@datagrok/sequence-translator 1.10.13 → 1.10.15

package/files/samples/sirna-demo.csv

@@ -0,0 +1,38 @@
+id,target,status,length_s,length_as,sense_helm,antisense_helm,oligo_helm,tm_c,ic50_nm,kd_pct,off_target_count
+siR-0001,KRAS,lead,19,19,RNA1{m(G)[sp].m(A)[sp].m(C)p.m(U)p.m(G)p.m(A)p.m(A)p.m(U)p.m(A)p.m(U)p.m(A)p.m(A)p.m(A)p.m(C)p.m(U)p.m(U)p.m(G)[sp].m(U)[sp].m(G).[L3]}$$$$,RNA1{m(C)[sp].m(A)[sp].m(C)p.m(A)p.m(A)p.m(G)p.m(U)p.m(U)p.m(U)p.m(A)p.m(U)p.m(A)p.m(U)p.m(U)p.m(C)p.m(A)p.m(G)[sp].m(U)[sp].m(C)}$$$$,RNA1{m(G)[sp].m(A)[sp].m(C)p.m(U)p.m(G)p.m(A)p.m(A)p.m(U)p.m(A)p.m(U)p.m(A)p.m(A)p.m(A)p.m(C)p.m(U)p.m(U)p.m(G)[sp].m(U)[sp].m(G).[L3]}|RNA2{m(C)[sp].m(A)[sp].m(C)p.m(A)p.m(A)p.m(G)p.m(U)p.m(U)p.m(U)p.m(A)p.m(U)p.m(A)p.m(U)p.m(U)p.m(C)p.m(A)p.m(G)[sp].m(U)[sp].m(C)}$$$$,76.9,0.29,99,7
+siR-0002,KRAS,clinical,19,19,RNA1{[Chol].m(G)[sp].[fl2r](A)[sp].m(C)p.[fl2r](U)p.m(G)p.[fl2r](A)p.m(A)p.[fl2r](U)p.m(A)p.[fl2r](U)p.m(A)p.[fl2r](A)p.m(A)p.[fl2r](C)p.m(U)p.[fl2r](U)p.m(G)[sp].[fl2r](U)[sp].m(G).[L3]}$$$$,RNA1{m(C)[sp].[fl2r](A)[sp].m(C)p.[fl2r](A)p.m(A)p.[fl2r](G)p.m(U)p.[fl2r](U)p.m(U)p.[fl2r](A)p.m(U)p.[fl2r](A)p.m(U)p.[fl2r](U)p.m(C)p.[fl2r](A)p.m(G)[sp].[fl2r](U)[sp].m(C)}$$$$,RNA1{[Chol].m(G)[sp].[fl2r](A)[sp].m(C)p.[fl2r](U)p.m(G)p.[fl2r](A)p.m(A)p.[fl2r](U)p.m(A)p.[fl2r](U)p.m(A)p.[fl2r](A)p.m(A)p.[fl2r](C)p.m(U)p.[fl2r](U)p.m(G)[sp].[fl2r](U)[sp].m(G).[L3]}|RNA2{m(C)[sp].[fl2r](A)[sp].m(C)p.[fl2r](A)p.m(A)p.[fl2r](G)p.m(U)p.[fl2r](U)p.m(U)p.[fl2r](A)p.m(U)p.[fl2r](A)p.m(U)p.[fl2r](U)p.m(C)p.[fl2r](A)p.m(G)[sp].[fl2r](U)[sp].m(C)}$$$$,83.8,0.28,99,7
+siR-0003,KRAS,parent,19,19,RNA1{r(G)p.r(A)p.r(C)p.r(U)p.r(G)p.r(A)p.r(A)p.r(U)p.r(A)p.r(U)p.r(A)p.r(A)p.r(A)p.r(C)p.r(U)p.r(U)p.r(G)p.r(U)p.r(G)}$$$$,RNA1{r(C)p.r(A)p.r(C)p.r(A)p.r(A)p.r(G)p.r(U)p.r(U)p.r(U)p.r(A)p.r(U)p.r(A)p.r(U)p.r(U)p.r(C)p.r(A)p.r(G)p.r(U)p.r(C)}$$$$,RNA1{r(G)p.r(A)p.r(C)p.r(U)p.r(G)p.r(A)p.r(A)p.r(U)p.r(A)p.r(U)p.r(A)p.r(A)p.r(A)p.r(C)p.r(U)p.r(U)p.r(G)p.r(U)p.r(G)}|RNA2{r(C)p.r(A)p.r(C)p.r(A)p.r(A)p.r(G)p.r(U)p.r(U)p.r(U)p.r(A)p.r(U)p.r(A)p.r(U)p.r(U)p.r(C)p.r(A)p.r(G)p.r(U)p.r(C)}$$$$,59.6,0.17,65,4
+siR-0004,PCSK9,lead,19,19,RNA1{m(U)[sp].m(C)[sp].m(A)p.m(G)p.m(G)p.m(A)p.m(C)p.m(A)p.m(U)p.m(G)p.m(G)p.m(A)p.m(A)p.m(G)p.m(C)p.m(U)p.m(G)[sp].m(A)[sp].m(A).[L3]}$$$$,RNA1{m(U)[sp].m(U)[sp].m(C)p.m(A)p.m(G)p.m(C)p.m(U)p.m(U)p.m(C)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(C)p.m(C)p.m(U)[sp].m(G)[sp].m(A)}$$$$,RNA1{m(U)[sp].m(C)[sp].m(A)p.m(G)p.m(G)p.m(A)p.m(C)p.m(A)p.m(U)p.m(G)p.m(G)p.m(A)p.m(A)p.m(G)p.m(C)p.m(U)p.m(G)[sp].m(A)[sp].m(A).[L3]}|RNA2{m(U)[sp].m(U)[sp].m(C)p.m(A)p.m(G)p.m(C)p.m(U)p.m(U)p.m(C)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(C)p.m(C)p.m(U)[sp].m(G)[sp].m(A)}$$$$,79,0.38,99,10
+siR-0005,PCSK9,clinical,19,19,RNA1{[Chol].m(U)[sp].[fl2r](C)[sp].m(A)p.[fl2r](G)p.m(G)p.[fl2r](A)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(G)p.[fl2r](A)p.m(A)p.[fl2r](G)p.m(C)p.[fl2r](U)p.m(G)[sp].[fl2r](A)[sp].m(A).[L3]}$$$$,RNA1{m(U)[sp].[fl2r](U)[sp].m(C)p.[fl2r](A)p.m(G)p.[fl2r](C)p.m(U)p.[fl2r](U)p.m(C)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](U)p.m(C)p.[fl2r](C)p.m(U)[sp].[fl2r](G)[sp].m(A)}$$$$,RNA1{[Chol].m(U)[sp].[fl2r](C)[sp].m(A)p.[fl2r](G)p.m(G)p.[fl2r](A)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(G)p.[fl2r](A)p.m(A)p.[fl2r](G)p.m(C)p.[fl2r](U)p.m(G)[sp].[fl2r](A)[sp].m(A).[L3]}|RNA2{m(U)[sp].[fl2r](U)[sp].m(C)p.[fl2r](A)p.m(G)p.[fl2r](C)p.m(U)p.[fl2r](U)p.m(C)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](U)p.m(C)p.[fl2r](C)p.m(U)[sp].[fl2r](G)[sp].m(A)}$$$$,82.1,0.23,99,5
+siR-0006,PCSK9,parent,19,19,RNA1{r(U)p.r(C)p.r(A)p.r(G)p.r(G)p.r(A)p.r(C)p.r(A)p.r(U)p.r(G)p.r(G)p.r(A)p.r(A)p.r(G)p.r(C)p.r(U)p.r(G)p.r(A)p.r(A)}$$$$,RNA1{r(U)p.r(U)p.r(C)p.r(A)p.r(G)p.r(C)p.r(U)p.r(U)p.r(C)p.r(C)p.r(A)p.r(U)p.r(G)p.r(U)p.r(C)p.r(C)p.r(U)p.r(G)p.r(A)}$$$$,RNA1{r(U)p.r(C)p.r(A)p.r(G)p.r(G)p.r(A)p.r(C)p.r(A)p.r(U)p.r(G)p.r(G)p.r(A)p.r(A)p.r(G)p.r(C)p.r(U)p.r(G)p.r(A)p.r(A)}|RNA2{r(U)p.r(U)p.r(C)p.r(A)p.r(G)p.r(C)p.r(U)p.r(U)p.r(C)p.r(C)p.r(A)p.r(U)p.r(G)p.r(U)p.r(C)p.r(C)p.r(U)p.r(G)p.r(A)}$$$$,64.8,0.56,81,15
+siR-0007,TTR,lead,19,19,RNA1{m(A)[sp].m(U)[sp].m(U)p.m(G)p.m(G)p.m(G)p.m(A)p.m(U)p.m(U)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(G)p.m(A)[sp].m(A)[sp].m(U).[L3]}$$$$,RNA1{m(A)[sp].m(U)[sp].m(U)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(A)p.m(A)p.m(U)p.m(C)p.m(C)p.m(C)p.m(A)[sp].m(A)[sp].m(U)}$$$$,RNA1{m(A)[sp].m(U)[sp].m(U)p.m(G)p.m(G)p.m(G)p.m(A)p.m(U)p.m(U)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(G)p.m(A)[sp].m(A)[sp].m(U).[L3]}|RNA2{m(A)[sp].m(U)[sp].m(U)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(A)p.m(A)p.m(U)p.m(C)p.m(C)p.m(C)p.m(A)[sp].m(A)[sp].m(U)}$$$$,78.1,0.34,99,9
+siR-0008,TTR,clinical,19,19,RNA1{[Chol].m(A)[sp].[fl2r](U)[sp].m(U)p.[fl2r](G)p.m(G)p.[fl2r](G)p.m(A)p.[fl2r](U)p.m(U)p.[fl2r](U)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](G)p.m(A)[sp].[fl2r](A)[sp].m(U).[L3]}$$$$,RNA1{m(A)[sp].[fl2r](U)[sp].m(U)p.[fl2r](C)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](A)p.m(A)p.[fl2r](A)p.m(U)p.[fl2r](C)p.m(C)p.[fl2r](C)p.m(A)[sp].[fl2r](A)[sp].m(U)}$$$$,RNA1{[Chol].m(A)[sp].[fl2r](U)[sp].m(U)p.[fl2r](G)p.m(G)p.[fl2r](G)p.m(A)p.[fl2r](U)p.m(U)p.[fl2r](U)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](G)p.m(A)[sp].[fl2r](A)[sp].m(U).[L3]}|RNA2{m(A)[sp].[fl2r](U)[sp].m(U)p.[fl2r](C)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](A)p.m(A)p.[fl2r](A)p.m(U)p.[fl2r](C)p.m(C)p.[fl2r](C)p.m(A)[sp].[fl2r](A)[sp].m(U)}$$$$,80.7,0.19,99,4
+siR-0009,TTR,parent,19,19,RNA1{r(A)p.r(U)p.r(U)p.r(G)p.r(G)p.r(G)p.r(A)p.r(U)p.r(U)p.r(U)p.r(C)p.r(A)p.r(U)p.r(G)p.r(A)p.r(G)p.r(A)p.r(A)p.r(U)}$$$$,RNA1{r(A)p.r(U)p.r(U)p.r(C)p.r(U)p.r(C)p.r(A)p.r(U)p.r(G)p.r(A)p.r(A)p.r(A)p.r(U)p.r(C)p.r(C)p.r(C)p.r(A)p.r(A)p.r(U)}$$$$,RNA1{r(A)p.r(U)p.r(U)p.r(G)p.r(G)p.r(G)p.r(A)p.r(U)p.r(U)p.r(U)p.r(C)p.r(A)p.r(U)p.r(G)p.r(A)p.r(G)p.r(A)p.r(A)p.r(U)}|RNA2{r(A)p.r(U)p.r(U)p.r(C)p.r(U)p.r(C)p.r(A)p.r(U)p.r(G)p.r(A)p.r(A)p.r(A)p.r(U)p.r(C)p.r(C)p.r(C)p.r(A)p.r(A)p.r(U)}$$$$,59.5,0.16,65,3
+siR-0010,APOC3,lead,19,19,RNA1{m(A)[sp].m(U)[sp].m(C)p.m(A)p.m(G)p.m(U)p.m(A)p.m(C)p.m(G)p.m(U)p.m(U)p.m(G)p.m(U)p.m(C)p.m(A)p.m(A)p.m(C)[sp].m(G)[sp].m(G).[L3]}$$$$,RNA1{m(C)[sp].m(C)[sp].m(G)p.m(U)p.m(U)p.m(G)p.m(A)p.m(C)p.m(A)p.m(A)p.m(C)p.m(G)p.m(U)p.m(A)p.m(C)p.m(U)p.m(G)[sp].m(A)[sp].m(U)}$$$$,RNA1{m(A)[sp].m(U)[sp].m(C)p.m(A)p.m(G)p.m(U)p.m(A)p.m(C)p.m(G)p.m(U)p.m(U)p.m(G)p.m(U)p.m(C)p.m(A)p.m(A)p.m(C)[sp].m(G)[sp].m(G).[L3]}|RNA2{m(C)[sp].m(C)[sp].m(G)p.m(U)p.m(U)p.m(G)p.m(A)p.m(C)p.m(A)p.m(A)p.m(C)p.m(G)p.m(U)p.m(A)p.m(C)p.m(U)p.m(G)[sp].m(A)[sp].m(U)}$$$$,77.5,0.32,99,8
+siR-0011,APOC3,clinical,19,19,RNA1{[Chol].m(A)[sp].[fl2r](U)[sp].m(C)p.[fl2r](A)p.m(G)p.[fl2r](U)p.m(A)p.[fl2r](C)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](A)p.m(C)[sp].[fl2r](G)[sp].m(G).[L3]}$$$$,RNA1{m(C)[sp].[fl2r](C)[sp].m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](C)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](G)p.m(U)p.[fl2r](A)p.m(C)p.[fl2r](U)p.m(G)[sp].[fl2r](A)[sp].m(U)}$$$$,RNA1{[Chol].m(A)[sp].[fl2r](U)[sp].m(C)p.[fl2r](A)p.m(G)p.[fl2r](U)p.m(A)p.[fl2r](C)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](A)p.m(C)[sp].[fl2r](G)[sp].m(G).[L3]}|RNA2{m(C)[sp].[fl2r](C)[sp].m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](C)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](G)p.m(U)p.[fl2r](A)p.m(C)p.[fl2r](U)p.m(G)[sp].[fl2r](A)[sp].m(U)}$$$$,76.8,0.07,92,1
+siR-0012,APOC3,parent,19,19,RNA1{r(A)p.r(U)p.r(C)p.r(A)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(U)p.r(G)p.r(U)p.r(C)p.r(A)p.r(A)p.r(C)p.r(G)p.r(G)}$$$$,RNA1{r(C)p.r(C)p.r(G)p.r(U)p.r(U)p.r(G)p.r(A)p.r(C)p.r(A)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(U)p.r(G)p.r(A)p.r(U)}$$$$,RNA1{r(A)p.r(U)p.r(C)p.r(A)p.r(G)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(U)p.r(G)p.r(U)p.r(C)p.r(A)p.r(A)p.r(C)p.r(G)p.r(G)}|RNA2{r(C)p.r(C)p.r(G)p.r(U)p.r(U)p.r(G)p.r(A)p.r(C)p.r(A)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(C)p.r(U)p.r(G)p.r(A)p.r(U)}$$$$,60.2,0.21,67,5
+siR-0013,ANGPTL3,lead,19,19,RNA1{m(G)[sp].m(A)[sp].m(A)p.m(C)p.m(U)p.m(C)p.m(U)p.m(G)p.m(A)p.m(U)p.m(G)p.m(A)p.m(G)p.m(G)p.m(C)p.m(A)p.m(U)[sp].m(U)[sp].m(C).[L3]}$$$$,RNA1{m(G)[sp].m(A)[sp].m(A)p.m(U)p.m(G)p.m(C)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(C)p.m(A)p.m(G)p.m(A)p.m(G)p.m(U)[sp].m(U)[sp].m(C)}$$$$,RNA1{m(G)[sp].m(A)[sp].m(A)p.m(C)p.m(U)p.m(C)p.m(U)p.m(G)p.m(A)p.m(U)p.m(G)p.m(A)p.m(G)p.m(G)p.m(C)p.m(A)p.m(U)[sp].m(U)[sp].m(C).[L3]}|RNA2{m(G)[sp].m(A)[sp].m(A)p.m(U)p.m(G)p.m(C)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(C)p.m(A)p.m(G)p.m(A)p.m(G)p.m(U)[sp].m(U)[sp].m(C)}$$$$,76.6,0.28,99,7
+siR-0014,ANGPTL3,clinical,19,19,RNA1{[Chol].m(G)[sp].[fl2r](A)[sp].m(A)p.[fl2r](C)p.m(U)p.[fl2r](C)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](A)p.m(G)p.[fl2r](G)p.m(C)p.[fl2r](A)p.m(U)[sp].[fl2r](U)[sp].m(C).[L3]}$$$$,RNA1{m(G)[sp].[fl2r](A)[sp].m(A)p.[fl2r](U)p.m(G)p.[fl2r](C)p.m(C)p.[fl2r](U)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](G)p.m(A)p.[fl2r](G)p.m(U)[sp].[fl2r](U)[sp].m(C)}$$$$,RNA1{[Chol].m(G)[sp].[fl2r](A)[sp].m(A)p.[fl2r](C)p.m(U)p.[fl2r](C)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](A)p.m(G)p.[fl2r](G)p.m(C)p.[fl2r](A)p.m(U)[sp].[fl2r](U)[sp].m(C).[L3]}|RNA2{m(G)[sp].[fl2r](A)[sp].m(A)p.[fl2r](U)p.m(G)p.[fl2r](C)p.m(C)p.[fl2r](U)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](G)p.m(A)p.[fl2r](G)p.m(U)[sp].[fl2r](U)[sp].m(C)}$$$$,76.6,0.07,92,1
+siR-0015,ANGPTL3,parent,19,19,RNA1{r(G)p.r(A)p.r(A)p.r(C)p.r(U)p.r(C)p.r(U)p.r(G)p.r(A)p.r(U)p.r(G)p.r(A)p.r(G)p.r(G)p.r(C)p.r(A)p.r(U)p.r(U)p.r(C)}$$$$,RNA1{r(G)p.r(A)p.r(A)p.r(U)p.r(G)p.r(C)p.r(C)p.r(U)p.r(C)p.r(A)p.r(U)p.r(C)p.r(A)p.r(G)p.r(A)p.r(G)p.r(U)p.r(U)p.r(C)}$$$$,RNA1{r(G)p.r(A)p.r(A)p.r(C)p.r(U)p.r(C)p.r(U)p.r(G)p.r(A)p.r(U)p.r(G)p.r(A)p.r(G)p.r(G)p.r(C)p.r(A)p.r(U)p.r(U)p.r(C)}|RNA2{r(G)p.r(A)p.r(A)p.r(U)p.r(G)p.r(C)p.r(C)p.r(U)p.r(C)p.r(A)p.r(U)p.r(C)p.r(A)p.r(G)p.r(A)p.r(G)p.r(U)p.r(U)p.r(C)}$$$$,65,0.58,82,16
+siR-0016,HBV,lead,19,19,RNA1{m(G)[sp].m(G)[sp].m(A)p.m(A)p.m(C)p.m(U)p.m(C)p.m(U)p.m(U)p.m(U)p.m(A)p.m(C)p.m(A)p.m(U)p.m(G)p.m(C)p.m(U)[sp].m(G)[sp].m(U).[L3]}$$$$,RNA1{m(A)[sp].m(C)[sp].m(A)p.m(G)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(A)p.m(A)p.m(A)p.m(G)p.m(A)p.m(G)p.m(U)p.m(U)[sp].m(C)[sp].m(C)}$$$$,RNA1{m(G)[sp].m(G)[sp].m(A)p.m(A)p.m(C)p.m(U)p.m(C)p.m(U)p.m(U)p.m(U)p.m(A)p.m(C)p.m(A)p.m(U)p.m(G)p.m(C)p.m(U)[sp].m(G)[sp].m(U).[L3]}|RNA2{m(A)[sp].m(C)[sp].m(A)p.m(G)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(A)p.m(A)p.m(A)p.m(G)p.m(A)p.m(G)p.m(U)p.m(U)[sp].m(C)[sp].m(C)}$$$$,78.9,0.37,99,10
+siR-0017,HBV,clinical,19,19,RNA1{[Chol].m(G)[sp].[fl2r](G)[sp].m(A)p.[fl2r](A)p.m(C)p.[fl2r](U)p.m(C)p.[fl2r](U)p.m(U)p.[fl2r](U)p.m(A)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](C)p.m(U)[sp].[fl2r](G)[sp].m(U).[L3]}$$$$,RNA1{m(A)[sp].[fl2r](C)[sp].m(A)p.[fl2r](G)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(U)p.[fl2r](A)p.m(A)p.[fl2r](A)p.m(G)p.[fl2r](A)p.m(G)p.[fl2r](U)p.m(U)[sp].[fl2r](C)[sp].m(C)}$$$$,RNA1{[Chol].m(G)[sp].[fl2r](G)[sp].m(A)p.[fl2r](A)p.m(C)p.[fl2r](U)p.m(C)p.[fl2r](U)p.m(U)p.[fl2r](U)p.m(A)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](C)p.m(U)[sp].[fl2r](G)[sp].m(U).[L3]}|RNA2{m(A)[sp].[fl2r](C)[sp].m(A)p.[fl2r](G)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(U)p.[fl2r](A)p.m(A)p.[fl2r](A)p.m(G)p.[fl2r](A)p.m(G)p.[fl2r](U)p.m(U)[sp].[fl2r](C)[sp].m(C)}$$$$,76.2,0.06,91,0
+siR-0018,HBV,parent,19,19,RNA1{r(G)p.r(G)p.r(A)p.r(A)p.r(C)p.r(U)p.r(C)p.r(U)p.r(U)p.r(U)p.r(A)p.r(C)p.r(A)p.r(U)p.r(G)p.r(C)p.r(U)p.r(G)p.r(U)}$$$$,RNA1{r(A)p.r(C)p.r(A)p.r(G)p.r(C)p.r(A)p.r(U)p.r(G)p.r(U)p.r(A)p.r(A)p.r(A)p.r(G)p.r(A)p.r(G)p.r(U)p.r(U)p.r(C)p.r(C)}$$$$,RNA1{r(G)p.r(G)p.r(A)p.r(A)p.r(C)p.r(U)p.r(C)p.r(U)p.r(U)p.r(U)p.r(A)p.r(C)p.r(A)p.r(U)p.r(G)p.r(C)p.r(U)p.r(G)p.r(U)}|RNA2{r(A)p.r(C)p.r(A)p.r(G)p.r(C)p.r(A)p.r(U)p.r(G)p.r(U)p.r(A)p.r(A)p.r(A)p.r(G)p.r(A)p.r(G)p.r(U)p.r(U)p.r(C)p.r(C)}$$$$,59,0.13,63,2
+siR-0019,HSD17B13,lead,19,19,RNA1{m(C)[sp].m(A)[sp].m(U)p.m(G)p.m(G)p.m(U)p.m(U)p.m(G)p.m(A)p.m(A)p.m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(G)p.m(C)[sp].m(A)[sp].m(A).[L3]}$$$$,RNA1{m(U)[sp].m(U)[sp].m(G)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(U)p.m(C)p.m(A)p.m(A)p.m(C)p.m(C)p.m(A)[sp].m(U)[sp].m(G)}$$$$,RNA1{m(C)[sp].m(A)[sp].m(U)p.m(G)p.m(G)p.m(U)p.m(U)p.m(G)p.m(A)p.m(A)p.m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(G)p.m(C)[sp].m(A)[sp].m(A).[L3]}|RNA2{m(U)[sp].m(U)[sp].m(G)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(U)p.m(C)p.m(A)p.m(A)p.m(C)p.m(C)p.m(A)[sp].m(U)[sp].m(G)}$$$$,77.4,0.31,99,8
+siR-0020,HSD17B13,clinical,19,19,RNA1{[Chol].m(C)[sp].[fl2r](A)[sp].m(U)p.[fl2r](G)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](G)p.m(C)[sp].[fl2r](A)[sp].m(A).[L3]}$$$$,RNA1{m(U)[sp].[fl2r](U)[sp].m(G)p.[fl2r](C)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](C)p.m(A)[sp].[fl2r](U)[sp].m(G)}$$$$,RNA1{[Chol].m(C)[sp].[fl2r](A)[sp].m(U)p.[fl2r](G)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](G)p.m(C)[sp].[fl2r](A)[sp].m(A).[L3]}|RNA2{m(U)[sp].[fl2r](U)[sp].m(G)p.[fl2r](C)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](C)p.m(A)[sp].[fl2r](U)[sp].m(G)}$$$$,79.6,0.16,99,3
+siR-0021,HSD17B13,parent,19,19,RNA1{r(C)p.r(A)p.r(U)p.r(G)p.r(G)p.r(U)p.r(U)p.r(G)p.r(A)p.r(A)p.r(C)p.r(A)p.r(U)p.r(G)p.r(A)p.r(G)p.r(C)p.r(A)p.r(A)}$$$$,RNA1{r(U)p.r(U)p.r(G)p.r(C)p.r(U)p.r(C)p.r(A)p.r(U)p.r(G)p.r(U)p.r(U)p.r(C)p.r(A)p.r(A)p.r(C)p.r(C)p.r(A)p.r(U)p.r(G)}$$$$,RNA1{r(C)p.r(A)p.r(U)p.r(G)p.r(G)p.r(U)p.r(U)p.r(G)p.r(A)p.r(A)p.r(C)p.r(A)p.r(U)p.r(G)p.r(A)p.r(G)p.r(C)p.r(A)p.r(A)}|RNA2{r(U)p.r(U)p.r(G)p.r(C)p.r(U)p.r(C)p.r(A)p.r(U)p.r(G)p.r(U)p.r(U)p.r(C)p.r(A)p.r(A)p.r(C)p.r(C)p.r(A)p.r(U)p.r(G)}$$$$,62.5,0.38,74,10
+siR-0022,AGT,lead,19,19,RNA1{m(A)[sp].m(A)[sp].m(A)p.m(C)p.m(U)p.m(A)p.m(C)p.m(G)p.m(U)p.m(G)p.m(G)p.m(U)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)[sp].m(G)[sp].m(C).[L3]}$$$$,RNA1{m(G)[sp].m(C)[sp].m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(A)p.m(C)p.m(C)p.m(A)p.m(C)p.m(G)p.m(U)p.m(A)p.m(G)p.m(U)[sp].m(U)[sp].m(U)}$$$$,RNA1{m(A)[sp].m(A)[sp].m(A)p.m(C)p.m(U)p.m(A)p.m(C)p.m(G)p.m(U)p.m(G)p.m(G)p.m(U)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)[sp].m(G)[sp].m(C).[L3]}|RNA2{m(G)[sp].m(C)[sp].m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(A)p.m(C)p.m(C)p.m(A)p.m(C)p.m(G)p.m(U)p.m(A)p.m(G)p.m(U)[sp].m(U)[sp].m(U)}$$$$,75.1,0.21,94,5
+siR-0023,AGT,clinical,19,19,RNA1{[Chol].m(A)[sp].[fl2r](A)[sp].m(A)p.[fl2r](C)p.m(U)p.[fl2r](A)p.m(C)p.[fl2r](G)p.m(U)p.[fl2r](G)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)[sp].[fl2r](G)[sp].m(C).[L3]}$$$$,RNA1{m(G)[sp].[fl2r](C)[sp].m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](C)p.m(A)p.[fl2r](C)p.m(G)p.[fl2r](U)p.m(A)p.[fl2r](G)p.m(U)[sp].[fl2r](U)[sp].m(U)}$$$$,RNA1{[Chol].m(A)[sp].[fl2r](A)[sp].m(A)p.[fl2r](C)p.m(U)p.[fl2r](A)p.m(C)p.[fl2r](G)p.m(U)p.[fl2r](G)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)[sp].[fl2r](G)[sp].m(C).[L3]}|RNA2{m(G)[sp].[fl2r](C)[sp].m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](C)p.m(A)p.[fl2r](C)p.m(G)p.[fl2r](U)p.m(A)p.[fl2r](G)p.m(U)[sp].[fl2r](U)[sp].m(U)}$$$$,82.4,0.24,99,6
+siR-0024,AGT,parent,19,19,RNA1{r(A)p.r(A)p.r(A)p.r(C)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(G)p.r(G)p.r(U)p.r(U)p.r(C)p.r(A)p.r(U)p.r(G)p.r(G)p.r(C)}$$$$,RNA1{r(G)p.r(C)p.r(C)p.r(A)p.r(U)p.r(G)p.r(A)p.r(A)p.r(C)p.r(C)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(G)p.r(U)p.r(U)p.r(U)}$$$$,RNA1{r(A)p.r(A)p.r(A)p.r(C)p.r(U)p.r(A)p.r(C)p.r(G)p.r(U)p.r(G)p.r(G)p.r(U)p.r(U)p.r(C)p.r(A)p.r(U)p.r(G)p.r(G)p.r(C)}|RNA2{r(G)p.r(C)p.r(C)p.r(A)p.r(U)p.r(G)p.r(A)p.r(A)p.r(C)p.r(C)p.r(A)p.r(C)p.r(G)p.r(U)p.r(A)p.r(G)p.r(U)p.r(U)p.r(U)}$$$$,59.7,0.18,65,4
+siR-0025,KRAS,backup,19,19,RNA1{[Chol].m(G)[sp].[fl2r](A)[sp].m(C)p.[fl2r](U)p.m(G)p.[fl2r](A)p.m(A)p.[fl2r](U)p.m(A)p.[fl2r](U)p.m(A)p.[fl2r](A)p.m(A)p.[fl2r](C)p.m(U)p.[fl2r](U)p.m(G)[sp].[fl2r](U)[sp].m(G)}$$$$,RNA1{m(C)[sp].[fl2r](A)[sp].m(C)p.[fl2r](A)p.m(A)p.[fl2r](G)p.m(U)p.[fl2r](U)p.m(U)p.[fl2r](A)p.m(U)p.[fl2r](A)p.m(U)p.[fl2r](U)p.m(C)p.[fl2r](A)p.m(G)[sp].[fl2r](U)[sp].m(C)}$$$$,RNA1{[Chol].m(G)[sp].[fl2r](A)[sp].m(C)p.[fl2r](U)p.m(G)p.[fl2r](A)p.m(A)p.[fl2r](U)p.m(A)p.[fl2r](U)p.m(A)p.[fl2r](A)p.m(A)p.[fl2r](C)p.m(U)p.[fl2r](U)p.m(G)[sp].[fl2r](U)[sp].m(G)}|RNA2{m(C)[sp].[fl2r](A)[sp].m(C)p.[fl2r](A)p.m(A)p.[fl2r](G)p.m(U)p.[fl2r](U)p.m(U)p.[fl2r](A)p.m(U)p.[fl2r](A)p.m(U)p.[fl2r](U)p.m(C)p.[fl2r](A)p.m(G)[sp].[fl2r](U)[sp].m(C)}$$$$,72.7,0.24,90,6
+siR-0026,PCSK9,backup,19,19,RNA1{[Chol].m(U)[sp].m(C)[sp].m(A)p.m(G)p.m(G)p.m(A)p.m(C)p.m(A)p.m(U)p.m(G)p.m(G)p.m(A)p.m(A)p.m(G)p.m(C)p.m(U)p.m(G)[sp].m(A)[sp].m(A)}$$$$,RNA1{m(U)[sp].m(U)[sp].m(C)p.m(A)p.m(G)p.m(C)p.m(U)p.m(U)p.m(C)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(C)p.m(C)p.m(U)[sp].m(G)[sp].m(A).[Toc]}$$$$,RNA1{[Chol].m(U)[sp].m(C)[sp].m(A)p.m(G)p.m(G)p.m(A)p.m(C)p.m(A)p.m(U)p.m(G)p.m(G)p.m(A)p.m(A)p.m(G)p.m(C)p.m(U)p.m(G)[sp].m(A)[sp].m(A)}|RNA2{m(U)[sp].m(U)[sp].m(C)p.m(A)p.m(G)p.m(C)p.m(U)p.m(U)p.m(C)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(C)p.m(C)p.m(U)[sp].m(G)[sp].m(A).[Toc]}$$$$,78.3,0.22,99,5
+siR-0027,TTR,lead,19,19,RNA1{m(A)[sp].[fl2r](U)[sp].m(U)p.[fl2r](G)p.m(G)p.[fl2r](G)p.m(A)p.[fl2r](U)p.m(U)p.[fl2r](U)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](G)p.m(A)[sp].[fl2r](A)[sp].m(U).[L3]}$$$$,RNA1{m(A)[sp].[fl2r](U)[sp].m(U)p.[fl2r](C)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](A)p.m(A)p.[fl2r](A)p.m(U)p.[fl2r](C)p.m(C)p.[fl2r](C)p.m(A)[sp].[fl2r](A)[sp].m(U).[Bio]}$$$$,RNA1{m(A)[sp].[fl2r](U)[sp].m(U)p.[fl2r](G)p.m(G)p.[fl2r](G)p.m(A)p.[fl2r](U)p.m(U)p.[fl2r](U)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](G)p.m(A)[sp].[fl2r](A)[sp].m(U).[L3]}|RNA2{m(A)[sp].[fl2r](U)[sp].m(U)p.[fl2r](C)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](A)p.m(A)p.[fl2r](A)p.m(U)p.[fl2r](C)p.m(C)p.[fl2r](C)p.m(A)[sp].[fl2r](A)[sp].m(U).[Bio]}$$$$,78.5,0.29,99,7
+siR-0028,APOC3,backup,19,19,RNA1{m(A)[sp].[fl2r](U)[sp].m(C)p.[fl2r](A)p.m(G)p.[fl2r](U)p.m(A)p.[fl2r](C)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](A)p.m(C)[sp].[fl2r](G)[sp].m(G)}$$$$,RNA1{[Bio].m(C)[sp].[fl2r](C)[sp].m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](C)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](G)p.m(U)p.[fl2r](A)p.m(C)p.[fl2r](U)p.m(G)[sp].[fl2r](A)[sp].m(U)}$$$$,RNA1{m(A)[sp].[fl2r](U)[sp].m(C)p.[fl2r](A)p.m(G)p.[fl2r](U)p.m(A)p.[fl2r](C)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(U)p.[fl2r](C)p.m(A)p.[fl2r](A)p.m(C)[sp].[fl2r](G)[sp].m(G)}|RNA2{[Bio].m(C)[sp].[fl2r](C)[sp].m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](C)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](G)p.m(U)p.[fl2r](A)p.m(C)p.[fl2r](U)p.m(G)[sp].[fl2r](A)[sp].m(U)}$$$$,70.5,0.07,81,1
+siR-0029,ANGPTL3,deprio,19,19,RNA1{[Chol].m(G)[sp].m(A)[sp].m(A)p.m(C)p.m(U)p.m(C)p.m(U)p.m(G)p.m(A)p.m(U)p.m(G)p.m(A)p.m(G)p.m(G)p.m(C)p.m(A)p.m(U)[sp].m(U)[sp].m(C).[L3]}$$$$,RNA1{[Pal].m(G)[sp].m(A)[sp].m(A)p.m(U)p.m(G)p.m(C)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(C)p.m(A)p.m(G)p.m(A)p.m(G)p.m(U)[sp].m(U)[sp].m(C).[Bio]}$$$$,RNA1{[Chol].m(G)[sp].m(A)[sp].m(A)p.m(C)p.m(U)p.m(C)p.m(U)p.m(G)p.m(A)p.m(U)p.m(G)p.m(A)p.m(G)p.m(G)p.m(C)p.m(A)p.m(U)[sp].m(U)[sp].m(C).[L3]}|RNA2{[Pal].m(G)[sp].m(A)[sp].m(A)p.m(U)p.m(G)p.m(C)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(C)p.m(A)p.m(G)p.m(A)p.m(G)p.m(U)[sp].m(U)[sp].m(C).[Bio]}$$$$,80.1,0.22,99,5
+siR-0030,HBV,lead,19,19,RNA1{[Pal].m(G)[sp].[fl2r](G)[sp].m(A)p.[fl2r](A)p.m(C)p.[fl2r](U)p.m(C)p.[fl2r](U)p.m(U)p.[fl2r](U)p.m(A)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](C)p.m(U)[sp].[fl2r](G)[sp].m(U)}$$$$,RNA1{m(A)[sp].m(C)[sp].m(A)p.m(G)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(A)p.m(A)p.m(A)p.m(G)p.m(A)p.m(G)p.m(U)p.m(U)[sp].m(C)[sp].m(C).[L3]}$$$$,RNA1{[Pal].m(G)[sp].[fl2r](G)[sp].m(A)p.[fl2r](A)p.m(C)p.[fl2r](U)p.m(C)p.[fl2r](U)p.m(U)p.[fl2r](U)p.m(A)p.[fl2r](C)p.m(A)p.[fl2r](U)p.m(G)p.[fl2r](C)p.m(U)[sp].[fl2r](G)[sp].m(U)}|RNA2{m(A)[sp].m(C)[sp].m(A)p.m(G)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(A)p.m(A)p.m(A)p.m(G)p.m(A)p.m(G)p.m(U)p.m(U)[sp].m(C)[sp].m(C).[L3]}$$$$,76.7,0.28,99,7
+siR-0031,HSD17B13,backup,19,19,RNA1{[DBCO].m(C)[sp].[fl2r](A)[sp].m(U)p.[fl2r](G)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](G)p.m(C)[sp].[fl2r](A)[sp].m(A)}$$$$,RNA1{m(U)[sp].m(U)[sp].m(G)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(U)p.m(C)p.m(A)p.m(A)p.m(C)p.m(C)p.m(A)[sp].m(U)[sp].m(G)}$$$$,RNA1{[DBCO].m(C)[sp].[fl2r](A)[sp].m(U)p.[fl2r](G)p.m(G)p.[fl2r](U)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](A)p.m(C)p.[fl2r](A)p.m(U)p.[fl2r](G)p.m(A)p.[fl2r](G)p.m(C)[sp].[fl2r](A)[sp].m(A)}|RNA2{m(U)[sp].m(U)[sp].m(G)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(U)p.m(U)p.m(C)p.m(A)p.m(A)p.m(C)p.m(C)p.m(A)[sp].m(U)[sp].m(G)}$$$$,72.6,0.3,92,8
+siR-0032,TTR,backup,19,19,RNA1{m(A)[sp].m(U)[sp].[fl2r](U)p.[fl2r](G)p.[fl2r](G)p.[fl2r](G)p.[fl2r](A)p.[fl2r](U)p.m(U)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(G)p.m(A)[sp].m(A)[sp].m(U).[L3]}$$$$,RNA1{m(A)[sp].m(U)[sp].m(U)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(A)p.m(A)p.m(U)p.m(C)p.m(C)p.m(C)p.m(A)[sp].m(A)[sp].m(U)}$$$$,RNA1{m(A)[sp].m(U)[sp].[fl2r](U)p.[fl2r](G)p.[fl2r](G)p.[fl2r](G)p.[fl2r](A)p.[fl2r](U)p.m(U)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(G)p.m(A)[sp].m(A)[sp].m(U).[L3]}|RNA2{m(A)[sp].m(U)[sp].m(U)p.m(C)p.m(U)p.m(C)p.m(A)p.m(U)p.m(G)p.m(A)p.m(A)p.m(A)p.m(U)p.m(C)p.m(C)p.m(C)p.m(A)[sp].m(A)[sp].m(U)}$$$$,69.7,0.16,83,3
+siR-0033,KRAS,deprio,19,19,RNA1{[r](G)p.m(A)p.m(C)p.m(U)p.m(G)p.[r](A)p.m(A)p.m(U)p.m(A)p.m(U)p.m(A)p.m(A)p.m(A)p.m(C)p.m(U)p.m(U)p.m(G)p.m(U)p.m(G)}$$$$,RNA1{m(C)[sp].m(A)[sp].m(C)p.m(A)p.m(A)p.m(G)p.m(U)p.m(U)p.m(U)p.m(A)p.m(U)p.m(A)p.m(U)p.m(U)p.m(C)p.m(A)p.m(G)[sp].m(U)[sp].m(C)}$$$$,RNA1{[r](G)p.m(A)p.m(C)p.m(U)p.m(G)p.[r](A)p.m(A)p.m(U)p.m(A)p.m(U)p.m(A)p.m(A)p.m(A)p.m(C)p.m(U)p.m(U)p.m(G)p.m(U)p.m(G)}|RNA2{m(C)[sp].m(A)[sp].m(C)p.m(A)p.m(A)p.m(G)p.m(U)p.m(U)p.m(U)p.m(A)p.m(U)p.m(A)p.m(U)p.m(U)p.m(C)p.m(A)p.m(G)[sp].m(U)[sp].m(C)}$$$$,63.7,0.11,71,2
+aso-0034,TTR_ASO,clinical,19,0,RNA1{[lna](C)[sp].[lna](A)[sp].[lna](G)[sp].d(T)[sp].d(G)[sp].d(T)[sp].d(T)[sp].d(C)[sp].d(T)[sp].d(T)[sp].d(G)[sp].d(C)[sp].d(T)[sp].d(C)[sp].d(T)[sp].d(A)[sp].[lna](T)[sp].[lna](A)[sp].[lna](A)}$$$$,,RNA1{[lna](C)[sp].[lna](A)[sp].[lna](G)[sp].d(T)[sp].d(G)[sp].d(T)[sp].d(T)[sp].d(C)[sp].d(T)[sp].d(T)[sp].d(G)[sp].d(C)[sp].d(T)[sp].d(C)[sp].d(T)[sp].d(A)[sp].[lna](T)[sp].[lna](A)[sp].[lna](A)}$$$$,79.6,0.3,99,7
+aso-0035,PCSK9_ASO,lead,19,0,RNA1{[moe](C)[sp].[moe](C)[sp].[moe](A)[sp].[moe](G)[sp].[moe](G)[sp].d(A)[sp].d(C)[sp].d(T)[sp].d(G)[sp].d(A)[sp].d(G)[sp].d(G)[sp].d(C)[sp].d(T)[sp].[moe](T)[sp].[moe](A)[sp].[moe](C)[sp].[moe](G)[sp].[moe](T)}$$$$,,RNA1{[moe](C)[sp].[moe](C)[sp].[moe](A)[sp].[moe](G)[sp].[moe](G)[sp].d(A)[sp].d(C)[sp].d(T)[sp].d(G)[sp].d(A)[sp].d(G)[sp].d(G)[sp].d(C)[sp].d(T)[sp].[moe](T)[sp].[moe](A)[sp].[moe](C)[sp].[moe](G)[sp].[moe](T)}$$$$,74.4,0.1,89,2
+aso-0036,AGT_ASO,lead,19,0,RNA1{[Chol].[lna](C)[sp].[lna](A)[sp].[lna](C)[sp].d(A)[sp].d(G)[sp].d(T)[sp].d(A)[sp].d(C)[sp].d(T)[sp].d(G)[sp].d(G)[sp].d(A)[sp].d(G)[sp].d(C)[sp].d(A)[sp].d(T)[sp].[lna](G)[sp].[lna](G)[sp].[lna](T).[GalNAc]}$$$$,,RNA1{[Chol].[lna](C)[sp].[lna](A)[sp].[lna](C)[sp].d(A)[sp].d(G)[sp].d(T)[sp].d(A)[sp].d(C)[sp].d(T)[sp].d(G)[sp].d(G)[sp].d(A)[sp].d(G)[sp].d(C)[sp].d(A)[sp].d(T)[sp].[lna](G)[sp].[lna](G)[sp].[lna](T).[GalNAc]}$$$$,74.7,0.11,90,2
+aso-0037,TTR_ASO,backup,19,0,RNA1{[Bio].[moe](C)[sp].[moe](A)[sp].[moe](G)[sp].[moe](T)[sp].[moe](G)[sp].d(T)[sp].d(T)[sp].d(C)[sp].d(T)[sp].d(T)[sp].d(G)[sp].d(C)[sp].d(T)[sp].d(C)[sp].[moe](T)[sp].[moe](A)[sp].[moe](T)[sp].[moe](A)[sp].[moe](A)}$$$$,,RNA1{[Bio].[moe](C)[sp].[moe](A)[sp].[moe](G)[sp].[moe](T)[sp].[moe](G)[sp].d(T)[sp].d(T)[sp].d(C)[sp].d(T)[sp].d(T)[sp].d(G)[sp].d(C)[sp].d(T)[sp].d(C)[sp].[moe](T)[sp].[moe](A)[sp].[moe](T)[sp].[moe](A)[sp].[moe](A)}$$$$,77.9,0.24,99,6

package/files/tests/chem_enum_cores.csv

@@ -0,0 +1,5 @@
+Core
+n1nc([*:3])n([*:2])c1[*:1]
+C1C2CN([*:2])CC2CN1[*:1]
+OC1CN([*:2])CCC1N[*:1]
+CC1(N[*:1])CCN([*:2])C1

package/files/tests/chem_enum_rgroups.csv

@@ -0,0 +1,5 @@
+R1,R2,R3
+CC1CCN([*:1])C1C,O=C(C[*:2])NCC(F)(F)F,Cc1cccc([*:3])n1
+NCCC(=O)[*:1],O=C1NC(C(=O)[*:2])CO1,
+CC(=O)[*:1],O=C(CCCF)[*:2],
+O=C(c1cc[nH]n1)[*:1],c1ccc(C[*:2])nc1,

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.10.13",
+  "version": "1.10.15",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -22,7 +22,7 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.63.6",
+    "@datagrok-libraries/bio": "^5.65.0",
     "@datagrok-libraries/chem-meta": "^1.2.8",
     "@datagrok-libraries/tutorials": "^1.6.1",
     "@datagrok-libraries/utils": "^4.6.5",

package/src/apps/structure/view/ui.ts

@@ -140,7 +140,7 @@ class StructureAppLayout {
     const clearBlock = Object.fromEntries(
       STRANDS.map(
         (key) => {
-          const clearIcon = ui.icons.delete(() => { coloredInput[key].inputBase.value = ''; });
+          const clearIcon = ui.icons.delete(() => { coloredInput[key].inputBase.value = ''; }, 'Delete');
           const clearButton = ui.button(clearIcon, () => {});
           ui.tooltip.bind(clearButton, `Clear ${key.toUpperCase()}`);
           return [key, clearIcon];

package/src/apps/translator/view/ui.ts

@@ -202,7 +202,7 @@ class TranslatorAppLayout {
     const formatChoiceInput = ui.div([this.formatChoiceInput]);
 
     const clearButton = ui.button(
-      ui.icons.delete(() => { sequenceColoredInput.inputBase.value = ''; }),
+      ui.icons.delete(() => { sequenceColoredInput.inputBase.value = ''; }, 'Delete'),
       () => {}
     );
     ui.tooltip.bind(clearButton, 'Clear input');

package/src/oligo-renderer/canvas-renderer.ts

@@ -0,0 +1,500 @@
+/**
+ * Canvas drawing for the OligoNucleotide cell renderer.
+ *
+ * Pure functions — no DG / DOM dependencies — so the renderer is easy to
+ * unit-test and to drive from the HTML prototype as well.
+ *
+ * Visual model:
+ *   - Chip body uses base-canonical color (A green / C blue / G tan / U pink).
+ *   - Sugar modifications are shown as a colored stripe at the bottom of the
+ *     chip (so the chip itself stays readable for the base sequence, and the
+ *     modification track scans easily horizontally).
+ *   - Phosphate linkage modifications (PS) are shown as a saturated bar in
+ *     the gap *between* chips — this is the actual chemistry: the linkage
+ *     belongs to the bond, not to either nucleotide.
+ *   - Wide gaps between chips give the modification markers room to breathe.
+ *   - Antisense is rendered 3'→5' (reversed) so position N of sense visually
+ *     pairs with position N of antisense (anti-parallel base-pair register).
+ *   - Conjugates are rendered as wider pills at the chain ends; their actual
+ *     width is propagated through layout so adjacent chips don't overlap.
+ *
+ * Sizing is fully adaptive: chip dimensions scale to fit the cell, preserving
+ * aspect ratio, down to a minimum below which the cell falls back to a text
+ * summary.
+ */
+
+import {
+  BASE_COLORS, FALLBACK_COLOR,
+  canonicalSugarSymbol,
+  ParsedDuplex, ParsedMonomer, ParsedNucleotide, ParsedStrand,
+  resolveConjugate, resolvePhosphate, resolveSugar,
+} from './types';
+
+export interface RenderOpts {
+  /** Show base letter inside chip. False at very small sizes. */
+  showLetters: boolean;
+  /** Draw antisense 3'→5' for base-pair alignment with sense. Default true. */
+  pairAlign: boolean;
+  /** Optional column-level scheme name (currently ignored — palette is fixed). */
+  scheme?: string;
+}
+
+const DEFAULT_OPTS: RenderOpts = {showLetters: true, pairAlign: true};
+
+/* Visual tuning. */
+const ASPECT_H_OVER_W = 1.25;
+const STRAND_GAP_RATIO = 0.5;
+const CHIP_GAP_RATIO = 0.32; // wider — gives PS bar room to breathe
+const MIN_CHIP_W = 5;
+const MAX_CHIP_W = 17;
+const PAD = 4;
+const LABEL_W = 30;
+const CHIP_FILL_ALPHA = 0.85; // chip body, base-canonical pale color
+const CHIP_BORDER_W = 0.5;
+const SUGAR_STRIPE_RATIO = 0.22; // height of bottom sugar-mod stripe
+const PS_BAR_RATIO = 0.55; // PS bar width as fraction of chip gap
+
+/** Cached layout for one rendered cell. */
+export interface DuplexLayout {
+  chipW: number;
+  chipH: number;
+  chipGap: number;
+  strandGap: number;
+  fontSize: number;
+  labelW: number;
+  padding: number;
+  senseY: number;
+  antiY: number; // -1 if no antisense
+  seqX: number;
+  textOnlyFallback: boolean;
+  senseChips: ChipPos[];
+  antiChips: ChipPos[];
+  senseLinks: LinkagePos[];
+  antiLinks: LinkagePos[];
+  /** Whether antisense was rendered in reversed (3'→5') order. */
+  antiReversed: boolean;
+}
+
+export interface ChipPos {
+  x: number;
+  w: number;
+  monomer: ParsedMonomer;
+  /** Original 0-based index in the data strand (regardless of display order). */
+  origIdx: number;
+  strand: StrandSide;
+}
+
+export interface LinkagePos {
+  x: number; w: number; y: number; h: number;
+  phosphateSymbol: string;
+  /** Original index of the nucleotide that owns the 3' phosphate. */
+  ownerOrigIdx: number;
+  strand: StrandSide;
+}
+
+export type StrandSide = 'sense' | 'antisense';
+
+/* ---------------------------------------------------------------- *
+ * Layout
+ * ---------------------------------------------------------------- */
+
+export function computeLayout(
+  cellW: number, cellH: number, model: ParsedDuplex, opts: Partial<RenderOpts> = {},
+): DuplexLayout {
+  const o: RenderOpts = {...DEFAULT_OPTS, ...opts};
+  const senseLen = model.sense.monomers.length;
+  const antiLen = model.antisense ? model.antisense.monomers.length : 0;
+  const hasAnti = antiLen > 0;
+  const strandsCount = hasAnti ? 2 : 1;
+  const maxLen = Math.max(1, senseLen, antiLen);
+
+  const availW = Math.max(0, cellW - LABEL_W - 2 * PAD);
+  const wChipW = availW / (maxLen + Math.max(0, maxLen - 1) * CHIP_GAP_RATIO);
+
+  const heightFactor = strandsCount + Math.max(0, strandsCount - 1) * STRAND_GAP_RATIO;
+  const hChipH = (cellH - 2 * PAD) / heightFactor;
+  const hChipW = hChipH / ASPECT_H_OVER_W;
+
+  let chipW = Math.min(MAX_CHIP_W, wChipW, hChipW);
+  const textOnlyFallback = chipW < MIN_CHIP_W;
+  if (chipW < MIN_CHIP_W) chipW = MIN_CHIP_W;
+
+  const chipH = chipW * ASPECT_H_OVER_W;
+  const chipGap = Math.max(2, chipW * CHIP_GAP_RATIO);
+  const strandGap = chipH * STRAND_GAP_RATIO;
+  const fontSize = Math.max(7, Math.min(13, chipW * 0.62));
+
+  const blockH = strandsCount * chipH + (strandsCount - 1) * strandGap;
+  const blockTop = Math.max(PAD, (cellH - blockH) / 2);
+  const senseY = blockTop;
+  const antiY = hasAnti ? blockTop + chipH + strandGap : -1;
+  const seqX = PAD + LABEL_W;
+  const seqEndX = cellW - PAD;
+
+  const layoutBase: Omit<DuplexLayout, 'senseChips' | 'antiChips' | 'senseLinks' | 'antiLinks' | 'antiReversed'> = {
+    chipW, chipH, chipGap, strandGap, fontSize,
+    labelW: LABEL_W, padding: PAD,
+    senseY, antiY, seqX, textOnlyFallback,
+  };
+
+  if (textOnlyFallback) {
+    return {
+      ...layoutBase,
+      senseChips: [], antiChips: [], senseLinks: [], antiLinks: [],
+      antiReversed: false,
+    };
+  }
+
+  // Conjugates on either strand's leftmost end push back the start of
+  // *that* strand's nucleotide region. To keep base pairs aligned across
+  // strands, we measure the leading-conjugate width of each strand (in
+  // its display order — antisense is reversed when pair-aligned) and
+  // shift each strand right by the difference, so the first NUCLEOTIDE
+  // of each strand sits at the same X coordinate.
+  const antiReversed = hasAnti && o.pairAlign;
+  const senseLeadW = leadingConjugateWidth(model.sense.monomers, false, chipW, fontSize, chipGap);
+  const antiLeadW = hasAnti ?
+    leadingConjugateWidth(model.antisense!.monomers, antiReversed, chipW, fontSize, chipGap) : 0;
+  const alignAt = Math.max(senseLeadW, antiLeadW);
+  const senseStartX = seqX + (alignAt - senseLeadW);
+  const antiStartX = seqX + (alignAt - antiLeadW);
+
+  const senseRes = placeStrand(model.sense, false, senseY, senseStartX, seqEndX, layoutBase, 'sense');
+  const antiRes = hasAnti ?
+    placeStrand(model.antisense!, antiReversed, antiY, antiStartX, seqEndX, layoutBase, 'antisense') :
+    {chips: [], links: []};
+
+  return {
+    ...layoutBase,
+    senseChips: senseRes.chips,
+    antiChips: antiRes.chips,
+    senseLinks: senseRes.links,
+    antiLinks: antiRes.links,
+    antiReversed,
+  };
+}
+
+/** Place chips for one strand, optionally reversed. Returns chip and linkage positions. */
+function placeStrand(
+  strand: ParsedStrand, reverse: boolean, y: number, startX: number, endX: number,
+  layout: Omit<DuplexLayout, 'senseChips' | 'antiChips' | 'senseLinks' | 'antiLinks' | 'antiReversed'>,
+  side: StrandSide,
+): { chips: ChipPos[]; links: LinkagePos[] } {
+  const monomers = reverse ? strand.monomers.slice().reverse() : strand.monomers;
+  const chips: ChipPos[] = [];
+  const links: LinkagePos[] = [];
+  let x = startX;
+
+  for (let i = 0; i < monomers.length; i++) {
+    const m = monomers[i];
+    const w = m.kind === 'conjugate' ?
+      estimateConjugateWidth(m.symbol, layout.chipW, layout.fontSize) :
+      layout.chipW;
+
+    if (x + w > endX) break; // truncate at cell edge
+
+    chips.push({x, w, monomer: m, origIdx: m.position, strand: side});
+
+    // Linkage from this monomer's 3'-phosphate goes in the gap to the right.
+    // When the strand is reversed (anti-parallel), the linkage that was
+    // "owned by monomer N's 3' end" connects monomer N to monomer N+1 in the
+    // data; in display these are still adjacent, so the gap-to-right is still
+    // the right place to draw it. We just need to look up the correct owner.
+    if (m.kind === 'nucleotide' && i < monomers.length - 1) {
+      const nt = m as ParsedNucleotide;
+      if (nt.phosphate) {
+        links.push({
+          x: x + w, w: layout.chipGap, y, h: layout.chipH,
+          phosphateSymbol: nt.phosphate,
+          ownerOrigIdx: nt.position,
+          strand: side,
+        });
+      }
+    }
+    x += w + layout.chipGap;
+  }
+  return {chips, links};
+}
+
+/** Width estimate for a conjugate pill, using only chip metrics (no canvas measure). */
+function estimateConjugateWidth(symbol: string, chipW: number, fontSize: number): number {
+  const meta = resolveConjugate(symbol).meta;
+  const charW = fontSize * 0.55;
+  const textW = meta.short.length * charW;
+  const padding = chipW * 0.6;
+  return Math.max(chipW, Math.min(chipW * 4, textW + padding));
+}
+
+/** Sum of widths of leading conjugates in display order (after reversal if any),
+ * including their trailing chipGap, so antisense and sense can be shifted
+ * independently to align their first nucleotides at the same X coordinate. */
+function leadingConjugateWidth(
+  monomers: ParsedMonomer[], reversed: boolean,
+  chipW: number, fontSize: number, chipGap: number,
+): number {
+  const seq = reversed ? monomers.slice().reverse() : monomers;
+  let w = 0;
+  for (const m of seq) {
+    if (m.kind !== 'conjugate') break;
+    w += estimateConjugateWidth(m.symbol, chipW, fontSize) + chipGap;
+  }
+  return w;
+}
+
+/* ---------------------------------------------------------------- *
+ * Drawing
+ * ---------------------------------------------------------------- */
+
+export function drawDuplex(
+  g: CanvasRenderingContext2D, cellX: number, cellY: number,
+  cellW: number, cellH: number, model: ParsedDuplex,
+  opts: Partial<RenderOpts> = {},
+): DuplexLayout {
+  const o: RenderOpts = {...DEFAULT_OPTS, ...opts};
+  const layout = computeLayout(cellW, cellH, model, o);
+
+  g.save();
+  g.beginPath();
+  g.rect(cellX, cellY, cellW, cellH);
+  g.clip();
+  g.translate(cellX, cellY);
+
+  if (layout.textOnlyFallback) {
+    drawFallbackText(g, cellW, cellH, model, layout);
+    g.restore();
+    return layout;
+  }
+
+  // Strand label "S 5'" left of sense
+  drawStrandLabel(g, 'S', '5\'', layout.padding, layout.senseY + layout.chipH / 2, layout);
+
+  // Linkages first (so chips paint over their rounded edges cleanly)
+  for (const link of layout.senseLinks) drawLinkage(g, link);
+  drawChips(g, layout.senseChips, layout, o);
+  drawTruncationMarker(g, layout.senseChips, model.sense.monomers.length, layout);
+
+  if (layout.antiY >= 0 && model.antisense) {
+    // When reversed, the leftmost chip in display is the 3' end of antisense.
+    const leftLabel = layout.antiReversed ? '3\'' : '5\'';
+    drawStrandLabel(g, 'AS', leftLabel, layout.padding, layout.antiY + layout.chipH / 2, layout);
+    for (const link of layout.antiLinks) drawLinkage(g, link);
+    drawChips(g, layout.antiChips, layout, o);
+    drawTruncationMarker(g, layout.antiChips, model.antisense.monomers.length, layout);
+  }
+
+  g.restore();
+  return layout;
+}
+
+function drawStrandLabel(
+  g: CanvasRenderingContext2D, strand: string, terminus: string, x: number, y: number, layout: DuplexLayout,
+): void {
+  g.fillStyle = '#8b949e';
+  g.font = `${Math.max(8, layout.fontSize - 1)}px ui-monospace, Menlo, monospace`;
+  g.textBaseline = 'middle';
+  g.textAlign = 'left';
+  g.fillText(`${strand} ${terminus}`, x, y);
+}
+
+function drawTruncationMarker(
+  g: CanvasRenderingContext2D, chips: ChipPos[], totalCount: number, layout: DuplexLayout,
+): void {
+  if (chips.length >= totalCount) return;
+  const last = chips[chips.length - 1];
+  if (!last) return;
+  g.fillStyle = '#6e7681';
+  g.font = `${Math.max(7, layout.fontSize - 1)}px ui-monospace, Menlo, monospace`;
+  g.textBaseline = 'middle';
+  g.textAlign = 'left';
+  g.fillText('…', last.x + last.w + 1, layout.senseY + layout.chipH / 2);
+}
+
+function drawChips(g: CanvasRenderingContext2D, chips: ChipPos[], layout: DuplexLayout, opts: RenderOpts): void {
+  const y = chips[0]?.strand === 'sense' ? layout.senseY : layout.antiY;
+  for (const cp of chips) {
+    if (cp.monomer.kind === 'conjugate')
+      drawConjugate(g, cp.monomer.symbol, cp.x, y, cp.w, layout.chipH, layout.fontSize);
+    else
+      drawChip(g, cp.monomer as ParsedNucleotide, cp.x, y, cp.w, layout.chipH, layout.fontSize, opts);
+  }
+}
+
+function drawChip(
+  g: CanvasRenderingContext2D, m: ParsedNucleotide, x: number, y: number,
+  w: number, h: number, fontSize: number, opts: RenderOpts,
+): void {
+  const sugarRes = resolveSugar(m.sugar, m.base);
+  const baseColor = BASE_COLORS[m.base ?? ''] ?? FALLBACK_COLOR;
+  const isModSugar = isModifiedSugar(m.sugar);
+  const r = Math.min(2.5, w / 4);
+
+  // Chip body — base-canonical pale color
+  drawRoundRect(g, x, y, w, h, r);
+  g.fillStyle = withAlpha(baseColor, CHIP_FILL_ALPHA);
+  g.fill();
+  g.lineWidth = CHIP_BORDER_W;
+  g.strokeStyle = 'rgba(0,0,0,0.22)';
+  g.stroke();
+
+  // Sugar modification stripe at chip bottom — clipped to rounded shape
+  if (isModSugar) {
+    const stripeH = Math.max(2, h * SUGAR_STRIPE_RATIO);
+    g.save();
+    drawRoundRect(g, x, y, w, h, r);
+    g.clip();
+    g.fillStyle = sugarRes.color;
+    g.fillRect(x, y + h - stripeH, w, stripeH);
+    g.restore();
+  }
+
+  // Base letter — biased upward to leave room for stripe
+  if (opts.showLetters && m.base && fontSize >= 8) {
+    const stripeH = isModSugar ? Math.max(2, h * SUGAR_STRIPE_RATIO) : 0;
+    g.fillStyle = '#1a1a1a';
+    g.font = `600 ${fontSize}px system-ui, -apple-system, "Segoe UI", Helvetica, Arial, sans-serif`;
+    g.textBaseline = 'middle';
+    g.textAlign = 'center';
+    g.fillText(m.base, x + w / 2, y + (h - stripeH) / 2 + 0.5);
+  }
+}
+
+function isModifiedSugar(sugar: string): boolean {
+  const c = canonicalSugarSymbol(sugar);
+  return c !== 'r' && c !== 'd';
+}
+
+function drawLinkage(g: CanvasRenderingContext2D, link: LinkagePos): void {
+  const ps = resolvePhosphate(link.phosphateSymbol);
+  if (ps.meta.short !== 'PS' && ps.meta.short !== 'PS₂' && ps.meta.short !== 'MeP')
+    return; // only draw markers for non-canonical linkages
+  const barW = Math.max(2.5, link.w * PS_BAR_RATIO);
+  const barX = link.x + (link.w - barW) / 2;
+  g.fillStyle = ps.color;
+  g.fillRect(barX, link.y + 1, barW, link.h - 2);
+}
+
+function drawConjugate(
+  g: CanvasRenderingContext2D, symbol: string, x: number, y: number,
+  w: number, chipH: number, fontSize: number,
+): void {
+  const conj = resolveConjugate(symbol);
+  const r = chipH / 2;
+  drawRoundRect(g, x, y, w, chipH, r);
+  g.fillStyle = conj.color;
+  g.fill();
+  g.lineWidth = 0.5;
+  g.strokeStyle = 'rgba(0,0,0,0.2)';
+  g.stroke();
+
+  if (fontSize >= 8) {
+    g.fillStyle = '#ffffff';
+    g.font = `600 ${Math.max(8, fontSize - 1)}px system-ui, sans-serif`;
+    g.textBaseline = 'middle';
+    g.textAlign = 'center';
+    g.fillText(conj.meta.short, x + w / 2, y + chipH / 2 + 0.5);
+  }
+}
+
+function drawRoundRect(
+  g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, r: number,
+): void {
+  g.beginPath();
+  g.moveTo(x + r, y);
+  g.lineTo(x + w - r, y);
+  g.quadraticCurveTo(x + w, y, x + w, y + r);
+  g.lineTo(x + w, y + h - r);
+  g.quadraticCurveTo(x + w, y + h, x + w - r, y + h);
+  g.lineTo(x + r, y + h);
+  g.quadraticCurveTo(x, y + h, x, y + h - r);
+  g.lineTo(x, y + r);
+  g.quadraticCurveTo(x, y, x + r, y);
+  g.closePath();
+}
+
+function drawFallbackText(
+  g: CanvasRenderingContext2D, _w: number, h: number, model: ParsedDuplex, layout: DuplexLayout,
+): void {
+  const sLen = model.sense.monomers.length;
+  const aLen = model.antisense ? model.antisense.monomers.length : 0;
+  const summary = model.antisense ? `${sLen}+${aLen} nt duplex` : `${sLen} nt`;
+  g.fillStyle = '#8b949e';
+  g.font = `${Math.max(8, layout.fontSize)}px ui-monospace, Menlo, monospace`;
+  g.textBaseline = 'middle';
+  g.textAlign = 'left';
+  g.fillText(summary, 4, h / 2);
+}
+
+/** Apply alpha to any CSS color string, returning rgba(...). Memoized. */
+const _alphaCache = new Map<string, string>();
+function withAlpha(color: string, alpha: number): string {
+  const key = `${color}|${alpha}`;
+  const cached = _alphaCache.get(key);
+  if (cached) return cached;
+  const probe = document.createElement('span');
+  probe.style.color = color;
+  document.body.appendChild(probe);
+  const rgb = getComputedStyle(probe).color;
+  document.body.removeChild(probe);
+  const m = rgb.match(/\d+/g);
+  const out = m ? `rgba(${m[0]},${m[1]},${m[2]},${alpha})` : color;
+  if (_alphaCache.size > 256) _alphaCache.clear();
+  _alphaCache.set(key, out);
+  return out;
+}
+
+/* ---------------------------------------------------------------- *
+ * Hit testing — uses the cached chip / linkage positions so it works
+ * correctly with variable widths (conjugate pills) and reversed antisense.
+ * ---------------------------------------------------------------- */
+
+export interface HitResult {
+  strand: StrandSide;
+  /** Original 0-based index in the data strand. */
+  position: number;
+  monomer: ParsedMonomer;
+  /** Set if the hit is on an inter-chip linkage marker (PS, etc.). */
+  linkage?: { phosphateSymbol: string };
+}
+
+export function hitTest(
+  localX: number, localY: number, model: ParsedDuplex, layout: DuplexLayout,
+): HitResult | null {
+  if (layout.textOnlyFallback) return null;
+
+  // Sense chip?
+  if (localY >= layout.senseY && localY <= layout.senseY + layout.chipH) {
+    const cp = findChip(localX, layout.senseChips);
+    if (cp) return {strand: 'sense', position: cp.origIdx, monomer: cp.monomer};
+    const link = findLink(localX, localY, layout.senseLinks);
+    if (link) return resolveLinkHit(link, model.sense, 'sense');
+  }
+  // Antisense chip?
+  if (layout.antiY >= 0 && localY >= layout.antiY && localY <= layout.antiY + layout.chipH) {
+    const cp = findChip(localX, layout.antiChips);
+    if (cp) return {strand: 'antisense', position: cp.origIdx, monomer: cp.monomer};
+    const link = findLink(localX, localY, layout.antiLinks);
+    if (link && model.antisense) return resolveLinkHit(link, model.antisense, 'antisense');
+  }
+  return null;
+}
+
+function findChip(x: number, chips: ChipPos[]): ChipPos | null {
+  for (const cp of chips) if (x >= cp.x && x < cp.x + cp.w) return cp;
+  return null;
+}
+
+function findLink(x: number, y: number, links: LinkagePos[]): LinkagePos | null {
+  for (const l of links)
+    if (x >= l.x && x < l.x + l.w && y >= l.y && y < l.y + l.h) return l;
+  return null;
+}
+
+function resolveLinkHit(link: LinkagePos, strand: ParsedStrand, side: StrandSide): HitResult {
+  const owner = strand.monomers.find((m) => m.position === link.ownerOrigIdx)!;
+  return {
+    strand: side,
+    position: link.ownerOrigIdx,
+    monomer: owner,
+    linkage: {phosphateSymbol: link.phosphateSymbol},
+  };
+}