Multiple sequence alignment - TraesCS3A01G498600

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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 TraesCS3A01G498600 chr3A 100.000 3554 0 0 1 3554 724139478 724135925 0.000000e+00 6564.0
1 TraesCS3A01G498600 chr3A 80.662 1360 237 18 1097 2446 724199467 724200810 0.000000e+00 1031.0
2 TraesCS3A01G498600 chr3A 97.782 541 11 1 1 541 165095786 165096325 0.000000e+00 931.0
3 TraesCS3A01G498600 chr3A 81.502 1065 178 14 1380 2436 724107613 724108666 0.000000e+00 857.0
4 TraesCS3A01G498600 chr3B 94.856 1905 70 11 745 2640 795167734 795169619 0.000000e+00 2950.0
5 TraesCS3A01G498600 chr3B 80.730 1370 233 22 1166 2527 795176739 795178085 0.000000e+00 1038.0
6 TraesCS3A01G498600 chr3B 91.928 223 16 2 2770 2992 795169909 795170129 9.580000e-81 311.0
7 TraesCS3A01G498600 chr3B 95.349 129 6 0 2639 2767 795169743 795169871 4.650000e-49 206.0
8 TraesCS3A01G498600 chr3B 88.194 144 16 1 551 693 720203216 720203073 1.700000e-38 171.0
9 TraesCS3A01G498600 chr3D 79.945 1446 249 26 1097 2526 592904405 592902985 0.000000e+00 1026.0
10 TraesCS3A01G498600 chr5A 98.507 536 8 0 1 536 682896976 682896441 0.000000e+00 946.0
11 TraesCS3A01G498600 chr5A 84.211 285 27 12 272 553 607947404 607947135 9.790000e-66 261.0
12 TraesCS3A01G498600 chr5A 88.073 109 8 4 55 161 607947569 607947464 1.340000e-24 124.0
13 TraesCS3A01G498600 chr5A 100.000 47 0 0 114 160 671555754 671555800 1.760000e-13 87.9
14 TraesCS3A01G498600 chr7A 95.636 550 14 2 1 541 8544283 8544831 0.000000e+00 874.0
15 TraesCS3A01G498600 chr7A 80.186 323 43 13 227 541 78704954 78705263 4.620000e-54 222.0
16 TraesCS3A01G498600 chr7A 79.751 321 45 13 229 541 148408640 148408948 7.730000e-52 215.0
17 TraesCS3A01G498600 chr7A 87.500 152 18 1 543 693 243356984 243356833 1.310000e-39 174.0
18 TraesCS3A01G498600 chr7A 83.065 124 16 2 34 157 254431644 254431526 1.350000e-19 108.0
19 TraesCS3A01G498600 chr7A 90.196 51 5 0 96 146 15523485 15523435 2.290000e-07 67.6
20 TraesCS3A01G498600 chr1A 94.291 543 16 1 1 543 150861792 150861265 0.000000e+00 817.0
21 TraesCS3A01G498600 chrUn 89.869 612 48 12 2908 3512 45767234 45767838 0.000000e+00 774.0
22 TraesCS3A01G498600 chrUn 86.890 328 15 1 214 541 12351868 12351569 3.400000e-90 342.0
23 TraesCS3A01G498600 chrUn 96.739 184 6 0 1 184 12352141 12351958 1.240000e-79 307.0
24 TraesCS3A01G498600 chr4D 89.286 420 42 3 3093 3510 122693393 122692975 1.130000e-144 523.0
25 TraesCS3A01G498600 chr6D 85.269 353 43 2 3107 3450 91766908 91766556 4.360000e-94 355.0
26 TraesCS3A01G498600 chr6A 81.560 423 62 6 3037 3447 111393425 111393007 5.690000e-88 335.0
27 TraesCS3A01G498600 chr6A 83.951 162 19 4 551 705 127170980 127171141 7.950000e-32 148.0
28 TraesCS3A01G498600 chr7D 84.699 183 27 1 361 543 16699393 16699212 7.840000e-42 182.0
29 TraesCS3A01G498600 chr6B 86.538 156 20 1 551 705 233671497 233671652 1.700000e-38 171.0
30 TraesCS3A01G498600 chr4A 88.194 144 16 1 551 693 744026708 744026851 1.700000e-38 171.0
31 TraesCS3A01G498600 chr1B 86.842 152 19 1 543 693 371440213 371440062 6.100000e-38 169.0
32 TraesCS3A01G498600 chr2B 87.500 144 17 1 551 693 572683990 572683847 7.890000e-37 165.0
33 TraesCS3A01G498600 chr7B 86.184 152 20 1 543 693 599856206 599856357 2.840000e-36 163.0
34 TraesCS3A01G498600 chr7B 86.275 153 18 3 543 693 641334968 641335119 2.840000e-36 163.0
35 TraesCS3A01G498600 chr2A 82.407 108 14 4 3032 3139 761129208 761129310 4.890000e-14 89.8


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 TraesCS3A01G498600 chr3A 724135925 724139478 3553 True 6564.000000 6564 100.000000 1 3554 1 chr3A.!!$R1 3553
1 TraesCS3A01G498600 chr3A 724199467 724200810 1343 False 1031.000000 1031 80.662000 1097 2446 1 chr3A.!!$F3 1349
2 TraesCS3A01G498600 chr3A 165095786 165096325 539 False 931.000000 931 97.782000 1 541 1 chr3A.!!$F1 540
3 TraesCS3A01G498600 chr3A 724107613 724108666 1053 False 857.000000 857 81.502000 1380 2436 1 chr3A.!!$F2 1056
4 TraesCS3A01G498600 chr3B 795167734 795170129 2395 False 1155.666667 2950 94.044333 745 2992 3 chr3B.!!$F2 2247
5 TraesCS3A01G498600 chr3B 795176739 795178085 1346 False 1038.000000 1038 80.730000 1166 2527 1 chr3B.!!$F1 1361
6 TraesCS3A01G498600 chr3D 592902985 592904405 1420 True 1026.000000 1026 79.945000 1097 2526 1 chr3D.!!$R1 1429
7 TraesCS3A01G498600 chr5A 682896441 682896976 535 True 946.000000 946 98.507000 1 536 1 chr5A.!!$R1 535
8 TraesCS3A01G498600 chr7A 8544283 8544831 548 False 874.000000 874 95.636000 1 541 1 chr7A.!!$F1 540
9 TraesCS3A01G498600 chr1A 150861265 150861792 527 True 817.000000 817 94.291000 1 543 1 chr1A.!!$R1 542
10 TraesCS3A01G498600 chrUn 45767234 45767838 604 False 774.000000 774 89.869000 2908 3512 1 chrUn.!!$F1 604
11 TraesCS3A01G498600 chrUn 12351569 12352141 572 True 324.500000 342 91.814500 1 541 2 chrUn.!!$R1 540

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
603 673 0.035439 TGGGAGGAGCCGTTTTCATC 60.035 55.0 0.00 0.0 37.63 2.92 F
772 842 0.038744 ACAAAGCTAGCCAGGTGCAT 59.961 50.0 12.13 0.0 44.83 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2452 2537 1.078214 CATCCCTCGGAAGCTGCAA 60.078 57.895 1.02 0.0 34.34 4.08 R
2767 2977 3.441222 TCTGAAACTGCTGCCATGTAATG 59.559 43.478 0.00 0.0 46.21 1.90 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
254 315 2.885113 CCGCGACTGATCAGGACA 59.115 61.111 26.08 0.00 0.00 4.02
257 318 0.101219 CGCGACTGATCAGGACATCA 59.899 55.000 26.08 0.00 0.00 3.07
335 396 0.397941 CCACTTGAAGGGCACTCAGA 59.602 55.000 0.00 0.00 0.00 3.27
543 613 6.266168 TGATGCACCGTAAAAATTCTCAAT 57.734 33.333 0.00 0.00 0.00 2.57
544 614 6.686630 TGATGCACCGTAAAAATTCTCAATT 58.313 32.000 0.00 0.00 0.00 2.32
545 615 7.151308 TGATGCACCGTAAAAATTCTCAATTT 58.849 30.769 0.00 0.00 42.62 1.82
546 616 7.328249 TGATGCACCGTAAAAATTCTCAATTTC 59.672 33.333 0.00 0.00 40.05 2.17
547 617 6.744112 TGCACCGTAAAAATTCTCAATTTCT 58.256 32.000 0.00 0.00 40.05 2.52
548 618 7.877003 TGCACCGTAAAAATTCTCAATTTCTA 58.123 30.769 0.00 0.00 40.05 2.10
549 619 8.353684 TGCACCGTAAAAATTCTCAATTTCTAA 58.646 29.630 0.00 0.00 40.05 2.10
550 620 9.187455 GCACCGTAAAAATTCTCAATTTCTAAA 57.813 29.630 0.00 0.00 40.05 1.85
575 645 7.719689 TTTATTTCAGAATTTTCGACGATGC 57.280 32.000 0.00 0.00 0.00 3.91
576 646 3.368321 TTCAGAATTTTCGACGATGCG 57.632 42.857 0.00 0.00 0.00 4.73
577 647 1.060553 TCAGAATTTTCGACGATGCGC 59.939 47.619 0.00 0.00 0.00 6.09
578 648 1.061131 CAGAATTTTCGACGATGCGCT 59.939 47.619 9.73 0.00 0.00 5.92
579 649 1.732259 AGAATTTTCGACGATGCGCTT 59.268 42.857 9.73 0.55 0.00 4.68
580 650 2.159627 AGAATTTTCGACGATGCGCTTT 59.840 40.909 9.73 0.00 0.00 3.51
581 651 2.159467 ATTTTCGACGATGCGCTTTC 57.841 45.000 9.73 4.77 0.00 2.62
582 652 0.862490 TTTTCGACGATGCGCTTTCA 59.138 45.000 9.73 0.00 0.00 2.69
583 653 0.438445 TTTCGACGATGCGCTTTCAG 59.562 50.000 9.73 5.25 0.00 3.02
584 654 0.666274 TTCGACGATGCGCTTTCAGT 60.666 50.000 9.73 8.32 0.00 3.41
585 655 1.057822 CGACGATGCGCTTTCAGTG 59.942 57.895 9.73 0.00 0.00 3.66
586 656 1.421485 GACGATGCGCTTTCAGTGG 59.579 57.895 9.73 0.00 0.00 4.00
587 657 1.970917 GACGATGCGCTTTCAGTGGG 61.971 60.000 9.73 0.00 0.00 4.61
588 658 1.741401 CGATGCGCTTTCAGTGGGA 60.741 57.895 9.73 0.00 0.00 4.37
589 659 1.699656 CGATGCGCTTTCAGTGGGAG 61.700 60.000 9.73 0.00 0.00 4.30
590 660 1.372087 GATGCGCTTTCAGTGGGAGG 61.372 60.000 9.73 0.00 0.00 4.30
591 661 1.841302 ATGCGCTTTCAGTGGGAGGA 61.841 55.000 9.73 0.00 0.00 3.71
592 662 1.743252 GCGCTTTCAGTGGGAGGAG 60.743 63.158 0.00 0.00 0.00 3.69
593 663 1.743252 CGCTTTCAGTGGGAGGAGC 60.743 63.158 0.00 0.00 34.80 4.70
594 664 1.377856 GCTTTCAGTGGGAGGAGCC 60.378 63.158 0.00 0.00 33.08 4.70
595 665 1.078848 CTTTCAGTGGGAGGAGCCG 60.079 63.158 0.00 0.00 37.63 5.52
596 666 1.831652 CTTTCAGTGGGAGGAGCCGT 61.832 60.000 0.00 0.00 37.63 5.68
597 667 1.415672 TTTCAGTGGGAGGAGCCGTT 61.416 55.000 0.00 0.00 37.63 4.44
598 668 1.415672 TTCAGTGGGAGGAGCCGTTT 61.416 55.000 0.00 0.00 37.63 3.60
599 669 1.073199 CAGTGGGAGGAGCCGTTTT 59.927 57.895 0.00 0.00 37.63 2.43
600 670 0.955919 CAGTGGGAGGAGCCGTTTTC 60.956 60.000 0.00 0.00 37.63 2.29
601 671 1.072505 GTGGGAGGAGCCGTTTTCA 59.927 57.895 0.00 0.00 37.63 2.69
602 672 0.322546 GTGGGAGGAGCCGTTTTCAT 60.323 55.000 0.00 0.00 37.63 2.57
603 673 0.035439 TGGGAGGAGCCGTTTTCATC 60.035 55.000 0.00 0.00 37.63 2.92
604 674 1.090052 GGGAGGAGCCGTTTTCATCG 61.090 60.000 0.00 0.00 37.63 3.84
605 675 0.108329 GGAGGAGCCGTTTTCATCGA 60.108 55.000 0.00 0.00 0.00 3.59
606 676 1.000145 GAGGAGCCGTTTTCATCGAC 59.000 55.000 0.00 0.00 0.00 4.20
607 677 0.736325 AGGAGCCGTTTTCATCGACG 60.736 55.000 0.00 0.00 38.90 5.12
608 678 0.734942 GGAGCCGTTTTCATCGACGA 60.735 55.000 0.00 0.00 41.53 4.20
609 679 1.278238 GAGCCGTTTTCATCGACGAT 58.722 50.000 4.05 4.05 41.53 3.73
610 680 1.659098 GAGCCGTTTTCATCGACGATT 59.341 47.619 7.83 0.00 41.53 3.34
611 681 2.855963 GAGCCGTTTTCATCGACGATTA 59.144 45.455 7.83 0.00 41.53 1.75
612 682 2.858344 AGCCGTTTTCATCGACGATTAG 59.142 45.455 7.83 0.00 41.53 1.73
613 683 2.034001 GCCGTTTTCATCGACGATTAGG 60.034 50.000 7.83 6.62 41.53 2.69
614 684 2.034001 CCGTTTTCATCGACGATTAGGC 60.034 50.000 7.83 0.00 41.53 3.93
625 695 3.577649 ACGATTAGGCGTCTATGATGG 57.422 47.619 0.00 0.00 41.22 3.51
626 696 2.263077 CGATTAGGCGTCTATGATGGC 58.737 52.381 0.00 5.37 43.20 4.40
630 700 2.522060 GGCGTCTATGATGGCTTCG 58.478 57.895 6.16 0.00 40.34 3.79
631 701 0.249489 GGCGTCTATGATGGCTTCGT 60.249 55.000 6.16 0.49 40.34 3.85
632 702 1.000607 GGCGTCTATGATGGCTTCGTA 60.001 52.381 6.16 2.73 40.34 3.43
633 703 2.545113 GGCGTCTATGATGGCTTCGTAA 60.545 50.000 6.16 0.00 40.34 3.18
634 704 3.120792 GCGTCTATGATGGCTTCGTAAA 58.879 45.455 4.17 0.00 0.00 2.01
635 705 3.741344 GCGTCTATGATGGCTTCGTAAAT 59.259 43.478 4.17 0.00 0.00 1.40
636 706 4.143305 GCGTCTATGATGGCTTCGTAAATC 60.143 45.833 4.17 0.00 0.00 2.17
637 707 5.223382 CGTCTATGATGGCTTCGTAAATCT 58.777 41.667 4.17 0.00 0.00 2.40
638 708 5.343593 CGTCTATGATGGCTTCGTAAATCTC 59.656 44.000 4.17 0.00 0.00 2.75
639 709 6.216569 GTCTATGATGGCTTCGTAAATCTCA 58.783 40.000 4.17 0.00 0.00 3.27
640 710 6.701841 GTCTATGATGGCTTCGTAAATCTCAA 59.298 38.462 4.17 0.00 0.00 3.02
641 711 5.998454 ATGATGGCTTCGTAAATCTCAAG 57.002 39.130 0.00 0.00 0.00 3.02
642 712 5.084818 TGATGGCTTCGTAAATCTCAAGA 57.915 39.130 0.00 0.00 0.00 3.02
643 713 5.674525 TGATGGCTTCGTAAATCTCAAGAT 58.325 37.500 0.00 0.00 36.07 2.40
644 714 5.525012 TGATGGCTTCGTAAATCTCAAGATG 59.475 40.000 0.00 0.00 34.49 2.90
645 715 5.084818 TGGCTTCGTAAATCTCAAGATGA 57.915 39.130 0.00 0.00 34.49 2.92
646 716 5.674525 TGGCTTCGTAAATCTCAAGATGAT 58.325 37.500 0.00 0.00 34.49 2.45
647 717 6.816136 TGGCTTCGTAAATCTCAAGATGATA 58.184 36.000 0.00 0.00 34.49 2.15
648 718 7.445121 TGGCTTCGTAAATCTCAAGATGATAT 58.555 34.615 0.00 0.00 34.49 1.63
649 719 7.386025 TGGCTTCGTAAATCTCAAGATGATATG 59.614 37.037 0.00 0.00 34.49 1.78
650 720 7.386299 GGCTTCGTAAATCTCAAGATGATATGT 59.614 37.037 0.00 0.00 34.49 2.29
651 721 8.431593 GCTTCGTAAATCTCAAGATGATATGTC 58.568 37.037 0.00 0.00 34.49 3.06
652 722 8.507470 TTCGTAAATCTCAAGATGATATGTCG 57.493 34.615 0.00 0.00 34.49 4.35
653 723 7.871853 TCGTAAATCTCAAGATGATATGTCGA 58.128 34.615 0.00 0.00 34.49 4.20
654 724 8.515414 TCGTAAATCTCAAGATGATATGTCGAT 58.485 33.333 0.00 0.00 34.49 3.59
655 725 9.133627 CGTAAATCTCAAGATGATATGTCGATT 57.866 33.333 0.00 0.00 34.49 3.34
658 728 8.760103 AATCTCAAGATGATATGTCGATTCAG 57.240 34.615 0.00 0.00 34.49 3.02
659 729 7.282332 TCTCAAGATGATATGTCGATTCAGT 57.718 36.000 0.00 0.00 0.00 3.41
660 730 7.366513 TCTCAAGATGATATGTCGATTCAGTC 58.633 38.462 0.00 0.00 0.00 3.51
661 731 7.230309 TCTCAAGATGATATGTCGATTCAGTCT 59.770 37.037 0.00 0.00 0.00 3.24
662 732 7.366513 TCAAGATGATATGTCGATTCAGTCTC 58.633 38.462 0.00 0.00 0.00 3.36
663 733 7.230309 TCAAGATGATATGTCGATTCAGTCTCT 59.770 37.037 0.00 0.00 0.00 3.10
664 734 7.144722 AGATGATATGTCGATTCAGTCTCTC 57.855 40.000 0.00 0.00 0.00 3.20
665 735 5.349824 TGATATGTCGATTCAGTCTCTCG 57.650 43.478 0.00 0.00 0.00 4.04
666 736 4.214332 TGATATGTCGATTCAGTCTCTCGG 59.786 45.833 0.00 0.00 33.38 4.63
667 737 2.109425 TGTCGATTCAGTCTCTCGGA 57.891 50.000 0.00 0.00 33.38 4.55
668 738 2.010497 TGTCGATTCAGTCTCTCGGAG 58.990 52.381 0.00 0.00 33.38 4.63
669 739 2.281517 GTCGATTCAGTCTCTCGGAGA 58.718 52.381 7.60 7.60 36.22 3.71
670 740 2.875933 GTCGATTCAGTCTCTCGGAGAT 59.124 50.000 8.39 0.00 40.98 2.75
671 741 2.875317 TCGATTCAGTCTCTCGGAGATG 59.125 50.000 8.39 4.48 40.98 2.90
672 742 2.616376 CGATTCAGTCTCTCGGAGATGT 59.384 50.000 8.39 0.00 40.98 3.06
673 743 3.066064 CGATTCAGTCTCTCGGAGATGTT 59.934 47.826 8.39 0.00 40.98 2.71
674 744 4.606961 GATTCAGTCTCTCGGAGATGTTC 58.393 47.826 8.39 3.35 40.98 3.18
675 745 3.073274 TCAGTCTCTCGGAGATGTTCA 57.927 47.619 8.39 0.00 40.98 3.18
676 746 3.625853 TCAGTCTCTCGGAGATGTTCAT 58.374 45.455 8.39 0.00 40.98 2.57
677 747 4.781934 TCAGTCTCTCGGAGATGTTCATA 58.218 43.478 8.39 0.00 40.98 2.15
678 748 4.819088 TCAGTCTCTCGGAGATGTTCATAG 59.181 45.833 8.39 0.00 40.98 2.23
679 749 4.023279 CAGTCTCTCGGAGATGTTCATAGG 60.023 50.000 8.39 0.00 40.98 2.57
680 750 4.138290 GTCTCTCGGAGATGTTCATAGGA 58.862 47.826 8.39 0.00 40.98 2.94
681 751 4.215399 GTCTCTCGGAGATGTTCATAGGAG 59.785 50.000 8.39 0.00 40.98 3.69
682 752 4.141287 CTCTCGGAGATGTTCATAGGAGT 58.859 47.826 8.39 0.00 33.89 3.85
683 753 5.071923 TCTCTCGGAGATGTTCATAGGAGTA 59.928 44.000 8.39 0.00 33.35 2.59
684 754 5.309638 TCTCGGAGATGTTCATAGGAGTAG 58.690 45.833 2.97 0.00 33.89 2.57
685 755 4.399219 TCGGAGATGTTCATAGGAGTAGG 58.601 47.826 0.00 0.00 0.00 3.18
686 756 4.141228 TCGGAGATGTTCATAGGAGTAGGT 60.141 45.833 0.00 0.00 0.00 3.08
687 757 4.022762 CGGAGATGTTCATAGGAGTAGGTG 60.023 50.000 0.00 0.00 0.00 4.00
688 758 4.896482 GGAGATGTTCATAGGAGTAGGTGT 59.104 45.833 0.00 0.00 0.00 4.16
689 759 5.221342 GGAGATGTTCATAGGAGTAGGTGTG 60.221 48.000 0.00 0.00 0.00 3.82
690 760 3.887621 TGTTCATAGGAGTAGGTGTGC 57.112 47.619 0.00 0.00 0.00 4.57
691 761 2.165641 TGTTCATAGGAGTAGGTGTGCG 59.834 50.000 0.00 0.00 0.00 5.34
692 762 2.139323 TCATAGGAGTAGGTGTGCGT 57.861 50.000 0.00 0.00 0.00 5.24
693 763 2.453521 TCATAGGAGTAGGTGTGCGTT 58.546 47.619 0.00 0.00 0.00 4.84
694 764 2.426024 TCATAGGAGTAGGTGTGCGTTC 59.574 50.000 0.00 0.00 0.00 3.95
695 765 1.913778 TAGGAGTAGGTGTGCGTTCA 58.086 50.000 0.00 0.00 0.00 3.18
696 766 1.267121 AGGAGTAGGTGTGCGTTCAT 58.733 50.000 0.00 0.00 0.00 2.57
697 767 2.453521 AGGAGTAGGTGTGCGTTCATA 58.546 47.619 0.00 0.00 0.00 2.15
698 768 2.427453 AGGAGTAGGTGTGCGTTCATAG 59.573 50.000 0.00 0.00 0.00 2.23
699 769 2.481449 GGAGTAGGTGTGCGTTCATAGG 60.481 54.545 0.00 0.00 0.00 2.57
700 770 1.480954 AGTAGGTGTGCGTTCATAGGG 59.519 52.381 0.00 0.00 0.00 3.53
701 771 1.479323 GTAGGTGTGCGTTCATAGGGA 59.521 52.381 0.00 0.00 0.00 4.20
702 772 1.204146 AGGTGTGCGTTCATAGGGAT 58.796 50.000 0.00 0.00 0.00 3.85
703 773 1.134401 AGGTGTGCGTTCATAGGGATG 60.134 52.381 0.00 0.00 0.00 3.51
704 774 1.134521 GGTGTGCGTTCATAGGGATGA 60.135 52.381 0.00 0.00 40.45 2.92
714 784 3.599343 TCATAGGGATGAACATATGCGC 58.401 45.455 0.00 0.00 39.20 6.09
715 785 3.007831 TCATAGGGATGAACATATGCGCA 59.992 43.478 14.96 14.96 39.20 6.09
716 786 2.574006 AGGGATGAACATATGCGCAT 57.426 45.000 28.23 28.23 0.00 4.73
717 787 3.701205 AGGGATGAACATATGCGCATA 57.299 42.857 30.72 30.72 0.00 3.14
718 788 4.226427 AGGGATGAACATATGCGCATAT 57.774 40.909 32.21 32.21 34.50 1.78
719 789 6.293244 CATAGGGATGAACATATGCGCATATG 60.293 42.308 45.71 45.71 43.79 1.78
729 799 6.270096 CATATGCGCATATGTATGAGTCAG 57.730 41.667 42.31 24.60 43.40 3.51
730 800 3.733443 TGCGCATATGTATGAGTCAGT 57.267 42.857 5.66 0.00 36.14 3.41
731 801 4.846779 TGCGCATATGTATGAGTCAGTA 57.153 40.909 5.66 0.00 36.14 2.74
732 802 4.546570 TGCGCATATGTATGAGTCAGTAC 58.453 43.478 5.66 2.78 36.14 2.73
733 803 4.278419 TGCGCATATGTATGAGTCAGTACT 59.722 41.667 5.66 0.00 39.21 2.73
734 804 5.472137 TGCGCATATGTATGAGTCAGTACTA 59.528 40.000 5.66 0.00 35.56 1.82
735 805 6.151144 TGCGCATATGTATGAGTCAGTACTAT 59.849 38.462 5.66 0.00 35.56 2.12
736 806 6.470556 GCGCATATGTATGAGTCAGTACTATG 59.529 42.308 0.30 5.31 35.56 2.23
737 807 7.530863 CGCATATGTATGAGTCAGTACTATGT 58.469 38.462 4.29 0.00 35.56 2.29
738 808 8.023706 CGCATATGTATGAGTCAGTACTATGTT 58.976 37.037 4.29 0.00 35.56 2.71
772 842 0.038744 ACAAAGCTAGCCAGGTGCAT 59.961 50.000 12.13 0.00 44.83 3.96
787 857 2.331194 GTGCATGCACATCTCAAAACC 58.669 47.619 39.12 12.88 45.53 3.27
792 862 4.487948 CATGCACATCTCAAAACCGAAAT 58.512 39.130 0.00 0.00 0.00 2.17
836 912 3.576356 CATCGGCGCATGTGGACC 61.576 66.667 10.83 0.37 0.00 4.46
849 925 1.909302 TGTGGACCCTCCTGAAAGATC 59.091 52.381 0.00 0.00 37.46 2.75
884 960 4.667420 GTGTACCACACGGACAGG 57.333 61.111 0.00 0.00 39.53 4.00
917 993 1.053424 TACACCAGACCAGACCCAAC 58.947 55.000 0.00 0.00 0.00 3.77
931 1007 3.201266 AGACCCAACTGTTAAACCTCACA 59.799 43.478 0.00 0.00 0.00 3.58
932 1008 3.284617 ACCCAACTGTTAAACCTCACAC 58.715 45.455 0.00 0.00 0.00 3.82
933 1009 3.283751 CCCAACTGTTAAACCTCACACA 58.716 45.455 0.00 0.00 0.00 3.72
937 1013 5.505654 CCAACTGTTAAACCTCACACATCAC 60.506 44.000 0.00 0.00 0.00 3.06
938 1014 4.776349 ACTGTTAAACCTCACACATCACA 58.224 39.130 0.00 0.00 0.00 3.58
939 1015 5.189928 ACTGTTAAACCTCACACATCACAA 58.810 37.500 0.00 0.00 0.00 3.33
940 1016 5.650266 ACTGTTAAACCTCACACATCACAAA 59.350 36.000 0.00 0.00 0.00 2.83
941 1017 6.321181 ACTGTTAAACCTCACACATCACAAAT 59.679 34.615 0.00 0.00 0.00 2.32
942 1018 6.734137 TGTTAAACCTCACACATCACAAATC 58.266 36.000 0.00 0.00 0.00 2.17
943 1019 6.319911 TGTTAAACCTCACACATCACAAATCA 59.680 34.615 0.00 0.00 0.00 2.57
944 1020 4.836125 AACCTCACACATCACAAATCAC 57.164 40.909 0.00 0.00 0.00 3.06
945 1021 3.819368 ACCTCACACATCACAAATCACA 58.181 40.909 0.00 0.00 0.00 3.58
946 1022 4.206375 ACCTCACACATCACAAATCACAA 58.794 39.130 0.00 0.00 0.00 3.33
947 1023 4.828939 ACCTCACACATCACAAATCACAAT 59.171 37.500 0.00 0.00 0.00 2.71
948 1024 5.302568 ACCTCACACATCACAAATCACAATT 59.697 36.000 0.00 0.00 0.00 2.32
949 1025 5.860182 CCTCACACATCACAAATCACAATTC 59.140 40.000 0.00 0.00 0.00 2.17
950 1026 6.388435 TCACACATCACAAATCACAATTCA 57.612 33.333 0.00 0.00 0.00 2.57
951 1027 6.983984 TCACACATCACAAATCACAATTCAT 58.016 32.000 0.00 0.00 0.00 2.57
967 1043 2.357327 TCATAGCGCACAAGTACGTT 57.643 45.000 11.47 0.00 0.00 3.99
990 1066 1.266989 TGCATAGTACATCTCGCGAGG 59.733 52.381 33.98 21.94 0.00 4.63
1017 1096 1.007479 ACAATGGCCATGTCCTCCAAT 59.993 47.619 21.63 0.00 33.04 3.16
1209 1294 1.876664 CACTCTCGCCGAGAAGACA 59.123 57.895 18.59 0.00 42.62 3.41
1278 1363 2.606519 AACGACTGGCAGGGGCTA 60.607 61.111 20.34 0.00 40.87 3.93
1356 1441 0.905337 AGGCCTGCTACGACTCCTTT 60.905 55.000 3.11 0.00 0.00 3.11
1425 1510 0.951040 GCACCTTCTTCCAGGACGTG 60.951 60.000 0.00 0.00 37.39 4.49
1475 1560 0.248907 CGGTACCTCTACGCCACATG 60.249 60.000 10.90 0.00 0.00 3.21
1692 1777 2.357881 CTGAAGCCGCTCACTGCA 60.358 61.111 0.00 0.00 43.06 4.41
1767 1852 1.691976 CTATACATCGGCAAGGACCCA 59.308 52.381 0.00 0.00 0.00 4.51
1950 2035 2.432628 GGAGCCAACGTGTCTCCG 60.433 66.667 13.11 0.00 37.28 4.63
2107 2192 1.592400 GCCTAAGGTGCCCGGTTTTC 61.592 60.000 0.00 0.00 0.00 2.29
2412 2497 2.688666 TGGCGGCAGGAGGAGAAT 60.689 61.111 7.97 0.00 0.00 2.40
2452 2537 1.449601 GACGGACGATGGGCATTGT 60.450 57.895 0.00 0.00 38.11 2.71
2559 2644 4.753233 AGCAAGATGGTATATGATCGAGC 58.247 43.478 0.00 0.00 0.00 5.03
2563 2648 5.929058 AGATGGTATATGATCGAGCACAT 57.071 39.130 5.03 1.32 0.00 3.21
2578 2663 5.990996 TCGAGCACATGATTCATATAGCAAA 59.009 36.000 0.00 2.94 0.00 3.68
2589 2674 8.000709 TGATTCATATAGCAAACCAAAGAGGAT 58.999 33.333 0.00 0.00 41.22 3.24
2593 2678 7.500227 TCATATAGCAAACCAAAGAGGATTCAG 59.500 37.037 0.00 0.00 41.22 3.02
2595 2680 4.670765 AGCAAACCAAAGAGGATTCAGAT 58.329 39.130 0.00 0.00 41.22 2.90
2598 2683 5.623141 GCAAACCAAAGAGGATTCAGATTCC 60.623 44.000 3.40 3.40 41.22 3.01
2601 2686 5.896963 ACCAAAGAGGATTCAGATTCCTTT 58.103 37.500 14.02 6.90 43.75 3.11
2605 2690 5.786121 AGAGGATTCAGATTCCTTTCCAA 57.214 39.130 14.02 0.00 43.75 3.53
2623 2708 7.565323 TTTCCAAGGATTTTCAATGTTTTGG 57.435 32.000 0.00 0.00 36.13 3.28
2627 2712 7.661027 TCCAAGGATTTTCAATGTTTTGGAATC 59.339 33.333 0.48 0.00 39.69 2.52
2640 2725 9.533253 AATGTTTTGGAATCTAACTCTTTTGTG 57.467 29.630 0.00 0.00 0.00 3.33
2652 2862 8.617809 TCTAACTCTTTTGTGTGTTTATTGTCC 58.382 33.333 0.00 0.00 0.00 4.02
2748 2958 6.325919 TGTTTACATTTCTTCACATGTCCC 57.674 37.500 0.00 0.00 35.24 4.46
2755 2965 4.478206 TTCTTCACATGTCCCTCTCATC 57.522 45.455 0.00 0.00 0.00 2.92
2767 2977 3.821600 TCCCTCTCATCGCTGTTATAGTC 59.178 47.826 0.00 0.00 0.00 2.59
2768 2978 3.570125 CCCTCTCATCGCTGTTATAGTCA 59.430 47.826 0.00 0.00 0.00 3.41
2781 3026 5.679601 TGTTATAGTCATTACATGGCAGCA 58.320 37.500 0.00 0.00 37.34 4.41
2788 3033 3.441222 TCATTACATGGCAGCAGTTTCAG 59.559 43.478 0.00 0.00 0.00 3.02
2894 3139 7.732140 AGTATTCCAGGACAATCATAGATCTCA 59.268 37.037 0.00 0.00 0.00 3.27
3006 3259 7.432350 TGTTATTTTGAATGTCAATTTGCCC 57.568 32.000 0.00 0.00 36.11 5.36
3007 3260 7.222872 TGTTATTTTGAATGTCAATTTGCCCT 58.777 30.769 0.00 0.00 36.11 5.19
3009 3262 9.213799 GTTATTTTGAATGTCAATTTGCCCTAA 57.786 29.630 0.00 0.00 36.11 2.69
3013 3266 8.688747 TTTGAATGTCAATTTGCCCTAATTTT 57.311 26.923 0.00 0.00 36.11 1.82
3014 3267 8.688747 TTGAATGTCAATTTGCCCTAATTTTT 57.311 26.923 0.00 0.00 30.26 1.94
3024 3277 5.159273 TGCCCTAATTTTTGTTTCCCATC 57.841 39.130 0.00 0.00 0.00 3.51
3025 3278 4.843516 TGCCCTAATTTTTGTTTCCCATCT 59.156 37.500 0.00 0.00 0.00 2.90
3067 3320 1.663695 CACATTACGGGTTAGGGCTG 58.336 55.000 0.00 0.00 0.00 4.85
3074 3327 0.243636 CGGGTTAGGGCTGCAAAAAG 59.756 55.000 0.50 0.00 0.00 2.27
3078 3331 2.094700 GGTTAGGGCTGCAAAAAGCTAC 60.095 50.000 0.50 0.00 45.94 3.58
3210 3463 2.584791 GCATGTTTGTTTGACCGCTAG 58.415 47.619 0.00 0.00 0.00 3.42
3229 3482 4.162509 GCTAGGTTGACCCTTAAGTCTGAT 59.837 45.833 0.97 0.00 42.73 2.90
3248 3501 0.039035 TGTTATGACAAGTGGGCCCC 59.961 55.000 22.27 11.17 31.49 5.80
3272 3525 0.773644 TCAGCTTCTTCTTTGCCCCT 59.226 50.000 0.00 0.00 0.00 4.79
3283 3536 1.916181 CTTTGCCCCTTCTTCCCTAGA 59.084 52.381 0.00 0.00 0.00 2.43
3289 3542 1.560146 CCCTTCTTCCCTAGAACCACC 59.440 57.143 0.00 0.00 37.96 4.61
3291 3544 2.176889 CTTCTTCCCTAGAACCACCGA 58.823 52.381 0.00 0.00 37.96 4.69
3314 3567 2.091541 TCATTTTCCTCCGTCAATGGC 58.908 47.619 0.00 0.00 0.00 4.40
3322 3575 0.545646 TCCGTCAATGGCCATCATCA 59.454 50.000 21.08 0.00 34.44 3.07
3347 3600 3.257561 CCGCGTCTGAAGCCATCG 61.258 66.667 4.92 0.00 0.00 3.84
3351 3604 1.227089 CGTCTGAAGCCATCGGGAG 60.227 63.158 0.00 0.00 34.95 4.30
3412 3665 3.934962 GGGGAGGATGAGCTCGCC 61.935 72.222 15.60 15.60 43.62 5.54
3413 3666 4.292178 GGGAGGATGAGCTCGCCG 62.292 72.222 16.91 0.00 0.00 6.46
3529 3782 3.250323 CGACGGCGATGACAGCAG 61.250 66.667 16.62 0.00 40.82 4.24
3530 3783 3.558411 GACGGCGATGACAGCAGC 61.558 66.667 16.62 0.00 36.08 5.25
3548 3801 4.347453 GGCTGCGGGCAACAACAG 62.347 66.667 15.36 0.00 44.01 3.16
3549 3802 3.595758 GCTGCGGGCAACAACAGT 61.596 61.111 0.00 0.00 41.63 3.55
3550 3803 2.332514 CTGCGGGCAACAACAGTG 59.667 61.111 0.00 0.00 36.57 3.66
3551 3804 2.124529 TGCGGGCAACAACAGTGA 60.125 55.556 0.00 0.00 39.74 3.41
3552 3805 2.121564 CTGCGGGCAACAACAGTGAG 62.122 60.000 0.00 0.00 36.57 3.51
3553 3806 2.639286 CGGGCAACAACAGTGAGC 59.361 61.111 0.00 0.00 39.74 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
254 315 0.179084 CACAGAACCGGCGGTATGAT 60.179 55.000 36.33 23.06 33.12 2.45
257 318 2.582436 CCACAGAACCGGCGGTAT 59.418 61.111 34.37 21.59 33.12 2.73
335 396 2.031120 GATCAGAGCTAGCCTGACTGT 58.969 52.381 27.59 17.56 42.68 3.55
549 619 8.798153 GCATCGTCGAAAATTCTGAAATAAATT 58.202 29.630 0.00 0.00 0.00 1.82
550 620 7.164171 CGCATCGTCGAAAATTCTGAAATAAAT 59.836 33.333 0.00 0.00 0.00 1.40
551 621 6.464519 CGCATCGTCGAAAATTCTGAAATAAA 59.535 34.615 0.00 0.00 0.00 1.40
552 622 5.957220 CGCATCGTCGAAAATTCTGAAATAA 59.043 36.000 0.00 0.00 0.00 1.40
553 623 5.489335 CGCATCGTCGAAAATTCTGAAATA 58.511 37.500 0.00 0.00 0.00 1.40
554 624 4.334443 CGCATCGTCGAAAATTCTGAAAT 58.666 39.130 0.00 0.00 0.00 2.17
555 625 3.731855 CGCATCGTCGAAAATTCTGAAA 58.268 40.909 0.00 0.00 0.00 2.69
556 626 2.473868 GCGCATCGTCGAAAATTCTGAA 60.474 45.455 0.30 0.00 0.00 3.02
557 627 1.060553 GCGCATCGTCGAAAATTCTGA 59.939 47.619 0.30 0.00 0.00 3.27
558 628 1.061131 AGCGCATCGTCGAAAATTCTG 59.939 47.619 11.47 0.00 0.00 3.02
559 629 1.359848 AGCGCATCGTCGAAAATTCT 58.640 45.000 11.47 0.00 0.00 2.40
560 630 2.159467 AAGCGCATCGTCGAAAATTC 57.841 45.000 11.47 0.00 0.00 2.17
561 631 2.095969 TGAAAGCGCATCGTCGAAAATT 60.096 40.909 11.47 0.00 0.00 1.82
562 632 1.463056 TGAAAGCGCATCGTCGAAAAT 59.537 42.857 11.47 0.00 0.00 1.82
563 633 0.862490 TGAAAGCGCATCGTCGAAAA 59.138 45.000 11.47 0.00 0.00 2.29
564 634 0.438445 CTGAAAGCGCATCGTCGAAA 59.562 50.000 11.47 0.00 0.00 3.46
565 635 0.666274 ACTGAAAGCGCATCGTCGAA 60.666 50.000 11.47 0.00 37.60 3.71
566 636 1.080772 ACTGAAAGCGCATCGTCGA 60.081 52.632 11.47 0.00 37.60 4.20
567 637 1.057822 CACTGAAAGCGCATCGTCG 59.942 57.895 11.47 3.02 37.60 5.12
568 638 1.421485 CCACTGAAAGCGCATCGTC 59.579 57.895 11.47 0.92 37.60 4.20
569 639 2.034879 CCCACTGAAAGCGCATCGT 61.035 57.895 11.47 7.45 37.60 3.73
570 640 1.699656 CTCCCACTGAAAGCGCATCG 61.700 60.000 11.47 6.82 37.60 3.84
571 641 1.372087 CCTCCCACTGAAAGCGCATC 61.372 60.000 11.47 8.39 37.60 3.91
572 642 1.377725 CCTCCCACTGAAAGCGCAT 60.378 57.895 11.47 0.00 37.60 4.73
573 643 2.032528 CCTCCCACTGAAAGCGCA 59.967 61.111 11.47 0.00 37.60 6.09
574 644 1.743252 CTCCTCCCACTGAAAGCGC 60.743 63.158 0.00 0.00 37.60 5.92
575 645 1.743252 GCTCCTCCCACTGAAAGCG 60.743 63.158 0.00 0.00 37.60 4.68
576 646 1.377856 GGCTCCTCCCACTGAAAGC 60.378 63.158 0.00 0.00 37.60 3.51
577 647 1.078848 CGGCTCCTCCCACTGAAAG 60.079 63.158 0.00 0.00 42.29 2.62
578 648 1.415672 AACGGCTCCTCCCACTGAAA 61.416 55.000 0.00 0.00 0.00 2.69
579 649 1.415672 AAACGGCTCCTCCCACTGAA 61.416 55.000 0.00 0.00 0.00 3.02
580 650 1.415672 AAAACGGCTCCTCCCACTGA 61.416 55.000 0.00 0.00 0.00 3.41
581 651 0.955919 GAAAACGGCTCCTCCCACTG 60.956 60.000 0.00 0.00 0.00 3.66
582 652 1.375326 GAAAACGGCTCCTCCCACT 59.625 57.895 0.00 0.00 0.00 4.00
583 653 0.322546 ATGAAAACGGCTCCTCCCAC 60.323 55.000 0.00 0.00 0.00 4.61
584 654 0.035439 GATGAAAACGGCTCCTCCCA 60.035 55.000 0.00 0.00 0.00 4.37
585 655 1.090052 CGATGAAAACGGCTCCTCCC 61.090 60.000 0.00 0.00 0.00 4.30
586 656 0.108329 TCGATGAAAACGGCTCCTCC 60.108 55.000 0.00 0.00 30.83 4.30
587 657 1.000145 GTCGATGAAAACGGCTCCTC 59.000 55.000 0.00 0.00 32.43 3.71
588 658 0.736325 CGTCGATGAAAACGGCTCCT 60.736 55.000 0.00 0.00 33.25 3.69
589 659 0.734942 TCGTCGATGAAAACGGCTCC 60.735 55.000 4.45 0.00 33.25 4.70
590 660 1.278238 ATCGTCGATGAAAACGGCTC 58.722 50.000 12.12 0.00 33.25 4.70
591 661 1.722011 AATCGTCGATGAAAACGGCT 58.278 45.000 12.12 0.00 33.25 5.52
592 662 2.034001 CCTAATCGTCGATGAAAACGGC 60.034 50.000 12.12 0.00 39.31 5.68
593 663 2.034001 GCCTAATCGTCGATGAAAACGG 60.034 50.000 12.12 10.69 39.31 4.44
594 664 2.346376 CGCCTAATCGTCGATGAAAACG 60.346 50.000 12.12 7.81 40.17 3.60
595 665 2.601763 ACGCCTAATCGTCGATGAAAAC 59.398 45.455 12.12 0.00 38.44 2.43
596 666 2.883574 ACGCCTAATCGTCGATGAAAA 58.116 42.857 12.12 1.78 38.44 2.29
597 667 2.572191 ACGCCTAATCGTCGATGAAA 57.428 45.000 12.12 2.16 38.44 2.69
605 675 2.352814 GCCATCATAGACGCCTAATCGT 60.353 50.000 0.00 0.00 46.38 3.73
606 676 2.094494 AGCCATCATAGACGCCTAATCG 60.094 50.000 0.00 0.00 0.00 3.34
607 677 3.601443 AGCCATCATAGACGCCTAATC 57.399 47.619 0.00 0.00 0.00 1.75
608 678 3.615110 CGAAGCCATCATAGACGCCTAAT 60.615 47.826 0.00 0.00 0.00 1.73
609 679 2.288213 CGAAGCCATCATAGACGCCTAA 60.288 50.000 0.00 0.00 0.00 2.69
610 680 1.269723 CGAAGCCATCATAGACGCCTA 59.730 52.381 0.00 0.00 0.00 3.93
611 681 0.032678 CGAAGCCATCATAGACGCCT 59.967 55.000 0.00 0.00 0.00 5.52
612 682 0.249489 ACGAAGCCATCATAGACGCC 60.249 55.000 0.00 0.00 0.00 5.68
613 683 2.417339 TACGAAGCCATCATAGACGC 57.583 50.000 0.00 0.00 0.00 5.19
614 684 5.223382 AGATTTACGAAGCCATCATAGACG 58.777 41.667 0.00 0.00 0.00 4.18
615 685 6.216569 TGAGATTTACGAAGCCATCATAGAC 58.783 40.000 0.00 0.00 0.00 2.59
616 686 6.405278 TGAGATTTACGAAGCCATCATAGA 57.595 37.500 0.00 0.00 0.00 1.98
617 687 6.925718 TCTTGAGATTTACGAAGCCATCATAG 59.074 38.462 0.00 0.00 0.00 2.23
618 688 6.816136 TCTTGAGATTTACGAAGCCATCATA 58.184 36.000 0.00 0.00 0.00 2.15
619 689 5.674525 TCTTGAGATTTACGAAGCCATCAT 58.325 37.500 0.00 0.00 0.00 2.45
620 690 5.084818 TCTTGAGATTTACGAAGCCATCA 57.915 39.130 0.00 0.00 0.00 3.07
621 691 5.755375 TCATCTTGAGATTTACGAAGCCATC 59.245 40.000 0.00 0.00 31.21 3.51
622 692 5.674525 TCATCTTGAGATTTACGAAGCCAT 58.325 37.500 0.00 0.00 31.21 4.40
623 693 5.084818 TCATCTTGAGATTTACGAAGCCA 57.915 39.130 0.00 0.00 31.21 4.75
624 694 7.386299 ACATATCATCTTGAGATTTACGAAGCC 59.614 37.037 0.00 0.00 31.21 4.35
625 695 8.304202 ACATATCATCTTGAGATTTACGAAGC 57.696 34.615 0.00 0.00 31.21 3.86
626 696 8.634265 CGACATATCATCTTGAGATTTACGAAG 58.366 37.037 0.00 0.00 31.21 3.79
627 697 8.349983 TCGACATATCATCTTGAGATTTACGAA 58.650 33.333 0.00 0.00 29.21 3.85
628 698 7.871853 TCGACATATCATCTTGAGATTTACGA 58.128 34.615 0.00 0.00 31.21 3.43
629 699 8.680707 ATCGACATATCATCTTGAGATTTACG 57.319 34.615 0.00 0.00 31.21 3.18
632 702 9.205719 CTGAATCGACATATCATCTTGAGATTT 57.794 33.333 0.00 0.00 31.21 2.17
633 703 8.366401 ACTGAATCGACATATCATCTTGAGATT 58.634 33.333 0.00 0.00 31.21 2.40
634 704 7.894708 ACTGAATCGACATATCATCTTGAGAT 58.105 34.615 0.00 0.00 34.56 2.75
635 705 7.230309 AGACTGAATCGACATATCATCTTGAGA 59.770 37.037 0.00 0.00 0.00 3.27
636 706 7.369607 AGACTGAATCGACATATCATCTTGAG 58.630 38.462 0.00 0.00 0.00 3.02
637 707 7.230309 AGAGACTGAATCGACATATCATCTTGA 59.770 37.037 0.00 0.00 0.00 3.02
638 708 7.369607 AGAGACTGAATCGACATATCATCTTG 58.630 38.462 0.00 0.00 0.00 3.02
639 709 7.523293 AGAGACTGAATCGACATATCATCTT 57.477 36.000 0.00 0.00 0.00 2.40
640 710 6.128309 CGAGAGACTGAATCGACATATCATCT 60.128 42.308 0.00 0.00 38.72 2.90
641 711 6.020984 CGAGAGACTGAATCGACATATCATC 58.979 44.000 0.00 0.00 38.72 2.92
642 712 5.106357 CCGAGAGACTGAATCGACATATCAT 60.106 44.000 0.00 0.00 38.72 2.45
643 713 4.214332 CCGAGAGACTGAATCGACATATCA 59.786 45.833 0.00 0.00 38.72 2.15
644 714 4.452795 TCCGAGAGACTGAATCGACATATC 59.547 45.833 0.00 0.00 38.72 1.63
645 715 4.390264 TCCGAGAGACTGAATCGACATAT 58.610 43.478 0.00 0.00 38.72 1.78
646 716 3.805207 TCCGAGAGACTGAATCGACATA 58.195 45.455 0.00 0.00 38.72 2.29
647 717 2.616376 CTCCGAGAGACTGAATCGACAT 59.384 50.000 0.00 0.00 38.72 3.06
648 718 2.010497 CTCCGAGAGACTGAATCGACA 58.990 52.381 0.00 0.00 38.72 4.35
649 719 2.281517 TCTCCGAGAGACTGAATCGAC 58.718 52.381 0.00 0.00 38.72 4.20
650 720 2.693267 TCTCCGAGAGACTGAATCGA 57.307 50.000 0.00 0.00 38.72 3.59
651 721 2.616376 ACATCTCCGAGAGACTGAATCG 59.384 50.000 4.07 0.00 41.76 3.34
652 722 4.097135 TGAACATCTCCGAGAGACTGAATC 59.903 45.833 4.07 3.56 41.76 2.52
653 723 4.019858 TGAACATCTCCGAGAGACTGAAT 58.980 43.478 4.07 0.00 41.76 2.57
654 724 3.421844 TGAACATCTCCGAGAGACTGAA 58.578 45.455 4.07 0.00 41.76 3.02
655 725 3.073274 TGAACATCTCCGAGAGACTGA 57.927 47.619 4.07 0.00 41.76 3.41
656 726 4.023279 CCTATGAACATCTCCGAGAGACTG 60.023 50.000 4.07 0.28 41.76 3.51
657 727 4.141287 CCTATGAACATCTCCGAGAGACT 58.859 47.826 4.07 0.00 41.76 3.24
658 728 4.138290 TCCTATGAACATCTCCGAGAGAC 58.862 47.826 4.07 0.00 41.76 3.36
659 729 4.141367 ACTCCTATGAACATCTCCGAGAGA 60.141 45.833 4.07 6.14 43.20 3.10
660 730 4.141287 ACTCCTATGAACATCTCCGAGAG 58.859 47.826 4.07 0.00 0.00 3.20
661 731 4.171878 ACTCCTATGAACATCTCCGAGA 57.828 45.455 0.00 0.00 0.00 4.04
662 732 4.457603 CCTACTCCTATGAACATCTCCGAG 59.542 50.000 0.00 0.00 0.00 4.63
663 733 4.141228 ACCTACTCCTATGAACATCTCCGA 60.141 45.833 0.00 0.00 0.00 4.55
664 734 4.022762 CACCTACTCCTATGAACATCTCCG 60.023 50.000 0.00 0.00 0.00 4.63
665 735 4.896482 ACACCTACTCCTATGAACATCTCC 59.104 45.833 0.00 0.00 0.00 3.71
666 736 5.737635 GCACACCTACTCCTATGAACATCTC 60.738 48.000 0.00 0.00 0.00 2.75
667 737 4.100189 GCACACCTACTCCTATGAACATCT 59.900 45.833 0.00 0.00 0.00 2.90
668 738 4.372656 GCACACCTACTCCTATGAACATC 58.627 47.826 0.00 0.00 0.00 3.06
669 739 3.181475 CGCACACCTACTCCTATGAACAT 60.181 47.826 0.00 0.00 0.00 2.71
670 740 2.165641 CGCACACCTACTCCTATGAACA 59.834 50.000 0.00 0.00 0.00 3.18
671 741 2.165845 ACGCACACCTACTCCTATGAAC 59.834 50.000 0.00 0.00 0.00 3.18
672 742 2.453521 ACGCACACCTACTCCTATGAA 58.546 47.619 0.00 0.00 0.00 2.57
673 743 2.139323 ACGCACACCTACTCCTATGA 57.861 50.000 0.00 0.00 0.00 2.15
674 744 2.165641 TGAACGCACACCTACTCCTATG 59.834 50.000 0.00 0.00 0.00 2.23
675 745 2.453521 TGAACGCACACCTACTCCTAT 58.546 47.619 0.00 0.00 0.00 2.57
676 746 1.913778 TGAACGCACACCTACTCCTA 58.086 50.000 0.00 0.00 0.00 2.94
677 747 1.267121 ATGAACGCACACCTACTCCT 58.733 50.000 0.00 0.00 0.00 3.69
678 748 2.481449 CCTATGAACGCACACCTACTCC 60.481 54.545 0.00 0.00 0.00 3.85
679 749 2.481449 CCCTATGAACGCACACCTACTC 60.481 54.545 0.00 0.00 0.00 2.59
680 750 1.480954 CCCTATGAACGCACACCTACT 59.519 52.381 0.00 0.00 0.00 2.57
681 751 1.479323 TCCCTATGAACGCACACCTAC 59.521 52.381 0.00 0.00 0.00 3.18
682 752 1.855295 TCCCTATGAACGCACACCTA 58.145 50.000 0.00 0.00 0.00 3.08
683 753 1.134401 CATCCCTATGAACGCACACCT 60.134 52.381 0.00 0.00 34.84 4.00
684 754 1.134521 TCATCCCTATGAACGCACACC 60.135 52.381 0.00 0.00 39.20 4.16
685 755 2.309528 TCATCCCTATGAACGCACAC 57.690 50.000 0.00 0.00 39.20 3.82
692 762 7.852091 ATATGCGCATATGTTCATCCCTATGAA 60.852 37.037 35.68 10.42 42.02 2.57
693 763 3.007831 TGCGCATATGTTCATCCCTATGA 59.992 43.478 5.66 0.00 40.43 2.15
694 764 3.337358 TGCGCATATGTTCATCCCTATG 58.663 45.455 5.66 0.00 0.00 2.23
695 765 3.701205 TGCGCATATGTTCATCCCTAT 57.299 42.857 5.66 0.00 0.00 2.57
696 766 3.701205 ATGCGCATATGTTCATCCCTA 57.299 42.857 24.02 0.00 0.00 3.53
697 767 2.574006 ATGCGCATATGTTCATCCCT 57.426 45.000 24.02 0.00 0.00 4.20
698 768 4.282950 CATATGCGCATATGTTCATCCC 57.717 45.455 42.31 1.36 43.40 3.85
707 777 5.970592 ACTGACTCATACATATGCGCATAT 58.029 37.500 32.21 32.21 34.50 1.78
708 778 5.391312 ACTGACTCATACATATGCGCATA 57.609 39.130 30.72 30.72 33.76 3.14
709 779 4.263018 ACTGACTCATACATATGCGCAT 57.737 40.909 28.23 28.23 33.76 4.73
710 780 3.733443 ACTGACTCATACATATGCGCA 57.267 42.857 14.96 14.96 33.76 6.09
711 781 4.799678 AGTACTGACTCATACATATGCGC 58.200 43.478 0.00 0.00 33.76 6.09
712 782 7.530863 ACATAGTACTGACTCATACATATGCG 58.469 38.462 5.39 0.00 37.10 4.73
742 812 6.100404 TGGCTAGCTTTGTGAATCATTTTT 57.900 33.333 15.72 0.00 0.00 1.94
743 813 5.337009 CCTGGCTAGCTTTGTGAATCATTTT 60.337 40.000 15.72 0.00 0.00 1.82
749 819 2.440409 CACCTGGCTAGCTTTGTGAAT 58.560 47.619 15.72 0.00 0.00 2.57
764 834 1.170442 TTGAGATGTGCATGCACCTG 58.830 50.000 40.01 0.00 45.63 4.00
772 842 5.697473 TTATTTCGGTTTTGAGATGTGCA 57.303 34.783 0.00 0.00 0.00 4.57
777 847 8.360390 AGCTTTTCTTTATTTCGGTTTTGAGAT 58.640 29.630 0.00 0.00 0.00 2.75
779 849 7.930513 AGCTTTTCTTTATTTCGGTTTTGAG 57.069 32.000 0.00 0.00 0.00 3.02
786 856 5.920273 TGCAGAAAGCTTTTCTTTATTTCGG 59.080 36.000 14.05 0.00 44.58 4.30
787 857 6.991485 TGCAGAAAGCTTTTCTTTATTTCG 57.009 33.333 14.05 0.52 44.58 3.46
792 862 5.199024 TGCATGCAGAAAGCTTTTCTTTA 57.801 34.783 18.46 0.05 44.58 1.85
831 907 2.191400 CTGATCTTTCAGGAGGGTCCA 58.809 52.381 0.00 0.00 44.78 4.02
849 925 4.340246 TGGCCAGGCTGACAGCTG 62.340 66.667 25.92 20.08 41.99 4.24
884 960 8.400184 TGGTCTGGTGTATATATACAGTACAC 57.600 38.462 23.03 14.64 43.32 2.90
888 964 6.720288 GGTCTGGTCTGGTGTATATATACAGT 59.280 42.308 23.03 0.00 43.32 3.55
889 965 6.153000 GGGTCTGGTCTGGTGTATATATACAG 59.847 46.154 23.03 13.35 43.32 2.74
901 977 0.694444 ACAGTTGGGTCTGGTCTGGT 60.694 55.000 0.00 0.00 39.48 4.00
902 978 0.474184 AACAGTTGGGTCTGGTCTGG 59.526 55.000 0.00 0.00 39.48 3.86
903 979 3.485463 TTAACAGTTGGGTCTGGTCTG 57.515 47.619 0.00 0.00 39.48 3.51
904 980 3.434596 GGTTTAACAGTTGGGTCTGGTCT 60.435 47.826 0.00 0.00 39.48 3.85
905 981 2.882761 GGTTTAACAGTTGGGTCTGGTC 59.117 50.000 0.00 0.00 39.48 4.02
917 993 5.749596 TTGTGATGTGTGAGGTTTAACAG 57.250 39.130 0.00 0.00 0.00 3.16
931 1007 6.260377 CGCTATGAATTGTGATTTGTGATGT 58.740 36.000 0.00 0.00 0.00 3.06
932 1008 5.172591 GCGCTATGAATTGTGATTTGTGATG 59.827 40.000 0.00 0.00 0.00 3.07
933 1009 5.163632 TGCGCTATGAATTGTGATTTGTGAT 60.164 36.000 9.73 0.00 0.00 3.06
937 1013 4.413969 TGTGCGCTATGAATTGTGATTTG 58.586 39.130 9.73 0.00 0.00 2.32
938 1014 4.700268 TGTGCGCTATGAATTGTGATTT 57.300 36.364 9.73 0.00 0.00 2.17
939 1015 4.156556 ACTTGTGCGCTATGAATTGTGATT 59.843 37.500 9.73 0.00 0.00 2.57
940 1016 3.691118 ACTTGTGCGCTATGAATTGTGAT 59.309 39.130 9.73 0.00 0.00 3.06
941 1017 3.073678 ACTTGTGCGCTATGAATTGTGA 58.926 40.909 9.73 0.00 0.00 3.58
942 1018 3.476295 ACTTGTGCGCTATGAATTGTG 57.524 42.857 9.73 0.00 0.00 3.33
943 1019 3.062099 CGTACTTGTGCGCTATGAATTGT 59.938 43.478 9.73 0.00 0.00 2.71
944 1020 3.062099 ACGTACTTGTGCGCTATGAATTG 59.938 43.478 9.73 0.00 0.00 2.32
945 1021 3.259064 ACGTACTTGTGCGCTATGAATT 58.741 40.909 9.73 0.00 0.00 2.17
946 1022 2.888594 ACGTACTTGTGCGCTATGAAT 58.111 42.857 9.73 0.00 0.00 2.57
947 1023 2.357327 ACGTACTTGTGCGCTATGAA 57.643 45.000 9.73 0.00 0.00 2.57
948 1024 2.256174 GAACGTACTTGTGCGCTATGA 58.744 47.619 9.73 0.00 0.00 2.15
949 1025 1.007422 CGAACGTACTTGTGCGCTATG 60.007 52.381 9.73 0.00 33.46 2.23
950 1026 1.265568 CGAACGTACTTGTGCGCTAT 58.734 50.000 9.73 0.00 33.46 2.97
951 1027 0.040157 ACGAACGTACTTGTGCGCTA 60.040 50.000 9.73 0.00 44.97 4.26
967 1043 1.333791 CGCGAGATGTACTATGCACGA 60.334 52.381 0.00 0.00 32.55 4.35
990 1066 2.423538 GGACATGGCCATTGTTACTGTC 59.576 50.000 17.92 19.46 0.00 3.51
1062 1141 4.778415 TTCGAGAGCAGCGACGCC 62.778 66.667 17.79 1.43 37.52 5.68
1278 1363 2.646175 CGTGTCGATGGGGTCCAGT 61.646 63.158 0.00 0.00 36.75 4.00
1356 1441 1.310933 GGGAGAAGCGGTCGTAGTCA 61.311 60.000 0.00 0.00 0.00 3.41
1475 1560 1.202891 AGTTTGGGTAGCTTGGGTGAC 60.203 52.381 0.00 0.00 0.00 3.67
2107 2192 3.871594 GGGAATATCACCTCGTTGAACAG 59.128 47.826 0.00 0.00 0.00 3.16
2412 2497 1.622607 CCGTCCTCACCATGCCCTTA 61.623 60.000 0.00 0.00 0.00 2.69
2452 2537 1.078214 CATCCCTCGGAAGCTGCAA 60.078 57.895 1.02 0.00 34.34 4.08
2559 2644 8.407832 TCTTTGGTTTGCTATATGAATCATGTG 58.592 33.333 5.91 0.00 0.00 3.21
2563 2648 7.345691 TCCTCTTTGGTTTGCTATATGAATCA 58.654 34.615 0.00 0.00 37.07 2.57
2578 2663 5.527026 AAGGAATCTGAATCCTCTTTGGT 57.473 39.130 14.45 0.00 46.65 3.67
2598 2683 7.498570 TCCAAAACATTGAAAATCCTTGGAAAG 59.501 33.333 0.00 0.00 45.69 2.62
2601 2686 6.491714 TCCAAAACATTGAAAATCCTTGGA 57.508 33.333 0.00 0.00 38.93 3.53
2605 2690 9.710900 GTTAGATTCCAAAACATTGAAAATCCT 57.289 29.630 0.00 0.00 30.79 3.24
2627 2712 8.621286 AGGACAATAAACACACAAAAGAGTTAG 58.379 33.333 0.00 0.00 0.00 2.34
2633 2718 7.920682 AGCTAAAGGACAATAAACACACAAAAG 59.079 33.333 0.00 0.00 0.00 2.27
2640 2725 7.971004 GCAATAGCTAAAGGACAATAAACAC 57.029 36.000 0.00 0.00 37.91 3.32
2681 2891 8.148807 TCAAAAACATTGATACAAACTCGAGA 57.851 30.769 21.68 0.00 0.00 4.04
2723 2933 7.233348 AGGGACATGTGAAGAAATGTAAACAAT 59.767 33.333 1.15 0.00 37.15 2.71
2748 2958 7.363431 TGTAATGACTATAACAGCGATGAGAG 58.637 38.462 8.12 0.81 0.00 3.20
2767 2977 3.441222 TCTGAAACTGCTGCCATGTAATG 59.559 43.478 0.00 0.00 46.21 1.90
2768 2978 3.441572 GTCTGAAACTGCTGCCATGTAAT 59.558 43.478 0.00 0.00 0.00 1.89
2781 3026 8.455682 TGAATTTCGTTTTTAGTGTCTGAAACT 58.544 29.630 5.69 5.69 31.58 2.66
2788 3033 8.115491 AGCTTTTGAATTTCGTTTTTAGTGTC 57.885 30.769 0.00 0.00 0.00 3.67
2867 3112 9.249053 GAGATCTATGATTGTCCTGGAATACTA 57.751 37.037 0.00 0.00 0.00 1.82
2869 3114 7.901029 TGAGATCTATGATTGTCCTGGAATAC 58.099 38.462 0.00 0.00 0.00 1.89
2992 3238 8.462589 AACAAAAATTAGGGCAAATTGACATT 57.537 26.923 0.00 0.00 0.00 2.71
2994 3240 7.012799 GGAAACAAAAATTAGGGCAAATTGACA 59.987 33.333 0.00 0.00 0.00 3.58
2997 3243 6.264067 TGGGAAACAAAAATTAGGGCAAATTG 59.736 34.615 0.00 0.00 0.00 2.32
2998 3244 6.368805 TGGGAAACAAAAATTAGGGCAAATT 58.631 32.000 0.00 0.00 0.00 1.82
2999 3245 5.946486 TGGGAAACAAAAATTAGGGCAAAT 58.054 33.333 0.00 0.00 0.00 2.32
3000 3246 5.373812 TGGGAAACAAAAATTAGGGCAAA 57.626 34.783 0.00 0.00 0.00 3.68
3002 3248 4.843516 AGATGGGAAACAAAAATTAGGGCA 59.156 37.500 0.00 0.00 0.00 5.36
3042 3295 2.290450 CCTAACCCGTAATGTGGTGGTT 60.290 50.000 0.00 0.00 41.85 3.67
3043 3296 1.279846 CCTAACCCGTAATGTGGTGGT 59.720 52.381 0.00 0.00 34.34 4.16
3044 3297 1.407712 CCCTAACCCGTAATGTGGTGG 60.408 57.143 0.00 0.00 34.34 4.61
3045 3298 2.015081 GCCCTAACCCGTAATGTGGTG 61.015 57.143 0.00 0.00 34.34 4.17
3163 3416 1.625818 GCCCTGTCATAATCCGGATCT 59.374 52.381 19.43 10.69 0.00 2.75
3169 3422 1.600916 GCCCGCCCTGTCATAATCC 60.601 63.158 0.00 0.00 0.00 3.01
3190 3443 2.584791 CTAGCGGTCAAACAAACATGC 58.415 47.619 0.00 0.00 0.00 4.06
3210 3463 4.287766 ACATCAGACTTAAGGGTCAACC 57.712 45.455 7.53 0.00 38.57 3.77
3213 3466 6.212589 TGTCATAACATCAGACTTAAGGGTCA 59.787 38.462 7.53 0.00 38.57 4.02
3218 3471 7.065085 CCCACTTGTCATAACATCAGACTTAAG 59.935 40.741 0.00 0.00 34.73 1.85
3229 3482 0.039035 GGGGCCCACTTGTCATAACA 59.961 55.000 26.86 0.00 0.00 2.41
3248 3501 2.094854 GGCAAAGAAGAAGCTGACATGG 60.095 50.000 0.00 0.00 0.00 3.66
3272 3525 1.897802 GTCGGTGGTTCTAGGGAAGAA 59.102 52.381 0.00 0.00 42.07 2.52
3283 3536 1.423921 AGGAAAATGAGGTCGGTGGTT 59.576 47.619 0.00 0.00 0.00 3.67
3289 3542 1.067142 TGACGGAGGAAAATGAGGTCG 60.067 52.381 0.00 0.00 0.00 4.79
3291 3544 3.347216 CATTGACGGAGGAAAATGAGGT 58.653 45.455 0.00 0.00 32.86 3.85
3314 3567 1.228063 CGGCTCCCCTTGATGATGG 60.228 63.158 0.00 0.00 0.00 3.51
3338 3591 2.768344 TCCCCTCCCGATGGCTTC 60.768 66.667 0.00 0.00 0.00 3.86
3340 3593 4.888325 CCTCCCCTCCCGATGGCT 62.888 72.222 0.00 0.00 0.00 4.75
3347 3600 1.547760 CTACCCTACCTCCCCTCCC 59.452 68.421 0.00 0.00 0.00 4.30
3351 3604 2.022848 TCCCCTACCCTACCTCCCC 61.023 68.421 0.00 0.00 0.00 4.81
3358 3611 1.957822 GCACCTCCTCCCCTACCCTA 61.958 65.000 0.00 0.00 0.00 3.53
3450 3703 1.026182 TCAGCCATGGACGCACATTC 61.026 55.000 18.40 0.00 0.00 2.67
3451 3704 1.002257 TCAGCCATGGACGCACATT 60.002 52.632 18.40 0.00 0.00 2.71
3455 3708 3.635191 TGGTCAGCCATGGACGCA 61.635 61.111 18.40 2.69 40.46 5.24
3488 3741 1.375140 GCTGCTGCTCACTACTGCA 60.375 57.895 8.53 0.00 39.31 4.41
3493 3746 3.654173 CTGCGGCTGCTGCTCACTA 62.654 63.158 31.19 12.20 43.34 2.74
3512 3765 3.250323 CTGCTGTCATCGCCGTCG 61.250 66.667 0.00 0.00 0.00 5.12
3513 3766 3.558411 GCTGCTGTCATCGCCGTC 61.558 66.667 0.00 0.00 0.00 4.79
3531 3784 4.347453 CTGTTGTTGCCCGCAGCC 62.347 66.667 0.87 0.00 42.71 4.85
3532 3785 3.595758 ACTGTTGTTGCCCGCAGC 61.596 61.111 0.00 0.00 44.14 5.25
3533 3786 2.121564 CTCACTGTTGTTGCCCGCAG 62.122 60.000 0.00 0.00 35.31 5.18
3534 3787 2.124529 TCACTGTTGTTGCCCGCA 60.125 55.556 0.00 0.00 0.00 5.69
3535 3788 2.639286 CTCACTGTTGTTGCCCGC 59.361 61.111 0.00 0.00 0.00 6.13
3536 3789 2.639286 GCTCACTGTTGTTGCCCG 59.361 61.111 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.