Multiple sequence alignment - TraesCS2A01G027900

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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 TraesCS2A01G027900 chr2A 100.000 3035 0 0 1 3035 12905622 12902588 0.000000e+00 5605
1 TraesCS2A01G027900 chr2A 93.401 1985 113 14 1061 3035 677222422 677220446 0.000000e+00 2924
2 TraesCS2A01G027900 chr2A 93.902 1476 74 9 1571 3035 70125564 70124094 0.000000e+00 2213
3 TraesCS2A01G027900 chr2A 93.426 791 38 3 775 1551 70134931 70134141 0.000000e+00 1160
4 TraesCS2A01G027900 chr2A 90.714 280 13 2 775 1041 70118941 70118662 8.000000e-96 361
5 TraesCS2A01G027900 chr1A 94.092 2285 107 10 775 3035 561407392 561405112 0.000000e+00 3446
6 TraesCS2A01G027900 chr1A 93.010 2289 126 12 773 3035 327713819 327711539 0.000000e+00 3310
7 TraesCS2A01G027900 chr1A 90.877 285 14 1 775 1047 561391728 561391444 3.700000e-99 372
8 TraesCS2A01G027900 chr7A 93.950 2281 117 15 770 3035 17110598 17112872 0.000000e+00 3428
9 TraesCS2A01G027900 chr7A 96.302 676 25 0 1 676 42300830 42301505 0.000000e+00 1110
10 TraesCS2A01G027900 chr7B 93.488 2288 115 18 775 3035 648721063 648718783 0.000000e+00 3369
11 TraesCS2A01G027900 chr5A 93.360 2289 120 16 773 3035 649442264 649444546 0.000000e+00 3356
12 TraesCS2A01G027900 chr4A 93.409 2276 98 17 773 3035 125038526 125036290 0.000000e+00 3325
13 TraesCS2A01G027900 chr4A 90.750 2292 142 30 776 3035 621705814 621708067 0.000000e+00 2994
14 TraesCS2A01G027900 chr4A 81.899 674 120 2 3 675 36286757 36286085 4.390000e-158 568
15 TraesCS2A01G027900 chr4A 86.145 332 32 5 775 1093 713599907 713600237 2.240000e-91 346
16 TraesCS2A01G027900 chr3D 95.210 1023 36 5 2023 3035 35718570 35719589 0.000000e+00 1605
17 TraesCS2A01G027900 chr3D 82.085 681 120 2 1 680 593232057 593231378 5.640000e-162 580
18 TraesCS2A01G027900 chr3D 81.858 678 121 2 1 677 425142985 425143661 1.220000e-158 569
19 TraesCS2A01G027900 chr3D 91.791 268 10 1 775 1030 35724746 35725013 2.220000e-96 363
20 TraesCS2A01G027900 chr6B 95.126 677 30 3 1 677 132332014 132332687 0.000000e+00 1064
21 TraesCS2A01G027900 chr5B 88.496 678 66 7 1 677 584607711 584608377 0.000000e+00 809
22 TraesCS2A01G027900 chrUn 90.510 569 48 3 1 569 63034303 63033741 0.000000e+00 747
23 TraesCS2A01G027900 chr2D 82.448 678 117 2 1 677 348981659 348982335 2.610000e-165 592
24 TraesCS2A01G027900 chr2D 81.711 678 122 2 1 677 74940323 74939647 5.680000e-157 564
25 TraesCS2A01G027900 chr7D 90.361 332 19 4 775 1093 168818006 168817675 1.010000e-114 424


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 TraesCS2A01G027900 chr2A 12902588 12905622 3034 True 5605 5605 100.000 1 3035 1 chr2A.!!$R1 3034
1 TraesCS2A01G027900 chr2A 677220446 677222422 1976 True 2924 2924 93.401 1061 3035 1 chr2A.!!$R5 1974
2 TraesCS2A01G027900 chr2A 70124094 70125564 1470 True 2213 2213 93.902 1571 3035 1 chr2A.!!$R3 1464
3 TraesCS2A01G027900 chr2A 70134141 70134931 790 True 1160 1160 93.426 775 1551 1 chr2A.!!$R4 776
4 TraesCS2A01G027900 chr1A 561405112 561407392 2280 True 3446 3446 94.092 775 3035 1 chr1A.!!$R3 2260
5 TraesCS2A01G027900 chr1A 327711539 327713819 2280 True 3310 3310 93.010 773 3035 1 chr1A.!!$R1 2262
6 TraesCS2A01G027900 chr7A 17110598 17112872 2274 False 3428 3428 93.950 770 3035 1 chr7A.!!$F1 2265
7 TraesCS2A01G027900 chr7A 42300830 42301505 675 False 1110 1110 96.302 1 676 1 chr7A.!!$F2 675
8 TraesCS2A01G027900 chr7B 648718783 648721063 2280 True 3369 3369 93.488 775 3035 1 chr7B.!!$R1 2260
9 TraesCS2A01G027900 chr5A 649442264 649444546 2282 False 3356 3356 93.360 773 3035 1 chr5A.!!$F1 2262
10 TraesCS2A01G027900 chr4A 125036290 125038526 2236 True 3325 3325 93.409 773 3035 1 chr4A.!!$R2 2262
11 TraesCS2A01G027900 chr4A 621705814 621708067 2253 False 2994 2994 90.750 776 3035 1 chr4A.!!$F1 2259
12 TraesCS2A01G027900 chr4A 36286085 36286757 672 True 568 568 81.899 3 675 1 chr4A.!!$R1 672
13 TraesCS2A01G027900 chr3D 35718570 35719589 1019 False 1605 1605 95.210 2023 3035 1 chr3D.!!$F1 1012
14 TraesCS2A01G027900 chr3D 593231378 593232057 679 True 580 580 82.085 1 680 1 chr3D.!!$R1 679
15 TraesCS2A01G027900 chr3D 425142985 425143661 676 False 569 569 81.858 1 677 1 chr3D.!!$F3 676
16 TraesCS2A01G027900 chr6B 132332014 132332687 673 False 1064 1064 95.126 1 677 1 chr6B.!!$F1 676
17 TraesCS2A01G027900 chr5B 584607711 584608377 666 False 809 809 88.496 1 677 1 chr5B.!!$F1 676
18 TraesCS2A01G027900 chrUn 63033741 63034303 562 True 747 747 90.510 1 569 1 chrUn.!!$R1 568
19 TraesCS2A01G027900 chr2D 348981659 348982335 676 False 592 592 82.448 1 677 1 chr2D.!!$F1 676
20 TraesCS2A01G027900 chr2D 74939647 74940323 676 True 564 564 81.711 1 677 1 chr2D.!!$R1 676

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
597 598 0.179004 TGTTTGGTTGCACTCGGGAT 60.179 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2255 1.817099 GCCCATGCACCGAAGAGAG 60.817 63.158 0.0 0.0 37.47 3.2 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
35 36 2.368875 ACGCTTCCTTCAGGGGTATATG 59.631 50.000 0.00 0.00 35.41 1.78
48 49 6.778069 TCAGGGGTATATGAACTCACTCTTAG 59.222 42.308 0.00 0.00 0.00 2.18
400 401 1.372087 GAGCTTGATTGTGCGGAGGG 61.372 60.000 0.00 0.00 0.00 4.30
479 480 6.424032 TGAGGACATTAAGAGACTAGTAGCA 58.576 40.000 0.00 0.00 0.00 3.49
497 498 0.533032 CAACGGAGGGAAGAGAGGTC 59.467 60.000 0.00 0.00 0.00 3.85
520 521 7.586664 GGTCTCTTTTAATCTTTGTTGTCGTTC 59.413 37.037 0.00 0.00 0.00 3.95
521 522 7.318205 GTCTCTTTTAATCTTTGTTGTCGTTCG 59.682 37.037 0.00 0.00 0.00 3.95
522 523 5.905181 TCTTTTAATCTTTGTTGTCGTTCGC 59.095 36.000 0.00 0.00 0.00 4.70
523 524 4.797693 TTAATCTTTGTTGTCGTTCGCA 57.202 36.364 0.00 0.00 0.00 5.10
524 525 2.949714 ATCTTTGTTGTCGTTCGCAG 57.050 45.000 0.00 0.00 0.00 5.18
525 526 1.929230 TCTTTGTTGTCGTTCGCAGA 58.071 45.000 0.00 0.00 0.00 4.26
526 527 2.272678 TCTTTGTTGTCGTTCGCAGAA 58.727 42.857 0.00 0.00 45.90 3.02
527 528 2.029970 TCTTTGTTGTCGTTCGCAGAAC 59.970 45.455 10.23 10.23 45.90 3.01
528 529 1.360820 TTGTTGTCGTTCGCAGAACA 58.639 45.000 17.37 1.78 45.90 3.18
529 530 1.360820 TGTTGTCGTTCGCAGAACAA 58.639 45.000 17.37 6.33 45.90 2.83
530 531 1.732809 TGTTGTCGTTCGCAGAACAAA 59.267 42.857 17.37 8.64 45.90 2.83
531 532 2.222931 TGTTGTCGTTCGCAGAACAAAG 60.223 45.455 17.37 5.73 45.90 2.77
532 533 1.647346 TGTCGTTCGCAGAACAAAGT 58.353 45.000 17.37 0.00 45.90 2.66
533 534 2.004017 TGTCGTTCGCAGAACAAAGTT 58.996 42.857 17.37 0.00 45.90 2.66
534 535 3.188492 TGTCGTTCGCAGAACAAAGTTA 58.812 40.909 17.37 0.67 45.90 2.24
535 536 3.244345 TGTCGTTCGCAGAACAAAGTTAG 59.756 43.478 17.37 4.14 45.90 2.34
536 537 3.244579 GTCGTTCGCAGAACAAAGTTAGT 59.755 43.478 17.37 0.00 45.90 2.24
537 538 3.488310 TCGTTCGCAGAACAAAGTTAGTC 59.512 43.478 17.37 0.00 45.90 2.59
538 539 3.244345 CGTTCGCAGAACAAAGTTAGTCA 59.756 43.478 17.37 0.00 45.90 3.41
539 540 4.084537 CGTTCGCAGAACAAAGTTAGTCAT 60.085 41.667 17.37 0.00 45.90 3.06
540 541 4.990543 TCGCAGAACAAAGTTAGTCATG 57.009 40.909 0.00 0.00 0.00 3.07
541 542 4.627058 TCGCAGAACAAAGTTAGTCATGA 58.373 39.130 0.00 0.00 0.00 3.07
542 543 4.686091 TCGCAGAACAAAGTTAGTCATGAG 59.314 41.667 0.00 0.00 0.00 2.90
543 544 4.667668 CGCAGAACAAAGTTAGTCATGAGC 60.668 45.833 0.00 0.00 0.00 4.26
544 545 4.453819 GCAGAACAAAGTTAGTCATGAGCT 59.546 41.667 0.00 0.00 0.00 4.09
545 546 5.390356 GCAGAACAAAGTTAGTCATGAGCTC 60.390 44.000 6.82 6.82 0.00 4.09
546 547 5.698089 CAGAACAAAGTTAGTCATGAGCTCA 59.302 40.000 20.79 20.79 0.00 4.26
547 548 5.698545 AGAACAAAGTTAGTCATGAGCTCAC 59.301 40.000 20.97 6.64 0.00 3.51
548 549 4.319177 ACAAAGTTAGTCATGAGCTCACC 58.681 43.478 20.97 10.17 0.00 4.02
549 550 4.202357 ACAAAGTTAGTCATGAGCTCACCA 60.202 41.667 20.97 5.31 0.00 4.17
550 551 4.623932 AAGTTAGTCATGAGCTCACCAA 57.376 40.909 20.97 4.32 0.00 3.67
551 552 4.199432 AGTTAGTCATGAGCTCACCAAG 57.801 45.455 20.97 9.69 0.00 3.61
552 553 3.580458 AGTTAGTCATGAGCTCACCAAGT 59.420 43.478 20.97 12.44 0.00 3.16
553 554 4.772624 AGTTAGTCATGAGCTCACCAAGTA 59.227 41.667 20.97 11.44 0.00 2.24
554 555 5.423610 AGTTAGTCATGAGCTCACCAAGTAT 59.576 40.000 20.97 0.00 0.00 2.12
555 556 4.134379 AGTCATGAGCTCACCAAGTATG 57.866 45.455 20.97 11.80 0.00 2.39
567 568 3.460857 CCAAGTATGGTAGGAGCACTC 57.539 52.381 0.00 0.00 42.18 3.51
568 569 2.103263 CCAAGTATGGTAGGAGCACTCC 59.897 54.545 8.74 8.74 44.84 3.85
569 570 5.071091 CCAAGTATGGTAGGAGCACTCCC 62.071 56.522 13.15 0.00 45.23 4.30
586 587 3.591835 CCGCACCGCTGTTTGGTT 61.592 61.111 0.00 0.00 37.72 3.67
587 588 2.353376 CGCACCGCTGTTTGGTTG 60.353 61.111 0.00 0.00 37.72 3.77
588 589 2.658268 GCACCGCTGTTTGGTTGC 60.658 61.111 0.00 0.00 37.72 4.17
589 590 2.804167 CACCGCTGTTTGGTTGCA 59.196 55.556 0.00 0.00 37.72 4.08
590 591 1.588667 CACCGCTGTTTGGTTGCAC 60.589 57.895 0.00 0.00 37.72 4.57
591 592 1.752694 ACCGCTGTTTGGTTGCACT 60.753 52.632 0.00 0.00 35.82 4.40
592 593 1.008538 CCGCTGTTTGGTTGCACTC 60.009 57.895 0.00 0.00 0.00 3.51
593 594 1.369209 CGCTGTTTGGTTGCACTCG 60.369 57.895 0.00 0.00 0.00 4.18
594 595 1.008538 GCTGTTTGGTTGCACTCGG 60.009 57.895 0.00 0.00 0.00 4.63
595 596 1.654220 CTGTTTGGTTGCACTCGGG 59.346 57.895 0.00 0.00 0.00 5.14
596 597 0.817634 CTGTTTGGTTGCACTCGGGA 60.818 55.000 0.00 0.00 0.00 5.14
597 598 0.179004 TGTTTGGTTGCACTCGGGAT 60.179 50.000 0.00 0.00 0.00 3.85
598 599 0.958822 GTTTGGTTGCACTCGGGATT 59.041 50.000 0.00 0.00 0.00 3.01
599 600 2.156098 GTTTGGTTGCACTCGGGATTA 58.844 47.619 0.00 0.00 0.00 1.75
600 601 2.107950 TTGGTTGCACTCGGGATTAG 57.892 50.000 0.00 0.00 0.00 1.73
601 602 1.271856 TGGTTGCACTCGGGATTAGA 58.728 50.000 0.00 0.00 0.00 2.10
602 603 1.066430 TGGTTGCACTCGGGATTAGAC 60.066 52.381 0.00 0.00 0.00 2.59
603 604 1.653151 GTTGCACTCGGGATTAGACC 58.347 55.000 0.00 0.00 0.00 3.85
604 605 1.207329 GTTGCACTCGGGATTAGACCT 59.793 52.381 0.00 0.00 0.00 3.85
605 606 1.112113 TGCACTCGGGATTAGACCTC 58.888 55.000 0.00 0.00 0.00 3.85
606 607 1.112113 GCACTCGGGATTAGACCTCA 58.888 55.000 0.00 0.00 0.00 3.86
607 608 1.689273 GCACTCGGGATTAGACCTCAT 59.311 52.381 0.00 0.00 0.00 2.90
608 609 2.103263 GCACTCGGGATTAGACCTCATT 59.897 50.000 0.00 0.00 0.00 2.57
609 610 3.722147 CACTCGGGATTAGACCTCATTG 58.278 50.000 0.00 0.00 0.00 2.82
610 611 3.133003 CACTCGGGATTAGACCTCATTGT 59.867 47.826 0.00 0.00 0.00 2.71
611 612 4.341235 CACTCGGGATTAGACCTCATTGTA 59.659 45.833 0.00 0.00 0.00 2.41
612 613 4.960469 ACTCGGGATTAGACCTCATTGTAA 59.040 41.667 0.00 0.00 0.00 2.41
613 614 5.069251 ACTCGGGATTAGACCTCATTGTAAG 59.931 44.000 0.00 0.00 0.00 2.34
614 615 4.058817 CGGGATTAGACCTCATTGTAAGC 58.941 47.826 0.00 0.00 0.00 3.09
615 616 4.202264 CGGGATTAGACCTCATTGTAAGCT 60.202 45.833 0.00 0.00 0.00 3.74
616 617 5.685075 CGGGATTAGACCTCATTGTAAGCTT 60.685 44.000 3.48 3.48 0.00 3.74
617 618 5.529060 GGGATTAGACCTCATTGTAAGCTTG 59.471 44.000 9.86 0.00 0.00 4.01
618 619 5.529060 GGATTAGACCTCATTGTAAGCTTGG 59.471 44.000 9.86 1.80 0.00 3.61
619 620 2.716217 AGACCTCATTGTAAGCTTGGC 58.284 47.619 9.86 2.36 0.00 4.52
620 621 2.307098 AGACCTCATTGTAAGCTTGGCT 59.693 45.455 9.86 0.00 42.56 4.75
621 622 2.680339 GACCTCATTGTAAGCTTGGCTC 59.320 50.000 9.86 0.00 38.25 4.70
622 623 2.307098 ACCTCATTGTAAGCTTGGCTCT 59.693 45.455 9.86 0.00 38.25 4.09
623 624 2.681848 CCTCATTGTAAGCTTGGCTCTG 59.318 50.000 9.86 0.51 38.25 3.35
624 625 2.681848 CTCATTGTAAGCTTGGCTCTGG 59.318 50.000 9.86 0.00 38.25 3.86
625 626 1.133790 CATTGTAAGCTTGGCTCTGGC 59.866 52.381 9.86 0.00 38.25 4.85
626 627 0.401738 TTGTAAGCTTGGCTCTGGCT 59.598 50.000 9.86 0.00 38.25 4.75
627 628 1.275666 TGTAAGCTTGGCTCTGGCTA 58.724 50.000 9.86 0.00 38.25 3.93
628 629 1.628340 TGTAAGCTTGGCTCTGGCTAA 59.372 47.619 9.86 0.00 38.25 3.09
642 643 3.354131 GCTAAGAAGCCTCCGTGAG 57.646 57.895 0.00 0.00 43.40 3.51
643 644 0.533032 GCTAAGAAGCCTCCGTGAGT 59.467 55.000 1.12 0.00 43.40 3.41
644 645 1.749634 GCTAAGAAGCCTCCGTGAGTA 59.250 52.381 1.12 0.00 43.40 2.59
645 646 2.165845 GCTAAGAAGCCTCCGTGAGTAA 59.834 50.000 1.12 0.00 43.40 2.24
646 647 3.181474 GCTAAGAAGCCTCCGTGAGTAAT 60.181 47.826 1.12 0.00 43.40 1.89
647 648 2.969628 AGAAGCCTCCGTGAGTAATG 57.030 50.000 1.12 0.00 0.00 1.90
648 649 2.457598 AGAAGCCTCCGTGAGTAATGA 58.542 47.619 1.12 0.00 0.00 2.57
649 650 2.428890 AGAAGCCTCCGTGAGTAATGAG 59.571 50.000 1.12 0.00 0.00 2.90
650 651 2.145397 AGCCTCCGTGAGTAATGAGA 57.855 50.000 0.00 0.00 0.00 3.27
651 652 2.457598 AGCCTCCGTGAGTAATGAGAA 58.542 47.619 0.00 0.00 0.00 2.87
652 653 2.832129 AGCCTCCGTGAGTAATGAGAAA 59.168 45.455 0.00 0.00 0.00 2.52
653 654 3.452627 AGCCTCCGTGAGTAATGAGAAAT 59.547 43.478 0.00 0.00 0.00 2.17
654 655 4.649674 AGCCTCCGTGAGTAATGAGAAATA 59.350 41.667 0.00 0.00 0.00 1.40
655 656 5.305644 AGCCTCCGTGAGTAATGAGAAATAT 59.694 40.000 0.00 0.00 0.00 1.28
656 657 5.635700 GCCTCCGTGAGTAATGAGAAATATC 59.364 44.000 0.00 0.00 0.00 1.63
657 658 6.517529 GCCTCCGTGAGTAATGAGAAATATCT 60.518 42.308 0.00 0.00 39.10 1.98
658 659 7.437748 CCTCCGTGAGTAATGAGAAATATCTT 58.562 38.462 0.00 0.00 35.54 2.40
659 660 7.928706 CCTCCGTGAGTAATGAGAAATATCTTT 59.071 37.037 0.00 0.00 35.54 2.52
660 661 9.319143 CTCCGTGAGTAATGAGAAATATCTTTT 57.681 33.333 0.00 0.00 35.54 2.27
661 662 9.314321 TCCGTGAGTAATGAGAAATATCTTTTC 57.686 33.333 0.00 0.00 35.54 2.29
662 663 9.098355 CCGTGAGTAATGAGAAATATCTTTTCA 57.902 33.333 1.41 0.00 35.54 2.69
663 664 9.907576 CGTGAGTAATGAGAAATATCTTTTCAC 57.092 33.333 1.41 0.00 35.54 3.18
665 666 9.396022 TGAGTAATGAGAAATATCTTTTCACCC 57.604 33.333 1.41 0.00 35.54 4.61
666 667 8.438676 AGTAATGAGAAATATCTTTTCACCCG 57.561 34.615 1.41 0.00 35.54 5.28
667 668 5.757850 ATGAGAAATATCTTTTCACCCGC 57.242 39.130 1.41 0.00 35.54 6.13
668 669 4.584874 TGAGAAATATCTTTTCACCCGCA 58.415 39.130 1.41 0.00 35.54 5.69
669 670 5.007034 TGAGAAATATCTTTTCACCCGCAA 58.993 37.500 1.41 0.00 35.54 4.85
670 671 5.475220 TGAGAAATATCTTTTCACCCGCAAA 59.525 36.000 1.41 0.00 35.54 3.68
671 672 6.015856 TGAGAAATATCTTTTCACCCGCAAAA 60.016 34.615 1.41 0.00 35.54 2.44
672 673 6.754193 AGAAATATCTTTTCACCCGCAAAAA 58.246 32.000 1.41 0.00 29.15 1.94
699 700 8.956533 AAATTAAGGTGTGCATAAACTTTTGT 57.043 26.923 7.83 0.00 0.00 2.83
700 701 7.945033 ATTAAGGTGTGCATAAACTTTTGTG 57.055 32.000 7.83 0.00 33.13 3.33
710 711 6.072112 CATAAACTTTTGTGCACTAGTGGT 57.928 37.500 23.95 8.77 0.00 4.16
711 712 7.197071 CATAAACTTTTGTGCACTAGTGGTA 57.803 36.000 23.95 13.52 0.00 3.25
712 713 5.494632 AAACTTTTGTGCACTAGTGGTAC 57.505 39.130 23.95 14.10 0.00 3.34
713 714 4.145365 ACTTTTGTGCACTAGTGGTACA 57.855 40.909 23.95 16.27 0.00 2.90
714 715 4.519213 ACTTTTGTGCACTAGTGGTACAA 58.481 39.130 23.95 20.34 44.16 2.41
715 716 4.944930 ACTTTTGTGCACTAGTGGTACAAA 59.055 37.500 23.95 23.86 44.16 2.83
716 717 5.416326 ACTTTTGTGCACTAGTGGTACAAAA 59.584 36.000 29.23 29.23 44.16 2.44
717 718 5.493133 TTTGTGCACTAGTGGTACAAAAG 57.507 39.130 24.61 3.85 44.16 2.27
718 719 3.472652 TGTGCACTAGTGGTACAAAAGG 58.527 45.455 23.95 0.00 44.16 3.11
719 720 2.812011 GTGCACTAGTGGTACAAAAGGG 59.188 50.000 23.95 0.00 44.16 3.95
720 721 2.706723 TGCACTAGTGGTACAAAAGGGA 59.293 45.455 23.95 0.00 44.16 4.20
721 722 3.136809 TGCACTAGTGGTACAAAAGGGAA 59.863 43.478 23.95 0.00 44.16 3.97
722 723 4.139038 GCACTAGTGGTACAAAAGGGAAA 58.861 43.478 23.95 0.00 44.16 3.13
723 724 4.215613 GCACTAGTGGTACAAAAGGGAAAG 59.784 45.833 23.95 0.00 44.16 2.62
724 725 5.617252 CACTAGTGGTACAAAAGGGAAAGA 58.383 41.667 15.49 0.00 44.16 2.52
725 726 6.059484 CACTAGTGGTACAAAAGGGAAAGAA 58.941 40.000 15.49 0.00 44.16 2.52
726 727 6.544564 CACTAGTGGTACAAAAGGGAAAGAAA 59.455 38.462 15.49 0.00 44.16 2.52
727 728 6.771267 ACTAGTGGTACAAAAGGGAAAGAAAG 59.229 38.462 0.00 0.00 44.16 2.62
728 729 4.893524 AGTGGTACAAAAGGGAAAGAAAGG 59.106 41.667 0.00 0.00 44.16 3.11
729 730 4.038763 GTGGTACAAAAGGGAAAGAAAGGG 59.961 45.833 0.00 0.00 44.16 3.95
730 731 4.079096 TGGTACAAAAGGGAAAGAAAGGGA 60.079 41.667 0.00 0.00 31.92 4.20
731 732 4.897076 GGTACAAAAGGGAAAGAAAGGGAA 59.103 41.667 0.00 0.00 0.00 3.97
732 733 5.364446 GGTACAAAAGGGAAAGAAAGGGAAA 59.636 40.000 0.00 0.00 0.00 3.13
733 734 5.353394 ACAAAAGGGAAAGAAAGGGAAAC 57.647 39.130 0.00 0.00 0.00 2.78
734 735 4.780554 ACAAAAGGGAAAGAAAGGGAAACA 59.219 37.500 0.00 0.00 0.00 2.83
735 736 5.428457 ACAAAAGGGAAAGAAAGGGAAACAT 59.572 36.000 0.00 0.00 0.00 2.71
736 737 5.551305 AAAGGGAAAGAAAGGGAAACATG 57.449 39.130 0.00 0.00 0.00 3.21
737 738 2.899900 AGGGAAAGAAAGGGAAACATGC 59.100 45.455 0.00 0.00 0.00 4.06
738 739 2.632512 GGGAAAGAAAGGGAAACATGCA 59.367 45.455 0.00 0.00 0.00 3.96
739 740 3.070878 GGGAAAGAAAGGGAAACATGCAA 59.929 43.478 0.00 0.00 0.00 4.08
740 741 4.309933 GGAAAGAAAGGGAAACATGCAAG 58.690 43.478 0.00 0.00 0.00 4.01
741 742 3.391506 AAGAAAGGGAAACATGCAAGC 57.608 42.857 0.00 0.00 0.00 4.01
742 743 2.318908 AGAAAGGGAAACATGCAAGCA 58.681 42.857 0.00 0.00 0.00 3.91
743 744 2.298163 AGAAAGGGAAACATGCAAGCAG 59.702 45.455 0.00 0.00 0.00 4.24
744 745 0.971386 AAGGGAAACATGCAAGCAGG 59.029 50.000 5.03 5.03 0.00 4.85
745 746 0.901580 AGGGAAACATGCAAGCAGGG 60.902 55.000 11.58 3.50 31.33 4.45
746 747 0.899717 GGGAAACATGCAAGCAGGGA 60.900 55.000 11.58 0.00 31.33 4.20
747 748 0.968405 GGAAACATGCAAGCAGGGAA 59.032 50.000 11.58 0.00 31.33 3.97
748 749 1.337167 GGAAACATGCAAGCAGGGAAC 60.337 52.381 11.58 1.89 31.33 3.62
749 750 1.615392 GAAACATGCAAGCAGGGAACT 59.385 47.619 11.58 0.00 46.44 3.01
750 751 1.708341 AACATGCAAGCAGGGAACTT 58.292 45.000 11.58 0.00 40.21 2.66
751 752 2.584835 ACATGCAAGCAGGGAACTTA 57.415 45.000 11.58 0.00 40.21 2.24
752 753 2.162681 ACATGCAAGCAGGGAACTTAC 58.837 47.619 11.58 0.00 40.21 2.34
753 754 2.224867 ACATGCAAGCAGGGAACTTACT 60.225 45.455 11.58 0.00 40.21 2.24
754 755 2.185004 TGCAAGCAGGGAACTTACTC 57.815 50.000 0.00 0.00 40.21 2.59
755 756 1.699634 TGCAAGCAGGGAACTTACTCT 59.300 47.619 0.00 0.00 40.21 3.24
756 757 2.079925 GCAAGCAGGGAACTTACTCTG 58.920 52.381 0.00 0.00 40.21 3.35
757 758 2.704572 CAAGCAGGGAACTTACTCTGG 58.295 52.381 0.00 0.00 40.21 3.86
758 759 0.615850 AGCAGGGAACTTACTCTGGC 59.384 55.000 0.00 0.00 40.21 4.85
759 760 0.615850 GCAGGGAACTTACTCTGGCT 59.384 55.000 0.00 0.00 40.21 4.75
760 761 1.831736 GCAGGGAACTTACTCTGGCTA 59.168 52.381 0.00 0.00 40.21 3.93
761 762 2.159028 GCAGGGAACTTACTCTGGCTAG 60.159 54.545 0.00 0.00 40.21 3.42
762 763 2.432510 CAGGGAACTTACTCTGGCTAGG 59.567 54.545 0.00 0.00 40.21 3.02
763 764 2.044630 AGGGAACTTACTCTGGCTAGGT 59.955 50.000 0.00 0.00 37.44 3.08
764 765 2.431419 GGGAACTTACTCTGGCTAGGTC 59.569 54.545 0.00 0.00 0.00 3.85
765 766 3.097614 GGAACTTACTCTGGCTAGGTCA 58.902 50.000 0.00 0.00 0.00 4.02
766 767 3.514309 GGAACTTACTCTGGCTAGGTCAA 59.486 47.826 0.00 0.00 0.00 3.18
767 768 4.162509 GGAACTTACTCTGGCTAGGTCAAT 59.837 45.833 0.00 0.00 0.00 2.57
768 769 5.338463 GGAACTTACTCTGGCTAGGTCAATT 60.338 44.000 0.00 0.00 0.00 2.32
855 868 6.018016 GGAACCGACTATGTACTCTCTAACTC 60.018 46.154 0.00 0.00 0.00 3.01
884 897 5.265191 AGCAGTTGTACTTCCTCTCTCATA 58.735 41.667 0.00 0.00 0.00 2.15
1093 1116 0.835941 AGAGAGCCATCGCAGGAAAT 59.164 50.000 0.00 0.00 37.52 2.17
1349 1373 4.269523 GGTGCACCAGGCTGGACA 62.270 66.667 38.99 30.37 40.96 4.02
1387 1411 3.291611 CAAACCATGCTGGGCCTC 58.708 61.111 4.53 0.00 43.37 4.70
1534 1558 1.347707 AGATGTTCCCTTGCGAACTCA 59.652 47.619 3.41 0.00 42.22 3.41
1838 1911 0.543174 GTGACACCACCTCCTCCTCT 60.543 60.000 0.00 0.00 37.33 3.69
2131 2227 2.284625 TGGCAGAGACGTGGGGAT 60.285 61.111 0.00 0.00 0.00 3.85
2150 2246 3.263425 GGATACTCTCGATCCTCCTCTCT 59.737 52.174 0.00 0.00 39.94 3.10
2158 2254 5.068215 TCGATCCTCCTCTCTTTATCCTT 57.932 43.478 0.00 0.00 0.00 3.36
2159 2255 5.074115 TCGATCCTCCTCTCTTTATCCTTC 58.926 45.833 0.00 0.00 0.00 3.46
2198 2297 4.148825 CCCAACTCTCCCCGCTCG 62.149 72.222 0.00 0.00 0.00 5.03
2319 2428 7.464710 CGGTTCTGTTTATTTGAGAGTGCTATC 60.465 40.741 0.00 0.00 0.00 2.08
2343 2452 9.877178 ATCTTATTGTACTAAGAACCTCTGTTG 57.123 33.333 8.24 0.00 40.23 3.33
2562 2680 5.735354 GCACTTTGCAGATTATCCTCATTGG 60.735 44.000 0.00 0.00 44.26 3.16
2682 2801 4.829064 CTTGCAAAGCACAAGGTAACTA 57.171 40.909 0.00 0.00 43.49 2.24
2952 3071 6.942891 GCATCAGCTATACTTCAGAACTTTC 58.057 40.000 0.00 0.00 37.91 2.62
3031 3150 3.692791 CATGATCACAACATGCAGGAG 57.307 47.619 4.84 0.00 38.58 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.855858 CTTCAGGCCTAAGAGTGAGTTC 58.144 50.000 3.98 0.00 0.00 3.01
48 49 2.729028 TTAGGGTATTGCTTCAGGCC 57.271 50.000 0.00 0.00 40.92 5.19
400 401 1.224075 CGCTGTGATCATGGACATCC 58.776 55.000 0.00 0.00 0.00 3.51
447 448 5.118817 GTCTCTTAATGTCCTCAACAACGAC 59.881 44.000 0.00 0.00 42.37 4.34
479 480 0.410270 AGACCTCTCTTCCCTCCGTT 59.590 55.000 0.00 0.00 0.00 4.44
497 498 6.085068 GCGAACGACAACAAAGATTAAAAGAG 59.915 38.462 0.00 0.00 0.00 2.85
520 521 4.667668 GCTCATGACTAACTTTGTTCTGCG 60.668 45.833 0.00 0.00 0.00 5.18
521 522 4.453819 AGCTCATGACTAACTTTGTTCTGC 59.546 41.667 0.00 0.00 0.00 4.26
522 523 5.698089 TGAGCTCATGACTAACTTTGTTCTG 59.302 40.000 13.74 0.00 0.00 3.02
523 524 5.698545 GTGAGCTCATGACTAACTTTGTTCT 59.301 40.000 21.47 0.00 0.00 3.01
524 525 5.106908 GGTGAGCTCATGACTAACTTTGTTC 60.107 44.000 21.47 0.19 0.00 3.18
525 526 4.757149 GGTGAGCTCATGACTAACTTTGTT 59.243 41.667 21.47 0.00 0.00 2.83
526 527 4.202357 TGGTGAGCTCATGACTAACTTTGT 60.202 41.667 21.47 0.00 0.00 2.83
527 528 4.318332 TGGTGAGCTCATGACTAACTTTG 58.682 43.478 21.47 0.00 0.00 2.77
528 529 4.623932 TGGTGAGCTCATGACTAACTTT 57.376 40.909 21.47 0.00 0.00 2.66
529 530 4.040952 ACTTGGTGAGCTCATGACTAACTT 59.959 41.667 21.47 0.00 0.00 2.66
530 531 3.580458 ACTTGGTGAGCTCATGACTAACT 59.420 43.478 21.47 0.00 0.00 2.24
531 532 3.931578 ACTTGGTGAGCTCATGACTAAC 58.068 45.455 21.47 4.57 0.00 2.34
532 533 5.395657 CCATACTTGGTGAGCTCATGACTAA 60.396 44.000 21.47 10.37 38.30 2.24
533 534 4.100035 CCATACTTGGTGAGCTCATGACTA 59.900 45.833 21.47 9.50 38.30 2.59
534 535 3.118482 CCATACTTGGTGAGCTCATGACT 60.118 47.826 21.47 4.49 38.30 3.41
535 536 3.201290 CCATACTTGGTGAGCTCATGAC 58.799 50.000 21.47 13.83 38.30 3.06
536 537 3.548745 CCATACTTGGTGAGCTCATGA 57.451 47.619 21.47 6.61 38.30 3.07
547 548 2.103263 GGAGTGCTCCTACCATACTTGG 59.897 54.545 10.80 0.00 46.37 3.61
548 549 2.103263 GGGAGTGCTCCTACCATACTTG 59.897 54.545 16.80 0.00 44.69 3.16
549 550 2.399580 GGGAGTGCTCCTACCATACTT 58.600 52.381 16.80 0.00 44.69 2.24
550 551 2.089600 GGGAGTGCTCCTACCATACT 57.910 55.000 16.80 0.00 44.69 2.12
569 570 3.591835 AACCAAACAGCGGTGCGG 61.592 61.111 15.82 15.12 36.67 5.69
570 571 2.353376 CAACCAAACAGCGGTGCG 60.353 61.111 15.82 3.26 36.67 5.34
571 572 2.658268 GCAACCAAACAGCGGTGC 60.658 61.111 15.82 0.00 36.67 5.01
572 573 1.588667 GTGCAACCAAACAGCGGTG 60.589 57.895 14.13 14.13 36.67 4.94
573 574 1.724582 GAGTGCAACCAAACAGCGGT 61.725 55.000 0.00 0.00 37.80 5.68
574 575 1.008538 GAGTGCAACCAAACAGCGG 60.009 57.895 0.00 0.00 37.80 5.52
575 576 1.369209 CGAGTGCAACCAAACAGCG 60.369 57.895 0.00 0.00 37.80 5.18
576 577 1.008538 CCGAGTGCAACCAAACAGC 60.009 57.895 0.00 0.00 37.80 4.40
577 578 0.817634 TCCCGAGTGCAACCAAACAG 60.818 55.000 0.00 0.00 37.80 3.16
578 579 0.179004 ATCCCGAGTGCAACCAAACA 60.179 50.000 0.00 0.00 37.80 2.83
579 580 0.958822 AATCCCGAGTGCAACCAAAC 59.041 50.000 0.00 0.00 37.80 2.93
580 581 2.039216 TCTAATCCCGAGTGCAACCAAA 59.961 45.455 0.00 0.00 37.80 3.28
581 582 1.626321 TCTAATCCCGAGTGCAACCAA 59.374 47.619 0.00 0.00 37.80 3.67
582 583 1.066430 GTCTAATCCCGAGTGCAACCA 60.066 52.381 0.00 0.00 37.80 3.67
583 584 1.653151 GTCTAATCCCGAGTGCAACC 58.347 55.000 0.00 0.00 37.80 3.77
584 585 1.207329 AGGTCTAATCCCGAGTGCAAC 59.793 52.381 0.00 0.00 0.00 4.17
585 586 1.480954 GAGGTCTAATCCCGAGTGCAA 59.519 52.381 0.00 0.00 0.00 4.08
586 587 1.112113 GAGGTCTAATCCCGAGTGCA 58.888 55.000 0.00 0.00 0.00 4.57
587 588 1.112113 TGAGGTCTAATCCCGAGTGC 58.888 55.000 0.00 0.00 0.00 4.40
588 589 3.133003 ACAATGAGGTCTAATCCCGAGTG 59.867 47.826 0.00 0.00 0.00 3.51
589 590 3.375699 ACAATGAGGTCTAATCCCGAGT 58.624 45.455 0.00 0.00 0.00 4.18
590 591 5.531122 TTACAATGAGGTCTAATCCCGAG 57.469 43.478 0.00 0.00 0.00 4.63
591 592 4.202223 GCTTACAATGAGGTCTAATCCCGA 60.202 45.833 0.00 0.00 0.00 5.14
592 593 4.058817 GCTTACAATGAGGTCTAATCCCG 58.941 47.826 0.00 0.00 0.00 5.14
593 594 5.297569 AGCTTACAATGAGGTCTAATCCC 57.702 43.478 0.00 0.00 0.00 3.85
594 595 5.529060 CCAAGCTTACAATGAGGTCTAATCC 59.471 44.000 0.00 0.00 0.00 3.01
595 596 5.008118 GCCAAGCTTACAATGAGGTCTAATC 59.992 44.000 0.00 0.00 0.00 1.75
596 597 4.884164 GCCAAGCTTACAATGAGGTCTAAT 59.116 41.667 0.00 0.00 0.00 1.73
597 598 4.019321 AGCCAAGCTTACAATGAGGTCTAA 60.019 41.667 0.00 0.00 33.89 2.10
598 599 3.519510 AGCCAAGCTTACAATGAGGTCTA 59.480 43.478 0.00 0.00 33.89 2.59
599 600 2.307098 AGCCAAGCTTACAATGAGGTCT 59.693 45.455 0.00 0.00 33.89 3.85
600 601 2.680339 GAGCCAAGCTTACAATGAGGTC 59.320 50.000 0.00 0.00 39.88 3.85
601 602 2.307098 AGAGCCAAGCTTACAATGAGGT 59.693 45.455 0.00 0.00 39.88 3.85
602 603 2.681848 CAGAGCCAAGCTTACAATGAGG 59.318 50.000 0.00 0.00 39.88 3.86
603 604 2.681848 CCAGAGCCAAGCTTACAATGAG 59.318 50.000 0.00 0.00 39.88 2.90
604 605 2.715046 CCAGAGCCAAGCTTACAATGA 58.285 47.619 0.00 0.00 39.88 2.57
605 606 1.133790 GCCAGAGCCAAGCTTACAATG 59.866 52.381 0.00 0.00 39.88 2.82
606 607 1.005215 AGCCAGAGCCAAGCTTACAAT 59.995 47.619 0.00 0.00 39.88 2.71
607 608 0.401738 AGCCAGAGCCAAGCTTACAA 59.598 50.000 0.00 0.00 39.88 2.41
608 609 1.275666 TAGCCAGAGCCAAGCTTACA 58.724 50.000 0.00 0.00 39.88 2.41
609 610 2.093447 TCTTAGCCAGAGCCAAGCTTAC 60.093 50.000 0.00 0.00 39.88 2.34
610 611 2.187958 TCTTAGCCAGAGCCAAGCTTA 58.812 47.619 0.00 0.00 39.88 3.09
611 612 0.987294 TCTTAGCCAGAGCCAAGCTT 59.013 50.000 0.00 0.00 39.88 3.74
612 613 0.987294 TTCTTAGCCAGAGCCAAGCT 59.013 50.000 0.00 0.00 43.88 3.74
613 614 1.377536 CTTCTTAGCCAGAGCCAAGC 58.622 55.000 0.00 0.00 37.61 4.01
614 615 1.377536 GCTTCTTAGCCAGAGCCAAG 58.622 55.000 0.00 0.00 41.74 3.61
615 616 3.558674 GCTTCTTAGCCAGAGCCAA 57.441 52.632 0.00 0.00 41.74 4.52
625 626 4.098044 TCATTACTCACGGAGGCTTCTTAG 59.902 45.833 0.00 0.00 33.35 2.18
626 627 4.021229 TCATTACTCACGGAGGCTTCTTA 58.979 43.478 0.00 0.00 33.35 2.10
627 628 2.832129 TCATTACTCACGGAGGCTTCTT 59.168 45.455 0.00 0.00 33.35 2.52
628 629 2.428890 CTCATTACTCACGGAGGCTTCT 59.571 50.000 0.00 0.00 33.35 2.85
629 630 2.427453 TCTCATTACTCACGGAGGCTTC 59.573 50.000 5.98 0.00 33.35 3.86
630 631 2.457598 TCTCATTACTCACGGAGGCTT 58.542 47.619 5.98 0.00 33.35 4.35
631 632 2.145397 TCTCATTACTCACGGAGGCT 57.855 50.000 5.98 0.00 33.35 4.58
632 633 2.961526 TTCTCATTACTCACGGAGGC 57.038 50.000 5.98 0.00 33.35 4.70
633 634 6.987386 AGATATTTCTCATTACTCACGGAGG 58.013 40.000 5.98 0.00 33.35 4.30
634 635 8.879342 AAAGATATTTCTCATTACTCACGGAG 57.121 34.615 0.03 0.03 35.52 4.63
635 636 9.314321 GAAAAGATATTTCTCATTACTCACGGA 57.686 33.333 0.00 0.00 0.00 4.69
636 637 9.098355 TGAAAAGATATTTCTCATTACTCACGG 57.902 33.333 2.98 0.00 0.00 4.94
637 638 9.907576 GTGAAAAGATATTTCTCATTACTCACG 57.092 33.333 2.98 0.00 0.00 4.35
639 640 9.396022 GGGTGAAAAGATATTTCTCATTACTCA 57.604 33.333 2.98 0.00 0.00 3.41
640 641 8.552034 CGGGTGAAAAGATATTTCTCATTACTC 58.448 37.037 2.98 0.00 0.00 2.59
641 642 7.012421 GCGGGTGAAAAGATATTTCTCATTACT 59.988 37.037 2.98 0.00 0.00 2.24
642 643 7.132863 GCGGGTGAAAAGATATTTCTCATTAC 58.867 38.462 2.98 0.00 0.00 1.89
643 644 6.826231 TGCGGGTGAAAAGATATTTCTCATTA 59.174 34.615 2.98 0.00 0.00 1.90
644 645 5.652014 TGCGGGTGAAAAGATATTTCTCATT 59.348 36.000 2.98 0.00 0.00 2.57
645 646 5.192927 TGCGGGTGAAAAGATATTTCTCAT 58.807 37.500 2.98 0.00 0.00 2.90
646 647 4.584874 TGCGGGTGAAAAGATATTTCTCA 58.415 39.130 2.98 1.01 0.00 3.27
647 648 5.560966 TTGCGGGTGAAAAGATATTTCTC 57.439 39.130 2.98 0.00 0.00 2.87
648 649 5.975693 TTTGCGGGTGAAAAGATATTTCT 57.024 34.783 2.98 0.00 0.00 2.52
673 674 9.389755 ACAAAAGTTTATGCACACCTTAATTTT 57.610 25.926 0.00 0.00 0.00 1.82
674 675 8.825745 CACAAAAGTTTATGCACACCTTAATTT 58.174 29.630 0.00 0.00 0.00 1.82
675 676 7.042119 GCACAAAAGTTTATGCACACCTTAATT 60.042 33.333 16.20 0.00 38.00 1.40
676 677 6.423604 GCACAAAAGTTTATGCACACCTTAAT 59.576 34.615 16.20 0.00 38.00 1.40
677 678 5.751028 GCACAAAAGTTTATGCACACCTTAA 59.249 36.000 16.20 0.00 38.00 1.85
678 679 5.163509 TGCACAAAAGTTTATGCACACCTTA 60.164 36.000 18.71 0.79 42.92 2.69
679 680 4.119136 GCACAAAAGTTTATGCACACCTT 58.881 39.130 16.20 0.00 38.00 3.50
680 681 3.131933 TGCACAAAAGTTTATGCACACCT 59.868 39.130 18.71 0.00 42.92 4.00
681 682 3.452474 TGCACAAAAGTTTATGCACACC 58.548 40.909 18.71 0.00 42.92 4.16
685 686 5.507149 CCACTAGTGCACAAAAGTTTATGCA 60.507 40.000 21.04 18.71 45.45 3.96
686 687 4.917415 CCACTAGTGCACAAAAGTTTATGC 59.083 41.667 21.04 14.84 38.59 3.14
687 688 6.072112 ACCACTAGTGCACAAAAGTTTATG 57.928 37.500 21.04 7.30 0.00 1.90
688 689 6.768861 TGTACCACTAGTGCACAAAAGTTTAT 59.231 34.615 21.04 9.03 36.01 1.40
689 690 6.114089 TGTACCACTAGTGCACAAAAGTTTA 58.886 36.000 21.04 9.60 36.01 2.01
690 691 4.944930 TGTACCACTAGTGCACAAAAGTTT 59.055 37.500 21.04 10.48 36.01 2.66
691 692 4.519213 TGTACCACTAGTGCACAAAAGTT 58.481 39.130 21.04 7.84 36.01 2.66
692 693 4.145365 TGTACCACTAGTGCACAAAAGT 57.855 40.909 21.04 15.90 36.01 2.66
693 694 5.493133 TTTGTACCACTAGTGCACAAAAG 57.507 39.130 31.30 15.23 41.17 2.27
694 695 5.163602 CCTTTTGTACCACTAGTGCACAAAA 60.164 40.000 34.97 34.97 43.48 2.44
695 696 4.336993 CCTTTTGTACCACTAGTGCACAAA 59.663 41.667 30.52 30.52 41.17 2.83
696 697 3.880490 CCTTTTGTACCACTAGTGCACAA 59.120 43.478 25.51 25.51 41.17 3.33
697 698 3.472652 CCTTTTGTACCACTAGTGCACA 58.527 45.455 21.04 18.62 41.17 4.57
698 699 2.812011 CCCTTTTGTACCACTAGTGCAC 59.188 50.000 17.86 16.39 41.17 4.57
699 700 2.706723 TCCCTTTTGTACCACTAGTGCA 59.293 45.455 17.86 7.45 39.57 4.57
700 701 3.412237 TCCCTTTTGTACCACTAGTGC 57.588 47.619 17.86 4.70 0.00 4.40
701 702 5.617252 TCTTTCCCTTTTGTACCACTAGTG 58.383 41.667 16.34 16.34 0.00 2.74
702 703 5.899631 TCTTTCCCTTTTGTACCACTAGT 57.100 39.130 0.00 0.00 0.00 2.57
703 704 6.206829 CCTTTCTTTCCCTTTTGTACCACTAG 59.793 42.308 0.00 0.00 0.00 2.57
704 705 6.066032 CCTTTCTTTCCCTTTTGTACCACTA 58.934 40.000 0.00 0.00 0.00 2.74
705 706 4.893524 CCTTTCTTTCCCTTTTGTACCACT 59.106 41.667 0.00 0.00 0.00 4.00
706 707 4.038763 CCCTTTCTTTCCCTTTTGTACCAC 59.961 45.833 0.00 0.00 0.00 4.16
707 708 4.079096 TCCCTTTCTTTCCCTTTTGTACCA 60.079 41.667 0.00 0.00 0.00 3.25
708 709 4.476297 TCCCTTTCTTTCCCTTTTGTACC 58.524 43.478 0.00 0.00 0.00 3.34
709 710 6.127281 TGTTTCCCTTTCTTTCCCTTTTGTAC 60.127 38.462 0.00 0.00 0.00 2.90
710 711 5.958987 TGTTTCCCTTTCTTTCCCTTTTGTA 59.041 36.000 0.00 0.00 0.00 2.41
711 712 4.780554 TGTTTCCCTTTCTTTCCCTTTTGT 59.219 37.500 0.00 0.00 0.00 2.83
712 713 5.351948 TGTTTCCCTTTCTTTCCCTTTTG 57.648 39.130 0.00 0.00 0.00 2.44
713 714 5.687441 GCATGTTTCCCTTTCTTTCCCTTTT 60.687 40.000 0.00 0.00 0.00 2.27
714 715 4.202357 GCATGTTTCCCTTTCTTTCCCTTT 60.202 41.667 0.00 0.00 0.00 3.11
715 716 3.324846 GCATGTTTCCCTTTCTTTCCCTT 59.675 43.478 0.00 0.00 0.00 3.95
716 717 2.899900 GCATGTTTCCCTTTCTTTCCCT 59.100 45.455 0.00 0.00 0.00 4.20
717 718 2.632512 TGCATGTTTCCCTTTCTTTCCC 59.367 45.455 0.00 0.00 0.00 3.97
718 719 4.309933 CTTGCATGTTTCCCTTTCTTTCC 58.690 43.478 0.00 0.00 0.00 3.13
719 720 3.742882 GCTTGCATGTTTCCCTTTCTTTC 59.257 43.478 1.14 0.00 0.00 2.62
720 721 3.134442 TGCTTGCATGTTTCCCTTTCTTT 59.866 39.130 1.14 0.00 0.00 2.52
721 722 2.699846 TGCTTGCATGTTTCCCTTTCTT 59.300 40.909 1.14 0.00 0.00 2.52
722 723 2.298163 CTGCTTGCATGTTTCCCTTTCT 59.702 45.455 1.14 0.00 0.00 2.52
723 724 2.611224 CCTGCTTGCATGTTTCCCTTTC 60.611 50.000 1.14 0.00 0.00 2.62
724 725 1.345415 CCTGCTTGCATGTTTCCCTTT 59.655 47.619 1.14 0.00 0.00 3.11
725 726 0.971386 CCTGCTTGCATGTTTCCCTT 59.029 50.000 1.14 0.00 0.00 3.95
726 727 0.901580 CCCTGCTTGCATGTTTCCCT 60.902 55.000 1.14 0.00 0.00 4.20
727 728 0.899717 TCCCTGCTTGCATGTTTCCC 60.900 55.000 1.14 0.00 0.00 3.97
728 729 0.968405 TTCCCTGCTTGCATGTTTCC 59.032 50.000 1.14 0.00 0.00 3.13
729 730 1.615392 AGTTCCCTGCTTGCATGTTTC 59.385 47.619 1.14 0.00 0.00 2.78
730 731 1.708341 AGTTCCCTGCTTGCATGTTT 58.292 45.000 1.14 0.00 0.00 2.83
731 732 1.708341 AAGTTCCCTGCTTGCATGTT 58.292 45.000 1.14 0.00 0.00 2.71
732 733 2.162681 GTAAGTTCCCTGCTTGCATGT 58.837 47.619 1.14 0.00 0.00 3.21
733 734 2.421424 GAGTAAGTTCCCTGCTTGCATG 59.579 50.000 0.00 0.00 32.26 4.06
734 735 2.307098 AGAGTAAGTTCCCTGCTTGCAT 59.693 45.455 0.00 0.00 32.26 3.96
735 736 1.699634 AGAGTAAGTTCCCTGCTTGCA 59.300 47.619 0.00 0.00 32.26 4.08
736 737 2.079925 CAGAGTAAGTTCCCTGCTTGC 58.920 52.381 0.00 0.00 0.00 4.01
737 738 2.704572 CCAGAGTAAGTTCCCTGCTTG 58.295 52.381 0.00 0.00 0.00 4.01
738 739 1.003696 GCCAGAGTAAGTTCCCTGCTT 59.996 52.381 0.00 0.00 0.00 3.91
739 740 0.615850 GCCAGAGTAAGTTCCCTGCT 59.384 55.000 0.00 0.00 0.00 4.24
740 741 0.615850 AGCCAGAGTAAGTTCCCTGC 59.384 55.000 0.00 0.00 0.00 4.85
741 742 2.432510 CCTAGCCAGAGTAAGTTCCCTG 59.567 54.545 0.00 0.00 0.00 4.45
742 743 2.044630 ACCTAGCCAGAGTAAGTTCCCT 59.955 50.000 0.00 0.00 0.00 4.20
743 744 2.431419 GACCTAGCCAGAGTAAGTTCCC 59.569 54.545 0.00 0.00 0.00 3.97
744 745 3.097614 TGACCTAGCCAGAGTAAGTTCC 58.902 50.000 0.00 0.00 0.00 3.62
745 746 4.803098 TTGACCTAGCCAGAGTAAGTTC 57.197 45.455 0.00 0.00 0.00 3.01
746 747 5.763876 AATTGACCTAGCCAGAGTAAGTT 57.236 39.130 0.00 0.00 0.00 2.66
747 748 6.195700 TCTAATTGACCTAGCCAGAGTAAGT 58.804 40.000 0.00 0.00 0.00 2.24
748 749 6.716934 TCTAATTGACCTAGCCAGAGTAAG 57.283 41.667 0.00 0.00 0.00 2.34
749 750 7.676683 AATCTAATTGACCTAGCCAGAGTAA 57.323 36.000 0.00 0.00 0.00 2.24
750 751 7.125811 ACAAATCTAATTGACCTAGCCAGAGTA 59.874 37.037 0.00 0.00 34.38 2.59
751 752 6.069963 ACAAATCTAATTGACCTAGCCAGAGT 60.070 38.462 0.00 0.00 34.38 3.24
752 753 6.352516 ACAAATCTAATTGACCTAGCCAGAG 58.647 40.000 0.00 0.00 34.38 3.35
753 754 6.313519 ACAAATCTAATTGACCTAGCCAGA 57.686 37.500 0.00 0.00 34.38 3.86
754 755 7.227512 CCTAACAAATCTAATTGACCTAGCCAG 59.772 40.741 0.00 0.00 34.38 4.85
755 756 7.054124 CCTAACAAATCTAATTGACCTAGCCA 58.946 38.462 0.00 0.00 34.38 4.75
756 757 7.280356 TCCTAACAAATCTAATTGACCTAGCC 58.720 38.462 0.00 0.00 34.38 3.93
757 758 8.732746 TTCCTAACAAATCTAATTGACCTAGC 57.267 34.615 0.00 0.00 34.38 3.42
855 868 4.464597 AGAGGAAGTACAACTGCTTCTAGG 59.535 45.833 0.00 0.00 38.32 3.02
910 923 4.273480 GGTTGCTAATGCGTGAGACATAAT 59.727 41.667 0.00 0.00 43.34 1.28
941 954 8.504005 CAAATCTGTGAGAGTATTTTTAACCGT 58.496 33.333 0.00 0.00 0.00 4.83
948 961 7.360946 GCGGTTACAAATCTGTGAGAGTATTTT 60.361 37.037 0.00 0.00 36.96 1.82
1269 1293 4.351938 CCACGACGGCGGTTCTGA 62.352 66.667 18.49 0.00 43.17 3.27
1577 1613 4.865761 TACGCGCTGGGCACGATC 62.866 66.667 17.13 0.00 43.84 3.69
1677 1713 2.122369 GGGGATGGGAGATCCGGT 60.122 66.667 0.00 0.00 39.07 5.28
2131 2227 4.781775 AAAGAGAGGAGGATCGAGAGTA 57.218 45.455 0.00 0.00 34.37 2.59
2150 2246 3.513912 TGCACCGAAGAGAGAAGGATAAA 59.486 43.478 0.00 0.00 0.00 1.40
2158 2254 1.900351 CCCATGCACCGAAGAGAGA 59.100 57.895 0.00 0.00 0.00 3.10
2159 2255 1.817099 GCCCATGCACCGAAGAGAG 60.817 63.158 0.00 0.00 37.47 3.20
2198 2297 4.781934 AGTTATTGGCCTGATTAGGTGAC 58.218 43.478 3.32 0.00 46.41 3.67
2319 2428 9.877178 ATCAACAGAGGTTCTTAGTACAATAAG 57.123 33.333 0.00 0.00 34.21 1.73
2505 2623 4.047166 TCATCTACCCTGTGATCCCAAAT 58.953 43.478 0.00 0.00 0.00 2.32
2508 2626 2.682594 CTCATCTACCCTGTGATCCCA 58.317 52.381 0.00 0.00 0.00 4.37
2562 2680 4.691216 AGAGGCAAAACGTAGATCTTTCAC 59.309 41.667 0.00 0.00 0.00 3.18
2682 2801 5.828747 GCAATTTGATGCAGTAGATCACAT 58.171 37.500 0.00 0.00 45.70 3.21
2707 2826 4.948621 ACCTCGCAGTAAGAGTGTATAGTT 59.051 41.667 0.00 0.00 34.08 2.24
2713 2832 1.912417 AGACCTCGCAGTAAGAGTGT 58.088 50.000 0.00 0.00 34.08 3.55
2952 3071 4.326504 ACAACAAATGCTTCAAAGGAGG 57.673 40.909 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.