Multiple sequence alignment - TraesCS2D01G394700

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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 TraesCS2D01G394700 chr2D 100.000 4279 0 0 1 4279 506147678 506143400 0.000000e+00 7902.0
1 TraesCS2D01G394700 chr2D 93.023 43 1 2 1273 1315 192301035 192301075 1.280000e-05 62.1
2 TraesCS2D01G394700 chr2B 92.637 3015 131 41 1305 4279 593657209 593654246 0.000000e+00 4253.0
3 TraesCS2D01G394700 chr2B 89.115 689 21 20 573 1243 593657869 593657217 0.000000e+00 808.0
4 TraesCS2D01G394700 chr2B 91.262 515 15 12 1 500 593658370 593657871 0.000000e+00 675.0
5 TraesCS2D01G394700 chr2A 93.265 2539 102 27 1771 4272 650628946 650626440 0.000000e+00 3677.0
6 TraesCS2D01G394700 chr2A 95.136 514 9 3 1 500 650629740 650629229 0.000000e+00 797.0
7 TraesCS2D01G394700 chr2A 81.034 290 19 21 573 840 650629227 650628952 9.390000e-47 198.0
8 TraesCS2D01G394700 chr7D 83.846 130 10 9 1111 1230 104566732 104566604 3.500000e-21 113.0
9 TraesCS2D01G394700 chr7B 93.506 77 3 2 1155 1230 62687421 62687346 3.500000e-21 113.0
10 TraesCS2D01G394700 chr7B 90.000 50 4 1 1273 1322 537838483 537838435 3.570000e-06 63.9
11 TraesCS2D01G394700 chr7A 94.366 71 2 2 1155 1225 108808848 108808780 1.630000e-19 108.0
12 TraesCS2D01G394700 chr5D 89.041 73 7 1 505 577 219645671 219645742 5.890000e-14 89.8
13 TraesCS2D01G394700 chr5D 97.436 39 1 0 1273 1311 42040556 42040594 2.760000e-07 67.6
14 TraesCS2D01G394700 chr4B 97.619 42 1 0 1266 1307 95869603 95869562 5.940000e-09 73.1
15 TraesCS2D01G394700 chr5B 93.617 47 2 1 1261 1307 589820324 589820369 7.680000e-08 69.4
16 TraesCS2D01G394700 chr5B 93.478 46 2 1 1273 1317 534303459 534303414 2.760000e-07 67.6
17 TraesCS2D01G394700 chrUn 95.349 43 0 2 1266 1307 112408738 112408697 2.760000e-07 67.6
18 TraesCS2D01G394700 chr3B 91.837 49 3 1 1261 1309 803635381 803635334 2.760000e-07 67.6
19 TraesCS2D01G394700 chr3B 96.774 31 1 0 3649 3679 794705295 794705265 8.000000e-03 52.8
20 TraesCS2D01G394700 chr1B 93.023 43 3 0 1273 1315 507106436 507106478 3.570000e-06 63.9


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 TraesCS2D01G394700 chr2D 506143400 506147678 4278 True 7902.000000 7902 100.000000 1 4279 1 chr2D.!!$R1 4278
1 TraesCS2D01G394700 chr2B 593654246 593658370 4124 True 1912.000000 4253 91.004667 1 4279 3 chr2B.!!$R1 4278
2 TraesCS2D01G394700 chr2A 650626440 650629740 3300 True 1557.333333 3677 89.811667 1 4272 3 chr2A.!!$R1 4271

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
550 565 0.036164 TGCACATCGGGCAGTAAAGT 59.964 50.0 0.0 0.0 36.11 2.66 F
1071 1114 0.036952 CCGCAGAGTCCATGTTCAGT 60.037 55.0 0.0 0.0 0.00 3.41 F
2365 2437 0.105760 TGTGGTTGGGTTGGCAGATT 60.106 50.0 0.0 0.0 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 1997 0.474854 TGTTGGCCTTGGAGAGGGTA 60.475 55.0 3.32 0.00 46.40 3.69 R
2551 2623 1.089920 CCTGAAAATCTGCAGGGTCG 58.910 55.0 15.13 3.53 46.24 4.79 R
3585 3674 0.028242 CGTGCGCTACCAGTCTCTAG 59.972 60.0 9.73 0.00 0.00 2.43 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
66 67 0.255318 ATGCTCCCAGAGAAGCAAGG 59.745 55.000 0.69 0.00 40.82 3.61
86 87 2.821969 GGCAAGCTTGGGTATGATATGG 59.178 50.000 27.10 0.00 0.00 2.74
100 101 7.501559 GGGTATGATATGGTAGCGAGATAGTAA 59.498 40.741 0.00 0.00 0.00 2.24
101 102 9.069082 GGTATGATATGGTAGCGAGATAGTAAT 57.931 37.037 0.00 0.00 0.00 1.89
434 449 7.955750 AGTATATATTCCATTTTTCCAAGGGGG 59.044 37.037 0.00 0.00 38.37 5.40
489 504 0.170339 GCATTTGCCTTGGTACGGAC 59.830 55.000 0.00 0.00 34.31 4.79
500 515 1.447140 GTACGGACGCATCTGCCAA 60.447 57.895 0.00 0.00 37.91 4.52
501 516 0.810031 GTACGGACGCATCTGCCAAT 60.810 55.000 0.00 0.00 37.91 3.16
502 517 0.809636 TACGGACGCATCTGCCAATG 60.810 55.000 0.00 0.00 37.91 2.82
503 518 2.827051 CGGACGCATCTGCCAATGG 61.827 63.158 0.00 0.00 37.91 3.16
513 528 3.776158 GCCAATGGCTCACAACCA 58.224 55.556 18.47 0.00 46.69 3.67
522 537 2.754552 TGGCTCACAACCATTGATTAGC 59.245 45.455 0.00 1.67 34.71 3.09
523 538 2.223340 GGCTCACAACCATTGATTAGCG 60.223 50.000 0.00 0.00 35.57 4.26
524 539 2.420022 GCTCACAACCATTGATTAGCGT 59.580 45.455 0.00 0.00 0.00 5.07
525 540 3.728864 GCTCACAACCATTGATTAGCGTG 60.729 47.826 0.00 0.00 0.00 5.34
526 541 3.407698 TCACAACCATTGATTAGCGTGT 58.592 40.909 0.00 0.00 0.00 4.49
527 542 3.435327 TCACAACCATTGATTAGCGTGTC 59.565 43.478 0.00 0.00 0.00 3.67
528 543 2.415168 ACAACCATTGATTAGCGTGTCG 59.585 45.455 0.00 0.00 0.00 4.35
529 544 2.380084 ACCATTGATTAGCGTGTCGT 57.620 45.000 0.00 0.00 0.00 4.34
530 545 1.999735 ACCATTGATTAGCGTGTCGTG 59.000 47.619 0.00 0.00 0.00 4.35
531 546 1.999735 CCATTGATTAGCGTGTCGTGT 59.000 47.619 0.00 0.00 0.00 4.49
532 547 2.222796 CCATTGATTAGCGTGTCGTGTG 60.223 50.000 0.00 0.00 0.00 3.82
533 548 0.787787 TTGATTAGCGTGTCGTGTGC 59.212 50.000 0.00 0.00 0.00 4.57
534 549 0.319125 TGATTAGCGTGTCGTGTGCA 60.319 50.000 0.00 0.00 0.00 4.57
535 550 0.093026 GATTAGCGTGTCGTGTGCAC 59.907 55.000 10.75 10.75 0.00 4.57
536 551 0.598942 ATTAGCGTGTCGTGTGCACA 60.599 50.000 17.42 17.42 36.71 4.57
537 552 0.598942 TTAGCGTGTCGTGTGCACAT 60.599 50.000 24.69 6.69 36.71 3.21
538 553 1.006825 TAGCGTGTCGTGTGCACATC 61.007 55.000 24.69 16.44 36.71 3.06
539 554 2.465486 CGTGTCGTGTGCACATCG 59.535 61.111 24.69 25.36 36.71 3.84
540 555 2.853210 GTGTCGTGTGCACATCGG 59.147 61.111 28.68 19.92 36.88 4.18
541 556 2.356913 TGTCGTGTGCACATCGGG 60.357 61.111 28.68 17.96 0.00 5.14
542 557 3.788766 GTCGTGTGCACATCGGGC 61.789 66.667 28.68 21.45 0.00 6.13
543 558 4.306967 TCGTGTGCACATCGGGCA 62.307 61.111 28.68 15.42 39.32 5.36
544 559 3.792047 CGTGTGCACATCGGGCAG 61.792 66.667 24.69 5.13 42.85 4.85
545 560 2.669569 GTGTGCACATCGGGCAGT 60.670 61.111 24.69 0.00 42.85 4.40
546 561 1.375396 GTGTGCACATCGGGCAGTA 60.375 57.895 24.69 0.00 42.85 2.74
547 562 0.953471 GTGTGCACATCGGGCAGTAA 60.953 55.000 24.69 0.00 42.85 2.24
548 563 0.250510 TGTGCACATCGGGCAGTAAA 60.251 50.000 17.42 0.00 42.85 2.01
549 564 0.447801 GTGCACATCGGGCAGTAAAG 59.552 55.000 13.17 0.00 42.85 1.85
550 565 0.036164 TGCACATCGGGCAGTAAAGT 59.964 50.000 0.00 0.00 36.11 2.66
551 566 0.447801 GCACATCGGGCAGTAAAGTG 59.552 55.000 0.00 0.00 0.00 3.16
552 567 1.808411 CACATCGGGCAGTAAAGTGT 58.192 50.000 0.00 0.00 0.00 3.55
553 568 1.732259 CACATCGGGCAGTAAAGTGTC 59.268 52.381 0.00 0.00 0.00 3.67
554 569 0.999406 CATCGGGCAGTAAAGTGTCG 59.001 55.000 0.00 0.00 0.00 4.35
555 570 0.606604 ATCGGGCAGTAAAGTGTCGT 59.393 50.000 0.00 0.00 0.00 4.34
556 571 0.038892 TCGGGCAGTAAAGTGTCGTC 60.039 55.000 0.00 0.00 0.00 4.20
557 572 0.038526 CGGGCAGTAAAGTGTCGTCT 60.039 55.000 0.00 0.00 0.00 4.18
558 573 1.429463 GGGCAGTAAAGTGTCGTCTG 58.571 55.000 0.00 0.00 0.00 3.51
559 574 1.270147 GGGCAGTAAAGTGTCGTCTGT 60.270 52.381 0.00 0.00 0.00 3.41
560 575 2.029649 GGGCAGTAAAGTGTCGTCTGTA 60.030 50.000 0.00 0.00 0.00 2.74
561 576 2.985139 GGCAGTAAAGTGTCGTCTGTAC 59.015 50.000 0.00 0.00 0.00 2.90
562 577 3.551454 GGCAGTAAAGTGTCGTCTGTACA 60.551 47.826 0.00 0.00 32.31 2.90
563 578 3.669122 GCAGTAAAGTGTCGTCTGTACAG 59.331 47.826 17.17 17.17 32.31 2.74
564 579 4.792057 GCAGTAAAGTGTCGTCTGTACAGT 60.792 45.833 21.99 2.56 32.31 3.55
565 580 4.910456 CAGTAAAGTGTCGTCTGTACAGTC 59.090 45.833 21.99 15.74 32.31 3.51
566 581 4.577693 AGTAAAGTGTCGTCTGTACAGTCA 59.422 41.667 21.99 13.81 32.31 3.41
567 582 4.585955 AAAGTGTCGTCTGTACAGTCAT 57.414 40.909 21.99 0.90 30.21 3.06
568 583 4.585955 AAGTGTCGTCTGTACAGTCATT 57.414 40.909 21.99 11.16 30.21 2.57
569 584 4.585955 AGTGTCGTCTGTACAGTCATTT 57.414 40.909 21.99 7.98 0.00 2.32
570 585 4.547532 AGTGTCGTCTGTACAGTCATTTC 58.452 43.478 21.99 10.33 0.00 2.17
571 586 3.361053 GTGTCGTCTGTACAGTCATTTCG 59.639 47.826 21.99 16.23 0.00 3.46
600 615 1.159713 TCAGTGCAGCTGTGGAAACG 61.160 55.000 16.64 0.00 45.23 3.60
602 617 1.009675 GTGCAGCTGTGGAAACGTG 60.010 57.895 16.64 0.00 0.00 4.49
603 618 1.451207 TGCAGCTGTGGAAACGTGT 60.451 52.632 16.64 0.00 0.00 4.49
611 628 5.173131 CAGCTGTGGAAACGTGTTTTATTTC 59.827 40.000 5.25 0.00 32.11 2.17
613 630 5.746721 GCTGTGGAAACGTGTTTTATTTCTT 59.253 36.000 0.00 0.00 33.68 2.52
614 631 6.291585 GCTGTGGAAACGTGTTTTATTTCTTG 60.292 38.462 0.00 0.00 33.68 3.02
631 648 5.356882 TTCTTGTTTTTAGGACAGATGCG 57.643 39.130 0.00 0.00 0.00 4.73
641 658 2.819595 CAGATGCGTTCCCCCGTG 60.820 66.667 0.00 0.00 0.00 4.94
649 667 1.971695 GTTCCCCCGTGAGCCAAAG 60.972 63.158 0.00 0.00 0.00 2.77
715 743 1.126488 TCATCTCATCCAGGTCCAGC 58.874 55.000 0.00 0.00 0.00 4.85
735 763 2.879103 TGGGACAGTTCAAATCTCCC 57.121 50.000 0.00 0.00 36.52 4.30
887 926 2.677848 GCCTCCCCTTCCCAAGTC 59.322 66.667 0.00 0.00 0.00 3.01
888 927 2.231380 GCCTCCCCTTCCCAAGTCA 61.231 63.158 0.00 0.00 0.00 3.41
889 928 1.789576 GCCTCCCCTTCCCAAGTCAA 61.790 60.000 0.00 0.00 0.00 3.18
890 929 0.329596 CCTCCCCTTCCCAAGTCAAG 59.670 60.000 0.00 0.00 0.00 3.02
891 930 1.068121 CTCCCCTTCCCAAGTCAAGT 58.932 55.000 0.00 0.00 0.00 3.16
927 966 2.183046 GTCGAGCTGCTCCTGGTC 59.817 66.667 22.97 4.52 0.00 4.02
936 979 2.970639 CTCCTGGTCGCGAGGAAA 59.029 61.111 10.24 0.00 37.88 3.13
970 1013 0.535797 GTTACTCCCGGTGGAAGGAG 59.464 60.000 0.00 4.52 41.17 3.69
971 1014 0.616679 TTACTCCCGGTGGAAGGAGG 60.617 60.000 10.61 0.00 41.17 4.30
972 1015 3.787001 CTCCCGGTGGAAGGAGGC 61.787 72.222 0.00 0.00 41.17 4.70
1038 1081 0.802494 GTGGTGGTAATTGCAGGTCG 59.198 55.000 0.00 0.00 0.00 4.79
1040 1083 1.338674 TGGTGGTAATTGCAGGTCGAG 60.339 52.381 0.00 0.00 0.00 4.04
1069 1112 0.247460 CTCCGCAGAGTCCATGTTCA 59.753 55.000 0.00 0.00 35.21 3.18
1070 1113 0.247460 TCCGCAGAGTCCATGTTCAG 59.753 55.000 0.00 0.00 0.00 3.02
1071 1114 0.036952 CCGCAGAGTCCATGTTCAGT 60.037 55.000 0.00 0.00 0.00 3.41
1072 1115 1.073964 CGCAGAGTCCATGTTCAGTG 58.926 55.000 0.00 0.00 0.00 3.66
1073 1116 1.446907 GCAGAGTCCATGTTCAGTGG 58.553 55.000 0.00 0.00 38.11 4.00
1074 1117 1.446907 CAGAGTCCATGTTCAGTGGC 58.553 55.000 0.00 0.00 36.66 5.01
1075 1118 0.326264 AGAGTCCATGTTCAGTGGCC 59.674 55.000 0.00 0.00 36.66 5.36
1076 1119 1.003355 AGTCCATGTTCAGTGGCCG 60.003 57.895 0.00 0.00 36.66 6.13
1077 1120 2.040544 GTCCATGTTCAGTGGCCGG 61.041 63.158 0.00 0.00 36.66 6.13
1078 1121 3.443045 CCATGTTCAGTGGCCGGC 61.443 66.667 21.18 21.18 0.00 6.13
1079 1122 2.360350 CATGTTCAGTGGCCGGCT 60.360 61.111 28.56 2.77 0.00 5.52
1080 1123 2.360350 ATGTTCAGTGGCCGGCTG 60.360 61.111 28.56 17.63 35.43 4.85
1081 1124 2.894257 ATGTTCAGTGGCCGGCTGA 61.894 57.895 28.56 19.92 40.76 4.26
1082 1125 3.050275 GTTCAGTGGCCGGCTGAC 61.050 66.667 28.56 22.55 42.00 3.51
1083 1126 4.329545 TTCAGTGGCCGGCTGACC 62.330 66.667 28.56 10.32 42.00 4.02
1141 1184 2.739609 GCTGCTTGTTGGTGCTTTTCTT 60.740 45.455 0.00 0.00 0.00 2.52
1142 1185 3.524541 CTGCTTGTTGGTGCTTTTCTTT 58.475 40.909 0.00 0.00 0.00 2.52
1144 1187 3.932089 TGCTTGTTGGTGCTTTTCTTTTC 59.068 39.130 0.00 0.00 0.00 2.29
1145 1188 4.183865 GCTTGTTGGTGCTTTTCTTTTCT 58.816 39.130 0.00 0.00 0.00 2.52
1147 1190 5.398603 TTGTTGGTGCTTTTCTTTTCTGA 57.601 34.783 0.00 0.00 0.00 3.27
1148 1191 5.596836 TGTTGGTGCTTTTCTTTTCTGAT 57.403 34.783 0.00 0.00 0.00 2.90
1149 1192 5.350633 TGTTGGTGCTTTTCTTTTCTGATG 58.649 37.500 0.00 0.00 0.00 3.07
1150 1193 5.126869 TGTTGGTGCTTTTCTTTTCTGATGA 59.873 36.000 0.00 0.00 0.00 2.92
1151 1194 5.443185 TGGTGCTTTTCTTTTCTGATGAG 57.557 39.130 0.00 0.00 0.00 2.90
1152 1195 4.233005 GGTGCTTTTCTTTTCTGATGAGC 58.767 43.478 0.00 0.00 0.00 4.26
1232 1275 5.180868 CAGCATCTAAGGTTGGCAATCTATC 59.819 44.000 14.43 0.00 0.00 2.08
1233 1276 5.065914 GCATCTAAGGTTGGCAATCTATCA 58.934 41.667 14.43 0.37 0.00 2.15
1234 1277 5.709164 GCATCTAAGGTTGGCAATCTATCAT 59.291 40.000 14.43 0.00 0.00 2.45
1235 1278 6.128063 GCATCTAAGGTTGGCAATCTATCATC 60.128 42.308 14.43 0.00 0.00 2.92
1236 1279 5.869579 TCTAAGGTTGGCAATCTATCATCC 58.130 41.667 14.43 2.03 0.00 3.51
1237 1280 4.524802 AAGGTTGGCAATCTATCATCCA 57.475 40.909 14.43 0.00 0.00 3.41
1241 1284 3.213206 TGGCAATCTATCATCCACACC 57.787 47.619 0.00 0.00 0.00 4.16
1242 1285 2.509131 TGGCAATCTATCATCCACACCA 59.491 45.455 0.00 0.00 0.00 4.17
1243 1286 3.053768 TGGCAATCTATCATCCACACCAA 60.054 43.478 0.00 0.00 0.00 3.67
1245 1288 4.202050 GGCAATCTATCATCCACACCAAAC 60.202 45.833 0.00 0.00 0.00 2.93
1246 1289 4.398988 GCAATCTATCATCCACACCAAACA 59.601 41.667 0.00 0.00 0.00 2.83
1248 1291 3.950397 TCTATCATCCACACCAAACACC 58.050 45.455 0.00 0.00 0.00 4.16
1249 1292 2.673775 ATCATCCACACCAAACACCA 57.326 45.000 0.00 0.00 0.00 4.17
1250 1293 2.673775 TCATCCACACCAAACACCAT 57.326 45.000 0.00 0.00 0.00 3.55
1251 1294 2.237643 TCATCCACACCAAACACCATG 58.762 47.619 0.00 0.00 0.00 3.66
1252 1295 2.158549 TCATCCACACCAAACACCATGA 60.159 45.455 0.00 0.00 0.00 3.07
1253 1296 2.673775 TCCACACCAAACACCATGAT 57.326 45.000 0.00 0.00 0.00 2.45
1254 1297 2.237643 TCCACACCAAACACCATGATG 58.762 47.619 0.00 0.00 0.00 3.07
1255 1298 1.337074 CCACACCAAACACCATGATGC 60.337 52.381 0.00 0.00 0.00 3.91
1256 1299 1.614903 CACACCAAACACCATGATGCT 59.385 47.619 0.00 0.00 0.00 3.79
1257 1300 2.036217 CACACCAAACACCATGATGCTT 59.964 45.455 0.00 0.00 0.00 3.91
1258 1301 2.036217 ACACCAAACACCATGATGCTTG 59.964 45.455 0.00 0.00 0.00 4.01
1259 1302 2.296752 CACCAAACACCATGATGCTTGA 59.703 45.455 4.68 0.00 0.00 3.02
1260 1303 3.056393 CACCAAACACCATGATGCTTGAT 60.056 43.478 4.68 0.00 0.00 2.57
1261 1304 4.158209 CACCAAACACCATGATGCTTGATA 59.842 41.667 4.68 0.00 0.00 2.15
1262 1305 4.771577 ACCAAACACCATGATGCTTGATAA 59.228 37.500 4.68 0.00 0.00 1.75
1263 1306 5.104374 CCAAACACCATGATGCTTGATAAC 58.896 41.667 4.68 0.00 0.00 1.89
1264 1307 5.336610 CCAAACACCATGATGCTTGATAACA 60.337 40.000 4.68 0.00 0.00 2.41
1265 1308 6.334989 CAAACACCATGATGCTTGATAACAT 58.665 36.000 0.00 0.00 0.00 2.71
1266 1309 7.416551 CCAAACACCATGATGCTTGATAACATA 60.417 37.037 4.68 0.00 0.00 2.29
1267 1310 6.872628 ACACCATGATGCTTGATAACATAG 57.127 37.500 0.00 0.00 0.00 2.23
1268 1311 5.240183 ACACCATGATGCTTGATAACATAGC 59.760 40.000 0.00 0.00 33.85 2.97
1269 1312 5.472478 CACCATGATGCTTGATAACATAGCT 59.528 40.000 0.00 0.00 34.13 3.32
1270 1313 6.016527 CACCATGATGCTTGATAACATAGCTT 60.017 38.462 0.00 0.00 34.13 3.74
1271 1314 6.016527 ACCATGATGCTTGATAACATAGCTTG 60.017 38.462 0.00 0.00 34.13 4.01
1272 1315 6.206048 CCATGATGCTTGATAACATAGCTTGA 59.794 38.462 0.00 0.00 34.13 3.02
1273 1316 7.255346 CCATGATGCTTGATAACATAGCTTGAA 60.255 37.037 0.00 0.00 34.13 2.69
1274 1317 7.628769 TGATGCTTGATAACATAGCTTGAAA 57.371 32.000 0.00 0.00 34.13 2.69
1275 1318 8.054152 TGATGCTTGATAACATAGCTTGAAAA 57.946 30.769 0.00 0.00 34.13 2.29
1276 1319 8.522003 TGATGCTTGATAACATAGCTTGAAAAA 58.478 29.630 0.00 0.00 34.13 1.94
1277 1320 8.693542 ATGCTTGATAACATAGCTTGAAAAAC 57.306 30.769 0.00 0.00 34.13 2.43
1278 1321 7.885297 TGCTTGATAACATAGCTTGAAAAACT 58.115 30.769 0.00 0.00 34.13 2.66
1279 1322 8.359642 TGCTTGATAACATAGCTTGAAAAACTT 58.640 29.630 0.00 0.00 34.13 2.66
1280 1323 9.196552 GCTTGATAACATAGCTTGAAAAACTTT 57.803 29.630 0.00 0.00 32.09 2.66
1300 1343 9.765795 AAACTTTCTTATATTATGAGACGGAGG 57.234 33.333 0.00 0.00 0.00 4.30
1301 1344 7.897864 ACTTTCTTATATTATGAGACGGAGGG 58.102 38.462 0.00 0.00 0.00 4.30
1302 1345 7.728981 ACTTTCTTATATTATGAGACGGAGGGA 59.271 37.037 0.00 0.00 0.00 4.20
1303 1346 7.704578 TTCTTATATTATGAGACGGAGGGAG 57.295 40.000 0.00 0.00 0.00 4.30
1336 1379 0.533755 GTCAATAGCTCAGCGGCCAT 60.534 55.000 2.24 0.00 0.00 4.40
1399 1442 3.780294 TCAAGCCTATCTCCTTTGCCTAA 59.220 43.478 0.00 0.00 0.00 2.69
1400 1443 4.413520 TCAAGCCTATCTCCTTTGCCTAAT 59.586 41.667 0.00 0.00 0.00 1.73
1401 1444 5.606749 TCAAGCCTATCTCCTTTGCCTAATA 59.393 40.000 0.00 0.00 0.00 0.98
1402 1445 6.273260 TCAAGCCTATCTCCTTTGCCTAATAT 59.727 38.462 0.00 0.00 0.00 1.28
1403 1446 6.710499 AGCCTATCTCCTTTGCCTAATATT 57.290 37.500 0.00 0.00 0.00 1.28
1404 1447 7.096402 AGCCTATCTCCTTTGCCTAATATTT 57.904 36.000 0.00 0.00 0.00 1.40
1405 1448 7.530435 AGCCTATCTCCTTTGCCTAATATTTT 58.470 34.615 0.00 0.00 0.00 1.82
1406 1449 8.007153 AGCCTATCTCCTTTGCCTAATATTTTT 58.993 33.333 0.00 0.00 0.00 1.94
1480 1523 6.154192 TGCCATTGCTAATTGAATTTGGTCTA 59.846 34.615 7.25 0.00 38.71 2.59
1512 1555 6.981559 GGACTAGGATATGTTCTGTTCAGAAC 59.018 42.308 28.17 28.17 46.00 3.01
1526 1569 4.022935 TGTTCAGAACATTTGAGATGCACC 60.023 41.667 12.24 0.00 36.25 5.01
1569 1615 7.643569 TTTGTGCAAGTTATGTGATCCATAT 57.356 32.000 0.00 0.00 35.96 1.78
1570 1616 7.643569 TTGTGCAAGTTATGTGATCCATATT 57.356 32.000 0.00 0.00 35.96 1.28
1571 1617 8.744568 TTGTGCAAGTTATGTGATCCATATTA 57.255 30.769 0.00 0.00 35.96 0.98
1607 1653 4.970003 GTGATTACTTGGTTATTCGCATGC 59.030 41.667 7.91 7.91 0.00 4.06
1615 1661 3.252944 TGGTTATTCGCATGCATATGTGG 59.747 43.478 19.57 0.00 43.40 4.17
1621 1667 3.737850 TCGCATGCATATGTGGTATTCA 58.262 40.909 19.57 0.00 43.40 2.57
1686 1732 2.732282 GCTGAAACGCTAAATTGGGCTC 60.732 50.000 2.26 0.00 0.00 4.70
1710 1756 3.119792 GCACGACTATAGCGTTTCATAGC 59.880 47.826 16.21 12.62 40.44 2.97
1727 1773 2.656646 CTTTTTCCCCAAGCCGCC 59.343 61.111 0.00 0.00 0.00 6.13
1798 1848 1.305219 GCTCCACGGTTGCAGCATAA 61.305 55.000 2.05 0.00 0.00 1.90
1875 1925 2.354259 CTGCTCTTGTTCTGTCCATCC 58.646 52.381 0.00 0.00 0.00 3.51
2077 2130 7.919091 TCGGTAATAGTAGCAAGTATGAGTTTG 59.081 37.037 0.00 0.00 0.00 2.93
2098 2151 8.416329 AGTTTGCATGAGAAACTTTGTTTAGAT 58.584 29.630 14.42 0.00 40.04 1.98
2099 2152 8.694394 GTTTGCATGAGAAACTTTGTTTAGATC 58.306 33.333 11.57 0.00 31.74 2.75
2106 2159 8.092068 TGAGAAACTTTGTTTAGATCGTCCATA 58.908 33.333 0.00 0.00 0.00 2.74
2110 2163 9.840427 AAACTTTGTTTAGATCGTCCATATTTG 57.160 29.630 0.00 0.00 0.00 2.32
2137 2190 4.154015 TGACGAAAATGTCTTGGTGCTATG 59.846 41.667 0.00 0.00 39.64 2.23
2139 2192 3.127548 CGAAAATGTCTTGGTGCTATGCT 59.872 43.478 0.00 0.00 0.00 3.79
2183 2236 2.302019 AGCTTTGCTCCTCCCTACC 58.698 57.895 0.00 0.00 30.62 3.18
2328 2395 2.229784 CCTTGGCTTGATTTGGTCTGAC 59.770 50.000 0.00 0.00 0.00 3.51
2336 2403 4.771590 TGATTTGGTCTGACTTGCAATC 57.228 40.909 7.85 10.19 0.00 2.67
2365 2437 0.105760 TGTGGTTGGGTTGGCAGATT 60.106 50.000 0.00 0.00 0.00 2.40
2383 2455 1.497309 TTGGAAGGGTGCCACTAGGG 61.497 60.000 0.00 0.00 34.56 3.53
2551 2623 1.446272 CTTCGGACGACAGAAGCCC 60.446 63.158 13.61 0.00 40.19 5.19
2630 2702 3.157881 CCACTCACCTCTAACTCACTCA 58.842 50.000 0.00 0.00 0.00 3.41
2692 2772 4.019792 TCTGAGCTTACCATCTTGCAAA 57.980 40.909 0.00 0.00 0.00 3.68
3287 3372 1.069159 CGATACGGATGAACGAGGAGG 60.069 57.143 0.00 0.00 37.61 4.30
3341 3426 1.821753 CATCGCGGAATATCTCCTCCT 59.178 52.381 6.13 0.00 42.85 3.69
3342 3427 1.996798 TCGCGGAATATCTCCTCCTT 58.003 50.000 6.13 0.00 42.85 3.36
3343 3428 1.887198 TCGCGGAATATCTCCTCCTTC 59.113 52.381 6.13 0.00 42.85 3.46
3346 3431 2.896039 CGGAATATCTCCTCCTTCCCT 58.104 52.381 0.00 0.00 42.85 4.20
3353 3438 4.521062 CCTCCTTCCCTCGCGCAG 62.521 72.222 8.75 3.84 0.00 5.18
3417 3502 3.788766 GACTTTGACGCGCGGCAT 61.789 61.111 41.79 26.74 30.63 4.40
3418 3503 3.308878 GACTTTGACGCGCGGCATT 62.309 57.895 41.79 26.91 30.63 3.56
3445 3531 6.136541 TCTTTTCTTTTTCCTTGTCTCTGC 57.863 37.500 0.00 0.00 0.00 4.26
3480 3566 1.604604 CTTTGTGAAGGCCGGAAAGA 58.395 50.000 5.05 0.00 0.00 2.52
3561 3650 1.651240 TACGTGCGGTCTACAGAGGC 61.651 60.000 0.00 0.00 0.00 4.70
3714 3811 0.526211 TGGACTCGATCTGTTGACGG 59.474 55.000 0.00 0.00 0.00 4.79
3817 3914 2.857992 GTCGTCGTCGTCGTCGTG 60.858 66.667 18.44 6.23 45.27 4.35
3820 3917 2.794166 GTCGTCGTCGTCGTGGTG 60.794 66.667 11.41 0.00 38.33 4.17
4126 4231 1.483004 TGCCGAATCCATTCTTCCGTA 59.517 47.619 0.00 0.00 34.69 4.02
4153 4258 2.223479 GCAGTAGCTTCTCTTCTCTCGG 60.223 54.545 0.00 0.00 37.91 4.63
4214 4319 1.583986 CTCGCTCCGGGATCAGATC 59.416 63.158 0.00 1.18 0.00 2.75
4215 4320 2.193865 CTCGCTCCGGGATCAGATCG 62.194 65.000 0.00 0.00 0.00 3.69
4218 4323 1.960612 CTCCGGGATCAGATCGGAC 59.039 63.158 8.79 0.00 46.48 4.79
4220 4325 1.531840 CCGGGATCAGATCGGACCT 60.532 63.158 4.80 0.00 45.96 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 3.490348 ACCATATCATACCCAAGCTTGC 58.510 45.455 21.43 0.00 0.00 4.01
86 87 6.456501 ACAATCCCAATTACTATCTCGCTAC 58.543 40.000 0.00 0.00 0.00 3.58
100 101 8.231007 TCCATTACCATTACATACAATCCCAAT 58.769 33.333 0.00 0.00 0.00 3.16
101 102 7.587258 TCCATTACCATTACATACAATCCCAA 58.413 34.615 0.00 0.00 0.00 4.12
266 268 2.617250 TGATGCAATCTTTCACACGC 57.383 45.000 0.00 0.00 45.81 5.34
434 449 1.094785 ACTGGCAATACCGAATGCAC 58.905 50.000 0.00 0.00 44.32 4.57
465 480 2.667481 CGTACCAAGGCAAATGCATTTG 59.333 45.455 36.80 36.80 42.92 2.32
501 516 2.754552 GCTAATCAATGGTTGTGAGCCA 59.245 45.455 0.00 0.00 40.68 4.75
502 517 2.223340 CGCTAATCAATGGTTGTGAGCC 60.223 50.000 0.00 0.00 31.66 4.70
503 518 2.420022 ACGCTAATCAATGGTTGTGAGC 59.580 45.455 0.00 0.00 0.00 4.26
504 519 3.436704 ACACGCTAATCAATGGTTGTGAG 59.563 43.478 2.77 0.00 0.00 3.51
505 520 3.407698 ACACGCTAATCAATGGTTGTGA 58.592 40.909 2.77 0.00 0.00 3.58
506 521 3.724716 CGACACGCTAATCAATGGTTGTG 60.725 47.826 0.00 0.00 0.00 3.33
507 522 2.415168 CGACACGCTAATCAATGGTTGT 59.585 45.455 0.00 0.00 0.00 3.32
508 523 2.415168 ACGACACGCTAATCAATGGTTG 59.585 45.455 0.00 0.00 0.00 3.77
509 524 2.415168 CACGACACGCTAATCAATGGTT 59.585 45.455 0.00 0.00 0.00 3.67
510 525 1.999735 CACGACACGCTAATCAATGGT 59.000 47.619 0.00 0.00 0.00 3.55
511 526 1.999735 ACACGACACGCTAATCAATGG 59.000 47.619 0.00 0.00 0.00 3.16
512 527 2.784327 GCACACGACACGCTAATCAATG 60.784 50.000 0.00 0.00 0.00 2.82
513 528 1.393539 GCACACGACACGCTAATCAAT 59.606 47.619 0.00 0.00 0.00 2.57
514 529 0.787787 GCACACGACACGCTAATCAA 59.212 50.000 0.00 0.00 0.00 2.57
515 530 0.319125 TGCACACGACACGCTAATCA 60.319 50.000 0.00 0.00 0.00 2.57
516 531 0.093026 GTGCACACGACACGCTAATC 59.907 55.000 13.17 0.00 0.00 1.75
517 532 0.598942 TGTGCACACGACACGCTAAT 60.599 50.000 17.42 0.00 41.03 1.73
518 533 0.598942 ATGTGCACACGACACGCTAA 60.599 50.000 24.37 0.00 41.03 3.09
519 534 1.006688 ATGTGCACACGACACGCTA 60.007 52.632 24.37 0.00 41.03 4.26
520 535 2.280119 ATGTGCACACGACACGCT 60.280 55.556 24.37 0.00 41.03 5.07
521 536 2.170985 GATGTGCACACGACACGC 59.829 61.111 24.37 1.97 41.03 5.34
522 537 2.465486 CGATGTGCACACGACACG 59.535 61.111 24.37 17.84 41.03 4.49
523 538 2.667318 CCCGATGTGCACACGACAC 61.667 63.158 30.26 16.88 38.55 3.67
524 539 2.356913 CCCGATGTGCACACGACA 60.357 61.111 30.26 9.50 0.00 4.35
525 540 3.788766 GCCCGATGTGCACACGAC 61.789 66.667 30.26 21.76 0.00 4.34
526 541 4.306967 TGCCCGATGTGCACACGA 62.307 61.111 30.26 16.04 32.85 4.35
527 542 3.792047 CTGCCCGATGTGCACACG 61.792 66.667 24.37 24.87 34.46 4.49
528 543 0.953471 TTACTGCCCGATGTGCACAC 60.953 55.000 24.37 14.98 34.46 3.82
529 544 0.250510 TTTACTGCCCGATGTGCACA 60.251 50.000 24.08 24.08 34.46 4.57
530 545 0.447801 CTTTACTGCCCGATGTGCAC 59.552 55.000 10.75 10.75 34.46 4.57
531 546 0.036164 ACTTTACTGCCCGATGTGCA 59.964 50.000 0.00 0.00 37.17 4.57
532 547 0.447801 CACTTTACTGCCCGATGTGC 59.552 55.000 0.00 0.00 0.00 4.57
533 548 1.732259 GACACTTTACTGCCCGATGTG 59.268 52.381 0.00 0.00 0.00 3.21
534 549 1.671850 CGACACTTTACTGCCCGATGT 60.672 52.381 0.00 0.00 0.00 3.06
535 550 0.999406 CGACACTTTACTGCCCGATG 59.001 55.000 0.00 0.00 0.00 3.84
536 551 0.606604 ACGACACTTTACTGCCCGAT 59.393 50.000 0.00 0.00 0.00 4.18
537 552 0.038892 GACGACACTTTACTGCCCGA 60.039 55.000 0.00 0.00 0.00 5.14
538 553 0.038526 AGACGACACTTTACTGCCCG 60.039 55.000 0.00 0.00 0.00 6.13
539 554 1.270147 ACAGACGACACTTTACTGCCC 60.270 52.381 0.00 0.00 32.67 5.36
540 555 2.150397 ACAGACGACACTTTACTGCC 57.850 50.000 0.00 0.00 32.67 4.85
541 556 3.635331 TGTACAGACGACACTTTACTGC 58.365 45.455 0.00 0.00 32.67 4.40
542 557 4.856664 ACTGTACAGACGACACTTTACTG 58.143 43.478 29.30 0.00 32.39 2.74
543 558 4.577693 TGACTGTACAGACGACACTTTACT 59.422 41.667 29.30 1.42 0.00 2.24
544 559 4.852138 TGACTGTACAGACGACACTTTAC 58.148 43.478 29.30 6.08 0.00 2.01
545 560 5.700722 ATGACTGTACAGACGACACTTTA 57.299 39.130 29.30 5.12 0.00 1.85
546 561 4.585955 ATGACTGTACAGACGACACTTT 57.414 40.909 29.30 3.01 0.00 2.66
547 562 4.585955 AATGACTGTACAGACGACACTT 57.414 40.909 29.30 3.81 0.00 3.16
548 563 4.547532 GAAATGACTGTACAGACGACACT 58.452 43.478 29.30 10.36 0.00 3.55
549 564 3.361053 CGAAATGACTGTACAGACGACAC 59.639 47.826 29.30 14.06 0.00 3.67
550 565 3.004002 ACGAAATGACTGTACAGACGACA 59.996 43.478 29.30 20.44 0.00 4.35
551 566 3.562505 ACGAAATGACTGTACAGACGAC 58.437 45.455 29.30 16.10 0.00 4.34
552 567 3.501062 AGACGAAATGACTGTACAGACGA 59.499 43.478 29.30 13.65 0.00 4.20
553 568 3.822996 AGACGAAATGACTGTACAGACG 58.177 45.455 29.30 21.73 0.00 4.18
554 569 5.049398 AGAGACGAAATGACTGTACAGAC 57.951 43.478 29.30 22.83 0.00 3.51
555 570 7.094334 ACAATAGAGACGAAATGACTGTACAGA 60.094 37.037 29.30 8.39 0.00 3.41
556 571 7.030165 ACAATAGAGACGAAATGACTGTACAG 58.970 38.462 21.44 21.44 0.00 2.74
557 572 6.920817 ACAATAGAGACGAAATGACTGTACA 58.079 36.000 0.00 0.00 0.00 2.90
558 573 7.027760 TGACAATAGAGACGAAATGACTGTAC 58.972 38.462 0.00 0.00 0.00 2.90
559 574 7.094334 ACTGACAATAGAGACGAAATGACTGTA 60.094 37.037 0.00 0.00 0.00 2.74
560 575 6.025749 TGACAATAGAGACGAAATGACTGT 57.974 37.500 0.00 0.00 0.00 3.55
561 576 6.034363 CACTGACAATAGAGACGAAATGACTG 59.966 42.308 0.00 0.00 0.00 3.51
562 577 6.096036 CACTGACAATAGAGACGAAATGACT 58.904 40.000 0.00 0.00 0.00 3.41
563 578 5.220303 GCACTGACAATAGAGACGAAATGAC 60.220 44.000 0.00 0.00 0.00 3.06
564 579 4.864806 GCACTGACAATAGAGACGAAATGA 59.135 41.667 0.00 0.00 0.00 2.57
565 580 4.627035 TGCACTGACAATAGAGACGAAATG 59.373 41.667 0.00 0.00 0.00 2.32
566 581 4.820897 TGCACTGACAATAGAGACGAAAT 58.179 39.130 0.00 0.00 0.00 2.17
567 582 4.237724 CTGCACTGACAATAGAGACGAAA 58.762 43.478 0.00 0.00 0.00 3.46
568 583 3.838120 CTGCACTGACAATAGAGACGAA 58.162 45.455 0.00 0.00 0.00 3.85
569 584 2.416027 GCTGCACTGACAATAGAGACGA 60.416 50.000 0.00 0.00 0.00 4.20
570 585 1.923204 GCTGCACTGACAATAGAGACG 59.077 52.381 0.00 0.00 0.00 4.18
571 586 3.244033 AGCTGCACTGACAATAGAGAC 57.756 47.619 1.02 0.00 0.00 3.36
611 628 4.749245 ACGCATCTGTCCTAAAAACAAG 57.251 40.909 0.00 0.00 0.00 3.16
613 630 3.500680 GGAACGCATCTGTCCTAAAAACA 59.499 43.478 0.00 0.00 0.00 2.83
614 631 3.119955 GGGAACGCATCTGTCCTAAAAAC 60.120 47.826 0.00 0.00 0.00 2.43
621 638 2.124695 GGGGGAACGCATCTGTCC 60.125 66.667 0.00 0.00 45.96 4.02
631 648 1.971695 CTTTGGCTCACGGGGGAAC 60.972 63.158 0.00 0.00 0.00 3.62
641 658 2.354199 GACATGCTAGCTTCTTTGGCTC 59.646 50.000 17.23 0.00 40.74 4.70
645 662 3.999001 TGTCAGACATGCTAGCTTCTTTG 59.001 43.478 17.23 9.23 0.00 2.77
646 664 4.252073 CTGTCAGACATGCTAGCTTCTTT 58.748 43.478 17.23 0.00 0.00 2.52
649 667 1.932511 GCTGTCAGACATGCTAGCTTC 59.067 52.381 17.23 9.66 34.34 3.86
684 712 5.818887 TGGATGAGATGATTTTCTGTTGGA 58.181 37.500 0.00 0.00 0.00 3.53
715 743 2.716217 GGGAGATTTGAACTGTCCCAG 58.284 52.381 12.12 0.00 45.58 4.45
735 763 2.740981 GTCATGTCTGACTGCTTCAAGG 59.259 50.000 9.51 0.00 46.84 3.61
813 852 5.679894 GCATATATCCCATCCTCGTACACTG 60.680 48.000 0.00 0.00 0.00 3.66
887 926 2.880890 CAAGGAGGAGGACAACAACTTG 59.119 50.000 0.00 0.00 0.00 3.16
888 927 2.158608 CCAAGGAGGAGGACAACAACTT 60.159 50.000 0.00 0.00 41.22 2.66
889 928 1.421646 CCAAGGAGGAGGACAACAACT 59.578 52.381 0.00 0.00 41.22 3.16
890 929 1.545651 CCCAAGGAGGAGGACAACAAC 60.546 57.143 0.00 0.00 41.22 3.32
891 930 0.771127 CCCAAGGAGGAGGACAACAA 59.229 55.000 0.00 0.00 41.22 2.83
927 966 1.437986 CTACCCCTCTTTCCTCGCG 59.562 63.158 0.00 0.00 0.00 5.87
936 979 3.367321 GAGTAACTTCAGCTACCCCTCT 58.633 50.000 0.00 0.00 0.00 3.69
1040 1083 2.232298 CTCTGCGGAGAGGTTGGACC 62.232 65.000 24.95 0.00 42.03 4.46
1074 1117 3.775654 GAGAGGTGGGTCAGCCGG 61.776 72.222 0.00 0.00 34.97 6.13
1075 1118 2.681778 AGAGAGGTGGGTCAGCCG 60.682 66.667 0.00 0.00 34.97 5.52
1076 1119 2.664081 CCAGAGAGGTGGGTCAGCC 61.664 68.421 0.00 0.00 33.46 4.85
1077 1120 2.985456 CCAGAGAGGTGGGTCAGC 59.015 66.667 0.00 0.00 33.46 4.26
1086 1129 6.550938 TGGCATTATATATCACCAGAGAGG 57.449 41.667 0.00 0.00 45.67 3.69
1097 1140 8.186163 CAGCACATCGAAAATGGCATTATATAT 58.814 33.333 14.05 2.92 0.00 0.86
1098 1141 7.529158 CAGCACATCGAAAATGGCATTATATA 58.471 34.615 14.05 0.47 0.00 0.86
1099 1142 6.384224 CAGCACATCGAAAATGGCATTATAT 58.616 36.000 14.05 2.89 0.00 0.86
1100 1143 5.761003 CAGCACATCGAAAATGGCATTATA 58.239 37.500 14.05 0.00 0.00 0.98
1106 1149 0.171903 AGCAGCACATCGAAAATGGC 59.828 50.000 0.00 0.00 0.00 4.40
1151 1194 0.932399 CACAAAGCAAAGCAACAGGC 59.068 50.000 0.00 0.00 45.30 4.85
1152 1195 1.928503 CACACAAAGCAAAGCAACAGG 59.071 47.619 0.00 0.00 0.00 4.00
1205 1248 1.020437 GCCAACCTTAGATGCTGCTC 58.980 55.000 0.00 0.00 0.00 4.26
1232 1275 2.237643 TCATGGTGTTTGGTGTGGATG 58.762 47.619 0.00 0.00 0.00 3.51
1233 1276 2.673775 TCATGGTGTTTGGTGTGGAT 57.326 45.000 0.00 0.00 0.00 3.41
1234 1277 2.237643 CATCATGGTGTTTGGTGTGGA 58.762 47.619 0.00 0.00 0.00 4.02
1235 1278 1.337074 GCATCATGGTGTTTGGTGTGG 60.337 52.381 8.00 0.00 0.00 4.17
1236 1279 1.614903 AGCATCATGGTGTTTGGTGTG 59.385 47.619 8.00 0.00 0.00 3.82
1237 1280 1.999648 AGCATCATGGTGTTTGGTGT 58.000 45.000 8.00 0.00 0.00 4.16
1241 1284 5.712004 TGTTATCAAGCATCATGGTGTTTG 58.288 37.500 24.88 24.88 40.37 2.93
1242 1285 5.981088 TGTTATCAAGCATCATGGTGTTT 57.019 34.783 8.00 4.82 0.00 2.83
1243 1286 6.238842 GCTATGTTATCAAGCATCATGGTGTT 60.239 38.462 8.00 0.00 36.26 3.32
1245 1288 5.472478 AGCTATGTTATCAAGCATCATGGTG 59.528 40.000 0.10 0.10 38.75 4.17
1246 1289 5.628130 AGCTATGTTATCAAGCATCATGGT 58.372 37.500 0.00 0.00 38.75 3.55
1248 1291 7.198306 TCAAGCTATGTTATCAAGCATCATG 57.802 36.000 0.00 0.00 38.75 3.07
1249 1292 7.812690 TTCAAGCTATGTTATCAAGCATCAT 57.187 32.000 0.00 0.00 38.75 2.45
1250 1293 7.628769 TTTCAAGCTATGTTATCAAGCATCA 57.371 32.000 0.00 0.00 38.75 3.07
1251 1294 8.801913 GTTTTTCAAGCTATGTTATCAAGCATC 58.198 33.333 0.00 0.00 38.75 3.91
1252 1295 8.526147 AGTTTTTCAAGCTATGTTATCAAGCAT 58.474 29.630 0.00 0.00 38.75 3.79
1253 1296 7.885297 AGTTTTTCAAGCTATGTTATCAAGCA 58.115 30.769 0.00 0.00 38.75 3.91
1254 1297 8.748380 AAGTTTTTCAAGCTATGTTATCAAGC 57.252 30.769 0.00 0.00 36.48 4.01
1274 1317 9.765795 CCTCCGTCTCATAATATAAGAAAGTTT 57.234 33.333 0.00 0.00 0.00 2.66
1275 1318 8.368668 CCCTCCGTCTCATAATATAAGAAAGTT 58.631 37.037 0.00 0.00 0.00 2.66
1276 1319 7.728981 TCCCTCCGTCTCATAATATAAGAAAGT 59.271 37.037 0.00 0.00 0.00 2.66
1277 1320 8.123639 TCCCTCCGTCTCATAATATAAGAAAG 57.876 38.462 0.00 0.00 0.00 2.62
1278 1321 7.728981 ACTCCCTCCGTCTCATAATATAAGAAA 59.271 37.037 0.00 0.00 0.00 2.52
1279 1322 7.239438 ACTCCCTCCGTCTCATAATATAAGAA 58.761 38.462 0.00 0.00 0.00 2.52
1280 1323 6.791371 ACTCCCTCCGTCTCATAATATAAGA 58.209 40.000 0.00 0.00 0.00 2.10
1281 1324 8.754991 ATACTCCCTCCGTCTCATAATATAAG 57.245 38.462 0.00 0.00 0.00 1.73
1282 1325 9.543231 AAATACTCCCTCCGTCTCATAATATAA 57.457 33.333 0.00 0.00 0.00 0.98
1283 1326 8.967918 CAAATACTCCCTCCGTCTCATAATATA 58.032 37.037 0.00 0.00 0.00 0.86
1284 1327 7.455008 ACAAATACTCCCTCCGTCTCATAATAT 59.545 37.037 0.00 0.00 0.00 1.28
1285 1328 6.781014 ACAAATACTCCCTCCGTCTCATAATA 59.219 38.462 0.00 0.00 0.00 0.98
1286 1329 5.602978 ACAAATACTCCCTCCGTCTCATAAT 59.397 40.000 0.00 0.00 0.00 1.28
1287 1330 4.960469 ACAAATACTCCCTCCGTCTCATAA 59.040 41.667 0.00 0.00 0.00 1.90
1288 1331 4.341235 CACAAATACTCCCTCCGTCTCATA 59.659 45.833 0.00 0.00 0.00 2.15
1289 1332 3.133003 CACAAATACTCCCTCCGTCTCAT 59.867 47.826 0.00 0.00 0.00 2.90
1290 1333 2.496070 CACAAATACTCCCTCCGTCTCA 59.504 50.000 0.00 0.00 0.00 3.27
1291 1334 2.496470 ACACAAATACTCCCTCCGTCTC 59.504 50.000 0.00 0.00 0.00 3.36
1292 1335 2.537143 ACACAAATACTCCCTCCGTCT 58.463 47.619 0.00 0.00 0.00 4.18
1293 1336 3.446516 ACTACACAAATACTCCCTCCGTC 59.553 47.826 0.00 0.00 0.00 4.79
1294 1337 3.438183 ACTACACAAATACTCCCTCCGT 58.562 45.455 0.00 0.00 0.00 4.69
1295 1338 4.181578 CAACTACACAAATACTCCCTCCG 58.818 47.826 0.00 0.00 0.00 4.63
1296 1339 5.161943 ACAACTACACAAATACTCCCTCC 57.838 43.478 0.00 0.00 0.00 4.30
1297 1340 5.790593 TGACAACTACACAAATACTCCCTC 58.209 41.667 0.00 0.00 0.00 4.30
1298 1341 5.818678 TGACAACTACACAAATACTCCCT 57.181 39.130 0.00 0.00 0.00 4.20
1299 1342 7.201617 GCTATTGACAACTACACAAATACTCCC 60.202 40.741 0.00 0.00 0.00 4.30
1300 1343 7.549488 AGCTATTGACAACTACACAAATACTCC 59.451 37.037 0.00 0.00 0.00 3.85
1301 1344 8.480643 AGCTATTGACAACTACACAAATACTC 57.519 34.615 0.00 0.00 0.00 2.59
1302 1345 8.094548 TGAGCTATTGACAACTACACAAATACT 58.905 33.333 0.00 0.00 0.00 2.12
1303 1346 8.251750 TGAGCTATTGACAACTACACAAATAC 57.748 34.615 0.00 0.00 0.00 1.89
1364 1407 1.509923 GCTTGACTTGCCATGGAGC 59.490 57.895 18.40 9.97 0.00 4.70
1403 1446 6.369629 TCATGTTCAACTCTTAGGGGAAAAA 58.630 36.000 0.00 0.00 0.00 1.94
1404 1447 5.947663 TCATGTTCAACTCTTAGGGGAAAA 58.052 37.500 0.00 0.00 0.00 2.29
1405 1448 5.576563 TCATGTTCAACTCTTAGGGGAAA 57.423 39.130 0.00 0.00 0.00 3.13
1406 1449 5.576563 TTCATGTTCAACTCTTAGGGGAA 57.423 39.130 0.00 0.00 0.00 3.97
1407 1450 5.779241 ATTCATGTTCAACTCTTAGGGGA 57.221 39.130 0.00 0.00 0.00 4.81
1480 1523 7.588169 ACAGAACATATCCTAGTCCTACTTCT 58.412 38.462 0.00 0.00 0.00 2.85
1512 1555 3.021695 AGGTCATGGTGCATCTCAAATG 58.978 45.455 0.00 0.00 0.00 2.32
1621 1667 9.423061 GAAAAGGTAAACATACAATCAAGCATT 57.577 29.630 0.00 0.00 0.00 3.56
1662 1708 3.181491 GCCCAATTTAGCGTTTCAGCATA 60.181 43.478 0.00 0.00 40.15 3.14
1686 1732 0.844503 GAAACGCTATAGTCGTGCCG 59.155 55.000 18.47 7.97 40.36 5.69
1693 1739 6.260271 GGGAAAAAGCTATGAAACGCTATAGT 59.740 38.462 0.84 0.00 34.96 2.12
1710 1756 2.656646 GGCGGCTTGGGGAAAAAG 59.343 61.111 0.00 0.00 0.00 2.27
1798 1848 1.522569 GGAGCACGGCCATCTTACT 59.477 57.895 2.24 0.00 0.00 2.24
1947 1997 0.474854 TGTTGGCCTTGGAGAGGGTA 60.475 55.000 3.32 0.00 46.40 3.69
2077 2130 6.603095 ACGATCTAAACAAAGTTTCTCATGC 58.397 36.000 0.00 0.00 0.00 4.06
2098 2151 4.911514 TCGTCAGATCAAATATGGACGA 57.088 40.909 10.21 10.21 40.71 4.20
2099 2152 5.966636 TTTCGTCAGATCAAATATGGACG 57.033 39.130 0.00 0.00 36.33 4.79
2106 2159 6.207417 ACCAAGACATTTTCGTCAGATCAAAT 59.793 34.615 0.00 0.00 38.43 2.32
2110 2163 4.670221 GCACCAAGACATTTTCGTCAGATC 60.670 45.833 0.00 0.00 38.43 2.75
2183 2236 1.277557 AGCACTAGAGTTTGGAGCCAG 59.722 52.381 0.00 0.00 0.00 4.85
2289 2342 8.658840 AGCCAAGGGAATTATACAAGTTAAAA 57.341 30.769 0.00 0.00 0.00 1.52
2303 2361 2.833943 GACCAAATCAAGCCAAGGGAAT 59.166 45.455 0.00 0.00 0.00 3.01
2328 2395 3.426191 CCACATTTTCACACGATTGCAAG 59.574 43.478 4.94 0.00 0.00 4.01
2336 2403 1.407258 ACCCAACCACATTTTCACACG 59.593 47.619 0.00 0.00 0.00 4.49
2365 2437 1.923395 CCCTAGTGGCACCCTTCCA 60.923 63.158 15.27 0.00 0.00 3.53
2383 2455 3.438087 TCTCAAAGTAGCTGATTTGCTGC 59.562 43.478 16.53 0.00 43.87 5.25
2455 2527 3.978571 GAGCGCCTCCCCCAAGAAC 62.979 68.421 2.29 0.00 0.00 3.01
2551 2623 1.089920 CCTGAAAATCTGCAGGGTCG 58.910 55.000 15.13 3.53 46.24 4.79
2618 2690 4.981812 TGGTGACTAGTGAGTGAGTTAGA 58.018 43.478 0.00 0.00 35.45 2.10
2630 2702 4.891992 AATTACAGTGCTGGTGACTAGT 57.108 40.909 0.00 0.00 34.19 2.57
2692 2772 1.670811 CCGCTTAGTTTTGGATGCGAT 59.329 47.619 6.74 0.00 45.15 4.58
2697 2777 2.488153 GTTCAGCCGCTTAGTTTTGGAT 59.512 45.455 0.00 0.00 0.00 3.41
2766 2846 1.299620 GCGGACGTACGGTATGCAT 60.300 57.895 23.80 3.79 0.00 3.96
2814 2894 2.664851 TTGTTCACAGCCGCCGAG 60.665 61.111 0.00 0.00 0.00 4.63
3000 3080 2.002586 CTCAGTCCACGAAATGCGAAT 58.997 47.619 0.00 0.00 44.57 3.34
3341 3426 4.314440 AAGTGCTGCGCGAGGGAA 62.314 61.111 12.10 0.00 0.00 3.97
3418 3503 9.423061 CAGAGACAAGGAAAAAGAAAAGAAAAA 57.577 29.630 0.00 0.00 0.00 1.94
3438 3523 0.595095 CCAAAGGCAACAGCAGAGAC 59.405 55.000 0.00 0.00 41.41 3.36
3480 3566 2.069273 CCTTTCGACAACAGCGATCTT 58.931 47.619 0.00 0.00 37.64 2.40
3573 3662 4.127171 CCAGTCTCTAGTCTCTACTGCTC 58.873 52.174 0.00 0.00 36.96 4.26
3585 3674 0.028242 CGTGCGCTACCAGTCTCTAG 59.972 60.000 9.73 0.00 0.00 2.43
3686 3783 1.344438 AGATCGAGTCCAAGTGTTGCA 59.656 47.619 0.00 0.00 0.00 4.08
3734 3831 0.458669 CCATGGAAGGCTACGTACGT 59.541 55.000 25.98 25.98 0.00 3.57
4126 4231 0.534412 AGAGAAGCTACTGCATGCGT 59.466 50.000 14.09 15.84 42.74 5.24
4165 4270 5.343325 GCAGCAGAGCAAACTAATTAAACAC 59.657 40.000 0.00 0.00 0.00 3.32
4214 4319 1.135083 GTGTACATCTGGTCAGGTCCG 60.135 57.143 0.00 0.00 0.00 4.79
4215 4320 1.899814 TGTGTACATCTGGTCAGGTCC 59.100 52.381 0.00 0.00 0.00 4.46
4218 4323 1.406069 GGCTGTGTACATCTGGTCAGG 60.406 57.143 0.00 0.00 0.00 3.86
4220 4325 1.347062 TGGCTGTGTACATCTGGTCA 58.653 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.