Multiple sequence alignment - TraesCS3A01G514200

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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 TraesCS3A01G514200 chr3A 100.000 2543 0 0 1 2543 733023801 733021259 0.000000e+00 4697
1 TraesCS3A01G514200 chr3D 83.535 1324 102 52 713 1996 602818289 602819536 0.000000e+00 1131
2 TraesCS3A01G514200 chr3D 86.945 383 21 10 2175 2543 602819683 602820050 1.100000e-108 403
3 TraesCS3A01G514200 chr3B 83.221 1341 88 50 713 2002 810936405 810935151 0.000000e+00 1103
4 TraesCS3A01G514200 chr3B 84.858 634 78 11 1 620 810937580 810936951 7.730000e-175 623
5 TraesCS3A01G514200 chr3B 90.492 305 17 2 2246 2543 810784002 810783703 2.370000e-105 392
6 TraesCS3A01G514200 chr3B 87.179 195 12 9 2193 2375 810935071 810934878 2.560000e-50 209
7 TraesCS3A01G514200 chr3B 90.816 98 9 0 1899 1996 810787409 810787312 5.710000e-27 132


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 TraesCS3A01G514200 chr3A 733021259 733023801 2542 True 4697 4697 100.000 1 2543 1 chr3A.!!$R1 2542
1 TraesCS3A01G514200 chr3D 602818289 602820050 1761 False 767 1131 85.240 713 2543 2 chr3D.!!$F1 1830
2 TraesCS3A01G514200 chr3B 810934878 810937580 2702 True 645 1103 85.086 1 2375 3 chr3B.!!$R2 2374
3 TraesCS3A01G514200 chr3B 810783703 810787409 3706 True 262 392 90.654 1899 2543 2 chr3B.!!$R1 644

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
850 1385 0.034059 AGTCCAGTCCAGTCAAAGCG 59.966 55.0 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 2503 0.108138 AGTAACTCCACTCCGCATGC 60.108 55.0 7.91 7.91 0.0 4.06 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
46 47 3.136123 CATGAGGCGTTGCTGGGG 61.136 66.667 0.00 0.00 0.00 4.96
89 90 9.481340 TCACTTCAATCTTGTATATGAGTATGC 57.519 33.333 0.00 0.00 0.00 3.14
92 93 6.711277 TCAATCTTGTATATGAGTATGCCCC 58.289 40.000 0.00 0.00 0.00 5.80
113 114 1.742761 CAAGATGGGTGTGTGGCTAG 58.257 55.000 0.00 0.00 0.00 3.42
134 135 2.161609 GTCCACGTGATAAAGCCTTTGG 59.838 50.000 19.30 0.00 0.00 3.28
135 136 1.472480 CCACGTGATAAAGCCTTTGGG 59.528 52.381 19.30 0.00 0.00 4.12
142 143 4.636206 GTGATAAAGCCTTTGGGTGACTAG 59.364 45.833 0.00 0.00 31.90 2.57
144 145 4.320910 GCCTTTGGGTGACTAGGC 57.679 61.111 0.00 0.00 45.57 3.93
157 158 4.804665 GGTGACTAGGCTTTTCGAGTTATC 59.195 45.833 0.00 0.00 0.00 1.75
158 159 5.408356 GTGACTAGGCTTTTCGAGTTATCA 58.592 41.667 0.00 0.00 0.00 2.15
160 161 5.012328 ACTAGGCTTTTCGAGTTATCAGG 57.988 43.478 0.00 0.00 0.00 3.86
183 184 0.108804 ATGTCCATCCGTGTCGTGTC 60.109 55.000 0.00 0.00 0.00 3.67
197 198 2.866762 GTCGTGTCATCCATCTTTAGGC 59.133 50.000 0.00 0.00 0.00 3.93
207 208 0.179145 ATCTTTAGGCGTGACGACGG 60.179 55.000 10.10 0.00 46.20 4.79
216 217 0.996462 CGTGACGACGGCACAATAAT 59.004 50.000 31.63 0.00 42.18 1.28
221 222 0.300491 CGACGGCACAATAATCGTGG 59.700 55.000 0.00 0.00 35.91 4.94
224 225 2.538449 GACGGCACAATAATCGTGGTAG 59.462 50.000 0.00 0.00 35.91 3.18
257 258 6.808321 TCACTGTAGACCCTTATGCTTATT 57.192 37.500 0.00 0.00 0.00 1.40
259 260 8.313944 TCACTGTAGACCCTTATGCTTATTTA 57.686 34.615 0.00 0.00 0.00 1.40
299 301 6.289745 TGTGTAAGATTGTTTGTAACGGAC 57.710 37.500 0.00 0.00 0.00 4.79
332 334 1.986698 TTTACGCACTTCCGCTACTC 58.013 50.000 0.00 0.00 0.00 2.59
361 363 1.007964 CCTCGTATGCTCCAGCTCG 60.008 63.158 0.00 3.09 42.66 5.03
366 368 1.065701 CGTATGCTCCAGCTCGTACTT 59.934 52.381 0.00 0.00 42.66 2.24
367 369 2.464865 GTATGCTCCAGCTCGTACTTG 58.535 52.381 0.00 0.00 42.66 3.16
368 370 0.176680 ATGCTCCAGCTCGTACTTGG 59.823 55.000 0.00 0.00 42.66 3.61
391 393 5.406477 GGTAAAGAATTGCCAAAGAAAGCAG 59.594 40.000 0.00 0.00 40.69 4.24
392 394 3.036075 AGAATTGCCAAAGAAAGCAGC 57.964 42.857 0.00 0.00 40.73 5.25
393 395 2.366266 AGAATTGCCAAAGAAAGCAGCA 59.634 40.909 0.00 0.00 40.73 4.41
394 396 2.914695 ATTGCCAAAGAAAGCAGCAA 57.085 40.000 0.00 0.00 46.43 3.91
403 405 4.470334 AAGAAAGCAGCAAGTGGAAAAA 57.530 36.364 0.00 0.00 0.00 1.94
419 421 3.434310 GGAAAAACCAAAATTGCCCCTCA 60.434 43.478 0.00 0.00 38.79 3.86
423 425 3.252554 ACCAAAATTGCCCCTCAAGTA 57.747 42.857 0.00 0.00 38.22 2.24
432 434 4.023726 TGCCCCTCAAGTAAACGTTAAT 57.976 40.909 0.00 0.00 0.00 1.40
438 440 6.259387 CCCCTCAAGTAAACGTTAATGGTATC 59.741 42.308 0.00 0.00 0.00 2.24
457 473 0.092351 CACGACGTGATGCCGTTTAC 59.908 55.000 23.39 0.00 41.98 2.01
458 474 0.038892 ACGACGTGATGCCGTTTACT 60.039 50.000 0.00 0.00 41.98 2.24
459 475 0.638746 CGACGTGATGCCGTTTACTC 59.361 55.000 0.00 0.00 41.98 2.59
460 476 0.997196 GACGTGATGCCGTTTACTCC 59.003 55.000 0.00 0.00 41.98 3.85
461 477 0.606604 ACGTGATGCCGTTTACTCCT 59.393 50.000 0.00 0.00 37.96 3.69
462 478 1.820519 ACGTGATGCCGTTTACTCCTA 59.179 47.619 0.00 0.00 37.96 2.94
472 488 4.521256 GCCGTTTACTCCTAGATGATCTCT 59.479 45.833 0.00 0.00 38.06 3.10
490 509 5.762179 TCTCTGGACTGATTTGTGGTATT 57.238 39.130 0.00 0.00 0.00 1.89
491 510 6.126863 TCTCTGGACTGATTTGTGGTATTT 57.873 37.500 0.00 0.00 0.00 1.40
492 511 7.252612 TCTCTGGACTGATTTGTGGTATTTA 57.747 36.000 0.00 0.00 0.00 1.40
495 514 6.653320 TCTGGACTGATTTGTGGTATTTACAC 59.347 38.462 0.00 0.00 39.26 2.90
497 516 5.410439 GGACTGATTTGTGGTATTTACACGT 59.590 40.000 0.00 0.00 41.64 4.49
498 517 6.236017 ACTGATTTGTGGTATTTACACGTG 57.764 37.500 15.48 15.48 41.64 4.49
516 535 3.135225 CGTGTGTGTATGTTGGGAAGAA 58.865 45.455 0.00 0.00 0.00 2.52
525 544 1.286553 TGTTGGGAAGAACTGGGTGTT 59.713 47.619 0.00 0.00 42.38 3.32
526 545 1.681264 GTTGGGAAGAACTGGGTGTTG 59.319 52.381 0.00 0.00 39.30 3.33
535 554 1.046472 ACTGGGTGTTGTCCTCGACA 61.046 55.000 0.00 0.00 41.09 4.35
539 558 0.600255 GGTGTTGTCCTCGACAGTGG 60.600 60.000 0.00 0.00 43.69 4.00
556 575 6.026947 ACAGTGGTGTCTATTAACAGTCTC 57.973 41.667 0.00 0.00 26.76 3.36
558 577 6.041637 ACAGTGGTGTCTATTAACAGTCTCAA 59.958 38.462 0.00 0.00 26.76 3.02
561 580 7.819900 AGTGGTGTCTATTAACAGTCTCAAATC 59.180 37.037 0.00 0.00 0.00 2.17
572 591 3.037549 AGTCTCAAATCCAGGGCTAGAG 58.962 50.000 0.00 0.00 0.00 2.43
585 604 3.228085 CTAGAGAAGCACGAGACGC 57.772 57.895 0.00 0.00 0.00 5.19
606 625 2.561569 CCCCTAGGCTGTGTTATTTCG 58.438 52.381 2.05 0.00 0.00 3.46
609 628 2.858344 CCTAGGCTGTGTTATTTCGACG 59.142 50.000 0.00 0.00 0.00 5.12
611 630 0.096454 GGCTGTGTTATTTCGACGGC 59.904 55.000 0.00 0.00 40.62 5.68
620 639 0.462789 ATTTCGACGGCGGGTTAGAT 59.537 50.000 12.58 0.00 38.28 1.98
622 641 1.033746 TTCGACGGCGGGTTAGATCT 61.034 55.000 12.58 0.00 38.28 2.75
623 642 1.299165 CGACGGCGGGTTAGATCTG 60.299 63.158 13.24 0.00 0.00 2.90
625 644 1.673808 GACGGCGGGTTAGATCTGGT 61.674 60.000 13.24 0.00 0.00 4.00
626 645 0.396139 ACGGCGGGTTAGATCTGGTA 60.396 55.000 13.24 0.00 0.00 3.25
627 646 0.966920 CGGCGGGTTAGATCTGGTAT 59.033 55.000 5.18 0.00 0.00 2.73
628 647 2.165167 CGGCGGGTTAGATCTGGTATA 58.835 52.381 5.18 0.00 0.00 1.47
629 648 2.758979 CGGCGGGTTAGATCTGGTATAT 59.241 50.000 5.18 0.00 0.00 0.86
630 649 3.428999 CGGCGGGTTAGATCTGGTATATG 60.429 52.174 5.18 0.00 0.00 1.78
631 650 3.767673 GGCGGGTTAGATCTGGTATATGA 59.232 47.826 5.18 0.00 0.00 2.15
632 651 4.142138 GGCGGGTTAGATCTGGTATATGAG 60.142 50.000 5.18 0.00 0.00 2.90
633 652 4.463186 GCGGGTTAGATCTGGTATATGAGT 59.537 45.833 5.18 0.00 0.00 3.41
634 653 5.651139 GCGGGTTAGATCTGGTATATGAGTA 59.349 44.000 5.18 0.00 0.00 2.59
635 654 6.321690 GCGGGTTAGATCTGGTATATGAGTAT 59.678 42.308 5.18 0.00 0.00 2.12
636 655 7.682261 GCGGGTTAGATCTGGTATATGAGTATG 60.682 44.444 5.18 0.00 0.00 2.39
637 656 7.339721 CGGGTTAGATCTGGTATATGAGTATGT 59.660 40.741 5.18 0.00 0.00 2.29
638 657 8.688151 GGGTTAGATCTGGTATATGAGTATGTC 58.312 40.741 5.18 0.00 0.00 3.06
639 658 8.688151 GGTTAGATCTGGTATATGAGTATGTCC 58.312 40.741 5.18 0.00 0.00 4.02
640 659 9.469097 GTTAGATCTGGTATATGAGTATGTCCT 57.531 37.037 5.18 0.00 0.00 3.85
641 660 9.688091 TTAGATCTGGTATATGAGTATGTCCTC 57.312 37.037 5.18 0.00 0.00 3.71
642 661 7.122715 AGATCTGGTATATGAGTATGTCCTCC 58.877 42.308 0.00 0.00 0.00 4.30
643 662 6.214177 TCTGGTATATGAGTATGTCCTCCA 57.786 41.667 0.00 0.00 0.00 3.86
644 663 6.620429 TCTGGTATATGAGTATGTCCTCCAA 58.380 40.000 0.00 0.00 0.00 3.53
645 664 7.073208 TCTGGTATATGAGTATGTCCTCCAAA 58.927 38.462 0.00 0.00 0.00 3.28
646 665 7.567250 TCTGGTATATGAGTATGTCCTCCAAAA 59.433 37.037 0.00 0.00 0.00 2.44
647 666 8.275187 TGGTATATGAGTATGTCCTCCAAAAT 57.725 34.615 0.00 0.00 0.00 1.82
648 667 9.387397 TGGTATATGAGTATGTCCTCCAAAATA 57.613 33.333 0.00 0.00 0.00 1.40
649 668 9.877178 GGTATATGAGTATGTCCTCCAAAATAG 57.123 37.037 0.00 0.00 0.00 1.73
650 669 9.877178 GTATATGAGTATGTCCTCCAAAATAGG 57.123 37.037 0.00 0.00 35.26 2.57
651 670 6.831664 ATGAGTATGTCCTCCAAAATAGGT 57.168 37.500 0.00 0.00 35.48 3.08
652 671 5.989477 TGAGTATGTCCTCCAAAATAGGTG 58.011 41.667 0.00 0.00 35.48 4.00
653 672 5.487488 TGAGTATGTCCTCCAAAATAGGTGT 59.513 40.000 0.00 0.00 35.48 4.16
654 673 5.745227 AGTATGTCCTCCAAAATAGGTGTG 58.255 41.667 0.00 0.00 35.48 3.82
655 674 4.657814 ATGTCCTCCAAAATAGGTGTGT 57.342 40.909 0.00 0.00 35.48 3.72
656 675 3.750371 TGTCCTCCAAAATAGGTGTGTG 58.250 45.455 0.00 0.00 35.48 3.82
657 676 3.081804 GTCCTCCAAAATAGGTGTGTGG 58.918 50.000 0.00 0.00 35.48 4.17
658 677 1.818674 CCTCCAAAATAGGTGTGTGGC 59.181 52.381 0.00 0.00 0.00 5.01
659 678 2.555227 CCTCCAAAATAGGTGTGTGGCT 60.555 50.000 0.00 0.00 0.00 4.75
660 679 3.308117 CCTCCAAAATAGGTGTGTGGCTA 60.308 47.826 0.00 0.00 0.00 3.93
661 680 3.681593 TCCAAAATAGGTGTGTGGCTAC 58.318 45.455 0.00 0.00 0.00 3.58
662 681 3.329520 TCCAAAATAGGTGTGTGGCTACT 59.670 43.478 0.64 0.00 0.00 2.57
663 682 3.440173 CCAAAATAGGTGTGTGGCTACTG 59.560 47.826 0.64 0.00 0.00 2.74
664 683 2.403252 AATAGGTGTGTGGCTACTGC 57.597 50.000 0.64 0.00 38.76 4.40
665 684 1.275666 ATAGGTGTGTGGCTACTGCA 58.724 50.000 0.64 0.00 41.91 4.41
666 685 0.320374 TAGGTGTGTGGCTACTGCAC 59.680 55.000 15.91 15.91 41.91 4.57
667 686 1.966451 GGTGTGTGGCTACTGCACC 60.966 63.158 23.21 23.21 41.99 5.01
668 687 1.071471 GTGTGTGGCTACTGCACCT 59.929 57.895 14.17 0.00 41.91 4.00
669 688 0.951040 GTGTGTGGCTACTGCACCTC 60.951 60.000 14.17 0.00 41.91 3.85
670 689 1.371183 GTGTGGCTACTGCACCTCA 59.629 57.895 0.64 0.00 41.91 3.86
693 712 4.453480 AAAGTCTTTGGGTGATGAGGAA 57.547 40.909 0.00 0.00 0.00 3.36
706 725 5.415221 GTGATGAGGAATTTCGAGTTCTCT 58.585 41.667 11.03 7.54 0.00 3.10
707 726 5.872070 GTGATGAGGAATTTCGAGTTCTCTT 59.128 40.000 11.03 2.22 0.00 2.85
709 728 3.997021 TGAGGAATTTCGAGTTCTCTTGC 59.003 43.478 11.03 0.00 0.00 4.01
711 730 3.748568 AGGAATTTCGAGTTCTCTTGCAC 59.251 43.478 11.03 0.00 0.00 4.57
742 1260 3.168528 ACCTGACCAACCACCGCT 61.169 61.111 0.00 0.00 0.00 5.52
799 1334 1.445518 CCACCACCCAAAGCCAAAC 59.554 57.895 0.00 0.00 0.00 2.93
808 1343 2.489802 CCCAAAGCCAAACCTCTTCTCT 60.490 50.000 0.00 0.00 0.00 3.10
813 1348 3.247162 AGCCAAACCTCTTCTCTCTCTT 58.753 45.455 0.00 0.00 0.00 2.85
820 1355 2.666317 CTCTTCTCTCTCTTCCTCCCC 58.334 57.143 0.00 0.00 0.00 4.81
821 1356 2.003830 TCTTCTCTCTCTTCCTCCCCA 58.996 52.381 0.00 0.00 0.00 4.96
822 1357 2.024464 TCTTCTCTCTCTTCCTCCCCAG 60.024 54.545 0.00 0.00 0.00 4.45
823 1358 1.388174 TCTCTCTCTTCCTCCCCAGT 58.612 55.000 0.00 0.00 0.00 4.00
824 1359 1.006519 TCTCTCTCTTCCTCCCCAGTG 59.993 57.143 0.00 0.00 0.00 3.66
825 1360 0.616111 TCTCTCTTCCTCCCCAGTGC 60.616 60.000 0.00 0.00 0.00 4.40
826 1361 0.906756 CTCTCTTCCTCCCCAGTGCA 60.907 60.000 0.00 0.00 0.00 4.57
827 1362 0.906756 TCTCTTCCTCCCCAGTGCAG 60.907 60.000 0.00 0.00 0.00 4.41
828 1363 1.152030 TCTTCCTCCCCAGTGCAGT 60.152 57.895 0.00 0.00 0.00 4.40
829 1364 1.194781 TCTTCCTCCCCAGTGCAGTC 61.195 60.000 0.00 0.00 0.00 3.51
830 1365 2.190488 CTTCCTCCCCAGTGCAGTCC 62.190 65.000 0.00 0.00 0.00 3.85
831 1366 2.930019 CCTCCCCAGTGCAGTCCA 60.930 66.667 0.00 0.00 0.00 4.02
832 1367 2.667418 CTCCCCAGTGCAGTCCAG 59.333 66.667 0.00 0.00 0.00 3.86
833 1368 2.122413 TCCCCAGTGCAGTCCAGT 60.122 61.111 0.00 0.00 0.00 4.00
850 1385 0.034059 AGTCCAGTCCAGTCAAAGCG 59.966 55.000 0.00 0.00 0.00 4.68
897 1434 6.456795 AAAGACAAAAACTCTCTTTCCCTG 57.543 37.500 0.00 0.00 29.98 4.45
899 1436 4.079730 AGACAAAAACTCTCTTTCCCTGGT 60.080 41.667 0.00 0.00 0.00 4.00
900 1437 4.610333 ACAAAAACTCTCTTTCCCTGGTT 58.390 39.130 0.00 0.00 0.00 3.67
901 1438 4.645136 ACAAAAACTCTCTTTCCCTGGTTC 59.355 41.667 0.00 0.00 0.00 3.62
902 1439 4.519906 AAAACTCTCTTTCCCTGGTTCA 57.480 40.909 0.00 0.00 0.00 3.18
903 1440 3.493767 AACTCTCTTTCCCTGGTTCAC 57.506 47.619 0.00 0.00 0.00 3.18
904 1441 2.408565 ACTCTCTTTCCCTGGTTCACA 58.591 47.619 0.00 0.00 0.00 3.58
905 1442 2.982488 ACTCTCTTTCCCTGGTTCACAT 59.018 45.455 0.00 0.00 0.00 3.21
906 1443 4.168101 ACTCTCTTTCCCTGGTTCACATA 58.832 43.478 0.00 0.00 0.00 2.29
934 1479 1.469423 GCCGTCTAGTACCAGCAGAAC 60.469 57.143 0.00 0.00 0.00 3.01
965 1510 0.820871 CACTCCACTCCTAGTCCTGC 59.179 60.000 0.00 0.00 0.00 4.85
975 1520 0.461961 CTAGTCCTGCTACCACCAGC 59.538 60.000 0.00 0.00 42.15 4.85
1292 1855 2.596851 GGGAGGTTCAGCTGGAGCA 61.597 63.158 25.60 0.00 45.16 4.26
1294 1857 1.548357 GGAGGTTCAGCTGGAGCAGA 61.548 60.000 25.60 0.00 45.16 4.26
1296 1859 0.540923 AGGTTCAGCTGGAGCAGATC 59.459 55.000 25.60 0.00 45.16 2.75
1300 1863 4.218578 AGCTGGAGCAGATCGCCG 62.219 66.667 0.65 0.00 45.16 6.46
1508 2089 4.819761 GCCGCACGATGGAGAGCA 62.820 66.667 0.00 0.00 0.00 4.26
1509 2090 2.125552 CCGCACGATGGAGAGCAA 60.126 61.111 0.00 0.00 0.00 3.91
1512 2093 1.742880 GCACGATGGAGAGCAAGCA 60.743 57.895 0.00 0.00 0.00 3.91
1515 2096 0.108424 ACGATGGAGAGCAAGCAGAC 60.108 55.000 0.00 0.00 0.00 3.51
1614 2199 0.240945 CTTTGGGTTCTTTCGCGCAT 59.759 50.000 8.75 0.00 0.00 4.73
1621 2206 2.244436 TTCTTTCGCGCATCAGCAGC 62.244 55.000 8.75 0.00 42.27 5.25
1622 2207 3.030763 CTTTCGCGCATCAGCAGCA 62.031 57.895 8.75 0.00 42.27 4.41
1623 2208 2.898087 CTTTCGCGCATCAGCAGCAG 62.898 60.000 8.75 0.00 42.27 4.24
1626 2211 4.538283 GCGCATCAGCAGCAGCAG 62.538 66.667 0.30 0.00 45.49 4.24
1627 2212 2.818274 CGCATCAGCAGCAGCAGA 60.818 61.111 3.17 0.11 45.49 4.26
1664 2252 3.384816 CAAGGCGTGCATGATAGGA 57.615 52.632 10.93 0.00 0.00 2.94
1675 2263 3.647590 TGCATGATAGGATTGGCTAGTCA 59.352 43.478 0.00 0.00 0.00 3.41
1679 2267 6.393990 CATGATAGGATTGGCTAGTCAGTAC 58.606 44.000 0.00 0.00 0.00 2.73
1728 2316 0.108207 GAGGCAGGAGTGGATGGATG 59.892 60.000 0.00 0.00 0.00 3.51
1729 2317 1.150081 GGCAGGAGTGGATGGATGG 59.850 63.158 0.00 0.00 0.00 3.51
1730 2318 1.348008 GGCAGGAGTGGATGGATGGA 61.348 60.000 0.00 0.00 0.00 3.41
1731 2319 0.179034 GCAGGAGTGGATGGATGGAC 60.179 60.000 0.00 0.00 0.00 4.02
1750 2338 5.379187 TGGACATGCATGCAGATTAATACT 58.621 37.500 26.69 2.26 0.00 2.12
1751 2339 6.532826 TGGACATGCATGCAGATTAATACTA 58.467 36.000 26.69 6.46 0.00 1.82
1752 2340 6.427853 TGGACATGCATGCAGATTAATACTAC 59.572 38.462 26.69 3.73 0.00 2.73
1753 2341 6.652481 GGACATGCATGCAGATTAATACTACT 59.348 38.462 26.69 0.61 0.00 2.57
1755 2343 8.539770 ACATGCATGCAGATTAATACTACTAC 57.460 34.615 26.69 0.00 0.00 2.73
1756 2344 7.329471 ACATGCATGCAGATTAATACTACTACG 59.671 37.037 26.69 0.00 0.00 3.51
1757 2345 6.156519 TGCATGCAGATTAATACTACTACGG 58.843 40.000 18.46 0.00 0.00 4.02
1758 2346 5.062308 GCATGCAGATTAATACTACTACGGC 59.938 44.000 14.21 0.00 0.00 5.68
1760 2348 4.516321 TGCAGATTAATACTACTACGGCGA 59.484 41.667 16.62 0.00 0.00 5.54
1761 2349 5.008911 TGCAGATTAATACTACTACGGCGAA 59.991 40.000 16.62 0.00 0.00 4.70
1762 2350 6.091437 GCAGATTAATACTACTACGGCGAAT 58.909 40.000 16.62 0.00 0.00 3.34
1763 2351 6.250951 GCAGATTAATACTACTACGGCGAATC 59.749 42.308 16.62 8.21 0.00 2.52
1765 2353 7.482113 CAGATTAATACTACTACGGCGAATCTG 59.518 40.741 16.62 18.36 40.50 2.90
1766 2354 3.555917 ATACTACTACGGCGAATCTGC 57.444 47.619 16.62 0.00 0.00 4.26
1767 2355 1.100510 ACTACTACGGCGAATCTGCA 58.899 50.000 16.62 0.00 36.28 4.41
1769 2357 2.054363 CTACTACGGCGAATCTGCATG 58.946 52.381 16.62 0.00 36.28 4.06
1770 2358 0.175760 ACTACGGCGAATCTGCATGT 59.824 50.000 16.62 0.00 36.28 3.21
1771 2359 1.407618 ACTACGGCGAATCTGCATGTA 59.592 47.619 16.62 0.00 36.28 2.29
1773 2361 1.953559 ACGGCGAATCTGCATGTATT 58.046 45.000 16.62 0.00 36.28 1.89
1774 2362 3.106242 ACGGCGAATCTGCATGTATTA 57.894 42.857 16.62 0.00 36.28 0.98
1775 2363 3.462982 ACGGCGAATCTGCATGTATTAA 58.537 40.909 16.62 0.00 36.28 1.40
1776 2364 4.065088 ACGGCGAATCTGCATGTATTAAT 58.935 39.130 16.62 0.00 36.28 1.40
1777 2365 4.152402 ACGGCGAATCTGCATGTATTAATC 59.848 41.667 16.62 0.00 36.28 1.75
1778 2366 4.389992 CGGCGAATCTGCATGTATTAATCT 59.610 41.667 0.00 0.00 36.28 2.40
1779 2367 5.625251 GGCGAATCTGCATGTATTAATCTG 58.375 41.667 0.00 0.00 36.28 2.90
1780 2368 5.084722 GCGAATCTGCATGTATTAATCTGC 58.915 41.667 9.49 9.49 35.21 4.26
1781 2369 5.334337 GCGAATCTGCATGTATTAATCTGCA 60.334 40.000 15.42 15.42 41.98 4.41
1782 2370 6.622245 GCGAATCTGCATGTATTAATCTGCAT 60.622 38.462 16.19 7.25 43.12 3.96
1783 2371 6.741358 CGAATCTGCATGTATTAATCTGCATG 59.259 38.462 16.19 16.46 43.12 4.06
1784 2372 7.360607 CGAATCTGCATGTATTAATCTGCATGA 60.361 37.037 21.59 17.77 43.12 3.07
1785 2373 7.754851 ATCTGCATGTATTAATCTGCATGAA 57.245 32.000 21.59 14.90 43.12 2.57
1786 2374 7.754851 TCTGCATGTATTAATCTGCATGAAT 57.245 32.000 21.59 0.00 43.12 2.57
1787 2375 8.173542 TCTGCATGTATTAATCTGCATGAATT 57.826 30.769 21.59 0.00 43.12 2.17
1788 2376 8.079809 TCTGCATGTATTAATCTGCATGAATTG 58.920 33.333 21.59 11.00 43.12 2.32
1789 2377 7.149307 TGCATGTATTAATCTGCATGAATTGG 58.851 34.615 21.59 4.88 39.54 3.16
1790 2378 7.014422 TGCATGTATTAATCTGCATGAATTGGA 59.986 33.333 21.59 4.57 39.54 3.53
1791 2379 7.541091 GCATGTATTAATCTGCATGAATTGGAG 59.459 37.037 21.59 0.00 44.66 3.86
1792 2380 6.973843 TGTATTAATCTGCATGAATTGGAGC 58.026 36.000 0.00 0.00 43.10 4.70
1793 2381 4.924305 TTAATCTGCATGAATTGGAGCC 57.076 40.909 0.00 0.00 43.10 4.70
1794 2382 1.700955 ATCTGCATGAATTGGAGCCC 58.299 50.000 0.00 0.00 43.10 5.19
1795 2383 0.396139 TCTGCATGAATTGGAGCCCC 60.396 55.000 0.00 0.00 43.10 5.80
1796 2384 1.381599 TGCATGAATTGGAGCCCCC 60.382 57.895 0.00 0.00 0.00 5.40
1819 2431 0.320946 TTTTACGGAGCAGGAACGGG 60.321 55.000 0.00 0.00 0.00 5.28
1864 2478 6.090763 CCAATTCTTTGGCGGACTTTAATTTC 59.909 38.462 0.00 0.00 45.71 2.17
1877 2491 2.004583 TAATTTCACAGCTAGCGCGT 57.995 45.000 9.55 8.10 42.32 6.01
1953 2576 3.571571 CATGCATGTCAACTTTGAGTGG 58.428 45.455 18.91 0.00 37.98 4.00
1954 2577 1.337703 TGCATGTCAACTTTGAGTGGC 59.662 47.619 0.00 0.00 37.98 5.01
1955 2578 1.664016 GCATGTCAACTTTGAGTGGCG 60.664 52.381 0.00 0.00 37.98 5.69
1956 2579 1.603802 CATGTCAACTTTGAGTGGCGT 59.396 47.619 0.00 0.00 37.98 5.68
1957 2580 1.295792 TGTCAACTTTGAGTGGCGTC 58.704 50.000 0.00 0.00 37.98 5.19
1958 2581 0.232303 GTCAACTTTGAGTGGCGTCG 59.768 55.000 0.00 0.00 37.98 5.12
1959 2582 1.082756 CAACTTTGAGTGGCGTCGC 60.083 57.895 9.22 9.22 0.00 5.19
1960 2583 1.227556 AACTTTGAGTGGCGTCGCT 60.228 52.632 18.11 0.87 36.27 4.93
1961 2584 1.498865 AACTTTGAGTGGCGTCGCTG 61.499 55.000 18.11 0.00 33.25 5.18
1998 2621 1.080569 CCTTTGTGCAATGCGTCCC 60.081 57.895 0.00 0.00 0.00 4.46
1999 2622 1.659233 CTTTGTGCAATGCGTCCCA 59.341 52.632 0.00 0.00 0.00 4.37
2000 2623 0.244450 CTTTGTGCAATGCGTCCCAT 59.756 50.000 0.00 0.00 35.06 4.00
2003 2626 1.139520 GTGCAATGCGTCCCATTCC 59.860 57.895 0.00 0.00 42.15 3.01
2006 2629 2.016961 CAATGCGTCCCATTCCTCG 58.983 57.895 0.00 0.00 42.15 4.63
2009 2632 2.435938 GCGTCCCATTCCTCGCAA 60.436 61.111 0.00 0.00 46.40 4.85
2010 2633 2.038269 GCGTCCCATTCCTCGCAAA 61.038 57.895 0.00 0.00 46.40 3.68
2012 2635 0.168128 CGTCCCATTCCTCGCAAAAC 59.832 55.000 0.00 0.00 0.00 2.43
2013 2636 1.243902 GTCCCATTCCTCGCAAAACA 58.756 50.000 0.00 0.00 0.00 2.83
2015 2638 0.958091 CCCATTCCTCGCAAAACACA 59.042 50.000 0.00 0.00 0.00 3.72
2016 2639 1.068333 CCCATTCCTCGCAAAACACAG 60.068 52.381 0.00 0.00 0.00 3.66
2018 2641 2.350772 CCATTCCTCGCAAAACACAGAC 60.351 50.000 0.00 0.00 0.00 3.51
2021 2644 0.508641 CCTCGCAAAACACAGACTCG 59.491 55.000 0.00 0.00 0.00 4.18
2022 2645 0.111089 CTCGCAAAACACAGACTCGC 60.111 55.000 0.00 0.00 0.00 5.03
2024 2647 1.771073 CGCAAAACACAGACTCGCCA 61.771 55.000 0.00 0.00 0.00 5.69
2025 2648 0.380378 GCAAAACACAGACTCGCCAA 59.620 50.000 0.00 0.00 0.00 4.52
2027 2650 1.670811 CAAAACACAGACTCGCCAAGT 59.329 47.619 0.00 0.00 42.42 3.16
2040 2663 4.452455 ACTCGCCAAGTCTCAAAATAAGTG 59.548 41.667 0.00 0.00 30.02 3.16
2043 2666 4.452455 CGCCAAGTCTCAAAATAAGTGTCT 59.548 41.667 0.00 0.00 0.00 3.41
2046 2669 6.017109 GCCAAGTCTCAAAATAAGTGTCTCAA 60.017 38.462 0.00 0.00 0.00 3.02
2047 2670 7.308830 GCCAAGTCTCAAAATAAGTGTCTCAAT 60.309 37.037 0.00 0.00 0.00 2.57
2049 2672 9.956720 CAAGTCTCAAAATAAGTGTCTCAATTT 57.043 29.630 0.00 0.00 0.00 1.82
2055 2678 9.554724 TCAAAATAAGTGTCTCAATTTTATCGC 57.445 29.630 0.00 0.00 31.97 4.58
2059 2682 8.942338 ATAAGTGTCTCAATTTTATCGCACTA 57.058 30.769 0.00 0.00 35.26 2.74
2060 2683 7.849804 AAGTGTCTCAATTTTATCGCACTAT 57.150 32.000 0.00 0.00 35.26 2.12
2103 2877 8.907222 AGGTTAAAACACTTATTTTAGGACGA 57.093 30.769 0.00 0.00 35.88 4.20
2104 2878 9.341078 AGGTTAAAACACTTATTTTAGGACGAA 57.659 29.630 0.00 0.00 35.88 3.85
2105 2879 9.603298 GGTTAAAACACTTATTTTAGGACGAAG 57.397 33.333 0.00 0.00 35.88 3.79
2106 2880 9.603298 GTTAAAACACTTATTTTAGGACGAAGG 57.397 33.333 0.00 0.00 35.88 3.46
2107 2881 9.558396 TTAAAACACTTATTTTAGGACGAAGGA 57.442 29.630 0.00 0.00 35.88 3.36
2109 2883 7.668525 AACACTTATTTTAGGACGAAGGAAG 57.331 36.000 0.00 0.00 0.00 3.46
2110 2884 6.766429 ACACTTATTTTAGGACGAAGGAAGT 58.234 36.000 0.00 0.00 0.00 3.01
2111 2885 7.899973 ACACTTATTTTAGGACGAAGGAAGTA 58.100 34.615 0.00 0.00 0.00 2.24
2112 2886 7.816513 ACACTTATTTTAGGACGAAGGAAGTAC 59.183 37.037 0.00 0.00 0.00 2.73
2113 2887 8.033626 CACTTATTTTAGGACGAAGGAAGTACT 58.966 37.037 0.00 0.00 36.60 2.73
2114 2888 9.247861 ACTTATTTTAGGACGAAGGAAGTACTA 57.752 33.333 0.00 0.00 34.13 1.82
2144 2918 4.933400 ACGGTGTCAATATTGAACTGTACC 59.067 41.667 26.53 22.34 39.21 3.34
2149 4518 7.361799 GGTGTCAATATTGAACTGTACCCTTTC 60.362 40.741 19.55 3.66 39.21 2.62
2153 4522 6.759497 ATATTGAACTGTACCCTTTCAAGC 57.241 37.500 15.01 0.00 41.33 4.01
2158 4527 3.660865 ACTGTACCCTTTCAAGCTAACG 58.339 45.455 0.00 0.00 0.00 3.18
2160 4529 3.395639 TGTACCCTTTCAAGCTAACGTG 58.604 45.455 0.00 0.00 0.00 4.49
2163 4532 2.369532 ACCCTTTCAAGCTAACGTGGTA 59.630 45.455 0.00 0.00 0.00 3.25
2171 4540 7.760131 TTCAAGCTAACGTGGTATTACATAC 57.240 36.000 0.00 0.00 35.00 2.39
2172 4541 6.865411 TCAAGCTAACGTGGTATTACATACA 58.135 36.000 0.00 0.00 37.48 2.29
2221 4772 0.388520 GTGCGCCCACCTTGATTTTC 60.389 55.000 4.18 0.00 35.92 2.29
2231 4782 2.092375 ACCTTGATTTTCCGAGGGATCC 60.092 50.000 1.92 1.92 41.18 3.36
2238 4795 1.983119 TTCCGAGGGATCCATGTGCC 61.983 60.000 15.23 0.00 0.00 5.01
2286 6020 1.005340 GCAAGCATCTTCTCCACTCG 58.995 55.000 0.00 0.00 0.00 4.18
2504 6249 1.268999 TGATGGCGCAACTGTTGTTTC 60.269 47.619 20.57 11.07 33.52 2.78
2527 6272 0.030638 GTGCAAAACCACGACATGCT 59.969 50.000 0.00 0.00 37.86 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.271102 GCTTCTCTAGCCCTGGATACG 59.729 57.143 0.00 0.00 44.48 3.06
36 37 3.242608 CGAAATAATACACCCCAGCAACG 60.243 47.826 0.00 0.00 0.00 4.10
39 40 3.916359 TCGAAATAATACACCCCAGCA 57.084 42.857 0.00 0.00 0.00 4.41
40 41 4.385825 TCATCGAAATAATACACCCCAGC 58.614 43.478 0.00 0.00 0.00 4.85
43 44 6.231211 AGTGATCATCGAAATAATACACCCC 58.769 40.000 0.00 0.00 0.00 4.95
92 93 2.981560 GCCACACACCCATCTTGCG 61.982 63.158 0.00 0.00 0.00 4.85
113 114 2.161609 CCAAAGGCTTTATCACGTGGAC 59.838 50.000 17.00 0.25 0.00 4.02
119 120 3.421844 AGTCACCCAAAGGCTTTATCAC 58.578 45.455 12.95 5.53 36.11 3.06
121 122 4.200092 CCTAGTCACCCAAAGGCTTTATC 58.800 47.826 12.95 0.41 36.11 1.75
134 135 2.745515 ACTCGAAAAGCCTAGTCACC 57.254 50.000 0.00 0.00 0.00 4.02
135 136 5.408356 TGATAACTCGAAAAGCCTAGTCAC 58.592 41.667 0.00 0.00 0.00 3.67
142 143 4.504858 TCTTCCTGATAACTCGAAAAGCC 58.495 43.478 0.00 0.00 0.00 4.35
144 145 6.256757 GGACATCTTCCTGATAACTCGAAAAG 59.743 42.308 0.00 0.00 41.95 2.27
157 158 1.208052 ACACGGATGGACATCTTCCTG 59.792 52.381 11.67 5.31 46.10 3.86
158 159 1.482593 GACACGGATGGACATCTTCCT 59.517 52.381 11.67 0.00 46.10 3.36
160 161 1.135083 ACGACACGGATGGACATCTTC 60.135 52.381 11.67 3.83 37.92 2.87
183 184 1.860950 CGTCACGCCTAAAGATGGATG 59.139 52.381 0.00 0.00 0.00 3.51
197 198 0.996462 ATTATTGTGCCGTCGTCACG 59.004 50.000 1.58 0.00 46.29 4.35
207 208 4.516092 GTGTCTACCACGATTATTGTGC 57.484 45.455 7.05 0.00 36.01 4.57
221 222 6.016943 GGGTCTACAGTGATATCTGTGTCTAC 60.017 46.154 12.20 11.37 46.36 2.59
224 225 4.890581 AGGGTCTACAGTGATATCTGTGTC 59.109 45.833 12.20 1.90 46.36 3.67
232 233 8.492415 AATAAGCATAAGGGTCTACAGTGATA 57.508 34.615 0.00 0.00 0.00 2.15
265 266 7.639113 AACAATCTTACACAAAAGTCCTCAA 57.361 32.000 0.00 0.00 0.00 3.02
266 267 7.122055 ACAAACAATCTTACACAAAAGTCCTCA 59.878 33.333 0.00 0.00 0.00 3.86
271 272 7.698970 CCGTTACAAACAATCTTACACAAAAGT 59.301 33.333 0.00 0.00 0.00 2.66
320 322 5.517322 CTACATAAAGGAGTAGCGGAAGT 57.483 43.478 0.00 0.00 32.25 3.01
332 334 4.238514 GAGCATACGAGGCTACATAAAGG 58.761 47.826 0.00 0.00 42.78 3.11
361 363 6.977213 TCTTTGGCAATTCTTTACCAAGTAC 58.023 36.000 0.00 0.00 39.03 2.73
366 368 5.163364 TGCTTTCTTTGGCAATTCTTTACCA 60.163 36.000 0.00 0.00 35.40 3.25
367 369 5.296748 TGCTTTCTTTGGCAATTCTTTACC 58.703 37.500 0.00 0.00 35.40 2.85
368 370 5.107337 GCTGCTTTCTTTGGCAATTCTTTAC 60.107 40.000 0.00 0.00 38.02 2.01
385 387 2.235898 TGGTTTTTCCACTTGCTGCTTT 59.764 40.909 0.00 0.00 41.93 3.51
403 405 2.101640 ACTTGAGGGGCAATTTTGGT 57.898 45.000 0.00 0.00 35.59 3.67
419 421 6.033831 CGTCGTGATACCATTAACGTTTACTT 59.966 38.462 5.91 0.00 37.32 2.24
423 425 4.090354 CACGTCGTGATACCATTAACGTTT 59.910 41.667 20.75 0.00 36.28 3.60
457 473 4.984295 TCAGTCCAGAGATCATCTAGGAG 58.016 47.826 8.30 0.09 36.50 3.69
458 474 5.597430 ATCAGTCCAGAGATCATCTAGGA 57.403 43.478 4.51 4.51 36.10 2.94
459 475 6.041865 ACAAATCAGTCCAGAGATCATCTAGG 59.958 42.308 0.00 0.00 36.10 3.02
460 476 6.924612 CACAAATCAGTCCAGAGATCATCTAG 59.075 42.308 0.00 0.00 36.10 2.43
461 477 6.183360 CCACAAATCAGTCCAGAGATCATCTA 60.183 42.308 0.00 0.00 36.10 1.98
462 478 5.396548 CCACAAATCAGTCCAGAGATCATCT 60.397 44.000 0.00 0.00 39.56 2.90
472 488 5.410132 CGTGTAAATACCACAAATCAGTCCA 59.590 40.000 0.00 0.00 0.00 4.02
495 514 2.761559 TCTTCCCAACATACACACACG 58.238 47.619 0.00 0.00 0.00 4.49
497 516 4.133820 CAGTTCTTCCCAACATACACACA 58.866 43.478 0.00 0.00 0.00 3.72
498 517 3.502211 CCAGTTCTTCCCAACATACACAC 59.498 47.826 0.00 0.00 0.00 3.82
510 529 1.143073 AGGACAACACCCAGTTCTTCC 59.857 52.381 0.00 0.00 38.74 3.46
516 535 1.046472 TGTCGAGGACAACACCCAGT 61.046 55.000 0.00 0.00 39.78 4.00
525 544 2.038690 GACACCACTGTCGAGGACA 58.961 57.895 0.00 0.00 40.50 4.02
526 545 4.968197 GACACCACTGTCGAGGAC 57.032 61.111 0.00 0.00 37.67 3.85
535 554 6.665992 TTGAGACTGTTAATAGACACCACT 57.334 37.500 6.19 0.00 0.00 4.00
539 558 7.278868 CCTGGATTTGAGACTGTTAATAGACAC 59.721 40.741 6.19 0.00 0.00 3.67
556 575 2.570135 GCTTCTCTAGCCCTGGATTTG 58.430 52.381 0.00 0.00 44.48 2.32
585 604 2.745152 CGAAATAACACAGCCTAGGGGG 60.745 54.545 11.72 0.00 38.36 5.40
598 617 1.589779 CTAACCCGCCGTCGAAATAAC 59.410 52.381 0.00 0.00 38.10 1.89
606 625 1.067582 CCAGATCTAACCCGCCGTC 59.932 63.158 0.00 0.00 0.00 4.79
609 628 3.767673 TCATATACCAGATCTAACCCGCC 59.232 47.826 0.00 0.00 0.00 6.13
611 630 7.339721 ACATACTCATATACCAGATCTAACCCG 59.660 40.741 0.00 0.00 0.00 5.28
620 639 6.214177 TGGAGGACATACTCATATACCAGA 57.786 41.667 0.00 0.00 39.27 3.86
622 641 7.684317 TTTTGGAGGACATACTCATATACCA 57.316 36.000 0.00 0.00 39.27 3.25
623 642 9.877178 CTATTTTGGAGGACATACTCATATACC 57.123 37.037 0.00 0.00 39.27 2.73
625 644 9.615660 ACCTATTTTGGAGGACATACTCATATA 57.384 33.333 0.00 0.00 39.27 0.86
626 645 8.378565 CACCTATTTTGGAGGACATACTCATAT 58.621 37.037 0.00 0.00 39.27 1.78
627 646 7.347222 ACACCTATTTTGGAGGACATACTCATA 59.653 37.037 0.00 0.00 39.27 2.15
628 647 6.158695 ACACCTATTTTGGAGGACATACTCAT 59.841 38.462 0.00 0.00 39.27 2.90
629 648 5.487488 ACACCTATTTTGGAGGACATACTCA 59.513 40.000 0.00 0.00 39.27 3.41
630 649 5.817816 CACACCTATTTTGGAGGACATACTC 59.182 44.000 0.00 0.00 37.53 2.59
631 650 5.250774 ACACACCTATTTTGGAGGACATACT 59.749 40.000 0.00 0.00 37.53 2.12
632 651 5.354234 CACACACCTATTTTGGAGGACATAC 59.646 44.000 0.00 0.00 37.53 2.39
633 652 5.496556 CACACACCTATTTTGGAGGACATA 58.503 41.667 0.00 0.00 37.53 2.29
634 653 4.335416 CACACACCTATTTTGGAGGACAT 58.665 43.478 0.00 0.00 37.53 3.06
635 654 3.497763 CCACACACCTATTTTGGAGGACA 60.498 47.826 0.00 0.00 37.53 4.02
636 655 3.081804 CCACACACCTATTTTGGAGGAC 58.918 50.000 0.00 0.00 37.53 3.85
637 656 2.554344 GCCACACACCTATTTTGGAGGA 60.554 50.000 0.00 0.00 37.53 3.71
638 657 1.818674 GCCACACACCTATTTTGGAGG 59.181 52.381 0.00 0.00 40.22 4.30
639 658 2.795329 AGCCACACACCTATTTTGGAG 58.205 47.619 0.00 0.00 0.00 3.86
640 659 2.969821 AGCCACACACCTATTTTGGA 57.030 45.000 0.00 0.00 0.00 3.53
641 660 3.440173 CAGTAGCCACACACCTATTTTGG 59.560 47.826 0.00 0.00 0.00 3.28
642 661 3.119849 GCAGTAGCCACACACCTATTTTG 60.120 47.826 0.00 0.00 33.58 2.44
643 662 3.081804 GCAGTAGCCACACACCTATTTT 58.918 45.455 0.00 0.00 33.58 1.82
644 663 2.039746 TGCAGTAGCCACACACCTATTT 59.960 45.455 0.00 0.00 41.13 1.40
645 664 1.628340 TGCAGTAGCCACACACCTATT 59.372 47.619 0.00 0.00 41.13 1.73
646 665 1.066143 GTGCAGTAGCCACACACCTAT 60.066 52.381 0.00 0.00 41.13 2.57
647 666 0.320374 GTGCAGTAGCCACACACCTA 59.680 55.000 0.00 0.00 41.13 3.08
648 667 1.071471 GTGCAGTAGCCACACACCT 59.929 57.895 0.00 0.00 41.13 4.00
649 668 1.966451 GGTGCAGTAGCCACACACC 60.966 63.158 10.74 10.74 43.02 4.16
650 669 0.951040 GAGGTGCAGTAGCCACACAC 60.951 60.000 0.00 0.83 41.13 3.82
651 670 1.371183 GAGGTGCAGTAGCCACACA 59.629 57.895 0.00 0.00 41.13 3.72
652 671 0.036010 ATGAGGTGCAGTAGCCACAC 60.036 55.000 0.00 0.00 41.13 3.82
653 672 1.567357 TATGAGGTGCAGTAGCCACA 58.433 50.000 0.00 0.00 41.13 4.17
654 673 2.691409 TTATGAGGTGCAGTAGCCAC 57.309 50.000 0.00 0.00 41.13 5.01
655 674 2.571653 ACTTTATGAGGTGCAGTAGCCA 59.428 45.455 0.00 0.00 41.13 4.75
656 675 3.118592 AGACTTTATGAGGTGCAGTAGCC 60.119 47.826 0.00 0.00 41.13 3.93
657 676 4.130286 AGACTTTATGAGGTGCAGTAGC 57.870 45.455 0.00 0.00 42.57 3.58
658 677 5.352569 CCAAAGACTTTATGAGGTGCAGTAG 59.647 44.000 0.00 0.00 0.00 2.57
659 678 5.245531 CCAAAGACTTTATGAGGTGCAGTA 58.754 41.667 0.00 0.00 0.00 2.74
660 679 4.074970 CCAAAGACTTTATGAGGTGCAGT 58.925 43.478 0.00 0.00 0.00 4.40
661 680 3.441572 CCCAAAGACTTTATGAGGTGCAG 59.558 47.826 0.00 0.00 0.00 4.41
662 681 3.181434 ACCCAAAGACTTTATGAGGTGCA 60.181 43.478 0.00 0.00 0.00 4.57
663 682 3.191371 CACCCAAAGACTTTATGAGGTGC 59.809 47.826 18.21 0.00 37.34 5.01
664 683 4.651778 TCACCCAAAGACTTTATGAGGTG 58.348 43.478 21.41 21.41 43.89 4.00
665 684 4.993705 TCACCCAAAGACTTTATGAGGT 57.006 40.909 0.00 3.08 0.00 3.85
666 685 5.500234 TCATCACCCAAAGACTTTATGAGG 58.500 41.667 0.00 7.13 0.00 3.86
667 686 5.587844 CCTCATCACCCAAAGACTTTATGAG 59.412 44.000 20.98 20.98 39.05 2.90
668 687 5.250543 TCCTCATCACCCAAAGACTTTATGA 59.749 40.000 0.00 5.31 0.00 2.15
669 688 5.500234 TCCTCATCACCCAAAGACTTTATG 58.500 41.667 0.00 1.01 0.00 1.90
670 689 5.779241 TCCTCATCACCCAAAGACTTTAT 57.221 39.130 0.00 0.00 0.00 1.40
693 712 3.070018 CTGGTGCAAGAGAACTCGAAAT 58.930 45.455 0.00 0.00 34.09 2.17
709 728 1.302033 GGTGGAGTCACTGCTGGTG 60.302 63.158 0.00 4.43 46.60 4.17
711 730 1.004080 CAGGTGGAGTCACTGCTGG 60.004 63.158 0.00 0.00 43.17 4.85
742 1260 3.500680 GGCTTTAAGTCGAATGTTCACCA 59.499 43.478 0.00 0.00 0.00 4.17
799 1334 2.666317 GGGAGGAAGAGAGAGAAGAGG 58.334 57.143 0.00 0.00 0.00 3.69
808 1343 0.906756 CTGCACTGGGGAGGAAGAGA 60.907 60.000 0.00 0.00 0.00 3.10
813 1348 2.607750 GGACTGCACTGGGGAGGA 60.608 66.667 2.79 0.00 39.67 3.71
820 1355 0.320247 GACTGGACTGGACTGCACTG 60.320 60.000 0.00 0.00 0.00 3.66
821 1356 1.476007 GGACTGGACTGGACTGCACT 61.476 60.000 0.00 0.00 0.00 4.40
822 1357 1.004440 GGACTGGACTGGACTGCAC 60.004 63.158 0.00 0.00 0.00 4.57
823 1358 1.459348 TGGACTGGACTGGACTGCA 60.459 57.895 0.00 0.00 0.00 4.41
824 1359 1.294780 CTGGACTGGACTGGACTGC 59.705 63.158 0.00 0.00 0.00 4.40
825 1360 0.605589 GACTGGACTGGACTGGACTG 59.394 60.000 0.00 0.00 0.00 3.51
826 1361 0.188587 TGACTGGACTGGACTGGACT 59.811 55.000 0.00 0.00 0.00 3.85
827 1362 1.048601 TTGACTGGACTGGACTGGAC 58.951 55.000 0.00 0.00 0.00 4.02
828 1363 1.694150 CTTTGACTGGACTGGACTGGA 59.306 52.381 0.00 0.00 0.00 3.86
829 1364 1.879796 GCTTTGACTGGACTGGACTGG 60.880 57.143 0.00 0.00 0.00 4.00
830 1365 1.517242 GCTTTGACTGGACTGGACTG 58.483 55.000 0.00 0.00 0.00 3.51
831 1366 0.034059 CGCTTTGACTGGACTGGACT 59.966 55.000 0.00 0.00 0.00 3.85
832 1367 0.033504 TCGCTTTGACTGGACTGGAC 59.966 55.000 0.00 0.00 0.00 4.02
833 1368 0.756294 TTCGCTTTGACTGGACTGGA 59.244 50.000 0.00 0.00 0.00 3.86
860 1395 4.536364 TTGTCTTTTGTCTTTGAGAGCG 57.464 40.909 0.00 0.00 0.00 5.03
861 1396 6.808704 AGTTTTTGTCTTTTGTCTTTGAGAGC 59.191 34.615 0.00 0.00 0.00 4.09
869 1406 7.363007 GGGAAAGAGAGTTTTTGTCTTTTGTCT 60.363 37.037 1.58 0.00 46.15 3.41
897 1434 1.670811 CGGCAATGGAGTATGTGAACC 59.329 52.381 0.00 0.00 0.00 3.62
899 1436 2.236146 AGACGGCAATGGAGTATGTGAA 59.764 45.455 0.00 0.00 0.00 3.18
900 1437 1.831106 AGACGGCAATGGAGTATGTGA 59.169 47.619 0.00 0.00 0.00 3.58
901 1438 2.315925 AGACGGCAATGGAGTATGTG 57.684 50.000 0.00 0.00 0.00 3.21
902 1439 3.031736 ACTAGACGGCAATGGAGTATGT 58.968 45.455 0.00 0.00 0.00 2.29
903 1440 3.735237 ACTAGACGGCAATGGAGTATG 57.265 47.619 0.00 0.00 0.00 2.39
904 1441 3.573110 GGTACTAGACGGCAATGGAGTAT 59.427 47.826 0.00 0.00 0.00 2.12
905 1442 2.954318 GGTACTAGACGGCAATGGAGTA 59.046 50.000 0.00 0.00 0.00 2.59
906 1443 1.755380 GGTACTAGACGGCAATGGAGT 59.245 52.381 0.00 0.00 0.00 3.85
934 1479 2.352805 GGAGTGAACTGCTGGGGG 59.647 66.667 0.00 0.00 0.00 5.40
965 1510 4.625800 GCCTCTTGCTGGTGGTAG 57.374 61.111 0.00 0.00 36.87 3.18
975 1520 2.360852 CCCACAGCCAGCCTCTTG 60.361 66.667 0.00 0.00 0.00 3.02
980 1525 4.437587 ATCAGCCCACAGCCAGCC 62.438 66.667 0.00 0.00 45.47 4.85
1134 1679 4.577677 TTCCTGCTGGCGTTGGCA 62.578 61.111 4.42 0.00 42.47 4.92
1135 1680 3.741476 CTTCCTGCTGGCGTTGGC 61.741 66.667 4.42 0.00 38.90 4.52
1136 1681 3.058160 CCTTCCTGCTGGCGTTGG 61.058 66.667 4.42 0.65 0.00 3.77
1137 1682 2.032528 TCCTTCCTGCTGGCGTTG 59.967 61.111 4.42 0.00 0.00 4.10
1138 1683 2.348998 CTCCTTCCTGCTGGCGTT 59.651 61.111 4.42 0.00 0.00 4.84
1139 1684 4.400961 GCTCCTTCCTGCTGGCGT 62.401 66.667 4.42 0.00 0.00 5.68
1331 1894 2.283966 CCACACCCTCCTCCTCGT 60.284 66.667 0.00 0.00 0.00 4.18
1500 2081 1.675801 CTGGTCTGCTTGCTCTCCA 59.324 57.895 0.00 0.00 0.00 3.86
1501 2082 1.744741 GCTGGTCTGCTTGCTCTCC 60.745 63.158 0.00 0.00 0.00 3.71
1502 2083 1.744741 GGCTGGTCTGCTTGCTCTC 60.745 63.158 0.24 0.00 0.00 3.20
1503 2084 2.350514 GGCTGGTCTGCTTGCTCT 59.649 61.111 0.24 0.00 0.00 4.09
1504 2085 3.123620 CGGCTGGTCTGCTTGCTC 61.124 66.667 0.24 0.00 0.00 4.26
1505 2086 4.711949 CCGGCTGGTCTGCTTGCT 62.712 66.667 2.29 0.00 0.00 3.91
1506 2087 4.704833 TCCGGCTGGTCTGCTTGC 62.705 66.667 12.43 0.00 36.30 4.01
1507 2088 2.435586 CTCCGGCTGGTCTGCTTG 60.436 66.667 12.43 0.00 36.30 4.01
1508 2089 4.400961 GCTCCGGCTGGTCTGCTT 62.401 66.667 12.43 0.00 36.30 3.91
1535 2116 0.104304 ATCGCCGGCTAACTAACTGG 59.896 55.000 26.68 4.37 35.26 4.00
1573 2158 9.055248 CAAAGAAAATTGTCGAATCTATGACAC 57.945 33.333 0.00 0.00 44.25 3.67
1614 2199 1.228033 TGCTTTCTGCTGCTGCTGA 60.228 52.632 18.88 18.88 43.70 4.26
1649 2237 0.877071 CCAATCCTATCATGCACGCC 59.123 55.000 0.00 0.00 0.00 5.68
1664 2252 8.763601 AGAAAGAATTAGTACTGACTAGCCAAT 58.236 33.333 5.39 0.00 39.36 3.16
1675 2263 6.736179 AGGAGGGGAAAGAAAGAATTAGTACT 59.264 38.462 0.00 0.00 0.00 2.73
1679 2267 6.249192 ACAAGGAGGGGAAAGAAAGAATTAG 58.751 40.000 0.00 0.00 0.00 1.73
1713 2301 1.206878 TGTCCATCCATCCACTCCTG 58.793 55.000 0.00 0.00 0.00 3.86
1728 2316 5.954296 AGTATTAATCTGCATGCATGTCC 57.046 39.130 26.79 12.52 0.00 4.02
1729 2317 7.664082 AGTAGTATTAATCTGCATGCATGTC 57.336 36.000 26.79 18.98 0.00 3.06
1730 2318 7.329471 CGTAGTAGTATTAATCTGCATGCATGT 59.671 37.037 26.79 10.13 0.00 3.21
1731 2319 7.201470 CCGTAGTAGTATTAATCTGCATGCATG 60.201 40.741 22.97 22.70 0.00 4.06
1750 2338 1.407618 ACATGCAGATTCGCCGTAGTA 59.592 47.619 0.00 0.00 0.00 1.82
1751 2339 0.175760 ACATGCAGATTCGCCGTAGT 59.824 50.000 0.00 0.00 0.00 2.73
1752 2340 2.134201 TACATGCAGATTCGCCGTAG 57.866 50.000 0.00 0.00 0.00 3.51
1753 2341 2.812358 ATACATGCAGATTCGCCGTA 57.188 45.000 0.00 0.00 0.00 4.02
1755 2343 4.389992 AGATTAATACATGCAGATTCGCCG 59.610 41.667 0.00 0.00 0.00 6.46
1756 2344 5.625251 CAGATTAATACATGCAGATTCGCC 58.375 41.667 0.00 0.00 0.00 5.54
1757 2345 5.084722 GCAGATTAATACATGCAGATTCGC 58.915 41.667 12.52 0.00 38.54 4.70
1758 2346 6.232139 TGCAGATTAATACATGCAGATTCG 57.768 37.500 14.99 0.00 43.34 3.34
1765 2353 7.372714 TCCAATTCATGCAGATTAATACATGC 58.627 34.615 15.70 13.54 39.75 4.06
1766 2354 7.541091 GCTCCAATTCATGCAGATTAATACATG 59.459 37.037 14.87 14.87 40.97 3.21
1767 2355 7.309621 GGCTCCAATTCATGCAGATTAATACAT 60.310 37.037 0.00 0.00 0.00 2.29
1769 2357 6.385033 GGCTCCAATTCATGCAGATTAATAC 58.615 40.000 0.00 0.00 0.00 1.89
1770 2358 5.477984 GGGCTCCAATTCATGCAGATTAATA 59.522 40.000 0.00 0.00 0.00 0.98
1771 2359 4.282703 GGGCTCCAATTCATGCAGATTAAT 59.717 41.667 0.00 0.00 0.00 1.40
1773 2361 3.225104 GGGCTCCAATTCATGCAGATTA 58.775 45.455 0.00 0.00 0.00 1.75
1774 2362 2.037144 GGGCTCCAATTCATGCAGATT 58.963 47.619 0.00 0.00 0.00 2.40
1775 2363 1.700955 GGGCTCCAATTCATGCAGAT 58.299 50.000 0.00 0.00 0.00 2.90
1776 2364 0.396139 GGGGCTCCAATTCATGCAGA 60.396 55.000 0.00 0.00 0.00 4.26
1777 2365 1.397390 GGGGGCTCCAATTCATGCAG 61.397 60.000 4.16 0.00 35.00 4.41
1778 2366 1.381599 GGGGGCTCCAATTCATGCA 60.382 57.895 4.16 0.00 35.00 3.96
1779 2367 0.688749 AAGGGGGCTCCAATTCATGC 60.689 55.000 5.99 0.00 38.24 4.06
1780 2368 1.870064 AAAGGGGGCTCCAATTCATG 58.130 50.000 5.99 0.00 38.24 3.07
1781 2369 2.647846 AAAAGGGGGCTCCAATTCAT 57.352 45.000 5.99 0.00 38.24 2.57
1782 2370 2.414250 AAAAAGGGGGCTCCAATTCA 57.586 45.000 5.99 0.00 38.24 2.57
1802 2390 1.607178 TCCCGTTCCTGCTCCGTAA 60.607 57.895 0.00 0.00 0.00 3.18
1819 2431 0.595825 CCCCGTAATTACTCGCCGTC 60.596 60.000 13.56 0.00 0.00 4.79
1888 2502 0.391130 GTAACTCCACTCCGCATGCA 60.391 55.000 19.57 0.00 0.00 3.96
1889 2503 0.108138 AGTAACTCCACTCCGCATGC 60.108 55.000 7.91 7.91 0.00 4.06
1890 2504 1.927895 GAGTAACTCCACTCCGCATG 58.072 55.000 0.00 0.00 39.26 4.06
1954 2577 3.898627 AAGACTGTCGGCAGCGACG 62.899 63.158 18.84 0.00 46.30 5.12
1955 2578 2.049063 AAGACTGTCGGCAGCGAC 60.049 61.111 18.84 9.15 46.30 5.19
1956 2579 1.806461 AAGAAGACTGTCGGCAGCGA 61.806 55.000 18.84 0.00 46.30 4.93
1957 2580 0.946221 AAAGAAGACTGTCGGCAGCG 60.946 55.000 18.84 0.00 46.30 5.18
1958 2581 1.230324 AAAAGAAGACTGTCGGCAGC 58.770 50.000 18.84 10.23 46.30 5.25
1979 2602 1.523154 GGGACGCATTGCACAAAGGA 61.523 55.000 9.69 0.00 0.00 3.36
1980 2603 1.080569 GGGACGCATTGCACAAAGG 60.081 57.895 9.69 0.00 0.00 3.11
1998 2621 2.549754 AGTCTGTGTTTTGCGAGGAATG 59.450 45.455 0.00 0.00 0.00 2.67
1999 2622 2.808543 GAGTCTGTGTTTTGCGAGGAAT 59.191 45.455 0.00 0.00 0.00 3.01
2000 2623 2.210116 GAGTCTGTGTTTTGCGAGGAA 58.790 47.619 0.00 0.00 0.00 3.36
2003 2626 0.111089 GCGAGTCTGTGTTTTGCGAG 60.111 55.000 0.00 0.00 0.00 5.03
2006 2629 0.380378 TTGGCGAGTCTGTGTTTTGC 59.620 50.000 0.00 0.00 0.00 3.68
2008 2631 2.038387 ACTTGGCGAGTCTGTGTTTT 57.962 45.000 0.18 0.00 31.20 2.43
2009 2632 3.780624 ACTTGGCGAGTCTGTGTTT 57.219 47.368 0.18 0.00 31.20 2.83
2018 2641 4.452455 ACACTTATTTTGAGACTTGGCGAG 59.548 41.667 0.00 0.00 0.00 5.03
2021 2644 5.470098 TGAGACACTTATTTTGAGACTTGGC 59.530 40.000 0.00 0.00 0.00 4.52
2022 2645 7.496529 TTGAGACACTTATTTTGAGACTTGG 57.503 36.000 0.00 0.00 0.00 3.61
2029 2652 9.554724 GCGATAAAATTGAGACACTTATTTTGA 57.445 29.630 0.00 0.00 33.59 2.69
2030 2653 9.340695 TGCGATAAAATTGAGACACTTATTTTG 57.659 29.630 0.00 0.00 33.59 2.44
2032 2655 8.730680 AGTGCGATAAAATTGAGACACTTATTT 58.269 29.630 0.00 0.00 33.56 1.40
2034 2657 7.849804 AGTGCGATAAAATTGAGACACTTAT 57.150 32.000 0.00 0.00 33.56 1.73
2037 2660 7.849804 AATAGTGCGATAAAATTGAGACACT 57.150 32.000 0.00 0.00 40.10 3.55
2077 2851 9.995003 TCGTCCTAAAATAAGTGTTTTAACCTA 57.005 29.630 0.00 0.00 34.26 3.08
2080 2854 9.603298 CCTTCGTCCTAAAATAAGTGTTTTAAC 57.397 33.333 0.00 0.00 34.26 2.01
2081 2855 9.558396 TCCTTCGTCCTAAAATAAGTGTTTTAA 57.442 29.630 0.00 0.00 34.26 1.52
2082 2856 9.558396 TTCCTTCGTCCTAAAATAAGTGTTTTA 57.442 29.630 0.00 0.00 33.62 1.52
2083 2857 8.454570 TTCCTTCGTCCTAAAATAAGTGTTTT 57.545 30.769 0.00 0.00 35.60 2.43
2085 2859 7.222161 ACTTCCTTCGTCCTAAAATAAGTGTT 58.778 34.615 0.00 0.00 0.00 3.32
2087 2861 8.033626 AGTACTTCCTTCGTCCTAAAATAAGTG 58.966 37.037 0.00 0.00 0.00 3.16
2088 2862 8.131847 AGTACTTCCTTCGTCCTAAAATAAGT 57.868 34.615 0.00 0.00 0.00 2.24
2092 2866 9.783081 TTTTTAGTACTTCCTTCGTCCTAAAAT 57.217 29.630 0.00 0.00 34.65 1.82
2117 2891 6.801575 ACAGTTCAATATTGACACCGTTTTT 58.198 32.000 17.76 1.25 36.83 1.94
2131 2905 5.876357 AGCTTGAAAGGGTACAGTTCAATA 58.124 37.500 14.50 0.06 39.74 1.90
2140 2914 2.740447 CCACGTTAGCTTGAAAGGGTAC 59.260 50.000 0.00 0.00 0.00 3.34
2144 2918 5.640357 TGTAATACCACGTTAGCTTGAAAGG 59.360 40.000 0.00 0.00 0.00 3.11
2163 4532 6.132658 TCTCTTCAGCCTCTCTGTATGTAAT 58.867 40.000 0.00 0.00 43.32 1.89
2171 4540 3.674528 TGTTTCTCTTCAGCCTCTCTG 57.325 47.619 0.00 0.00 44.21 3.35
2172 4541 3.645687 ACTTGTTTCTCTTCAGCCTCTCT 59.354 43.478 0.00 0.00 0.00 3.10
2221 4772 2.111878 GGCACATGGATCCCTCGG 59.888 66.667 9.90 0.00 0.00 4.63
2313 6047 4.994471 CAGCCAGCCAGCGTCACA 62.994 66.667 0.00 0.00 38.01 3.58
2338 6079 0.811281 GGAAAGGATGGTTCGCCTTG 59.189 55.000 0.00 0.00 43.46 3.61
2391 6132 2.991540 GCCCCTGCTTTGTCCACC 60.992 66.667 0.00 0.00 33.53 4.61
2415 6156 0.251354 ATATATCCGGCCAGCTGCTG 59.749 55.000 22.44 22.44 46.56 4.41
2449 6190 0.695803 ATGTGTCCCATCCCCTCTCC 60.696 60.000 0.00 0.00 0.00 3.71
2450 6191 0.471617 CATGTGTCCCATCCCCTCTC 59.528 60.000 0.00 0.00 0.00 3.20
2451 6192 1.639635 GCATGTGTCCCATCCCCTCT 61.640 60.000 0.00 0.00 0.00 3.69
2452 6193 1.152881 GCATGTGTCCCATCCCCTC 60.153 63.158 0.00 0.00 0.00 4.30
2453 6194 1.929860 CTGCATGTGTCCCATCCCCT 61.930 60.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.