qu-cmdwrapper 1.0.0
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- checksums.yaml +7 -0
- data/.gitignore +17 -0
- data/Gemfile +5 -0
- data/LICENSE.txt +22 -0
- data/README.md +32 -0
- data/Rakefile +1 -0
- data/lib/qu/cmdwrapper.rb +10 -0
- data/lib/qu/cmdwrapper/cmd.rb +109 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/32/faToTwoBit +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/32/ntdpal +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/32/ntthal +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/32/oligotm +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/32/primer3_core +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/32/twoBitToFa +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/64/faToTwoBit +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/64/ntdpal +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/64/ntthal +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/64/oligotm +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/64/primer3_core +0 -0
- data/lib/qu/cmdwrapper/ext_bin/linux/64/twoBitToFa +0 -0
- data/lib/qu/cmdwrapper/ext_bin/mac/32/faToTwoBit +0 -0
- data/lib/qu/cmdwrapper/ext_bin/mac/32/ntthal +0 -0
- data/lib/qu/cmdwrapper/ext_bin/mac/32/oligotm +0 -0
- data/lib/qu/cmdwrapper/ext_bin/mac/32/primer3_core +0 -0
- data/lib/qu/cmdwrapper/ext_bin/mac/32/twoBitToFa +0 -0
- data/lib/qu/cmdwrapper/ext_bin/mac/64/faToTwoBit +0 -0
- data/lib/qu/cmdwrapper/ext_bin/mac/64/ntthal +0 -0
- data/lib/qu/cmdwrapper/ext_bin/mac/64/oligotm +0 -0
- data/lib/qu/cmdwrapper/ext_bin/mac/64/primer3_core +0 -0
- data/lib/qu/cmdwrapper/ext_bin/mac/64/twoBitToFa +0 -0
- data/lib/qu/cmdwrapper/primer3_config/dangle.dh +128 -0
- data/lib/qu/cmdwrapper/primer3_config/dangle.ds +128 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.dh +131 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.ds +131 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.dh +34 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.ds +31 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.dh +257 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.ds +256 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.dh +79 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.ds +81 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.dh +21 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.ds +18 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.dh +256 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.ds +256 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.dh +256 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.ds +256 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
- data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
- data/lib/qu/cmdwrapper/primer3_config/loops.dh +30 -0
- data/lib/qu/cmdwrapper/primer3_config/loops.ds +30 -0
- data/lib/qu/cmdwrapper/primer3_config/stack.dh +256 -0
- data/lib/qu/cmdwrapper/primer3_config/stack.ds +256 -0
- data/lib/qu/cmdwrapper/primer3_config/stackmm.dh +256 -0
- data/lib/qu/cmdwrapper/primer3_config/stackmm.ds +256 -0
- data/lib/qu/cmdwrapper/primer3_config/tetraloop.dh +77 -0
- data/lib/qu/cmdwrapper/primer3_config/tetraloop.ds +77 -0
- data/lib/qu/cmdwrapper/primer3_config/triloop.dh +16 -0
- data/lib/qu/cmdwrapper/primer3_config/triloop.ds +16 -0
- data/lib/qu/cmdwrapper/primer3_config/tstack.dh +256 -0
- data/lib/qu/cmdwrapper/primer3_config/tstack2.dh +256 -0
- data/lib/qu/cmdwrapper/primer3_config/tstack2.ds +256 -0
- data/lib/qu/cmdwrapper/primer3_config/tstack_tm_inf.ds +256 -0
- data/lib/qu/cmdwrapper/version.rb +5 -0
- data/qu-cmdwrapper.gemspec +24 -0
- metadata +137 -0
@@ -0,0 +1,131 @@
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/* Entropy of dangling end */
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@@ -0,0 +1,34 @@
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DESTABILIZING ENTHALPIES BY SIZE OF LOOP (INTERPOLATE WHERE NEEDED)
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hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges
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SIZE INTERNAL BULGE HAIRPIN
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-------------------------------------------------------
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1 . 0.0 .
|
6
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2 0.0 0.0 .
|
7
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3 0.0 0.0 0.0
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8
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4 0.0 0.0 0.0
|
9
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5 0.0 0.0 0.0
|
10
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6 0.0 0.0 0.0
|
11
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7 0.0 0.0 0.0
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12
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8 0.0 0.0 0.0
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13
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9 0.0 0.0 0.0
|
14
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10 0.0 0.0 0.0
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15
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11 0.0 0.0 0.0
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16
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12 0.0 0.0 0.0
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13 0.0 0.0 0.0
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14 0.0 0.0 0.0
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19
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15 0.0 0.0 0.0
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16 0.0 0.0 0.0
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21
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17 0.0 0.0 0.0
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18 0.0 0.0 0.0
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19 0.0 0.0 0.0
|
24
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20 0.0 0.0 0.0
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25
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21 0.0 0.0 0.0
|
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22 0.0 0.0 0.0
|
27
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23 0.0 0.0 0.0
|
28
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24 0.0 0.0 0.0
|
29
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25 0.0 0.0 0.0
|
30
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+
26 0.0 0.0 0.0
|
31
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+
27 0.0 0.0 0.0
|
32
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+
28 0.0 0.0 0.0
|
33
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+
29 0.0 0.0 0.0
|
34
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+
30 0.0 0.0 0.0
|
@@ -0,0 +1,31 @@
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SIZE INTERNAL BULGE HAIRPIN
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1 . -128.9 .
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2 . -93.5 .
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3 -103.1 -99.9 -112.8
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4 -116 -103.1 -112.8
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5 -128.9 -106.4 -106.4
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6 -141.8 -112.8 -128.9
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7 -148.3 -119.2 -135.4
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9
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8 -154.7 -125.7 -138.6
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9 -157.9 -132.1 -145
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10 -157.9 -138.6 -148.3
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12
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11 -162.6 -143.2 -152.9
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12 -167.6 -145 -161.2
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13 -171.5 -148.9 -165
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14 -174.1 -154.7 -164.4
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15 -177.4 -158.1 -167.7
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16 -180.5 -161.2 -170.8
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17 -183.4 -164.1 -173.8
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18 -187 -167.6 -177.3
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19 -189.6 -170.2 -179.9
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20 -190.2 -170.8 -183.7
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21 -192.5 -173.2 -186.1
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22 -194.8 -175.5 -188.4
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23 -197 -177.6 -190.5
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24 -199 -179.7 -192.6
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25 -203.1 -180.5 -196.6
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26 -205 -182.4 -198.5
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27 -206.8 -184.2 -200.4
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28 -208.6 -186 -202.1
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29 -210.3 -187.7 -203.8
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31
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30 -212.8 -190.2 -203.1
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@@ -0,0 +1,257 @@
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1
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+
/* values in articles are modified as follows: dS *(-10) and dH *(-10) */
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2
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+
AA_AA inf
|
3
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+
AA_AC inf
|
4
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+
AA_AG inf
|
5
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+
AA_AT inf
|
6
|
+
AA_CA inf
|
7
|
+
AA_CC inf
|
8
|
+
AA_CG inf
|
9
|
+
AA_CT inf
|
10
|
+
AA_GA inf
|
11
|
+
AA_GC inf
|
12
|
+
AA_GG inf
|
13
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+
AA_GT inf
|
14
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+
AA_TA inf
|
15
|
+
AA_TC inf
|
16
|
+
AA_TG inf
|
17
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+
AA_TT -7900
|
18
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+
AC_AA inf
|
19
|
+
AC_AC inf
|
20
|
+
AC_AG inf
|
21
|
+
AC_AT inf
|
22
|
+
AC_CA inf
|
23
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+
AC_CC inf
|
24
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+
AC_CG inf
|
25
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+
AC_CT inf
|
26
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+
AC_GA inf
|
27
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+
AC_GC inf
|
28
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+
AC_GG inf
|
29
|
+
AC_GT inf
|
30
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+
AC_TA inf
|
31
|
+
AC_TC inf
|
32
|
+
AC_TG -8400
|
33
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+
AC_TT inf
|
34
|
+
AG_AA inf
|
35
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+
AG_AC inf
|
36
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+
AG_AG inf
|
37
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+
AG_AT inf
|
38
|
+
AG_CA inf
|
39
|
+
AG_CC inf
|
40
|
+
AG_CG inf
|
41
|
+
AG_CT inf
|
42
|
+
AG_GA inf
|
43
|
+
AG_GC inf
|
44
|
+
AG_GG inf
|
45
|
+
AG_GT inf
|
46
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+
AG_TA inf
|
47
|
+
AG_TC -7800
|
48
|
+
AG_TG inf
|
49
|
+
AG_TT inf
|
50
|
+
AT_AA inf
|
51
|
+
AT_AC inf
|
52
|
+
AT_AG inf
|
53
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+
AT_AT inf
|
54
|
+
AT_CA inf
|
55
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+
AT_CC inf
|
56
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+
AT_CG inf
|
57
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+
AT_CT inf
|
58
|
+
AT_GA inf
|
59
|
+
AT_GC inf
|
60
|
+
AT_GG inf
|
61
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+
AT_GT inf
|
62
|
+
AT_TA -7200
|
63
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+
AT_TC inf
|
64
|
+
AT_TG inf
|
65
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+
AT_TT inf
|
66
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+
CA_AA inf
|
67
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+
CA_AC inf
|
68
|
+
CA_AG inf
|
69
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+
CA_AT inf
|
70
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+
CA_CA inf
|
71
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+
CA_CC inf
|
72
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+
CA_CG inf
|
73
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+
CA_CT inf
|
74
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+
CA_GA inf
|
75
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+
CA_GC inf
|
76
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+
CA_GG inf
|
77
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+
CA_GT -8500
|
78
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+
CA_TA inf
|
79
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+
CA_TC inf
|
80
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+
CA_TG inf
|
81
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+
CA_TT inf
|
82
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+
CC_AA inf
|
83
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+
CC_AC inf
|
84
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+
CC_AG -52
|
85
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+
CC_AT inf
|
86
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+
CC_CA inf
|
87
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+
CC_CC inf
|
88
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+
CC_CG -36
|
89
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+
CC_CT inf
|
90
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+
CC_GA inf
|
91
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+
CC_GC inf
|
92
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+
CC_GG -8000
|
93
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+
CC_GT inf
|
94
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+
CC_TA inf
|
95
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+
CC_TC inf
|
96
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+
CC_TG inf
|
97
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+
CC_TT inf
|
98
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+
CG_AA inf
|
99
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+
CG_AC inf
|
100
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+
CG_AG inf
|
101
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+
CG_AT inf
|
102
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+
CG_CA inf
|
103
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+
CG_CC inf
|
104
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+
CG_CG inf
|
105
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+
CG_CT inf
|
106
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+
CG_GA inf
|
107
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+
CG_GC -10600
|
108
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+
CG_GG inf
|
109
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+
CG_GT inf
|
110
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+
CG_TA inf
|
111
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+
CG_TC inf
|
112
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+
CG_TG inf
|
113
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+
CG_TT inf
|
114
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+
CT_AA inf
|
115
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+
CT_AC inf
|
116
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+
CT_AG inf
|
117
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+
CT_AT inf
|
118
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+
CT_CA inf
|
119
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+
CT_CC inf
|
120
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+
CT_CG inf
|
121
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+
CT_CT inf
|
122
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+
CT_GA -7800
|
123
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+
CT_GC inf
|
124
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+
CT_GG inf
|
125
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+
CT_GT inf
|
126
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+
CT_TA inf
|
127
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+
CT_TC inf
|
128
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+
CT_TG inf
|
129
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+
CT_TT inf
|
130
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+
GA_AA inf
|
131
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+
GA_AC inf
|
132
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+
GA_AG inf
|
133
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+
GA_AT inf
|
134
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+
GA_CA inf
|
135
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+
GA_CC inf
|
136
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+
GA_CG inf
|
137
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+
GA_CT -8200
|
138
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+
GA_GA inf
|
139
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+
GA_GC inf
|
140
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+
GA_GG inf
|
141
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+
GA_GT inf
|
142
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+
GA_TA inf
|
143
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+
GA_TC inf
|
144
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+
GA_TG inf
|
145
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+
GA_TT inf
|
146
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+
GC_AA inf
|
147
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+
GC_AC inf
|
148
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+
GC_AG inf
|
149
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+
GC_AT inf
|
150
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+
GC_CA inf
|
151
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+
GC_CC inf
|
152
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+
GC_CG -9800
|
153
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+
GC_CT inf
|
154
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+
GC_GA inf
|
155
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+
GC_GC inf
|
156
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+
GC_GG inf
|
157
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+
GC_GT inf
|
158
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+
GC_TA inf
|
159
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+
GC_TC inf
|
160
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+
GC_TG inf
|
161
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+
GC_TT inf
|
162
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+
GG_AA inf
|
163
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+
GG_AC inf
|
164
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+
GG_AG inf
|
165
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+
GG_AT inf
|
166
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+
GG_CA inf
|
167
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+
GG_CC -8000
|
168
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+
GG_CG inf
|
169
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+
GG_CT inf
|
170
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+
GG_GA inf
|
171
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+
GG_GC inf
|
172
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+
GG_GG inf
|
173
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+
GG_GT inf
|
174
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+
GG_TA inf
|
175
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+
GG_TC inf
|
176
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+
GG_TG inf
|
177
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+
GG_TT inf
|
178
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+
GT_AA inf
|
179
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+
GT_AC inf
|
180
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+
GT_AG inf
|
181
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+
GT_AT inf
|
182
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+
GT_CA -8400
|
183
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+
GT_CC inf
|
184
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+
GT_CG inf
|
185
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+
GT_CT inf
|
186
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+
GT_GA inf
|
187
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+
GT_GC inf
|
188
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+
GT_GG inf
|
189
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+
GT_GT inf
|
190
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+
GT_TA inf
|
191
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+
GT_TC inf
|
192
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+
GT_TG inf
|
193
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+
GT_TT inf
|
194
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+
TA_AA inf
|
195
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+
TA_AC inf
|
196
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+
TA_AG inf
|
197
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+
TA_AT -7200
|
198
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+
TA_CA inf
|
199
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+
TA_CC inf
|
200
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+
TA_CG inf
|
201
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+
TA_CT inf
|
202
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+
TA_GA inf
|
203
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+
TA_GC inf
|
204
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+
TA_GG inf
|
205
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+
TA_GT inf
|
206
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+
TA_TA inf
|
207
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+
TA_TC inf
|
208
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+
TA_TG inf
|
209
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+
TA_TT inf
|
210
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+
TC_AA inf
|
211
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+
TC_AC inf
|
212
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+
TC_AG -8200
|
213
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+
TC_AT inf
|
214
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+
TC_CA inf
|
215
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+
TC_CC inf
|
216
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+
TC_CG inf
|
217
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+
TC_CT inf
|
218
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+
TC_GA inf
|
219
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+
TC_GC inf
|
220
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+
TC_GG inf
|
221
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+
TC_GT inf
|
222
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+
TC_TA inf
|
223
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+
TC_TC inf
|
224
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+
TC_TG inf
|
225
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+
TC_TT inf
|
226
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+
TG_AA inf
|
227
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+
TG_AC -8500
|
228
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+
TG_AG inf
|
229
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+
TG_AT inf
|
230
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+
TG_CA inf
|
231
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+
TG_CC inf
|
232
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+
TG_CG inf
|
233
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+
TG_CT inf
|
234
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+
TG_GA inf
|
235
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+
TG_GC inf
|
236
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+
TG_GG inf
|
237
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+
TG_GT inf
|
238
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+
TG_TA inf
|
239
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+
TG_TC inf
|
240
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+
TG_TG inf
|
241
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+
TG_TT inf
|
242
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+
TT_AA -7900
|
243
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+
TT_AC inf
|
244
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+
TT_AG inf
|
245
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+
TT_AT inf
|
246
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+
TT_CA inf
|
247
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+
TT_CC inf
|
248
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+
TT_CG inf
|
249
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+
TT_CT inf
|
250
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+
TT_GA inf
|
251
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+
TT_GC inf
|
252
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+
TT_GG inf
|
253
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+
TT_GT inf
|
254
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+
TT_TA inf
|
255
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+
TT_TC inf
|
256
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+
TT_TG inf
|
257
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+
TT_TT inf
|