Multiple sequence alignment - TraesCS7D01G322500

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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 TraesCS7D01G322500 chr7D 100.000 6322 0 0 1 6322 412677638 412671317 0.000000e+00 11675.0
1 TraesCS7D01G322500 chr7D 97.649 638 13 2 1 638 572637173 572636538 0.000000e+00 1094.0
2 TraesCS7D01G322500 chr7D 91.304 92 7 1 638 728 209524012 209523921 2.390000e-24 124.0
3 TraesCS7D01G322500 chr7B 93.774 3951 162 29 2409 6322 426883751 426879848 0.000000e+00 5856.0
4 TraesCS7D01G322500 chr7B 89.244 1441 91 27 1087 2489 426885374 426883960 0.000000e+00 1744.0
5 TraesCS7D01G322500 chr7B 94.258 209 4 1 882 1082 426885674 426885466 4.760000e-81 313.0
6 TraesCS7D01G322500 chr7B 94.118 68 4 0 822 889 426886200 426886133 3.120000e-18 104.0
7 TraesCS7D01G322500 chr7B 97.619 42 1 0 2407 2448 426883712 426883671 8.790000e-09 73.1
8 TraesCS7D01G322500 chr7A 96.448 2421 76 5 2529 4949 473912533 473910123 0.000000e+00 3986.0
9 TraesCS7D01G322500 chr7A 87.968 1122 44 32 769 1859 473914205 473913144 0.000000e+00 1240.0
10 TraesCS7D01G322500 chr7A 97.188 640 15 3 2 640 80976704 80977341 0.000000e+00 1079.0
11 TraesCS7D01G322500 chr7A 94.572 608 30 2 1898 2502 473913138 473912531 0.000000e+00 937.0
12 TraesCS7D01G322500 chr7A 95.440 307 11 1 5045 5348 473910089 473909783 2.650000e-133 486.0
13 TraesCS7D01G322500 chr7A 85.900 461 31 15 5429 5855 473909783 473909323 1.610000e-125 460.0
14 TraesCS7D01G322500 chr7A 87.209 344 41 2 5979 6322 473908930 473908590 7.690000e-104 388.0
15 TraesCS7D01G322500 chr5D 98.589 638 8 1 1 638 142520837 142521473 0.000000e+00 1127.0
16 TraesCS7D01G322500 chr5D 97.966 639 9 3 1 638 432501890 432502525 0.000000e+00 1105.0
17 TraesCS7D01G322500 chr5D 97.022 638 14 4 2 639 477305185 477305817 0.000000e+00 1068.0
18 TraesCS7D01G322500 chr2D 98.276 638 10 1 1 638 306491385 306490749 0.000000e+00 1116.0
19 TraesCS7D01G322500 chr2D 97.496 639 15 1 1 639 549939116 549939753 0.000000e+00 1090.0
20 TraesCS7D01G322500 chr2D 95.846 650 25 2 1 649 644653950 644654598 0.000000e+00 1050.0
21 TraesCS7D01G322500 chr3A 97.653 639 14 1 1 639 644720436 644719799 0.000000e+00 1096.0
22 TraesCS7D01G322500 chrUn 91.000 100 9 0 638 737 137677290 137677389 1.110000e-27 135.0
23 TraesCS7D01G322500 chr2A 89.320 103 10 1 638 739 127001605 127001707 1.850000e-25 128.0
24 TraesCS7D01G322500 chr1B 85.849 106 14 1 638 742 517506430 517506325 1.860000e-20 111.0
25 TraesCS7D01G322500 chr1B 84.158 101 15 1 640 739 647229031 647229131 5.220000e-16 97.1
26 TraesCS7D01G322500 chr3B 85.437 103 14 1 638 739 386386035 386386137 8.670000e-19 106.0
27 TraesCS7D01G322500 chr5B 84.615 104 15 1 640 742 525601202 525601099 1.120000e-17 102.0
28 TraesCS7D01G322500 chr6B 84.848 99 14 1 640 737 144421534 144421632 1.450000e-16 99.0
29 TraesCS7D01G322500 chr2B 84.848 99 14 1 640 737 70923284 70923382 1.450000e-16 99.0


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 TraesCS7D01G322500 chr7D 412671317 412677638 6321 True 11675.00 11675 100.000000 1 6322 1 chr7D.!!$R2 6321
1 TraesCS7D01G322500 chr7D 572636538 572637173 635 True 1094.00 1094 97.649000 1 638 1 chr7D.!!$R3 637
2 TraesCS7D01G322500 chr7B 426879848 426886200 6352 True 1618.02 5856 93.802600 822 6322 5 chr7B.!!$R1 5500
3 TraesCS7D01G322500 chr7A 473908590 473914205 5615 True 1249.50 3986 91.256167 769 6322 6 chr7A.!!$R1 5553
4 TraesCS7D01G322500 chr7A 80976704 80977341 637 False 1079.00 1079 97.188000 2 640 1 chr7A.!!$F1 638
5 TraesCS7D01G322500 chr5D 142520837 142521473 636 False 1127.00 1127 98.589000 1 638 1 chr5D.!!$F1 637
6 TraesCS7D01G322500 chr5D 432501890 432502525 635 False 1105.00 1105 97.966000 1 638 1 chr5D.!!$F2 637
7 TraesCS7D01G322500 chr5D 477305185 477305817 632 False 1068.00 1068 97.022000 2 639 1 chr5D.!!$F3 637
8 TraesCS7D01G322500 chr2D 306490749 306491385 636 True 1116.00 1116 98.276000 1 638 1 chr2D.!!$R1 637
9 TraesCS7D01G322500 chr2D 549939116 549939753 637 False 1090.00 1090 97.496000 1 639 1 chr2D.!!$F1 638
10 TraesCS7D01G322500 chr2D 644653950 644654598 648 False 1050.00 1050 95.846000 1 649 1 chr2D.!!$F2 648
11 TraesCS7D01G322500 chr3A 644719799 644720436 637 True 1096.00 1096 97.653000 1 639 1 chr3A.!!$R1 638

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
717 720 0.108329 TAAGCACCTCACCTAAGCGC 60.108 55.000 0.0 0.0 0.00 5.92 F
1371 1966 0.949105 GCCACCTATGCGTAATCCCG 60.949 60.000 0.0 0.0 0.00 5.14 F
1761 2362 1.378119 CTACCGAGGTTTTGGGGCC 60.378 63.158 0.0 0.0 31.40 5.80 F
2365 2990 1.135721 GAATGGACTGATTGCTTGCCC 59.864 52.381 0.0 0.0 0.00 5.36 F
2756 3671 2.868583 CGGATTCAAGGCTGTGATAGTG 59.131 50.000 0.0 0.0 0.00 2.74 F
4429 5346 2.046023 CTCCGCACCTTGCATCCA 60.046 61.111 0.0 0.0 45.36 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2633 0.759346 AGAAGAGCAAACACCGACCT 59.241 50.000 0.00 0.0 0.00 3.85 R
2363 2986 2.103263 GTCTAACTACCAGGATGCAGGG 59.897 54.545 0.00 0.0 31.97 4.45 R
2772 3687 2.718563 ACTTGAAACAAGGACACCGTT 58.281 42.857 14.51 0.0 0.00 4.44 R
3662 4577 4.040068 GCACAGGCATCGAGATCC 57.960 61.111 0.00 0.0 40.72 3.36 R
4700 5617 2.098280 GCTGAAGCTGATAGACTCGTCA 59.902 50.000 0.00 0.0 38.21 4.35 R
6136 7413 0.037232 ACCTTGTACTTCCGCTCTGC 60.037 55.000 0.00 0.0 0.00 4.26 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
46 47 6.672593 ACCTTATTAAGAGGAATTGGCATGA 58.327 36.000 13.15 0.00 37.72 3.07
284 285 7.661437 TCGCTTTGGCTATGTAGAAATGATAAT 59.339 33.333 0.00 0.00 36.09 1.28
315 316 6.295719 ACGATAAAAGTACTTCCCTGATGT 57.704 37.500 8.95 0.00 0.00 3.06
368 369 4.430908 GTTTATGGTCCTCTCTACAACGG 58.569 47.826 0.00 0.00 0.00 4.44
440 441 2.092807 GGCGAGGGATACTTTTACCCAA 60.093 50.000 0.00 0.00 45.43 4.12
658 661 7.787725 AAAAATTAAGCGTCTACCCTCTATG 57.212 36.000 0.00 0.00 0.00 2.23
659 662 6.726490 AAATTAAGCGTCTACCCTCTATGA 57.274 37.500 0.00 0.00 0.00 2.15
660 663 6.726490 AATTAAGCGTCTACCCTCTATGAA 57.274 37.500 0.00 0.00 0.00 2.57
661 664 6.919775 ATTAAGCGTCTACCCTCTATGAAT 57.080 37.500 0.00 0.00 0.00 2.57
662 665 8.418597 AATTAAGCGTCTACCCTCTATGAATA 57.581 34.615 0.00 0.00 0.00 1.75
663 666 7.828508 TTAAGCGTCTACCCTCTATGAATAA 57.171 36.000 0.00 0.00 0.00 1.40
664 667 5.968528 AGCGTCTACCCTCTATGAATAAG 57.031 43.478 0.00 0.00 0.00 1.73
665 668 4.218852 AGCGTCTACCCTCTATGAATAAGC 59.781 45.833 0.00 0.00 0.00 3.09
666 669 4.022242 GCGTCTACCCTCTATGAATAAGCA 60.022 45.833 0.00 0.00 0.00 3.91
667 670 5.462405 CGTCTACCCTCTATGAATAAGCAC 58.538 45.833 0.00 0.00 0.00 4.40
668 671 5.241949 CGTCTACCCTCTATGAATAAGCACT 59.758 44.000 0.00 0.00 0.00 4.40
669 672 6.451393 GTCTACCCTCTATGAATAAGCACTG 58.549 44.000 0.00 0.00 0.00 3.66
670 673 4.078639 ACCCTCTATGAATAAGCACTGC 57.921 45.455 0.00 0.00 0.00 4.40
671 674 3.713764 ACCCTCTATGAATAAGCACTGCT 59.286 43.478 0.00 0.00 42.56 4.24
672 675 4.063689 CCCTCTATGAATAAGCACTGCTG 58.936 47.826 3.73 0.00 39.62 4.41
673 676 3.497640 CCTCTATGAATAAGCACTGCTGC 59.502 47.826 3.73 0.00 44.63 5.25
707 710 9.771534 ATACTGATTTATTTCTCTAAGCACCTC 57.228 33.333 0.00 0.00 0.00 3.85
708 711 7.624549 ACTGATTTATTTCTCTAAGCACCTCA 58.375 34.615 0.00 0.00 0.00 3.86
709 712 7.550906 ACTGATTTATTTCTCTAAGCACCTCAC 59.449 37.037 0.00 0.00 0.00 3.51
710 713 6.823689 TGATTTATTTCTCTAAGCACCTCACC 59.176 38.462 0.00 0.00 0.00 4.02
711 714 6.374417 TTTATTTCTCTAAGCACCTCACCT 57.626 37.500 0.00 0.00 0.00 4.00
712 715 7.490657 TTTATTTCTCTAAGCACCTCACCTA 57.509 36.000 0.00 0.00 0.00 3.08
713 716 7.490657 TTATTTCTCTAAGCACCTCACCTAA 57.509 36.000 0.00 0.00 0.00 2.69
714 717 5.407407 TTTCTCTAAGCACCTCACCTAAG 57.593 43.478 0.00 0.00 0.00 2.18
715 718 2.761208 TCTCTAAGCACCTCACCTAAGC 59.239 50.000 0.00 0.00 0.00 3.09
716 719 1.476891 TCTAAGCACCTCACCTAAGCG 59.523 52.381 0.00 0.00 0.00 4.68
717 720 0.108329 TAAGCACCTCACCTAAGCGC 60.108 55.000 0.00 0.00 0.00 5.92
718 721 2.804828 AAGCACCTCACCTAAGCGCC 62.805 60.000 2.29 0.00 0.00 6.53
719 722 2.982130 CACCTCACCTAAGCGCCT 59.018 61.111 2.29 0.00 0.00 5.52
720 723 1.296715 CACCTCACCTAAGCGCCTT 59.703 57.895 2.29 0.00 0.00 4.35
721 724 1.021390 CACCTCACCTAAGCGCCTTG 61.021 60.000 2.29 0.00 0.00 3.61
722 725 2.109126 CCTCACCTAAGCGCCTTGC 61.109 63.158 2.29 0.00 46.98 4.01
733 736 2.405892 GCGCCTTGCATTGTATAAGG 57.594 50.000 0.00 10.32 45.45 2.69
740 743 6.463995 CCTTGCATTGTATAAGGCCTTAAA 57.536 37.500 28.50 18.56 42.60 1.52
741 744 6.507023 CCTTGCATTGTATAAGGCCTTAAAG 58.493 40.000 28.50 21.75 42.60 1.85
742 745 6.096846 CCTTGCATTGTATAAGGCCTTAAAGT 59.903 38.462 28.50 15.21 42.60 2.66
743 746 7.363793 CCTTGCATTGTATAAGGCCTTAAAGTT 60.364 37.037 28.50 14.85 42.60 2.66
744 747 7.475137 TGCATTGTATAAGGCCTTAAAGTTT 57.525 32.000 28.50 14.47 42.60 2.66
745 748 7.543756 TGCATTGTATAAGGCCTTAAAGTTTC 58.456 34.615 28.50 14.98 42.60 2.78
746 749 6.978659 GCATTGTATAAGGCCTTAAAGTTTCC 59.021 38.462 28.50 11.82 37.62 3.13
747 750 7.147897 GCATTGTATAAGGCCTTAAAGTTTCCT 60.148 37.037 28.50 12.30 37.62 3.36
748 751 8.749354 CATTGTATAAGGCCTTAAAGTTTCCTT 58.251 33.333 28.50 11.58 40.05 3.36
749 752 7.696992 TGTATAAGGCCTTAAAGTTTCCTTG 57.303 36.000 28.50 0.00 37.66 3.61
750 753 7.463431 TGTATAAGGCCTTAAAGTTTCCTTGA 58.537 34.615 28.50 3.59 37.66 3.02
751 754 7.945664 TGTATAAGGCCTTAAAGTTTCCTTGAA 59.054 33.333 28.50 3.11 37.66 2.69
752 755 5.531122 AAGGCCTTAAAGTTTCCTTGAAC 57.469 39.130 18.87 0.00 35.95 3.18
753 756 4.804597 AGGCCTTAAAGTTTCCTTGAACT 58.195 39.130 0.00 0.00 41.44 3.01
754 757 4.584743 AGGCCTTAAAGTTTCCTTGAACTG 59.415 41.667 0.00 0.00 39.68 3.16
755 758 4.341235 GGCCTTAAAGTTTCCTTGAACTGT 59.659 41.667 0.00 0.00 39.68 3.55
756 759 5.281727 GCCTTAAAGTTTCCTTGAACTGTG 58.718 41.667 0.00 0.00 39.68 3.66
757 760 5.163550 GCCTTAAAGTTTCCTTGAACTGTGT 60.164 40.000 0.00 0.00 39.68 3.72
758 761 6.627287 GCCTTAAAGTTTCCTTGAACTGTGTT 60.627 38.462 0.00 0.00 39.68 3.32
759 762 7.320399 CCTTAAAGTTTCCTTGAACTGTGTTT 58.680 34.615 0.00 0.00 39.68 2.83
760 763 7.817478 CCTTAAAGTTTCCTTGAACTGTGTTTT 59.183 33.333 0.00 0.00 39.68 2.43
761 764 9.203421 CTTAAAGTTTCCTTGAACTGTGTTTTT 57.797 29.630 0.00 0.00 39.68 1.94
800 804 4.259650 CGCGCGAATGTTTAGTAGAAATGA 60.260 41.667 28.94 0.00 0.00 2.57
806 810 6.750501 CGAATGTTTAGTAGAAATGAGTCCGA 59.249 38.462 0.00 0.00 0.00 4.55
811 815 8.525316 TGTTTAGTAGAAATGAGTCCGATTGTA 58.475 33.333 0.00 0.00 0.00 2.41
816 820 5.053145 AGAAATGAGTCCGATTGTAGATGC 58.947 41.667 0.00 0.00 0.00 3.91
819 823 3.291584 TGAGTCCGATTGTAGATGCTCT 58.708 45.455 0.00 0.00 0.00 4.09
820 824 3.316588 TGAGTCCGATTGTAGATGCTCTC 59.683 47.826 0.00 0.00 0.00 3.20
826 830 5.948758 TCCGATTGTAGATGCTCTCATAGAT 59.051 40.000 0.00 0.00 31.96 1.98
829 833 4.797800 TGTAGATGCTCTCATAGATGCC 57.202 45.455 0.00 0.00 31.96 4.40
875 879 2.658548 ACACCTGTGATCAGCTCGA 58.341 52.632 3.94 0.00 40.09 4.04
929 1403 4.072088 GCGTCGGTGGCTTCGTTG 62.072 66.667 0.00 0.00 0.00 4.10
957 1439 3.577667 TCAATTCAGAGCCGCAAAAATG 58.422 40.909 0.00 0.00 0.00 2.32
1082 1567 4.017126 CCACCAGTGACAGACATCTACTA 58.983 47.826 0.00 0.00 0.00 1.82
1083 1568 4.097135 CCACCAGTGACAGACATCTACTAG 59.903 50.000 0.00 0.00 0.00 2.57
1085 1570 3.696548 CCAGTGACAGACATCTACTAGCA 59.303 47.826 0.00 0.00 0.00 3.49
1112 1684 4.061596 GCACACAGATTAATCCCTAGAGC 58.938 47.826 11.92 6.29 0.00 4.09
1113 1685 4.202305 GCACACAGATTAATCCCTAGAGCT 60.202 45.833 11.92 0.00 0.00 4.09
1114 1686 5.011125 GCACACAGATTAATCCCTAGAGCTA 59.989 44.000 11.92 0.00 0.00 3.32
1115 1687 6.686630 CACACAGATTAATCCCTAGAGCTAG 58.313 44.000 11.92 0.00 0.00 3.42
1116 1688 6.491745 CACACAGATTAATCCCTAGAGCTAGA 59.508 42.308 11.92 0.00 35.21 2.43
1117 1689 6.719370 ACACAGATTAATCCCTAGAGCTAGAG 59.281 42.308 11.92 0.00 35.21 2.43
1206 1795 6.519679 AAATAGTTAAAAATCCCCACGGAC 57.480 37.500 0.00 0.00 42.48 4.79
1371 1966 0.949105 GCCACCTATGCGTAATCCCG 60.949 60.000 0.00 0.00 0.00 5.14
1424 2019 4.222847 GCCGACGTCTCCATCCCC 62.223 72.222 14.70 0.00 0.00 4.81
1445 2040 2.498726 CCGCCTCTCTGCCTTCTC 59.501 66.667 0.00 0.00 0.00 2.87
1461 2056 2.282251 TCGTCTCCTCACAGCCGT 60.282 61.111 0.00 0.00 0.00 5.68
1525 2122 3.893753 TTCCAGGTGAAAAATCCCTCA 57.106 42.857 0.00 0.00 0.00 3.86
1526 2123 3.439857 TCCAGGTGAAAAATCCCTCAG 57.560 47.619 0.00 0.00 0.00 3.35
1528 2125 3.084786 CCAGGTGAAAAATCCCTCAGTC 58.915 50.000 0.00 0.00 0.00 3.51
1531 2128 4.829492 CAGGTGAAAAATCCCTCAGTCTTT 59.171 41.667 0.00 0.00 0.00 2.52
1532 2129 5.302823 CAGGTGAAAAATCCCTCAGTCTTTT 59.697 40.000 0.00 0.00 0.00 2.27
1533 2130 5.899547 AGGTGAAAAATCCCTCAGTCTTTTT 59.100 36.000 0.00 0.00 34.46 1.94
1534 2131 7.014230 CAGGTGAAAAATCCCTCAGTCTTTTTA 59.986 37.037 0.00 0.00 32.56 1.52
1535 2132 7.563556 AGGTGAAAAATCCCTCAGTCTTTTTAA 59.436 33.333 0.00 0.00 32.56 1.52
1536 2133 8.201464 GGTGAAAAATCCCTCAGTCTTTTTAAA 58.799 33.333 0.00 0.00 32.56 1.52
1537 2134 9.249457 GTGAAAAATCCCTCAGTCTTTTTAAAG 57.751 33.333 0.00 0.00 32.56 1.85
1538 2135 9.196139 TGAAAAATCCCTCAGTCTTTTTAAAGA 57.804 29.630 0.89 0.89 42.41 2.52
1585 2182 6.655062 GCTAAATTTGGCCAAGTTTTTGTAC 58.345 36.000 34.97 20.00 33.31 2.90
1647 2245 2.819608 TGAATTCCAGCTAAAGTGCCAC 59.180 45.455 2.27 0.00 0.00 5.01
1653 2251 2.554344 CCAGCTAAAGTGCCACCCTTTA 60.554 50.000 0.00 0.00 34.20 1.85
1721 2322 5.594317 CCCACGGATTGATAGGATTCTTTTT 59.406 40.000 0.00 0.00 0.00 1.94
1761 2362 1.378119 CTACCGAGGTTTTGGGGCC 60.378 63.158 0.00 0.00 31.40 5.80
1844 2464 5.047872 TGTGTGCTACATTTGAATGAATGCT 60.048 36.000 10.48 0.00 39.97 3.79
1845 2465 6.150809 TGTGTGCTACATTTGAATGAATGCTA 59.849 34.615 10.48 3.59 39.97 3.49
1846 2466 6.690098 GTGTGCTACATTTGAATGAATGCTAG 59.310 38.462 10.48 3.14 39.97 3.42
1886 2506 5.746990 ATTGTTCTGTTCCTACTACTGCT 57.253 39.130 0.00 0.00 0.00 4.24
1893 2513 6.188407 TCTGTTCCTACTACTGCTCAGTTAT 58.812 40.000 7.92 0.01 42.54 1.89
2013 2633 3.960102 AGGTTTTGAGTTCTCATTTGGCA 59.040 39.130 3.28 0.00 0.00 4.92
2062 2683 3.555966 CACCAAAGGAAAGGAAGTCTGT 58.444 45.455 0.00 0.00 0.00 3.41
2168 2789 2.034687 AGTGTGGTGCTGATGGCC 59.965 61.111 0.00 0.00 40.92 5.36
2363 2986 3.703420 GATGAATGGACTGATTGCTTGC 58.297 45.455 0.00 0.00 0.00 4.01
2365 2990 1.135721 GAATGGACTGATTGCTTGCCC 59.864 52.381 0.00 0.00 0.00 5.36
2389 3015 5.269991 TGCATCCTGGTAGTTAGACTAGTT 58.730 41.667 0.00 0.00 30.12 2.24
2394 3020 7.607615 TCCTGGTAGTTAGACTAGTTTTTGT 57.392 36.000 0.00 0.00 30.12 2.83
2403 3029 5.023533 AGACTAGTTTTTGTCAGTGCTGA 57.976 39.130 0.00 0.00 35.81 4.26
2413 3039 9.463443 GTTTTTGTCAGTGCTGATTTTATTACT 57.537 29.630 5.11 0.00 42.18 2.24
2533 3448 7.282224 TGCTTGACCCAATCTATATGTGTTAAC 59.718 37.037 0.00 0.00 0.00 2.01
2756 3671 2.868583 CGGATTCAAGGCTGTGATAGTG 59.131 50.000 0.00 0.00 0.00 2.74
2772 3687 9.586435 CTGTGATAGTGTATGATAACAAAGACA 57.414 33.333 0.00 0.00 0.00 3.41
2803 3718 7.139392 GTCCTTGTTTCAAGTAATGTTCCTTC 58.861 38.462 8.37 0.00 0.00 3.46
2824 3739 3.652869 TCACTTCTCCTTTTGGTCCTGAT 59.347 43.478 0.00 0.00 41.38 2.90
2952 3867 5.128008 AGAGGTCAGAGGAATAACAAGTAGC 59.872 44.000 0.00 0.00 0.00 3.58
3221 4136 5.763088 CTCATCCGGTATCGACATATATGG 58.237 45.833 16.96 0.39 39.00 2.74
3222 4137 5.442391 TCATCCGGTATCGACATATATGGA 58.558 41.667 16.96 5.96 39.00 3.41
3303 4218 5.104569 TGCTCAGGTGTGGATAATATCAACA 60.105 40.000 6.38 6.38 40.82 3.33
3324 4239 3.990469 CACGTGATAACTCAGCTTTGTCT 59.010 43.478 10.90 0.00 30.18 3.41
3662 4577 6.005823 TGCATAATAGGATCTGATGGTTTGG 58.994 40.000 0.00 0.00 0.00 3.28
3727 4642 8.293699 TCTGTCTACTAGTCATTGCTGATTTA 57.706 34.615 0.00 0.00 32.98 1.40
3781 4696 7.584122 TTACTACCAGAATAGTAGCAAGAGG 57.416 40.000 0.00 0.00 40.77 3.69
3806 4721 5.996219 TGGTGTCATTGATCAAAACTTACG 58.004 37.500 13.09 0.00 0.00 3.18
3849 4764 9.130661 TCCACATAATATCCCTTTGTATGTTTG 57.869 33.333 0.00 0.00 34.07 2.93
3850 4765 9.130661 CCACATAATATCCCTTTGTATGTTTGA 57.869 33.333 0.00 0.00 34.07 2.69
3939 4856 8.942338 ATAAATCTACACTGCGAATTCTACAA 57.058 30.769 3.52 0.00 0.00 2.41
3988 4905 4.532521 ACTGCTACTGAACCCTCTGTTATT 59.467 41.667 0.00 0.00 37.29 1.40
4001 4918 6.207614 ACCCTCTGTTATTTCAAGCTTTCTTC 59.792 38.462 0.00 0.00 0.00 2.87
4002 4919 6.432472 CCCTCTGTTATTTCAAGCTTTCTTCT 59.568 38.462 0.00 0.00 0.00 2.85
4003 4920 7.040132 CCCTCTGTTATTTCAAGCTTTCTTCTT 60.040 37.037 0.00 0.00 0.00 2.52
4429 5346 2.046023 CTCCGCACCTTGCATCCA 60.046 61.111 0.00 0.00 45.36 3.41
4700 5617 3.771160 GGATGGTGGCGACTCGGT 61.771 66.667 0.00 0.00 0.00 4.69
4775 5692 0.313043 CATTGCCCCGATTCTGATGC 59.687 55.000 0.00 0.00 0.00 3.91
4806 5723 4.057428 GCGACGTCAGCCCAGTCT 62.057 66.667 17.16 0.00 33.10 3.24
4847 5764 4.148838 CCCTTACAGGTTCACCATTGAAA 58.851 43.478 0.00 0.00 43.52 2.69
4880 5797 6.611642 AGACCTGTTACCATAGAATAAGCTCA 59.388 38.462 0.00 0.00 0.00 4.26
4887 5804 6.252599 ACCATAGAATAAGCTCACCATGAA 57.747 37.500 0.00 0.00 0.00 2.57
4889 5806 6.126652 ACCATAGAATAAGCTCACCATGAAGT 60.127 38.462 0.00 0.00 0.00 3.01
4890 5807 6.769822 CCATAGAATAAGCTCACCATGAAGTT 59.230 38.462 0.00 0.00 0.00 2.66
4909 5826 0.742990 TTTCATCGGTCGCCACCATC 60.743 55.000 0.16 0.00 44.02 3.51
4910 5827 2.899345 TTCATCGGTCGCCACCATCG 62.899 60.000 0.16 0.00 44.02 3.84
4920 5837 1.215382 CCACCATCGAGTGAAGCGA 59.785 57.895 6.39 0.00 40.34 4.93
4949 5866 1.604593 GCAAAAGGGAGCTGCCTGA 60.605 57.895 29.25 0.00 36.66 3.86
4952 5869 1.688197 CAAAAGGGAGCTGCCTGAAAA 59.312 47.619 29.25 0.00 36.66 2.29
4994 5911 5.070685 GGTGACCTTTAATCTGACCAACTT 58.929 41.667 0.00 0.00 0.00 2.66
4995 5912 5.048713 GGTGACCTTTAATCTGACCAACTTG 60.049 44.000 0.00 0.00 0.00 3.16
4996 5913 4.518970 TGACCTTTAATCTGACCAACTTGC 59.481 41.667 0.00 0.00 0.00 4.01
4997 5914 4.729868 ACCTTTAATCTGACCAACTTGCT 58.270 39.130 0.00 0.00 0.00 3.91
4998 5915 4.762251 ACCTTTAATCTGACCAACTTGCTC 59.238 41.667 0.00 0.00 0.00 4.26
4999 5916 4.142816 CCTTTAATCTGACCAACTTGCTCG 60.143 45.833 0.00 0.00 0.00 5.03
5000 5917 1.813513 AATCTGACCAACTTGCTCGG 58.186 50.000 0.00 0.00 0.00 4.63
5001 5918 0.976641 ATCTGACCAACTTGCTCGGA 59.023 50.000 0.00 0.00 0.00 4.55
5002 5919 0.756294 TCTGACCAACTTGCTCGGAA 59.244 50.000 0.00 0.00 0.00 4.30
5003 5920 0.868406 CTGACCAACTTGCTCGGAAC 59.132 55.000 0.00 0.00 0.00 3.62
5004 5921 0.534203 TGACCAACTTGCTCGGAACC 60.534 55.000 0.00 0.00 0.00 3.62
5005 5922 0.250338 GACCAACTTGCTCGGAACCT 60.250 55.000 0.00 0.00 0.00 3.50
5006 5923 0.182775 ACCAACTTGCTCGGAACCTT 59.817 50.000 0.00 0.00 0.00 3.50
5007 5924 0.593128 CCAACTTGCTCGGAACCTTG 59.407 55.000 0.00 0.00 0.00 3.61
5008 5925 1.593196 CAACTTGCTCGGAACCTTGA 58.407 50.000 0.00 0.00 0.00 3.02
5009 5926 1.946768 CAACTTGCTCGGAACCTTGAA 59.053 47.619 0.00 0.00 0.00 2.69
5010 5927 1.884235 ACTTGCTCGGAACCTTGAAG 58.116 50.000 0.00 0.00 0.00 3.02
5011 5928 1.416401 ACTTGCTCGGAACCTTGAAGA 59.584 47.619 0.00 0.00 0.00 2.87
5012 5929 1.801178 CTTGCTCGGAACCTTGAAGAC 59.199 52.381 0.00 0.00 0.00 3.01
5013 5930 1.048601 TGCTCGGAACCTTGAAGACT 58.951 50.000 0.00 0.00 0.00 3.24
5014 5931 1.270305 TGCTCGGAACCTTGAAGACTG 60.270 52.381 0.00 0.00 0.00 3.51
5015 5932 1.941668 GCTCGGAACCTTGAAGACTGG 60.942 57.143 0.00 0.00 0.00 4.00
5016 5933 1.618837 CTCGGAACCTTGAAGACTGGA 59.381 52.381 0.00 0.00 0.00 3.86
5017 5934 2.037251 CTCGGAACCTTGAAGACTGGAA 59.963 50.000 0.00 0.00 0.00 3.53
5018 5935 2.436542 TCGGAACCTTGAAGACTGGAAA 59.563 45.455 0.00 0.00 0.00 3.13
5019 5936 3.072476 TCGGAACCTTGAAGACTGGAAAT 59.928 43.478 0.00 0.00 0.00 2.17
5020 5937 3.189287 CGGAACCTTGAAGACTGGAAATG 59.811 47.826 0.00 0.00 0.00 2.32
5021 5938 4.398319 GGAACCTTGAAGACTGGAAATGA 58.602 43.478 0.00 0.00 0.00 2.57
5022 5939 4.216472 GGAACCTTGAAGACTGGAAATGAC 59.784 45.833 0.00 0.00 0.00 3.06
5023 5940 4.713792 ACCTTGAAGACTGGAAATGACT 57.286 40.909 0.00 0.00 0.00 3.41
5024 5941 4.646572 ACCTTGAAGACTGGAAATGACTC 58.353 43.478 0.00 0.00 0.00 3.36
5025 5942 4.349342 ACCTTGAAGACTGGAAATGACTCT 59.651 41.667 0.00 0.00 0.00 3.24
5026 5943 4.694509 CCTTGAAGACTGGAAATGACTCTG 59.305 45.833 0.00 0.00 0.00 3.35
5027 5944 3.668447 TGAAGACTGGAAATGACTCTGC 58.332 45.455 0.00 0.00 0.00 4.26
5028 5945 3.326006 TGAAGACTGGAAATGACTCTGCT 59.674 43.478 0.00 0.00 0.00 4.24
5029 5946 3.331478 AGACTGGAAATGACTCTGCTG 57.669 47.619 0.00 0.00 0.00 4.41
5030 5947 2.902486 AGACTGGAAATGACTCTGCTGA 59.098 45.455 0.00 0.00 0.00 4.26
5031 5948 2.999355 GACTGGAAATGACTCTGCTGAC 59.001 50.000 0.00 0.00 0.00 3.51
5032 5949 2.289945 ACTGGAAATGACTCTGCTGACC 60.290 50.000 0.00 0.00 0.00 4.02
5033 5950 1.699083 TGGAAATGACTCTGCTGACCA 59.301 47.619 0.00 0.00 0.00 4.02
5034 5951 2.079925 GGAAATGACTCTGCTGACCAC 58.920 52.381 0.00 0.00 0.00 4.16
5035 5952 2.550855 GGAAATGACTCTGCTGACCACA 60.551 50.000 0.00 0.00 0.00 4.17
5036 5953 3.341823 GAAATGACTCTGCTGACCACAT 58.658 45.455 0.00 0.00 0.00 3.21
5037 5954 3.430042 AATGACTCTGCTGACCACATT 57.570 42.857 0.00 0.00 0.00 2.71
5038 5955 2.174363 TGACTCTGCTGACCACATTG 57.826 50.000 0.00 0.00 0.00 2.82
5039 5956 1.693606 TGACTCTGCTGACCACATTGA 59.306 47.619 0.00 0.00 0.00 2.57
5040 5957 2.289257 TGACTCTGCTGACCACATTGAG 60.289 50.000 0.00 0.00 0.00 3.02
5041 5958 1.696336 ACTCTGCTGACCACATTGAGT 59.304 47.619 0.00 0.00 0.00 3.41
5042 5959 2.105477 ACTCTGCTGACCACATTGAGTT 59.895 45.455 0.00 0.00 31.33 3.01
5043 5960 3.144506 CTCTGCTGACCACATTGAGTTT 58.855 45.455 0.00 0.00 0.00 2.66
5135 6105 4.629200 GGATCTGTTAGTTGCAGTCAGAAG 59.371 45.833 10.56 0.00 38.38 2.85
5227 6199 5.006153 TCGTTCTCACTCTGTTTTGAAGA 57.994 39.130 0.00 0.00 0.00 2.87
5348 6320 0.104120 GGTTTTTGGTTGCCTTCGCT 59.896 50.000 0.00 0.00 35.36 4.93
5353 6325 2.217429 TTGGTTGCCTTCGCTTTTTC 57.783 45.000 0.00 0.00 35.36 2.29
5363 6335 3.417185 CTTCGCTTTTTCGTATTGGAGC 58.583 45.455 0.00 0.00 0.00 4.70
5364 6336 1.735571 TCGCTTTTTCGTATTGGAGCC 59.264 47.619 0.00 0.00 0.00 4.70
5365 6337 1.202143 CGCTTTTTCGTATTGGAGCCC 60.202 52.381 0.00 0.00 0.00 5.19
5433 6405 1.151777 CTGCGTGCCCTAACCATACG 61.152 60.000 0.00 0.00 37.77 3.06
5517 6491 9.583765 GGTACACCTAAGACTGTAAAAAGATAG 57.416 37.037 0.00 0.00 0.00 2.08
5550 6524 1.620323 GATTGGGGCAACTGAAGCTTT 59.380 47.619 0.00 0.00 0.00 3.51
5554 6528 0.540597 GGGCAACTGAAGCTTTCCCT 60.541 55.000 0.00 0.00 0.00 4.20
5653 6640 8.862325 TCCTTCTTGAAATCTTAGTGCAAATA 57.138 30.769 0.00 0.00 0.00 1.40
5770 6758 2.289382 TGGCGATTCTGACTTTGCACTA 60.289 45.455 0.00 0.00 0.00 2.74
5905 6914 7.180229 TCAGGATAACTTGAACTTAGATGGTGA 59.820 37.037 0.00 0.00 0.00 4.02
5931 6940 2.093447 CCAATCTACTCTTTCAGCGGGT 60.093 50.000 0.00 0.00 0.00 5.28
6037 7314 3.390521 CGGTGCTGCCTCAGGGTA 61.391 66.667 0.00 0.00 34.25 3.69
6049 7326 0.898326 TCAGGGTAGCTCAGTTGCGA 60.898 55.000 0.00 0.00 38.13 5.10
6074 7351 3.376078 CACATGTGCACTGGCCCC 61.376 66.667 19.41 0.00 40.13 5.80
6128 7405 0.481567 AGCTAGTCCGCCAGGGTATA 59.518 55.000 0.00 0.00 38.33 1.47
6131 7408 2.803956 CTAGTCCGCCAGGGTATATGA 58.196 52.381 0.00 0.00 38.33 2.15
6136 7413 0.667487 CGCCAGGGTATATGACTGCG 60.667 60.000 0.00 0.00 0.00 5.18
6138 7415 0.392706 CCAGGGTATATGACTGCGCA 59.607 55.000 10.98 10.98 0.00 6.09
6163 7440 1.534729 GAAGTACAAGGTGGCTTGGG 58.465 55.000 0.00 0.00 38.55 4.12
6230 7507 1.137513 GGCGTTCGTGATGGCTATAC 58.862 55.000 0.00 0.00 36.91 1.47
6285 7562 0.107508 CTCGCCTCCATGGTGTCATT 60.108 55.000 12.58 0.00 46.10 2.57
6295 7572 0.107643 TGGTGTCATTGTGGCTCGAA 59.892 50.000 0.00 0.00 0.00 3.71
6314 7591 4.338118 TCGAACAAAGACTCAAATTTGGCT 59.662 37.500 17.90 10.17 40.05 4.75
6316 7593 5.343307 AACAAAGACTCAAATTTGGCTGT 57.657 34.783 17.90 13.67 40.05 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 3.130340 ACAAAAGACACATTGCGGACTTT 59.870 39.130 0.00 0.00 0.00 2.66
284 285 9.341078 AGGGAAGTACTTTTATCGTTAAAAACA 57.659 29.630 10.02 1.89 36.97 2.83
315 316 4.458397 CCGGTACATCTGTAGAGAACCTA 58.542 47.826 7.44 0.00 0.00 3.08
368 369 1.187087 ACAGGTCTCGATTCTCCACC 58.813 55.000 0.00 0.00 0.00 4.61
440 441 1.006281 AGATCATGTTGCCACCCATGT 59.994 47.619 0.00 0.00 39.53 3.21
556 558 2.566833 ACTAAGATGCACACAGCCAA 57.433 45.000 0.00 0.00 44.83 4.52
639 642 7.523380 GCTTATTCATAGAGGGTAGACGCTTAA 60.523 40.741 0.33 0.00 39.39 1.85
640 643 6.072064 GCTTATTCATAGAGGGTAGACGCTTA 60.072 42.308 0.33 0.00 39.39 3.09
641 644 5.279056 GCTTATTCATAGAGGGTAGACGCTT 60.279 44.000 0.33 0.00 39.39 4.68
642 645 4.218852 GCTTATTCATAGAGGGTAGACGCT 59.781 45.833 0.00 0.00 42.17 5.07
643 646 4.022242 TGCTTATTCATAGAGGGTAGACGC 60.022 45.833 0.00 0.00 0.00 5.19
644 647 5.241949 AGTGCTTATTCATAGAGGGTAGACG 59.758 44.000 0.00 0.00 0.00 4.18
645 648 6.451393 CAGTGCTTATTCATAGAGGGTAGAC 58.549 44.000 0.00 0.00 0.00 2.59
646 649 5.011125 GCAGTGCTTATTCATAGAGGGTAGA 59.989 44.000 8.18 0.00 0.00 2.59
647 650 5.011533 AGCAGTGCTTATTCATAGAGGGTAG 59.988 44.000 13.14 0.00 33.89 3.18
648 651 4.901849 AGCAGTGCTTATTCATAGAGGGTA 59.098 41.667 13.14 0.00 33.89 3.69
649 652 3.713764 AGCAGTGCTTATTCATAGAGGGT 59.286 43.478 13.14 0.00 33.89 4.34
650 653 4.063689 CAGCAGTGCTTATTCATAGAGGG 58.936 47.826 16.89 0.00 36.40 4.30
681 684 9.771534 GAGGTGCTTAGAGAAATAAATCAGTAT 57.228 33.333 0.00 0.00 0.00 2.12
682 685 8.758829 TGAGGTGCTTAGAGAAATAAATCAGTA 58.241 33.333 0.00 0.00 0.00 2.74
683 686 7.550906 GTGAGGTGCTTAGAGAAATAAATCAGT 59.449 37.037 0.00 0.00 0.00 3.41
684 687 7.011857 GGTGAGGTGCTTAGAGAAATAAATCAG 59.988 40.741 0.00 0.00 0.00 2.90
685 688 6.823689 GGTGAGGTGCTTAGAGAAATAAATCA 59.176 38.462 0.00 0.00 0.00 2.57
686 689 7.051000 AGGTGAGGTGCTTAGAGAAATAAATC 58.949 38.462 0.00 0.00 0.00 2.17
687 690 6.963322 AGGTGAGGTGCTTAGAGAAATAAAT 58.037 36.000 0.00 0.00 0.00 1.40
688 691 6.374417 AGGTGAGGTGCTTAGAGAAATAAA 57.626 37.500 0.00 0.00 0.00 1.40
689 692 7.490657 TTAGGTGAGGTGCTTAGAGAAATAA 57.509 36.000 0.00 0.00 0.00 1.40
690 693 6.407074 GCTTAGGTGAGGTGCTTAGAGAAATA 60.407 42.308 0.00 0.00 0.00 1.40
691 694 5.627968 GCTTAGGTGAGGTGCTTAGAGAAAT 60.628 44.000 0.00 0.00 0.00 2.17
692 695 4.322801 GCTTAGGTGAGGTGCTTAGAGAAA 60.323 45.833 0.00 0.00 0.00 2.52
693 696 3.195825 GCTTAGGTGAGGTGCTTAGAGAA 59.804 47.826 0.00 0.00 0.00 2.87
694 697 2.761208 GCTTAGGTGAGGTGCTTAGAGA 59.239 50.000 0.00 0.00 0.00 3.10
695 698 2.480416 CGCTTAGGTGAGGTGCTTAGAG 60.480 54.545 0.00 0.00 0.00 2.43
696 699 1.476891 CGCTTAGGTGAGGTGCTTAGA 59.523 52.381 0.00 0.00 0.00 2.10
697 700 1.927895 CGCTTAGGTGAGGTGCTTAG 58.072 55.000 0.00 0.00 0.00 2.18
698 701 0.108329 GCGCTTAGGTGAGGTGCTTA 60.108 55.000 0.00 0.00 34.21 3.09
699 702 1.376037 GCGCTTAGGTGAGGTGCTT 60.376 57.895 0.00 0.00 34.21 3.91
700 703 2.266055 GCGCTTAGGTGAGGTGCT 59.734 61.111 0.00 0.00 34.21 4.40
701 704 2.804828 AAGGCGCTTAGGTGAGGTGC 62.805 60.000 7.64 0.00 35.98 5.01
702 705 1.021390 CAAGGCGCTTAGGTGAGGTG 61.021 60.000 7.64 0.00 0.00 4.00
703 706 1.296715 CAAGGCGCTTAGGTGAGGT 59.703 57.895 7.64 0.00 0.00 3.85
704 707 2.109126 GCAAGGCGCTTAGGTGAGG 61.109 63.158 7.64 0.00 37.77 3.86
705 708 0.745845 ATGCAAGGCGCTTAGGTGAG 60.746 55.000 7.64 0.00 43.06 3.51
706 709 0.322456 AATGCAAGGCGCTTAGGTGA 60.322 50.000 7.64 0.00 43.06 4.02
707 710 0.179156 CAATGCAAGGCGCTTAGGTG 60.179 55.000 7.64 0.00 43.06 4.00
708 711 0.609131 ACAATGCAAGGCGCTTAGGT 60.609 50.000 7.64 0.00 43.06 3.08
709 712 1.378531 TACAATGCAAGGCGCTTAGG 58.621 50.000 7.64 0.00 43.06 2.69
710 713 4.319766 CCTTATACAATGCAAGGCGCTTAG 60.320 45.833 7.64 0.00 43.06 2.18
711 714 3.563808 CCTTATACAATGCAAGGCGCTTA 59.436 43.478 7.64 0.00 43.06 3.09
712 715 2.358898 CCTTATACAATGCAAGGCGCTT 59.641 45.455 7.64 0.00 43.06 4.68
713 716 1.949525 CCTTATACAATGCAAGGCGCT 59.050 47.619 7.64 0.00 43.06 5.92
714 717 2.405892 CCTTATACAATGCAAGGCGC 57.594 50.000 0.00 0.00 42.89 6.53
717 720 6.096846 ACTTTAAGGCCTTATACAATGCAAGG 59.903 38.462 25.70 12.03 41.53 3.61
718 721 7.100458 ACTTTAAGGCCTTATACAATGCAAG 57.900 36.000 25.70 22.49 0.00 4.01
719 722 7.475137 AACTTTAAGGCCTTATACAATGCAA 57.525 32.000 25.70 13.04 0.00 4.08
720 723 7.363443 GGAAACTTTAAGGCCTTATACAATGCA 60.363 37.037 25.70 5.59 0.00 3.96
721 724 6.978659 GGAAACTTTAAGGCCTTATACAATGC 59.021 38.462 25.70 13.54 0.00 3.56
722 725 8.293699 AGGAAACTTTAAGGCCTTATACAATG 57.706 34.615 25.70 16.15 37.44 2.82
780 783 6.508088 CGGACTCATTTCTACTAAACATTCGC 60.508 42.308 0.00 0.00 0.00 4.70
785 788 7.383687 ACAATCGGACTCATTTCTACTAAACA 58.616 34.615 0.00 0.00 0.00 2.83
816 820 3.624861 GTGTTTGTGGGCATCTATGAGAG 59.375 47.826 0.00 0.00 0.00 3.20
819 823 2.290008 ACGTGTTTGTGGGCATCTATGA 60.290 45.455 0.00 0.00 0.00 2.15
820 824 2.083774 ACGTGTTTGTGGGCATCTATG 58.916 47.619 0.00 0.00 0.00 2.23
826 830 1.078072 AGACACGTGTTTGTGGGCA 60.078 52.632 24.26 0.00 44.21 5.36
829 833 3.548014 GGAATTCAGACACGTGTTTGTGG 60.548 47.826 31.07 16.34 44.21 4.17
875 879 1.675641 GGAACATTCAGGCCAGCGT 60.676 57.895 5.01 0.00 0.00 5.07
929 1403 2.478539 GCGGCTCTGAATTGATTTGTCC 60.479 50.000 0.00 0.00 0.00 4.02
957 1439 3.457234 TCATGGTATGTTGACGCTGATC 58.543 45.455 0.00 0.00 0.00 2.92
1082 1567 0.321564 TAATCTGTGTGCCGCTTGCT 60.322 50.000 0.00 0.00 42.00 3.91
1083 1568 0.521291 TTAATCTGTGTGCCGCTTGC 59.479 50.000 0.00 0.00 41.77 4.01
1085 1570 2.017049 GGATTAATCTGTGTGCCGCTT 58.983 47.619 14.95 0.00 0.00 4.68
1139 1711 1.817209 GACCTCGTCCTGGATCCAC 59.183 63.158 11.44 0.00 0.00 4.02
1206 1795 0.181114 TTTCCGCCCATCCATCTCTG 59.819 55.000 0.00 0.00 0.00 3.35
1265 1860 1.066152 GGGAATTGAAATCGCAGGCTC 59.934 52.381 0.00 0.00 0.00 4.70
1267 1862 0.817013 TGGGAATTGAAATCGCAGGC 59.183 50.000 0.00 0.00 35.17 4.85
1385 1980 3.774336 ATGGGAGGGGCGGGTAGA 61.774 66.667 0.00 0.00 0.00 2.59
1430 2025 1.140804 GACGAGAAGGCAGAGAGGC 59.859 63.158 0.00 0.00 44.61 4.70
1441 2036 2.268022 GGCTGTGAGGAGACGAGAA 58.732 57.895 0.00 0.00 0.00 2.87
1534 2131 9.311916 CTGACTTTCGAATCTAATCTGATCTTT 57.688 33.333 0.00 0.00 0.00 2.52
1535 2132 7.925483 CCTGACTTTCGAATCTAATCTGATCTT 59.075 37.037 0.00 0.00 0.00 2.40
1536 2133 7.432869 CCTGACTTTCGAATCTAATCTGATCT 58.567 38.462 0.00 0.00 0.00 2.75
1537 2134 6.145371 GCCTGACTTTCGAATCTAATCTGATC 59.855 42.308 0.00 0.00 0.00 2.92
1538 2135 5.988561 GCCTGACTTTCGAATCTAATCTGAT 59.011 40.000 0.00 0.00 0.00 2.90
1539 2136 5.127845 AGCCTGACTTTCGAATCTAATCTGA 59.872 40.000 0.00 0.00 0.00 3.27
1540 2137 5.355596 AGCCTGACTTTCGAATCTAATCTG 58.644 41.667 0.00 0.00 0.00 2.90
1585 2182 4.899239 GGCATCTGGCGACTCGGG 62.899 72.222 0.00 0.00 46.16 5.14
1647 2245 3.193479 AGAAAAGCAATTCGGCTAAAGGG 59.807 43.478 0.00 0.00 45.07 3.95
1721 2322 7.227910 GGTAGACTCCAAAATTATGCGGATAAA 59.772 37.037 13.61 0.00 0.00 1.40
1724 2325 5.063880 GGTAGACTCCAAAATTATGCGGAT 58.936 41.667 0.00 0.00 0.00 4.18
1761 2362 4.431131 ATGGGAGGCCGCAACCTG 62.431 66.667 9.31 0.00 41.32 4.00
1770 2378 3.359950 AGAAGATGTTTTCATGGGAGGC 58.640 45.455 0.00 0.00 41.05 4.70
1859 2479 8.630917 GCAGTAGTAGGAACAGAACAATATCTA 58.369 37.037 0.00 0.00 0.00 1.98
1860 2480 7.343316 AGCAGTAGTAGGAACAGAACAATATCT 59.657 37.037 0.00 0.00 0.00 1.98
1861 2481 7.493367 AGCAGTAGTAGGAACAGAACAATATC 58.507 38.462 0.00 0.00 0.00 1.63
1862 2482 7.124298 TGAGCAGTAGTAGGAACAGAACAATAT 59.876 37.037 0.00 0.00 0.00 1.28
1863 2483 6.436218 TGAGCAGTAGTAGGAACAGAACAATA 59.564 38.462 0.00 0.00 0.00 1.90
1864 2484 5.246203 TGAGCAGTAGTAGGAACAGAACAAT 59.754 40.000 0.00 0.00 0.00 2.71
1865 2485 4.587262 TGAGCAGTAGTAGGAACAGAACAA 59.413 41.667 0.00 0.00 0.00 2.83
1867 2487 4.218852 ACTGAGCAGTAGTAGGAACAGAAC 59.781 45.833 0.41 0.00 40.43 3.01
1868 2488 4.408276 ACTGAGCAGTAGTAGGAACAGAA 58.592 43.478 0.41 0.00 40.43 3.02
1869 2489 4.035612 ACTGAGCAGTAGTAGGAACAGA 57.964 45.455 0.41 0.00 40.43 3.41
1870 2490 4.792521 AACTGAGCAGTAGTAGGAACAG 57.207 45.455 3.21 0.00 41.58 3.16
2013 2633 0.759346 AGAAGAGCAAACACCGACCT 59.241 50.000 0.00 0.00 0.00 3.85
2062 2683 2.542020 TCTTGCACGGTTCATCTTGA 57.458 45.000 0.00 0.00 0.00 3.02
2168 2789 3.562141 TGAACGACAGGGTTGTGTTATTG 59.438 43.478 0.00 0.00 37.76 1.90
2363 2986 2.103263 GTCTAACTACCAGGATGCAGGG 59.897 54.545 0.00 0.00 31.97 4.45
2365 2990 4.890581 ACTAGTCTAACTACCAGGATGCAG 59.109 45.833 0.00 0.00 31.97 4.41
2389 3015 9.677567 GAAGTAATAAAATCAGCACTGACAAAA 57.322 29.630 1.71 0.00 43.11 2.44
2394 3020 8.621532 ACAAGAAGTAATAAAATCAGCACTGA 57.378 30.769 2.25 2.25 44.59 3.41
2413 3039 5.634439 GCATGTGCAAATTGTCATACAAGAA 59.366 36.000 0.00 0.00 40.30 2.52
2423 3338 8.550710 AACATTATAAAGCATGTGCAAATTGT 57.449 26.923 7.83 1.14 45.16 2.71
2464 3379 7.623770 CACATTATAAAGCATGTGGAAATTGC 58.376 34.615 8.46 0.00 44.47 3.56
2533 3448 9.840427 AATGTTCAAATACCAATAAGTTCTTCG 57.160 29.630 0.00 0.00 0.00 3.79
2553 3468 3.005155 ACTTCTGGAGCTGCAAAATGTTC 59.995 43.478 9.92 0.00 0.00 3.18
2756 3671 6.476243 ACACCGTTGTCTTTGTTATCATAC 57.524 37.500 0.00 0.00 0.00 2.39
2772 3687 2.718563 ACTTGAAACAAGGACACCGTT 58.281 42.857 14.51 0.00 0.00 4.44
2803 3718 3.492102 TCAGGACCAAAAGGAGAAGTG 57.508 47.619 0.00 0.00 0.00 3.16
2974 3889 7.753132 TGCGTCTAACCATTTAAATTTCATGAC 59.247 33.333 10.53 4.56 0.00 3.06
3303 4218 4.258702 AGACAAAGCTGAGTTATCACGT 57.741 40.909 0.00 0.00 0.00 4.49
3324 4239 6.016860 GTGCTGTGAAAGATATTGCCATGATA 60.017 38.462 0.00 0.00 0.00 2.15
3662 4577 4.040068 GCACAGGCATCGAGATCC 57.960 61.111 0.00 0.00 40.72 3.36
3727 4642 9.700831 AGCAAGTATATTCTAATTCCCAACTTT 57.299 29.630 0.00 0.00 0.00 2.66
3781 4696 6.742718 CGTAAGTTTTGATCAATGACACCATC 59.257 38.462 9.40 0.00 31.40 3.51
3850 4765 9.911788 AGACCATATTCAATTGAGTTTGTATCT 57.088 29.630 16.32 15.07 0.00 1.98
3949 4866 8.792633 TCAGTAGCAGTGCAATACTTAATTTTT 58.207 29.630 19.20 0.00 37.60 1.94
3966 4883 4.744795 ATAACAGAGGGTTCAGTAGCAG 57.255 45.455 0.00 0.00 40.96 4.24
4001 4918 6.272318 TCAGTGCACTGGTTGAAAAATAAAG 58.728 36.000 39.04 14.13 43.91 1.85
4002 4919 6.214191 TCAGTGCACTGGTTGAAAAATAAA 57.786 33.333 39.04 17.72 43.91 1.40
4003 4920 5.843673 TCAGTGCACTGGTTGAAAAATAA 57.156 34.783 39.04 17.91 43.91 1.40
4429 5346 4.954118 TCCACCCAGGGAGTGCGT 62.954 66.667 14.54 0.00 38.24 5.24
4700 5617 2.098280 GCTGAAGCTGATAGACTCGTCA 59.902 50.000 0.00 0.00 38.21 4.35
4775 5692 1.535636 CGTCGCAGCAGATAAGCTCG 61.536 60.000 0.00 0.00 44.54 5.03
4806 5723 1.001764 CAATCAGCACCCTGGCAGA 60.002 57.895 17.94 0.00 39.61 4.26
4887 5804 0.953960 GGTGGCGACCGATGAAAACT 60.954 55.000 0.71 0.00 30.61 2.66
4889 5806 0.322098 ATGGTGGCGACCGATGAAAA 60.322 50.000 13.67 0.00 46.62 2.29
4890 5807 0.742990 GATGGTGGCGACCGATGAAA 60.743 55.000 13.67 0.00 46.62 2.69
4899 5816 1.215382 CTTCACTCGATGGTGGCGA 59.785 57.895 5.11 0.00 37.75 5.54
4900 5817 2.456119 GCTTCACTCGATGGTGGCG 61.456 63.158 5.11 0.00 37.75 5.69
4902 5819 0.389817 TTCGCTTCACTCGATGGTGG 60.390 55.000 5.11 0.00 37.75 4.61
4909 5826 4.326413 TCATTCAAATTCGCTTCACTCG 57.674 40.909 0.00 0.00 0.00 4.18
4910 5827 4.094212 GCTCATTCAAATTCGCTTCACTC 58.906 43.478 0.00 0.00 0.00 3.51
4920 5837 4.285260 AGCTCCCTTTTGCTCATTCAAATT 59.715 37.500 0.00 0.00 36.04 1.82
4952 5869 4.708421 TCACCGGTTCTAGCTAGTATGTTT 59.292 41.667 20.10 0.24 0.00 2.83
4955 5872 3.004524 GGTCACCGGTTCTAGCTAGTATG 59.995 52.174 20.10 6.52 0.00 2.39
4959 5876 1.765230 AGGTCACCGGTTCTAGCTAG 58.235 55.000 15.01 15.01 0.00 3.42
4960 5877 2.226962 AAGGTCACCGGTTCTAGCTA 57.773 50.000 2.97 0.00 0.00 3.32
4961 5878 1.349067 AAAGGTCACCGGTTCTAGCT 58.651 50.000 2.97 5.72 0.00 3.32
4962 5879 3.323751 TTAAAGGTCACCGGTTCTAGC 57.676 47.619 2.97 2.98 0.00 3.42
4994 5911 1.048601 AGTCTTCAAGGTTCCGAGCA 58.951 50.000 0.00 0.00 0.00 4.26
4995 5912 1.433534 CAGTCTTCAAGGTTCCGAGC 58.566 55.000 0.00 0.00 0.00 5.03
4996 5913 1.618837 TCCAGTCTTCAAGGTTCCGAG 59.381 52.381 0.00 0.00 0.00 4.63
4997 5914 1.712056 TCCAGTCTTCAAGGTTCCGA 58.288 50.000 0.00 0.00 0.00 4.55
4998 5915 2.543777 TTCCAGTCTTCAAGGTTCCG 57.456 50.000 0.00 0.00 0.00 4.30
4999 5916 4.216472 GTCATTTCCAGTCTTCAAGGTTCC 59.784 45.833 0.00 0.00 0.00 3.62
5000 5917 5.066593 AGTCATTTCCAGTCTTCAAGGTTC 58.933 41.667 0.00 0.00 0.00 3.62
5001 5918 5.053978 AGTCATTTCCAGTCTTCAAGGTT 57.946 39.130 0.00 0.00 0.00 3.50
5002 5919 4.349342 AGAGTCATTTCCAGTCTTCAAGGT 59.651 41.667 0.00 0.00 0.00 3.50
5003 5920 4.694509 CAGAGTCATTTCCAGTCTTCAAGG 59.305 45.833 0.00 0.00 0.00 3.61
5004 5921 4.153835 GCAGAGTCATTTCCAGTCTTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
5005 5922 4.067896 GCAGAGTCATTTCCAGTCTTCAA 58.932 43.478 0.00 0.00 0.00 2.69
5006 5923 3.326006 AGCAGAGTCATTTCCAGTCTTCA 59.674 43.478 0.00 0.00 0.00 3.02
5007 5924 3.683822 CAGCAGAGTCATTTCCAGTCTTC 59.316 47.826 0.00 0.00 0.00 2.87
5008 5925 3.326006 TCAGCAGAGTCATTTCCAGTCTT 59.674 43.478 0.00 0.00 0.00 3.01
5009 5926 2.902486 TCAGCAGAGTCATTTCCAGTCT 59.098 45.455 0.00 0.00 0.00 3.24
5010 5927 2.999355 GTCAGCAGAGTCATTTCCAGTC 59.001 50.000 0.00 0.00 0.00 3.51
5011 5928 2.289945 GGTCAGCAGAGTCATTTCCAGT 60.290 50.000 0.00 0.00 0.00 4.00
5012 5929 2.289882 TGGTCAGCAGAGTCATTTCCAG 60.290 50.000 0.00 0.00 0.00 3.86
5013 5930 1.699083 TGGTCAGCAGAGTCATTTCCA 59.301 47.619 0.00 0.00 0.00 3.53
5014 5931 2.079925 GTGGTCAGCAGAGTCATTTCC 58.920 52.381 0.00 0.00 0.00 3.13
5015 5932 2.771089 TGTGGTCAGCAGAGTCATTTC 58.229 47.619 0.00 0.00 0.00 2.17
5016 5933 2.936919 TGTGGTCAGCAGAGTCATTT 57.063 45.000 0.00 0.00 0.00 2.32
5017 5934 3.079578 CAATGTGGTCAGCAGAGTCATT 58.920 45.455 0.00 0.00 0.00 2.57
5018 5935 2.303890 TCAATGTGGTCAGCAGAGTCAT 59.696 45.455 0.00 0.00 0.00 3.06
5019 5936 1.693606 TCAATGTGGTCAGCAGAGTCA 59.306 47.619 0.00 0.00 0.00 3.41
5020 5937 2.289320 ACTCAATGTGGTCAGCAGAGTC 60.289 50.000 0.00 0.00 31.90 3.36
5021 5938 1.696336 ACTCAATGTGGTCAGCAGAGT 59.304 47.619 0.00 0.00 32.29 3.24
5022 5939 2.469274 ACTCAATGTGGTCAGCAGAG 57.531 50.000 0.00 0.00 0.00 3.35
5023 5940 2.880268 CAAACTCAATGTGGTCAGCAGA 59.120 45.455 0.00 0.00 0.00 4.26
5024 5941 2.606308 GCAAACTCAATGTGGTCAGCAG 60.606 50.000 0.00 0.00 0.00 4.24
5025 5942 1.337703 GCAAACTCAATGTGGTCAGCA 59.662 47.619 0.00 0.00 0.00 4.41
5026 5943 1.337703 TGCAAACTCAATGTGGTCAGC 59.662 47.619 0.00 0.00 0.00 4.26
5027 5944 3.551454 CCTTGCAAACTCAATGTGGTCAG 60.551 47.826 0.00 0.00 0.00 3.51
5028 5945 2.361757 CCTTGCAAACTCAATGTGGTCA 59.638 45.455 0.00 0.00 0.00 4.02
5029 5946 2.622942 TCCTTGCAAACTCAATGTGGTC 59.377 45.455 0.00 0.00 0.00 4.02
5030 5947 2.665165 TCCTTGCAAACTCAATGTGGT 58.335 42.857 0.00 0.00 0.00 4.16
5031 5948 3.947910 ATCCTTGCAAACTCAATGTGG 57.052 42.857 0.00 0.00 0.00 4.17
5032 5949 4.624015 ACAATCCTTGCAAACTCAATGTG 58.376 39.130 0.00 0.00 0.00 3.21
5033 5950 4.586001 AGACAATCCTTGCAAACTCAATGT 59.414 37.500 0.00 1.32 0.00 2.71
5034 5951 5.130292 AGACAATCCTTGCAAACTCAATG 57.870 39.130 0.00 0.00 0.00 2.82
5035 5952 5.302568 TCAAGACAATCCTTGCAAACTCAAT 59.697 36.000 0.00 0.00 42.34 2.57
5036 5953 4.644234 TCAAGACAATCCTTGCAAACTCAA 59.356 37.500 0.00 0.00 42.34 3.02
5037 5954 4.206375 TCAAGACAATCCTTGCAAACTCA 58.794 39.130 0.00 0.00 42.34 3.41
5038 5955 4.320788 CCTCAAGACAATCCTTGCAAACTC 60.321 45.833 0.00 0.00 42.34 3.01
5039 5956 3.571401 CCTCAAGACAATCCTTGCAAACT 59.429 43.478 0.00 0.00 42.34 2.66
5040 5957 3.858503 GCCTCAAGACAATCCTTGCAAAC 60.859 47.826 0.00 0.00 42.34 2.93
5041 5958 2.297033 GCCTCAAGACAATCCTTGCAAA 59.703 45.455 0.00 0.00 42.34 3.68
5042 5959 1.888512 GCCTCAAGACAATCCTTGCAA 59.111 47.619 0.00 0.00 42.34 4.08
5043 5960 1.538047 GCCTCAAGACAATCCTTGCA 58.462 50.000 0.00 0.00 42.34 4.08
5169 6141 4.997905 TTTCTCTGAAGCGTTCATGAAG 57.002 40.909 8.80 4.54 39.30 3.02
5449 6421 5.748592 ACTTCTCTCGTTGTATTTTGCAAC 58.251 37.500 0.00 0.00 41.81 4.17
5450 6422 7.667043 ATACTTCTCTCGTTGTATTTTGCAA 57.333 32.000 0.00 0.00 0.00 4.08
5528 6502 1.203100 AGCTTCAGTTGCCCCAATCTT 60.203 47.619 0.00 0.00 0.00 2.40
5550 6524 0.259065 AGTGATCTCGTAGGCAGGGA 59.741 55.000 0.00 0.00 0.00 4.20
5554 6528 1.847328 TGGAAGTGATCTCGTAGGCA 58.153 50.000 0.00 0.00 0.00 4.75
5653 6640 8.260114 ACCAATGAAGTTTTTCTTTCAACATCT 58.740 29.630 0.00 0.00 36.40 2.90
5770 6758 0.679002 GGAGCGCATCCCATATGCAT 60.679 55.000 11.47 3.79 44.75 3.96
5800 6808 8.270080 CTCTAGTAGAGTCGCCATAATGATAA 57.730 38.462 17.70 0.00 37.57 1.75
5828 6836 1.667212 GAAAACCGACACGTTTGGAGT 59.333 47.619 10.01 0.00 36.12 3.85
5832 6840 2.836479 AAGGAAAACCGACACGTTTG 57.164 45.000 0.00 0.00 36.12 2.93
5835 6843 4.277257 GTTTTAAGGAAAACCGACACGT 57.723 40.909 2.53 0.00 45.86 4.49
5862 6870 4.523083 TCCTGAAATTCCATTTCCTACCG 58.477 43.478 6.73 0.00 46.18 4.02
5905 6914 5.411781 CGCTGAAAGAGTAGATTGGTAACT 58.588 41.667 0.00 0.00 34.07 2.24
5921 6930 0.246635 GTCTAGCTCACCCGCTGAAA 59.753 55.000 0.00 0.00 41.12 2.69
5931 6940 7.921214 CCGAAAAGATAAACTATGTCTAGCTCA 59.079 37.037 0.00 0.00 0.00 4.26
5999 7276 1.491668 TCACGCCCACTACATACCAT 58.508 50.000 0.00 0.00 0.00 3.55
6004 7281 1.327690 ACCGATCACGCCCACTACAT 61.328 55.000 0.00 0.00 38.29 2.29
6037 7314 0.251354 ACCATCATCGCAACTGAGCT 59.749 50.000 0.00 0.00 0.00 4.09
6049 7326 2.089201 CAGTGCACATGTGACCATCAT 58.911 47.619 29.80 6.51 0.00 2.45
6136 7413 0.037232 ACCTTGTACTTCCGCTCTGC 60.037 55.000 0.00 0.00 0.00 4.26
6138 7415 0.608640 CCACCTTGTACTTCCGCTCT 59.391 55.000 0.00 0.00 0.00 4.09
6148 7425 3.176297 CCCCCAAGCCACCTTGTA 58.824 61.111 3.13 0.00 45.57 2.41
6182 7459 2.939261 CGCCACCACTAGGACCGTT 61.939 63.158 0.00 0.00 38.69 4.44
6230 7507 3.119173 ACAACACCACCACAACTGAATTG 60.119 43.478 0.00 0.00 44.60 2.32
6285 7562 1.138069 TGAGTCTTTGTTCGAGCCACA 59.862 47.619 0.00 0.00 0.00 4.17
6295 7572 4.402155 TGACAGCCAAATTTGAGTCTTTGT 59.598 37.500 24.99 17.16 31.83 2.83


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

AutoCloner maintained by Alex Coulton.