Multiple sequence alignment - TraesCS1A01G378100

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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 TraesCS1A01G378100 chr1A 100.000 3352 0 0 1 3352 551048165 551051516 0.000000e+00 6191
1 TraesCS1A01G378100 chr1D 91.813 1930 94 28 1455 3352 458676585 458678482 0.000000e+00 2630
2 TraesCS1A01G378100 chr1D 88.247 970 48 29 441 1396 458675665 458676582 0.000000e+00 1099
3 TraesCS1A01G378100 chr1B 90.409 1856 93 38 1534 3352 630060991 630062798 0.000000e+00 2362
4 TraesCS1A01G378100 chr1B 87.297 984 55 38 440 1393 630059948 630060891 0.000000e+00 1061
5 TraesCS1A01G378100 chr1B 88.843 242 25 2 6 245 630058309 630058550 2.530000e-76 296
6 TraesCS1A01G378100 chr5B 85.647 634 55 18 1041 1666 668600746 668600141 4.720000e-178 634
7 TraesCS1A01G378100 chr7B 85.000 640 60 18 1035 1666 253370762 253371373 4.750000e-173 617
8 TraesCS1A01G378100 chr3B 85.150 633 60 16 1041 1666 36492396 36493001 4.750000e-173 617


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 TraesCS1A01G378100 chr1A 551048165 551051516 3351 False 6191.000000 6191 100.000000 1 3352 1 chr1A.!!$F1 3351
1 TraesCS1A01G378100 chr1D 458675665 458678482 2817 False 1864.500000 2630 90.030000 441 3352 2 chr1D.!!$F1 2911
2 TraesCS1A01G378100 chr1B 630058309 630062798 4489 False 1239.666667 2362 88.849667 6 3352 3 chr1B.!!$F1 3346
3 TraesCS1A01G378100 chr5B 668600141 668600746 605 True 634.000000 634 85.647000 1041 1666 1 chr5B.!!$R1 625
4 TraesCS1A01G378100 chr7B 253370762 253371373 611 False 617.000000 617 85.000000 1035 1666 1 chr7B.!!$F1 631
5 TraesCS1A01G378100 chr3B 36492396 36493001 605 False 617.000000 617 85.150000 1041 1666 1 chr3B.!!$F1 625

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
325 1596 0.032952 TGAATATACAGGCGGCCGTC 59.967 55.0 25.39 25.39 0.0 4.79 F
522 1804 0.036858 GCTCCACCTGTCAACCTCTC 60.037 60.0 0.00 0.00 0.0 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 2758 0.249489 GATTAGCTCGTCGGGCATGT 60.249 55.0 21.18 3.62 0.0 3.21 R
2397 3760 0.036732 AGCTCAAAACCGCATCCAGA 59.963 50.0 0.00 0.00 0.0 3.86 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
25 26 8.508800 GACGATGTGTAGAGGAAACATATTAG 57.491 38.462 0.00 0.00 34.74 1.73
47 49 3.293262 CAAACGACCAAACATAACACGG 58.707 45.455 0.00 0.00 0.00 4.94
99 101 5.967088 ACTCACATATGTGTTACTCTCACC 58.033 41.667 30.03 0.00 45.76 4.02
100 102 5.105310 ACTCACATATGTGTTACTCTCACCC 60.105 44.000 30.03 0.00 45.76 4.61
101 103 4.161565 TCACATATGTGTTACTCTCACCCC 59.838 45.833 30.03 0.00 45.76 4.95
128 130 0.539986 TCCGGTTTGGCATCCTCTAC 59.460 55.000 0.00 0.00 37.80 2.59
131 133 2.643551 CGGTTTGGCATCCTCTACATT 58.356 47.619 7.46 0.00 0.00 2.71
140 142 4.141846 GGCATCCTCTACATTGTTCTCTGA 60.142 45.833 0.00 0.00 0.00 3.27
144 146 6.030548 TCCTCTACATTGTTCTCTGAGTTG 57.969 41.667 4.32 0.00 0.00 3.16
159 161 0.907230 AGTTGAGAGAGTCCCCAGCC 60.907 60.000 0.00 0.00 0.00 4.85
163 165 3.474570 GAGAGTCCCCAGCCGCAT 61.475 66.667 0.00 0.00 0.00 4.73
167 169 2.252072 GAGTCCCCAGCCGCATGTTA 62.252 60.000 0.00 0.00 0.00 2.41
188 190 8.058667 TGTTACGACTGAATAGAGGAAATGTA 57.941 34.615 0.00 0.00 0.00 2.29
194 196 9.967346 CGACTGAATAGAGGAAATGTATTTAGA 57.033 33.333 4.32 0.00 35.49 2.10
245 248 2.530460 TGGGAGGAATGGGAAATGTG 57.470 50.000 0.00 0.00 0.00 3.21
248 251 2.024941 GGGAGGAATGGGAAATGTGAGT 60.025 50.000 0.00 0.00 0.00 3.41
265 1536 4.141711 TGTGAGTAATATTGGGAGACAGCC 60.142 45.833 0.00 0.00 0.00 4.85
273 1544 0.320374 TGGGAGACAGCCTACGTTTG 59.680 55.000 0.00 0.00 0.00 2.93
274 1545 0.606604 GGGAGACAGCCTACGTTTGA 59.393 55.000 0.00 0.00 0.00 2.69
275 1546 1.001633 GGGAGACAGCCTACGTTTGAA 59.998 52.381 0.00 0.00 0.00 2.69
276 1547 2.354805 GGGAGACAGCCTACGTTTGAAT 60.355 50.000 0.00 0.00 0.00 2.57
277 1548 3.118884 GGGAGACAGCCTACGTTTGAATA 60.119 47.826 0.00 0.00 0.00 1.75
278 1549 4.443034 GGGAGACAGCCTACGTTTGAATAT 60.443 45.833 0.00 0.00 0.00 1.28
279 1550 5.116882 GGAGACAGCCTACGTTTGAATATT 58.883 41.667 0.00 0.00 0.00 1.28
280 1551 5.585047 GGAGACAGCCTACGTTTGAATATTT 59.415 40.000 0.00 0.00 0.00 1.40
281 1552 6.093633 GGAGACAGCCTACGTTTGAATATTTT 59.906 38.462 0.00 0.00 0.00 1.82
282 1553 7.073342 AGACAGCCTACGTTTGAATATTTTC 57.927 36.000 0.00 0.00 0.00 2.29
283 1554 6.093633 AGACAGCCTACGTTTGAATATTTTCC 59.906 38.462 0.00 0.00 0.00 3.13
284 1555 5.708230 ACAGCCTACGTTTGAATATTTTCCA 59.292 36.000 0.00 0.00 0.00 3.53
285 1556 6.128007 ACAGCCTACGTTTGAATATTTTCCAG 60.128 38.462 0.00 0.00 0.00 3.86
286 1557 5.944007 AGCCTACGTTTGAATATTTTCCAGT 59.056 36.000 0.00 0.00 0.00 4.00
287 1558 6.027749 GCCTACGTTTGAATATTTTCCAGTG 58.972 40.000 0.00 0.00 0.00 3.66
288 1559 6.027749 CCTACGTTTGAATATTTTCCAGTGC 58.972 40.000 0.00 0.00 0.00 4.40
289 1560 5.446143 ACGTTTGAATATTTTCCAGTGCA 57.554 34.783 0.00 0.00 0.00 4.57
290 1561 6.024552 ACGTTTGAATATTTTCCAGTGCAT 57.975 33.333 0.00 0.00 0.00 3.96
291 1562 6.092748 ACGTTTGAATATTTTCCAGTGCATC 58.907 36.000 0.00 0.00 0.00 3.91
292 1563 5.516339 CGTTTGAATATTTTCCAGTGCATCC 59.484 40.000 0.00 0.00 0.00 3.51
293 1564 6.397272 GTTTGAATATTTTCCAGTGCATCCA 58.603 36.000 0.00 0.00 0.00 3.41
294 1565 6.602410 TTGAATATTTTCCAGTGCATCCAA 57.398 33.333 0.00 0.00 0.00 3.53
295 1566 5.964758 TGAATATTTTCCAGTGCATCCAAC 58.035 37.500 0.00 0.00 0.00 3.77
296 1567 5.479724 TGAATATTTTCCAGTGCATCCAACA 59.520 36.000 0.00 0.00 0.00 3.33
297 1568 3.947910 ATTTTCCAGTGCATCCAACAG 57.052 42.857 0.00 0.00 0.00 3.16
298 1569 0.961019 TTTCCAGTGCATCCAACAGC 59.039 50.000 0.00 0.00 0.00 4.40
299 1570 0.111061 TTCCAGTGCATCCAACAGCT 59.889 50.000 0.00 0.00 0.00 4.24
300 1571 0.111061 TCCAGTGCATCCAACAGCTT 59.889 50.000 0.00 0.00 0.00 3.74
301 1572 0.242825 CCAGTGCATCCAACAGCTTG 59.757 55.000 0.00 0.00 0.00 4.01
302 1573 0.388134 CAGTGCATCCAACAGCTTGC 60.388 55.000 0.00 0.00 35.67 4.01
303 1574 1.443194 GTGCATCCAACAGCTTGCG 60.443 57.895 0.00 0.00 37.92 4.85
304 1575 1.898094 TGCATCCAACAGCTTGCGT 60.898 52.632 1.66 0.00 37.92 5.24
305 1576 1.286880 GCATCCAACAGCTTGCGTT 59.713 52.632 0.00 0.00 0.00 4.84
306 1577 0.318955 GCATCCAACAGCTTGCGTTT 60.319 50.000 0.00 0.00 0.00 3.60
307 1578 1.411394 CATCCAACAGCTTGCGTTTG 58.589 50.000 0.00 3.35 0.00 2.93
316 1587 5.221891 ACAGCTTGCGTTTGAATATACAG 57.778 39.130 0.00 0.00 0.00 2.74
325 1596 0.032952 TGAATATACAGGCGGCCGTC 59.967 55.000 25.39 25.39 0.00 4.79
351 1622 5.235186 CGCGGAGAGATTCTTCACATTAATT 59.765 40.000 0.00 0.00 0.00 1.40
353 1624 7.042725 CGCGGAGAGATTCTTCACATTAATTAA 60.043 37.037 0.00 0.00 0.00 1.40
382 1653 3.300590 GCAACAAGACAAGAAAACGTGTG 59.699 43.478 0.00 0.00 0.00 3.82
383 1654 3.757745 ACAAGACAAGAAAACGTGTGG 57.242 42.857 0.00 0.00 0.00 4.17
384 1655 3.078837 ACAAGACAAGAAAACGTGTGGT 58.921 40.909 0.00 0.00 0.00 4.16
390 1661 4.263435 ACAAGAAAACGTGTGGTAAGGAA 58.737 39.130 0.00 0.00 0.00 3.36
394 1665 2.561478 AACGTGTGGTAAGGAAGCAT 57.439 45.000 0.00 0.00 38.03 3.79
398 1669 2.359900 GTGTGGTAAGGAAGCATGAGG 58.640 52.381 0.00 0.00 38.03 3.86
408 1679 0.911769 AAGCATGAGGGATTCGGTCA 59.088 50.000 0.00 0.00 0.00 4.02
409 1680 0.467384 AGCATGAGGGATTCGGTCAG 59.533 55.000 0.00 0.00 0.00 3.51
410 1681 0.465705 GCATGAGGGATTCGGTCAGA 59.534 55.000 0.00 0.00 0.00 3.27
411 1682 1.071385 GCATGAGGGATTCGGTCAGAT 59.929 52.381 0.00 0.00 0.00 2.90
412 1683 2.763933 CATGAGGGATTCGGTCAGATG 58.236 52.381 0.00 0.00 0.00 2.90
413 1684 1.866015 TGAGGGATTCGGTCAGATGT 58.134 50.000 0.00 0.00 0.00 3.06
414 1685 2.187958 TGAGGGATTCGGTCAGATGTT 58.812 47.619 0.00 0.00 0.00 2.71
415 1686 2.168521 TGAGGGATTCGGTCAGATGTTC 59.831 50.000 0.00 0.00 0.00 3.18
416 1687 1.486726 AGGGATTCGGTCAGATGTTCC 59.513 52.381 0.00 0.00 0.00 3.62
417 1688 1.486726 GGGATTCGGTCAGATGTTCCT 59.513 52.381 0.00 0.00 0.00 3.36
418 1689 2.698797 GGGATTCGGTCAGATGTTCCTA 59.301 50.000 0.00 0.00 0.00 2.94
419 1690 3.134081 GGGATTCGGTCAGATGTTCCTAA 59.866 47.826 0.00 0.00 0.00 2.69
420 1691 4.120589 GGATTCGGTCAGATGTTCCTAAC 58.879 47.826 0.00 0.00 0.00 2.34
421 1692 4.141914 GGATTCGGTCAGATGTTCCTAACT 60.142 45.833 0.00 0.00 0.00 2.24
422 1693 4.884668 TTCGGTCAGATGTTCCTAACTT 57.115 40.909 0.00 0.00 0.00 2.66
423 1694 4.884668 TCGGTCAGATGTTCCTAACTTT 57.115 40.909 0.00 0.00 0.00 2.66
424 1695 4.566004 TCGGTCAGATGTTCCTAACTTTG 58.434 43.478 0.00 0.00 0.00 2.77
425 1696 4.039973 TCGGTCAGATGTTCCTAACTTTGT 59.960 41.667 0.00 0.00 0.00 2.83
426 1697 4.389077 CGGTCAGATGTTCCTAACTTTGTC 59.611 45.833 0.00 0.00 0.00 3.18
427 1698 5.305585 GGTCAGATGTTCCTAACTTTGTCA 58.694 41.667 0.00 0.00 0.00 3.58
428 1699 5.763204 GGTCAGATGTTCCTAACTTTGTCAA 59.237 40.000 0.00 0.00 0.00 3.18
429 1700 6.262273 GGTCAGATGTTCCTAACTTTGTCAAA 59.738 38.462 0.00 0.00 0.00 2.69
430 1701 7.201785 GGTCAGATGTTCCTAACTTTGTCAAAA 60.202 37.037 0.00 0.00 0.00 2.44
431 1702 8.188139 GTCAGATGTTCCTAACTTTGTCAAAAA 58.812 33.333 0.00 0.00 0.00 1.94
488 1765 1.250840 AAGCCGCCTCATCCAAAACC 61.251 55.000 0.00 0.00 0.00 3.27
489 1766 1.678970 GCCGCCTCATCCAAAACCT 60.679 57.895 0.00 0.00 0.00 3.50
490 1767 0.393808 GCCGCCTCATCCAAAACCTA 60.394 55.000 0.00 0.00 0.00 3.08
521 1803 0.472734 AGCTCCACCTGTCAACCTCT 60.473 55.000 0.00 0.00 0.00 3.69
522 1804 0.036858 GCTCCACCTGTCAACCTCTC 60.037 60.000 0.00 0.00 0.00 3.20
523 1805 0.244994 CTCCACCTGTCAACCTCTCG 59.755 60.000 0.00 0.00 0.00 4.04
524 1806 0.178973 TCCACCTGTCAACCTCTCGA 60.179 55.000 0.00 0.00 0.00 4.04
525 1807 0.244994 CCACCTGTCAACCTCTCGAG 59.755 60.000 5.93 5.93 0.00 4.04
526 1808 0.962489 CACCTGTCAACCTCTCGAGT 59.038 55.000 13.13 0.00 0.00 4.18
527 1809 1.068194 CACCTGTCAACCTCTCGAGTC 60.068 57.143 13.13 0.00 0.00 3.36
578 1862 3.921677 ACCAATGCAAGCAAGAAAGATG 58.078 40.909 0.00 0.00 0.00 2.90
617 1901 0.297820 CGCGCGGAATAACTCACTTC 59.702 55.000 24.84 0.00 0.00 3.01
690 1988 6.078202 GCATTCTGACAGACTGCTATACTA 57.922 41.667 30.30 4.83 44.47 1.82
691 1989 6.148948 GCATTCTGACAGACTGCTATACTAG 58.851 44.000 30.30 4.20 44.47 2.57
710 2008 5.904941 ACTAGCACTTCATCTCAGAATCAG 58.095 41.667 0.00 0.00 0.00 2.90
711 2009 5.655974 ACTAGCACTTCATCTCAGAATCAGA 59.344 40.000 0.00 0.00 0.00 3.27
712 2010 4.757594 AGCACTTCATCTCAGAATCAGAC 58.242 43.478 0.00 0.00 0.00 3.51
713 2011 4.467082 AGCACTTCATCTCAGAATCAGACT 59.533 41.667 0.00 0.00 0.00 3.24
714 2012 4.567558 GCACTTCATCTCAGAATCAGACTG 59.432 45.833 0.00 0.00 36.80 3.51
715 2013 4.567558 CACTTCATCTCAGAATCAGACTGC 59.432 45.833 0.00 0.00 35.61 4.40
716 2014 3.815856 TCATCTCAGAATCAGACTGCC 57.184 47.619 0.00 0.00 35.61 4.85
717 2015 2.100418 TCATCTCAGAATCAGACTGCCG 59.900 50.000 0.00 0.00 35.61 5.69
718 2016 0.174389 TCTCAGAATCAGACTGCCGC 59.826 55.000 0.00 0.00 35.61 6.53
719 2017 0.108472 CTCAGAATCAGACTGCCGCA 60.108 55.000 0.00 0.00 35.61 5.69
720 2018 0.321346 TCAGAATCAGACTGCCGCAA 59.679 50.000 0.00 0.00 35.61 4.85
721 2019 0.725686 CAGAATCAGACTGCCGCAAG 59.274 55.000 0.00 0.00 0.00 4.01
722 2020 0.610174 AGAATCAGACTGCCGCAAGA 59.390 50.000 0.00 0.00 43.02 3.02
723 2021 1.005340 GAATCAGACTGCCGCAAGAG 58.995 55.000 0.00 0.00 43.02 2.85
724 2022 1.023513 AATCAGACTGCCGCAAGAGC 61.024 55.000 0.00 0.00 43.02 4.09
725 2023 2.866085 ATCAGACTGCCGCAAGAGCC 62.866 60.000 0.00 0.00 43.02 4.70
726 2024 3.630013 AGACTGCCGCAAGAGCCA 61.630 61.111 0.00 0.00 43.02 4.75
727 2025 3.426568 GACTGCCGCAAGAGCCAC 61.427 66.667 0.00 0.00 43.02 5.01
832 2135 3.726144 GCCTGCAAGCCTCCTCCT 61.726 66.667 0.00 0.00 0.00 3.69
834 2137 2.588989 CTGCAAGCCTCCTCCTCC 59.411 66.667 0.00 0.00 0.00 4.30
835 2138 1.994507 CTGCAAGCCTCCTCCTCCT 60.995 63.158 0.00 0.00 0.00 3.69
837 2140 2.741055 GCAAGCCTCCTCCTCCTCC 61.741 68.421 0.00 0.00 0.00 4.30
838 2141 1.002792 CAAGCCTCCTCCTCCTCCT 59.997 63.158 0.00 0.00 0.00 3.69
839 2142 1.048160 CAAGCCTCCTCCTCCTCCTC 61.048 65.000 0.00 0.00 0.00 3.71
840 2143 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
841 2144 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
843 2146 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
847 2150 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
848 2151 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
849 2152 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
850 2153 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
851 2154 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
852 2155 0.998945 CCTCCTCCTCCTCCTCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
853 2156 1.700907 CCTCCTCCTCCTCCTCCTCTA 60.701 61.905 0.00 0.00 0.00 2.43
854 2157 1.423921 CTCCTCCTCCTCCTCCTCTAC 59.576 61.905 0.00 0.00 0.00 2.59
855 2158 0.481128 CCTCCTCCTCCTCCTCTACC 59.519 65.000 0.00 0.00 0.00 3.18
865 2168 1.008449 CCTCCTCTACCTTCCCTTCCA 59.992 57.143 0.00 0.00 0.00 3.53
885 2188 2.038863 TTCCCTCCTGACCTTGCTTA 57.961 50.000 0.00 0.00 0.00 3.09
908 2211 4.415332 TCCGTCCACGCTTCTCGC 62.415 66.667 0.00 0.00 43.23 5.03
985 2292 5.065704 ACGCTAGCTATATGTGATCCTTG 57.934 43.478 13.93 0.00 0.00 3.61
988 2295 5.240891 GCTAGCTATATGTGATCCTTGCAA 58.759 41.667 7.70 0.00 0.00 4.08
992 2299 2.804986 TATGTGATCCTTGCAAGCCA 57.195 45.000 21.43 14.48 0.00 4.75
998 2305 2.097978 ATCCTTGCAAGCCAGGGGTT 62.098 55.000 21.43 0.00 40.91 4.11
1083 2391 2.586792 GACGAGGCCTCCAATGCT 59.413 61.111 27.20 2.31 0.00 3.79
1128 2436 1.227321 TGAAAAGGCCGTCGTCGTT 60.227 52.632 0.00 0.00 35.01 3.85
1134 2445 2.370393 GGCCGTCGTCGTTGAAGAC 61.370 63.158 0.71 3.27 37.61 3.01
1257 2568 3.729217 GCTTGAAGGTAAAAACGTCTTGC 59.271 43.478 0.00 0.00 0.00 4.01
1258 2569 4.732355 GCTTGAAGGTAAAAACGTCTTGCA 60.732 41.667 0.00 0.00 0.00 4.08
1259 2570 5.508200 TTGAAGGTAAAAACGTCTTGCAT 57.492 34.783 0.00 0.00 0.00 3.96
1260 2571 6.621316 TTGAAGGTAAAAACGTCTTGCATA 57.379 33.333 0.00 0.00 0.00 3.14
1261 2572 6.811253 TGAAGGTAAAAACGTCTTGCATAT 57.189 33.333 0.00 0.00 0.00 1.78
1262 2573 6.607689 TGAAGGTAAAAACGTCTTGCATATG 58.392 36.000 0.00 0.00 0.00 1.78
1263 2574 5.560966 AGGTAAAAACGTCTTGCATATGG 57.439 39.130 4.56 0.00 0.00 2.74
1264 2575 5.250200 AGGTAAAAACGTCTTGCATATGGA 58.750 37.500 4.56 0.00 0.00 3.41
1396 2716 3.311871 GTGAGATATGCTTGCAGGTGAAG 59.688 47.826 0.87 0.00 0.00 3.02
1397 2717 3.054875 TGAGATATGCTTGCAGGTGAAGT 60.055 43.478 0.87 0.00 0.00 3.01
1398 2718 3.944015 GAGATATGCTTGCAGGTGAAGTT 59.056 43.478 0.87 0.00 0.00 2.66
1399 2719 3.944015 AGATATGCTTGCAGGTGAAGTTC 59.056 43.478 0.87 0.00 0.00 3.01
1400 2720 1.985473 ATGCTTGCAGGTGAAGTTCA 58.015 45.000 0.08 0.08 0.00 3.18
1401 2721 1.761449 TGCTTGCAGGTGAAGTTCAA 58.239 45.000 7.25 0.00 0.00 2.69
1402 2722 2.098614 TGCTTGCAGGTGAAGTTCAAA 58.901 42.857 7.25 0.00 0.00 2.69
1403 2723 2.694628 TGCTTGCAGGTGAAGTTCAAAT 59.305 40.909 7.25 0.00 0.00 2.32
1404 2724 3.132646 TGCTTGCAGGTGAAGTTCAAATT 59.867 39.130 7.25 0.00 0.00 1.82
1405 2725 3.737774 GCTTGCAGGTGAAGTTCAAATTC 59.262 43.478 7.25 0.00 0.00 2.17
1406 2726 3.624326 TGCAGGTGAAGTTCAAATTCG 57.376 42.857 7.25 0.00 0.00 3.34
1412 2732 6.129088 GCAGGTGAAGTTCAAATTCGAAATTC 60.129 38.462 11.41 11.41 45.54 2.17
1419 2739 9.237846 GAAGTTCAAATTCGAAATTCAGTTTCT 57.762 29.630 13.01 0.00 44.99 2.52
1420 2740 8.788409 AGTTCAAATTCGAAATTCAGTTTCTC 57.212 30.769 0.00 0.00 43.26 2.87
1421 2741 8.624776 AGTTCAAATTCGAAATTCAGTTTCTCT 58.375 29.630 0.00 0.00 43.26 3.10
1422 2742 9.878599 GTTCAAATTCGAAATTCAGTTTCTCTA 57.121 29.630 0.00 0.00 43.26 2.43
1426 2746 9.436957 AAATTCGAAATTCAGTTTCTCTAGCTA 57.563 29.630 0.00 0.00 43.26 3.32
1436 2756 8.859236 TCAGTTTCTCTAGCTAGTAACTTGTA 57.141 34.615 23.50 15.18 0.00 2.41
1438 2758 8.512956 CAGTTTCTCTAGCTAGTAACTTGTACA 58.487 37.037 23.50 0.00 0.00 2.90
1443 2763 6.561614 TCTAGCTAGTAACTTGTACACATGC 58.438 40.000 20.10 0.00 0.00 4.06
1445 2765 3.621715 GCTAGTAACTTGTACACATGCCC 59.378 47.826 0.00 0.00 0.00 5.36
1449 2769 0.669318 ACTTGTACACATGCCCGACG 60.669 55.000 0.00 0.00 0.00 5.12
1451 2771 0.389296 TTGTACACATGCCCGACGAG 60.389 55.000 0.00 0.00 0.00 4.18
1452 2772 2.165301 GTACACATGCCCGACGAGC 61.165 63.158 0.00 0.00 0.00 5.03
1453 2773 2.348104 TACACATGCCCGACGAGCT 61.348 57.895 2.23 0.00 0.00 4.09
1464 2790 2.600731 CCGACGAGCTAATCATCATCC 58.399 52.381 0.00 0.00 0.00 3.51
1528 2854 9.764363 TCCACTGACATATGTAGATTGTATTTC 57.236 33.333 8.71 0.00 0.00 2.17
1567 2893 1.588674 TCACACCAAACTACAAGGCG 58.411 50.000 0.00 0.00 0.00 5.52
1577 2903 0.321653 CTACAAGGCGCCTTCCAAGT 60.322 55.000 38.34 31.74 33.42 3.16
1603 2929 2.376518 TCAGCAGGGAAGAAACTCCATT 59.623 45.455 0.00 0.00 37.20 3.16
1620 2946 7.027874 ACTCCATTTTCTTCAGGTACCAATA 57.972 36.000 15.94 0.00 0.00 1.90
1621 2947 7.466804 ACTCCATTTTCTTCAGGTACCAATAA 58.533 34.615 15.94 4.07 0.00 1.40
1623 2949 8.893563 TCCATTTTCTTCAGGTACCAATAATT 57.106 30.769 15.94 0.00 0.00 1.40
1624 2950 8.966868 TCCATTTTCTTCAGGTACCAATAATTC 58.033 33.333 15.94 0.00 0.00 2.17
1639 2965 7.582719 ACCAATAATTCCTAATGCTTCACCTA 58.417 34.615 0.00 0.00 0.00 3.08
1651 2977 6.889301 ATGCTTCACCTATCAAACATATGG 57.111 37.500 7.80 0.00 0.00 2.74
1657 2983 5.999600 TCACCTATCAAACATATGGCATCTG 59.000 40.000 1.65 7.38 0.00 2.90
1753 3079 3.099362 CACATCGACAAGCTACGAGTAC 58.901 50.000 13.95 0.00 41.63 2.73
1777 3103 1.820010 GCCAAGCTTCCACCCCAAAG 61.820 60.000 0.00 0.00 0.00 2.77
1828 3154 2.969443 CTGTAAGTGCCGGTGAAAAG 57.031 50.000 1.90 0.00 0.00 2.27
1830 3156 2.616842 CTGTAAGTGCCGGTGAAAAGTT 59.383 45.455 1.90 0.00 0.00 2.66
1831 3157 2.614983 TGTAAGTGCCGGTGAAAAGTTC 59.385 45.455 1.90 0.00 0.00 3.01
1840 3166 3.403038 CGGTGAAAAGTTCCAGACATCT 58.597 45.455 0.00 0.00 0.00 2.90
1877 3208 4.521256 ACGGCTTCAAAAATTAACAGCCTA 59.479 37.500 6.45 0.00 44.02 3.93
1969 3300 4.112341 GGCGTCTACACCGTCGCT 62.112 66.667 8.18 0.00 46.37 4.93
1972 3303 1.500844 CGTCTACACCGTCGCTCTT 59.499 57.895 0.00 0.00 0.00 2.85
1994 3326 3.358554 ACCGTAAGTGAGGCTCTGA 57.641 52.632 16.72 0.00 0.00 3.27
2230 3589 5.850557 TGAAGTTTCTTGCTGAAATGGAA 57.149 34.783 8.28 0.00 45.19 3.53
2382 3741 3.406764 GGGAACAGATATGGACATCAGC 58.593 50.000 0.00 0.00 0.00 4.26
2390 3749 0.615331 ATGGACATCAGCCGTCAAGT 59.385 50.000 0.00 0.00 34.97 3.16
2419 3782 0.179189 GGATGCGGTTTTGAGCTTCG 60.179 55.000 0.00 0.00 38.10 3.79
2435 3798 0.676466 TTCGGGTGTGCCATCATGTC 60.676 55.000 0.00 0.00 36.17 3.06
2436 3799 2.463620 CGGGTGTGCCATCATGTCG 61.464 63.158 0.00 0.00 36.17 4.35
2455 3818 3.632604 GTCGACACAAGAGATGGAGGATA 59.367 47.826 11.55 0.00 0.00 2.59
2482 3845 8.664798 TGTACATAATAATTGTGAGTTGTGAGC 58.335 33.333 0.00 0.00 0.00 4.26
2483 3846 7.928307 ACATAATAATTGTGAGTTGTGAGCT 57.072 32.000 0.00 0.00 0.00 4.09
2484 3847 8.340618 ACATAATAATTGTGAGTTGTGAGCTT 57.659 30.769 0.00 0.00 0.00 3.74
2485 3848 8.239314 ACATAATAATTGTGAGTTGTGAGCTTG 58.761 33.333 0.00 0.00 0.00 4.01
2486 3849 6.639632 AATAATTGTGAGTTGTGAGCTTGT 57.360 33.333 0.00 0.00 0.00 3.16
2487 3850 3.976793 ATTGTGAGTTGTGAGCTTGTG 57.023 42.857 0.00 0.00 0.00 3.33
2504 3867 5.491070 GCTTGTGGCTGTCCATATATCATA 58.509 41.667 0.00 0.00 45.62 2.15
2536 3900 9.661563 ATACCTGTGTATATCGAAAGAAAAACA 57.338 29.630 0.00 0.00 35.89 2.83
2686 4050 4.082354 GCAGAGAAAATGCAGGAATCACTT 60.082 41.667 0.00 0.00 43.31 3.16
2733 4100 1.014044 TGCTCGACAATTCGCCAGTC 61.014 55.000 0.00 0.00 45.46 3.51
2824 4191 9.698309 CAAATTTCGATACCATAGACAGAGTAT 57.302 33.333 0.00 0.00 0.00 2.12
2843 4211 7.542477 CAGAGTATATCCGATAAAAGTCGCAAT 59.458 37.037 0.00 0.00 40.17 3.56
2848 4216 5.961395 TCCGATAAAAGTCGCAATACTTC 57.039 39.130 0.00 0.00 38.76 3.01
2859 4227 6.349300 AGTCGCAATACTTCAGGATTAACAT 58.651 36.000 0.00 0.00 0.00 2.71
2898 4266 0.248289 ATCAAATGGGCAGCAACAGC 59.752 50.000 0.00 0.00 0.00 4.40
2973 4343 3.266510 TGAGCCTATAACAAGGTGCAG 57.733 47.619 0.00 0.00 39.02 4.41
2993 4363 3.875727 CAGGTTAGGTCATCATGCTTCTG 59.124 47.826 0.00 0.00 0.00 3.02
2999 4369 5.939764 AGGTCATCATGCTTCTGTAAGTA 57.060 39.130 0.00 0.00 34.99 2.24
3121 4491 1.271001 CCACCTCTGATGAAGTGCACA 60.271 52.381 21.04 0.00 34.27 4.57
3131 4501 1.303309 GAAGTGCACAGTGAGCAACT 58.697 50.000 21.04 13.05 44.64 3.16
3220 4590 9.098355 CACTTCTCTATGATTTGAATTCCGTAA 57.902 33.333 2.27 0.00 0.00 3.18
3320 4691 5.533482 GAGTACTTTCTGTTCTTCTGCTGA 58.467 41.667 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.115095 GCTAATATGTTTCCTCTACACATCGTC 59.885 40.741 0.00 0.00 33.19 4.20
1 2 6.924060 GCTAATATGTTTCCTCTACACATCGT 59.076 38.462 0.00 0.00 33.19 3.73
2 3 6.923508 TGCTAATATGTTTCCTCTACACATCG 59.076 38.462 0.00 0.00 33.19 3.84
3 4 8.662781 TTGCTAATATGTTTCCTCTACACATC 57.337 34.615 0.00 0.00 33.19 3.06
4 5 8.893727 GTTTGCTAATATGTTTCCTCTACACAT 58.106 33.333 0.00 0.00 35.33 3.21
11 12 5.353123 TGGTCGTTTGCTAATATGTTTCCTC 59.647 40.000 0.00 0.00 0.00 3.71
12 13 5.250200 TGGTCGTTTGCTAATATGTTTCCT 58.750 37.500 0.00 0.00 0.00 3.36
17 18 5.950758 TGTTTGGTCGTTTGCTAATATGT 57.049 34.783 0.00 0.00 0.00 2.29
25 26 2.717011 CGTGTTATGTTTGGTCGTTTGC 59.283 45.455 0.00 0.00 0.00 3.68
82 84 5.487488 TGAAAGGGGTGAGAGTAACACATAT 59.513 40.000 0.00 0.00 39.65 1.78
85 87 3.042682 TGAAAGGGGTGAGAGTAACACA 58.957 45.455 0.00 0.00 39.65 3.72
89 91 3.775316 GGAGATGAAAGGGGTGAGAGTAA 59.225 47.826 0.00 0.00 0.00 2.24
92 94 1.137872 CGGAGATGAAAGGGGTGAGAG 59.862 57.143 0.00 0.00 0.00 3.20
99 101 1.463674 CCAAACCGGAGATGAAAGGG 58.536 55.000 9.46 0.00 36.56 3.95
100 102 0.811281 GCCAAACCGGAGATGAAAGG 59.189 55.000 9.46 0.00 36.56 3.11
101 103 1.533625 TGCCAAACCGGAGATGAAAG 58.466 50.000 9.46 0.00 36.56 2.62
128 130 5.782047 ACTCTCTCAACTCAGAGAACAATG 58.218 41.667 3.79 0.00 46.72 2.82
131 133 3.823873 GGACTCTCTCAACTCAGAGAACA 59.176 47.826 3.79 0.00 46.72 3.18
140 142 0.907230 GGCTGGGGACTCTCTCAACT 60.907 60.000 0.00 0.00 0.00 3.16
144 146 3.844090 GCGGCTGGGGACTCTCTC 61.844 72.222 0.00 0.00 0.00 3.20
151 153 2.270850 GTAACATGCGGCTGGGGA 59.729 61.111 0.00 0.00 0.00 4.81
159 161 3.731216 CCTCTATTCAGTCGTAACATGCG 59.269 47.826 0.00 0.00 0.00 4.73
163 165 6.931838 ACATTTCCTCTATTCAGTCGTAACA 58.068 36.000 0.00 0.00 0.00 2.41
167 169 9.751542 CTAAATACATTTCCTCTATTCAGTCGT 57.248 33.333 0.00 0.00 0.00 4.34
188 190 5.044030 TCCTCACAGTCCTAGACCTCTAAAT 60.044 44.000 0.00 0.00 32.18 1.40
191 193 3.461824 TCCTCACAGTCCTAGACCTCTA 58.538 50.000 0.00 0.00 32.18 2.43
194 196 3.544698 TTTCCTCACAGTCCTAGACCT 57.455 47.619 0.00 0.00 32.18 3.85
198 200 8.919145 AGTCTTATATTTTCCTCACAGTCCTAG 58.081 37.037 0.00 0.00 0.00 3.02
245 248 4.965200 AGGCTGTCTCCCAATATTACTC 57.035 45.455 0.00 0.00 0.00 2.59
248 251 4.220724 ACGTAGGCTGTCTCCCAATATTA 58.779 43.478 0.00 0.00 0.00 0.98
265 1536 6.607689 TGCACTGGAAAATATTCAAACGTAG 58.392 36.000 0.00 0.00 37.29 3.51
273 1544 5.964758 TGTTGGATGCACTGGAAAATATTC 58.035 37.500 0.00 0.00 34.66 1.75
274 1545 5.625197 GCTGTTGGATGCACTGGAAAATATT 60.625 40.000 0.00 0.00 0.00 1.28
275 1546 4.142093 GCTGTTGGATGCACTGGAAAATAT 60.142 41.667 0.00 0.00 0.00 1.28
276 1547 3.193267 GCTGTTGGATGCACTGGAAAATA 59.807 43.478 0.00 0.00 0.00 1.40
277 1548 2.028748 GCTGTTGGATGCACTGGAAAAT 60.029 45.455 0.00 0.00 0.00 1.82
278 1549 1.340889 GCTGTTGGATGCACTGGAAAA 59.659 47.619 0.00 0.00 0.00 2.29
279 1550 0.961019 GCTGTTGGATGCACTGGAAA 59.039 50.000 0.00 0.00 0.00 3.13
280 1551 0.111061 AGCTGTTGGATGCACTGGAA 59.889 50.000 0.00 0.00 0.00 3.53
281 1552 0.111061 AAGCTGTTGGATGCACTGGA 59.889 50.000 0.00 0.00 0.00 3.86
282 1553 0.242825 CAAGCTGTTGGATGCACTGG 59.757 55.000 0.00 0.00 0.00 4.00
283 1554 0.388134 GCAAGCTGTTGGATGCACTG 60.388 55.000 0.95 0.00 38.63 3.66
284 1555 1.859427 CGCAAGCTGTTGGATGCACT 61.859 55.000 6.62 0.00 38.69 4.40
285 1556 1.443194 CGCAAGCTGTTGGATGCAC 60.443 57.895 6.62 0.00 38.69 4.57
286 1557 1.454572 AACGCAAGCTGTTGGATGCA 61.455 50.000 6.62 0.00 45.62 3.96
287 1558 0.318955 AAACGCAAGCTGTTGGATGC 60.319 50.000 0.00 0.00 45.62 3.91
288 1559 1.001487 TCAAACGCAAGCTGTTGGATG 60.001 47.619 0.00 0.00 45.62 3.51
289 1560 1.317613 TCAAACGCAAGCTGTTGGAT 58.682 45.000 0.00 0.00 45.62 3.41
290 1561 1.098869 TTCAAACGCAAGCTGTTGGA 58.901 45.000 0.00 0.00 45.62 3.53
291 1562 2.138596 ATTCAAACGCAAGCTGTTGG 57.861 45.000 0.00 0.00 45.62 3.77
292 1563 5.389778 TGTATATTCAAACGCAAGCTGTTG 58.610 37.500 0.00 1.84 45.62 3.33
293 1564 5.391950 CCTGTATATTCAAACGCAAGCTGTT 60.392 40.000 0.00 0.00 45.62 3.16
294 1565 4.094887 CCTGTATATTCAAACGCAAGCTGT 59.905 41.667 0.00 0.00 45.62 4.40
295 1566 4.591202 CCTGTATATTCAAACGCAAGCTG 58.409 43.478 0.00 0.00 45.62 4.24
296 1567 3.065371 GCCTGTATATTCAAACGCAAGCT 59.935 43.478 0.00 0.00 45.62 3.74
297 1568 3.363178 GCCTGTATATTCAAACGCAAGC 58.637 45.455 0.00 0.00 45.62 4.01
299 1570 2.353269 CCGCCTGTATATTCAAACGCAA 59.647 45.455 0.00 0.00 0.00 4.85
300 1571 1.937223 CCGCCTGTATATTCAAACGCA 59.063 47.619 0.00 0.00 0.00 5.24
301 1572 1.333791 GCCGCCTGTATATTCAAACGC 60.334 52.381 0.00 0.00 0.00 4.84
302 1573 1.263217 GGCCGCCTGTATATTCAAACG 59.737 52.381 0.71 0.00 0.00 3.60
303 1574 1.263217 CGGCCGCCTGTATATTCAAAC 59.737 52.381 14.67 0.00 0.00 2.93
304 1575 1.134340 ACGGCCGCCTGTATATTCAAA 60.134 47.619 28.58 0.00 0.00 2.69
305 1576 0.466543 ACGGCCGCCTGTATATTCAA 59.533 50.000 28.58 0.00 0.00 2.69
306 1577 0.032952 GACGGCCGCCTGTATATTCA 59.967 55.000 28.58 0.00 0.00 2.57
307 1578 0.317479 AGACGGCCGCCTGTATATTC 59.683 55.000 28.58 12.14 0.00 1.75
325 1596 1.133216 TGTGAAGAATCTCTCCGCGAG 59.867 52.381 8.23 3.02 41.30 5.03
351 1622 9.677567 GTTTTCTTGTCTTGTTGCTCATTATTA 57.322 29.630 0.00 0.00 0.00 0.98
353 1624 6.857964 CGTTTTCTTGTCTTGTTGCTCATTAT 59.142 34.615 0.00 0.00 0.00 1.28
356 1627 4.096382 ACGTTTTCTTGTCTTGTTGCTCAT 59.904 37.500 0.00 0.00 0.00 2.90
357 1628 3.438781 ACGTTTTCTTGTCTTGTTGCTCA 59.561 39.130 0.00 0.00 0.00 4.26
359 1630 3.190535 ACACGTTTTCTTGTCTTGTTGCT 59.809 39.130 0.00 0.00 0.00 3.91
360 1631 3.300590 CACACGTTTTCTTGTCTTGTTGC 59.699 43.478 0.00 0.00 29.73 4.17
361 1632 3.851403 CCACACGTTTTCTTGTCTTGTTG 59.149 43.478 0.00 0.00 29.73 3.33
372 1643 2.614983 TGCTTCCTTACCACACGTTTTC 59.385 45.455 0.00 0.00 0.00 2.29
373 1644 2.645802 TGCTTCCTTACCACACGTTTT 58.354 42.857 0.00 0.00 0.00 2.43
382 1653 3.481453 GAATCCCTCATGCTTCCTTACC 58.519 50.000 0.00 0.00 0.00 2.85
383 1654 3.134458 CGAATCCCTCATGCTTCCTTAC 58.866 50.000 0.00 0.00 0.00 2.34
384 1655 2.104792 CCGAATCCCTCATGCTTCCTTA 59.895 50.000 0.00 0.00 0.00 2.69
390 1661 0.467384 CTGACCGAATCCCTCATGCT 59.533 55.000 0.00 0.00 0.00 3.79
394 1665 1.866015 ACATCTGACCGAATCCCTCA 58.134 50.000 0.00 0.00 0.00 3.86
398 1669 2.990066 AGGAACATCTGACCGAATCC 57.010 50.000 0.00 0.00 0.00 3.01
431 1702 9.331282 GCTGTTAGGAACATCTGATTATTACTT 57.669 33.333 2.33 0.00 41.26 2.24
432 1703 7.934120 GGCTGTTAGGAACATCTGATTATTACT 59.066 37.037 2.56 2.56 41.26 2.24
433 1704 7.715249 TGGCTGTTAGGAACATCTGATTATTAC 59.285 37.037 0.00 0.00 41.26 1.89
434 1705 7.801104 TGGCTGTTAGGAACATCTGATTATTA 58.199 34.615 0.00 0.00 41.26 0.98
435 1706 6.662755 TGGCTGTTAGGAACATCTGATTATT 58.337 36.000 0.00 0.00 41.26 1.40
436 1707 6.252599 TGGCTGTTAGGAACATCTGATTAT 57.747 37.500 0.00 0.00 41.26 1.28
437 1708 5.692115 TGGCTGTTAGGAACATCTGATTA 57.308 39.130 0.00 0.00 41.26 1.75
438 1709 4.574674 TGGCTGTTAGGAACATCTGATT 57.425 40.909 0.00 0.00 41.26 2.57
451 1722 2.170166 CTTTCCATGGCTTGGCTGTTA 58.830 47.619 14.30 0.00 46.01 2.41
488 1765 5.297776 CAGGTGGAGCTGTTGGAAATTATAG 59.702 44.000 0.00 0.00 0.00 1.31
489 1766 5.192927 CAGGTGGAGCTGTTGGAAATTATA 58.807 41.667 0.00 0.00 0.00 0.98
490 1767 4.019174 CAGGTGGAGCTGTTGGAAATTAT 58.981 43.478 0.00 0.00 0.00 1.28
524 1806 4.323868 GCTTTAATCTTGGAGTGGGAGACT 60.324 45.833 0.00 0.00 37.76 3.24
525 1807 3.942115 GCTTTAATCTTGGAGTGGGAGAC 59.058 47.826 0.00 0.00 0.00 3.36
526 1808 3.587061 TGCTTTAATCTTGGAGTGGGAGA 59.413 43.478 0.00 0.00 0.00 3.71
527 1809 3.691609 GTGCTTTAATCTTGGAGTGGGAG 59.308 47.826 0.00 0.00 0.00 4.30
617 1901 5.851047 TTGTCATATCATATCTTGCTGCG 57.149 39.130 0.00 0.00 0.00 5.18
684 1982 8.697507 TGATTCTGAGATGAAGTGCTAGTATA 57.302 34.615 0.00 0.00 0.00 1.47
688 1986 5.978919 GTCTGATTCTGAGATGAAGTGCTAG 59.021 44.000 0.00 0.00 0.00 3.42
690 1988 4.467082 AGTCTGATTCTGAGATGAAGTGCT 59.533 41.667 0.00 0.00 0.00 4.40
691 1989 4.567558 CAGTCTGATTCTGAGATGAAGTGC 59.432 45.833 0.00 0.00 35.20 4.40
692 1990 4.567558 GCAGTCTGATTCTGAGATGAAGTG 59.432 45.833 3.32 0.00 35.20 3.16
696 1994 2.100418 CGGCAGTCTGATTCTGAGATGA 59.900 50.000 3.32 0.00 35.20 2.92
698 1996 1.202510 GCGGCAGTCTGATTCTGAGAT 60.203 52.381 3.32 0.00 35.20 2.75
701 1999 0.321346 TTGCGGCAGTCTGATTCTGA 59.679 50.000 3.32 0.00 35.20 3.27
702 2000 0.725686 CTTGCGGCAGTCTGATTCTG 59.274 55.000 3.32 0.00 36.18 3.02
703 2001 0.610174 TCTTGCGGCAGTCTGATTCT 59.390 50.000 3.32 0.00 0.00 2.40
704 2002 1.005340 CTCTTGCGGCAGTCTGATTC 58.995 55.000 3.32 0.00 0.00 2.52
705 2003 1.023513 GCTCTTGCGGCAGTCTGATT 61.024 55.000 3.32 0.00 0.00 2.57
707 2005 2.047844 GCTCTTGCGGCAGTCTGA 60.048 61.111 3.32 0.15 0.00 3.27
708 2006 3.123620 GGCTCTTGCGGCAGTCTG 61.124 66.667 1.67 0.00 40.82 3.51
710 2008 3.426568 GTGGCTCTTGCGGCAGTC 61.427 66.667 1.67 0.00 40.35 3.51
784 2087 1.107538 TCGGCCGGGTATCTGAAGAG 61.108 60.000 27.83 0.00 0.00 2.85
831 2134 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
832 2135 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
834 2137 1.423921 GTAGAGGAGGAGGAGGAGGAG 59.576 61.905 0.00 0.00 0.00 3.69
835 2138 1.525175 GTAGAGGAGGAGGAGGAGGA 58.475 60.000 0.00 0.00 0.00 3.71
837 2140 1.529744 AGGTAGAGGAGGAGGAGGAG 58.470 60.000 0.00 0.00 0.00 3.69
838 2141 1.854280 GAAGGTAGAGGAGGAGGAGGA 59.146 57.143 0.00 0.00 0.00 3.71
839 2142 1.133294 GGAAGGTAGAGGAGGAGGAGG 60.133 61.905 0.00 0.00 0.00 4.30
840 2143 1.133294 GGGAAGGTAGAGGAGGAGGAG 60.133 61.905 0.00 0.00 0.00 3.69
841 2144 0.935194 GGGAAGGTAGAGGAGGAGGA 59.065 60.000 0.00 0.00 0.00 3.71
843 2146 2.673258 GAAGGGAAGGTAGAGGAGGAG 58.327 57.143 0.00 0.00 0.00 3.69
847 2150 3.385115 GAATGGAAGGGAAGGTAGAGGA 58.615 50.000 0.00 0.00 0.00 3.71
848 2151 2.439880 GGAATGGAAGGGAAGGTAGAGG 59.560 54.545 0.00 0.00 0.00 3.69
849 2152 2.439880 GGGAATGGAAGGGAAGGTAGAG 59.560 54.545 0.00 0.00 0.00 2.43
850 2153 2.047296 AGGGAATGGAAGGGAAGGTAGA 59.953 50.000 0.00 0.00 0.00 2.59
851 2154 2.439880 GAGGGAATGGAAGGGAAGGTAG 59.560 54.545 0.00 0.00 0.00 3.18
852 2155 2.488836 GAGGGAATGGAAGGGAAGGTA 58.511 52.381 0.00 0.00 0.00 3.08
853 2156 1.299939 GAGGGAATGGAAGGGAAGGT 58.700 55.000 0.00 0.00 0.00 3.50
854 2157 0.553333 GGAGGGAATGGAAGGGAAGG 59.447 60.000 0.00 0.00 0.00 3.46
855 2158 1.213926 CAGGAGGGAATGGAAGGGAAG 59.786 57.143 0.00 0.00 0.00 3.46
865 2168 1.376649 AAGCAAGGTCAGGAGGGAAT 58.623 50.000 0.00 0.00 0.00 3.01
885 2188 2.564553 GAAGCGTGGACGGAGATGCT 62.565 60.000 0.71 0.00 40.23 3.79
908 2211 3.518068 GGAAGCGGGGGAATTGCG 61.518 66.667 0.00 0.00 0.00 4.85
985 2292 2.353610 CCATCAACCCCTGGCTTGC 61.354 63.158 0.00 0.00 0.00 4.01
992 2299 3.728373 GGTCCGCCATCAACCCCT 61.728 66.667 0.00 0.00 34.09 4.79
1108 2416 2.851104 GACGACGGCCTTTTCACG 59.149 61.111 0.00 0.00 0.00 4.35
1112 2420 0.810823 TTCAACGACGACGGCCTTTT 60.811 50.000 12.58 0.00 44.46 2.27
1113 2421 1.219522 CTTCAACGACGACGGCCTTT 61.220 55.000 12.58 0.00 44.46 3.11
1114 2422 1.663702 CTTCAACGACGACGGCCTT 60.664 57.895 12.58 0.00 44.46 4.35
1128 2436 4.680237 CTGCCGCCACCGTCTTCA 62.680 66.667 0.00 0.00 0.00 3.02
1203 2514 2.281091 CAAGGGGCCTCCATGCAT 59.719 61.111 0.00 0.00 38.24 3.96
1257 2568 6.202379 CAGACAAGAGCAATGTACTCCATATG 59.798 42.308 0.00 0.00 34.56 1.78
1258 2569 6.098838 TCAGACAAGAGCAATGTACTCCATAT 59.901 38.462 0.00 0.00 34.56 1.78
1259 2570 5.422012 TCAGACAAGAGCAATGTACTCCATA 59.578 40.000 0.00 0.00 34.56 2.74
1260 2571 4.223700 TCAGACAAGAGCAATGTACTCCAT 59.776 41.667 0.00 0.00 34.56 3.41
1261 2572 3.578282 TCAGACAAGAGCAATGTACTCCA 59.422 43.478 0.00 0.00 34.56 3.86
1262 2573 4.193826 TCAGACAAGAGCAATGTACTCC 57.806 45.455 0.00 0.00 34.56 3.85
1263 2574 5.390356 GCTTTCAGACAAGAGCAATGTACTC 60.390 44.000 0.00 0.00 35.29 2.59
1264 2575 4.453819 GCTTTCAGACAAGAGCAATGTACT 59.546 41.667 0.00 0.00 35.29 2.73
1406 2726 9.863845 AGTTACTAGCTAGAGAAACTGAATTTC 57.136 33.333 27.45 5.84 46.21 2.17
1412 2732 8.512956 TGTACAAGTTACTAGCTAGAGAAACTG 58.487 37.037 27.45 22.29 30.73 3.16
1413 2733 8.513774 GTGTACAAGTTACTAGCTAGAGAAACT 58.486 37.037 27.45 24.78 0.00 2.66
1419 2739 6.405508 GGCATGTGTACAAGTTACTAGCTAGA 60.406 42.308 27.45 8.20 0.00 2.43
1420 2740 5.749109 GGCATGTGTACAAGTTACTAGCTAG 59.251 44.000 19.44 19.44 0.00 3.42
1421 2741 5.394883 GGGCATGTGTACAAGTTACTAGCTA 60.395 44.000 0.00 0.00 0.00 3.32
1422 2742 4.504858 GGCATGTGTACAAGTTACTAGCT 58.495 43.478 0.00 0.00 0.00 3.32
1423 2743 3.621715 GGGCATGTGTACAAGTTACTAGC 59.378 47.826 0.00 0.00 0.00 3.42
1426 2746 2.300723 TCGGGCATGTGTACAAGTTACT 59.699 45.455 0.00 0.00 0.00 2.24
1436 2756 1.884075 TTAGCTCGTCGGGCATGTGT 61.884 55.000 21.18 0.00 0.00 3.72
1438 2758 0.249489 GATTAGCTCGTCGGGCATGT 60.249 55.000 21.18 3.62 0.00 3.21
1443 2763 2.600731 GATGATGATTAGCTCGTCGGG 58.399 52.381 0.00 0.00 42.00 5.14
1445 2765 2.230025 AGGGATGATGATTAGCTCGTCG 59.770 50.000 0.00 0.00 42.00 5.12
1449 2769 7.337167 ACATGATTAGGGATGATGATTAGCTC 58.663 38.462 0.00 0.00 33.58 4.09
1451 2771 9.107177 CTTACATGATTAGGGATGATGATTAGC 57.893 37.037 0.00 0.00 33.58 3.09
1464 2790 9.784531 AATTATCCACACTCTTACATGATTAGG 57.215 33.333 0.00 0.00 0.00 2.69
1479 2805 3.129113 TGACAGCATGCAATTATCCACAC 59.871 43.478 21.98 0.00 42.53 3.82
1528 2854 6.144402 GTGTGAATTGCTGTTTTATCACCAAG 59.856 38.462 0.00 0.00 37.07 3.61
1567 2893 1.408702 TGCTGAAACAACTTGGAAGGC 59.591 47.619 0.00 0.00 0.00 4.35
1577 2903 3.631250 AGTTTCTTCCCTGCTGAAACAA 58.369 40.909 16.57 0.00 46.82 2.83
1620 2946 7.615365 TGTTTGATAGGTGAAGCATTAGGAATT 59.385 33.333 0.00 0.00 0.00 2.17
1621 2947 7.118723 TGTTTGATAGGTGAAGCATTAGGAAT 58.881 34.615 0.00 0.00 0.00 3.01
1623 2949 6.061022 TGTTTGATAGGTGAAGCATTAGGA 57.939 37.500 0.00 0.00 0.00 2.94
1624 2950 6.949352 ATGTTTGATAGGTGAAGCATTAGG 57.051 37.500 0.00 0.00 0.00 2.69
1639 2965 6.778834 TTTGTCAGATGCCATATGTTTGAT 57.221 33.333 1.24 0.00 0.00 2.57
1651 2977 6.872628 TTAGATGATCCATTTGTCAGATGC 57.127 37.500 0.00 0.00 0.00 3.91
1657 2983 7.444792 AGAAGAGCATTAGATGATCCATTTGTC 59.555 37.037 2.84 0.00 46.35 3.18
1735 3061 2.274437 TCGTACTCGTAGCTTGTCGAT 58.726 47.619 0.00 0.00 38.33 3.59
1753 3079 2.464459 GGTGGAAGCTTGGCGATCG 61.464 63.158 11.69 11.69 0.00 3.69
1777 3103 1.305219 TGCGGCAACAGATTACAGCC 61.305 55.000 0.00 0.00 41.86 4.85
1840 3166 0.806884 AGCCGTCGAACGAAACAACA 60.807 50.000 8.63 0.00 46.05 3.33
1877 3208 3.118665 AGCTGAGGTTGCAACAATGTTTT 60.119 39.130 29.55 7.73 0.00 2.43
2027 3381 1.818674 CCAGGTTACATTTGCCAGGTC 59.181 52.381 0.00 0.00 0.00 3.85
2031 3385 1.959985 CACACCAGGTTACATTTGCCA 59.040 47.619 0.00 0.00 0.00 4.92
2032 3386 1.336795 GCACACCAGGTTACATTTGCC 60.337 52.381 0.00 0.00 0.00 4.52
2167 3523 5.480422 AGGATCAAGATGGTTTTACAAACCC 59.520 40.000 14.47 0.00 39.54 4.11
2230 3589 2.028294 TGCATTGCGTTCCATTTCCATT 60.028 40.909 3.84 0.00 0.00 3.16
2382 3741 1.138859 TCCAGATGCCATACTTGACGG 59.861 52.381 0.00 0.00 0.00 4.79
2397 3760 0.036732 AGCTCAAAACCGCATCCAGA 59.963 50.000 0.00 0.00 0.00 3.86
2435 3798 4.038522 ACATATCCTCCATCTCTTGTGTCG 59.961 45.833 0.00 0.00 0.00 4.35
2436 3799 5.543507 ACATATCCTCCATCTCTTGTGTC 57.456 43.478 0.00 0.00 0.00 3.67
2487 3850 9.197694 GTATTCGAATATGATATATGGACAGCC 57.802 37.037 20.21 0.00 0.00 4.85
2501 3864 9.783256 TTCGATATACACAGGTATTCGAATATG 57.217 33.333 20.21 16.97 43.86 1.78
2504 3867 8.573885 TCTTTCGATATACACAGGTATTCGAAT 58.426 33.333 16.15 16.15 45.41 3.34
2535 3899 6.074142 CGAGTGTCCATGAATGTACATATGTG 60.074 42.308 18.81 7.89 29.33 3.21
2536 3900 5.985530 CGAGTGTCCATGAATGTACATATGT 59.014 40.000 13.93 13.93 29.33 2.29
2572 3936 3.188048 CAGCAGGAACACTTCATCTTCAC 59.812 47.826 0.00 0.00 0.00 3.18
2640 4004 4.353737 GCATCGAATGTACATTGCACATT 58.646 39.130 25.42 13.80 46.58 2.71
2641 4005 3.546616 CGCATCGAATGTACATTGCACAT 60.547 43.478 25.42 8.71 38.25 3.21
2686 4050 2.425312 ACAACAACAATGAAGGCGACAA 59.575 40.909 0.00 0.00 0.00 3.18
2733 4100 2.353011 CCTTACACAAGCAGCATTTGGG 60.353 50.000 0.00 0.00 35.10 4.12
2824 4191 7.204604 TGAAGTATTGCGACTTTTATCGGATA 58.795 34.615 0.00 0.00 42.30 2.59
2843 4211 9.567776 TTTGAACTCAATGTTAATCCTGAAGTA 57.432 29.630 0.00 0.00 39.30 2.24
2859 4227 9.757227 ATTTGATCCGTAAAATTTTGAACTCAA 57.243 25.926 13.76 11.93 0.00 3.02
2874 4242 0.254462 TGCTGCCCATTTGATCCGTA 59.746 50.000 0.00 0.00 0.00 4.02
2898 4266 2.879026 CTGATTGCTGGACATGGATGAG 59.121 50.000 0.00 0.00 0.00 2.90
2973 4343 3.878778 ACAGAAGCATGATGACCTAACC 58.121 45.455 0.00 0.00 0.00 2.85
3121 4491 2.113986 GCCCACCAGTTGCTCACT 59.886 61.111 0.00 0.00 35.35 3.41
3220 4590 1.163420 TCATTCTTGCCGTGTGCGTT 61.163 50.000 0.00 0.00 45.60 4.84
3320 4691 2.903135 ACTAGCTTGCTTCTGGAGAACT 59.097 45.455 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.