Multiple sequence alignment - TraesCS3D01G096300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G096300 chr3D 100.000 2985 0 0 1 2985 48819008 48821992 0.000000e+00 5513.0
1 TraesCS3D01G096300 chr3D 89.333 300 32 0 1685 1984 48820623 48820922 7.810000e-101 377.0
2 TraesCS3D01G096300 chr3D 89.333 300 32 0 1616 1915 48820692 48820991 7.810000e-101 377.0
3 TraesCS3D01G096300 chr3D 89.823 226 23 0 1754 1979 48820623 48820848 1.050000e-74 291.0
4 TraesCS3D01G096300 chr3D 89.823 226 23 0 1616 1841 48820761 48820986 1.050000e-74 291.0
5 TraesCS3D01G096300 chr3D 83.764 271 36 5 1 266 190271937 190272204 1.780000e-62 250.0
6 TraesCS3D01G096300 chr3D 82.014 278 45 5 1220 1497 568582946 568583218 6.430000e-57 231.0
7 TraesCS3D01G096300 chr3D 87.654 162 20 0 1823 1984 48820623 48820784 3.930000e-44 189.0
8 TraesCS3D01G096300 chr3D 87.654 162 20 0 1616 1777 48820830 48820991 3.930000e-44 189.0
9 TraesCS3D01G096300 chr3B 86.786 1226 126 20 1749 2963 77852079 77853279 0.000000e+00 1334.0
10 TraesCS3D01G096300 chr3B 86.035 401 34 10 678 1075 77851663 77852044 7.700000e-111 411.0
11 TraesCS3D01G096300 chr3A 92.998 914 53 6 1753 2662 61308801 61309707 0.000000e+00 1323.0
12 TraesCS3D01G096300 chr3A 88.640 1118 77 19 1 1075 61307060 61308170 0.000000e+00 1315.0
13 TraesCS3D01G096300 chr3A 88.742 302 16 2 1553 1854 61308164 61308447 1.320000e-93 353.0
14 TraesCS3D01G096300 chr3A 94.222 225 13 0 1616 1840 61308802 61309026 7.920000e-91 344.0
15 TraesCS3D01G096300 chr3A 92.760 221 16 0 1705 1925 61308229 61308449 1.340000e-83 320.0
16 TraesCS3D01G096300 chr3A 90.517 232 22 0 1684 1915 61308801 61309032 1.040000e-79 307.0
17 TraesCS3D01G096300 chr3A 89.076 238 23 3 1748 1984 61308204 61308439 2.910000e-75 292.0
18 TraesCS3D01G096300 chr3A 95.930 172 7 0 1616 1787 61308278 61308449 2.270000e-71 279.0
19 TraesCS3D01G096300 chr3A 93.902 164 10 0 1614 1777 61308869 61309032 6.390000e-62 248.0
20 TraesCS3D01G096300 chr3A 89.571 163 17 0 1822 1984 61308801 61308963 1.080000e-49 207.0
21 TraesCS3D01G096300 chr3A 95.833 72 3 0 2658 2729 61309851 61309922 1.880000e-22 117.0
22 TraesCS3D01G096300 chr7D 94.958 238 11 1 1316 1552 47608762 47608525 3.630000e-99 372.0
23 TraesCS3D01G096300 chr7D 94.372 231 7 4 1324 1552 47605117 47604891 1.700000e-92 350.0
24 TraesCS3D01G096300 chr7D 84.270 267 38 4 1 265 510848550 510848286 1.060000e-64 257.0
25 TraesCS3D01G096300 chr7D 88.636 88 9 1 1307 1393 621775501 621775588 4.070000e-19 106.0
26 TraesCS3D01G096300 chr2D 82.500 360 55 6 1 354 524046673 524046316 2.890000e-80 309.0
27 TraesCS3D01G096300 chr2D 83.333 270 37 8 1 266 73464112 73463847 2.970000e-60 243.0
28 TraesCS3D01G096300 chr1A 91.031 223 19 1 1332 1553 48987085 48986863 1.740000e-77 300.0
29 TraesCS3D01G096300 chr6D 81.016 374 60 11 1 368 386650218 386649850 1.350000e-73 287.0
30 TraesCS3D01G096300 chr6D 80.376 372 53 10 1 354 267726947 267726578 6.340000e-67 265.0
31 TraesCS3D01G096300 chr6D 83.582 268 34 8 1 266 57465678 57465419 2.970000e-60 243.0
32 TraesCS3D01G096300 chr6D 79.805 307 40 16 1081 1381 472052662 472052952 1.400000e-48 204.0
33 TraesCS3D01G096300 chr2A 80.939 362 56 12 1 354 670639448 670639092 1.050000e-69 274.0
34 TraesCS3D01G096300 chr7A 94.928 138 6 1 1416 1552 733431943 733431806 6.480000e-52 215.0
35 TraesCS3D01G096300 chr7A 88.172 93 11 0 1332 1424 733432219 733432127 8.750000e-21 111.0
36 TraesCS3D01G096300 chr4B 80.899 267 33 12 1121 1381 205077781 205078035 8.440000e-46 195.0
37 TraesCS3D01G096300 chr4B 78.010 191 26 10 155 332 2634452 2634265 4.070000e-19 106.0
38 TraesCS3D01G096300 chr5D 96.154 78 3 0 1316 1393 440243495 440243418 8.680000e-26 128.0
39 TraesCS3D01G096300 chr4D 86.735 98 11 2 1307 1402 115530302 115530205 1.130000e-19 108.0
40 TraesCS3D01G096300 chr1B 83.178 107 15 3 2782 2887 155678211 155678315 8.810000e-16 95.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G096300 chr3D 48819008 48821992 2984 False 1032.428571 5513 90.517143 1 2985 7 chr3D.!!$F3 2984
1 TraesCS3D01G096300 chr3B 77851663 77853279 1616 False 872.500000 1334 86.410500 678 2963 2 chr3B.!!$F1 2285
2 TraesCS3D01G096300 chr3A 61307060 61309922 2862 False 464.090909 1323 92.017364 1 2729 11 chr3A.!!$F1 2728
3 TraesCS3D01G096300 chr7D 47604891 47608762 3871 True 361.000000 372 94.665000 1316 1552 2 chr7D.!!$R2 236

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
246 251 0.464735 TTGTGTCTCCGGTTTGTGGG 60.465 55.0 0.00 0.0 0.0 4.61 F
290 307 1.359459 GACCGGCGTTGGATGACTTC 61.359 60.0 6.01 0.0 0.0 3.01 F
1106 1157 0.171903 TAGTACTTTCCGGCAGCGAC 59.828 55.0 0.00 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1087 1138 0.171903 GTCGCTGCCGGAAAGTACTA 59.828 55.0 5.05 0.0 34.56 1.82 R
1122 1173 0.179307 CTTCGCTTCGTCGTCGTTTG 60.179 55.0 1.33 0.0 38.33 2.93 R
2608 4571 0.676184 CGCAGAGCTTAGGATGCCTA 59.324 55.0 0.00 0.0 34.61 3.93 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 83 0.465705 TCCGCCTAAGCCATCTTCAG 59.534 55.000 0.00 0.00 34.57 3.02
194 199 3.435186 GTCAGAAGCGGGCTTGGC 61.435 66.667 11.17 0.00 36.26 4.52
216 221 2.258726 GGTCCGGACTGCCACAAAC 61.259 63.158 32.52 10.15 0.00 2.93
229 234 0.827507 CACAAACCCTCCCCCACTTG 60.828 60.000 0.00 0.00 0.00 3.16
236 241 1.679898 CTCCCCCACTTGTGTCTCC 59.320 63.158 0.00 0.00 0.00 3.71
238 243 2.347490 CCCCACTTGTGTCTCCGG 59.653 66.667 0.00 0.00 0.00 5.14
245 250 0.944386 CTTGTGTCTCCGGTTTGTGG 59.056 55.000 0.00 0.00 0.00 4.17
246 251 0.464735 TTGTGTCTCCGGTTTGTGGG 60.465 55.000 0.00 0.00 0.00 4.61
265 282 3.252484 GAAATCGCGTCCGGACCG 61.252 66.667 28.52 28.64 34.56 4.79
272 289 2.475466 GCGTCCGGACCGATACAGA 61.475 63.158 28.52 0.00 0.00 3.41
290 307 1.359459 GACCGGCGTTGGATGACTTC 61.359 60.000 6.01 0.00 0.00 3.01
318 335 1.512996 GGATAGCGTGATCCGGACGA 61.513 60.000 17.44 0.00 39.21 4.20
322 339 1.518572 GCGTGATCCGGACGATTGT 60.519 57.895 17.44 0.00 39.21 2.71
323 340 1.752501 GCGTGATCCGGACGATTGTG 61.753 60.000 17.44 0.83 39.21 3.33
345 362 2.675075 GTTTGCAGGCCCGCCTTA 60.675 61.111 8.88 0.00 45.70 2.69
354 371 3.106986 GCCCGCCTTAGAGATGCCA 62.107 63.158 0.00 0.00 0.00 4.92
406 424 7.979444 TTTTCAGATAGAAGTAGGTGTTTGG 57.021 36.000 0.00 0.00 37.57 3.28
410 428 6.380274 TCAGATAGAAGTAGGTGTTTGGGTAG 59.620 42.308 0.00 0.00 0.00 3.18
417 435 2.661718 AGGTGTTTGGGTAGTTTGGTG 58.338 47.619 0.00 0.00 0.00 4.17
479 497 6.248569 TCAGGGGTTCTTTAGGTCATATTC 57.751 41.667 0.00 0.00 0.00 1.75
510 528 9.783256 AACGGAAATTGCATATAAGTTAGAAAC 57.217 29.630 0.00 0.00 0.00 2.78
545 578 7.984391 TGTGCGATCTAATGATTGTTGTTATT 58.016 30.769 0.00 0.00 36.64 1.40
625 658 7.531280 AACGTCTGATTCAATATGAAGACTG 57.469 36.000 0.00 5.47 40.05 3.51
634 667 5.500234 TCAATATGAAGACTGTGAAAGGGG 58.500 41.667 0.00 0.00 0.00 4.79
635 668 2.206576 ATGAAGACTGTGAAAGGGGC 57.793 50.000 0.00 0.00 0.00 5.80
645 678 5.589831 ACTGTGAAAGGGGCCTTTATAATT 58.410 37.500 0.00 0.00 45.16 1.40
650 683 7.455008 TGTGAAAGGGGCCTTTATAATTTGTAA 59.545 33.333 0.00 0.00 45.16 2.41
653 686 9.899661 GAAAGGGGCCTTTATAATTTGTAAAAT 57.100 29.630 0.00 0.00 45.16 1.82
654 687 9.679661 AAAGGGGCCTTTATAATTTGTAAAATG 57.320 29.630 0.00 0.00 43.58 2.32
657 690 7.497579 GGGGCCTTTATAATTTGTAAAATGTGG 59.502 37.037 0.84 0.52 0.00 4.17
658 691 7.011950 GGGCCTTTATAATTTGTAAAATGTGGC 59.988 37.037 0.84 13.60 32.34 5.01
659 692 7.550906 GGCCTTTATAATTTGTAAAATGTGGCA 59.449 33.333 19.15 0.00 33.63 4.92
692 735 3.488678 CGAACGTGATGGATCTCTTCATG 59.511 47.826 13.21 13.21 40.41 3.07
701 744 3.843619 TGGATCTCTTCATGTAACCCACA 59.156 43.478 0.00 0.00 42.69 4.17
836 886 2.414138 ACGCTTACGCCAACTGATTTAC 59.586 45.455 0.00 0.00 45.53 2.01
837 887 2.671396 CGCTTACGCCAACTGATTTACT 59.329 45.455 0.00 0.00 0.00 2.24
838 888 3.861113 CGCTTACGCCAACTGATTTACTA 59.139 43.478 0.00 0.00 0.00 1.82
1078 1129 2.953466 CCAGATGATGGCAGTTTTGG 57.047 50.000 0.00 0.00 43.83 3.28
1085 1136 4.662961 GGCAGTTTTGGCCGGCAC 62.663 66.667 30.85 18.16 43.67 5.01
1086 1137 4.662961 GCAGTTTTGGCCGGCACC 62.663 66.667 30.85 12.89 0.00 5.01
1087 1138 2.912025 CAGTTTTGGCCGGCACCT 60.912 61.111 30.85 12.68 0.00 4.00
1088 1139 1.602323 CAGTTTTGGCCGGCACCTA 60.602 57.895 30.85 8.44 0.00 3.08
1089 1140 1.303317 AGTTTTGGCCGGCACCTAG 60.303 57.895 30.85 0.00 0.00 3.02
1090 1141 1.602605 GTTTTGGCCGGCACCTAGT 60.603 57.895 30.85 0.00 0.00 2.57
1091 1142 0.321830 GTTTTGGCCGGCACCTAGTA 60.322 55.000 30.85 2.99 0.00 1.82
1092 1143 0.321830 TTTTGGCCGGCACCTAGTAC 60.322 55.000 30.85 8.62 0.00 2.73
1093 1144 1.196104 TTTGGCCGGCACCTAGTACT 61.196 55.000 30.85 0.00 0.00 2.73
1094 1145 1.196104 TTGGCCGGCACCTAGTACTT 61.196 55.000 30.85 0.00 0.00 2.24
1095 1146 1.196104 TGGCCGGCACCTAGTACTTT 61.196 55.000 30.85 0.00 0.00 2.66
1096 1147 0.461516 GGCCGGCACCTAGTACTTTC 60.462 60.000 30.85 0.98 0.00 2.62
1097 1148 0.461516 GCCGGCACCTAGTACTTTCC 60.462 60.000 24.80 0.00 0.00 3.13
1098 1149 0.179119 CCGGCACCTAGTACTTTCCG 60.179 60.000 0.00 7.28 35.60 4.30
1099 1150 0.179119 CGGCACCTAGTACTTTCCGG 60.179 60.000 0.00 0.00 32.55 5.14
1100 1151 0.461516 GGCACCTAGTACTTTCCGGC 60.462 60.000 0.00 0.00 0.00 6.13
1101 1152 0.248289 GCACCTAGTACTTTCCGGCA 59.752 55.000 0.00 0.00 0.00 5.69
1102 1153 1.739371 GCACCTAGTACTTTCCGGCAG 60.739 57.143 0.00 0.00 0.00 4.85
1103 1154 0.535797 ACCTAGTACTTTCCGGCAGC 59.464 55.000 0.00 0.00 0.00 5.25
1104 1155 0.527817 CCTAGTACTTTCCGGCAGCG 60.528 60.000 0.00 0.00 0.00 5.18
1105 1156 0.454600 CTAGTACTTTCCGGCAGCGA 59.545 55.000 0.00 0.00 0.00 4.93
1106 1157 0.171903 TAGTACTTTCCGGCAGCGAC 59.828 55.000 0.00 0.00 0.00 5.19
1107 1158 2.126228 TACTTTCCGGCAGCGACG 60.126 61.111 0.00 0.00 0.00 5.12
1124 1175 4.853507 GGTGACGATCGACGACAA 57.146 55.556 24.34 0.00 46.03 3.18
1125 1176 3.096541 GGTGACGATCGACGACAAA 57.903 52.632 24.34 0.00 46.03 2.83
1126 1177 0.706729 GGTGACGATCGACGACAAAC 59.293 55.000 24.34 9.20 46.03 2.93
1127 1178 0.357894 GTGACGATCGACGACAAACG 59.642 55.000 24.34 6.85 46.03 3.60
1128 1179 0.235404 TGACGATCGACGACAAACGA 59.765 50.000 24.34 0.00 45.77 3.85
1129 1180 0.627307 GACGATCGACGACAAACGAC 59.373 55.000 24.34 10.58 45.77 4.34
1134 1185 4.194312 GACGACAAACGACGACGA 57.806 55.556 15.32 0.00 45.77 4.20
1135 1186 2.483793 GACGACAAACGACGACGAA 58.516 52.632 15.32 0.00 45.77 3.85
1136 1187 0.424920 GACGACAAACGACGACGAAG 59.575 55.000 15.32 5.63 45.77 3.79
1137 1188 1.125266 CGACAAACGACGACGAAGC 59.875 57.895 15.32 0.00 45.77 3.86
1138 1189 1.125266 GACAAACGACGACGAAGCG 59.875 57.895 15.32 4.89 42.66 4.68
1139 1190 1.264141 GACAAACGACGACGAAGCGA 61.264 55.000 15.32 0.00 42.66 4.93
1140 1191 0.866906 ACAAACGACGACGAAGCGAA 60.867 50.000 15.32 0.00 42.66 4.70
1141 1192 0.179307 CAAACGACGACGAAGCGAAG 60.179 55.000 15.32 0.00 42.66 3.79
1157 1208 3.455619 CGAAGCAACGCTGATTAACTT 57.544 42.857 0.00 0.00 39.62 2.66
1158 1209 3.155998 CGAAGCAACGCTGATTAACTTG 58.844 45.455 0.00 0.00 39.62 3.16
1159 1210 3.492313 GAAGCAACGCTGATTAACTTGG 58.508 45.455 0.00 0.00 39.62 3.61
1160 1211 2.778299 AGCAACGCTGATTAACTTGGA 58.222 42.857 0.00 0.00 37.57 3.53
1161 1212 3.347216 AGCAACGCTGATTAACTTGGAT 58.653 40.909 0.00 0.00 37.57 3.41
1162 1213 3.375299 AGCAACGCTGATTAACTTGGATC 59.625 43.478 0.00 0.00 37.57 3.36
1163 1214 3.487544 GCAACGCTGATTAACTTGGATCC 60.488 47.826 4.20 4.20 0.00 3.36
1164 1215 3.914426 ACGCTGATTAACTTGGATCCT 57.086 42.857 14.23 0.00 0.00 3.24
1165 1216 3.535561 ACGCTGATTAACTTGGATCCTG 58.464 45.455 14.23 8.50 0.00 3.86
1166 1217 2.289002 CGCTGATTAACTTGGATCCTGC 59.711 50.000 14.23 0.00 0.00 4.85
1167 1218 2.620585 GCTGATTAACTTGGATCCTGCC 59.379 50.000 14.23 0.00 0.00 4.85
1168 1219 3.217626 CTGATTAACTTGGATCCTGCCC 58.782 50.000 14.23 0.00 0.00 5.36
1169 1220 2.091885 TGATTAACTTGGATCCTGCCCC 60.092 50.000 14.23 0.00 0.00 5.80
1170 1221 1.377690 TTAACTTGGATCCTGCCCCA 58.622 50.000 14.23 0.00 0.00 4.96
1171 1222 1.377690 TAACTTGGATCCTGCCCCAA 58.622 50.000 14.23 0.00 39.88 4.12
1173 1224 3.936408 TTGGATCCTGCCCCAAGT 58.064 55.556 14.23 0.00 37.50 3.16
1174 1225 2.172900 TTGGATCCTGCCCCAAGTT 58.827 52.632 14.23 0.00 37.50 2.66
1175 1226 0.251742 TTGGATCCTGCCCCAAGTTG 60.252 55.000 14.23 0.00 37.50 3.16
1176 1227 1.380380 GGATCCTGCCCCAAGTTGG 60.380 63.158 15.52 15.52 37.25 3.77
1182 1233 4.645809 GCCCCAAGTTGGCTAGAG 57.354 61.111 17.07 2.17 45.70 2.43
1183 1234 1.991230 GCCCCAAGTTGGCTAGAGA 59.009 57.895 17.07 0.00 45.70 3.10
1184 1235 0.393132 GCCCCAAGTTGGCTAGAGAC 60.393 60.000 17.07 0.00 45.70 3.36
1185 1236 1.280457 CCCCAAGTTGGCTAGAGACT 58.720 55.000 17.07 0.00 35.79 3.24
1186 1237 1.208293 CCCCAAGTTGGCTAGAGACTC 59.792 57.143 17.07 0.00 35.79 3.36
1187 1238 1.902508 CCCAAGTTGGCTAGAGACTCA 59.097 52.381 17.07 0.00 35.79 3.41
1188 1239 2.354203 CCCAAGTTGGCTAGAGACTCAC 60.354 54.545 17.07 0.00 35.79 3.51
1189 1240 2.600731 CAAGTTGGCTAGAGACTCACG 58.399 52.381 5.02 0.00 0.00 4.35
1190 1241 1.912417 AGTTGGCTAGAGACTCACGT 58.088 50.000 5.02 0.00 0.00 4.49
1191 1242 3.069079 AGTTGGCTAGAGACTCACGTA 57.931 47.619 5.02 0.00 0.00 3.57
1192 1243 2.748532 AGTTGGCTAGAGACTCACGTAC 59.251 50.000 5.02 0.00 0.00 3.67
1193 1244 1.747709 TGGCTAGAGACTCACGTACC 58.252 55.000 5.02 0.00 0.00 3.34
1194 1245 1.003928 TGGCTAGAGACTCACGTACCA 59.996 52.381 5.02 2.20 0.00 3.25
1195 1246 2.089980 GGCTAGAGACTCACGTACCAA 58.910 52.381 5.02 0.00 0.00 3.67
1196 1247 2.490903 GGCTAGAGACTCACGTACCAAA 59.509 50.000 5.02 0.00 0.00 3.28
1197 1248 3.500014 GCTAGAGACTCACGTACCAAAC 58.500 50.000 5.02 0.00 0.00 2.93
1198 1249 3.190953 GCTAGAGACTCACGTACCAAACT 59.809 47.826 5.02 0.00 0.00 2.66
1199 1250 4.394300 GCTAGAGACTCACGTACCAAACTA 59.606 45.833 5.02 0.00 0.00 2.24
1200 1251 5.447548 GCTAGAGACTCACGTACCAAACTAG 60.448 48.000 5.02 0.00 0.00 2.57
1201 1252 3.190953 AGAGACTCACGTACCAAACTAGC 59.809 47.826 5.02 0.00 0.00 3.42
1202 1253 2.889045 AGACTCACGTACCAAACTAGCA 59.111 45.455 0.00 0.00 0.00 3.49
1203 1254 2.985139 GACTCACGTACCAAACTAGCAC 59.015 50.000 0.00 0.00 0.00 4.40
1204 1255 2.288640 ACTCACGTACCAAACTAGCACC 60.289 50.000 0.00 0.00 0.00 5.01
1205 1256 1.687660 TCACGTACCAAACTAGCACCA 59.312 47.619 0.00 0.00 0.00 4.17
1206 1257 2.102757 TCACGTACCAAACTAGCACCAA 59.897 45.455 0.00 0.00 0.00 3.67
1207 1258 2.478894 CACGTACCAAACTAGCACCAAG 59.521 50.000 0.00 0.00 0.00 3.61
1208 1259 1.463444 CGTACCAAACTAGCACCAAGC 59.537 52.381 0.00 0.00 46.19 4.01
1227 1278 4.292186 AGCTTGATTGCTTCTAGTTGGA 57.708 40.909 0.00 0.00 40.93 3.53
1228 1279 4.006319 AGCTTGATTGCTTCTAGTTGGAC 58.994 43.478 0.00 0.00 40.93 4.02
1229 1280 3.181516 GCTTGATTGCTTCTAGTTGGACG 60.182 47.826 0.00 0.00 30.81 4.79
1230 1281 3.678056 TGATTGCTTCTAGTTGGACGT 57.322 42.857 0.00 0.00 0.00 4.34
1231 1282 3.325870 TGATTGCTTCTAGTTGGACGTG 58.674 45.455 0.00 0.00 0.00 4.49
1232 1283 2.902705 TTGCTTCTAGTTGGACGTGT 57.097 45.000 0.00 0.00 0.00 4.49
1233 1284 4.021807 TGATTGCTTCTAGTTGGACGTGTA 60.022 41.667 0.00 0.00 0.00 2.90
1234 1285 3.293311 TGCTTCTAGTTGGACGTGTAC 57.707 47.619 0.00 0.00 0.00 2.90
1235 1286 2.889045 TGCTTCTAGTTGGACGTGTACT 59.111 45.455 0.00 0.00 0.00 2.73
1236 1287 4.074259 TGCTTCTAGTTGGACGTGTACTA 58.926 43.478 0.00 0.00 0.00 1.82
1237 1288 4.083110 TGCTTCTAGTTGGACGTGTACTAC 60.083 45.833 0.00 0.00 0.00 2.73
1238 1289 4.155644 GCTTCTAGTTGGACGTGTACTACT 59.844 45.833 0.00 4.77 0.00 2.57
1239 1290 5.335504 GCTTCTAGTTGGACGTGTACTACTT 60.336 44.000 4.69 0.00 0.00 2.24
1240 1291 5.618056 TCTAGTTGGACGTGTACTACTTG 57.382 43.478 4.69 3.69 0.00 3.16
1241 1292 3.022607 AGTTGGACGTGTACTACTTGC 57.977 47.619 0.00 0.00 0.00 4.01
1242 1293 2.626743 AGTTGGACGTGTACTACTTGCT 59.373 45.455 0.00 0.00 0.00 3.91
1243 1294 3.822735 AGTTGGACGTGTACTACTTGCTA 59.177 43.478 0.00 0.00 0.00 3.49
1244 1295 3.837213 TGGACGTGTACTACTTGCTAC 57.163 47.619 0.00 0.00 0.00 3.58
1245 1296 3.415212 TGGACGTGTACTACTTGCTACT 58.585 45.455 0.00 0.00 0.00 2.57
1246 1297 4.578871 TGGACGTGTACTACTTGCTACTA 58.421 43.478 0.00 0.00 0.00 1.82
1247 1298 4.633126 TGGACGTGTACTACTTGCTACTAG 59.367 45.833 0.00 0.00 0.00 2.57
1248 1299 4.495514 GGACGTGTACTACTTGCTACTAGC 60.496 50.000 0.00 0.61 42.82 3.42
1266 1317 3.467374 AGCAGAAGATAGCTAGCAACC 57.533 47.619 18.83 4.80 39.78 3.77
1267 1318 3.037549 AGCAGAAGATAGCTAGCAACCT 58.962 45.455 18.83 7.22 39.78 3.50
1268 1319 3.129871 GCAGAAGATAGCTAGCAACCTG 58.870 50.000 18.83 14.63 0.00 4.00
1269 1320 3.181471 GCAGAAGATAGCTAGCAACCTGA 60.181 47.826 18.83 0.00 0.00 3.86
1270 1321 4.502950 GCAGAAGATAGCTAGCAACCTGAT 60.503 45.833 18.83 0.00 0.00 2.90
1271 1322 5.229423 CAGAAGATAGCTAGCAACCTGATC 58.771 45.833 18.83 9.16 0.00 2.92
1272 1323 4.898265 AGAAGATAGCTAGCAACCTGATCA 59.102 41.667 18.83 0.00 0.00 2.92
1273 1324 5.365025 AGAAGATAGCTAGCAACCTGATCAA 59.635 40.000 18.83 0.00 0.00 2.57
1274 1325 5.822132 AGATAGCTAGCAACCTGATCAAT 57.178 39.130 18.83 0.00 0.00 2.57
1275 1326 5.792741 AGATAGCTAGCAACCTGATCAATC 58.207 41.667 18.83 4.00 0.00 2.67
1276 1327 5.543405 AGATAGCTAGCAACCTGATCAATCT 59.457 40.000 18.83 6.03 0.00 2.40
1277 1328 4.070630 AGCTAGCAACCTGATCAATCTC 57.929 45.455 18.83 0.00 0.00 2.75
1278 1329 3.453717 AGCTAGCAACCTGATCAATCTCA 59.546 43.478 18.83 0.00 0.00 3.27
1279 1330 3.559242 GCTAGCAACCTGATCAATCTCAC 59.441 47.826 10.63 0.00 0.00 3.51
1280 1331 2.625737 AGCAACCTGATCAATCTCACG 58.374 47.619 0.00 0.00 0.00 4.35
1281 1332 2.234661 AGCAACCTGATCAATCTCACGA 59.765 45.455 0.00 0.00 0.00 4.35
1282 1333 3.118482 AGCAACCTGATCAATCTCACGAT 60.118 43.478 0.00 0.00 0.00 3.73
1283 1334 3.624861 GCAACCTGATCAATCTCACGATT 59.375 43.478 0.00 0.00 40.43 3.34
1307 1358 4.288670 TCGATTCTGGTCGATACTCAAC 57.711 45.455 0.00 0.00 44.87 3.18
1308 1359 3.692593 TCGATTCTGGTCGATACTCAACA 59.307 43.478 0.00 0.00 44.87 3.33
1309 1360 3.791887 CGATTCTGGTCGATACTCAACAC 59.208 47.826 0.00 0.00 44.06 3.32
1310 1361 2.913777 TCTGGTCGATACTCAACACG 57.086 50.000 0.00 0.00 0.00 4.49
1311 1362 1.135489 TCTGGTCGATACTCAACACGC 60.135 52.381 0.00 0.00 0.00 5.34
1312 1363 0.599060 TGGTCGATACTCAACACGCA 59.401 50.000 0.00 0.00 0.00 5.24
1313 1364 1.203758 TGGTCGATACTCAACACGCAT 59.796 47.619 0.00 0.00 0.00 4.73
1314 1365 1.588404 GGTCGATACTCAACACGCATG 59.412 52.381 0.00 0.00 0.00 4.06
1319 1370 0.865111 TACTCAACACGCATGCACAC 59.135 50.000 19.57 0.00 0.00 3.82
1322 1373 1.010238 CAACACGCATGCACACGAA 60.010 52.632 19.57 0.00 0.00 3.85
1381 1432 9.944663 TGTTCTGATTTGTATTACTTCACAAAC 57.055 29.630 2.30 0.00 44.80 2.93
1425 1476 7.117667 TGGCTGATTACACGCATATAAATAGTG 59.882 37.037 0.00 0.00 38.63 2.74
1503 1554 0.531657 TACATGCATGCAAGCCAACC 59.468 50.000 26.68 0.00 0.00 3.77
1505 1556 0.818938 CATGCATGCAAGCCAACCTA 59.181 50.000 26.68 0.00 0.00 3.08
1517 1568 1.605202 GCCAACCTAAACACGTACCGA 60.605 52.381 0.00 0.00 0.00 4.69
1521 1572 4.545610 CAACCTAAACACGTACCGACTAA 58.454 43.478 0.00 0.00 0.00 2.24
1529 1581 1.341383 ACGTACCGACTAACAGGGGAT 60.341 52.381 0.00 0.00 0.00 3.85
1552 1604 4.116961 TGAGTCGTGTTTAACTCCAACAG 58.883 43.478 0.00 0.00 40.98 3.16
1553 1605 3.463944 AGTCGTGTTTAACTCCAACAGG 58.536 45.455 0.00 0.00 40.04 4.00
1556 1608 2.032030 CGTGTTTAACTCCAACAGGCAG 60.032 50.000 0.00 0.00 34.79 4.85
1557 1609 2.949644 GTGTTTAACTCCAACAGGCAGT 59.050 45.455 0.00 0.00 34.79 4.40
1558 1610 3.380320 GTGTTTAACTCCAACAGGCAGTT 59.620 43.478 0.00 0.00 42.42 3.16
1580 1808 4.615815 ATGCATCGGCTCCGCTCC 62.616 66.667 2.96 0.00 41.91 4.70
1619 1898 0.319900 GCGCTCAACCTCTGAAGTCA 60.320 55.000 0.00 0.00 32.17 3.41
1631 1910 2.507886 TCTGAAGTCACAAAACCCTCCA 59.492 45.455 0.00 0.00 0.00 3.86
1771 2482 0.601841 GAGTCGCAAAACCCTCCGAA 60.602 55.000 0.00 0.00 0.00 4.30
1847 2558 1.770294 AAAACCCTCCGAGTTTTGCA 58.230 45.000 1.12 0.00 43.80 4.08
1848 2559 1.029681 AAACCCTCCGAGTTTTGCAC 58.970 50.000 0.00 0.00 33.73 4.57
1863 2574 1.832167 GCACCTGCACCCCTGAAAA 60.832 57.895 0.00 0.00 41.59 2.29
1884 2595 1.228862 GGTGGTGTTGCCCTCCAAT 60.229 57.895 0.00 0.00 38.40 3.16
1978 2689 1.004918 AGTCGCAAAACCCTCCGAG 60.005 57.895 0.00 0.00 0.00 4.63
2000 2711 7.066284 CCGAGGATTGAACTAAAATCTTCATGT 59.934 37.037 8.41 0.00 39.07 3.21
2059 2770 0.669318 TACGGCCTGAACTTGAAGCG 60.669 55.000 0.00 0.00 0.00 4.68
2082 2835 6.349363 GCGTCATTTTCTTTTAGTTCCATCCT 60.349 38.462 0.00 0.00 0.00 3.24
2123 2876 5.461078 GTGTATTGTATGTGGTCGTATGTCC 59.539 44.000 0.00 0.00 0.00 4.02
2126 2879 3.093814 TGTATGTGGTCGTATGTCCTGT 58.906 45.455 0.00 0.00 0.00 4.00
2223 3359 5.311913 TGTGGGGATGATATGCCAGTTTATA 59.688 40.000 1.80 0.00 43.48 0.98
2410 4339 3.546724 CCTGTGATAGACCGAGAGAGAA 58.453 50.000 0.00 0.00 0.00 2.87
2435 4366 1.004277 GGGGCTCACTGTAATTGGTCA 59.996 52.381 0.00 0.00 0.00 4.02
2451 4382 9.793259 GTAATTGGTCAATAATTCTGAGGGATA 57.207 33.333 0.00 0.00 0.00 2.59
2489 4451 0.742281 CCATCAGACACAAGAGGCCG 60.742 60.000 0.00 0.00 0.00 6.13
2581 4544 3.954981 ACCCTAGGCCACCCAGGT 61.955 66.667 5.01 0.56 40.61 4.00
2623 4586 4.001618 CCTCTTTAGGCATCCTAAGCTC 57.998 50.000 5.58 0.00 45.40 4.09
2626 4589 2.918712 TTAGGCATCCTAAGCTCTGC 57.081 50.000 1.40 0.00 40.71 4.26
2629 4592 1.596477 GCATCCTAAGCTCTGCGGG 60.596 63.158 0.00 0.00 0.00 6.13
2822 4938 3.686016 ACGTATGAGCATCCCAAAACTT 58.314 40.909 0.00 0.00 0.00 2.66
2834 5650 4.671831 TCCCAAAACTTAATCCATGCTCA 58.328 39.130 0.00 0.00 0.00 4.26
2838 5654 5.361857 CCAAAACTTAATCCATGCTCATCCT 59.638 40.000 0.00 0.00 0.00 3.24
2849 5665 4.442052 CCATGCTCATCCTCGAGAGTTAAA 60.442 45.833 15.71 0.00 34.79 1.52
2896 5996 4.216257 GTGTGTGAATGCTACCTTTCATGT 59.784 41.667 0.00 0.00 37.43 3.21
2907 6007 8.492673 TGCTACCTTTCATGTACTTAATTCTG 57.507 34.615 0.00 0.00 0.00 3.02
2932 6032 3.620488 TGCAAACTCTTTTGGTGAGTCT 58.380 40.909 0.00 0.00 43.16 3.24
2963 6063 7.698836 ACAGTAAAGATGTTTTCACAATTGC 57.301 32.000 5.05 0.00 36.16 3.56
2964 6064 6.417635 ACAGTAAAGATGTTTTCACAATTGCG 59.582 34.615 5.05 0.00 36.16 4.85
2965 6065 6.636447 CAGTAAAGATGTTTTCACAATTGCGA 59.364 34.615 5.05 0.00 36.16 5.10
2966 6066 7.326789 CAGTAAAGATGTTTTCACAATTGCGAT 59.673 33.333 5.05 0.00 36.16 4.58
2967 6067 8.511321 AGTAAAGATGTTTTCACAATTGCGATA 58.489 29.630 5.05 0.00 36.16 2.92
2968 6068 9.123709 GTAAAGATGTTTTCACAATTGCGATAA 57.876 29.630 5.05 0.00 36.16 1.75
2970 6070 7.975866 AGATGTTTTCACAATTGCGATAATC 57.024 32.000 5.05 3.32 36.16 1.75
2972 6072 6.018589 TGTTTTCACAATTGCGATAATCCA 57.981 33.333 5.05 0.00 0.00 3.41
2973 6073 5.861251 TGTTTTCACAATTGCGATAATCCAC 59.139 36.000 5.05 0.00 0.00 4.02
2974 6074 5.895636 TTTCACAATTGCGATAATCCACT 57.104 34.783 5.05 0.00 0.00 4.00
2975 6075 5.895636 TTCACAATTGCGATAATCCACTT 57.104 34.783 5.05 0.00 0.00 3.16
2976 6076 5.895636 TCACAATTGCGATAATCCACTTT 57.104 34.783 5.05 0.00 0.00 2.66
2977 6077 6.266168 TCACAATTGCGATAATCCACTTTT 57.734 33.333 5.05 0.00 0.00 2.27
2980 6080 6.252015 CACAATTGCGATAATCCACTTTTGAG 59.748 38.462 5.05 0.00 0.00 3.02
2981 6081 4.355543 TTGCGATAATCCACTTTTGAGC 57.644 40.909 0.00 0.00 0.00 4.26
2982 6082 2.682856 TGCGATAATCCACTTTTGAGCC 59.317 45.455 0.00 0.00 0.00 4.70
2983 6083 2.033424 GCGATAATCCACTTTTGAGCCC 59.967 50.000 0.00 0.00 0.00 5.19
2984 6084 3.278574 CGATAATCCACTTTTGAGCCCA 58.721 45.455 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.803426 CGTCTCACTGCCTCCGCC 62.803 72.222 0.00 0.00 0.00 6.13
69 71 0.392193 CTCCGCACTGAAGATGGCTT 60.392 55.000 0.00 0.00 36.96 4.35
136 138 1.746991 CTTTCCCCTTCCTGCGCTC 60.747 63.158 9.73 0.00 0.00 5.03
137 139 2.352805 CTTTCCCCTTCCTGCGCT 59.647 61.111 9.73 0.00 0.00 5.92
138 140 2.751837 CCTTTCCCCTTCCTGCGC 60.752 66.667 0.00 0.00 0.00 6.09
139 141 2.044946 CCCTTTCCCCTTCCTGCG 60.045 66.667 0.00 0.00 0.00 5.18
162 167 3.338250 GACCACCCTGGCCCATCA 61.338 66.667 0.00 0.00 42.67 3.07
163 168 3.338250 TGACCACCCTGGCCCATC 61.338 66.667 0.00 0.00 42.67 3.51
164 169 3.341629 CTGACCACCCTGGCCCAT 61.342 66.667 0.00 0.00 42.67 4.00
165 170 4.590553 TCTGACCACCCTGGCCCA 62.591 66.667 0.00 0.00 42.67 5.36
167 172 2.352805 CTTCTGACCACCCTGGCC 59.647 66.667 0.00 0.00 42.67 5.36
168 173 2.360475 GCTTCTGACCACCCTGGC 60.360 66.667 0.00 0.00 42.67 4.85
170 175 2.046892 CCGCTTCTGACCACCCTG 60.047 66.667 0.00 0.00 0.00 4.45
171 176 3.322466 CCCGCTTCTGACCACCCT 61.322 66.667 0.00 0.00 0.00 4.34
174 179 2.032681 AAGCCCGCTTCTGACCAC 59.967 61.111 0.00 0.00 0.00 4.16
175 180 2.032528 CAAGCCCGCTTCTGACCA 59.967 61.111 0.00 0.00 33.42 4.02
216 221 1.842381 GAGACACAAGTGGGGGAGGG 61.842 65.000 5.08 0.00 34.19 4.30
229 234 1.448497 TCCCACAAACCGGAGACAC 59.552 57.895 9.46 0.00 0.00 3.67
236 241 0.168128 GCGATTTCTCCCACAAACCG 59.832 55.000 0.00 0.00 0.00 4.44
238 243 0.872388 ACGCGATTTCTCCCACAAAC 59.128 50.000 15.93 0.00 0.00 2.93
245 250 1.877165 GTCCGGACGCGATTTCTCC 60.877 63.158 20.85 8.07 0.00 3.71
246 251 1.877165 GGTCCGGACGCGATTTCTC 60.877 63.158 27.68 7.22 0.00 2.87
265 282 0.104304 ATCCAACGCCGGTCTGTATC 59.896 55.000 1.90 0.00 0.00 2.24
272 289 1.375523 GAAGTCATCCAACGCCGGT 60.376 57.895 1.90 0.00 0.00 5.28
302 319 0.030235 CAATCGTCCGGATCACGCTA 59.970 55.000 7.81 0.00 42.52 4.26
306 323 0.810031 CCCACAATCGTCCGGATCAC 60.810 60.000 7.81 0.00 33.02 3.06
318 335 1.187567 GCCTGCAAACCTCCCACAAT 61.188 55.000 0.00 0.00 0.00 2.71
322 339 4.299796 GGGCCTGCAAACCTCCCA 62.300 66.667 0.84 0.00 36.96 4.37
386 403 5.422214 ACCCAAACACCTACTTCTATCTG 57.578 43.478 0.00 0.00 0.00 2.90
509 527 8.382030 TCATTAGATCGCACATATTTCAATGT 57.618 30.769 0.00 0.00 40.75 2.71
510 528 9.836076 AATCATTAGATCGCACATATTTCAATG 57.164 29.630 0.00 0.00 31.90 2.82
595 628 9.270576 CTTCATATTGAATCAGACGTTTGAAAG 57.729 33.333 13.27 5.11 35.59 2.62
602 635 6.533012 CACAGTCTTCATATTGAATCAGACGT 59.467 38.462 0.00 0.00 35.51 4.34
610 643 5.945784 CCCCTTTCACAGTCTTCATATTGAA 59.054 40.000 0.00 0.00 34.79 2.69
625 658 6.294361 ACAAATTATAAAGGCCCCTTTCAC 57.706 37.500 15.16 0.00 44.17 3.18
634 667 8.387354 GTGCCACATTTTACAAATTATAAAGGC 58.613 33.333 12.05 12.05 33.18 4.35
635 668 9.651913 AGTGCCACATTTTACAAATTATAAAGG 57.348 29.630 0.00 0.00 0.00 3.11
645 678 2.736978 CGCAAGTGCCACATTTTACAA 58.263 42.857 0.00 0.00 37.91 2.41
692 735 1.133025 GAGTGCATGCATGTGGGTTAC 59.867 52.381 25.64 15.59 0.00 2.50
701 744 0.036105 TCTTGTCCGAGTGCATGCAT 60.036 50.000 25.64 12.95 0.00 3.96
838 888 9.507329 CCCAGCTTACATGTTAGTTAATGATAT 57.493 33.333 13.05 0.00 0.00 1.63
879 929 6.392625 TCACTCCCTTTTATAGACATCTCG 57.607 41.667 0.00 0.00 0.00 4.04
1075 1126 1.196104 AAGTACTAGGTGCCGGCCAA 61.196 55.000 26.77 2.06 0.00 4.52
1076 1127 1.196104 AAAGTACTAGGTGCCGGCCA 61.196 55.000 26.77 9.53 0.00 5.36
1077 1128 0.461516 GAAAGTACTAGGTGCCGGCC 60.462 60.000 26.77 15.53 0.00 6.13
1078 1129 0.461516 GGAAAGTACTAGGTGCCGGC 60.462 60.000 22.73 22.73 0.00 6.13
1079 1130 0.179119 CGGAAAGTACTAGGTGCCGG 60.179 60.000 4.72 0.00 34.08 6.13
1080 1131 0.179119 CCGGAAAGTACTAGGTGCCG 60.179 60.000 5.58 5.58 37.20 5.69
1081 1132 0.461516 GCCGGAAAGTACTAGGTGCC 60.462 60.000 5.05 0.00 0.00 5.01
1082 1133 0.248289 TGCCGGAAAGTACTAGGTGC 59.752 55.000 5.05 0.00 0.00 5.01
1083 1134 1.739371 GCTGCCGGAAAGTACTAGGTG 60.739 57.143 5.05 0.00 0.00 4.00
1084 1135 0.535797 GCTGCCGGAAAGTACTAGGT 59.464 55.000 5.05 0.00 0.00 3.08
1085 1136 0.527817 CGCTGCCGGAAAGTACTAGG 60.528 60.000 5.05 0.00 0.00 3.02
1086 1137 0.454600 TCGCTGCCGGAAAGTACTAG 59.545 55.000 5.05 0.00 34.56 2.57
1087 1138 0.171903 GTCGCTGCCGGAAAGTACTA 59.828 55.000 5.05 0.00 34.56 1.82
1088 1139 1.080025 GTCGCTGCCGGAAAGTACT 60.080 57.895 5.05 0.00 34.56 2.73
1089 1140 2.442188 CGTCGCTGCCGGAAAGTAC 61.442 63.158 5.05 4.03 34.56 2.73
1090 1141 2.126228 CGTCGCTGCCGGAAAGTA 60.126 61.111 5.05 0.00 34.56 2.24
1098 1149 4.796231 ATCGTCACCGTCGCTGCC 62.796 66.667 0.00 0.00 35.01 4.85
1099 1150 3.248171 GATCGTCACCGTCGCTGC 61.248 66.667 0.00 0.00 35.01 5.25
1100 1151 2.944557 CGATCGTCACCGTCGCTG 60.945 66.667 7.03 0.00 33.43 5.18
1101 1152 3.122971 TCGATCGTCACCGTCGCT 61.123 61.111 15.94 0.00 37.45 4.93
1102 1153 2.943034 GTCGATCGTCACCGTCGC 60.943 66.667 15.94 0.00 37.45 5.19
1103 1154 2.643790 CGTCGATCGTCACCGTCG 60.644 66.667 15.94 6.26 38.25 5.12
1104 1155 1.579626 GTCGTCGATCGTCACCGTC 60.580 63.158 15.94 7.67 40.80 4.79
1105 1156 1.844771 TTGTCGTCGATCGTCACCGT 61.845 55.000 15.94 0.00 37.33 4.83
1106 1157 0.726787 TTTGTCGTCGATCGTCACCG 60.727 55.000 15.94 12.97 37.33 4.94
1107 1158 0.706729 GTTTGTCGTCGATCGTCACC 59.293 55.000 15.94 3.29 37.33 4.02
1108 1159 0.357894 CGTTTGTCGTCGATCGTCAC 59.642 55.000 15.94 10.52 37.33 3.67
1109 1160 0.235404 TCGTTTGTCGTCGATCGTCA 59.765 50.000 15.94 7.84 40.80 4.35
1110 1161 0.627307 GTCGTTTGTCGTCGATCGTC 59.373 55.000 15.94 8.82 40.80 4.20
1111 1162 2.704758 GTCGTTTGTCGTCGATCGT 58.295 52.632 15.94 0.00 40.80 3.73
1117 1168 0.424920 CTTCGTCGTCGTTTGTCGTC 59.575 55.000 1.33 0.00 40.80 4.20
1118 1169 1.534811 GCTTCGTCGTCGTTTGTCGT 61.535 55.000 1.33 0.00 40.80 4.34
1119 1170 1.125266 GCTTCGTCGTCGTTTGTCG 59.875 57.895 1.33 0.00 41.41 4.35
1120 1171 1.125266 CGCTTCGTCGTCGTTTGTC 59.875 57.895 1.33 0.00 38.33 3.18
1121 1172 0.866906 TTCGCTTCGTCGTCGTTTGT 60.867 50.000 1.33 0.00 38.33 2.83
1122 1173 0.179307 CTTCGCTTCGTCGTCGTTTG 60.179 55.000 1.33 0.00 38.33 2.93
1123 1174 1.873355 GCTTCGCTTCGTCGTCGTTT 61.873 55.000 1.33 0.00 38.33 3.60
1124 1175 2.362800 GCTTCGCTTCGTCGTCGTT 61.363 57.895 1.33 0.00 38.33 3.85
1125 1176 2.799916 GCTTCGCTTCGTCGTCGT 60.800 61.111 1.33 0.00 38.33 4.34
1126 1177 2.362047 TTGCTTCGCTTCGTCGTCG 61.362 57.895 0.00 0.00 38.55 5.12
1127 1178 1.128015 GTTGCTTCGCTTCGTCGTC 59.872 57.895 0.00 0.00 0.00 4.20
1128 1179 2.645510 CGTTGCTTCGCTTCGTCGT 61.646 57.895 0.00 0.00 0.00 4.34
1129 1180 2.092148 CGTTGCTTCGCTTCGTCG 59.908 61.111 0.00 0.00 0.00 5.12
1137 1188 3.155998 CAAGTTAATCAGCGTTGCTTCG 58.844 45.455 0.00 0.00 36.40 3.79
1138 1189 3.188460 TCCAAGTTAATCAGCGTTGCTTC 59.812 43.478 0.00 0.00 36.40 3.86
1139 1190 3.146066 TCCAAGTTAATCAGCGTTGCTT 58.854 40.909 0.00 0.00 36.40 3.91
1140 1191 2.778299 TCCAAGTTAATCAGCGTTGCT 58.222 42.857 0.00 0.00 40.77 3.91
1141 1192 3.487544 GGATCCAAGTTAATCAGCGTTGC 60.488 47.826 6.95 0.00 0.00 4.17
1142 1193 3.941483 AGGATCCAAGTTAATCAGCGTTG 59.059 43.478 15.82 0.00 0.00 4.10
1143 1194 3.941483 CAGGATCCAAGTTAATCAGCGTT 59.059 43.478 15.82 0.00 0.00 4.84
1144 1195 3.535561 CAGGATCCAAGTTAATCAGCGT 58.464 45.455 15.82 0.00 0.00 5.07
1145 1196 2.289002 GCAGGATCCAAGTTAATCAGCG 59.711 50.000 15.82 0.00 0.00 5.18
1146 1197 2.620585 GGCAGGATCCAAGTTAATCAGC 59.379 50.000 15.82 1.83 0.00 4.26
1147 1198 3.217626 GGGCAGGATCCAAGTTAATCAG 58.782 50.000 15.82 0.00 0.00 2.90
1148 1199 2.091885 GGGGCAGGATCCAAGTTAATCA 60.092 50.000 15.82 0.00 0.00 2.57
1149 1200 2.091885 TGGGGCAGGATCCAAGTTAATC 60.092 50.000 15.82 0.00 0.00 1.75
1150 1201 1.929494 TGGGGCAGGATCCAAGTTAAT 59.071 47.619 15.82 0.00 0.00 1.40
1151 1202 1.377690 TGGGGCAGGATCCAAGTTAA 58.622 50.000 15.82 0.00 0.00 2.01
1152 1203 1.377690 TTGGGGCAGGATCCAAGTTA 58.622 50.000 15.82 0.00 38.04 2.24
1153 1204 2.172900 TTGGGGCAGGATCCAAGTT 58.827 52.632 15.82 0.00 38.04 2.66
1154 1205 3.936408 TTGGGGCAGGATCCAAGT 58.064 55.556 15.82 0.00 38.04 3.16
1156 1207 0.251742 CAACTTGGGGCAGGATCCAA 60.252 55.000 15.82 0.00 40.36 3.53
1157 1208 1.383799 CAACTTGGGGCAGGATCCA 59.616 57.895 15.82 0.00 0.00 3.41
1158 1209 1.380380 CCAACTTGGGGCAGGATCC 60.380 63.158 2.48 2.48 32.67 3.36
1159 1210 4.344237 CCAACTTGGGGCAGGATC 57.656 61.111 0.00 0.00 32.67 3.36
1166 1217 1.208293 GAGTCTCTAGCCAACTTGGGG 59.792 57.143 9.95 0.00 38.19 4.96
1167 1218 1.902508 TGAGTCTCTAGCCAACTTGGG 59.097 52.381 9.95 0.00 38.19 4.12
1168 1219 2.672478 CGTGAGTCTCTAGCCAACTTGG 60.672 54.545 3.10 3.10 41.55 3.61
1169 1220 2.029828 ACGTGAGTCTCTAGCCAACTTG 60.030 50.000 0.65 0.00 44.19 3.16
1170 1221 2.240279 ACGTGAGTCTCTAGCCAACTT 58.760 47.619 0.65 0.00 44.19 2.66
1171 1222 1.912417 ACGTGAGTCTCTAGCCAACT 58.088 50.000 0.65 0.00 44.19 3.16
1184 1235 2.288579 TGGTGCTAGTTTGGTACGTGAG 60.289 50.000 0.00 0.00 0.00 3.51
1185 1236 1.687660 TGGTGCTAGTTTGGTACGTGA 59.312 47.619 0.00 0.00 0.00 4.35
1186 1237 2.157834 TGGTGCTAGTTTGGTACGTG 57.842 50.000 0.00 0.00 0.00 4.49
1187 1238 2.762745 CTTGGTGCTAGTTTGGTACGT 58.237 47.619 0.00 0.00 0.00 3.57
1188 1239 1.463444 GCTTGGTGCTAGTTTGGTACG 59.537 52.381 0.00 0.00 38.95 3.67
1207 1258 3.181516 CGTCCAACTAGAAGCAATCAAGC 60.182 47.826 0.00 0.00 0.00 4.01
1208 1259 3.997021 ACGTCCAACTAGAAGCAATCAAG 59.003 43.478 0.00 0.00 0.00 3.02
1209 1260 3.745975 CACGTCCAACTAGAAGCAATCAA 59.254 43.478 0.00 0.00 0.00 2.57
1210 1261 3.244078 ACACGTCCAACTAGAAGCAATCA 60.244 43.478 0.00 0.00 0.00 2.57
1211 1262 3.326747 ACACGTCCAACTAGAAGCAATC 58.673 45.455 0.00 0.00 0.00 2.67
1212 1263 3.402628 ACACGTCCAACTAGAAGCAAT 57.597 42.857 0.00 0.00 0.00 3.56
1213 1264 2.902705 ACACGTCCAACTAGAAGCAA 57.097 45.000 0.00 0.00 0.00 3.91
1214 1265 2.889045 AGTACACGTCCAACTAGAAGCA 59.111 45.455 0.00 0.00 0.00 3.91
1215 1266 3.572604 AGTACACGTCCAACTAGAAGC 57.427 47.619 0.00 0.00 0.00 3.86
1216 1267 5.876612 AGTAGTACACGTCCAACTAGAAG 57.123 43.478 2.52 0.00 0.00 2.85
1217 1268 5.563475 GCAAGTAGTACACGTCCAACTAGAA 60.563 44.000 2.52 0.00 0.00 2.10
1218 1269 4.083110 GCAAGTAGTACACGTCCAACTAGA 60.083 45.833 2.52 0.00 0.00 2.43
1219 1270 4.082895 AGCAAGTAGTACACGTCCAACTAG 60.083 45.833 2.52 0.00 0.00 2.57
1220 1271 3.822735 AGCAAGTAGTACACGTCCAACTA 59.177 43.478 2.52 0.00 0.00 2.24
1221 1272 2.626743 AGCAAGTAGTACACGTCCAACT 59.373 45.455 2.52 0.00 0.00 3.16
1222 1273 3.022607 AGCAAGTAGTACACGTCCAAC 57.977 47.619 2.52 0.00 0.00 3.77
1223 1274 3.822735 AGTAGCAAGTAGTACACGTCCAA 59.177 43.478 2.52 0.00 0.00 3.53
1224 1275 3.415212 AGTAGCAAGTAGTACACGTCCA 58.585 45.455 2.52 0.00 0.00 4.02
1225 1276 4.495514 GCTAGTAGCAAGTAGTACACGTCC 60.496 50.000 17.47 0.00 41.89 4.79
1226 1277 4.586334 GCTAGTAGCAAGTAGTACACGTC 58.414 47.826 17.47 0.00 41.89 4.34
1227 1278 4.612932 GCTAGTAGCAAGTAGTACACGT 57.387 45.455 17.47 0.00 41.89 4.49
1245 1296 4.038522 CAGGTTGCTAGCTATCTTCTGCTA 59.961 45.833 17.23 0.00 40.35 3.49
1246 1297 3.037549 AGGTTGCTAGCTATCTTCTGCT 58.962 45.455 17.23 0.00 42.67 4.24
1247 1298 3.129871 CAGGTTGCTAGCTATCTTCTGC 58.870 50.000 17.23 0.00 0.00 4.26
1248 1299 4.662468 TCAGGTTGCTAGCTATCTTCTG 57.338 45.455 17.23 13.85 0.00 3.02
1249 1300 4.898265 TGATCAGGTTGCTAGCTATCTTCT 59.102 41.667 17.23 3.29 0.00 2.85
1250 1301 5.207110 TGATCAGGTTGCTAGCTATCTTC 57.793 43.478 17.23 9.93 0.00 2.87
1251 1302 5.620738 TTGATCAGGTTGCTAGCTATCTT 57.379 39.130 17.23 0.00 0.00 2.40
1252 1303 5.543405 AGATTGATCAGGTTGCTAGCTATCT 59.457 40.000 17.23 11.60 0.00 1.98
1253 1304 5.792741 AGATTGATCAGGTTGCTAGCTATC 58.207 41.667 17.23 9.04 0.00 2.08
1254 1305 5.306419 TGAGATTGATCAGGTTGCTAGCTAT 59.694 40.000 17.23 0.00 0.00 2.97
1255 1306 4.651045 TGAGATTGATCAGGTTGCTAGCTA 59.349 41.667 17.23 5.31 0.00 3.32
1256 1307 3.453717 TGAGATTGATCAGGTTGCTAGCT 59.546 43.478 17.23 0.00 0.00 3.32
1257 1308 3.559242 GTGAGATTGATCAGGTTGCTAGC 59.441 47.826 8.10 8.10 0.00 3.42
1258 1309 3.801050 CGTGAGATTGATCAGGTTGCTAG 59.199 47.826 0.00 0.00 31.91 3.42
1259 1310 3.447229 TCGTGAGATTGATCAGGTTGCTA 59.553 43.478 0.00 0.00 36.64 3.49
1260 1311 2.234661 TCGTGAGATTGATCAGGTTGCT 59.765 45.455 0.00 0.00 36.64 3.91
1261 1312 2.621338 TCGTGAGATTGATCAGGTTGC 58.379 47.619 0.00 0.00 36.64 4.17
1275 1326 7.704475 TCGACCAGAATCGATCAATCGTGAG 62.704 48.000 11.77 1.62 45.84 3.51
1276 1327 5.981716 TCGACCAGAATCGATCAATCGTGA 61.982 45.833 11.77 0.00 45.84 4.35
1277 1328 3.792124 TCGACCAGAATCGATCAATCGTG 60.792 47.826 11.77 3.54 45.84 4.35
1278 1329 2.357952 TCGACCAGAATCGATCAATCGT 59.642 45.455 11.77 0.00 45.84 3.73
1279 1330 3.000082 TCGACCAGAATCGATCAATCG 58.000 47.619 0.00 6.05 45.84 3.34
1296 1347 1.277326 GCATGCGTGTTGAGTATCGA 58.723 50.000 0.00 0.00 38.61 3.59
1297 1348 0.998669 TGCATGCGTGTTGAGTATCG 59.001 50.000 14.09 0.00 38.61 2.92
1298 1349 1.731709 TGTGCATGCGTGTTGAGTATC 59.268 47.619 14.09 0.00 0.00 2.24
1299 1350 1.464608 GTGTGCATGCGTGTTGAGTAT 59.535 47.619 14.09 0.00 0.00 2.12
1300 1351 0.865111 GTGTGCATGCGTGTTGAGTA 59.135 50.000 14.09 0.00 0.00 2.59
1301 1352 1.648720 GTGTGCATGCGTGTTGAGT 59.351 52.632 14.09 0.00 0.00 3.41
1302 1353 1.439201 CGTGTGCATGCGTGTTGAG 60.439 57.895 14.09 0.00 0.00 3.02
1303 1354 1.432270 TTCGTGTGCATGCGTGTTGA 61.432 50.000 14.09 4.27 0.00 3.18
1304 1355 0.993251 CTTCGTGTGCATGCGTGTTG 60.993 55.000 14.09 1.69 0.00 3.33
1305 1356 1.279539 CTTCGTGTGCATGCGTGTT 59.720 52.632 14.09 0.00 0.00 3.32
1306 1357 2.938253 CTTCGTGTGCATGCGTGT 59.062 55.556 14.09 0.00 0.00 4.49
1307 1358 2.500369 GCTTCGTGTGCATGCGTG 60.500 61.111 14.09 0.09 0.00 5.34
1308 1359 3.726517 GGCTTCGTGTGCATGCGT 61.727 61.111 14.09 0.00 0.00 5.24
1309 1360 4.799473 CGGCTTCGTGTGCATGCG 62.799 66.667 14.09 6.54 0.00 4.73
1310 1361 4.465512 CCGGCTTCGTGTGCATGC 62.466 66.667 11.82 11.82 0.00 4.06
1311 1362 4.465512 GCCGGCTTCGTGTGCATG 62.466 66.667 22.15 0.00 0.00 4.06
1356 1407 9.394477 GGTTTGTGAAGTAATACAAATCAGAAC 57.606 33.333 7.90 3.42 45.28 3.01
1381 1432 2.352388 CCATGTAACTTGTACCGTGGG 58.648 52.381 0.00 0.00 0.00 4.61
1425 1476 3.006003 GTCCTGGATAACTAGGTGCTAGC 59.994 52.174 8.10 8.10 43.83 3.42
1437 1488 5.698104 TCCGAGTAGTATTGTCCTGGATAA 58.302 41.667 8.39 8.39 0.00 1.75
1517 1568 2.233922 CACGACTCAATCCCCTGTTAGT 59.766 50.000 0.00 0.00 0.00 2.24
1521 1572 1.056660 AACACGACTCAATCCCCTGT 58.943 50.000 0.00 0.00 0.00 4.00
1529 1581 4.505808 TGTTGGAGTTAAACACGACTCAA 58.494 39.130 5.93 0.00 32.71 3.02
1552 1604 0.940126 CCGATGCATCAGTAACTGCC 59.060 55.000 25.70 0.00 37.59 4.85
1553 1605 0.305922 GCCGATGCATCAGTAACTGC 59.694 55.000 25.70 11.90 38.87 4.40
1556 1608 1.221414 GGAGCCGATGCATCAGTAAC 58.779 55.000 25.70 12.22 41.13 2.50
1557 1609 0.249447 CGGAGCCGATGCATCAGTAA 60.249 55.000 25.70 0.00 42.83 2.24
1558 1610 1.363807 CGGAGCCGATGCATCAGTA 59.636 57.895 25.70 0.00 42.83 2.74
1619 1898 1.970640 GCAATCCTTGGAGGGTTTTGT 59.029 47.619 0.00 0.00 34.28 2.83
1651 1930 1.595093 GGCAACACCACCATGTAGCC 61.595 60.000 0.00 0.00 38.86 3.93
1792 2503 1.228552 AGGGCAACACCACCATGTC 60.229 57.895 0.00 0.00 42.05 3.06
1821 2532 1.005394 TCGGAGGGTTTTGCGACTC 60.005 57.895 0.00 0.00 35.97 3.36
1847 2558 1.341080 CATTTTTCAGGGGTGCAGGT 58.659 50.000 0.00 0.00 0.00 4.00
1848 2559 0.609662 CCATTTTTCAGGGGTGCAGG 59.390 55.000 0.00 0.00 0.00 4.85
1860 2571 1.416030 GAGGGCAACACCACCATTTTT 59.584 47.619 0.00 0.00 42.05 1.94
1861 2572 1.047801 GAGGGCAACACCACCATTTT 58.952 50.000 0.00 0.00 42.05 1.82
1863 2574 1.228862 GGAGGGCAACACCACCATT 60.229 57.895 0.00 0.00 42.05 3.16
1957 2668 2.033194 GGAGGGTTTTGCGACTCCG 61.033 63.158 0.00 0.00 40.01 4.63
1978 2689 7.260603 CCCACATGAAGATTTTAGTTCAATCC 58.739 38.462 0.00 0.00 36.31 3.01
2059 2770 7.329471 GCAAGGATGGAACTAAAAGAAAATGAC 59.671 37.037 0.00 0.00 0.00 3.06
2082 2835 2.634600 ACACACAAAAGACGTAGGCAA 58.365 42.857 0.00 0.00 0.00 4.52
2123 2876 4.174411 TCTTTATCGAGACACACCACAG 57.826 45.455 0.00 0.00 0.00 3.66
2126 2879 4.594123 TGTTCTTTATCGAGACACACCA 57.406 40.909 0.00 0.00 0.00 4.17
2185 3320 1.481871 CCCACACGGACCTACATAGT 58.518 55.000 0.00 0.00 0.00 2.12
2193 3328 1.056660 ATATCATCCCCACACGGACC 58.943 55.000 0.00 0.00 33.77 4.46
2223 3359 2.158534 TGGCTACAACATCAACCCAACT 60.159 45.455 0.00 0.00 0.00 3.16
2435 4366 7.018769 CCCCCAAAATATCCCTCAGAATTATT 58.981 38.462 0.00 0.00 0.00 1.40
2451 4382 6.629156 TGATGGCTTTATATACCCCCAAAAT 58.371 36.000 0.00 0.00 0.00 1.82
2581 4544 2.384933 ATTGGAGCCAAGGCCCAACA 62.385 55.000 25.94 13.03 46.23 3.33
2608 4571 0.676184 CGCAGAGCTTAGGATGCCTA 59.324 55.000 0.00 0.00 34.61 3.93
2786 4902 7.762382 TGCTCATACGTATCCAATGTATCTAG 58.238 38.462 4.74 0.00 38.07 2.43
2789 4905 6.477033 GGATGCTCATACGTATCCAATGTATC 59.523 42.308 4.74 8.25 43.25 2.24
2797 4913 3.678056 TTGGGATGCTCATACGTATCC 57.322 47.619 4.74 4.59 43.10 2.59
2822 4938 3.500343 TCTCGAGGATGAGCATGGATTA 58.500 45.455 13.56 0.00 35.90 1.75
2871 5687 4.203226 TGAAAGGTAGCATTCACACACAA 58.797 39.130 8.41 0.00 30.94 3.33
2878 5694 9.461312 AATTAAGTACATGAAAGGTAGCATTCA 57.539 29.630 14.22 14.22 39.66 2.57
2896 5996 8.621532 AAGAGTTTGCATCACAGAATTAAGTA 57.378 30.769 0.00 0.00 0.00 2.24
2907 6007 4.202050 ACTCACCAAAAGAGTTTGCATCAC 60.202 41.667 0.00 0.00 43.47 3.06
2949 6049 5.861251 GTGGATTATCGCAATTGTGAAAACA 59.139 36.000 24.43 15.75 38.15 2.83
2950 6050 6.092748 AGTGGATTATCGCAATTGTGAAAAC 58.907 36.000 24.43 16.68 38.15 2.43
2955 6055 6.092092 TCAAAAGTGGATTATCGCAATTGTG 58.908 36.000 12.92 12.92 0.00 3.33
2963 6063 3.278574 TGGGCTCAAAAGTGGATTATCG 58.721 45.455 0.00 0.00 0.00 2.92


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.