Multiple sequence alignment - TraesCS3A01G338900

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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 TraesCS3A01G338900 chr3A 100.000 3313 0 0 1 3313 585569096 585565784 0.000000e+00 6119.0
1 TraesCS3A01G338900 chr3B 84.627 1275 95 44 330 1571 582754186 582752980 0.000000e+00 1175.0
2 TraesCS3A01G338900 chr3B 89.200 750 69 8 2576 3313 252593406 252592657 0.000000e+00 926.0
3 TraesCS3A01G338900 chr3B 87.615 436 26 13 1995 2419 582752468 582752050 6.430000e-132 481.0
4 TraesCS3A01G338900 chr3B 91.582 297 18 3 1684 1977 582752962 582752670 1.430000e-108 403.0
5 TraesCS3A01G338900 chr3D 90.723 733 56 8 2576 3297 173712896 173712165 0.000000e+00 966.0
6 TraesCS3A01G338900 chr3D 87.895 760 63 16 397 1145 444715037 444714296 0.000000e+00 867.0
7 TraesCS3A01G338900 chr3D 84.022 920 64 26 1680 2568 444713861 444712994 0.000000e+00 808.0
8 TraesCS3A01G338900 chr3D 87.339 466 28 19 1168 1630 444714298 444713861 3.820000e-139 505.0
9 TraesCS3A01G338900 chr3D 84.983 293 26 10 21 303 444715383 444715099 7.000000e-72 281.0
10 TraesCS3A01G338900 chr2B 89.799 745 67 5 2576 3313 418961002 418961744 0.000000e+00 946.0
11 TraesCS3A01G338900 chr2D 89.706 748 65 8 2578 3313 19606254 19607001 0.000000e+00 944.0
12 TraesCS3A01G338900 chr7D 89.637 743 64 7 2582 3313 43373333 43372593 0.000000e+00 933.0
13 TraesCS3A01G338900 chr4B 88.859 745 74 6 2576 3313 417227929 417228671 0.000000e+00 907.0
14 TraesCS3A01G338900 chr2A 88.785 749 71 8 2576 3313 423780792 423781538 0.000000e+00 905.0
15 TraesCS3A01G338900 chr5D 88.606 746 77 5 2576 3313 376704121 376703376 0.000000e+00 900.0
16 TraesCS3A01G338900 chr6B 88.606 746 75 6 2576 3313 648167615 648166872 0.000000e+00 898.0
17 TraesCS3A01G338900 chr7A 76.471 153 27 8 23 171 637295507 637295360 1.280000e-09 75.0
18 TraesCS3A01G338900 chr7A 95.349 43 1 1 140 181 59018661 59018619 2.130000e-07 67.6
19 TraesCS3A01G338900 chr1A 100.000 28 0 0 1627 1654 262943729 262943756 6.000000e-03 52.8


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 TraesCS3A01G338900 chr3A 585565784 585569096 3312 True 6119.000000 6119 100.000000 1 3313 1 chr3A.!!$R1 3312
1 TraesCS3A01G338900 chr3B 252592657 252593406 749 True 926.000000 926 89.200000 2576 3313 1 chr3B.!!$R1 737
2 TraesCS3A01G338900 chr3B 582752050 582754186 2136 True 686.333333 1175 87.941333 330 2419 3 chr3B.!!$R2 2089
3 TraesCS3A01G338900 chr3D 173712165 173712896 731 True 966.000000 966 90.723000 2576 3297 1 chr3D.!!$R1 721
4 TraesCS3A01G338900 chr3D 444712994 444715383 2389 True 615.250000 867 86.059750 21 2568 4 chr3D.!!$R2 2547
5 TraesCS3A01G338900 chr2B 418961002 418961744 742 False 946.000000 946 89.799000 2576 3313 1 chr2B.!!$F1 737
6 TraesCS3A01G338900 chr2D 19606254 19607001 747 False 944.000000 944 89.706000 2578 3313 1 chr2D.!!$F1 735
7 TraesCS3A01G338900 chr7D 43372593 43373333 740 True 933.000000 933 89.637000 2582 3313 1 chr7D.!!$R1 731
8 TraesCS3A01G338900 chr4B 417227929 417228671 742 False 907.000000 907 88.859000 2576 3313 1 chr4B.!!$F1 737
9 TraesCS3A01G338900 chr2A 423780792 423781538 746 False 905.000000 905 88.785000 2576 3313 1 chr2A.!!$F1 737
10 TraesCS3A01G338900 chr5D 376703376 376704121 745 True 900.000000 900 88.606000 2576 3313 1 chr5D.!!$R1 737
11 TraesCS3A01G338900 chr6B 648166872 648167615 743 True 898.000000 898 88.606000 2576 3313 1 chr6B.!!$R1 737

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
986 1041 0.099791 CGTTTTCGTTGTGGCCTTGT 59.9 50.0 3.32 0.0 38.65 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2724 3030 0.034089 GTGGGGCTGCAACCTAGATT 60.034 55.0 6.03 0.0 0.0 2.4 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
102 103 8.520351 AGTAAAAAGGAAAGAAATCAATACGGG 58.480 33.333 0.00 0.00 0.00 5.28
103 104 7.533289 AAAAAGGAAAGAAATCAATACGGGA 57.467 32.000 0.00 0.00 0.00 5.14
104 105 7.533289 AAAAGGAAAGAAATCAATACGGGAA 57.467 32.000 0.00 0.00 0.00 3.97
105 106 7.533289 AAAGGAAAGAAATCAATACGGGAAA 57.467 32.000 0.00 0.00 0.00 3.13
106 107 6.510879 AGGAAAGAAATCAATACGGGAAAC 57.489 37.500 0.00 0.00 0.00 2.78
138 139 1.278985 ACGATTCAGTGGATTCCTGCA 59.721 47.619 3.95 0.00 0.00 4.41
139 140 2.092753 ACGATTCAGTGGATTCCTGCAT 60.093 45.455 3.95 0.00 0.00 3.96
148 149 4.764771 TTCCTGCATGCCTGGGCC 62.765 66.667 21.70 0.00 41.09 5.80
233 241 2.267961 CCCTTGCCGTACCCTCAC 59.732 66.667 0.00 0.00 0.00 3.51
259 267 3.366440 AATCTACGAATGCCGGACTAC 57.634 47.619 5.05 0.00 43.93 2.73
266 274 2.287069 CGAATGCCGGACTACTCTACAG 60.287 54.545 5.05 0.00 33.91 2.74
275 283 3.181512 GGACTACTCTACAGAAACGGACG 60.182 52.174 0.00 0.00 0.00 4.79
278 286 1.544691 ACTCTACAGAAACGGACGCAT 59.455 47.619 0.00 0.00 0.00 4.73
291 299 0.855349 GACGCATGGAACGCAGATAG 59.145 55.000 0.00 0.00 0.00 2.08
303 311 1.071894 CGCAGATAGAAATGCACGACG 60.072 52.381 0.00 0.00 42.68 5.12
304 312 2.193447 GCAGATAGAAATGCACGACGA 58.807 47.619 0.00 0.00 42.11 4.20
305 313 2.797156 GCAGATAGAAATGCACGACGAT 59.203 45.455 0.00 0.00 42.11 3.73
307 315 4.623167 GCAGATAGAAATGCACGACGATAT 59.377 41.667 0.00 0.00 42.11 1.63
308 316 5.119279 GCAGATAGAAATGCACGACGATATT 59.881 40.000 0.00 0.00 42.11 1.28
309 317 6.346919 GCAGATAGAAATGCACGACGATATTT 60.347 38.462 0.00 5.21 42.11 1.40
310 318 7.223339 CAGATAGAAATGCACGACGATATTTC 58.777 38.462 18.92 18.92 38.93 2.17
311 319 4.795970 AGAAATGCACGACGATATTTCC 57.204 40.909 20.97 11.23 39.27 3.13
312 320 3.560068 AGAAATGCACGACGATATTTCCC 59.440 43.478 20.97 8.43 39.27 3.97
313 321 1.497991 ATGCACGACGATATTTCCCG 58.502 50.000 0.00 0.00 0.00 5.14
314 322 0.173935 TGCACGACGATATTTCCCGT 59.826 50.000 0.00 0.00 42.17 5.28
316 324 1.205657 CACGACGATATTTCCCGTGG 58.794 55.000 0.00 0.00 44.51 4.94
317 325 1.105457 ACGACGATATTTCCCGTGGA 58.895 50.000 0.00 0.00 39.30 4.02
318 326 1.684983 ACGACGATATTTCCCGTGGAT 59.315 47.619 0.00 0.00 39.30 3.41
319 327 2.886523 ACGACGATATTTCCCGTGGATA 59.113 45.455 0.00 0.00 39.30 2.59
320 328 3.508793 ACGACGATATTTCCCGTGGATAT 59.491 43.478 0.00 0.00 39.30 1.63
321 329 4.021719 ACGACGATATTTCCCGTGGATATT 60.022 41.667 0.00 0.00 39.30 1.28
322 330 4.326278 CGACGATATTTCCCGTGGATATTG 59.674 45.833 0.00 2.10 39.30 1.90
323 331 5.475719 GACGATATTTCCCGTGGATATTGA 58.524 41.667 0.00 0.00 39.30 2.57
324 332 6.049955 ACGATATTTCCCGTGGATATTGAT 57.950 37.500 0.00 0.00 37.64 2.57
325 333 7.177832 ACGATATTTCCCGTGGATATTGATA 57.822 36.000 0.00 0.00 37.64 2.15
326 334 7.792032 ACGATATTTCCCGTGGATATTGATAT 58.208 34.615 0.00 0.00 37.64 1.63
327 335 8.265055 ACGATATTTCCCGTGGATATTGATATT 58.735 33.333 0.00 0.00 37.64 1.28
328 336 9.109393 CGATATTTCCCGTGGATATTGATATTT 57.891 33.333 2.30 0.00 0.00 1.40
345 353 9.815306 ATTGATATTTCCTCTACTAGCTACTGA 57.185 33.333 0.00 0.00 0.00 3.41
346 354 9.815306 TTGATATTTCCTCTACTAGCTACTGAT 57.185 33.333 0.00 0.00 0.00 2.90
355 368 8.394877 CCTCTACTAGCTACTGATGATATTTCG 58.605 40.741 0.00 0.00 0.00 3.46
364 377 3.588955 TGATGATATTTCGCCTGGATCG 58.411 45.455 0.00 0.00 0.00 3.69
374 387 2.528743 CCTGGATCGACGCATGTGC 61.529 63.158 6.08 0.00 37.78 4.57
458 481 3.698463 GCGTCGTTGACCACCACG 61.698 66.667 0.00 0.00 0.00 4.94
501 525 1.375908 GATGTTCAGCCTCCGCACA 60.376 57.895 0.00 0.00 37.52 4.57
609 635 1.748403 GTCAGTGTCACCCAGCTCA 59.252 57.895 0.00 0.00 0.00 4.26
684 721 3.752339 GAAAAGGCCCCAGCGCAG 61.752 66.667 11.47 0.00 41.24 5.18
719 756 3.123620 GCACGCAGAGCCAAGAGG 61.124 66.667 0.00 0.00 38.43 3.69
760 797 1.546476 GACTTTTGAGCGAGAGGGAGA 59.454 52.381 0.00 0.00 0.00 3.71
771 808 2.815158 GAGAGGGAGAGACAAAGGACT 58.185 52.381 0.00 0.00 0.00 3.85
772 809 2.758423 GAGAGGGAGAGACAAAGGACTC 59.242 54.545 0.00 0.00 36.29 3.36
824 861 1.994885 CTCACACCCACCACCCAAGT 61.995 60.000 0.00 0.00 0.00 3.16
857 894 1.356979 GCAGCAGCTCGATCGTAGA 59.643 57.895 15.94 0.00 38.54 2.59
882 919 2.159627 GTGCAGTGTATACTTGTGTGGC 59.840 50.000 4.17 0.00 34.07 5.01
930 985 2.038295 GAGCTTGGAGGTGGATCATAGG 59.962 54.545 0.00 0.00 0.00 2.57
931 986 1.544314 GCTTGGAGGTGGATCATAGGC 60.544 57.143 0.00 0.00 0.00 3.93
932 987 2.053244 CTTGGAGGTGGATCATAGGCT 58.947 52.381 0.00 0.00 0.00 4.58
933 988 1.427809 TGGAGGTGGATCATAGGCTG 58.572 55.000 0.00 0.00 0.00 4.85
934 989 1.062198 TGGAGGTGGATCATAGGCTGA 60.062 52.381 0.00 0.00 38.53 4.26
936 991 3.181407 TGGAGGTGGATCATAGGCTGATA 60.181 47.826 0.00 0.00 44.83 2.15
937 992 3.450457 GGAGGTGGATCATAGGCTGATAG 59.550 52.174 0.00 0.00 44.83 2.08
938 993 2.836981 AGGTGGATCATAGGCTGATAGC 59.163 50.000 0.00 0.00 44.83 2.97
939 994 2.417924 GGTGGATCATAGGCTGATAGCG 60.418 54.545 0.00 0.00 44.83 4.26
940 995 1.205655 TGGATCATAGGCTGATAGCGC 59.794 52.381 0.00 0.00 44.83 5.92
941 996 1.554392 GATCATAGGCTGATAGCGCG 58.446 55.000 0.00 0.00 44.83 6.86
959 1014 3.775654 CACGGTGCTCCCCTCTCC 61.776 72.222 0.00 0.00 0.00 3.71
961 1016 3.151022 CGGTGCTCCCCTCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
965 1020 2.249125 TGCTCCCCTCTCCTCCTCA 61.249 63.158 0.00 0.00 0.00 3.86
981 1036 1.399727 CCTCATCGTTTTCGTTGTGGC 60.400 52.381 6.78 0.00 44.07 5.01
982 1037 0.589223 TCATCGTTTTCGTTGTGGCC 59.411 50.000 0.00 0.00 44.46 5.36
983 1038 0.591170 CATCGTTTTCGTTGTGGCCT 59.409 50.000 3.32 0.00 44.46 5.19
984 1039 1.001815 CATCGTTTTCGTTGTGGCCTT 60.002 47.619 3.32 0.00 44.46 4.35
985 1040 0.378962 TCGTTTTCGTTGTGGCCTTG 59.621 50.000 3.32 0.00 44.46 3.61
986 1041 0.099791 CGTTTTCGTTGTGGCCTTGT 59.900 50.000 3.32 0.00 38.65 3.16
987 1042 1.555477 GTTTTCGTTGTGGCCTTGTG 58.445 50.000 3.32 0.00 0.00 3.33
988 1043 1.135228 GTTTTCGTTGTGGCCTTGTGT 60.135 47.619 3.32 0.00 0.00 3.72
989 1044 0.453793 TTTCGTTGTGGCCTTGTGTG 59.546 50.000 3.32 0.00 0.00 3.82
990 1045 1.380403 TTCGTTGTGGCCTTGTGTGG 61.380 55.000 3.32 0.00 0.00 4.17
991 1046 2.118404 CGTTGTGGCCTTGTGTGGT 61.118 57.895 3.32 0.00 0.00 4.16
1080 1141 0.251832 TTCTTCCGCTGGTCTCCTCT 60.252 55.000 0.00 0.00 0.00 3.69
1101 1162 1.174078 TGCCCGTGTCGAGTAAGTGA 61.174 55.000 0.00 0.00 0.00 3.41
1110 1171 2.232941 GTCGAGTAAGTGATTGACCCCA 59.767 50.000 0.00 0.00 0.00 4.96
1111 1172 3.104512 TCGAGTAAGTGATTGACCCCAT 58.895 45.455 0.00 0.00 0.00 4.00
1125 1187 0.398806 CCCCATCCCCATGCATTCAA 60.399 55.000 0.00 0.00 0.00 2.69
1127 1189 1.411930 CCCATCCCCATGCATTCAAGA 60.412 52.381 0.00 0.00 0.00 3.02
1141 1203 4.679662 CATTCAAGAATGCATGGACCTTC 58.320 43.478 9.60 0.00 41.27 3.46
1142 1204 2.726821 TCAAGAATGCATGGACCTTCC 58.273 47.619 0.00 0.00 36.96 3.46
1143 1205 2.309755 TCAAGAATGCATGGACCTTCCT 59.690 45.455 0.00 0.00 37.46 3.36
1144 1206 3.094572 CAAGAATGCATGGACCTTCCTT 58.905 45.455 0.00 0.00 37.46 3.36
1145 1207 3.463048 AGAATGCATGGACCTTCCTTT 57.537 42.857 0.00 0.00 37.46 3.11
1146 1208 3.359950 AGAATGCATGGACCTTCCTTTC 58.640 45.455 0.00 0.00 37.46 2.62
1147 1209 2.905415 ATGCATGGACCTTCCTTTCA 57.095 45.000 0.00 0.00 37.46 2.69
1148 1210 2.673775 TGCATGGACCTTCCTTTCAA 57.326 45.000 0.00 0.00 37.46 2.69
1149 1211 2.956132 TGCATGGACCTTCCTTTCAAA 58.044 42.857 0.00 0.00 37.46 2.69
1150 1212 3.303938 TGCATGGACCTTCCTTTCAAAA 58.696 40.909 0.00 0.00 37.46 2.44
1151 1213 3.708631 TGCATGGACCTTCCTTTCAAAAA 59.291 39.130 0.00 0.00 37.46 1.94
1202 1264 4.216902 TCATCTTCTTTCTTGGCATGTGTG 59.783 41.667 0.00 0.00 0.00 3.82
1203 1265 3.819368 TCTTCTTTCTTGGCATGTGTGA 58.181 40.909 0.00 0.00 0.00 3.58
1204 1266 4.401022 TCTTCTTTCTTGGCATGTGTGAT 58.599 39.130 0.00 0.00 0.00 3.06
1205 1267 4.216902 TCTTCTTTCTTGGCATGTGTGATG 59.783 41.667 0.00 0.00 0.00 3.07
1206 1268 3.489355 TCTTTCTTGGCATGTGTGATGT 58.511 40.909 0.00 0.00 0.00 3.06
1207 1269 3.253921 TCTTTCTTGGCATGTGTGATGTG 59.746 43.478 0.00 0.00 0.00 3.21
1208 1270 2.275134 TCTTGGCATGTGTGATGTGT 57.725 45.000 0.00 0.00 0.00 3.72
1223 1285 0.876399 TGTGTCTGTGCATGCATGTC 59.124 50.000 25.64 18.98 0.00 3.06
1225 1287 1.135774 GTGTCTGTGCATGCATGTCAG 60.136 52.381 30.09 30.09 35.19 3.51
1234 1299 0.523072 ATGCATGTCAGTTTCGTGCC 59.477 50.000 0.00 0.00 44.28 5.01
1237 1302 1.229428 CATGTCAGTTTCGTGCCTGT 58.771 50.000 0.00 0.00 0.00 4.00
1245 1310 4.094294 TCAGTTTCGTGCCTGTATTTATGC 59.906 41.667 0.00 0.00 0.00 3.14
1281 1346 1.019805 GTAGGAAGCGTGTCCTTGGC 61.020 60.000 13.35 3.08 46.42 4.52
1345 1410 2.235898 GCCTGTTCAGGTCAATCTCTCT 59.764 50.000 18.42 0.00 0.00 3.10
1346 1411 3.678529 GCCTGTTCAGGTCAATCTCTCTC 60.679 52.174 18.42 0.00 0.00 3.20
1374 1439 0.881118 TGATGCCTTTGCCGTTCTTC 59.119 50.000 0.00 0.00 36.33 2.87
1377 1442 2.489938 TGCCTTTGCCGTTCTTCTAT 57.510 45.000 0.00 0.00 36.33 1.98
1409 1479 6.490566 TTCTGTTCCTTAAGCGGATTAAAC 57.509 37.500 0.00 0.00 32.98 2.01
1487 1561 1.002868 TCTGGCTGCTTCCTGCTTC 60.003 57.895 0.00 0.00 43.37 3.86
1581 1655 1.136565 GCGCATAACATTGTGCCGT 59.863 52.632 0.30 0.00 45.21 5.68
1596 1670 1.509463 CCGTGACGGCACTAGCTAA 59.491 57.895 21.24 0.00 41.17 3.09
1606 1680 2.615493 GGCACTAGCTAAGCAGGAAACA 60.615 50.000 16.86 0.00 41.70 2.83
1607 1681 3.274288 GCACTAGCTAAGCAGGAAACAT 58.726 45.455 11.77 0.00 37.91 2.71
1608 1682 4.442706 GCACTAGCTAAGCAGGAAACATA 58.557 43.478 11.77 0.00 37.91 2.29
1636 1710 6.793505 TTGATAGTTCTTTCTACTCCCTCC 57.206 41.667 0.00 0.00 0.00 4.30
1637 1711 4.888239 TGATAGTTCTTTCTACTCCCTCCG 59.112 45.833 0.00 0.00 0.00 4.63
1638 1712 3.172471 AGTTCTTTCTACTCCCTCCGT 57.828 47.619 0.00 0.00 0.00 4.69
1639 1713 3.090790 AGTTCTTTCTACTCCCTCCGTC 58.909 50.000 0.00 0.00 0.00 4.79
1640 1714 2.140839 TCTTTCTACTCCCTCCGTCC 57.859 55.000 0.00 0.00 0.00 4.79
1641 1715 1.639628 TCTTTCTACTCCCTCCGTCCT 59.360 52.381 0.00 0.00 0.00 3.85
1642 1716 2.848694 TCTTTCTACTCCCTCCGTCCTA 59.151 50.000 0.00 0.00 0.00 2.94
1643 1717 3.462579 TCTTTCTACTCCCTCCGTCCTAT 59.537 47.826 0.00 0.00 0.00 2.57
1644 1718 4.662179 TCTTTCTACTCCCTCCGTCCTATA 59.338 45.833 0.00 0.00 0.00 1.31
1645 1719 5.133322 TCTTTCTACTCCCTCCGTCCTATAA 59.867 44.000 0.00 0.00 0.00 0.98
1646 1720 5.595814 TTCTACTCCCTCCGTCCTATAAT 57.404 43.478 0.00 0.00 0.00 1.28
1647 1721 4.919793 TCTACTCCCTCCGTCCTATAATG 58.080 47.826 0.00 0.00 0.00 1.90
1648 1722 3.614568 ACTCCCTCCGTCCTATAATGT 57.385 47.619 0.00 0.00 0.00 2.71
1649 1723 4.736611 ACTCCCTCCGTCCTATAATGTA 57.263 45.455 0.00 0.00 0.00 2.29
1650 1724 4.664392 ACTCCCTCCGTCCTATAATGTAG 58.336 47.826 0.00 0.00 0.00 2.74
1651 1725 4.017808 CTCCCTCCGTCCTATAATGTAGG 58.982 52.174 0.00 0.00 36.06 3.18
1652 1726 3.659195 TCCCTCCGTCCTATAATGTAGGA 59.341 47.826 1.33 1.33 41.14 2.94
1653 1727 4.294168 TCCCTCCGTCCTATAATGTAGGAT 59.706 45.833 9.01 0.00 44.67 3.24
1654 1728 5.024118 CCCTCCGTCCTATAATGTAGGATT 58.976 45.833 9.01 0.00 44.67 3.01
1655 1729 6.011362 TCCCTCCGTCCTATAATGTAGGATTA 60.011 42.308 9.01 0.00 44.67 1.75
1656 1730 6.666546 CCCTCCGTCCTATAATGTAGGATTAA 59.333 42.308 9.01 0.00 44.67 1.40
1657 1731 7.147880 CCCTCCGTCCTATAATGTAGGATTAAG 60.148 44.444 9.01 6.76 44.67 1.85
1658 1732 7.614583 CCTCCGTCCTATAATGTAGGATTAAGA 59.385 40.741 9.01 3.82 44.67 2.10
1659 1733 8.345724 TCCGTCCTATAATGTAGGATTAAGAC 57.654 38.462 9.01 0.00 44.67 3.01
1660 1734 7.946219 TCCGTCCTATAATGTAGGATTAAGACA 59.054 37.037 9.01 0.00 44.67 3.41
1661 1735 8.750298 CCGTCCTATAATGTAGGATTAAGACAT 58.250 37.037 9.01 0.00 44.67 3.06
1703 1777 6.072452 GCATATTAACCATTTGACTAGGGAGC 60.072 42.308 0.00 0.00 0.00 4.70
1704 1778 5.717119 ATTAACCATTTGACTAGGGAGCT 57.283 39.130 0.00 0.00 0.00 4.09
1717 1794 2.161486 GGAGCTAAGCGCACTCACG 61.161 63.158 11.47 0.00 42.61 4.35
1740 1817 4.137543 CTGAGGGTTTAAGTCAAGTGCTT 58.862 43.478 0.00 0.00 0.00 3.91
1759 1836 0.317160 TTCTGTAGCTGGTGTCCACG 59.683 55.000 0.00 0.00 0.00 4.94
1846 1923 0.321653 ATGTGACCTTTGGACGCTCC 60.322 55.000 0.00 0.00 36.96 4.70
1867 1944 0.462759 AAGAGCATACCCGAAGCTGC 60.463 55.000 0.00 0.00 39.02 5.25
1885 1962 4.452733 GTCGGCCGGTTGCTAGCT 62.453 66.667 27.83 0.00 40.92 3.32
1886 1963 2.756691 TCGGCCGGTTGCTAGCTA 60.757 61.111 27.83 5.31 40.92 3.32
1887 1964 2.279517 CGGCCGGTTGCTAGCTAG 60.280 66.667 20.10 16.84 40.92 3.42
1892 1969 0.807667 CCGGTTGCTAGCTAGTGCAG 60.808 60.000 21.62 12.08 42.74 4.41
1940 2017 2.340443 GCTAGATAAGCGCGGCCT 59.660 61.111 8.83 0.42 42.53 5.19
1977 2054 4.722700 ACATGCGTGGCCACTCCC 62.723 66.667 32.28 20.33 0.00 4.30
1988 2065 0.771127 GCCACTCCCCATAAGCCATA 59.229 55.000 0.00 0.00 0.00 2.74
1990 2067 2.057922 CCACTCCCCATAAGCCATACT 58.942 52.381 0.00 0.00 0.00 2.12
1991 2068 2.443255 CCACTCCCCATAAGCCATACTT 59.557 50.000 0.00 0.00 42.76 2.24
1992 2069 3.480470 CACTCCCCATAAGCCATACTTG 58.520 50.000 0.00 0.00 39.58 3.16
1993 2070 3.117888 CACTCCCCATAAGCCATACTTGT 60.118 47.826 0.00 0.00 39.58 3.16
2001 2262 5.220854 CCATAAGCCATACTTGTGTAGTTGC 60.221 44.000 2.25 0.00 43.84 4.17
2012 2273 1.545582 GTGTAGTTGCATTGCACCCAT 59.454 47.619 11.66 0.18 38.71 4.00
2047 2308 2.664851 CCACCTCGCTCGTGCAAA 60.665 61.111 10.43 0.00 39.64 3.68
2061 2322 2.223688 CGTGCAAACAAGAACATTCCCA 60.224 45.455 0.00 0.00 0.00 4.37
2154 2415 1.930567 GTGTGTGACACCACTAACGT 58.069 50.000 13.85 0.00 43.05 3.99
2180 2441 1.463444 GTGTTGTTCATACAGGGCGTC 59.537 52.381 0.00 0.00 35.28 5.19
2244 2511 2.721859 CGCGGATGGACATCGAGA 59.278 61.111 0.00 0.00 38.69 4.04
2381 2653 7.499895 GGTTAGTCTAGTCTAGATAGCACTTGT 59.500 40.741 12.74 0.00 37.13 3.16
2382 2654 8.895737 GTTAGTCTAGTCTAGATAGCACTTGTT 58.104 37.037 12.74 0.00 37.13 2.83
2384 2656 6.320164 AGTCTAGTCTAGATAGCACTTGTTGG 59.680 42.308 12.74 0.00 37.13 3.77
2385 2657 6.095720 GTCTAGTCTAGATAGCACTTGTTGGT 59.904 42.308 12.74 0.00 37.13 3.67
2386 2658 5.078411 AGTCTAGATAGCACTTGTTGGTG 57.922 43.478 0.00 0.00 36.33 4.17
2387 2659 4.772624 AGTCTAGATAGCACTTGTTGGTGA 59.227 41.667 0.00 0.00 39.34 4.02
2388 2660 5.423610 AGTCTAGATAGCACTTGTTGGTGAT 59.576 40.000 0.00 0.00 39.34 3.06
2389 2661 5.521735 GTCTAGATAGCACTTGTTGGTGATG 59.478 44.000 0.00 0.00 39.34 3.07
2391 2663 4.256920 AGATAGCACTTGTTGGTGATGAC 58.743 43.478 0.00 0.00 39.34 3.06
2392 2664 2.645838 AGCACTTGTTGGTGATGACT 57.354 45.000 0.00 0.00 39.34 3.41
2393 2665 2.498167 AGCACTTGTTGGTGATGACTC 58.502 47.619 0.00 0.00 39.34 3.36
2400 2683 4.356405 TGTTGGTGATGACTCATGAGTT 57.644 40.909 28.46 14.70 42.66 3.01
2419 2702 3.566742 AGTTCAACGGGTTAAACATGTCC 59.433 43.478 0.00 0.00 0.00 4.02
2481 2778 8.474025 AGTGTCAAAATTGGTCTTACATTTTGA 58.526 29.630 12.91 12.91 44.14 2.69
2482 2779 9.260002 GTGTCAAAATTGGTCTTACATTTTGAT 57.740 29.630 17.67 0.00 46.24 2.57
2509 2806 8.807118 ACAGAGGGAGTATATTATATGTGTGTG 58.193 37.037 0.00 0.00 0.00 3.82
2513 2810 6.113411 GGAGTATATTATATGTGTGTGCCCC 58.887 44.000 0.00 0.00 0.00 5.80
2568 2865 3.140623 TGTCCATGTGTGTCTGTCAATG 58.859 45.455 0.00 0.00 0.00 2.82
2569 2866 2.095567 GTCCATGTGTGTCTGTCAATGC 60.096 50.000 0.00 0.00 0.00 3.56
2570 2867 1.200716 CCATGTGTGTCTGTCAATGCC 59.799 52.381 0.00 0.00 0.00 4.40
2571 2868 1.135888 CATGTGTGTCTGTCAATGCCG 60.136 52.381 0.00 0.00 0.00 5.69
2572 2869 0.105778 TGTGTGTCTGTCAATGCCGA 59.894 50.000 0.00 0.00 0.00 5.54
2573 2870 0.512952 GTGTGTCTGTCAATGCCGAC 59.487 55.000 0.00 0.00 36.40 4.79
2574 2871 0.602638 TGTGTCTGTCAATGCCGACC 60.603 55.000 0.00 0.00 34.88 4.79
2602 2901 2.439104 GGGCTCCCTCAATCGCTCT 61.439 63.158 0.00 0.00 0.00 4.09
2672 2978 2.361357 CTCCACCTCGTCGTCCCT 60.361 66.667 0.00 0.00 0.00 4.20
2687 2993 3.506096 CCTAGAGACGTGCGCCGA 61.506 66.667 22.10 0.00 40.70 5.54
2717 3023 3.809013 GCCACCGGTGATGGGGAT 61.809 66.667 36.07 0.00 37.73 3.85
2724 3030 2.070039 GGTGATGGGGATGACGGGA 61.070 63.158 0.00 0.00 0.00 5.14
2742 3048 0.255890 GAATCTAGGTTGCAGCCCCA 59.744 55.000 16.95 3.52 0.00 4.96
2747 3053 4.338710 GGTTGCAGCCCCACGGTA 62.339 66.667 8.70 0.00 0.00 4.02
2825 3131 3.718210 CTACTCCGGCGGCTTGGTC 62.718 68.421 23.83 0.00 0.00 4.02
2945 3256 2.281692 TTCGTCGGAGGTGGTCGA 60.282 61.111 0.00 0.00 0.00 4.20
2956 3267 4.357947 TGGTCGACACGAGGCTGC 62.358 66.667 18.91 0.00 36.23 5.25
2985 3296 1.524848 TCTCGAGATCCGCCATCTAC 58.475 55.000 12.08 0.00 42.48 2.59
3163 3480 2.554462 CCAGATCAGACGATGACGGTAT 59.446 50.000 0.00 0.00 41.91 2.73
3186 3503 1.192534 CGGTGTCGTTTTCTCTCTTGC 59.807 52.381 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 8.520351 CCCGTATTGATTTCTTTCCTTTTTACT 58.480 33.333 0.00 0.00 0.00 2.24
77 78 8.517056 TCCCGTATTGATTTCTTTCCTTTTTAC 58.483 33.333 0.00 0.00 0.00 2.01
78 79 8.638629 TCCCGTATTGATTTCTTTCCTTTTTA 57.361 30.769 0.00 0.00 0.00 1.52
79 80 7.533289 TCCCGTATTGATTTCTTTCCTTTTT 57.467 32.000 0.00 0.00 0.00 1.94
83 84 5.417894 GGTTTCCCGTATTGATTTCTTTCCT 59.582 40.000 0.00 0.00 0.00 3.36
84 85 5.393787 GGGTTTCCCGTATTGATTTCTTTCC 60.394 44.000 0.00 0.00 32.13 3.13
85 86 5.393787 GGGGTTTCCCGTATTGATTTCTTTC 60.394 44.000 0.00 0.00 46.66 2.62
87 88 4.021229 GGGGTTTCCCGTATTGATTTCTT 58.979 43.478 0.00 0.00 46.66 2.52
88 89 3.628008 GGGGTTTCCCGTATTGATTTCT 58.372 45.455 0.00 0.00 46.66 2.52
116 117 2.749621 GCAGGAATCCACTGAATCGTTT 59.250 45.455 0.61 0.00 38.20 3.60
119 120 2.028420 TGCAGGAATCCACTGAATCG 57.972 50.000 0.61 0.00 38.20 3.34
219 220 3.420300 TTATTTGTGAGGGTACGGCAA 57.580 42.857 0.00 0.00 0.00 4.52
233 241 5.236478 AGTCCGGCATTCGTAGATTTATTTG 59.764 40.000 0.00 0.00 35.04 2.32
259 267 1.920574 CATGCGTCCGTTTCTGTAGAG 59.079 52.381 0.00 0.00 0.00 2.43
266 274 1.131826 CGTTCCATGCGTCCGTTTC 59.868 57.895 0.00 0.00 0.00 2.78
275 283 3.851105 GCATTTCTATCTGCGTTCCATGC 60.851 47.826 0.00 0.00 0.00 4.06
278 286 2.677836 GTGCATTTCTATCTGCGTTCCA 59.322 45.455 0.00 0.00 41.32 3.53
291 299 3.603857 CGGGAAATATCGTCGTGCATTTC 60.604 47.826 14.76 14.76 36.90 2.17
304 312 9.408648 GGAAATATCAATATCCACGGGAAATAT 57.591 33.333 0.00 0.00 34.34 1.28
305 313 8.611257 AGGAAATATCAATATCCACGGGAAATA 58.389 33.333 0.00 0.00 34.34 1.40
307 315 6.848069 AGGAAATATCAATATCCACGGGAAA 58.152 36.000 0.00 0.00 34.34 3.13
308 316 6.272324 AGAGGAAATATCAATATCCACGGGAA 59.728 38.462 0.00 0.00 34.34 3.97
309 317 5.785423 AGAGGAAATATCAATATCCACGGGA 59.215 40.000 0.00 0.00 34.30 5.14
310 318 6.054860 AGAGGAAATATCAATATCCACGGG 57.945 41.667 0.00 0.00 34.30 5.28
311 319 7.841956 AGTAGAGGAAATATCAATATCCACGG 58.158 38.462 0.00 0.00 34.30 4.94
313 321 9.810545 GCTAGTAGAGGAAATATCAATATCCAC 57.189 37.037 0.00 0.00 34.30 4.02
314 322 9.775539 AGCTAGTAGAGGAAATATCAATATCCA 57.224 33.333 0.00 0.00 34.30 3.41
319 327 9.815306 TCAGTAGCTAGTAGAGGAAATATCAAT 57.185 33.333 0.00 0.00 0.00 2.57
320 328 9.815306 ATCAGTAGCTAGTAGAGGAAATATCAA 57.185 33.333 0.00 0.00 0.00 2.57
321 329 9.237187 CATCAGTAGCTAGTAGAGGAAATATCA 57.763 37.037 0.00 0.00 0.00 2.15
322 330 9.456147 TCATCAGTAGCTAGTAGAGGAAATATC 57.544 37.037 0.00 0.00 0.00 1.63
323 331 9.989296 ATCATCAGTAGCTAGTAGAGGAAATAT 57.011 33.333 14.77 2.33 0.00 1.28
325 333 9.989296 ATATCATCAGTAGCTAGTAGAGGAAAT 57.011 33.333 14.77 6.69 0.00 2.17
326 334 9.815306 AATATCATCAGTAGCTAGTAGAGGAAA 57.185 33.333 14.77 0.81 0.00 3.13
327 335 9.815306 AAATATCATCAGTAGCTAGTAGAGGAA 57.185 33.333 14.77 8.43 0.00 3.36
328 336 9.456147 GAAATATCATCAGTAGCTAGTAGAGGA 57.544 37.037 13.78 13.78 0.00 3.71
343 351 3.258123 TCGATCCAGGCGAAATATCATCA 59.742 43.478 0.00 0.00 34.45 3.07
345 353 3.589988 GTCGATCCAGGCGAAATATCAT 58.410 45.455 0.00 0.00 39.73 2.45
346 354 2.607038 CGTCGATCCAGGCGAAATATCA 60.607 50.000 0.00 0.00 42.53 2.15
355 368 2.202932 ACATGCGTCGATCCAGGC 60.203 61.111 0.00 0.00 0.00 4.85
412 432 2.511829 TCGGAGTCGGAGAGCTCG 60.512 66.667 8.37 0.00 36.95 5.03
458 481 1.600916 GCTCCCGTATGATTGGGCC 60.601 63.158 0.00 0.00 45.60 5.80
481 504 1.375908 TGCGGAGGCTGAACATCAC 60.376 57.895 0.00 0.00 40.82 3.06
638 673 0.663153 GATTTTTCCGGCTGGATCCG 59.337 55.000 16.96 3.14 45.91 4.18
639 674 1.032794 GGATTTTTCCGGCTGGATCC 58.967 55.000 16.96 15.69 45.91 3.36
640 675 1.678101 CTGGATTTTTCCGGCTGGATC 59.322 52.381 16.96 9.88 45.91 3.36
712 749 1.811266 CGCCATGTCGACCTCTTGG 60.811 63.158 14.12 15.06 39.83 3.61
719 756 3.071459 CTTCACGCGCCATGTCGAC 62.071 63.158 9.11 9.11 0.00 4.20
722 759 1.154413 CAACTTCACGCGCCATGTC 60.154 57.895 5.73 0.00 0.00 3.06
760 797 2.534990 CCTCTCCTGAGTCCTTTGTCT 58.465 52.381 0.00 0.00 38.61 3.41
852 889 4.982999 AGTATACACTGCACTTGTCTACG 58.017 43.478 5.50 0.00 33.78 3.51
896 933 0.459934 CAAGCTCCGCCTCTCTTCTG 60.460 60.000 0.00 0.00 0.00 3.02
931 986 3.620428 CACCGTGCGCGCTATCAG 61.620 66.667 33.29 18.00 36.67 2.90
941 996 4.459089 GAGAGGGGAGCACCGTGC 62.459 72.222 16.04 16.04 45.46 5.34
957 1012 2.036733 ACAACGAAAACGATGAGGAGGA 59.963 45.455 6.86 0.00 0.00 3.71
959 1014 2.157668 CCACAACGAAAACGATGAGGAG 59.842 50.000 9.67 0.00 0.00 3.69
961 1016 1.399727 GCCACAACGAAAACGATGAGG 60.400 52.381 10.56 10.56 0.00 3.86
965 1020 1.001815 CAAGGCCACAACGAAAACGAT 60.002 47.619 5.01 0.00 0.00 3.73
981 1036 1.079127 CGCCCTCTACCACACAAGG 60.079 63.158 0.00 0.00 0.00 3.61
982 1037 0.537188 ATCGCCCTCTACCACACAAG 59.463 55.000 0.00 0.00 0.00 3.16
983 1038 0.249120 CATCGCCCTCTACCACACAA 59.751 55.000 0.00 0.00 0.00 3.33
984 1039 1.613317 CCATCGCCCTCTACCACACA 61.613 60.000 0.00 0.00 0.00 3.72
985 1040 1.144057 CCATCGCCCTCTACCACAC 59.856 63.158 0.00 0.00 0.00 3.82
986 1041 1.001120 TCCATCGCCCTCTACCACA 59.999 57.895 0.00 0.00 0.00 4.17
987 1042 1.043673 ACTCCATCGCCCTCTACCAC 61.044 60.000 0.00 0.00 0.00 4.16
988 1043 1.043116 CACTCCATCGCCCTCTACCA 61.043 60.000 0.00 0.00 0.00 3.25
989 1044 1.742768 CACTCCATCGCCCTCTACC 59.257 63.158 0.00 0.00 0.00 3.18
990 1045 1.068250 GCACTCCATCGCCCTCTAC 59.932 63.158 0.00 0.00 0.00 2.59
991 1046 1.381191 TGCACTCCATCGCCCTCTA 60.381 57.895 0.00 0.00 0.00 2.43
1080 1141 1.287815 CTTACTCGACACGGGCACA 59.712 57.895 0.00 0.00 0.00 4.57
1101 1162 1.233949 GCATGGGGATGGGGTCAAT 59.766 57.895 0.00 0.00 0.00 2.57
1125 1187 3.245371 TGAAAGGAAGGTCCATGCATTCT 60.245 43.478 0.00 0.00 39.61 2.40
1127 1189 3.173953 TGAAAGGAAGGTCCATGCATT 57.826 42.857 0.00 0.00 39.61 3.56
1150 1212 8.980596 TGATATTAAGGTCCATGCATTCTTTTT 58.019 29.630 0.00 0.00 0.00 1.94
1151 1213 8.537728 TGATATTAAGGTCCATGCATTCTTTT 57.462 30.769 0.00 0.00 0.00 2.27
1152 1214 7.781693 ACTGATATTAAGGTCCATGCATTCTTT 59.218 33.333 0.00 0.00 0.00 2.52
1153 1215 7.293073 ACTGATATTAAGGTCCATGCATTCTT 58.707 34.615 0.00 1.64 0.00 2.52
1154 1216 6.845908 ACTGATATTAAGGTCCATGCATTCT 58.154 36.000 0.00 0.00 0.00 2.40
1155 1217 7.229306 TGAACTGATATTAAGGTCCATGCATTC 59.771 37.037 0.00 0.00 29.77 2.67
1156 1218 7.062322 TGAACTGATATTAAGGTCCATGCATT 58.938 34.615 0.00 0.00 29.77 3.56
1202 1264 1.471287 ACATGCATGCACAGACACATC 59.529 47.619 25.37 0.00 0.00 3.06
1203 1265 1.471287 GACATGCATGCACAGACACAT 59.529 47.619 25.37 0.38 0.00 3.21
1204 1266 0.876399 GACATGCATGCACAGACACA 59.124 50.000 25.37 0.00 0.00 3.72
1205 1267 0.876399 TGACATGCATGCACAGACAC 59.124 50.000 25.37 14.77 0.00 3.67
1206 1268 1.161843 CTGACATGCATGCACAGACA 58.838 50.000 32.48 21.92 37.55 3.41
1207 1269 1.162698 ACTGACATGCATGCACAGAC 58.837 50.000 37.62 23.45 38.20 3.51
1208 1270 1.900245 AACTGACATGCATGCACAGA 58.100 45.000 37.62 17.51 38.20 3.41
1223 1285 4.142708 TGCATAAATACAGGCACGAAACTG 60.143 41.667 0.00 0.00 40.48 3.16
1225 1287 4.349663 TGCATAAATACAGGCACGAAAC 57.650 40.909 0.00 0.00 0.00 2.78
1234 1299 7.067372 TCCAAGAACAAGGATGCATAAATACAG 59.933 37.037 0.00 0.00 0.00 2.74
1345 1410 1.839994 CAAAGGCATCAGGTAGAGGGA 59.160 52.381 0.00 0.00 0.00 4.20
1346 1411 1.748591 GCAAAGGCATCAGGTAGAGGG 60.749 57.143 0.00 0.00 40.72 4.30
1377 1442 8.644216 TCCGCTTAAGGAACAGAAATATACATA 58.356 33.333 4.29 0.00 37.36 2.29
1409 1479 5.178996 GCATCTATCATCAAGCCACAACTAG 59.821 44.000 0.00 0.00 0.00 2.57
1511 1585 1.000396 GGGAACAGGCAAGCCATCT 60.000 57.895 14.40 0.00 38.92 2.90
1581 1655 0.173481 CTGCTTAGCTAGTGCCGTCA 59.827 55.000 5.60 0.35 40.80 4.35
1619 1693 2.166050 GGACGGAGGGAGTAGAAAGAAC 59.834 54.545 0.00 0.00 0.00 3.01
1629 1703 4.017808 CCTACATTATAGGACGGAGGGAG 58.982 52.174 0.00 0.00 36.85 4.30
1630 1704 3.659195 TCCTACATTATAGGACGGAGGGA 59.341 47.826 0.00 0.00 38.71 4.20
1631 1705 4.043608 TCCTACATTATAGGACGGAGGG 57.956 50.000 0.00 0.00 38.71 4.30
1632 1706 7.614583 TCTTAATCCTACATTATAGGACGGAGG 59.385 40.741 4.81 0.00 45.56 4.30
1633 1707 8.460428 GTCTTAATCCTACATTATAGGACGGAG 58.540 40.741 4.81 4.07 45.56 4.63
1634 1708 7.946219 TGTCTTAATCCTACATTATAGGACGGA 59.054 37.037 4.81 0.00 45.56 4.69
1635 1709 8.118976 TGTCTTAATCCTACATTATAGGACGG 57.881 38.462 4.81 0.00 45.56 4.79
1670 1744 6.095440 GTCAAATGGTTAATATGCACTCCAGT 59.905 38.462 0.00 0.00 0.00 4.00
1671 1745 6.319658 AGTCAAATGGTTAATATGCACTCCAG 59.680 38.462 0.00 0.00 0.00 3.86
1672 1746 6.186957 AGTCAAATGGTTAATATGCACTCCA 58.813 36.000 0.00 0.00 0.00 3.86
1673 1747 6.699575 AGTCAAATGGTTAATATGCACTCC 57.300 37.500 0.00 0.00 0.00 3.85
1674 1748 7.041098 CCCTAGTCAAATGGTTAATATGCACTC 60.041 40.741 0.00 0.00 0.00 3.51
1675 1749 6.772716 CCCTAGTCAAATGGTTAATATGCACT 59.227 38.462 0.00 0.00 0.00 4.40
1676 1750 6.770785 TCCCTAGTCAAATGGTTAATATGCAC 59.229 38.462 0.00 0.00 0.00 4.57
1677 1751 6.905736 TCCCTAGTCAAATGGTTAATATGCA 58.094 36.000 0.00 0.00 0.00 3.96
1678 1752 6.072452 GCTCCCTAGTCAAATGGTTAATATGC 60.072 42.308 0.00 0.00 0.00 3.14
1717 1794 2.226674 GCACTTGACTTAAACCCTCAGC 59.773 50.000 0.00 0.00 0.00 4.26
1723 1800 5.500645 ACAGAAAGCACTTGACTTAAACC 57.499 39.130 0.00 0.00 0.00 3.27
1740 1817 0.317160 CGTGGACACCAGCTACAGAA 59.683 55.000 0.00 0.00 32.34 3.02
1759 1836 3.552684 GGCTGACTGATGAGTGCTCTATC 60.553 52.174 0.00 3.53 30.16 2.08
1846 1923 0.103208 AGCTTCGGGTATGCTCTTCG 59.897 55.000 0.00 0.00 33.49 3.79
1881 1958 2.159179 TGGGATCACTGCACTAGCTA 57.841 50.000 0.00 0.00 42.74 3.32
1884 1961 2.484417 GGACATGGGATCACTGCACTAG 60.484 54.545 0.00 0.00 0.00 2.57
1885 1962 1.486310 GGACATGGGATCACTGCACTA 59.514 52.381 0.00 0.00 0.00 2.74
1886 1963 0.254178 GGACATGGGATCACTGCACT 59.746 55.000 0.00 0.00 0.00 4.40
1887 1964 0.035152 TGGACATGGGATCACTGCAC 60.035 55.000 0.00 0.00 0.00 4.57
1892 1969 1.278985 TGTGACTGGACATGGGATCAC 59.721 52.381 0.00 4.45 37.54 3.06
1948 2025 2.987547 GCATGTGGGCTGCACTGT 60.988 61.111 2.50 0.00 39.46 3.55
1977 2054 5.220854 GCAACTACACAAGTATGGCTTATGG 60.221 44.000 0.00 0.00 36.00 2.74
1988 2065 2.034558 GGTGCAATGCAACTACACAAGT 59.965 45.455 17.07 0.00 43.73 3.16
1990 2067 1.339610 GGGTGCAATGCAACTACACAA 59.660 47.619 23.36 0.00 46.64 3.33
1991 2068 0.958091 GGGTGCAATGCAACTACACA 59.042 50.000 23.36 0.00 46.64 3.72
1992 2069 0.958091 TGGGTGCAATGCAACTACAC 59.042 50.000 23.36 6.02 46.64 2.90
1993 2070 1.818060 GATGGGTGCAATGCAACTACA 59.182 47.619 23.36 13.76 46.64 2.74
2001 2262 0.959867 TCGTGTGGATGGGTGCAATG 60.960 55.000 0.00 0.00 0.00 2.82
2012 2273 0.245539 GGACCTTTCGATCGTGTGGA 59.754 55.000 22.26 0.24 0.00 4.02
2047 2308 1.238439 CGCACTGGGAATGTTCTTGT 58.762 50.000 0.00 0.00 0.00 3.16
2061 2322 4.849310 AACACCACACCGCGCACT 62.849 61.111 8.75 0.00 0.00 4.40
2148 2409 4.343811 TGAACAACACAAACCACGTTAG 57.656 40.909 0.00 0.00 0.00 2.34
2149 2410 4.966965 ATGAACAACACAAACCACGTTA 57.033 36.364 0.00 0.00 0.00 3.18
2150 2411 3.859411 ATGAACAACACAAACCACGTT 57.141 38.095 0.00 0.00 0.00 3.99
2151 2412 3.690139 TGTATGAACAACACAAACCACGT 59.310 39.130 0.00 0.00 30.91 4.49
2152 2413 4.278858 CTGTATGAACAACACAAACCACG 58.721 43.478 0.00 0.00 34.49 4.94
2153 2414 4.499019 CCCTGTATGAACAACACAAACCAC 60.499 45.833 0.00 0.00 34.49 4.16
2154 2415 3.634448 CCCTGTATGAACAACACAAACCA 59.366 43.478 0.00 0.00 34.49 3.67
2157 2418 2.292016 CGCCCTGTATGAACAACACAAA 59.708 45.455 0.00 0.00 34.49 2.83
2160 2421 1.463444 GACGCCCTGTATGAACAACAC 59.537 52.381 0.00 0.00 34.49 3.32
2195 2462 2.430921 ACGACGCTTTGCTCCTCG 60.431 61.111 0.00 0.00 0.00 4.63
2244 2511 2.040178 GGATCCAGGGTAGTCGTTGAT 58.960 52.381 6.95 0.00 0.00 2.57
2300 2567 2.471084 ATCGACTTCACCCCCTCCCA 62.471 60.000 0.00 0.00 0.00 4.37
2381 2653 4.622260 TGAACTCATGAGTCATCACCAA 57.378 40.909 28.01 5.17 41.58 3.67
2382 2654 4.318332 GTTGAACTCATGAGTCATCACCA 58.682 43.478 28.01 12.34 41.58 4.17
2384 2656 3.369147 CCGTTGAACTCATGAGTCATCAC 59.631 47.826 28.01 19.38 41.58 3.06
2385 2657 3.588955 CCGTTGAACTCATGAGTCATCA 58.411 45.455 28.01 24.18 41.58 3.07
2386 2658 2.932614 CCCGTTGAACTCATGAGTCATC 59.067 50.000 28.01 21.99 41.58 2.92
2387 2659 2.303022 ACCCGTTGAACTCATGAGTCAT 59.697 45.455 28.01 14.30 41.58 3.06
2388 2660 1.691976 ACCCGTTGAACTCATGAGTCA 59.308 47.619 28.01 22.30 41.58 3.41
2389 2661 2.457366 ACCCGTTGAACTCATGAGTC 57.543 50.000 28.01 20.22 41.58 3.36
2391 2663 4.513692 TGTTTAACCCGTTGAACTCATGAG 59.486 41.667 21.37 21.37 39.08 2.90
2392 2664 4.452825 TGTTTAACCCGTTGAACTCATGA 58.547 39.130 14.09 0.00 39.08 3.07
2393 2665 4.822036 TGTTTAACCCGTTGAACTCATG 57.178 40.909 14.09 0.00 39.08 3.07
2400 2683 2.144730 CGGACATGTTTAACCCGTTGA 58.855 47.619 13.29 0.00 35.83 3.18
2419 2702 2.746362 AGAATGCTTCTTTCCTTGCTCG 59.254 45.455 0.00 0.00 36.36 5.03
2465 2762 6.884295 CCCTCTGTATCAAAATGTAAGACCAA 59.116 38.462 0.00 0.00 0.00 3.67
2485 2782 7.093289 GGCACACACATATAATATACTCCCTCT 60.093 40.741 0.00 0.00 0.00 3.69
2486 2783 7.042335 GGCACACACATATAATATACTCCCTC 58.958 42.308 0.00 0.00 0.00 4.30
2504 2801 1.354031 ACATGAACATAGGGGCACACA 59.646 47.619 0.00 0.00 0.00 3.72
2509 2806 4.799564 TGAAAAACATGAACATAGGGGC 57.200 40.909 0.00 0.00 0.00 5.80
2538 2835 8.023021 ACAGACACACATGGACATACTATATT 57.977 34.615 0.00 0.00 0.00 1.28
2542 2839 4.770010 TGACAGACACACATGGACATACTA 59.230 41.667 0.00 0.00 0.00 1.82
2549 2846 2.153645 GCATTGACAGACACACATGGA 58.846 47.619 0.00 0.00 0.00 3.41
2550 2847 1.200716 GGCATTGACAGACACACATGG 59.799 52.381 0.00 0.00 0.00 3.66
2554 2851 0.512952 GTCGGCATTGACAGACACAC 59.487 55.000 8.87 0.00 38.75 3.82
2560 2857 2.009108 CGATGGTCGGCATTGACAG 58.991 57.895 5.51 0.00 40.72 3.51
2568 2865 4.899239 CCTGGAGCGATGGTCGGC 62.899 72.222 1.29 0.00 40.84 5.54
2569 2866 4.227134 CCCTGGAGCGATGGTCGG 62.227 72.222 0.00 0.00 40.84 4.79
2570 2867 4.899239 GCCCTGGAGCGATGGTCG 62.899 72.222 0.00 0.00 43.89 4.79
2571 2868 3.453070 GAGCCCTGGAGCGATGGTC 62.453 68.421 0.00 0.00 38.01 4.02
2572 2869 3.474570 GAGCCCTGGAGCGATGGT 61.475 66.667 0.00 0.00 38.01 3.55
2573 2870 4.247380 GGAGCCCTGGAGCGATGG 62.247 72.222 0.00 0.00 38.01 3.51
2574 2871 4.247380 GGGAGCCCTGGAGCGATG 62.247 72.222 0.00 0.00 38.01 3.84
2602 2901 0.470080 CCCCTTGATCGCCCTAGAGA 60.470 60.000 0.00 0.00 0.00 3.10
2648 2947 1.303615 GACGAGGTGGAGGAGAGGA 59.696 63.158 0.00 0.00 0.00 3.71
2672 2978 1.020861 TTAGTCGGCGCACGTCTCTA 61.021 55.000 17.55 14.39 44.69 2.43
2703 3009 2.731571 CGTCATCCCCATCACCGGT 61.732 63.158 0.00 0.00 0.00 5.28
2717 3023 1.207089 CTGCAACCTAGATTCCCGTCA 59.793 52.381 0.00 0.00 0.00 4.35
2724 3030 0.034089 GTGGGGCTGCAACCTAGATT 60.034 55.000 6.03 0.00 0.00 2.40
2945 3256 0.461516 CTGATCATGCAGCCTCGTGT 60.462 55.000 0.00 0.00 0.00 4.49
2948 3259 1.001068 AGATCTGATCATGCAGCCTCG 59.999 52.381 19.12 0.00 35.86 4.63
3030 3343 4.552365 CCATCGCCTGCCATCGGT 62.552 66.667 0.00 0.00 0.00 4.69
3050 3363 2.066262 CAAGGTAACGACGCAGAACAT 58.934 47.619 0.00 0.00 46.39 2.71
3163 3480 1.202486 AGAGAGAAAACGACACCGCAA 60.202 47.619 0.00 0.00 39.95 4.85
3186 3503 0.592637 TGCTCCACAAACAATGCTCG 59.407 50.000 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.