Multiple sequence alignment - TraesCS7B01G335800

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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 TraesCS7B01G335800 chr7B 100.000 2432 0 0 1 2432 590847845 590850276 0.000000e+00 4492.0
1 TraesCS7B01G335800 chr7B 95.054 829 39 2 1605 2432 667387972 667388799 0.000000e+00 1303.0
2 TraesCS7B01G335800 chr5B 94.673 826 42 2 1609 2432 513856754 513857579 0.000000e+00 1280.0
3 TraesCS7B01G335800 chr5B 91.908 828 59 7 1608 2429 688568416 688569241 0.000000e+00 1151.0
4 TraesCS7B01G335800 chr5B 91.758 825 63 5 1608 2429 695847923 695848745 0.000000e+00 1142.0
5 TraesCS7B01G335800 chr5B 91.505 824 64 5 1611 2429 246872251 246871429 0.000000e+00 1129.0
6 TraesCS7B01G335800 chr6B 92.745 827 55 5 1606 2429 633488976 633489800 0.000000e+00 1190.0
7 TraesCS7B01G335800 chr6B 91.576 831 66 4 1606 2432 209591184 209592014 0.000000e+00 1144.0
8 TraesCS7B01G335800 chr1B 91.898 827 62 5 1610 2432 82739279 82740104 0.000000e+00 1151.0
9 TraesCS7B01G335800 chr2B 91.215 831 69 4 1605 2432 499584048 499583219 0.000000e+00 1127.0
10 TraesCS7B01G335800 chr7A 87.486 903 60 27 24 896 630695178 630694299 0.000000e+00 992.0
11 TraesCS7B01G335800 chr7A 92.514 521 35 2 973 1489 630694171 630693651 0.000000e+00 743.0
12 TraesCS7B01G335800 chr7A 82.407 432 71 4 1020 1447 630695114 630694684 2.950000e-99 372.0
13 TraesCS7B01G335800 chr7D 96.970 33 1 0 187 219 42901387 42901419 3.380000e-04 56.5
14 TraesCS7B01G335800 chr4A 96.970 33 1 0 187 219 650410019 650410051 3.380000e-04 56.5


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 TraesCS7B01G335800 chr7B 590847845 590850276 2431 False 4492.000000 4492 100.000 1 2432 1 chr7B.!!$F1 2431
1 TraesCS7B01G335800 chr7B 667387972 667388799 827 False 1303.000000 1303 95.054 1605 2432 1 chr7B.!!$F2 827
2 TraesCS7B01G335800 chr5B 513856754 513857579 825 False 1280.000000 1280 94.673 1609 2432 1 chr5B.!!$F1 823
3 TraesCS7B01G335800 chr5B 688568416 688569241 825 False 1151.000000 1151 91.908 1608 2429 1 chr5B.!!$F2 821
4 TraesCS7B01G335800 chr5B 695847923 695848745 822 False 1142.000000 1142 91.758 1608 2429 1 chr5B.!!$F3 821
5 TraesCS7B01G335800 chr5B 246871429 246872251 822 True 1129.000000 1129 91.505 1611 2429 1 chr5B.!!$R1 818
6 TraesCS7B01G335800 chr6B 633488976 633489800 824 False 1190.000000 1190 92.745 1606 2429 1 chr6B.!!$F2 823
7 TraesCS7B01G335800 chr6B 209591184 209592014 830 False 1144.000000 1144 91.576 1606 2432 1 chr6B.!!$F1 826
8 TraesCS7B01G335800 chr1B 82739279 82740104 825 False 1151.000000 1151 91.898 1610 2432 1 chr1B.!!$F1 822
9 TraesCS7B01G335800 chr2B 499583219 499584048 829 True 1127.000000 1127 91.215 1605 2432 1 chr2B.!!$R1 827
10 TraesCS7B01G335800 chr7A 630693651 630695178 1527 True 702.333333 992 87.469 24 1489 3 chr7A.!!$R1 1465

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
816 846 0.106149 AGTCAAACTTCGTCGCCCTT 59.894 50.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2200 0.710588 GGAGGGAAGGGGGAAAATGT 59.289 55.0 0.0 0.0 0.0 2.71 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
38 39 1.532437 CAATCGACAGCAGCTCAACAA 59.468 47.619 0.00 0.00 0.00 2.83
53 54 2.372504 TCAACAACCCTCCCATTTACGA 59.627 45.455 0.00 0.00 0.00 3.43
159 165 3.882825 CCAGAGAGATGGCCGGAT 58.117 61.111 5.05 0.00 32.48 4.18
401 407 3.069318 GAGGAGGGCTTCGACGGT 61.069 66.667 0.00 0.00 0.00 4.83
408 414 0.672401 GGGCTTCGACGGTTTCATGA 60.672 55.000 0.00 0.00 0.00 3.07
437 443 1.955080 GATCTCGGGAAGTACGTCCAT 59.045 52.381 26.20 13.04 39.70 3.41
451 457 1.086634 GTCCATGGAGACTGCTTCGC 61.087 60.000 16.81 0.00 33.79 4.70
452 458 1.220206 CCATGGAGACTGCTTCGCT 59.780 57.895 5.56 0.00 0.00 4.93
511 517 6.909448 AAGGCACTAGGACAAATCCGTTCC 62.909 50.000 0.00 0.00 45.88 3.62
521 527 5.414765 GGACAAATCCGTTCCATTAACTTCT 59.585 40.000 0.00 0.00 34.48 2.85
524 530 2.343101 TCCGTTCCATTAACTTCTGCG 58.657 47.619 0.00 0.00 35.81 5.18
525 531 1.202031 CCGTTCCATTAACTTCTGCGC 60.202 52.381 0.00 0.00 35.81 6.09
527 533 2.095853 CGTTCCATTAACTTCTGCGCAT 59.904 45.455 12.24 0.00 35.81 4.73
528 534 3.685058 GTTCCATTAACTTCTGCGCATC 58.315 45.455 12.24 0.00 35.05 3.91
529 535 3.266510 TCCATTAACTTCTGCGCATCT 57.733 42.857 12.24 0.00 0.00 2.90
530 536 4.400529 TCCATTAACTTCTGCGCATCTA 57.599 40.909 12.24 0.00 0.00 1.98
531 537 4.765273 TCCATTAACTTCTGCGCATCTAA 58.235 39.130 12.24 5.08 0.00 2.10
532 538 5.182487 TCCATTAACTTCTGCGCATCTAAA 58.818 37.500 12.24 2.31 0.00 1.85
533 539 5.064707 TCCATTAACTTCTGCGCATCTAAAC 59.935 40.000 12.24 0.00 0.00 2.01
534 540 5.065218 CCATTAACTTCTGCGCATCTAAACT 59.935 40.000 12.24 0.00 0.00 2.66
535 541 5.779806 TTAACTTCTGCGCATCTAAACTC 57.220 39.130 12.24 0.00 0.00 3.01
536 542 3.319137 ACTTCTGCGCATCTAAACTCA 57.681 42.857 12.24 0.00 0.00 3.41
537 543 3.664107 ACTTCTGCGCATCTAAACTCAA 58.336 40.909 12.24 0.00 0.00 3.02
538 544 4.256920 ACTTCTGCGCATCTAAACTCAAT 58.743 39.130 12.24 0.00 0.00 2.57
539 545 4.697352 ACTTCTGCGCATCTAAACTCAATT 59.303 37.500 12.24 0.00 0.00 2.32
540 546 5.182001 ACTTCTGCGCATCTAAACTCAATTT 59.818 36.000 12.24 0.00 0.00 1.82
541 547 5.627499 TCTGCGCATCTAAACTCAATTTT 57.373 34.783 12.24 0.00 0.00 1.82
542 548 6.012658 TCTGCGCATCTAAACTCAATTTTT 57.987 33.333 12.24 0.00 0.00 1.94
543 549 5.858049 TCTGCGCATCTAAACTCAATTTTTG 59.142 36.000 12.24 0.00 0.00 2.44
544 550 5.527951 TGCGCATCTAAACTCAATTTTTGT 58.472 33.333 5.66 0.00 0.00 2.83
554 560 6.849588 AACTCAATTTTTGTTCCATTGCTC 57.150 33.333 0.00 0.00 0.00 4.26
555 561 5.916318 ACTCAATTTTTGTTCCATTGCTCA 58.084 33.333 0.00 0.00 0.00 4.26
557 563 6.993902 ACTCAATTTTTGTTCCATTGCTCAAT 59.006 30.769 0.00 0.00 0.00 2.57
583 589 3.181466 TGGTAGTTGCGTGCATCATCTAT 60.181 43.478 5.77 0.00 0.00 1.98
584 590 3.809832 GGTAGTTGCGTGCATCATCTATT 59.190 43.478 5.77 0.00 0.00 1.73
585 591 4.084328 GGTAGTTGCGTGCATCATCTATTC 60.084 45.833 5.77 5.82 0.00 1.75
586 592 3.801698 AGTTGCGTGCATCATCTATTCT 58.198 40.909 5.77 0.00 0.00 2.40
587 593 4.948847 AGTTGCGTGCATCATCTATTCTA 58.051 39.130 5.77 0.00 0.00 2.10
591 597 3.121944 GCGTGCATCATCTATTCTAACGG 59.878 47.826 0.00 0.00 0.00 4.44
595 601 5.934625 GTGCATCATCTATTCTAACGGGAAT 59.065 40.000 0.00 5.99 39.06 3.01
603 609 9.929180 CATCTATTCTAACGGGAATCTGAATTA 57.071 33.333 4.32 0.00 37.20 1.40
607 613 8.839310 ATTCTAACGGGAATCTGAATTATCTG 57.161 34.615 0.00 0.00 31.08 2.90
617 623 7.919621 GGAATCTGAATTATCTGCTTTTTGAGG 59.080 37.037 0.00 0.00 0.00 3.86
621 627 8.517878 TCTGAATTATCTGCTTTTTGAGGAAAG 58.482 33.333 0.00 0.00 39.16 2.62
635 641 5.576563 TGAGGAAAGTACTCAAAATCCCA 57.423 39.130 0.00 0.00 41.66 4.37
639 645 6.133356 AGGAAAGTACTCAAAATCCCAAACA 58.867 36.000 0.00 0.00 0.00 2.83
671 677 3.809832 ACTCCAAGTTCAAACGTGAGATG 59.190 43.478 9.88 0.00 40.18 2.90
673 679 3.559655 TCCAAGTTCAAACGTGAGATGTG 59.440 43.478 9.88 0.00 40.18 3.21
685 691 3.547868 CGTGAGATGTGTACATTTCCGAG 59.452 47.826 11.56 2.06 36.85 4.63
705 712 4.515191 CGAGTGGAGGTTCTGAATTTGAAA 59.485 41.667 0.00 0.00 0.00 2.69
720 727 7.873910 TGAATTTGAAATGAAATTCCAAAGCC 58.126 30.769 13.17 0.00 45.69 4.35
721 728 7.720515 TGAATTTGAAATGAAATTCCAAAGCCT 59.279 29.630 13.17 0.00 45.69 4.58
722 729 6.864360 TTTGAAATGAAATTCCAAAGCCTG 57.136 33.333 0.00 0.00 33.67 4.85
725 732 6.454795 TGAAATGAAATTCCAAAGCCTGTAC 58.545 36.000 0.00 0.00 33.67 2.90
727 734 5.904362 ATGAAATTCCAAAGCCTGTACTC 57.096 39.130 0.00 0.00 0.00 2.59
728 735 4.724399 TGAAATTCCAAAGCCTGTACTCA 58.276 39.130 0.00 0.00 0.00 3.41
729 736 5.136828 TGAAATTCCAAAGCCTGTACTCAA 58.863 37.500 0.00 0.00 0.00 3.02
730 737 5.241506 TGAAATTCCAAAGCCTGTACTCAAG 59.758 40.000 0.00 0.00 0.00 3.02
731 738 3.857157 TTCCAAAGCCTGTACTCAAGT 57.143 42.857 0.00 0.00 0.00 3.16
733 740 2.703536 TCCAAAGCCTGTACTCAAGTCA 59.296 45.455 0.00 0.00 0.00 3.41
734 741 3.135712 TCCAAAGCCTGTACTCAAGTCAA 59.864 43.478 0.00 0.00 0.00 3.18
735 742 4.074970 CCAAAGCCTGTACTCAAGTCAAT 58.925 43.478 0.00 0.00 0.00 2.57
736 743 4.083110 CCAAAGCCTGTACTCAAGTCAATG 60.083 45.833 0.00 0.00 0.00 2.82
737 744 4.357918 AAGCCTGTACTCAAGTCAATGT 57.642 40.909 0.00 0.00 0.00 2.71
738 745 4.357918 AGCCTGTACTCAAGTCAATGTT 57.642 40.909 0.00 0.00 0.00 2.71
740 747 5.133221 AGCCTGTACTCAAGTCAATGTTTT 58.867 37.500 0.00 0.00 0.00 2.43
741 748 5.009010 AGCCTGTACTCAAGTCAATGTTTTG 59.991 40.000 0.00 0.00 0.00 2.44
742 749 5.008613 GCCTGTACTCAAGTCAATGTTTTGA 59.991 40.000 0.00 3.22 39.54 2.69
746 753 4.214980 CTCAAGTCAATGTTTTGAGCGT 57.785 40.909 13.28 0.00 42.41 5.07
747 754 4.209452 TCAAGTCAATGTTTTGAGCGTC 57.791 40.909 0.00 0.00 42.41 5.19
748 755 2.949714 AGTCAATGTTTTGAGCGTCG 57.050 45.000 0.00 0.00 42.41 5.12
749 756 2.479837 AGTCAATGTTTTGAGCGTCGA 58.520 42.857 0.00 0.00 42.41 4.20
755 785 1.529438 TGTTTTGAGCGTCGAACATCC 59.471 47.619 0.00 0.00 0.00 3.51
759 789 0.669318 TGAGCGTCGAACATCCAACC 60.669 55.000 0.00 0.00 0.00 3.77
760 790 1.359459 GAGCGTCGAACATCCAACCC 61.359 60.000 0.00 0.00 0.00 4.11
769 799 3.186205 CGAACATCCAACCCAAAAATTGC 59.814 43.478 0.00 0.00 0.00 3.56
772 802 4.530875 ACATCCAACCCAAAAATTGCAAA 58.469 34.783 1.71 0.00 0.00 3.68
773 803 5.139001 ACATCCAACCCAAAAATTGCAAAT 58.861 33.333 1.71 0.00 0.00 2.32
775 805 4.785301 TCCAACCCAAAAATTGCAAATCA 58.215 34.783 1.71 0.00 0.00 2.57
780 810 5.683681 ACCCAAAAATTGCAAATCAGAGTT 58.316 33.333 1.71 0.00 0.00 3.01
784 814 9.434420 CCCAAAAATTGCAAATCAGAGTTAATA 57.566 29.630 1.71 0.00 0.00 0.98
813 843 0.938168 ACGAGTCAAACTTCGTCGCC 60.938 55.000 0.00 0.00 30.36 5.54
816 846 0.106149 AGTCAAACTTCGTCGCCCTT 59.894 50.000 0.00 0.00 0.00 3.95
826 856 2.198406 TCGTCGCCCTTTATGATTTCG 58.802 47.619 0.00 0.00 0.00 3.46
834 864 3.555966 CCTTTATGATTTCGGGCTCCTT 58.444 45.455 0.00 0.00 0.00 3.36
896 927 4.179579 GCTCCCATTCGTTGGCGC 62.180 66.667 0.00 0.00 44.97 6.53
897 928 3.508840 CTCCCATTCGTTGGCGCC 61.509 66.667 22.73 22.73 44.97 6.53
923 974 3.358707 ACACGACGACTTGTTCATGTA 57.641 42.857 0.00 0.00 0.00 2.29
924 975 3.305964 ACACGACGACTTGTTCATGTAG 58.694 45.455 0.00 0.00 0.00 2.74
925 976 3.243301 ACACGACGACTTGTTCATGTAGT 60.243 43.478 0.00 4.82 0.00 2.73
926 977 4.023792 ACACGACGACTTGTTCATGTAGTA 60.024 41.667 0.00 0.00 0.00 1.82
936 987 7.568349 ACTTGTTCATGTAGTATCCACATCAT 58.432 34.615 0.00 0.00 34.39 2.45
952 1007 7.615403 TCCACATCATCTATTTATAGTGCTCC 58.385 38.462 0.00 0.00 0.00 4.70
965 1020 4.385405 GCTCCACCAGCGCAGTCT 62.385 66.667 11.47 0.00 38.76 3.24
992 1079 2.091555 TCAGCCCAACAACCTTTACCTT 60.092 45.455 0.00 0.00 0.00 3.50
994 1081 2.177016 AGCCCAACAACCTTTACCTTCT 59.823 45.455 0.00 0.00 0.00 2.85
998 1085 4.202472 CCCAACAACCTTTACCTTCTCTCT 60.202 45.833 0.00 0.00 0.00 3.10
1005 1092 5.033522 ACCTTTACCTTCTCTCTAATGGCT 58.966 41.667 0.00 0.00 0.00 4.75
1034 1121 1.520342 GGATGAGCCTCACTGTCGC 60.520 63.158 0.00 0.00 0.00 5.19
1057 1144 3.659364 CGCAAGAAGAGTTTTCGACTTCG 60.659 47.826 6.98 0.00 40.18 3.79
1083 1170 1.819903 GAAGACTACTCCTTGGCTCGT 59.180 52.381 0.00 0.00 0.00 4.18
1098 1185 2.025727 CGTACGATGGCCGGAGTC 59.974 66.667 10.44 0.00 43.93 3.36
1182 1269 1.269166 CGTGGAGTACATCGCTCAAC 58.731 55.000 0.00 0.00 34.43 3.18
1198 1285 0.662619 CAACCTCGTGCTTTTGAGCA 59.337 50.000 0.00 0.00 43.22 4.26
1293 1380 1.265365 GCTGTGTGGAAGAAGAAGTGC 59.735 52.381 0.00 0.00 0.00 4.40
1305 1392 2.217510 AGAAGTGCTCGGAGTTCCTA 57.782 50.000 6.90 0.00 0.00 2.94
1306 1393 2.526432 AGAAGTGCTCGGAGTTCCTAA 58.474 47.619 6.90 0.00 0.00 2.69
1307 1394 2.897969 AGAAGTGCTCGGAGTTCCTAAA 59.102 45.455 6.90 0.00 0.00 1.85
1368 1455 2.435805 TGCAGATCTGGGGAAGTACATC 59.564 50.000 23.89 3.45 0.00 3.06
1370 1457 3.041211 CAGATCTGGGGAAGTACATCCA 58.959 50.000 18.38 7.70 41.55 3.41
1372 1459 1.580059 TCTGGGGAAGTACATCCACC 58.420 55.000 16.55 15.27 42.62 4.61
1438 1525 1.069227 CAACAAGGCGCTAGGACAAAC 60.069 52.381 7.64 0.00 0.00 2.93
1448 1535 2.295349 GCTAGGACAAACCCGATCGATA 59.705 50.000 18.66 0.00 40.05 2.92
1459 1546 5.243426 ACCCGATCGATATTTTTGGTTTG 57.757 39.130 18.66 0.00 0.00 2.93
1471 1560 1.780806 TTGGTTTGATGCATGCGTTG 58.219 45.000 14.88 0.00 0.00 4.10
1472 1561 0.957362 TGGTTTGATGCATGCGTTGA 59.043 45.000 14.88 2.85 0.00 3.18
1480 1569 1.432514 TGCATGCGTTGACTTCTCTC 58.567 50.000 14.09 0.00 0.00 3.20
1486 1575 3.123804 TGCGTTGACTTCTCTCTTGTTC 58.876 45.455 0.00 0.00 0.00 3.18
1489 1578 4.611943 CGTTGACTTCTCTCTTGTTCAGA 58.388 43.478 0.00 0.00 0.00 3.27
1490 1579 5.226396 CGTTGACTTCTCTCTTGTTCAGAT 58.774 41.667 0.00 0.00 0.00 2.90
1491 1580 5.118357 CGTTGACTTCTCTCTTGTTCAGATG 59.882 44.000 0.00 0.00 0.00 2.90
1492 1581 4.564041 TGACTTCTCTCTTGTTCAGATGC 58.436 43.478 0.00 0.00 0.00 3.91
1493 1582 4.282957 TGACTTCTCTCTTGTTCAGATGCT 59.717 41.667 0.00 0.00 0.00 3.79
1494 1583 4.567971 ACTTCTCTCTTGTTCAGATGCTG 58.432 43.478 0.00 0.00 0.00 4.41
1495 1584 4.040217 ACTTCTCTCTTGTTCAGATGCTGT 59.960 41.667 0.00 0.00 32.61 4.40
1496 1585 4.613925 TCTCTCTTGTTCAGATGCTGTT 57.386 40.909 0.00 0.00 32.61 3.16
1497 1586 4.965814 TCTCTCTTGTTCAGATGCTGTTT 58.034 39.130 0.00 0.00 32.61 2.83
1498 1587 4.753610 TCTCTCTTGTTCAGATGCTGTTTG 59.246 41.667 0.00 0.00 32.61 2.93
1499 1588 3.251729 TCTCTTGTTCAGATGCTGTTTGC 59.748 43.478 0.00 0.00 43.25 3.68
1510 1599 2.566952 GCTGTTTGCACTTGTCAAGT 57.433 45.000 12.62 12.62 44.06 3.16
1511 1600 2.879826 GCTGTTTGCACTTGTCAAGTT 58.120 42.857 15.73 0.00 40.46 2.66
1512 1601 3.253230 GCTGTTTGCACTTGTCAAGTTT 58.747 40.909 15.73 0.00 40.46 2.66
1513 1602 3.061161 GCTGTTTGCACTTGTCAAGTTTG 59.939 43.478 15.73 7.12 40.46 2.93
1514 1603 4.484236 CTGTTTGCACTTGTCAAGTTTGA 58.516 39.130 15.73 1.90 40.46 2.69
1529 1618 7.815840 TCAAGTTTGACCATTGTATCAGAAA 57.184 32.000 0.00 0.00 31.01 2.52
1530 1619 8.231692 TCAAGTTTGACCATTGTATCAGAAAA 57.768 30.769 0.00 0.00 31.01 2.29
1531 1620 8.134895 TCAAGTTTGACCATTGTATCAGAAAAC 58.865 33.333 0.00 0.00 31.01 2.43
1532 1621 6.668323 AGTTTGACCATTGTATCAGAAAACG 58.332 36.000 0.00 0.00 0.00 3.60
1533 1622 4.678509 TGACCATTGTATCAGAAAACGC 57.321 40.909 0.00 0.00 0.00 4.84
1534 1623 3.438781 TGACCATTGTATCAGAAAACGCC 59.561 43.478 0.00 0.00 0.00 5.68
1535 1624 3.686016 ACCATTGTATCAGAAAACGCCT 58.314 40.909 0.00 0.00 0.00 5.52
1536 1625 4.079253 ACCATTGTATCAGAAAACGCCTT 58.921 39.130 0.00 0.00 0.00 4.35
1537 1626 4.156008 ACCATTGTATCAGAAAACGCCTTC 59.844 41.667 0.00 0.00 0.00 3.46
1538 1627 4.155826 CCATTGTATCAGAAAACGCCTTCA 59.844 41.667 0.50 0.00 0.00 3.02
1539 1628 5.163622 CCATTGTATCAGAAAACGCCTTCAT 60.164 40.000 0.50 0.00 0.00 2.57
1540 1629 5.545658 TTGTATCAGAAAACGCCTTCATC 57.454 39.130 0.50 0.00 0.00 2.92
1541 1630 3.938963 TGTATCAGAAAACGCCTTCATCC 59.061 43.478 0.50 0.00 0.00 3.51
1542 1631 1.821216 TCAGAAAACGCCTTCATCCC 58.179 50.000 0.50 0.00 0.00 3.85
1543 1632 1.351017 TCAGAAAACGCCTTCATCCCT 59.649 47.619 0.50 0.00 0.00 4.20
1544 1633 2.569853 TCAGAAAACGCCTTCATCCCTA 59.430 45.455 0.50 0.00 0.00 3.53
1545 1634 2.939103 CAGAAAACGCCTTCATCCCTAG 59.061 50.000 0.50 0.00 0.00 3.02
1546 1635 1.671328 GAAAACGCCTTCATCCCTAGC 59.329 52.381 0.00 0.00 0.00 3.42
1547 1636 0.618458 AAACGCCTTCATCCCTAGCA 59.382 50.000 0.00 0.00 0.00 3.49
1548 1637 0.179000 AACGCCTTCATCCCTAGCAG 59.821 55.000 0.00 0.00 0.00 4.24
1549 1638 0.978146 ACGCCTTCATCCCTAGCAGT 60.978 55.000 0.00 0.00 0.00 4.40
1550 1639 0.249657 CGCCTTCATCCCTAGCAGTC 60.250 60.000 0.00 0.00 0.00 3.51
1551 1640 0.249657 GCCTTCATCCCTAGCAGTCG 60.250 60.000 0.00 0.00 0.00 4.18
1552 1641 1.403814 CCTTCATCCCTAGCAGTCGA 58.596 55.000 0.00 0.00 0.00 4.20
1553 1642 1.967066 CCTTCATCCCTAGCAGTCGAT 59.033 52.381 0.00 0.00 0.00 3.59
1554 1643 2.288702 CCTTCATCCCTAGCAGTCGATG 60.289 54.545 0.00 0.00 34.66 3.84
1555 1644 2.364972 TCATCCCTAGCAGTCGATGA 57.635 50.000 0.00 0.00 38.96 2.92
1556 1645 2.881734 TCATCCCTAGCAGTCGATGAT 58.118 47.619 0.00 0.00 36.95 2.45
1557 1646 3.234353 TCATCCCTAGCAGTCGATGATT 58.766 45.455 0.00 0.00 36.95 2.57
1558 1647 3.643320 TCATCCCTAGCAGTCGATGATTT 59.357 43.478 0.00 0.00 36.95 2.17
1559 1648 3.459232 TCCCTAGCAGTCGATGATTTG 57.541 47.619 0.00 0.00 0.00 2.32
1560 1649 1.869767 CCCTAGCAGTCGATGATTTGC 59.130 52.381 0.00 0.00 36.83 3.68
1561 1650 1.524355 CCTAGCAGTCGATGATTTGCG 59.476 52.381 0.00 0.00 41.27 4.85
1562 1651 1.524355 CTAGCAGTCGATGATTTGCGG 59.476 52.381 0.00 0.00 41.27 5.69
1563 1652 0.391661 AGCAGTCGATGATTTGCGGT 60.392 50.000 0.00 0.00 41.27 5.68
1564 1653 1.134818 AGCAGTCGATGATTTGCGGTA 60.135 47.619 0.00 0.00 41.27 4.02
1565 1654 1.867233 GCAGTCGATGATTTGCGGTAT 59.133 47.619 0.00 0.00 0.00 2.73
1566 1655 2.348872 GCAGTCGATGATTTGCGGTATG 60.349 50.000 0.00 0.00 0.00 2.39
1567 1656 1.867233 AGTCGATGATTTGCGGTATGC 59.133 47.619 0.00 0.00 46.70 3.14
1568 1657 1.069906 GTCGATGATTTGCGGTATGCC 60.070 52.381 0.00 0.00 45.60 4.40
1569 1658 0.943673 CGATGATTTGCGGTATGCCA 59.056 50.000 0.00 0.00 45.60 4.92
1570 1659 1.333308 CGATGATTTGCGGTATGCCAA 59.667 47.619 0.00 0.00 45.60 4.52
1571 1660 2.223456 CGATGATTTGCGGTATGCCAAA 60.223 45.455 0.00 0.00 45.60 3.28
1572 1661 3.733380 CGATGATTTGCGGTATGCCAAAA 60.733 43.478 0.00 0.29 45.60 2.44
1573 1662 3.883830 TGATTTGCGGTATGCCAAAAT 57.116 38.095 9.39 9.39 45.60 1.82
1574 1663 4.199432 TGATTTGCGGTATGCCAAAATT 57.801 36.364 10.54 0.00 45.60 1.82
1575 1664 4.180057 TGATTTGCGGTATGCCAAAATTC 58.820 39.130 10.54 5.95 45.60 2.17
1576 1665 2.270275 TTGCGGTATGCCAAAATTCG 57.730 45.000 0.00 0.00 45.60 3.34
1577 1666 1.454201 TGCGGTATGCCAAAATTCGA 58.546 45.000 0.00 0.00 45.60 3.71
1578 1667 1.131504 TGCGGTATGCCAAAATTCGAC 59.868 47.619 0.00 0.00 45.60 4.20
1579 1668 1.533129 GCGGTATGCCAAAATTCGACC 60.533 52.381 0.00 0.00 37.76 4.79
1580 1669 1.740585 CGGTATGCCAAAATTCGACCA 59.259 47.619 0.00 0.00 34.09 4.02
1581 1670 2.357637 CGGTATGCCAAAATTCGACCAT 59.642 45.455 0.00 0.00 34.09 3.55
1582 1671 3.181491 CGGTATGCCAAAATTCGACCATT 60.181 43.478 0.00 0.00 34.09 3.16
1583 1672 4.676723 CGGTATGCCAAAATTCGACCATTT 60.677 41.667 0.00 0.00 34.09 2.32
1584 1673 4.803613 GGTATGCCAAAATTCGACCATTTC 59.196 41.667 0.00 0.00 34.09 2.17
1585 1674 6.460289 GGTATGCCAAAATTCGACCATTTCG 61.460 44.000 0.00 0.00 41.12 3.46
1586 1675 8.761811 GGTATGCCAAAATTCGACCATTTCGT 62.762 42.308 0.00 0.00 40.81 3.85
1595 1684 3.804518 CGACCATTTCGTCATGTTCAA 57.195 42.857 0.00 0.00 43.24 2.69
1596 1685 3.736213 CGACCATTTCGTCATGTTCAAG 58.264 45.455 0.00 0.00 43.24 3.02
1597 1686 3.431912 CGACCATTTCGTCATGTTCAAGA 59.568 43.478 0.00 0.00 43.24 3.02
1598 1687 4.434725 CGACCATTTCGTCATGTTCAAGAG 60.435 45.833 0.00 0.00 43.24 2.85
1599 1688 4.389374 ACCATTTCGTCATGTTCAAGAGT 58.611 39.130 0.00 0.00 0.00 3.24
1600 1689 4.821805 ACCATTTCGTCATGTTCAAGAGTT 59.178 37.500 0.00 0.00 0.00 3.01
1601 1690 5.995282 ACCATTTCGTCATGTTCAAGAGTTA 59.005 36.000 0.00 0.00 0.00 2.24
1602 1691 6.485313 ACCATTTCGTCATGTTCAAGAGTTAA 59.515 34.615 0.00 0.00 0.00 2.01
1603 1692 6.797033 CCATTTCGTCATGTTCAAGAGTTAAC 59.203 38.462 0.00 0.00 0.00 2.01
1604 1693 7.307989 CCATTTCGTCATGTTCAAGAGTTAACT 60.308 37.037 8.13 8.13 0.00 2.24
1605 1694 7.548196 TTTCGTCATGTTCAAGAGTTAACTT 57.452 32.000 10.02 0.00 0.00 2.66
1606 1695 7.548196 TTCGTCATGTTCAAGAGTTAACTTT 57.452 32.000 10.02 0.23 0.00 2.66
1670 1759 1.376424 CCACACGCAAGCATCTCCT 60.376 57.895 0.00 0.00 45.62 3.69
1903 1992 1.918800 CCCCTCTCCCTCACGGTTT 60.919 63.158 0.00 0.00 0.00 3.27
2084 2175 1.948611 GCGGGTTGAAGGTAATGCTCA 60.949 52.381 0.00 0.00 0.00 4.26
2109 2200 2.038863 TCTCTTGCAACCCCTTCCTA 57.961 50.000 0.00 0.00 0.00 2.94
2233 2329 2.111162 CCGTTTTTGGTGGCACTGA 58.889 52.632 18.45 3.36 0.00 3.41
2319 2415 5.109210 CACTAGTCTTGCGTATGGATTTGA 58.891 41.667 0.00 0.00 0.00 2.69
2393 2490 4.149922 CAGTCAGTTCGTGCGAGAATTTTA 59.850 41.667 0.00 0.00 32.25 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.819825 TCGATTGCGATAGATAGCACTAT 57.180 39.130 0.00 0.00 43.69 2.12
15 16 1.807165 GAGCTGCTGTCGATTGCGA 60.807 57.895 7.01 0.00 45.71 5.10
16 17 1.629345 TTGAGCTGCTGTCGATTGCG 61.629 55.000 7.01 4.77 39.35 4.85
17 18 0.179205 GTTGAGCTGCTGTCGATTGC 60.179 55.000 7.01 5.78 0.00 3.56
18 19 1.150827 TGTTGAGCTGCTGTCGATTG 58.849 50.000 7.01 0.00 0.00 2.67
19 20 1.532868 GTTGTTGAGCTGCTGTCGATT 59.467 47.619 7.01 0.00 0.00 3.34
20 21 1.151668 GTTGTTGAGCTGCTGTCGAT 58.848 50.000 7.01 0.00 0.00 3.59
21 22 0.880278 GGTTGTTGAGCTGCTGTCGA 60.880 55.000 7.01 0.00 0.00 4.20
22 23 1.571460 GGTTGTTGAGCTGCTGTCG 59.429 57.895 7.01 0.00 0.00 4.35
28 29 0.038744 ATGGGAGGGTTGTTGAGCTG 59.961 55.000 0.00 0.00 0.00 4.24
61 62 0.539051 CATCGGAGAGCAGGGAAGTT 59.461 55.000 0.00 0.00 43.63 2.66
63 64 0.539051 AACATCGGAGAGCAGGGAAG 59.461 55.000 0.00 0.00 43.63 3.46
64 65 0.250234 CAACATCGGAGAGCAGGGAA 59.750 55.000 0.00 0.00 43.63 3.97
65 66 0.614697 TCAACATCGGAGAGCAGGGA 60.615 55.000 0.00 0.00 43.63 4.20
66 67 0.179089 CTCAACATCGGAGAGCAGGG 60.179 60.000 0.00 0.00 43.63 4.45
67 68 3.359194 CTCAACATCGGAGAGCAGG 57.641 57.895 0.00 0.00 43.63 4.85
103 109 1.801178 CCTCGAAGTCCAAAACTCTGC 59.199 52.381 0.00 0.00 37.17 4.26
104 110 3.060602 GACCTCGAAGTCCAAAACTCTG 58.939 50.000 2.55 0.00 37.17 3.35
159 165 2.606519 CTGGAAGGACACCCCGGA 60.607 66.667 0.73 0.00 40.87 5.14
166 172 2.927580 GCGTCGGACTGGAAGGACA 61.928 63.158 6.57 0.00 39.30 4.02
232 238 1.403647 CGAGTTTGAGCGATACACCCA 60.404 52.381 0.00 0.00 0.00 4.51
257 263 2.708255 GCTTGCATCTCGCTCAGC 59.292 61.111 0.00 0.00 43.06 4.26
284 290 2.738480 CCGAACTTCACCCCGACA 59.262 61.111 0.00 0.00 0.00 4.35
307 313 3.175240 CGGACTTGTCGAGCAGCG 61.175 66.667 0.00 0.00 42.69 5.18
344 350 0.320771 TTGAGAACTTCTCCCGCAGC 60.321 55.000 14.98 0.00 42.73 5.25
346 352 1.416401 ACTTTGAGAACTTCTCCCGCA 59.584 47.619 14.98 0.00 42.73 5.69
401 407 4.052159 GAGATCCTTCTCGCTCATGAAA 57.948 45.455 0.00 0.00 39.14 2.69
424 430 2.100989 AGTCTCCATGGACGTACTTCC 58.899 52.381 11.44 11.42 40.76 3.46
511 517 6.111768 AGTTTAGATGCGCAGAAGTTAATG 57.888 37.500 18.32 0.00 0.00 1.90
513 519 5.234752 TGAGTTTAGATGCGCAGAAGTTAA 58.765 37.500 18.32 6.97 0.00 2.01
514 520 4.816392 TGAGTTTAGATGCGCAGAAGTTA 58.184 39.130 18.32 5.14 0.00 2.24
517 523 4.871993 ATTGAGTTTAGATGCGCAGAAG 57.128 40.909 18.32 0.00 0.00 2.85
521 527 5.527951 ACAAAAATTGAGTTTAGATGCGCA 58.472 33.333 14.96 14.96 0.00 6.09
524 530 7.945033 TGGAACAAAAATTGAGTTTAGATGC 57.055 32.000 0.00 0.00 31.92 3.91
543 549 7.100458 ACTACCATAAATTGAGCAATGGAAC 57.900 36.000 7.18 0.00 41.20 3.62
544 550 7.546358 CAACTACCATAAATTGAGCAATGGAA 58.454 34.615 7.18 0.00 41.20 3.53
554 560 4.090138 TGCACGCAACTACCATAAATTG 57.910 40.909 0.00 0.00 0.00 2.32
555 561 4.397730 TGATGCACGCAACTACCATAAATT 59.602 37.500 0.00 0.00 0.00 1.82
557 563 3.339141 TGATGCACGCAACTACCATAAA 58.661 40.909 0.00 0.00 0.00 1.40
583 589 6.706270 GCAGATAATTCAGATTCCCGTTAGAA 59.294 38.462 0.00 0.00 0.00 2.10
584 590 6.042093 AGCAGATAATTCAGATTCCCGTTAGA 59.958 38.462 0.00 0.00 0.00 2.10
585 591 6.226787 AGCAGATAATTCAGATTCCCGTTAG 58.773 40.000 0.00 0.00 0.00 2.34
586 592 6.174720 AGCAGATAATTCAGATTCCCGTTA 57.825 37.500 0.00 0.00 0.00 3.18
587 593 5.041191 AGCAGATAATTCAGATTCCCGTT 57.959 39.130 0.00 0.00 0.00 4.44
591 597 7.919621 CCTCAAAAAGCAGATAATTCAGATTCC 59.080 37.037 0.00 0.00 0.00 3.01
595 601 8.408043 TTTCCTCAAAAAGCAGATAATTCAGA 57.592 30.769 0.00 0.00 0.00 3.27
603 609 6.299141 TGAGTACTTTCCTCAAAAAGCAGAT 58.701 36.000 0.00 0.00 39.39 2.90
617 623 8.141268 TCAATGTTTGGGATTTTGAGTACTTTC 58.859 33.333 0.00 0.00 0.00 2.62
621 627 5.863935 GCTCAATGTTTGGGATTTTGAGTAC 59.136 40.000 11.34 0.00 43.21 2.73
635 641 4.843220 CTTGGAGTCAAGCTCAATGTTT 57.157 40.909 0.00 0.00 45.88 2.83
671 677 2.028385 ACCTCCACTCGGAAATGTACAC 60.028 50.000 0.00 0.00 42.21 2.90
673 679 3.056035 AGAACCTCCACTCGGAAATGTAC 60.056 47.826 0.00 0.00 42.21 2.90
685 691 6.331369 TCATTTCAAATTCAGAACCTCCAC 57.669 37.500 0.00 0.00 0.00 4.02
705 712 5.324409 TGAGTACAGGCTTTGGAATTTCAT 58.676 37.500 0.00 0.00 0.00 2.57
720 727 6.138761 GCTCAAAACATTGACTTGAGTACAG 58.861 40.000 22.05 8.24 45.13 2.74
721 728 5.277297 CGCTCAAAACATTGACTTGAGTACA 60.277 40.000 22.05 0.00 45.13 2.90
722 729 5.140177 CGCTCAAAACATTGACTTGAGTAC 58.860 41.667 22.05 12.58 45.13 2.73
725 732 4.214437 GACGCTCAAAACATTGACTTGAG 58.786 43.478 19.37 19.37 45.78 3.02
727 734 2.966708 CGACGCTCAAAACATTGACTTG 59.033 45.455 0.00 0.00 0.00 3.16
728 735 2.869801 TCGACGCTCAAAACATTGACTT 59.130 40.909 0.00 0.00 0.00 3.01
729 736 2.479837 TCGACGCTCAAAACATTGACT 58.520 42.857 0.00 0.00 0.00 3.41
730 737 2.941891 TCGACGCTCAAAACATTGAC 57.058 45.000 0.00 0.00 0.00 3.18
731 738 2.609916 TGTTCGACGCTCAAAACATTGA 59.390 40.909 0.00 0.00 0.00 2.57
733 740 3.364964 GGATGTTCGACGCTCAAAACATT 60.365 43.478 11.66 0.00 41.18 2.71
734 741 2.159627 GGATGTTCGACGCTCAAAACAT 59.840 45.455 10.55 10.55 43.15 2.71
735 742 1.529438 GGATGTTCGACGCTCAAAACA 59.471 47.619 2.10 2.10 36.19 2.83
736 743 1.529438 TGGATGTTCGACGCTCAAAAC 59.471 47.619 0.00 0.00 0.00 2.43
737 744 1.872388 TGGATGTTCGACGCTCAAAA 58.128 45.000 0.00 0.00 0.00 2.44
738 745 1.529438 GTTGGATGTTCGACGCTCAAA 59.471 47.619 0.00 0.00 0.00 2.69
740 747 0.669318 GGTTGGATGTTCGACGCTCA 60.669 55.000 0.00 0.00 0.00 4.26
741 748 1.359459 GGGTTGGATGTTCGACGCTC 61.359 60.000 0.00 0.00 32.99 5.03
742 749 1.375523 GGGTTGGATGTTCGACGCT 60.376 57.895 0.00 0.00 32.99 5.07
743 750 1.231958 TTGGGTTGGATGTTCGACGC 61.232 55.000 0.00 0.00 35.36 5.19
745 752 3.719173 TTTTTGGGTTGGATGTTCGAC 57.281 42.857 0.00 0.00 0.00 4.20
746 753 4.626042 CAATTTTTGGGTTGGATGTTCGA 58.374 39.130 0.00 0.00 0.00 3.71
747 754 3.186205 GCAATTTTTGGGTTGGATGTTCG 59.814 43.478 0.00 0.00 0.00 3.95
748 755 4.133078 TGCAATTTTTGGGTTGGATGTTC 58.867 39.130 0.00 0.00 0.00 3.18
749 756 4.162040 TGCAATTTTTGGGTTGGATGTT 57.838 36.364 0.00 0.00 0.00 2.71
755 785 5.528320 ACTCTGATTTGCAATTTTTGGGTTG 59.472 36.000 0.00 0.00 0.00 3.77
772 802 9.469807 CTCGTAGCTCAAAATATTAACTCTGAT 57.530 33.333 0.00 0.00 0.00 2.90
773 803 8.467598 ACTCGTAGCTCAAAATATTAACTCTGA 58.532 33.333 0.00 0.00 0.00 3.27
775 805 8.467598 TGACTCGTAGCTCAAAATATTAACTCT 58.532 33.333 0.00 0.00 0.00 3.24
780 810 8.997621 AGTTTGACTCGTAGCTCAAAATATTA 57.002 30.769 0.00 0.00 37.96 0.98
784 814 5.107453 CGAAGTTTGACTCGTAGCTCAAAAT 60.107 40.000 0.00 0.00 37.96 1.82
813 843 3.214696 AGGAGCCCGAAATCATAAAGG 57.785 47.619 0.00 0.00 0.00 3.11
816 846 3.054728 TGACAAGGAGCCCGAAATCATAA 60.055 43.478 0.00 0.00 0.00 1.90
826 856 1.376037 CTCGGTTGACAAGGAGCCC 60.376 63.158 3.88 0.00 0.00 5.19
834 864 1.891919 GCTGGTTGCTCGGTTGACA 60.892 57.895 0.00 0.00 38.95 3.58
896 927 1.081641 AAGTCGTCGTGTACTGCGG 60.082 57.895 9.73 0.00 0.00 5.69
897 928 0.659417 ACAAGTCGTCGTGTACTGCG 60.659 55.000 0.00 0.00 34.79 5.18
905 956 3.637998 ACTACATGAACAAGTCGTCGT 57.362 42.857 0.00 0.00 0.00 4.34
926 977 8.263640 GGAGCACTATAAATAGATGATGTGGAT 58.736 37.037 4.02 0.00 34.50 3.41
952 1007 2.176273 GCCATAGACTGCGCTGGTG 61.176 63.158 18.98 10.85 0.00 4.17
976 1031 4.974399 AGAGAGAAGGTAAAGGTTGTTGG 58.026 43.478 0.00 0.00 0.00 3.77
1005 1092 0.393808 GGCTCATCCGGTTTGGCTTA 60.394 55.000 0.00 0.00 37.80 3.09
1034 1121 2.135933 AGTCGAAAACTCTTCTTGCGG 58.864 47.619 0.00 0.00 30.02 5.69
1057 1144 2.424246 CCAAGGAGTAGTCTTCGACCTC 59.576 54.545 0.00 0.00 32.18 3.85
1098 1185 2.359967 GGACTGGAAGGACTCCCCG 61.360 68.421 0.00 0.00 44.69 5.73
1171 1258 1.738099 GCACGAGGTTGAGCGATGT 60.738 57.895 0.00 0.00 0.00 3.06
1198 1285 2.124819 CTCGATGGCCTGCAGCTT 60.125 61.111 8.66 0.00 43.05 3.74
1279 1366 1.273606 CTCCGAGCACTTCTTCTTCCA 59.726 52.381 0.00 0.00 0.00 3.53
1305 1392 1.693606 CCATGTTCTTGGCCCTTGTTT 59.306 47.619 0.00 0.00 0.00 2.83
1306 1393 1.341080 CCATGTTCTTGGCCCTTGTT 58.659 50.000 0.00 0.00 0.00 2.83
1307 1394 3.056213 CCATGTTCTTGGCCCTTGT 57.944 52.632 0.00 0.00 0.00 3.16
1368 1455 1.444553 GACGAAGCAGTCTCGGTGG 60.445 63.158 0.00 0.00 38.09 4.61
1370 1457 2.259439 ACGACGAAGCAGTCTCGGT 61.259 57.895 0.00 0.00 38.90 4.69
1372 1459 2.429351 GCACGACGAAGCAGTCTCG 61.429 63.158 0.00 6.59 38.90 4.04
1404 1491 0.534203 TTGTTGGTCGCCTGAGAACC 60.534 55.000 0.00 0.00 0.00 3.62
1438 1525 5.493133 TCAAACCAAAAATATCGATCGGG 57.507 39.130 16.41 8.24 0.00 5.14
1448 1535 3.401182 ACGCATGCATCAAACCAAAAAT 58.599 36.364 19.57 0.00 0.00 1.82
1459 1546 2.005451 AGAGAAGTCAACGCATGCATC 58.995 47.619 19.57 3.83 0.00 3.91
1471 1560 4.626604 CAGCATCTGAACAAGAGAGAAGTC 59.373 45.833 0.00 0.00 38.67 3.01
1472 1561 4.040217 ACAGCATCTGAACAAGAGAGAAGT 59.960 41.667 0.29 0.00 38.67 3.01
1489 1578 8.726623 TCAAACTTGACAAGTGCAAACAGCAT 62.727 38.462 21.24 0.00 43.53 3.79
1490 1579 7.512580 TCAAACTTGACAAGTGCAAACAGCA 62.513 40.000 21.24 0.00 41.91 4.41
1491 1580 2.566952 ACTTGACAAGTGCAAACAGC 57.433 45.000 19.96 0.00 41.01 4.40
1492 1581 4.484236 TCAAACTTGACAAGTGCAAACAG 58.516 39.130 21.24 6.99 41.91 3.16
1493 1582 4.511617 TCAAACTTGACAAGTGCAAACA 57.488 36.364 21.24 0.74 41.91 2.83
1505 1594 7.815840 TTTCTGATACAATGGTCAAACTTGA 57.184 32.000 0.00 0.00 34.20 3.02
1506 1595 7.113404 CGTTTTCTGATACAATGGTCAAACTTG 59.887 37.037 0.00 0.00 0.00 3.16
1507 1596 7.138736 CGTTTTCTGATACAATGGTCAAACTT 58.861 34.615 0.00 0.00 0.00 2.66
1508 1597 6.668323 CGTTTTCTGATACAATGGTCAAACT 58.332 36.000 0.00 0.00 0.00 2.66
1509 1598 5.342259 GCGTTTTCTGATACAATGGTCAAAC 59.658 40.000 0.00 0.00 0.00 2.93
1510 1599 5.457140 GCGTTTTCTGATACAATGGTCAAA 58.543 37.500 0.00 0.00 0.00 2.69
1511 1600 4.083003 GGCGTTTTCTGATACAATGGTCAA 60.083 41.667 0.00 0.00 0.00 3.18
1512 1601 3.438781 GGCGTTTTCTGATACAATGGTCA 59.561 43.478 0.00 0.00 0.00 4.02
1513 1602 3.689649 AGGCGTTTTCTGATACAATGGTC 59.310 43.478 0.00 0.00 0.00 4.02
1514 1603 3.686016 AGGCGTTTTCTGATACAATGGT 58.314 40.909 0.00 0.00 0.00 3.55
1515 1604 4.155826 TGAAGGCGTTTTCTGATACAATGG 59.844 41.667 0.00 0.00 0.00 3.16
1516 1605 5.295431 TGAAGGCGTTTTCTGATACAATG 57.705 39.130 0.00 0.00 0.00 2.82
1517 1606 5.066505 GGATGAAGGCGTTTTCTGATACAAT 59.933 40.000 0.00 0.00 0.00 2.71
1518 1607 4.394920 GGATGAAGGCGTTTTCTGATACAA 59.605 41.667 0.00 0.00 0.00 2.41
1519 1608 3.938963 GGATGAAGGCGTTTTCTGATACA 59.061 43.478 0.00 0.00 0.00 2.29
1520 1609 3.312697 GGGATGAAGGCGTTTTCTGATAC 59.687 47.826 0.00 0.00 0.00 2.24
1521 1610 3.199946 AGGGATGAAGGCGTTTTCTGATA 59.800 43.478 0.00 0.00 0.00 2.15
1522 1611 2.025887 AGGGATGAAGGCGTTTTCTGAT 60.026 45.455 0.00 0.00 0.00 2.90
1523 1612 1.351017 AGGGATGAAGGCGTTTTCTGA 59.649 47.619 0.00 0.00 0.00 3.27
1524 1613 1.826385 AGGGATGAAGGCGTTTTCTG 58.174 50.000 0.00 0.00 0.00 3.02
1525 1614 2.681097 GCTAGGGATGAAGGCGTTTTCT 60.681 50.000 0.00 0.00 0.00 2.52
1526 1615 1.671328 GCTAGGGATGAAGGCGTTTTC 59.329 52.381 0.00 0.00 0.00 2.29
1527 1616 1.004277 TGCTAGGGATGAAGGCGTTTT 59.996 47.619 0.00 0.00 0.00 2.43
1528 1617 0.618458 TGCTAGGGATGAAGGCGTTT 59.382 50.000 0.00 0.00 0.00 3.60
1529 1618 0.179000 CTGCTAGGGATGAAGGCGTT 59.821 55.000 0.00 0.00 0.00 4.84
1530 1619 0.978146 ACTGCTAGGGATGAAGGCGT 60.978 55.000 0.00 0.00 0.00 5.68
1531 1620 0.249657 GACTGCTAGGGATGAAGGCG 60.250 60.000 0.00 0.00 0.00 5.52
1532 1621 0.249657 CGACTGCTAGGGATGAAGGC 60.250 60.000 0.00 0.00 0.00 4.35
1533 1622 1.403814 TCGACTGCTAGGGATGAAGG 58.596 55.000 0.00 0.00 0.00 3.46
1534 1623 2.625314 TCATCGACTGCTAGGGATGAAG 59.375 50.000 14.02 0.00 41.50 3.02
1535 1624 2.666317 TCATCGACTGCTAGGGATGAA 58.334 47.619 14.02 4.96 41.50 2.57
1536 1625 2.364972 TCATCGACTGCTAGGGATGA 57.635 50.000 13.13 13.13 42.02 2.92
1537 1626 3.674528 AATCATCGACTGCTAGGGATG 57.325 47.619 0.00 10.41 38.06 3.51
1538 1627 3.805108 GCAAATCATCGACTGCTAGGGAT 60.805 47.826 0.00 0.00 0.00 3.85
1539 1628 2.483714 GCAAATCATCGACTGCTAGGGA 60.484 50.000 0.00 0.00 0.00 4.20
1540 1629 1.869767 GCAAATCATCGACTGCTAGGG 59.130 52.381 0.00 0.00 0.00 3.53
1541 1630 1.524355 CGCAAATCATCGACTGCTAGG 59.476 52.381 0.00 0.00 32.52 3.02
1542 1631 1.524355 CCGCAAATCATCGACTGCTAG 59.476 52.381 0.00 0.00 32.52 3.42
1543 1632 1.134818 ACCGCAAATCATCGACTGCTA 60.135 47.619 0.00 0.00 32.52 3.49
1544 1633 0.391661 ACCGCAAATCATCGACTGCT 60.392 50.000 0.00 0.00 32.52 4.24
1545 1634 1.286501 TACCGCAAATCATCGACTGC 58.713 50.000 0.00 0.00 0.00 4.40
1546 1635 2.348872 GCATACCGCAAATCATCGACTG 60.349 50.000 0.00 0.00 41.79 3.51
1547 1636 1.867233 GCATACCGCAAATCATCGACT 59.133 47.619 0.00 0.00 41.79 4.18
1548 1637 1.069906 GGCATACCGCAAATCATCGAC 60.070 52.381 0.00 0.00 45.17 4.20
1549 1638 1.225855 GGCATACCGCAAATCATCGA 58.774 50.000 0.00 0.00 45.17 3.59
1550 1639 0.943673 TGGCATACCGCAAATCATCG 59.056 50.000 0.00 0.00 45.17 3.84
1551 1640 3.435105 TTTGGCATACCGCAAATCATC 57.565 42.857 0.00 0.00 45.17 2.92
1552 1641 3.883830 TTTTGGCATACCGCAAATCAT 57.116 38.095 0.00 0.00 45.17 2.45
1553 1642 3.883830 ATTTTGGCATACCGCAAATCA 57.116 38.095 0.00 0.00 45.17 2.57
1554 1643 3.242712 CGAATTTTGGCATACCGCAAATC 59.757 43.478 0.00 0.00 45.17 2.17
1555 1644 3.119316 TCGAATTTTGGCATACCGCAAAT 60.119 39.130 0.00 0.00 45.17 2.32
1556 1645 2.229062 TCGAATTTTGGCATACCGCAAA 59.771 40.909 0.00 0.00 45.17 3.68
1557 1646 1.813178 TCGAATTTTGGCATACCGCAA 59.187 42.857 0.00 0.00 45.17 4.85
1558 1647 1.131504 GTCGAATTTTGGCATACCGCA 59.868 47.619 0.00 0.00 45.17 5.69
1559 1648 1.533129 GGTCGAATTTTGGCATACCGC 60.533 52.381 0.00 0.00 39.70 5.68
1560 1649 1.740585 TGGTCGAATTTTGGCATACCG 59.259 47.619 0.00 0.00 39.70 4.02
1561 1650 4.385358 AATGGTCGAATTTTGGCATACC 57.615 40.909 0.00 0.00 0.00 2.73
1562 1651 5.949233 GAAATGGTCGAATTTTGGCATAC 57.051 39.130 0.00 0.00 29.89 2.39
1576 1665 4.452455 ACTCTTGAACATGACGAAATGGTC 59.548 41.667 0.00 11.57 43.37 4.02
1577 1666 4.389374 ACTCTTGAACATGACGAAATGGT 58.611 39.130 0.00 0.00 31.46 3.55
1578 1667 5.362556 AACTCTTGAACATGACGAAATGG 57.637 39.130 0.00 0.00 31.46 3.16
1579 1668 7.576236 AGTTAACTCTTGAACATGACGAAATG 58.424 34.615 1.12 0.00 0.00 2.32
1580 1669 7.730364 AGTTAACTCTTGAACATGACGAAAT 57.270 32.000 1.12 0.00 0.00 2.17
1581 1670 7.548196 AAGTTAACTCTTGAACATGACGAAA 57.452 32.000 8.95 0.00 0.00 3.46
1582 1671 7.548196 AAAGTTAACTCTTGAACATGACGAA 57.452 32.000 8.95 0.00 0.00 3.85
1583 1672 7.548196 AAAAGTTAACTCTTGAACATGACGA 57.452 32.000 8.95 0.00 0.00 4.20
1584 1673 7.526186 CGTAAAAGTTAACTCTTGAACATGACG 59.474 37.037 8.95 2.73 0.00 4.35
1585 1674 7.797123 CCGTAAAAGTTAACTCTTGAACATGAC 59.203 37.037 8.95 0.00 0.00 3.06
1586 1675 7.711772 TCCGTAAAAGTTAACTCTTGAACATGA 59.288 33.333 8.95 0.00 0.00 3.07
1587 1676 7.857569 TCCGTAAAAGTTAACTCTTGAACATG 58.142 34.615 8.95 0.00 0.00 3.21
1588 1677 8.441312 TTCCGTAAAAGTTAACTCTTGAACAT 57.559 30.769 8.95 0.00 0.00 2.71
1589 1678 7.846644 TTCCGTAAAAGTTAACTCTTGAACA 57.153 32.000 8.95 0.00 0.00 3.18
1597 1686 9.759259 GCGTTAATATTTCCGTAAAAGTTAACT 57.241 29.630 1.12 1.12 38.35 2.24
1598 1687 8.998989 GGCGTTAATATTTCCGTAAAAGTTAAC 58.001 33.333 0.00 0.00 37.84 2.01
1599 1688 8.180920 GGGCGTTAATATTTCCGTAAAAGTTAA 58.819 33.333 0.00 0.00 0.00 2.01
1600 1689 7.335422 TGGGCGTTAATATTTCCGTAAAAGTTA 59.665 33.333 0.00 0.00 0.00 2.24
1601 1690 6.150809 TGGGCGTTAATATTTCCGTAAAAGTT 59.849 34.615 0.00 0.00 0.00 2.66
1602 1691 5.647225 TGGGCGTTAATATTTCCGTAAAAGT 59.353 36.000 0.00 0.00 0.00 2.66
1603 1692 5.967088 GTGGGCGTTAATATTTCCGTAAAAG 59.033 40.000 0.00 0.00 0.00 2.27
1604 1693 5.413833 TGTGGGCGTTAATATTTCCGTAAAA 59.586 36.000 0.00 0.00 0.00 1.52
1605 1694 4.940046 TGTGGGCGTTAATATTTCCGTAAA 59.060 37.500 0.00 0.00 0.00 2.01
1606 1695 4.332268 GTGTGGGCGTTAATATTTCCGTAA 59.668 41.667 0.00 0.00 0.00 3.18
1616 1705 1.658994 CCATACGTGTGGGCGTTAAT 58.341 50.000 22.66 0.00 43.04 1.40
1632 1721 2.275418 GGGATGGTGAACGCCCAT 59.725 61.111 0.00 0.00 45.37 4.00
1670 1759 1.226916 CGTGCACAAAGCTGCCAAA 60.227 52.632 18.64 0.00 45.94 3.28
1903 1992 1.743623 CGTGCGGCAGGGTAAATGA 60.744 57.895 14.53 0.00 0.00 2.57
2084 2175 2.269940 AGGGGTTGCAAGAGATGTAGT 58.730 47.619 0.00 0.00 0.00 2.73
2109 2200 0.710588 GGAGGGAAGGGGGAAAATGT 59.289 55.000 0.00 0.00 0.00 2.71
2233 2329 3.127533 GGCGGCGATGAAACTGCT 61.128 61.111 12.98 0.00 38.28 4.24
2319 2415 2.122099 AAACCGGGGGACACCTCT 60.122 61.111 6.32 0.00 40.03 3.69
2393 2490 4.461198 ACTTCGACTTCAAAATCACCCTT 58.539 39.130 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.