Multiple sequence alignment - TraesCS2B01G187600

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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 TraesCS2B01G187600 chr2B 100.000 3525 0 0 1 3525 162930589 162927065 0.000000e+00 6510.0
1 TraesCS2B01G187600 chr2A 85.696 2321 189 71 606 2839 113930326 113928062 0.000000e+00 2314.0
2 TraesCS2B01G187600 chr2A 88.182 220 12 6 277 489 113930607 113930395 2.100000e-62 250.0
3 TraesCS2B01G187600 chr2A 86.341 205 21 5 3202 3404 113924220 113924021 2.130000e-52 217.0
4 TraesCS2B01G187600 chr2A 86.709 158 9 6 1 151 113930845 113930693 7.830000e-37 165.0
5 TraesCS2B01G187600 chr2A 92.537 67 5 0 3082 3148 113925542 113925476 2.900000e-16 97.1
6 TraesCS2B01G187600 chr2D 89.924 1181 60 35 621 1796 112721743 112720617 0.000000e+00 1467.0
7 TraesCS2B01G187600 chr2D 87.023 1048 81 27 1802 2826 112720437 112719422 0.000000e+00 1131.0
8 TraesCS2B01G187600 chr2D 87.892 702 51 10 2840 3525 112696831 112696148 0.000000e+00 795.0
9 TraesCS2B01G187600 chr2D 91.481 270 20 2 2475 2741 112697341 112697072 5.560000e-98 368.0
10 TraesCS2B01G187600 chr2D 84.255 235 25 5 1 224 112722347 112722114 5.920000e-53 219.0
11 TraesCS2B01G187600 chr7B 88.304 1120 71 32 1007 2104 386119991 386121072 0.000000e+00 1288.0
12 TraesCS2B01G187600 chr6B 92.718 412 21 2 1007 1410 82498198 82498608 1.410000e-163 586.0
13 TraesCS2B01G187600 chr4A 87.580 467 39 14 1085 1550 732529086 732529534 1.120000e-144 523.0
14 TraesCS2B01G187600 chr5B 88.889 414 26 2 1007 1412 333010692 333011093 3.160000e-135 492.0


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 TraesCS2B01G187600 chr2B 162927065 162930589 3524 True 6510.00 6510 100.000000 1 3525 1 chr2B.!!$R1 3524
1 TraesCS2B01G187600 chr2A 113924021 113930845 6824 True 608.62 2314 87.893000 1 3404 5 chr2A.!!$R1 3403
2 TraesCS2B01G187600 chr2D 112719422 112722347 2925 True 939.00 1467 87.067333 1 2826 3 chr2D.!!$R2 2825
3 TraesCS2B01G187600 chr2D 112696148 112697341 1193 True 581.50 795 89.686500 2475 3525 2 chr2D.!!$R1 1050
4 TraesCS2B01G187600 chr7B 386119991 386121072 1081 False 1288.00 1288 88.304000 1007 2104 1 chr7B.!!$F1 1097

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
512 552 0.038166 ACTTTGACCCGACATGGCAT 59.962 50.0 0.0 0.0 35.87 4.40 F
687 760 0.179023 AAAAGGCGGTTCCCAACGTA 60.179 50.0 0.0 0.0 34.51 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2375 2719 0.310854 GTTGGTGTAGGTGCTGCAAC 59.689 55.000 10.28 10.28 34.44 4.17 R
2577 2921 1.475280 AGTAGTCACTAAATCGCGGCA 59.525 47.619 6.13 0.00 31.45 5.69 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
28 29 0.451783 AAGGCGCATCACGGAATTTC 59.548 50.000 10.83 0.00 43.93 2.17
36 37 2.033448 ACGGAATTTCGGCTGGCA 59.967 55.556 11.59 0.00 0.00 4.92
37 38 2.332654 ACGGAATTTCGGCTGGCAC 61.333 57.895 11.59 0.00 0.00 5.01
38 39 2.331893 CGGAATTTCGGCTGGCACA 61.332 57.895 0.00 0.00 0.00 4.57
39 40 1.656818 CGGAATTTCGGCTGGCACAT 61.657 55.000 0.00 0.00 38.20 3.21
88 96 3.596046 TGTTCAGGGGGAAATACCTTCAT 59.404 43.478 0.00 0.00 37.23 2.57
95 103 4.354087 GGGGGAAATACCTTCATATGGACT 59.646 45.833 2.13 0.00 38.98 3.85
104 112 1.882912 TCATATGGACTGCGGAATGC 58.117 50.000 0.00 0.00 46.70 3.56
107 115 0.473755 TATGGACTGCGGAATGCCAT 59.526 50.000 0.00 9.16 45.60 4.40
113 121 2.050714 GCGGAATGCCATCATGCG 60.051 61.111 0.00 0.00 37.76 4.73
116 124 1.656441 GGAATGCCATCATGCGGAC 59.344 57.895 5.26 0.00 32.23 4.79
123 131 1.683943 CCATCATGCGGACCAAAGAT 58.316 50.000 0.00 0.00 0.00 2.40
126 134 3.251729 CCATCATGCGGACCAAAGATAAG 59.748 47.826 0.00 0.00 0.00 1.73
163 195 1.883275 CCATTGGCGGTTAAAGTCACA 59.117 47.619 0.00 0.00 0.00 3.58
166 198 0.250553 TGGCGGTTAAAGTCACAGGG 60.251 55.000 0.00 0.00 0.00 4.45
170 202 1.071071 CGGTTAAAGTCACAGGGTGGA 59.929 52.381 0.00 0.00 33.87 4.02
174 206 2.938956 AAAGTCACAGGGTGGAGAAG 57.061 50.000 0.00 0.00 33.87 2.85
179 211 2.633481 GTCACAGGGTGGAGAAGTACTT 59.367 50.000 8.13 8.13 33.87 2.24
180 212 3.830755 GTCACAGGGTGGAGAAGTACTTA 59.169 47.826 8.42 0.00 33.87 2.24
181 213 4.282703 GTCACAGGGTGGAGAAGTACTTAA 59.717 45.833 8.42 0.00 33.87 1.85
215 248 1.003116 CATCGAGCAGCCAAATAGTGC 60.003 52.381 0.00 0.00 37.48 4.40
224 257 4.692155 GCAGCCAAATAGTGCTTGAATTTT 59.308 37.500 0.00 0.00 35.12 1.82
225 258 5.179929 GCAGCCAAATAGTGCTTGAATTTTT 59.820 36.000 0.00 0.00 35.12 1.94
259 292 8.498054 TTTTTGCAAATGAAATAGTGGTTGAA 57.502 26.923 13.65 0.00 0.00 2.69
260 293 8.674263 TTTTGCAAATGAAATAGTGGTTGAAT 57.326 26.923 13.65 0.00 0.00 2.57
261 294 8.674263 TTTGCAAATGAAATAGTGGTTGAATT 57.326 26.923 8.05 0.00 0.00 2.17
262 295 8.674263 TTGCAAATGAAATAGTGGTTGAATTT 57.326 26.923 0.00 0.00 0.00 1.82
263 296 8.674263 TGCAAATGAAATAGTGGTTGAATTTT 57.326 26.923 0.00 0.00 0.00 1.82
264 297 9.118300 TGCAAATGAAATAGTGGTTGAATTTTT 57.882 25.926 0.00 0.00 0.00 1.94
311 344 2.356695 ACAAGGAACTAAGCGCGTTTTT 59.643 40.909 14.84 2.44 38.49 1.94
364 400 5.744345 AGAATAAGAGCACGTAGTCGATTTG 59.256 40.000 0.00 0.00 41.61 2.32
365 401 3.570926 AAGAGCACGTAGTCGATTTGA 57.429 42.857 0.00 0.00 41.61 2.69
412 452 5.138125 TCTTTCAAATTCATTGTGGAGGC 57.862 39.130 0.00 0.00 40.11 4.70
426 466 1.915769 GAGGCAGGGTGTCTCCAGT 60.916 63.158 0.00 0.00 42.99 4.00
441 481 4.335647 AGTTGGAGGCTGCACGGG 62.336 66.667 8.71 0.00 0.00 5.28
489 529 2.687935 TGCACTCCACCACTTCTTTTTC 59.312 45.455 0.00 0.00 0.00 2.29
490 530 2.034685 GCACTCCACCACTTCTTTTTCC 59.965 50.000 0.00 0.00 0.00 3.13
491 531 3.555966 CACTCCACCACTTCTTTTTCCT 58.444 45.455 0.00 0.00 0.00 3.36
492 532 4.714632 CACTCCACCACTTCTTTTTCCTA 58.285 43.478 0.00 0.00 0.00 2.94
493 533 5.130350 CACTCCACCACTTCTTTTTCCTAA 58.870 41.667 0.00 0.00 0.00 2.69
494 534 5.008712 CACTCCACCACTTCTTTTTCCTAAC 59.991 44.000 0.00 0.00 0.00 2.34
495 535 5.104067 ACTCCACCACTTCTTTTTCCTAACT 60.104 40.000 0.00 0.00 0.00 2.24
496 536 5.762279 TCCACCACTTCTTTTTCCTAACTT 58.238 37.500 0.00 0.00 0.00 2.66
497 537 6.192044 TCCACCACTTCTTTTTCCTAACTTT 58.808 36.000 0.00 0.00 0.00 2.66
498 538 6.096282 TCCACCACTTCTTTTTCCTAACTTTG 59.904 38.462 0.00 0.00 0.00 2.77
499 539 6.096282 CCACCACTTCTTTTTCCTAACTTTGA 59.904 38.462 0.00 0.00 0.00 2.69
500 540 6.972901 CACCACTTCTTTTTCCTAACTTTGAC 59.027 38.462 0.00 0.00 0.00 3.18
501 541 6.096423 ACCACTTCTTTTTCCTAACTTTGACC 59.904 38.462 0.00 0.00 0.00 4.02
502 542 6.461092 CCACTTCTTTTTCCTAACTTTGACCC 60.461 42.308 0.00 0.00 0.00 4.46
503 543 5.298527 ACTTCTTTTTCCTAACTTTGACCCG 59.701 40.000 0.00 0.00 0.00 5.28
504 544 5.038651 TCTTTTTCCTAACTTTGACCCGA 57.961 39.130 0.00 0.00 0.00 5.14
505 545 4.818005 TCTTTTTCCTAACTTTGACCCGAC 59.182 41.667 0.00 0.00 0.00 4.79
506 546 3.842007 TTTCCTAACTTTGACCCGACA 57.158 42.857 0.00 0.00 0.00 4.35
507 547 4.360951 TTTCCTAACTTTGACCCGACAT 57.639 40.909 0.00 0.00 0.00 3.06
508 548 3.328382 TCCTAACTTTGACCCGACATG 57.672 47.619 0.00 0.00 0.00 3.21
509 549 2.027561 TCCTAACTTTGACCCGACATGG 60.028 50.000 0.00 0.00 37.55 3.66
510 550 1.737793 CTAACTTTGACCCGACATGGC 59.262 52.381 0.00 0.00 35.87 4.40
511 551 0.179004 AACTTTGACCCGACATGGCA 60.179 50.000 0.00 0.00 35.87 4.92
512 552 0.038166 ACTTTGACCCGACATGGCAT 59.962 50.000 0.00 0.00 35.87 4.40
513 553 1.176527 CTTTGACCCGACATGGCATT 58.823 50.000 0.00 0.00 35.87 3.56
514 554 1.545582 CTTTGACCCGACATGGCATTT 59.454 47.619 0.00 0.00 35.87 2.32
515 555 1.173043 TTGACCCGACATGGCATTTC 58.827 50.000 0.00 0.00 35.87 2.17
516 556 0.327924 TGACCCGACATGGCATTTCT 59.672 50.000 11.53 0.00 35.87 2.52
517 557 1.271871 TGACCCGACATGGCATTTCTT 60.272 47.619 11.53 0.00 35.87 2.52
518 558 1.818674 GACCCGACATGGCATTTCTTT 59.181 47.619 11.53 0.00 35.87 2.52
519 559 2.231235 GACCCGACATGGCATTTCTTTT 59.769 45.455 11.53 0.00 35.87 2.27
520 560 2.231235 ACCCGACATGGCATTTCTTTTC 59.769 45.455 11.53 0.00 35.87 2.29
521 561 2.417243 CCCGACATGGCATTTCTTTTCC 60.417 50.000 11.53 0.00 35.87 3.13
522 562 2.417243 CCGACATGGCATTTCTTTTCCC 60.417 50.000 11.53 0.00 0.00 3.97
523 563 2.731968 CGACATGGCATTTCTTTTCCCG 60.732 50.000 11.53 0.00 0.00 5.14
524 564 1.066929 ACATGGCATTTCTTTTCCCGC 60.067 47.619 0.00 0.00 0.00 6.13
525 565 1.067000 CATGGCATTTCTTTTCCCGCA 60.067 47.619 0.00 0.00 0.00 5.69
526 566 1.043816 TGGCATTTCTTTTCCCGCAA 58.956 45.000 0.00 0.00 0.00 4.85
527 567 1.414181 TGGCATTTCTTTTCCCGCAAA 59.586 42.857 0.00 0.00 0.00 3.68
528 568 2.158900 TGGCATTTCTTTTCCCGCAAAA 60.159 40.909 0.00 0.00 32.77 2.44
529 569 2.875317 GGCATTTCTTTTCCCGCAAAAA 59.125 40.909 0.00 0.00 33.40 1.94
551 591 1.766494 TGGCTGCGAAATGATTCCAT 58.234 45.000 0.00 0.00 31.52 3.41
555 595 4.341806 TGGCTGCGAAATGATTCCATAAAT 59.658 37.500 0.00 0.00 31.59 1.40
597 637 7.830940 AAAAATTGCTGCGAAATGATTATCA 57.169 28.000 0.00 0.00 0.00 2.15
598 638 6.817270 AAATTGCTGCGAAATGATTATCAC 57.183 33.333 0.00 0.00 0.00 3.06
599 639 3.590720 TGCTGCGAAATGATTATCACG 57.409 42.857 0.00 0.00 0.00 4.35
602 642 3.604772 GCTGCGAAATGATTATCACGACC 60.605 47.826 7.69 0.00 0.00 4.79
603 643 2.869801 TGCGAAATGATTATCACGACCC 59.130 45.455 7.69 0.00 0.00 4.46
604 644 3.131396 GCGAAATGATTATCACGACCCT 58.869 45.455 7.69 0.00 0.00 4.34
605 645 3.560068 GCGAAATGATTATCACGACCCTT 59.440 43.478 7.69 0.00 0.00 3.95
606 646 4.552767 GCGAAATGATTATCACGACCCTTG 60.553 45.833 7.69 0.00 0.00 3.61
607 647 4.808895 CGAAATGATTATCACGACCCTTGA 59.191 41.667 0.00 0.00 0.00 3.02
608 648 5.466728 CGAAATGATTATCACGACCCTTGAT 59.533 40.000 0.00 0.00 37.47 2.57
609 649 6.346919 CGAAATGATTATCACGACCCTTGATC 60.347 42.308 0.00 0.00 35.31 2.92
610 650 5.815233 ATGATTATCACGACCCTTGATCT 57.185 39.130 0.00 0.00 35.31 2.75
611 651 5.614324 TGATTATCACGACCCTTGATCTT 57.386 39.130 0.00 0.00 35.31 2.40
612 652 5.989477 TGATTATCACGACCCTTGATCTTT 58.011 37.500 0.00 0.00 35.31 2.52
613 653 5.817296 TGATTATCACGACCCTTGATCTTTG 59.183 40.000 0.00 0.00 35.31 2.77
614 654 3.981071 ATCACGACCCTTGATCTTTGA 57.019 42.857 0.00 0.00 0.00 2.69
615 655 3.762407 TCACGACCCTTGATCTTTGAA 57.238 42.857 0.00 0.00 0.00 2.69
618 658 4.515191 TCACGACCCTTGATCTTTGAAAAG 59.485 41.667 0.00 0.00 37.36 2.27
638 711 9.958180 TGAAAAGAAAATGGAGTGAGTATATGA 57.042 29.630 0.00 0.00 0.00 2.15
687 760 0.179023 AAAAGGCGGTTCCCAACGTA 60.179 50.000 0.00 0.00 34.51 3.57
688 761 0.886043 AAAGGCGGTTCCCAACGTAC 60.886 55.000 0.00 0.00 34.51 3.67
689 762 3.113979 GGCGGTTCCCAACGTACG 61.114 66.667 15.01 15.01 0.00 3.67
690 763 2.356194 GCGGTTCCCAACGTACGT 60.356 61.111 16.72 16.72 0.00 3.57
691 764 2.660612 GCGGTTCCCAACGTACGTG 61.661 63.158 23.57 15.40 0.00 4.49
692 765 2.660612 CGGTTCCCAACGTACGTGC 61.661 63.158 23.57 8.07 0.00 5.34
723 796 1.803519 GCGCTGGAGACTTGACTCG 60.804 63.158 0.00 0.00 37.74 4.18
798 894 1.008079 CGGCCCGGTAGATAACGAC 60.008 63.158 0.00 0.00 0.00 4.34
799 895 1.008079 GGCCCGGTAGATAACGACG 60.008 63.158 0.00 0.00 0.00 5.12
835 947 0.984995 AGGAGGAAACCCTACTGTGC 59.015 55.000 0.00 0.00 43.43 4.57
836 948 0.984995 GGAGGAAACCCTACTGTGCT 59.015 55.000 0.00 0.00 33.25 4.40
843 955 3.629142 AACCCTACTGTGCTACAATCC 57.371 47.619 0.00 0.00 0.00 3.01
920 1032 4.603535 GCCCACAGCCCACCAGTT 62.604 66.667 0.00 0.00 34.35 3.16
928 1040 1.600916 GCCCACCAGTTCAGTCCAC 60.601 63.158 0.00 0.00 0.00 4.02
1156 1271 2.072487 GGCTGCCTCCCCTACATCA 61.072 63.158 12.43 0.00 0.00 3.07
1376 1499 2.027385 GCCATCTTCCCATCTTGTTCC 58.973 52.381 0.00 0.00 0.00 3.62
1381 1509 3.873910 TCTTCCCATCTTGTTCCGATTC 58.126 45.455 0.00 0.00 0.00 2.52
1413 1541 2.673368 GTGTCGATTTGTGATCTGTCCC 59.327 50.000 0.00 0.00 0.00 4.46
1416 1544 1.405526 CGATTTGTGATCTGTCCCCGT 60.406 52.381 0.00 0.00 0.00 5.28
1458 1590 0.320771 ATGCGGTGTTGGTCTGACTC 60.321 55.000 7.85 0.00 0.00 3.36
1459 1591 1.069090 GCGGTGTTGGTCTGACTCA 59.931 57.895 7.85 1.44 0.00 3.41
1600 1734 3.007506 TCCTGTAGATCCGTGCAGAAAAA 59.992 43.478 2.21 0.00 0.00 1.94
1798 2094 2.111384 GGACACCTCTGGCATCTAGAA 58.889 52.381 0.00 0.00 0.00 2.10
1800 2096 3.135530 GGACACCTCTGGCATCTAGAATT 59.864 47.826 0.00 0.00 0.00 2.17
1941 2262 8.072567 GCACATAGCAGACCTTCAAAATATTAG 58.927 37.037 0.00 0.00 44.79 1.73
1948 2269 8.624776 GCAGACCTTCAAAATATTAGCTTGTAT 58.375 33.333 0.00 0.00 0.00 2.29
2007 2328 1.006337 TGGCGGTGCTTTTCAATGC 60.006 52.632 0.00 0.00 0.00 3.56
2054 2380 1.276138 AGATGTTGCACTGGATCACGA 59.724 47.619 0.00 0.00 0.00 4.35
2058 2384 1.195448 GTTGCACTGGATCACGAACAG 59.805 52.381 0.00 0.00 38.19 3.16
2063 2389 3.329386 CACTGGATCACGAACAGAACAT 58.671 45.455 8.54 0.00 36.17 2.71
2085 2411 8.876275 ACATAATTGACAAACCATTATGATGC 57.124 30.769 19.16 0.00 38.12 3.91
2110 2443 2.415776 CAACCACCAAATGATGCCAAC 58.584 47.619 0.00 0.00 0.00 3.77
2112 2445 2.328319 ACCACCAAATGATGCCAACTT 58.672 42.857 0.00 0.00 0.00 2.66
2139 2472 6.433766 GCCTTCAATTAGTGATAGAATGTGC 58.566 40.000 0.00 0.00 35.70 4.57
2140 2473 6.514048 GCCTTCAATTAGTGATAGAATGTGCC 60.514 42.308 0.00 0.00 35.70 5.01
2143 2476 5.528690 TCAATTAGTGATAGAATGTGCCAGC 59.471 40.000 0.00 0.00 0.00 4.85
2155 2488 1.814394 TGTGCCAGCTGCTAAAAGATG 59.186 47.619 8.66 0.00 42.00 2.90
2168 2506 6.598525 TGCTAAAAGATGTGATTTGTGTACG 58.401 36.000 0.00 0.00 0.00 3.67
2184 2522 5.471257 TGTGTACGTGCATCAGTTTGTATA 58.529 37.500 10.21 0.00 0.00 1.47
2185 2523 6.103330 TGTGTACGTGCATCAGTTTGTATAT 58.897 36.000 10.21 0.00 0.00 0.86
2196 2534 9.884465 GCATCAGTTTGTATATTAAGTTCATCC 57.116 33.333 0.00 0.00 0.00 3.51
2220 2558 2.422597 TGGATTGTTCATCGGTGTGAC 58.577 47.619 0.00 0.00 31.73 3.67
2221 2559 2.224402 TGGATTGTTCATCGGTGTGACA 60.224 45.455 0.00 0.00 31.73 3.58
2222 2560 2.159627 GGATTGTTCATCGGTGTGACAC 59.840 50.000 7.29 7.29 31.73 3.67
2223 2561 1.213491 TTGTTCATCGGTGTGACACG 58.787 50.000 9.90 5.48 34.83 4.49
2224 2562 0.386113 TGTTCATCGGTGTGACACGA 59.614 50.000 9.90 10.76 43.85 4.35
2225 2563 1.202428 TGTTCATCGGTGTGACACGAA 60.202 47.619 9.90 4.73 42.88 3.85
2235 2573 2.738846 GTGTGACACGAAAGCTGATGAT 59.261 45.455 0.00 0.00 0.00 2.45
2236 2574 3.926527 GTGTGACACGAAAGCTGATGATA 59.073 43.478 0.00 0.00 0.00 2.15
2239 2577 5.046529 GTGACACGAAAGCTGATGATAGAT 58.953 41.667 0.00 0.00 0.00 1.98
2240 2578 5.521735 GTGACACGAAAGCTGATGATAGATT 59.478 40.000 0.00 0.00 0.00 2.40
2241 2579 6.697455 GTGACACGAAAGCTGATGATAGATTA 59.303 38.462 0.00 0.00 0.00 1.75
2242 2580 7.383572 GTGACACGAAAGCTGATGATAGATTAT 59.616 37.037 0.00 0.00 0.00 1.28
2243 2581 8.576442 TGACACGAAAGCTGATGATAGATTATA 58.424 33.333 0.00 0.00 0.00 0.98
2244 2582 9.579768 GACACGAAAGCTGATGATAGATTATAT 57.420 33.333 0.00 0.00 0.00 0.86
2245 2583 9.363763 ACACGAAAGCTGATGATAGATTATATG 57.636 33.333 0.00 0.00 0.00 1.78
2246 2584 9.363763 CACGAAAGCTGATGATAGATTATATGT 57.636 33.333 0.00 0.00 0.00 2.29
2247 2585 9.935241 ACGAAAGCTGATGATAGATTATATGTT 57.065 29.630 0.00 0.00 0.00 2.71
2267 2605 4.709397 TGTTGTGATTGAGAAAAACCACCT 59.291 37.500 0.00 0.00 0.00 4.00
2268 2606 4.916983 TGTGATTGAGAAAAACCACCTG 57.083 40.909 0.00 0.00 0.00 4.00
2269 2607 4.277476 TGTGATTGAGAAAAACCACCTGT 58.723 39.130 0.00 0.00 0.00 4.00
2284 2624 4.282449 ACCACCTGTTTTACTTTATTGCCC 59.718 41.667 0.00 0.00 0.00 5.36
2310 2654 6.089249 AGTCCTGAATTGAAATGTTGGTTC 57.911 37.500 0.00 0.00 0.00 3.62
2321 2665 5.596361 TGAAATGTTGGTTCCTGCTTTTCTA 59.404 36.000 16.26 7.98 0.00 2.10
2324 2668 3.751175 TGTTGGTTCCTGCTTTTCTATCG 59.249 43.478 0.00 0.00 0.00 2.92
2335 2679 6.314896 CCTGCTTTTCTATCGTCTGAATCTTT 59.685 38.462 0.00 0.00 0.00 2.52
2336 2680 7.148340 CCTGCTTTTCTATCGTCTGAATCTTTT 60.148 37.037 0.00 0.00 0.00 2.27
2337 2681 8.771920 TGCTTTTCTATCGTCTGAATCTTTTA 57.228 30.769 0.00 0.00 0.00 1.52
2338 2682 8.656849 TGCTTTTCTATCGTCTGAATCTTTTAC 58.343 33.333 0.00 0.00 0.00 2.01
2339 2683 8.874816 GCTTTTCTATCGTCTGAATCTTTTACT 58.125 33.333 0.00 0.00 0.00 2.24
2342 2686 8.928270 TTCTATCGTCTGAATCTTTTACTTCC 57.072 34.615 0.00 0.00 0.00 3.46
2343 2687 8.063200 TCTATCGTCTGAATCTTTTACTTCCA 57.937 34.615 0.00 0.00 0.00 3.53
2351 2695 9.312904 TCTGAATCTTTTACTTCCATCCATTTT 57.687 29.630 0.00 0.00 0.00 1.82
2411 2755 2.226330 CAACTTCCGGATCAACACCAA 58.774 47.619 4.15 0.00 0.00 3.67
2452 2796 1.447838 GAAATCGGCAGCGACCAGA 60.448 57.895 0.00 0.00 0.00 3.86
2474 2818 4.680237 CTGTCTCGGCGGCAACCA 62.680 66.667 10.53 0.00 0.00 3.67
2530 2874 9.403583 CTTTCTTACTACTACCTCTGAAGATCT 57.596 37.037 0.00 0.00 0.00 2.75
2531 2875 8.740123 TTCTTACTACTACCTCTGAAGATCTG 57.260 38.462 0.00 0.00 0.00 2.90
2533 2877 4.211920 ACTACTACCTCTGAAGATCTGCC 58.788 47.826 0.00 0.00 0.00 4.85
2577 2921 3.018856 CTGTGATGTGTATGGGCATTGT 58.981 45.455 0.00 0.00 0.00 2.71
2613 2959 5.463724 GTGACTACTTTGTGGAGAGAACTTG 59.536 44.000 0.00 0.00 0.00 3.16
2725 3071 7.425595 GTCTTCGGAATAAAGTTGATAAAAGCG 59.574 37.037 0.00 0.00 0.00 4.68
2817 3163 7.554835 GTGTTAAATGGGTATACAATGTGGAGA 59.445 37.037 5.01 0.00 0.00 3.71
2830 3177 1.558294 TGTGGAGAAGAGCAGATGCAT 59.442 47.619 0.00 0.00 45.16 3.96
2833 3180 2.211806 GGAGAAGAGCAGATGCATGAC 58.788 52.381 2.46 0.00 45.16 3.06
2849 3380 3.338249 CATGACGGAAACCTGATCAGTT 58.662 45.455 21.11 10.00 0.00 3.16
2856 3387 1.813513 AACCTGATCAGTTTCTGCCG 58.186 50.000 21.11 5.94 0.00 5.69
2878 3412 4.269363 CGTTTCCTTGTTATATCCACGGAC 59.731 45.833 1.33 0.00 30.75 4.79
2911 3445 2.884320 TGTGCCAGACCTAGTGAAGTA 58.116 47.619 0.00 0.00 0.00 2.24
2915 3449 5.061179 GTGCCAGACCTAGTGAAGTAAAAA 58.939 41.667 0.00 0.00 0.00 1.94
2974 3582 2.916716 CCATGAACGGCAAATTCGAAAG 59.083 45.455 0.00 0.00 0.00 2.62
3025 3633 0.171903 AAATGCTTGAGTGCGCATCC 59.828 50.000 15.91 9.42 45.41 3.51
3052 3660 2.293122 TGGCCTTTTCTTGACGATGTTG 59.707 45.455 3.32 0.00 0.00 3.33
3142 5838 3.204306 TGATGCAGAAGGATCATCCAC 57.796 47.619 6.42 0.00 46.03 4.02
3146 5842 1.964552 CAGAAGGATCATCCACAGCC 58.035 55.000 6.42 0.00 39.61 4.85
3147 5843 1.211212 CAGAAGGATCATCCACAGCCA 59.789 52.381 6.42 0.00 39.61 4.75
3148 5844 2.133520 AGAAGGATCATCCACAGCCAT 58.866 47.619 6.42 0.00 39.61 4.40
3149 5845 2.106166 AGAAGGATCATCCACAGCCATC 59.894 50.000 6.42 0.00 39.61 3.51
3150 5846 1.817087 AGGATCATCCACAGCCATCT 58.183 50.000 6.42 0.00 39.61 2.90
3151 5847 2.981921 AGGATCATCCACAGCCATCTA 58.018 47.619 6.42 0.00 39.61 1.98
3152 5848 3.528976 AGGATCATCCACAGCCATCTAT 58.471 45.455 6.42 0.00 39.61 1.98
3153 5849 3.518705 AGGATCATCCACAGCCATCTATC 59.481 47.826 6.42 0.00 39.61 2.08
3154 5850 3.262660 GGATCATCCACAGCCATCTATCA 59.737 47.826 0.00 0.00 36.28 2.15
3155 5851 4.080469 GGATCATCCACAGCCATCTATCAT 60.080 45.833 0.00 0.00 36.28 2.45
3156 5852 4.548451 TCATCCACAGCCATCTATCATC 57.452 45.455 0.00 0.00 0.00 2.92
3157 5853 3.262660 TCATCCACAGCCATCTATCATCC 59.737 47.826 0.00 0.00 0.00 3.51
3158 5854 2.981921 TCCACAGCCATCTATCATCCT 58.018 47.619 0.00 0.00 0.00 3.24
3159 5855 2.902486 TCCACAGCCATCTATCATCCTC 59.098 50.000 0.00 0.00 0.00 3.71
3160 5856 2.353505 CCACAGCCATCTATCATCCTCG 60.354 54.545 0.00 0.00 0.00 4.63
3161 5857 2.560105 CACAGCCATCTATCATCCTCGA 59.440 50.000 0.00 0.00 0.00 4.04
3162 5858 2.560542 ACAGCCATCTATCATCCTCGAC 59.439 50.000 0.00 0.00 0.00 4.20
3163 5859 1.815613 AGCCATCTATCATCCTCGACG 59.184 52.381 0.00 0.00 0.00 5.12
3164 5860 1.542030 GCCATCTATCATCCTCGACGT 59.458 52.381 0.00 0.00 0.00 4.34
3165 5861 2.029828 GCCATCTATCATCCTCGACGTT 60.030 50.000 0.00 0.00 0.00 3.99
3166 5862 3.569548 CCATCTATCATCCTCGACGTTG 58.430 50.000 0.00 0.00 0.00 4.10
3167 5863 3.569548 CATCTATCATCCTCGACGTTGG 58.430 50.000 2.20 0.00 0.00 3.77
3168 5864 1.337071 TCTATCATCCTCGACGTTGGC 59.663 52.381 2.20 0.00 0.00 4.52
3169 5865 0.030235 TATCATCCTCGACGTTGGCG 59.970 55.000 2.20 0.00 44.93 5.69
3170 5866 2.629050 ATCATCCTCGACGTTGGCGG 62.629 60.000 2.20 4.40 43.45 6.13
3171 5867 4.814294 ATCCTCGACGTTGGCGGC 62.814 66.667 0.00 0.00 44.04 6.53
3217 5946 3.814005 AAGGTTAGGGTGTGCTATACG 57.186 47.619 0.00 0.00 0.00 3.06
3218 7182 2.037144 AGGTTAGGGTGTGCTATACGG 58.963 52.381 0.00 0.00 0.00 4.02
3219 7183 1.758862 GGTTAGGGTGTGCTATACGGT 59.241 52.381 0.00 0.00 0.00 4.83
3225 7189 0.174162 GTGTGCTATACGGTTCCGGT 59.826 55.000 15.66 6.44 0.00 5.28
3230 7194 1.598924 GCTATACGGTTCCGGTTCGAG 60.599 57.143 15.66 6.41 0.00 4.04
3258 7223 5.392811 GCCTGATCAAACTGAGAATTCCTTG 60.393 44.000 0.65 0.00 0.00 3.61
3298 7264 8.035165 TGATTAGATCGAATCGGAAACAAAAA 57.965 30.769 19.61 0.44 38.46 1.94
3348 7314 2.096417 CCGTTGTTTAAGTTCCGCTCAG 60.096 50.000 0.00 0.00 0.00 3.35
3354 7320 1.195115 TAAGTTCCGCTCAGAGCCAT 58.805 50.000 17.16 0.00 38.18 4.40
3356 7322 1.418334 AGTTCCGCTCAGAGCCATAT 58.582 50.000 17.16 0.00 38.18 1.78
3357 7323 2.598565 AGTTCCGCTCAGAGCCATATA 58.401 47.619 17.16 0.00 38.18 0.86
3358 7324 3.169099 AGTTCCGCTCAGAGCCATATAT 58.831 45.455 17.16 0.00 38.18 0.86
3359 7325 4.344978 AGTTCCGCTCAGAGCCATATATA 58.655 43.478 17.16 0.00 38.18 0.86
3360 7326 4.772624 AGTTCCGCTCAGAGCCATATATAA 59.227 41.667 17.16 0.00 38.18 0.98
3382 7355 5.528043 ACTGATTCATACGCTCTCATCTT 57.472 39.130 0.00 0.00 0.00 2.40
3392 7365 1.605202 GCTCTCATCTTCTGCGGATCC 60.605 57.143 0.00 0.00 0.00 3.36
3421 7394 3.125376 GCCATGGCGGGGAAGAGAT 62.125 63.158 23.48 0.00 34.06 2.75
3423 7396 1.528824 CATGGCGGGGAAGAGATGT 59.471 57.895 0.00 0.00 0.00 3.06
3444 7417 2.833582 GATCTCCCCGCGTCTCCA 60.834 66.667 4.92 0.00 0.00 3.86
3447 7420 4.135153 CTCCCCGCGTCTCCACAG 62.135 72.222 4.92 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.807538 GCTGTGATGTGCCAGCCG 61.808 66.667 0.24 0.00 46.55 5.52
88 96 0.473755 ATGGCATTCCGCAGTCCATA 59.526 50.000 0.00 0.00 45.17 2.74
95 103 2.836793 CGCATGATGGCATTCCGCA 61.837 57.895 0.00 0.00 45.17 5.69
104 112 1.683943 ATCTTTGGTCCGCATGATGG 58.316 50.000 0.00 0.00 0.00 3.51
107 115 3.904800 TCTTATCTTTGGTCCGCATGA 57.095 42.857 0.00 0.00 0.00 3.07
163 195 6.758806 TCTTTTTAAGTACTTCTCCACCCT 57.241 37.500 12.39 0.00 0.00 4.34
166 198 8.606602 TCGTTTTCTTTTTAAGTACTTCTCCAC 58.393 33.333 12.39 0.00 0.00 4.02
170 202 8.938906 TGTGTCGTTTTCTTTTTAAGTACTTCT 58.061 29.630 12.39 0.00 0.00 2.85
174 206 8.184524 CGATGTGTCGTTTTCTTTTTAAGTAC 57.815 34.615 0.00 0.00 42.78 2.73
234 267 8.498054 TTCAACCACTATTTCATTTGCAAAAA 57.502 26.923 17.19 6.60 0.00 1.94
235 268 8.674263 ATTCAACCACTATTTCATTTGCAAAA 57.326 26.923 17.19 0.00 0.00 2.44
236 269 8.674263 AATTCAACCACTATTTCATTTGCAAA 57.326 26.923 15.44 15.44 0.00 3.68
237 270 8.674263 AAATTCAACCACTATTTCATTTGCAA 57.326 26.923 0.00 0.00 0.00 4.08
238 271 8.674263 AAAATTCAACCACTATTTCATTTGCA 57.326 26.923 0.00 0.00 0.00 4.08
269 302 9.408648 CCTTGTAAATTCAACCACTATTATCCT 57.591 33.333 0.00 0.00 0.00 3.24
270 303 9.403583 TCCTTGTAAATTCAACCACTATTATCC 57.596 33.333 0.00 0.00 0.00 2.59
273 306 9.802039 AGTTCCTTGTAAATTCAACCACTATTA 57.198 29.630 0.00 0.00 0.00 0.98
274 307 8.706322 AGTTCCTTGTAAATTCAACCACTATT 57.294 30.769 0.00 0.00 0.00 1.73
275 308 9.802039 TTAGTTCCTTGTAAATTCAACCACTAT 57.198 29.630 0.00 0.00 0.00 2.12
276 309 9.280174 CTTAGTTCCTTGTAAATTCAACCACTA 57.720 33.333 0.00 0.00 0.00 2.74
277 310 7.255486 GCTTAGTTCCTTGTAAATTCAACCACT 60.255 37.037 0.00 0.00 0.00 4.00
278 311 6.861572 GCTTAGTTCCTTGTAAATTCAACCAC 59.138 38.462 0.00 0.00 0.00 4.16
279 312 6.293735 CGCTTAGTTCCTTGTAAATTCAACCA 60.294 38.462 0.00 0.00 0.00 3.67
280 313 6.084277 CGCTTAGTTCCTTGTAAATTCAACC 58.916 40.000 0.00 0.00 0.00 3.77
281 314 5.567915 GCGCTTAGTTCCTTGTAAATTCAAC 59.432 40.000 0.00 0.00 0.00 3.18
282 315 5.615984 CGCGCTTAGTTCCTTGTAAATTCAA 60.616 40.000 5.56 0.00 0.00 2.69
283 316 4.142988 CGCGCTTAGTTCCTTGTAAATTCA 60.143 41.667 5.56 0.00 0.00 2.57
284 317 4.142966 ACGCGCTTAGTTCCTTGTAAATTC 60.143 41.667 5.73 0.00 0.00 2.17
285 318 3.749609 ACGCGCTTAGTTCCTTGTAAATT 59.250 39.130 5.73 0.00 0.00 1.82
286 319 3.332034 ACGCGCTTAGTTCCTTGTAAAT 58.668 40.909 5.73 0.00 0.00 1.40
287 320 2.758009 ACGCGCTTAGTTCCTTGTAAA 58.242 42.857 5.73 0.00 0.00 2.01
288 321 2.443887 ACGCGCTTAGTTCCTTGTAA 57.556 45.000 5.73 0.00 0.00 2.41
289 322 2.443887 AACGCGCTTAGTTCCTTGTA 57.556 45.000 5.73 0.00 0.00 2.41
290 323 1.589803 AAACGCGCTTAGTTCCTTGT 58.410 45.000 5.73 0.00 0.00 3.16
291 324 2.681152 AAAACGCGCTTAGTTCCTTG 57.319 45.000 5.73 0.00 0.00 3.61
292 325 2.876550 AGAAAAACGCGCTTAGTTCCTT 59.123 40.909 5.73 0.00 0.00 3.36
364 400 9.665264 AAAAGAAACAAATACGACAAGATCTTC 57.335 29.630 4.57 0.00 0.00 2.87
365 401 9.665264 GAAAAGAAACAAATACGACAAGATCTT 57.335 29.630 0.88 0.88 0.00 2.40
405 445 2.665603 GAGACACCCTGCCTCCAC 59.334 66.667 0.00 0.00 0.00 4.02
412 452 2.452116 TCCAACTGGAGACACCCTG 58.548 57.895 0.00 0.00 39.78 4.45
424 464 4.335647 CCCGTGCAGCCTCCAACT 62.336 66.667 0.00 0.00 0.00 3.16
426 466 4.641645 CACCCGTGCAGCCTCCAA 62.642 66.667 0.00 0.00 0.00 3.53
445 485 2.045045 ATGACATGGTGGCCACGG 60.045 61.111 29.08 22.13 35.80 4.94
447 487 0.322816 AGACATGACATGGTGGCCAC 60.323 55.000 28.57 28.57 35.80 5.01
449 489 0.322816 ACAGACATGACATGGTGGCC 60.323 55.000 19.39 0.00 33.60 5.36
450 490 0.806868 CACAGACATGACATGGTGGC 59.193 55.000 19.39 6.14 33.60 5.01
451 491 0.806868 GCACAGACATGACATGGTGG 59.193 55.000 19.39 10.04 33.60 4.61
452 492 1.198408 GTGCACAGACATGACATGGTG 59.802 52.381 19.39 16.98 33.60 4.17
453 493 1.072806 AGTGCACAGACATGACATGGT 59.927 47.619 21.04 5.28 33.60 3.55
454 494 1.736126 GAGTGCACAGACATGACATGG 59.264 52.381 21.04 4.65 33.60 3.66
489 529 2.356135 CCATGTCGGGTCAAAGTTAGG 58.644 52.381 0.00 0.00 0.00 2.69
490 530 1.737793 GCCATGTCGGGTCAAAGTTAG 59.262 52.381 0.00 0.00 34.06 2.34
491 531 1.072489 TGCCATGTCGGGTCAAAGTTA 59.928 47.619 0.00 0.00 34.06 2.24
492 532 0.179004 TGCCATGTCGGGTCAAAGTT 60.179 50.000 0.00 0.00 34.06 2.66
493 533 0.038166 ATGCCATGTCGGGTCAAAGT 59.962 50.000 0.00 0.00 34.06 2.66
494 534 1.176527 AATGCCATGTCGGGTCAAAG 58.823 50.000 0.00 0.00 34.06 2.77
495 535 1.543802 GAAATGCCATGTCGGGTCAAA 59.456 47.619 0.00 0.00 34.06 2.69
496 536 1.173043 GAAATGCCATGTCGGGTCAA 58.827 50.000 0.00 0.00 34.06 3.18
497 537 0.327924 AGAAATGCCATGTCGGGTCA 59.672 50.000 0.00 0.00 34.06 4.02
498 538 1.463674 AAGAAATGCCATGTCGGGTC 58.536 50.000 0.00 0.00 34.06 4.46
499 539 1.923356 AAAGAAATGCCATGTCGGGT 58.077 45.000 0.00 0.00 34.06 5.28
500 540 2.417243 GGAAAAGAAATGCCATGTCGGG 60.417 50.000 0.00 0.00 34.06 5.14
501 541 2.417243 GGGAAAAGAAATGCCATGTCGG 60.417 50.000 0.00 0.00 38.11 4.79
502 542 2.731968 CGGGAAAAGAAATGCCATGTCG 60.732 50.000 0.00 0.00 0.00 4.35
503 543 2.879826 CGGGAAAAGAAATGCCATGTC 58.120 47.619 0.00 0.00 0.00 3.06
504 544 1.066929 GCGGGAAAAGAAATGCCATGT 60.067 47.619 0.00 0.00 0.00 3.21
505 545 1.067000 TGCGGGAAAAGAAATGCCATG 60.067 47.619 0.00 0.00 0.00 3.66
506 546 1.265236 TGCGGGAAAAGAAATGCCAT 58.735 45.000 0.00 0.00 0.00 4.40
507 547 1.043816 TTGCGGGAAAAGAAATGCCA 58.956 45.000 0.00 0.00 0.00 4.92
508 548 2.162319 TTTGCGGGAAAAGAAATGCC 57.838 45.000 0.00 0.00 0.00 4.40
527 567 3.934579 GGAATCATTTCGCAGCCATTTTT 59.065 39.130 0.00 0.00 32.28 1.94
528 568 3.055963 TGGAATCATTTCGCAGCCATTTT 60.056 39.130 0.00 0.00 32.28 1.82
529 569 2.496871 TGGAATCATTTCGCAGCCATTT 59.503 40.909 0.00 0.00 32.28 2.32
530 570 2.101783 TGGAATCATTTCGCAGCCATT 58.898 42.857 0.00 0.00 32.28 3.16
531 571 1.766494 TGGAATCATTTCGCAGCCAT 58.234 45.000 0.00 0.00 32.28 4.40
532 572 1.766494 ATGGAATCATTTCGCAGCCA 58.234 45.000 0.00 0.00 32.28 4.75
533 573 3.988379 TTATGGAATCATTTCGCAGCC 57.012 42.857 0.00 0.00 34.96 4.85
534 574 5.817616 CATTTATGGAATCATTTCGCAGC 57.182 39.130 0.00 0.00 34.96 5.25
551 591 1.558756 CAGCATTTTGGGGCCCATTTA 59.441 47.619 29.34 15.26 31.53 1.40
555 595 0.765903 TTTCAGCATTTTGGGGCCCA 60.766 50.000 24.76 24.76 0.00 5.36
577 617 4.273235 TCGTGATAATCATTTCGCAGCAAT 59.727 37.500 0.00 0.00 0.00 3.56
578 618 3.620821 TCGTGATAATCATTTCGCAGCAA 59.379 39.130 0.00 0.00 0.00 3.91
579 619 3.001228 GTCGTGATAATCATTTCGCAGCA 59.999 43.478 0.00 0.00 0.00 4.41
580 620 3.535860 GTCGTGATAATCATTTCGCAGC 58.464 45.455 0.00 0.00 0.00 5.25
581 621 3.059597 GGGTCGTGATAATCATTTCGCAG 60.060 47.826 0.00 0.00 0.00 5.18
582 622 2.869801 GGGTCGTGATAATCATTTCGCA 59.130 45.455 0.00 0.00 0.00 5.10
583 623 3.131396 AGGGTCGTGATAATCATTTCGC 58.869 45.455 0.00 0.00 0.00 4.70
584 624 4.808895 TCAAGGGTCGTGATAATCATTTCG 59.191 41.667 0.00 0.00 0.00 3.46
585 625 6.708054 AGATCAAGGGTCGTGATAATCATTTC 59.292 38.462 0.00 0.00 35.84 2.17
586 626 6.595682 AGATCAAGGGTCGTGATAATCATTT 58.404 36.000 0.00 0.00 35.84 2.32
587 627 6.179906 AGATCAAGGGTCGTGATAATCATT 57.820 37.500 0.00 0.00 35.84 2.57
588 628 5.815233 AGATCAAGGGTCGTGATAATCAT 57.185 39.130 0.00 0.00 35.84 2.45
589 629 5.614324 AAGATCAAGGGTCGTGATAATCA 57.386 39.130 0.00 0.00 35.84 2.57
590 630 6.049149 TCAAAGATCAAGGGTCGTGATAATC 58.951 40.000 0.00 0.00 35.84 1.75
591 631 5.989477 TCAAAGATCAAGGGTCGTGATAAT 58.011 37.500 0.00 0.00 35.84 1.28
592 632 5.414789 TCAAAGATCAAGGGTCGTGATAA 57.585 39.130 0.00 0.00 35.84 1.75
594 634 3.981071 TCAAAGATCAAGGGTCGTGAT 57.019 42.857 0.00 0.00 38.44 3.06
596 636 4.515191 TCTTTTCAAAGATCAAGGGTCGTG 59.485 41.667 0.00 0.00 39.95 4.35
597 637 4.714632 TCTTTTCAAAGATCAAGGGTCGT 58.285 39.130 0.00 0.00 39.95 4.34
598 638 5.689383 TTCTTTTCAAAGATCAAGGGTCG 57.311 39.130 2.83 0.00 43.92 4.79
599 639 7.386025 CCATTTTCTTTTCAAAGATCAAGGGTC 59.614 37.037 12.90 0.00 43.92 4.46
602 642 8.146412 ACTCCATTTTCTTTTCAAAGATCAAGG 58.854 33.333 2.83 4.50 43.92 3.61
603 643 8.975439 CACTCCATTTTCTTTTCAAAGATCAAG 58.025 33.333 2.83 0.00 43.92 3.02
604 644 8.694540 TCACTCCATTTTCTTTTCAAAGATCAA 58.305 29.630 2.83 0.91 43.92 2.57
605 645 8.236585 TCACTCCATTTTCTTTTCAAAGATCA 57.763 30.769 2.83 0.00 43.92 2.92
606 646 8.355913 ACTCACTCCATTTTCTTTTCAAAGATC 58.644 33.333 2.83 0.00 43.92 2.75
607 647 8.242729 ACTCACTCCATTTTCTTTTCAAAGAT 57.757 30.769 2.83 0.00 43.92 2.40
608 648 7.645058 ACTCACTCCATTTTCTTTTCAAAGA 57.355 32.000 0.00 0.00 42.91 2.52
612 652 9.958180 TCATATACTCACTCCATTTTCTTTTCA 57.042 29.630 0.00 0.00 0.00 2.69
614 654 9.739276 TGTCATATACTCACTCCATTTTCTTTT 57.261 29.630 0.00 0.00 0.00 2.27
615 655 9.911788 ATGTCATATACTCACTCCATTTTCTTT 57.088 29.630 0.00 0.00 0.00 2.52
618 658 8.893219 TGATGTCATATACTCACTCCATTTTC 57.107 34.615 0.00 0.00 0.00 2.29
638 711 4.217550 CCTTGGAAACGGTAAACATGATGT 59.782 41.667 0.00 0.00 0.00 3.06
687 760 4.664677 GCGACTGGACTGGCACGT 62.665 66.667 0.00 0.00 0.00 4.49
748 821 1.909781 ACCGGAGAGCGGTTGGTTA 60.910 57.895 9.46 0.00 36.12 2.85
798 894 4.636435 GGTGGGTGGTGGTGACCG 62.636 72.222 0.00 0.00 46.62 4.79
799 895 3.491598 CTGGTGGGTGGTGGTGACC 62.492 68.421 0.00 0.00 43.48 4.02
834 946 0.462047 CGGTGAGGTGGGATTGTAGC 60.462 60.000 0.00 0.00 0.00 3.58
835 947 0.462047 GCGGTGAGGTGGGATTGTAG 60.462 60.000 0.00 0.00 0.00 2.74
836 948 1.600107 GCGGTGAGGTGGGATTGTA 59.400 57.895 0.00 0.00 0.00 2.41
920 1032 1.074850 TGGTGGTGGAGTGGACTGA 60.075 57.895 0.00 0.00 0.00 3.41
1376 1499 2.594654 CGACACGAGGAAAAGAGAATCG 59.405 50.000 0.00 0.00 42.67 3.34
1381 1509 3.741344 ACAAATCGACACGAGGAAAAGAG 59.259 43.478 0.00 0.00 39.91 2.85
1413 1541 1.377202 CCCCTCCATGAACACACGG 60.377 63.158 0.00 0.00 0.00 4.94
1416 1544 1.074775 GTGCCCCTCCATGAACACA 59.925 57.895 0.00 0.00 0.00 3.72
1458 1590 3.556775 CACTGCAGGACAACCAAAAATTG 59.443 43.478 19.93 0.00 38.94 2.32
1459 1591 3.450457 TCACTGCAGGACAACCAAAAATT 59.550 39.130 19.93 0.00 38.94 1.82
1529 1662 2.968574 ACTGCAAAGGAGAAGAGAGTGA 59.031 45.455 0.00 0.00 0.00 3.41
1531 1664 3.244387 GGAACTGCAAAGGAGAAGAGAGT 60.244 47.826 0.00 0.00 0.00 3.24
1798 2094 3.890756 TCACATGCAGACCACTGAAAAAT 59.109 39.130 0.00 0.00 46.03 1.82
1800 2096 2.929641 TCACATGCAGACCACTGAAAA 58.070 42.857 0.00 0.00 46.03 2.29
1847 2156 6.162777 TGTTTTTCTTTTCAAGTGGAGGTTG 58.837 36.000 0.00 0.00 0.00 3.77
1850 2159 6.476706 GTGATGTTTTTCTTTTCAAGTGGAGG 59.523 38.462 0.00 0.00 0.00 4.30
1900 2215 6.741109 TGCTATGTGCCAATTTCATTCTATG 58.259 36.000 0.00 0.00 42.00 2.23
1902 2217 6.038603 GTCTGCTATGTGCCAATTTCATTCTA 59.961 38.462 0.00 0.00 42.00 2.10
1941 2262 7.011482 AGGAATGTCTTCGATTACAATACAAGC 59.989 37.037 4.66 0.00 31.75 4.01
1954 2275 7.705325 GCAGTACTTTATTAGGAATGTCTTCGA 59.295 37.037 0.00 0.00 35.18 3.71
2007 2328 3.065371 GTCAGCCCTCAAAATTACGATGG 59.935 47.826 0.00 0.00 0.00 3.51
2025 2351 0.520404 GTGCAACATCTGGCTGTCAG 59.480 55.000 2.07 2.07 40.10 3.51
2063 2389 7.927092 CCATGCATCATAATGGTTTGTCAATTA 59.073 33.333 0.00 0.00 38.85 1.40
2085 2411 2.623535 CATCATTTGGTGGTTGCCATG 58.376 47.619 0.00 0.00 38.48 3.66
2110 2443 7.630242 TTCTATCACTAATTGAAGGCCAAAG 57.370 36.000 5.01 0.00 37.92 2.77
2112 2445 7.067372 CACATTCTATCACTAATTGAAGGCCAA 59.933 37.037 5.01 0.00 37.92 4.52
2139 2472 4.978083 AATCACATCTTTTAGCAGCTGG 57.022 40.909 17.12 0.00 0.00 4.85
2140 2473 5.571741 CACAAATCACATCTTTTAGCAGCTG 59.428 40.000 10.11 10.11 0.00 4.24
2143 2476 6.738200 CGTACACAAATCACATCTTTTAGCAG 59.262 38.462 0.00 0.00 0.00 4.24
2155 2488 3.186409 ACTGATGCACGTACACAAATCAC 59.814 43.478 0.00 0.00 0.00 3.06
2196 2534 3.064408 CACACCGATGAACAATCCATGAG 59.936 47.826 0.00 0.00 30.80 2.90
2200 2538 2.224402 TGTCACACCGATGAACAATCCA 60.224 45.455 0.00 0.00 30.80 3.41
2220 2558 9.363763 ACATATAATCTATCATCAGCTTTCGTG 57.636 33.333 0.00 0.00 0.00 4.35
2221 2559 9.935241 AACATATAATCTATCATCAGCTTTCGT 57.065 29.630 0.00 0.00 0.00 3.85
2239 2577 9.906660 GTGGTTTTTCTCAATCACAACATATAA 57.093 29.630 0.00 0.00 0.00 0.98
2240 2578 8.519526 GGTGGTTTTTCTCAATCACAACATATA 58.480 33.333 0.00 0.00 0.00 0.86
2241 2579 7.233348 AGGTGGTTTTTCTCAATCACAACATAT 59.767 33.333 0.00 0.00 0.00 1.78
2242 2580 6.549364 AGGTGGTTTTTCTCAATCACAACATA 59.451 34.615 0.00 0.00 0.00 2.29
2243 2581 5.363580 AGGTGGTTTTTCTCAATCACAACAT 59.636 36.000 0.00 0.00 0.00 2.71
2244 2582 4.709397 AGGTGGTTTTTCTCAATCACAACA 59.291 37.500 0.00 0.00 0.00 3.33
2245 2583 5.043248 CAGGTGGTTTTTCTCAATCACAAC 58.957 41.667 0.00 0.00 0.00 3.32
2246 2584 4.709397 ACAGGTGGTTTTTCTCAATCACAA 59.291 37.500 0.00 0.00 0.00 3.33
2247 2585 4.277476 ACAGGTGGTTTTTCTCAATCACA 58.723 39.130 0.00 0.00 0.00 3.58
2248 2586 4.918810 ACAGGTGGTTTTTCTCAATCAC 57.081 40.909 0.00 0.00 0.00 3.06
2267 2605 5.048573 GGACTTCGGGCAATAAAGTAAAACA 60.049 40.000 0.00 0.00 33.54 2.83
2268 2606 5.182570 AGGACTTCGGGCAATAAAGTAAAAC 59.817 40.000 0.00 0.00 33.54 2.43
2269 2607 5.182380 CAGGACTTCGGGCAATAAAGTAAAA 59.818 40.000 0.00 0.00 33.54 1.52
2284 2624 5.156355 CCAACATTTCAATTCAGGACTTCG 58.844 41.667 0.00 0.00 0.00 3.79
2310 2654 5.355596 AGATTCAGACGATAGAAAAGCAGG 58.644 41.667 0.00 0.00 41.38 4.85
2321 2665 6.763610 GGATGGAAGTAAAAGATTCAGACGAT 59.236 38.462 0.00 0.00 0.00 3.73
2324 2668 7.872113 ATGGATGGAAGTAAAAGATTCAGAC 57.128 36.000 0.00 0.00 0.00 3.51
2340 2684 9.489084 CGATTTCAGTATAGTAAAATGGATGGA 57.511 33.333 0.00 0.00 0.00 3.41
2341 2685 9.489084 TCGATTTCAGTATAGTAAAATGGATGG 57.511 33.333 0.00 0.00 0.00 3.51
2372 2716 1.349357 TGGTGTAGGTGCTGCAACATA 59.651 47.619 21.23 6.61 38.75 2.29
2375 2719 0.310854 GTTGGTGTAGGTGCTGCAAC 59.689 55.000 10.28 10.28 34.44 4.17
2411 2755 2.594592 GCTTGGGCTGACGGTTGT 60.595 61.111 0.00 0.00 35.22 3.32
2452 2796 3.532155 GCCGCCGAGACAGGAGAT 61.532 66.667 0.00 0.00 32.51 2.75
2474 2818 3.227276 CACCGCGGCTAGGAGGAT 61.227 66.667 28.58 0.00 0.00 3.24
2530 2874 1.829970 TGGAACAAACCATGCGGCA 60.830 52.632 4.58 4.58 34.77 5.69
2531 2875 3.046870 TGGAACAAACCATGCGGC 58.953 55.556 0.00 0.00 34.77 6.53
2577 2921 1.475280 AGTAGTCACTAAATCGCGGCA 59.525 47.619 6.13 0.00 31.45 5.69
2613 2959 4.377124 GCTAAACCGAACAACTAGCAGAAC 60.377 45.833 0.00 0.00 35.98 3.01
2725 3071 2.579207 TCGGCACAACACTAGCTATC 57.421 50.000 0.00 0.00 0.00 2.08
2776 3122 2.645838 AACACCAAGCACACTGATCT 57.354 45.000 0.00 0.00 0.00 2.75
2817 3163 0.538584 TCCGTCATGCATCTGCTCTT 59.461 50.000 0.00 0.00 42.66 2.85
2830 3177 3.399330 GAAACTGATCAGGTTTCCGTCA 58.601 45.455 26.31 0.00 43.68 4.35
2849 3380 4.879545 GGATATAACAAGGAAACGGCAGAA 59.120 41.667 0.00 0.00 0.00 3.02
2856 3387 4.269363 CGTCCGTGGATATAACAAGGAAAC 59.731 45.833 13.56 5.41 45.63 2.78
2915 3449 7.343357 TCGGGATATCTGTGAATTACCTTTTT 58.657 34.615 2.05 0.00 0.00 1.94
2919 3453 4.021016 GCTCGGGATATCTGTGAATTACCT 60.021 45.833 2.05 0.00 0.00 3.08
3012 3620 1.402613 CATTCATGGATGCGCACTCAA 59.597 47.619 14.90 5.73 0.00 3.02
3013 3621 1.018910 CATTCATGGATGCGCACTCA 58.981 50.000 14.90 15.20 0.00 3.41
3014 3622 3.839654 CATTCATGGATGCGCACTC 57.160 52.632 14.90 11.87 0.00 3.51
3025 3633 3.191162 TCGTCAAGAAAAGGCCATTCATG 59.809 43.478 19.76 17.90 0.00 3.07
3034 3642 5.424121 ACTTCAACATCGTCAAGAAAAGG 57.576 39.130 0.00 0.00 0.00 3.11
3039 3647 2.058798 GCGACTTCAACATCGTCAAGA 58.941 47.619 0.00 0.00 40.49 3.02
3141 5837 2.560542 GTCGAGGATGATAGATGGCTGT 59.439 50.000 0.00 0.00 0.00 4.40
3142 5838 2.415224 CGTCGAGGATGATAGATGGCTG 60.415 54.545 0.00 0.00 0.00 4.85
3146 5842 3.569548 CCAACGTCGAGGATGATAGATG 58.430 50.000 15.87 0.00 0.00 2.90
3147 5843 2.029828 GCCAACGTCGAGGATGATAGAT 60.030 50.000 15.87 0.00 0.00 1.98
3148 5844 1.337071 GCCAACGTCGAGGATGATAGA 59.663 52.381 15.87 0.00 0.00 1.98
3149 5845 1.772182 GCCAACGTCGAGGATGATAG 58.228 55.000 15.87 2.04 0.00 2.08
3150 5846 0.030235 CGCCAACGTCGAGGATGATA 59.970 55.000 15.87 0.00 33.53 2.15
3151 5847 1.226974 CGCCAACGTCGAGGATGAT 60.227 57.895 15.87 0.00 33.53 2.45
3152 5848 2.180769 CGCCAACGTCGAGGATGA 59.819 61.111 15.87 0.00 33.53 2.92
3153 5849 2.885644 CCGCCAACGTCGAGGATG 60.886 66.667 12.85 10.32 37.70 3.51
3154 5850 4.814294 GCCGCCAACGTCGAGGAT 62.814 66.667 12.85 0.00 37.70 3.24
3172 5868 4.664677 ACAGAGTCGGTGCGGTGC 62.665 66.667 0.00 0.00 0.00 5.01
3173 5869 1.157870 AAAACAGAGTCGGTGCGGTG 61.158 55.000 0.00 0.00 0.00 4.94
3174 5870 0.463116 AAAAACAGAGTCGGTGCGGT 60.463 50.000 0.00 0.00 0.00 5.68
3175 5871 0.234884 GAAAAACAGAGTCGGTGCGG 59.765 55.000 0.00 0.00 0.00 5.69
3176 5872 0.234884 GGAAAAACAGAGTCGGTGCG 59.765 55.000 0.00 0.00 0.00 5.34
3177 5873 1.305201 TGGAAAAACAGAGTCGGTGC 58.695 50.000 0.00 0.00 0.00 5.01
3217 5946 2.677979 GCAAGCTCGAACCGGAACC 61.678 63.158 9.46 0.00 0.00 3.62
3218 7182 2.677979 GGCAAGCTCGAACCGGAAC 61.678 63.158 9.46 0.00 0.00 3.62
3219 7183 2.358247 GGCAAGCTCGAACCGGAA 60.358 61.111 9.46 0.00 0.00 4.30
3225 7189 1.806542 GTTTGATCAGGCAAGCTCGAA 59.193 47.619 0.00 0.00 0.00 3.71
3230 7194 2.430465 TCTCAGTTTGATCAGGCAAGC 58.570 47.619 0.00 0.00 0.00 4.01
3258 7223 9.424319 TCGATCTAATCAGGCAGAAAATTATAC 57.576 33.333 0.00 0.00 0.00 1.47
3268 7233 3.057245 TCCGATTCGATCTAATCAGGCAG 60.057 47.826 17.35 3.68 35.93 4.85
3298 7264 4.081807 GGATTATATAAGGAAGGACGCGGT 60.082 45.833 12.47 0.00 0.00 5.68
3348 7314 7.923344 AGCGTATGAATCAGTTATATATGGCTC 59.077 37.037 0.00 0.00 0.00 4.70
3356 7322 8.341892 AGATGAGAGCGTATGAATCAGTTATA 57.658 34.615 0.00 0.00 0.00 0.98
3357 7323 7.225784 AGATGAGAGCGTATGAATCAGTTAT 57.774 36.000 0.00 0.00 0.00 1.89
3358 7324 6.641169 AGATGAGAGCGTATGAATCAGTTA 57.359 37.500 0.00 0.00 0.00 2.24
3359 7325 5.528043 AGATGAGAGCGTATGAATCAGTT 57.472 39.130 0.00 0.00 0.00 3.16
3360 7326 5.301551 AGAAGATGAGAGCGTATGAATCAGT 59.698 40.000 0.00 0.00 0.00 3.41
3382 7355 0.392998 GAAGCCTTTGGATCCGCAGA 60.393 55.000 7.39 0.00 0.00 4.26
3405 7378 0.816825 CACATCTCTTCCCCGCCATG 60.817 60.000 0.00 0.00 0.00 3.66
3421 7394 4.147449 CGCGGGGAGATCTGCACA 62.147 66.667 17.38 0.00 38.88 4.57
3423 7396 3.838271 GACGCGGGGAGATCTGCA 61.838 66.667 16.72 0.00 38.88 4.41
3444 7417 4.314440 TTCTTGCGAGGCGGCTGT 62.314 61.111 19.63 0.00 0.00 4.40
3447 7420 3.028366 GAACTTCTTGCGAGGCGGC 62.028 63.158 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.