Multiple sequence alignment - TraesCS1D01G052000

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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 TraesCS1D01G052000 chr1D 100.000 4079 0 0 1 4079 32736966 32741044 0.000000e+00 7533
1 TraesCS1D01G052000 chr1A 88.281 3234 208 88 45 3187 31255459 31252306 0.000000e+00 3714
2 TraesCS1D01G052000 chr1A 96.259 294 11 0 3786 4079 31251262 31250969 2.200000e-132 483
3 TraesCS1D01G052000 chr1A 88.889 315 24 4 3337 3640 31252207 31251893 1.070000e-100 377
4 TraesCS1D01G052000 chr1B 91.842 2660 139 37 560 3184 50203496 50206112 0.000000e+00 3639
5 TraesCS1D01G052000 chr1B 84.993 753 47 26 3344 4079 50206239 50206942 0.000000e+00 704
6 TraesCS1D01G052000 chr1B 86.707 331 27 8 68 392 50203062 50203381 6.490000e-93 351
7 TraesCS1D01G052000 chr5D 85.449 1883 244 18 1200 3077 102331935 102330078 0.000000e+00 1932
8 TraesCS1D01G052000 chr5A 84.898 1907 252 24 1180 3077 96983762 96985641 0.000000e+00 1893
9 TraesCS1D01G052000 chr5B 84.995 1886 247 22 1200 3077 112021376 112019519 0.000000e+00 1882
10 TraesCS1D01G052000 chr3B 83.615 1892 280 18 1203 3088 24019167 24017300 0.000000e+00 1749
11 TraesCS1D01G052000 chr3A 82.333 2015 315 22 1078 3088 19988359 19990336 0.000000e+00 1711
12 TraesCS1D01G052000 chr3A 78.105 1900 357 55 1208 3079 602224992 602226860 0.000000e+00 1149
13 TraesCS1D01G052000 chr3D 78.188 1921 358 57 1188 3079 460180030 460181918 0.000000e+00 1170
14 TraesCS1D01G052000 chr4B 78.594 939 176 20 2155 3079 428900282 428901209 7.550000e-167 597


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 TraesCS1D01G052000 chr1D 32736966 32741044 4078 False 7533.000000 7533 100.000000 1 4079 1 chr1D.!!$F1 4078
1 TraesCS1D01G052000 chr1A 31250969 31255459 4490 True 1524.666667 3714 91.143000 45 4079 3 chr1A.!!$R1 4034
2 TraesCS1D01G052000 chr1B 50203062 50206942 3880 False 1564.666667 3639 87.847333 68 4079 3 chr1B.!!$F1 4011
3 TraesCS1D01G052000 chr5D 102330078 102331935 1857 True 1932.000000 1932 85.449000 1200 3077 1 chr5D.!!$R1 1877
4 TraesCS1D01G052000 chr5A 96983762 96985641 1879 False 1893.000000 1893 84.898000 1180 3077 1 chr5A.!!$F1 1897
5 TraesCS1D01G052000 chr5B 112019519 112021376 1857 True 1882.000000 1882 84.995000 1200 3077 1 chr5B.!!$R1 1877
6 TraesCS1D01G052000 chr3B 24017300 24019167 1867 True 1749.000000 1749 83.615000 1203 3088 1 chr3B.!!$R1 1885
7 TraesCS1D01G052000 chr3A 19988359 19990336 1977 False 1711.000000 1711 82.333000 1078 3088 1 chr3A.!!$F1 2010
8 TraesCS1D01G052000 chr3A 602224992 602226860 1868 False 1149.000000 1149 78.105000 1208 3079 1 chr3A.!!$F2 1871
9 TraesCS1D01G052000 chr3D 460180030 460181918 1888 False 1170.000000 1170 78.188000 1188 3079 1 chr3D.!!$F1 1891
10 TraesCS1D01G052000 chr4B 428900282 428901209 927 False 597.000000 597 78.594000 2155 3079 1 chr4B.!!$F1 924

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
513 548 0.035630 ACTCAATGAGTCCCAGCTGC 60.036 55.0 10.56 0.00 38.71 5.25 F
514 549 0.035725 CTCAATGAGTCCCAGCTGCA 60.036 55.0 8.66 0.00 0.00 4.41 F
719 798 0.106894 GCACGGAGGGGATTAAGGAG 59.893 60.0 0.00 0.00 0.00 3.69 F
785 887 0.886490 ACGGCAGGCACAAAGAGAAG 60.886 55.0 0.00 0.00 0.00 2.85 F
2928 3091 0.396435 ACATGACGTCCCACACATGT 59.604 50.0 14.12 12.47 45.19 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1780 2.612672 CTCGTCGAGGAACAGCAGTATA 59.387 50.000 14.68 0.00 0.00 1.47 R
2532 2689 2.997897 AGGAAAGACGAGGCGCCT 60.998 61.111 33.48 33.48 0.00 5.52 R
2709 2866 2.320781 CAGATCCAGTAGTCGGGGATT 58.679 52.381 0.00 0.00 41.39 3.01 R
3015 3178 2.125512 AGCGCGCGGAAGAAGAAT 60.126 55.556 33.06 0.00 0.00 2.40 R
3807 4522 0.976641 CTGGTCTCCTAGTGTTGCCA 59.023 55.000 0.00 0.00 0.00 4.92 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
22 23 5.567138 CCATAGTAGGGCTTGAAACAAAG 57.433 43.478 0.00 0.00 0.00 2.77
23 24 5.253330 CCATAGTAGGGCTTGAAACAAAGA 58.747 41.667 0.00 0.00 0.00 2.52
24 25 5.710099 CCATAGTAGGGCTTGAAACAAAGAA 59.290 40.000 0.00 0.00 0.00 2.52
25 26 6.378280 CCATAGTAGGGCTTGAAACAAAGAAT 59.622 38.462 0.00 0.00 0.00 2.40
26 27 7.093771 CCATAGTAGGGCTTGAAACAAAGAATT 60.094 37.037 0.00 0.00 0.00 2.17
27 28 6.089249 AGTAGGGCTTGAAACAAAGAATTG 57.911 37.500 0.00 0.00 42.46 2.32
28 29 4.341366 AGGGCTTGAAACAAAGAATTGG 57.659 40.909 0.00 0.00 41.01 3.16
29 30 3.711190 AGGGCTTGAAACAAAGAATTGGT 59.289 39.130 0.00 0.00 41.01 3.67
30 31 3.809279 GGGCTTGAAACAAAGAATTGGTG 59.191 43.478 0.00 0.00 41.01 4.17
31 32 4.442753 GGGCTTGAAACAAAGAATTGGTGA 60.443 41.667 0.00 0.00 41.01 4.02
32 33 4.507756 GGCTTGAAACAAAGAATTGGTGAC 59.492 41.667 0.00 0.00 41.01 3.67
33 34 5.108517 GCTTGAAACAAAGAATTGGTGACA 58.891 37.500 0.00 0.00 41.01 3.58
74 78 5.359194 TGGAGAAATGGCTTCTTAGTAGG 57.641 43.478 0.00 0.00 44.82 3.18
77 81 5.104900 GGAGAAATGGCTTCTTAGTAGGTGA 60.105 44.000 0.00 0.00 44.82 4.02
103 107 6.208644 AGTGTAAAGATTTGACACATTGTGC 58.791 36.000 16.62 9.97 44.77 4.57
105 109 5.976534 TGTAAAGATTTGACACATTGTGCAC 59.023 36.000 16.62 10.75 36.98 4.57
169 175 8.574251 TGTTAAACAGTGCCATGATAGTTAAT 57.426 30.769 0.00 0.00 0.00 1.40
170 176 9.674068 TGTTAAACAGTGCCATGATAGTTAATA 57.326 29.630 0.00 0.00 0.00 0.98
280 286 5.964887 TTTGTTCTTTTGCGAGGAAATTG 57.035 34.783 0.00 0.00 0.00 2.32
318 324 6.961359 TCGAACACTCCACATTTGTAATAG 57.039 37.500 0.00 0.00 0.00 1.73
319 325 6.460781 TCGAACACTCCACATTTGTAATAGT 58.539 36.000 0.00 0.00 0.00 2.12
320 326 7.604549 TCGAACACTCCACATTTGTAATAGTA 58.395 34.615 0.00 0.00 0.00 1.82
346 355 4.643387 AGGGCCAGGAACGTGCAC 62.643 66.667 6.82 6.82 33.46 4.57
351 360 2.616330 CCAGGAACGTGCACGCATT 61.616 57.895 37.35 25.58 44.43 3.56
392 411 8.137437 CCAATCTGTGAGAGTAAAACACAAAAT 58.863 33.333 0.00 0.00 42.55 1.82
394 413 7.857734 TCTGTGAGAGTAAAACACAAAATCA 57.142 32.000 0.00 0.00 42.55 2.57
395 414 7.919690 TCTGTGAGAGTAAAACACAAAATCAG 58.080 34.615 0.00 0.00 42.55 2.90
401 420 8.738645 AGAGTAAAACACAAAATCAGAACTCT 57.261 30.769 0.00 0.00 36.15 3.24
432 451 5.411361 TGCACATTGTGAGTATACTTCCAAC 59.589 40.000 20.77 9.78 35.23 3.77
434 453 6.183360 GCACATTGTGAGTATACTTCCAACTC 60.183 42.308 20.77 2.31 40.05 3.01
435 454 6.035005 CACATTGTGAGTATACTTCCAACTCG 59.965 42.308 11.45 11.78 42.05 4.18
436 455 5.717078 TTGTGAGTATACTTCCAACTCGT 57.283 39.130 6.88 0.00 42.05 4.18
438 457 6.432607 TGTGAGTATACTTCCAACTCGTAG 57.567 41.667 6.88 0.00 42.05 3.51
439 458 5.942236 TGTGAGTATACTTCCAACTCGTAGT 59.058 40.000 6.88 0.00 42.05 2.73
440 459 7.105588 TGTGAGTATACTTCCAACTCGTAGTA 58.894 38.462 6.88 0.00 42.05 1.82
441 460 7.772292 TGTGAGTATACTTCCAACTCGTAGTAT 59.228 37.037 6.88 0.00 42.05 2.12
442 461 9.265901 GTGAGTATACTTCCAACTCGTAGTATA 57.734 37.037 6.88 0.00 42.05 1.47
449 468 7.948357 ACTTCCAACTCGTAGTATATTATGCA 58.052 34.615 0.00 0.00 0.00 3.96
451 470 6.684686 TCCAACTCGTAGTATATTATGCACC 58.315 40.000 0.00 0.00 0.00 5.01
452 471 6.492429 TCCAACTCGTAGTATATTATGCACCT 59.508 38.462 0.00 0.00 0.00 4.00
453 472 7.014905 TCCAACTCGTAGTATATTATGCACCTT 59.985 37.037 0.00 0.00 0.00 3.50
454 473 7.116376 CCAACTCGTAGTATATTATGCACCTTG 59.884 40.741 0.00 0.00 0.00 3.61
457 476 6.755206 TCGTAGTATATTATGCACCTTGCTT 58.245 36.000 0.00 0.00 45.31 3.91
471 498 0.681733 TTGCTTCTCGTCAGGCTCTT 59.318 50.000 0.00 0.00 0.00 2.85
493 528 2.447089 CTGCATGCAGTACAATGACG 57.553 50.000 34.76 10.48 39.10 4.35
494 529 2.001872 CTGCATGCAGTACAATGACGA 58.998 47.619 34.76 2.37 39.10 4.20
495 530 1.731709 TGCATGCAGTACAATGACGAC 59.268 47.619 18.46 0.00 0.00 4.34
496 531 2.002586 GCATGCAGTACAATGACGACT 58.997 47.619 14.21 0.00 0.00 4.18
498 533 3.253230 CATGCAGTACAATGACGACTCA 58.747 45.455 0.00 0.00 0.00 3.41
499 534 3.378911 TGCAGTACAATGACGACTCAA 57.621 42.857 0.00 0.00 0.00 3.02
500 535 3.925379 TGCAGTACAATGACGACTCAAT 58.075 40.909 0.00 0.00 0.00 2.57
502 537 3.926527 GCAGTACAATGACGACTCAATGA 59.073 43.478 0.00 0.00 32.36 2.57
503 538 4.032217 GCAGTACAATGACGACTCAATGAG 59.968 45.833 8.98 8.98 32.36 2.90
504 539 5.164233 CAGTACAATGACGACTCAATGAGT 58.836 41.667 16.70 16.70 46.42 3.41
513 548 0.035630 ACTCAATGAGTCCCAGCTGC 60.036 55.000 10.56 0.00 38.71 5.25
514 549 0.035725 CTCAATGAGTCCCAGCTGCA 60.036 55.000 8.66 0.00 0.00 4.41
515 550 0.321919 TCAATGAGTCCCAGCTGCAC 60.322 55.000 8.66 7.08 0.00 4.57
522 557 4.020617 CCCAGCTGCACCCTCGAA 62.021 66.667 8.66 0.00 0.00 3.71
545 580 2.029380 TCCTTCACACCACGTATGTCTG 60.029 50.000 1.76 0.00 0.00 3.51
546 581 2.029380 CCTTCACACCACGTATGTCTGA 60.029 50.000 1.76 0.00 0.00 3.27
547 582 2.717580 TCACACCACGTATGTCTGAC 57.282 50.000 0.00 0.00 0.00 3.51
548 583 2.235891 TCACACCACGTATGTCTGACT 58.764 47.619 9.51 0.00 0.00 3.41
549 584 2.228103 TCACACCACGTATGTCTGACTC 59.772 50.000 9.51 0.00 0.00 3.36
550 585 2.229062 CACACCACGTATGTCTGACTCT 59.771 50.000 9.51 0.00 0.00 3.24
551 586 2.229062 ACACCACGTATGTCTGACTCTG 59.771 50.000 9.51 0.00 0.00 3.35
552 587 2.229062 CACCACGTATGTCTGACTCTGT 59.771 50.000 9.51 0.02 0.00 3.41
553 588 3.439129 CACCACGTATGTCTGACTCTGTA 59.561 47.826 9.51 0.00 0.00 2.74
554 589 3.439476 ACCACGTATGTCTGACTCTGTAC 59.561 47.826 9.51 6.33 0.00 2.90
555 590 3.485381 CCACGTATGTCTGACTCTGTACG 60.485 52.174 21.64 21.64 40.30 3.67
557 592 4.328169 CACGTATGTCTGACTCTGTACGTA 59.672 45.833 24.97 0.00 44.06 3.57
558 593 4.328440 ACGTATGTCTGACTCTGTACGTAC 59.672 45.833 24.60 18.90 44.06 3.67
586 638 2.743928 CCTTCACACGAGGCAGGC 60.744 66.667 0.00 0.00 0.00 4.85
587 639 2.031012 CTTCACACGAGGCAGGCA 59.969 61.111 0.00 0.00 0.00 4.75
588 640 2.031012 TTCACACGAGGCAGGCAG 59.969 61.111 0.00 0.00 0.00 4.85
589 641 3.535629 TTCACACGAGGCAGGCAGG 62.536 63.158 0.00 0.00 0.00 4.85
590 642 4.320456 CACACGAGGCAGGCAGGT 62.320 66.667 0.00 0.00 0.00 4.00
591 643 4.008933 ACACGAGGCAGGCAGGTC 62.009 66.667 0.00 0.00 0.00 3.85
693 766 1.115467 AGTTATGGAGGGAGTGCGAG 58.885 55.000 0.00 0.00 0.00 5.03
700 779 1.452145 GAGGGAGTGCGAGAGGCTAG 61.452 65.000 0.00 0.00 44.05 3.42
710 789 3.541713 GAGGCTAGCACGGAGGGG 61.542 72.222 18.24 0.00 0.00 4.79
711 790 4.075793 AGGCTAGCACGGAGGGGA 62.076 66.667 18.24 0.00 0.00 4.81
713 792 2.444256 GGCTAGCACGGAGGGGATT 61.444 63.158 18.24 0.00 0.00 3.01
715 794 0.756903 GCTAGCACGGAGGGGATTAA 59.243 55.000 10.63 0.00 0.00 1.40
716 795 1.270358 GCTAGCACGGAGGGGATTAAG 60.270 57.143 10.63 0.00 0.00 1.85
717 796 1.344763 CTAGCACGGAGGGGATTAAGG 59.655 57.143 0.00 0.00 0.00 2.69
718 797 0.326238 AGCACGGAGGGGATTAAGGA 60.326 55.000 0.00 0.00 0.00 3.36
719 798 0.106894 GCACGGAGGGGATTAAGGAG 59.893 60.000 0.00 0.00 0.00 3.69
780 882 2.906897 ACCACGGCAGGCACAAAG 60.907 61.111 0.00 0.00 0.00 2.77
782 884 2.620112 CCACGGCAGGCACAAAGAG 61.620 63.158 0.00 0.00 0.00 2.85
783 885 1.597854 CACGGCAGGCACAAAGAGA 60.598 57.895 0.00 0.00 0.00 3.10
784 886 1.148273 ACGGCAGGCACAAAGAGAA 59.852 52.632 0.00 0.00 0.00 2.87
785 887 0.886490 ACGGCAGGCACAAAGAGAAG 60.886 55.000 0.00 0.00 0.00 2.85
786 888 1.583477 GGCAGGCACAAAGAGAAGC 59.417 57.895 0.00 0.00 0.00 3.86
787 889 0.892814 GGCAGGCACAAAGAGAAGCT 60.893 55.000 0.00 0.00 0.00 3.74
788 890 1.611673 GGCAGGCACAAAGAGAAGCTA 60.612 52.381 0.00 0.00 0.00 3.32
789 891 1.466558 GCAGGCACAAAGAGAAGCTAC 59.533 52.381 0.00 0.00 0.00 3.58
790 892 2.873649 GCAGGCACAAAGAGAAGCTACT 60.874 50.000 0.00 0.00 0.00 2.57
802 904 5.297547 AGAGAAGCTACTCTACTCTGATCG 58.702 45.833 0.00 0.00 44.17 3.69
803 905 4.385825 AGAAGCTACTCTACTCTGATCGG 58.614 47.826 0.00 0.00 0.00 4.18
804 906 3.134574 AGCTACTCTACTCTGATCGGG 57.865 52.381 0.62 0.00 0.00 5.14
805 907 2.706723 AGCTACTCTACTCTGATCGGGA 59.293 50.000 0.62 0.00 0.00 5.14
806 908 3.329520 AGCTACTCTACTCTGATCGGGAT 59.670 47.826 0.62 0.00 0.00 3.85
807 909 3.687698 GCTACTCTACTCTGATCGGGATC 59.312 52.174 0.62 1.69 38.29 3.36
855 957 1.900545 CTCGGAAACCACCTCCTCCC 61.901 65.000 0.00 0.00 0.00 4.30
856 958 1.918800 CGGAAACCACCTCCTCCCT 60.919 63.158 0.00 0.00 0.00 4.20
866 968 4.144727 TCCTCCCTCTCCGCCCTC 62.145 72.222 0.00 0.00 0.00 4.30
882 989 2.846827 GCCCTCCCTATATAACCTGCAT 59.153 50.000 0.00 0.00 0.00 3.96
888 995 4.841813 TCCCTATATAACCTGCATTCCGAA 59.158 41.667 0.00 0.00 0.00 4.30
892 999 2.570415 TAACCTGCATTCCGAACCAA 57.430 45.000 0.00 0.00 0.00 3.67
916 1025 2.159272 GACACACGCAGCCGAGTTTC 62.159 60.000 0.00 0.00 36.13 2.78
952 1061 2.285442 AAACCCCTCCCTCCCTCG 60.285 66.667 0.00 0.00 0.00 4.63
953 1062 2.877018 AAACCCCTCCCTCCCTCGA 61.877 63.158 0.00 0.00 0.00 4.04
957 1066 2.609339 CCTCCCTCCCTCGATCCA 59.391 66.667 0.00 0.00 0.00 3.41
961 1070 1.152247 CCCTCCCTCGATCCATCCA 60.152 63.158 0.00 0.00 0.00 3.41
962 1071 1.476007 CCCTCCCTCGATCCATCCAC 61.476 65.000 0.00 0.00 0.00 4.02
968 1077 0.961753 CTCGATCCATCCACCGATCA 59.038 55.000 0.00 0.00 35.61 2.92
972 1081 2.289010 CGATCCATCCACCGATCAATCA 60.289 50.000 0.00 0.00 35.61 2.57
973 1082 2.620251 TCCATCCACCGATCAATCAC 57.380 50.000 0.00 0.00 0.00 3.06
974 1083 1.140852 TCCATCCACCGATCAATCACC 59.859 52.381 0.00 0.00 0.00 4.02
978 1087 1.154205 CCACCGATCAATCACCGAGC 61.154 60.000 0.00 0.00 0.00 5.03
1005 1114 1.900585 CTGACCGCAACACCATGTCG 61.901 60.000 0.00 0.00 0.00 4.35
1007 1116 1.897398 GACCGCAACACCATGTCGAC 61.897 60.000 9.11 9.11 0.00 4.20
1647 1780 1.676678 CCGACATCATCCACGACCCT 61.677 60.000 0.00 0.00 0.00 4.34
2198 2355 3.276091 CGCCTTCACCAACACGCA 61.276 61.111 0.00 0.00 0.00 5.24
2472 2629 3.379445 GTCGTCTCCTTCCCGCCA 61.379 66.667 0.00 0.00 0.00 5.69
2709 2866 0.601057 TCTTCATCAACCGCGACAGA 59.399 50.000 8.23 1.51 0.00 3.41
2925 3088 1.596752 GCACATGACGTCCCACACA 60.597 57.895 14.12 0.00 0.00 3.72
2928 3091 0.396435 ACATGACGTCCCACACATGT 59.604 50.000 14.12 12.47 45.19 3.21
3106 3276 3.337358 TCAATCGATCGGCATGCATTAT 58.663 40.909 21.36 9.22 0.00 1.28
3111 3281 2.413239 CGATCGGCATGCATTATGTTCC 60.413 50.000 21.36 0.00 39.08 3.62
3119 3294 6.282930 GGCATGCATTATGTTCCTGTATTTT 58.717 36.000 21.36 0.00 39.08 1.82
3153 3329 0.608856 TGTAGAGTAACGGACGGCCA 60.609 55.000 8.76 0.00 0.00 5.36
3155 3331 1.067635 GTAGAGTAACGGACGGCCAAA 60.068 52.381 8.76 0.00 0.00 3.28
3166 3342 2.415893 GGACGGCCAAAGAATCAATGTG 60.416 50.000 0.00 0.00 0.00 3.21
3168 3344 3.417101 ACGGCCAAAGAATCAATGTGTA 58.583 40.909 2.24 0.00 0.00 2.90
3172 3348 5.104374 GGCCAAAGAATCAATGTGTATGTG 58.896 41.667 0.00 0.00 0.00 3.21
3187 3374 7.793927 TGTGTATGTGAAATGTTCAGTGTTA 57.206 32.000 0.00 0.00 41.01 2.41
3188 3375 8.389779 TGTGTATGTGAAATGTTCAGTGTTAT 57.610 30.769 0.00 0.00 41.01 1.89
3191 3378 8.845227 TGTATGTGAAATGTTCAGTGTTATTGT 58.155 29.630 0.00 0.00 41.01 2.71
3193 3380 7.984002 TGTGAAATGTTCAGTGTTATTGTTG 57.016 32.000 0.00 0.00 41.01 3.33
3194 3381 6.977502 TGTGAAATGTTCAGTGTTATTGTTGG 59.022 34.615 0.00 0.00 41.01 3.77
3196 3383 7.491048 GTGAAATGTTCAGTGTTATTGTTGGTT 59.509 33.333 0.00 0.00 41.01 3.67
3197 3384 8.037758 TGAAATGTTCAGTGTTATTGTTGGTTT 58.962 29.630 0.00 0.00 34.08 3.27
3198 3385 7.769272 AATGTTCAGTGTTATTGTTGGTTTG 57.231 32.000 0.00 0.00 0.00 2.93
3201 3388 7.155328 TGTTCAGTGTTATTGTTGGTTTGTTT 58.845 30.769 0.00 0.00 0.00 2.83
3202 3389 7.657761 TGTTCAGTGTTATTGTTGGTTTGTTTT 59.342 29.630 0.00 0.00 0.00 2.43
3203 3390 8.499967 GTTCAGTGTTATTGTTGGTTTGTTTTT 58.500 29.630 0.00 0.00 0.00 1.94
3204 3391 9.706691 TTCAGTGTTATTGTTGGTTTGTTTTTA 57.293 25.926 0.00 0.00 0.00 1.52
3205 3392 9.877178 TCAGTGTTATTGTTGGTTTGTTTTTAT 57.123 25.926 0.00 0.00 0.00 1.40
3206 3393 9.913451 CAGTGTTATTGTTGGTTTGTTTTTATG 57.087 29.630 0.00 0.00 0.00 1.90
3245 3432 9.499479 AAATGCATAGTATATCTTTCTCACCAG 57.501 33.333 0.00 0.00 0.00 4.00
3248 3435 7.158021 GCATAGTATATCTTTCTCACCAGCTT 58.842 38.462 0.00 0.00 0.00 3.74
3251 3438 6.815089 AGTATATCTTTCTCACCAGCTTGAG 58.185 40.000 8.85 8.85 43.93 3.02
3252 3439 5.690464 ATATCTTTCTCACCAGCTTGAGT 57.310 39.130 13.78 0.00 43.19 3.41
3253 3440 3.845781 TCTTTCTCACCAGCTTGAGTT 57.154 42.857 13.78 0.00 43.19 3.01
3255 3442 4.526970 TCTTTCTCACCAGCTTGAGTTTT 58.473 39.130 13.78 0.00 43.19 2.43
3256 3443 4.949856 TCTTTCTCACCAGCTTGAGTTTTT 59.050 37.500 13.78 0.00 43.19 1.94
3277 3464 4.804868 TTGATGAATTGATTGGTGTGGG 57.195 40.909 0.00 0.00 0.00 4.61
3278 3465 3.777087 TGATGAATTGATTGGTGTGGGT 58.223 40.909 0.00 0.00 0.00 4.51
3279 3466 3.510753 TGATGAATTGATTGGTGTGGGTG 59.489 43.478 0.00 0.00 0.00 4.61
3280 3467 2.956132 TGAATTGATTGGTGTGGGTGT 58.044 42.857 0.00 0.00 0.00 4.16
3281 3468 2.627221 TGAATTGATTGGTGTGGGTGTG 59.373 45.455 0.00 0.00 0.00 3.82
3282 3469 0.968405 ATTGATTGGTGTGGGTGTGC 59.032 50.000 0.00 0.00 0.00 4.57
3283 3470 1.451337 TTGATTGGTGTGGGTGTGCG 61.451 55.000 0.00 0.00 0.00 5.34
3284 3471 1.896660 GATTGGTGTGGGTGTGCGT 60.897 57.895 0.00 0.00 0.00 5.24
3285 3472 2.128853 GATTGGTGTGGGTGTGCGTG 62.129 60.000 0.00 0.00 0.00 5.34
3288 3475 3.952675 GTGTGGGTGTGCGTGCAG 61.953 66.667 0.00 0.00 0.00 4.41
3289 3476 4.481617 TGTGGGTGTGCGTGCAGT 62.482 61.111 0.00 0.00 0.00 4.40
3290 3477 3.209097 GTGGGTGTGCGTGCAGTT 61.209 61.111 0.00 0.00 0.00 3.16
3291 3478 2.899838 TGGGTGTGCGTGCAGTTC 60.900 61.111 0.00 0.00 0.00 3.01
3292 3479 2.591715 GGGTGTGCGTGCAGTTCT 60.592 61.111 0.00 0.00 0.00 3.01
3293 3480 1.301401 GGGTGTGCGTGCAGTTCTA 60.301 57.895 0.00 0.00 0.00 2.10
3294 3481 0.673644 GGGTGTGCGTGCAGTTCTAT 60.674 55.000 0.00 0.00 0.00 1.98
3295 3482 1.404986 GGGTGTGCGTGCAGTTCTATA 60.405 52.381 0.00 0.00 0.00 1.31
3296 3483 2.550978 GGTGTGCGTGCAGTTCTATAT 58.449 47.619 0.00 0.00 0.00 0.86
3297 3484 2.285220 GGTGTGCGTGCAGTTCTATATG 59.715 50.000 0.00 0.00 0.00 1.78
3298 3485 2.285220 GTGTGCGTGCAGTTCTATATGG 59.715 50.000 0.00 0.00 0.00 2.74
3299 3486 1.261619 GTGCGTGCAGTTCTATATGGC 59.738 52.381 0.00 0.00 0.00 4.40
3300 3487 1.134551 TGCGTGCAGTTCTATATGGCA 60.135 47.619 0.00 0.00 0.00 4.92
3301 3488 2.146342 GCGTGCAGTTCTATATGGCAT 58.854 47.619 4.88 4.88 36.79 4.40
3302 3489 2.158449 GCGTGCAGTTCTATATGGCATC 59.842 50.000 1.65 0.00 36.79 3.91
3303 3490 3.392882 CGTGCAGTTCTATATGGCATCA 58.607 45.455 1.65 0.00 36.79 3.07
3304 3491 3.431233 CGTGCAGTTCTATATGGCATCAG 59.569 47.826 1.65 2.67 36.79 2.90
3305 3492 4.635223 GTGCAGTTCTATATGGCATCAGA 58.365 43.478 1.65 5.37 36.79 3.27
3306 3493 4.689812 GTGCAGTTCTATATGGCATCAGAG 59.310 45.833 1.65 0.00 36.79 3.35
3307 3494 3.683822 GCAGTTCTATATGGCATCAGAGC 59.316 47.826 1.65 10.26 0.00 4.09
3319 3506 4.924305 GCATCAGAGCCAATAAATTCCA 57.076 40.909 0.00 0.00 0.00 3.53
3320 3507 5.266733 GCATCAGAGCCAATAAATTCCAA 57.733 39.130 0.00 0.00 0.00 3.53
3321 3508 5.287226 GCATCAGAGCCAATAAATTCCAAG 58.713 41.667 0.00 0.00 0.00 3.61
3322 3509 5.163478 GCATCAGAGCCAATAAATTCCAAGT 60.163 40.000 0.00 0.00 0.00 3.16
3323 3510 6.628844 GCATCAGAGCCAATAAATTCCAAGTT 60.629 38.462 0.00 0.00 0.00 2.66
3324 3511 6.515272 TCAGAGCCAATAAATTCCAAGTTC 57.485 37.500 0.00 0.00 0.00 3.01
3325 3512 6.009589 TCAGAGCCAATAAATTCCAAGTTCA 58.990 36.000 0.00 0.00 0.00 3.18
3326 3513 6.493115 TCAGAGCCAATAAATTCCAAGTTCAA 59.507 34.615 0.00 0.00 0.00 2.69
3327 3514 6.810182 CAGAGCCAATAAATTCCAAGTTCAAG 59.190 38.462 0.00 0.00 0.00 3.02
3328 3515 6.721208 AGAGCCAATAAATTCCAAGTTCAAGA 59.279 34.615 0.00 0.00 0.00 3.02
3332 3519 5.897377 ATAAATTCCAAGTTCAAGACCCG 57.103 39.130 0.00 0.00 0.00 5.28
3334 3521 2.249844 TTCCAAGTTCAAGACCCGAC 57.750 50.000 0.00 0.00 0.00 4.79
3335 3522 1.420430 TCCAAGTTCAAGACCCGACT 58.580 50.000 0.00 0.00 0.00 4.18
3342 3532 3.640029 AGTTCAAGACCCGACTTCTTACA 59.360 43.478 0.00 0.00 31.86 2.41
3345 3535 5.988310 TCAAGACCCGACTTCTTACATTA 57.012 39.130 0.00 0.00 31.86 1.90
3349 3539 5.903810 AGACCCGACTTCTTACATTATGAC 58.096 41.667 0.00 0.00 0.00 3.06
3378 3568 7.894376 AAATTGCATGTCTGTAAATCAAAGG 57.106 32.000 0.00 0.00 30.46 3.11
3434 3627 2.507484 TGAGCATCACTTCCAGTTTGG 58.493 47.619 0.00 0.00 42.56 3.28
3437 3630 0.523072 CATCACTTCCAGTTTGGGCG 59.477 55.000 0.00 0.00 38.32 6.13
3438 3631 1.244019 ATCACTTCCAGTTTGGGCGC 61.244 55.000 0.00 0.00 38.32 6.53
3441 3634 2.123683 TTCCAGTTTGGGCGCCAA 60.124 55.556 30.85 16.59 42.29 4.52
3443 3636 3.222855 CCAGTTTGGGCGCCAACA 61.223 61.111 30.85 15.86 43.82 3.33
3445 3638 1.591327 CAGTTTGGGCGCCAACAAC 60.591 57.895 30.85 25.02 43.82 3.32
3487 3680 6.588204 TGTTACATTGTCTTAACCACACTCT 58.412 36.000 0.00 0.00 0.00 3.24
3499 3692 5.930837 AACCACACTCTTGAAATTTCCAA 57.069 34.783 15.48 8.83 0.00 3.53
3510 3711 4.692228 TGAAATTTCCAAACAACCTCTGC 58.308 39.130 15.48 0.00 0.00 4.26
3609 3810 8.552296 AGATCATAAACAAATCTTCCTGTACCT 58.448 33.333 0.00 0.00 0.00 3.08
3640 3841 2.354403 GCAAGCCTCAGCAAATCCAAAT 60.354 45.455 0.00 0.00 43.56 2.32
3642 3843 4.442472 GCAAGCCTCAGCAAATCCAAATAT 60.442 41.667 0.00 0.00 43.56 1.28
3643 3844 5.667466 CAAGCCTCAGCAAATCCAAATATT 58.333 37.500 0.00 0.00 43.56 1.28
3644 3845 5.945144 AGCCTCAGCAAATCCAAATATTT 57.055 34.783 0.00 0.00 43.56 1.40
3645 3846 7.267128 CAAGCCTCAGCAAATCCAAATATTTA 58.733 34.615 0.00 0.00 43.56 1.40
3646 3847 6.809869 AGCCTCAGCAAATCCAAATATTTAC 58.190 36.000 0.00 0.00 43.56 2.01
3647 3848 5.985530 GCCTCAGCAAATCCAAATATTTACC 59.014 40.000 0.00 0.00 39.53 2.85
3648 3849 6.208644 CCTCAGCAAATCCAAATATTTACCG 58.791 40.000 0.00 0.00 0.00 4.02
3649 3850 6.142818 TCAGCAAATCCAAATATTTACCGG 57.857 37.500 0.00 0.00 0.00 5.28
3650 3851 4.744631 CAGCAAATCCAAATATTTACCGGC 59.255 41.667 0.00 1.18 0.00 6.13
3651 3852 4.649218 AGCAAATCCAAATATTTACCGGCT 59.351 37.500 0.00 3.37 0.00 5.52
3652 3853 5.128663 AGCAAATCCAAATATTTACCGGCTT 59.871 36.000 0.00 0.00 0.00 4.35
3653 3854 5.815222 GCAAATCCAAATATTTACCGGCTTT 59.185 36.000 0.00 0.37 0.00 3.51
3654 3855 6.315144 GCAAATCCAAATATTTACCGGCTTTT 59.685 34.615 0.00 0.59 0.00 2.27
3655 3856 7.465379 GCAAATCCAAATATTTACCGGCTTTTC 60.465 37.037 0.00 0.00 0.00 2.29
3656 3857 6.783708 ATCCAAATATTTACCGGCTTTTCA 57.216 33.333 0.00 0.00 0.00 2.69
3657 3858 6.591750 TCCAAATATTTACCGGCTTTTCAA 57.408 33.333 0.00 0.00 0.00 2.69
3658 3859 6.994221 TCCAAATATTTACCGGCTTTTCAAA 58.006 32.000 0.00 0.00 0.00 2.69
3659 3860 7.442656 TCCAAATATTTACCGGCTTTTCAAAA 58.557 30.769 0.00 0.00 0.00 2.44
3660 3861 7.931948 TCCAAATATTTACCGGCTTTTCAAAAA 59.068 29.630 0.00 0.00 0.00 1.94
3724 4363 1.729472 CGTCAGACAACGAGCCTGTAG 60.729 57.143 0.41 0.00 45.37 2.74
3736 4375 1.079503 GCCTGTAGGAAAACTCTGCG 58.920 55.000 1.17 0.00 37.39 5.18
3745 4384 0.669625 AAAACTCTGCGACCGTAGCC 60.670 55.000 0.82 0.00 0.00 3.93
3750 4389 1.064296 CTGCGACCGTAGCCACTAG 59.936 63.158 0.82 0.00 0.00 2.57
3751 4390 1.654954 CTGCGACCGTAGCCACTAGT 61.655 60.000 0.82 0.00 0.00 2.57
3752 4391 0.392863 TGCGACCGTAGCCACTAGTA 60.393 55.000 0.00 0.00 0.00 1.82
3754 4393 1.069364 GCGACCGTAGCCACTAGTATC 60.069 57.143 0.00 0.00 0.00 2.24
3756 4395 2.877168 CGACCGTAGCCACTAGTATCTT 59.123 50.000 0.00 0.00 0.00 2.40
3758 4397 4.608951 GACCGTAGCCACTAGTATCTTTG 58.391 47.826 0.00 0.00 0.00 2.77
3762 4401 4.202020 CGTAGCCACTAGTATCTTTGCTCA 60.202 45.833 0.00 0.00 0.00 4.26
3766 4405 4.744570 CCACTAGTATCTTTGCTCAACGA 58.255 43.478 0.00 0.00 0.00 3.85
3769 4408 5.633601 CACTAGTATCTTTGCTCAACGACAA 59.366 40.000 0.00 0.00 0.00 3.18
3770 4409 5.864474 ACTAGTATCTTTGCTCAACGACAAG 59.136 40.000 0.00 0.00 0.00 3.16
3772 4411 5.779922 AGTATCTTTGCTCAACGACAAGTA 58.220 37.500 0.00 0.00 0.00 2.24
3773 4412 5.864474 AGTATCTTTGCTCAACGACAAGTAG 59.136 40.000 0.00 0.00 0.00 2.57
3774 4413 3.390135 TCTTTGCTCAACGACAAGTAGG 58.610 45.455 0.00 0.00 0.00 3.18
3776 4415 4.038282 TCTTTGCTCAACGACAAGTAGGTA 59.962 41.667 0.00 0.00 0.00 3.08
3778 4417 5.648178 TTGCTCAACGACAAGTAGGTATA 57.352 39.130 0.00 0.00 0.00 1.47
3779 4418 4.990257 TGCTCAACGACAAGTAGGTATAC 58.010 43.478 0.00 0.00 0.00 1.47
3780 4419 4.460034 TGCTCAACGACAAGTAGGTATACA 59.540 41.667 5.01 0.00 34.07 2.29
3783 4422 6.534079 GCTCAACGACAAGTAGGTATACATTT 59.466 38.462 5.01 0.00 34.07 2.32
3784 4423 7.464178 GCTCAACGACAAGTAGGTATACATTTG 60.464 40.741 5.01 2.95 34.07 2.32
3926 4641 1.298157 TTCAGACGGAATTGGCTGCG 61.298 55.000 0.00 0.00 36.08 5.18
3995 4710 1.202782 CCAAGGCCAGATGGAGAGATG 60.203 57.143 15.19 0.00 39.12 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.253330 TCTTTGTTTCAAGCCCTACTATGG 58.747 41.667 0.00 0.00 0.00 2.74
1 2 6.817765 TTCTTTGTTTCAAGCCCTACTATG 57.182 37.500 0.00 0.00 0.00 2.23
2 3 7.093771 CCAATTCTTTGTTTCAAGCCCTACTAT 60.094 37.037 0.00 0.00 0.00 2.12
3 4 6.208599 CCAATTCTTTGTTTCAAGCCCTACTA 59.791 38.462 0.00 0.00 0.00 1.82
4 5 5.011023 CCAATTCTTTGTTTCAAGCCCTACT 59.989 40.000 0.00 0.00 0.00 2.57
5 6 5.221441 ACCAATTCTTTGTTTCAAGCCCTAC 60.221 40.000 0.00 0.00 0.00 3.18
6 7 4.898861 ACCAATTCTTTGTTTCAAGCCCTA 59.101 37.500 0.00 0.00 0.00 3.53
7 8 3.711190 ACCAATTCTTTGTTTCAAGCCCT 59.289 39.130 0.00 0.00 0.00 5.19
8 9 3.809279 CACCAATTCTTTGTTTCAAGCCC 59.191 43.478 0.00 0.00 0.00 5.19
9 10 4.507756 GTCACCAATTCTTTGTTTCAAGCC 59.492 41.667 0.00 0.00 0.00 4.35
10 11 5.108517 TGTCACCAATTCTTTGTTTCAAGC 58.891 37.500 0.00 0.00 0.00 4.01
11 12 7.412891 GGTTTGTCACCAATTCTTTGTTTCAAG 60.413 37.037 0.00 0.00 46.42 3.02
12 13 6.370166 GGTTTGTCACCAATTCTTTGTTTCAA 59.630 34.615 0.00 0.00 46.42 2.69
13 14 5.872070 GGTTTGTCACCAATTCTTTGTTTCA 59.128 36.000 0.00 0.00 46.42 2.69
14 15 6.344572 GGTTTGTCACCAATTCTTTGTTTC 57.655 37.500 0.00 0.00 46.42 2.78
27 28 4.023193 CCAAACTCATACTGGTTTGTCACC 60.023 45.833 14.53 0.00 46.04 4.02
28 29 4.578928 ACCAAACTCATACTGGTTTGTCAC 59.421 41.667 14.53 0.00 46.04 3.67
29 30 4.787551 ACCAAACTCATACTGGTTTGTCA 58.212 39.130 14.53 0.00 46.04 3.58
35 36 3.650942 TCTCCAACCAAACTCATACTGGT 59.349 43.478 0.00 0.00 45.50 4.00
36 37 4.286297 TCTCCAACCAAACTCATACTGG 57.714 45.455 0.00 0.00 36.24 4.00
37 38 6.349611 CCATTTCTCCAACCAAACTCATACTG 60.350 42.308 0.00 0.00 0.00 2.74
38 39 5.711976 CCATTTCTCCAACCAAACTCATACT 59.288 40.000 0.00 0.00 0.00 2.12
39 40 5.622233 GCCATTTCTCCAACCAAACTCATAC 60.622 44.000 0.00 0.00 0.00 2.39
40 41 4.462483 GCCATTTCTCCAACCAAACTCATA 59.538 41.667 0.00 0.00 0.00 2.15
41 42 3.259123 GCCATTTCTCCAACCAAACTCAT 59.741 43.478 0.00 0.00 0.00 2.90
42 43 2.627699 GCCATTTCTCCAACCAAACTCA 59.372 45.455 0.00 0.00 0.00 3.41
43 44 2.893489 AGCCATTTCTCCAACCAAACTC 59.107 45.455 0.00 0.00 0.00 3.01
74 78 8.745837 CAATGTGTCAAATCTTTACACTTTCAC 58.254 33.333 0.00 0.00 43.09 3.18
77 81 7.222611 GCACAATGTGTCAAATCTTTACACTTT 59.777 33.333 15.36 0.00 43.09 2.66
103 107 5.448438 ACACATGTGCTAATAACAAACGTG 58.552 37.500 25.68 0.00 34.76 4.49
105 109 6.984740 AAACACATGTGCTAATAACAAACG 57.015 33.333 25.68 0.00 0.00 3.60
185 191 7.417612 GTTTAGCATCACTTCTCTTTCAACAA 58.582 34.615 0.00 0.00 0.00 2.83
243 249 9.748708 CAAAAGAACAAAAATGAAGAGGATACA 57.251 29.630 0.00 0.00 41.41 2.29
244 250 8.703336 GCAAAAGAACAAAAATGAAGAGGATAC 58.297 33.333 0.00 0.00 0.00 2.24
280 286 1.317904 GTTCGAACGAATGAGCGTCTC 59.682 52.381 13.36 0.58 44.86 3.36
318 324 4.514066 CGTTCCTGGCCCTGTATTTTATAC 59.486 45.833 0.00 0.00 0.00 1.47
319 325 4.164604 ACGTTCCTGGCCCTGTATTTTATA 59.835 41.667 0.00 0.00 0.00 0.98
320 326 3.053917 ACGTTCCTGGCCCTGTATTTTAT 60.054 43.478 0.00 0.00 0.00 1.40
326 335 3.065306 CACGTTCCTGGCCCTGTA 58.935 61.111 0.00 0.00 0.00 2.74
404 423 7.826744 TGGAAGTATACTCACAATGTGCATAAA 59.173 33.333 8.78 0.00 32.98 1.40
414 433 5.717078 ACGAGTTGGAAGTATACTCACAA 57.283 39.130 5.70 11.36 38.52 3.33
428 447 6.688578 AGGTGCATAATATACTACGAGTTGG 58.311 40.000 0.00 0.00 0.00 3.77
432 451 6.633668 GCAAGGTGCATAATATACTACGAG 57.366 41.667 0.00 0.00 44.26 4.18
447 466 1.294659 CCTGACGAGAAGCAAGGTGC 61.295 60.000 0.00 0.00 45.46 5.01
448 467 1.294659 GCCTGACGAGAAGCAAGGTG 61.295 60.000 0.00 0.00 0.00 4.00
449 468 1.004440 GCCTGACGAGAAGCAAGGT 60.004 57.895 0.00 0.00 0.00 3.50
451 470 0.246086 AGAGCCTGACGAGAAGCAAG 59.754 55.000 0.00 0.00 0.00 4.01
452 471 0.681733 AAGAGCCTGACGAGAAGCAA 59.318 50.000 0.00 0.00 0.00 3.91
453 472 0.244994 GAAGAGCCTGACGAGAAGCA 59.755 55.000 0.00 0.00 0.00 3.91
454 473 0.244994 TGAAGAGCCTGACGAGAAGC 59.755 55.000 0.00 0.00 0.00 3.86
457 476 0.884514 CAGTGAAGAGCCTGACGAGA 59.115 55.000 0.00 0.00 0.00 4.04
494 529 0.035630 GCAGCTGGGACTCATTGAGT 60.036 55.000 19.05 19.05 46.42 3.41
495 530 0.035725 TGCAGCTGGGACTCATTGAG 60.036 55.000 17.12 12.17 35.52 3.02
496 531 0.321919 GTGCAGCTGGGACTCATTGA 60.322 55.000 17.12 0.00 34.56 2.57
498 533 1.001641 GGTGCAGCTGGGACTCATT 60.002 57.895 17.12 0.00 38.05 2.57
499 534 2.673523 GGTGCAGCTGGGACTCAT 59.326 61.111 17.12 0.00 38.05 2.90
500 535 3.640407 GGGTGCAGCTGGGACTCA 61.640 66.667 17.12 0.71 38.39 3.41
502 537 3.325753 GAGGGTGCAGCTGGGACT 61.326 66.667 17.12 3.36 38.05 3.85
503 538 4.767255 CGAGGGTGCAGCTGGGAC 62.767 72.222 17.12 7.53 37.06 4.46
505 540 4.020617 TTCGAGGGTGCAGCTGGG 62.021 66.667 17.12 5.13 0.00 4.45
506 541 2.743928 GTTCGAGGGTGCAGCTGG 60.744 66.667 17.12 5.50 0.00 4.85
507 542 1.739562 GAGTTCGAGGGTGCAGCTG 60.740 63.158 16.65 10.11 0.00 4.24
508 543 2.659610 GAGTTCGAGGGTGCAGCT 59.340 61.111 16.65 1.37 0.00 4.24
509 544 2.435059 GGAGTTCGAGGGTGCAGC 60.435 66.667 7.55 7.55 0.00 5.25
510 545 0.390472 GAAGGAGTTCGAGGGTGCAG 60.390 60.000 0.00 0.00 0.00 4.41
511 546 1.118965 TGAAGGAGTTCGAGGGTGCA 61.119 55.000 0.00 0.00 35.17 4.57
512 547 0.670854 GTGAAGGAGTTCGAGGGTGC 60.671 60.000 0.00 0.00 35.17 5.01
513 548 0.679505 TGTGAAGGAGTTCGAGGGTG 59.320 55.000 0.00 0.00 35.17 4.61
514 549 0.680061 GTGTGAAGGAGTTCGAGGGT 59.320 55.000 0.00 0.00 35.17 4.34
515 550 0.037232 GGTGTGAAGGAGTTCGAGGG 60.037 60.000 0.00 0.00 35.17 4.30
522 557 1.968493 ACATACGTGGTGTGAAGGAGT 59.032 47.619 0.00 0.00 0.00 3.85
545 580 5.730010 GCTTGATGGTAGTACGTACAGAGTC 60.730 48.000 26.55 16.79 32.62 3.36
546 581 4.096081 GCTTGATGGTAGTACGTACAGAGT 59.904 45.833 26.55 9.30 32.62 3.24
547 582 4.497674 GGCTTGATGGTAGTACGTACAGAG 60.498 50.000 26.55 12.52 32.62 3.35
548 583 3.379372 GGCTTGATGGTAGTACGTACAGA 59.621 47.826 26.55 11.98 32.62 3.41
549 584 3.380637 AGGCTTGATGGTAGTACGTACAG 59.619 47.826 26.55 13.63 32.62 2.74
550 585 3.359033 AGGCTTGATGGTAGTACGTACA 58.641 45.455 26.55 10.68 32.62 2.90
551 586 4.142315 TGAAGGCTTGATGGTAGTACGTAC 60.142 45.833 18.10 18.10 0.00 3.67
552 587 4.018490 TGAAGGCTTGATGGTAGTACGTA 58.982 43.478 3.46 0.00 0.00 3.57
553 588 2.829720 TGAAGGCTTGATGGTAGTACGT 59.170 45.455 3.46 0.00 0.00 3.57
554 589 3.187700 GTGAAGGCTTGATGGTAGTACG 58.812 50.000 3.46 0.00 0.00 3.67
555 590 3.933332 GTGTGAAGGCTTGATGGTAGTAC 59.067 47.826 3.46 0.00 0.00 2.73
557 592 2.612972 CGTGTGAAGGCTTGATGGTAGT 60.613 50.000 3.46 0.00 0.00 2.73
558 593 2.002586 CGTGTGAAGGCTTGATGGTAG 58.997 52.381 3.46 0.00 0.00 3.18
607 659 2.438868 AATTTTCTTTCGGCTGTGCC 57.561 45.000 0.00 0.00 46.75 5.01
617 689 3.816523 TGCGACCGGAGTAAATTTTCTTT 59.183 39.130 9.46 0.00 0.00 2.52
693 766 3.541713 CCCCTCCGTGCTAGCCTC 61.542 72.222 13.29 4.56 0.00 4.70
700 779 0.106894 CTCCTTAATCCCCTCCGTGC 59.893 60.000 0.00 0.00 0.00 5.34
710 789 0.463833 CACGCCACCCCTCCTTAATC 60.464 60.000 0.00 0.00 0.00 1.75
711 790 1.607612 CACGCCACCCCTCCTTAAT 59.392 57.895 0.00 0.00 0.00 1.40
713 792 3.006728 CCACGCCACCCCTCCTTA 61.007 66.667 0.00 0.00 0.00 2.69
780 882 4.451096 CCGATCAGAGTAGAGTAGCTTCTC 59.549 50.000 12.14 12.14 40.29 2.87
782 884 3.500680 CCCGATCAGAGTAGAGTAGCTTC 59.499 52.174 0.00 0.00 0.00 3.86
783 885 3.136809 TCCCGATCAGAGTAGAGTAGCTT 59.863 47.826 0.00 0.00 0.00 3.74
784 886 2.706723 TCCCGATCAGAGTAGAGTAGCT 59.293 50.000 0.00 0.00 0.00 3.32
785 887 3.128852 TCCCGATCAGAGTAGAGTAGC 57.871 52.381 0.00 0.00 0.00 3.58
786 888 3.930229 CGATCCCGATCAGAGTAGAGTAG 59.070 52.174 5.59 0.00 37.69 2.57
787 889 3.306849 CCGATCCCGATCAGAGTAGAGTA 60.307 52.174 5.59 0.00 37.69 2.59
788 890 2.551287 CCGATCCCGATCAGAGTAGAGT 60.551 54.545 5.59 0.00 37.69 3.24
789 891 2.080693 CCGATCCCGATCAGAGTAGAG 58.919 57.143 5.59 0.00 37.69 2.43
790 892 1.271434 CCCGATCCCGATCAGAGTAGA 60.271 57.143 5.59 0.00 37.69 2.59
802 904 3.225061 GGTCCGAGTCCCGATCCC 61.225 72.222 0.00 0.00 41.76 3.85
807 909 4.493747 GAAGCGGTCCGAGTCCCG 62.494 72.222 17.49 2.27 46.90 5.14
855 957 3.025262 GTTATATAGGGAGGGCGGAGAG 58.975 54.545 0.00 0.00 0.00 3.20
856 958 2.292061 GGTTATATAGGGAGGGCGGAGA 60.292 54.545 0.00 0.00 0.00 3.71
866 968 4.819105 TCGGAATGCAGGTTATATAGGG 57.181 45.455 0.00 0.00 0.00 3.53
882 989 1.144276 TGTCGTGCTTGGTTCGGAA 59.856 52.632 0.00 0.00 0.00 4.30
888 995 3.269347 GCGTGTGTCGTGCTTGGT 61.269 61.111 0.00 0.00 42.13 3.67
911 1018 1.087202 TGTGTTGTGCGAGCGAAACT 61.087 50.000 11.93 0.00 0.00 2.66
916 1025 1.154599 GTGATGTGTTGTGCGAGCG 60.155 57.895 0.00 0.00 0.00 5.03
952 1061 3.070018 GTGATTGATCGGTGGATGGATC 58.930 50.000 0.00 0.00 39.56 3.36
953 1062 2.224621 GGTGATTGATCGGTGGATGGAT 60.225 50.000 0.00 0.00 31.51 3.41
957 1066 1.069204 CTCGGTGATTGATCGGTGGAT 59.931 52.381 0.00 0.00 34.96 3.41
961 1070 0.103208 GAGCTCGGTGATTGATCGGT 59.897 55.000 0.00 0.00 0.00 4.69
962 1071 0.387202 AGAGCTCGGTGATTGATCGG 59.613 55.000 8.37 0.00 0.00 4.18
978 1087 4.069232 TTGCGGTCAGGGCGAGAG 62.069 66.667 0.00 0.00 0.00 3.20
1647 1780 2.612672 CTCGTCGAGGAACAGCAGTATA 59.387 50.000 14.68 0.00 0.00 1.47
2532 2689 2.997897 AGGAAAGACGAGGCGCCT 60.998 61.111 33.48 33.48 0.00 5.52
2544 2701 4.017126 TGATGAGCGAGAAGTAGAGGAAA 58.983 43.478 0.00 0.00 0.00 3.13
2709 2866 2.320781 CAGATCCAGTAGTCGGGGATT 58.679 52.381 0.00 0.00 41.39 3.01
3015 3178 2.125512 AGCGCGCGGAAGAAGAAT 60.126 55.556 33.06 0.00 0.00 2.40
3129 3305 3.756069 CCGTCCGTTACTCTACAGAAAG 58.244 50.000 0.00 0.00 0.00 2.62
3134 3310 0.608856 TGGCCGTCCGTTACTCTACA 60.609 55.000 0.00 0.00 34.14 2.74
3139 3315 0.393820 TTCTTTGGCCGTCCGTTACT 59.606 50.000 0.00 0.00 34.14 2.24
3140 3316 1.395954 GATTCTTTGGCCGTCCGTTAC 59.604 52.381 0.00 0.00 34.14 2.50
3144 3320 1.094785 ATTGATTCTTTGGCCGTCCG 58.905 50.000 0.00 0.00 34.14 4.79
3145 3321 1.818674 ACATTGATTCTTTGGCCGTCC 59.181 47.619 0.00 0.00 0.00 4.79
3153 3329 9.985730 AACATTTCACATACACATTGATTCTTT 57.014 25.926 0.00 0.00 0.00 2.52
3155 3331 8.795513 TGAACATTTCACATACACATTGATTCT 58.204 29.630 0.00 0.00 34.08 2.40
3166 3342 9.677567 AACAATAACACTGAACATTTCACATAC 57.322 29.630 0.00 0.00 35.46 2.39
3168 3344 7.652909 CCAACAATAACACTGAACATTTCACAT 59.347 33.333 0.00 0.00 35.46 3.21
3172 3348 8.327429 CAAACCAACAATAACACTGAACATTTC 58.673 33.333 0.00 0.00 0.00 2.17
3218 3405 9.276590 TGGTGAGAAAGATATACTATGCATTTG 57.723 33.333 3.54 0.60 0.00 2.32
3219 3406 9.499479 CTGGTGAGAAAGATATACTATGCATTT 57.501 33.333 3.54 0.00 0.00 2.32
3220 3407 7.605691 GCTGGTGAGAAAGATATACTATGCATT 59.394 37.037 3.54 0.00 0.00 3.56
3222 3409 6.268617 AGCTGGTGAGAAAGATATACTATGCA 59.731 38.462 0.00 0.00 0.00 3.96
3223 3410 6.696411 AGCTGGTGAGAAAGATATACTATGC 58.304 40.000 0.00 0.00 0.00 3.14
3224 3411 8.363390 TCAAGCTGGTGAGAAAGATATACTATG 58.637 37.037 0.00 0.00 0.00 2.23
3225 3412 8.484214 TCAAGCTGGTGAGAAAGATATACTAT 57.516 34.615 0.00 0.00 0.00 2.12
3227 3414 6.382570 ACTCAAGCTGGTGAGAAAGATATACT 59.617 38.462 19.91 0.00 46.76 2.12
3228 3415 6.578023 ACTCAAGCTGGTGAGAAAGATATAC 58.422 40.000 19.91 0.00 46.76 1.47
3230 3417 5.690464 ACTCAAGCTGGTGAGAAAGATAT 57.310 39.130 19.91 0.00 46.76 1.63
3232 3419 4.363991 AACTCAAGCTGGTGAGAAAGAT 57.636 40.909 19.91 0.00 46.76 2.40
3234 3421 4.907879 AAAACTCAAGCTGGTGAGAAAG 57.092 40.909 19.91 0.00 46.76 2.62
3253 3440 5.996513 CCCACACCAATCAATTCATCAAAAA 59.003 36.000 0.00 0.00 0.00 1.94
3255 3442 4.592351 ACCCACACCAATCAATTCATCAAA 59.408 37.500 0.00 0.00 0.00 2.69
3256 3443 4.021280 CACCCACACCAATCAATTCATCAA 60.021 41.667 0.00 0.00 0.00 2.57
3257 3444 3.510753 CACCCACACCAATCAATTCATCA 59.489 43.478 0.00 0.00 0.00 3.07
3258 3445 3.511146 ACACCCACACCAATCAATTCATC 59.489 43.478 0.00 0.00 0.00 2.92
3259 3446 3.258872 CACACCCACACCAATCAATTCAT 59.741 43.478 0.00 0.00 0.00 2.57
3261 3448 2.610232 GCACACCCACACCAATCAATTC 60.610 50.000 0.00 0.00 0.00 2.17
3263 3450 0.968405 GCACACCCACACCAATCAAT 59.032 50.000 0.00 0.00 0.00 2.57
3264 3451 1.451337 CGCACACCCACACCAATCAA 61.451 55.000 0.00 0.00 0.00 2.57
3265 3452 1.896183 CGCACACCCACACCAATCA 60.896 57.895 0.00 0.00 0.00 2.57
3266 3453 1.896660 ACGCACACCCACACCAATC 60.897 57.895 0.00 0.00 0.00 2.67
3267 3454 2.192861 CACGCACACCCACACCAAT 61.193 57.895 0.00 0.00 0.00 3.16
3268 3455 2.826287 CACGCACACCCACACCAA 60.826 61.111 0.00 0.00 0.00 3.67
3271 3458 3.952675 CTGCACGCACACCCACAC 61.953 66.667 0.00 0.00 0.00 3.82
3272 3459 3.986072 AACTGCACGCACACCCACA 62.986 57.895 0.00 0.00 0.00 4.17
3273 3460 3.181169 GAACTGCACGCACACCCAC 62.181 63.158 0.00 0.00 0.00 4.61
3274 3461 2.034048 TAGAACTGCACGCACACCCA 62.034 55.000 0.00 0.00 0.00 4.51
3275 3462 0.673644 ATAGAACTGCACGCACACCC 60.674 55.000 0.00 0.00 0.00 4.61
3277 3464 2.285220 CCATATAGAACTGCACGCACAC 59.715 50.000 0.00 0.00 0.00 3.82
3278 3465 2.549926 CCATATAGAACTGCACGCACA 58.450 47.619 0.00 0.00 0.00 4.57
3279 3466 1.261619 GCCATATAGAACTGCACGCAC 59.738 52.381 0.00 0.00 0.00 5.34
3280 3467 1.134551 TGCCATATAGAACTGCACGCA 60.135 47.619 0.00 0.00 0.00 5.24
3281 3468 1.581934 TGCCATATAGAACTGCACGC 58.418 50.000 0.00 0.00 0.00 5.34
3282 3469 3.392882 TGATGCCATATAGAACTGCACG 58.607 45.455 0.00 0.00 34.33 5.34
3283 3470 4.635223 TCTGATGCCATATAGAACTGCAC 58.365 43.478 0.00 0.00 34.33 4.57
3284 3471 4.801914 GCTCTGATGCCATATAGAACTGCA 60.802 45.833 0.00 0.00 36.23 4.41
3285 3472 3.683822 GCTCTGATGCCATATAGAACTGC 59.316 47.826 0.00 0.00 0.00 4.40
3298 3485 4.924305 TGGAATTTATTGGCTCTGATGC 57.076 40.909 0.00 0.00 0.00 3.91
3299 3486 6.461110 ACTTGGAATTTATTGGCTCTGATG 57.539 37.500 0.00 0.00 0.00 3.07
3300 3487 6.664816 TGAACTTGGAATTTATTGGCTCTGAT 59.335 34.615 0.00 0.00 0.00 2.90
3301 3488 6.009589 TGAACTTGGAATTTATTGGCTCTGA 58.990 36.000 0.00 0.00 0.00 3.27
3302 3489 6.271488 TGAACTTGGAATTTATTGGCTCTG 57.729 37.500 0.00 0.00 0.00 3.35
3303 3490 6.721208 TCTTGAACTTGGAATTTATTGGCTCT 59.279 34.615 0.00 0.00 0.00 4.09
3304 3491 6.808704 GTCTTGAACTTGGAATTTATTGGCTC 59.191 38.462 0.00 0.00 0.00 4.70
3305 3492 6.295292 GGTCTTGAACTTGGAATTTATTGGCT 60.295 38.462 0.00 0.00 0.00 4.75
3306 3493 5.869344 GGTCTTGAACTTGGAATTTATTGGC 59.131 40.000 0.00 0.00 0.00 4.52
3307 3494 6.398095 GGGTCTTGAACTTGGAATTTATTGG 58.602 40.000 0.00 0.00 0.00 3.16
3308 3495 6.072175 TCGGGTCTTGAACTTGGAATTTATTG 60.072 38.462 0.00 0.00 0.00 1.90
3309 3496 6.007703 TCGGGTCTTGAACTTGGAATTTATT 58.992 36.000 0.00 0.00 0.00 1.40
3310 3497 5.414765 GTCGGGTCTTGAACTTGGAATTTAT 59.585 40.000 0.00 0.00 0.00 1.40
3311 3498 4.758165 GTCGGGTCTTGAACTTGGAATTTA 59.242 41.667 0.00 0.00 0.00 1.40
3312 3499 3.568430 GTCGGGTCTTGAACTTGGAATTT 59.432 43.478 0.00 0.00 0.00 1.82
3313 3500 3.146847 GTCGGGTCTTGAACTTGGAATT 58.853 45.455 0.00 0.00 0.00 2.17
3314 3501 2.372172 AGTCGGGTCTTGAACTTGGAAT 59.628 45.455 0.00 0.00 0.00 3.01
3315 3502 1.766496 AGTCGGGTCTTGAACTTGGAA 59.234 47.619 0.00 0.00 0.00 3.53
3316 3503 1.420430 AGTCGGGTCTTGAACTTGGA 58.580 50.000 0.00 0.00 0.00 3.53
3317 3504 2.143925 GAAGTCGGGTCTTGAACTTGG 58.856 52.381 0.00 0.00 0.00 3.61
3318 3505 3.113260 AGAAGTCGGGTCTTGAACTTG 57.887 47.619 0.00 0.00 0.00 3.16
3319 3506 3.840124 AAGAAGTCGGGTCTTGAACTT 57.160 42.857 0.00 0.00 34.03 2.66
3320 3507 3.640029 TGTAAGAAGTCGGGTCTTGAACT 59.360 43.478 6.46 0.00 36.06 3.01
3321 3508 3.986277 TGTAAGAAGTCGGGTCTTGAAC 58.014 45.455 6.46 0.35 36.06 3.18
3322 3509 4.884668 ATGTAAGAAGTCGGGTCTTGAA 57.115 40.909 6.46 0.00 36.06 2.69
3323 3510 4.884668 AATGTAAGAAGTCGGGTCTTGA 57.115 40.909 6.46 0.00 36.06 3.02
3324 3511 6.255887 GTCATAATGTAAGAAGTCGGGTCTTG 59.744 42.308 6.46 0.00 36.06 3.02
3325 3512 6.154706 AGTCATAATGTAAGAAGTCGGGTCTT 59.845 38.462 0.00 0.00 38.80 3.01
3326 3513 5.657302 AGTCATAATGTAAGAAGTCGGGTCT 59.343 40.000 0.00 0.00 0.00 3.85
3327 3514 5.903810 AGTCATAATGTAAGAAGTCGGGTC 58.096 41.667 0.00 0.00 0.00 4.46
3328 3515 5.934402 AGTCATAATGTAAGAAGTCGGGT 57.066 39.130 0.00 0.00 0.00 5.28
3364 3554 4.216257 GCTCAAGTGCCTTTGATTTACAGA 59.784 41.667 1.05 0.00 36.55 3.41
3368 3558 4.397420 TGAGCTCAAGTGCCTTTGATTTA 58.603 39.130 15.67 0.00 36.55 1.40
3378 3568 3.137533 AGAAGAAGTTGAGCTCAAGTGC 58.862 45.455 32.19 30.34 39.29 4.40
3428 3621 1.326951 AAGTTGTTGGCGCCCAAACT 61.327 50.000 26.77 25.51 45.73 2.66
3434 3627 1.483316 GTACAAAAGTTGTTGGCGCC 58.517 50.000 22.73 22.73 42.22 6.53
3437 3630 3.548616 GGGTACGTACAAAAGTTGTTGGC 60.549 47.826 26.02 4.81 42.22 4.52
3438 3631 3.626670 TGGGTACGTACAAAAGTTGTTGG 59.373 43.478 26.02 0.00 42.22 3.77
3443 3636 3.135994 CAGCTGGGTACGTACAAAAGTT 58.864 45.455 26.02 14.71 0.00 2.66
3445 3638 2.762745 ACAGCTGGGTACGTACAAAAG 58.237 47.619 26.02 19.25 0.00 2.27
3487 3680 5.104982 AGCAGAGGTTGTTTGGAAATTTCAA 60.105 36.000 19.49 5.77 0.00 2.69
3499 3692 3.558746 CCTCATTCAGAGCAGAGGTTGTT 60.559 47.826 0.00 0.00 43.31 2.83
3510 3711 3.347077 AGGTTCTTGCCTCATTCAGAG 57.653 47.619 0.00 0.00 44.31 3.35
3609 3810 2.739932 GCTGAGGCTTGCGAATCTAGAA 60.740 50.000 0.00 0.00 35.22 2.10
3685 3886 5.412640 TGACGAAACACTCTTTACTGTCAA 58.587 37.500 0.00 0.00 31.55 3.18
3687 3888 5.173492 GTCTGACGAAACACTCTTTACTGTC 59.827 44.000 0.00 0.00 0.00 3.51
3688 3889 5.041940 GTCTGACGAAACACTCTTTACTGT 58.958 41.667 0.00 0.00 0.00 3.55
3689 3890 5.041287 TGTCTGACGAAACACTCTTTACTG 58.959 41.667 2.98 0.00 0.00 2.74
3690 3891 5.258456 TGTCTGACGAAACACTCTTTACT 57.742 39.130 2.98 0.00 0.00 2.24
3692 3893 4.501559 CGTTGTCTGACGAAACACTCTTTA 59.498 41.667 0.00 0.00 45.47 1.85
3693 3894 3.306166 CGTTGTCTGACGAAACACTCTTT 59.694 43.478 0.00 0.00 45.47 2.52
3695 3896 2.460918 CGTTGTCTGACGAAACACTCT 58.539 47.619 0.00 0.00 45.47 3.24
3718 4357 2.338500 GTCGCAGAGTTTTCCTACAGG 58.662 52.381 0.00 0.00 36.95 4.00
3724 4363 1.347320 CTACGGTCGCAGAGTTTTCC 58.653 55.000 0.00 0.00 36.95 3.13
3736 4375 4.608951 CAAAGATACTAGTGGCTACGGTC 58.391 47.826 5.39 0.00 0.00 4.79
3745 4384 5.161358 TGTCGTTGAGCAAAGATACTAGTG 58.839 41.667 5.39 0.00 31.94 2.74
3750 4389 4.992381 ACTTGTCGTTGAGCAAAGATAC 57.008 40.909 2.41 0.00 31.94 2.24
3751 4390 5.168569 CCTACTTGTCGTTGAGCAAAGATA 58.831 41.667 2.41 0.00 31.94 1.98
3752 4391 3.997021 CCTACTTGTCGTTGAGCAAAGAT 59.003 43.478 2.41 0.00 31.94 2.40
3754 4393 3.131396 ACCTACTTGTCGTTGAGCAAAG 58.869 45.455 0.00 0.00 0.00 2.77
3756 4395 2.902705 ACCTACTTGTCGTTGAGCAA 57.097 45.000 0.00 0.00 0.00 3.91
3758 4397 4.990257 TGTATACCTACTTGTCGTTGAGC 58.010 43.478 0.00 0.00 0.00 4.26
3762 4401 7.117236 CACACAAATGTATACCTACTTGTCGTT 59.883 37.037 0.00 0.00 36.72 3.85
3766 4405 6.775708 ACCACACAAATGTATACCTACTTGT 58.224 36.000 0.00 2.32 36.72 3.16
3769 4408 6.614694 TGACCACACAAATGTATACCTACT 57.385 37.500 0.00 0.00 36.72 2.57
3770 4409 7.675962 TTTGACCACACAAATGTATACCTAC 57.324 36.000 0.00 0.00 36.72 3.18
3772 4411 8.276252 GTATTTGACCACACAAATGTATACCT 57.724 34.615 14.26 0.00 45.85 3.08
3807 4522 0.976641 CTGGTCTCCTAGTGTTGCCA 59.023 55.000 0.00 0.00 0.00 4.92
3808 4523 0.977395 ACTGGTCTCCTAGTGTTGCC 59.023 55.000 0.00 0.00 0.00 4.52
3926 4641 2.558359 CCTGTGATTTCAGACCAAACCC 59.442 50.000 0.00 0.00 37.61 4.11
3995 4710 6.405731 GGCAGATAGATGTATCTCTGATCACC 60.406 46.154 9.37 7.11 43.13 4.02


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

AutoCloner maintained by Alex Coulton.