Multiple sequence alignment - TraesCS3D01G132700

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 TraesCS3D01G132700 chr3D 100.000 2563 0 0 1 2563 92269145 92271707 0.000000e+00 4734.0
1 TraesCS3D01G132700 chr3D 81.567 1595 241 22 1 1569 48803372 48801805 0.000000e+00 1267.0
2 TraesCS3D01G132700 chr3D 95.756 589 25 0 1975 2563 380929118 380929706 0.000000e+00 950.0
3 TraesCS3D01G132700 chr3D 95.756 589 24 1 1975 2563 92305884 92306471 0.000000e+00 948.0
4 TraesCS3D01G132700 chr3D 95.076 589 29 0 1975 2563 123027917 123027329 0.000000e+00 928.0
5 TraesCS3D01G132700 chr3D 94.737 589 30 1 1975 2563 590799343 590798756 0.000000e+00 915.0
6 TraesCS3D01G132700 chr3D 94.407 590 31 2 1975 2563 527594218 527594806 0.000000e+00 905.0
7 TraesCS3D01G132700 chr3D 94.017 117 7 0 1860 1976 567243951 567243835 7.290000e-41 178.0
8 TraesCS3D01G132700 chr5D 95.235 1616 49 9 1 1589 193141146 193142760 0.000000e+00 2532.0
9 TraesCS3D01G132700 chr5D 94.595 592 31 1 1973 2563 269932004 269932595 0.000000e+00 915.0
10 TraesCS3D01G132700 chr5D 94.068 118 7 0 1859 1976 300326833 300326950 2.030000e-41 180.0
11 TraesCS3D01G132700 chr7D 94.056 1615 54 10 1 1589 277449254 277447656 0.000000e+00 2412.0
12 TraesCS3D01G132700 chr7D 91.939 1253 69 17 369 1592 137612406 137611157 0.000000e+00 1725.0
13 TraesCS3D01G132700 chr7D 90.253 1303 69 16 317 1592 137573731 137572460 0.000000e+00 1650.0
14 TraesCS3D01G132700 chr7B 93.065 1615 81 9 1 1589 15584517 15582908 0.000000e+00 2333.0
15 TraesCS3D01G132700 chr5B 92.498 1613 79 9 1 1589 692244268 692245862 0.000000e+00 2270.0
16 TraesCS3D01G132700 chr2A 92.343 1306 77 8 1 1283 291311202 291309897 0.000000e+00 1836.0
17 TraesCS3D01G132700 chr2A 92.219 1221 69 11 329 1523 751523891 751525111 0.000000e+00 1705.0
18 TraesCS3D01G132700 chr2A 94.197 741 39 2 854 1590 771491870 771491130 0.000000e+00 1127.0
19 TraesCS3D01G132700 chr2A 88.108 185 18 4 1672 1854 67210213 67210395 1.540000e-52 217.0
20 TraesCS3D01G132700 chr2A 94.215 121 5 2 1856 1974 780741174 780741054 1.570000e-42 183.0
21 TraesCS3D01G132700 chrUn 91.939 1253 70 17 369 1592 91678601 91677351 0.000000e+00 1725.0
22 TraesCS3D01G132700 chrUn 82.222 90 11 3 1595 1679 45758325 45758236 3.540000e-09 73.1
23 TraesCS3D01G132700 chr5A 91.948 1155 65 10 456 1582 631966863 631965709 0.000000e+00 1592.0
24 TraesCS3D01G132700 chr5A 94.915 118 5 1 1860 1976 4006598 4006715 1.570000e-42 183.0
25 TraesCS3D01G132700 chr5A 94.068 118 6 1 1860 1976 4001165 4001282 7.290000e-41 178.0
26 TraesCS3D01G132700 chr6B 80.714 1597 275 19 1 1569 8731204 8732795 0.000000e+00 1212.0
27 TraesCS3D01G132700 chr6B 80.651 1597 276 19 1 1569 8745997 8747588 0.000000e+00 1206.0
28 TraesCS3D01G132700 chr6B 88.406 69 6 2 1610 1676 8598557 8598625 5.880000e-12 82.4
29 TraesCS3D01G132700 chr2D 94.728 588 31 0 1976 2563 257683403 257682816 0.000000e+00 915.0
30 TraesCS3D01G132700 chr2D 94.397 589 33 0 1975 2563 404217275 404216687 0.000000e+00 905.0
31 TraesCS3D01G132700 chr2D 94.068 590 35 0 1974 2563 266787403 266786814 0.000000e+00 896.0
32 TraesCS3D01G132700 chr2D 94.118 119 6 1 1859 1976 513544673 513544791 2.030000e-41 180.0
33 TraesCS3D01G132700 chr1D 83.570 846 131 8 1 841 269321852 269321010 0.000000e+00 785.0
34 TraesCS3D01G132700 chr1D 88.636 176 18 2 1680 1854 298561813 298561639 2.000000e-51 213.0
35 TraesCS3D01G132700 chr1D 94.068 118 6 1 1860 1976 397294597 397294714 7.290000e-41 178.0
36 TraesCS3D01G132700 chr1D 85.185 81 9 2 1603 1681 483255545 483255624 2.110000e-11 80.5
37 TraesCS3D01G132700 chr3A 91.954 174 14 0 1681 1854 631129208 631129381 7.080000e-61 244.0
38 TraesCS3D01G132700 chr3A 83.146 89 10 4 1595 1678 599377190 599377278 2.730000e-10 76.8
39 TraesCS3D01G132700 chr7A 89.080 174 19 0 1681 1854 535388070 535388243 1.540000e-52 217.0
40 TraesCS3D01G132700 chr7A 94.915 118 5 1 1860 1976 48070701 48070818 1.570000e-42 183.0
41 TraesCS3D01G132700 chr7A 81.818 77 11 3 1603 1677 133628373 133628448 7.660000e-06 62.1
42 TraesCS3D01G132700 chr7A 84.375 64 7 2 1603 1663 168846425 168846488 2.750000e-05 60.2
43 TraesCS3D01G132700 chr4A 87.302 189 24 0 1670 1858 166585400 166585212 1.540000e-52 217.0
44 TraesCS3D01G132700 chr4A 89.286 56 4 2 1623 1677 3987626 3987572 4.580000e-08 69.4
45 TraesCS3D01G132700 chr3B 87.568 185 20 3 1680 1862 50941214 50941031 7.180000e-51 211.0
46 TraesCS3D01G132700 chr3B 87.500 56 5 1 1610 1663 24245761 24245816 2.130000e-06 63.9
47 TraesCS3D01G132700 chr6A 86.772 189 22 3 1677 1862 457327749 457327561 9.290000e-50 207.0
48 TraesCS3D01G132700 chr6A 96.581 117 4 0 1860 1976 4707433 4707317 7.240000e-46 195.0
49 TraesCS3D01G132700 chr2B 87.293 181 21 2 1679 1858 795197482 795197303 3.340000e-49 206.0
50 TraesCS3D01G132700 chr2B 86.486 185 23 2 1679 1862 736213387 736213204 4.320000e-48 202.0
51 TraesCS3D01G132700 chr1B 84.706 85 7 5 1598 1677 101228180 101228263 2.110000e-11 80.5


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 TraesCS3D01G132700 chr3D 92269145 92271707 2562 False 4734 4734 100.000 1 2563 1 chr3D.!!$F1 2562
1 TraesCS3D01G132700 chr3D 48801805 48803372 1567 True 1267 1267 81.567 1 1569 1 chr3D.!!$R1 1568
2 TraesCS3D01G132700 chr3D 380929118 380929706 588 False 950 950 95.756 1975 2563 1 chr3D.!!$F3 588
3 TraesCS3D01G132700 chr3D 92305884 92306471 587 False 948 948 95.756 1975 2563 1 chr3D.!!$F2 588
4 TraesCS3D01G132700 chr3D 123027329 123027917 588 True 928 928 95.076 1975 2563 1 chr3D.!!$R2 588
5 TraesCS3D01G132700 chr3D 590798756 590799343 587 True 915 915 94.737 1975 2563 1 chr3D.!!$R4 588
6 TraesCS3D01G132700 chr3D 527594218 527594806 588 False 905 905 94.407 1975 2563 1 chr3D.!!$F4 588
7 TraesCS3D01G132700 chr5D 193141146 193142760 1614 False 2532 2532 95.235 1 1589 1 chr5D.!!$F1 1588
8 TraesCS3D01G132700 chr5D 269932004 269932595 591 False 915 915 94.595 1973 2563 1 chr5D.!!$F2 590
9 TraesCS3D01G132700 chr7D 277447656 277449254 1598 True 2412 2412 94.056 1 1589 1 chr7D.!!$R3 1588
10 TraesCS3D01G132700 chr7D 137611157 137612406 1249 True 1725 1725 91.939 369 1592 1 chr7D.!!$R2 1223
11 TraesCS3D01G132700 chr7D 137572460 137573731 1271 True 1650 1650 90.253 317 1592 1 chr7D.!!$R1 1275
12 TraesCS3D01G132700 chr7B 15582908 15584517 1609 True 2333 2333 93.065 1 1589 1 chr7B.!!$R1 1588
13 TraesCS3D01G132700 chr5B 692244268 692245862 1594 False 2270 2270 92.498 1 1589 1 chr5B.!!$F1 1588
14 TraesCS3D01G132700 chr2A 291309897 291311202 1305 True 1836 1836 92.343 1 1283 1 chr2A.!!$R1 1282
15 TraesCS3D01G132700 chr2A 751523891 751525111 1220 False 1705 1705 92.219 329 1523 1 chr2A.!!$F2 1194
16 TraesCS3D01G132700 chr2A 771491130 771491870 740 True 1127 1127 94.197 854 1590 1 chr2A.!!$R2 736
17 TraesCS3D01G132700 chrUn 91677351 91678601 1250 True 1725 1725 91.939 369 1592 1 chrUn.!!$R2 1223
18 TraesCS3D01G132700 chr5A 631965709 631966863 1154 True 1592 1592 91.948 456 1582 1 chr5A.!!$R1 1126
19 TraesCS3D01G132700 chr6B 8731204 8732795 1591 False 1212 1212 80.714 1 1569 1 chr6B.!!$F2 1568
20 TraesCS3D01G132700 chr6B 8745997 8747588 1591 False 1206 1206 80.651 1 1569 1 chr6B.!!$F3 1568
21 TraesCS3D01G132700 chr2D 257682816 257683403 587 True 915 915 94.728 1976 2563 1 chr2D.!!$R1 587
22 TraesCS3D01G132700 chr2D 404216687 404217275 588 True 905 905 94.397 1975 2563 1 chr2D.!!$R3 588
23 TraesCS3D01G132700 chr2D 266786814 266787403 589 True 896 896 94.068 1974 2563 1 chr2D.!!$R2 589
24 TraesCS3D01G132700 chr1D 269321010 269321852 842 True 785 785 83.570 1 841 1 chr1D.!!$R1 840

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
931 990 0.097674 GCTGATTGCTGTAACCGCAG 59.902 55.0 0.0 0.0 38.8 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1959 2025 0.031585 GACATATAGCGCGGGTCACA 59.968 55.0 8.83 0.0 0.0 3.58 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
27 28 2.558359 GTGTGTTCCCAAAGATCAAGGG 59.442 50.000 10.09 10.09 44.22 3.95
105 106 1.048601 GGCGTCTCCTGGATAATCCA 58.951 55.000 0.00 0.00 45.98 3.41
126 127 4.345288 CAGATTCGTTATGTGCCACAATG 58.655 43.478 0.00 0.00 0.00 2.82
294 299 2.270352 TTTGGACAGACGCTTGGATT 57.730 45.000 0.00 0.00 0.00 3.01
349 354 1.334243 GACGAGGGATACTTCTGACGG 59.666 57.143 0.00 0.00 41.35 4.79
629 641 4.959839 TGGGGTAAGATTTGGAAATTAGCC 59.040 41.667 3.95 3.95 32.44 3.93
825 840 5.660864 GGGAAAATTTGGGGATGTATGAAGA 59.339 40.000 0.00 0.00 0.00 2.87
851 866 2.888834 AAAAGCTTGTGCGGTTGATT 57.111 40.000 0.00 0.00 45.42 2.57
931 990 0.097674 GCTGATTGCTGTAACCGCAG 59.902 55.000 0.00 0.00 38.80 5.18
1468 1534 1.959899 GCACATGAGTTGGCTCGACG 61.960 60.000 0.00 0.00 44.48 5.12
1657 1723 9.722056 ATGTTTTATCTCTTAAATCATGCGTTC 57.278 29.630 0.00 0.00 38.16 3.95
1658 1724 8.726068 TGTTTTATCTCTTAAATCATGCGTTCA 58.274 29.630 0.00 0.00 28.91 3.18
1659 1725 9.554724 GTTTTATCTCTTAAATCATGCGTTCAA 57.445 29.630 0.00 0.00 30.03 2.69
1662 1728 9.935682 TTATCTCTTAAATCATGCGTTCAAATC 57.064 29.630 0.00 0.00 0.00 2.17
1663 1729 6.477742 TCTCTTAAATCATGCGTTCAAATCG 58.522 36.000 0.00 0.00 0.00 3.34
1674 1740 4.707210 CGTTCAAATCGCAAACCATTTT 57.293 36.364 0.00 0.00 0.00 1.82
1675 1741 4.687047 CGTTCAAATCGCAAACCATTTTC 58.313 39.130 0.00 0.00 0.00 2.29
1676 1742 4.208047 CGTTCAAATCGCAAACCATTTTCA 59.792 37.500 0.00 0.00 0.00 2.69
1677 1743 5.431309 GTTCAAATCGCAAACCATTTTCAC 58.569 37.500 0.00 0.00 0.00 3.18
1678 1744 4.942852 TCAAATCGCAAACCATTTTCACT 58.057 34.783 0.00 0.00 0.00 3.41
1679 1745 5.355596 TCAAATCGCAAACCATTTTCACTT 58.644 33.333 0.00 0.00 0.00 3.16
1680 1746 5.233902 TCAAATCGCAAACCATTTTCACTTG 59.766 36.000 0.00 0.00 0.00 3.16
1681 1747 4.582701 ATCGCAAACCATTTTCACTTGA 57.417 36.364 0.00 0.00 0.00 3.02
1682 1748 3.963665 TCGCAAACCATTTTCACTTGAG 58.036 40.909 0.00 0.00 0.00 3.02
1683 1749 3.629855 TCGCAAACCATTTTCACTTGAGA 59.370 39.130 0.00 0.00 0.00 3.27
1684 1750 4.097135 TCGCAAACCATTTTCACTTGAGAA 59.903 37.500 0.00 0.00 0.00 2.87
1685 1751 4.803088 CGCAAACCATTTTCACTTGAGAAA 59.197 37.500 0.00 0.00 35.82 2.52
1702 1768 9.343539 ACTTGAGAAAATTCCTTATATAGCACC 57.656 33.333 0.00 0.00 0.00 5.01
1703 1769 7.962964 TGAGAAAATTCCTTATATAGCACCG 57.037 36.000 0.00 0.00 0.00 4.94
1704 1770 7.506114 TGAGAAAATTCCTTATATAGCACCGT 58.494 34.615 0.00 0.00 0.00 4.83
1705 1771 7.990886 TGAGAAAATTCCTTATATAGCACCGTT 59.009 33.333 0.00 0.00 0.00 4.44
1706 1772 8.747538 AGAAAATTCCTTATATAGCACCGTTT 57.252 30.769 0.00 0.00 0.00 3.60
1707 1773 9.185680 AGAAAATTCCTTATATAGCACCGTTTT 57.814 29.630 0.00 0.00 0.00 2.43
1720 1786 6.352682 AGCACCGTTTTAAATTTTGTTTCC 57.647 33.333 0.00 0.00 0.00 3.13
1721 1787 5.294799 AGCACCGTTTTAAATTTTGTTTCCC 59.705 36.000 0.00 0.00 0.00 3.97
1722 1788 5.294799 GCACCGTTTTAAATTTTGTTTCCCT 59.705 36.000 0.00 0.00 0.00 4.20
1723 1789 6.479331 GCACCGTTTTAAATTTTGTTTCCCTA 59.521 34.615 0.00 0.00 0.00 3.53
1724 1790 7.171848 GCACCGTTTTAAATTTTGTTTCCCTAT 59.828 33.333 0.00 0.00 0.00 2.57
1725 1791 9.047371 CACCGTTTTAAATTTTGTTTCCCTATT 57.953 29.630 0.00 0.00 0.00 1.73
1726 1792 9.616156 ACCGTTTTAAATTTTGTTTCCCTATTT 57.384 25.926 0.00 0.00 0.00 1.40
1727 1793 9.871299 CCGTTTTAAATTTTGTTTCCCTATTTG 57.129 29.630 0.00 0.00 0.00 2.32
1733 1799 8.661352 AAATTTTGTTTCCCTATTTGACACTG 57.339 30.769 0.00 0.00 0.00 3.66
1734 1800 7.595819 ATTTTGTTTCCCTATTTGACACTGA 57.404 32.000 0.00 0.00 0.00 3.41
1735 1801 7.411486 TTTTGTTTCCCTATTTGACACTGAA 57.589 32.000 0.00 0.00 0.00 3.02
1736 1802 7.411486 TTTGTTTCCCTATTTGACACTGAAA 57.589 32.000 0.00 0.00 0.00 2.69
1737 1803 7.411486 TTGTTTCCCTATTTGACACTGAAAA 57.589 32.000 0.00 0.00 0.00 2.29
1738 1804 7.411486 TGTTTCCCTATTTGACACTGAAAAA 57.589 32.000 0.00 0.00 0.00 1.94
1739 1805 7.262048 TGTTTCCCTATTTGACACTGAAAAAC 58.738 34.615 0.00 0.00 0.00 2.43
1740 1806 7.123547 TGTTTCCCTATTTGACACTGAAAAACT 59.876 33.333 0.00 0.00 0.00 2.66
1741 1807 7.654022 TTCCCTATTTGACACTGAAAAACTT 57.346 32.000 0.00 0.00 0.00 2.66
1742 1808 7.654022 TCCCTATTTGACACTGAAAAACTTT 57.346 32.000 0.00 0.00 0.00 2.66
1743 1809 8.073467 TCCCTATTTGACACTGAAAAACTTTT 57.927 30.769 0.00 0.00 0.00 2.27
1744 1810 8.536175 TCCCTATTTGACACTGAAAAACTTTTT 58.464 29.630 0.00 0.00 0.00 1.94
1745 1811 8.817100 CCCTATTTGACACTGAAAAACTTTTTC 58.183 33.333 16.92 16.92 0.00 2.29
1746 1812 9.586435 CCTATTTGACACTGAAAAACTTTTTCT 57.414 29.630 21.95 7.19 0.00 2.52
1749 1815 7.883229 TTGACACTGAAAAACTTTTTCTTCC 57.117 32.000 21.95 11.00 0.00 3.46
1750 1816 6.394809 TGACACTGAAAAACTTTTTCTTCCC 58.605 36.000 21.95 11.50 0.00 3.97
1751 1817 6.210584 TGACACTGAAAAACTTTTTCTTCCCT 59.789 34.615 21.95 6.54 0.00 4.20
1752 1818 7.394923 TGACACTGAAAAACTTTTTCTTCCCTA 59.605 33.333 21.95 5.72 0.00 3.53
1753 1819 8.306313 ACACTGAAAAACTTTTTCTTCCCTAT 57.694 30.769 21.95 4.94 0.00 2.57
1754 1820 9.416284 ACACTGAAAAACTTTTTCTTCCCTATA 57.584 29.630 21.95 4.60 0.00 1.31
1781 1847 8.838649 AACACCTTATCTAAATTTTATGCCCT 57.161 30.769 0.00 0.00 0.00 5.19
1782 1848 8.838649 ACACCTTATCTAAATTTTATGCCCTT 57.161 30.769 0.00 0.00 0.00 3.95
1783 1849 9.267071 ACACCTTATCTAAATTTTATGCCCTTT 57.733 29.630 0.00 0.00 0.00 3.11
1786 1852 9.893305 CCTTATCTAAATTTTATGCCCTTTACG 57.107 33.333 0.00 0.00 0.00 3.18
1789 1855 7.925043 TCTAAATTTTATGCCCTTTACGACA 57.075 32.000 0.00 0.00 0.00 4.35
1790 1856 7.754625 TCTAAATTTTATGCCCTTTACGACAC 58.245 34.615 0.00 0.00 0.00 3.67
1791 1857 6.584185 AAATTTTATGCCCTTTACGACACT 57.416 33.333 0.00 0.00 0.00 3.55
1792 1858 6.584185 AATTTTATGCCCTTTACGACACTT 57.416 33.333 0.00 0.00 0.00 3.16
1793 1859 5.616488 TTTTATGCCCTTTACGACACTTC 57.384 39.130 0.00 0.00 0.00 3.01
1794 1860 2.109425 ATGCCCTTTACGACACTTCC 57.891 50.000 0.00 0.00 0.00 3.46
1795 1861 0.759959 TGCCCTTTACGACACTTCCA 59.240 50.000 0.00 0.00 0.00 3.53
1796 1862 1.349688 TGCCCTTTACGACACTTCCAT 59.650 47.619 0.00 0.00 0.00 3.41
1797 1863 2.007608 GCCCTTTACGACACTTCCATC 58.992 52.381 0.00 0.00 0.00 3.51
1798 1864 2.614481 GCCCTTTACGACACTTCCATCA 60.614 50.000 0.00 0.00 0.00 3.07
1799 1865 3.670625 CCCTTTACGACACTTCCATCAA 58.329 45.455 0.00 0.00 0.00 2.57
1800 1866 4.261801 CCCTTTACGACACTTCCATCAAT 58.738 43.478 0.00 0.00 0.00 2.57
1801 1867 4.700213 CCCTTTACGACACTTCCATCAATT 59.300 41.667 0.00 0.00 0.00 2.32
1802 1868 5.183140 CCCTTTACGACACTTCCATCAATTT 59.817 40.000 0.00 0.00 0.00 1.82
1803 1869 6.294508 CCCTTTACGACACTTCCATCAATTTT 60.295 38.462 0.00 0.00 0.00 1.82
1804 1870 7.094549 CCCTTTACGACACTTCCATCAATTTTA 60.095 37.037 0.00 0.00 0.00 1.52
1805 1871 8.293867 CCTTTACGACACTTCCATCAATTTTAA 58.706 33.333 0.00 0.00 0.00 1.52
1806 1872 9.329913 CTTTACGACACTTCCATCAATTTTAAG 57.670 33.333 0.00 0.00 0.00 1.85
1807 1873 5.699839 ACGACACTTCCATCAATTTTAAGC 58.300 37.500 0.00 0.00 0.00 3.09
1808 1874 5.095490 CGACACTTCCATCAATTTTAAGCC 58.905 41.667 0.00 0.00 0.00 4.35
1809 1875 5.106157 CGACACTTCCATCAATTTTAAGCCT 60.106 40.000 0.00 0.00 0.00 4.58
1810 1876 6.570378 CGACACTTCCATCAATTTTAAGCCTT 60.570 38.462 0.00 0.00 0.00 4.35
1811 1877 7.361713 CGACACTTCCATCAATTTTAAGCCTTA 60.362 37.037 0.00 0.00 0.00 2.69
1812 1878 8.189119 ACACTTCCATCAATTTTAAGCCTTAA 57.811 30.769 0.00 0.00 0.00 1.85
1813 1879 8.088365 ACACTTCCATCAATTTTAAGCCTTAAC 58.912 33.333 0.00 0.00 0.00 2.01
1814 1880 7.273381 CACTTCCATCAATTTTAAGCCTTAACG 59.727 37.037 0.00 0.00 0.00 3.18
1815 1881 6.202516 TCCATCAATTTTAAGCCTTAACGG 57.797 37.500 0.00 0.00 0.00 4.44
1816 1882 5.712917 TCCATCAATTTTAAGCCTTAACGGT 59.287 36.000 0.00 0.00 34.25 4.83
1817 1883 5.804979 CCATCAATTTTAAGCCTTAACGGTG 59.195 40.000 0.00 0.00 34.25 4.94
1818 1884 6.386654 CATCAATTTTAAGCCTTAACGGTGT 58.613 36.000 0.00 0.00 34.25 4.16
1819 1885 6.394025 TCAATTTTAAGCCTTAACGGTGTT 57.606 33.333 0.00 0.00 34.25 3.32
1820 1886 6.210078 TCAATTTTAAGCCTTAACGGTGTTG 58.790 36.000 0.00 0.00 34.25 3.33
1821 1887 6.039493 TCAATTTTAAGCCTTAACGGTGTTGA 59.961 34.615 0.00 1.73 34.25 3.18
1822 1888 5.831702 TTTTAAGCCTTAACGGTGTTGAA 57.168 34.783 0.00 0.00 34.25 2.69
1823 1889 6.394025 TTTTAAGCCTTAACGGTGTTGAAT 57.606 33.333 0.00 0.00 34.25 2.57
1824 1890 3.915437 AAGCCTTAACGGTGTTGAATG 57.085 42.857 0.00 0.00 34.25 2.67
1825 1891 3.134574 AGCCTTAACGGTGTTGAATGA 57.865 42.857 0.00 0.00 34.25 2.57
1826 1892 2.812011 AGCCTTAACGGTGTTGAATGAC 59.188 45.455 0.00 0.00 34.25 3.06
1827 1893 2.550606 GCCTTAACGGTGTTGAATGACA 59.449 45.455 0.00 0.00 34.25 3.58
1836 1902 4.214980 GTGTTGAATGACACCTGAACAG 57.785 45.455 0.00 0.00 43.16 3.16
1837 1903 3.876914 GTGTTGAATGACACCTGAACAGA 59.123 43.478 3.19 0.00 43.16 3.41
1838 1904 3.876914 TGTTGAATGACACCTGAACAGAC 59.123 43.478 3.19 0.00 0.00 3.51
1839 1905 3.126001 TGAATGACACCTGAACAGACC 57.874 47.619 3.19 0.00 0.00 3.85
1840 1906 2.705658 TGAATGACACCTGAACAGACCT 59.294 45.455 3.19 0.00 0.00 3.85
1841 1907 3.901222 TGAATGACACCTGAACAGACCTA 59.099 43.478 3.19 0.00 0.00 3.08
1842 1908 4.532126 TGAATGACACCTGAACAGACCTAT 59.468 41.667 3.19 0.00 0.00 2.57
1843 1909 5.013079 TGAATGACACCTGAACAGACCTATT 59.987 40.000 3.19 0.00 0.00 1.73
1844 1910 4.974645 TGACACCTGAACAGACCTATTT 57.025 40.909 3.19 0.00 0.00 1.40
1845 1911 4.641396 TGACACCTGAACAGACCTATTTG 58.359 43.478 3.19 0.00 0.00 2.32
1846 1912 3.412386 ACACCTGAACAGACCTATTTGC 58.588 45.455 3.19 0.00 0.00 3.68
1847 1913 2.749621 CACCTGAACAGACCTATTTGCC 59.250 50.000 3.19 0.00 0.00 4.52
1848 1914 2.290960 ACCTGAACAGACCTATTTGCCC 60.291 50.000 3.19 0.00 0.00 5.36
1849 1915 2.369394 CTGAACAGACCTATTTGCCCC 58.631 52.381 0.00 0.00 0.00 5.80
1850 1916 1.992557 TGAACAGACCTATTTGCCCCT 59.007 47.619 0.00 0.00 0.00 4.79
1851 1917 2.026262 TGAACAGACCTATTTGCCCCTC 60.026 50.000 0.00 0.00 0.00 4.30
1852 1918 1.668826 ACAGACCTATTTGCCCCTCA 58.331 50.000 0.00 0.00 0.00 3.86
1853 1919 2.208872 ACAGACCTATTTGCCCCTCAT 58.791 47.619 0.00 0.00 0.00 2.90
1854 1920 2.092212 ACAGACCTATTTGCCCCTCATG 60.092 50.000 0.00 0.00 0.00 3.07
1855 1921 2.173356 CAGACCTATTTGCCCCTCATGA 59.827 50.000 0.00 0.00 0.00 3.07
1856 1922 2.441001 AGACCTATTTGCCCCTCATGAG 59.559 50.000 16.24 16.24 0.00 2.90
1869 1935 4.286297 CCTCATGAGGTTGTTAGGTTGA 57.714 45.455 30.55 0.00 43.61 3.18
1870 1936 4.848357 CCTCATGAGGTTGTTAGGTTGAT 58.152 43.478 30.55 0.00 43.61 2.57
1871 1937 4.878397 CCTCATGAGGTTGTTAGGTTGATC 59.122 45.833 30.55 0.00 43.61 2.92
1872 1938 5.338708 CCTCATGAGGTTGTTAGGTTGATCT 60.339 44.000 30.55 0.00 43.61 2.75
1873 1939 5.734720 TCATGAGGTTGTTAGGTTGATCTC 58.265 41.667 0.00 0.00 0.00 2.75
1874 1940 4.553330 TGAGGTTGTTAGGTTGATCTCC 57.447 45.455 0.00 0.00 0.00 3.71
1875 1941 3.907474 TGAGGTTGTTAGGTTGATCTCCA 59.093 43.478 9.47 0.00 0.00 3.86
1876 1942 4.254492 GAGGTTGTTAGGTTGATCTCCAC 58.746 47.826 9.47 2.17 0.00 4.02
1877 1943 3.009143 AGGTTGTTAGGTTGATCTCCACC 59.991 47.826 9.47 5.90 0.00 4.61
1878 1944 3.244770 GGTTGTTAGGTTGATCTCCACCA 60.245 47.826 10.72 2.52 0.00 4.17
1879 1945 4.567747 GGTTGTTAGGTTGATCTCCACCAT 60.568 45.833 10.72 1.44 0.00 3.55
1880 1946 4.220693 TGTTAGGTTGATCTCCACCATG 57.779 45.455 10.72 0.00 0.00 3.66
1881 1947 3.587061 TGTTAGGTTGATCTCCACCATGT 59.413 43.478 10.72 0.00 0.00 3.21
1882 1948 2.795231 AGGTTGATCTCCACCATGTG 57.205 50.000 10.72 0.00 0.00 3.21
1891 1957 4.403137 CACCATGTGGGCGCAACG 62.403 66.667 10.83 0.00 42.05 4.10
1910 1976 2.772622 CCCACCGGGCCCTTAGAT 60.773 66.667 22.43 0.00 35.35 1.98
1911 1977 2.819284 CCCACCGGGCCCTTAGATC 61.819 68.421 22.43 0.00 35.35 2.75
1912 1978 2.819284 CCACCGGGCCCTTAGATCC 61.819 68.421 22.43 0.00 0.00 3.36
1913 1979 2.842936 ACCGGGCCCTTAGATCCG 60.843 66.667 22.43 3.11 41.90 4.18
1914 1980 4.315941 CCGGGCCCTTAGATCCGC 62.316 72.222 22.43 0.00 41.02 5.54
1915 1981 4.664677 CGGGCCCTTAGATCCGCG 62.665 72.222 22.43 0.00 35.95 6.46
1916 1982 4.990553 GGGCCCTTAGATCCGCGC 62.991 72.222 17.04 0.00 0.00 6.86
1917 1983 4.990553 GGCCCTTAGATCCGCGCC 62.991 72.222 0.00 0.00 0.00 6.53
1918 1984 4.990553 GCCCTTAGATCCGCGCCC 62.991 72.222 0.00 0.00 0.00 6.13
1919 1985 3.234730 CCCTTAGATCCGCGCCCT 61.235 66.667 0.00 0.00 0.00 5.19
1920 1986 2.029666 CCTTAGATCCGCGCCCTG 59.970 66.667 0.00 0.00 0.00 4.45
1921 1987 2.498941 CCTTAGATCCGCGCCCTGA 61.499 63.158 0.00 0.00 0.00 3.86
1922 1988 1.668294 CTTAGATCCGCGCCCTGAT 59.332 57.895 0.00 0.88 0.00 2.90
1923 1989 0.389166 CTTAGATCCGCGCCCTGATC 60.389 60.000 17.05 17.05 38.10 2.92
1924 1990 2.142357 TTAGATCCGCGCCCTGATCG 62.142 60.000 18.09 0.00 41.76 3.69
1944 2010 4.035102 GGCGCCCAACCCTCTTCT 62.035 66.667 18.11 0.00 0.00 2.85
1945 2011 2.747855 GCGCCCAACCCTCTTCTG 60.748 66.667 0.00 0.00 0.00 3.02
1946 2012 2.045926 CGCCCAACCCTCTTCTGG 60.046 66.667 0.00 0.00 0.00 3.86
1947 2013 2.895424 CGCCCAACCCTCTTCTGGT 61.895 63.158 0.00 0.00 37.85 4.00
1948 2014 1.460699 GCCCAACCCTCTTCTGGTT 59.539 57.895 0.00 0.00 46.92 3.67
1953 2019 0.478507 AACCCTCTTCTGGTTGGTGG 59.521 55.000 0.00 0.00 44.30 4.61
1954 2020 1.380302 CCCTCTTCTGGTTGGTGGG 59.620 63.158 0.00 0.00 0.00 4.61
1955 2021 1.303643 CCTCTTCTGGTTGGTGGGC 60.304 63.158 0.00 0.00 0.00 5.36
1956 2022 1.303643 CTCTTCTGGTTGGTGGGCC 60.304 63.158 0.00 0.00 0.00 5.80
1957 2023 2.283173 CTTCTGGTTGGTGGGCCC 60.283 66.667 17.59 17.59 0.00 5.80
1958 2024 3.886550 CTTCTGGTTGGTGGGCCCC 62.887 68.421 22.27 10.91 0.00 5.80
1959 2025 4.938756 TCTGGTTGGTGGGCCCCT 62.939 66.667 22.27 0.00 0.00 4.79
1960 2026 4.684134 CTGGTTGGTGGGCCCCTG 62.684 72.222 22.27 2.24 0.00 4.45
1962 2028 4.994756 GGTTGGTGGGCCCCTGTG 62.995 72.222 22.27 0.00 0.00 3.66
1963 2029 3.897122 GTTGGTGGGCCCCTGTGA 61.897 66.667 22.27 0.00 0.00 3.58
1964 2030 3.897122 TTGGTGGGCCCCTGTGAC 61.897 66.667 22.27 10.43 0.00 3.67
2026 2092 5.487488 TCACAAGAATCCCTACTATGGTTGT 59.513 40.000 0.00 0.00 0.00 3.32
2082 2148 3.935203 CAGTCAGCACAAGGATCGTTTAT 59.065 43.478 0.00 0.00 0.00 1.40
2123 2189 1.972795 TGCGTAAAACCCTAGTCCTGT 59.027 47.619 0.00 0.00 0.00 4.00
2287 2353 6.403878 GTGAAAAGGCCTACAGTACTATGAA 58.596 40.000 5.16 0.00 0.00 2.57
2293 2359 7.916077 AGGCCTACAGTACTATGAACTTATT 57.084 36.000 1.29 0.00 0.00 1.40
2483 2549 1.823169 GCGGTGGTAGGGTCTTCACA 61.823 60.000 0.00 0.00 32.29 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.978156 TATCATGAAAGCCCATCCCC 57.022 50.000 0.00 0.00 0.00 4.81
105 106 3.181497 GCATTGTGGCACATAACGAATCT 60.181 43.478 22.73 0.00 43.40 2.40
126 127 3.879892 CTGGGAAATACTTGGCTCTTAGC 59.120 47.826 0.00 0.00 41.46 3.09
294 299 4.214986 TCTCCTATTCGCACAATTTGGA 57.785 40.909 0.78 0.00 0.00 3.53
349 354 5.734720 TGGGTCAATAAGATCAGACACTTC 58.265 41.667 0.00 0.00 35.50 3.01
629 641 0.673644 AATTCACCTTCGCCGGACAG 60.674 55.000 5.05 0.00 0.00 3.51
851 866 2.571202 TGTGGCATGAGGAGTAATGACA 59.429 45.455 0.00 0.00 39.52 3.58
931 990 5.861727 ACGTCTATTCCACCATAAATACCC 58.138 41.667 0.00 0.00 0.00 3.69
1022 1085 5.046231 GGGGAATGGGCACTTACAAAATTTA 60.046 40.000 0.00 0.00 0.00 1.40
1034 1097 0.396974 TGCATTAGGGGAATGGGCAC 60.397 55.000 0.00 0.00 44.53 5.01
1468 1534 3.001330 CCTCGTCACGGAATATTTTGCTC 59.999 47.826 0.00 0.00 0.00 4.26
1631 1697 9.722056 GAACGCATGATTTAAGAGATAAAACAT 57.278 29.630 0.00 0.00 43.66 2.71
1632 1698 8.726068 TGAACGCATGATTTAAGAGATAAAACA 58.274 29.630 0.00 0.00 39.61 2.83
1633 1699 9.554724 TTGAACGCATGATTTAAGAGATAAAAC 57.445 29.630 0.00 0.00 37.06 2.43
1636 1702 9.935682 GATTTGAACGCATGATTTAAGAGATAA 57.064 29.630 0.00 0.00 0.00 1.75
1637 1703 8.275632 CGATTTGAACGCATGATTTAAGAGATA 58.724 33.333 0.00 0.00 0.00 1.98
1638 1704 7.128331 CGATTTGAACGCATGATTTAAGAGAT 58.872 34.615 0.00 0.00 0.00 2.75
1639 1705 6.477742 CGATTTGAACGCATGATTTAAGAGA 58.522 36.000 0.00 0.00 0.00 3.10
1640 1706 6.707752 CGATTTGAACGCATGATTTAAGAG 57.292 37.500 0.00 0.00 0.00 2.85
1653 1719 4.208047 TGAAAATGGTTTGCGATTTGAACG 59.792 37.500 0.00 0.00 34.13 3.95
1654 1720 5.234116 AGTGAAAATGGTTTGCGATTTGAAC 59.766 36.000 0.00 0.00 34.13 3.18
1655 1721 5.355596 AGTGAAAATGGTTTGCGATTTGAA 58.644 33.333 0.00 0.00 34.13 2.69
1656 1722 4.942852 AGTGAAAATGGTTTGCGATTTGA 58.057 34.783 0.00 0.00 34.13 2.69
1657 1723 5.233902 TCAAGTGAAAATGGTTTGCGATTTG 59.766 36.000 0.00 0.00 34.13 2.32
1658 1724 5.355596 TCAAGTGAAAATGGTTTGCGATTT 58.644 33.333 0.00 0.00 35.09 2.17
1659 1725 4.942852 TCAAGTGAAAATGGTTTGCGATT 58.057 34.783 0.00 0.00 0.00 3.34
1660 1726 4.278170 TCTCAAGTGAAAATGGTTTGCGAT 59.722 37.500 0.00 0.00 0.00 4.58
1661 1727 3.629855 TCTCAAGTGAAAATGGTTTGCGA 59.370 39.130 0.00 0.00 0.00 5.10
1662 1728 3.963665 TCTCAAGTGAAAATGGTTTGCG 58.036 40.909 0.00 0.00 0.00 4.85
1663 1729 6.660887 TTTTCTCAAGTGAAAATGGTTTGC 57.339 33.333 6.08 0.00 39.92 3.68
1676 1742 9.343539 GGTGCTATATAAGGAATTTTCTCAAGT 57.656 33.333 0.00 0.00 0.00 3.16
1677 1743 8.499162 CGGTGCTATATAAGGAATTTTCTCAAG 58.501 37.037 0.00 0.00 0.00 3.02
1678 1744 7.990886 ACGGTGCTATATAAGGAATTTTCTCAA 59.009 33.333 0.00 0.00 0.00 3.02
1679 1745 7.506114 ACGGTGCTATATAAGGAATTTTCTCA 58.494 34.615 0.00 0.00 0.00 3.27
1680 1746 7.964604 ACGGTGCTATATAAGGAATTTTCTC 57.035 36.000 0.00 0.00 0.00 2.87
1681 1747 8.747538 AAACGGTGCTATATAAGGAATTTTCT 57.252 30.769 0.00 0.00 0.00 2.52
1694 1760 9.194271 GGAAACAAAATTTAAAACGGTGCTATA 57.806 29.630 0.00 0.00 0.00 1.31
1695 1761 7.171848 GGGAAACAAAATTTAAAACGGTGCTAT 59.828 33.333 0.00 0.00 0.00 2.97
1696 1762 6.479331 GGGAAACAAAATTTAAAACGGTGCTA 59.521 34.615 0.00 0.00 0.00 3.49
1697 1763 5.294799 GGGAAACAAAATTTAAAACGGTGCT 59.705 36.000 0.00 0.00 0.00 4.40
1698 1764 5.294799 AGGGAAACAAAATTTAAAACGGTGC 59.705 36.000 0.00 0.00 0.00 5.01
1699 1765 6.912203 AGGGAAACAAAATTTAAAACGGTG 57.088 33.333 0.00 0.00 0.00 4.94
1700 1766 9.616156 AAATAGGGAAACAAAATTTAAAACGGT 57.384 25.926 0.00 0.00 0.00 4.83
1701 1767 9.871299 CAAATAGGGAAACAAAATTTAAAACGG 57.129 29.630 0.00 0.00 0.00 4.44
1707 1773 9.757227 CAGTGTCAAATAGGGAAACAAAATTTA 57.243 29.630 0.00 0.00 0.00 1.40
1708 1774 8.482128 TCAGTGTCAAATAGGGAAACAAAATTT 58.518 29.630 0.00 0.00 0.00 1.82
1709 1775 8.017418 TCAGTGTCAAATAGGGAAACAAAATT 57.983 30.769 0.00 0.00 0.00 1.82
1710 1776 7.595819 TCAGTGTCAAATAGGGAAACAAAAT 57.404 32.000 0.00 0.00 0.00 1.82
1711 1777 7.411486 TTCAGTGTCAAATAGGGAAACAAAA 57.589 32.000 0.00 0.00 0.00 2.44
1712 1778 7.411486 TTTCAGTGTCAAATAGGGAAACAAA 57.589 32.000 0.00 0.00 0.00 2.83
1713 1779 7.411486 TTTTCAGTGTCAAATAGGGAAACAA 57.589 32.000 0.00 0.00 0.00 2.83
1714 1780 7.123547 AGTTTTTCAGTGTCAAATAGGGAAACA 59.876 33.333 0.00 0.00 0.00 2.83
1715 1781 7.489160 AGTTTTTCAGTGTCAAATAGGGAAAC 58.511 34.615 0.00 0.00 0.00 2.78
1716 1782 7.654022 AGTTTTTCAGTGTCAAATAGGGAAA 57.346 32.000 0.00 0.00 0.00 3.13
1717 1783 7.654022 AAGTTTTTCAGTGTCAAATAGGGAA 57.346 32.000 0.00 0.00 0.00 3.97
1718 1784 7.654022 AAAGTTTTTCAGTGTCAAATAGGGA 57.346 32.000 0.00 0.00 0.00 4.20
1719 1785 8.716646 AAAAAGTTTTTCAGTGTCAAATAGGG 57.283 30.769 7.79 0.00 0.00 3.53
1720 1786 9.586435 AGAAAAAGTTTTTCAGTGTCAAATAGG 57.414 29.630 32.23 0.00 0.00 2.57
1723 1789 8.935844 GGAAGAAAAAGTTTTTCAGTGTCAAAT 58.064 29.630 32.23 13.50 31.07 2.32
1724 1790 7.386573 GGGAAGAAAAAGTTTTTCAGTGTCAAA 59.613 33.333 32.23 0.00 31.07 2.69
1725 1791 6.871492 GGGAAGAAAAAGTTTTTCAGTGTCAA 59.129 34.615 32.23 0.00 31.07 3.18
1726 1792 6.210584 AGGGAAGAAAAAGTTTTTCAGTGTCA 59.789 34.615 32.23 0.00 31.07 3.58
1727 1793 6.631016 AGGGAAGAAAAAGTTTTTCAGTGTC 58.369 36.000 32.23 23.96 31.07 3.67
1728 1794 6.605471 AGGGAAGAAAAAGTTTTTCAGTGT 57.395 33.333 32.23 19.32 31.07 3.55
1755 1821 9.930158 AGGGCATAAAATTTAGATAAGGTGTTA 57.070 29.630 0.00 0.00 0.00 2.41
1756 1822 8.838649 AGGGCATAAAATTTAGATAAGGTGTT 57.161 30.769 0.00 0.00 0.00 3.32
1757 1823 8.838649 AAGGGCATAAAATTTAGATAAGGTGT 57.161 30.769 0.00 0.00 0.00 4.16
1760 1826 9.893305 CGTAAAGGGCATAAAATTTAGATAAGG 57.107 33.333 0.00 0.00 0.00 2.69
1763 1829 9.616156 TGTCGTAAAGGGCATAAAATTTAGATA 57.384 29.630 0.00 0.00 0.00 1.98
1764 1830 8.403236 GTGTCGTAAAGGGCATAAAATTTAGAT 58.597 33.333 0.00 0.00 0.00 1.98
1765 1831 7.608761 AGTGTCGTAAAGGGCATAAAATTTAGA 59.391 33.333 0.00 0.00 0.00 2.10
1766 1832 7.758495 AGTGTCGTAAAGGGCATAAAATTTAG 58.242 34.615 0.00 0.00 0.00 1.85
1767 1833 7.690952 AGTGTCGTAAAGGGCATAAAATTTA 57.309 32.000 0.00 0.00 0.00 1.40
1768 1834 6.584185 AGTGTCGTAAAGGGCATAAAATTT 57.416 33.333 0.00 0.00 0.00 1.82
1769 1835 6.349860 GGAAGTGTCGTAAAGGGCATAAAATT 60.350 38.462 0.00 0.00 0.00 1.82
1770 1836 5.124936 GGAAGTGTCGTAAAGGGCATAAAAT 59.875 40.000 0.00 0.00 0.00 1.82
1771 1837 4.456566 GGAAGTGTCGTAAAGGGCATAAAA 59.543 41.667 0.00 0.00 0.00 1.52
1772 1838 4.004982 GGAAGTGTCGTAAAGGGCATAAA 58.995 43.478 0.00 0.00 0.00 1.40
1773 1839 3.008157 TGGAAGTGTCGTAAAGGGCATAA 59.992 43.478 0.00 0.00 0.00 1.90
1774 1840 2.568062 TGGAAGTGTCGTAAAGGGCATA 59.432 45.455 0.00 0.00 0.00 3.14
1775 1841 1.349688 TGGAAGTGTCGTAAAGGGCAT 59.650 47.619 0.00 0.00 0.00 4.40
1776 1842 0.759959 TGGAAGTGTCGTAAAGGGCA 59.240 50.000 0.00 0.00 0.00 5.36
1777 1843 2.007608 GATGGAAGTGTCGTAAAGGGC 58.992 52.381 0.00 0.00 0.00 5.19
1778 1844 3.328382 TGATGGAAGTGTCGTAAAGGG 57.672 47.619 0.00 0.00 0.00 3.95
1779 1845 5.880054 AATTGATGGAAGTGTCGTAAAGG 57.120 39.130 0.00 0.00 0.00 3.11
1780 1846 9.329913 CTTAAAATTGATGGAAGTGTCGTAAAG 57.670 33.333 0.00 0.00 0.00 1.85
1781 1847 7.806014 GCTTAAAATTGATGGAAGTGTCGTAAA 59.194 33.333 0.00 0.00 0.00 2.01
1782 1848 7.302524 GCTTAAAATTGATGGAAGTGTCGTAA 58.697 34.615 0.00 0.00 0.00 3.18
1783 1849 6.128117 GGCTTAAAATTGATGGAAGTGTCGTA 60.128 38.462 0.00 0.00 0.00 3.43
1784 1850 5.335661 GGCTTAAAATTGATGGAAGTGTCGT 60.336 40.000 0.00 0.00 0.00 4.34
1785 1851 5.095490 GGCTTAAAATTGATGGAAGTGTCG 58.905 41.667 0.00 0.00 0.00 4.35
1786 1852 6.272822 AGGCTTAAAATTGATGGAAGTGTC 57.727 37.500 0.00 0.00 0.00 3.67
1787 1853 6.670695 AAGGCTTAAAATTGATGGAAGTGT 57.329 33.333 0.00 0.00 0.00 3.55
1788 1854 7.273381 CGTTAAGGCTTAAAATTGATGGAAGTG 59.727 37.037 20.57 0.00 0.00 3.16
1789 1855 7.312899 CGTTAAGGCTTAAAATTGATGGAAGT 58.687 34.615 20.57 0.00 0.00 3.01
1790 1856 6.751888 CCGTTAAGGCTTAAAATTGATGGAAG 59.248 38.462 20.57 0.00 0.00 3.46
1791 1857 6.209788 ACCGTTAAGGCTTAAAATTGATGGAA 59.790 34.615 20.57 0.00 46.52 3.53
1792 1858 5.712917 ACCGTTAAGGCTTAAAATTGATGGA 59.287 36.000 20.57 0.00 46.52 3.41
1793 1859 5.804979 CACCGTTAAGGCTTAAAATTGATGG 59.195 40.000 20.57 14.56 46.52 3.51
1794 1860 6.386654 ACACCGTTAAGGCTTAAAATTGATG 58.613 36.000 20.57 14.56 46.52 3.07
1795 1861 6.584185 ACACCGTTAAGGCTTAAAATTGAT 57.416 33.333 20.57 3.61 46.52 2.57
1796 1862 6.039493 TCAACACCGTTAAGGCTTAAAATTGA 59.961 34.615 20.57 19.35 46.52 2.57
1797 1863 6.210078 TCAACACCGTTAAGGCTTAAAATTG 58.790 36.000 20.57 17.77 46.52 2.32
1798 1864 6.394025 TCAACACCGTTAAGGCTTAAAATT 57.606 33.333 20.57 8.50 46.52 1.82
1799 1865 6.394025 TTCAACACCGTTAAGGCTTAAAAT 57.606 33.333 20.57 7.12 46.52 1.82
1800 1866 5.831702 TTCAACACCGTTAAGGCTTAAAA 57.168 34.783 20.57 6.81 46.52 1.52
1801 1867 5.531659 TCATTCAACACCGTTAAGGCTTAAA 59.468 36.000 20.57 3.20 46.52 1.52
1802 1868 5.049267 GTCATTCAACACCGTTAAGGCTTAA 60.049 40.000 15.49 15.49 46.52 1.85
1803 1869 4.453136 GTCATTCAACACCGTTAAGGCTTA 59.547 41.667 2.04 2.04 46.52 3.09
1804 1870 3.252458 GTCATTCAACACCGTTAAGGCTT 59.748 43.478 4.58 4.58 46.52 4.35
1805 1871 2.812011 GTCATTCAACACCGTTAAGGCT 59.188 45.455 0.00 0.00 46.52 4.58
1806 1872 2.550606 TGTCATTCAACACCGTTAAGGC 59.449 45.455 0.00 0.00 46.52 4.35
1807 1873 4.141855 GTGTCATTCAACACCGTTAAGG 57.858 45.455 0.00 0.00 43.01 2.69
1816 1882 3.876914 GTCTGTTCAGGTGTCATTCAACA 59.123 43.478 0.00 0.00 35.97 3.33
1817 1883 3.251004 GGTCTGTTCAGGTGTCATTCAAC 59.749 47.826 0.00 0.00 0.00 3.18
1818 1884 3.136443 AGGTCTGTTCAGGTGTCATTCAA 59.864 43.478 0.00 0.00 0.00 2.69
1819 1885 2.705658 AGGTCTGTTCAGGTGTCATTCA 59.294 45.455 0.00 0.00 0.00 2.57
1820 1886 3.409026 AGGTCTGTTCAGGTGTCATTC 57.591 47.619 0.00 0.00 0.00 2.67
1821 1887 5.505181 AATAGGTCTGTTCAGGTGTCATT 57.495 39.130 0.00 0.00 0.00 2.57
1822 1888 5.248640 CAAATAGGTCTGTTCAGGTGTCAT 58.751 41.667 0.00 0.00 0.00 3.06
1823 1889 4.641396 CAAATAGGTCTGTTCAGGTGTCA 58.359 43.478 0.00 0.00 0.00 3.58
1824 1890 3.437049 GCAAATAGGTCTGTTCAGGTGTC 59.563 47.826 0.00 0.00 0.00 3.67
1825 1891 3.412386 GCAAATAGGTCTGTTCAGGTGT 58.588 45.455 0.00 0.00 0.00 4.16
1826 1892 2.749621 GGCAAATAGGTCTGTTCAGGTG 59.250 50.000 0.00 0.00 0.00 4.00
1827 1893 2.290960 GGGCAAATAGGTCTGTTCAGGT 60.291 50.000 0.00 0.00 0.00 4.00
1828 1894 2.369394 GGGCAAATAGGTCTGTTCAGG 58.631 52.381 0.00 0.00 0.00 3.86
1829 1895 2.025887 AGGGGCAAATAGGTCTGTTCAG 60.026 50.000 0.00 0.00 0.00 3.02
1830 1896 1.992557 AGGGGCAAATAGGTCTGTTCA 59.007 47.619 0.00 0.00 0.00 3.18
1831 1897 2.026262 TGAGGGGCAAATAGGTCTGTTC 60.026 50.000 0.00 0.00 0.00 3.18
1832 1898 1.992557 TGAGGGGCAAATAGGTCTGTT 59.007 47.619 0.00 0.00 0.00 3.16
1833 1899 1.668826 TGAGGGGCAAATAGGTCTGT 58.331 50.000 0.00 0.00 0.00 3.41
1834 1900 2.173356 TCATGAGGGGCAAATAGGTCTG 59.827 50.000 0.00 0.00 0.00 3.51
1835 1901 2.441001 CTCATGAGGGGCAAATAGGTCT 59.559 50.000 15.38 0.00 0.00 3.85
1836 1902 2.487986 CCTCATGAGGGGCAAATAGGTC 60.488 54.545 31.14 0.00 44.87 3.85
1837 1903 1.496429 CCTCATGAGGGGCAAATAGGT 59.504 52.381 31.14 0.00 44.87 3.08
1838 1904 2.283145 CCTCATGAGGGGCAAATAGG 57.717 55.000 31.14 4.89 44.87 2.57
1849 1915 5.738909 AGATCAACCTAACAACCTCATGAG 58.261 41.667 16.24 16.24 0.00 2.90
1850 1916 5.338381 GGAGATCAACCTAACAACCTCATGA 60.338 44.000 0.00 0.00 0.00 3.07
1851 1917 4.878397 GGAGATCAACCTAACAACCTCATG 59.122 45.833 0.00 0.00 0.00 3.07
1852 1918 4.536090 TGGAGATCAACCTAACAACCTCAT 59.464 41.667 9.71 0.00 0.00 2.90
1853 1919 3.907474 TGGAGATCAACCTAACAACCTCA 59.093 43.478 9.71 0.00 0.00 3.86
1854 1920 4.254492 GTGGAGATCAACCTAACAACCTC 58.746 47.826 9.71 0.00 0.00 3.85
1855 1921 3.009143 GGTGGAGATCAACCTAACAACCT 59.991 47.826 0.00 0.00 0.00 3.50
1856 1922 3.244770 TGGTGGAGATCAACCTAACAACC 60.245 47.826 7.89 9.76 30.29 3.77
1857 1923 4.015872 TGGTGGAGATCAACCTAACAAC 57.984 45.455 7.89 2.28 30.29 3.32
1858 1924 4.042809 ACATGGTGGAGATCAACCTAACAA 59.957 41.667 7.89 0.00 30.29 2.83
1859 1925 3.587061 ACATGGTGGAGATCAACCTAACA 59.413 43.478 7.89 7.37 30.29 2.41
1860 1926 3.941483 CACATGGTGGAGATCAACCTAAC 59.059 47.826 7.89 3.41 30.29 2.34
1861 1927 4.220693 CACATGGTGGAGATCAACCTAA 57.779 45.455 7.89 0.00 30.29 2.69
1862 1928 3.912496 CACATGGTGGAGATCAACCTA 57.088 47.619 7.89 0.00 30.29 3.08
1863 1929 2.795231 CACATGGTGGAGATCAACCT 57.205 50.000 7.89 0.00 30.29 3.50
1894 1960 2.819284 GGATCTAAGGGCCCGGTGG 61.819 68.421 18.44 11.09 0.00 4.61
1895 1961 2.829592 GGATCTAAGGGCCCGGTG 59.170 66.667 18.44 10.51 0.00 4.94
1896 1962 2.842936 CGGATCTAAGGGCCCGGT 60.843 66.667 18.44 11.65 38.42 5.28
1897 1963 4.315941 GCGGATCTAAGGGCCCGG 62.316 72.222 18.44 11.27 42.02 5.73
1898 1964 4.664677 CGCGGATCTAAGGGCCCG 62.665 72.222 18.44 1.51 44.34 6.13
1899 1965 4.990553 GCGCGGATCTAAGGGCCC 62.991 72.222 16.46 16.46 39.91 5.80
1901 1967 4.990553 GGGCGCGGATCTAAGGGC 62.991 72.222 8.83 13.72 44.19 5.19
1902 1968 3.234730 AGGGCGCGGATCTAAGGG 61.235 66.667 8.83 0.00 0.00 3.95
1903 1969 1.821061 ATCAGGGCGCGGATCTAAGG 61.821 60.000 8.83 0.00 0.00 2.69
1904 1970 0.389166 GATCAGGGCGCGGATCTAAG 60.389 60.000 28.34 1.14 37.52 2.18
1905 1971 1.666011 GATCAGGGCGCGGATCTAA 59.334 57.895 28.34 0.00 37.52 2.10
1906 1972 2.626780 CGATCAGGGCGCGGATCTA 61.627 63.158 30.69 2.82 38.18 1.98
1907 1973 3.983494 CGATCAGGGCGCGGATCT 61.983 66.667 30.69 9.16 38.18 2.75
1927 1993 4.035102 AGAAGAGGGTTGGGCGCC 62.035 66.667 21.18 21.18 0.00 6.53
1928 1994 2.747855 CAGAAGAGGGTTGGGCGC 60.748 66.667 0.00 0.00 0.00 6.53
1929 1995 2.045926 CCAGAAGAGGGTTGGGCG 60.046 66.667 0.00 0.00 0.00 6.13
1930 1996 1.460699 AACCAGAAGAGGGTTGGGC 59.539 57.895 0.00 0.00 46.53 5.36
1935 2001 1.427072 CCCACCAACCAGAAGAGGGT 61.427 60.000 0.00 0.00 41.41 4.34
1936 2002 1.380302 CCCACCAACCAGAAGAGGG 59.620 63.158 0.00 0.00 0.00 4.30
1937 2003 1.303643 GCCCACCAACCAGAAGAGG 60.304 63.158 0.00 0.00 0.00 3.69
1938 2004 1.303643 GGCCCACCAACCAGAAGAG 60.304 63.158 0.00 0.00 35.26 2.85
1939 2005 2.840753 GGGCCCACCAACCAGAAGA 61.841 63.158 19.95 0.00 39.85 2.87
1940 2006 2.283173 GGGCCCACCAACCAGAAG 60.283 66.667 19.95 0.00 39.85 2.85
1941 2007 3.909651 GGGGCCCACCAACCAGAA 61.910 66.667 26.86 0.00 42.91 3.02
1942 2008 4.938756 AGGGGCCCACCAACCAGA 62.939 66.667 27.72 0.00 42.91 3.86
1943 2009 4.684134 CAGGGGCCCACCAACCAG 62.684 72.222 27.72 0.00 42.91 4.00
1945 2011 4.994756 CACAGGGGCCCACCAACC 62.995 72.222 27.72 4.38 42.91 3.77
1946 2012 3.897122 TCACAGGGGCCCACCAAC 61.897 66.667 27.72 5.28 42.91 3.77
1947 2013 3.897122 GTCACAGGGGCCCACCAA 61.897 66.667 27.72 4.22 42.91 3.67
1956 2022 1.816863 ATATAGCGCGGGTCACAGGG 61.817 60.000 8.83 0.00 0.00 4.45
1957 2023 0.667487 CATATAGCGCGGGTCACAGG 60.667 60.000 8.83 0.00 0.00 4.00
1958 2024 0.032130 ACATATAGCGCGGGTCACAG 59.968 55.000 8.83 0.00 0.00 3.66
1959 2025 0.031585 GACATATAGCGCGGGTCACA 59.968 55.000 8.83 0.00 0.00 3.58
1960 2026 1.002250 CGACATATAGCGCGGGTCAC 61.002 60.000 8.83 0.00 0.00 3.67
1961 2027 1.284715 CGACATATAGCGCGGGTCA 59.715 57.895 8.83 0.00 0.00 4.02
1962 2028 1.443872 CCGACATATAGCGCGGGTC 60.444 63.158 8.83 5.84 40.08 4.46
1963 2029 2.649034 CCGACATATAGCGCGGGT 59.351 61.111 8.83 0.00 40.08 5.28
1966 2032 1.733041 CCCACCGACATATAGCGCG 60.733 63.158 0.00 0.00 0.00 6.86
1967 2033 0.032952 TTCCCACCGACATATAGCGC 59.967 55.000 0.00 0.00 0.00 5.92
1968 2034 2.132762 GTTTCCCACCGACATATAGCG 58.867 52.381 0.00 0.00 0.00 4.26
1969 2035 2.132762 CGTTTCCCACCGACATATAGC 58.867 52.381 0.00 0.00 0.00 2.97
1970 2036 3.720949 TCGTTTCCCACCGACATATAG 57.279 47.619 0.00 0.00 0.00 1.31
2123 2189 3.904717 ACACTCAATACACCCACCAAAA 58.095 40.909 0.00 0.00 0.00 2.44
2266 2332 6.622427 AGTTCATAGTACTGTAGGCCTTTT 57.378 37.500 12.58 0.00 0.00 2.27
2287 2353 4.162698 TGTCCTGTAATACGGGCAATAAGT 59.837 41.667 13.34 0.00 44.40 2.24
2293 2359 2.093869 GTCTTGTCCTGTAATACGGGCA 60.094 50.000 13.34 11.46 44.40 5.36
2483 2549 1.001020 TGGTGGCATGCGGATCTTT 60.001 52.632 12.44 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.