Multiple sequence alignment - TraesCS5A01G444100

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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 TraesCS5A01G444100 chr5A 100.000 4073 0 0 1 4073 624213309 624209237 0.000000e+00 7522.0
1 TraesCS5A01G444100 chr5D 90.755 2185 139 27 1495 3647 499870020 499867867 0.000000e+00 2857.0
2 TraesCS5A01G444100 chr5D 85.185 999 77 32 1 960 499871525 499870559 0.000000e+00 959.0
3 TraesCS5A01G444100 chr5D 92.400 500 33 2 959 1456 499870520 499870024 0.000000e+00 708.0
4 TraesCS5A01G444100 chr5D 82.308 130 9 7 76 194 18193872 18193746 2.590000e-17 100.0
5 TraesCS5A01G444100 chr5D 81.343 134 11 11 70 193 294640229 294640358 3.350000e-16 97.1
6 TraesCS5A01G444100 chr5B 89.646 1893 120 30 1495 3359 621261242 621259398 0.000000e+00 2340.0
7 TraesCS5A01G444100 chr5B 87.359 443 49 6 1019 1456 621261686 621261246 6.080000e-138 501.0
8 TraesCS5A01G444100 chr5B 87.356 348 34 10 3462 3807 621259166 621258827 1.370000e-104 390.0
9 TraesCS5A01G444100 chr5B 78.148 540 51 29 186 685 621262533 621262021 8.620000e-72 281.0
10 TraesCS5A01G444100 chr5B 96.154 104 4 0 3926 4029 621258384 621258281 1.950000e-38 171.0
11 TraesCS5A01G444100 chr5B 84.733 131 10 7 75 199 265435469 265435343 5.530000e-24 122.0
12 TraesCS5A01G444100 chr5B 81.295 139 11 8 70 199 312761812 312761944 9.320000e-17 99.0
13 TraesCS5A01G444100 chr5B 95.918 49 2 0 3389 3437 621259397 621259349 3.370000e-11 80.5
14 TraesCS5A01G444100 chrUn 85.593 236 31 2 1957 2192 317044685 317044453 1.130000e-60 244.0
15 TraesCS5A01G444100 chr3B 85.593 236 31 2 1957 2192 510277799 510278031 1.130000e-60 244.0
16 TraesCS5A01G444100 chr4D 84.348 230 32 3 1946 2174 291789149 291789375 5.300000e-54 222.0
17 TraesCS5A01G444100 chr7D 83.913 230 33 3 1946 2174 608238893 608238667 2.470000e-52 217.0
18 TraesCS5A01G444100 chr6D 87.634 186 19 3 1946 2130 418331884 418332066 3.190000e-51 213.0
19 TraesCS5A01G444100 chr6D 84.496 129 8 6 73 195 221219671 221219549 2.570000e-22 117.0
20 TraesCS5A01G444100 chr6A 83.406 229 34 3 1946 2173 111246468 111246243 4.130000e-50 209.0
21 TraesCS5A01G444100 chr6B 81.933 238 33 6 1949 2186 266872813 266873040 4.150000e-45 193.0
22 TraesCS5A01G444100 chr6B 83.459 133 10 7 73 199 365700752 365700878 3.330000e-21 113.0
23 TraesCS5A01G444100 chr1B 82.946 129 16 4 70 193 240487906 240488033 1.200000e-20 111.0
24 TraesCS5A01G444100 chr1D 82.353 136 9 9 73 201 35756865 35756992 2.000000e-18 104.0
25 TraesCS5A01G444100 chr7B 83.333 126 3 9 76 194 475307981 475308095 2.590000e-17 100.0


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 TraesCS5A01G444100 chr5A 624209237 624213309 4072 True 7522.00 7522 100.000000 1 4073 1 chr5A.!!$R1 4072
1 TraesCS5A01G444100 chr5D 499867867 499871525 3658 True 1508.00 2857 89.446667 1 3647 3 chr5D.!!$R2 3646
2 TraesCS5A01G444100 chr5B 621258281 621262533 4252 True 627.25 2340 89.096833 186 4029 6 chr5B.!!$R2 3843

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
898 985 0.035056 CCATCTTGCCCTTCTCCGTT 60.035 55.0 0.00 0.0 0.0 4.44 F
1095 1247 0.106819 AATGGGTGCTGATCCTGCTC 60.107 55.0 8.84 5.6 0.0 4.26 F
2160 2349 0.315251 TGGTCGACACTGAAGCTGAG 59.685 55.0 18.91 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2330 0.034616 GCACTCCTCAGCTTCAGTGT 59.965 55.0 11.04 0.0 38.83 3.55 R
3048 3240 0.394192 TAGCAATGGCATCCTCTCCG 59.606 55.0 0.00 0.0 44.61 4.63 R
3447 3659 0.956410 TTGTACATGAAACGGGGGCG 60.956 55.0 0.00 0.0 0.00 6.13 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 3.812053 GGATGTGCCAGCTTTACATCTAG 59.188 47.826 23.39 0.00 46.10 2.43
28 29 5.500234 TGTGCCAGCTTTACATCTAGAAAT 58.500 37.500 0.00 0.00 0.00 2.17
46 47 9.224267 TCTAGAAATATGAAAGCATAAGCATCC 57.776 33.333 0.00 0.00 45.49 3.51
78 79 2.177016 GCCACCCCTGGGAAATAATACT 59.823 50.000 16.20 0.00 38.13 2.12
107 116 8.378172 TCCGTCCTAATATAAGAGCATTTTTG 57.622 34.615 0.00 0.00 0.00 2.44
150 159 8.397951 AATGCTCTTATATTATGGGATGGAGA 57.602 34.615 0.00 0.00 0.00 3.71
152 161 8.397951 TGCTCTTATATTATGGGATGGAGATT 57.602 34.615 0.00 0.00 0.00 2.40
153 162 8.270030 TGCTCTTATATTATGGGATGGAGATTG 58.730 37.037 0.00 0.00 0.00 2.67
154 163 8.270744 GCTCTTATATTATGGGATGGAGATTGT 58.729 37.037 0.00 0.00 0.00 2.71
189 198 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
315 352 9.732130 AGGATCTCAATTATTAGCAGATAAACC 57.268 33.333 0.00 0.00 0.00 3.27
340 377 5.538463 ACTTTTCCAAGCTCCATTTCCTGG 61.538 45.833 0.00 0.00 38.88 4.45
341 378 1.075601 TCCAAGCTCCATTTCCTGGT 58.924 50.000 0.00 0.00 46.08 4.00
351 388 0.991920 ATTTCCTGGTCCGGTGTCAT 59.008 50.000 0.00 0.00 0.00 3.06
352 389 0.323629 TTTCCTGGTCCGGTGTCATC 59.676 55.000 0.00 0.00 0.00 2.92
353 390 0.834261 TTCCTGGTCCGGTGTCATCA 60.834 55.000 0.00 0.00 0.00 3.07
370 407 8.542953 GGTGTCATCAGAAATGAAAAGAAAAAC 58.457 33.333 0.00 0.00 0.00 2.43
413 458 6.243811 TGGGACACAACGACATATTTAAAC 57.756 37.500 0.00 0.00 0.00 2.01
443 491 1.440618 TTGAGAAAGCCACCACCCTA 58.559 50.000 0.00 0.00 0.00 3.53
460 509 8.342634 CACCACCCTATTATGTTTATTTCGAAG 58.657 37.037 0.00 0.00 0.00 3.79
558 622 3.895025 CTGCCATGACAGGTTCCG 58.105 61.111 0.22 0.00 33.85 4.30
559 623 1.746615 CTGCCATGACAGGTTCCGG 60.747 63.158 0.22 0.00 33.85 5.14
560 624 2.438434 GCCATGACAGGTTCCGGG 60.438 66.667 0.00 0.00 0.00 5.73
561 625 2.272146 CCATGACAGGTTCCGGGG 59.728 66.667 0.00 0.00 0.00 5.73
562 626 2.272146 CATGACAGGTTCCGGGGG 59.728 66.667 0.00 0.00 0.00 5.40
563 627 2.204090 ATGACAGGTTCCGGGGGT 60.204 61.111 0.00 0.00 0.00 4.95
564 628 1.081462 ATGACAGGTTCCGGGGGTA 59.919 57.895 0.00 0.00 0.00 3.69
568 632 2.365237 AGGTTCCGGGGGTAGAGC 60.365 66.667 0.00 0.00 0.00 4.09
588 652 2.060383 CATCCCTCTCGCTGTCCCA 61.060 63.158 0.00 0.00 0.00 4.37
734 813 2.362077 GTCTGGAGGAGATCTGAGCTTC 59.638 54.545 0.00 0.00 31.63 3.86
737 816 2.292785 TGGAGGAGATCTGAGCTTCCTT 60.293 50.000 13.20 0.00 0.00 3.36
746 825 1.273606 CTGAGCTTCCTTCTCCGTGAA 59.726 52.381 0.00 0.00 0.00 3.18
761 840 3.502211 TCCGTGAAGAAGGAAATTTGCTC 59.498 43.478 13.01 6.83 32.86 4.26
763 842 4.261572 CCGTGAAGAAGGAAATTTGCTCAA 60.262 41.667 13.01 0.00 0.00 3.02
764 843 4.913924 CGTGAAGAAGGAAATTTGCTCAAG 59.086 41.667 13.01 5.58 0.00 3.02
765 844 5.506317 CGTGAAGAAGGAAATTTGCTCAAGT 60.506 40.000 13.01 0.00 0.00 3.16
767 846 5.010012 TGAAGAAGGAAATTTGCTCAAGTCC 59.990 40.000 13.01 0.00 0.00 3.85
768 847 4.473444 AGAAGGAAATTTGCTCAAGTCCA 58.527 39.130 13.01 0.00 0.00 4.02
771 850 2.627699 GGAAATTTGCTCAAGTCCACCA 59.372 45.455 1.93 0.00 0.00 4.17
795 874 4.363999 AGATTTCATCGACGATCACTTCC 58.636 43.478 7.54 0.00 0.00 3.46
848 927 2.417924 GCATCTCTTCTCGCCTTCTTCA 60.418 50.000 0.00 0.00 0.00 3.02
851 930 5.595885 CATCTCTTCTCGCCTTCTTCAATA 58.404 41.667 0.00 0.00 0.00 1.90
854 933 6.644347 TCTCTTCTCGCCTTCTTCAATAATT 58.356 36.000 0.00 0.00 0.00 1.40
858 937 3.620488 TCGCCTTCTTCAATAATTGGCT 58.380 40.909 0.00 0.00 37.01 4.75
898 985 0.035056 CCATCTTGCCCTTCTCCGTT 60.035 55.000 0.00 0.00 0.00 4.44
899 986 1.614317 CCATCTTGCCCTTCTCCGTTT 60.614 52.381 0.00 0.00 0.00 3.60
917 1004 9.810545 TCTCCGTTTAGAAATTTGTTCAAATTT 57.189 25.926 25.97 25.97 42.96 1.82
984 1125 2.815308 CTCGGTCCTTCCATCCCG 59.185 66.667 0.00 0.00 41.75 5.14
1009 1152 3.672397 CGAAGATCGATCAATGGCTACTG 59.328 47.826 26.47 1.56 43.74 2.74
1050 1202 2.743928 CACCGGCAGCAGTTCTCC 60.744 66.667 0.00 0.00 0.00 3.71
1095 1247 0.106819 AATGGGTGCTGATCCTGCTC 60.107 55.000 8.84 5.60 0.00 4.26
1325 1495 1.693083 GACGTTTTGGGAGATCGGCG 61.693 60.000 0.00 0.00 0.00 6.46
1328 1498 3.599285 TTTTGGGAGATCGGCGCGT 62.599 57.895 8.43 0.00 0.00 6.01
1332 1502 4.849329 GGAGATCGGCGCGTCGTT 62.849 66.667 33.52 25.83 0.00 3.85
1404 1574 2.223386 CGAGTCGGAGCTTAGAAGAAGG 60.223 54.545 4.10 0.00 0.00 3.46
1453 1623 1.138069 GGCTGAAGGAGGAGCTTACTC 59.862 57.143 10.07 10.07 42.66 2.59
1456 1626 2.430332 CTGAAGGAGGAGCTTACTCTGG 59.570 54.545 16.07 2.98 42.98 3.86
1457 1627 1.760029 GAAGGAGGAGCTTACTCTGGG 59.240 57.143 16.07 0.00 42.98 4.45
1458 1628 0.689412 AGGAGGAGCTTACTCTGGGC 60.689 60.000 16.07 3.34 42.98 5.36
1461 1631 0.980231 AGGAGCTTACTCTGGGCCAG 60.980 60.000 28.01 28.01 42.98 4.85
1463 1633 2.124529 GCTTACTCTGGGCCAGGC 60.125 66.667 32.23 22.92 31.51 4.85
1464 1634 2.187946 CTTACTCTGGGCCAGGCG 59.812 66.667 32.23 24.41 31.51 5.52
1465 1635 4.096003 TTACTCTGGGCCAGGCGC 62.096 66.667 32.23 21.72 41.94 6.53
1473 1643 3.741476 GGCCAGGCGCAGACAAAG 61.741 66.667 10.83 0.00 39.87 2.77
1474 1644 3.741476 GCCAGGCGCAGACAAAGG 61.741 66.667 10.83 0.33 39.87 3.11
1475 1645 2.281761 CCAGGCGCAGACAAAGGT 60.282 61.111 10.83 0.00 39.87 3.50
1476 1646 1.898574 CCAGGCGCAGACAAAGGTT 60.899 57.895 10.83 0.00 39.87 3.50
1477 1647 1.283793 CAGGCGCAGACAAAGGTTG 59.716 57.895 10.83 0.00 39.87 3.77
1478 1648 2.050077 GGCGCAGACAAAGGTTGC 60.050 61.111 10.83 0.00 31.66 4.17
1479 1649 2.721231 GCGCAGACAAAGGTTGCA 59.279 55.556 0.30 0.00 37.69 4.08
1480 1650 1.370900 GCGCAGACAAAGGTTGCAG 60.371 57.895 0.30 0.00 37.69 4.41
1481 1651 1.785041 GCGCAGACAAAGGTTGCAGA 61.785 55.000 0.30 0.00 37.69 4.26
1482 1652 0.877071 CGCAGACAAAGGTTGCAGAT 59.123 50.000 0.00 0.00 37.69 2.90
1483 1653 2.076100 CGCAGACAAAGGTTGCAGATA 58.924 47.619 0.00 0.00 37.69 1.98
1484 1654 2.094894 CGCAGACAAAGGTTGCAGATAG 59.905 50.000 0.00 0.00 37.69 2.08
1485 1655 2.159462 GCAGACAAAGGTTGCAGATAGC 60.159 50.000 0.00 0.00 45.96 2.97
1486 1656 2.421424 CAGACAAAGGTTGCAGATAGCC 59.579 50.000 0.00 0.00 44.83 3.93
1487 1657 2.307098 AGACAAAGGTTGCAGATAGCCT 59.693 45.455 0.00 0.00 44.83 4.58
1488 1658 3.084786 GACAAAGGTTGCAGATAGCCTT 58.915 45.455 0.00 0.00 42.22 4.35
1489 1659 3.084786 ACAAAGGTTGCAGATAGCCTTC 58.915 45.455 8.35 0.00 39.92 3.46
1490 1660 2.424956 CAAAGGTTGCAGATAGCCTTCC 59.575 50.000 8.35 0.00 39.92 3.46
1491 1661 1.589414 AGGTTGCAGATAGCCTTCCT 58.411 50.000 0.00 0.00 44.83 3.36
1492 1662 1.488393 AGGTTGCAGATAGCCTTCCTC 59.512 52.381 0.00 0.00 44.83 3.71
1493 1663 1.488393 GGTTGCAGATAGCCTTCCTCT 59.512 52.381 0.00 0.00 44.83 3.69
1494 1664 2.484594 GGTTGCAGATAGCCTTCCTCTC 60.485 54.545 0.00 0.00 44.83 3.20
1495 1665 2.165357 TGCAGATAGCCTTCCTCTCA 57.835 50.000 0.00 0.00 44.83 3.27
1496 1666 2.470990 TGCAGATAGCCTTCCTCTCAA 58.529 47.619 0.00 0.00 44.83 3.02
1497 1667 2.433604 TGCAGATAGCCTTCCTCTCAAG 59.566 50.000 0.00 0.00 44.83 3.02
1498 1668 2.697751 GCAGATAGCCTTCCTCTCAAGA 59.302 50.000 0.00 0.00 37.23 3.02
1505 1675 3.843027 AGCCTTCCTCTCAAGATTCAGAA 59.157 43.478 0.00 0.00 0.00 3.02
1509 1679 5.339035 CCTTCCTCTCAAGATTCAGAATGGT 60.339 44.000 0.00 0.00 36.16 3.55
1511 1681 4.080695 TCCTCTCAAGATTCAGAATGGTGG 60.081 45.833 0.00 0.00 36.16 4.61
1518 1688 1.570857 TTCAGAATGGTGGCCCGGAT 61.571 55.000 0.73 0.00 36.16 4.18
1520 1690 0.401738 CAGAATGGTGGCCCGGATAT 59.598 55.000 0.73 0.00 0.00 1.63
1521 1691 1.149101 AGAATGGTGGCCCGGATATT 58.851 50.000 0.73 0.00 0.00 1.28
1528 1698 1.140252 GTGGCCCGGATATTACACACT 59.860 52.381 0.73 0.00 0.00 3.55
1593 1766 4.022589 CAGTCAACTGATCTTGCCACAAAT 60.023 41.667 4.05 0.00 46.59 2.32
1611 1784 6.183360 CCACAAATGATGAAGAACCTCATACC 60.183 42.308 0.00 0.00 36.15 2.73
1627 1800 0.698238 TACCAAGGTTGCAGATGGCT 59.302 50.000 0.00 1.42 45.15 4.75
1632 1805 1.831580 AGGTTGCAGATGGCTTTCTC 58.168 50.000 0.00 0.00 45.15 2.87
1640 1813 1.133976 AGATGGCTTTCTCCAATCCGG 60.134 52.381 0.00 0.00 39.96 5.14
1664 1837 1.864862 CGCAAGTTCAGAGTGGCAG 59.135 57.895 0.00 0.00 0.00 4.85
1681 1854 6.951971 AGTGGCAGATTACACTCTAAAGATT 58.048 36.000 0.00 0.00 44.08 2.40
1684 1857 6.818644 TGGCAGATTACACTCTAAAGATTCAC 59.181 38.462 0.00 0.00 0.00 3.18
1728 1901 6.129179 TCTTCCAACAAAAGATGAAGAACCT 58.871 36.000 0.00 0.00 38.68 3.50
1730 1903 4.515191 TCCAACAAAAGATGAAGAACCTCG 59.485 41.667 0.00 0.00 0.00 4.63
1741 1914 5.306532 TGAAGAACCTCGTACAGATACAC 57.693 43.478 0.00 0.00 0.00 2.90
1742 1915 4.763279 TGAAGAACCTCGTACAGATACACA 59.237 41.667 0.00 0.00 0.00 3.72
1762 1935 0.609131 AGGTGTGTGCAGCATTACCC 60.609 55.000 17.37 13.45 44.89 3.69
1770 1943 2.095059 GTGCAGCATTACCCTTGACAAG 60.095 50.000 8.31 8.31 0.00 3.16
1780 1957 2.308570 ACCCTTGACAAGCATACCATCA 59.691 45.455 9.85 0.00 0.00 3.07
1781 1958 3.245229 ACCCTTGACAAGCATACCATCAA 60.245 43.478 9.85 0.00 0.00 2.57
1821 1998 5.805486 CCAATCTGAATTTCTGACAATGCTG 59.195 40.000 7.99 1.29 0.00 4.41
1822 1999 4.430137 TCTGAATTTCTGACAATGCTGC 57.570 40.909 2.19 0.00 0.00 5.25
1824 2001 2.892215 TGAATTTCTGACAATGCTGCCA 59.108 40.909 0.00 0.00 0.00 4.92
1829 2006 3.581024 TCTGACAATGCTGCCATTTTC 57.419 42.857 0.00 1.20 39.60 2.29
1845 2025 7.345691 TGCCATTTTCTCCTGTAGATCATAAA 58.654 34.615 0.00 0.00 33.05 1.40
1857 2037 8.260818 CCTGTAGATCATAAACCAGAAGAAGAA 58.739 37.037 0.00 0.00 0.00 2.52
1858 2038 9.311916 CTGTAGATCATAAACCAGAAGAAGAAG 57.688 37.037 0.00 0.00 0.00 2.85
1859 2039 9.035890 TGTAGATCATAAACCAGAAGAAGAAGA 57.964 33.333 0.00 0.00 0.00 2.87
1862 2042 8.766476 AGATCATAAACCAGAAGAAGAAGATGA 58.234 33.333 0.00 0.00 0.00 2.92
1923 2106 2.588314 GCAGCAGATGAGCCGGAG 60.588 66.667 5.05 0.00 34.23 4.63
1933 2116 0.677731 TGAGCCGGAGCCTGAATTTG 60.678 55.000 5.05 0.00 41.25 2.32
2029 2212 2.609737 GCTTCTTCGTCTTCTTTCCGGA 60.610 50.000 0.00 0.00 0.00 5.14
2160 2349 0.315251 TGGTCGACACTGAAGCTGAG 59.685 55.000 18.91 0.00 0.00 3.35
2186 2375 1.364626 GGCACGGTTGATGAGCTGAG 61.365 60.000 0.00 0.00 0.00 3.35
2250 2439 4.219999 GAGCTGGAGGAGGAGCGC 62.220 72.222 0.00 0.00 40.34 5.92
2319 2508 4.521062 CAGGAGGAGAAGGCGGCG 62.521 72.222 0.51 0.51 0.00 6.46
2385 2574 1.009335 CGCGTACGATCGGGATGAA 60.009 57.895 21.65 0.00 44.40 2.57
2514 2703 1.374758 CCTTCCGTGCCAGACAGAC 60.375 63.158 0.00 0.00 0.00 3.51
2661 2853 1.577328 CGAACAACAGCAGCGGGATT 61.577 55.000 0.00 0.00 0.00 3.01
2740 2932 1.212229 GAGGAGGACACGACGGAAC 59.788 63.158 0.00 0.00 0.00 3.62
2751 2943 1.666872 GACGGAACCTTCGGTGGTG 60.667 63.158 3.20 0.00 40.26 4.17
2754 2946 2.033602 GAACCTTCGGTGGTGGGG 59.966 66.667 1.22 0.00 40.73 4.96
2756 2948 2.465055 GAACCTTCGGTGGTGGGGAG 62.465 65.000 1.22 0.00 40.73 4.30
2862 3054 4.274700 CACCACGGACACGACGGT 62.275 66.667 0.00 0.00 45.48 4.83
2886 3078 3.986006 GAGGGTGACGACACGGCA 61.986 66.667 11.73 0.00 45.13 5.69
3048 3240 0.454196 GAGAGCTCCGGAAGACACTC 59.546 60.000 10.93 7.98 0.00 3.51
3098 3290 4.431131 CTGGCCGGGGTTGCTCAT 62.431 66.667 2.57 0.00 0.00 2.90
3099 3291 4.738998 TGGCCGGGGTTGCTCATG 62.739 66.667 2.18 0.00 0.00 3.07
3136 3331 6.881602 ACAGAGGTGATTAATTCTTCAACCTC 59.118 38.462 18.81 18.81 38.75 3.85
3142 3337 7.391833 GGTGATTAATTCTTCAACCTCTGAACT 59.608 37.037 0.00 0.00 39.20 3.01
3143 3338 8.233190 GTGATTAATTCTTCAACCTCTGAACTG 58.767 37.037 0.00 0.00 39.20 3.16
3144 3339 8.156820 TGATTAATTCTTCAACCTCTGAACTGA 58.843 33.333 0.00 0.00 39.20 3.41
3153 3348 5.474532 TCAACCTCTGAACTGATGAAAATGG 59.525 40.000 0.00 0.00 0.00 3.16
3248 3447 2.744202 CACCGCTGCTAATCTCACTTTT 59.256 45.455 0.00 0.00 0.00 2.27
3269 3468 4.220693 TGATCCTTGTGATTTGATCGGT 57.779 40.909 0.00 0.00 37.11 4.69
3329 3528 4.035675 GGTTGTAAATAGTGATGAGGCTGC 59.964 45.833 0.00 0.00 0.00 5.25
3331 3530 4.697514 TGTAAATAGTGATGAGGCTGCTC 58.302 43.478 0.00 0.00 0.00 4.26
3334 3533 1.697284 TAGTGATGAGGCTGCTCGAT 58.303 50.000 0.00 0.00 0.00 3.59
3440 3652 1.896220 TTGCAGAATCAGGGTGTCAC 58.104 50.000 0.00 0.00 0.00 3.67
3447 3659 4.394300 CAGAATCAGGGTGTCACTGAATTC 59.606 45.833 5.80 9.74 46.89 2.17
3450 3662 0.321653 AGGGTGTCACTGAATTCGCC 60.322 55.000 2.35 0.00 0.00 5.54
3522 3892 7.502226 TGAAATTTTGAGAGGATGTAAGTGTGT 59.498 33.333 0.00 0.00 0.00 3.72
3524 3894 7.823745 ATTTTGAGAGGATGTAAGTGTGTTT 57.176 32.000 0.00 0.00 0.00 2.83
3534 3904 9.823647 AGGATGTAAGTGTGTTTCATATCTAAG 57.176 33.333 0.00 0.00 0.00 2.18
3555 3925 9.476202 TCTAAGATGGTGTAATGTTTCATATCG 57.524 33.333 0.00 0.00 0.00 2.92
3569 3939 6.522855 TGTTTCATATCGAAATTCAAAGTGCG 59.477 34.615 0.00 0.00 45.21 5.34
3570 3940 4.587306 TCATATCGAAATTCAAAGTGCGC 58.413 39.130 0.00 0.00 0.00 6.09
3651 4023 8.717821 GCCTTTAATTCAACCCATTTTCTTTAC 58.282 33.333 0.00 0.00 0.00 2.01
3653 4025 7.876896 TTAATTCAACCCATTTTCTTTACGC 57.123 32.000 0.00 0.00 0.00 4.42
3654 4026 4.920640 TTCAACCCATTTTCTTTACGCA 57.079 36.364 0.00 0.00 0.00 5.24
3655 4027 5.461032 TTCAACCCATTTTCTTTACGCAT 57.539 34.783 0.00 0.00 0.00 4.73
3656 4028 5.054390 TCAACCCATTTTCTTTACGCATC 57.946 39.130 0.00 0.00 0.00 3.91
3658 4030 4.434713 ACCCATTTTCTTTACGCATCAC 57.565 40.909 0.00 0.00 0.00 3.06
3659 4031 3.192633 ACCCATTTTCTTTACGCATCACC 59.807 43.478 0.00 0.00 0.00 4.02
3661 4033 4.321601 CCCATTTTCTTTACGCATCACCAA 60.322 41.667 0.00 0.00 0.00 3.67
3663 4035 5.289193 CCATTTTCTTTACGCATCACCAATG 59.711 40.000 0.00 0.00 38.50 2.82
3664 4036 5.697473 TTTTCTTTACGCATCACCAATGA 57.303 34.783 0.00 0.00 37.59 2.57
3665 4037 5.697473 TTTCTTTACGCATCACCAATGAA 57.303 34.783 0.00 0.00 38.69 2.57
3666 4038 5.895636 TTCTTTACGCATCACCAATGAAT 57.104 34.783 0.00 0.00 38.69 2.57
3667 4039 5.233957 TCTTTACGCATCACCAATGAATG 57.766 39.130 0.00 0.00 38.69 2.67
3668 4040 4.699735 TCTTTACGCATCACCAATGAATGT 59.300 37.500 0.00 0.00 38.69 2.71
3669 4041 5.182950 TCTTTACGCATCACCAATGAATGTT 59.817 36.000 0.00 0.00 38.69 2.71
3670 4042 3.220507 ACGCATCACCAATGAATGTTG 57.779 42.857 0.00 0.00 38.69 3.33
3671 4043 2.819019 ACGCATCACCAATGAATGTTGA 59.181 40.909 0.00 0.00 38.69 3.18
3685 4057 9.199982 CAATGAATGTTGACATTTTTAGCTCTT 57.800 29.630 10.42 0.00 45.72 2.85
3807 4179 6.313744 AGAAAGACTAATTTCAAACGGGTG 57.686 37.500 2.41 0.00 40.86 4.61
3808 4180 4.499037 AAGACTAATTTCAAACGGGTGC 57.501 40.909 0.00 0.00 0.00 5.01
3809 4181 3.482436 AGACTAATTTCAAACGGGTGCA 58.518 40.909 0.00 0.00 0.00 4.57
3810 4182 3.252458 AGACTAATTTCAAACGGGTGCAC 59.748 43.478 8.80 8.80 0.00 4.57
3811 4183 2.295070 ACTAATTTCAAACGGGTGCACC 59.705 45.455 28.57 28.57 0.00 5.01
3812 4184 1.115467 AATTTCAAACGGGTGCACCA 58.885 45.000 35.78 14.50 40.22 4.17
3813 4185 1.115467 ATTTCAAACGGGTGCACCAA 58.885 45.000 35.78 20.36 40.22 3.67
3814 4186 0.895530 TTTCAAACGGGTGCACCAAA 59.104 45.000 35.78 22.96 40.22 3.28
3815 4187 1.115467 TTCAAACGGGTGCACCAAAT 58.885 45.000 35.78 18.41 40.22 2.32
3816 4188 1.982660 TCAAACGGGTGCACCAAATA 58.017 45.000 35.78 13.89 40.22 1.40
3817 4189 2.520069 TCAAACGGGTGCACCAAATAT 58.480 42.857 35.78 15.64 40.22 1.28
3818 4190 2.490115 TCAAACGGGTGCACCAAATATC 59.510 45.455 35.78 17.13 40.22 1.63
3819 4191 1.470051 AACGGGTGCACCAAATATCC 58.530 50.000 35.78 16.40 40.22 2.59
3820 4192 0.395173 ACGGGTGCACCAAATATCCC 60.395 55.000 35.78 16.13 40.22 3.85
3821 4193 1.106944 CGGGTGCACCAAATATCCCC 61.107 60.000 35.78 15.37 40.22 4.81
3822 4194 0.759060 GGGTGCACCAAATATCCCCC 60.759 60.000 35.78 12.14 39.85 5.40
3869 4241 9.801873 ATTGTAGATACATGTGGCAAAAATTAC 57.198 29.630 9.11 0.00 35.89 1.89
3870 4242 8.341892 TGTAGATACATGTGGCAAAAATTACA 57.658 30.769 9.11 1.68 0.00 2.41
3871 4243 8.965819 TGTAGATACATGTGGCAAAAATTACAT 58.034 29.630 9.11 0.00 34.31 2.29
3874 4246 9.189156 AGATACATGTGGCAAAAATTACATACT 57.811 29.630 9.11 0.00 32.86 2.12
3875 4247 9.801873 GATACATGTGGCAAAAATTACATACTT 57.198 29.630 9.11 0.00 32.86 2.24
3877 4249 8.309163 ACATGTGGCAAAAATTACATACTTTG 57.691 30.769 0.00 0.00 32.86 2.77
3878 4250 8.147058 ACATGTGGCAAAAATTACATACTTTGA 58.853 29.630 0.00 0.00 32.86 2.69
3879 4251 8.986847 CATGTGGCAAAAATTACATACTTTGAA 58.013 29.630 0.00 0.00 32.86 2.69
3880 4252 9.723601 ATGTGGCAAAAATTACATACTTTGAAT 57.276 25.926 0.00 0.00 32.41 2.57
3881 4253 9.553064 TGTGGCAAAAATTACATACTTTGAATT 57.447 25.926 0.00 0.00 31.77 2.17
3989 4685 1.824852 GACCATTTTGGACATCACCCC 59.175 52.381 0.00 0.00 40.96 4.95
4019 4715 8.263940 TGATTTTATGAAACCGGTTCTCTTAG 57.736 34.615 22.53 0.00 37.13 2.18
4022 4718 6.845758 TTATGAAACCGGTTCTCTTAGAGA 57.154 37.500 22.53 8.00 36.86 3.10
4029 4725 4.998672 ACCGGTTCTCTTAGAGATCTATCG 59.001 45.833 13.14 10.09 38.56 2.92
4030 4726 4.393680 CCGGTTCTCTTAGAGATCTATCGG 59.606 50.000 16.55 16.55 38.56 4.18
4031 4727 4.998672 CGGTTCTCTTAGAGATCTATCGGT 59.001 45.833 13.14 0.00 38.56 4.69
4032 4728 5.470777 CGGTTCTCTTAGAGATCTATCGGTT 59.529 44.000 13.14 0.00 38.56 4.44
4033 4729 6.649973 CGGTTCTCTTAGAGATCTATCGGTTA 59.350 42.308 13.14 0.00 38.56 2.85
4034 4730 7.172875 CGGTTCTCTTAGAGATCTATCGGTTAA 59.827 40.741 13.14 0.00 38.56 2.01
4035 4731 9.016438 GGTTCTCTTAGAGATCTATCGGTTAAT 57.984 37.037 13.14 0.00 38.56 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.508687 TCATATTTCTAGATGTAAAGCTGGCA 58.491 34.615 0.00 0.00 0.00 4.92
8 9 7.969536 TCATATTTCTAGATGTAAAGCTGGC 57.030 36.000 0.00 0.00 0.00 4.85
24 25 6.015180 TGGGGATGCTTATGCTTTCATATTTC 60.015 38.462 1.96 0.00 40.48 2.17
28 29 4.451891 TGGGGATGCTTATGCTTTCATA 57.548 40.909 1.96 0.00 40.48 2.15
58 59 3.181433 GGAGTATTATTTCCCAGGGGTGG 60.181 52.174 5.33 0.00 36.47 4.61
78 79 4.202641 TGCTCTTATATTAGGACGGAGGGA 60.203 45.833 0.00 0.00 0.00 4.20
125 134 8.397951 TCTCCATCCCATAATATAAGAGCATT 57.602 34.615 0.00 0.00 0.00 3.56
126 135 8.578593 ATCTCCATCCCATAATATAAGAGCAT 57.421 34.615 0.00 0.00 0.00 3.79
127 136 8.270030 CAATCTCCATCCCATAATATAAGAGCA 58.730 37.037 0.00 0.00 0.00 4.26
128 137 8.270744 ACAATCTCCATCCCATAATATAAGAGC 58.729 37.037 0.00 0.00 0.00 4.09
158 167 9.396022 CCGTCCCATAATATAAGAGCATTATTT 57.604 33.333 0.20 0.00 0.00 1.40
159 168 8.768397 TCCGTCCCATAATATAAGAGCATTATT 58.232 33.333 0.20 0.00 0.00 1.40
160 169 8.319057 TCCGTCCCATAATATAAGAGCATTAT 57.681 34.615 0.00 0.00 0.00 1.28
161 170 7.147724 CCTCCGTCCCATAATATAAGAGCATTA 60.148 40.741 0.00 0.00 0.00 1.90
217 226 2.259917 TGTGAATGCTCCTTCTCTCCA 58.740 47.619 0.00 0.00 0.00 3.86
218 227 3.557228 ATGTGAATGCTCCTTCTCTCC 57.443 47.619 0.00 0.00 0.00 3.71
315 352 3.366374 GGAAATGGAGCTTGGAAAAGTCG 60.366 47.826 0.00 0.00 0.00 4.18
340 377 2.972625 TCATTTCTGATGACACCGGAC 58.027 47.619 9.46 0.00 0.00 4.79
341 378 3.694043 TTCATTTCTGATGACACCGGA 57.306 42.857 9.46 0.00 0.00 5.14
351 388 9.369904 CCTTTCTGTTTTTCTTTTCATTTCTGA 57.630 29.630 0.00 0.00 0.00 3.27
352 389 9.369904 TCCTTTCTGTTTTTCTTTTCATTTCTG 57.630 29.630 0.00 0.00 0.00 3.02
353 390 9.942850 TTCCTTTCTGTTTTTCTTTTCATTTCT 57.057 25.926 0.00 0.00 0.00 2.52
370 407 6.010219 TCCCATCTAAACCTTTTCCTTTCTG 58.990 40.000 0.00 0.00 0.00 3.02
413 458 5.335191 GGTGGCTTTCTCAATTAGTTGTCAG 60.335 44.000 0.00 0.00 36.69 3.51
460 509 7.133513 GTGAATGCTGATGATGATCTTTTCTC 58.866 38.462 0.00 0.00 0.00 2.87
553 617 1.049289 ATGAGCTCTACCCCCGGAAC 61.049 60.000 16.19 0.00 0.00 3.62
554 618 0.759436 GATGAGCTCTACCCCCGGAA 60.759 60.000 16.19 0.00 0.00 4.30
556 620 2.210711 GGATGAGCTCTACCCCCGG 61.211 68.421 16.19 0.00 0.00 5.73
558 622 0.834261 GAGGGATGAGCTCTACCCCC 60.834 65.000 30.79 25.10 42.97 5.40
559 623 0.189822 AGAGGGATGAGCTCTACCCC 59.810 60.000 30.79 26.95 42.97 4.95
560 624 1.627864 GAGAGGGATGAGCTCTACCC 58.372 60.000 28.85 28.85 42.36 3.69
561 625 1.243902 CGAGAGGGATGAGCTCTACC 58.756 60.000 16.19 16.86 0.00 3.18
562 626 0.596082 GCGAGAGGGATGAGCTCTAC 59.404 60.000 16.19 8.63 0.00 2.59
563 627 0.476338 AGCGAGAGGGATGAGCTCTA 59.524 55.000 16.19 1.49 31.94 2.43
564 628 1.108727 CAGCGAGAGGGATGAGCTCT 61.109 60.000 16.19 0.00 35.82 4.09
568 632 1.739049 GGACAGCGAGAGGGATGAG 59.261 63.158 0.00 0.00 0.00 2.90
588 652 9.261180 CTACGTGTATCAATAATTCCAGTCAAT 57.739 33.333 0.00 0.00 0.00 2.57
609 686 3.626930 AGGCTGAGAGAGATTTCTACGT 58.373 45.455 0.00 0.00 32.53 3.57
704 783 1.889530 CTCCTCCAGACCCACGTTCC 61.890 65.000 0.00 0.00 0.00 3.62
737 816 3.502211 GCAAATTTCCTTCTTCACGGAGA 59.498 43.478 0.00 0.00 0.00 3.71
746 825 4.279420 GTGGACTTGAGCAAATTTCCTTCT 59.721 41.667 0.00 0.00 0.00 2.85
761 840 4.455533 TCGATGAAATCTTTGGTGGACTTG 59.544 41.667 0.00 0.00 42.58 3.16
763 842 4.003648 GTCGATGAAATCTTTGGTGGACT 58.996 43.478 0.00 0.00 42.58 3.85
764 843 3.181520 CGTCGATGAAATCTTTGGTGGAC 60.182 47.826 0.00 0.00 42.58 4.02
765 844 3.000041 CGTCGATGAAATCTTTGGTGGA 59.000 45.455 0.00 0.00 42.58 4.02
767 846 4.329801 TGATCGTCGATGAAATCTTTGGTG 59.670 41.667 13.54 0.00 42.58 4.17
768 847 4.330074 GTGATCGTCGATGAAATCTTTGGT 59.670 41.667 13.54 0.00 42.58 3.67
771 850 5.292101 GGAAGTGATCGTCGATGAAATCTTT 59.708 40.000 13.54 5.11 42.58 2.52
795 874 7.440198 ACATACATACCTTCATCTCATCTGTG 58.560 38.462 0.00 0.00 0.00 3.66
848 927 6.646267 AGATGTGCAAATTGAGCCAATTATT 58.354 32.000 11.87 0.00 42.32 1.40
851 930 4.501071 GAGATGTGCAAATTGAGCCAATT 58.499 39.130 0.00 7.18 44.62 2.32
854 933 1.820519 GGAGATGTGCAAATTGAGCCA 59.179 47.619 0.00 0.00 0.00 4.75
858 937 3.949754 GGATCAGGAGATGTGCAAATTGA 59.050 43.478 0.00 0.00 33.72 2.57
940 1027 3.883489 CACTGCAGATCATGGTGATTGAT 59.117 43.478 23.35 0.00 37.20 2.57
984 1125 1.458827 GCCATTGATCGATCTTCGCTC 59.541 52.381 25.02 7.51 40.21 5.03
1009 1152 1.461911 CCCCAGGCCGTACTACTAGC 61.462 65.000 0.00 0.00 0.00 3.42
1050 1202 4.671569 GCCGAGGATAGCAGGGCG 62.672 72.222 0.00 0.00 33.58 6.13
1095 1247 4.124943 AGGCCCTCCAGCAGCATG 62.125 66.667 0.00 0.00 34.65 4.06
1350 1520 0.538746 TCAGCTCACTGTACCCGACA 60.539 55.000 0.00 0.00 44.77 4.35
1352 1522 0.965866 CCTCAGCTCACTGTACCCGA 60.966 60.000 0.00 0.00 44.77 5.14
1389 1559 1.471851 GGCGACCTTCTTCTAAGCTCC 60.472 57.143 0.00 0.00 0.00 4.70
1395 1565 1.035932 CCTCCGGCGACCTTCTTCTA 61.036 60.000 9.30 0.00 0.00 2.10
1429 1599 1.040339 AGCTCCTCCTTCAGCCTACG 61.040 60.000 0.00 0.00 36.17 3.51
1430 1600 1.199615 AAGCTCCTCCTTCAGCCTAC 58.800 55.000 0.00 0.00 36.17 3.18
1432 1602 1.199615 GTAAGCTCCTCCTTCAGCCT 58.800 55.000 0.00 0.00 36.17 4.58
1435 1605 2.430332 CCAGAGTAAGCTCCTCCTTCAG 59.570 54.545 9.18 0.00 42.59 3.02
1444 1614 1.524482 CCTGGCCCAGAGTAAGCTC 59.476 63.158 13.74 0.00 41.94 4.09
1456 1626 3.741476 CTTTGTCTGCGCCTGGCC 61.741 66.667 14.12 6.66 42.61 5.36
1457 1627 3.741476 CCTTTGTCTGCGCCTGGC 61.741 66.667 9.11 9.11 43.96 4.85
1458 1628 1.898574 AACCTTTGTCTGCGCCTGG 60.899 57.895 4.18 0.00 0.00 4.45
1461 1631 2.050077 GCAACCTTTGTCTGCGCC 60.050 61.111 4.18 0.00 0.00 6.53
1463 1633 0.877071 ATCTGCAACCTTTGTCTGCG 59.123 50.000 0.00 0.00 38.97 5.18
1464 1634 2.159462 GCTATCTGCAACCTTTGTCTGC 60.159 50.000 0.00 0.00 42.31 4.26
1465 1635 2.421424 GGCTATCTGCAACCTTTGTCTG 59.579 50.000 0.00 0.00 45.15 3.51
1466 1636 2.307098 AGGCTATCTGCAACCTTTGTCT 59.693 45.455 0.00 0.00 45.15 3.41
1467 1637 2.716217 AGGCTATCTGCAACCTTTGTC 58.284 47.619 0.00 0.00 45.15 3.18
1468 1638 2.887151 AGGCTATCTGCAACCTTTGT 57.113 45.000 0.00 0.00 45.15 2.83
1469 1639 2.424956 GGAAGGCTATCTGCAACCTTTG 59.575 50.000 6.21 0.00 42.54 2.77
1470 1640 2.310052 AGGAAGGCTATCTGCAACCTTT 59.690 45.455 6.21 0.00 42.54 3.11
1471 1641 1.918957 AGGAAGGCTATCTGCAACCTT 59.081 47.619 4.78 4.78 45.13 3.50
1472 1642 1.488393 GAGGAAGGCTATCTGCAACCT 59.512 52.381 0.00 0.00 45.15 3.50
1473 1643 1.488393 AGAGGAAGGCTATCTGCAACC 59.512 52.381 0.00 0.00 45.15 3.77
1474 1644 2.169352 TGAGAGGAAGGCTATCTGCAAC 59.831 50.000 1.93 0.00 45.15 4.17
1475 1645 2.470990 TGAGAGGAAGGCTATCTGCAA 58.529 47.619 1.93 0.00 45.15 4.08
1476 1646 2.165357 TGAGAGGAAGGCTATCTGCA 57.835 50.000 1.93 0.00 45.15 4.41
1477 1647 2.697751 TCTTGAGAGGAAGGCTATCTGC 59.302 50.000 1.93 0.00 41.94 4.26
1478 1648 5.070180 TGAATCTTGAGAGGAAGGCTATCTG 59.930 44.000 1.93 0.00 0.00 2.90
1479 1649 5.215069 TGAATCTTGAGAGGAAGGCTATCT 58.785 41.667 0.00 0.00 0.00 1.98
1480 1650 5.304101 TCTGAATCTTGAGAGGAAGGCTATC 59.696 44.000 0.00 0.00 0.00 2.08
1481 1651 5.215069 TCTGAATCTTGAGAGGAAGGCTAT 58.785 41.667 0.00 0.00 0.00 2.97
1482 1652 4.614475 TCTGAATCTTGAGAGGAAGGCTA 58.386 43.478 0.00 0.00 0.00 3.93
1483 1653 3.448934 TCTGAATCTTGAGAGGAAGGCT 58.551 45.455 0.00 0.00 0.00 4.58
1484 1654 3.902881 TCTGAATCTTGAGAGGAAGGC 57.097 47.619 0.00 0.00 0.00 4.35
1485 1655 5.124645 CCATTCTGAATCTTGAGAGGAAGG 58.875 45.833 0.00 0.00 0.00 3.46
1486 1656 5.585445 CACCATTCTGAATCTTGAGAGGAAG 59.415 44.000 0.00 0.00 0.00 3.46
1487 1657 5.494724 CACCATTCTGAATCTTGAGAGGAA 58.505 41.667 0.00 0.00 0.00 3.36
1488 1658 4.080695 CCACCATTCTGAATCTTGAGAGGA 60.081 45.833 0.00 0.00 0.00 3.71
1489 1659 4.197750 CCACCATTCTGAATCTTGAGAGG 58.802 47.826 0.00 0.00 0.00 3.69
1490 1660 3.626670 GCCACCATTCTGAATCTTGAGAG 59.373 47.826 0.00 0.00 0.00 3.20
1491 1661 3.614092 GCCACCATTCTGAATCTTGAGA 58.386 45.455 0.00 0.00 0.00 3.27
1492 1662 2.686915 GGCCACCATTCTGAATCTTGAG 59.313 50.000 0.00 0.00 0.00 3.02
1493 1663 2.621407 GGGCCACCATTCTGAATCTTGA 60.621 50.000 4.39 0.00 36.50 3.02
1494 1664 1.753073 GGGCCACCATTCTGAATCTTG 59.247 52.381 4.39 0.78 36.50 3.02
1495 1665 1.683011 CGGGCCACCATTCTGAATCTT 60.683 52.381 4.39 0.00 36.13 2.40
1496 1666 0.107017 CGGGCCACCATTCTGAATCT 60.107 55.000 4.39 0.00 36.13 2.40
1497 1667 1.103398 CCGGGCCACCATTCTGAATC 61.103 60.000 4.39 0.00 36.13 2.52
1498 1668 1.076777 CCGGGCCACCATTCTGAAT 60.077 57.895 4.39 0.00 36.13 2.57
1505 1675 1.073284 GTGTAATATCCGGGCCACCAT 59.927 52.381 4.39 0.00 36.13 3.55
1509 1679 1.414919 GAGTGTGTAATATCCGGGCCA 59.585 52.381 4.39 0.00 0.00 5.36
1511 1681 2.364324 TCAGAGTGTGTAATATCCGGGC 59.636 50.000 0.00 0.00 0.00 6.13
1518 1688 7.180229 TCCCTTGAATCTTCAGAGTGTGTAATA 59.820 37.037 0.00 0.00 38.61 0.98
1520 1690 5.306937 TCCCTTGAATCTTCAGAGTGTGTAA 59.693 40.000 0.00 0.00 38.61 2.41
1521 1691 4.838423 TCCCTTGAATCTTCAGAGTGTGTA 59.162 41.667 0.00 0.00 38.61 2.90
1528 1698 1.208052 CGGCTCCCTTGAATCTTCAGA 59.792 52.381 0.00 0.00 38.61 3.27
1585 1758 3.507233 TGAGGTTCTTCATCATTTGTGGC 59.493 43.478 0.00 0.00 31.68 5.01
1593 1766 4.536090 ACCTTGGTATGAGGTTCTTCATCA 59.464 41.667 0.86 0.00 45.06 3.07
1611 1784 1.891150 AGAAAGCCATCTGCAACCTTG 59.109 47.619 0.00 0.00 44.83 3.61
1627 1800 2.702261 CGTTAACCCGGATTGGAGAAA 58.298 47.619 0.73 0.00 42.00 2.52
1632 1805 0.450184 CTTGCGTTAACCCGGATTGG 59.550 55.000 0.73 0.00 37.55 3.16
1640 1813 2.223377 CCACTCTGAACTTGCGTTAACC 59.777 50.000 0.00 0.00 32.39 2.85
1664 1837 8.988934 TGTTGTGTGAATCTTTAGAGTGTAATC 58.011 33.333 0.00 0.00 0.00 1.75
1675 1848 6.698008 TGTCTGAATGTTGTGTGAATCTTT 57.302 33.333 0.00 0.00 0.00 2.52
1681 1854 4.512484 TCACTTGTCTGAATGTTGTGTGA 58.488 39.130 0.00 0.00 0.00 3.58
1684 1857 5.936686 AGATCACTTGTCTGAATGTTGTG 57.063 39.130 0.00 0.00 0.00 3.33
1728 1901 4.168922 CACACCTTGTGTATCTGTACGA 57.831 45.455 0.00 0.00 45.65 3.43
1741 1914 1.068333 GGTAATGCTGCACACACCTTG 60.068 52.381 17.32 0.00 34.97 3.61
1742 1915 1.247567 GGTAATGCTGCACACACCTT 58.752 50.000 17.32 5.71 34.97 3.50
1762 1935 9.590451 AATTTAATTGATGGTATGCTTGTCAAG 57.410 29.630 8.31 8.31 32.93 3.02
1770 1943 8.819974 CAGGACAAAATTTAATTGATGGTATGC 58.180 33.333 0.00 0.00 0.00 3.14
1780 1957 7.678837 TCAGATTGGCAGGACAAAATTTAATT 58.321 30.769 0.00 0.00 33.48 1.40
1781 1958 7.243604 TCAGATTGGCAGGACAAAATTTAAT 57.756 32.000 0.00 0.00 33.48 1.40
1821 1998 7.255277 GGTTTATGATCTACAGGAGAAAATGGC 60.255 40.741 0.00 0.00 37.85 4.40
1822 1999 7.775093 TGGTTTATGATCTACAGGAGAAAATGG 59.225 37.037 0.00 0.00 37.85 3.16
1824 2001 8.772250 TCTGGTTTATGATCTACAGGAGAAAAT 58.228 33.333 0.00 0.00 37.85 1.82
1829 2006 7.353414 TCTTCTGGTTTATGATCTACAGGAG 57.647 40.000 0.00 0.00 33.80 3.69
1845 2025 3.307339 GCCACTCATCTTCTTCTTCTGGT 60.307 47.826 0.00 0.00 0.00 4.00
1857 2037 3.972227 GCGTTGTGCCACTCATCT 58.028 55.556 0.00 0.00 37.76 2.90
1887 2070 1.532437 GCAGCTTTGGTTTCAAATGGC 59.468 47.619 0.00 0.00 41.45 4.40
1892 2075 0.822811 TGCTGCAGCTTTGGTTTCAA 59.177 45.000 36.61 12.08 42.66 2.69
1923 2106 0.449388 CTCTGTCGGCAAATTCAGGC 59.551 55.000 0.00 0.00 0.00 4.85
1933 2116 4.314440 TGTGGTGGCTCTGTCGGC 62.314 66.667 0.00 0.00 0.00 5.54
2008 2191 1.727335 CCGGAAAGAAGACGAAGAAGC 59.273 52.381 0.00 0.00 0.00 3.86
2009 2192 2.987821 GTCCGGAAAGAAGACGAAGAAG 59.012 50.000 5.23 0.00 0.00 2.85
2010 2193 3.022607 GTCCGGAAAGAAGACGAAGAA 57.977 47.619 5.23 0.00 0.00 2.52
2011 2194 2.719426 GTCCGGAAAGAAGACGAAGA 57.281 50.000 5.23 0.00 0.00 2.87
2144 2327 0.884514 CTCCTCAGCTTCAGTGTCGA 59.115 55.000 0.00 0.00 0.00 4.20
2147 2330 0.034616 GCACTCCTCAGCTTCAGTGT 59.965 55.000 11.04 0.00 38.83 3.55
2149 2332 1.291588 CGCACTCCTCAGCTTCAGT 59.708 57.895 0.00 0.00 0.00 3.41
2154 2343 4.385405 GTGCCGCACTCCTCAGCT 62.385 66.667 16.51 0.00 0.00 4.24
2160 2349 4.980805 TCAACCGTGCCGCACTCC 62.981 66.667 20.87 0.00 31.34 3.85
2570 2759 1.004080 TTCTCGTCGTCCTCGGAGT 60.004 57.895 4.02 0.00 37.69 3.85
2661 2853 2.747686 GGCTCCGGTTCTTGGACA 59.252 61.111 0.00 0.00 0.00 4.02
2874 3066 3.911698 AGTGCTGCCGTGTCGTCA 61.912 61.111 0.00 0.00 0.00 4.35
2886 3078 0.754957 CGATCTCCTCCTCCAGTGCT 60.755 60.000 0.00 0.00 0.00 4.40
3048 3240 0.394192 TAGCAATGGCATCCTCTCCG 59.606 55.000 0.00 0.00 44.61 4.63
3058 3250 3.637297 GCTTTCAGCTAGCAATGGC 57.363 52.632 18.83 10.41 38.45 4.40
3081 3273 4.431131 ATGAGCAACCCCGGCCAG 62.431 66.667 2.24 0.00 0.00 4.85
3094 3286 3.463944 TCTGTATGTGCATGCTCATGAG 58.536 45.455 34.28 28.63 41.20 2.90
3095 3287 3.463944 CTCTGTATGTGCATGCTCATGA 58.536 45.455 34.28 24.72 41.20 3.07
3097 3289 2.172082 ACCTCTGTATGTGCATGCTCAT 59.828 45.455 31.24 31.24 34.92 2.90
3098 3290 1.556451 ACCTCTGTATGTGCATGCTCA 59.444 47.619 23.37 23.37 0.00 4.26
3099 3291 1.938577 CACCTCTGTATGTGCATGCTC 59.061 52.381 20.33 16.39 0.00 4.26
3105 3300 7.280876 TGAAGAATTAATCACCTCTGTATGTGC 59.719 37.037 0.00 0.00 32.51 4.57
3110 3305 7.918076 AGGTTGAAGAATTAATCACCTCTGTA 58.082 34.615 0.00 0.00 0.00 2.74
3136 3331 5.049474 TCACGAACCATTTTCATCAGTTCAG 60.049 40.000 0.00 0.00 37.31 3.02
3142 3337 5.956068 TTGATCACGAACCATTTTCATCA 57.044 34.783 0.00 0.00 0.00 3.07
3143 3338 6.690098 CAGATTGATCACGAACCATTTTCATC 59.310 38.462 0.00 0.00 0.00 2.92
3144 3339 6.558009 CAGATTGATCACGAACCATTTTCAT 58.442 36.000 0.00 0.00 0.00 2.57
3153 3348 2.621338 TCCAGCAGATTGATCACGAAC 58.379 47.619 0.00 0.00 0.00 3.95
3201 3399 1.109920 ACTGGATCGATCGGAGGTGG 61.110 60.000 18.81 4.49 0.00 4.61
3248 3447 4.220693 ACCGATCAAATCACAAGGATCA 57.779 40.909 0.00 0.00 36.75 2.92
3290 3489 3.485394 ACAACCTACATCATGCACAACA 58.515 40.909 0.00 0.00 0.00 3.33
3329 3528 6.187480 CACACATGCTTATTGTACAATCGAG 58.813 40.000 24.00 21.50 32.50 4.04
3367 3579 1.331214 CTGGTCCACTTGCAAACCAT 58.669 50.000 18.61 0.00 40.81 3.55
3399 3611 1.336240 GCATTGCAGAACAACCACTCC 60.336 52.381 3.15 0.00 42.27 3.85
3440 3652 0.958382 TGAAACGGGGGCGAATTCAG 60.958 55.000 6.22 0.00 0.00 3.02
3447 3659 0.956410 TTGTACATGAAACGGGGGCG 60.956 55.000 0.00 0.00 0.00 6.13
3450 3662 8.032451 AGATAAAATTTTGTACATGAAACGGGG 58.968 33.333 13.76 0.00 0.00 5.73
3504 3874 5.545063 TGAAACACACTTACATCCTCTCA 57.455 39.130 0.00 0.00 0.00 3.27
3506 3876 8.083828 AGATATGAAACACACTTACATCCTCT 57.916 34.615 0.00 0.00 0.00 3.69
3551 3921 4.332543 AGATGCGCACTTTGAATTTCGATA 59.667 37.500 14.90 0.00 0.00 2.92
3555 3925 5.221891 TCTAGATGCGCACTTTGAATTTC 57.778 39.130 14.90 2.26 0.00 2.17
3569 3939 6.142817 ACGTGTCATTTTTGTTTCTAGATGC 58.857 36.000 0.00 0.00 0.00 3.91
3570 3940 7.321271 GTGACGTGTCATTTTTGTTTCTAGATG 59.679 37.037 5.91 0.00 42.18 2.90
3656 4028 7.385752 AGCTAAAAATGTCAACATTCATTGGTG 59.614 33.333 8.72 4.97 45.06 4.17
3658 4030 7.816031 AGAGCTAAAAATGTCAACATTCATTGG 59.184 33.333 8.72 9.89 45.06 3.16
3659 4031 8.752766 AGAGCTAAAAATGTCAACATTCATTG 57.247 30.769 8.72 4.14 45.06 2.82
3731 4103 9.672673 AATTATGTTCTAGCAGTGACAAGTATT 57.327 29.630 0.00 0.00 0.00 1.89
3734 4106 7.986085 AAATTATGTTCTAGCAGTGACAAGT 57.014 32.000 0.00 0.00 0.00 3.16
3789 4161 3.561503 GTGCACCCGTTTGAAATTAGTC 58.438 45.455 5.22 0.00 0.00 2.59
3843 4215 9.801873 GTAATTTTTGCCACATGTATCTACAAT 57.198 29.630 0.00 0.00 39.99 2.71
3844 4216 8.797438 TGTAATTTTTGCCACATGTATCTACAA 58.203 29.630 0.00 0.00 39.99 2.41
3845 4217 8.341892 TGTAATTTTTGCCACATGTATCTACA 57.658 30.769 0.00 0.00 40.98 2.74
3848 4220 9.189156 AGTATGTAATTTTTGCCACATGTATCT 57.811 29.630 0.00 0.00 33.78 1.98
3849 4221 9.801873 AAGTATGTAATTTTTGCCACATGTATC 57.198 29.630 0.00 0.00 33.78 2.24
3851 4223 9.416794 CAAAGTATGTAATTTTTGCCACATGTA 57.583 29.630 0.00 0.00 33.78 2.29
3852 4224 8.147058 TCAAAGTATGTAATTTTTGCCACATGT 58.853 29.630 0.00 0.00 32.84 3.21
3853 4225 8.531622 TCAAAGTATGTAATTTTTGCCACATG 57.468 30.769 0.00 0.00 32.84 3.21
3854 4226 9.723601 ATTCAAAGTATGTAATTTTTGCCACAT 57.276 25.926 0.00 0.00 32.84 3.21
3855 4227 9.553064 AATTCAAAGTATGTAATTTTTGCCACA 57.447 25.926 0.00 0.00 32.84 4.17
3915 4287 9.772973 ACATAATAACTAATTGTCGATAAGCCA 57.227 29.630 0.02 0.00 0.00 4.75
3989 4685 5.744666 ACCGGTTTCATAAAATCATACGG 57.255 39.130 0.00 0.00 42.88 4.02


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

AutoCloner maintained by Alex Coulton.