Multiple sequence alignment - TraesCS2D01G179700

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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 TraesCS2D01G179700 chr2D 100.000 3568 0 0 1 3568 123812565 123808998 0.000000e+00 6589
1 TraesCS2D01G179700 chr2D 98.279 523 8 1 1 523 366135835 366135314 0.000000e+00 915
2 TraesCS2D01G179700 chr2D 98.276 522 9 0 1 522 441061291 441060770 0.000000e+00 915
3 TraesCS2D01G179700 chr2D 95.098 102 5 0 523 624 335090953 335090852 1.030000e-35 161
4 TraesCS2D01G179700 chr2A 90.520 2173 92 53 843 2956 129105914 129103797 0.000000e+00 2767
5 TraesCS2D01G179700 chr2A 89.460 389 25 6 820 1207 129873574 129873947 8.960000e-131 477
6 TraesCS2D01G179700 chr2A 83.491 527 26 26 3102 3568 129103594 129103069 5.470000e-118 435
7 TraesCS2D01G179700 chr2B 90.253 1939 80 44 731 2604 176415249 176413355 0.000000e+00 2433
8 TraesCS2D01G179700 chr2B 89.384 292 14 8 2683 2958 176412986 176412696 5.670000e-93 351
9 TraesCS2D01G179700 chr2B 81.839 435 28 18 3181 3568 176412322 176411892 5.750000e-83 318
10 TraesCS2D01G179700 chr7D 98.279 523 9 0 1 523 266864447 266863925 0.000000e+00 917
11 TraesCS2D01G179700 chr7D 97.897 523 11 0 1 523 163984549 163985071 0.000000e+00 905
12 TraesCS2D01G179700 chr6D 98.279 523 9 0 1 523 433629695 433629173 0.000000e+00 917
13 TraesCS2D01G179700 chr6D 95.098 102 5 0 523 624 188519881 188519982 1.030000e-35 161
14 TraesCS2D01G179700 chr6D 95.098 102 5 0 523 624 339138718 339138819 1.030000e-35 161
15 TraesCS2D01G179700 chr6D 93.396 106 7 0 519 624 67059629 67059524 1.330000e-34 158
16 TraesCS2D01G179700 chr6D 87.097 93 12 0 523 615 111453335 111453427 4.870000e-19 106
17 TraesCS2D01G179700 chr5D 98.084 522 10 0 1 522 261263388 261263909 0.000000e+00 909
18 TraesCS2D01G179700 chr5D 97.897 523 11 0 1 523 442524458 442524980 0.000000e+00 905
19 TraesCS2D01G179700 chr4D 98.088 523 9 1 1 523 393910085 393910606 0.000000e+00 909
20 TraesCS2D01G179700 chr3D 97.180 532 14 1 1 532 500171495 500172025 0.000000e+00 898
21 TraesCS2D01G179700 chr3D 95.098 102 5 0 523 624 130022434 130022535 1.030000e-35 161
22 TraesCS2D01G179700 chr3D 91.398 93 8 0 523 615 173160147 173160055 1.040000e-25 128
23 TraesCS2D01G179700 chr5B 96.078 102 4 0 523 624 422393749 422393648 2.200000e-37 167
24 TraesCS2D01G179700 chr5B 91.398 93 8 0 523 615 580798274 580798182 1.040000e-25 128
25 TraesCS2D01G179700 chr4A 96.078 102 4 0 523 624 255392386 255392487 2.200000e-37 167
26 TraesCS2D01G179700 chr6A 95.098 102 5 0 523 624 130933883 130933782 1.030000e-35 161
27 TraesCS2D01G179700 chr6A 94.118 102 6 0 523 624 399598854 399598753 4.770000e-34 156
28 TraesCS2D01G179700 chr1A 93.548 93 6 0 523 615 409708090 409708182 4.800000e-29 139
29 TraesCS2D01G179700 chr3B 90.217 92 9 0 524 615 683568141 683568232 1.740000e-23 121


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 TraesCS2D01G179700 chr2D 123808998 123812565 3567 True 6589 6589 100.000000 1 3568 1 chr2D.!!$R1 3567
1 TraesCS2D01G179700 chr2D 366135314 366135835 521 True 915 915 98.279000 1 523 1 chr2D.!!$R3 522
2 TraesCS2D01G179700 chr2D 441060770 441061291 521 True 915 915 98.276000 1 522 1 chr2D.!!$R4 521
3 TraesCS2D01G179700 chr2A 129103069 129105914 2845 True 1601 2767 87.005500 843 3568 2 chr2A.!!$R1 2725
4 TraesCS2D01G179700 chr2B 176411892 176415249 3357 True 1034 2433 87.158667 731 3568 3 chr2B.!!$R1 2837
5 TraesCS2D01G179700 chr7D 266863925 266864447 522 True 917 917 98.279000 1 523 1 chr7D.!!$R1 522
6 TraesCS2D01G179700 chr7D 163984549 163985071 522 False 905 905 97.897000 1 523 1 chr7D.!!$F1 522
7 TraesCS2D01G179700 chr6D 433629173 433629695 522 True 917 917 98.279000 1 523 1 chr6D.!!$R2 522
8 TraesCS2D01G179700 chr5D 261263388 261263909 521 False 909 909 98.084000 1 522 1 chr5D.!!$F1 521
9 TraesCS2D01G179700 chr5D 442524458 442524980 522 False 905 905 97.897000 1 523 1 chr5D.!!$F2 522
10 TraesCS2D01G179700 chr4D 393910085 393910606 521 False 909 909 98.088000 1 523 1 chr4D.!!$F1 522
11 TraesCS2D01G179700 chr3D 500171495 500172025 530 False 898 898 97.180000 1 532 1 chr3D.!!$F2 531

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
645 647 0.038526 ACTTGACGTCTGCCTTACCG 60.039 55.0 17.92 0.0 0.00 4.02 F
1654 1673 0.104120 CAACACGGTGAGACCAGTGA 59.896 55.0 16.29 0.0 41.74 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1862 0.102300 GGAAGCAAGTGCCAAAACGT 59.898 50.0 0.00 0.0 43.38 3.99 R
3130 3690 0.106894 GGGCCTAGGAAGGTTCATCG 59.893 60.0 14.75 0.0 45.64 3.84 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
80 81 1.475403 ATCCCAGTCTCGATTCGTGT 58.525 50.000 5.89 0.00 0.00 4.49
193 194 1.084289 GTATCCGGGAGTTGCACAAC 58.916 55.000 0.00 5.36 41.45 3.32
435 437 8.551205 GTGGTCTATGTATTCACACATGTATTG 58.449 37.037 0.00 0.00 39.46 1.90
523 525 4.272489 CTCAAGGGCATATTTCCAACAGA 58.728 43.478 0.00 0.00 0.00 3.41
524 526 4.870636 TCAAGGGCATATTTCCAACAGAT 58.129 39.130 0.00 0.00 0.00 2.90
525 527 6.012337 TCAAGGGCATATTTCCAACAGATA 57.988 37.500 0.00 0.00 0.00 1.98
526 528 6.430864 TCAAGGGCATATTTCCAACAGATAA 58.569 36.000 0.00 0.00 0.00 1.75
529 531 4.280929 GGGCATATTTCCAACAGATAACCC 59.719 45.833 0.00 0.00 0.00 4.11
530 532 4.892934 GGCATATTTCCAACAGATAACCCA 59.107 41.667 0.00 0.00 0.00 4.51
531 533 5.221244 GGCATATTTCCAACAGATAACCCAC 60.221 44.000 0.00 0.00 0.00 4.61
532 534 5.359576 GCATATTTCCAACAGATAACCCACA 59.640 40.000 0.00 0.00 0.00 4.17
533 535 6.127479 GCATATTTCCAACAGATAACCCACAA 60.127 38.462 0.00 0.00 0.00 3.33
534 536 5.982890 ATTTCCAACAGATAACCCACAAG 57.017 39.130 0.00 0.00 0.00 3.16
535 537 4.447138 TTCCAACAGATAACCCACAAGT 57.553 40.909 0.00 0.00 0.00 3.16
536 538 5.570205 TTCCAACAGATAACCCACAAGTA 57.430 39.130 0.00 0.00 0.00 2.24
537 539 5.772393 TCCAACAGATAACCCACAAGTAT 57.228 39.130 0.00 0.00 0.00 2.12
538 540 6.877668 TCCAACAGATAACCCACAAGTATA 57.122 37.500 0.00 0.00 0.00 1.47
539 541 6.884832 TCCAACAGATAACCCACAAGTATAG 58.115 40.000 0.00 0.00 0.00 1.31
540 542 6.055588 CCAACAGATAACCCACAAGTATAGG 58.944 44.000 0.00 0.00 0.00 2.57
547 549 2.326428 CCCACAAGTATAGGGGATCGT 58.674 52.381 0.00 0.00 43.57 3.73
548 550 2.704065 CCCACAAGTATAGGGGATCGTT 59.296 50.000 0.00 0.00 43.57 3.85
549 551 3.135895 CCCACAAGTATAGGGGATCGTTT 59.864 47.826 0.00 0.00 43.57 3.60
550 552 4.127171 CCACAAGTATAGGGGATCGTTTG 58.873 47.826 0.00 0.00 0.00 2.93
551 553 4.383770 CCACAAGTATAGGGGATCGTTTGT 60.384 45.833 0.00 0.00 0.00 2.83
552 554 5.163385 CCACAAGTATAGGGGATCGTTTGTA 60.163 44.000 0.00 0.00 0.00 2.41
553 555 6.463897 CCACAAGTATAGGGGATCGTTTGTAT 60.464 42.308 0.00 0.00 0.00 2.29
554 556 6.645415 CACAAGTATAGGGGATCGTTTGTATC 59.355 42.308 0.00 0.00 0.00 2.24
555 557 5.997384 AGTATAGGGGATCGTTTGTATCC 57.003 43.478 0.00 0.00 41.96 2.59
556 558 5.652324 AGTATAGGGGATCGTTTGTATCCT 58.348 41.667 0.00 0.00 42.27 3.24
557 559 6.082707 AGTATAGGGGATCGTTTGTATCCTT 58.917 40.000 0.00 0.00 42.27 3.36
558 560 5.906772 ATAGGGGATCGTTTGTATCCTTT 57.093 39.130 0.00 0.00 42.27 3.11
559 561 4.586306 AGGGGATCGTTTGTATCCTTTT 57.414 40.909 0.00 0.00 42.27 2.27
560 562 4.930696 AGGGGATCGTTTGTATCCTTTTT 58.069 39.130 0.00 0.00 42.27 1.94
582 584 7.878477 TTTTGATAAATACGAGTGTCGAACT 57.122 32.000 2.82 0.00 43.74 3.01
590 592 3.267900 AGTGTCGAACTCAACGTGG 57.732 52.632 0.00 0.00 31.64 4.94
591 593 0.742505 AGTGTCGAACTCAACGTGGA 59.257 50.000 0.00 0.00 31.64 4.02
592 594 1.129326 GTGTCGAACTCAACGTGGAG 58.871 55.000 18.70 18.70 40.79 3.86
593 595 0.596600 TGTCGAACTCAACGTGGAGC 60.597 55.000 20.19 3.67 38.50 4.70
594 596 0.318784 GTCGAACTCAACGTGGAGCT 60.319 55.000 20.19 7.86 38.50 4.09
595 597 1.068748 GTCGAACTCAACGTGGAGCTA 60.069 52.381 20.19 0.00 38.50 3.32
596 598 1.610038 TCGAACTCAACGTGGAGCTAA 59.390 47.619 20.19 0.36 38.50 3.09
597 599 2.034939 TCGAACTCAACGTGGAGCTAAA 59.965 45.455 20.19 0.74 38.50 1.85
598 600 2.408704 CGAACTCAACGTGGAGCTAAAG 59.591 50.000 20.19 3.71 38.50 1.85
599 601 2.457366 ACTCAACGTGGAGCTAAAGG 57.543 50.000 20.19 0.00 38.50 3.11
600 602 1.692519 ACTCAACGTGGAGCTAAAGGT 59.307 47.619 20.19 0.00 38.50 3.50
601 603 2.895404 ACTCAACGTGGAGCTAAAGGTA 59.105 45.455 20.19 0.00 38.50 3.08
602 604 3.056749 ACTCAACGTGGAGCTAAAGGTAG 60.057 47.826 20.19 0.00 38.50 3.18
603 605 3.159472 TCAACGTGGAGCTAAAGGTAGA 58.841 45.455 0.00 0.00 0.00 2.59
604 606 3.575256 TCAACGTGGAGCTAAAGGTAGAA 59.425 43.478 0.00 0.00 0.00 2.10
605 607 3.589495 ACGTGGAGCTAAAGGTAGAAC 57.411 47.619 0.00 0.00 0.00 3.01
606 608 2.895404 ACGTGGAGCTAAAGGTAGAACA 59.105 45.455 0.00 0.00 0.00 3.18
607 609 3.322828 ACGTGGAGCTAAAGGTAGAACAA 59.677 43.478 0.00 0.00 0.00 2.83
608 610 4.202284 ACGTGGAGCTAAAGGTAGAACAAA 60.202 41.667 0.00 0.00 0.00 2.83
609 611 4.935808 CGTGGAGCTAAAGGTAGAACAAAT 59.064 41.667 0.00 0.00 0.00 2.32
610 612 6.103997 CGTGGAGCTAAAGGTAGAACAAATA 58.896 40.000 0.00 0.00 0.00 1.40
611 613 6.761714 CGTGGAGCTAAAGGTAGAACAAATAT 59.238 38.462 0.00 0.00 0.00 1.28
612 614 7.280205 CGTGGAGCTAAAGGTAGAACAAATATT 59.720 37.037 0.00 0.00 0.00 1.28
613 615 8.613482 GTGGAGCTAAAGGTAGAACAAATATTC 58.387 37.037 0.00 0.00 0.00 1.75
614 616 7.773690 TGGAGCTAAAGGTAGAACAAATATTCC 59.226 37.037 0.00 0.00 0.00 3.01
615 617 7.993758 GGAGCTAAAGGTAGAACAAATATTCCT 59.006 37.037 0.00 0.00 0.00 3.36
616 618 9.397280 GAGCTAAAGGTAGAACAAATATTCCTT 57.603 33.333 0.00 0.00 35.68 3.36
617 619 9.397280 AGCTAAAGGTAGAACAAATATTCCTTC 57.603 33.333 3.55 1.28 33.48 3.46
618 620 9.174166 GCTAAAGGTAGAACAAATATTCCTTCA 57.826 33.333 3.55 0.00 33.48 3.02
621 623 9.588096 AAAGGTAGAACAAATATTCCTTCAAGT 57.412 29.630 3.55 0.00 33.48 3.16
622 624 9.588096 AAGGTAGAACAAATATTCCTTCAAGTT 57.412 29.630 7.47 0.00 0.00 2.66
623 625 9.232473 AGGTAGAACAAATATTCCTTCAAGTTC 57.768 33.333 0.00 0.00 35.58 3.01
624 626 9.010029 GGTAGAACAAATATTCCTTCAAGTTCA 57.990 33.333 0.00 0.00 37.25 3.18
625 627 9.827411 GTAGAACAAATATTCCTTCAAGTTCAC 57.173 33.333 0.00 0.00 37.25 3.18
626 628 8.463930 AGAACAAATATTCCTTCAAGTTCACA 57.536 30.769 0.00 0.00 37.25 3.58
627 629 8.352942 AGAACAAATATTCCTTCAAGTTCACAC 58.647 33.333 0.00 0.00 37.25 3.82
628 630 7.823745 ACAAATATTCCTTCAAGTTCACACT 57.176 32.000 0.00 0.00 33.11 3.55
629 631 8.237811 ACAAATATTCCTTCAAGTTCACACTT 57.762 30.769 0.00 0.00 44.72 3.16
638 640 1.571919 AGTTCACACTTGACGTCTGC 58.428 50.000 17.92 0.00 0.00 4.26
639 641 0.582005 GTTCACACTTGACGTCTGCC 59.418 55.000 17.92 0.00 0.00 4.85
640 642 0.464036 TTCACACTTGACGTCTGCCT 59.536 50.000 17.92 0.00 0.00 4.75
641 643 0.464036 TCACACTTGACGTCTGCCTT 59.536 50.000 17.92 0.00 0.00 4.35
642 644 1.684450 TCACACTTGACGTCTGCCTTA 59.316 47.619 17.92 0.00 0.00 2.69
643 645 1.792949 CACACTTGACGTCTGCCTTAC 59.207 52.381 17.92 0.00 0.00 2.34
644 646 1.270147 ACACTTGACGTCTGCCTTACC 60.270 52.381 17.92 0.00 0.00 2.85
645 647 0.038526 ACTTGACGTCTGCCTTACCG 60.039 55.000 17.92 0.00 0.00 4.02
646 648 0.242825 CTTGACGTCTGCCTTACCGA 59.757 55.000 17.92 0.00 0.00 4.69
647 649 0.675083 TTGACGTCTGCCTTACCGAA 59.325 50.000 17.92 0.00 0.00 4.30
648 650 0.675083 TGACGTCTGCCTTACCGAAA 59.325 50.000 17.92 0.00 0.00 3.46
649 651 1.068895 TGACGTCTGCCTTACCGAAAA 59.931 47.619 17.92 0.00 0.00 2.29
650 652 1.458445 GACGTCTGCCTTACCGAAAAC 59.542 52.381 8.70 0.00 0.00 2.43
651 653 1.202557 ACGTCTGCCTTACCGAAAACA 60.203 47.619 0.00 0.00 0.00 2.83
652 654 1.868498 CGTCTGCCTTACCGAAAACAA 59.132 47.619 0.00 0.00 0.00 2.83
653 655 2.096417 CGTCTGCCTTACCGAAAACAAG 60.096 50.000 0.00 0.00 0.00 3.16
654 656 2.876550 GTCTGCCTTACCGAAAACAAGT 59.123 45.455 0.00 0.00 0.00 3.16
655 657 4.060205 GTCTGCCTTACCGAAAACAAGTA 58.940 43.478 0.00 0.00 0.00 2.24
656 658 4.694037 GTCTGCCTTACCGAAAACAAGTAT 59.306 41.667 0.00 0.00 0.00 2.12
657 659 4.693566 TCTGCCTTACCGAAAACAAGTATG 59.306 41.667 0.00 0.00 0.00 2.39
658 660 4.643463 TGCCTTACCGAAAACAAGTATGA 58.357 39.130 0.00 0.00 0.00 2.15
659 661 5.064558 TGCCTTACCGAAAACAAGTATGAA 58.935 37.500 0.00 0.00 0.00 2.57
660 662 5.531659 TGCCTTACCGAAAACAAGTATGAAA 59.468 36.000 0.00 0.00 0.00 2.69
661 663 5.854866 GCCTTACCGAAAACAAGTATGAAAC 59.145 40.000 0.00 0.00 0.00 2.78
662 664 6.293790 GCCTTACCGAAAACAAGTATGAAACT 60.294 38.462 0.00 0.00 41.49 2.66
663 665 7.095102 GCCTTACCGAAAACAAGTATGAAACTA 60.095 37.037 0.00 0.00 37.50 2.24
664 666 8.440833 CCTTACCGAAAACAAGTATGAAACTAG 58.559 37.037 0.00 0.00 37.50 2.57
665 667 8.891671 TTACCGAAAACAAGTATGAAACTAGT 57.108 30.769 0.00 0.00 37.50 2.57
666 668 9.979578 TTACCGAAAACAAGTATGAAACTAGTA 57.020 29.630 0.00 0.00 37.50 1.82
668 670 9.498176 ACCGAAAACAAGTATGAAACTAGTATT 57.502 29.630 0.00 0.00 37.50 1.89
695 697 8.786937 TTTCAATTTATCAGCGATAAAGCATC 57.213 30.769 20.37 0.00 44.30 3.91
727 729 6.861065 TTTTATCAGCGGTAAAGGATCATC 57.139 37.500 0.00 0.00 0.00 2.92
728 730 5.808366 TTATCAGCGGTAAAGGATCATCT 57.192 39.130 0.00 0.00 0.00 2.90
729 731 6.911250 TTATCAGCGGTAAAGGATCATCTA 57.089 37.500 0.00 0.00 0.00 1.98
776 780 9.416794 TGCTTTTTAGCGAATAAAATGAAATGA 57.583 25.926 16.52 0.55 41.74 2.57
824 828 2.158667 AGACGATCCAAACTTGTGGGTT 60.159 45.455 0.00 0.00 39.34 4.11
829 833 3.593442 TCCAAACTTGTGGGTTGATCT 57.407 42.857 0.00 0.00 44.88 2.75
838 842 3.073678 TGTGGGTTGATCTGAAACATCG 58.926 45.455 0.00 0.00 0.00 3.84
840 844 2.039746 TGGGTTGATCTGAAACATCGGT 59.960 45.455 0.00 0.00 0.00 4.69
1289 1296 1.123077 CCCCCATTCGATCACTCAGA 58.877 55.000 0.00 0.00 0.00 3.27
1299 1306 7.307632 CCATTCGATCACTCAGATTAATTCACC 60.308 40.741 0.00 0.00 37.00 4.02
1300 1307 6.220726 TCGATCACTCAGATTAATTCACCA 57.779 37.500 0.00 0.00 37.00 4.17
1301 1308 6.820335 TCGATCACTCAGATTAATTCACCAT 58.180 36.000 0.00 0.00 37.00 3.55
1302 1309 6.703165 TCGATCACTCAGATTAATTCACCATG 59.297 38.462 0.00 0.00 37.00 3.66
1303 1310 6.565435 CGATCACTCAGATTAATTCACCATGC 60.565 42.308 0.00 0.00 37.00 4.06
1304 1311 4.883585 TCACTCAGATTAATTCACCATGCC 59.116 41.667 0.00 0.00 0.00 4.40
1320 1327 0.625316 TGCCATGCCATTAGGAGTGT 59.375 50.000 0.00 0.00 36.89 3.55
1355 1362 1.133253 CATCCGCGCTGTTCTTGTG 59.867 57.895 5.56 0.00 0.00 3.33
1578 1597 3.165071 GGAAGAGATCATCCCTCCTCTC 58.835 54.545 0.00 0.00 35.16 3.20
1648 1667 1.202486 TCCAGAACAACACGGTGAGAC 60.202 52.381 16.29 7.05 0.00 3.36
1654 1673 0.104120 CAACACGGTGAGACCAGTGA 59.896 55.000 16.29 0.00 41.74 3.41
1697 1724 0.538057 CACAGTCACAGGCCCAACAT 60.538 55.000 0.00 0.00 0.00 2.71
1700 1727 1.003580 CAGTCACAGGCCCAACATACT 59.996 52.381 0.00 0.00 0.00 2.12
1715 1742 4.142609 ACATACTCGTGATTTGGCATCT 57.857 40.909 0.00 0.00 0.00 2.90
1805 1851 3.088194 CATATTTGCATGCCACAGGAC 57.912 47.619 16.68 0.00 0.00 3.85
1806 1852 2.212812 TATTTGCATGCCACAGGACA 57.787 45.000 16.68 0.00 0.00 4.02
1807 1853 0.892755 ATTTGCATGCCACAGGACAG 59.107 50.000 16.68 0.00 0.00 3.51
1808 1854 1.180456 TTTGCATGCCACAGGACAGG 61.180 55.000 16.68 0.00 0.00 4.00
1809 1855 2.034687 GCATGCCACAGGACAGGT 59.965 61.111 6.36 0.00 0.00 4.00
1810 1856 1.299648 GCATGCCACAGGACAGGTA 59.700 57.895 6.36 0.00 0.00 3.08
1812 1858 1.683011 GCATGCCACAGGACAGGTATT 60.683 52.381 6.36 0.00 0.00 1.89
1813 1859 2.421388 GCATGCCACAGGACAGGTATTA 60.421 50.000 6.36 0.00 0.00 0.98
1814 1860 3.470709 CATGCCACAGGACAGGTATTAG 58.529 50.000 0.00 0.00 0.00 1.73
1815 1861 2.546899 TGCCACAGGACAGGTATTAGT 58.453 47.619 0.00 0.00 0.00 2.24
1816 1862 3.715287 TGCCACAGGACAGGTATTAGTA 58.285 45.455 0.00 0.00 0.00 1.82
1817 1863 3.449737 TGCCACAGGACAGGTATTAGTAC 59.550 47.826 0.00 0.00 0.00 2.73
1875 1931 2.601763 GCAATGCTAGCAACTTCAATGC 59.398 45.455 23.54 17.81 44.15 3.56
1878 1934 2.507484 TGCTAGCAACTTCAATGCACT 58.493 42.857 16.84 0.00 46.22 4.40
2049 2108 1.862602 GCCGTTTCTTCCCGTGCAAT 61.863 55.000 0.00 0.00 0.00 3.56
2050 2109 0.109781 CCGTTTCTTCCCGTGCAATG 60.110 55.000 0.00 0.00 0.00 2.82
2051 2110 0.729140 CGTTTCTTCCCGTGCAATGC 60.729 55.000 0.00 0.00 0.00 3.56
2052 2111 0.313672 GTTTCTTCCCGTGCAATGCA 59.686 50.000 2.72 2.72 35.60 3.96
2053 2112 1.035923 TTTCTTCCCGTGCAATGCAA 58.964 45.000 10.44 0.00 41.47 4.08
2054 2113 1.255882 TTCTTCCCGTGCAATGCAAT 58.744 45.000 10.44 0.00 41.47 3.56
2055 2114 0.527113 TCTTCCCGTGCAATGCAATG 59.473 50.000 10.44 5.54 41.47 2.82
2056 2115 1.079875 CTTCCCGTGCAATGCAATGC 61.080 55.000 19.99 19.99 46.58 3.56
2057 2116 1.534336 TTCCCGTGCAATGCAATGCT 61.534 50.000 26.10 0.00 46.54 3.79
2058 2117 1.079681 CCCGTGCAATGCAATGCTT 60.080 52.632 26.10 0.00 46.54 3.91
2059 2118 0.671163 CCCGTGCAATGCAATGCTTT 60.671 50.000 26.10 3.26 46.54 3.51
2060 2119 0.717224 CCGTGCAATGCAATGCTTTC 59.283 50.000 26.10 15.39 46.54 2.62
2061 2120 1.670674 CCGTGCAATGCAATGCTTTCT 60.671 47.619 26.10 0.00 46.54 2.52
2062 2121 2.063266 CGTGCAATGCAATGCTTTCTT 58.937 42.857 26.10 0.00 46.54 2.52
2063 2122 2.477375 CGTGCAATGCAATGCTTTCTTT 59.523 40.909 26.10 0.00 46.54 2.52
2064 2123 3.422603 CGTGCAATGCAATGCTTTCTTTC 60.423 43.478 26.10 8.09 46.54 2.62
2065 2124 3.744426 GTGCAATGCAATGCTTTCTTTCT 59.256 39.130 26.10 0.00 46.54 2.52
2066 2125 4.212636 GTGCAATGCAATGCTTTCTTTCTT 59.787 37.500 26.10 0.00 46.54 2.52
2067 2126 4.817464 TGCAATGCAATGCTTTCTTTCTTT 59.183 33.333 26.10 0.00 46.54 2.52
2068 2127 5.297278 TGCAATGCAATGCTTTCTTTCTTTT 59.703 32.000 26.10 0.00 46.54 2.27
2069 2128 6.183360 TGCAATGCAATGCTTTCTTTCTTTTT 60.183 30.769 26.10 0.00 46.54 1.94
2098 2157 1.192757 CGTGCAATGCAATGTTGGTTG 59.807 47.619 10.44 0.00 41.47 3.77
2110 2169 2.564771 TGTTGGTTGACTTGCTGAGAG 58.435 47.619 0.00 0.00 0.00 3.20
2153 2212 4.689612 TCTTGACCTAGTTTGCTGTTCT 57.310 40.909 0.00 0.00 0.00 3.01
2159 2228 5.827797 TGACCTAGTTTGCTGTTCTTGAAAT 59.172 36.000 0.00 0.00 0.00 2.17
2170 2239 1.581147 CTTGAAATTCTCGGCGCGC 60.581 57.895 25.94 25.94 0.00 6.86
2209 2278 5.472137 TCACTTCATAGCCCAAAAACTACAC 59.528 40.000 0.00 0.00 0.00 2.90
2212 2281 6.493458 ACTTCATAGCCCAAAAACTACACAAT 59.507 34.615 0.00 0.00 0.00 2.71
2381 2459 1.053424 ACGTGGTGTTCTGGGTGTAT 58.947 50.000 0.00 0.00 0.00 2.29
2483 2561 5.805486 AGTAGTAACACATGCAAGATACACG 59.195 40.000 0.00 0.00 0.00 4.49
2503 2581 3.004419 ACGACATACAGGGTGATCATACG 59.996 47.826 0.00 0.00 0.00 3.06
2504 2582 3.611766 CGACATACAGGGTGATCATACGG 60.612 52.174 0.00 0.00 0.00 4.02
2514 2592 1.152963 ATCATACGGGGGCACAAGC 60.153 57.895 0.00 0.00 41.10 4.01
2538 2616 7.288852 AGCTACTCTGTGTATAAGATGTCCATT 59.711 37.037 0.00 0.00 0.00 3.16
2579 2657 5.726980 AAAGATGCTGCAAAAGGTTCATA 57.273 34.783 6.36 0.00 0.00 2.15
2604 2682 7.880160 TGATTCTTTTTCTTCTGAAGTCCAA 57.120 32.000 16.43 6.37 33.28 3.53
2606 2684 7.557719 TGATTCTTTTTCTTCTGAAGTCCAACT 59.442 33.333 16.43 0.00 33.28 3.16
2671 2781 8.523915 ACCATATATTGTGAGCAAAGAAATGA 57.476 30.769 0.00 0.00 38.21 2.57
2757 3143 1.270907 AGGTTCCTGACGATCAGCTT 58.729 50.000 8.85 0.00 42.98 3.74
2761 3147 3.585862 GTTCCTGACGATCAGCTTGTAA 58.414 45.455 8.85 0.00 42.98 2.41
2922 3311 1.813092 GCCACCACATGATAGCCTGAG 60.813 57.143 0.00 0.00 0.00 3.35
2942 3331 2.011349 CGCCGCGTAGTGCTAGATG 61.011 63.158 4.92 0.00 43.27 2.90
2998 3441 4.431809 AGTCGAGCAATCTGAAGATCAAG 58.568 43.478 0.00 0.00 32.75 3.02
3004 3447 5.426504 AGCAATCTGAAGATCAAGAACGAT 58.573 37.500 0.00 0.00 32.75 3.73
3007 3450 7.714377 AGCAATCTGAAGATCAAGAACGATAAT 59.286 33.333 0.00 0.00 32.75 1.28
3008 3451 7.797587 GCAATCTGAAGATCAAGAACGATAATG 59.202 37.037 0.00 0.00 32.75 1.90
3044 3489 5.509163 CCGAGTTACCGAATCCAGTGATAAT 60.509 44.000 0.00 0.00 0.00 1.28
3045 3490 6.294342 CCGAGTTACCGAATCCAGTGATAATA 60.294 42.308 0.00 0.00 0.00 0.98
3046 3491 7.143340 CGAGTTACCGAATCCAGTGATAATAA 58.857 38.462 0.00 0.00 0.00 1.40
3048 3493 8.658499 AGTTACCGAATCCAGTGATAATAAAC 57.342 34.615 0.00 0.00 0.00 2.01
3050 3495 6.248569 ACCGAATCCAGTGATAATAAACCT 57.751 37.500 0.00 0.00 0.00 3.50
3051 3496 6.289064 ACCGAATCCAGTGATAATAAACCTC 58.711 40.000 0.00 0.00 0.00 3.85
3054 3499 5.888982 ATCCAGTGATAATAAACCTCGGT 57.111 39.130 0.00 0.00 0.00 4.69
3055 3500 5.687166 TCCAGTGATAATAAACCTCGGTT 57.313 39.130 0.00 0.00 40.45 4.44
3060 3505 7.414098 CCAGTGATAATAAACCTCGGTTGAAAG 60.414 40.741 1.44 0.00 38.47 2.62
3061 3506 7.119262 CAGTGATAATAAACCTCGGTTGAAAGT 59.881 37.037 1.44 0.00 38.47 2.66
3062 3507 7.119262 AGTGATAATAAACCTCGGTTGAAAGTG 59.881 37.037 1.44 0.00 38.47 3.16
3063 3508 7.118680 GTGATAATAAACCTCGGTTGAAAGTGA 59.881 37.037 1.44 0.00 38.47 3.41
3064 3509 7.827236 TGATAATAAACCTCGGTTGAAAGTGAT 59.173 33.333 1.44 0.00 38.47 3.06
3065 3510 6.894339 AATAAACCTCGGTTGAAAGTGATT 57.106 33.333 1.44 0.00 38.47 2.57
3067 3512 4.830826 AACCTCGGTTGAAAGTGATTTC 57.169 40.909 0.00 0.00 36.91 2.17
3068 3513 2.806244 ACCTCGGTTGAAAGTGATTTCG 59.194 45.455 0.00 0.00 33.80 3.46
3069 3514 2.159627 CCTCGGTTGAAAGTGATTTCGG 59.840 50.000 0.00 0.00 33.80 4.30
3070 3515 3.064207 CTCGGTTGAAAGTGATTTCGGA 58.936 45.455 0.00 0.00 33.80 4.55
3071 3516 3.670625 TCGGTTGAAAGTGATTTCGGAT 58.329 40.909 0.00 0.00 33.80 4.18
3072 3517 4.823157 TCGGTTGAAAGTGATTTCGGATA 58.177 39.130 0.00 0.00 33.80 2.59
3089 3569 9.712305 ATTTCGGATAGTTTGAGATATTACCTG 57.288 33.333 0.00 0.00 0.00 4.00
3090 3570 7.228314 TCGGATAGTTTGAGATATTACCTGG 57.772 40.000 0.00 0.00 0.00 4.45
3091 3571 6.210784 TCGGATAGTTTGAGATATTACCTGGG 59.789 42.308 0.00 0.00 0.00 4.45
3092 3572 6.014499 CGGATAGTTTGAGATATTACCTGGGT 60.014 42.308 0.00 0.00 0.00 4.51
3094 3574 7.878644 GGATAGTTTGAGATATTACCTGGGTTC 59.121 40.741 0.00 0.00 0.00 3.62
3105 3665 1.633432 ACCTGGGTTCATTCCATCGAA 59.367 47.619 0.00 0.00 33.29 3.71
3113 3673 4.859245 GGTTCATTCCATCGAAAAGAAAGC 59.141 41.667 0.00 0.00 31.74 3.51
3130 3690 1.299089 GCAAGAAACCGTGCACCAC 60.299 57.895 12.15 0.00 38.59 4.16
3147 3715 1.473434 CCACGATGAACCTTCCTAGGC 60.473 57.143 2.96 0.00 46.22 3.93
3149 3717 0.106894 CGATGAACCTTCCTAGGCCC 59.893 60.000 2.96 0.00 46.22 5.80
3188 3769 3.875737 TGACATGTCACGCACACTTGTG 61.876 50.000 24.56 4.92 40.72 3.33
3191 3772 7.963256 TGACATGTCACGCACACTTGTGATA 62.963 44.000 24.56 0.00 45.90 2.15
3209 3790 6.108687 TGTGATACACAGCTCTTATCCAAAG 58.891 40.000 0.25 0.00 39.62 2.77
3251 3834 3.627123 CCGCATGGTTGATTAGATGTTGA 59.373 43.478 0.00 0.00 0.00 3.18
3268 3851 8.812513 AGATGTTGAATTTGGATGATAGTTCA 57.187 30.769 0.00 0.00 36.00 3.18
3270 3853 9.859427 GATGTTGAATTTGGATGATAGTTCAAA 57.141 29.630 0.00 0.00 37.33 2.69
3314 3919 8.928270 AAAAGATCTACGTAGTGTTTCTATGG 57.072 34.615 21.53 0.00 45.73 2.74
3315 3920 7.876936 AAGATCTACGTAGTGTTTCTATGGA 57.123 36.000 21.53 0.00 45.73 3.41
3316 3921 7.261829 AGATCTACGTAGTGTTTCTATGGAC 57.738 40.000 21.53 0.00 45.73 4.02
3317 3922 5.824904 TCTACGTAGTGTTTCTATGGACC 57.175 43.478 21.53 0.00 45.73 4.46
3321 3926 5.416947 ACGTAGTGTTTCTATGGACCAATC 58.583 41.667 0.00 0.00 42.51 2.67
3324 3929 7.069578 ACGTAGTGTTTCTATGGACCAATCTAT 59.930 37.037 0.00 0.00 42.51 1.98
3351 3973 2.744741 CTCGCTTCTCCTTTTTCCTTCC 59.255 50.000 0.00 0.00 0.00 3.46
3398 4028 1.202806 TGGCAAACCTGAAGGAGTGAG 60.203 52.381 2.62 0.00 38.94 3.51
3439 4081 2.617021 CCCACGGTTTACAGTTAGCCAT 60.617 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 2.285083 CGAAAGTGTCTGTTGGGTTGA 58.715 47.619 0.00 0.00 0.00 3.18
193 194 7.072263 AGTATCATTTCCTTAGACCATGAGG 57.928 40.000 0.00 0.00 42.21 3.86
435 437 7.801783 GCTATAATTGTATTAACTGGAAACCGC 59.198 37.037 0.00 0.00 0.00 5.68
504 506 5.598417 GGTTATCTGTTGGAAATATGCCCTT 59.402 40.000 0.00 0.00 0.00 3.95
523 525 4.530946 CGATCCCCTATACTTGTGGGTTAT 59.469 45.833 0.00 0.00 39.31 1.89
524 526 3.899360 CGATCCCCTATACTTGTGGGTTA 59.101 47.826 0.00 0.00 39.31 2.85
525 527 2.704065 CGATCCCCTATACTTGTGGGTT 59.296 50.000 0.00 0.00 39.31 4.11
526 528 2.326428 CGATCCCCTATACTTGTGGGT 58.674 52.381 0.00 0.00 39.31 4.51
529 531 4.766375 ACAAACGATCCCCTATACTTGTG 58.234 43.478 0.00 0.00 0.00 3.33
530 532 6.239515 GGATACAAACGATCCCCTATACTTGT 60.240 42.308 0.00 0.00 37.49 3.16
531 533 6.014499 AGGATACAAACGATCCCCTATACTTG 60.014 42.308 0.00 0.00 43.52 3.16
532 534 6.082707 AGGATACAAACGATCCCCTATACTT 58.917 40.000 0.00 0.00 43.52 2.24
533 535 5.652324 AGGATACAAACGATCCCCTATACT 58.348 41.667 0.00 0.00 43.52 2.12
534 536 5.997384 AGGATACAAACGATCCCCTATAC 57.003 43.478 0.00 0.00 43.52 1.47
535 537 7.383156 AAAAGGATACAAACGATCCCCTATA 57.617 36.000 0.00 0.00 43.52 1.31
536 538 5.906772 AAAGGATACAAACGATCCCCTAT 57.093 39.130 0.00 0.00 43.52 2.57
537 539 5.703730 AAAAGGATACAAACGATCCCCTA 57.296 39.130 0.00 0.00 43.52 3.53
538 540 4.586306 AAAAGGATACAAACGATCCCCT 57.414 40.909 0.00 0.00 43.52 4.79
557 559 8.301730 AGTTCGACACTCGTATTTATCAAAAA 57.698 30.769 0.00 0.00 41.35 1.94
558 560 7.878477 AGTTCGACACTCGTATTTATCAAAA 57.122 32.000 0.00 0.00 41.35 2.44
559 561 7.502177 GAGTTCGACACTCGTATTTATCAAA 57.498 36.000 10.56 0.00 42.82 2.69
572 574 0.742505 TCCACGTTGAGTTCGACACT 59.257 50.000 0.00 0.00 39.07 3.55
573 575 1.129326 CTCCACGTTGAGTTCGACAC 58.871 55.000 8.45 0.00 0.00 3.67
574 576 0.596600 GCTCCACGTTGAGTTCGACA 60.597 55.000 17.09 0.00 34.74 4.35
575 577 0.318784 AGCTCCACGTTGAGTTCGAC 60.319 55.000 17.09 1.39 34.74 4.20
576 578 1.241165 TAGCTCCACGTTGAGTTCGA 58.759 50.000 17.09 0.00 34.74 3.71
577 579 2.060326 TTAGCTCCACGTTGAGTTCG 57.940 50.000 17.09 0.00 34.74 3.95
578 580 2.737252 CCTTTAGCTCCACGTTGAGTTC 59.263 50.000 17.09 2.75 34.74 3.01
579 581 2.104281 ACCTTTAGCTCCACGTTGAGTT 59.896 45.455 17.09 13.94 34.74 3.01
580 582 1.692519 ACCTTTAGCTCCACGTTGAGT 59.307 47.619 17.09 7.53 34.74 3.41
581 583 2.457366 ACCTTTAGCTCCACGTTGAG 57.543 50.000 12.15 12.15 35.40 3.02
582 584 3.159472 TCTACCTTTAGCTCCACGTTGA 58.841 45.455 0.00 0.00 0.00 3.18
583 585 3.587797 TCTACCTTTAGCTCCACGTTG 57.412 47.619 0.00 0.00 0.00 4.10
584 586 3.322828 TGTTCTACCTTTAGCTCCACGTT 59.677 43.478 0.00 0.00 0.00 3.99
585 587 2.895404 TGTTCTACCTTTAGCTCCACGT 59.105 45.455 0.00 0.00 0.00 4.49
586 588 3.587797 TGTTCTACCTTTAGCTCCACG 57.412 47.619 0.00 0.00 0.00 4.94
587 589 8.507524 AATATTTGTTCTACCTTTAGCTCCAC 57.492 34.615 0.00 0.00 0.00 4.02
588 590 7.773690 GGAATATTTGTTCTACCTTTAGCTCCA 59.226 37.037 0.00 0.00 0.00 3.86
589 591 7.993758 AGGAATATTTGTTCTACCTTTAGCTCC 59.006 37.037 0.00 0.00 0.00 4.70
590 592 8.966069 AGGAATATTTGTTCTACCTTTAGCTC 57.034 34.615 0.00 0.00 0.00 4.09
591 593 9.397280 GAAGGAATATTTGTTCTACCTTTAGCT 57.603 33.333 0.00 0.00 36.58 3.32
592 594 9.174166 TGAAGGAATATTTGTTCTACCTTTAGC 57.826 33.333 0.00 0.00 36.58 3.09
595 597 9.588096 ACTTGAAGGAATATTTGTTCTACCTTT 57.412 29.630 0.00 0.00 36.58 3.11
596 598 9.588096 AACTTGAAGGAATATTTGTTCTACCTT 57.412 29.630 0.00 0.00 38.68 3.50
597 599 9.232473 GAACTTGAAGGAATATTTGTTCTACCT 57.768 33.333 0.00 0.00 32.48 3.08
598 600 9.010029 TGAACTTGAAGGAATATTTGTTCTACC 57.990 33.333 0.00 0.00 35.16 3.18
599 601 9.827411 GTGAACTTGAAGGAATATTTGTTCTAC 57.173 33.333 0.00 0.00 35.16 2.59
600 602 9.567776 TGTGAACTTGAAGGAATATTTGTTCTA 57.432 29.630 0.00 4.47 35.16 2.10
601 603 8.352942 GTGTGAACTTGAAGGAATATTTGTTCT 58.647 33.333 0.00 0.00 35.16 3.01
602 604 8.352942 AGTGTGAACTTGAAGGAATATTTGTTC 58.647 33.333 0.00 0.00 34.82 3.18
603 605 8.237811 AGTGTGAACTTGAAGGAATATTTGTT 57.762 30.769 0.00 0.00 0.00 2.83
604 606 7.823745 AGTGTGAACTTGAAGGAATATTTGT 57.176 32.000 0.00 0.00 0.00 2.83
617 619 2.285834 GCAGACGTCAAGTGTGAACTTG 60.286 50.000 19.50 11.49 45.98 3.16
618 620 1.933853 GCAGACGTCAAGTGTGAACTT 59.066 47.619 19.50 0.00 45.98 2.66
619 621 1.571919 GCAGACGTCAAGTGTGAACT 58.428 50.000 19.50 0.00 45.98 3.01
620 622 0.582005 GGCAGACGTCAAGTGTGAAC 59.418 55.000 19.50 0.12 45.98 3.18
621 623 0.464036 AGGCAGACGTCAAGTGTGAA 59.536 50.000 19.50 0.00 45.98 3.18
622 624 0.464036 AAGGCAGACGTCAAGTGTGA 59.536 50.000 19.50 0.00 45.98 3.58
623 625 1.792949 GTAAGGCAGACGTCAAGTGTG 59.207 52.381 19.50 7.89 45.87 3.82
624 626 1.270147 GGTAAGGCAGACGTCAAGTGT 60.270 52.381 19.50 2.26 0.00 3.55
625 627 1.429463 GGTAAGGCAGACGTCAAGTG 58.571 55.000 19.50 8.69 0.00 3.16
626 628 0.038526 CGGTAAGGCAGACGTCAAGT 60.039 55.000 19.50 0.00 0.00 3.16
627 629 0.242825 TCGGTAAGGCAGACGTCAAG 59.757 55.000 19.50 11.01 0.00 3.02
628 630 0.675083 TTCGGTAAGGCAGACGTCAA 59.325 50.000 19.50 0.00 0.00 3.18
629 631 0.675083 TTTCGGTAAGGCAGACGTCA 59.325 50.000 19.50 0.00 0.00 4.35
630 632 1.458445 GTTTTCGGTAAGGCAGACGTC 59.542 52.381 7.70 7.70 0.00 4.34
631 633 1.202557 TGTTTTCGGTAAGGCAGACGT 60.203 47.619 0.00 0.00 0.00 4.34
632 634 1.504359 TGTTTTCGGTAAGGCAGACG 58.496 50.000 0.00 0.00 0.00 4.18
633 635 2.876550 ACTTGTTTTCGGTAAGGCAGAC 59.123 45.455 0.00 0.00 0.00 3.51
634 636 3.202829 ACTTGTTTTCGGTAAGGCAGA 57.797 42.857 0.00 0.00 0.00 4.26
635 637 4.693566 TCATACTTGTTTTCGGTAAGGCAG 59.306 41.667 0.00 0.00 0.00 4.85
636 638 4.643463 TCATACTTGTTTTCGGTAAGGCA 58.357 39.130 0.00 0.00 0.00 4.75
637 639 5.616488 TTCATACTTGTTTTCGGTAAGGC 57.384 39.130 0.00 0.00 0.00 4.35
638 640 7.198306 AGTTTCATACTTGTTTTCGGTAAGG 57.802 36.000 0.00 0.00 31.29 2.69
639 641 8.985805 ACTAGTTTCATACTTGTTTTCGGTAAG 58.014 33.333 0.00 0.00 39.34 2.34
640 642 8.891671 ACTAGTTTCATACTTGTTTTCGGTAA 57.108 30.769 0.00 0.00 39.34 2.85
642 644 9.498176 AATACTAGTTTCATACTTGTTTTCGGT 57.502 29.630 0.00 0.00 41.88 4.69
669 671 9.403110 GATGCTTTATCGCTGATAAATTGAAAT 57.597 29.630 17.81 10.78 41.63 2.17
670 672 8.786937 GATGCTTTATCGCTGATAAATTGAAA 57.213 30.769 17.81 7.99 41.63 2.69
703 705 7.054124 AGATGATCCTTTACCGCTGATAAAAA 58.946 34.615 0.00 0.00 0.00 1.94
704 706 6.591935 AGATGATCCTTTACCGCTGATAAAA 58.408 36.000 0.00 0.00 0.00 1.52
705 707 6.174720 AGATGATCCTTTACCGCTGATAAA 57.825 37.500 0.00 0.00 0.00 1.40
706 708 5.808366 AGATGATCCTTTACCGCTGATAA 57.192 39.130 0.00 0.00 0.00 1.75
707 709 6.911250 TTAGATGATCCTTTACCGCTGATA 57.089 37.500 0.00 0.00 0.00 2.15
708 710 5.808366 TTAGATGATCCTTTACCGCTGAT 57.192 39.130 0.00 0.00 0.00 2.90
709 711 5.357257 GTTTAGATGATCCTTTACCGCTGA 58.643 41.667 0.00 0.00 0.00 4.26
710 712 4.511826 GGTTTAGATGATCCTTTACCGCTG 59.488 45.833 0.00 0.00 0.00 5.18
711 713 4.163458 TGGTTTAGATGATCCTTTACCGCT 59.837 41.667 0.00 0.00 0.00 5.52
712 714 4.448210 TGGTTTAGATGATCCTTTACCGC 58.552 43.478 0.00 0.00 0.00 5.68
713 715 6.204882 GGAATGGTTTAGATGATCCTTTACCG 59.795 42.308 0.00 0.00 0.00 4.02
714 716 6.204882 CGGAATGGTTTAGATGATCCTTTACC 59.795 42.308 0.00 0.00 0.00 2.85
715 717 6.990349 TCGGAATGGTTTAGATGATCCTTTAC 59.010 38.462 0.00 0.00 0.00 2.01
716 718 7.131907 TCGGAATGGTTTAGATGATCCTTTA 57.868 36.000 0.00 0.00 0.00 1.85
717 719 6.001449 TCGGAATGGTTTAGATGATCCTTT 57.999 37.500 0.00 0.00 0.00 3.11
718 720 5.630415 TCGGAATGGTTTAGATGATCCTT 57.370 39.130 0.00 0.00 0.00 3.36
719 721 5.366768 TCTTCGGAATGGTTTAGATGATCCT 59.633 40.000 0.00 0.00 0.00 3.24
720 722 5.611374 TCTTCGGAATGGTTTAGATGATCC 58.389 41.667 0.00 0.00 0.00 3.36
721 723 7.064016 GCTATCTTCGGAATGGTTTAGATGATC 59.936 40.741 0.00 0.00 31.30 2.92
722 724 6.876257 GCTATCTTCGGAATGGTTTAGATGAT 59.124 38.462 0.00 0.00 32.78 2.45
723 725 6.183360 TGCTATCTTCGGAATGGTTTAGATGA 60.183 38.462 0.00 0.00 0.00 2.92
724 726 5.991606 TGCTATCTTCGGAATGGTTTAGATG 59.008 40.000 0.00 0.00 0.00 2.90
725 727 6.174720 TGCTATCTTCGGAATGGTTTAGAT 57.825 37.500 0.00 0.00 0.00 1.98
726 728 5.607939 TGCTATCTTCGGAATGGTTTAGA 57.392 39.130 0.00 0.00 0.00 2.10
727 729 6.662616 CATTGCTATCTTCGGAATGGTTTAG 58.337 40.000 0.00 0.00 36.80 1.85
728 730 5.008613 GCATTGCTATCTTCGGAATGGTTTA 59.991 40.000 0.16 0.00 39.61 2.01
729 731 4.202050 GCATTGCTATCTTCGGAATGGTTT 60.202 41.667 0.16 0.00 39.61 3.27
776 780 2.755655 CTGGAGAAGATAGACCACGTGT 59.244 50.000 15.65 2.26 0.00 4.49
778 782 3.367646 TCTGGAGAAGATAGACCACGT 57.632 47.619 0.00 0.00 0.00 4.49
824 828 7.240674 CGATTAAAAACCGATGTTTCAGATCA 58.759 34.615 0.00 0.00 43.80 2.92
829 833 4.616373 GCCCGATTAAAAACCGATGTTTCA 60.616 41.667 0.00 0.00 43.80 2.69
838 842 0.099968 GAGCCGCCCGATTAAAAACC 59.900 55.000 0.00 0.00 0.00 3.27
840 844 0.806241 GTGAGCCGCCCGATTAAAAA 59.194 50.000 0.00 0.00 0.00 1.94
1289 1296 3.039743 TGGCATGGCATGGTGAATTAAT 58.960 40.909 27.48 0.00 0.00 1.40
1299 1306 1.611977 CACTCCTAATGGCATGGCATG 59.388 52.381 32.77 22.99 0.00 4.06
1300 1307 1.216175 ACACTCCTAATGGCATGGCAT 59.784 47.619 27.75 27.75 0.00 4.40
1301 1308 0.625316 ACACTCCTAATGGCATGGCA 59.375 50.000 25.52 25.52 0.00 4.92
1302 1309 1.406539 CAACACTCCTAATGGCATGGC 59.593 52.381 13.29 13.29 0.00 4.40
1303 1310 2.726821 ACAACACTCCTAATGGCATGG 58.273 47.619 0.00 0.00 0.00 3.66
1304 1311 3.309682 CGTACAACACTCCTAATGGCATG 59.690 47.826 0.00 0.00 0.00 4.06
1320 1327 3.457234 GGATGATCATCACTGCGTACAA 58.543 45.455 31.49 0.00 39.54 2.41
1395 1414 5.537674 AGATTCAGAACAGGCAAAATTCAGT 59.462 36.000 0.00 0.00 0.00 3.41
1449 1468 0.955919 CTTCCTTCTTGTCACCGCCC 60.956 60.000 0.00 0.00 0.00 6.13
1648 1667 3.181507 CGCTTGTTGGTATGAATCACTGG 60.182 47.826 0.00 0.00 0.00 4.00
1654 1673 3.487376 CGCAATCGCTTGTTGGTATGAAT 60.487 43.478 0.42 0.00 34.69 2.57
1697 1724 4.645136 AGTAGAGATGCCAAATCACGAGTA 59.355 41.667 0.00 0.00 0.00 2.59
1700 1727 3.785486 CAGTAGAGATGCCAAATCACGA 58.215 45.455 0.00 0.00 0.00 4.35
1796 1827 3.490419 CGTACTAATACCTGTCCTGTGGC 60.490 52.174 0.00 0.00 0.00 5.01
1800 1846 5.579511 CCAAAACGTACTAATACCTGTCCTG 59.420 44.000 0.00 0.00 0.00 3.86
1801 1847 5.727434 CCAAAACGTACTAATACCTGTCCT 58.273 41.667 0.00 0.00 0.00 3.85
1802 1848 4.330894 GCCAAAACGTACTAATACCTGTCC 59.669 45.833 0.00 0.00 0.00 4.02
1803 1849 4.931002 TGCCAAAACGTACTAATACCTGTC 59.069 41.667 0.00 0.00 0.00 3.51
1804 1850 4.692155 GTGCCAAAACGTACTAATACCTGT 59.308 41.667 0.00 0.00 0.00 4.00
1805 1851 4.933400 AGTGCCAAAACGTACTAATACCTG 59.067 41.667 0.00 0.00 0.00 4.00
1806 1852 5.156608 AGTGCCAAAACGTACTAATACCT 57.843 39.130 0.00 0.00 0.00 3.08
1807 1853 5.624292 CAAGTGCCAAAACGTACTAATACC 58.376 41.667 0.00 0.00 0.00 2.73
1808 1854 5.084055 GCAAGTGCCAAAACGTACTAATAC 58.916 41.667 0.00 0.00 34.31 1.89
1809 1855 4.998672 AGCAAGTGCCAAAACGTACTAATA 59.001 37.500 0.00 0.00 43.38 0.98
1810 1856 3.818773 AGCAAGTGCCAAAACGTACTAAT 59.181 39.130 0.00 0.00 43.38 1.73
1812 1858 2.841215 AGCAAGTGCCAAAACGTACTA 58.159 42.857 0.00 0.00 43.38 1.82
1813 1859 1.675552 AGCAAGTGCCAAAACGTACT 58.324 45.000 0.00 0.00 43.38 2.73
1814 1860 2.381589 GAAGCAAGTGCCAAAACGTAC 58.618 47.619 0.00 0.00 43.38 3.67
1815 1861 1.335496 GGAAGCAAGTGCCAAAACGTA 59.665 47.619 0.00 0.00 43.38 3.57
1816 1862 0.102300 GGAAGCAAGTGCCAAAACGT 59.898 50.000 0.00 0.00 43.38 3.99
1817 1863 0.385390 AGGAAGCAAGTGCCAAAACG 59.615 50.000 0.00 0.00 43.38 3.60
2006 2065 4.781775 TGGACAGAAGGGTTTCAAAGTA 57.218 40.909 0.00 0.00 35.70 2.24
2066 2125 3.064408 TGCATTGCACGCAATTTCAAAAA 59.936 34.783 14.41 0.00 43.32 1.94
2067 2126 2.610833 TGCATTGCACGCAATTTCAAAA 59.389 36.364 14.41 0.00 43.32 2.44
2068 2127 2.207590 TGCATTGCACGCAATTTCAAA 58.792 38.095 14.41 0.00 43.32 2.69
2069 2128 1.861971 TGCATTGCACGCAATTTCAA 58.138 40.000 14.41 0.00 43.32 2.69
2070 2129 1.861971 TTGCATTGCACGCAATTTCA 58.138 40.000 16.69 12.21 44.13 2.69
2076 2135 0.944788 CCAACATTGCATTGCACGCA 60.945 50.000 11.66 5.89 38.71 5.24
2077 2136 0.945265 ACCAACATTGCATTGCACGC 60.945 50.000 11.66 0.20 38.71 5.34
2078 2137 1.192757 CAACCAACATTGCATTGCACG 59.807 47.619 11.66 8.25 38.71 5.34
2079 2138 2.221517 GTCAACCAACATTGCATTGCAC 59.778 45.455 11.66 0.00 38.71 4.57
2092 2151 3.388024 AGTACTCTCAGCAAGTCAACCAA 59.612 43.478 0.00 0.00 0.00 3.67
2098 2157 3.984633 GTCAACAGTACTCTCAGCAAGTC 59.015 47.826 0.00 0.00 0.00 3.01
2110 2169 5.992217 AGAAGGATTGTCTTGTCAACAGTAC 59.008 40.000 0.00 0.00 0.00 2.73
2153 2212 1.643868 ATGCGCGCCGAGAATTTCAA 61.644 50.000 30.77 4.99 0.00 2.69
2159 2228 2.164663 CAGTAATGCGCGCCGAGAA 61.165 57.895 30.77 10.13 0.00 2.87
2226 2295 8.770438 AAGTGAGAATTCAGATTAGTTGAGAC 57.230 34.615 8.44 0.00 32.98 3.36
2228 2297 7.757173 TCGAAGTGAGAATTCAGATTAGTTGAG 59.243 37.037 8.44 0.00 32.98 3.02
2276 2354 1.135315 CGTCATCGCAAAGCCCTTG 59.865 57.895 0.00 0.00 38.15 3.61
2483 2561 3.306088 CCCGTATGATCACCCTGTATGTC 60.306 52.174 0.00 0.00 0.00 3.06
2503 2581 1.078143 CAGAGTAGCTTGTGCCCCC 60.078 63.158 0.00 0.00 40.80 5.40
2504 2582 0.674895 CACAGAGTAGCTTGTGCCCC 60.675 60.000 3.44 0.00 40.80 5.80
2514 2592 9.469807 GAAATGGACATCTTATACACAGAGTAG 57.530 37.037 0.00 0.00 35.85 2.57
2579 2657 8.355913 GTTGGACTTCAGAAGAAAAAGAATCAT 58.644 33.333 17.56 0.00 32.35 2.45
2604 2682 4.460382 CAGGGCAACAGTTATCATCAAAGT 59.540 41.667 0.00 0.00 39.74 2.66
2606 2684 4.661222 TCAGGGCAACAGTTATCATCAAA 58.339 39.130 0.00 0.00 39.74 2.69
2671 2781 5.353956 GCCCTTTTTCATTTCAACAACAACT 59.646 36.000 0.00 0.00 0.00 3.16
2757 3143 7.604657 AACATACTGGGTTTTGGATTTTACA 57.395 32.000 0.00 0.00 0.00 2.41
2761 3147 5.604650 TGGAAACATACTGGGTTTTGGATTT 59.395 36.000 0.00 0.00 38.50 2.17
2966 3391 6.924111 TCAGATTGCTCGACTTGCATATATA 58.076 36.000 0.00 0.00 40.34 0.86
2967 3392 5.787380 TCAGATTGCTCGACTTGCATATAT 58.213 37.500 0.00 0.00 40.34 0.86
2968 3393 5.200368 TCAGATTGCTCGACTTGCATATA 57.800 39.130 0.00 0.00 40.34 0.86
2970 3395 3.525268 TCAGATTGCTCGACTTGCATA 57.475 42.857 0.00 0.00 40.34 3.14
2971 3396 2.391616 TCAGATTGCTCGACTTGCAT 57.608 45.000 0.00 0.00 40.34 3.96
2972 3397 2.071540 CTTCAGATTGCTCGACTTGCA 58.928 47.619 0.00 0.00 38.80 4.08
2973 3398 2.341257 TCTTCAGATTGCTCGACTTGC 58.659 47.619 0.00 0.00 0.00 4.01
2975 3400 4.462508 TGATCTTCAGATTGCTCGACTT 57.537 40.909 0.00 0.00 34.37 3.01
2976 3401 4.159321 TCTTGATCTTCAGATTGCTCGACT 59.841 41.667 0.00 0.00 34.37 4.18
2977 3402 4.428209 TCTTGATCTTCAGATTGCTCGAC 58.572 43.478 0.00 0.00 34.37 4.20
2978 3403 4.725790 TCTTGATCTTCAGATTGCTCGA 57.274 40.909 0.00 0.00 34.37 4.04
2979 3404 4.259730 CGTTCTTGATCTTCAGATTGCTCG 60.260 45.833 0.00 0.00 34.37 5.03
3004 3447 9.414295 CGGTAACTCGGTATATTCAAATCATTA 57.586 33.333 0.00 0.00 0.00 1.90
3007 3450 7.041635 TCGGTAACTCGGTATATTCAAATCA 57.958 36.000 0.00 0.00 0.00 2.57
3008 3451 7.935338 TTCGGTAACTCGGTATATTCAAATC 57.065 36.000 0.00 0.00 0.00 2.17
3019 3464 1.203994 CACTGGATTCGGTAACTCGGT 59.796 52.381 0.00 0.00 0.00 4.69
3044 3489 5.049954 CGAAATCACTTTCAACCGAGGTTTA 60.050 40.000 4.52 0.00 40.72 2.01
3045 3490 4.261031 CGAAATCACTTTCAACCGAGGTTT 60.261 41.667 4.52 0.00 40.72 3.27
3046 3491 3.250040 CGAAATCACTTTCAACCGAGGTT 59.750 43.478 0.93 0.93 40.72 3.50
3048 3493 2.159627 CCGAAATCACTTTCAACCGAGG 59.840 50.000 0.00 0.00 40.72 4.63
3050 3495 3.114668 TCCGAAATCACTTTCAACCGA 57.885 42.857 0.00 0.00 40.72 4.69
3051 3496 4.630069 ACTATCCGAAATCACTTTCAACCG 59.370 41.667 0.00 0.00 40.72 4.44
3054 3499 7.659799 TCTCAAACTATCCGAAATCACTTTCAA 59.340 33.333 0.00 0.00 40.72 2.69
3055 3500 7.158697 TCTCAAACTATCCGAAATCACTTTCA 58.841 34.615 0.00 0.00 40.72 2.69
3061 3506 9.706691 GGTAATATCTCAAACTATCCGAAATCA 57.293 33.333 0.00 0.00 0.00 2.57
3062 3507 9.930693 AGGTAATATCTCAAACTATCCGAAATC 57.069 33.333 0.00 0.00 0.00 2.17
3063 3508 9.712305 CAGGTAATATCTCAAACTATCCGAAAT 57.288 33.333 0.00 0.00 0.00 2.17
3064 3509 8.148351 CCAGGTAATATCTCAAACTATCCGAAA 58.852 37.037 0.00 0.00 0.00 3.46
3065 3510 7.256190 CCCAGGTAATATCTCAAACTATCCGAA 60.256 40.741 0.00 0.00 0.00 4.30
3067 3512 6.014499 ACCCAGGTAATATCTCAAACTATCCG 60.014 42.308 0.00 0.00 0.00 4.18
3068 3513 7.317722 ACCCAGGTAATATCTCAAACTATCC 57.682 40.000 0.00 0.00 0.00 2.59
3069 3514 8.429641 TGAACCCAGGTAATATCTCAAACTATC 58.570 37.037 0.00 0.00 0.00 2.08
3070 3515 8.331931 TGAACCCAGGTAATATCTCAAACTAT 57.668 34.615 0.00 0.00 0.00 2.12
3071 3516 7.743116 TGAACCCAGGTAATATCTCAAACTA 57.257 36.000 0.00 0.00 0.00 2.24
3072 3517 6.636454 TGAACCCAGGTAATATCTCAAACT 57.364 37.500 0.00 0.00 0.00 2.66
3089 3569 5.385509 TTTCTTTTCGATGGAATGAACCC 57.614 39.130 6.11 0.00 30.25 4.11
3090 3570 4.859245 GCTTTCTTTTCGATGGAATGAACC 59.141 41.667 6.11 0.00 30.25 3.62
3091 3571 5.460646 TGCTTTCTTTTCGATGGAATGAAC 58.539 37.500 6.11 0.00 30.25 3.18
3092 3572 5.703978 TGCTTTCTTTTCGATGGAATGAA 57.296 34.783 0.00 0.00 30.88 2.57
3094 3574 5.702865 TCTTGCTTTCTTTTCGATGGAATG 58.297 37.500 0.00 0.00 30.88 2.67
3105 3665 2.165437 TGCACGGTTTCTTGCTTTCTTT 59.835 40.909 0.00 0.00 38.73 2.52
3130 3690 0.106894 GGGCCTAGGAAGGTTCATCG 59.893 60.000 14.75 0.00 45.64 3.84
3147 3715 1.014352 CTGGATTTTTACGAGGCGGG 58.986 55.000 0.00 0.00 0.00 6.13
3149 3717 2.093783 GTCACTGGATTTTTACGAGGCG 59.906 50.000 0.00 0.00 0.00 5.52
3178 3746 2.146342 AGCTGTGTATCACAAGTGTGC 58.854 47.619 6.56 4.03 44.08 4.57
3188 3769 4.210120 CGCTTTGGATAAGAGCTGTGTATC 59.790 45.833 0.00 0.00 34.33 2.24
3191 3772 2.350522 CGCTTTGGATAAGAGCTGTGT 58.649 47.619 0.00 0.00 34.33 3.72
3209 3790 1.918609 GATAGAGTTGTCGTGTTCCGC 59.081 52.381 0.00 0.00 36.19 5.54
3224 3805 5.012046 ACATCTAATCAACCATGCGGATAGA 59.988 40.000 0.00 0.00 35.59 1.98
3225 3806 5.240891 ACATCTAATCAACCATGCGGATAG 58.759 41.667 0.00 0.00 35.59 2.08
3299 3904 5.661458 AGATTGGTCCATAGAAACACTACG 58.339 41.667 0.00 0.00 33.62 3.51
3300 3905 9.614792 AAATAGATTGGTCCATAGAAACACTAC 57.385 33.333 0.00 0.00 33.62 2.73
3302 3907 9.533831 AAAAATAGATTGGTCCATAGAAACACT 57.466 29.630 0.00 0.00 0.00 3.55
3398 4028 2.851104 GCGCGTGTGTTCTGTACC 59.149 61.111 8.43 0.00 0.00 3.34
3439 4081 1.884464 GCGATTGGCAGAGATGCGA 60.884 57.895 0.00 0.00 42.87 5.10


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

AutoCloner maintained by Alex Coulton.