Multiple sequence alignment - TraesCS2B01G474300

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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 TraesCS2B01G474300 chr2B 100.000 2617 0 0 1 2617 671214700 671212084 0.000000e+00 4833
1 TraesCS2B01G474300 chr2B 89.938 646 39 6 1851 2495 671239625 671239005 0.000000e+00 809
2 TraesCS2B01G474300 chr2B 95.164 517 16 3 55 571 671240129 671239622 0.000000e+00 808
3 TraesCS2B01G474300 chr2B 88.293 205 22 2 1786 1988 472991134 472991338 7.230000e-61 244
4 TraesCS2B01G474300 chr2B 86.957 207 23 3 1786 1988 407320372 407320578 2.030000e-56 230
5 TraesCS2B01G474300 chr2B 86.957 207 23 3 1786 1988 407416164 407416370 2.030000e-56 230
6 TraesCS2B01G474300 chr2B 96.032 126 5 0 2492 2617 620628592 620628717 3.410000e-49 206
7 TraesCS2B01G474300 chr2A 88.319 1130 68 18 672 1789 702194413 702193336 0.000000e+00 1297
8 TraesCS2B01G474300 chr2A 91.503 306 13 7 55 356 702194819 702194523 2.420000e-110 409
9 TraesCS2B01G474300 chr2A 89.456 294 22 4 2202 2495 702192586 702192302 1.910000e-96 363
10 TraesCS2B01G474300 chr2A 75.403 248 53 8 1044 1287 717878439 717878196 2.130000e-21 113
11 TraesCS2B01G474300 chr2D 88.866 952 61 19 864 1802 561935475 561934556 0.000000e+00 1129
12 TraesCS2B01G474300 chr2D 90.816 294 18 3 2202 2495 561933952 561933668 4.090000e-103 385
13 TraesCS2B01G474300 chr2D 94.531 128 6 1 2488 2614 426427794 426427921 2.050000e-46 196
14 TraesCS2B01G474300 chr2D 84.135 208 27 4 1989 2193 561934566 561934362 2.050000e-46 196
15 TraesCS2B01G474300 chr2D 90.972 144 8 4 2475 2614 388429967 388430109 3.440000e-44 189
16 TraesCS2B01G474300 chr2D 75.610 246 56 4 1044 1287 580003863 580003620 4.580000e-23 119
17 TraesCS2B01G474300 chr3B 80.066 908 145 27 823 1703 5588135 5589033 2.200000e-180 641
18 TraesCS2B01G474300 chr3B 98.276 58 1 0 1 58 467282859 467282916 4.610000e-18 102
19 TraesCS2B01G474300 chr7B 88.293 205 22 2 1785 1988 120376792 120376589 7.230000e-61 244
20 TraesCS2B01G474300 chr7B 94.531 128 6 1 2488 2614 588861675 588861802 2.050000e-46 196
21 TraesCS2B01G474300 chr1B 86.473 207 23 4 1786 1988 351567740 351567535 3.390000e-54 222
22 TraesCS2B01G474300 chr1B 90.845 142 10 3 2475 2614 308157159 308157299 1.240000e-43 187
23 TraesCS2B01G474300 chr4B 86.700 203 22 3 1786 1984 550364051 550363850 1.220000e-53 220
24 TraesCS2B01G474300 chr4B 98.276 58 1 0 1 58 490549093 490549150 4.610000e-18 102
25 TraesCS2B01G474300 chr4B 98.276 58 1 0 1 58 563422691 563422634 4.610000e-18 102
26 TraesCS2B01G474300 chr6B 86.139 202 23 4 1786 1983 638388977 638389177 2.040000e-51 213
27 TraesCS2B01G474300 chr5D 86.139 202 23 5 1786 1983 460210861 460210661 2.040000e-51 213
28 TraesCS2B01G474300 chr4D 95.276 127 5 1 2492 2617 74373295 74373169 1.590000e-47 200
29 TraesCS2B01G474300 chr4D 98.276 58 1 0 1 58 149415926 149415983 4.610000e-18 102
30 TraesCS2B01G474300 chr4D 98.276 58 1 0 1 58 286608918 286608861 4.610000e-18 102
31 TraesCS2B01G474300 chr4D 98.276 58 1 0 1 58 334289610 334289667 4.610000e-18 102
32 TraesCS2B01G474300 chr5B 94.574 129 6 1 2487 2614 540367706 540367834 5.710000e-47 198
33 TraesCS2B01G474300 chr6D 93.284 134 6 3 2483 2614 145463871 145464003 7.390000e-46 195
34 TraesCS2B01G474300 chr6D 98.276 58 1 0 1 58 268268515 268268572 4.610000e-18 102
35 TraesCS2B01G474300 chr1D 90.345 145 11 3 2475 2617 277745925 277745782 1.240000e-43 187
36 TraesCS2B01G474300 chrUn 98.276 58 1 0 1 58 342114398 342114341 4.610000e-18 102
37 TraesCS2B01G474300 chr4A 98.276 58 1 0 1 58 610740032 610740089 4.610000e-18 102


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 TraesCS2B01G474300 chr2B 671212084 671214700 2616 True 4833.000000 4833 100.000000 1 2617 1 chr2B.!!$R1 2616
1 TraesCS2B01G474300 chr2B 671239005 671240129 1124 True 808.500000 809 92.551000 55 2495 2 chr2B.!!$R2 2440
2 TraesCS2B01G474300 chr2A 702192302 702194819 2517 True 689.666667 1297 89.759333 55 2495 3 chr2A.!!$R2 2440
3 TraesCS2B01G474300 chr2D 561933668 561935475 1807 True 570.000000 1129 87.939000 864 2495 3 chr2D.!!$R2 1631
4 TraesCS2B01G474300 chr3B 5588135 5589033 898 False 641.000000 641 80.066000 823 1703 1 chr3B.!!$F1 880

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
43 44 0.10339 TTCGAGGTGTGAACTTGCGA 59.897 50.0 0.0 0.0 0.0 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1963 0.034089 AGAGGCATGGCACTAAACCC 60.034 55.0 22.64 0.0 0.0 4.11 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
21 22 2.972625 TCTAGGTTTGCCAGAATGACG 58.027 47.619 0.00 0.00 39.69 4.35
22 23 1.398390 CTAGGTTTGCCAGAATGACGC 59.602 52.381 0.00 0.00 39.69 5.19
23 24 1.212751 GGTTTGCCAGAATGACGCC 59.787 57.895 0.00 0.00 39.69 5.68
24 25 1.244019 GGTTTGCCAGAATGACGCCT 61.244 55.000 0.00 0.00 39.69 5.52
25 26 0.598065 GTTTGCCAGAATGACGCCTT 59.402 50.000 0.00 0.00 39.69 4.35
26 27 0.881118 TTTGCCAGAATGACGCCTTC 59.119 50.000 0.00 0.00 39.69 3.46
27 28 1.298157 TTGCCAGAATGACGCCTTCG 61.298 55.000 0.00 0.00 39.69 3.79
28 29 1.447838 GCCAGAATGACGCCTTCGA 60.448 57.895 0.00 0.00 39.69 3.71
29 30 1.424493 GCCAGAATGACGCCTTCGAG 61.424 60.000 0.00 0.00 39.69 4.04
30 31 0.807667 CCAGAATGACGCCTTCGAGG 60.808 60.000 0.00 0.00 39.69 4.63
31 32 0.108615 CAGAATGACGCCTTCGAGGT 60.109 55.000 0.00 0.00 39.69 3.85
37 38 3.550656 CGCCTTCGAGGTGTGAAC 58.449 61.111 6.37 0.00 40.92 3.18
38 39 1.006102 CGCCTTCGAGGTGTGAACT 60.006 57.895 6.37 0.00 40.92 3.01
39 40 0.600255 CGCCTTCGAGGTGTGAACTT 60.600 55.000 6.37 0.00 40.92 2.66
40 41 0.868406 GCCTTCGAGGTGTGAACTTG 59.132 55.000 0.00 0.00 37.80 3.16
41 42 0.868406 CCTTCGAGGTGTGAACTTGC 59.132 55.000 0.00 0.00 0.00 4.01
42 43 0.508641 CTTCGAGGTGTGAACTTGCG 59.491 55.000 0.00 0.00 0.00 4.85
43 44 0.103390 TTCGAGGTGTGAACTTGCGA 59.897 50.000 0.00 0.00 0.00 5.10
44 45 0.596600 TCGAGGTGTGAACTTGCGAC 60.597 55.000 0.00 0.00 0.00 5.19
45 46 0.597637 CGAGGTGTGAACTTGCGACT 60.598 55.000 0.00 0.00 0.00 4.18
46 47 1.583054 GAGGTGTGAACTTGCGACTT 58.417 50.000 0.00 0.00 0.00 3.01
47 48 1.261619 GAGGTGTGAACTTGCGACTTG 59.738 52.381 0.00 0.00 0.00 3.16
48 49 0.317020 GGTGTGAACTTGCGACTTGC 60.317 55.000 0.00 0.00 46.70 4.01
49 50 0.317020 GTGTGAACTTGCGACTTGCC 60.317 55.000 0.00 0.00 45.60 4.52
50 51 1.082756 GTGAACTTGCGACTTGCCG 60.083 57.895 0.00 0.00 45.60 5.69
51 52 2.250939 TGAACTTGCGACTTGCCGG 61.251 57.895 0.00 0.00 45.60 6.13
52 53 2.203153 AACTTGCGACTTGCCGGT 60.203 55.556 1.90 0.00 45.60 5.28
53 54 2.171489 GAACTTGCGACTTGCCGGTC 62.171 60.000 1.90 0.00 45.60 4.79
450 465 3.336138 AGAAATCAGACGGGAACTTCC 57.664 47.619 0.00 0.00 35.23 3.46
467 482 2.899303 TCCAGAAGGATCCCAAAACC 57.101 50.000 8.55 0.00 39.61 3.27
549 564 1.939934 TGCGAGAAATAGGAAATGCCG 59.060 47.619 0.00 0.00 43.43 5.69
554 569 2.097466 AGAAATAGGAAATGCCGCAACG 59.903 45.455 0.00 0.00 43.43 4.10
567 582 4.426313 CAACGCCCTTCCCCTCCC 62.426 72.222 0.00 0.00 0.00 4.30
568 583 4.995058 AACGCCCTTCCCCTCCCA 62.995 66.667 0.00 0.00 0.00 4.37
569 584 4.995058 ACGCCCTTCCCCTCCCAA 62.995 66.667 0.00 0.00 0.00 4.12
570 585 3.657350 CGCCCTTCCCCTCCCAAA 61.657 66.667 0.00 0.00 0.00 3.28
571 586 2.996330 CGCCCTTCCCCTCCCAAAT 61.996 63.158 0.00 0.00 0.00 2.32
572 587 1.392131 GCCCTTCCCCTCCCAAATT 59.608 57.895 0.00 0.00 0.00 1.82
573 588 0.252696 GCCCTTCCCCTCCCAAATTT 60.253 55.000 0.00 0.00 0.00 1.82
574 589 1.835386 GCCCTTCCCCTCCCAAATTTT 60.835 52.381 0.00 0.00 0.00 1.82
575 590 2.187958 CCCTTCCCCTCCCAAATTTTC 58.812 52.381 0.00 0.00 0.00 2.29
576 591 2.225624 CCCTTCCCCTCCCAAATTTTCT 60.226 50.000 0.00 0.00 0.00 2.52
577 592 3.520696 CCTTCCCCTCCCAAATTTTCTT 58.479 45.455 0.00 0.00 0.00 2.52
578 593 3.909995 CCTTCCCCTCCCAAATTTTCTTT 59.090 43.478 0.00 0.00 0.00 2.52
579 594 4.350816 CCTTCCCCTCCCAAATTTTCTTTT 59.649 41.667 0.00 0.00 0.00 2.27
580 595 5.163099 CCTTCCCCTCCCAAATTTTCTTTTT 60.163 40.000 0.00 0.00 0.00 1.94
581 596 5.303259 TCCCCTCCCAAATTTTCTTTTTG 57.697 39.130 0.00 0.00 34.55 2.44
582 597 4.971924 TCCCCTCCCAAATTTTCTTTTTGA 59.028 37.500 0.00 0.00 36.40 2.69
583 598 5.071653 TCCCCTCCCAAATTTTCTTTTTGAG 59.928 40.000 0.00 0.00 36.40 3.02
584 599 5.163205 CCCCTCCCAAATTTTCTTTTTGAGT 60.163 40.000 0.00 0.00 36.40 3.41
585 600 6.356556 CCCTCCCAAATTTTCTTTTTGAGTT 58.643 36.000 0.00 0.00 36.40 3.01
586 601 6.260714 CCCTCCCAAATTTTCTTTTTGAGTTG 59.739 38.462 0.00 0.00 36.40 3.16
587 602 6.260714 CCTCCCAAATTTTCTTTTTGAGTTGG 59.739 38.462 0.00 0.00 36.40 3.77
588 603 6.118852 TCCCAAATTTTCTTTTTGAGTTGGG 58.881 36.000 12.76 12.76 36.40 4.12
589 604 5.221028 CCCAAATTTTCTTTTTGAGTTGGGC 60.221 40.000 7.42 0.00 36.40 5.36
590 605 5.356470 CCAAATTTTCTTTTTGAGTTGGGCA 59.644 36.000 0.00 0.00 36.40 5.36
591 606 6.039605 CCAAATTTTCTTTTTGAGTTGGGCAT 59.960 34.615 0.00 0.00 36.40 4.40
592 607 6.866010 AATTTTCTTTTTGAGTTGGGCATC 57.134 33.333 0.00 0.00 0.00 3.91
593 608 4.335400 TTTCTTTTTGAGTTGGGCATCC 57.665 40.909 0.00 0.00 0.00 3.51
594 609 2.247358 TCTTTTTGAGTTGGGCATCCC 58.753 47.619 0.00 0.00 45.71 3.85
606 621 2.849942 GGGCATCCCAATATTTTTGGC 58.150 47.619 0.69 0.00 44.65 4.52
607 622 2.172293 GGGCATCCCAATATTTTTGGCA 59.828 45.455 0.69 0.00 44.65 4.92
608 623 3.181441 GGGCATCCCAATATTTTTGGCAT 60.181 43.478 0.69 0.00 44.65 4.40
609 624 4.041444 GGGCATCCCAATATTTTTGGCATA 59.959 41.667 0.69 0.00 44.65 3.14
610 625 5.455899 GGGCATCCCAATATTTTTGGCATAA 60.456 40.000 0.69 0.00 44.65 1.90
611 626 6.060788 GGCATCCCAATATTTTTGGCATAAA 58.939 36.000 5.59 5.59 38.23 1.40
612 627 6.017192 GGCATCCCAATATTTTTGGCATAAAC 60.017 38.462 5.23 0.00 38.23 2.01
613 628 6.541641 GCATCCCAATATTTTTGGCATAAACA 59.458 34.615 5.23 0.00 38.23 2.83
614 629 7.467131 GCATCCCAATATTTTTGGCATAAACAC 60.467 37.037 5.23 0.00 38.23 3.32
615 630 6.410540 TCCCAATATTTTTGGCATAAACACC 58.589 36.000 5.23 0.00 38.23 4.16
616 631 5.588246 CCCAATATTTTTGGCATAAACACCC 59.412 40.000 5.23 0.00 38.23 4.61
617 632 5.588246 CCAATATTTTTGGCATAAACACCCC 59.412 40.000 5.23 0.00 32.18 4.95
618 633 3.712016 ATTTTTGGCATAAACACCCCC 57.288 42.857 5.23 0.00 0.00 5.40
619 634 2.103153 TTTTGGCATAAACACCCCCA 57.897 45.000 0.00 0.00 0.00 4.96
620 635 2.103153 TTTGGCATAAACACCCCCAA 57.897 45.000 0.00 0.00 34.02 4.12
621 636 1.638529 TTGGCATAAACACCCCCAAG 58.361 50.000 0.00 0.00 32.25 3.61
622 637 0.485099 TGGCATAAACACCCCCAAGT 59.515 50.000 0.00 0.00 0.00 3.16
623 638 1.133009 TGGCATAAACACCCCCAAGTT 60.133 47.619 0.00 0.00 0.00 2.66
624 639 1.974957 GGCATAAACACCCCCAAGTTT 59.025 47.619 0.00 0.00 40.68 2.66
625 640 2.370519 GGCATAAACACCCCCAAGTTTT 59.629 45.455 0.00 0.00 38.71 2.43
626 641 3.579151 GGCATAAACACCCCCAAGTTTTA 59.421 43.478 0.00 0.00 38.71 1.52
627 642 4.224147 GGCATAAACACCCCCAAGTTTTAT 59.776 41.667 0.00 0.00 38.71 1.40
628 643 5.280266 GGCATAAACACCCCCAAGTTTTATT 60.280 40.000 0.00 0.00 38.71 1.40
629 644 6.070710 GGCATAAACACCCCCAAGTTTTATTA 60.071 38.462 0.00 0.00 38.71 0.98
630 645 7.039270 GCATAAACACCCCCAAGTTTTATTAG 58.961 38.462 0.00 0.00 38.71 1.73
631 646 7.552459 CATAAACACCCCCAAGTTTTATTAGG 58.448 38.462 0.00 0.00 38.71 2.69
632 647 5.342361 AACACCCCCAAGTTTTATTAGGA 57.658 39.130 0.00 0.00 0.00 2.94
633 648 5.342361 ACACCCCCAAGTTTTATTAGGAA 57.658 39.130 0.00 0.00 0.00 3.36
634 649 5.910931 ACACCCCCAAGTTTTATTAGGAAT 58.089 37.500 0.00 0.00 0.00 3.01
635 650 7.046891 ACACCCCCAAGTTTTATTAGGAATA 57.953 36.000 0.00 0.00 0.00 1.75
636 651 7.480437 ACACCCCCAAGTTTTATTAGGAATAA 58.520 34.615 0.00 0.00 0.00 1.40
637 652 7.398047 ACACCCCCAAGTTTTATTAGGAATAAC 59.602 37.037 0.00 0.00 33.32 1.89
638 653 7.618117 CACCCCCAAGTTTTATTAGGAATAACT 59.382 37.037 0.00 0.00 33.32 2.24
639 654 8.181524 ACCCCCAAGTTTTATTAGGAATAACTT 58.818 33.333 0.00 0.00 33.32 2.66
640 655 8.474831 CCCCCAAGTTTTATTAGGAATAACTTG 58.525 37.037 15.43 15.43 39.57 3.16
641 656 9.250246 CCCCAAGTTTTATTAGGAATAACTTGA 57.750 33.333 21.15 0.00 40.91 3.02
652 667 6.901081 AGGAATAACTTGAGTCCAAAAAGG 57.099 37.500 0.00 0.00 35.99 3.11
653 668 6.610830 AGGAATAACTTGAGTCCAAAAAGGA 58.389 36.000 0.00 0.00 46.75 3.36
669 684 7.953493 TCCAAAAAGGAATACAATTACTCCCTT 59.047 33.333 0.00 0.00 45.65 3.95
671 686 7.625828 AAAAGGAATACAATTACTCCCTTCG 57.374 36.000 0.00 0.00 31.97 3.79
687 702 7.390027 ACTCCCTTCGATCCATATTAATTCTG 58.610 38.462 0.00 0.00 0.00 3.02
689 704 8.150827 TCCCTTCGATCCATATTAATTCTGAT 57.849 34.615 0.00 0.00 0.00 2.90
736 751 9.585099 TTAAATGAGCAACAATTAACATGGATC 57.415 29.630 0.00 0.00 31.47 3.36
738 753 4.940654 TGAGCAACAATTAACATGGATCGA 59.059 37.500 0.00 0.00 0.00 3.59
739 754 5.589855 TGAGCAACAATTAACATGGATCGAT 59.410 36.000 0.00 0.00 0.00 3.59
742 757 6.095300 AGCAACAATTAACATGGATCGATGAA 59.905 34.615 22.78 9.14 0.00 2.57
800 893 2.344025 ACTTTGGACTAAATCGGCGAC 58.656 47.619 13.76 0.00 0.00 5.19
806 899 4.699637 TGGACTAAATCGGCGACAATTAT 58.300 39.130 13.76 0.00 0.00 1.28
889 982 9.454859 ACCTTTTTCATTGGTTTGTTCAAATTA 57.545 25.926 1.33 0.00 0.00 1.40
954 1055 6.772605 TCATGGCTATATATATGCACCATCC 58.227 40.000 16.94 1.09 34.26 3.51
955 1056 5.213891 TGGCTATATATATGCACCATCCG 57.786 43.478 5.44 0.00 0.00 4.18
1060 1187 1.720694 CTCCTCGTCCTCCTCTTCGC 61.721 65.000 0.00 0.00 0.00 4.70
1067 1194 2.352032 CCTCCTCTTCGCCCTCGTT 61.352 63.158 0.00 0.00 36.96 3.85
1094 1221 2.303175 GAGGCTTCCACTCTAGACGAT 58.697 52.381 0.00 0.00 32.28 3.73
1102 1229 3.565902 TCCACTCTAGACGATACATGCAG 59.434 47.826 0.00 0.00 0.00 4.41
1107 1234 1.485124 AGACGATACATGCAGGTCCA 58.515 50.000 7.56 0.00 0.00 4.02
1175 1302 4.988598 CAGGCCGACAACGCCAGT 62.989 66.667 0.00 0.00 37.85 4.00
1228 1355 1.112113 GCCACTAAGATCACCCGAGA 58.888 55.000 0.00 0.00 0.00 4.04
1253 1380 3.564027 GCGAACATCCGGAAGCGG 61.564 66.667 9.01 0.56 0.00 5.52
1330 1457 2.387445 GCCGCATGCACTACACGAA 61.387 57.895 19.57 0.00 40.77 3.85
1386 1513 3.071479 GTCAAGTCGGGTAATTTGCAGA 58.929 45.455 0.00 0.00 0.00 4.26
1388 1515 3.751175 TCAAGTCGGGTAATTTGCAGAAG 59.249 43.478 0.00 0.00 0.00 2.85
1508 1635 0.839853 AGTTCTCCAAGGGCTGCTCT 60.840 55.000 0.00 0.00 0.00 4.09
1565 1693 2.100631 CCGCCGAGGATGTGTGAAC 61.101 63.158 0.00 0.00 45.00 3.18
1635 1769 4.590850 AAACTCTTGGAACCTGCAATTC 57.409 40.909 2.37 2.37 0.00 2.17
1667 1801 5.687285 GTGAACTTTGCAAGTATGTTTGGAG 59.313 40.000 0.00 0.00 41.91 3.86
1669 1803 4.469657 ACTTTGCAAGTATGTTTGGAGGA 58.530 39.130 0.00 0.00 40.69 3.71
1674 1808 6.024552 TGCAAGTATGTTTGGAGGAAAATC 57.975 37.500 0.00 0.00 0.00 2.17
1675 1809 5.047377 TGCAAGTATGTTTGGAGGAAAATCC 60.047 40.000 0.00 0.00 40.03 3.01
1795 1940 2.598589 CATGTTTACATGCAGCCACAC 58.401 47.619 9.69 0.00 45.92 3.82
1796 1941 1.979855 TGTTTACATGCAGCCACACT 58.020 45.000 0.00 0.00 0.00 3.55
1797 1942 2.305928 TGTTTACATGCAGCCACACTT 58.694 42.857 0.00 0.00 0.00 3.16
1798 1943 2.034432 TGTTTACATGCAGCCACACTTG 59.966 45.455 0.00 0.00 0.00 3.16
1799 1944 1.979855 TTACATGCAGCCACACTTGT 58.020 45.000 0.00 0.00 0.00 3.16
1800 1945 1.522668 TACATGCAGCCACACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
1801 1946 0.179009 ACATGCAGCCACACTTGTCT 60.179 50.000 0.00 0.00 0.00 3.41
1802 1947 0.956633 CATGCAGCCACACTTGTCTT 59.043 50.000 0.00 0.00 0.00 3.01
1803 1948 2.153645 CATGCAGCCACACTTGTCTTA 58.846 47.619 0.00 0.00 0.00 2.10
1804 1949 2.566833 TGCAGCCACACTTGTCTTAT 57.433 45.000 0.00 0.00 0.00 1.73
1805 1950 3.694043 TGCAGCCACACTTGTCTTATA 57.306 42.857 0.00 0.00 0.00 0.98
1806 1951 3.599343 TGCAGCCACACTTGTCTTATAG 58.401 45.455 0.00 0.00 0.00 1.31
1807 1952 2.939103 GCAGCCACACTTGTCTTATAGG 59.061 50.000 0.00 0.00 0.00 2.57
1808 1953 3.535561 CAGCCACACTTGTCTTATAGGG 58.464 50.000 0.00 0.00 0.00 3.53
1809 1954 2.505819 AGCCACACTTGTCTTATAGGGG 59.494 50.000 0.00 0.00 0.00 4.79
1810 1955 2.238898 GCCACACTTGTCTTATAGGGGT 59.761 50.000 0.00 0.00 0.00 4.95
1811 1956 3.681874 GCCACACTTGTCTTATAGGGGTC 60.682 52.174 0.00 0.00 0.00 4.46
1812 1957 3.118371 CCACACTTGTCTTATAGGGGTCC 60.118 52.174 0.00 0.00 0.00 4.46
1813 1958 3.775316 CACACTTGTCTTATAGGGGTCCT 59.225 47.826 0.00 0.00 37.71 3.85
1814 1959 4.960469 CACACTTGTCTTATAGGGGTCCTA 59.040 45.833 0.00 0.00 40.71 2.94
1815 1960 5.424252 CACACTTGTCTTATAGGGGTCCTAA 59.576 44.000 0.00 0.00 39.77 2.69
1816 1961 5.424573 ACACTTGTCTTATAGGGGTCCTAAC 59.575 44.000 0.00 0.00 39.77 2.34
1817 1962 5.661759 CACTTGTCTTATAGGGGTCCTAACT 59.338 44.000 0.00 0.00 39.77 2.24
1818 1963 5.661759 ACTTGTCTTATAGGGGTCCTAACTG 59.338 44.000 0.00 0.00 39.77 3.16
1819 1964 4.553678 TGTCTTATAGGGGTCCTAACTGG 58.446 47.826 0.00 0.00 39.77 4.00
1820 1965 3.902467 GTCTTATAGGGGTCCTAACTGGG 59.098 52.174 0.00 0.00 39.77 4.45
1821 1966 3.538980 TCTTATAGGGGTCCTAACTGGGT 59.461 47.826 0.00 0.00 39.77 4.51
1822 1967 2.984989 ATAGGGGTCCTAACTGGGTT 57.015 50.000 0.00 0.00 39.77 4.11
1823 1968 2.747083 TAGGGGTCCTAACTGGGTTT 57.253 50.000 0.00 0.00 32.55 3.27
1824 1969 2.747083 AGGGGTCCTAACTGGGTTTA 57.253 50.000 0.00 0.00 36.20 2.01
1825 1970 2.558974 AGGGGTCCTAACTGGGTTTAG 58.441 52.381 0.00 0.00 36.20 1.85
1826 1971 2.157895 AGGGGTCCTAACTGGGTTTAGT 60.158 50.000 0.00 0.00 36.20 2.24
1827 1972 2.026542 GGGGTCCTAACTGGGTTTAGTG 60.027 54.545 0.00 0.00 36.20 2.74
1828 1973 2.617276 GGGTCCTAACTGGGTTTAGTGC 60.617 54.545 0.00 0.00 36.20 4.40
1829 1974 2.617276 GGTCCTAACTGGGTTTAGTGCC 60.617 54.545 0.00 0.00 36.20 5.01
1830 1975 2.039348 GTCCTAACTGGGTTTAGTGCCA 59.961 50.000 0.00 0.00 36.20 4.92
1831 1976 2.916934 TCCTAACTGGGTTTAGTGCCAT 59.083 45.455 0.00 0.00 36.20 4.40
1832 1977 3.016736 CCTAACTGGGTTTAGTGCCATG 58.983 50.000 0.00 0.00 0.00 3.66
1833 1978 1.256812 AACTGGGTTTAGTGCCATGC 58.743 50.000 0.00 0.00 0.00 4.06
1834 1979 0.611896 ACTGGGTTTAGTGCCATGCC 60.612 55.000 0.00 0.00 0.00 4.40
1835 1980 0.323725 CTGGGTTTAGTGCCATGCCT 60.324 55.000 0.00 0.00 0.00 4.75
1836 1981 0.323360 TGGGTTTAGTGCCATGCCTC 60.323 55.000 0.00 0.00 0.00 4.70
1837 1982 0.034089 GGGTTTAGTGCCATGCCTCT 60.034 55.000 0.00 0.00 0.00 3.69
1838 1983 1.616994 GGGTTTAGTGCCATGCCTCTT 60.617 52.381 0.00 0.00 0.00 2.85
1839 1984 1.474077 GGTTTAGTGCCATGCCTCTTG 59.526 52.381 0.00 0.00 0.00 3.02
1840 1985 1.135286 GTTTAGTGCCATGCCTCTTGC 60.135 52.381 0.00 0.00 41.77 4.01
1841 1986 0.680921 TTAGTGCCATGCCTCTTGCC 60.681 55.000 0.00 0.00 40.16 4.52
1842 1987 2.874648 TAGTGCCATGCCTCTTGCCG 62.875 60.000 0.00 0.00 40.16 5.69
1845 1990 3.136123 CCATGCCTCTTGCCGGTG 61.136 66.667 1.90 0.00 40.16 4.94
1846 1991 3.818787 CATGCCTCTTGCCGGTGC 61.819 66.667 1.90 0.00 40.16 5.01
1857 2002 2.335712 GCCGGTGCCTTCAAAGAGG 61.336 63.158 1.90 0.00 39.93 3.69
1871 2016 0.905357 AAGAGGGAAGGTCATGGACG 59.095 55.000 0.00 0.00 32.65 4.79
1872 2017 1.153349 GAGGGAAGGTCATGGACGC 60.153 63.158 0.00 0.00 32.65 5.19
1873 2018 2.511600 GGGAAGGTCATGGACGCG 60.512 66.667 3.53 3.53 32.65 6.01
1889 2034 3.120105 CGCGCTACCCTGATCAGA 58.880 61.111 24.62 3.20 0.00 3.27
1893 2038 2.163509 GCGCTACCCTGATCAGATAGA 58.836 52.381 24.62 5.45 0.00 1.98
1895 2040 3.149981 CGCTACCCTGATCAGATAGACA 58.850 50.000 24.62 2.22 0.00 3.41
1909 2054 4.749099 CAGATAGACAGACATAAGCCTTGC 59.251 45.833 0.00 0.00 0.00 4.01
1911 2056 1.550524 AGACAGACATAAGCCTTGCGA 59.449 47.619 0.00 0.00 0.00 5.10
1912 2057 1.929836 GACAGACATAAGCCTTGCGAG 59.070 52.381 0.00 0.00 0.00 5.03
1927 2072 0.743345 GCGAGCCCGAGTTTGGTTAT 60.743 55.000 0.00 0.00 38.22 1.89
1938 2083 4.475944 GAGTTTGGTTATGTGCACATGTC 58.524 43.478 36.72 27.58 37.15 3.06
1939 2084 3.255642 AGTTTGGTTATGTGCACATGTCC 59.744 43.478 36.72 33.24 37.15 4.02
1947 2092 1.149401 TGCACATGTCCCCGTTTGA 59.851 52.632 0.00 0.00 0.00 2.69
1950 2095 1.950484 GCACATGTCCCCGTTTGAGAT 60.950 52.381 0.00 0.00 0.00 2.75
1959 2104 3.936453 TCCCCGTTTGAGATCGTTTATTG 59.064 43.478 0.00 0.00 0.00 1.90
1975 2120 5.220006 CGTTTATTGTTTTGCCACGATGATG 60.220 40.000 0.00 0.00 0.00 3.07
2012 2158 1.529438 ACAGTTTGCGTACGATTGTGG 59.471 47.619 21.65 6.14 0.00 4.17
2109 2256 4.458829 AGACCCTCGGATCCGCCA 62.459 66.667 29.62 12.52 39.59 5.69
2140 2322 4.101448 GGGCTGCCCGTCACTGAT 62.101 66.667 24.16 0.00 32.13 2.90
2211 2904 2.124320 ACTGCCCGTGCACTGTTT 60.124 55.556 16.19 0.00 44.23 2.83
2241 2934 7.380870 CCAAAATGATCGACACACATGTTTTTA 59.619 33.333 0.00 0.00 39.95 1.52
2391 3084 1.518367 AGGGATCCGGATTAGGCAAA 58.482 50.000 20.22 0.00 0.00 3.68
2501 3194 8.933522 ATCTCTATCTCTATCTTCTACTCCCT 57.066 38.462 0.00 0.00 0.00 4.20
2502 3195 8.375493 TCTCTATCTCTATCTTCTACTCCCTC 57.625 42.308 0.00 0.00 0.00 4.30
2503 3196 7.402071 TCTCTATCTCTATCTTCTACTCCCTCC 59.598 44.444 0.00 0.00 0.00 4.30
2504 3197 4.627284 TCTCTATCTTCTACTCCCTCCG 57.373 50.000 0.00 0.00 0.00 4.63
2505 3198 3.975312 TCTCTATCTTCTACTCCCTCCGT 59.025 47.826 0.00 0.00 0.00 4.69
2506 3199 4.412858 TCTCTATCTTCTACTCCCTCCGTT 59.587 45.833 0.00 0.00 0.00 4.44
2507 3200 4.716794 TCTATCTTCTACTCCCTCCGTTC 58.283 47.826 0.00 0.00 0.00 3.95
2508 3201 2.140839 TCTTCTACTCCCTCCGTTCC 57.859 55.000 0.00 0.00 0.00 3.62
2509 3202 1.639628 TCTTCTACTCCCTCCGTTCCT 59.360 52.381 0.00 0.00 0.00 3.36
2510 3203 2.848694 TCTTCTACTCCCTCCGTTCCTA 59.151 50.000 0.00 0.00 0.00 2.94
2511 3204 3.267812 TCTTCTACTCCCTCCGTTCCTAA 59.732 47.826 0.00 0.00 0.00 2.69
2512 3205 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2513 3206 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2514 3207 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
2515 3208 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
2516 3209 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
2517 3210 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2518 3211 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2519 3212 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2520 3213 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2521 3214 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2522 3215 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2523 3216 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2524 3217 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2525 3218 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2556 3249 9.923143 TTTCAAATAGACTACCATATACGGATG 57.077 33.333 0.00 0.00 0.00 3.51
2557 3250 8.645814 TCAAATAGACTACCATATACGGATGT 57.354 34.615 0.00 0.00 0.00 3.06
2558 3251 9.743581 TCAAATAGACTACCATATACGGATGTA 57.256 33.333 0.00 0.00 34.45 2.29
2599 3292 9.606631 AGAATGTAGATTCACTCATTTTACTCC 57.393 33.333 14.46 0.00 40.59 3.85
2600 3293 8.425577 AATGTAGATTCACTCATTTTACTCCG 57.574 34.615 0.00 0.00 0.00 4.63
2601 3294 6.931838 TGTAGATTCACTCATTTTACTCCGT 58.068 36.000 0.00 0.00 0.00 4.69
2602 3295 8.058667 TGTAGATTCACTCATTTTACTCCGTA 57.941 34.615 0.00 0.00 0.00 4.02
2603 3296 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
2604 3297 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
2605 3298 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
2606 3299 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
2607 3300 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
2608 3301 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2609 3302 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2610 3303 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
2611 3304 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
2612 3305 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
2613 3306 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
2614 3307 8.959548 TCATTTTACTCCGTATGTAGTCACTTA 58.040 33.333 0.00 0.00 0.00 2.24
2615 3308 9.745880 CATTTTACTCCGTATGTAGTCACTTAT 57.254 33.333 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.535561 CGTCATTCTGGCAAACCTAGAT 58.464 45.455 0.00 0.00 36.63 1.98
1 2 2.935238 GCGTCATTCTGGCAAACCTAGA 60.935 50.000 0.00 0.00 36.63 2.43
2 3 1.398390 GCGTCATTCTGGCAAACCTAG 59.602 52.381 0.00 0.00 36.63 3.02
3 4 1.448985 GCGTCATTCTGGCAAACCTA 58.551 50.000 0.00 0.00 36.63 3.08
4 5 1.244019 GGCGTCATTCTGGCAAACCT 61.244 55.000 0.00 0.00 36.63 3.50
5 6 1.212751 GGCGTCATTCTGGCAAACC 59.787 57.895 0.00 0.00 0.00 3.27
6 7 0.598065 AAGGCGTCATTCTGGCAAAC 59.402 50.000 0.00 0.00 0.00 2.93
7 8 0.881118 GAAGGCGTCATTCTGGCAAA 59.119 50.000 0.00 0.00 0.00 3.68
8 9 1.298157 CGAAGGCGTCATTCTGGCAA 61.298 55.000 0.55 0.00 0.00 4.52
9 10 1.741401 CGAAGGCGTCATTCTGGCA 60.741 57.895 0.55 0.00 0.00 4.92
10 11 1.424493 CTCGAAGGCGTCATTCTGGC 61.424 60.000 0.55 0.00 38.98 4.85
11 12 0.807667 CCTCGAAGGCGTCATTCTGG 60.808 60.000 0.55 0.00 38.98 3.86
12 13 0.108615 ACCTCGAAGGCGTCATTCTG 60.109 55.000 0.55 0.00 39.63 3.02
13 14 0.108615 CACCTCGAAGGCGTCATTCT 60.109 55.000 0.55 0.00 39.63 2.40
14 15 0.389948 ACACCTCGAAGGCGTCATTC 60.390 55.000 0.55 0.00 39.63 2.67
15 16 0.670546 CACACCTCGAAGGCGTCATT 60.671 55.000 0.55 0.00 39.63 2.57
16 17 1.079819 CACACCTCGAAGGCGTCAT 60.080 57.895 0.55 0.00 39.63 3.06
17 18 1.740332 TTCACACCTCGAAGGCGTCA 61.740 55.000 0.55 0.00 39.63 4.35
18 19 1.006571 TTCACACCTCGAAGGCGTC 60.007 57.895 1.36 0.00 39.63 5.19
19 20 1.300697 GTTCACACCTCGAAGGCGT 60.301 57.895 1.36 0.00 39.63 5.68
20 21 0.600255 AAGTTCACACCTCGAAGGCG 60.600 55.000 1.36 0.00 39.63 5.52
21 22 0.868406 CAAGTTCACACCTCGAAGGC 59.132 55.000 1.36 0.00 39.63 4.35
22 23 0.868406 GCAAGTTCACACCTCGAAGG 59.132 55.000 0.00 0.00 42.49 3.46
23 24 0.508641 CGCAAGTTCACACCTCGAAG 59.491 55.000 0.00 0.00 0.00 3.79
24 25 0.103390 TCGCAAGTTCACACCTCGAA 59.897 50.000 0.00 0.00 39.48 3.71
25 26 0.596600 GTCGCAAGTTCACACCTCGA 60.597 55.000 0.00 0.00 39.48 4.04
26 27 0.597637 AGTCGCAAGTTCACACCTCG 60.598 55.000 0.00 0.00 39.48 4.63
27 28 1.261619 CAAGTCGCAAGTTCACACCTC 59.738 52.381 0.00 0.00 39.48 3.85
28 29 1.299541 CAAGTCGCAAGTTCACACCT 58.700 50.000 0.00 0.00 39.48 4.00
29 30 0.317020 GCAAGTCGCAAGTTCACACC 60.317 55.000 0.00 0.00 41.79 4.16
30 31 0.317020 GGCAAGTCGCAAGTTCACAC 60.317 55.000 0.00 0.00 45.17 3.82
31 32 1.771073 CGGCAAGTCGCAAGTTCACA 61.771 55.000 0.00 0.00 45.17 3.58
32 33 1.082756 CGGCAAGTCGCAAGTTCAC 60.083 57.895 0.00 0.00 45.17 3.18
33 34 2.250939 CCGGCAAGTCGCAAGTTCA 61.251 57.895 0.00 0.00 45.17 3.18
34 35 2.171489 GACCGGCAAGTCGCAAGTTC 62.171 60.000 0.00 0.00 45.17 3.01
35 36 2.203153 ACCGGCAAGTCGCAAGTT 60.203 55.556 0.00 0.00 45.17 2.66
36 37 2.665185 GACCGGCAAGTCGCAAGT 60.665 61.111 0.00 0.00 45.17 3.16
37 38 3.423154 GGACCGGCAAGTCGCAAG 61.423 66.667 0.00 0.00 45.17 4.01
210 213 8.039603 AGTTTGGGAAATTCAAAACTCAAAAC 57.960 30.769 15.72 5.37 36.11 2.43
211 214 9.898152 ATAGTTTGGGAAATTCAAAACTCAAAA 57.102 25.926 21.39 10.61 36.11 2.44
212 215 9.898152 AATAGTTTGGGAAATTCAAAACTCAAA 57.102 25.926 21.39 10.86 36.11 2.69
213 216 9.898152 AAATAGTTTGGGAAATTCAAAACTCAA 57.102 25.926 21.39 11.36 36.11 3.02
214 217 9.898152 AAAATAGTTTGGGAAATTCAAAACTCA 57.102 25.926 21.39 12.88 36.11 3.41
216 219 9.898152 TCAAAATAGTTTGGGAAATTCAAAACT 57.102 25.926 21.45 21.45 43.70 2.66
426 441 5.294552 GGAAGTTCCCGTCTGATTTCTATTG 59.705 44.000 11.17 0.00 0.00 1.90
450 465 1.463674 CCGGTTTTGGGATCCTTCTG 58.536 55.000 12.58 3.30 0.00 3.02
467 482 0.395312 AACTGTACACTGGTTCCCCG 59.605 55.000 0.00 0.00 0.00 5.73
554 569 0.252696 AAATTTGGGAGGGGAAGGGC 60.253 55.000 0.00 0.00 0.00 5.19
567 582 6.434018 TGCCCAACTCAAAAAGAAAATTTG 57.566 33.333 0.00 0.00 38.76 2.32
568 583 6.262944 GGATGCCCAACTCAAAAAGAAAATTT 59.737 34.615 0.00 0.00 0.00 1.82
569 584 5.764686 GGATGCCCAACTCAAAAAGAAAATT 59.235 36.000 0.00 0.00 0.00 1.82
570 585 5.308014 GGATGCCCAACTCAAAAAGAAAAT 58.692 37.500 0.00 0.00 0.00 1.82
571 586 4.444164 GGGATGCCCAACTCAAAAAGAAAA 60.444 41.667 0.00 0.00 44.65 2.29
572 587 3.070878 GGGATGCCCAACTCAAAAAGAAA 59.929 43.478 0.00 0.00 44.65 2.52
573 588 2.632512 GGGATGCCCAACTCAAAAAGAA 59.367 45.455 0.00 0.00 44.65 2.52
574 589 2.247358 GGGATGCCCAACTCAAAAAGA 58.753 47.619 0.00 0.00 44.65 2.52
575 590 2.749280 GGGATGCCCAACTCAAAAAG 57.251 50.000 0.00 0.00 44.65 2.27
586 601 2.172293 TGCCAAAAATATTGGGATGCCC 59.828 45.455 0.00 0.00 45.71 5.36
587 602 3.557228 TGCCAAAAATATTGGGATGCC 57.443 42.857 9.12 0.00 39.90 4.40
591 606 6.410540 GGTGTTTATGCCAAAAATATTGGGA 58.589 36.000 9.12 6.62 44.00 4.37
592 607 5.588246 GGGTGTTTATGCCAAAAATATTGGG 59.412 40.000 9.12 0.00 39.90 4.12
593 608 5.588246 GGGGTGTTTATGCCAAAAATATTGG 59.412 40.000 2.84 2.84 42.37 3.16
594 609 5.588246 GGGGGTGTTTATGCCAAAAATATTG 59.412 40.000 0.00 0.00 0.00 1.90
595 610 5.251700 TGGGGGTGTTTATGCCAAAAATATT 59.748 36.000 0.00 0.00 0.00 1.28
596 611 4.785376 TGGGGGTGTTTATGCCAAAAATAT 59.215 37.500 0.00 0.00 0.00 1.28
597 612 4.168101 TGGGGGTGTTTATGCCAAAAATA 58.832 39.130 0.00 0.00 0.00 1.40
598 613 2.982488 TGGGGGTGTTTATGCCAAAAAT 59.018 40.909 0.00 0.00 0.00 1.82
599 614 2.408565 TGGGGGTGTTTATGCCAAAAA 58.591 42.857 0.00 0.00 0.00 1.94
600 615 2.103153 TGGGGGTGTTTATGCCAAAA 57.897 45.000 0.00 0.00 0.00 2.44
601 616 1.974236 CTTGGGGGTGTTTATGCCAAA 59.026 47.619 0.00 0.00 0.00 3.28
602 617 1.133009 ACTTGGGGGTGTTTATGCCAA 60.133 47.619 0.00 0.00 0.00 4.52
603 618 0.485099 ACTTGGGGGTGTTTATGCCA 59.515 50.000 0.00 0.00 0.00 4.92
604 619 1.639722 AACTTGGGGGTGTTTATGCC 58.360 50.000 0.00 0.00 0.00 4.40
605 620 3.762407 AAAACTTGGGGGTGTTTATGC 57.238 42.857 0.00 0.00 35.63 3.14
606 621 7.397761 TCCTAATAAAACTTGGGGGTGTTTATG 59.602 37.037 0.00 0.00 35.63 1.90
607 622 7.480437 TCCTAATAAAACTTGGGGGTGTTTAT 58.520 34.615 0.00 0.00 35.63 1.40
608 623 6.861129 TCCTAATAAAACTTGGGGGTGTTTA 58.139 36.000 0.00 0.00 35.63 2.01
609 624 5.718039 TCCTAATAAAACTTGGGGGTGTTT 58.282 37.500 0.00 0.00 37.92 2.83
610 625 5.342361 TCCTAATAAAACTTGGGGGTGTT 57.658 39.130 0.00 0.00 0.00 3.32
611 626 5.342361 TTCCTAATAAAACTTGGGGGTGT 57.658 39.130 0.00 0.00 0.00 4.16
612 627 7.618117 AGTTATTCCTAATAAAACTTGGGGGTG 59.382 37.037 0.00 0.00 35.29 4.61
613 628 7.715482 AGTTATTCCTAATAAAACTTGGGGGT 58.285 34.615 0.00 0.00 35.29 4.95
614 629 8.474831 CAAGTTATTCCTAATAAAACTTGGGGG 58.525 37.037 15.15 0.00 37.94 5.40
615 630 9.250246 TCAAGTTATTCCTAATAAAACTTGGGG 57.750 33.333 20.10 2.47 39.92 4.96
626 641 9.025041 CCTTTTTGGACTCAAGTTATTCCTAAT 57.975 33.333 0.00 0.00 38.35 1.73
627 642 8.221944 TCCTTTTTGGACTCAAGTTATTCCTAA 58.778 33.333 0.00 0.00 40.56 2.69
628 643 7.751646 TCCTTTTTGGACTCAAGTTATTCCTA 58.248 34.615 0.00 0.00 40.56 2.94
629 644 6.610830 TCCTTTTTGGACTCAAGTTATTCCT 58.389 36.000 0.00 0.00 40.56 3.36
630 645 6.894339 TCCTTTTTGGACTCAAGTTATTCC 57.106 37.500 0.00 0.00 40.56 3.01
631 646 9.841880 GTATTCCTTTTTGGACTCAAGTTATTC 57.158 33.333 0.00 0.00 46.14 1.75
632 647 9.362151 TGTATTCCTTTTTGGACTCAAGTTATT 57.638 29.630 0.00 0.00 46.14 1.40
633 648 8.934023 TGTATTCCTTTTTGGACTCAAGTTAT 57.066 30.769 0.00 0.00 46.14 1.89
634 649 8.754991 TTGTATTCCTTTTTGGACTCAAGTTA 57.245 30.769 0.00 0.00 46.14 2.24
635 650 7.654022 TTGTATTCCTTTTTGGACTCAAGTT 57.346 32.000 0.00 0.00 46.14 2.66
636 651 7.839680 ATTGTATTCCTTTTTGGACTCAAGT 57.160 32.000 0.00 0.00 46.14 3.16
637 652 9.626045 GTAATTGTATTCCTTTTTGGACTCAAG 57.374 33.333 0.00 0.00 46.14 3.02
638 653 9.362151 AGTAATTGTATTCCTTTTTGGACTCAA 57.638 29.630 0.00 0.00 46.14 3.02
639 654 8.934023 AGTAATTGTATTCCTTTTTGGACTCA 57.066 30.769 0.00 0.00 46.14 3.41
640 655 8.459635 GGAGTAATTGTATTCCTTTTTGGACTC 58.540 37.037 0.00 0.00 46.14 3.36
641 656 7.396339 GGGAGTAATTGTATTCCTTTTTGGACT 59.604 37.037 0.00 0.00 46.14 3.85
642 657 7.396339 AGGGAGTAATTGTATTCCTTTTTGGAC 59.604 37.037 0.00 0.00 46.14 4.02
643 658 7.475299 AGGGAGTAATTGTATTCCTTTTTGGA 58.525 34.615 0.00 0.00 44.51 3.53
644 659 7.718334 AGGGAGTAATTGTATTCCTTTTTGG 57.282 36.000 0.00 0.00 36.56 3.28
645 660 7.968405 CGAAGGGAGTAATTGTATTCCTTTTTG 59.032 37.037 0.00 0.00 36.09 2.44
646 661 7.886446 TCGAAGGGAGTAATTGTATTCCTTTTT 59.114 33.333 0.00 0.00 36.09 1.94
647 662 7.399634 TCGAAGGGAGTAATTGTATTCCTTTT 58.600 34.615 0.00 0.00 36.09 2.27
648 663 6.954232 TCGAAGGGAGTAATTGTATTCCTTT 58.046 36.000 0.00 0.00 37.90 3.11
649 664 6.555463 TCGAAGGGAGTAATTGTATTCCTT 57.445 37.500 0.00 0.00 36.56 3.36
650 665 6.239629 GGATCGAAGGGAGTAATTGTATTCCT 60.240 42.308 0.00 0.00 36.56 3.36
651 666 5.932883 GGATCGAAGGGAGTAATTGTATTCC 59.067 44.000 0.00 0.00 35.77 3.01
652 667 6.522054 TGGATCGAAGGGAGTAATTGTATTC 58.478 40.000 0.00 0.00 0.00 1.75
653 668 6.494666 TGGATCGAAGGGAGTAATTGTATT 57.505 37.500 0.00 0.00 0.00 1.89
654 669 6.688073 ATGGATCGAAGGGAGTAATTGTAT 57.312 37.500 0.00 0.00 0.00 2.29
655 670 7.792364 ATATGGATCGAAGGGAGTAATTGTA 57.208 36.000 0.00 0.00 0.00 2.41
656 671 6.688073 ATATGGATCGAAGGGAGTAATTGT 57.312 37.500 0.00 0.00 0.00 2.71
657 672 9.672673 ATTAATATGGATCGAAGGGAGTAATTG 57.327 33.333 0.00 0.00 0.00 2.32
710 725 9.585099 GATCCATGTTAATTGTTGCTCATTTAA 57.415 29.630 0.00 0.00 32.80 1.52
800 893 5.179452 ACTCCCCCGATCCATAATAATTG 57.821 43.478 0.00 0.00 0.00 2.32
806 899 6.963117 ATAAATTACTCCCCCGATCCATAA 57.037 37.500 0.00 0.00 0.00 1.90
850 943 8.997323 CCAATGAAAAAGGTATGTATTGCAAAA 58.003 29.630 1.71 0.00 0.00 2.44
889 982 9.736414 CCTCATGAGTATATCAATCTTCCAATT 57.264 33.333 21.11 0.00 42.53 2.32
890 983 8.888419 ACCTCATGAGTATATCAATCTTCCAAT 58.112 33.333 21.11 0.00 42.53 3.16
891 984 8.267620 ACCTCATGAGTATATCAATCTTCCAA 57.732 34.615 21.11 0.00 42.53 3.53
892 985 7.862274 ACCTCATGAGTATATCAATCTTCCA 57.138 36.000 21.11 0.00 42.53 3.53
1067 1194 1.229209 AGTGGAAGCCTCGGAGGAA 60.229 57.895 27.95 4.12 37.67 3.36
1094 1221 1.146041 GCCGATGGACCTGCATGTA 59.854 57.895 0.00 0.00 0.00 2.29
1107 1234 2.401766 CCTTCTTGCTTGCGCCGAT 61.402 57.895 4.18 0.00 34.43 4.18
1228 1355 2.125106 GGATGTTCGCGGCCTCTT 60.125 61.111 6.13 0.00 0.00 2.85
1247 1374 1.666234 GAGGGCATCGATCCGCTTC 60.666 63.158 7.41 2.88 0.00 3.86
1330 1457 3.490759 CGAGCCATTTCAGCGCGT 61.491 61.111 8.43 0.00 46.45 6.01
1386 1513 1.347707 TGTGAGGTTCATCTTCGCCTT 59.652 47.619 0.00 0.00 32.72 4.35
1388 1515 1.363744 CTGTGAGGTTCATCTTCGCC 58.636 55.000 0.00 0.00 32.72 5.54
1565 1693 4.625800 GCCAGAGCTGTTACCAGG 57.374 61.111 0.00 0.00 39.22 4.45
1635 1769 4.156664 CTTGCAAAGTTCACTGATCTGG 57.843 45.455 0.00 0.00 39.70 3.86
1778 1923 2.034558 ACAAGTGTGGCTGCATGTAAAC 59.965 45.455 0.50 0.00 0.00 2.01
1789 1934 2.238898 ACCCCTATAAGACAAGTGTGGC 59.761 50.000 0.00 0.00 0.00 5.01
1790 1935 3.118371 GGACCCCTATAAGACAAGTGTGG 60.118 52.174 0.00 0.00 0.00 4.17
1791 1936 3.775316 AGGACCCCTATAAGACAAGTGTG 59.225 47.826 0.00 0.00 28.47 3.82
1792 1937 4.076175 AGGACCCCTATAAGACAAGTGT 57.924 45.455 0.00 0.00 28.47 3.55
1793 1938 5.661759 AGTTAGGACCCCTATAAGACAAGTG 59.338 44.000 0.00 0.00 35.87 3.16
1794 1939 5.661759 CAGTTAGGACCCCTATAAGACAAGT 59.338 44.000 0.00 0.00 35.87 3.16
1795 1940 5.070580 CCAGTTAGGACCCCTATAAGACAAG 59.929 48.000 0.00 0.00 41.22 3.16
1796 1941 4.966805 CCAGTTAGGACCCCTATAAGACAA 59.033 45.833 0.00 0.00 41.22 3.18
1797 1942 4.553678 CCAGTTAGGACCCCTATAAGACA 58.446 47.826 0.00 0.00 41.22 3.41
1798 1943 3.902467 CCCAGTTAGGACCCCTATAAGAC 59.098 52.174 0.00 0.00 41.22 3.01
1799 1944 3.538980 ACCCAGTTAGGACCCCTATAAGA 59.461 47.826 0.00 0.00 41.22 2.10
1800 1945 3.937751 ACCCAGTTAGGACCCCTATAAG 58.062 50.000 0.00 0.00 41.22 1.73
1801 1946 4.372953 AACCCAGTTAGGACCCCTATAA 57.627 45.455 0.00 0.00 41.22 0.98
1802 1947 4.372953 AAACCCAGTTAGGACCCCTATA 57.627 45.455 0.00 0.00 41.22 1.31
1803 1948 2.984989 AACCCAGTTAGGACCCCTAT 57.015 50.000 0.00 0.00 41.22 2.57
1804 1949 2.747083 AAACCCAGTTAGGACCCCTA 57.253 50.000 0.00 0.00 41.22 3.53
1805 1950 2.157895 ACTAAACCCAGTTAGGACCCCT 60.158 50.000 0.00 0.00 41.22 4.79
1806 1951 2.026542 CACTAAACCCAGTTAGGACCCC 60.027 54.545 0.00 0.00 41.22 4.95
1807 1952 2.617276 GCACTAAACCCAGTTAGGACCC 60.617 54.545 0.00 0.00 41.22 4.46
1808 1953 2.617276 GGCACTAAACCCAGTTAGGACC 60.617 54.545 0.00 0.00 41.22 4.46
1809 1954 2.039348 TGGCACTAAACCCAGTTAGGAC 59.961 50.000 0.00 0.00 41.22 3.85
1810 1955 2.340731 TGGCACTAAACCCAGTTAGGA 58.659 47.619 0.00 0.00 41.22 2.94
1811 1956 2.871096 TGGCACTAAACCCAGTTAGG 57.129 50.000 0.00 0.00 35.72 2.69
1812 1957 2.423538 GCATGGCACTAAACCCAGTTAG 59.576 50.000 0.00 0.00 37.16 2.34
1813 1958 2.442413 GCATGGCACTAAACCCAGTTA 58.558 47.619 0.00 0.00 34.01 2.24
1814 1959 1.256812 GCATGGCACTAAACCCAGTT 58.743 50.000 0.00 0.00 34.01 3.16
1815 1960 0.611896 GGCATGGCACTAAACCCAGT 60.612 55.000 15.47 0.00 34.01 4.00
1816 1961 0.323725 AGGCATGGCACTAAACCCAG 60.324 55.000 22.64 0.00 34.01 4.45
1817 1962 0.323360 GAGGCATGGCACTAAACCCA 60.323 55.000 22.64 0.00 35.21 4.51
1818 1963 0.034089 AGAGGCATGGCACTAAACCC 60.034 55.000 22.64 0.00 0.00 4.11
1819 1964 1.474077 CAAGAGGCATGGCACTAAACC 59.526 52.381 22.64 0.00 0.00 3.27
1820 1965 1.135286 GCAAGAGGCATGGCACTAAAC 60.135 52.381 22.64 9.55 43.97 2.01
1821 1966 1.176527 GCAAGAGGCATGGCACTAAA 58.823 50.000 22.64 0.00 43.97 1.85
1822 1967 2.872408 GCAAGAGGCATGGCACTAA 58.128 52.632 22.64 0.00 43.97 2.24
1823 1968 4.643795 GCAAGAGGCATGGCACTA 57.356 55.556 22.64 0.00 43.97 2.74
1833 1978 2.747855 GAAGGCACCGGCAAGAGG 60.748 66.667 0.00 0.00 43.71 3.69
1834 1979 1.172180 TTTGAAGGCACCGGCAAGAG 61.172 55.000 0.00 0.00 43.71 2.85
1835 1980 1.152860 TTTGAAGGCACCGGCAAGA 60.153 52.632 0.00 0.00 43.71 3.02
1836 1981 1.172180 TCTTTGAAGGCACCGGCAAG 61.172 55.000 0.00 0.00 43.71 4.01
1837 1982 1.152860 TCTTTGAAGGCACCGGCAA 60.153 52.632 0.00 0.00 43.71 4.52
1838 1983 1.600636 CTCTTTGAAGGCACCGGCA 60.601 57.895 0.00 0.00 43.71 5.69
1839 1984 2.335712 CCTCTTTGAAGGCACCGGC 61.336 63.158 0.00 0.00 40.13 6.13
1840 1985 1.675641 CCCTCTTTGAAGGCACCGG 60.676 63.158 0.00 0.00 34.88 5.28
1841 1986 0.250727 TTCCCTCTTTGAAGGCACCG 60.251 55.000 0.00 0.00 34.88 4.94
1842 1987 1.539157 CTTCCCTCTTTGAAGGCACC 58.461 55.000 0.00 0.00 36.43 5.01
1847 1992 3.009473 TCCATGACCTTCCCTCTTTGAAG 59.991 47.826 0.00 0.00 39.13 3.02
1848 1993 2.986019 TCCATGACCTTCCCTCTTTGAA 59.014 45.455 0.00 0.00 0.00 2.69
1849 1994 2.305927 GTCCATGACCTTCCCTCTTTGA 59.694 50.000 0.00 0.00 0.00 2.69
1857 2002 3.195698 GCGCGTCCATGACCTTCC 61.196 66.667 8.43 0.00 0.00 3.46
1871 2016 2.427540 ATCTGATCAGGGTAGCGCGC 62.428 60.000 26.66 26.66 0.00 6.86
1872 2017 0.881796 TATCTGATCAGGGTAGCGCG 59.118 55.000 22.42 0.00 0.00 6.86
1873 2018 2.094957 GTCTATCTGATCAGGGTAGCGC 60.095 54.545 22.42 14.99 0.00 5.92
1881 2026 6.209192 AGGCTTATGTCTGTCTATCTGATCAG 59.791 42.308 17.07 17.07 0.00 2.90
1889 2034 3.384789 TCGCAAGGCTTATGTCTGTCTAT 59.615 43.478 0.00 0.00 38.47 1.98
1893 2038 2.009042 GCTCGCAAGGCTTATGTCTGT 61.009 52.381 0.00 0.00 38.47 3.41
1895 2040 0.462759 GGCTCGCAAGGCTTATGTCT 60.463 55.000 0.00 0.00 44.47 3.41
1909 2054 1.006832 CATAACCAAACTCGGGCTCG 58.993 55.000 0.00 0.00 37.82 5.03
1911 2056 1.821216 CACATAACCAAACTCGGGCT 58.179 50.000 0.00 0.00 0.00 5.19
1912 2057 0.170339 GCACATAACCAAACTCGGGC 59.830 55.000 0.00 0.00 0.00 6.13
1927 2072 1.152860 AAACGGGGACATGTGCACA 60.153 52.632 24.08 24.08 0.00 4.57
1938 2083 3.687698 ACAATAAACGATCTCAAACGGGG 59.312 43.478 0.00 0.00 0.00 5.73
1939 2084 4.939509 ACAATAAACGATCTCAAACGGG 57.060 40.909 0.00 0.00 0.00 5.28
1947 2092 4.214545 TCGTGGCAAAACAATAAACGATCT 59.785 37.500 0.00 0.00 34.04 2.75
1950 2095 3.965292 TCGTGGCAAAACAATAAACGA 57.035 38.095 0.00 0.00 36.35 3.85
1975 2120 3.364441 TGCGCACACTCAATGGCC 61.364 61.111 5.66 0.00 0.00 5.36
2012 2158 6.739565 GCCAAATCCATTATTTCCTCCATCAC 60.740 42.308 0.00 0.00 35.54 3.06
2153 2335 1.832998 TGGAACCCGGTTGGATACTAC 59.167 52.381 7.78 0.00 41.95 2.73
2211 2904 3.879892 TGTGTGTCGATCATTTTGGTCAA 59.120 39.130 0.00 0.00 0.00 3.18
2495 3188 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2496 3189 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2497 3190 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2498 3191 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2499 3192 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2530 3223 9.923143 CATCCGTATATGGTAGTCTATTTGAAA 57.077 33.333 10.85 0.00 0.00 2.69
2531 3224 9.085645 ACATCCGTATATGGTAGTCTATTTGAA 57.914 33.333 10.85 0.00 0.00 2.69
2532 3225 8.645814 ACATCCGTATATGGTAGTCTATTTGA 57.354 34.615 10.85 0.00 0.00 2.69
2573 3266 9.606631 GGAGTAAAATGAGTGAATCTACATTCT 57.393 33.333 0.00 0.00 39.49 2.40
2574 3267 8.543774 CGGAGTAAAATGAGTGAATCTACATTC 58.456 37.037 0.00 0.00 39.24 2.67
2575 3268 8.041323 ACGGAGTAAAATGAGTGAATCTACATT 58.959 33.333 0.00 0.00 41.94 2.71
2576 3269 7.556844 ACGGAGTAAAATGAGTGAATCTACAT 58.443 34.615 0.00 0.00 41.94 2.29
2577 3270 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74


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

AutoCloner maintained by Alex Coulton.