Multiple sequence alignment - TraesCS4B01G023200

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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 TraesCS4B01G023200 chr4B 100.000 2615 0 0 1 2615 16896391 16893777 0.000000e+00 4830.0
1 TraesCS4B01G023200 chr4B 90.909 99 9 0 1576 1674 436272723 436272821 1.630000e-27 134.0
2 TraesCS4B01G023200 chr4B 97.368 38 1 0 1683 1720 30731079 30731042 6.040000e-07 65.8
3 TraesCS4B01G023200 chr4D 88.412 1096 76 28 666 1739 8998598 8997532 0.000000e+00 1273.0
4 TraesCS4B01G023200 chr4D 85.687 524 43 13 1769 2261 8997538 8997016 8.290000e-145 523.0
5 TraesCS4B01G023200 chr4D 84.753 446 36 12 58 500 8999321 8998905 4.030000e-113 418.0
6 TraesCS4B01G023200 chr4D 91.500 200 13 3 2416 2615 8993340 8993145 3.320000e-69 272.0
7 TraesCS4B01G023200 chr4D 89.320 206 13 4 417 614 8999138 8998934 1.550000e-62 250.0
8 TraesCS4B01G023200 chr4D 89.744 78 8 0 274 351 8998982 8998905 1.660000e-17 100.0
9 TraesCS4B01G023200 chr4D 97.368 38 1 0 1683 1720 18695339 18695302 6.040000e-07 65.8
10 TraesCS4B01G023200 chr4D 80.412 97 10 7 323 419 413008364 413008277 6.040000e-07 65.8
11 TraesCS4B01G023200 chr4A 86.835 1071 67 40 661 1680 594363801 594364848 0.000000e+00 1129.0
12 TraesCS4B01G023200 chr4A 80.495 364 37 22 1880 2224 594365365 594365713 5.590000e-62 248.0
13 TraesCS4B01G023200 chrUn 90.909 99 9 0 1576 1674 445913620 445913522 1.630000e-27 134.0
14 TraesCS4B01G023200 chrUn 90.909 99 9 0 1576 1674 467212383 467212285 1.630000e-27 134.0
15 TraesCS4B01G023200 chr5B 90.909 99 9 0 1576 1674 708639203 708639105 1.630000e-27 134.0
16 TraesCS4B01G023200 chr5B 87.500 48 6 0 1673 1720 638762144 638762191 3.640000e-04 56.5
17 TraesCS4B01G023200 chr5A 90.909 99 9 0 1576 1674 555960251 555960153 1.630000e-27 134.0
18 TraesCS4B01G023200 chr3A 90.909 99 9 0 1576 1674 48416725 48416627 1.630000e-27 134.0
19 TraesCS4B01G023200 chr3A 90.909 99 9 0 1576 1674 717054645 717054547 1.630000e-27 134.0
20 TraesCS4B01G023200 chr2B 83.942 137 16 6 1541 1674 360732365 360732498 2.730000e-25 126.0
21 TraesCS4B01G023200 chr2B 94.737 38 2 0 1683 1720 434103107 434103144 2.810000e-05 60.2
22 TraesCS4B01G023200 chr5D 97.368 38 1 0 1683 1720 335051236 335051199 6.040000e-07 65.8
23 TraesCS4B01G023200 chr2D 94.737 38 2 0 1683 1720 365781766 365781803 2.810000e-05 60.2
24 TraesCS4B01G023200 chr7B 97.059 34 1 0 1687 1720 91790743 91790776 1.010000e-04 58.4
25 TraesCS4B01G023200 chr2A 100.000 30 0 0 1691 1720 718335748 718335719 3.640000e-04 56.5
26 TraesCS4B01G023200 chr3B 100.000 28 0 0 1852 1879 806154100 806154127 5.000000e-03 52.8


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 TraesCS4B01G023200 chr4B 16893777 16896391 2614 True 4830.000000 4830 100.000 1 2615 1 chr4B.!!$R1 2614
1 TraesCS4B01G023200 chr4D 8993145 8999321 6176 True 472.666667 1273 88.236 58 2615 6 chr4D.!!$R3 2557
2 TraesCS4B01G023200 chr4A 594363801 594365713 1912 False 688.500000 1129 83.665 661 2224 2 chr4A.!!$F1 1563

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
977 1165 0.036388 TCCCATTCAACTCTGACCGC 60.036 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 2881 1.135972 CGTGCTTTGGATTGTTCTCGG 60.136 52.381 0.0 0.0 0.0 4.63 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
24 25 6.973229 AGTACCAAAACACATAATACGGTC 57.027 37.500 0.00 0.00 0.00 4.79
25 26 6.465948 AGTACCAAAACACATAATACGGTCA 58.534 36.000 0.00 0.00 0.00 4.02
26 27 7.107542 AGTACCAAAACACATAATACGGTCAT 58.892 34.615 0.00 0.00 0.00 3.06
27 28 8.259411 AGTACCAAAACACATAATACGGTCATA 58.741 33.333 0.00 0.00 0.00 2.15
28 29 9.048446 GTACCAAAACACATAATACGGTCATAT 57.952 33.333 0.00 0.00 0.00 1.78
29 30 7.925993 ACCAAAACACATAATACGGTCATATG 58.074 34.615 0.00 0.00 34.08 1.78
30 31 7.554835 ACCAAAACACATAATACGGTCATATGT 59.445 33.333 1.90 11.03 40.04 2.29
31 32 9.047371 CCAAAACACATAATACGGTCATATGTA 57.953 33.333 14.60 0.00 37.99 2.29
34 35 9.472361 AAACACATAATACGGTCATATGTAGAC 57.528 33.333 14.60 0.00 37.99 2.59
35 36 7.303261 ACACATAATACGGTCATATGTAGACG 58.697 38.462 14.60 6.15 37.99 4.18
36 37 7.173735 ACACATAATACGGTCATATGTAGACGA 59.826 37.037 14.60 0.00 37.99 4.20
37 38 8.019094 CACATAATACGGTCATATGTAGACGAA 58.981 37.037 14.60 0.00 37.99 3.85
38 39 8.737175 ACATAATACGGTCATATGTAGACGAAT 58.263 33.333 13.82 0.05 38.22 3.34
43 44 7.918536 ACGGTCATATGTAGACGAATATAGT 57.081 36.000 1.90 0.00 36.87 2.12
44 45 8.332996 ACGGTCATATGTAGACGAATATAGTT 57.667 34.615 1.90 0.00 36.87 2.24
45 46 9.440773 ACGGTCATATGTAGACGAATATAGTTA 57.559 33.333 1.90 0.00 36.87 2.24
60 61 9.651718 CGAATATAGTTAAAGAATCCAACAAGC 57.348 33.333 0.00 0.00 0.00 4.01
74 75 5.076182 TCCAACAAGCATCCAACAAAGATA 58.924 37.500 0.00 0.00 0.00 1.98
103 104 8.650490 AGGTCATGTGTATATATGTCAATCACA 58.350 33.333 0.00 0.00 40.18 3.58
118 119 7.304735 TGTCAATCACATACTATTTTGTGTGC 58.695 34.615 4.13 0.00 42.95 4.57
129 130 6.797454 ACTATTTTGTGTGCGTTTTTAGGAA 58.203 32.000 0.00 0.00 0.00 3.36
136 137 4.206200 GTGTGCGTTTTTAGGAACACAATG 59.794 41.667 4.65 0.00 39.50 2.82
137 138 4.096532 TGTGCGTTTTTAGGAACACAATGA 59.903 37.500 0.00 0.00 35.28 2.57
146 147 2.143122 GGAACACAATGAAGACGCAGA 58.857 47.619 0.00 0.00 0.00 4.26
152 153 2.744202 ACAATGAAGACGCAGACATTCC 59.256 45.455 0.00 0.00 31.85 3.01
169 170 2.496899 TCCTTTCTCCCTGAATGTGC 57.503 50.000 0.00 0.00 34.24 4.57
183 184 5.854866 CCTGAATGTGCGCATAATTGATAAG 59.145 40.000 21.60 14.08 34.39 1.73
264 265 6.476380 ACAAACTAAACACACATGCATTCAAG 59.524 34.615 0.00 0.00 0.00 3.02
265 266 5.125100 ACTAAACACACATGCATTCAAGG 57.875 39.130 0.00 0.00 0.00 3.61
294 295 4.884164 AGTTCCTAAGCCTTGTTCATATGC 59.116 41.667 0.00 0.00 0.00 3.14
312 313 6.707608 TCATATGCTAATCATTTGCTCGAAGT 59.292 34.615 5.40 0.00 35.12 3.01
314 315 4.252878 TGCTAATCATTTGCTCGAAGTGA 58.747 39.130 5.40 0.00 35.01 3.41
317 318 5.906285 GCTAATCATTTGCTCGAAGTGAATC 59.094 40.000 0.00 0.00 34.28 2.52
319 320 3.325870 TCATTTGCTCGAAGTGAATCGT 58.674 40.909 0.00 0.00 43.19 3.73
332 333 6.292381 CGAAGTGAATCGTGAGGGATTAATTC 60.292 42.308 0.00 0.00 36.79 2.17
358 360 6.131961 CCCATAAGTCAAATTCCTCTCCAAT 58.868 40.000 0.00 0.00 0.00 3.16
370 372 2.041620 CCTCTCCAATCCCCTTCAAACA 59.958 50.000 0.00 0.00 0.00 2.83
381 383 3.129287 CCCCTTCAAACATCTCCAATTCG 59.871 47.826 0.00 0.00 0.00 3.34
385 388 4.764679 TCAAACATCTCCAATTCGTTGG 57.235 40.909 0.76 0.76 43.40 3.77
389 392 1.064758 CATCTCCAATTCGTTGGGGGA 60.065 52.381 7.19 6.71 42.88 4.81
407 410 3.014623 GGGAGGGATTAAACGAACAAGG 58.985 50.000 0.00 0.00 0.00 3.61
411 414 2.823747 GGGATTAAACGAACAAGGCCTT 59.176 45.455 13.78 13.78 0.00 4.35
413 416 4.460034 GGGATTAAACGAACAAGGCCTTAA 59.540 41.667 20.00 6.60 0.00 1.85
421 424 4.202388 ACGAACAAGGCCTTAAGGAGTTTA 60.202 41.667 26.21 0.00 37.39 2.01
422 425 4.392138 CGAACAAGGCCTTAAGGAGTTTAG 59.608 45.833 26.21 11.66 37.39 1.85
423 426 4.995624 ACAAGGCCTTAAGGAGTTTAGT 57.004 40.909 26.21 11.63 37.39 2.24
424 427 5.320488 ACAAGGCCTTAAGGAGTTTAGTT 57.680 39.130 26.21 3.93 37.39 2.24
425 428 5.702266 ACAAGGCCTTAAGGAGTTTAGTTT 58.298 37.500 26.21 3.94 37.39 2.66
430 433 7.395617 AGGCCTTAAGGAGTTTAGTTTCTAAG 58.604 38.462 26.21 0.00 37.39 2.18
434 437 7.334671 CCTTAAGGAGTTTAGTTTCTAAGCCTG 59.665 40.741 17.21 0.00 37.39 4.85
461 464 7.495135 TCATATGCTAATCATTTGCTCGAAA 57.505 32.000 5.40 0.00 35.12 3.46
475 478 1.220749 CGAAAGGGATTGCGAGGGA 59.779 57.895 0.00 0.00 0.00 4.20
500 504 4.586306 ATTCCCCGTAAGTCAAATTCCT 57.414 40.909 0.00 0.00 0.00 3.36
501 505 3.622166 TCCCCGTAAGTCAAATTCCTC 57.378 47.619 0.00 0.00 0.00 3.71
502 506 3.178865 TCCCCGTAAGTCAAATTCCTCT 58.821 45.455 0.00 0.00 0.00 3.69
503 507 3.197116 TCCCCGTAAGTCAAATTCCTCTC 59.803 47.826 0.00 0.00 0.00 3.20
504 508 3.532542 CCCGTAAGTCAAATTCCTCTCC 58.467 50.000 0.00 0.00 0.00 3.71
505 509 3.055385 CCCGTAAGTCAAATTCCTCTCCA 60.055 47.826 0.00 0.00 0.00 3.86
506 510 4.564821 CCCGTAAGTCAAATTCCTCTCCAA 60.565 45.833 0.00 0.00 0.00 3.53
507 511 5.001232 CCGTAAGTCAAATTCCTCTCCAAA 58.999 41.667 0.00 0.00 0.00 3.28
508 512 5.106673 CCGTAAGTCAAATTCCTCTCCAAAC 60.107 44.000 0.00 0.00 0.00 2.93
509 513 5.106673 CGTAAGTCAAATTCCTCTCCAAACC 60.107 44.000 0.00 0.00 0.00 3.27
510 514 3.767711 AGTCAAATTCCTCTCCAAACCC 58.232 45.455 0.00 0.00 0.00 4.11
511 515 2.826128 GTCAAATTCCTCTCCAAACCCC 59.174 50.000 0.00 0.00 0.00 4.95
512 516 2.721906 TCAAATTCCTCTCCAAACCCCT 59.278 45.455 0.00 0.00 0.00 4.79
513 517 3.142028 TCAAATTCCTCTCCAAACCCCTT 59.858 43.478 0.00 0.00 0.00 3.95
514 518 3.458044 AATTCCTCTCCAAACCCCTTC 57.542 47.619 0.00 0.00 0.00 3.46
515 519 1.827792 TTCCTCTCCAAACCCCTTCA 58.172 50.000 0.00 0.00 0.00 3.02
516 520 1.827792 TCCTCTCCAAACCCCTTCAA 58.172 50.000 0.00 0.00 0.00 2.69
517 521 2.140224 TCCTCTCCAAACCCCTTCAAA 58.860 47.619 0.00 0.00 0.00 2.69
518 522 2.158519 TCCTCTCCAAACCCCTTCAAAC 60.159 50.000 0.00 0.00 0.00 2.93
519 523 2.239400 CTCTCCAAACCCCTTCAAACC 58.761 52.381 0.00 0.00 0.00 3.27
520 524 1.856920 TCTCCAAACCCCTTCAAACCT 59.143 47.619 0.00 0.00 0.00 3.50
521 525 2.158519 TCTCCAAACCCCTTCAAACCTC 60.159 50.000 0.00 0.00 0.00 3.85
522 526 1.856920 TCCAAACCCCTTCAAACCTCT 59.143 47.619 0.00 0.00 0.00 3.69
523 527 2.246327 TCCAAACCCCTTCAAACCTCTT 59.754 45.455 0.00 0.00 0.00 2.85
524 528 2.628178 CCAAACCCCTTCAAACCTCTTC 59.372 50.000 0.00 0.00 0.00 2.87
525 529 3.295973 CAAACCCCTTCAAACCTCTTCA 58.704 45.455 0.00 0.00 0.00 3.02
526 530 3.680777 AACCCCTTCAAACCTCTTCAA 57.319 42.857 0.00 0.00 0.00 2.69
527 531 3.903530 ACCCCTTCAAACCTCTTCAAT 57.096 42.857 0.00 0.00 0.00 2.57
528 532 4.199002 ACCCCTTCAAACCTCTTCAATT 57.801 40.909 0.00 0.00 0.00 2.32
529 533 4.152647 ACCCCTTCAAACCTCTTCAATTC 58.847 43.478 0.00 0.00 0.00 2.17
530 534 3.511540 CCCCTTCAAACCTCTTCAATTCC 59.488 47.826 0.00 0.00 0.00 3.01
553 557 0.393944 GGGGGAGGGATTGAACGAAC 60.394 60.000 0.00 0.00 0.00 3.95
554 558 0.326927 GGGGAGGGATTGAACGAACA 59.673 55.000 0.00 0.00 0.00 3.18
574 578 3.149981 CAAGACCTCAAGGAGTTTTCCC 58.850 50.000 2.30 0.00 45.24 3.97
575 579 2.707554 AGACCTCAAGGAGTTTTCCCT 58.292 47.619 2.30 0.00 45.24 4.20
576 580 2.640332 AGACCTCAAGGAGTTTTCCCTC 59.360 50.000 2.30 0.00 45.24 4.30
580 589 3.067833 CTCAAGGAGTTTTCCCTCGTTC 58.932 50.000 0.00 0.00 45.24 3.95
590 599 5.585047 AGTTTTCCCTCGTTCATATGCTAAC 59.415 40.000 0.00 0.00 0.00 2.34
620 629 1.508088 GGCAACTTGCGATTGGGAG 59.492 57.895 7.67 0.00 46.21 4.30
624 633 1.789576 AACTTGCGATTGGGAGGGGT 61.790 55.000 0.00 0.00 0.00 4.95
638 647 2.369203 GGAGGGGTCTTATAGAAGTGCC 59.631 54.545 0.00 1.52 34.03 5.01
639 648 3.039011 GAGGGGTCTTATAGAAGTGCCA 58.961 50.000 12.78 0.00 33.45 4.92
640 649 2.772515 AGGGGTCTTATAGAAGTGCCAC 59.227 50.000 12.78 10.21 34.55 5.01
641 650 2.158798 GGGGTCTTATAGAAGTGCCACC 60.159 54.545 12.78 6.51 33.45 4.61
642 651 2.504175 GGGTCTTATAGAAGTGCCACCA 59.496 50.000 12.78 0.00 30.71 4.17
643 652 3.532542 GGTCTTATAGAAGTGCCACCAC 58.467 50.000 0.00 0.00 42.39 4.16
644 653 3.532542 GTCTTATAGAAGTGCCACCACC 58.467 50.000 0.00 0.00 43.09 4.61
646 655 3.585289 TCTTATAGAAGTGCCACCACCAA 59.415 43.478 0.00 0.00 43.09 3.67
647 656 4.227300 TCTTATAGAAGTGCCACCACCAAT 59.773 41.667 0.00 0.00 43.09 3.16
648 657 5.427157 TCTTATAGAAGTGCCACCACCAATA 59.573 40.000 0.00 0.00 43.09 1.90
649 658 2.969821 AGAAGTGCCACCACCAATAA 57.030 45.000 0.00 0.00 43.09 1.40
650 659 2.514803 AGAAGTGCCACCACCAATAAC 58.485 47.619 0.00 0.00 43.09 1.89
651 660 2.158534 AGAAGTGCCACCACCAATAACA 60.159 45.455 0.00 0.00 43.09 2.41
652 661 2.373335 AGTGCCACCACCAATAACAA 57.627 45.000 0.00 0.00 43.09 2.83
653 662 2.888212 AGTGCCACCACCAATAACAAT 58.112 42.857 0.00 0.00 43.09 2.71
654 663 3.238597 AGTGCCACCACCAATAACAATT 58.761 40.909 0.00 0.00 43.09 2.32
655 664 3.645687 AGTGCCACCACCAATAACAATTT 59.354 39.130 0.00 0.00 43.09 1.82
657 666 5.047377 AGTGCCACCACCAATAACAATTTAG 60.047 40.000 0.00 0.00 43.09 1.85
658 667 4.835615 TGCCACCACCAATAACAATTTAGT 59.164 37.500 0.00 0.00 0.00 2.24
659 668 5.305644 TGCCACCACCAATAACAATTTAGTT 59.694 36.000 0.00 0.00 35.55 2.24
660 669 5.867174 GCCACCACCAATAACAATTTAGTTC 59.133 40.000 0.00 0.00 33.07 3.01
661 670 6.295067 GCCACCACCAATAACAATTTAGTTCT 60.295 38.462 0.00 0.00 33.07 3.01
663 672 8.458843 CCACCACCAATAACAATTTAGTTCTAG 58.541 37.037 0.00 0.00 33.07 2.43
664 673 7.968405 CACCACCAATAACAATTTAGTTCTAGC 59.032 37.037 0.00 0.00 33.07 3.42
667 676 7.698130 CACCAATAACAATTTAGTTCTAGCAGC 59.302 37.037 0.00 0.00 33.07 5.25
668 677 6.907212 CCAATAACAATTTAGTTCTAGCAGCG 59.093 38.462 0.00 0.00 33.07 5.18
670 679 4.928661 ACAATTTAGTTCTAGCAGCGTG 57.071 40.909 0.00 0.00 0.00 5.34
671 680 4.566004 ACAATTTAGTTCTAGCAGCGTGA 58.434 39.130 0.00 0.00 0.00 4.35
672 681 4.389077 ACAATTTAGTTCTAGCAGCGTGAC 59.611 41.667 0.00 0.00 0.00 3.67
673 682 2.257974 TTAGTTCTAGCAGCGTGACG 57.742 50.000 0.00 0.00 0.00 4.35
674 683 1.162698 TAGTTCTAGCAGCGTGACGT 58.837 50.000 6.91 0.00 0.00 4.34
714 891 7.338449 CCATATAAAAGGACCCGAAGAAAAAGA 59.662 37.037 0.00 0.00 0.00 2.52
715 892 8.736244 CATATAAAAGGACCCGAAGAAAAAGAA 58.264 33.333 0.00 0.00 0.00 2.52
716 893 5.925506 AAAAGGACCCGAAGAAAAAGAAA 57.074 34.783 0.00 0.00 0.00 2.52
717 894 5.925506 AAAGGACCCGAAGAAAAAGAAAA 57.074 34.783 0.00 0.00 0.00 2.29
718 895 5.925506 AAGGACCCGAAGAAAAAGAAAAA 57.074 34.783 0.00 0.00 0.00 1.94
719 896 5.515797 AGGACCCGAAGAAAAAGAAAAAG 57.484 39.130 0.00 0.00 0.00 2.27
728 905 6.479990 CGAAGAAAAAGAAAAAGCCCTCAAAT 59.520 34.615 0.00 0.00 0.00 2.32
761 941 4.499188 CGGTCACATCCACACGAACTATAT 60.499 45.833 0.00 0.00 0.00 0.86
763 943 5.462398 GGTCACATCCACACGAACTATATTC 59.538 44.000 0.00 0.00 0.00 1.75
787 967 3.157087 AGAATCCAACAACCAATTCGCT 58.843 40.909 0.00 0.00 34.17 4.93
823 1003 3.043340 CGTGATGGCATACGTGTCA 57.957 52.632 16.24 0.00 45.37 3.58
976 1164 1.276421 AGTCCCATTCAACTCTGACCG 59.724 52.381 0.00 0.00 0.00 4.79
977 1165 0.036388 TCCCATTCAACTCTGACCGC 60.036 55.000 0.00 0.00 0.00 5.68
1069 1259 3.326210 CGATCAAGCTCGCTCGCC 61.326 66.667 0.00 0.00 0.00 5.54
1097 1296 1.038130 CCGACGACCAGGAAGAGGAT 61.038 60.000 0.00 0.00 0.00 3.24
1100 1299 0.034380 ACGACCAGGAAGAGGATCGA 60.034 55.000 0.00 0.00 42.67 3.59
1256 1455 4.008933 GTGCAGAGGCTCACCGGT 62.009 66.667 18.26 0.00 42.76 5.28
1373 1584 3.263503 CTCGTCGTGGTTCTCCGCA 62.264 63.158 0.00 0.00 43.79 5.69
1382 1593 4.314440 TTCTCCGCACCGCTGCTT 62.314 61.111 0.54 0.00 41.77 3.91
1440 1651 2.105930 GCGCTCTGCTGTAGGAGG 59.894 66.667 0.00 0.00 41.73 4.30
1441 1652 2.418910 GCGCTCTGCTGTAGGAGGA 61.419 63.158 0.00 0.00 41.73 3.71
1442 1653 1.732917 CGCTCTGCTGTAGGAGGAG 59.267 63.158 0.45 0.00 41.50 3.69
1443 1654 0.749818 CGCTCTGCTGTAGGAGGAGA 60.750 60.000 0.45 0.00 46.29 3.71
1446 1657 2.136298 TCTGCTGTAGGAGGAGAGTG 57.864 55.000 0.45 0.00 43.80 3.51
1447 1658 1.110442 CTGCTGTAGGAGGAGAGTGG 58.890 60.000 0.00 0.00 42.77 4.00
1448 1659 0.409876 TGCTGTAGGAGGAGAGTGGT 59.590 55.000 0.00 0.00 0.00 4.16
1449 1660 1.639108 TGCTGTAGGAGGAGAGTGGTA 59.361 52.381 0.00 0.00 0.00 3.25
1450 1661 2.025898 GCTGTAGGAGGAGAGTGGTAC 58.974 57.143 0.00 0.00 0.00 3.34
1452 1663 1.997791 TGTAGGAGGAGAGTGGTACCA 59.002 52.381 11.60 11.60 0.00 3.25
1453 1664 2.291411 TGTAGGAGGAGAGTGGTACCAC 60.291 54.545 33.72 33.72 46.50 4.16
1496 1718 1.303309 ATCGAGCTAAATGCCACAGC 58.697 50.000 0.00 0.00 44.23 4.40
1531 1753 9.586732 TTCTTCCCTTCTCATTATTTTCTTTCA 57.413 29.630 0.00 0.00 0.00 2.69
1560 1783 2.368548 TGACACAGGACAGTGCTTACAT 59.631 45.455 0.00 0.00 43.23 2.29
1561 1784 2.738846 GACACAGGACAGTGCTTACATG 59.261 50.000 0.00 0.00 43.23 3.21
1562 1785 2.079158 CACAGGACAGTGCTTACATGG 58.921 52.381 0.00 0.00 32.04 3.66
1564 1787 1.278985 CAGGACAGTGCTTACATGGGA 59.721 52.381 0.00 0.00 0.00 4.37
1565 1788 2.092753 CAGGACAGTGCTTACATGGGAT 60.093 50.000 0.00 0.00 0.00 3.85
1566 1789 2.092753 AGGACAGTGCTTACATGGGATG 60.093 50.000 0.00 0.00 0.00 3.51
1569 1792 2.305635 ACAGTGCTTACATGGGATGACA 59.694 45.455 0.00 0.00 0.00 3.58
1570 1793 2.679837 CAGTGCTTACATGGGATGACAC 59.320 50.000 0.00 0.00 0.00 3.67
1572 1795 3.054139 AGTGCTTACATGGGATGACACAT 60.054 43.478 0.00 0.00 41.25 3.21
1635 1862 2.481568 TGCTCTGCAATTCTCTGTTTCG 59.518 45.455 0.00 0.00 34.76 3.46
1706 2063 8.012957 TCTCCCTCTATCTCAAAATAAGTGTC 57.987 38.462 0.00 0.00 0.00 3.67
1712 2069 9.307121 CTCTATCTCAAAATAAGTGTCGTTGAT 57.693 33.333 0.00 0.00 0.00 2.57
1731 2088 2.380084 TTTAGTACTGCTTGCCTCGG 57.620 50.000 5.39 0.00 0.00 4.63
1734 2091 0.461961 AGTACTGCTTGCCTCGGATC 59.538 55.000 0.00 0.00 0.00 3.36
1735 2092 0.530870 GTACTGCTTGCCTCGGATCC 60.531 60.000 0.00 0.00 0.00 3.36
1736 2093 0.975556 TACTGCTTGCCTCGGATCCA 60.976 55.000 13.41 0.00 0.00 3.41
1737 2094 1.078214 CTGCTTGCCTCGGATCCAA 60.078 57.895 13.41 0.00 0.00 3.53
1738 2095 0.677731 CTGCTTGCCTCGGATCCAAA 60.678 55.000 13.41 0.00 0.00 3.28
1739 2096 0.251121 TGCTTGCCTCGGATCCAAAA 60.251 50.000 13.41 0.00 0.00 2.44
1740 2097 1.106285 GCTTGCCTCGGATCCAAAAT 58.894 50.000 13.41 0.00 0.00 1.82
1741 2098 2.297701 GCTTGCCTCGGATCCAAAATA 58.702 47.619 13.41 0.00 0.00 1.40
1743 2100 3.304928 GCTTGCCTCGGATCCAAAATATG 60.305 47.826 13.41 0.00 0.00 1.78
1744 2101 2.229792 TGCCTCGGATCCAAAATATGC 58.770 47.619 13.41 4.63 0.00 3.14
1745 2102 1.197721 GCCTCGGATCCAAAATATGCG 59.802 52.381 13.41 0.00 39.24 4.73
1747 2104 2.480419 CCTCGGATCCAAAATATGCGTC 59.520 50.000 13.41 0.00 38.99 5.19
1748 2105 2.131972 TCGGATCCAAAATATGCGTCG 58.868 47.619 13.41 0.00 38.99 5.12
1750 2107 2.348498 CGGATCCAAAATATGCGTCGTG 60.348 50.000 13.41 0.00 34.02 4.35
1751 2108 2.869801 GGATCCAAAATATGCGTCGTGA 59.130 45.455 6.95 0.00 0.00 4.35
1753 2110 4.024048 GGATCCAAAATATGCGTCGTGATT 60.024 41.667 6.95 0.00 0.00 2.57
1754 2111 4.955925 TCCAAAATATGCGTCGTGATTT 57.044 36.364 0.00 0.00 0.00 2.17
1755 2112 5.303747 TCCAAAATATGCGTCGTGATTTT 57.696 34.783 0.00 1.59 32.97 1.82
1757 2114 7.022055 TCCAAAATATGCGTCGTGATTTTAT 57.978 32.000 11.12 0.00 31.86 1.40
1758 2115 7.476667 TCCAAAATATGCGTCGTGATTTTATT 58.523 30.769 11.12 0.00 31.86 1.40
1759 2116 7.430793 TCCAAAATATGCGTCGTGATTTTATTG 59.569 33.333 11.12 4.13 31.86 1.90
1762 2119 9.776158 AAAATATGCGTCGTGATTTTATTGTAA 57.224 25.926 10.27 0.00 31.43 2.41
1763 2120 8.987599 AATATGCGTCGTGATTTTATTGTAAG 57.012 30.769 0.00 0.00 0.00 2.34
1765 2122 6.230849 TGCGTCGTGATTTTATTGTAAGTT 57.769 33.333 0.00 0.00 0.00 2.66
1767 2124 7.794880 TGCGTCGTGATTTTATTGTAAGTTTA 58.205 30.769 0.00 0.00 0.00 2.01
1791 2148 7.085052 AGTTCAAACTTCAACTAAACTCACC 57.915 36.000 0.00 0.00 35.21 4.02
1795 2152 6.093495 TCAAACTTCAACTAAACTCACCACAG 59.907 38.462 0.00 0.00 0.00 3.66
1809 2166 8.553459 AACTCACCACAGTTATTTTAGATCAG 57.447 34.615 0.00 0.00 34.70 2.90
1814 2171 7.012704 CACCACAGTTATTTTAGATCAGATGGG 59.987 40.741 0.00 0.00 0.00 4.00
1818 2175 8.211629 ACAGTTATTTTAGATCAGATGGGGTAC 58.788 37.037 0.00 0.00 0.00 3.34
1834 2343 6.578163 TGGGGTACAATTTTAGTGTAAAGC 57.422 37.500 0.00 0.00 33.40 3.51
1835 2344 5.181622 TGGGGTACAATTTTAGTGTAAAGCG 59.818 40.000 0.00 0.00 33.40 4.68
1839 2348 7.066163 GGGTACAATTTTAGTGTAAAGCGGTAT 59.934 37.037 0.00 0.00 33.40 2.73
1848 2357 9.439500 TTTAGTGTAAAGCGGTATTAAGTCAAT 57.561 29.630 0.00 0.00 0.00 2.57
1883 2408 8.937634 TTTAAGACGAAGGGAGTATATGTTTC 57.062 34.615 0.00 0.00 0.00 2.78
1888 2413 6.994221 ACGAAGGGAGTATATGTTTCTATGG 58.006 40.000 0.00 0.00 0.00 2.74
1890 2415 7.039644 ACGAAGGGAGTATATGTTTCTATGGAG 60.040 40.741 0.00 0.00 0.00 3.86
1891 2416 7.039644 CGAAGGGAGTATATGTTTCTATGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
1904 2455 9.321562 TGTTTCTATGGAGTAATTATCCGTTTC 57.678 33.333 11.52 0.00 39.91 2.78
1911 2462 7.617225 TGGAGTAATTATCCGTTTCTCTTGAA 58.383 34.615 8.50 0.00 39.91 2.69
1960 2511 1.934589 CAGGCGTGTGATTATTCGGA 58.065 50.000 0.00 0.00 0.00 4.55
2022 2575 1.599606 ATGAAGCAGTCGTCCTCGCT 61.600 55.000 0.00 0.00 36.96 4.93
2032 2589 3.381908 AGTCGTCCTCGCTGATAGAAAAT 59.618 43.478 0.00 0.00 36.96 1.82
2034 2591 5.067413 AGTCGTCCTCGCTGATAGAAAATTA 59.933 40.000 0.00 0.00 36.96 1.40
2137 2695 4.631377 TCACATTTTCTCATCCTACTTGCG 59.369 41.667 0.00 0.00 0.00 4.85
2143 2701 5.607119 TTCTCATCCTACTTGCGTTTTTC 57.393 39.130 0.00 0.00 0.00 2.29
2218 2779 3.148412 CAAAAGGGCCCAAGGAAAATTG 58.852 45.455 27.56 12.37 0.00 2.32
2228 2789 2.368655 AGGAAAATTGTTCGCATGGC 57.631 45.000 0.00 0.00 0.00 4.40
2261 2828 0.179100 TTCACATCGCAGGAGCTAGC 60.179 55.000 6.62 6.62 39.10 3.42
2262 2829 1.142531 CACATCGCAGGAGCTAGCA 59.857 57.895 18.83 0.00 39.10 3.49
2263 2830 1.142748 ACATCGCAGGAGCTAGCAC 59.857 57.895 18.83 11.05 39.10 4.40
2271 2877 2.583593 GAGCTAGCACGGCCGAAG 60.584 66.667 35.90 24.47 0.00 3.79
2275 2881 1.805945 CTAGCACGGCCGAAGACAC 60.806 63.158 35.90 13.68 0.00 3.67
2285 2891 1.939838 GCCGAAGACACCGAGAACAAT 60.940 52.381 0.00 0.00 0.00 2.71
2286 2892 1.993370 CCGAAGACACCGAGAACAATC 59.007 52.381 0.00 0.00 0.00 2.67
2292 2898 1.880027 ACACCGAGAACAATCCAAAGC 59.120 47.619 0.00 0.00 0.00 3.51
2301 2907 1.072505 AATCCAAAGCACGGACGGT 59.927 52.632 0.00 0.00 34.69 4.83
2306 2912 3.141522 AAAGCACGGACGGTCGACA 62.142 57.895 18.91 0.00 0.00 4.35
2308 2914 3.179265 GCACGGACGGTCGACATG 61.179 66.667 18.91 11.68 0.00 3.21
2309 2915 2.506217 CACGGACGGTCGACATGG 60.506 66.667 18.91 8.40 0.00 3.66
2320 2926 2.622436 GTCGACATGGAGAAGAAAGGG 58.378 52.381 11.55 0.00 0.00 3.95
2324 2930 3.013219 GACATGGAGAAGAAAGGGAAGC 58.987 50.000 0.00 0.00 0.00 3.86
2325 2931 2.646798 ACATGGAGAAGAAAGGGAAGCT 59.353 45.455 0.00 0.00 0.00 3.74
2327 2933 2.625639 TGGAGAAGAAAGGGAAGCTCT 58.374 47.619 0.00 0.00 0.00 4.09
2340 6319 2.678336 GGAAGCTCTTTTATCACCGTGG 59.322 50.000 0.00 0.00 0.00 4.94
2356 6336 1.293924 GTGGAGATCAGACATTGGCG 58.706 55.000 0.00 0.00 0.00 5.69
2362 6342 2.437281 AGATCAGACATTGGCGAGGAAT 59.563 45.455 0.00 0.00 0.00 3.01
2367 6347 3.012518 AGACATTGGCGAGGAATTTCAG 58.987 45.455 0.00 0.00 0.00 3.02
2370 6350 4.331968 ACATTGGCGAGGAATTTCAGTAA 58.668 39.130 0.00 0.00 0.00 2.24
2374 6354 5.155278 TGGCGAGGAATTTCAGTAAAGTA 57.845 39.130 0.00 0.00 0.00 2.24
2375 6355 5.553123 TGGCGAGGAATTTCAGTAAAGTAA 58.447 37.500 0.00 0.00 0.00 2.24
2380 6360 9.062674 GCGAGGAATTTCAGTAAAGTAATTTTC 57.937 33.333 0.00 0.00 0.00 2.29
2389 6369 9.607988 TTCAGTAAAGTAATTTTCTGTCACAGA 57.392 29.630 17.91 2.36 38.87 3.41
2390 6370 9.607988 TCAGTAAAGTAATTTTCTGTCACAGAA 57.392 29.630 16.67 16.67 46.93 3.02
2400 6380 5.815233 TTCTGTCACAGAAAAGAGAGGAT 57.185 39.130 18.28 0.00 45.84 3.24
2403 6383 5.305386 TCTGTCACAGAAAAGAGAGGATCAA 59.695 40.000 4.55 0.00 37.57 2.57
2439 6528 7.472543 ACGCTCATAATCTTGTGAAATTTACC 58.527 34.615 0.00 0.00 0.00 2.85
2440 6529 7.120579 ACGCTCATAATCTTGTGAAATTTACCA 59.879 33.333 0.00 0.00 0.00 3.25
2467 6556 1.986882 AGAAACAGCAAGACCCAAGG 58.013 50.000 0.00 0.00 0.00 3.61
2544 6633 4.436998 CACCCAGGAGGCGACGAC 62.437 72.222 0.00 0.00 40.58 4.34
2557 6646 1.927174 GCGACGACATTACAGCTGATT 59.073 47.619 23.35 0.27 0.00 2.57
2561 6650 5.481472 CGACGACATTACAGCTGATTAAAC 58.519 41.667 23.35 6.66 0.00 2.01
2585 6674 1.657094 CGGGGAAGAAACATACGTTCG 59.343 52.381 0.00 0.00 32.91 3.95
2586 6675 2.691927 GGGGAAGAAACATACGTTCGT 58.308 47.619 0.00 2.91 32.91 3.85
2597 6686 8.006590 AGAAACATACGTTCGTATAGTCGTATC 58.993 37.037 15.75 12.18 44.06 2.24
2598 6687 5.837068 ACATACGTTCGTATAGTCGTATCG 58.163 41.667 15.75 5.20 44.06 2.92
2599 6688 5.402568 ACATACGTTCGTATAGTCGTATCGT 59.597 40.000 15.75 5.72 44.06 3.73
2600 6689 6.581166 ACATACGTTCGTATAGTCGTATCGTA 59.419 38.462 15.75 0.00 44.06 3.43
2601 6690 7.273598 ACATACGTTCGTATAGTCGTATCGTAT 59.726 37.037 15.75 0.00 44.06 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.935771 TGACCGTATTATGTGTTTTGGTACTT 59.064 34.615 0.00 0.00 0.00 2.24
1 2 6.465948 TGACCGTATTATGTGTTTTGGTACT 58.534 36.000 0.00 0.00 0.00 2.73
2 3 6.724694 TGACCGTATTATGTGTTTTGGTAC 57.275 37.500 0.00 0.00 0.00 3.34
3 4 9.047371 CATATGACCGTATTATGTGTTTTGGTA 57.953 33.333 0.00 0.00 0.00 3.25
4 5 7.554835 ACATATGACCGTATTATGTGTTTTGGT 59.445 33.333 10.38 0.00 31.05 3.67
8 9 9.472361 GTCTACATATGACCGTATTATGTGTTT 57.528 33.333 10.38 0.00 33.88 2.83
9 10 7.806487 CGTCTACATATGACCGTATTATGTGTT 59.194 37.037 10.38 0.00 33.88 3.32
10 11 7.173735 TCGTCTACATATGACCGTATTATGTGT 59.826 37.037 10.38 6.74 33.88 3.72
11 12 7.524065 TCGTCTACATATGACCGTATTATGTG 58.476 38.462 10.38 2.36 33.88 3.21
12 13 7.677454 TCGTCTACATATGACCGTATTATGT 57.323 36.000 10.38 9.57 35.75 2.29
17 18 9.610705 ACTATATTCGTCTACATATGACCGTAT 57.389 33.333 10.38 7.39 0.00 3.06
18 19 9.440773 AACTATATTCGTCTACATATGACCGTA 57.559 33.333 10.38 0.41 0.00 4.02
19 20 7.918536 ACTATATTCGTCTACATATGACCGT 57.081 36.000 10.38 0.00 0.00 4.83
34 35 9.651718 GCTTGTTGGATTCTTTAACTATATTCG 57.348 33.333 0.00 0.00 0.00 3.34
38 39 9.120538 GGATGCTTGTTGGATTCTTTAACTATA 57.879 33.333 0.00 0.00 0.00 1.31
39 40 7.615365 TGGATGCTTGTTGGATTCTTTAACTAT 59.385 33.333 0.00 0.00 0.00 2.12
40 41 6.945435 TGGATGCTTGTTGGATTCTTTAACTA 59.055 34.615 0.00 0.00 0.00 2.24
41 42 5.774690 TGGATGCTTGTTGGATTCTTTAACT 59.225 36.000 0.00 0.00 0.00 2.24
42 43 6.024552 TGGATGCTTGTTGGATTCTTTAAC 57.975 37.500 0.00 0.00 0.00 2.01
43 44 6.041409 TGTTGGATGCTTGTTGGATTCTTTAA 59.959 34.615 0.00 0.00 0.00 1.52
44 45 5.538053 TGTTGGATGCTTGTTGGATTCTTTA 59.462 36.000 0.00 0.00 0.00 1.85
45 46 4.344679 TGTTGGATGCTTGTTGGATTCTTT 59.655 37.500 0.00 0.00 0.00 2.52
46 47 3.896888 TGTTGGATGCTTGTTGGATTCTT 59.103 39.130 0.00 0.00 0.00 2.52
47 48 3.499338 TGTTGGATGCTTGTTGGATTCT 58.501 40.909 0.00 0.00 0.00 2.40
48 49 3.940209 TGTTGGATGCTTGTTGGATTC 57.060 42.857 0.00 0.00 0.00 2.52
49 50 4.344679 TCTTTGTTGGATGCTTGTTGGATT 59.655 37.500 0.00 0.00 0.00 3.01
50 51 3.896888 TCTTTGTTGGATGCTTGTTGGAT 59.103 39.130 0.00 0.00 0.00 3.41
51 52 3.295093 TCTTTGTTGGATGCTTGTTGGA 58.705 40.909 0.00 0.00 0.00 3.53
52 53 3.731652 TCTTTGTTGGATGCTTGTTGG 57.268 42.857 0.00 0.00 0.00 3.77
53 54 5.771469 TGTATCTTTGTTGGATGCTTGTTG 58.229 37.500 0.00 0.00 0.00 3.33
54 55 6.403866 TTGTATCTTTGTTGGATGCTTGTT 57.596 33.333 0.00 0.00 0.00 2.83
55 56 5.047802 CCTTGTATCTTTGTTGGATGCTTGT 60.048 40.000 0.00 0.00 0.00 3.16
56 57 5.047802 ACCTTGTATCTTTGTTGGATGCTTG 60.048 40.000 0.00 0.00 0.00 4.01
60 61 6.151648 ACATGACCTTGTATCTTTGTTGGATG 59.848 38.462 0.00 0.00 0.00 3.51
74 75 9.494271 GATTGACATATATACACATGACCTTGT 57.506 33.333 0.00 0.00 0.00 3.16
103 104 8.101654 TCCTAAAAACGCACACAAAATAGTAT 57.898 30.769 0.00 0.00 0.00 2.12
112 113 2.747989 TGTGTTCCTAAAAACGCACACA 59.252 40.909 0.00 0.00 42.88 3.72
118 119 5.619607 CGTCTTCATTGTGTTCCTAAAAACG 59.380 40.000 0.00 0.00 31.58 3.60
129 130 2.238942 TGTCTGCGTCTTCATTGTGT 57.761 45.000 0.00 0.00 0.00 3.72
136 137 3.330267 AGAAAGGAATGTCTGCGTCTTC 58.670 45.455 0.00 0.00 0.00 2.87
137 138 3.330267 GAGAAAGGAATGTCTGCGTCTT 58.670 45.455 0.00 0.00 0.00 3.01
152 153 0.449388 GCGCACATTCAGGGAGAAAG 59.551 55.000 0.30 0.00 40.22 2.62
226 227 9.877178 TGTGTTTAGTTTGTCATGGTTAATTTT 57.123 25.926 0.00 0.00 0.00 1.82
227 228 9.308318 GTGTGTTTAGTTTGTCATGGTTAATTT 57.692 29.630 0.00 0.00 0.00 1.82
245 246 4.826733 ACTCCTTGAATGCATGTGTGTTTA 59.173 37.500 0.00 0.00 0.00 2.01
250 251 5.072741 ACTAAACTCCTTGAATGCATGTGT 58.927 37.500 0.00 0.00 0.00 3.72
294 295 6.125419 CGATTCACTTCGAGCAAATGATTAG 58.875 40.000 0.00 0.00 41.62 1.73
332 333 4.464947 GAGAGGAATTTGACTTATGGGGG 58.535 47.826 0.00 0.00 0.00 5.40
337 338 6.368805 GGGATTGGAGAGGAATTTGACTTAT 58.631 40.000 0.00 0.00 0.00 1.73
358 360 4.344104 GAATTGGAGATGTTTGAAGGGGA 58.656 43.478 0.00 0.00 0.00 4.81
381 383 1.282738 TCGTTTAATCCCTCCCCCAAC 59.717 52.381 0.00 0.00 0.00 3.77
385 388 2.793288 TGTTCGTTTAATCCCTCCCC 57.207 50.000 0.00 0.00 0.00 4.81
389 392 2.041216 AGGCCTTGTTCGTTTAATCCCT 59.959 45.455 0.00 0.00 0.00 4.20
407 410 6.093771 GGCTTAGAAACTAAACTCCTTAAGGC 59.906 42.308 17.32 0.00 34.44 4.35
411 414 6.271624 ACCAGGCTTAGAAACTAAACTCCTTA 59.728 38.462 0.00 0.00 0.00 2.69
413 416 4.597940 ACCAGGCTTAGAAACTAAACTCCT 59.402 41.667 0.00 0.00 0.00 3.69
421 424 4.884164 GCATATGAACCAGGCTTAGAAACT 59.116 41.667 6.97 0.00 0.00 2.66
422 425 4.884164 AGCATATGAACCAGGCTTAGAAAC 59.116 41.667 6.97 0.00 0.00 2.78
423 426 5.116084 AGCATATGAACCAGGCTTAGAAA 57.884 39.130 6.97 0.00 0.00 2.52
424 427 4.778213 AGCATATGAACCAGGCTTAGAA 57.222 40.909 6.97 0.00 0.00 2.10
425 428 5.887214 TTAGCATATGAACCAGGCTTAGA 57.113 39.130 6.97 0.00 36.10 2.10
430 433 5.972107 AATGATTAGCATATGAACCAGGC 57.028 39.130 6.97 0.00 35.78 4.85
434 437 6.073058 TCGAGCAAATGATTAGCATATGAACC 60.073 38.462 6.97 0.00 35.78 3.62
461 464 3.498661 GGAATTAATCCCTCGCAATCCCT 60.499 47.826 0.00 0.00 43.00 4.20
475 478 7.123383 AGGAATTTGACTTACGGGGAATTAAT 58.877 34.615 0.00 0.00 0.00 1.40
500 504 1.856920 AGGTTTGAAGGGGTTTGGAGA 59.143 47.619 0.00 0.00 0.00 3.71
501 505 2.158460 AGAGGTTTGAAGGGGTTTGGAG 60.158 50.000 0.00 0.00 0.00 3.86
502 506 1.856920 AGAGGTTTGAAGGGGTTTGGA 59.143 47.619 0.00 0.00 0.00 3.53
503 507 2.381752 AGAGGTTTGAAGGGGTTTGG 57.618 50.000 0.00 0.00 0.00 3.28
504 508 3.295973 TGAAGAGGTTTGAAGGGGTTTG 58.704 45.455 0.00 0.00 0.00 2.93
505 509 3.680777 TGAAGAGGTTTGAAGGGGTTT 57.319 42.857 0.00 0.00 0.00 3.27
506 510 3.680777 TTGAAGAGGTTTGAAGGGGTT 57.319 42.857 0.00 0.00 0.00 4.11
507 511 3.903530 ATTGAAGAGGTTTGAAGGGGT 57.096 42.857 0.00 0.00 0.00 4.95
508 512 3.511540 GGAATTGAAGAGGTTTGAAGGGG 59.488 47.826 0.00 0.00 0.00 4.79
509 513 3.511540 GGGAATTGAAGAGGTTTGAAGGG 59.488 47.826 0.00 0.00 0.00 3.95
510 514 4.411013 AGGGAATTGAAGAGGTTTGAAGG 58.589 43.478 0.00 0.00 0.00 3.46
511 515 5.279156 CCAAGGGAATTGAAGAGGTTTGAAG 60.279 44.000 0.00 0.00 41.83 3.02
512 516 4.588528 CCAAGGGAATTGAAGAGGTTTGAA 59.411 41.667 0.00 0.00 41.83 2.69
513 517 4.151883 CCAAGGGAATTGAAGAGGTTTGA 58.848 43.478 0.00 0.00 41.83 2.69
514 518 3.259123 CCCAAGGGAATTGAAGAGGTTTG 59.741 47.826 0.00 0.00 41.83 2.93
515 519 3.510459 CCCAAGGGAATTGAAGAGGTTT 58.490 45.455 0.00 0.00 41.83 3.27
516 520 3.175438 CCCAAGGGAATTGAAGAGGTT 57.825 47.619 0.00 0.00 41.83 3.50
517 521 2.907458 CCCAAGGGAATTGAAGAGGT 57.093 50.000 0.00 0.00 41.83 3.85
530 534 0.033109 GTTCAATCCCTCCCCCAAGG 60.033 60.000 0.00 0.00 36.08 3.61
546 550 3.060602 CTCCTTGAGGTCTTGTTCGTTC 58.939 50.000 0.00 0.00 36.34 3.95
553 557 3.149981 GGGAAAACTCCTTGAGGTCTTG 58.850 50.000 0.00 0.00 33.35 3.02
554 558 3.056832 AGGGAAAACTCCTTGAGGTCTT 58.943 45.455 0.00 0.00 33.35 3.01
574 578 5.008019 AGCAAATGGTTAGCATATGAACGAG 59.992 40.000 6.97 0.00 0.00 4.18
575 579 4.881273 AGCAAATGGTTAGCATATGAACGA 59.119 37.500 6.97 0.59 0.00 3.85
576 580 5.173774 AGCAAATGGTTAGCATATGAACG 57.826 39.130 6.97 0.00 0.00 3.95
580 589 4.083643 CCTCGAGCAAATGGTTAGCATATG 60.084 45.833 6.99 0.00 0.00 1.78
616 625 2.369203 GCACTTCTATAAGACCCCTCCC 59.631 54.545 0.00 0.00 36.50 4.30
620 629 2.158798 GGTGGCACTTCTATAAGACCCC 60.159 54.545 18.45 0.00 36.50 4.95
624 633 3.178046 TGGTGGTGGCACTTCTATAAGA 58.822 45.455 18.45 0.00 36.50 2.10
638 647 7.968405 GCTAGAACTAAATTGTTATTGGTGGTG 59.032 37.037 0.00 0.00 0.00 4.17
639 648 7.668052 TGCTAGAACTAAATTGTTATTGGTGGT 59.332 33.333 0.00 0.00 0.00 4.16
640 649 8.050778 TGCTAGAACTAAATTGTTATTGGTGG 57.949 34.615 0.00 0.00 0.00 4.61
641 650 7.698130 GCTGCTAGAACTAAATTGTTATTGGTG 59.302 37.037 0.00 0.00 0.00 4.17
642 651 7.414098 CGCTGCTAGAACTAAATTGTTATTGGT 60.414 37.037 0.00 0.00 0.00 3.67
643 652 6.907212 CGCTGCTAGAACTAAATTGTTATTGG 59.093 38.462 0.00 0.00 0.00 3.16
644 653 7.426456 CACGCTGCTAGAACTAAATTGTTATTG 59.574 37.037 0.00 0.00 0.00 1.90
646 655 6.816640 TCACGCTGCTAGAACTAAATTGTTAT 59.183 34.615 0.00 0.00 0.00 1.89
647 656 6.090358 GTCACGCTGCTAGAACTAAATTGTTA 59.910 38.462 0.00 0.00 0.00 2.41
648 657 4.994852 TCACGCTGCTAGAACTAAATTGTT 59.005 37.500 0.00 0.00 0.00 2.83
649 658 4.389077 GTCACGCTGCTAGAACTAAATTGT 59.611 41.667 0.00 0.00 0.00 2.71
650 659 4.490959 CGTCACGCTGCTAGAACTAAATTG 60.491 45.833 0.00 0.00 0.00 2.32
651 660 3.612860 CGTCACGCTGCTAGAACTAAATT 59.387 43.478 0.00 0.00 0.00 1.82
652 661 3.179830 CGTCACGCTGCTAGAACTAAAT 58.820 45.455 0.00 0.00 0.00 1.40
653 662 2.030540 ACGTCACGCTGCTAGAACTAAA 60.031 45.455 0.00 0.00 0.00 1.85
654 663 1.538512 ACGTCACGCTGCTAGAACTAA 59.461 47.619 0.00 0.00 0.00 2.24
655 664 1.162698 ACGTCACGCTGCTAGAACTA 58.837 50.000 0.00 0.00 0.00 2.24
657 666 1.973138 TTACGTCACGCTGCTAGAAC 58.027 50.000 0.00 0.00 0.00 3.01
658 667 2.710220 TTTACGTCACGCTGCTAGAA 57.290 45.000 0.00 0.00 0.00 2.10
659 668 2.933495 ATTTACGTCACGCTGCTAGA 57.067 45.000 0.00 0.00 0.00 2.43
660 669 3.366724 TGAAATTTACGTCACGCTGCTAG 59.633 43.478 0.00 0.00 0.00 3.42
661 670 3.318886 TGAAATTTACGTCACGCTGCTA 58.681 40.909 0.00 0.00 0.00 3.49
663 672 2.587612 TGAAATTTACGTCACGCTGC 57.412 45.000 0.00 0.00 0.00 5.25
664 673 3.867665 TGTTGAAATTTACGTCACGCTG 58.132 40.909 0.00 0.00 0.00 5.18
667 676 3.969981 GGGTTGTTGAAATTTACGTCACG 59.030 43.478 0.00 0.00 0.00 4.35
668 677 4.922719 TGGGTTGTTGAAATTTACGTCAC 58.077 39.130 0.00 0.00 0.00 3.67
670 679 9.843334 TTTATATGGGTTGTTGAAATTTACGTC 57.157 29.630 0.00 0.00 0.00 4.34
714 891 2.955660 TGACGTGATTTGAGGGCTTTTT 59.044 40.909 0.00 0.00 0.00 1.94
715 892 2.293399 GTGACGTGATTTGAGGGCTTTT 59.707 45.455 0.00 0.00 0.00 2.27
716 893 1.880027 GTGACGTGATTTGAGGGCTTT 59.120 47.619 0.00 0.00 0.00 3.51
717 894 1.202758 TGTGACGTGATTTGAGGGCTT 60.203 47.619 0.00 0.00 0.00 4.35
718 895 0.396435 TGTGACGTGATTTGAGGGCT 59.604 50.000 0.00 0.00 0.00 5.19
719 896 0.517316 GTGTGACGTGATTTGAGGGC 59.483 55.000 0.00 0.00 0.00 5.19
728 905 0.318360 GATGTGACCGTGTGACGTGA 60.318 55.000 0.00 0.00 40.58 4.35
761 941 5.982516 CGAATTGGTTGTTGGATTCTTTGAA 59.017 36.000 0.00 0.00 0.00 2.69
763 943 4.150451 GCGAATTGGTTGTTGGATTCTTTG 59.850 41.667 0.00 0.00 0.00 2.77
783 963 1.219124 GCAGACTTGGGATCAGCGA 59.781 57.895 0.00 0.00 0.00 4.93
787 967 1.831106 ACGTATGCAGACTTGGGATCA 59.169 47.619 10.18 0.00 0.00 2.92
1049 1239 3.326210 GAGCGAGCTTGATCGGCG 61.326 66.667 4.70 0.00 42.94 6.46
1074 1264 4.351938 TTCCTGGTCGTCGGTGCG 62.352 66.667 0.00 0.00 0.00 5.34
1075 1265 2.432628 CTTCCTGGTCGTCGGTGC 60.433 66.667 0.00 0.00 0.00 5.01
1076 1266 1.213013 CTCTTCCTGGTCGTCGGTG 59.787 63.158 0.00 0.00 0.00 4.94
1097 1296 3.822192 CCGTGCTCCATCGGTCGA 61.822 66.667 0.00 0.00 41.58 4.20
1288 1487 3.414700 CCGCGTGAACCTCTGCAC 61.415 66.667 4.92 0.00 0.00 4.57
1440 1651 1.505353 CGACCGTGGTACCACTCTC 59.495 63.158 35.83 27.78 44.16 3.20
1441 1652 2.633509 GCGACCGTGGTACCACTCT 61.634 63.158 35.83 23.47 44.16 3.24
1442 1653 2.126189 GCGACCGTGGTACCACTC 60.126 66.667 35.83 27.43 44.16 3.51
1443 1654 3.688159 GGCGACCGTGGTACCACT 61.688 66.667 35.83 22.75 44.16 4.00
1461 1683 1.730064 TCGATTTTACAAGTGCCGAGC 59.270 47.619 0.00 0.00 0.00 5.03
1496 1718 1.484240 AGAAGGGAAGAAGCGATGGAG 59.516 52.381 0.00 0.00 0.00 3.86
1531 1753 1.905215 CTGTCCTGTGTCATCTCCCTT 59.095 52.381 0.00 0.00 0.00 3.95
1560 1783 5.948742 TTATACTGTCATGTGTCATCCCA 57.051 39.130 0.00 0.00 0.00 4.37
1561 1784 7.220030 AGAATTATACTGTCATGTGTCATCCC 58.780 38.462 0.00 0.00 0.00 3.85
1562 1785 8.668510 AAGAATTATACTGTCATGTGTCATCC 57.331 34.615 0.00 0.00 0.00 3.51
1566 1789 9.869844 GCATAAAGAATTATACTGTCATGTGTC 57.130 33.333 0.00 0.00 30.50 3.67
1635 1862 3.346315 TGTCATGTGTCATCCCATGAAC 58.654 45.455 6.26 3.34 46.46 3.18
1681 1913 7.201830 CGACACTTATTTTGAGATAGAGGGAGA 60.202 40.741 0.00 0.00 0.00 3.71
1702 2059 5.609088 CAAGCAGTACTAAATCAACGACAC 58.391 41.667 0.00 0.00 0.00 3.67
1706 2063 3.684788 AGGCAAGCAGTACTAAATCAACG 59.315 43.478 0.00 0.00 0.00 4.10
1712 2069 1.897133 TCCGAGGCAAGCAGTACTAAA 59.103 47.619 0.00 0.00 0.00 1.85
1731 2088 4.732285 ATCACGACGCATATTTTGGATC 57.268 40.909 0.00 0.00 0.00 3.36
1734 2091 7.219917 ACAATAAAATCACGACGCATATTTTGG 59.780 33.333 18.24 12.75 34.37 3.28
1735 2092 8.103101 ACAATAAAATCACGACGCATATTTTG 57.897 30.769 18.24 10.05 34.37 2.44
1736 2093 9.776158 TTACAATAAAATCACGACGCATATTTT 57.224 25.926 15.33 15.33 36.04 1.82
1737 2094 9.433317 CTTACAATAAAATCACGACGCATATTT 57.567 29.630 0.00 0.00 0.00 1.40
1738 2095 8.609176 ACTTACAATAAAATCACGACGCATATT 58.391 29.630 0.00 0.00 0.00 1.28
1739 2096 8.138365 ACTTACAATAAAATCACGACGCATAT 57.862 30.769 0.00 0.00 0.00 1.78
1740 2097 7.528481 ACTTACAATAAAATCACGACGCATA 57.472 32.000 0.00 0.00 0.00 3.14
1741 2098 6.417191 ACTTACAATAAAATCACGACGCAT 57.583 33.333 0.00 0.00 0.00 4.73
1743 2100 7.953710 ACTAAACTTACAATAAAATCACGACGC 59.046 33.333 0.00 0.00 0.00 5.19
1744 2101 9.801714 AACTAAACTTACAATAAAATCACGACG 57.198 29.630 0.00 0.00 0.00 5.12
1765 2122 8.671028 GGTGAGTTTAGTTGAAGTTTGAACTAA 58.329 33.333 11.07 11.07 42.36 2.24
1767 2124 6.657541 TGGTGAGTTTAGTTGAAGTTTGAACT 59.342 34.615 2.47 2.47 42.04 3.01
1777 2134 8.514330 AAAATAACTGTGGTGAGTTTAGTTGA 57.486 30.769 0.00 0.00 37.38 3.18
1778 2135 9.878599 CTAAAATAACTGTGGTGAGTTTAGTTG 57.121 33.333 0.00 0.00 38.58 3.16
1786 2143 8.824781 CATCTGATCTAAAATAACTGTGGTGAG 58.175 37.037 0.00 0.00 0.00 3.51
1791 2148 7.056635 ACCCCATCTGATCTAAAATAACTGTG 58.943 38.462 0.00 0.00 0.00 3.66
1795 2152 8.974060 TTGTACCCCATCTGATCTAAAATAAC 57.026 34.615 0.00 0.00 0.00 1.89
1809 2166 7.255569 GCTTTACACTAAAATTGTACCCCATC 58.744 38.462 0.00 0.00 0.00 3.51
1814 2171 6.245115 ACCGCTTTACACTAAAATTGTACC 57.755 37.500 0.00 0.00 0.00 3.34
1848 2357 8.370182 ACTCCCTTCGTCTTAAAATAAGTGTTA 58.630 33.333 0.00 0.00 0.00 2.41
1861 2386 6.793505 AGAAACATATACTCCCTTCGTCTT 57.206 37.500 0.00 0.00 0.00 3.01
1862 2387 7.039644 CCATAGAAACATATACTCCCTTCGTCT 60.040 40.741 0.00 0.00 0.00 4.18
1863 2388 7.039923 TCCATAGAAACATATACTCCCTTCGTC 60.040 40.741 0.00 0.00 0.00 4.20
1867 2392 9.670442 TTACTCCATAGAAACATATACTCCCTT 57.330 33.333 0.00 0.00 0.00 3.95
1883 2408 9.197694 CAAGAGAAACGGATAATTACTCCATAG 57.802 37.037 11.89 0.00 32.72 2.23
1888 2413 7.011202 GGGTTCAAGAGAAACGGATAATTACTC 59.989 40.741 0.00 0.00 42.53 2.59
1890 2415 6.596497 TGGGTTCAAGAGAAACGGATAATTAC 59.404 38.462 0.00 0.00 42.53 1.89
1891 2416 6.713276 TGGGTTCAAGAGAAACGGATAATTA 58.287 36.000 0.00 0.00 42.53 1.40
1896 2446 3.502123 TTGGGTTCAAGAGAAACGGAT 57.498 42.857 0.00 0.00 42.53 4.18
1899 2449 4.455533 TCATCATTGGGTTCAAGAGAAACG 59.544 41.667 0.00 0.00 42.53 3.60
1904 2455 6.514541 GCATATGTCATCATTGGGTTCAAGAG 60.515 42.308 4.29 0.00 36.19 2.85
1911 2462 4.202182 GCAAAGCATATGTCATCATTGGGT 60.202 41.667 4.29 0.00 35.70 4.51
1993 2546 2.223203 CGACTGCTTCATCTTGCCAATC 60.223 50.000 0.00 0.00 0.00 2.67
2032 2589 7.526142 CCACACTCTAGGCATCTAACTATAA 57.474 40.000 0.00 0.00 0.00 0.98
2137 2695 4.618920 TGACTCCCTGGTCTAGAAAAAC 57.381 45.455 0.00 0.00 37.16 2.43
2143 2701 4.559862 ACAAAATGACTCCCTGGTCTAG 57.440 45.455 0.00 0.00 37.16 2.43
2201 2762 1.977854 GAACAATTTTCCTTGGGCCCT 59.022 47.619 25.70 0.00 0.00 5.19
2231 2792 2.672996 ATGTGAACCAGCACCCGC 60.673 61.111 0.00 0.00 37.99 6.13
2233 2794 2.690778 GCGATGTGAACCAGCACCC 61.691 63.158 0.00 0.00 37.99 4.61
2235 2796 1.499056 CTGCGATGTGAACCAGCAC 59.501 57.895 0.00 0.00 39.22 4.40
2261 2828 4.351938 TCGGTGTCTTCGGCCGTG 62.352 66.667 27.15 19.13 45.11 4.94
2262 2829 4.052229 CTCGGTGTCTTCGGCCGT 62.052 66.667 27.15 0.00 45.11 5.68
2263 2830 3.277211 TTCTCGGTGTCTTCGGCCG 62.277 63.158 22.12 22.12 46.12 6.13
2266 2872 1.993370 GATTGTTCTCGGTGTCTTCGG 59.007 52.381 0.00 0.00 0.00 4.30
2267 2873 1.993370 GGATTGTTCTCGGTGTCTTCG 59.007 52.381 0.00 0.00 0.00 3.79
2271 2877 2.095718 GCTTTGGATTGTTCTCGGTGTC 60.096 50.000 0.00 0.00 0.00 3.67
2275 2881 1.135972 CGTGCTTTGGATTGTTCTCGG 60.136 52.381 0.00 0.00 0.00 4.63
2285 2891 2.029964 GACCGTCCGTGCTTTGGA 59.970 61.111 0.00 0.00 0.00 3.53
2286 2892 3.411351 CGACCGTCCGTGCTTTGG 61.411 66.667 0.00 0.00 0.00 3.28
2292 2898 2.506217 CCATGTCGACCGTCCGTG 60.506 66.667 14.12 0.00 0.00 4.94
2301 2907 2.536066 TCCCTTTCTTCTCCATGTCGA 58.464 47.619 0.00 0.00 0.00 4.20
2306 2912 3.188773 AGAGCTTCCCTTTCTTCTCCAT 58.811 45.455 0.00 0.00 0.00 3.41
2308 2914 3.712016 AAGAGCTTCCCTTTCTTCTCC 57.288 47.619 0.00 0.00 0.00 3.71
2309 2915 6.881602 TGATAAAAGAGCTTCCCTTTCTTCTC 59.118 38.462 0.00 0.00 33.15 2.87
2320 2926 3.596214 TCCACGGTGATAAAAGAGCTTC 58.404 45.455 10.28 0.00 0.00 3.86
2324 2930 5.011090 TGATCTCCACGGTGATAAAAGAG 57.989 43.478 10.28 6.60 0.00 2.85
2325 2931 4.709886 TCTGATCTCCACGGTGATAAAAGA 59.290 41.667 10.28 4.88 0.00 2.52
2327 2933 4.221924 TGTCTGATCTCCACGGTGATAAAA 59.778 41.667 10.28 0.00 0.00 1.52
2340 6319 1.410517 TCCTCGCCAATGTCTGATCTC 59.589 52.381 0.00 0.00 0.00 2.75
2380 6360 5.144692 TGATCCTCTCTTTTCTGTGACAG 57.855 43.478 6.18 6.18 0.00 3.51
2381 6361 5.551305 TTGATCCTCTCTTTTCTGTGACA 57.449 39.130 0.00 0.00 0.00 3.58
2382 6362 8.729805 ATATTTGATCCTCTCTTTTCTGTGAC 57.270 34.615 0.00 0.00 0.00 3.67
2390 6370 8.754080 CGTCCCTATATATTTGATCCTCTCTTT 58.246 37.037 0.00 0.00 0.00 2.52
2393 6373 6.322712 AGCGTCCCTATATATTTGATCCTCTC 59.677 42.308 0.00 0.00 0.00 3.20
2394 6374 6.198639 AGCGTCCCTATATATTTGATCCTCT 58.801 40.000 0.00 0.00 0.00 3.69
2395 6375 6.096987 TGAGCGTCCCTATATATTTGATCCTC 59.903 42.308 0.00 0.00 0.00 3.71
2396 6376 5.958380 TGAGCGTCCCTATATATTTGATCCT 59.042 40.000 0.00 0.00 0.00 3.24
2397 6377 6.222038 TGAGCGTCCCTATATATTTGATCC 57.778 41.667 0.00 0.00 0.00 3.36
2398 6378 9.988815 ATTATGAGCGTCCCTATATATTTGATC 57.011 33.333 0.00 0.00 0.00 2.92
2399 6379 9.988815 GATTATGAGCGTCCCTATATATTTGAT 57.011 33.333 0.00 0.00 0.00 2.57
2400 6380 9.201989 AGATTATGAGCGTCCCTATATATTTGA 57.798 33.333 0.00 0.00 0.00 2.69
2403 6383 8.982723 ACAAGATTATGAGCGTCCCTATATATT 58.017 33.333 0.00 0.00 0.00 1.28
2409 6389 3.958147 TCACAAGATTATGAGCGTCCCTA 59.042 43.478 0.00 0.00 0.00 3.53
2411 6391 3.179443 TCACAAGATTATGAGCGTCCC 57.821 47.619 0.00 0.00 0.00 4.46
2412 6392 5.741388 ATTTCACAAGATTATGAGCGTCC 57.259 39.130 0.00 0.00 0.00 4.79
2413 6393 7.640240 GGTAAATTTCACAAGATTATGAGCGTC 59.360 37.037 0.00 0.00 0.00 5.19
2414 6394 7.120579 TGGTAAATTTCACAAGATTATGAGCGT 59.879 33.333 0.00 0.00 0.00 5.07
2439 6528 4.214437 GTCTTGCTGTTTCTTCGAATGTG 58.786 43.478 0.00 0.00 0.00 3.21
2440 6529 3.251004 GGTCTTGCTGTTTCTTCGAATGT 59.749 43.478 0.00 0.00 0.00 2.71
2445 6534 1.593196 TGGGTCTTGCTGTTTCTTCG 58.407 50.000 0.00 0.00 0.00 3.79
2471 6560 9.919416 AGCAGAGAGATATGTACTATGATATGT 57.081 33.333 0.00 0.00 0.00 2.29
2480 6569 9.757227 GAACAAATAAGCAGAGAGATATGTACT 57.243 33.333 0.00 0.00 0.00 2.73
2481 6570 9.534565 TGAACAAATAAGCAGAGAGATATGTAC 57.465 33.333 0.00 0.00 0.00 2.90
2544 6633 5.277974 CCCGATGGTTTAATCAGCTGTAATG 60.278 44.000 14.67 0.00 0.00 1.90
2557 6646 3.791953 TGTTTCTTCCCCGATGGTTTA 57.208 42.857 0.00 0.00 34.77 2.01
2561 6650 2.210116 CGTATGTTTCTTCCCCGATGG 58.790 52.381 0.00 0.00 0.00 3.51
2585 6674 4.874966 AGGAGGCATACGATACGACTATAC 59.125 45.833 0.00 0.00 0.00 1.47
2586 6675 5.095145 AGGAGGCATACGATACGACTATA 57.905 43.478 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.