Multiple sequence alignment - TraesCS5D01G566500

Loading Multiple Alignment...

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 TraesCS5D01G566500 chr5D 100.000 3424 0 0 1 3424 564836825 564833402 0.000000e+00 6324.0
1 TraesCS5D01G566500 chr4A 90.368 1765 89 30 1 1722 606348445 606346719 0.000000e+00 2242.0
2 TraesCS5D01G566500 chr4A 83.852 675 51 32 1759 2429 606346736 606346116 1.060000e-164 590.0
3 TraesCS5D01G566500 chr4A 84.663 489 26 24 2678 3135 606345927 606345457 3.140000e-120 442.0
4 TraesCS5D01G566500 chr4A 90.833 120 6 1 3201 3315 606345459 606345340 4.580000e-34 156.0
5 TraesCS5D01G566500 chr5B 86.513 1735 109 52 65 1732 708963608 708961932 0.000000e+00 1792.0
6 TraesCS5D01G566500 chr5B 86.041 874 53 33 1751 2584 708961955 708961111 0.000000e+00 874.0
7 TraesCS5D01G566500 chr5B 92.343 431 19 7 2736 3153 708960931 708960502 4.890000e-168 601.0
8 TraesCS5D01G566500 chr5B 84.434 212 22 3 3224 3424 708960461 708960250 7.490000e-47 198.0
9 TraesCS5D01G566500 chr5B 89.333 150 14 2 2 150 530653531 530653383 1.620000e-43 187.0
10 TraesCS5D01G566500 chr5B 85.263 95 4 5 2636 2720 708961021 708960927 4.710000e-14 89.8
11 TraesCS5D01G566500 chr3A 84.553 492 27 24 2675 3135 744091794 744092267 3.140000e-120 442.0
12 TraesCS5D01G566500 chr3A 90.833 120 6 1 3201 3315 744092265 744092384 4.580000e-34 156.0
13 TraesCS5D01G566500 chr6B 88.079 151 15 3 1 150 184635853 184636001 3.510000e-40 176.0
14 TraesCS5D01G566500 chr6B 97.436 39 1 0 2387 2425 702385302 702385340 2.210000e-07 67.6
15 TraesCS5D01G566500 chr4D 88.435 147 16 1 1 146 41907123 41907269 3.510000e-40 176.0
16 TraesCS5D01G566500 chr3D 88.435 147 16 1 1 146 93254504 93254358 3.510000e-40 176.0
17 TraesCS5D01G566500 chr3D 87.013 154 16 4 1 153 354087614 354087464 1.630000e-38 171.0
18 TraesCS5D01G566500 chr2B 87.500 152 17 2 1 151 599602282 599602132 1.260000e-39 174.0
19 TraesCS5D01G566500 chr7B 86.624 157 18 3 1 156 200717281 200717127 1.630000e-38 171.0
20 TraesCS5D01G566500 chr5A 82.270 141 22 1 148 288 12197880 12198017 6.000000e-23 119.0
21 TraesCS5D01G566500 chr5A 82.301 113 16 3 474 583 291792639 291792528 1.010000e-15 95.3
22 TraesCS5D01G566500 chr6D 97.368 38 1 0 2387 2424 460855442 460855479 7.930000e-07 65.8
23 TraesCS5D01G566500 chr6A 94.872 39 2 0 2387 2425 607426974 607427012 1.030000e-05 62.1


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 TraesCS5D01G566500 chr5D 564833402 564836825 3423 True 6324.00 6324 100.0000 1 3424 1 chr5D.!!$R1 3423
1 TraesCS5D01G566500 chr4A 606345340 606348445 3105 True 857.50 2242 87.4290 1 3315 4 chr4A.!!$R1 3314
2 TraesCS5D01G566500 chr5B 708960250 708963608 3358 True 710.96 1792 86.9188 65 3424 5 chr5B.!!$R2 3359
3 TraesCS5D01G566500 chr3A 744091794 744092384 590 False 299.00 442 87.6930 2675 3315 2 chr3A.!!$F1 640

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
958 1019 0.170116 ACAACACAGGCACAACAACG 59.830 50.000 0.0 0.0 0.00 4.10 F
1290 1351 1.997874 CCCCTGGGACCTCAAGGAG 60.998 68.421 16.2 0.0 38.94 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 1873 0.032130 GCATGATGCATGGCAGGAAG 59.968 55.0 13.36 0.0 43.65 3.46 R
3153 3417 0.106918 AGTGTGGAGGCCGAACAAAA 60.107 50.0 9.40 0.0 0.00 2.44 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
140 142 9.000018 GTATGAATGAAATTACAAGCGTTTCTC 58.000 33.333 0.00 0.00 36.07 2.87
143 145 7.918033 TGAATGAAATTACAAGCGTTTCTCAAA 59.082 29.630 0.00 0.00 36.07 2.69
144 146 8.641499 AATGAAATTACAAGCGTTTCTCAAAA 57.359 26.923 0.00 0.00 32.46 2.44
145 147 8.641499 ATGAAATTACAAGCGTTTCTCAAAAA 57.359 26.923 0.00 0.00 33.99 1.94
146 148 7.890763 TGAAATTACAAGCGTTTCTCAAAAAC 58.109 30.769 0.00 0.00 33.99 2.43
284 291 1.541588 GTCTCATTGCAGGTTTGACCC 59.458 52.381 0.00 0.00 39.75 4.46
392 399 3.867600 GCATCCGGTCATTATCTGCTCAT 60.868 47.826 0.00 0.00 0.00 2.90
393 400 4.621510 GCATCCGGTCATTATCTGCTCATA 60.622 45.833 0.00 0.00 0.00 2.15
461 468 1.450025 TCCGATCCGATCCATCTACG 58.550 55.000 2.69 0.00 0.00 3.51
468 475 2.107031 TCCGATCCATCTACGTCCCTTA 59.893 50.000 0.00 0.00 0.00 2.69
469 476 3.090037 CCGATCCATCTACGTCCCTTAT 58.910 50.000 0.00 0.00 0.00 1.73
472 479 2.511659 TCCATCTACGTCCCTTATCGG 58.488 52.381 0.00 0.00 0.00 4.18
506 513 6.952935 AATTTAGTTTGCAAACACGACAAA 57.047 29.167 36.46 26.43 41.30 2.83
511 518 6.952935 AGTTTGCAAACACGACAAATTTTA 57.047 29.167 36.46 0.00 41.30 1.52
540 548 4.853924 AATGAACCAAGACGAATTTGCT 57.146 36.364 0.00 0.00 0.00 3.91
555 563 6.039717 ACGAATTTGCTATGCTCACCAAATAT 59.960 34.615 0.00 0.00 37.02 1.28
593 625 6.154877 TGAAGAACATAATTTGCCATGGTCAT 59.845 34.615 14.67 0.00 40.62 3.06
745 788 2.360165 GGAGTAGAAAGATTCGGGCGTA 59.640 50.000 0.00 0.00 34.02 4.42
746 789 3.005578 GGAGTAGAAAGATTCGGGCGTAT 59.994 47.826 0.00 0.00 34.02 3.06
747 790 3.978687 AGTAGAAAGATTCGGGCGTATG 58.021 45.455 0.00 0.00 34.02 2.39
748 791 1.583054 AGAAAGATTCGGGCGTATGC 58.417 50.000 0.00 0.00 35.90 3.14
749 792 1.134521 AGAAAGATTCGGGCGTATGCA 60.135 47.619 9.59 0.00 37.56 3.96
750 793 1.873591 GAAAGATTCGGGCGTATGCAT 59.126 47.619 9.59 3.79 45.35 3.96
751 794 1.229428 AAGATTCGGGCGTATGCATG 58.771 50.000 10.16 0.00 45.35 4.06
752 795 1.207593 GATTCGGGCGTATGCATGC 59.792 57.895 11.82 11.82 45.35 4.06
777 820 1.368641 TGCATGCATGGAACGTACTC 58.631 50.000 27.34 8.37 0.00 2.59
778 821 0.657840 GCATGCATGGAACGTACTCC 59.342 55.000 27.34 3.43 35.88 3.85
779 822 1.743772 GCATGCATGGAACGTACTCCT 60.744 52.381 27.34 0.00 36.35 3.69
780 823 2.632377 CATGCATGGAACGTACTCCTT 58.368 47.619 19.40 0.00 36.35 3.36
848 904 2.262471 CTACGACGACCAAGTCCCGG 62.262 65.000 0.00 0.00 37.85 5.73
931 992 4.093011 TCTCTCCCTTTCTTCTTCCTCTG 58.907 47.826 0.00 0.00 0.00 3.35
935 996 2.431454 CCTTTCTTCTTCCTCTGGCAC 58.569 52.381 0.00 0.00 0.00 5.01
936 997 2.224621 CCTTTCTTCTTCCTCTGGCACA 60.225 50.000 0.00 0.00 0.00 4.57
951 1012 0.801836 GCACAACACAACACAGGCAC 60.802 55.000 0.00 0.00 0.00 5.01
956 1017 1.252175 ACACAACACAGGCACAACAA 58.748 45.000 0.00 0.00 0.00 2.83
957 1018 1.067915 ACACAACACAGGCACAACAAC 60.068 47.619 0.00 0.00 0.00 3.32
958 1019 0.170116 ACAACACAGGCACAACAACG 59.830 50.000 0.00 0.00 0.00 4.10
1290 1351 1.997874 CCCCTGGGACCTCAAGGAG 60.998 68.421 16.20 0.00 38.94 3.69
1452 1516 2.932614 CGGCGATGACAAGAAGAAGAAT 59.067 45.455 0.00 0.00 0.00 2.40
1470 1540 8.152023 AGAAGAATAACAAGGAGGTGATTAGT 57.848 34.615 0.00 0.00 0.00 2.24
1473 1543 8.567285 AGAATAACAAGGAGGTGATTAGTTTG 57.433 34.615 0.00 0.00 0.00 2.93
1474 1544 8.383175 AGAATAACAAGGAGGTGATTAGTTTGA 58.617 33.333 0.00 0.00 0.00 2.69
1475 1545 9.178758 GAATAACAAGGAGGTGATTAGTTTGAT 57.821 33.333 0.00 0.00 0.00 2.57
1476 1546 6.824305 AACAAGGAGGTGATTAGTTTGATG 57.176 37.500 0.00 0.00 0.00 3.07
1477 1547 6.126863 ACAAGGAGGTGATTAGTTTGATGA 57.873 37.500 0.00 0.00 0.00 2.92
1479 1549 7.177878 ACAAGGAGGTGATTAGTTTGATGATT 58.822 34.615 0.00 0.00 0.00 2.57
1481 1551 9.177608 CAAGGAGGTGATTAGTTTGATGATTAA 57.822 33.333 0.00 0.00 0.00 1.40
1483 1553 8.552296 AGGAGGTGATTAGTTTGATGATTAACT 58.448 33.333 0.00 0.00 38.16 2.24
1484 1554 9.832445 GGAGGTGATTAGTTTGATGATTAACTA 57.168 33.333 0.00 0.00 36.16 2.24
1486 1556 9.331282 AGGTGATTAGTTTGATGATTAACTAGC 57.669 33.333 0.00 0.00 37.92 3.42
1487 1557 9.109393 GGTGATTAGTTTGATGATTAACTAGCA 57.891 33.333 0.00 0.00 37.92 3.49
1492 1562 7.944729 AGTTTGATGATTAACTAGCATTGGT 57.055 32.000 0.00 0.00 33.06 3.67
1494 1564 6.942532 TTGATGATTAACTAGCATTGGTCC 57.057 37.500 0.00 0.00 0.00 4.46
1495 1565 6.252599 TGATGATTAACTAGCATTGGTCCT 57.747 37.500 0.00 0.00 0.00 3.85
1508 1580 7.427989 AGCATTGGTCCTTAATCAATCAAAT 57.572 32.000 0.00 0.00 0.00 2.32
1521 1602 7.510549 AATCAATCAAATGGGATTAGTACGG 57.489 36.000 0.00 0.00 35.79 4.02
1523 1604 6.654959 TCAATCAAATGGGATTAGTACGGAA 58.345 36.000 0.00 0.00 35.79 4.30
1524 1605 7.287061 TCAATCAAATGGGATTAGTACGGAAT 58.713 34.615 0.00 0.00 35.79 3.01
1529 1610 7.663905 TCAAATGGGATTAGTACGGAATTATGG 59.336 37.037 0.00 0.00 0.00 2.74
1530 1611 6.945636 ATGGGATTAGTACGGAATTATGGA 57.054 37.500 0.00 0.00 0.00 3.41
1533 1614 5.585047 GGGATTAGTACGGAATTATGGATGC 59.415 44.000 0.00 0.00 0.00 3.91
1534 1615 6.170506 GGATTAGTACGGAATTATGGATGCA 58.829 40.000 0.00 0.00 0.00 3.96
1535 1616 6.823689 GGATTAGTACGGAATTATGGATGCAT 59.176 38.462 4.68 4.68 0.00 3.96
1585 1666 5.271598 TGTTAACTAATTAGGGTCCGGAGA 58.728 41.667 16.73 0.00 0.00 3.71
1722 1823 4.404073 ACTGACTCTCTCTCTCTCTCTCTC 59.596 50.000 0.00 0.00 0.00 3.20
1723 1824 4.614475 TGACTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
1726 1827 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
1727 1828 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1728 1829 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1729 1830 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1730 1831 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1731 1832 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1732 1833 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1733 1834 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1734 1835 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1735 1836 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1736 1837 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1737 1838 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1738 1839 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1739 1840 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1740 1841 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1741 1842 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1742 1843 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1743 1844 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1744 1845 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1745 1846 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1746 1847 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1747 1848 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1748 1849 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1749 1850 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1750 1851 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1751 1852 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1752 1853 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1753 1854 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1754 1855 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1755 1856 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1756 1857 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1757 1858 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1758 1859 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1759 1860 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1760 1861 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1761 1862 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1762 1863 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1763 1864 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1764 1865 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1765 1866 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1766 1867 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1767 1868 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1768 1869 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1769 1870 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1770 1871 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1771 1872 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1772 1873 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1773 1874 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1774 1875 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
1775 1876 5.596361 TCTCTCTCTCTCTCTCTCTCTCTTC 59.404 48.000 0.00 0.00 0.00 2.87
1776 1877 4.651503 TCTCTCTCTCTCTCTCTCTCTTCC 59.348 50.000 0.00 0.00 0.00 3.46
1777 1878 4.624913 TCTCTCTCTCTCTCTCTCTTCCT 58.375 47.826 0.00 0.00 0.00 3.36
1778 1879 4.406972 TCTCTCTCTCTCTCTCTCTTCCTG 59.593 50.000 0.00 0.00 0.00 3.86
1779 1880 3.118261 TCTCTCTCTCTCTCTCTTCCTGC 60.118 52.174 0.00 0.00 0.00 4.85
1780 1881 2.092429 TCTCTCTCTCTCTCTTCCTGCC 60.092 54.545 0.00 0.00 0.00 4.85
1781 1882 1.638070 TCTCTCTCTCTCTTCCTGCCA 59.362 52.381 0.00 0.00 0.00 4.92
1782 1883 2.244510 TCTCTCTCTCTCTTCCTGCCAT 59.755 50.000 0.00 0.00 0.00 4.40
1783 1884 2.363038 CTCTCTCTCTCTTCCTGCCATG 59.637 54.545 0.00 0.00 0.00 3.66
1784 1885 0.829333 TCTCTCTCTTCCTGCCATGC 59.171 55.000 0.00 0.00 0.00 4.06
1785 1886 0.540454 CTCTCTCTTCCTGCCATGCA 59.460 55.000 0.00 0.00 36.92 3.96
1786 1887 1.141254 CTCTCTCTTCCTGCCATGCAT 59.859 52.381 0.00 0.00 38.13 3.96
1901 2024 4.065423 TCGAAATGATTGACGTTCTTGC 57.935 40.909 0.00 0.00 0.00 4.01
1904 2027 2.198827 ATGATTGACGTTCTTGCCCA 57.801 45.000 0.00 0.00 0.00 5.36
1917 2040 3.845259 GCCCATGGGTGCTGCATG 61.845 66.667 31.58 3.44 37.65 4.06
1918 2041 2.043752 CCCATGGGTGCTGCATGA 60.044 61.111 23.93 0.00 0.00 3.07
1919 2042 1.683025 CCCATGGGTGCTGCATGAA 60.683 57.895 23.93 0.00 0.00 2.57
2078 2203 1.247567 CAACGGCCAAGAACAAGGAT 58.752 50.000 2.24 0.00 0.00 3.24
2084 2209 1.508088 CAAGAACAAGGATGGCGGC 59.492 57.895 0.00 0.00 0.00 6.53
2085 2210 2.040544 AAGAACAAGGATGGCGGCG 61.041 57.895 0.51 0.51 0.00 6.46
2086 2211 2.435938 GAACAAGGATGGCGGCGA 60.436 61.111 12.98 0.00 0.00 5.54
2087 2212 2.746277 AACAAGGATGGCGGCGAC 60.746 61.111 12.98 9.31 0.00 5.19
2088 2213 3.545124 AACAAGGATGGCGGCGACA 62.545 57.895 21.84 21.84 0.00 4.35
2089 2214 2.745884 CAAGGATGGCGGCGACAA 60.746 61.111 23.82 2.64 0.00 3.18
2090 2215 2.436646 AAGGATGGCGGCGACAAG 60.437 61.111 23.82 0.00 0.00 3.16
2091 2216 2.954684 AAGGATGGCGGCGACAAGA 61.955 57.895 23.82 0.00 0.00 3.02
2092 2217 2.435938 GGATGGCGGCGACAAGAA 60.436 61.111 23.82 0.00 0.00 2.52
2093 2218 2.464459 GGATGGCGGCGACAAGAAG 61.464 63.158 23.82 0.00 0.00 2.85
2094 2219 1.447838 GATGGCGGCGACAAGAAGA 60.448 57.895 23.82 0.00 0.00 2.87
2095 2220 1.003839 ATGGCGGCGACAAGAAGAA 60.004 52.632 23.82 0.00 0.00 2.52
2096 2221 1.021390 ATGGCGGCGACAAGAAGAAG 61.021 55.000 23.82 0.00 0.00 2.85
2097 2222 2.476499 GCGGCGACAAGAAGAAGC 59.524 61.111 12.98 0.00 0.00 3.86
2098 2223 2.317609 GCGGCGACAAGAAGAAGCA 61.318 57.895 12.98 0.00 0.00 3.91
2099 2224 1.784062 CGGCGACAAGAAGAAGCAG 59.216 57.895 0.00 0.00 0.00 4.24
2100 2225 1.499502 GGCGACAAGAAGAAGCAGC 59.500 57.895 0.00 0.00 0.00 5.25
2101 2226 1.230635 GGCGACAAGAAGAAGCAGCA 61.231 55.000 0.00 0.00 0.00 4.41
2102 2227 0.165511 GCGACAAGAAGAAGCAGCAG 59.834 55.000 0.00 0.00 0.00 4.24
2103 2228 1.788258 CGACAAGAAGAAGCAGCAGA 58.212 50.000 0.00 0.00 0.00 4.26
2104 2229 2.138320 CGACAAGAAGAAGCAGCAGAA 58.862 47.619 0.00 0.00 0.00 3.02
2105 2230 2.157279 CGACAAGAAGAAGCAGCAGAAG 59.843 50.000 0.00 0.00 0.00 2.85
2106 2231 2.483491 GACAAGAAGAAGCAGCAGAAGG 59.517 50.000 0.00 0.00 0.00 3.46
2107 2232 2.105477 ACAAGAAGAAGCAGCAGAAGGA 59.895 45.455 0.00 0.00 0.00 3.36
2108 2233 2.470983 AGAAGAAGCAGCAGAAGGAC 57.529 50.000 0.00 0.00 0.00 3.85
2109 2234 1.696336 AGAAGAAGCAGCAGAAGGACA 59.304 47.619 0.00 0.00 0.00 4.02
2110 2235 2.075338 GAAGAAGCAGCAGAAGGACAG 58.925 52.381 0.00 0.00 0.00 3.51
2111 2236 0.321475 AGAAGCAGCAGAAGGACAGC 60.321 55.000 0.00 0.00 0.00 4.40
2112 2237 1.633852 GAAGCAGCAGAAGGACAGCG 61.634 60.000 0.00 0.00 36.14 5.18
2113 2238 3.123620 GCAGCAGAAGGACAGCGG 61.124 66.667 0.00 0.00 36.14 5.52
2139 2267 1.696336 AGAAGAAGCAGCAGAAGGACA 59.304 47.619 0.00 0.00 0.00 4.02
2209 2349 1.532868 CGGTGGCAAGAAGAAGAACAG 59.467 52.381 0.00 0.00 0.00 3.16
2390 2536 3.121030 GCGCCGCAGATGTTCAGT 61.121 61.111 3.15 0.00 0.00 3.41
2424 2570 3.190849 CCTGCGCCGTCATGTGAG 61.191 66.667 4.18 0.00 0.00 3.51
2426 2572 3.647649 CTGCGCCGTCATGTGAGGA 62.648 63.158 4.18 0.00 32.08 3.71
2427 2573 2.434185 GCGCCGTCATGTGAGGAA 60.434 61.111 0.00 0.00 32.08 3.36
2429 2575 1.970917 GCGCCGTCATGTGAGGAAAG 61.971 60.000 0.00 0.00 32.08 2.62
2471 2637 3.668100 CACTCGTACTTAGTCGTAGTGC 58.332 50.000 15.28 0.00 33.06 4.40
2507 2679 7.504403 AGTAGCTAAGCCATGCCTATATATTG 58.496 38.462 0.00 0.00 0.00 1.90
2524 2697 1.624336 TTGCTACGTACTGGTGGACT 58.376 50.000 0.00 0.00 0.00 3.85
2526 2699 1.171308 GCTACGTACTGGTGGACTGA 58.829 55.000 0.00 0.00 0.00 3.41
2529 2702 1.215647 CGTACTGGTGGACTGAGCC 59.784 63.158 0.00 0.00 0.00 4.70
2530 2703 1.597461 GTACTGGTGGACTGAGCCC 59.403 63.158 0.00 0.00 0.00 5.19
2531 2704 1.982395 TACTGGTGGACTGAGCCCG 60.982 63.158 0.00 0.00 0.00 6.13
2532 2705 4.767255 CTGGTGGACTGAGCCCGC 62.767 72.222 0.00 0.00 0.00 6.13
2605 2778 3.992427 ACTTTAGTAGCCAAAGTACGTGC 59.008 43.478 0.00 0.00 42.83 5.34
2607 2780 2.762535 AGTAGCCAAAGTACGTGCAT 57.237 45.000 6.38 0.00 0.00 3.96
2608 2781 2.346803 AGTAGCCAAAGTACGTGCATG 58.653 47.619 6.38 3.82 0.00 4.06
2609 2782 1.396996 GTAGCCAAAGTACGTGCATGG 59.603 52.381 19.45 19.45 0.00 3.66
2610 2783 0.250727 AGCCAAAGTACGTGCATGGT 60.251 50.000 22.71 4.68 33.63 3.55
2611 2784 0.596082 GCCAAAGTACGTGCATGGTT 59.404 50.000 22.71 0.00 33.63 3.67
2613 2786 2.226912 GCCAAAGTACGTGCATGGTTAA 59.773 45.455 22.71 0.00 33.63 2.01
2614 2787 3.817238 CCAAAGTACGTGCATGGTTAAC 58.183 45.455 16.72 0.00 0.00 2.01
2615 2788 3.475242 CAAAGTACGTGCATGGTTAACG 58.525 45.455 11.36 0.00 42.82 3.18
2616 2789 1.717194 AGTACGTGCATGGTTAACGG 58.283 50.000 11.36 0.00 41.50 4.44
2617 2790 0.095762 GTACGTGCATGGTTAACGGC 59.904 55.000 11.36 4.19 41.50 5.68
2618 2791 0.037139 TACGTGCATGGTTAACGGCT 60.037 50.000 11.36 0.00 41.50 5.52
2619 2792 1.134487 CGTGCATGGTTAACGGCTG 59.866 57.895 14.10 0.00 33.77 4.85
2621 2794 1.303236 TGCATGGTTAACGGCTGCT 60.303 52.632 19.73 0.00 34.02 4.24
2622 2795 1.137404 GCATGGTTAACGGCTGCTG 59.863 57.895 6.98 6.98 0.00 4.41
2626 2799 1.081442 GGTTAACGGCTGCTGTTGC 60.081 57.895 31.41 23.45 34.54 4.17
2649 2860 7.140705 TGCATTGCAGCATATGTATAAGTTTC 58.859 34.615 7.38 1.83 40.11 2.78
2676 2889 3.502211 GGTTGGTGACACGATTCATTTCT 59.498 43.478 0.00 0.00 42.67 2.52
2785 3015 3.718480 GCCGTACGTACGTCCGGTC 62.718 68.421 40.12 31.17 46.99 4.79
2818 3056 0.107508 TGCAGGTAGAGATTGGCAGC 60.108 55.000 0.00 0.00 0.00 5.25
2859 3105 4.996434 GGGCAGACGCACAGCAGT 62.996 66.667 0.00 0.00 43.03 4.40
2912 3158 1.300233 GCCACAGATCGATCGACCC 60.300 63.158 22.06 15.21 0.00 4.46
2940 3191 0.179148 CGATCGACGTCCATCCAACA 60.179 55.000 16.17 0.00 37.22 3.33
2942 3193 0.606096 ATCGACGTCCATCCAACACA 59.394 50.000 10.58 0.00 0.00 3.72
3072 3327 1.299541 CATCCCGTTCATTTCCCTCG 58.700 55.000 0.00 0.00 0.00 4.63
3073 3328 0.180406 ATCCCGTTCATTTCCCTCGG 59.820 55.000 0.00 0.00 40.72 4.63
3132 3396 0.803380 CATGACGACGAGCATGCAGA 60.803 55.000 21.98 0.00 35.93 4.26
3133 3397 0.108662 ATGACGACGAGCATGCAGAA 60.109 50.000 21.98 0.00 0.00 3.02
3134 3398 1.008875 TGACGACGAGCATGCAGAAC 61.009 55.000 21.98 11.56 0.00 3.01
3135 3399 2.002963 GACGACGAGCATGCAGAACG 62.003 60.000 21.98 22.25 0.00 3.95
3136 3400 2.792290 CGACGAGCATGCAGAACGG 61.792 63.158 21.98 4.36 0.00 4.44
3137 3401 3.088500 GACGAGCATGCAGAACGGC 62.089 63.158 21.98 17.38 0.00 5.68
3152 3416 2.736995 GGCAGACGCACGCACTAA 60.737 61.111 0.00 0.00 41.24 2.24
3153 3417 2.100631 GGCAGACGCACGCACTAAT 61.101 57.895 0.00 0.00 41.24 1.73
3154 3418 1.635663 GGCAGACGCACGCACTAATT 61.636 55.000 0.00 0.00 41.24 1.40
3155 3419 0.165944 GCAGACGCACGCACTAATTT 59.834 50.000 0.00 0.00 38.36 1.82
3156 3420 1.399727 GCAGACGCACGCACTAATTTT 60.400 47.619 0.00 0.00 38.36 1.82
3157 3421 2.233355 CAGACGCACGCACTAATTTTG 58.767 47.619 0.00 0.00 0.00 2.44
3158 3422 1.871039 AGACGCACGCACTAATTTTGT 59.129 42.857 0.00 0.00 0.00 2.83
3159 3423 2.289547 AGACGCACGCACTAATTTTGTT 59.710 40.909 0.00 0.00 0.00 2.83
3160 3424 2.646250 ACGCACGCACTAATTTTGTTC 58.354 42.857 0.00 0.00 0.00 3.18
3161 3425 1.637086 CGCACGCACTAATTTTGTTCG 59.363 47.619 2.14 2.14 0.00 3.95
3162 3426 1.976045 GCACGCACTAATTTTGTTCGG 59.024 47.619 7.71 0.00 0.00 4.30
3163 3427 1.976045 CACGCACTAATTTTGTTCGGC 59.024 47.619 7.71 0.00 0.00 5.54
3164 3428 1.068816 ACGCACTAATTTTGTTCGGCC 60.069 47.619 7.71 0.00 0.00 6.13
3165 3429 1.199097 CGCACTAATTTTGTTCGGCCT 59.801 47.619 0.00 0.00 0.00 5.19
3166 3430 2.727916 CGCACTAATTTTGTTCGGCCTC 60.728 50.000 0.00 0.00 0.00 4.70
3167 3431 2.415491 GCACTAATTTTGTTCGGCCTCC 60.415 50.000 0.00 0.00 0.00 4.30
3168 3432 2.817258 CACTAATTTTGTTCGGCCTCCA 59.183 45.455 0.00 0.00 0.00 3.86
3169 3433 2.817844 ACTAATTTTGTTCGGCCTCCAC 59.182 45.455 0.00 0.00 0.00 4.02
3170 3434 1.698506 AATTTTGTTCGGCCTCCACA 58.301 45.000 0.00 0.00 0.00 4.17
3171 3435 0.958822 ATTTTGTTCGGCCTCCACAC 59.041 50.000 0.00 0.00 0.00 3.82
3172 3436 0.106918 TTTTGTTCGGCCTCCACACT 60.107 50.000 0.00 0.00 0.00 3.55
3173 3437 0.106918 TTTGTTCGGCCTCCACACTT 60.107 50.000 0.00 0.00 0.00 3.16
3174 3438 0.817634 TTGTTCGGCCTCCACACTTG 60.818 55.000 0.00 0.00 0.00 3.16
3175 3439 2.281484 TTCGGCCTCCACACTTGC 60.281 61.111 0.00 0.00 0.00 4.01
3176 3440 3.842925 TTCGGCCTCCACACTTGCC 62.843 63.158 0.00 0.00 40.54 4.52
3177 3441 4.335647 CGGCCTCCACACTTGCCT 62.336 66.667 0.00 0.00 41.80 4.75
3178 3442 2.674380 GGCCTCCACACTTGCCTG 60.674 66.667 0.00 0.00 40.77 4.85
3179 3443 2.113986 GCCTCCACACTTGCCTGT 59.886 61.111 0.00 0.00 0.00 4.00
3180 3444 1.529244 GCCTCCACACTTGCCTGTT 60.529 57.895 0.00 0.00 0.00 3.16
3181 3445 1.109323 GCCTCCACACTTGCCTGTTT 61.109 55.000 0.00 0.00 0.00 2.83
3182 3446 1.402787 CCTCCACACTTGCCTGTTTT 58.597 50.000 0.00 0.00 0.00 2.43
3183 3447 1.338020 CCTCCACACTTGCCTGTTTTC 59.662 52.381 0.00 0.00 0.00 2.29
3184 3448 2.301346 CTCCACACTTGCCTGTTTTCT 58.699 47.619 0.00 0.00 0.00 2.52
3185 3449 2.689983 CTCCACACTTGCCTGTTTTCTT 59.310 45.455 0.00 0.00 0.00 2.52
3186 3450 3.096092 TCCACACTTGCCTGTTTTCTTT 58.904 40.909 0.00 0.00 0.00 2.52
3187 3451 3.513515 TCCACACTTGCCTGTTTTCTTTT 59.486 39.130 0.00 0.00 0.00 2.27
3188 3452 4.020662 TCCACACTTGCCTGTTTTCTTTTT 60.021 37.500 0.00 0.00 0.00 1.94
3189 3453 5.186021 TCCACACTTGCCTGTTTTCTTTTTA 59.814 36.000 0.00 0.00 0.00 1.52
3190 3454 5.872070 CCACACTTGCCTGTTTTCTTTTTAA 59.128 36.000 0.00 0.00 0.00 1.52
3191 3455 6.538381 CCACACTTGCCTGTTTTCTTTTTAAT 59.462 34.615 0.00 0.00 0.00 1.40
3192 3456 7.065683 CCACACTTGCCTGTTTTCTTTTTAATT 59.934 33.333 0.00 0.00 0.00 1.40
3193 3457 8.450180 CACACTTGCCTGTTTTCTTTTTAATTT 58.550 29.630 0.00 0.00 0.00 1.82
3194 3458 9.660180 ACACTTGCCTGTTTTCTTTTTAATTTA 57.340 25.926 0.00 0.00 0.00 1.40
3234 3538 1.039785 TGGAGGTCTCTCGGAGCATG 61.040 60.000 0.00 0.00 44.16 4.06
3267 3576 1.017177 TCGTATCTGCACCAAACGCC 61.017 55.000 0.00 0.00 33.75 5.68
3318 3638 3.680786 GGCAAACCCAGCCCGAAC 61.681 66.667 0.00 0.00 46.50 3.95
3326 3646 2.125673 CAGCCCGAACGTCCGAAT 60.126 61.111 0.00 0.00 0.00 3.34
3327 3647 2.165301 CAGCCCGAACGTCCGAATC 61.165 63.158 0.00 0.00 0.00 2.52
3342 3662 1.606994 CGAATCGACCAACAACCCTCA 60.607 52.381 0.00 0.00 0.00 3.86
3357 3677 4.487282 ACCCTCATACTCAGCCCTTATA 57.513 45.455 0.00 0.00 0.00 0.98
3362 3682 5.152623 TCATACTCAGCCCTTATATGCAC 57.847 43.478 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 117 8.726068 TGAGAAACGCTTGTAATTTCATTCATA 58.274 29.630 0.00 0.00 35.26 2.15
122 124 7.890763 TGTTTTTGAGAAACGCTTGTAATTTC 58.109 30.769 0.00 0.00 33.05 2.17
167 174 4.882671 AGTGTTTGAAGTCATGACACAC 57.117 40.909 26.86 26.86 41.58 3.82
297 304 2.059541 GACTCGGACTGGAAACGAAAG 58.940 52.381 0.00 0.00 36.08 2.62
468 475 4.473444 ACTAAATTTGCCATCATCCCGAT 58.527 39.130 0.00 0.00 33.27 4.18
469 476 3.897239 ACTAAATTTGCCATCATCCCGA 58.103 40.909 0.00 0.00 0.00 5.14
516 523 6.048509 AGCAAATTCGTCTTGGTTCATTTTT 58.951 32.000 0.00 0.00 30.56 1.94
526 534 4.337763 GTGAGCATAGCAAATTCGTCTTG 58.662 43.478 0.00 0.00 0.00 3.02
540 548 7.661437 GGATGTCAAGTATATTTGGTGAGCATA 59.339 37.037 7.99 0.00 0.00 3.14
555 563 9.739276 AATTATGTTCTTCAAGGATGTCAAGTA 57.261 29.630 0.00 0.00 0.00 2.24
593 625 6.209192 TCCACTACAAATCTGACGTAGGTTTA 59.791 38.462 12.60 0.00 37.63 2.01
777 820 4.192317 GCTTCTCCTGTACATTACCAAGG 58.808 47.826 0.00 0.00 0.00 3.61
778 821 3.865745 CGCTTCTCCTGTACATTACCAAG 59.134 47.826 0.00 0.00 0.00 3.61
779 822 3.369052 CCGCTTCTCCTGTACATTACCAA 60.369 47.826 0.00 0.00 0.00 3.67
780 823 2.167693 CCGCTTCTCCTGTACATTACCA 59.832 50.000 0.00 0.00 0.00 3.25
848 904 1.002544 AGGGCGCATAAATAGGAGCTC 59.997 52.381 10.83 4.71 33.45 4.09
931 992 1.226945 GCCTGTGTTGTGTTGTGCC 60.227 57.895 0.00 0.00 0.00 5.01
935 996 1.067985 TGTTGTGCCTGTGTTGTGTTG 60.068 47.619 0.00 0.00 0.00 3.33
936 997 1.252175 TGTTGTGCCTGTGTTGTGTT 58.748 45.000 0.00 0.00 0.00 3.32
951 1012 1.842720 TGTACTCGTGGTCGTTGTTG 58.157 50.000 0.00 0.00 38.33 3.33
956 1017 1.404391 GATGGATGTACTCGTGGTCGT 59.596 52.381 0.00 0.00 38.33 4.34
957 1018 1.676529 AGATGGATGTACTCGTGGTCG 59.323 52.381 0.00 0.00 38.55 4.79
958 1019 2.287069 CGAGATGGATGTACTCGTGGTC 60.287 54.545 0.00 0.00 45.23 4.02
1056 1117 1.674651 GTTTGCCCTCTCGTTCCCC 60.675 63.158 0.00 0.00 0.00 4.81
1266 1327 3.899545 GAGGTCCCAGGGGTCGACA 62.900 68.421 18.91 0.00 36.47 4.35
1452 1516 7.685481 TCATCAAACTAATCACCTCCTTGTTA 58.315 34.615 0.00 0.00 0.00 2.41
1470 1540 7.118723 AGGACCAATGCTAGTTAATCATCAAA 58.881 34.615 0.00 0.00 0.00 2.69
1473 1543 8.677148 TTAAGGACCAATGCTAGTTAATCATC 57.323 34.615 0.00 0.00 0.00 2.92
1474 1544 9.289782 GATTAAGGACCAATGCTAGTTAATCAT 57.710 33.333 11.12 0.00 36.27 2.45
1475 1545 8.271458 TGATTAAGGACCAATGCTAGTTAATCA 58.729 33.333 13.32 13.32 40.49 2.57
1476 1546 8.677148 TGATTAAGGACCAATGCTAGTTAATC 57.323 34.615 9.85 9.85 36.55 1.75
1477 1547 9.646522 ATTGATTAAGGACCAATGCTAGTTAAT 57.353 29.630 0.00 0.00 0.00 1.40
1479 1549 8.271458 TGATTGATTAAGGACCAATGCTAGTTA 58.729 33.333 0.00 0.00 31.40 2.24
1481 1551 6.662755 TGATTGATTAAGGACCAATGCTAGT 58.337 36.000 0.00 0.00 31.40 2.57
1483 1553 7.953005 TTTGATTGATTAAGGACCAATGCTA 57.047 32.000 0.00 0.00 31.40 3.49
1484 1554 6.855763 TTTGATTGATTAAGGACCAATGCT 57.144 33.333 0.00 0.00 31.40 3.79
1485 1555 6.480981 CCATTTGATTGATTAAGGACCAATGC 59.519 38.462 0.00 0.00 31.40 3.56
1486 1556 6.987992 CCCATTTGATTGATTAAGGACCAATG 59.012 38.462 0.00 0.00 31.40 2.82
1487 1557 6.902416 TCCCATTTGATTGATTAAGGACCAAT 59.098 34.615 0.00 0.00 33.66 3.16
1488 1558 6.259893 TCCCATTTGATTGATTAAGGACCAA 58.740 36.000 0.00 0.00 0.00 3.67
1489 1559 5.836705 TCCCATTTGATTGATTAAGGACCA 58.163 37.500 0.00 0.00 0.00 4.02
1490 1560 6.983906 ATCCCATTTGATTGATTAAGGACC 57.016 37.500 0.00 0.00 0.00 4.46
1495 1565 9.062524 CCGTACTAATCCCATTTGATTGATTAA 57.937 33.333 0.00 0.00 35.77 1.40
1508 1580 6.707290 CATCCATAATTCCGTACTAATCCCA 58.293 40.000 0.00 0.00 0.00 4.37
1519 1600 5.231265 CATCAGATGCATCCATAATTCCG 57.769 43.478 23.06 0.00 0.00 4.30
1533 1614 5.306394 ACTAATCACCATCAGCATCAGATG 58.694 41.667 5.98 5.98 41.91 2.90
1534 1615 5.563876 ACTAATCACCATCAGCATCAGAT 57.436 39.130 0.00 0.00 0.00 2.90
1535 1616 5.363562 AACTAATCACCATCAGCATCAGA 57.636 39.130 0.00 0.00 0.00 3.27
1585 1666 1.469335 ATCTTCACCACCACCGTCGT 61.469 55.000 0.00 0.00 0.00 4.34
1722 1823 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1723 1824 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1726 1827 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1727 1828 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1728 1829 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1729 1830 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1730 1831 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1731 1832 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1732 1833 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1733 1834 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1734 1835 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1735 1836 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1736 1837 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1737 1838 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1738 1839 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1739 1840 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1740 1841 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1741 1842 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1742 1843 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1743 1844 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1744 1845 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1745 1846 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1746 1847 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1747 1848 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1748 1849 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1749 1850 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1750 1851 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1751 1852 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1752 1853 5.221422 GGAAGAGAGAGAGAGAGAGAGAGAG 60.221 52.000 0.00 0.00 0.00 3.20
1753 1854 4.651503 GGAAGAGAGAGAGAGAGAGAGAGA 59.348 50.000 0.00 0.00 0.00 3.10
1754 1855 4.653341 AGGAAGAGAGAGAGAGAGAGAGAG 59.347 50.000 0.00 0.00 0.00 3.20
1755 1856 4.406972 CAGGAAGAGAGAGAGAGAGAGAGA 59.593 50.000 0.00 0.00 0.00 3.10
1756 1857 4.701765 CAGGAAGAGAGAGAGAGAGAGAG 58.298 52.174 0.00 0.00 0.00 3.20
1757 1858 3.118261 GCAGGAAGAGAGAGAGAGAGAGA 60.118 52.174 0.00 0.00 0.00 3.10
1758 1859 3.209410 GCAGGAAGAGAGAGAGAGAGAG 58.791 54.545 0.00 0.00 0.00 3.20
1759 1860 2.092429 GGCAGGAAGAGAGAGAGAGAGA 60.092 54.545 0.00 0.00 0.00 3.10
1760 1861 2.301346 GGCAGGAAGAGAGAGAGAGAG 58.699 57.143 0.00 0.00 0.00 3.20
1761 1862 1.638070 TGGCAGGAAGAGAGAGAGAGA 59.362 52.381 0.00 0.00 0.00 3.10
1762 1863 2.142356 TGGCAGGAAGAGAGAGAGAG 57.858 55.000 0.00 0.00 0.00 3.20
1763 1864 2.386779 CATGGCAGGAAGAGAGAGAGA 58.613 52.381 0.00 0.00 0.00 3.10
1764 1865 1.202557 GCATGGCAGGAAGAGAGAGAG 60.203 57.143 1.99 0.00 0.00 3.20
1765 1866 0.829333 GCATGGCAGGAAGAGAGAGA 59.171 55.000 1.99 0.00 0.00 3.10
1766 1867 0.540454 TGCATGGCAGGAAGAGAGAG 59.460 55.000 1.99 0.00 33.32 3.20
1767 1868 1.140452 GATGCATGGCAGGAAGAGAGA 59.860 52.381 2.46 0.00 43.65 3.10
1768 1869 1.134189 TGATGCATGGCAGGAAGAGAG 60.134 52.381 2.46 0.00 43.65 3.20
1769 1870 0.913924 TGATGCATGGCAGGAAGAGA 59.086 50.000 2.46 0.00 43.65 3.10
1770 1871 1.609072 CATGATGCATGGCAGGAAGAG 59.391 52.381 2.46 0.00 43.65 2.85
1771 1872 1.687563 CATGATGCATGGCAGGAAGA 58.312 50.000 2.46 0.00 43.65 2.87
1772 1873 0.032130 GCATGATGCATGGCAGGAAG 59.968 55.000 13.36 0.00 43.65 3.46
1773 1874 2.120765 GCATGATGCATGGCAGGAA 58.879 52.632 13.36 0.00 43.65 3.36
1774 1875 3.850508 GCATGATGCATGGCAGGA 58.149 55.556 13.36 0.00 43.65 3.86
1812 1913 5.582269 CGACAACTCCATGAATGAATGTACT 59.418 40.000 0.00 0.00 0.00 2.73
1813 1914 5.351465 ACGACAACTCCATGAATGAATGTAC 59.649 40.000 0.00 0.00 0.00 2.90
1814 1915 5.351189 CACGACAACTCCATGAATGAATGTA 59.649 40.000 0.00 0.00 0.00 2.29
1855 1967 2.620112 GCGACAGCCATGCAGTGTT 61.620 57.895 0.00 0.00 37.42 3.32
1877 2000 5.225949 GCAAGAACGTCAATCATTTCGATTC 59.774 40.000 0.00 1.13 42.70 2.52
1894 2017 1.607467 AGCACCCATGGGCAAGAAC 60.607 57.895 31.73 13.44 39.32 3.01
1895 2018 1.607178 CAGCACCCATGGGCAAGAA 60.607 57.895 31.73 0.00 39.32 2.52
1896 2019 2.036098 CAGCACCCATGGGCAAGA 59.964 61.111 31.73 0.00 39.32 3.02
1897 2020 3.766691 GCAGCACCCATGGGCAAG 61.767 66.667 31.73 21.22 39.32 4.01
1901 2024 1.046472 ATTCATGCAGCACCCATGGG 61.046 55.000 30.23 30.23 40.29 4.00
1930 2055 0.671781 CTTCACCTCCTTCACGCCTG 60.672 60.000 0.00 0.00 0.00 4.85
2061 2186 0.609131 CCATCCTTGTTCTTGGCCGT 60.609 55.000 0.00 0.00 0.00 5.68
2078 2203 1.667830 CTTCTTCTTGTCGCCGCCA 60.668 57.895 0.00 0.00 0.00 5.69
2084 2209 1.788258 TCTGCTGCTTCTTCTTGTCG 58.212 50.000 0.00 0.00 0.00 4.35
2085 2210 2.483491 CCTTCTGCTGCTTCTTCTTGTC 59.517 50.000 0.00 0.00 0.00 3.18
2086 2211 2.105477 TCCTTCTGCTGCTTCTTCTTGT 59.895 45.455 0.00 0.00 0.00 3.16
2087 2212 2.483491 GTCCTTCTGCTGCTTCTTCTTG 59.517 50.000 0.00 0.00 0.00 3.02
2088 2213 2.105477 TGTCCTTCTGCTGCTTCTTCTT 59.895 45.455 0.00 0.00 0.00 2.52
2089 2214 1.696336 TGTCCTTCTGCTGCTTCTTCT 59.304 47.619 0.00 0.00 0.00 2.85
2090 2215 2.075338 CTGTCCTTCTGCTGCTTCTTC 58.925 52.381 0.00 0.00 0.00 2.87
2091 2216 1.881498 GCTGTCCTTCTGCTGCTTCTT 60.881 52.381 0.00 0.00 37.88 2.52
2092 2217 0.321475 GCTGTCCTTCTGCTGCTTCT 60.321 55.000 0.00 0.00 37.88 2.85
2093 2218 1.633852 CGCTGTCCTTCTGCTGCTTC 61.634 60.000 0.00 0.00 38.56 3.86
2094 2219 1.670406 CGCTGTCCTTCTGCTGCTT 60.670 57.895 0.00 0.00 38.56 3.91
2095 2220 2.047465 CGCTGTCCTTCTGCTGCT 60.047 61.111 0.00 0.00 38.56 4.24
2096 2221 3.123620 CCGCTGTCCTTCTGCTGC 61.124 66.667 0.00 0.00 38.56 5.25
2097 2222 3.123620 GCCGCTGTCCTTCTGCTG 61.124 66.667 0.00 0.00 38.56 4.41
2098 2223 4.749310 CGCCGCTGTCCTTCTGCT 62.749 66.667 0.00 0.00 38.56 4.24
2099 2224 4.742201 TCGCCGCTGTCCTTCTGC 62.742 66.667 0.00 0.00 37.59 4.26
2100 2225 2.811317 GTCGCCGCTGTCCTTCTG 60.811 66.667 0.00 0.00 0.00 3.02
2101 2226 2.771763 CTTGTCGCCGCTGTCCTTCT 62.772 60.000 0.00 0.00 0.00 2.85
2102 2227 2.357034 TTGTCGCCGCTGTCCTTC 60.357 61.111 0.00 0.00 0.00 3.46
2103 2228 2.357517 CTTGTCGCCGCTGTCCTT 60.358 61.111 0.00 0.00 0.00 3.36
2104 2229 2.771763 CTTCTTGTCGCCGCTGTCCT 62.772 60.000 0.00 0.00 0.00 3.85
2105 2230 2.357034 TTCTTGTCGCCGCTGTCC 60.357 61.111 0.00 0.00 0.00 4.02
2106 2231 0.944311 TTCTTCTTGTCGCCGCTGTC 60.944 55.000 0.00 0.00 0.00 3.51
2107 2232 0.946221 CTTCTTCTTGTCGCCGCTGT 60.946 55.000 0.00 0.00 0.00 4.40
2108 2233 1.784062 CTTCTTCTTGTCGCCGCTG 59.216 57.895 0.00 0.00 0.00 5.18
2109 2234 2.029844 GCTTCTTCTTGTCGCCGCT 61.030 57.895 0.00 0.00 0.00 5.52
2110 2235 2.233007 CTGCTTCTTCTTGTCGCCGC 62.233 60.000 0.00 0.00 0.00 6.53
2111 2236 1.784062 CTGCTTCTTCTTGTCGCCG 59.216 57.895 0.00 0.00 0.00 6.46
2112 2237 1.230635 TGCTGCTTCTTCTTGTCGCC 61.231 55.000 0.00 0.00 0.00 5.54
2113 2238 0.165511 CTGCTGCTTCTTCTTGTCGC 59.834 55.000 0.00 0.00 0.00 5.19
2209 2349 1.882623 CCTCCTGCTTGTTCTTGTTCC 59.117 52.381 0.00 0.00 0.00 3.62
2382 2528 1.002087 GGGGTTCTCGTCACTGAACAT 59.998 52.381 11.13 0.00 42.91 2.71
2390 2536 2.029964 GCGTTGGGGTTCTCGTCA 59.970 61.111 0.00 0.00 0.00 4.35
2424 2570 2.420022 ACTAACGCACATGCATCTTTCC 59.580 45.455 0.00 0.00 42.21 3.13
2426 2572 2.162208 CCACTAACGCACATGCATCTTT 59.838 45.455 0.00 0.00 42.21 2.52
2427 2573 1.739466 CCACTAACGCACATGCATCTT 59.261 47.619 0.00 0.00 42.21 2.40
2429 2575 1.086696 ACCACTAACGCACATGCATC 58.913 50.000 0.00 0.00 42.21 3.91
2452 2611 4.564372 TGTAGCACTACGACTAAGTACGAG 59.436 45.833 3.52 0.00 38.85 4.18
2488 2654 6.127168 ACGTAGCAATATATAGGCATGGCTTA 60.127 38.462 28.30 18.26 0.00 3.09
2493 2665 6.697455 CCAGTACGTAGCAATATATAGGCATG 59.303 42.308 0.00 0.00 0.00 4.06
2507 2679 1.132643 CTCAGTCCACCAGTACGTAGC 59.867 57.143 0.00 0.00 0.00 3.58
2586 2759 3.663995 TGCACGTACTTTGGCTACTAA 57.336 42.857 0.00 0.00 0.00 2.24
2588 2761 2.346803 CATGCACGTACTTTGGCTACT 58.653 47.619 0.00 0.00 0.00 2.57
2590 2763 1.002659 ACCATGCACGTACTTTGGCTA 59.997 47.619 7.89 0.00 0.00 3.93
2593 2766 3.665848 CGTTAACCATGCACGTACTTTGG 60.666 47.826 0.00 6.75 0.00 3.28
2594 2767 3.475242 CGTTAACCATGCACGTACTTTG 58.525 45.455 0.00 0.00 0.00 2.77
2595 2768 2.481185 CCGTTAACCATGCACGTACTTT 59.519 45.455 0.00 0.00 31.83 2.66
2597 2770 1.717194 CCGTTAACCATGCACGTACT 58.283 50.000 0.00 0.00 31.83 2.73
2601 2774 1.134487 CAGCCGTTAACCATGCACG 59.866 57.895 10.81 0.00 0.00 5.34
2603 2776 1.303236 AGCAGCCGTTAACCATGCA 60.303 52.632 20.18 0.00 39.34 3.96
2604 2777 1.137404 CAGCAGCCGTTAACCATGC 59.863 57.895 13.62 13.62 37.15 4.06
2605 2778 0.881118 AACAGCAGCCGTTAACCATG 59.119 50.000 0.00 0.00 0.00 3.66
2607 2780 1.791103 GCAACAGCAGCCGTTAACCA 61.791 55.000 0.00 0.00 0.00 3.67
2608 2781 1.081442 GCAACAGCAGCCGTTAACC 60.081 57.895 0.00 0.00 0.00 2.85
2609 2782 0.240945 ATGCAACAGCAGCCGTTAAC 59.759 50.000 0.00 0.00 42.36 2.01
2610 2783 0.958091 AATGCAACAGCAGCCGTTAA 59.042 45.000 0.00 0.00 42.36 2.01
2611 2784 0.240678 CAATGCAACAGCAGCCGTTA 59.759 50.000 0.00 0.00 42.36 3.18
2613 2786 2.646719 CAATGCAACAGCAGCCGT 59.353 55.556 0.00 0.00 42.36 5.68
2614 2787 2.807895 GCAATGCAACAGCAGCCG 60.808 61.111 0.00 0.00 42.36 5.52
2615 2788 2.340809 TGCAATGCAACAGCAGCC 59.659 55.556 5.01 0.00 42.36 4.85
2621 2794 4.922471 ATACATATGCTGCAATGCAACA 57.078 36.364 13.95 13.95 46.61 3.33
2622 2795 6.441274 ACTTATACATATGCTGCAATGCAAC 58.559 36.000 9.92 5.35 46.61 4.17
2626 2799 8.347771 ACAGAAACTTATACATATGCTGCAATG 58.652 33.333 6.36 13.80 0.00 2.82
2630 2803 7.134815 CCAACAGAAACTTATACATATGCTGC 58.865 38.462 1.58 0.00 0.00 5.25
2631 2804 8.213518 ACCAACAGAAACTTATACATATGCTG 57.786 34.615 1.58 1.35 0.00 4.41
2632 2805 8.677300 CAACCAACAGAAACTTATACATATGCT 58.323 33.333 1.58 0.00 0.00 3.79
2633 2806 7.915397 CCAACCAACAGAAACTTATACATATGC 59.085 37.037 1.58 0.00 0.00 3.14
2649 2860 1.593196 ATCGTGTCACCAACCAACAG 58.407 50.000 0.00 0.00 0.00 3.16
2676 2889 4.022416 GCCATTGTTATTGAATGCCCGATA 60.022 41.667 0.00 0.00 30.66 2.92
2785 3015 0.455972 CCTGCACAATTTAACGCCGG 60.456 55.000 0.00 0.00 0.00 6.13
2818 3056 1.164662 CCAGCTCCAGCAATGGATCG 61.165 60.000 0.48 0.00 45.16 3.69
2912 3158 2.894007 CGTCGATCGTACGTTGCG 59.106 61.111 23.03 16.37 35.66 4.85
2940 3191 1.674764 TTGACGGGTGGTACGTGTGT 61.675 55.000 0.00 0.00 45.68 3.72
2942 3193 0.320073 CATTGACGGGTGGTACGTGT 60.320 55.000 0.00 0.00 45.68 4.49
3089 3353 4.084171 ACACGATCGATGGTACGTATACAG 60.084 45.833 24.34 2.05 37.22 2.74
3092 3356 4.057432 TGACACGATCGATGGTACGTATA 58.943 43.478 24.34 0.00 37.22 1.47
3127 3391 4.600576 TGCGTCTGCCGTTCTGCA 62.601 61.111 0.00 0.00 41.78 4.41
3135 3399 1.635663 AATTAGTGCGTGCGTCTGCC 61.636 55.000 0.00 0.00 41.78 4.85
3136 3400 0.165944 AAATTAGTGCGTGCGTCTGC 59.834 50.000 0.00 0.00 43.20 4.26
3137 3401 2.233355 CAAAATTAGTGCGTGCGTCTG 58.767 47.619 0.00 0.00 0.00 3.51
3138 3402 1.871039 ACAAAATTAGTGCGTGCGTCT 59.129 42.857 0.00 0.00 0.00 4.18
3139 3403 2.309898 ACAAAATTAGTGCGTGCGTC 57.690 45.000 0.00 0.00 0.00 5.19
3140 3404 2.646250 GAACAAAATTAGTGCGTGCGT 58.354 42.857 0.00 0.00 0.00 5.24
3141 3405 1.637086 CGAACAAAATTAGTGCGTGCG 59.363 47.619 3.75 0.00 33.38 5.34
3142 3406 1.976045 CCGAACAAAATTAGTGCGTGC 59.024 47.619 9.66 0.00 36.29 5.34
3143 3407 1.976045 GCCGAACAAAATTAGTGCGTG 59.024 47.619 9.66 4.04 36.29 5.34
3144 3408 1.068816 GGCCGAACAAAATTAGTGCGT 60.069 47.619 9.66 0.00 36.29 5.24
3145 3409 1.199097 AGGCCGAACAAAATTAGTGCG 59.801 47.619 0.00 4.73 37.77 5.34
3146 3410 2.415491 GGAGGCCGAACAAAATTAGTGC 60.415 50.000 0.00 0.00 0.00 4.40
3147 3411 2.817258 TGGAGGCCGAACAAAATTAGTG 59.183 45.455 0.00 0.00 0.00 2.74
3148 3412 2.817844 GTGGAGGCCGAACAAAATTAGT 59.182 45.455 0.00 0.00 0.00 2.24
3149 3413 2.817258 TGTGGAGGCCGAACAAAATTAG 59.183 45.455 0.00 0.00 0.00 1.73
3150 3414 2.554893 GTGTGGAGGCCGAACAAAATTA 59.445 45.455 9.40 0.00 0.00 1.40
3151 3415 1.339929 GTGTGGAGGCCGAACAAAATT 59.660 47.619 9.40 0.00 0.00 1.82
3152 3416 0.958822 GTGTGGAGGCCGAACAAAAT 59.041 50.000 9.40 0.00 0.00 1.82
3153 3417 0.106918 AGTGTGGAGGCCGAACAAAA 60.107 50.000 9.40 0.00 0.00 2.44
3154 3418 0.106918 AAGTGTGGAGGCCGAACAAA 60.107 50.000 9.40 0.00 0.00 2.83
3155 3419 0.817634 CAAGTGTGGAGGCCGAACAA 60.818 55.000 9.40 0.00 0.00 2.83
3156 3420 1.227823 CAAGTGTGGAGGCCGAACA 60.228 57.895 0.00 0.00 0.00 3.18
3157 3421 2.617274 GCAAGTGTGGAGGCCGAAC 61.617 63.158 0.00 0.00 0.00 3.95
3158 3422 2.281484 GCAAGTGTGGAGGCCGAA 60.281 61.111 0.00 0.00 0.00 4.30
3159 3423 4.329545 GGCAAGTGTGGAGGCCGA 62.330 66.667 0.00 0.00 36.58 5.54
3161 3425 2.674380 CAGGCAAGTGTGGAGGCC 60.674 66.667 0.00 0.00 46.77 5.19
3162 3426 1.109323 AAACAGGCAAGTGTGGAGGC 61.109 55.000 0.00 0.00 0.00 4.70
3163 3427 1.338020 GAAAACAGGCAAGTGTGGAGG 59.662 52.381 0.00 0.00 0.00 4.30
3164 3428 2.301346 AGAAAACAGGCAAGTGTGGAG 58.699 47.619 0.00 0.00 0.00 3.86
3165 3429 2.435372 AGAAAACAGGCAAGTGTGGA 57.565 45.000 0.00 0.00 0.00 4.02
3166 3430 3.525268 AAAGAAAACAGGCAAGTGTGG 57.475 42.857 0.00 0.00 0.00 4.17
3167 3431 6.959671 TTAAAAAGAAAACAGGCAAGTGTG 57.040 33.333 0.00 0.00 0.00 3.82
3168 3432 8.560355 AAATTAAAAAGAAAACAGGCAAGTGT 57.440 26.923 0.00 0.00 0.00 3.55
3190 3454 9.638239 CAAAGTGTGCCTGTGTTATTATTAAAT 57.362 29.630 0.00 0.00 0.00 1.40
3191 3455 8.085296 CCAAAGTGTGCCTGTGTTATTATTAAA 58.915 33.333 0.00 0.00 0.00 1.52
3192 3456 7.448777 TCCAAAGTGTGCCTGTGTTATTATTAA 59.551 33.333 0.00 0.00 0.00 1.40
3193 3457 6.943146 TCCAAAGTGTGCCTGTGTTATTATTA 59.057 34.615 0.00 0.00 0.00 0.98
3194 3458 5.772672 TCCAAAGTGTGCCTGTGTTATTATT 59.227 36.000 0.00 0.00 0.00 1.40
3195 3459 5.321102 TCCAAAGTGTGCCTGTGTTATTAT 58.679 37.500 0.00 0.00 0.00 1.28
3196 3460 4.720046 TCCAAAGTGTGCCTGTGTTATTA 58.280 39.130 0.00 0.00 0.00 0.98
3197 3461 3.561143 TCCAAAGTGTGCCTGTGTTATT 58.439 40.909 0.00 0.00 0.00 1.40
3198 3462 3.149196 CTCCAAAGTGTGCCTGTGTTAT 58.851 45.455 0.00 0.00 0.00 1.89
3199 3463 2.571212 CTCCAAAGTGTGCCTGTGTTA 58.429 47.619 0.00 0.00 0.00 2.41
3250 3559 1.800681 GGGCGTTTGGTGCAGATAC 59.199 57.895 0.00 0.00 0.00 2.24
3279 3588 2.159014 CGATGGTAAATTCCTGGTCGGA 60.159 50.000 0.00 0.00 41.06 4.55
3315 3635 0.712222 GTTGGTCGATTCGGACGTTC 59.288 55.000 6.18 0.00 37.82 3.95
3318 3638 0.437295 GTTGTTGGTCGATTCGGACG 59.563 55.000 6.18 0.00 37.82 4.79
3324 3644 2.879103 ATGAGGGTTGTTGGTCGATT 57.121 45.000 0.00 0.00 0.00 3.34
3326 3646 2.232941 GAGTATGAGGGTTGTTGGTCGA 59.767 50.000 0.00 0.00 0.00 4.20
3327 3647 2.028476 TGAGTATGAGGGTTGTTGGTCG 60.028 50.000 0.00 0.00 0.00 4.79
3342 3662 4.019860 CCAGTGCATATAAGGGCTGAGTAT 60.020 45.833 0.00 0.00 0.00 2.12
3372 3692 0.744281 ACCTTTTTCAGCAACCCGTG 59.256 50.000 0.00 0.00 0.00 4.94
3376 3696 2.867647 GCCATGACCTTTTTCAGCAACC 60.868 50.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.