Multiple sequence alignment - TraesCS3D01G164600

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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 TraesCS3D01G164600 chr3D 100.000 5763 0 0 1 5763 136268690 136262928 0.000000e+00 10643
1 TraesCS3D01G164600 chr3D 98.986 592 6 0 5172 5763 370537049 370537640 0.000000e+00 1061
2 TraesCS3D01G164600 chr3A 93.119 4534 173 55 680 5161 153598984 153594538 0.000000e+00 6516
3 TraesCS3D01G164600 chr3A 85.660 530 50 15 19 531 153599550 153599030 8.500000e-148 534
4 TraesCS3D01G164600 chr3A 91.954 87 5 2 574 660 108878535 108878619 2.820000e-23 121
5 TraesCS3D01G164600 chr3B 93.023 4515 169 65 719 5178 194647160 194642737 0.000000e+00 6458
6 TraesCS3D01G164600 chr3B 97.973 592 12 0 5172 5763 466280506 466281097 0.000000e+00 1027
7 TraesCS3D01G164600 chr3B 92.042 289 16 5 293 577 194647862 194647577 3.240000e-107 399
8 TraesCS3D01G164600 chr3B 90.909 220 2 7 40 257 194648061 194647858 4.400000e-71 279
9 TraesCS3D01G164600 chr3B 95.588 68 3 0 655 722 194647590 194647523 6.110000e-20 110
10 TraesCS3D01G164600 chr1D 98.986 592 6 0 5172 5763 28071458 28072049 0.000000e+00 1061
11 TraesCS3D01G164600 chr1D 98.472 589 9 0 5175 5763 70344313 70343725 0.000000e+00 1038
12 TraesCS3D01G164600 chr1D 86.547 446 44 11 94 531 293195257 293195694 1.450000e-130 477
13 TraesCS3D01G164600 chr1D 90.283 247 11 5 665 901 293195737 293195980 1.560000e-80 311
14 TraesCS3D01G164600 chrUn 98.981 589 6 0 5175 5763 415563502 415562914 0.000000e+00 1055
15 TraesCS3D01G164600 chr7D 98.981 589 6 0 5175 5763 252066933 252066345 0.000000e+00 1055
16 TraesCS3D01G164600 chr7D 95.000 80 2 2 574 653 49638127 49638204 2.180000e-24 124
17 TraesCS3D01G164600 chr7D 93.976 83 4 1 574 656 610864710 610864629 2.180000e-24 124
18 TraesCS3D01G164600 chr7D 94.937 79 3 1 574 652 568905282 568905205 7.840000e-24 122
19 TraesCS3D01G164600 chr1B 98.472 589 9 0 5175 5763 654269270 654268682 0.000000e+00 1038
20 TraesCS3D01G164600 chr2B 98.142 592 11 0 5172 5763 543313152 543313743 0.000000e+00 1033
21 TraesCS3D01G164600 chr2A 98.302 589 10 0 5175 5763 677884719 677884131 0.000000e+00 1033
22 TraesCS3D01G164600 chr2A 94.118 85 4 1 574 658 672521760 672521843 1.690000e-25 128
23 TraesCS3D01G164600 chr6A 92.391 92 5 2 574 665 573475248 573475159 4.690000e-26 130
24 TraesCS3D01G164600 chr6D 96.203 79 2 1 574 652 340469712 340469635 1.690000e-25 128
25 TraesCS3D01G164600 chr4A 93.976 83 5 0 574 656 5470137 5470055 6.060000e-25 126
26 TraesCS3D01G164600 chr5D 95.000 80 2 2 574 651 474013415 474013494 2.180000e-24 124


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 TraesCS3D01G164600 chr3D 136262928 136268690 5762 True 10643.0 10643 100.0000 1 5763 1 chr3D.!!$R1 5762
1 TraesCS3D01G164600 chr3D 370537049 370537640 591 False 1061.0 1061 98.9860 5172 5763 1 chr3D.!!$F1 591
2 TraesCS3D01G164600 chr3A 153594538 153599550 5012 True 3525.0 6516 89.3895 19 5161 2 chr3A.!!$R1 5142
3 TraesCS3D01G164600 chr3B 194642737 194648061 5324 True 1811.5 6458 92.8905 40 5178 4 chr3B.!!$R1 5138
4 TraesCS3D01G164600 chr3B 466280506 466281097 591 False 1027.0 1027 97.9730 5172 5763 1 chr3B.!!$F1 591
5 TraesCS3D01G164600 chr1D 28071458 28072049 591 False 1061.0 1061 98.9860 5172 5763 1 chr1D.!!$F1 591
6 TraesCS3D01G164600 chr1D 70343725 70344313 588 True 1038.0 1038 98.4720 5175 5763 1 chr1D.!!$R1 588
7 TraesCS3D01G164600 chr1D 293195257 293195980 723 False 394.0 477 88.4150 94 901 2 chr1D.!!$F2 807
8 TraesCS3D01G164600 chrUn 415562914 415563502 588 True 1055.0 1055 98.9810 5175 5763 1 chrUn.!!$R1 588
9 TraesCS3D01G164600 chr7D 252066345 252066933 588 True 1055.0 1055 98.9810 5175 5763 1 chr7D.!!$R1 588
10 TraesCS3D01G164600 chr1B 654268682 654269270 588 True 1038.0 1038 98.4720 5175 5763 1 chr1B.!!$R1 588
11 TraesCS3D01G164600 chr2B 543313152 543313743 591 False 1033.0 1033 98.1420 5172 5763 1 chr2B.!!$F1 591
12 TraesCS3D01G164600 chr2A 677884131 677884719 588 True 1033.0 1033 98.3020 5175 5763 1 chr2A.!!$R1 588

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
597 662 0.961019 GGCATTGGAGTTTGCAGTGA 59.039 50.000 0.0 0.0 40.66 3.41 F
1509 2004 0.544357 TCCATCCTTCGGGGCGATAT 60.544 55.000 0.0 0.0 35.23 1.63 F
1789 2295 0.097674 GTGCGTTTCTGGCTGCTATG 59.902 55.000 0.0 0.0 0.00 2.23 F
1791 2297 0.375106 GCGTTTCTGGCTGCTATGTC 59.625 55.000 0.0 0.0 0.00 3.06 F
2041 2547 1.396301 GCGTGAGAGCAAGAGATTTGG 59.604 52.381 0.0 0.0 37.05 3.28 F
3996 4520 1.391485 CTGAAGTTTGAGATGACCGCG 59.609 52.381 0.0 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 2063 0.036164 ACGCTGCTGATTGGGTACAA 59.964 50.000 0.00 0.00 41.59 2.41 R
2394 2901 0.798776 GCAATGAGGAGTCACCGTTG 59.201 55.000 10.06 10.06 44.74 4.10 R
3662 4186 0.605050 TAAGCATGCAAGCGACACCA 60.605 50.000 21.98 0.00 40.15 4.17 R
3727 4251 9.729281 AAATGCCAATCAAGAGTAAATGAAAAT 57.271 25.926 0.00 0.00 0.00 1.82 R
4061 4585 5.303971 AGAGAAAGTGAGATTCAGTTGGTG 58.696 41.667 0.27 0.00 38.97 4.17 R
5144 5693 0.248289 AAACATCATGGCAGCCAAGC 59.752 50.000 20.84 0.00 36.95 4.01 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
33 34 2.278332 AGGGCGCTTTTCTTTCTTCT 57.722 45.000 7.64 0.00 0.00 2.85
34 35 2.587522 AGGGCGCTTTTCTTTCTTCTT 58.412 42.857 7.64 0.00 0.00 2.52
35 36 2.959030 AGGGCGCTTTTCTTTCTTCTTT 59.041 40.909 7.64 0.00 0.00 2.52
36 37 3.052745 GGGCGCTTTTCTTTCTTCTTTG 58.947 45.455 7.64 0.00 0.00 2.77
37 38 3.052745 GGCGCTTTTCTTTCTTCTTTGG 58.947 45.455 7.64 0.00 0.00 3.28
38 39 3.243401 GGCGCTTTTCTTTCTTCTTTGGA 60.243 43.478 7.64 0.00 0.00 3.53
82 83 4.132336 TCATGCCACGTACTAGTACTAGG 58.868 47.826 29.05 25.62 37.49 3.02
84 85 3.801698 TGCCACGTACTAGTACTAGGAG 58.198 50.000 29.88 21.62 37.49 3.69
85 86 3.137533 GCCACGTACTAGTACTAGGAGG 58.862 54.545 29.88 27.64 37.76 4.30
88 89 4.100808 CCACGTACTAGTACTAGGAGGAGT 59.899 50.000 32.03 21.20 35.89 3.85
89 90 5.049167 CACGTACTAGTACTAGGAGGAGTG 58.951 50.000 32.03 26.20 35.89 3.51
90 91 4.714308 ACGTACTAGTACTAGGAGGAGTGT 59.286 45.833 32.03 18.04 35.89 3.55
112 113 1.005630 GCATCGAGCGCTTCCCTAT 60.006 57.895 13.26 0.00 0.00 2.57
259 269 2.338500 GCCTTGGTTCTCTAACTCACG 58.662 52.381 0.00 0.00 35.81 4.35
264 274 3.151554 TGGTTCTCTAACTCACGCAGTA 58.848 45.455 0.00 0.00 35.52 2.74
267 277 4.159857 GTTCTCTAACTCACGCAGTACAG 58.840 47.826 0.00 0.00 32.30 2.74
268 278 3.409570 TCTCTAACTCACGCAGTACAGT 58.590 45.455 0.00 0.00 41.61 3.55
269 279 4.572909 TCTCTAACTCACGCAGTACAGTA 58.427 43.478 0.00 0.00 41.61 2.74
270 280 4.630505 TCTCTAACTCACGCAGTACAGTAG 59.369 45.833 0.00 0.00 41.61 2.57
271 281 4.321718 TCTAACTCACGCAGTACAGTAGT 58.678 43.478 0.00 0.00 41.61 2.73
272 282 5.482006 TCTAACTCACGCAGTACAGTAGTA 58.518 41.667 0.00 0.00 41.61 1.82
328 381 2.874701 CAATCTGGCCTGAACTAATCCG 59.125 50.000 17.04 0.00 0.00 4.18
365 420 7.914871 TCCGATGTGCAATTTTTGTATGAATAG 59.085 33.333 0.00 0.00 0.00 1.73
367 422 8.950961 CGATGTGCAATTTTTGTATGAATAGAG 58.049 33.333 0.00 0.00 0.00 2.43
431 490 9.495754 GTAATGCTATTTTCTCTTGCTAAAGTG 57.504 33.333 0.00 0.00 34.78 3.16
495 558 9.084533 TGTAAGTTTAATCCAGGCTACATTTTT 57.915 29.630 0.00 0.00 0.00 1.94
534 597 4.020573 CCCAACAAACTTAAAATCCTCCCC 60.021 45.833 0.00 0.00 0.00 4.81
536 599 5.510690 CCAACAAACTTAAAATCCTCCCCAC 60.511 44.000 0.00 0.00 0.00 4.61
541 606 6.816616 AACTTAAAATCCTCCCCACAAAAA 57.183 33.333 0.00 0.00 0.00 1.94
579 644 4.640789 GTACTGAGGTACATGTCAGAGG 57.359 50.000 20.18 2.13 45.41 3.69
580 645 1.827969 ACTGAGGTACATGTCAGAGGC 59.172 52.381 20.18 0.00 42.49 4.70
581 646 1.827344 CTGAGGTACATGTCAGAGGCA 59.173 52.381 0.00 0.00 42.49 4.75
582 647 2.433604 CTGAGGTACATGTCAGAGGCAT 59.566 50.000 0.00 0.00 42.49 4.40
583 648 2.840038 TGAGGTACATGTCAGAGGCATT 59.160 45.455 0.00 0.00 0.00 3.56
584 649 3.201290 GAGGTACATGTCAGAGGCATTG 58.799 50.000 0.00 0.00 0.00 2.82
585 650 2.092753 AGGTACATGTCAGAGGCATTGG 60.093 50.000 0.00 0.00 0.00 3.16
586 651 2.092968 GGTACATGTCAGAGGCATTGGA 60.093 50.000 0.00 0.00 0.00 3.53
587 652 2.414994 ACATGTCAGAGGCATTGGAG 57.585 50.000 0.00 0.00 0.00 3.86
588 653 1.632409 ACATGTCAGAGGCATTGGAGT 59.368 47.619 0.00 0.00 0.00 3.85
589 654 2.040813 ACATGTCAGAGGCATTGGAGTT 59.959 45.455 0.00 0.00 0.00 3.01
590 655 2.957402 TGTCAGAGGCATTGGAGTTT 57.043 45.000 0.00 0.00 0.00 2.66
591 656 2.507484 TGTCAGAGGCATTGGAGTTTG 58.493 47.619 0.00 0.00 0.00 2.93
592 657 1.200948 GTCAGAGGCATTGGAGTTTGC 59.799 52.381 0.00 0.00 38.14 3.68
593 658 1.202915 TCAGAGGCATTGGAGTTTGCA 60.203 47.619 0.00 0.00 40.66 4.08
594 659 1.201647 CAGAGGCATTGGAGTTTGCAG 59.798 52.381 0.00 0.00 40.66 4.41
595 660 1.202976 AGAGGCATTGGAGTTTGCAGT 60.203 47.619 0.00 0.00 40.66 4.40
596 661 0.963962 AGGCATTGGAGTTTGCAGTG 59.036 50.000 0.00 0.00 40.66 3.66
597 662 0.961019 GGCATTGGAGTTTGCAGTGA 59.039 50.000 0.00 0.00 40.66 3.41
598 663 1.547372 GGCATTGGAGTTTGCAGTGAT 59.453 47.619 0.00 0.00 40.66 3.06
599 664 2.028748 GGCATTGGAGTTTGCAGTGATT 60.029 45.455 0.00 0.00 40.66 2.57
600 665 2.991190 GCATTGGAGTTTGCAGTGATTG 59.009 45.455 0.00 0.00 38.72 2.67
601 666 3.305539 GCATTGGAGTTTGCAGTGATTGA 60.306 43.478 0.00 0.00 38.72 2.57
602 667 4.619863 GCATTGGAGTTTGCAGTGATTGAT 60.620 41.667 0.00 0.00 38.72 2.57
603 668 5.475719 CATTGGAGTTTGCAGTGATTGATT 58.524 37.500 0.00 0.00 27.08 2.57
604 669 4.508461 TGGAGTTTGCAGTGATTGATTG 57.492 40.909 0.00 0.00 0.00 2.67
605 670 3.890756 TGGAGTTTGCAGTGATTGATTGT 59.109 39.130 0.00 0.00 0.00 2.71
606 671 5.069318 TGGAGTTTGCAGTGATTGATTGTA 58.931 37.500 0.00 0.00 0.00 2.41
607 672 5.711506 TGGAGTTTGCAGTGATTGATTGTAT 59.288 36.000 0.00 0.00 0.00 2.29
608 673 6.032094 GGAGTTTGCAGTGATTGATTGTATG 58.968 40.000 0.00 0.00 0.00 2.39
609 674 6.127925 GGAGTTTGCAGTGATTGATTGTATGA 60.128 38.462 0.00 0.00 0.00 2.15
610 675 7.218228 AGTTTGCAGTGATTGATTGTATGAA 57.782 32.000 0.00 0.00 0.00 2.57
611 676 7.086376 AGTTTGCAGTGATTGATTGTATGAAC 58.914 34.615 0.00 0.00 0.00 3.18
612 677 5.565592 TGCAGTGATTGATTGTATGAACC 57.434 39.130 0.00 0.00 0.00 3.62
613 678 5.255687 TGCAGTGATTGATTGTATGAACCT 58.744 37.500 0.00 0.00 0.00 3.50
614 679 5.711506 TGCAGTGATTGATTGTATGAACCTT 59.288 36.000 0.00 0.00 0.00 3.50
615 680 6.032094 GCAGTGATTGATTGTATGAACCTTG 58.968 40.000 0.00 0.00 0.00 3.61
616 681 6.349611 GCAGTGATTGATTGTATGAACCTTGT 60.350 38.462 0.00 0.00 0.00 3.16
617 682 7.025365 CAGTGATTGATTGTATGAACCTTGTG 58.975 38.462 0.00 0.00 0.00 3.33
618 683 6.942005 AGTGATTGATTGTATGAACCTTGTGA 59.058 34.615 0.00 0.00 0.00 3.58
619 684 7.613022 AGTGATTGATTGTATGAACCTTGTGAT 59.387 33.333 0.00 0.00 0.00 3.06
620 685 8.246180 GTGATTGATTGTATGAACCTTGTGATT 58.754 33.333 0.00 0.00 0.00 2.57
621 686 8.245491 TGATTGATTGTATGAACCTTGTGATTG 58.755 33.333 0.00 0.00 0.00 2.67
622 687 7.757941 TTGATTGTATGAACCTTGTGATTGA 57.242 32.000 0.00 0.00 0.00 2.57
623 688 7.381766 TGATTGTATGAACCTTGTGATTGAG 57.618 36.000 0.00 0.00 0.00 3.02
624 689 6.942005 TGATTGTATGAACCTTGTGATTGAGT 59.058 34.615 0.00 0.00 0.00 3.41
625 690 8.100164 TGATTGTATGAACCTTGTGATTGAGTA 58.900 33.333 0.00 0.00 0.00 2.59
626 691 8.862325 ATTGTATGAACCTTGTGATTGAGTAA 57.138 30.769 0.00 0.00 0.00 2.24
627 692 8.862325 TTGTATGAACCTTGTGATTGAGTAAT 57.138 30.769 0.00 0.00 0.00 1.89
628 693 9.952030 TTGTATGAACCTTGTGATTGAGTAATA 57.048 29.630 0.00 0.00 0.00 0.98
629 694 9.378551 TGTATGAACCTTGTGATTGAGTAATAC 57.621 33.333 0.00 0.00 0.00 1.89
630 695 9.378551 GTATGAACCTTGTGATTGAGTAATACA 57.621 33.333 0.00 0.00 0.00 2.29
632 697 8.862325 TGAACCTTGTGATTGAGTAATACATT 57.138 30.769 0.00 0.00 0.00 2.71
633 698 9.952030 TGAACCTTGTGATTGAGTAATACATTA 57.048 29.630 0.00 0.00 0.00 1.90
642 707 9.051679 TGATTGAGTAATACATTATTTCACCCG 57.948 33.333 0.00 0.00 0.00 5.28
643 708 9.268268 GATTGAGTAATACATTATTTCACCCGA 57.732 33.333 0.00 0.00 0.00 5.14
644 709 9.621629 ATTGAGTAATACATTATTTCACCCGAA 57.378 29.630 0.00 0.00 0.00 4.30
645 710 9.451002 TTGAGTAATACATTATTTCACCCGAAA 57.549 29.630 0.00 0.00 44.99 3.46
646 711 9.451002 TGAGTAATACATTATTTCACCCGAAAA 57.549 29.630 0.00 0.00 44.12 2.29
647 712 9.931210 GAGTAATACATTATTTCACCCGAAAAG 57.069 33.333 0.00 0.00 44.12 2.27
648 713 9.675464 AGTAATACATTATTTCACCCGAAAAGA 57.325 29.630 0.00 0.00 44.12 2.52
792 1232 4.734843 TTTTCCTAATATAGCCACCCCC 57.265 45.455 0.00 0.00 0.00 5.40
793 1233 3.666975 TTCCTAATATAGCCACCCCCT 57.333 47.619 0.00 0.00 0.00 4.79
794 1234 3.666975 TCCTAATATAGCCACCCCCTT 57.333 47.619 0.00 0.00 0.00 3.95
851 1304 2.608988 CCCCAGGGCTCTGTCTGT 60.609 66.667 13.79 0.00 39.31 3.41
860 1314 3.633094 CTCTGTCTGTCGTGCCGGG 62.633 68.421 2.18 0.00 0.00 5.73
877 1335 2.112297 GACACCAAACCCTCGCCA 59.888 61.111 0.00 0.00 0.00 5.69
925 1391 1.077716 CAAATCCCACCCGAGGTCC 60.078 63.158 0.00 0.00 31.02 4.46
926 1392 1.540367 AAATCCCACCCGAGGTCCA 60.540 57.895 0.00 0.00 31.02 4.02
927 1393 1.848886 AAATCCCACCCGAGGTCCAC 61.849 60.000 0.00 0.00 31.02 4.02
1216 1692 2.573341 GAAGATCGCGGTCGTCACGA 62.573 60.000 26.94 0.00 40.53 4.35
1354 1844 4.799564 TTTGAATGGCTATGGTTGGAAC 57.200 40.909 0.00 0.00 0.00 3.62
1406 1896 1.874562 CTCCTGCTGTTGCTTCTGC 59.125 57.895 0.00 0.00 40.48 4.26
1487 1982 2.292267 GATGCGGAGATTTGGATGTGT 58.708 47.619 0.00 0.00 0.00 3.72
1501 1996 2.009774 GATGTGTTGTCCATCCTTCGG 58.990 52.381 0.00 0.00 34.02 4.30
1507 2002 2.445845 TCCATCCTTCGGGGCGAT 60.446 61.111 0.00 0.00 35.23 4.58
1509 2004 0.544357 TCCATCCTTCGGGGCGATAT 60.544 55.000 0.00 0.00 35.23 1.63
1529 2024 7.629845 GCGATATGTCAAACGTTTAGTAGTTTC 59.370 37.037 14.20 5.25 38.37 2.78
1566 2063 4.708177 ACATACTGCGATTTATTGCCTCT 58.292 39.130 0.00 0.00 36.33 3.69
1768 2273 5.550290 TCCCAAATTTTGATGCCTCTTTTC 58.450 37.500 10.72 0.00 0.00 2.29
1771 2276 5.993441 CCAAATTTTGATGCCTCTTTTCTGT 59.007 36.000 10.72 0.00 0.00 3.41
1789 2295 0.097674 GTGCGTTTCTGGCTGCTATG 59.902 55.000 0.00 0.00 0.00 2.23
1791 2297 0.375106 GCGTTTCTGGCTGCTATGTC 59.625 55.000 0.00 0.00 0.00 3.06
1856 2362 4.023707 CGGATCATATTTCAGGAGTTTGGC 60.024 45.833 0.00 0.00 0.00 4.52
1878 2384 4.082354 GCTCATGTTCTGGCAAGAATTCTT 60.082 41.667 15.11 15.11 44.18 2.52
2041 2547 1.396301 GCGTGAGAGCAAGAGATTTGG 59.604 52.381 0.00 0.00 37.05 3.28
2063 2569 9.517868 TTTGGAATCGGTTATTTACCTTTTCTA 57.482 29.630 0.00 0.00 45.40 2.10
2064 2570 8.726870 TGGAATCGGTTATTTACCTTTTCTAG 57.273 34.615 0.00 0.00 45.40 2.43
2394 2901 2.864343 CCCCGATTTCGAGTACATTGAC 59.136 50.000 0.67 0.00 43.02 3.18
2397 2904 4.201685 CCCGATTTCGAGTACATTGACAAC 60.202 45.833 0.67 0.00 43.02 3.32
2522 3029 2.165845 ACAGTTATGTCTAGGGCGTGTC 59.834 50.000 0.00 0.00 32.99 3.67
2536 3043 3.243334 GGGCGTGTCCTCTTATAGTGTAC 60.243 52.174 0.00 0.00 34.39 2.90
2537 3044 3.631227 GGCGTGTCCTCTTATAGTGTACT 59.369 47.826 0.00 0.00 0.00 2.73
2538 3045 4.261114 GGCGTGTCCTCTTATAGTGTACTC 60.261 50.000 0.00 0.00 0.00 2.59
2555 3062 8.209917 AGTGTACTCTTTTGTTAGACCTTTTG 57.790 34.615 0.00 0.00 0.00 2.44
2556 3063 7.827729 AGTGTACTCTTTTGTTAGACCTTTTGT 59.172 33.333 0.00 0.00 0.00 2.83
2557 3064 8.121086 GTGTACTCTTTTGTTAGACCTTTTGTC 58.879 37.037 0.00 0.00 44.82 3.18
2657 3172 6.231365 CGTTTGTGACGTTGATGATAACTAC 58.769 40.000 0.00 0.00 46.49 2.73
2739 3254 2.226437 GAGGTGCGCATTCTTTTCTTCA 59.774 45.455 15.91 0.00 0.00 3.02
2740 3255 2.227388 AGGTGCGCATTCTTTTCTTCAG 59.773 45.455 15.91 0.00 0.00 3.02
2862 3377 4.764679 TCAGTTTGCGCATGTTTCTTAT 57.235 36.364 12.75 0.00 0.00 1.73
2944 3459 5.957842 TTGTCAATTACCAGGAATGTGTC 57.042 39.130 0.00 0.00 0.00 3.67
2952 3467 3.139077 ACCAGGAATGTGTCGAAAGAAC 58.861 45.455 0.00 0.00 45.01 3.01
3013 3528 8.655970 CGAAAACATCAATCATAGACACTACAA 58.344 33.333 0.00 0.00 0.00 2.41
3076 3591 6.603599 ACCAGCCTCTGAAGAAATTATAAACC 59.396 38.462 0.00 0.00 32.44 3.27
3111 3633 9.051679 TGTCAGTACAAACACCATATAATATGC 57.948 33.333 0.00 0.00 30.91 3.14
3531 4055 5.560724 CCTGGAGGTCACTCTTTTTCATTA 58.439 41.667 0.00 0.00 43.46 1.90
3764 4288 4.422840 TGATTGGCATTTCATTGTTAGCG 58.577 39.130 0.00 0.00 0.00 4.26
3996 4520 1.391485 CTGAAGTTTGAGATGACCGCG 59.609 52.381 0.00 0.00 0.00 6.46
4031 4555 4.745125 GTGCTTTTTAAGGTTTTGCTCTCC 59.255 41.667 0.00 0.00 0.00 3.71
4061 4585 3.042871 TGGCAAATTTCATGGCTTCAC 57.957 42.857 4.10 0.00 43.24 3.18
4210 4743 9.820229 TTTGTAGCATTTTACTGATTACTTTCG 57.180 29.630 0.00 0.00 0.00 3.46
4407 4940 7.928908 TCACAAATCTTTGCAGTATCAAAAC 57.071 32.000 2.63 0.00 41.79 2.43
4455 4988 4.118168 ACTTCCCATTGTGAACTGGAAT 57.882 40.909 0.00 0.00 34.76 3.01
4494 5027 2.224185 CCACTACACACAGTACAAGCCA 60.224 50.000 0.00 0.00 0.00 4.75
4503 5036 0.461961 AGTACAAGCCATCGGAGCTC 59.538 55.000 4.71 4.71 40.49 4.09
4602 5135 3.054655 ACAGCCAACATAAGGTAACCGAT 60.055 43.478 0.00 0.00 37.17 4.18
4603 5136 3.560068 CAGCCAACATAAGGTAACCGATC 59.440 47.826 0.00 0.00 37.17 3.69
4604 5137 3.454812 AGCCAACATAAGGTAACCGATCT 59.545 43.478 0.00 0.00 37.17 2.75
4605 5138 3.808174 GCCAACATAAGGTAACCGATCTC 59.192 47.826 0.00 0.00 37.17 2.75
4606 5139 4.682320 GCCAACATAAGGTAACCGATCTCA 60.682 45.833 0.00 0.00 37.17 3.27
4607 5140 5.050490 CCAACATAAGGTAACCGATCTCAG 58.950 45.833 0.00 0.00 37.17 3.35
4608 5141 4.323553 ACATAAGGTAACCGATCTCAGC 57.676 45.455 0.00 0.00 37.17 4.26
4609 5142 3.069729 ACATAAGGTAACCGATCTCAGCC 59.930 47.826 0.00 0.00 37.17 4.85
4610 5143 1.568504 AAGGTAACCGATCTCAGCCA 58.431 50.000 0.00 0.00 37.17 4.75
4645 5178 7.309744 CCACCAAATTTCTTCAGTTATTAGGCA 60.310 37.037 0.00 0.00 0.00 4.75
4708 5241 4.517453 CCTCAGTACAAATTTGTCGGGAAA 59.483 41.667 26.46 6.11 42.35 3.13
4822 5355 2.787473 ATTCTTCATCTTGTGGCGGA 57.213 45.000 0.00 0.00 0.00 5.54
4890 5423 3.443045 CAAGACATGCCGGTGCCC 61.443 66.667 1.90 0.00 36.33 5.36
4950 5483 1.270785 TGATGCTGATGTCGTTGTGGT 60.271 47.619 0.00 0.00 0.00 4.16
4951 5484 2.028567 TGATGCTGATGTCGTTGTGGTA 60.029 45.455 0.00 0.00 0.00 3.25
4952 5485 2.078849 TGCTGATGTCGTTGTGGTAG 57.921 50.000 0.00 0.00 0.00 3.18
4953 5486 1.343142 TGCTGATGTCGTTGTGGTAGT 59.657 47.619 0.00 0.00 0.00 2.73
4954 5487 1.726791 GCTGATGTCGTTGTGGTAGTG 59.273 52.381 0.00 0.00 0.00 2.74
4955 5488 2.337583 CTGATGTCGTTGTGGTAGTGG 58.662 52.381 0.00 0.00 0.00 4.00
4956 5489 1.964933 TGATGTCGTTGTGGTAGTGGA 59.035 47.619 0.00 0.00 0.00 4.02
4957 5490 2.288579 TGATGTCGTTGTGGTAGTGGAC 60.289 50.000 0.00 0.00 0.00 4.02
5031 5579 4.274459 TGCTCTCTGCTGTTTTCTTTCTTC 59.726 41.667 0.00 0.00 43.37 2.87
5032 5580 4.320129 GCTCTCTGCTGTTTTCTTTCTTCC 60.320 45.833 0.00 0.00 38.95 3.46
5033 5581 5.041191 TCTCTGCTGTTTTCTTTCTTCCT 57.959 39.130 0.00 0.00 0.00 3.36
5034 5582 5.440610 TCTCTGCTGTTTTCTTTCTTCCTT 58.559 37.500 0.00 0.00 0.00 3.36
5111 5659 3.920144 GCTGCAGCAGAAGCATAAG 57.080 52.632 33.36 0.00 46.44 1.73
5144 5693 5.538118 TGTAATGGCATAATACTGGAGTCG 58.462 41.667 0.00 0.00 0.00 4.18
5161 5710 2.412323 CGCTTGGCTGCCATGATGT 61.412 57.895 31.69 0.00 31.53 3.06
5555 6104 1.152922 TTCAAAACCTTCCGGCGGT 60.153 52.632 27.32 9.21 35.97 5.68
5602 6151 4.828925 GCCTCCCGCTCTCTGTGC 62.829 72.222 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.000843 GCGCCCTTCCACATTTTCTTT 59.999 47.619 0.00 0.00 0.00 2.52
1 2 0.603065 GCGCCCTTCCACATTTTCTT 59.397 50.000 0.00 0.00 0.00 2.52
2 3 0.251341 AGCGCCCTTCCACATTTTCT 60.251 50.000 2.29 0.00 0.00 2.52
3 4 0.603065 AAGCGCCCTTCCACATTTTC 59.397 50.000 2.29 0.00 0.00 2.29
4 5 1.047801 AAAGCGCCCTTCCACATTTT 58.952 45.000 2.29 0.00 0.00 1.82
5 6 1.000843 GAAAAGCGCCCTTCCACATTT 59.999 47.619 2.29 0.00 0.00 2.32
6 7 0.603065 GAAAAGCGCCCTTCCACATT 59.397 50.000 2.29 0.00 0.00 2.71
7 8 0.251341 AGAAAAGCGCCCTTCCACAT 60.251 50.000 2.29 0.00 0.00 3.21
8 9 0.467290 AAGAAAAGCGCCCTTCCACA 60.467 50.000 2.29 0.00 0.00 4.17
9 10 0.673985 AAAGAAAAGCGCCCTTCCAC 59.326 50.000 2.29 0.00 0.00 4.02
10 11 0.958822 GAAAGAAAAGCGCCCTTCCA 59.041 50.000 2.29 0.00 0.00 3.53
11 12 1.248486 AGAAAGAAAAGCGCCCTTCC 58.752 50.000 2.29 0.00 0.00 3.46
12 13 2.554462 AGAAGAAAGAAAAGCGCCCTTC 59.446 45.455 2.29 7.45 0.00 3.46
13 14 2.587522 AGAAGAAAGAAAAGCGCCCTT 58.412 42.857 2.29 0.00 0.00 3.95
14 15 2.278332 AGAAGAAAGAAAAGCGCCCT 57.722 45.000 2.29 0.00 0.00 5.19
15 16 3.052745 CAAAGAAGAAAGAAAAGCGCCC 58.947 45.455 2.29 0.00 0.00 6.13
16 17 3.052745 CCAAAGAAGAAAGAAAAGCGCC 58.947 45.455 2.29 0.00 0.00 6.53
17 18 3.964909 TCCAAAGAAGAAAGAAAAGCGC 58.035 40.909 0.00 0.00 0.00 5.92
33 34 0.808125 CGCGTCCATCCAAATCCAAA 59.192 50.000 0.00 0.00 0.00 3.28
34 35 0.322098 ACGCGTCCATCCAAATCCAA 60.322 50.000 5.58 0.00 0.00 3.53
35 36 0.322098 AACGCGTCCATCCAAATCCA 60.322 50.000 14.44 0.00 0.00 3.41
36 37 0.098728 CAACGCGTCCATCCAAATCC 59.901 55.000 14.44 0.00 0.00 3.01
37 38 0.098728 CCAACGCGTCCATCCAAATC 59.901 55.000 14.44 0.00 0.00 2.17
38 39 0.322098 TCCAACGCGTCCATCCAAAT 60.322 50.000 14.44 0.00 0.00 2.32
82 83 1.354040 CTCGATGCACAACACTCCTC 58.646 55.000 0.00 0.00 0.00 3.71
84 85 1.790387 GCTCGATGCACAACACTCC 59.210 57.895 0.00 0.00 42.31 3.85
85 86 1.417592 CGCTCGATGCACAACACTC 59.582 57.895 0.00 0.00 43.06 3.51
88 89 1.900585 GAAGCGCTCGATGCACAACA 61.901 55.000 12.06 0.00 43.06 3.33
89 90 1.225854 GAAGCGCTCGATGCACAAC 60.226 57.895 12.06 0.00 43.06 3.32
90 91 2.390599 GGAAGCGCTCGATGCACAA 61.391 57.895 12.06 0.00 43.06 3.33
112 113 2.811431 CTCCTTTTGTCACGGTGCAATA 59.189 45.455 15.25 11.25 0.00 1.90
272 282 9.535878 CAGAGTTCTTCTTTTGAAACTACTAGT 57.464 33.333 0.00 0.00 38.07 2.57
273 283 8.491950 GCAGAGTTCTTCTTTTGAAACTACTAG 58.508 37.037 0.00 0.00 38.07 2.57
274 284 8.204836 AGCAGAGTTCTTCTTTTGAAACTACTA 58.795 33.333 0.00 0.00 38.07 1.82
275 285 7.011857 CAGCAGAGTTCTTCTTTTGAAACTACT 59.988 37.037 0.00 0.00 38.07 2.57
276 286 7.128976 CAGCAGAGTTCTTCTTTTGAAACTAC 58.871 38.462 0.00 0.00 38.07 2.73
277 287 6.823689 ACAGCAGAGTTCTTCTTTTGAAACTA 59.176 34.615 0.00 0.00 38.07 2.24
278 288 5.649831 ACAGCAGAGTTCTTCTTTTGAAACT 59.350 36.000 0.00 0.00 38.07 2.66
279 289 5.741040 CACAGCAGAGTTCTTCTTTTGAAAC 59.259 40.000 0.00 0.00 38.07 2.78
280 290 5.647658 TCACAGCAGAGTTCTTCTTTTGAAA 59.352 36.000 0.00 0.00 38.07 2.69
281 291 5.065218 GTCACAGCAGAGTTCTTCTTTTGAA 59.935 40.000 0.00 0.00 32.41 2.69
282 292 4.572389 GTCACAGCAGAGTTCTTCTTTTGA 59.428 41.667 0.00 0.00 32.41 2.69
283 293 4.333649 TGTCACAGCAGAGTTCTTCTTTTG 59.666 41.667 0.00 0.00 32.41 2.44
284 294 4.333926 GTGTCACAGCAGAGTTCTTCTTTT 59.666 41.667 0.00 0.00 32.41 2.27
285 295 3.873952 GTGTCACAGCAGAGTTCTTCTTT 59.126 43.478 0.00 0.00 32.41 2.52
286 296 3.118629 TGTGTCACAGCAGAGTTCTTCTT 60.119 43.478 0.18 0.00 32.41 2.52
287 297 2.432146 TGTGTCACAGCAGAGTTCTTCT 59.568 45.455 0.18 0.00 36.25 2.85
288 298 2.826428 TGTGTCACAGCAGAGTTCTTC 58.174 47.619 0.18 0.00 0.00 2.87
289 299 2.988010 TGTGTCACAGCAGAGTTCTT 57.012 45.000 0.18 0.00 0.00 2.52
290 300 2.988010 TTGTGTCACAGCAGAGTTCT 57.012 45.000 5.67 0.00 0.00 3.01
291 301 3.186001 CAGATTGTGTCACAGCAGAGTTC 59.814 47.826 5.67 0.00 0.00 3.01
328 381 0.857311 CACATCGGAAAATGTCGCGC 60.857 55.000 0.00 0.00 37.78 6.86
431 490 4.082136 ACTTAGGGACGTGAAGTGAGATTC 60.082 45.833 0.00 0.00 32.25 2.52
507 570 3.006003 GGATTTTAAGTTTGTTGGGCGGA 59.994 43.478 0.00 0.00 0.00 5.54
513 576 5.069781 TGTGGGGAGGATTTTAAGTTTGTTG 59.930 40.000 0.00 0.00 0.00 3.33
560 625 1.827969 GCCTCTGACATGTACCTCAGT 59.172 52.381 0.00 0.00 36.16 3.41
561 626 1.827344 TGCCTCTGACATGTACCTCAG 59.173 52.381 0.00 1.67 36.07 3.35
562 627 1.937191 TGCCTCTGACATGTACCTCA 58.063 50.000 0.00 0.00 0.00 3.86
563 628 3.201290 CAATGCCTCTGACATGTACCTC 58.799 50.000 0.00 0.00 0.00 3.85
564 629 2.092753 CCAATGCCTCTGACATGTACCT 60.093 50.000 0.00 0.00 0.00 3.08
565 630 2.092968 TCCAATGCCTCTGACATGTACC 60.093 50.000 0.00 0.00 0.00 3.34
566 631 3.201290 CTCCAATGCCTCTGACATGTAC 58.799 50.000 0.00 0.00 0.00 2.90
567 632 2.840038 ACTCCAATGCCTCTGACATGTA 59.160 45.455 0.00 0.00 0.00 2.29
568 633 1.632409 ACTCCAATGCCTCTGACATGT 59.368 47.619 0.00 0.00 0.00 3.21
569 634 2.414994 ACTCCAATGCCTCTGACATG 57.585 50.000 0.00 0.00 0.00 3.21
570 635 3.087031 CAAACTCCAATGCCTCTGACAT 58.913 45.455 0.00 0.00 0.00 3.06
571 636 2.507484 CAAACTCCAATGCCTCTGACA 58.493 47.619 0.00 0.00 0.00 3.58
572 637 1.200948 GCAAACTCCAATGCCTCTGAC 59.799 52.381 0.00 0.00 36.56 3.51
573 638 1.202915 TGCAAACTCCAATGCCTCTGA 60.203 47.619 0.00 0.00 41.87 3.27
574 639 1.201647 CTGCAAACTCCAATGCCTCTG 59.798 52.381 0.00 0.00 41.87 3.35
575 640 1.202976 ACTGCAAACTCCAATGCCTCT 60.203 47.619 0.00 0.00 41.87 3.69
576 641 1.068055 CACTGCAAACTCCAATGCCTC 60.068 52.381 0.00 0.00 41.87 4.70
577 642 0.963962 CACTGCAAACTCCAATGCCT 59.036 50.000 0.00 0.00 41.87 4.75
578 643 0.961019 TCACTGCAAACTCCAATGCC 59.039 50.000 0.00 0.00 41.87 4.40
579 644 2.991190 CAATCACTGCAAACTCCAATGC 59.009 45.455 0.00 0.00 42.86 3.56
580 645 4.508461 TCAATCACTGCAAACTCCAATG 57.492 40.909 0.00 0.00 0.00 2.82
581 646 5.011329 ACAATCAATCACTGCAAACTCCAAT 59.989 36.000 0.00 0.00 0.00 3.16
582 647 4.341806 ACAATCAATCACTGCAAACTCCAA 59.658 37.500 0.00 0.00 0.00 3.53
583 648 3.890756 ACAATCAATCACTGCAAACTCCA 59.109 39.130 0.00 0.00 0.00 3.86
584 649 4.510038 ACAATCAATCACTGCAAACTCC 57.490 40.909 0.00 0.00 0.00 3.85
585 650 6.845302 TCATACAATCAATCACTGCAAACTC 58.155 36.000 0.00 0.00 0.00 3.01
586 651 6.822667 TCATACAATCAATCACTGCAAACT 57.177 33.333 0.00 0.00 0.00 2.66
587 652 6.308766 GGTTCATACAATCAATCACTGCAAAC 59.691 38.462 0.00 0.00 0.00 2.93
588 653 6.209192 AGGTTCATACAATCAATCACTGCAAA 59.791 34.615 0.00 0.00 0.00 3.68
589 654 5.711506 AGGTTCATACAATCAATCACTGCAA 59.288 36.000 0.00 0.00 0.00 4.08
590 655 5.255687 AGGTTCATACAATCAATCACTGCA 58.744 37.500 0.00 0.00 0.00 4.41
591 656 5.824904 AGGTTCATACAATCAATCACTGC 57.175 39.130 0.00 0.00 0.00 4.40
592 657 7.025365 CACAAGGTTCATACAATCAATCACTG 58.975 38.462 0.00 0.00 0.00 3.66
593 658 6.942005 TCACAAGGTTCATACAATCAATCACT 59.058 34.615 0.00 0.00 0.00 3.41
594 659 7.144722 TCACAAGGTTCATACAATCAATCAC 57.855 36.000 0.00 0.00 0.00 3.06
595 660 7.943079 ATCACAAGGTTCATACAATCAATCA 57.057 32.000 0.00 0.00 0.00 2.57
596 661 8.461222 TCAATCACAAGGTTCATACAATCAATC 58.539 33.333 0.00 0.00 0.00 2.67
597 662 8.352137 TCAATCACAAGGTTCATACAATCAAT 57.648 30.769 0.00 0.00 0.00 2.57
598 663 7.448161 ACTCAATCACAAGGTTCATACAATCAA 59.552 33.333 0.00 0.00 0.00 2.57
599 664 6.942005 ACTCAATCACAAGGTTCATACAATCA 59.058 34.615 0.00 0.00 0.00 2.57
600 665 7.383102 ACTCAATCACAAGGTTCATACAATC 57.617 36.000 0.00 0.00 0.00 2.67
601 666 8.862325 TTACTCAATCACAAGGTTCATACAAT 57.138 30.769 0.00 0.00 0.00 2.71
602 667 8.862325 ATTACTCAATCACAAGGTTCATACAA 57.138 30.769 0.00 0.00 0.00 2.41
603 668 9.378551 GTATTACTCAATCACAAGGTTCATACA 57.621 33.333 0.00 0.00 0.00 2.29
604 669 9.378551 TGTATTACTCAATCACAAGGTTCATAC 57.621 33.333 0.00 0.00 0.00 2.39
606 671 9.466497 AATGTATTACTCAATCACAAGGTTCAT 57.534 29.630 0.00 0.00 0.00 2.57
607 672 8.862325 AATGTATTACTCAATCACAAGGTTCA 57.138 30.769 0.00 0.00 0.00 3.18
616 681 9.051679 CGGGTGAAATAATGTATTACTCAATCA 57.948 33.333 0.00 0.00 0.00 2.57
617 682 9.268268 TCGGGTGAAATAATGTATTACTCAATC 57.732 33.333 0.00 0.00 0.00 2.67
618 683 9.621629 TTCGGGTGAAATAATGTATTACTCAAT 57.378 29.630 0.00 0.00 0.00 2.57
619 684 9.451002 TTTCGGGTGAAATAATGTATTACTCAA 57.549 29.630 0.00 0.00 39.13 3.02
620 685 9.451002 TTTTCGGGTGAAATAATGTATTACTCA 57.549 29.630 0.00 0.00 43.32 3.41
621 686 9.931210 CTTTTCGGGTGAAATAATGTATTACTC 57.069 33.333 0.00 0.00 43.32 2.59
622 687 9.675464 TCTTTTCGGGTGAAATAATGTATTACT 57.325 29.630 0.00 0.00 43.32 2.24
649 714 3.626217 GGACTTGACACGGACTTCTTTTT 59.374 43.478 0.00 0.00 0.00 1.94
650 715 3.203716 GGACTTGACACGGACTTCTTTT 58.796 45.455 0.00 0.00 0.00 2.27
651 716 2.169769 TGGACTTGACACGGACTTCTTT 59.830 45.455 0.00 0.00 0.00 2.52
652 717 1.760613 TGGACTTGACACGGACTTCTT 59.239 47.619 0.00 0.00 0.00 2.52
653 718 1.341531 CTGGACTTGACACGGACTTCT 59.658 52.381 0.00 0.00 0.00 2.85
661 726 3.181474 GCCCTCTATACTGGACTTGACAC 60.181 52.174 0.00 0.00 0.00 3.67
667 740 3.406512 AACTGCCCTCTATACTGGACT 57.593 47.619 0.00 0.00 0.00 3.85
860 1314 2.112297 TGGCGAGGGTTTGGTGTC 59.888 61.111 0.00 0.00 0.00 3.67
937 1403 4.657824 ACAACCACCGACCTCGCG 62.658 66.667 0.00 0.00 38.18 5.87
938 1404 3.041940 CACAACCACCGACCTCGC 61.042 66.667 0.00 0.00 38.18 5.03
939 1405 1.954146 CACACAACCACCGACCTCG 60.954 63.158 0.00 0.00 39.44 4.63
940 1406 1.597027 CCACACAACCACCGACCTC 60.597 63.158 0.00 0.00 0.00 3.85
941 1407 2.372074 ACCACACAACCACCGACCT 61.372 57.895 0.00 0.00 0.00 3.85
942 1408 2.184167 CACCACACAACCACCGACC 61.184 63.158 0.00 0.00 0.00 4.79
943 1409 2.184167 CCACCACACAACCACCGAC 61.184 63.158 0.00 0.00 0.00 4.79
944 1410 2.190843 CCACCACACAACCACCGA 59.809 61.111 0.00 0.00 0.00 4.69
945 1411 3.591835 GCCACCACACAACCACCG 61.592 66.667 0.00 0.00 0.00 4.94
946 1412 2.441164 TGCCACCACACAACCACC 60.441 61.111 0.00 0.00 0.00 4.61
947 1413 3.119193 CTGCCACCACACAACCAC 58.881 61.111 0.00 0.00 0.00 4.16
948 1414 2.832661 GCTGCCACCACACAACCA 60.833 61.111 0.00 0.00 0.00 3.67
949 1415 3.964875 CGCTGCCACCACACAACC 61.965 66.667 0.00 0.00 0.00 3.77
950 1416 2.896801 CTCGCTGCCACCACACAAC 61.897 63.158 0.00 0.00 0.00 3.32
951 1417 2.591429 CTCGCTGCCACCACACAA 60.591 61.111 0.00 0.00 0.00 3.33
1242 1718 1.942776 AAAAAGGCAATCCCTCAGGG 58.057 50.000 1.80 1.80 45.62 4.45
1268 1744 4.163078 ACCATTTCATCCCACAACAACAAA 59.837 37.500 0.00 0.00 0.00 2.83
1269 1745 3.708631 ACCATTTCATCCCACAACAACAA 59.291 39.130 0.00 0.00 0.00 2.83
1270 1746 3.303938 ACCATTTCATCCCACAACAACA 58.696 40.909 0.00 0.00 0.00 3.33
1271 1747 4.057432 CAACCATTTCATCCCACAACAAC 58.943 43.478 0.00 0.00 0.00 3.32
1415 1905 2.101415 TGCACTTGATCCATCCGTAGAG 59.899 50.000 0.00 0.00 0.00 2.43
1463 1958 0.104855 TCCAAATCTCCGCATCGAGG 59.895 55.000 0.00 0.00 0.00 4.63
1501 1996 3.619929 ACTAAACGTTTGACATATCGCCC 59.380 43.478 23.46 0.00 0.00 6.13
1507 2002 9.188588 CAGAGAAACTACTAAACGTTTGACATA 57.811 33.333 23.46 9.02 33.82 2.29
1509 2004 6.477688 CCAGAGAAACTACTAAACGTTTGACA 59.522 38.462 23.46 2.65 33.82 3.58
1548 2043 3.347216 ACAAGAGGCAATAAATCGCAGT 58.653 40.909 0.00 0.00 0.00 4.40
1566 2063 0.036164 ACGCTGCTGATTGGGTACAA 59.964 50.000 0.00 0.00 41.59 2.41
1768 2273 0.950555 TAGCAGCCAGAAACGCACAG 60.951 55.000 0.00 0.00 0.00 3.66
1771 2276 0.321564 ACATAGCAGCCAGAAACGCA 60.322 50.000 0.00 0.00 0.00 5.24
1789 2295 0.598065 AGGCGCAAAATTGAGTGGAC 59.402 50.000 10.83 0.00 0.00 4.02
1791 2297 2.153366 AAAGGCGCAAAATTGAGTGG 57.847 45.000 10.83 0.00 0.00 4.00
1856 2362 5.399858 CAAGAATTCTTGCCAGAACATGAG 58.600 41.667 29.90 7.03 45.59 2.90
1878 2384 5.414454 AGATTTTAACCATAAACGCTCAGCA 59.586 36.000 0.00 0.00 30.86 4.41
2063 2569 6.265196 TGAATTCAACCTCTGCATTACAAACT 59.735 34.615 5.45 0.00 0.00 2.66
2064 2570 6.446318 TGAATTCAACCTCTGCATTACAAAC 58.554 36.000 5.45 0.00 0.00 2.93
2328 2835 5.000012 ACATAGTCTCGTCAGTGGAAATC 58.000 43.478 0.00 0.00 0.00 2.17
2361 2868 3.492656 CGAAATCGGGGCTCTTCATAGAA 60.493 47.826 0.00 0.00 35.37 2.10
2394 2901 0.798776 GCAATGAGGAGTCACCGTTG 59.201 55.000 10.06 10.06 44.74 4.10
2397 2904 0.803768 CGAGCAATGAGGAGTCACCG 60.804 60.000 0.00 0.00 44.74 4.94
2551 3058 8.177119 AGAAAGGCACTACATTAATGACAAAA 57.823 30.769 22.16 1.54 38.49 2.44
2552 3059 7.759489 AGAAAGGCACTACATTAATGACAAA 57.241 32.000 22.16 3.83 38.49 2.83
2553 3060 7.665559 AGAAGAAAGGCACTACATTAATGACAA 59.334 33.333 22.16 6.16 38.49 3.18
2554 3061 7.168219 AGAAGAAAGGCACTACATTAATGACA 58.832 34.615 22.16 8.20 38.49 3.58
2555 3062 7.617041 AGAAGAAAGGCACTACATTAATGAC 57.383 36.000 22.16 0.00 38.49 3.06
2556 3063 8.635765 AAAGAAGAAAGGCACTACATTAATGA 57.364 30.769 22.16 5.10 38.49 2.57
2557 3064 7.693951 CGAAAGAAGAAAGGCACTACATTAATG 59.306 37.037 14.01 14.01 38.49 1.90
2558 3065 7.626452 GCGAAAGAAGAAAGGCACTACATTAAT 60.626 37.037 0.00 0.00 38.49 1.40
2657 3172 4.509756 CACAGCTGTGGATCCTCG 57.490 61.111 34.65 10.43 42.10 4.63
2739 3254 1.004511 AGCAGGCTGAAAGAAGATGCT 59.995 47.619 20.86 1.04 37.10 3.79
2740 3255 1.401199 GAGCAGGCTGAAAGAAGATGC 59.599 52.381 20.86 0.00 34.07 3.91
2862 3377 1.321474 CTGAGAAGGGCAAGCAACAA 58.679 50.000 0.00 0.00 0.00 2.83
2944 3459 4.391830 TGGCATTTGCTACTAGTTCTTTCG 59.608 41.667 0.00 0.00 41.70 3.46
2952 3467 4.644103 AGCATTTGGCATTTGCTACTAG 57.356 40.909 19.45 0.00 44.51 2.57
3033 3548 6.377146 AGGCTGGTTTAATCGTTTATGTGAAT 59.623 34.615 0.00 0.00 0.00 2.57
3076 3591 6.142817 GGTGTTTGTACTGACAATAGCTTTG 58.857 40.000 0.00 0.00 44.96 2.77
3106 3621 9.416794 TCAATTTGTGAAAAATGTAACGCATAT 57.583 25.926 0.00 0.00 32.50 1.78
3107 3622 8.803201 TCAATTTGTGAAAAATGTAACGCATA 57.197 26.923 0.00 0.00 32.50 3.14
3531 4055 5.050363 CCTGCACGAAGTAACGCATTAATAT 60.050 40.000 0.00 0.00 41.61 1.28
3662 4186 0.605050 TAAGCATGCAAGCGACACCA 60.605 50.000 21.98 0.00 40.15 4.17
3727 4251 9.729281 AAATGCCAATCAAGAGTAAATGAAAAT 57.271 25.926 0.00 0.00 0.00 1.82
4061 4585 5.303971 AGAGAAAGTGAGATTCAGTTGGTG 58.696 41.667 0.27 0.00 38.97 4.17
4407 4940 1.264020 TGTTAGCTCAAGCAAGCAACG 59.736 47.619 4.59 0.00 45.00 4.10
4455 4988 1.761174 GGCAAGGGTGGAGTTCTGA 59.239 57.895 0.00 0.00 0.00 3.27
4494 5027 0.529337 CACAATCGCAGAGCTCCGAT 60.529 55.000 18.53 18.53 45.17 4.18
4503 5036 1.133253 CGCCTTCACACAATCGCAG 59.867 57.895 0.00 0.00 0.00 5.18
4602 5135 3.138098 TGGTGGCATAATATTGGCTGAGA 59.862 43.478 12.02 0.00 42.34 3.27
4603 5136 3.489355 TGGTGGCATAATATTGGCTGAG 58.511 45.455 12.02 0.00 42.34 3.35
4604 5137 3.591695 TGGTGGCATAATATTGGCTGA 57.408 42.857 12.02 0.22 42.34 4.26
4605 5138 4.669206 TTTGGTGGCATAATATTGGCTG 57.331 40.909 12.02 3.03 42.34 4.85
4606 5139 5.892524 AATTTGGTGGCATAATATTGGCT 57.107 34.783 12.02 0.00 42.34 4.75
4607 5140 6.290605 AGAAATTTGGTGGCATAATATTGGC 58.709 36.000 0.00 1.81 42.20 4.52
4608 5141 7.986320 TGAAGAAATTTGGTGGCATAATATTGG 59.014 33.333 0.00 0.00 0.00 3.16
4609 5142 8.945481 TGAAGAAATTTGGTGGCATAATATTG 57.055 30.769 0.00 0.00 0.00 1.90
4610 5143 8.761689 ACTGAAGAAATTTGGTGGCATAATATT 58.238 29.630 0.00 0.00 0.00 1.28
4708 5241 2.041701 ACTGAAGTTGGGCATTGCTTT 58.958 42.857 8.82 0.00 0.00 3.51
4890 5423 4.383602 CACCCGAAACAAGCGCGG 62.384 66.667 8.83 0.00 44.42 6.46
4950 5483 5.889853 CCACTACAATACCACTAGTCCACTA 59.110 44.000 0.00 0.00 0.00 2.74
4951 5484 4.710375 CCACTACAATACCACTAGTCCACT 59.290 45.833 0.00 0.00 0.00 4.00
4952 5485 4.465305 ACCACTACAATACCACTAGTCCAC 59.535 45.833 0.00 0.00 0.00 4.02
4953 5486 4.464951 CACCACTACAATACCACTAGTCCA 59.535 45.833 0.00 0.00 0.00 4.02
4954 5487 4.465305 ACACCACTACAATACCACTAGTCC 59.535 45.833 0.00 0.00 0.00 3.85
4955 5488 5.408356 CACACCACTACAATACCACTAGTC 58.592 45.833 0.00 0.00 0.00 2.59
4956 5489 4.322499 GCACACCACTACAATACCACTAGT 60.322 45.833 0.00 0.00 0.00 2.57
4957 5490 4.081642 AGCACACCACTACAATACCACTAG 60.082 45.833 0.00 0.00 0.00 2.57
5031 5579 9.629878 TCTAGACTATAGGTACAGAAAGAAAGG 57.370 37.037 4.43 0.00 0.00 3.11
5033 5581 9.122779 GCTCTAGACTATAGGTACAGAAAGAAA 57.877 37.037 4.43 0.00 0.00 2.52
5034 5582 7.720515 GGCTCTAGACTATAGGTACAGAAAGAA 59.279 40.741 4.43 0.00 0.00 2.52
5111 5659 8.137437 AGTATTATGCCATTACAAACAAGATGC 58.863 33.333 0.00 0.00 0.00 3.91
5144 5693 0.248289 AAACATCATGGCAGCCAAGC 59.752 50.000 20.84 0.00 36.95 4.01
5462 6011 1.001633 GAAAGTTGGTGGCTAGACCGA 59.998 52.381 0.00 0.00 43.94 4.69


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

AutoCloner maintained by Alex Coulton.