Multiple sequence alignment - TraesCS5D01G258300

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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 TraesCS5D01G258300 chr5D 100.000 4406 0 0 1 4406 364743692 364748097 0.000000e+00 8137
1 TraesCS5D01G258300 chr5D 92.593 81 6 0 1669 1749 394160599 394160679 2.780000e-22 117
2 TraesCS5D01G258300 chr5D 88.172 93 11 0 1669 1761 387715459 387715367 1.300000e-20 111
3 TraesCS5D01G258300 chr5A 91.426 3324 142 72 595 3830 466025798 466029066 0.000000e+00 4427
4 TraesCS5D01G258300 chr5A 94.097 559 11 7 1 540 466025245 466025800 0.000000e+00 830
5 TraesCS5D01G258300 chr5A 78.116 329 39 15 4059 4376 466029364 466029670 1.260000e-40 178
6 TraesCS5D01G258300 chr5A 89.773 88 6 1 2350 2437 466027515 466027599 4.660000e-20 110
7 TraesCS5D01G258300 chr5B 93.934 1731 60 19 573 2292 430740032 430741728 0.000000e+00 2573
8 TraesCS5D01G258300 chr5B 87.662 1775 63 48 2348 4039 430741742 430743443 0.000000e+00 1921
9 TraesCS5D01G258300 chr5B 93.628 565 13 9 1 564 430739510 430740052 0.000000e+00 822
10 TraesCS5D01G258300 chr5B 90.441 136 8 2 4042 4172 430743545 430743680 1.630000e-39 174
11 TraesCS5D01G258300 chr2A 86.022 93 13 0 1669 1761 768206783 768206691 2.800000e-17 100


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 TraesCS5D01G258300 chr5D 364743692 364748097 4405 False 8137.00 8137 100.00000 1 4406 1 chr5D.!!$F1 4405
1 TraesCS5D01G258300 chr5A 466025245 466029670 4425 False 1386.25 4427 88.35300 1 4376 4 chr5A.!!$F1 4375
2 TraesCS5D01G258300 chr5B 430739510 430743680 4170 False 1372.50 2573 91.41625 1 4172 4 chr5B.!!$F1 4171

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
544 599 0.038618 CTAAAGCGGTTTGTTGCCCC 60.039 55.0 22.16 0.0 0.00 5.80 F
551 606 0.402121 GGTTTGTTGCCCCTCTCTCT 59.598 55.0 0.00 0.0 0.00 3.10 F
555 610 0.411452 TGTTGCCCCTCTCTCTCTCT 59.589 55.0 0.00 0.0 0.00 3.10 F
558 613 0.550914 TGCCCCTCTCTCTCTCTCTC 59.449 60.0 0.00 0.0 0.00 3.20 F
1566 1635 0.728129 CGTCGTGTGCTTCTCGCTTA 60.728 55.0 0.00 0.0 40.11 3.09 F
2629 2764 1.035139 CCAGTTGCCTGCTTTCAAGT 58.965 50.0 0.00 0.0 37.38 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2476 2610 0.244721 AAATTGCAAAGGGAGCGAGC 59.755 50.000 1.71 0.0 33.85 5.03 R
2598 2732 1.073284 GGCAACTGGTAGTCCAAGGAA 59.927 52.381 0.00 0.0 43.81 3.36 R
2600 2734 3.249687 GGCAACTGGTAGTCCAAGG 57.750 57.895 0.00 0.0 43.81 3.61 R
2636 2771 7.040132 TGTTGTTGGCATGAACATGATTAGTTA 60.040 33.333 17.40 0.0 41.20 2.24 R
2681 2832 0.243907 CCATGGACGACGAAGACACT 59.756 55.000 5.56 0.0 0.00 3.55 R
4376 4771 0.169009 GATCAACAGCCGAGTTTGCC 59.831 55.000 0.00 0.0 0.00 4.52 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
132 135 0.395173 ATAATTGCCCGTGTCCACCC 60.395 55.000 0.00 0.00 0.00 4.61
278 281 0.179097 CTCTTTACGCCTGCTCCTCC 60.179 60.000 0.00 0.00 0.00 4.30
279 282 0.614979 TCTTTACGCCTGCTCCTCCT 60.615 55.000 0.00 0.00 0.00 3.69
282 285 1.323271 TTACGCCTGCTCCTCCTCTG 61.323 60.000 0.00 0.00 0.00 3.35
283 286 4.527583 CGCCTGCTCCTCCTCTGC 62.528 72.222 0.00 0.00 0.00 4.26
284 287 3.082701 GCCTGCTCCTCCTCTGCT 61.083 66.667 0.00 0.00 0.00 4.24
285 288 3.092780 GCCTGCTCCTCCTCTGCTC 62.093 68.421 0.00 0.00 0.00 4.26
286 289 2.433994 CCTGCTCCTCCTCTGCTCC 61.434 68.421 0.00 0.00 0.00 4.70
287 290 1.381599 CTGCTCCTCCTCTGCTCCT 60.382 63.158 0.00 0.00 0.00 3.69
288 291 1.678598 CTGCTCCTCCTCTGCTCCTG 61.679 65.000 0.00 0.00 0.00 3.86
289 292 3.092780 GCTCCTCCTCTGCTCCTGC 62.093 68.421 0.00 0.00 40.20 4.85
290 293 1.381599 CTCCTCCTCTGCTCCTGCT 60.382 63.158 0.00 0.00 40.48 4.24
291 294 0.106268 CTCCTCCTCTGCTCCTGCTA 60.106 60.000 0.00 0.00 40.48 3.49
339 358 1.702957 AGCAAGTAAGTAACCCAGGCA 59.297 47.619 0.00 0.00 0.00 4.75
407 426 4.178956 AGGGCTGTTAACAAAGGAAAGA 57.821 40.909 10.03 0.00 0.00 2.52
436 455 1.003464 GGACGGTTAAGGTGCCCTAAA 59.997 52.381 0.00 0.00 31.13 1.85
437 456 2.079158 GACGGTTAAGGTGCCCTAAAC 58.921 52.381 0.00 0.00 31.13 2.01
438 457 1.420891 ACGGTTAAGGTGCCCTAAACA 59.579 47.619 0.00 0.00 31.13 2.83
439 458 2.040679 ACGGTTAAGGTGCCCTAAACAT 59.959 45.455 0.00 0.00 31.13 2.71
443 462 5.183522 CGGTTAAGGTGCCCTAAACATTTTA 59.816 40.000 0.00 0.00 31.13 1.52
444 463 6.294620 CGGTTAAGGTGCCCTAAACATTTTAA 60.295 38.462 0.00 0.00 31.13 1.52
540 595 0.958822 AGGGCTAAAGCGGTTTGTTG 59.041 50.000 22.16 12.74 43.26 3.33
541 596 0.666274 GGGCTAAAGCGGTTTGTTGC 60.666 55.000 22.16 20.29 43.26 4.17
542 597 0.666274 GGCTAAAGCGGTTTGTTGCC 60.666 55.000 25.62 25.62 43.26 4.52
543 598 0.666274 GCTAAAGCGGTTTGTTGCCC 60.666 55.000 22.16 1.09 0.00 5.36
544 599 0.038618 CTAAAGCGGTTTGTTGCCCC 60.039 55.000 22.16 0.00 0.00 5.80
545 600 0.468400 TAAAGCGGTTTGTTGCCCCT 60.468 50.000 22.16 0.00 0.00 4.79
546 601 1.744320 AAAGCGGTTTGTTGCCCCTC 61.744 55.000 12.53 0.00 0.00 4.30
547 602 2.597510 GCGGTTTGTTGCCCCTCT 60.598 61.111 0.00 0.00 0.00 3.69
548 603 2.626780 GCGGTTTGTTGCCCCTCTC 61.627 63.158 0.00 0.00 0.00 3.20
549 604 1.073199 CGGTTTGTTGCCCCTCTCT 59.927 57.895 0.00 0.00 0.00 3.10
550 605 0.955919 CGGTTTGTTGCCCCTCTCTC 60.956 60.000 0.00 0.00 0.00 3.20
551 606 0.402121 GGTTTGTTGCCCCTCTCTCT 59.598 55.000 0.00 0.00 0.00 3.10
552 607 1.611936 GGTTTGTTGCCCCTCTCTCTC 60.612 57.143 0.00 0.00 0.00 3.20
553 608 1.349357 GTTTGTTGCCCCTCTCTCTCT 59.651 52.381 0.00 0.00 0.00 3.10
554 609 1.270907 TTGTTGCCCCTCTCTCTCTC 58.729 55.000 0.00 0.00 0.00 3.20
555 610 0.411452 TGTTGCCCCTCTCTCTCTCT 59.589 55.000 0.00 0.00 0.00 3.10
556 611 1.111277 GTTGCCCCTCTCTCTCTCTC 58.889 60.000 0.00 0.00 0.00 3.20
557 612 1.006813 TTGCCCCTCTCTCTCTCTCT 58.993 55.000 0.00 0.00 0.00 3.10
558 613 0.550914 TGCCCCTCTCTCTCTCTCTC 59.449 60.000 0.00 0.00 0.00 3.20
559 614 0.846693 GCCCCTCTCTCTCTCTCTCT 59.153 60.000 0.00 0.00 0.00 3.10
560 615 1.202818 GCCCCTCTCTCTCTCTCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
561 616 2.412591 CCCCTCTCTCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
562 617 2.370189 CCCCTCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
563 618 3.312890 CCCTCTCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
564 619 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
565 620 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
566 621 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
567 622 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
568 623 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
569 624 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
570 625 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
571 626 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
572 627 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
573 628 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
574 629 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
575 630 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
576 631 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
577 632 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
578 633 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
579 634 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
580 635 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
581 636 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
582 637 4.078922 TCTCTCTCTCTCTCTCTCTCTCCT 60.079 50.000 0.00 0.00 0.00 3.69
583 638 4.219115 TCTCTCTCTCTCTCTCTCTCCTC 58.781 52.174 0.00 0.00 0.00 3.71
584 639 4.078922 TCTCTCTCTCTCTCTCTCTCCTCT 60.079 50.000 0.00 0.00 0.00 3.69
585 640 4.219115 TCTCTCTCTCTCTCTCTCCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
586 641 4.078922 TCTCTCTCTCTCTCTCTCCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
587 642 4.219115 TCTCTCTCTCTCTCTCCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
588 643 4.078922 TCTCTCTCTCTCTCTCCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
589 644 4.219115 TCTCTCTCTCTCTCCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
590 645 4.078922 TCTCTCTCTCTCTCCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
591 646 3.963374 TCTCTCTCTCTCCTCTCTCTCTG 59.037 52.174 0.00 0.00 0.00 3.35
592 647 3.708631 CTCTCTCTCTCCTCTCTCTCTGT 59.291 52.174 0.00 0.00 0.00 3.41
593 648 3.452264 TCTCTCTCTCCTCTCTCTCTGTG 59.548 52.174 0.00 0.00 0.00 3.66
594 649 2.505407 TCTCTCTCCTCTCTCTCTGTGG 59.495 54.545 0.00 0.00 0.00 4.17
595 650 2.239654 CTCTCTCCTCTCTCTCTGTGGT 59.760 54.545 0.00 0.00 0.00 4.16
596 651 2.647299 TCTCTCCTCTCTCTCTGTGGTT 59.353 50.000 0.00 0.00 0.00 3.67
880 943 4.211502 GCCCATCGCATTGCCCAC 62.212 66.667 2.41 0.00 37.47 4.61
975 1038 2.031245 TCCATTTGCTACGCTTGTTGTG 60.031 45.455 0.00 0.00 0.00 3.33
976 1039 1.715519 CATTTGCTACGCTTGTTGTGC 59.284 47.619 0.00 0.00 0.00 4.57
1155 1224 1.586564 GATGGACTCCTTCGCGTCG 60.587 63.158 5.77 0.00 0.00 5.12
1497 1566 1.371183 CTGCTCGTCCAAAGGGTCA 59.629 57.895 0.00 0.00 34.93 4.02
1539 1608 2.171840 CCCAGCGAGGTATATACTGCT 58.828 52.381 16.71 16.71 34.66 4.24
1548 1617 4.621991 AGGTATATACTGCTTGCTGTTCG 58.378 43.478 12.54 0.00 0.00 3.95
1555 1624 1.083401 GCTTGCTGTTCGTCGTGTG 60.083 57.895 0.00 0.00 0.00 3.82
1556 1625 1.083401 CTTGCTGTTCGTCGTGTGC 60.083 57.895 0.00 0.00 0.00 4.57
1557 1626 1.490693 CTTGCTGTTCGTCGTGTGCT 61.491 55.000 0.00 0.00 0.00 4.40
1558 1627 1.087202 TTGCTGTTCGTCGTGTGCTT 61.087 50.000 0.00 0.00 0.00 3.91
1559 1628 1.201825 GCTGTTCGTCGTGTGCTTC 59.798 57.895 0.00 0.00 0.00 3.86
1560 1629 1.215655 GCTGTTCGTCGTGTGCTTCT 61.216 55.000 0.00 0.00 0.00 2.85
1561 1630 0.778815 CTGTTCGTCGTGTGCTTCTC 59.221 55.000 0.00 0.00 0.00 2.87
1562 1631 0.933047 TGTTCGTCGTGTGCTTCTCG 60.933 55.000 0.00 0.00 34.85 4.04
1563 1632 2.014554 TTCGTCGTGTGCTTCTCGC 61.015 57.895 0.00 0.00 39.77 5.03
1564 1633 2.402282 TTCGTCGTGTGCTTCTCGCT 62.402 55.000 0.00 0.00 40.11 4.93
1565 1634 2.016704 CGTCGTGTGCTTCTCGCTT 61.017 57.895 0.00 0.00 40.11 4.68
1566 1635 0.728129 CGTCGTGTGCTTCTCGCTTA 60.728 55.000 0.00 0.00 40.11 3.09
1567 1636 1.415374 GTCGTGTGCTTCTCGCTTAA 58.585 50.000 0.00 0.00 40.11 1.85
1568 1637 1.790623 GTCGTGTGCTTCTCGCTTAAA 59.209 47.619 0.00 0.00 40.11 1.52
1569 1638 1.790623 TCGTGTGCTTCTCGCTTAAAC 59.209 47.619 0.00 0.00 40.11 2.01
1570 1639 1.792949 CGTGTGCTTCTCGCTTAAACT 59.207 47.619 0.00 0.00 40.11 2.66
1571 1640 2.410262 CGTGTGCTTCTCGCTTAAACTG 60.410 50.000 0.00 0.00 40.11 3.16
1572 1641 2.544267 GTGTGCTTCTCGCTTAAACTGT 59.456 45.455 0.00 0.00 40.11 3.55
1573 1642 2.800544 TGTGCTTCTCGCTTAAACTGTC 59.199 45.455 0.00 0.00 40.11 3.51
1595 1664 5.047943 GTCTCCAGCTTCAGTTCAGTACTTA 60.048 44.000 0.00 0.00 33.85 2.24
1596 1665 5.184096 TCTCCAGCTTCAGTTCAGTACTTAG 59.816 44.000 0.00 0.00 33.85 2.18
1597 1666 5.077564 TCCAGCTTCAGTTCAGTACTTAGA 58.922 41.667 0.00 0.00 33.85 2.10
1598 1667 5.538813 TCCAGCTTCAGTTCAGTACTTAGAA 59.461 40.000 0.00 0.00 33.85 2.10
1599 1668 6.041637 TCCAGCTTCAGTTCAGTACTTAGAAA 59.958 38.462 0.00 0.00 33.85 2.52
1600 1669 6.367422 CCAGCTTCAGTTCAGTACTTAGAAAG 59.633 42.308 0.00 0.00 33.85 2.62
1601 1670 5.929415 AGCTTCAGTTCAGTACTTAGAAAGC 59.071 40.000 12.90 12.90 36.63 3.51
1602 1671 5.696724 GCTTCAGTTCAGTACTTAGAAAGCA 59.303 40.000 14.70 0.00 36.52 3.91
1603 1672 6.202954 GCTTCAGTTCAGTACTTAGAAAGCAA 59.797 38.462 14.70 2.69 36.52 3.91
1608 1688 7.115663 CAGTTCAGTACTTAGAAAGCAAGTCTC 59.884 40.741 0.00 0.00 37.42 3.36
1612 1692 4.323553 ACTTAGAAAGCAAGTCTCGTGT 57.676 40.909 0.00 0.00 30.36 4.49
1623 1703 2.417719 AGTCTCGTGTTTCATTCAGGC 58.582 47.619 0.00 0.00 0.00 4.85
1628 1708 1.202065 CGTGTTTCATTCAGGCGATGG 60.202 52.381 0.00 0.00 0.00 3.51
1629 1709 1.133025 GTGTTTCATTCAGGCGATGGG 59.867 52.381 0.00 0.00 0.00 4.00
1630 1710 1.271871 TGTTTCATTCAGGCGATGGGT 60.272 47.619 0.00 0.00 0.00 4.51
2065 2145 4.505556 ACCGAAAGAAGTTACGTGTTTCTC 59.494 41.667 15.77 0.00 31.16 2.87
2201 2282 3.303791 GCAAAGACAAGTTGAGGTAACGG 60.304 47.826 10.54 0.00 44.15 4.44
2242 2323 3.581101 TCTATCTAGGCAACCTGAGCAT 58.419 45.455 0.00 0.00 34.61 3.79
2243 2324 4.740902 TCTATCTAGGCAACCTGAGCATA 58.259 43.478 0.00 0.00 34.61 3.14
2244 2325 3.760580 ATCTAGGCAACCTGAGCATAC 57.239 47.619 0.00 0.00 34.61 2.39
2245 2326 2.466846 TCTAGGCAACCTGAGCATACA 58.533 47.619 0.00 0.00 34.61 2.29
2269 2350 9.649316 ACATACTAGTAGGATTTTAGCTTCTCT 57.351 33.333 20.74 0.00 0.00 3.10
2280 2361 8.608317 GGATTTTAGCTTCTCTTGAACATACTC 58.392 37.037 0.00 0.00 0.00 2.59
2292 2373 1.629043 ACATACTCCGTGTCAGGTGT 58.371 50.000 0.00 0.00 40.60 4.16
2315 2396 4.559862 AGGGAAGAAGTACAATCACTGG 57.440 45.455 0.00 0.00 0.00 4.00
2316 2397 4.168101 AGGGAAGAAGTACAATCACTGGA 58.832 43.478 0.00 0.00 0.00 3.86
2317 2398 4.785376 AGGGAAGAAGTACAATCACTGGAT 59.215 41.667 0.00 0.00 34.43 3.41
2318 2399 5.964477 AGGGAAGAAGTACAATCACTGGATA 59.036 40.000 0.00 0.00 32.09 2.59
2319 2400 6.049790 GGGAAGAAGTACAATCACTGGATAC 58.950 44.000 0.00 0.00 32.09 2.24
2445 2579 4.083855 TGTGTTCTAGTAACTGGTACGTCG 60.084 45.833 0.00 0.00 37.81 5.12
2476 2610 2.014128 ACAACCACCAGAGTTTTGACG 58.986 47.619 0.00 0.00 0.00 4.35
2594 2728 7.042858 GGATGTAAGAGCATCATCGCTTATATG 60.043 40.741 8.11 0.00 45.11 1.78
2595 2729 6.924111 TGTAAGAGCATCATCGCTTATATGA 58.076 36.000 0.00 0.00 44.01 2.15
2596 2730 7.378181 TGTAAGAGCATCATCGCTTATATGAA 58.622 34.615 0.00 0.00 44.01 2.57
2597 2731 8.037166 TGTAAGAGCATCATCGCTTATATGAAT 58.963 33.333 0.00 0.00 44.01 2.57
2598 2732 7.918536 AAGAGCATCATCGCTTATATGAATT 57.081 32.000 0.00 0.00 44.01 2.17
2600 2734 7.972527 AGAGCATCATCGCTTATATGAATTTC 58.027 34.615 0.00 0.00 44.01 2.17
2604 2738 7.484007 GCATCATCGCTTATATGAATTTCCTTG 59.516 37.037 0.00 0.00 36.95 3.61
2605 2739 7.439157 TCATCGCTTATATGAATTTCCTTGG 57.561 36.000 0.00 0.00 30.52 3.61
2606 2740 7.223584 TCATCGCTTATATGAATTTCCTTGGA 58.776 34.615 0.00 0.00 30.52 3.53
2607 2741 6.861065 TCGCTTATATGAATTTCCTTGGAC 57.139 37.500 0.00 0.00 0.00 4.02
2629 2764 1.035139 CCAGTTGCCTGCTTTCAAGT 58.965 50.000 0.00 0.00 37.38 3.16
2636 2771 2.104792 TGCCTGCTTTCAAGTAGTGTCT 59.895 45.455 4.24 0.00 37.08 3.41
2643 2778 7.819900 CCTGCTTTCAAGTAGTGTCTAACTAAT 59.180 37.037 4.24 0.00 43.08 1.73
2650 2785 9.856488 TCAAGTAGTGTCTAACTAATCATGTTC 57.144 33.333 0.00 0.00 43.08 3.18
2651 2786 9.639601 CAAGTAGTGTCTAACTAATCATGTTCA 57.360 33.333 0.00 0.00 43.08 3.18
2653 2788 9.809096 AGTAGTGTCTAACTAATCATGTTCATG 57.191 33.333 6.46 6.46 43.08 3.07
2681 2832 1.194781 AGCTTCTTCGCTTCCCTGGA 61.195 55.000 0.00 0.00 36.74 3.86
2696 2847 0.109689 CTGGAGTGTCTTCGTCGTCC 60.110 60.000 0.00 0.00 0.00 4.79
2843 2994 3.303049 AGCAAAAGATGGATCCCATTCC 58.697 45.455 9.90 0.00 45.26 3.01
2853 3004 1.494721 GATCCCATTCCCAGGTTAGCA 59.505 52.381 0.00 0.00 0.00 3.49
2855 3006 1.215173 TCCCATTCCCAGGTTAGCATG 59.785 52.381 0.00 0.00 0.00 4.06
2856 3007 1.215173 CCCATTCCCAGGTTAGCATGA 59.785 52.381 0.00 0.00 0.00 3.07
2857 3008 2.158415 CCCATTCCCAGGTTAGCATGAT 60.158 50.000 0.00 0.00 0.00 2.45
2858 3009 3.074390 CCCATTCCCAGGTTAGCATGATA 59.926 47.826 0.00 0.00 0.00 2.15
2859 3010 4.330250 CCATTCCCAGGTTAGCATGATAG 58.670 47.826 0.00 0.00 0.00 2.08
2860 3011 3.492102 TTCCCAGGTTAGCATGATAGC 57.508 47.619 0.00 0.00 0.00 2.97
2861 3012 2.407562 TCCCAGGTTAGCATGATAGCA 58.592 47.619 7.15 0.00 36.85 3.49
2862 3013 2.981784 TCCCAGGTTAGCATGATAGCAT 59.018 45.455 7.15 0.00 36.85 3.79
2863 3014 3.008375 TCCCAGGTTAGCATGATAGCATC 59.992 47.826 7.15 0.00 36.85 3.91
2864 3015 3.008813 CCCAGGTTAGCATGATAGCATCT 59.991 47.826 7.15 0.00 36.85 2.90
2865 3016 4.252073 CCAGGTTAGCATGATAGCATCTC 58.748 47.826 7.15 0.00 36.85 2.75
2866 3017 4.020396 CCAGGTTAGCATGATAGCATCTCT 60.020 45.833 7.15 0.00 36.85 3.10
2867 3018 5.512749 CCAGGTTAGCATGATAGCATCTCTT 60.513 44.000 7.15 0.00 36.85 2.85
2868 3019 5.638657 CAGGTTAGCATGATAGCATCTCTTC 59.361 44.000 7.15 0.00 36.85 2.87
2869 3020 5.306419 AGGTTAGCATGATAGCATCTCTTCA 59.694 40.000 7.15 0.00 36.85 3.02
2870 3021 5.994054 GGTTAGCATGATAGCATCTCTTCAA 59.006 40.000 7.15 0.00 36.85 2.69
2871 3022 6.147492 GGTTAGCATGATAGCATCTCTTCAAG 59.853 42.308 7.15 0.00 36.85 3.02
2872 3023 4.066490 AGCATGATAGCATCTCTTCAAGC 58.934 43.478 0.00 0.00 36.85 4.01
2888 3039 5.466728 TCTTCAAGCTCAACAACTGACATAC 59.533 40.000 0.00 0.00 0.00 2.39
2890 3041 5.308014 TCAAGCTCAACAACTGACATACAT 58.692 37.500 0.00 0.00 0.00 2.29
2891 3042 6.463360 TCAAGCTCAACAACTGACATACATA 58.537 36.000 0.00 0.00 0.00 2.29
2892 3043 6.368791 TCAAGCTCAACAACTGACATACATAC 59.631 38.462 0.00 0.00 0.00 2.39
2893 3044 5.178797 AGCTCAACAACTGACATACATACC 58.821 41.667 0.00 0.00 0.00 2.73
2894 3045 4.935205 GCTCAACAACTGACATACATACCA 59.065 41.667 0.00 0.00 0.00 3.25
2895 3046 5.063944 GCTCAACAACTGACATACATACCAG 59.936 44.000 0.00 0.00 0.00 4.00
2923 3079 3.063588 GGTTAATTACTCCAGCAACGAGC 59.936 47.826 0.00 0.00 46.19 5.03
2941 3097 3.249799 CGAGCTAGTAGGAGATGACACAG 59.750 52.174 0.00 0.00 0.00 3.66
2978 3134 6.875948 ACAATTTAATTTGCTCCCAAAACC 57.124 33.333 9.46 0.00 43.58 3.27
2988 3144 2.914059 CTCCCAAAACCCCATAGTACG 58.086 52.381 0.00 0.00 0.00 3.67
3096 3256 3.936564 GCAGCTAGCAGCCTATTAGATT 58.063 45.455 20.58 0.00 43.77 2.40
3136 3301 6.876257 GGCCAGTAGGAGTATGAAATGAATAG 59.124 42.308 0.00 0.00 36.89 1.73
3178 3343 4.743151 TGCATACTTACATAGCTAACGTGC 59.257 41.667 0.00 1.36 0.00 5.34
3327 3509 3.425713 CACGTTGCGCAGATGGCT 61.426 61.111 11.31 0.00 41.67 4.75
3412 3594 3.627123 CGCCTACCAAATGTGATTGATGA 59.373 43.478 0.00 0.00 31.84 2.92
3651 3870 2.543848 CGTGTGTAAATCGATCCATGGG 59.456 50.000 13.02 0.00 0.00 4.00
3697 3916 1.244019 CGGGGCTGGAACTGGAAAAG 61.244 60.000 0.00 0.00 0.00 2.27
3702 3921 0.482887 CTGGAACTGGAAAAGGGGGT 59.517 55.000 0.00 0.00 0.00 4.95
3704 3923 1.338107 GGAACTGGAAAAGGGGGTTG 58.662 55.000 0.00 0.00 0.00 3.77
3818 4041 2.001361 GCAGCGGCTGATGAATTGCT 62.001 55.000 32.72 0.00 36.96 3.91
3819 4042 0.248498 CAGCGGCTGATGAATTGCTG 60.248 55.000 25.33 0.00 43.08 4.41
3820 4043 4.704007 CGGCTGATGAATTGCTGC 57.296 55.556 0.00 0.00 0.00 5.25
3821 4044 1.065273 CGGCTGATGAATTGCTGCC 59.935 57.895 0.00 0.00 43.26 4.85
3822 4045 1.065273 GGCTGATGAATTGCTGCCG 59.935 57.895 0.00 0.00 38.93 5.69
3823 4046 1.588139 GCTGATGAATTGCTGCCGC 60.588 57.895 0.00 0.00 0.00 6.53
3824 4047 2.001361 GCTGATGAATTGCTGCCGCT 62.001 55.000 0.70 0.00 36.97 5.52
3825 4048 0.248498 CTGATGAATTGCTGCCGCTG 60.248 55.000 0.70 0.00 36.97 5.18
3826 4049 1.588139 GATGAATTGCTGCCGCTGC 60.588 57.895 14.83 14.83 36.97 5.25
3827 4050 2.001361 GATGAATTGCTGCCGCTGCT 62.001 55.000 21.13 3.18 38.71 4.24
3828 4051 2.202570 GAATTGCTGCCGCTGCTG 60.203 61.111 21.13 1.71 38.71 4.41
3861 4084 2.936114 GCTGCTGCAGGATATCTCATCC 60.936 54.545 29.05 5.82 39.41 3.51
3883 4112 2.186826 GGACGCAAGCACAACCAGT 61.187 57.895 0.00 0.00 45.62 4.00
3913 4190 3.093172 TATGGGGGTGCATGGCGA 61.093 61.111 0.00 0.00 0.00 5.54
3914 4191 3.414136 TATGGGGGTGCATGGCGAC 62.414 63.158 0.00 0.00 0.00 5.19
3963 4240 0.601558 ACACCTGCACGAGTACGAAT 59.398 50.000 0.00 0.00 42.66 3.34
4039 4318 0.251033 GAACTTTTACCAGCCCCGGT 60.251 55.000 0.00 0.00 43.46 5.28
4055 4434 2.315386 GGTCACACGACGAAAGCCC 61.315 63.158 0.00 0.00 43.61 5.19
4061 4440 2.338015 ACGACGAAAGCCCTAGCGA 61.338 57.895 0.00 0.00 46.67 4.93
4136 4516 0.601558 ACCCACAGCACAGTACTACG 59.398 55.000 0.00 0.00 0.00 3.51
4137 4517 0.885879 CCCACAGCACAGTACTACGA 59.114 55.000 0.00 0.00 0.00 3.43
4138 4518 1.135373 CCCACAGCACAGTACTACGAG 60.135 57.143 0.00 0.00 0.00 4.18
4172 4556 2.480759 CGATCTTTGGGGTGGTACGTAG 60.481 54.545 0.00 0.00 0.00 3.51
4173 4557 2.307496 TCTTTGGGGTGGTACGTAGA 57.693 50.000 0.00 0.00 0.00 2.59
4176 4560 2.897271 TTGGGGTGGTACGTAGAGTA 57.103 50.000 0.00 0.00 0.00 2.59
4194 4578 4.083749 AGAGTACGTATATTCTGCTCTGCG 60.084 45.833 8.37 0.00 31.57 5.18
4198 4582 2.408050 GTATATTCTGCTCTGCGGGTG 58.592 52.381 0.00 0.00 35.34 4.61
4199 4583 0.833287 ATATTCTGCTCTGCGGGTGT 59.167 50.000 0.00 0.00 35.34 4.16
4200 4584 0.175760 TATTCTGCTCTGCGGGTGTC 59.824 55.000 0.00 0.00 35.34 3.67
4209 4593 4.634133 GCGGGTGTCGTCGTGTCA 62.634 66.667 0.00 0.00 41.72 3.58
4224 4613 0.616395 TGTCATCGCTAGGGGTTCCA 60.616 55.000 6.99 0.00 34.83 3.53
4248 4638 1.527380 GACAAGGGGTTTGGCACGA 60.527 57.895 0.00 0.00 44.72 4.35
4251 4641 1.674322 AAGGGGTTTGGCACGATCG 60.674 57.895 14.88 14.88 0.00 3.69
4252 4642 3.131478 GGGGTTTGGCACGATCGG 61.131 66.667 20.98 9.59 0.00 4.18
4259 4649 1.613317 TTGGCACGATCGGGATCAGT 61.613 55.000 24.26 0.00 37.69 3.41
4260 4650 1.144057 GGCACGATCGGGATCAGTT 59.856 57.895 24.26 0.00 37.69 3.16
4261 4651 0.462047 GGCACGATCGGGATCAGTTT 60.462 55.000 24.26 0.00 37.69 2.66
4262 4652 1.202486 GGCACGATCGGGATCAGTTTA 60.202 52.381 24.26 0.00 37.69 2.01
4293 4683 3.470888 GAGGGGCCGCTGCTTCTA 61.471 66.667 29.42 0.00 37.74 2.10
4294 4684 3.453070 GAGGGGCCGCTGCTTCTAG 62.453 68.421 29.42 0.00 37.74 2.43
4296 4686 2.512515 GGGCCGCTGCTTCTAGTG 60.513 66.667 0.00 0.00 37.74 2.74
4298 4688 1.376037 GGCCGCTGCTTCTAGTGTT 60.376 57.895 0.00 0.00 37.74 3.32
4299 4689 0.955919 GGCCGCTGCTTCTAGTGTTT 60.956 55.000 0.00 0.00 37.74 2.83
4300 4690 0.875059 GCCGCTGCTTCTAGTGTTTT 59.125 50.000 0.00 0.00 33.53 2.43
4301 4691 1.400242 GCCGCTGCTTCTAGTGTTTTG 60.400 52.381 0.00 0.00 33.53 2.44
4302 4692 1.873591 CCGCTGCTTCTAGTGTTTTGT 59.126 47.619 0.00 0.00 0.00 2.83
4305 4695 4.201724 CCGCTGCTTCTAGTGTTTTGTATC 60.202 45.833 0.00 0.00 0.00 2.24
4306 4696 4.627467 CGCTGCTTCTAGTGTTTTGTATCT 59.373 41.667 0.00 0.00 0.00 1.98
4307 4697 5.805486 CGCTGCTTCTAGTGTTTTGTATCTA 59.195 40.000 0.00 0.00 0.00 1.98
4308 4698 6.237595 CGCTGCTTCTAGTGTTTTGTATCTAC 60.238 42.308 0.00 0.00 0.00 2.59
4309 4699 6.237595 GCTGCTTCTAGTGTTTTGTATCTACG 60.238 42.308 0.00 0.00 0.00 3.51
4310 4700 6.684686 TGCTTCTAGTGTTTTGTATCTACGT 58.315 36.000 0.00 0.00 0.00 3.57
4319 4714 0.380733 TGTATCTACGTCTGCCTGCG 59.619 55.000 0.00 0.00 0.00 5.18
4340 4735 0.315869 CCTGCACACGTCGAAAACAC 60.316 55.000 0.00 0.00 0.00 3.32
4341 4736 0.315869 CTGCACACGTCGAAAACACC 60.316 55.000 0.00 0.00 0.00 4.16
4361 4756 2.976840 GCGCAAGGCAATTCCGTGA 61.977 57.895 0.30 0.00 45.67 4.35
4371 4766 2.738135 CAATTCCGTGAACGCCTTTTT 58.262 42.857 0.00 0.00 38.18 1.94
4390 4785 1.975660 TTTTAGGCAAACTCGGCTGT 58.024 45.000 0.00 0.00 42.62 4.40
4391 4786 1.975660 TTTAGGCAAACTCGGCTGTT 58.024 45.000 0.00 0.00 42.62 3.16
4392 4787 1.234821 TTAGGCAAACTCGGCTGTTG 58.765 50.000 0.00 0.00 42.62 3.33
4393 4788 0.394938 TAGGCAAACTCGGCTGTTGA 59.605 50.000 0.00 0.00 42.62 3.18
4394 4789 0.250901 AGGCAAACTCGGCTGTTGAT 60.251 50.000 0.00 0.00 40.87 2.57
4395 4790 0.169009 GGCAAACTCGGCTGTTGATC 59.831 55.000 0.00 0.00 0.00 2.92
4396 4791 0.179215 GCAAACTCGGCTGTTGATCG 60.179 55.000 0.00 0.00 0.00 3.69
4397 4792 1.148310 CAAACTCGGCTGTTGATCGT 58.852 50.000 0.00 0.00 0.00 3.73
4398 4793 1.136252 CAAACTCGGCTGTTGATCGTG 60.136 52.381 0.00 0.00 0.00 4.35
4399 4794 1.291877 AACTCGGCTGTTGATCGTGC 61.292 55.000 0.00 0.00 0.00 5.34
4400 4795 1.737735 CTCGGCTGTTGATCGTGCA 60.738 57.895 0.00 0.00 0.00 4.57
4401 4796 1.291184 CTCGGCTGTTGATCGTGCAA 61.291 55.000 0.00 0.00 0.00 4.08
4402 4797 1.133253 CGGCTGTTGATCGTGCAAG 59.867 57.895 0.00 0.00 0.00 4.01
4403 4798 1.503542 GGCTGTTGATCGTGCAAGG 59.496 57.895 0.00 0.00 0.00 3.61
4404 4799 0.955428 GGCTGTTGATCGTGCAAGGA 60.955 55.000 0.00 0.00 33.98 3.36
4405 4800 1.089920 GCTGTTGATCGTGCAAGGAT 58.910 50.000 0.00 0.00 45.38 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.562672 AACATTAGGAGGGGCTGCGT 61.563 55.000 0.00 0.00 0.00 5.24
132 135 7.754069 TTTGACTGTTTGCACTTCTTTAATG 57.246 32.000 0.00 0.00 0.00 1.90
278 281 2.561858 TCATAGCATAGCAGGAGCAGAG 59.438 50.000 0.00 0.00 45.49 3.35
279 282 2.561858 CTCATAGCATAGCAGGAGCAGA 59.438 50.000 0.00 0.00 45.49 4.26
282 285 1.724429 GCTCATAGCATAGCAGGAGC 58.276 55.000 11.65 11.65 41.89 4.70
283 286 1.403914 CCGCTCATAGCATAGCAGGAG 60.404 57.143 0.00 0.00 42.58 3.69
284 287 0.605083 CCGCTCATAGCATAGCAGGA 59.395 55.000 0.00 0.00 42.58 3.86
285 288 0.319728 ACCGCTCATAGCATAGCAGG 59.680 55.000 0.00 0.00 42.58 4.85
286 289 1.426423 CACCGCTCATAGCATAGCAG 58.574 55.000 0.00 0.00 42.58 4.24
287 290 0.601046 GCACCGCTCATAGCATAGCA 60.601 55.000 0.00 0.00 42.58 3.49
288 291 1.621301 CGCACCGCTCATAGCATAGC 61.621 60.000 0.00 0.00 42.58 2.97
289 292 1.010935 CCGCACCGCTCATAGCATAG 61.011 60.000 0.00 0.00 42.58 2.23
290 293 1.006220 CCGCACCGCTCATAGCATA 60.006 57.895 0.00 0.00 42.58 3.14
291 294 2.280389 CCGCACCGCTCATAGCAT 60.280 61.111 0.00 0.00 42.58 3.79
339 358 6.744622 GCTTTCCTTTAGTTACAACTCCCTCT 60.745 42.308 0.00 0.00 40.37 3.69
407 426 1.134310 CCTTAACCGTCCCCGCTTTAT 60.134 52.381 0.00 0.00 0.00 1.40
466 485 1.883021 CCATCCACGGCCAGTTTTC 59.117 57.895 2.24 0.00 0.00 2.29
493 512 1.623811 TCCTCCTAGTCACAAACTGGC 59.376 52.381 0.00 0.00 39.11 4.85
540 595 0.846693 AGAGAGAGAGAGAGAGGGGC 59.153 60.000 0.00 0.00 0.00 5.80
541 596 2.370189 GAGAGAGAGAGAGAGAGAGGGG 59.630 59.091 0.00 0.00 0.00 4.79
542 597 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
543 598 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
544 599 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
545 600 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
546 601 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
547 602 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
548 603 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
549 604 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
550 605 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
551 606 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
552 607 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
553 608 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
554 609 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
555 610 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
556 611 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
557 612 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
558 613 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
559 614 4.078922 AGGAGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
560 615 4.222336 AGGAGAGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
561 616 4.078922 AGAGGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
562 617 4.222336 AGAGGAGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
563 618 4.078922 AGAGAGGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
564 619 4.222336 AGAGAGGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
565 620 4.078922 AGAGAGAGGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
566 621 4.222336 AGAGAGAGGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
567 622 4.078922 AGAGAGAGAGGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
568 623 4.039004 CAGAGAGAGAGGAGAGAGAGAGAG 59.961 54.167 0.00 0.00 0.00 3.20
569 624 3.963374 CAGAGAGAGAGGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
570 625 3.708631 ACAGAGAGAGAGGAGAGAGAGAG 59.291 52.174 0.00 0.00 0.00 3.20
571 626 3.452264 CACAGAGAGAGAGGAGAGAGAGA 59.548 52.174 0.00 0.00 0.00 3.10
572 627 3.432749 CCACAGAGAGAGAGGAGAGAGAG 60.433 56.522 0.00 0.00 0.00 3.20
573 628 2.505407 CCACAGAGAGAGAGGAGAGAGA 59.495 54.545 0.00 0.00 0.00 3.10
574 629 2.239654 ACCACAGAGAGAGAGGAGAGAG 59.760 54.545 0.00 0.00 0.00 3.20
575 630 2.274542 ACCACAGAGAGAGAGGAGAGA 58.725 52.381 0.00 0.00 0.00 3.10
576 631 2.806945 ACCACAGAGAGAGAGGAGAG 57.193 55.000 0.00 0.00 0.00 3.20
577 632 4.337145 GTTAACCACAGAGAGAGAGGAGA 58.663 47.826 0.00 0.00 0.00 3.71
578 633 3.445805 GGTTAACCACAGAGAGAGAGGAG 59.554 52.174 20.12 0.00 35.64 3.69
579 634 3.181422 TGGTTAACCACAGAGAGAGAGGA 60.181 47.826 23.69 0.00 42.01 3.71
580 635 3.165875 TGGTTAACCACAGAGAGAGAGG 58.834 50.000 23.69 0.00 42.01 3.69
593 648 5.838529 ACTAGTTTTTGTGCATGGTTAACC 58.161 37.500 18.27 18.27 0.00 2.85
594 649 7.081976 CCTACTAGTTTTTGTGCATGGTTAAC 58.918 38.462 0.00 0.00 0.00 2.01
595 650 6.207810 CCCTACTAGTTTTTGTGCATGGTTAA 59.792 38.462 0.00 0.00 0.00 2.01
596 651 5.708230 CCCTACTAGTTTTTGTGCATGGTTA 59.292 40.000 0.00 0.00 0.00 2.85
780 843 1.077716 GATTGTGGCGCTAGGGGTT 60.078 57.895 7.64 0.00 0.00 4.11
783 846 2.182842 GCAGATTGTGGCGCTAGGG 61.183 63.158 7.64 1.65 0.00 3.53
889 952 2.932234 CGAAGTGCTCTGGTCGGGT 61.932 63.158 2.65 0.00 0.00 5.28
991 1054 2.804572 CGTTCATGTCCATGGCTCCTAG 60.805 54.545 6.96 0.00 39.24 3.02
1119 1188 2.043652 ATGTGGGGATGCTGGTGC 60.044 61.111 0.00 0.00 40.20 5.01
1122 1191 0.826256 CCATCATGTGGGGATGCTGG 60.826 60.000 6.46 0.00 44.79 4.85
1308 1377 3.807839 CCCATCATCCCACCGCCA 61.808 66.667 0.00 0.00 0.00 5.69
1539 1608 1.087202 AAGCACACGACGAACAGCAA 61.087 50.000 0.00 0.00 0.00 3.91
1555 1624 3.861131 TGGAGACAGTTTAAGCGAGAAGC 60.861 47.826 0.00 0.00 40.64 3.86
1556 1625 3.914312 TGGAGACAGTTTAAGCGAGAAG 58.086 45.455 0.00 0.00 35.01 2.85
1570 1639 2.042464 ACTGAACTGAAGCTGGAGACA 58.958 47.619 0.00 0.00 39.59 3.41
1571 1640 2.829741 ACTGAACTGAAGCTGGAGAC 57.170 50.000 0.00 0.00 0.00 3.36
1572 1641 3.501349 AGTACTGAACTGAAGCTGGAGA 58.499 45.455 0.00 0.00 36.93 3.71
1573 1642 3.951775 AGTACTGAACTGAAGCTGGAG 57.048 47.619 0.00 0.00 36.93 3.86
1595 1664 3.531538 TGAAACACGAGACTTGCTTTCT 58.468 40.909 11.90 0.00 0.00 2.52
1596 1665 3.944422 TGAAACACGAGACTTGCTTTC 57.056 42.857 0.00 6.54 0.00 2.62
1597 1666 4.335315 TGAATGAAACACGAGACTTGCTTT 59.665 37.500 0.00 0.00 0.00 3.51
1598 1667 3.876914 TGAATGAAACACGAGACTTGCTT 59.123 39.130 0.00 0.00 0.00 3.91
1599 1668 3.466836 TGAATGAAACACGAGACTTGCT 58.533 40.909 0.00 0.00 0.00 3.91
1600 1669 3.364366 CCTGAATGAAACACGAGACTTGC 60.364 47.826 0.00 0.00 0.00 4.01
1601 1670 3.364366 GCCTGAATGAAACACGAGACTTG 60.364 47.826 0.00 0.00 0.00 3.16
1602 1671 2.808543 GCCTGAATGAAACACGAGACTT 59.191 45.455 0.00 0.00 0.00 3.01
1603 1672 2.417719 GCCTGAATGAAACACGAGACT 58.582 47.619 0.00 0.00 0.00 3.24
1608 1688 1.202065 CCATCGCCTGAATGAAACACG 60.202 52.381 0.00 0.00 0.00 4.49
1612 1692 1.462616 CACCCATCGCCTGAATGAAA 58.537 50.000 0.00 0.00 0.00 2.69
1623 1703 2.029666 GATCGCCTCCACCCATCG 59.970 66.667 0.00 0.00 0.00 3.84
1628 1708 1.153349 GAACCTGATCGCCTCCACC 60.153 63.158 0.00 0.00 0.00 4.61
1629 1709 0.460987 CTGAACCTGATCGCCTCCAC 60.461 60.000 0.00 0.00 0.00 4.02
1630 1710 0.904865 ACTGAACCTGATCGCCTCCA 60.905 55.000 0.00 0.00 0.00 3.86
1928 2008 7.174107 AGGATAAAAACATCCATGGTTTCAG 57.826 36.000 12.58 1.02 46.22 3.02
2065 2145 6.073327 TGCTACGAAATACTAGGACTGATG 57.927 41.667 0.00 0.00 0.00 3.07
2201 2282 3.686726 AGATTCTCAGACGAATTGTTGGC 59.313 43.478 0.00 0.00 33.96 4.52
2243 2324 9.649316 AGAGAAGCTAAAATCCTACTAGTATGT 57.351 33.333 2.33 0.00 0.00 2.29
2266 2347 4.169508 CTGACACGGAGTATGTTCAAGAG 58.830 47.826 0.00 0.00 41.61 2.85
2267 2348 3.056821 CCTGACACGGAGTATGTTCAAGA 60.057 47.826 0.00 0.00 41.61 3.02
2268 2349 3.254060 CCTGACACGGAGTATGTTCAAG 58.746 50.000 0.00 0.00 41.61 3.02
2269 2350 2.631062 ACCTGACACGGAGTATGTTCAA 59.369 45.455 0.00 0.00 41.61 2.69
2280 2361 0.682852 TTCCCTTACACCTGACACGG 59.317 55.000 0.00 0.00 0.00 4.94
2292 2373 5.783360 TCCAGTGATTGTACTTCTTCCCTTA 59.217 40.000 0.00 0.00 0.00 2.69
2335 2416 9.500785 TCAGTTATCTGTATCAATGTTTCAACA 57.499 29.630 0.83 0.00 41.58 3.33
2345 2426 9.890629 AGCAAAGTATTCAGTTATCTGTATCAA 57.109 29.630 0.83 0.00 41.91 2.57
2346 2427 9.534565 GAGCAAAGTATTCAGTTATCTGTATCA 57.465 33.333 0.83 0.00 41.91 2.15
2403 2537 5.655488 ACACACTACTGATCAGTTATCTGC 58.345 41.667 32.14 0.00 42.54 4.26
2476 2610 0.244721 AAATTGCAAAGGGAGCGAGC 59.755 50.000 1.71 0.00 33.85 5.03
2594 2728 4.082733 GCAACTGGTAGTCCAAGGAAATTC 60.083 45.833 0.00 0.00 43.81 2.17
2595 2729 3.826729 GCAACTGGTAGTCCAAGGAAATT 59.173 43.478 0.00 0.00 43.81 1.82
2596 2730 3.421844 GCAACTGGTAGTCCAAGGAAAT 58.578 45.455 0.00 0.00 43.81 2.17
2597 2731 2.488347 GGCAACTGGTAGTCCAAGGAAA 60.488 50.000 0.00 0.00 43.81 3.13
2598 2732 1.073284 GGCAACTGGTAGTCCAAGGAA 59.927 52.381 0.00 0.00 43.81 3.36
2600 2734 3.249687 GGCAACTGGTAGTCCAAGG 57.750 57.895 0.00 0.00 43.81 3.61
2629 2764 7.710907 GGCATGAACATGATTAGTTAGACACTA 59.289 37.037 17.40 0.00 41.20 2.74
2636 2771 7.040132 TGTTGTTGGCATGAACATGATTAGTTA 60.040 33.333 17.40 0.00 41.20 2.24
2643 2778 2.288334 GCTGTTGTTGGCATGAACATGA 60.288 45.455 17.40 0.00 41.20 3.07
2648 2783 2.309613 AGAAGCTGTTGTTGGCATGAA 58.690 42.857 0.00 0.00 0.00 2.57
2649 2784 1.985473 AGAAGCTGTTGTTGGCATGA 58.015 45.000 0.00 0.00 0.00 3.07
2650 2785 2.669364 GAAGAAGCTGTTGTTGGCATG 58.331 47.619 0.00 0.00 0.00 4.06
2651 2786 1.267806 CGAAGAAGCTGTTGTTGGCAT 59.732 47.619 0.00 0.00 0.00 4.40
2652 2787 0.662619 CGAAGAAGCTGTTGTTGGCA 59.337 50.000 0.00 0.00 0.00 4.92
2653 2788 0.661483 GCGAAGAAGCTGTTGTTGGC 60.661 55.000 0.00 0.00 34.34 4.52
2681 2832 0.243907 CCATGGACGACGAAGACACT 59.756 55.000 5.56 0.00 0.00 3.55
2843 2994 4.020396 AGAGATGCTATCATGCTAACCTGG 60.020 45.833 0.00 0.00 31.96 4.45
2853 3004 5.548181 TGAGCTTGAAGAGATGCTATCAT 57.452 39.130 0.00 0.00 35.76 2.45
2855 3006 5.114780 TGTTGAGCTTGAAGAGATGCTATC 58.885 41.667 0.00 0.00 35.76 2.08
2856 3007 5.095145 TGTTGAGCTTGAAGAGATGCTAT 57.905 39.130 0.00 0.00 35.76 2.97
2857 3008 4.541973 TGTTGAGCTTGAAGAGATGCTA 57.458 40.909 0.00 0.00 35.76 3.49
2858 3009 3.413846 TGTTGAGCTTGAAGAGATGCT 57.586 42.857 0.00 0.00 38.59 3.79
2859 3010 3.501445 AGTTGTTGAGCTTGAAGAGATGC 59.499 43.478 0.00 0.00 0.00 3.91
2860 3011 4.753610 TCAGTTGTTGAGCTTGAAGAGATG 59.246 41.667 0.00 0.00 0.00 2.90
2861 3012 4.754114 GTCAGTTGTTGAGCTTGAAGAGAT 59.246 41.667 0.00 0.00 36.21 2.75
2862 3013 4.122776 GTCAGTTGTTGAGCTTGAAGAGA 58.877 43.478 0.00 0.00 36.21 3.10
2863 3014 3.873361 TGTCAGTTGTTGAGCTTGAAGAG 59.127 43.478 0.00 0.00 36.21 2.85
2864 3015 3.872696 TGTCAGTTGTTGAGCTTGAAGA 58.127 40.909 0.00 0.00 36.21 2.87
2865 3016 4.825546 ATGTCAGTTGTTGAGCTTGAAG 57.174 40.909 0.00 0.00 36.21 3.02
2866 3017 5.122519 TGTATGTCAGTTGTTGAGCTTGAA 58.877 37.500 0.00 0.00 36.21 2.69
2867 3018 4.702831 TGTATGTCAGTTGTTGAGCTTGA 58.297 39.130 0.00 0.00 36.21 3.02
2868 3019 5.618056 ATGTATGTCAGTTGTTGAGCTTG 57.382 39.130 0.00 0.00 36.21 4.01
2869 3020 5.643777 GGTATGTATGTCAGTTGTTGAGCTT 59.356 40.000 0.00 0.00 36.21 3.74
2870 3021 5.178797 GGTATGTATGTCAGTTGTTGAGCT 58.821 41.667 0.00 0.00 36.21 4.09
2871 3022 4.935205 TGGTATGTATGTCAGTTGTTGAGC 59.065 41.667 0.00 0.00 36.21 4.26
2872 3023 6.166279 ACTGGTATGTATGTCAGTTGTTGAG 58.834 40.000 0.00 0.00 37.18 3.02
2893 3044 4.565564 GCTGGAGTAATTAACCACGTACTG 59.434 45.833 8.12 1.46 0.00 2.74
2894 3045 4.221262 TGCTGGAGTAATTAACCACGTACT 59.779 41.667 8.12 0.00 0.00 2.73
2895 3046 4.497300 TGCTGGAGTAATTAACCACGTAC 58.503 43.478 8.12 0.00 0.00 3.67
2902 3058 4.260334 GCTCGTTGCTGGAGTAATTAAC 57.740 45.455 0.00 0.00 38.95 2.01
2923 3079 4.036262 GTGAGCTGTGTCATCTCCTACTAG 59.964 50.000 0.00 0.00 0.00 2.57
2927 3083 3.093057 AGTGAGCTGTGTCATCTCCTA 57.907 47.619 0.00 0.00 0.00 2.94
2928 3084 1.935799 AGTGAGCTGTGTCATCTCCT 58.064 50.000 0.00 0.00 0.00 3.69
2929 3085 3.445450 TCTTAGTGAGCTGTGTCATCTCC 59.555 47.826 0.00 0.00 0.00 3.71
2930 3086 4.710423 TCTTAGTGAGCTGTGTCATCTC 57.290 45.455 0.00 0.00 0.00 2.75
2931 3087 6.782082 TTATCTTAGTGAGCTGTGTCATCT 57.218 37.500 0.00 0.00 0.00 2.90
2978 3134 1.749063 TGACTGCTGACGTACTATGGG 59.251 52.381 0.00 0.00 0.00 4.00
3096 3256 2.356278 GCCAGGCCAGGTGAATGA 59.644 61.111 16.66 0.00 0.00 2.57
3136 3301 2.719046 GCATGCACGTACTTGTTCAAAC 59.281 45.455 14.21 0.00 0.00 2.93
3178 3343 2.050639 TTATGCATGAAGCTGCCGCG 62.051 55.000 10.16 0.00 45.94 6.46
3412 3594 1.455217 GGCTGGCAATGGCATCTCT 60.455 57.895 10.64 0.00 43.71 3.10
3480 3673 2.369860 CAGGTGATTGATAGCTAGGCCA 59.630 50.000 5.01 0.00 0.00 5.36
3651 3870 1.068474 CAAGAACACGACCGATCCAC 58.932 55.000 0.00 0.00 0.00 4.02
3711 3934 1.134946 CAGGATTTCATTTCACCCCGC 59.865 52.381 0.00 0.00 0.00 6.13
3861 4084 2.594303 TTGTGCTTGCGTCCCTGG 60.594 61.111 0.00 0.00 0.00 4.45
3936 4213 0.535335 TCGTGCAGGTGTAGATTCCC 59.465 55.000 6.26 0.00 0.00 3.97
3937 4214 1.204941 ACTCGTGCAGGTGTAGATTCC 59.795 52.381 12.04 0.00 0.00 3.01
3938 4215 2.656560 ACTCGTGCAGGTGTAGATTC 57.343 50.000 12.04 0.00 0.00 2.52
3939 4216 2.159421 CGTACTCGTGCAGGTGTAGATT 60.159 50.000 18.59 0.00 0.00 2.40
3940 4217 1.400846 CGTACTCGTGCAGGTGTAGAT 59.599 52.381 18.59 0.00 0.00 1.98
3941 4218 0.800631 CGTACTCGTGCAGGTGTAGA 59.199 55.000 18.59 1.45 0.00 2.59
3942 4219 0.800631 TCGTACTCGTGCAGGTGTAG 59.199 55.000 18.59 13.48 38.33 2.74
3943 4220 1.237533 TTCGTACTCGTGCAGGTGTA 58.762 50.000 15.23 15.23 38.33 2.90
3944 4221 0.601558 ATTCGTACTCGTGCAGGTGT 59.398 50.000 17.10 17.10 38.33 4.16
3963 4240 3.947196 ACGCTTAATCATCTTGCCATTCA 59.053 39.130 0.00 0.00 0.00 2.57
4039 4318 0.242825 CTAGGGCTTTCGTCGTGTGA 59.757 55.000 0.00 0.00 0.00 3.58
4055 4434 1.426816 CTGCATGCACTGGTCGCTAG 61.427 60.000 18.46 0.00 0.00 3.42
4061 4440 1.601759 GTCACCTGCATGCACTGGT 60.602 57.895 22.43 22.43 42.07 4.00
4118 4497 0.885879 TCGTAGTACTGTGCTGTGGG 59.114 55.000 5.39 0.00 0.00 4.61
4136 4516 6.363473 CCAAAGATCGACTTGTGTTTTACTC 58.637 40.000 0.00 0.00 38.98 2.59
4137 4517 5.238650 CCCAAAGATCGACTTGTGTTTTACT 59.761 40.000 0.00 0.00 38.98 2.24
4138 4518 5.449304 CCCAAAGATCGACTTGTGTTTTAC 58.551 41.667 0.00 0.00 38.98 2.01
4172 4556 4.152526 CGCAGAGCAGAATATACGTACTC 58.847 47.826 0.00 0.00 0.00 2.59
4173 4557 3.058155 CCGCAGAGCAGAATATACGTACT 60.058 47.826 0.00 0.00 0.00 2.73
4176 4560 1.000163 CCCGCAGAGCAGAATATACGT 60.000 52.381 0.00 0.00 0.00 3.57
4180 4564 0.833287 ACACCCGCAGAGCAGAATAT 59.167 50.000 0.00 0.00 0.00 1.28
4194 4578 1.800315 CGATGACACGACGACACCC 60.800 63.158 0.00 0.00 35.09 4.61
4198 4582 0.589229 CCTAGCGATGACACGACGAC 60.589 60.000 0.00 0.00 35.09 4.34
4199 4583 1.712018 CCCTAGCGATGACACGACGA 61.712 60.000 0.00 0.00 35.09 4.20
4200 4584 1.298413 CCCTAGCGATGACACGACG 60.298 63.158 0.00 0.00 35.09 5.12
4209 4593 2.444256 GGCTGGAACCCCTAGCGAT 61.444 63.158 0.00 0.00 37.42 4.58
4224 4613 1.153756 CAAACCCCTTGTCCTGGCT 59.846 57.895 0.00 0.00 0.00 4.75
4248 4638 4.412199 TGGAGGAATTAAACTGATCCCGAT 59.588 41.667 0.00 0.00 32.15 4.18
4251 4641 4.335594 CGTTGGAGGAATTAAACTGATCCC 59.664 45.833 0.00 0.00 32.15 3.85
4252 4642 5.183228 TCGTTGGAGGAATTAAACTGATCC 58.817 41.667 0.00 0.00 0.00 3.36
4282 4672 1.873591 ACAAAACACTAGAAGCAGCGG 59.126 47.619 0.00 0.00 0.00 5.52
4289 4679 6.805271 GCAGACGTAGATACAAAACACTAGAA 59.195 38.462 0.00 0.00 0.00 2.10
4292 4682 5.184479 AGGCAGACGTAGATACAAAACACTA 59.816 40.000 0.00 0.00 0.00 2.74
4293 4683 4.021368 AGGCAGACGTAGATACAAAACACT 60.021 41.667 0.00 0.00 0.00 3.55
4294 4684 4.091509 CAGGCAGACGTAGATACAAAACAC 59.908 45.833 0.00 0.00 0.00 3.32
4296 4686 3.062234 GCAGGCAGACGTAGATACAAAAC 59.938 47.826 0.00 0.00 0.00 2.43
4298 4688 2.734175 CGCAGGCAGACGTAGATACAAA 60.734 50.000 0.00 0.00 0.00 2.83
4299 4689 1.202256 CGCAGGCAGACGTAGATACAA 60.202 52.381 0.00 0.00 0.00 2.41
4300 4690 0.380733 CGCAGGCAGACGTAGATACA 59.619 55.000 0.00 0.00 0.00 2.29
4301 4691 0.317938 CCGCAGGCAGACGTAGATAC 60.318 60.000 0.00 0.00 46.14 2.24
4302 4692 2.030551 CCGCAGGCAGACGTAGATA 58.969 57.895 0.00 0.00 46.14 1.98
4319 4714 2.539338 TTTTCGACGTGTGCAGGCC 61.539 57.895 0.00 0.00 0.00 5.19
4340 4735 4.496927 GGAATTGCCTTGCGCCGG 62.497 66.667 4.18 6.72 36.24 6.13
4341 4736 4.834892 CGGAATTGCCTTGCGCCG 62.835 66.667 4.18 0.00 41.84 6.46
4371 4766 1.975660 ACAGCCGAGTTTGCCTAAAA 58.024 45.000 0.00 0.00 0.00 1.52
4376 4771 0.169009 GATCAACAGCCGAGTTTGCC 59.831 55.000 0.00 0.00 0.00 4.52
4377 4772 0.179215 CGATCAACAGCCGAGTTTGC 60.179 55.000 0.00 0.00 0.00 3.68
4378 4773 1.136252 CACGATCAACAGCCGAGTTTG 60.136 52.381 0.00 0.00 0.00 2.93
4379 4774 1.148310 CACGATCAACAGCCGAGTTT 58.852 50.000 0.00 0.00 0.00 2.66
4380 4775 1.291877 GCACGATCAACAGCCGAGTT 61.292 55.000 0.00 0.00 0.00 3.01
4381 4776 1.738099 GCACGATCAACAGCCGAGT 60.738 57.895 0.00 0.00 0.00 4.18
4382 4777 1.291184 TTGCACGATCAACAGCCGAG 61.291 55.000 0.00 0.00 0.00 4.63
4383 4778 1.291184 CTTGCACGATCAACAGCCGA 61.291 55.000 0.00 0.00 0.00 5.54
4384 4779 1.133253 CTTGCACGATCAACAGCCG 59.867 57.895 0.00 0.00 0.00 5.52
4385 4780 0.955428 TCCTTGCACGATCAACAGCC 60.955 55.000 0.00 0.00 0.00 4.85
4386 4781 1.089920 ATCCTTGCACGATCAACAGC 58.910 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.