gensplore 0.0.11 → 0.0.12

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (3) hide show
  1. package/dist/gensplore.cjs +3 -3
  2. package/dist/gensplore.js +14 -14
  3. package/package.json +1 -1
package/dist/gensplore.cjs CHANGED
@@ -6,7 +6,7 @@ var e=Object.create,t=Object.defineProperty,n=Object.getOwnPropertyDescriptor,r=
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  font-size: .6rem;
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  font-weight: bold;
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  color: hsl(${Math.max(0,Math.min(120-120*r,120))}deg 100% 31%);`,n?.key)}return n?.onChange&&!(a&&n.skipInitialOnChange)&&n.onChange(i),a=!1,i}return o.updateDeps=e=>{r=e},o}function Ze(e,t){if(e===void 0)throw Error(`Unexpected undefined${t?`: ${t}`:``}`);return e}var Qe=(e,t)=>Math.abs(e-t)<1.01,$e=(e,t,n)=>{let r;return Object.assign(function(...i){e.clearTimeout(r),r=e.setTimeout(()=>t.apply(this,i),n)},{cancel:()=>{e.clearTimeout(r)}})},et,tt=()=>{if(et!==void 0)return et;if(typeof navigator>`u`)return et=!1;if(/iP(hone|od|ad)/.test(navigator.userAgent))return et=!0;let e=navigator.maxTouchPoints;return et=navigator.platform===`MacIntel`&&e!==void 0&&e>0},nt=e=>e,rt=e=>{let t=Math.max(e.startIndex-e.overscan,0),n=Math.min(e.endIndex+e.overscan,e.count-1)-t+1,r=Array(n);for(let e=0;e<n;e++)r[e]=t+e;return r},it={passive:!0},at=(e,t)=>{let n=e.scrollElement;if(!n)return;let r=()=>{t({width:n.innerWidth,height:n.innerHeight})};return 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10
10
  ${t.startIsActual?`L ${i+ro} ${a}
11
11
  L ${i} ${a+5}
12
12
  L ${i+ro} ${a+10}`:`L ${i+io} ${a}
@@ -22,7 +22,7 @@ var e=Object.create,t=Object.defineProperty,n=Object.getOwnPropertyDescriptor,r=
22
22
  L ${c-io} ${a+10}`}
23
23
  L ${i} ${a+10}
24
24
  L ${i} ${a}
25
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{aliases:[`Sau96mI`,`Sau93I`,`Sau98I`,`Sau90I`],site:`ctyrag`,forwardRegex:`ct[cty][agr]ag`,reverseRegex:`ct[cty][agr]ag`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`TrsSII`],site:`gacnnnnnngtc`,forwardRegex:`gac[abcdghkmnrstvwy]{6}gtc`,reverseRegex:`gac[abcdghkmnrstvwy]{6}gtc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`ParI`,`BsiQI`,`BclI`,`AbaI`,`FbaI`,`Ksp22I`,`BstT7I`,`BspXII`],site:`tgatca`,forwardRegex:`tgatca`,reverseRegex:`tgatca`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`Eco255I`,`DpaI`,`BmcAI`,`ZrmI`,`ScaI`,`AssI`,`Bpa34I`,`Acc113I`,`RflFII`],site:`agtact`,forwardRegex:`agtact`,reverseRegex:`agtact`,topSnipOffset:3,bottomSnipOffset:3},{aliases:[`SplAII`,`TteI`,`TspI`,`TrsKTII`,`FsuI`,`SmaAII`,`NtaI`,`SplII`,`SpaPI`,`TtrI`],site:`gacnnngtc`,forwardRegex:`gac[abcdghkmnrstvwy]{3}gtc`,reverseRegex:`gac[abcdghkmnrstvwy]{3}gtc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`AspLEI`,`HhaI`,`BspLAI`,`CfoI`,`BstHHI`,`FnuDIII`],site:`gcgc`,forwardRegex:`gcgc`,reverseRegex:`gcgc`,topSnipOffset:3,bottomSnipOffset:1},{aliases:[`StyLTI`],site:`cagag`,forwardRegex:`cagag`,reverseRegex:`ctctg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BsoEI`,`Uba1289I`,`Uba1290I`,`BstWI`,`Uba1309I`,`Uba1308I`,`Uba1310I`,`Bpu1268I`],site:`cctnnnnnagg`,forwardRegex:`c{2}t[abcdghkmnrstvwy]{5}ag{2}`,reverseRegex:`c{2}t[abcdghkmnrstvwy]{5}ag{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Eco826I`,`Eco1455I`],site:`gcannnnnnctga`,forwardRegex:`gca[abcdghkmnrstvwy]{6}ctga`,reverseRegex:`tcag[abcdghkmnrstvwy]{6}tgc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`ApaI`,`PpeI`],site:`gggccc`,forwardRegex:`g{3}c{3}`,reverseRegex:`g{3}c{3}`,topSnipOffset:5,bottomSnipOffset:1},{aliases:[`KpnBI`],site:`caaannnnnnrtca`,forwardRegex:`ca{3}[abcdghkmnrstvwy]{6}[agr]tca`,reverseRegex:`tga[cty][abcdghkmnrstvwy]{6}t{3}g`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`UnbI`],site:`ggncc`,forwardRegex:`g{2}[abcdghkmnrstvwy]c{2}`,reverseRegex:`g{2}[abcdghkmnrstvwy]c{2}`,topSnipOffset:0,bottomSnipOffset:5},{aliases:[`Uba1384I`,`SmuCI`,`AvaIII`,`Uba1353I`,`PxyJKI`,`Uba1367I`,`BfrCI`,`SrlII`],site:`atgcat`,forwardRegex:`atgcat`,reverseRegex:`atgcat`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BspMKI`,`XciI`,`SalI`,`HgiCIII`,`Rtr63I`,`Rrh4273I`,`RflFI`,`HgiDII`,`NopI`,`RtrI`],site:`gtcgac`,forwardRegex:`gtcgac`,reverseRegex:`gtcgac`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`EcoR124I`],site:`gaannnnnnrtcg`,forwardRegex:`ga{2}[abcdghkmnrstvwy]{6}[agr]tcg`,reverseRegex:`cga[cty][abcdghkmnrstvwy]{6}t{2}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`SynII`,`Psc2I`],site:`gaannnnttc`,forwardRegex:`ga{2}[abcdghkmnrstvwy]{4}t{2}c`,reverseRegex:`ga{2}[abcdghkmnrstvwy]{4}t{2}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`CspI`,`Rsr2I`,`RsrII`,`CpoI`],site:`cggwccg`,forwardRegex:`cg{2}[atw]c{2}g`,reverseRegex:`cg{2}[atw]c{2}g`,topSnipOffset:2,bottomSnipOffset:5},{aliases:[`AscI`,`PalAI`,`SgsI`],site:`ggcgcgcc`,forwardRegex:`g{2}cgcgc{2}`,reverseRegex:`g{2}cgcgc{2}`,topSnipOffset:2,bottomSnipOffset:6},{aliases:[`Uba69I`,`TtmII`,`BscEI`,`BsrHI`,`Kpn30I`,`M.BssHIII`,`BssBI`,`Eco143I`,`Eco152I`,`Esp7I`,`Esp8I`,`CfrJ5I`,`BsoPI`],site:`gcgcgc`,forwardRegex:`gcgcgc`,reverseRegex:`gcgcgc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`EclHKI`,`BspOVI`,`AhdI`,`AspEI`,`Eam1105I`,`NruGI`,`BmeRI`,`DriI`],site:`gacnnnnngtc`,forwardRegex:`gac[abcdghkmnrstvwy]{5}gtc`,reverseRegex:`gac[abcdghkmnrstvwy]{5}gtc`,topSnipOffset:6,bottomSnipOffset:5},{aliases:[`Uba1222I`,`Uba1221I`,`BpuGCI`,`Uba1320I`,`Uba1284I`],site:`gctnagc`,forwardRegex:`gct[abcdghkmnrstvwy]agc`,reverseRegex:`gct[abcdghkmnrstvwy]agc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BpuCI`],site:`ggcgga`,forwardRegex:`g{2}cg{2}a`,reverseRegex:`tc{2}gc{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`EspI`,`BlpI`,`Bsp1720I`,`Bpu1102I`,`CelII`],site:`gctnagc`,forwardRegex:`gct[abcdghkmnrstvwy]agc`,reverseRegex:`gct[abcdghkmnrstvwy]agc`,topSnipOffset:2,bottomSnipOffset:5},{aliases:[`Eco1476I`,`Eco1427I`,`Eco1430I`,`Eco1323I`,`Eco377I`,`Eco1386I`,`Eco37I`,`Eco1344II`,`Eco1456I`],site:`ggannnnnnnnatgc`,forwardRegex:`g{2}a[abcdghkmnrstvwy]{8}atgc`,reverseRegex:`gcat[abcdghkmnrstvwy]{8}tc{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`MnnI`,`Hin1160II`,`ChuEII`,`Hin1161II`],site:`gtyrac`,forwardRegex:`gt[cty][agr]ac`,reverseRegex:`gt[cty][agr]ac`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`SstI`,`SacI`,`Psp124BI`],site:`gagctc`,forwardRegex:`gagctc`,reverseRegex:`gagctc`,topSnipOffset:5,bottomSnipOffset:1},{aliases:[`SspD5II`,`NsiI`,`PinBI`,`Asi372I`,`Mph1103I`,`Csp68KIII`,`Zsp2I`,`SepI`,`EcoT22I`,`BfrBI`],site:`atgcat`,forwardRegex:`atgcat`,reverseRegex:`atgcat`,topSnipOffset:5,bottomSnipOffset:1},{aliases:[`AsnI`,`AseI`,`VspI`,`PshBI`,`Sru4DI`,`BpoAI`],site:`attaat`,forwardRegex:`at{2}a{2}t`,reverseRegex:`at{2}a{2}t`,topSnipOffset:2,bottomSnipOffset:4},{aliases:[`BmrFI`,`Msp67I`,`MspR9I`,`ScrFI`,`Bme1390I`],site:`ccngg`,forwardRegex:`c{2}[abcdghkmnrstvwy]g{2}`,reverseRegex:`c{2}[abcd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gag[abcdghkmnrstvwy]{6}gt[agr]c`,reverseRegex:`g[cty]ac[abcdghkmnrstvwy]{6}ctc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BchI`,`BsaUI`,`BsrVI`,`LfeI`],site:`gcagc`,forwardRegex:`gcagc`,reverseRegex:`gctgc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BscAI`,`Bst19I`],site:`gcatc`,forwardRegex:`gcatc`,reverseRegex:`gatgc`,topSnipOffset:9,bottomSnipOffset:11,isType2S:!0},{aliases:[`KteAI`,`Uba1393I`,`Uba1220I`],site:`cccggg`,forwardRegex:`c{3}g{3}`,reverseRegex:`c{3}g{3}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BctI`],site:`acggc`,forwardRegex:`acg{2}c`,reverseRegex:`gc{2}gt`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BsePI`,`PteI`,`BssHII`,`BstBZ153I`,`PauI`],site:`gcgcgc`,forwardRegex:`gcgcgc`,reverseRegex:`gcgcgc`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`StyLTIII`],site:`gagnnnnnnrtayg`,forwardRegex:`gag[abcdghkmnrstvwy]{6}[agr]ta[cty]g`,reverseRegex:`c[agr]ta[cty][abcdghkmnrstvwy]{6}ctc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`VpaK32I`,`PciSI`,`LguI`,`BspQI`,`SapI`],isType2S:!0,site:`gctcttc`,forwardRegex:`gctct{2}c`,reverseRegex:`ga{2}gagc`,topSnipOffset:8,bottomSnipOffset:11},{aliases:[`BniI`],site:`gcnngc`,forwardRegex:`gc[abcdghkmnrstvwy]{2}gc`,reverseRegex:`gc[abcdghkmnrstvwy]{2}gc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`EcoDR2`],site:`tcannnnnngtcg`,forwardRegex:`tca[abcdghkmnrstvwy]{6}gtcg`,reverseRegex:`cgac[abcdghkmnrstvwy]{6}tga`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`TssI`],site:`gagnnnctc`,forwardRegex:`gag[abcdghkmnrstvwy]{3}ctc`,reverseRegex:`gag[abcdghkmnrstvwy]{3}ctc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Tth111II`],site:`caarca`,forwardRegex:`ca{2}[agr]ca`,reverseRegex:`tg[cty]t{2}g`,topSnipOffset:17,bottomSnipOffset:15,isType2S:!0},{aliases:[`BbvCI`,`AbeI`],site:`cctcagc`,forwardRegex:`c{2}tcagc`,reverseRegex:`gctgag{2}`,topSnipOffset:2,bottomSnipOffset:5},{aliases:[`MluI`,`Bbi24I`],site:`acgcgt`,forwardRegex:`acgcgt`,reverseRegex:`acgcgt`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`MnlI`],site:`cctc`,forwardRegex:`c{2}tc`,reverseRegex:`gag{2}`,topSnipOffset:11,bottomSnipOffset:10,isType2S:!0},{aliases:[`SspD5I`],site:`ggtga`,forwardRegex:`g{2}tga`,reverseRegex:`tcac{2}`,topSnipOffset:13,bottomSnipOffset:13,isType2S:!0},{aliases:[`AspCNI`],site:`gccgc`,forwardRegex:`gc{2}gc`,reverseRegex:`gcg{2}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`TauI`,`BspUI`],site:`gcsgc`,forwardRegex:`gc[cgs]gc`,reverseRegex:`gc[cgs]gc`,topSnipOffset:4,bottomSnipOffset:1},{aliases:[`BinSII`,`BbeI`],site:`ggcgcc`,forwardRegex:`g{2}cgc{2}`,reverseRegex:`g{2}cgc{2}`,topSnipOffset:5,bottomSnipOffset:1},{aliases:[`BpmI`,`GsuI`],site:`ctggag`,forwardRegex:`ctg{2}ag`,reverseRegex:`ctc{2}ag`,topSnipOffset:22,bottomSnipOffset:20,isType2S:!0},{aliases:[`NciI`,`AhaI`,`AseII`,`Mgl14481I`,`AsuC2I`,`BpuMI`,`HgiS22I`,`CauII`,`BcnI`],site:`ccsgg`,forwardRegex:`c{2}[cgs]g{2}`,reverseRegex:`c{2}[cgs]g{2}`,topSnipOffset:2,bottomSnipOffset:3},{aliases:[`Eco1348I`,`Eco777I`,`Eco1412I`],site:`ggannnnnntatc`,forwardRegex:`g{2}a[abcdghkmnrstvwy]{6}tatc`,reverseRegex:`gata[abcdghkmnrstvwy]{6}tc{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`AgsI`],site:`ttsaa`,forwardRegex:`t{2}[cgs]a{2}`,reverseRegex:`t{2}[cgs]a{2}`,topSnipOffset:3,bottomSnipOffset:2},{aliases:[`Pfl18I`,`Ssm4I`,`Ssm5I`,`NasSI`,`ScoI`,`Ecl137I`],site:`gagctc`,forwardRegex:`gagctc`,reverseRegex:`gagctc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`CfrBI`,`StyI`,`ErhB9II`,`Eco130I`,`ErhI`,`EcoT14I`,`BsmSI`,`BssT1I`],site:`ccwwgg`,forwardRegex:`c{2}[atw]{2}g{2}`,reverseRegex:`c{2}[atw]{2}g{2}`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`AlwFI`],site:`gaaaynnnnnrtg`,forwardRegex:`ga{3}[cty][abcdghkmnrstvwy]{5}[agr]tg`,reverseRegex:`ca[cty][abcdghkmnrstvwy]{5}[agr]t{3}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`CviRI`,`HpyCH4V`,`HpyF44III`],site:`tgca`,forwardRegex:`tgca`,reverseRegex:`tgca`,topSnipOffset:2,bottomSnipOffset:2},{aliases:[`Bse19I`,`AteI`,`NspSAIII`],site:`ccatgg`,forwardRegex:`c{2}atg{2}`,reverseRegex:`c{2}atg{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Srl65DI`,`Srr17I`,`Srl55DII`,`CprJK722I`,`Srl8DI`,`PbuMZI`],site:`attaat`,forwardRegex:`at{2}a{2}t`,reverseRegex:`at{2}a{2}t`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`ClcII`,`GspAII`,`NspHIII`,`Bco6I`,`NspLI`,`NspMI`,`BsaTI`,`CliII`,`ApcTR183I`,`AcaIII`],site:`tgcgca`,forwardRegex:`tgcgca`,reverseRegex:`tgcgca`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`CsiI`,`MabI`,`SexAI`],site:`accwggt`,forwardRegex:`ac{2}[atw]g{2}t`,reverseRegex:`ac{2}[atw]g{2}t`,topSnipOffset:1,bottomSnipOffset:6},{aliases:[`HgiEII`],site:`accnnnnnnggt`,forwardRegex:`ac{2}[abcdghkmnrstvwy]{6}g{2}t`,reverseRegex:`ac{2}[abcdghkmnrstvwy]{6}g{2}t`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`TseDI`,`BscRI`,`Bsp21I`],site:`rccggy`,forwardRegex:`[agr]c{2}g{2}[cty]`,reverseRegex:`[agr]c{2}g{2}[cty]`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Bse23I`,`BsmYI`],site:`ccnnnnnnngg`,forwardRegex:`c{2}[abcdghkmnrstvwy]{7}g{2}`,reverseRegex:`c{2}[abcdghkmnrstvwy]{7}g{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`NdeI`,`FauNDI`,`PfaAII`],site:`catatg`,forwardRegex:`catatg`,reverseRegex:`catatg`,topSnipOffset:2,bottomSnipOffset:4},{aliases:[`VneAI`,`Uba1326I`],site:`rggnccy`,forwardRegex:`[agr]g{2}[abcdghkmnrstvwy]c{2}[cty]`,reverseRegex:`[agr]g{2}[abcdghkmnrstvwy]c{2}[cty]`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`SrlI`,`NgoMIV`,`SceIII`,`NgoAIV`,`MroNI`,`Eco56I`],site:`gccggc`,forwardRegex:`gc{2}g{2}c`,reverseRegex:`gc{2}g{2}c`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`AsiSI`,`SfaAI`,`RgaI`,`SgfI`],site:`gcgatcgc`,forwardRegex:`gcgatcgc`,reverseRegex:`gcgatcgc`,topSnipOffset:5,bottomSnipOffset:3},{aliases:[`BtsPI`,`SaiI`,`ShaI`],site:`gggtc`,forwardRegex:`g{3}tc`,reverseRegex:`gac{3}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Pfl1108I`],site:`tcgtag`,forwardRegex:`tcgtag`,reverseRegex:`ctacga`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`EcoHK31I`,`Bfi89I`,`EaeI`,`CfrI`,`AcoI`],site:`yggccr`,forwardRegex:`[cty]g{2}c{2}[agr]`,reverseRegex:`[cty]g{2}c{2}[agr]`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`HphI`,`AsuHPI`],site:`ggtga`,forwardRegex:`g{2}tga`,reverseRegex:`tcac{2}`,topSnipOffset:13,bottomSnipOffset:12,isType2S:!0},{aliases:[`Uba1303I`,`BstZ5I`,`BscNI`],site:`cgrycg`,forwardRegex:`cg[agr][cty]cg`,reverseRegex:`cg[agr][cty]cg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Bsp6II`,`FsfI`,`BspD6II`,`Eco112I`,`Eco125I`],site:`ctgaag`,forwardRegex:`ctga{2}g`,reverseRegex:`ct{2}cag`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BstXI`,`BstHZ55I`],site:`ccannnnnntgg`,forwardRegex:`c{2}a[abcdghkmnrstvwy]{6}tg{2}`,reverseRegex:`c{2}a[abcdghkmnrstvwy]{6}tg{2}`,topSnipOffset:8,bottomSnipOffset:4},{aliases:[`Ppu11I`,`Ppu6I`],site:`yacgtr`,forwardRegex:`[cty]acgt[agr]`,reverseRegex:`[cty]acgt[agr]`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`EcoT104I`,`SblAI`,`SblBI`,`SblCI`,`Uba1311I`,`Eco208II`,`Bst224I`],site:`ccwwgg`,forwardRegex:`c{2}[atw]{2}g{2}`,reverseRegex:`c{2}[atw]{2}g{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`EcoR124II`],site:`gaannnnnnnrtcg`,forwardRegex:`ga{2}[abcdghkmnrstvwy]{7}[agr]tcg`,reverseRegex:`cga[cty][abcdghkmnrstvwy]{7}t{2}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`MamI`,`BseJI`,`Bse8I`,`BsrBRI`,`BsiBI`,`BsaBI`,`Bsh1365I`],site:`gatnnnnatc`,forwardRegex:`gat[abcdghkmnrstvwy]{4}atc`,reverseRegex:`gat[abcdghkmnrstvwy]{4}atc`,topSnipOffset:5,bottomSnipOffset:5},{aliases:[`Ssp5230I`,`AatII`],site:`gacgtc`,forwardRegex:`gacgtc`,reverseRegex:`gacgtc`,topSnipOffset:5,bottomSnipOffset:1},{aliases:[`Uba1240I`,`Bpu1831I`,`SspM1I`,`SspM2I`,`EciAI`,`SspJI`,`Eco158II`],site:`tacgta`,forwardRegex:`tacgta`,reverseRegex:`tacgta`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`MaqI`],site:`crttgac`,forwardRegex:`c[agr]t{2}gac`,reverseRegex:`gtca{2}[cty]g`,topSnipOffset:28,bottomSnipOffset:26,isType2S:!0},{aliases:[`CjeNII`],site:`gagnnnnngt`,forwardRegex:`gag[abcdghkmnrstvwy]{5}gt`,reverseRegex:`ac[abcdghkmnrstvwy]{5}ctc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`KpnAI`],site:`gaannnnnntgcc`,forwardRegex:`ga{2}[abcdghkmnrstvwy]{6}tgc{2}`,reverseRegex:`g{2}ca[abcdghkmnrstvwy]{6}t{2}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`SleI`,`AjnI`,`Psp6I`,`PspGI`,`SspAI`,`EcoRII`],site:`ccwgg`,forwardRegex:`c{2}[atw]g{2}`,reverseRegex:`c{2}[atw]g{2}`,topSnipOffset:0,bottomSnipOffset:5},{aliases:[`BstFZ438I`,`Bme585I`,`SmuI`,`FauI`],site:`cccgc`,forwardRegex:`c{3}gc`,reverseRegex:`gcg{3}`,topSnipOffset:9,bottomSnipOffset:11,isType2S:!0},{aliases:[`HpyCH4IV`,`MaeII`],site:`acgt`,forwardRegex:`acgt`,reverseRegex:`acgt`,topSnipOffset:1,bottomSnipOffset:3},{aliases:[`TaqII`],site:`caccca`,forwardRegex:`cac{3}a`,reverseRegex:`tg{3}tg`,topSnipOffset:17,bottomSnipOffset:15,isType2S:!0},{aliases:[`UbaN9I`],site:`aacgtt`,forwardRegex:`a{2}cgt{2}`,reverseRegex:`a{2}cgt{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`DrdII`],site:`gaacca`,forwardRegex:`ga{2}c{2}a`,reverseRegex:`tg{2}t{2}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`MalI`,`DpnI`,`CfuI`],site:`gatc`,forwardRegex:`gatc`,reverseRegex:`gatc`,topSnipOffset:2,bottomSnipOffset:2},{aliases:[`AarI`],isType2S:!0,site:`cacctgc`,forwardRegex:`cac{2}tgc`,reverseRegex:`gcag{2}tg`,topSnipOffset:11,bottomSnipOffset:15},{aliases:[`SrfI`],site:`gcccgggc`,forwardRegex:`gc{3}g{3}c`,reverseRegex:`gc{3}g{3}c`,topSnipOffset:4,bottomSnipOffset:4},{aliases:[`TatI`],site:`wgtacw`,forwardRegex:`[atw]gtac[atw]`,reverseRegex:`[atw]gtac[atw]`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`EcoDXXI`],site:`tcannnnnnnrttc`,forwardRegex:`tca[abcdghkmnrstvwy]{7}[agr]t{2}c`,reverseRegex:`ga{2}[cty][abcdghkmnrstvwy]{7}tga`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`HindII`,`HincII`,`HinJCI`],site:`gtyrac`,forwardRegex:`gt[cty][agr]ac`,reverseRegex:`gt[cty][agr]ac`,topSnipOffset:3,bottomSnipOffset:3},{aliases:[`BseMI`,`Bse3DI`,`BsrDI`],site:`gcaatg`,forwardRegex:`gca{2}tg`,reverseRegex:`cat{2}gc`,topSnipOffset:8,bottomSnipOffset:6,isType2S:!0},{aliases:[`HalI`,`Srl32DII`,`FunII`,`Ppu111I`,`EcoRI`,`RsrI`,`Kpn49kI`,`SsoI`,`Srl55DI`],site:`gaattc`,forwardRegex:`ga{2}t{2}c`,reverseRegex:`ga{2}t{2}c`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`Hpy166III`],site:`cctc`,forwardRegex:`c{2}tc`,reverseRegex:`gag{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`FspAI`],site:`rtgcgcay`,forwardRegex:`[agr]tgcgca[cty]`,reverseRegex:`[agr]tgcgca[cty]`,topSnipOffset:4,bottomSnipOffset:4},{aliases:[`Eco585I`],site:`gccnnnnnntgcg`,forwardRegex:`gc{2}[abcdghkmnrstvwy]{6}tgcg`,reverseRegex:`cgca[abcdghkmnrstvwy]{6}g{2}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`PlaDI`],site:`catcag`,forwardRegex:`catcag`,reverseRegex:`ctgatg`,topSnipOffset:27,bottomSnipOffset:25,isType2S:!0},{aliases:[`Hpy188I`],site:`tcnga`,forwardRegex:`tc[abcdghkmnrstvwy]ga`,reverseRegex:`tc[abcdghkmnrstvwy]ga`,topSnipOffset:3,bottomSnipOffset:2},{aliases:[`PciI`,`PscI`,`BspLU11I`],site:`acatgt`,forwardRegex:`acatgt`,reverseRegex:`acatgt`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`VchO25I`,`SnaI`],site:`gtatac`,forwardRegex:`gtatac`,reverseRegex:`gtatac`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`TseBI`,`M.BbvSI`,`TneI`],site:`gcwgc`,forwardRegex:`gc[atw]gc`,reverseRegex:`gc[atw]gc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`OliI`,`AleI`],site:`cacnnnngtg`,forwardRegex:`cac[abcdghkmnrstvwy]{4}gtg`,reverseRegex:`cac[abcdghkmnrstvwy]{4}gtg`,topSnipOffset:5,bottomSnipOffset:5},{aliases:[`GlaI`],site:`gcgc`,forwardRegex:`gcgc`,reverseRegex:`gcgc`,topSnipOffset:2,bottomSnipOffset:2},{aliases:[`BssGI`,`BscJI`,`BstTI`],site:`ccannnnnntgg`,forwardRegex:`c{2}a[abcdghkmnrstvwy]{6}tg{2}`,reverseRegex:`c{2}a[abcdghkmnrstvwy]{6}tg{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Tsp4CI`,`Bst4CI`,`HpyCH4III`,`TaaI`],site:`acngt`,forwardRegex:`ac[abcdghkmnrstvwy]gt`,reverseRegex:`ac[abcdghkmnrstvwy]gt`,topSnipOffset:3,bottomSnipOffset:2},{aliases:[`AceIII`],site:`cagctc`,forwardRegex:`cagctc`,reverseRegex:`gagctg`,topSnipOffset:13,bottomSnipOffset:17,isType2S:!0},{aliases:[`BseNI`,`BsrI`,`Bse1I`,`Tsp1I`,`BsrSI`,`Bst11I`],site:`actgg`,forwardRegex:`actg{2}`,reverseRegex:`c{2}agt`,topSnipOffset:6,bottomSnipOffset:4,isType2S:!0},{aliases:[`FnuAI`,`HinfI`,`CviBI`,`HhaII`,`SscL1I`],site:`gantc`,forwardRegex:`ga[abcdghkmnrstvwy]tc`,reverseRegex:`ga[abcdghkmnrstvwy]tc`,topSnipOffset:1,bottomSnipOffset:4},{aliases:[`CjuI`],site:`caynnnnnrtg`,forwardRegex:`ca[cty][abcdghkmnrstvwy]{5}[agr]tg`,reverseRegex:`ca[cty][abcdghkmnrstvwy]{5}[agr]tg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`HpyF2I`,`Bco163I`],site:`ctryag`,forwardRegex:`ct[agr][cty]ag`,reverseRegex:`ct[agr][cty]ag`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`AanI`,`PsiI`],site:`ttataa`,forwardRegex:`t{2}ata{2}`,reverseRegex:`t{2}ata{2}`,topSnipOffset:3,bottomSnipOffset:3},{aliases:[`StySPI`],site:`aacnnnnnngtrc`,forwardRegex:`a{2}c[abcdghkmnrstvwy]{6}gt[agr]c`,reverseRegex:`g[cty]ac[abcdghkmnrstvwy]{6}gt{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BpuJI`,`BstDZ247I`,`BscGI`],site:`cccgt`,forwardRegex:`c{3}gt`,reverseRegex:`acg{3}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Hpy99I`],site:`cgwcg`,forwardRegex:`cg[atw]cg`,reverseRegex:`cg[atw]cg`,topSnipOffset:5,bottomSnipOffset:0},{aliases:[`BceSI`],site:`mmcgaag`,forwardRegex:`[acm]{2}cga{2}g`,reverseRegex:`ct{2}cg[gkt]{2}`,topSnipOffset:32,bottomSnipOffset:34,isType2S:!0},{aliases:[`HaeI`],site:`wggccw`,forwardRegex:`[atw]g{2}c{2}[atw]`,reverseRegex:`[atw]g{2}c{2}[atw]`,topSnipOffset:3,bottomSnipOffset:3},{aliases:[`PspPRI`],site:`ccycag`,forwardRegex:`c{2}[cty]cag`,reverseRegex:`ctg[agr]g{2}`,topSnipOffset:21,bottomSnipOffset:19,isType2S:!0},{aliases:[`FokI`],site:`ggatg`,forwardRegex:`g{2}atg`,reverseRegex:`catc{2}`,topSnipOffset:14,bottomSnipOffset:18,isType2S:!0},{aliases:[`NgoBV`,`NgoGV`,`Bsp29I`,`HpyF44II`,`Uba1445I`,`Uba1305I`,`HpyF73I`,`BsaEI`,`BcrI`,`Rlu3I`,`BssI`],site:`ggnncc`,forwardRegex:`g{2}[abcdghkmnrstvwy]{2}c{2}`,reverseRegex:`g{2}[abcdghkmnrstvwy]{2}c{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Bce1247I`],site:`gcnnnnnnngc`,forwardRegex:`gc[abcdghkmnrstvwy]{7}gc`,reverseRegex:`gc[abcdghkmnrstvwy]{7}gc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`AasI`,`DrdI`,`DseDI`],site:`gacnnnnnngtc`,forwardRegex:`gac[abcdghkmnrstvwy]{6}gtc`,reverseRegex:`gac[abcdghkmnrstvwy]{6}gtc`,topSnipOffset:7,bottomSnipOffset:5},{aliases:[`M.SssI`],site:`cg`,forwardRegex:`cg`,reverseRegex:`cg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`HpyF61III`],site:`cgwcg`,forwardRegex:`cg[atw]cg`,reverseRegex:`cg[atw]cg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`AflIII`],site:`acrygt`,forwardRegex:`ac[agr][cty]gt`,reverseRegex:`ac[agr][cty]gt`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`Asp700I`,`BbvAI`,`MroXI`,`XmnI`,`PdmI`],site:`gaannnnttc`,forwardRegex:`ga{2}[abcdghkmnrstvwy]{4}t{2}c`,reverseRegex:`ga{2}[abcdghkmnrstvwy]{4}t{2}c`,topSnipOffset:5,bottomSnipOffset:5},{aliases:[`ChaI`],site:`gatc`,forwardRegex:`gatc`,reverseRegex:`gatc`,topSnipOffset:4,bottomSnipOffset:0},{aliases:[`EcoEI`],site:`gagnnnnnnnatgc`,forwardRegex:`gag[abcdghkmnrstvwy]{7}atgc`,reverseRegex:`gcat[abcdghkmnrstvwy]{7}ctc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BspAAII`,`XbaI`],site:`tctaga`,forwardRegex:`tctaga`,reverseRegex:`tctaga`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`Hpy188III`,`Hpy178III`],site:`tcnnga`,forwardRegex:`tc[abcdghkmnrstvwy]{2}ga`,reverseRegex:`tc[abcdghkmnrstvwy]{2}ga`,topSnipOffset:2,bottomSnipOffset:4},{aliases:[`McaTI`],site:`gcgcgc`,forwardRegex:`gcgcgc`,reverseRegex:`gcgcgc`,topSnipOffset:4,bottomSnipOffset:2},{aliases:[`BstZ9I`,`Uba6I`,`ApeI`],site:`acgcgt`,forwardRegex:`acgcgt`,reverseRegex:`acgcgt`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BspNCI`],site:`ccaga`,forwardRegex:`c{2}aga`,reverseRegex:`tctg{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`EcoHI`,`Eco1831I`,`Kpn49kII`],site:`ccsgg`,forwardRegex:`c{2}[cgs]g{2}`,reverseRegex:`c{2}[cgs]g{2}`,topSnipOffset:0,bottomSnipOffset:5},{aliases:[`PpsI`,`PleI`],site:`gagtc`,forwardRegex:`gagtc`,reverseRegex:`gactc`,topSnipOffset:9,bottomSnipOffset:10,isType2S:!0},{aliases:[`BfuI`,`BciVI`],site:`gtatcc`,forwardRegex:`gtatc{2}`,reverseRegex:`g{2}atac`,topSnipOffset:12,bottomSnipOffset:11,isType2S:!0},{aliases:[`TthHB27I`],site:`caarca`,forwardRegex:`ca{2}[agr]ca`,reverseRegex:`tg[cty]t{2}g`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`PspXI`],site:`vctcgagb`,forwardRegex:`[acgmrsv]ctcgag[bcgksty]`,reverseRegex:`[acgmrsv]ctcgag[bcgksty]`,topSnipOffset:2,bottomSnipOffset:6},{aliases:[`Lsp1270I`],site:`rcatgy`,forwardRegex:`[agr]catg[cty]`,reverseRegex:`[agr]catg[cty]`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`HpyC1I`,`BccI`],site:`ccatc`,forwardRegex:`c{2}atc`,reverseRegex:`gatg{2}`,topSnipOffset:9,bottomSnipOffset:10,isType2S:!0},{aliases:[`BseMII`],site:`ctcag`,forwardRegex:`ctcag`,reverseRegex:`ctgag`,topSnipOffset:15,bottomSnipOffset:13,isType2S:!0},{aliases:[`BstENI`,`EcoNI`,`XagI`],site:`cctnnnnnagg`,forwardRegex:`c{2}t[abcdghkmnrstvwy]{5}ag{2}`,reverseRegex:`c{2}t[abcdghkmnrstvwy]{5}ag{2}`,topSnipOffset:5,bottomSnipOffset:6},{aliases:[`EcoAI`,`Eco1446I`],site:`gagnnnnnnngtca`,forwardRegex:`gag[abcdghkmnrstvwy]{7}gtca`,reverseRegex:`tgac[abcdghkmnrstvwy]{7}ctc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`MmeI`],site:`tccrac`,forwardRegex:`tc{2}[agr]ac`,reverseRegex:`gt[cty]g{2}a`,topSnipOffset:26,bottomSnipOffset:24,isType2S:!0},{aliases:[`AjiI`,`BmgBI`,`BtrI`],site:`cacgtc`,forwardRegex:`cacgtc`,reverseRegex:`gacgtg`,topSnipOffset:3,bottomSnipOffset:3},{aliases:[`BlsI`],site:`gcngc`,forwardRegex:`gc[abcdghkmnrstvwy]gc`,reverseRegex:`gc[abcdghkmnrstvwy]gc`,topSnipOffset:3,bottomSnipOffset:2},{aliases:[`Bst170I`,`BsmGI`],site:`tgtaca`,forwardRegex:`tgtaca`,reverseRegex:`tgtaca`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`HpyBII`,`Hpy166II`,`Hpy8I`],site:`gtnnac`,forwardRegex:`gt[abcdghkmnrstvwy]{2}ac`,reverseRegex:`gt[abcdghkmnrstvwy]{2}ac`,topSnipOffset:3,bottomSnipOffset:3},{aliases:[`StySKI`],site:`cgatnnnnnnngtta`,forwardRegex:`cgat[abcdghkmnrstvwy]{7}gt{2}a`,reverseRegex:`ta{2}c[abcdghkmnrstvwy]{7}atcg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Esp23I`,`Esp16I`],site:`cgtctc`,forwardRegex:`cgtctc`,reverseRegex:`gagacg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BmgT120I`],site:`ggncc`,forwardRegex:`g{2}[abcdghkmnrstvwy]c{2}`,reverseRegex:`g{2}[abcdghkmnrstvwy]c{2}`,topSnipOffset:2,bottomSnipOffset:3},{aliases:[`BcoAI`,`BbrPI`,`PmlI`,`PspCI`,`PmaCI`,`Eco72I`,`AcvI`],site:`cacgtg`,forwardRegex:`cacgtg`,reverseRegex:`cacgtg`,topSnipOffset:3,bottomSnipOffset:3},{aliases:[`CjeP338II`,`BscUI`,`BsmNI`,`BhaI`],site:`gcatc`,forwardRegex:`gcatc`,reverseRegex:`gatgc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`KasI`,`SspDI`],site:`ggcgcc`,forwardRegex:`g{2}cgc{2}`,reverseRegex:`g{2}cgc{2}`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`FmuI`],site:`ggncc`,forwardRegex:`g{2}[abcdghkmnrstvwy]c{2}`,reverseRegex:`g{2}[abcdghkmnrstvwy]c{2}`,topSnipOffset:4,bottomSnipOffset:1},{aliases:[`RseI`,`MslI`,`SmiMI`],site:`caynnnnrtg`,forwardRegex:`ca[cty][abcdghkmnrstvwy]{4}[agr]tg`,reverseRegex:`ca[cty][abcdghkmnrstvwy]{4}[agr]tg`,topSnipOffset:5,bottomSnipOffset:5},{aliases:[`NmuCI`,`Tsp45I`,`Hpy51I`],site:`gtsac`,forwardRegex:`gt[cgs]ac`,reverseRegex:`gt[cgs]ac`,topSnipOffset:0,bottomSnipOffset:5},{aliases:[`Psp5II`,`PpuMI`,`PpuXI`,`Pfl27I`,`PspPPI`],site:`rggwccy`,forwardRegex:`[agr]g{2}[atw]c{2}[cty]`,reverseRegex:`[agr]g{2}[atw]c{2}[cty]`,topSnipOffset:2,bottomSnipOffset:5},{aliases:[`Bba179I`,`Bst1473I`,`UbaN10I`],site:`wccggw`,forwardRegex:`[atw]c{2}g{2}[atw]`,reverseRegex:`[atw]c{2}g{2}[atw]`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Eco912I`],site:`cacnnnnntggc`,forwardRegex:`cac[abcdghkmnrstvwy]{5}tg{2}c`,reverseRegex:`gc{2}a[abcdghkmnrstvwy]{5}gtg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`SsmI`],site:`ctgatg`,forwardRegex:`ctgatg`,reverseRegex:`catcag`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`EsaSSI`],site:`gaccac`,forwardRegex:`gac{2}ac`,reverseRegex:`gtg{2}tc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`EcoDI`],site:`ttannnnnnngtcy`,forwardRegex:`t{2}a[abcdghkmnrstvwy]{7}gtc[cty]`,reverseRegex:`[agr]gac[abcdghkmnrstvwy]{7}ta{2}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BsoHI`,`BscHI`],site:`actgg`,forwardRegex:`actg{2}`,reverseRegex:`c{2}agt`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`NmeBI`],site:`gacgc`,forwardRegex:`gacgc`,reverseRegex:`gcgtc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`NspBII`,`MspA1I`],site:`cmgckg`,forwardRegex:`c[acm]gc[gkt]g`,reverseRegex:`c[acm]gc[gkt]g`,topSnipOffset:3,bottomSnipOffset:3},{aliases:[`BmgAI`],site:`gkgcmc`,forwardRegex:`g[gkt]gc[acm]c`,reverseRegex:`g[gkt]gc[acm]c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`NmeAIII`],site:`gccgag`,forwardRegex:`gc{2}gag`,reverseRegex:`ctcg{2}c`,topSnipOffset:27,bottomSnipOffset:25,isType2S:!0},{aliases:[`DrdIV`],site:`tacgac`,forwardRegex:`tacgac`,reverseRegex:`gtcgta`,topSnipOffset:26,bottomSnipOffset:24,isType2S:!0},{aliases:[`BscQII`],site:`gtctc`,forwardRegex:`gtctc`,reverseRegex:`gagac`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`AbsI`],site:`cctcgagg`,forwardRegex:`c{2}tcgag{2}`,reverseRegex:`c{2}tcgag{2}`,topSnipOffset:2,bottomSnipOffset:6},{aliases:[`Psp03I`],site:`ggwcc`,forwardRegex:`g{2}[atw]c{2}`,reverseRegex:`g{2}[atw]c{2}`,topSnipOffset:4,bottomSnipOffset:1},{aliases:[`BmtI`,`BspOI`,`AceII`],site:`gctagc`,forwardRegex:`gctagc`,reverseRegex:`gctagc`,topSnipOffset:5,bottomSnipOffset:1},{aliases:[`GsaI`],site:`cccagc`,forwardRegex:`c{3}agc`,reverseRegex:`gctg{3}`,topSnipOffset:5,bottomSnipOffset:1},{aliases:[`UbaF9I`],site:`tacnnnnnrtgt`,forwardRegex:`tac[abcdghkmnrstvwy]{5}[agr]tgt`,reverseRegex:`aca[cty][abcdghkmnrstvwy]{5}gta`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Hin1II`,`NlaIII`,`FaeI`,`Hsp92II`,`HpyCH4I`],site:`catg`,forwardRegex:`catg`,reverseRegex:`catg`,topSnipOffset:4,bottomSnipOffset:0},{aliases:[`Bbr7I`],site:`gaagac`,forwardRegex:`ga{2}gac`,reverseRegex:`gtct{2}c`,topSnipOffset:13,bottomSnipOffset:17,isType2S:!0},{aliases:[`Kaz48kI`,`PssI`],site:`rggnccy`,forwardRegex:`[agr]g{2}[abcdghkmnrstvwy]c{2}[cty]`,reverseRegex:`[agr]g{2}[abcdghkmnrstvwy]c{2}[cty]`,topSnipOffset:5,bottomSnipOffset:2},{aliases:[`BoxI`,`BstPAI`,`PshAI`],site:`gacnnnngtc`,forwardRegex:`gac[abcdghkmnrstvwy]{4}gtc`,reverseRegex:`gac[abcdghkmnrstvwy]{4}gtc`,topSnipOffset:5,bottomSnipOffset:5},{aliases:[`SgrDI`],site:`cgtcgacg`,forwardRegex:`cgtcgacg`,reverseRegex:`cgtcgacg`,topSnipOffset:2,bottomSnipOffset:6},{aliases:[`BssIMI`,`SimI`],site:`gggtc`,forwardRegex:`g{3}tc`,reverseRegex:`gac{3}`,topSnipOffset:2,bottomSnipOffset:5},{aliases:[`RleAI`],site:`cccaca`,forwardRegex:`c{3}aca`,reverseRegex:`tgtg{3}`,topSnipOffset:18,bottomSnipOffset:15,isType2S:!0},{aliases:[`EciI`],site:`ggcgga`,forwardRegex:`g{2}cg{2}a`,reverseRegex:`tc{2}gc{2}`,topSnipOffset:17,bottomSnipOffset:15,isType2S:!0},{aliases:[`Eco57MI`],site:`ctgrag`,forwardRegex:`ctg[agr]ag`,reverseRegex:`ct[cty]cag`,topSnipOffset:22,bottomSnipOffset:20,isType2S:!0},{aliases:[`AspJI`,`Ppu1253I`],site:`gacgtc`,forwardRegex:`gacgtc`,reverseRegex:`gacgtc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`UbaF11I`],site:`tcgta`,forwardRegex:`tcgta`,reverseRegex:`tacga`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`SetI`],site:`asst`,forwardRegex:`a[cgs]{2}t`,reverseRegex:`a[cgs]{2}t`,topSnipOffset:4,bottomSnipOffset:0},{aliases:[`PspOMII`],site:`cgcccar`,forwardRegex:`cgc{3}a[agr]`,reverseRegex:`[cty]tg{3}cg`,topSnipOffset:27,bottomSnipOffset:25,isType2S:!0},{aliases:[`BsxI`],site:`actggg`,forwardRegex:`actg{3}`,reverseRegex:`c{3}agt`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Eco394I`],site:`gacnnnnnrtaay`,forwardRegex:`gac[abcdghkmnrstvwy]{5}[agr]ta{2}[cty]`,reverseRegex:`[agr]t{2}a[cty][abcdghkmnrstvwy]{5}gtc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`ApyPI`],site:`atcgac`,forwardRegex:`atcgac`,reverseRegex:`gtcgat`,topSnipOffset:26,bottomSnipOffset:24,isType2S:!0},{aliases:[`AlwNI`,`CaiI`],site:`cagnnnctg`,forwardRegex:`cag[abcdghkmnrstvwy]{3}ctg`,reverseRegex:`cag[abcdghkmnrstvwy]{3}ctg`,topSnipOffset:6,bottomSnipOffset:3},{aliases:[`TsuI`],site:`gcgac`,forwardRegex:`gcgac`,reverseRegex:`gtcgc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Bca77I`,`BsaWI`,`BetI`],site:`wccggw`,forwardRegex:`[atw]c{2}g{2}[atw]`,reverseRegex:`[atw]c{2}g{2}[atw]`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`EcoDR3`],site:`tcannnnnnnatcg`,forwardRegex:`tca[abcdghkmnrstvwy]{7}atcg`,reverseRegex:`cgat[abcdghkmnrstvwy]{7}tga`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`SgrAI`],site:`crccggyg`,forwardRegex:`c[agr]c{2}g{2}[cty]g`,reverseRegex:`c[agr]c{2}g{2}[cty]g`,topSnipOffset:2,bottomSnipOffset:6},{aliases:[`M.NgoMXV`],site:`gcchr`,forwardRegex:`gc{2}[achmtwy][agr]`,reverseRegex:`[cty][adgkrtw]g{2}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`EcoRD2`],site:`gaannnnnnrttc`,forwardRegex:`ga{2}[abcdghkmnrstvwy]{6}[agr]t{2}c`,reverseRegex:`ga{2}[cty][abcdghkmnrstvwy]{6}t{2}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`TspGWI`],site:`acgga`,forwardRegex:`acg{2}a`,reverseRegex:`tc{2}gt`,topSnipOffset:16,bottomSnipOffset:14,isType2S:!0},{aliases:[`CviAII`],site:`catg`,forwardRegex:`catg`,reverseRegex:`catg`,topSnipOffset:1,bottomSnipOffset:3},{aliases:[`XcmI`],site:`ccannnnnnnnntgg`,forwardRegex:`c{2}a[abcdghkmnrstvwy]{9}tg{2}`,reverseRegex:`c{2}a[abcdghkmnrstvwy]{9}tg{2}`,topSnipOffset:8,bottomSnipOffset:7},{aliases:[`EcoRD3`],site:`gaannnnnnnrttc`,forwardRegex:`ga{2}[abcdghkmnrstvwy]{7}[agr]t{2}c`,reverseRegex:`ga{2}[cty][abcdghkmnrstvwy]{7}t{2}c`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`SpoDI`],site:`gcggrag`,forwardRegex:`gcg{2}[agr]ag`,reverseRegex:`ct[cty]c{2}gc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`UbaN12I`],site:`cacgag`,forwardRegex:`cacgag`,reverseRegex:`ctcgtg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`PspFI`],site:`cccagc`,forwardRegex:`c{3}agc`,reverseRegex:`gctg{3}`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`PfoI`],site:`tccngga`,forwardRegex:`tc{2}[abcdghkmnrstvwy]g{2}a`,reverseRegex:`tc{2}[abcdghkmnrstvwy]g{2}a`,topSnipOffset:1,bottomSnipOffset:6},{aliases:[`Sse8647I`],site:`aggwcct`,forwardRegex:`ag{2}[atw]c{2}t`,reverseRegex:`ag{2}[atw]c{2}t`,topSnipOffset:2,bottomSnipOffset:5},{aliases:[`KflI`,`Sse1825I`,`SanDI`],site:`gggwccc`,forwardRegex:`g{3}[atw]c{3}`,reverseRegex:`g{3}[atw]c{3}`,topSnipOffset:2,bottomSnipOffset:5},{aliases:[`Sth132I`],site:`cccg`,forwardRegex:`c{3}g`,reverseRegex:`cg{3}`,topSnipOffset:8,bottomSnipOffset:12,isType2S:!0},{aliases:[`CdpI`],site:`gcggag`,forwardRegex:`gcg{2}ag`,reverseRegex:`ctc{2}gc`,topSnipOffset:26,bottomSnipOffset:24,isType2S:!0},{aliases:[`Asp90I`],site:`acrygt`,forwardRegex:`ac[agr][cty]gt`,reverseRegex:`ac[agr][cty]gt`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`M.CviPI`],site:`gc`,forwardRegex:`gc`,reverseRegex:`gc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`MauBI`],site:`cgcgcgcg`,forwardRegex:`cgcgcgcg`,reverseRegex:`cgcgcgcg`,topSnipOffset:2,bottomSnipOffset:6},{aliases:[`CfrAI`],site:`gcannnnnnnngtgg`,forwardRegex:`gca[abcdghkmnrstvwy]{8}gtg{2}`,reverseRegex:`c{2}ac[abcdghkmnrstvwy]{8}tgc`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Eco851I`],site:`gtcannnnnntgay`,forwardRegex:`gtca[abcdghkmnrstvwy]{6}tga[cty]`,reverseRegex:`[agr]tca[abcdghkmnrstvwy]{6}tgac`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`BsgI`],site:`gtgcag`,forwardRegex:`gtgcag`,reverseRegex:`ctgcac`,topSnipOffset:22,bottomSnipOffset:20,isType2S:!0},{aliases:[`AquIV`],site:`grggaag`,forwardRegex:`g[agr]g{2}a{2}g`,reverseRegex:`ct{2}c{2}[cty]c`,topSnipOffset:26,bottomSnipOffset:24,isType2S:!0},{aliases:[`SciI`],site:`ctcgag`,forwardRegex:`ctcgag`,reverseRegex:`ctcgag`,topSnipOffset:3,bottomSnipOffset:3},{aliases:[`VpaK11AI`],site:`ggwcc`,forwardRegex:`g{2}[atw]c{2}`,reverseRegex:`g{2}[atw]c{2}`,topSnipOffset:0,bottomSnipOffset:5},{aliases:[`CviKI`,`CviJI`,`CviKI-1`],site:`rgcy`,forwardRegex:`[agr]gc[cty]`,reverseRegex:`[agr]gc[cty]`,topSnipOffset:2,bottomSnipOffset:2},{aliases:[`SnoI`,`VneI`,`ApaLI`,`Alw44I`],site:`gtgcac`,forwardRegex:`gtgcac`,reverseRegex:`gtgcac`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`BspD6I`],site:`gactc`,forwardRegex:`gactc`,reverseRegex:`gagtc`,topSnipOffset:9,bottomSnipOffset:11,isType2S:!0},{aliases:[`FatI`],site:`catg`,forwardRegex:`catg`,reverseRegex:`catg`,topSnipOffset:0,bottomSnipOffset:4},{aliases:[`ZraI`],site:`gacgtc`,forwardRegex:`gacgtc`,reverseRegex:`gacgtc`,topSnipOffset:3,bottomSnipOffset:3},{aliases:[`HineI`,`HinfIII`],site:`cgaat`,forwardRegex:`cga{2}t`,reverseRegex:`at{2}cg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`UbaF12I`],site:`ctacnnngtc`,forwardRegex:`ctac[abcdghkmnrstvwy]{3}gtc`,reverseRegex:`gac[abcdghkmnrstvwy]{3}gtag`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`Ppu10I`],site:`atgcat`,forwardRegex:`atgcat`,reverseRegex:`atgcat`,topSnipOffset:1,bottomSnipOffset:5},{aliases:[`ApaBI`],site:`gcannnnntgc`,forwardRegex:`gca[abcdghkmnrstvwy]{5}tgc`,reverseRegex:`gca[abcdghkmnrstvwy]{5}tgc`,topSnipOffset:8,bottomSnipOffset:3},{aliases:[`NhaXI`],site:`caagrag`,forwardRegex:`ca{2}g[agr]ag`,reverseRegex:`ct[cty]ct{2}g`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`PabI`],site:`gtac`,forwardRegex:`gtac`,reverseRegex:`gtac`,topSnipOffset:3,bottomSnipOffset:1},{aliases:[`HindI`],site:`cac`,forwardRegex:`cac`,reverseRegex:`gtg`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`M.PhiMx8I`],site:`ctssag`,forwardRegex:`ct[cgs]{2}ag`,reverseRegex:`ct[cgs]{2}ag`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`RhcI`],site:`tcatga`,forwardRegex:`tcatga`,reverseRegex:`tcatga`,topSnipOffset:1,bottomSnipOffset:1},{aliases:[`KpnI`],site:`ggtacc`,forwardRegex:`g{2}tac{2}`,reverseRegex:`g{2}tac{2}`,topSnipOffset:5,bottomSnipOffset:1},{aliases:[`BpuDI`,`Bpu10I`],site:`cctnagc`,forwardRegex:`c{2}t[abcdghkmnrstvwy]agc`,reverseRegex:`gct[abcdghkmnrstvwy]ag{2}`,topSnipOffset:2,bottomSnipOffset:5},{aliases:[`EcoP15I`],site:`cagcag`,forwardRegex:`cagcag`,reverseRegex:`ctgctg`,topSnipOffset:31,bottomSnipOffset:33,isType2S:!0},{aliases:[`Nli3877I`],site:`cycg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49
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50
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51
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package/dist/gensplore.js CHANGED
@@ -2907,7 +2907,7 @@ var Pi = Re(ji), Fi = Object.assign(Mi, {
2907
2907
  Panel: Ni,
2908
2908
  Title: Pi,
2909
2909
  Description: dt
2910
- }), Ii = "function e(e,t){if(!t||typeof t.sequence!=`string`)throw Error(`Expected an aligned DNA sequence.`);let n=t.sequence.toUpperCase();if(!e.length||n.length!==e.length)throw Error(`Aligned sequence length must match the reference.`);if(/[^ACGTRYSWKMBDHVN-]/.test(n))throw Error(`Aligned sequences must contain IUPAC DNA bases or deletion gaps (-).`);let r=[],i=0;for(let t=0;t<n.length;){if(n[t]===e[t]){t++;continue}let a=n[t]===`-`?`Deletion`:/[^ACGT]/.test(n[t]+e[t])?`Ambiguous`:`Substitution`,o=t+1;if(a===`Deletion`||a===`Ambiguous`)for(;o<n.length&&n[o]!==e[o]&&(a===`Deletion`?n[o]===`-`:n[o]!==`-`&&/[^ACGT]/.test(n[o]+e[o]));)o++;r.push({type:a,start:t,end:o,reference:e.slice(t,o),alternative:a===`Deletion`?``:n.slice(t,o)}),i+=o-t,t=o}let a=new Set;for(let n of t.insertions||[]){let t=n.position,o=typeof n.sequence==`string`?n.sequence.toUpperCase():``;if(!Number.isInteger(t)||t<0||t>e.length||a.has(t))throw Error(`Insertions need unique integer positions from 0 to the reference length.`);if(!o||/[^ACGTRYSWKMBDHVN]/.test(o))throw Error(`Insertions must contain ungapped IUPAC DNA bases.`);a.add(t),r.push({type:`Insertion`,start:t,end:t,reference:``,alternative:o}),i+=o.length}return r.sort((e,t)=>e.start-t.start||e.end-t.end),{name:t.name||`Alternative`,distance:i,differences:r}}const t=e=>{switch(e){case`TTT`:case`TTC`:return`F`;case`TTA`:case`TTG`:case`CTT`:case`CTC`:case`CTA`:case`CTG`:return`L`;case`ATT`:case`ATC`:case`ATA`:return`I`;case`ATG`:return`M`;case`GTT`:case`GTC`:case`GTA`:case`GTG`:return`V`;case`TCT`:case`TCC`:case`TCA`:case`TCG`:case`AGT`:case`AGC`:return`S`;case`CCT`:case`CCC`:case`CCA`:case`CCG`:return`P`;case`ACT`:case`ACC`:case`ACA`:case`ACG`:return`T`;case`GCT`:case`GCC`:case`GCA`:case`GCG`:return`A`;case`TAT`:case`TAC`:return`Y`;case`TAA`:case`TAG`:case`TGA`:return`*`;case`CAT`:case`CAC`:return`H`;case`CAA`:case`CAG`:return`Q`;case`AAT`:case`AAC`:return`N`;case`AAA`:case`AAG`:return`K`;case`GAT`:case`GAC`:return`D`;case`GAA`:case`GAG`:return`E`;case`TGT`:case`TGC`:return`C`;case`TGG`:return`W`;case`CGT`:case`CGC`:case`CGA`:case`CGG`:case`AGA`:case`AGG`:return`R`;case`GGT`:case`GGC`:case`GGA`:case`GGG`:return`G`;default:return`X`}};function n(e){let t=e.trim().split(/\\r?\\n/);if(!t[0]?.startsWith(`>`))throw Error(`Expected a FASTA header starting with >.`);if(t.slice(1).some(e=>e.startsWith(`>`)))throw Error(`Please supply exactly one FASTA record.`);let n=t.slice(1).join(``).replace(/\\s/g,``).toUpperCase();if(!n||/[^ACGTRYSWKMBDHVN]/.test(n))throw Error(`Expected an ungapped DNA sequence (IUPAC bases).`);return{name:t[0].slice(1).trim()||`Alternative`,sequence:n}}function r(e,t,n=128){let r=e.length,i=t.length;if(!r||!i)throw Error(`Both sequences must contain bases.`);if(Math.max(r,i)>1e5)throw Error(`Comparison supports sequences up to 100,000 bases.`);let a=()=>Error(`Sequences exceed the ${n}-edit comparison limit. Use complete sequences in the same orientation and with the same starting point.`);if(Math.abs(r-i)>n)throw a();let o=2*n+1,s=n+1,c=s*s,l=new Uint8Array((r+1)*o),u=(e,t,n)=>e<=t&&e<=n?0:t<=n?1:2,d=new Uint32Array(o*3).fill(c);d[n*3]=0;for(let e=1;e<=Math.min(i,n);e++)d[(e+n)*3+2]=e*s+1,l[e+n]=(e===1?0:2)<<4;for(let a=1;a<=r;a++){let r=new Uint32Array(o*3).fill(c);for(let f=Math.max(0,a-n);f<=Math.min(i,a+n);f++){let i=f-a+n,p=i*3;if(f===0){r[p+1]=a*s+1,l[a*o+i]=(a===1?0:1)<<2;continue}let m=u(d[p],d[p+1],d[p+2]);r[p]=Math.min(c,d[p+m]+(e[a-1]===t[f-1]?0:s));let h=0,g=0;if(i+1<o){let e=p+3,t=d[e]+s+1,n=d[e+1]+s,i=d[e+2]+s+1;h=u(t,n,i),r[p+1]=Math.min(c,t,n,i)}if(i>0){let e=p-3,t=r[e]+s+1,n=r[e+1]+s+1,i=r[e+2]+s;g=u(t,n,i),r[p+2]=Math.min(c,t,n,i)}l[a*o+i]=m|h<<2|g<<4}d=r}let f=(i-r+n)*3,p=u(d[f],d[f+1],d[f+2]),m=Math.floor(d[f+p]/s);if(m>n)throw a();let h=r,g=i,_=[];for(;h||g;){let r=l[h*o+g-h+n]>>p*2&3;p===0?_.push([e[--h],t[--g]]):p===1?_.push([e[--h],`-`]):_.push([`-`,t[--g]]),p=r}_.reverse();let v=[],y=0;for(let[e,t]of _){if(e!==t){let n=e===`-`?`Insertion`:t===`-`?`Deletion`:/[^ACGT]/.test(e+t)?`Ambiguous`:`Substitution`,r=v.at(-1);r&&r.type===n&&n!==`Substitution`&&n!==`Ambiguous`&&r.end===y?(r.reference+=e===`-`?``:e,r.alternative+=t===`-`?``:t,r.end+=e===`-`?0:1):v.push({type:n,start:y,end:y+(e===`-`?0:1),reference:e===`-`?``:e,alternative:t===`-`?``:t})}e!==`-`&&y++}return{distance:m,differences:v}}function i(e,t){return e.locations?.length?e.locations:e.start>e.end?[{start:e.start,end:t-1},{start:0,end:e.end}]:[{start:e.start,end:e.end}]}const a={A:`T`,T:`A`,C:`G`,G:`C`,R:`Y`,Y:`R`,S:`S`,W:`W`,K:`M`,M:`K`,B:`V`,V:`B`,D:`H`,H:`D`,N:`N`},o=e=>[...e].reverse().map(e=>a[e]||`N`).join(``),s=e=>{let n=``;for(let r=0;r+2<e.length;r+=3)n+=t(e.slice(r,r+3));return n},c=(e,t,n)=>{let r=e.notes?.[t];return(Array.isArray(r)?r[0]:r)??n};function l(e,t,n){if(![`CDS`,`mat_peptide`].includes(t.type))return null;let a=i(t,e.length),l=[];for(let t of a){if(!Number.isInteger(t.start)||!Number.isInteger(t.end)||t.start<0||t.end>=e.length||t.end<t.start)return{warning:`Unsupported coding location`,codons:[],changes:[]};for(let e=t.start;e<=t.end;e++)l.push(e)}t.strand<0&&l.reverse();let u=Number(c(t,`codon_start`,1))-1;if(![0,1,2].includes(u))return{warning:`Unsupported codon_start`,codons:[],changes:[]};l.splice(0,u);let d=Number(c(t,`transl_table`,1));if(![1,11].includes(d)||[`transl_except`,`ribosomal_slippage`,`exception`].some(e=>t.notes?.[e]))return{warning:`AA comparison unavailable for this translation table or exception`,codons:[],changes:[]};let f=new Map(l.map((e,t)=>[e,t])),p=e=>t.strand<0?o(e):e,m=l.map(t=>p(e[t])).join(``),h=s(m),g=[...h].map((e,t)=>({positions:l.slice(t*3,t*3+3),aminoAcid:e,codonIndex:t})),_=new Set,v=new Map,y=new Map,b=1/0,x=!1;for(let e of n)if(e.type===`Insertion`){let n=t.strand<0?e.start-1:e.start,r=f.get(n),i=t.strand<0?e.start:e.start-1;r>0&&l[r-1]===i?(y.set(r,p(e.alternative)),e.alternative.length%3&&(b=Math.min(b,r))):(f.has(n)||f.has(i))&&(x=!0)}else if(e.type===`Deletion`){let t=[];for(let n=e.start;n<e.end;n++){let e=f.get(n);e!==void 0&&(_.add(e),t.push(e))}t.length%3&&(b=Math.min(b,...t))}else for(let t=e.start;t<e.end;t++){let n=f.get(t);n!==void 0&&v.set(n,p(e.alternative[t-e.start]))}let S=``,C=[];for(let e=0;e<l.length;e++)C[e]=S.length,S+=y.get(e)||``,_.has(e)||(S+=v.get(e)??m[e]);let w=Math.floor(b/3),T=Number.isFinite(b)?h.slice(0,w):h,E=s(Number.isFinite(b)?S.slice(0,C[w*3]):S),D=[],O=e=>{let n=Math.min(e.start,Math.max(0,g.length-1)),r=g[n],i=e.start<g.length?(r?.positions[0]??l[0])+(t.strand<0?.5:-.5):(r?.positions[2]??l[0])+(t.strand<0?-.5:.5);return{...e,anchor:r?.positions[1]??l[0],...e.type===`Insertion`?{pointerPosition:i}:{},aaPosition:e.type===`Insertion`?e.start:e.start+1}};try{T&&E?D=r(T,E).differences.map(e=>O({...e,type:e.type===`Ambiguous`?/X/.test(e.reference+e.alternative)?`Ambiguous`:`Substitution`:e.type})):(T||E)&&(D=[O({type:T?`Deletion`:`Insertion`,start:0,end:T.length,reference:T,alternative:E})])}catch{return{codons:g,changes:[],warning:`AA comparison exceeds the alignment limit`}}return Number.isFinite(b)&&D.push(O({type:`Frameshift`,start:w,end:w+1,reference:``,alternative:``})),{codons:g,changes:D,warning:x?`Insertion at a coding boundary: AA assignment is uncertain`:void 0}}function u(e,t,n){return t.map(t=>l(e,t,n))}self.onmessage=({data:t})=>{try{let i=t.alignedSequence||n(t.fasta),a=t.alignedSequence?e(t.reference,i):r(t.reference,i.sequence);self.postMessage({...a,name:i.name,proteins:u(t.reference,t.features||[],a.differences)})}catch(e){self.postMessage({error:e.message})}};", Li = typeof self < "u" && self.Blob && new Blob(["URL.revokeObjectURL(import.meta.url);", Ii], { type: "text/javascript;charset=utf-8" });
2910
+ }), Ii = "function e(e,t){if(!t||typeof t.sequence!=`string`)throw Error(`Expected an aligned DNA sequence.`);let n=t.sequence.toUpperCase();if(!e.length||n.length!==e.length)throw Error(`Aligned sequence length must match the reference.`);if(/[^ACGTRYSWKMBDHVN-]/.test(n))throw Error(`Aligned sequences must contain IUPAC DNA bases or deletion gaps (-).`);let r=[],i=0;for(let t=0;t<n.length;){if(n[t]===e[t]){t++;continue}let a=n[t]===`-`?`Deletion`:/[^ACGT]/.test(n[t]+e[t])?`Ambiguous`:`Substitution`,o=t+1;if(a===`Deletion`||a===`Ambiguous`)for(;o<n.length&&n[o]!==e[o]&&(a===`Deletion`?n[o]===`-`:n[o]!==`-`&&/[^ACGT]/.test(n[o]+e[o]));)o++;r.push({type:a,start:t,end:o,reference:e.slice(t,o),alternative:a===`Deletion`?``:n.slice(t,o)}),i+=o-t,t=o}let a=new Set;for(let n of t.insertions||[]){let t=n.position,o=typeof n.sequence==`string`?n.sequence.toUpperCase():``;if(!Number.isInteger(t)||t<0||t>e.length||a.has(t))throw Error(`Insertions need unique integer positions from 0 to the reference length.`);if(!o||/[^ACGTRYSWKMBDHVN]/.test(o))throw Error(`Insertions must contain ungapped IUPAC DNA bases.`);a.add(t),r.push({type:`Insertion`,start:t,end:t,reference:``,alternative:o}),i+=o.length}return r.sort((e,t)=>e.start-t.start||e.end-t.end),{name:t.name||`Alternative`,distance:i,differences:r}}const t=e=>{switch(e){case`TTT`:case`TTC`:return`F`;case`TTA`:case`TTG`:case`CTT`:case`CTC`:case`CTA`:case`CTG`:return`L`;case`ATT`:case`ATC`:case`ATA`:return`I`;case`ATG`:return`M`;case`GTT`:case`GTC`:case`GTA`:case`GTG`:return`V`;case`TCT`:case`TCC`:case`TCA`:case`TCG`:case`AGT`:case`AGC`:return`S`;case`CCT`:case`CCC`:case`CCA`:case`CCG`:return`P`;case`ACT`:case`ACC`:case`ACA`:case`ACG`:return`T`;case`GCT`:case`GCC`:case`GCA`:case`GCG`:return`A`;case`TAT`:case`TAC`:return`Y`;case`TAA`:case`TAG`:case`TGA`:return`*`;case`CAT`:case`CAC`:return`H`;case`CAA`:case`CAG`:return`Q`;case`AAT`:case`AAC`:return`N`;case`AAA`:case`AAG`:return`K`;case`GAT`:case`GAC`:return`D`;case`GAA`:case`GAG`:return`E`;case`TGT`:case`TGC`:return`C`;case`TGG`:return`W`;case`CGT`:case`CGC`:case`CGA`:case`CGG`:case`AGA`:case`AGG`:return`R`;case`GGT`:case`GGC`:case`GGA`:case`GGG`:return`G`;default:return`X`}};function n(e){let t=e.trim().split(/\\r?\\n/);if(!t[0]?.startsWith(`>`))throw Error(`Expected a FASTA header starting with >.`);if(t.slice(1).some(e=>e.startsWith(`>`)))throw Error(`Please supply exactly one FASTA record.`);let n=t.slice(1).join(``).replace(/\\s/g,``).toUpperCase();if(!n||/[^ACGTRYSWKMBDHVN]/.test(n))throw Error(`Expected an ungapped DNA sequence (IUPAC bases).`);return{name:t[0].slice(1).trim()||`Alternative`,sequence:n}}function r(e,t,n=128){let r=e.length,i=t.length;if(!r||!i)throw Error(`Both sequences must contain bases.`);if(Math.max(r,i)>1e5)throw Error(`Comparison supports sequences up to 100,000 bases.`);let a=()=>Error(`Sequences exceed the ${n}-edit comparison limit. Use complete sequences in the same orientation and with the same starting point.`);if(Math.abs(r-i)>n)throw a();let o=2*n+1,s=n+1,c=s*s,l=new Uint8Array((r+1)*o),u=(e,t,n)=>e<=t&&e<=n?0:t<=n?1:2,d=new Uint32Array(o*3).fill(c);d[n*3]=0;for(let e=1;e<=Math.min(i,n);e++)d[(e+n)*3+2]=e*s+1,l[e+n]=(e===1?0:2)<<4;for(let a=1;a<=r;a++){let r=new Uint32Array(o*3).fill(c);for(let f=Math.max(0,a-n);f<=Math.min(i,a+n);f++){let i=f-a+n,p=i*3;if(f===0){r[p+1]=a*s+1,l[a*o+i]=(a===1?0:1)<<2;continue}let m=u(d[p],d[p+1],d[p+2]);r[p]=Math.min(c,d[p+m]+(e[a-1]===t[f-1]?0:s));let h=0,g=0;if(i+1<o){let e=p+3,t=d[e]+s+1,n=d[e+1]+s,i=d[e+2]+s+1;h=u(t,n,i),r[p+1]=Math.min(c,t,n,i)}if(i>0){let e=p-3,t=r[e]+s+1,n=r[e+1]+s+1,i=r[e+2]+s;g=u(t,n,i),r[p+2]=Math.min(c,t,n,i)}l[a*o+i]=m|h<<2|g<<4}d=r}let f=(i-r+n)*3,p=u(d[f],d[f+1],d[f+2]),m=Math.floor(d[f+p]/s);if(m>n)throw a();let h=r,g=i,_=[];for(;h||g;){let r=l[h*o+g-h+n]>>p*2&3;p===0?_.push([e[--h],t[--g]]):p===1?_.push([e[--h],`-`]):_.push([`-`,t[--g]]),p=r}_.reverse();let v=[],y=0;for(let[e,t]of _){if(e!==t){let n=e===`-`?`Insertion`:t===`-`?`Deletion`:/[^ACGT]/.test(e+t)?`Ambiguous`:`Substitution`,r=v.at(-1);r&&r.type===n&&n!==`Substitution`&&n!==`Ambiguous`&&r.end===y?(r.reference+=e===`-`?``:e,r.alternative+=t===`-`?``:t,r.end+=e===`-`?0:1):v.push({type:n,start:y,end:y+(e===`-`?0:1),reference:e===`-`?``:e,alternative:t===`-`?``:t})}e!==`-`&&y++}return{distance:m,differences:v}}function i(e,t){return e.locations?.length?e.locations:e.start>e.end?[{start:e.start,end:t-1},{start:0,end:e.end}]:[{start:e.start,end:e.end}]}const a={A:`T`,T:`A`,C:`G`,G:`C`,R:`Y`,Y:`R`,S:`S`,W:`W`,K:`M`,M:`K`,B:`V`,V:`B`,D:`H`,H:`D`,N:`N`},o=e=>[...e].reverse().map(e=>a[e]||`N`).join(``),s=e=>{let n=``;for(let r=0;r+2<e.length;r+=3)n+=t(e.slice(r,r+3));return n},c=(e,t,n)=>{let r=e.notes?.[t];return(Array.isArray(r)?r[0]:r)??n};function l(e,t,n){if(![`CDS`,`mat_peptide`].includes(t.type))return null;let a=i(t,e.length),l=[];for(let t of a){if(!Number.isInteger(t.start)||!Number.isInteger(t.end)||t.start<0||t.end>=e.length||t.end<t.start)return{warning:`Unsupported coding location`,codons:[],changes:[]};for(let e=t.start;e<=t.end;e++)l.push(e)}t.strand<0&&l.reverse();let u=Number(c(t,`codon_start`,1))-1;if(![0,1,2].includes(u))return{warning:`Unsupported codon_start`,codons:[],changes:[]};l.splice(0,u);let d=Number(c(t,`transl_table`,1));if(![1,11].includes(d)||[`transl_except`,`ribosomal_slippage`,`exception`].some(e=>t.notes?.[e]))return{warning:`AA comparison unavailable for this translation table or exception`,codons:[],changes:[]};let f=new Map(l.map((e,t)=>[e,t])),p=e=>t.strand<0?o(e):e,m=l.map(t=>p(e[t])).join(``),h=s(m),g=[...h].map((e,t)=>({positions:l.slice(t*3,t*3+3),aminoAcid:e,codonIndex:t})),_=new Set,v=new Map,y=new Map,b=1/0,x=!1;for(let e of n)if(e.type===`Insertion`){let n=t.strand<0?e.start-1:e.start,r=f.get(n),i=t.strand<0?e.start:e.start-1;r>0&&l[r-1]===i?(y.set(r,p(e.alternative)),e.alternative.length%3&&(b=Math.min(b,r))):(f.has(n)||f.has(i))&&(x=!0)}else if(e.type===`Deletion`){let t=[];for(let n=e.start;n<e.end;n++){let e=f.get(n);e!==void 0&&(_.add(e),t.push(e))}t.length%3&&(b=Math.min(b,...t))}else for(let t=e.start;t<e.end;t++){let n=f.get(t);n!==void 0&&v.set(n,p(e.alternative[t-e.start]))}let S=``,C=[];for(let e=0;e<l.length;e++)C[e]=S.length,S+=y.get(e)||``,_.has(e)||(S+=v.get(e)??m[e]);let w=Math.floor(b/3),T=Number.isFinite(b)?h.slice(0,w):h,E=s(Number.isFinite(b)?S.slice(0,C[w*3]):S),D=[],O=e=>{let n=Math.min(e.start,Math.max(0,g.length-1)),r=g[n],i=e.start<g.length?(r?.positions[0]??l[0])+(t.strand<0?.5:-.5):(r?.positions[2]??l[0])+(t.strand<0?-.5:.5);return{...e,anchor:r?.positions[1]??l[0],...e.type===`Insertion`?{pointerPosition:i}:{},aaPosition:e.type===`Insertion`?e.start:e.start+1}};try{if(T&&E){let e=[];for(let t of r(T,E).differences){let n={...t,type:t.type===`Ambiguous`?/X/.test(t.reference+t.alternative)?`Ambiguous`:`Substitution`:t.type},r=e.at(-1);n.type===`Ambiguous`&&r?.type===`Ambiguous`&&r.end===n.start?(r.end=n.end,r.reference+=n.reference,r.alternative+=n.alternative):e.push(n)}D=e.map(O)}else(T||E)&&(D=[O({type:T?`Deletion`:`Insertion`,start:0,end:T.length,reference:T,alternative:E})])}catch{return{codons:g,changes:[],warning:`AA comparison exceeds the alignment limit`}}return Number.isFinite(b)&&D.push(O({type:`Frameshift`,start:w,end:w+1,reference:``,alternative:``})),{codons:g,changes:D,warning:x?`Insertion at a coding boundary: AA assignment is uncertain`:void 0}}function u(e,t,n){return t.map(t=>l(e,t,n))}self.onmessage=({data:t})=>{try{let i=t.alignedSequence||n(t.fasta),a=t.alignedSequence?e(t.reference,i):r(t.reference,i.sequence);self.postMessage({...a,name:i.name,proteins:u(t.reference,t.features||[],a.differences)})}catch(e){self.postMessage({error:e.message})}};", Li = typeof self < "u" && self.Blob && new Blob(["URL.revokeObjectURL(import.meta.url);", Ii], { type: "text/javascript;charset=utf-8" });
2911
2911
  function Ri(e) {
2912
2912
  let t;
2913
2913
  try {
@@ -4275,18 +4275,18 @@ var Ao = ({ parsedSequence: e, rowStart: t, rowEnd: n, setHoveredInfo: r, rowId:
4275
4275
  let i = ba(r, e.locations, w.length);
4276
4276
  return i >= t && i < n;
4277
4277
  }).sort((e, t) => e.anchor - t.anchor).map((n) => {
4278
- let r = n.end > n.start + 1 ? `${n.start + 1}–${n.end}` : n.start + 1, i = n.type === "Insertion" ? `AA INS +${n.alternative} · after ${n.aaPosition}` : n.type === "Deletion" ? `AA DEL ${n.reference} · ${r}` : n.type === "Frameshift" ? `Frame shift · AA ${n.aaPosition}` : `AA ${n.reference}${n.aaPosition} → ${n.alternative}`, a = Math.max(8, Math.floor((P - 20) / 7)), o = i.length > a ? `${i.slice(0, a - 1)}…` : i, s = Math.min(P, o.length * 7 + 16), c = ((n.pointerPosition ?? n.anchor) - t) * C, l = Math.max(-C / 2, Math.min(c - s / 2, P - s)), u = R[e.lane], d = u.findIndex((e) => e + 8 <= l);
4279
- d === -1 && (d = u.length), u[d] = l + s;
4280
- let f = n.type === "Insertion" ? "#1d4ed8" : n.type === "Deletion" ? "#b91c1c" : ["Frameshift", "Ambiguous"].includes(n.type) ? "#6d28d9" : "#92400e";
4278
+ let r = n.end > n.start + 1 ? `${n.start + 1}–${n.end}` : n.start + 1, i = n.type === "Insertion" ? `AA INS +${n.alternative} · after ${n.aaPosition}` : n.type === "Deletion" ? `AA DEL ${n.reference} · ${r}` : n.type === "Frameshift" ? `Frame shift · AA ${n.aaPosition}` : n.type === "Ambiguous" ? `Coverage gap · AA ${r}` : `AA ${n.reference}${n.aaPosition} → ${n.alternative}`, a = Math.max(8, Math.floor((P - 20) / 7)), o = n.type === "Ambiguous" ? "Coverage gap" : i, s = o.length > a ? `${o.slice(0, a - 1)}…` : o, c = Math.min(P, s.length * 7 + 16), l = ((n.pointerPosition ?? n.anchor) - t) * C, u = Math.max(-C / 2, Math.min(l - c / 2, P - c)), d = R[e.lane], f = d.findIndex((e) => e + 8 <= u);
4279
+ f === -1 && (f = d.length), d[f] = u + c;
4280
+ let p = n.type === "Insertion" ? "#1d4ed8" : n.type === "Deletion" ? "#b91c1c" : ["Frameshift", "Ambiguous"].includes(n.type) ? "#6d28d9" : "#92400e";
4281
4281
  return {
4282
4282
  ...n,
4283
4283
  text: i,
4284
- label: o,
4285
- labelWidth: s,
4286
- anchor: c,
4287
- left: l,
4288
- lane: d,
4289
- color: f
4284
+ label: s,
4285
+ labelWidth: c,
4286
+ anchor: l,
4287
+ left: u,
4288
+ lane: f,
4289
+ color: p
4290
4290
  };
4291
4291
  });
4292
4292
  });
@@ -4402,7 +4402,7 @@ var Ao = ({ parsedSequence: e, rowStart: t, rowEnd: n, setHoveredInfo: r, rowId:
4402
4402
  width: t.labelWidth,
4403
4403
  height: 20,
4404
4404
  rx: 4,
4405
- fill: "white",
4405
+ fill: t.type === "Ambiguous" ? "#f5f3ff" : "white",
4406
4406
  stroke: t.color
4407
4407
  }),
4408
4408
  /* @__PURE__ */ x("text", {
@@ -4482,7 +4482,7 @@ var Ao = ({ parsedSequence: e, rowStart: t, rowEnd: n, setHoveredInfo: r, rowId:
4482
4482
  locusTag: e.notes?.locus_tag || null
4483
4483
  }),
4484
4484
  onMouseLeave: () => r(null),
4485
- fillOpacity: .75,
4485
+ fillOpacity: e.proteinChanges.some((e) => e.type === "Ambiguous" && t.codonIndex >= e.start && t.codonIndex < e.end) ? .35 : .75,
4486
4486
  style: { cursor: "pointer" },
4487
4487
  children: t.aminoAcid
4488
4488
  }), t.middle > 2 && s > -.5 && /* @__PURE__ */ x("text", {
@@ -23730,8 +23730,8 @@ Z(wC, "jsonToJsonString");
23730
23730
  //#endregion
23731
23731
  //#region src/comparison/parseReference.mjs
23732
23732
  async function TC(e) {
23733
- let t = await Dv(e);
23734
- for (let e of t) e.parsedSequence?.sequence && (e.parsedSequence.sequence = e.parsedSequence.sequence.toUpperCase().replace(/U/g, "T"));
23733
+ let t = await Dv(e, { isOligo: !0 });
23734
+ for (let e of t) e.parsedSequence?.sequence && (e.parsedSequence.sequence = e.parsedSequence.sequence.toUpperCase());
23735
23735
  return t;
23736
23736
  }
23737
23737
  //#endregion
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "gensplore",
3
- "version": "0.0.11",
3
+ "version": "0.0.12",
4
4
  "description": "React component for displaying genbank files",
5
5
  "keywords": [
6
6
  "genbank",