Multiple sequence alignment - TraesCS4D01G127200

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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 TraesCS4D01G127200 chr4D 100.000 2714 0 0 1 2714 111609958 111612671 0.000000e+00 5012.0
1 TraesCS4D01G127200 chr4D 96.631 653 22 0 2062 2714 447592327 447591675 0.000000e+00 1085.0
2 TraesCS4D01G127200 chr4B 90.359 1701 107 26 3 1655 172396328 172398019 0.000000e+00 2180.0
3 TraesCS4D01G127200 chr4B 89.286 140 9 5 1824 1958 172450005 172450143 1.290000e-38 171.0
4 TraesCS4D01G127200 chr4B 91.489 47 2 2 1804 1849 172398114 172398159 2.260000e-06 63.9
5 TraesCS4D01G127200 chr5D 96.483 654 21 2 2062 2714 517330076 517329424 0.000000e+00 1079.0
6 TraesCS4D01G127200 chr5D 96.325 653 22 2 2062 2714 206338766 206339416 0.000000e+00 1072.0
7 TraesCS4D01G127200 chr5D 96.177 654 24 1 2061 2714 74630485 74629833 0.000000e+00 1068.0
8 TraesCS4D01G127200 chr3D 96.478 653 23 0 2062 2714 586216766 586217418 0.000000e+00 1079.0
9 TraesCS4D01G127200 chr3D 96.336 655 23 1 2060 2714 291912485 291911832 0.000000e+00 1075.0
10 TraesCS4D01G127200 chr3D 96.049 658 25 1 2057 2714 388924223 388924879 0.000000e+00 1070.0
11 TraesCS4D01G127200 chr7D 96.330 654 22 2 2061 2714 35196660 35197311 0.000000e+00 1074.0
12 TraesCS4D01G127200 chr7D 85.808 458 60 3 1197 1653 41592418 41592871 5.260000e-132 481.0
13 TraesCS4D01G127200 chr2D 96.183 655 23 2 2061 2714 59481720 59482373 0.000000e+00 1070.0
14 TraesCS4D01G127200 chr4A 92.288 765 40 2 891 1655 465524226 465523481 0.000000e+00 1068.0
15 TraesCS4D01G127200 chr4A 86.819 918 71 17 3 881 465525228 465524322 0.000000e+00 979.0
16 TraesCS4D01G127200 chr4A 86.871 457 60 0 1197 1653 648784639 648785095 1.860000e-141 512.0
17 TraesCS4D01G127200 chr4A 90.850 153 14 0 1806 1958 465523373 465523221 3.540000e-49 206.0
18 TraesCS4D01G127200 chr7A 87.965 457 55 0 1197 1653 40987988 40988444 8.550000e-150 540.0


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 TraesCS4D01G127200 chr4D 111609958 111612671 2713 False 5012.00 5012 100.000000 1 2714 1 chr4D.!!$F1 2713
1 TraesCS4D01G127200 chr4D 447591675 447592327 652 True 1085.00 1085 96.631000 2062 2714 1 chr4D.!!$R1 652
2 TraesCS4D01G127200 chr4B 172396328 172398159 1831 False 1121.95 2180 90.924000 3 1849 2 chr4B.!!$F2 1846
3 TraesCS4D01G127200 chr5D 517329424 517330076 652 True 1079.00 1079 96.483000 2062 2714 1 chr5D.!!$R2 652
4 TraesCS4D01G127200 chr5D 206338766 206339416 650 False 1072.00 1072 96.325000 2062 2714 1 chr5D.!!$F1 652
5 TraesCS4D01G127200 chr5D 74629833 74630485 652 True 1068.00 1068 96.177000 2061 2714 1 chr5D.!!$R1 653
6 TraesCS4D01G127200 chr3D 586216766 586217418 652 False 1079.00 1079 96.478000 2062 2714 1 chr3D.!!$F2 652
7 TraesCS4D01G127200 chr3D 291911832 291912485 653 True 1075.00 1075 96.336000 2060 2714 1 chr3D.!!$R1 654
8 TraesCS4D01G127200 chr3D 388924223 388924879 656 False 1070.00 1070 96.049000 2057 2714 1 chr3D.!!$F1 657
9 TraesCS4D01G127200 chr7D 35196660 35197311 651 False 1074.00 1074 96.330000 2061 2714 1 chr7D.!!$F1 653
10 TraesCS4D01G127200 chr2D 59481720 59482373 653 False 1070.00 1070 96.183000 2061 2714 1 chr2D.!!$F1 653
11 TraesCS4D01G127200 chr4A 465523221 465525228 2007 True 751.00 1068 89.985667 3 1958 3 chr4A.!!$R1 1955

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
317 328 1.014352 CCCCACGCTATGTTACTTGC 58.986 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2216 0.037975 TCTGAACGCCCGTAAAGTCC 60.038 55.0 0.0 0.0 0.0 3.85 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
47 48 4.021229 ACAACATATCAGGGAGACGTGTA 58.979 43.478 0.00 0.00 46.12 2.90
62 63 5.416947 AGACGTGTATAGGAACAACATTCC 58.583 41.667 0.00 0.00 38.86 3.01
130 131 4.544683 AGGTCTACTCGCCCTTATTAAGT 58.455 43.478 2.88 0.00 0.00 2.24
149 150 2.076863 GTAAACGCATTGGTGAGAGCT 58.923 47.619 0.00 0.00 0.00 4.09
200 208 6.057627 CATGTGTCTCATGCCTAGAAATTC 57.942 41.667 2.12 0.00 45.69 2.17
208 216 6.432162 TCTCATGCCTAGAAATTCCATATTGC 59.568 38.462 0.00 0.00 0.00 3.56
288 298 2.103432 TCGCTTTCTATGGCCCGATTTA 59.897 45.455 0.00 0.00 0.00 1.40
317 328 1.014352 CCCCACGCTATGTTACTTGC 58.986 55.000 0.00 0.00 0.00 4.01
328 339 6.400727 CGCTATGTTACTTGCGTTCTACTTTT 60.401 38.462 0.00 0.00 42.93 2.27
334 345 7.658575 TGTTACTTGCGTTCTACTTTTATTCCT 59.341 33.333 0.00 0.00 0.00 3.36
385 396 4.141144 CGGCCCGCTCATAATTGT 57.859 55.556 0.00 0.00 0.00 2.71
438 465 5.299531 TCGAGTCTCATTATTACCACCTCTG 59.700 44.000 0.00 0.00 0.00 3.35
439 466 5.299531 CGAGTCTCATTATTACCACCTCTGA 59.700 44.000 0.00 0.00 0.00 3.27
440 467 6.183360 CGAGTCTCATTATTACCACCTCTGAA 60.183 42.308 0.00 0.00 0.00 3.02
441 468 7.118496 AGTCTCATTATTACCACCTCTGAAG 57.882 40.000 0.00 0.00 0.00 3.02
442 469 5.755861 GTCTCATTATTACCACCTCTGAAGC 59.244 44.000 0.00 0.00 0.00 3.86
443 470 5.425217 TCTCATTATTACCACCTCTGAAGCA 59.575 40.000 0.00 0.00 0.00 3.91
444 471 5.428253 TCATTATTACCACCTCTGAAGCAC 58.572 41.667 0.00 0.00 0.00 4.40
447 474 3.402628 TTACCACCTCTGAAGCACTTC 57.597 47.619 3.37 3.37 39.91 3.01
480 509 7.104043 ACAATTGCATGCATAGTATTCTGTT 57.896 32.000 23.37 0.00 0.00 3.16
505 534 1.302913 TCGATTTGCAGGCCGGAAA 60.303 52.632 5.05 11.77 39.47 3.13
510 539 1.876322 TTTGCAGGCCGGAAAATTTG 58.124 45.000 5.05 0.00 31.16 2.32
523 552 5.333263 CCGGAAAATTTGCTCAAATCACAAC 60.333 40.000 0.00 0.00 39.88 3.32
550 579 8.514330 AAGGAAAACGAATATAGCCATTTGTA 57.486 30.769 0.00 0.00 32.41 2.41
554 583 8.967664 AAAACGAATATAGCCATTTGTAGGTA 57.032 30.769 0.00 0.00 32.41 3.08
571 600 4.258457 AGGTAGTAGAGTGAGGAGCAAT 57.742 45.455 0.00 0.00 0.00 3.56
671 708 1.870055 AAGTCCATTGCTTGCTGCGG 61.870 55.000 0.00 0.00 46.63 5.69
757 794 1.497278 CGTGACTCATTTGCACCGG 59.503 57.895 0.00 0.00 0.00 5.28
813 850 2.187946 GCTGCTAGCCACGTGGAT 59.812 61.111 38.30 34.37 34.48 3.41
819 856 1.743772 GCTAGCCACGTGGATGACAAT 60.744 52.381 38.30 15.16 37.39 2.71
825 862 3.438781 GCCACGTGGATGACAATTTTCTA 59.561 43.478 38.30 0.00 37.39 2.10
864 904 4.067896 TCTGAAGTGCCATTTCTCTGAAC 58.932 43.478 1.51 0.00 0.00 3.18
881 922 4.007659 CTGAACTACCGGGCAGTTTTAAT 58.992 43.478 20.72 2.88 36.38 1.40
883 924 3.428413 ACTACCGGGCAGTTTTAATGT 57.572 42.857 6.32 0.00 0.00 2.71
886 927 1.161843 CCGGGCAGTTTTAATGTCGT 58.838 50.000 0.00 0.00 0.00 4.34
887 928 2.289569 ACCGGGCAGTTTTAATGTCGTA 60.290 45.455 6.32 0.00 0.00 3.43
940 1067 2.771089 TGAGCATGAAGAACACTCCAC 58.229 47.619 0.00 0.00 0.00 4.02
982 1110 3.763360 TGGTGGCCAAATACAGAATCAAG 59.237 43.478 7.24 0.00 0.00 3.02
987 1115 4.394920 GGCCAAATACAGAATCAAGTCGAA 59.605 41.667 0.00 0.00 0.00 3.71
1050 1183 0.926155 CATCTGCCATCTTCGACACG 59.074 55.000 0.00 0.00 0.00 4.49
1114 1259 3.617284 TGTTCCTCTAGTAGCGTGATGA 58.383 45.455 0.00 0.00 0.00 2.92
1122 1267 1.135139 AGTAGCGTGATGAGCGTGATT 59.865 47.619 0.00 0.00 40.04 2.57
1194 1339 3.838271 TCGGCCAGCGACCAGATC 61.838 66.667 2.24 0.00 0.00 2.75
1362 1507 1.443407 CACGGAGGCCAAGATCGAT 59.557 57.895 5.01 0.00 0.00 3.59
1400 1545 2.742372 CGTGAAGGTCAAGCCGGG 60.742 66.667 2.18 0.00 43.70 5.73
1577 1722 1.374252 GCGGGTTCGAGAAGAGCAA 60.374 57.895 0.00 0.00 39.00 3.91
1655 1800 1.883544 TCGCGTTGCTCCGTTTTGA 60.884 52.632 5.77 0.00 0.00 2.69
1656 1801 1.721133 CGCGTTGCTCCGTTTTGAC 60.721 57.895 0.00 0.00 0.00 3.18
1657 1802 1.721133 GCGTTGCTCCGTTTTGACG 60.721 57.895 0.00 0.00 0.00 4.35
1658 1803 1.928653 CGTTGCTCCGTTTTGACGA 59.071 52.632 0.00 0.00 34.64 4.20
1659 1804 0.111266 CGTTGCTCCGTTTTGACGAG 60.111 55.000 0.00 0.00 34.64 4.18
1660 1805 1.214367 GTTGCTCCGTTTTGACGAGA 58.786 50.000 0.00 0.00 34.64 4.04
1662 1807 1.942677 TGCTCCGTTTTGACGAGAAA 58.057 45.000 0.00 0.00 34.64 2.52
1666 1866 3.810373 CTCCGTTTTGACGAGAAATTGG 58.190 45.455 0.00 0.00 34.64 3.16
1675 1881 5.403897 TGACGAGAAATTGGATATTTCGC 57.596 39.130 0.00 0.00 41.49 4.70
1676 1882 4.272504 TGACGAGAAATTGGATATTTCGCC 59.727 41.667 7.91 0.00 41.49 5.54
1677 1883 3.564225 ACGAGAAATTGGATATTTCGCCC 59.436 43.478 7.91 0.00 41.49 6.13
1678 1884 3.058224 CGAGAAATTGGATATTTCGCCCC 60.058 47.826 7.91 0.00 41.49 5.80
1679 1885 2.884639 AGAAATTGGATATTTCGCCCCG 59.115 45.455 0.00 0.00 41.49 5.73
1680 1886 0.958822 AATTGGATATTTCGCCCCGC 59.041 50.000 0.00 0.00 0.00 6.13
1681 1887 0.110486 ATTGGATATTTCGCCCCGCT 59.890 50.000 0.00 0.00 0.00 5.52
1682 1888 0.106918 TTGGATATTTCGCCCCGCTT 60.107 50.000 0.00 0.00 0.00 4.68
1683 1889 0.106918 TGGATATTTCGCCCCGCTTT 60.107 50.000 0.00 0.00 0.00 3.51
1684 1890 1.141254 TGGATATTTCGCCCCGCTTTA 59.859 47.619 0.00 0.00 0.00 1.85
1685 1891 1.534163 GGATATTTCGCCCCGCTTTAC 59.466 52.381 0.00 0.00 0.00 2.01
1686 1892 2.490991 GATATTTCGCCCCGCTTTACT 58.509 47.619 0.00 0.00 0.00 2.24
1687 1893 2.406596 TATTTCGCCCCGCTTTACTT 57.593 45.000 0.00 0.00 0.00 2.24
1688 1894 1.092348 ATTTCGCCCCGCTTTACTTC 58.908 50.000 0.00 0.00 0.00 3.01
1691 1897 0.390735 TCGCCCCGCTTTACTTCTTC 60.391 55.000 0.00 0.00 0.00 2.87
1692 1898 0.672401 CGCCCCGCTTTACTTCTTCA 60.672 55.000 0.00 0.00 0.00 3.02
1696 1902 3.673323 GCCCCGCTTTACTTCTTCATTTG 60.673 47.826 0.00 0.00 0.00 2.32
1697 1903 3.756434 CCCCGCTTTACTTCTTCATTTGA 59.244 43.478 0.00 0.00 0.00 2.69
1698 1904 4.399303 CCCCGCTTTACTTCTTCATTTGAT 59.601 41.667 0.00 0.00 0.00 2.57
1699 1905 5.449177 CCCCGCTTTACTTCTTCATTTGATC 60.449 44.000 0.00 0.00 0.00 2.92
1700 1906 5.123820 CCCGCTTTACTTCTTCATTTGATCA 59.876 40.000 0.00 0.00 0.00 2.92
1701 1907 6.183360 CCCGCTTTACTTCTTCATTTGATCAT 60.183 38.462 0.00 0.00 0.00 2.45
1702 1908 7.253422 CCGCTTTACTTCTTCATTTGATCATT 58.747 34.615 0.00 0.00 0.00 2.57
1704 1910 7.163195 CGCTTTACTTCTTCATTTGATCATTCG 59.837 37.037 0.00 0.00 0.00 3.34
1705 1911 7.044445 GCTTTACTTCTTCATTTGATCATTCGC 60.044 37.037 0.00 0.00 0.00 4.70
1706 1912 5.240713 ACTTCTTCATTTGATCATTCGCC 57.759 39.130 0.00 0.00 0.00 5.54
1707 1913 4.946157 ACTTCTTCATTTGATCATTCGCCT 59.054 37.500 0.00 0.00 0.00 5.52
1709 1915 5.490139 TCTTCATTTGATCATTCGCCTTC 57.510 39.130 0.00 0.00 0.00 3.46
1710 1916 4.336433 TCTTCATTTGATCATTCGCCTTCC 59.664 41.667 0.00 0.00 0.00 3.46
1712 1918 3.628942 TCATTTGATCATTCGCCTTCCTG 59.371 43.478 0.00 0.00 0.00 3.86
1713 1919 3.348647 TTTGATCATTCGCCTTCCTGA 57.651 42.857 0.00 0.00 0.00 3.86
1714 1920 2.609427 TGATCATTCGCCTTCCTGAG 57.391 50.000 0.00 0.00 0.00 3.35
1715 1921 2.110578 TGATCATTCGCCTTCCTGAGA 58.889 47.619 0.00 0.00 0.00 3.27
1716 1922 2.102084 TGATCATTCGCCTTCCTGAGAG 59.898 50.000 0.00 0.00 0.00 3.20
1717 1923 0.826715 TCATTCGCCTTCCTGAGAGG 59.173 55.000 0.00 0.00 36.46 3.69
1724 1930 0.965439 CCTTCCTGAGAGGCTATCGG 59.035 60.000 11.03 11.03 34.61 4.18
1725 1931 1.479573 CCTTCCTGAGAGGCTATCGGA 60.480 57.143 19.25 17.05 34.61 4.55
1726 1932 2.524306 CTTCCTGAGAGGCTATCGGAT 58.476 52.381 19.25 0.00 34.61 4.18
1727 1933 1.916506 TCCTGAGAGGCTATCGGATG 58.083 55.000 19.25 3.83 34.61 3.51
1728 1934 0.894141 CCTGAGAGGCTATCGGATGG 59.106 60.000 19.25 7.59 0.00 3.51
1729 1935 0.894141 CTGAGAGGCTATCGGATGGG 59.106 60.000 12.63 0.00 0.00 4.00
1730 1936 0.542938 TGAGAGGCTATCGGATGGGG 60.543 60.000 4.47 0.00 0.00 4.96
1731 1937 1.893919 GAGAGGCTATCGGATGGGGC 61.894 65.000 0.00 6.05 0.00 5.80
1732 1938 2.930562 AGGCTATCGGATGGGGCC 60.931 66.667 17.61 17.61 42.74 5.80
1733 1939 4.035102 GGCTATCGGATGGGGCCC 62.035 72.222 18.17 18.17 37.12 5.80
1735 1941 3.706373 CTATCGGATGGGGCCCGG 61.706 72.222 19.83 7.27 46.47 5.73
1736 1942 4.242586 TATCGGATGGGGCCCGGA 62.243 66.667 19.83 12.91 46.47 5.14
1748 1954 3.346426 GCCCGGAGCCATTATCATT 57.654 52.632 0.73 0.00 34.35 2.57
1749 1955 0.883833 GCCCGGAGCCATTATCATTG 59.116 55.000 0.73 0.00 34.35 2.82
1750 1956 1.545428 GCCCGGAGCCATTATCATTGA 60.545 52.381 0.73 0.00 34.35 2.57
1751 1957 2.430465 CCCGGAGCCATTATCATTGAG 58.570 52.381 0.73 0.00 0.00 3.02
1752 1958 2.038952 CCCGGAGCCATTATCATTGAGA 59.961 50.000 0.73 0.00 0.00 3.27
1753 1959 3.070018 CCGGAGCCATTATCATTGAGAC 58.930 50.000 0.00 0.00 0.00 3.36
1754 1960 3.494924 CCGGAGCCATTATCATTGAGACA 60.495 47.826 0.00 0.00 0.00 3.41
1755 1961 4.129380 CGGAGCCATTATCATTGAGACAA 58.871 43.478 0.00 0.00 0.00 3.18
1756 1962 4.758674 CGGAGCCATTATCATTGAGACAAT 59.241 41.667 0.00 0.00 0.00 2.71
1757 1963 5.106791 CGGAGCCATTATCATTGAGACAATC 60.107 44.000 0.00 0.00 0.00 2.67
1758 1964 5.766670 GGAGCCATTATCATTGAGACAATCA 59.233 40.000 0.00 0.00 35.62 2.57
1770 1976 5.034852 TGAGACAATCAAAGGACAAGTCA 57.965 39.130 2.29 0.00 34.02 3.41
1771 1977 5.624159 TGAGACAATCAAAGGACAAGTCAT 58.376 37.500 2.29 0.00 34.02 3.06
1772 1978 5.702670 TGAGACAATCAAAGGACAAGTCATC 59.297 40.000 2.29 0.00 34.02 2.92
1773 1979 5.006386 AGACAATCAAAGGACAAGTCATCC 58.994 41.667 2.29 0.00 36.38 3.51
1774 1980 4.728772 ACAATCAAAGGACAAGTCATCCA 58.271 39.130 2.29 0.00 38.86 3.41
1775 1981 5.139727 ACAATCAAAGGACAAGTCATCCAA 58.860 37.500 2.29 0.00 38.86 3.53
1776 1982 5.010012 ACAATCAAAGGACAAGTCATCCAAC 59.990 40.000 2.29 0.00 38.86 3.77
1777 1983 3.138304 TCAAAGGACAAGTCATCCAACG 58.862 45.455 2.29 0.00 38.86 4.10
1778 1984 1.523758 AAGGACAAGTCATCCAACGC 58.476 50.000 2.29 0.00 38.86 4.84
1779 1985 0.321653 AGGACAAGTCATCCAACGCC 60.322 55.000 2.29 0.00 38.86 5.68
1780 1986 0.321653 GGACAAGTCATCCAACGCCT 60.322 55.000 2.29 0.00 36.15 5.52
1781 1987 1.523758 GACAAGTCATCCAACGCCTT 58.476 50.000 0.00 0.00 0.00 4.35
1782 1988 1.197721 GACAAGTCATCCAACGCCTTG 59.802 52.381 0.00 0.00 38.71 3.61
1783 1989 1.202758 ACAAGTCATCCAACGCCTTGA 60.203 47.619 0.00 0.00 36.79 3.02
1784 1990 1.879380 CAAGTCATCCAACGCCTTGAA 59.121 47.619 0.00 0.00 35.64 2.69
1785 1991 2.270352 AGTCATCCAACGCCTTGAAA 57.730 45.000 0.00 0.00 0.00 2.69
1786 1992 2.582052 AGTCATCCAACGCCTTGAAAA 58.418 42.857 0.00 0.00 0.00 2.29
1787 1993 2.955660 AGTCATCCAACGCCTTGAAAAA 59.044 40.909 0.00 0.00 0.00 1.94
1788 1994 3.573967 AGTCATCCAACGCCTTGAAAAAT 59.426 39.130 0.00 0.00 0.00 1.82
1789 1995 4.764823 AGTCATCCAACGCCTTGAAAAATA 59.235 37.500 0.00 0.00 0.00 1.40
1790 1996 5.095490 GTCATCCAACGCCTTGAAAAATAG 58.905 41.667 0.00 0.00 0.00 1.73
1791 1997 4.157656 TCATCCAACGCCTTGAAAAATAGG 59.842 41.667 0.00 0.00 34.54 2.57
1792 1998 2.823154 TCCAACGCCTTGAAAAATAGGG 59.177 45.455 0.00 0.00 31.95 3.53
1793 1999 2.606108 CAACGCCTTGAAAAATAGGGC 58.394 47.619 0.00 0.00 39.43 5.19
1794 2000 1.917872 ACGCCTTGAAAAATAGGGCA 58.082 45.000 0.00 0.00 42.56 5.36
1795 2001 2.243810 ACGCCTTGAAAAATAGGGCAA 58.756 42.857 0.00 0.00 42.56 4.52
1796 2002 2.630580 ACGCCTTGAAAAATAGGGCAAA 59.369 40.909 0.00 0.00 42.56 3.68
1797 2003 3.260632 ACGCCTTGAAAAATAGGGCAAAT 59.739 39.130 0.00 0.00 42.56 2.32
1798 2004 3.865164 CGCCTTGAAAAATAGGGCAAATC 59.135 43.478 0.00 0.00 42.56 2.17
1799 2005 4.620332 CGCCTTGAAAAATAGGGCAAATCA 60.620 41.667 0.00 0.00 42.56 2.57
1800 2006 5.430886 GCCTTGAAAAATAGGGCAAATCAT 58.569 37.500 0.00 0.00 42.08 2.45
1801 2007 5.525012 GCCTTGAAAAATAGGGCAAATCATC 59.475 40.000 0.00 0.00 42.08 2.92
1802 2008 6.051074 CCTTGAAAAATAGGGCAAATCATCC 58.949 40.000 0.00 0.00 0.00 3.51
1803 2009 6.352051 CCTTGAAAAATAGGGCAAATCATCCA 60.352 38.462 0.00 0.00 0.00 3.41
1804 2010 6.617782 TGAAAAATAGGGCAAATCATCCAA 57.382 33.333 0.00 0.00 0.00 3.53
1878 2084 4.630069 GCGTTGTTGGTTAGATCATGTACT 59.370 41.667 0.00 0.00 0.00 2.73
1894 2100 5.359860 TCATGTACTGATGATCCTACGTGTT 59.640 40.000 14.39 0.00 31.01 3.32
1895 2101 6.544564 TCATGTACTGATGATCCTACGTGTTA 59.455 38.462 14.39 1.12 31.01 2.41
1900 2106 4.871513 TGATGATCCTACGTGTTATCTGC 58.128 43.478 0.00 0.00 0.00 4.26
1905 2111 2.096980 TCCTACGTGTTATCTGCTGTCG 59.903 50.000 0.00 0.00 0.00 4.35
1906 2112 2.451132 CTACGTGTTATCTGCTGTCGG 58.549 52.381 0.00 0.00 0.00 4.79
1907 2113 0.108804 ACGTGTTATCTGCTGTCGGG 60.109 55.000 0.00 0.00 0.00 5.14
1917 2123 3.314331 CTGTCGGGCAGTCAGGGT 61.314 66.667 0.34 0.00 40.27 4.34
1931 2137 5.048083 GCAGTCAGGGTGAAAATGTGAATTA 60.048 40.000 0.00 0.00 0.00 1.40
1940 2146 5.569059 GTGAAAATGTGAATTAAGGACTGCG 59.431 40.000 0.00 0.00 0.00 5.18
1949 2155 0.970937 TAAGGACTGCGGACCCTCTG 60.971 60.000 10.62 0.00 0.00 3.35
1955 2161 2.514824 GCGGACCCTCTGGCAATC 60.515 66.667 0.00 0.00 33.59 2.67
1958 2164 1.153349 GGACCCTCTGGCAATCGTC 60.153 63.158 0.00 0.00 33.59 4.20
1959 2165 1.153349 GACCCTCTGGCAATCGTCC 60.153 63.158 0.00 0.00 33.59 4.79
1960 2166 2.202932 CCCTCTGGCAATCGTCCG 60.203 66.667 0.00 0.00 0.00 4.79
1961 2167 2.721167 CCCTCTGGCAATCGTCCGA 61.721 63.158 0.00 0.00 0.00 4.55
1962 2168 1.218047 CCTCTGGCAATCGTCCGAA 59.782 57.895 0.00 0.00 0.00 4.30
1963 2169 1.084370 CCTCTGGCAATCGTCCGAAC 61.084 60.000 0.00 0.00 0.00 3.95
1974 2180 3.897819 GTCCGAACGATTTGCCATC 57.102 52.632 0.00 0.00 0.00 3.51
1975 2181 1.083489 GTCCGAACGATTTGCCATCA 58.917 50.000 0.00 0.00 0.00 3.07
1976 2182 1.062587 GTCCGAACGATTTGCCATCAG 59.937 52.381 0.00 0.00 0.00 2.90
1977 2183 1.086696 CCGAACGATTTGCCATCAGT 58.913 50.000 0.00 0.00 0.00 3.41
1978 2184 1.062587 CCGAACGATTTGCCATCAGTC 59.937 52.381 0.00 0.00 0.00 3.51
1979 2185 2.002586 CGAACGATTTGCCATCAGTCT 58.997 47.619 0.00 0.00 0.00 3.24
1980 2186 2.222886 CGAACGATTTGCCATCAGTCTG 60.223 50.000 0.00 0.00 0.00 3.51
1981 2187 1.089920 ACGATTTGCCATCAGTCTGC 58.910 50.000 0.00 0.00 0.00 4.26
1982 2188 1.339438 ACGATTTGCCATCAGTCTGCT 60.339 47.619 0.00 0.00 0.00 4.24
1983 2189 1.329906 CGATTTGCCATCAGTCTGCTC 59.670 52.381 0.00 0.00 0.00 4.26
1984 2190 1.329906 GATTTGCCATCAGTCTGCTCG 59.670 52.381 0.00 0.00 0.00 5.03
1985 2191 0.321346 TTTGCCATCAGTCTGCTCGA 59.679 50.000 0.00 0.00 0.00 4.04
1986 2192 0.390340 TTGCCATCAGTCTGCTCGAC 60.390 55.000 0.00 0.00 43.17 4.20
1993 2199 2.202324 GTCTGCTCGACGGACGTC 60.202 66.667 14.38 14.38 44.57 4.34
1994 2200 2.667199 TCTGCTCGACGGACGTCA 60.667 61.111 22.60 10.31 44.77 4.35
1995 2201 2.502080 CTGCTCGACGGACGTCAC 60.502 66.667 22.60 12.64 44.77 3.67
1996 2202 2.967473 CTGCTCGACGGACGTCACT 61.967 63.158 22.60 0.08 44.77 3.41
1997 2203 2.254651 GCTCGACGGACGTCACTT 59.745 61.111 22.60 0.00 44.77 3.16
1998 2204 1.371389 GCTCGACGGACGTCACTTT 60.371 57.895 22.60 0.00 44.77 2.66
1999 2205 0.938168 GCTCGACGGACGTCACTTTT 60.938 55.000 22.60 0.00 44.77 2.27
2000 2206 1.664016 GCTCGACGGACGTCACTTTTA 60.664 52.381 22.60 0.00 44.77 1.52
2001 2207 2.653890 CTCGACGGACGTCACTTTTAA 58.346 47.619 22.60 0.00 44.77 1.52
2002 2208 2.653890 TCGACGGACGTCACTTTTAAG 58.346 47.619 22.60 5.85 44.77 1.85
2003 2209 1.123756 CGACGGACGTCACTTTTAAGC 59.876 52.381 22.60 0.00 44.77 3.09
2004 2210 2.129607 GACGGACGTCACTTTTAAGCA 58.870 47.619 18.91 0.00 44.02 3.91
2005 2211 2.540931 GACGGACGTCACTTTTAAGCAA 59.459 45.455 18.91 0.00 44.02 3.91
2006 2212 3.135994 ACGGACGTCACTTTTAAGCAAT 58.864 40.909 18.91 0.00 0.00 3.56
2007 2213 3.059188 ACGGACGTCACTTTTAAGCAATG 60.059 43.478 18.91 0.00 0.00 2.82
2008 2214 3.185594 CGGACGTCACTTTTAAGCAATGA 59.814 43.478 18.91 0.00 0.00 2.57
2009 2215 4.666655 CGGACGTCACTTTTAAGCAATGAG 60.667 45.833 18.91 0.00 0.00 2.90
2010 2216 4.378459 GGACGTCACTTTTAAGCAATGAGG 60.378 45.833 18.91 0.00 0.00 3.86
2011 2217 3.502211 ACGTCACTTTTAAGCAATGAGGG 59.498 43.478 0.00 0.00 31.19 4.30
2012 2218 3.751175 CGTCACTTTTAAGCAATGAGGGA 59.249 43.478 0.00 0.00 0.00 4.20
2013 2219 4.378459 CGTCACTTTTAAGCAATGAGGGAC 60.378 45.833 0.00 0.00 0.00 4.46
2015 2221 5.241728 GTCACTTTTAAGCAATGAGGGACTT 59.758 40.000 0.00 0.00 41.55 3.01
2016 2222 5.833131 TCACTTTTAAGCAATGAGGGACTTT 59.167 36.000 0.00 0.00 41.55 2.66
2017 2223 7.001674 TCACTTTTAAGCAATGAGGGACTTTA 58.998 34.615 0.00 0.00 41.55 1.85
2018 2224 7.040686 TCACTTTTAAGCAATGAGGGACTTTAC 60.041 37.037 0.00 0.00 41.55 2.01
2019 2225 5.873179 TTTAAGCAATGAGGGACTTTACG 57.127 39.130 0.00 0.00 41.55 3.18
2020 2226 2.403252 AGCAATGAGGGACTTTACGG 57.597 50.000 0.00 0.00 41.55 4.02
2021 2227 1.065418 AGCAATGAGGGACTTTACGGG 60.065 52.381 0.00 0.00 41.55 5.28
2022 2228 1.379527 CAATGAGGGACTTTACGGGC 58.620 55.000 0.00 0.00 41.55 6.13
2023 2229 0.107848 AATGAGGGACTTTACGGGCG 60.108 55.000 0.00 0.00 41.55 6.13
2024 2230 1.262640 ATGAGGGACTTTACGGGCGT 61.263 55.000 0.00 0.00 41.55 5.68
2025 2231 1.294459 GAGGGACTTTACGGGCGTT 59.706 57.895 0.00 0.00 41.55 4.84
2026 2232 0.738762 GAGGGACTTTACGGGCGTTC 60.739 60.000 0.00 0.00 41.55 3.95
2027 2233 1.004679 GGGACTTTACGGGCGTTCA 60.005 57.895 0.00 0.00 0.00 3.18
2028 2234 1.017701 GGGACTTTACGGGCGTTCAG 61.018 60.000 0.00 0.00 0.00 3.02
2029 2235 0.037975 GGACTTTACGGGCGTTCAGA 60.038 55.000 0.00 0.00 0.00 3.27
2030 2236 1.066136 GACTTTACGGGCGTTCAGAC 58.934 55.000 0.00 0.00 0.00 3.51
2036 2242 3.195698 GGGCGTTCAGACCGATGC 61.196 66.667 0.00 0.00 38.99 3.91
2037 2243 3.195698 GGCGTTCAGACCGATGCC 61.196 66.667 0.00 0.00 38.08 4.40
2038 2244 2.434185 GCGTTCAGACCGATGCCA 60.434 61.111 0.00 0.00 0.00 4.92
2039 2245 2.740714 GCGTTCAGACCGATGCCAC 61.741 63.158 0.00 0.00 0.00 5.01
2040 2246 2.444624 CGTTCAGACCGATGCCACG 61.445 63.158 0.00 0.00 0.00 4.94
2041 2247 2.434185 TTCAGACCGATGCCACGC 60.434 61.111 0.00 0.00 0.00 5.34
2042 2248 3.233259 TTCAGACCGATGCCACGCA 62.233 57.895 0.00 0.00 44.86 5.24
2043 2249 2.723586 TTCAGACCGATGCCACGCAA 62.724 55.000 0.00 0.00 43.62 4.85
2044 2250 2.434884 AGACCGATGCCACGCAAG 60.435 61.111 0.00 0.00 43.62 4.01
2045 2251 4.166011 GACCGATGCCACGCAAGC 62.166 66.667 0.00 0.00 43.62 4.01
2051 2257 2.596923 TGCCACGCAAGCATCCAA 60.597 55.556 0.00 0.00 45.62 3.53
2052 2258 2.180017 GCCACGCAAGCATCCAAG 59.820 61.111 0.00 0.00 45.62 3.61
2053 2259 2.334946 GCCACGCAAGCATCCAAGA 61.335 57.895 0.00 0.00 45.62 3.02
2054 2260 1.865788 GCCACGCAAGCATCCAAGAA 61.866 55.000 0.00 0.00 45.62 2.52
2055 2261 0.109597 CCACGCAAGCATCCAAGAAC 60.110 55.000 0.00 0.00 45.62 3.01
2089 2295 1.074248 AAAACCGGCGGATCTTGGT 59.926 52.632 35.78 4.66 35.90 3.67
2124 2330 0.320858 TGTGCGTTTAAGGCGGATGA 60.321 50.000 5.18 0.00 31.50 2.92
2267 2473 5.587043 CGAGATCGTAGAGGCTAAATCCTAT 59.413 44.000 0.00 0.00 43.63 2.57
2367 2573 4.370917 GGTTACACAGAGTCGGTTACAAA 58.629 43.478 0.00 0.00 0.00 2.83
2538 2744 0.324738 CAGGACTCCCTCAGTAGCCA 60.325 60.000 0.00 0.00 42.02 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 3.439293 TCTTTTGAGAGCGCGAGAATAG 58.561 45.455 12.10 0.00 0.00 1.73
118 119 5.163591 ACCAATGCGTTTACTTAATAAGGGC 60.164 40.000 4.92 1.14 0.00 5.19
130 131 2.472695 AGCTCTCACCAATGCGTTTA 57.527 45.000 0.00 0.00 0.00 2.01
194 202 6.294397 GGATGTCTCCTGCAATATGGAATTTC 60.294 42.308 0.00 0.00 38.65 2.17
249 257 1.609061 CGACTGTGGTCCAGAAGCAAT 60.609 52.381 0.00 0.00 44.49 3.56
269 279 4.636206 CCTATAAATCGGGCCATAGAAAGC 59.364 45.833 4.39 0.00 0.00 3.51
272 282 6.442541 TTTCCTATAAATCGGGCCATAGAA 57.557 37.500 4.39 0.00 0.00 2.10
288 298 4.657952 GCGTGGGGCTTTTCCTAT 57.342 55.556 0.00 0.00 39.11 2.57
334 345 9.537192 TCTTGTCTGTCTATTTCTTACGAAAAA 57.463 29.630 0.00 0.00 42.03 1.94
459 488 7.337480 TGAAACAGAATACTATGCATGCAAT 57.663 32.000 26.68 15.66 0.00 3.56
480 509 2.288666 GGCCTGCAAATCGAGTATGAA 58.711 47.619 0.00 0.00 0.00 2.57
505 534 6.347696 TCCTTTGTTGTGATTTGAGCAAATT 58.652 32.000 9.57 0.00 40.77 1.82
510 539 5.276348 CGTTTTCCTTTGTTGTGATTTGAGC 60.276 40.000 0.00 0.00 0.00 4.26
523 552 7.759433 ACAAATGGCTATATTCGTTTTCCTTTG 59.241 33.333 0.00 0.00 0.00 2.77
550 579 3.741245 TTGCTCCTCACTCTACTACCT 57.259 47.619 0.00 0.00 0.00 3.08
554 583 5.423610 ACACATTATTGCTCCTCACTCTACT 59.576 40.000 0.00 0.00 0.00 2.57
645 679 0.877071 AAGCAATGGACTTGTCAGCG 59.123 50.000 3.08 0.00 37.18 5.18
653 690 2.338015 CCGCAGCAAGCAATGGACT 61.338 57.895 0.00 0.00 46.13 3.85
671 708 2.093447 ACATAACTAGCCAGTGAGCCAC 60.093 50.000 0.00 0.00 34.36 5.01
683 720 8.779354 AGCTTCTTTTAGACCAACATAACTAG 57.221 34.615 0.00 0.00 0.00 2.57
733 770 1.926510 TGCAAATGAGTCACGCTATCG 59.073 47.619 11.16 0.00 42.43 2.92
757 794 1.012486 ACTGCCAAACTACTACGCGC 61.012 55.000 5.73 0.00 0.00 6.86
811 848 6.758416 GGGAAAAGCCATAGAAAATTGTCATC 59.242 38.462 0.00 0.00 38.95 2.92
812 849 6.627953 CGGGAAAAGCCATAGAAAATTGTCAT 60.628 38.462 0.00 0.00 38.95 3.06
813 850 5.336372 CGGGAAAAGCCATAGAAAATTGTCA 60.336 40.000 0.00 0.00 38.95 3.58
819 856 2.745281 CGTCGGGAAAAGCCATAGAAAA 59.255 45.455 0.00 0.00 38.95 2.29
825 862 1.376812 GACCGTCGGGAAAAGCCAT 60.377 57.895 17.28 0.00 38.95 4.40
864 904 2.350498 CGACATTAAAACTGCCCGGTAG 59.650 50.000 0.00 0.13 0.00 3.18
881 922 8.497554 GTGTACTTTTGGATTTACATTACGACA 58.502 33.333 0.00 0.00 0.00 4.35
883 924 8.604640 TGTGTACTTTTGGATTTACATTACGA 57.395 30.769 0.00 0.00 0.00 3.43
949 1076 2.358615 GCCACCACGCTCATCACA 60.359 61.111 0.00 0.00 0.00 3.58
1008 1141 3.679389 ACATGTGAGGTGTTGGAAGATC 58.321 45.455 0.00 0.00 0.00 2.75
1114 1259 1.198637 GAAGAGCAGCAAAATCACGCT 59.801 47.619 0.00 0.00 39.66 5.07
1122 1267 0.320771 GGACGGAGAAGAGCAGCAAA 60.321 55.000 0.00 0.00 0.00 3.68
1286 1431 2.494918 CGAGGTCTTGGTAGCCGG 59.505 66.667 0.00 0.00 0.00 6.13
1387 1532 2.430367 GTCACCCGGCTTGACCTT 59.570 61.111 19.11 0.00 37.93 3.50
1506 1651 2.441164 AGGATCGCTGTCGCCTCT 60.441 61.111 0.00 0.00 35.26 3.69
1655 1800 3.564225 GGGCGAAATATCCAATTTCTCGT 59.436 43.478 8.39 0.00 36.24 4.18
1656 1801 3.058224 GGGGCGAAATATCCAATTTCTCG 60.058 47.826 8.39 0.00 36.24 4.04
1657 1802 3.058224 CGGGGCGAAATATCCAATTTCTC 60.058 47.826 8.39 1.55 36.24 2.87
1658 1803 2.884639 CGGGGCGAAATATCCAATTTCT 59.115 45.455 8.39 0.00 36.24 2.52
1659 1804 2.607038 GCGGGGCGAAATATCCAATTTC 60.607 50.000 0.00 1.26 35.34 2.17
1660 1805 1.339929 GCGGGGCGAAATATCCAATTT 59.660 47.619 0.00 0.00 0.00 1.82
1662 1807 0.110486 AGCGGGGCGAAATATCCAAT 59.890 50.000 0.00 0.00 0.00 3.16
1666 1866 2.490991 AGTAAAGCGGGGCGAAATATC 58.509 47.619 0.00 0.00 0.00 1.63
1675 1881 3.756434 TCAAATGAAGAAGTAAAGCGGGG 59.244 43.478 0.00 0.00 0.00 5.73
1676 1882 5.123820 TGATCAAATGAAGAAGTAAAGCGGG 59.876 40.000 0.00 0.00 0.00 6.13
1677 1883 6.182039 TGATCAAATGAAGAAGTAAAGCGG 57.818 37.500 0.00 0.00 0.00 5.52
1678 1884 7.163195 CGAATGATCAAATGAAGAAGTAAAGCG 59.837 37.037 0.00 0.00 0.00 4.68
1679 1885 7.044445 GCGAATGATCAAATGAAGAAGTAAAGC 60.044 37.037 0.00 0.00 0.00 3.51
1680 1886 7.430502 GGCGAATGATCAAATGAAGAAGTAAAG 59.569 37.037 0.00 0.00 0.00 1.85
1681 1887 7.121168 AGGCGAATGATCAAATGAAGAAGTAAA 59.879 33.333 0.00 0.00 0.00 2.01
1682 1888 6.599244 AGGCGAATGATCAAATGAAGAAGTAA 59.401 34.615 0.00 0.00 0.00 2.24
1683 1889 6.115446 AGGCGAATGATCAAATGAAGAAGTA 58.885 36.000 0.00 0.00 0.00 2.24
1684 1890 4.946157 AGGCGAATGATCAAATGAAGAAGT 59.054 37.500 0.00 0.00 0.00 3.01
1685 1891 5.496133 AGGCGAATGATCAAATGAAGAAG 57.504 39.130 0.00 0.00 0.00 2.85
1686 1892 5.163622 GGAAGGCGAATGATCAAATGAAGAA 60.164 40.000 0.00 0.00 0.00 2.52
1687 1893 4.336433 GGAAGGCGAATGATCAAATGAAGA 59.664 41.667 0.00 0.00 0.00 2.87
1688 1894 4.337555 AGGAAGGCGAATGATCAAATGAAG 59.662 41.667 0.00 0.00 0.00 3.02
1691 1897 3.628942 TCAGGAAGGCGAATGATCAAATG 59.371 43.478 0.00 0.00 0.00 2.32
1692 1898 3.881688 CTCAGGAAGGCGAATGATCAAAT 59.118 43.478 0.00 0.00 0.00 2.32
1696 1902 2.547642 CCTCTCAGGAAGGCGAATGATC 60.548 54.545 0.00 0.00 37.67 2.92
1697 1903 1.415659 CCTCTCAGGAAGGCGAATGAT 59.584 52.381 0.00 0.00 37.67 2.45
1698 1904 0.826715 CCTCTCAGGAAGGCGAATGA 59.173 55.000 0.00 0.00 37.67 2.57
1699 1905 0.813210 GCCTCTCAGGAAGGCGAATG 60.813 60.000 0.00 0.00 37.67 2.67
1700 1906 1.524482 GCCTCTCAGGAAGGCGAAT 59.476 57.895 0.00 0.00 37.67 3.34
1701 1907 2.982130 GCCTCTCAGGAAGGCGAA 59.018 61.111 0.00 0.00 37.67 4.70
1705 1911 0.965439 CCGATAGCCTCTCAGGAAGG 59.035 60.000 0.00 0.00 37.67 3.46
1706 1912 1.988293 TCCGATAGCCTCTCAGGAAG 58.012 55.000 0.00 0.00 37.67 3.46
1707 1913 2.242926 CATCCGATAGCCTCTCAGGAA 58.757 52.381 0.00 0.00 37.67 3.36
1709 1915 0.894141 CCATCCGATAGCCTCTCAGG 59.106 60.000 0.00 0.00 38.80 3.86
1710 1916 0.894141 CCCATCCGATAGCCTCTCAG 59.106 60.000 0.00 0.00 0.00 3.35
1712 1918 1.893919 GCCCCATCCGATAGCCTCTC 61.894 65.000 0.00 0.00 0.00 3.20
1713 1919 1.915769 GCCCCATCCGATAGCCTCT 60.916 63.158 0.00 0.00 0.00 3.69
1714 1920 2.665603 GCCCCATCCGATAGCCTC 59.334 66.667 0.00 0.00 0.00 4.70
1715 1921 2.930562 GGCCCCATCCGATAGCCT 60.931 66.667 0.00 0.00 40.57 4.58
1716 1922 4.035102 GGGCCCCATCCGATAGCC 62.035 72.222 12.23 7.45 43.09 3.93
1730 1936 0.883833 CAATGATAATGGCTCCGGGC 59.116 55.000 0.00 3.56 40.90 6.13
1731 1937 2.038952 TCTCAATGATAATGGCTCCGGG 59.961 50.000 0.00 0.00 0.00 5.73
1732 1938 3.070018 GTCTCAATGATAATGGCTCCGG 58.930 50.000 0.00 0.00 0.00 5.14
1733 1939 3.732212 TGTCTCAATGATAATGGCTCCG 58.268 45.455 0.00 0.00 0.00 4.63
1734 1940 5.766670 TGATTGTCTCAATGATAATGGCTCC 59.233 40.000 0.00 0.00 36.77 4.70
1735 1941 6.872628 TGATTGTCTCAATGATAATGGCTC 57.127 37.500 0.00 0.00 36.77 4.70
1736 1942 7.201884 CCTTTGATTGTCTCAATGATAATGGCT 60.202 37.037 0.00 0.00 43.30 4.75
1737 1943 6.921857 CCTTTGATTGTCTCAATGATAATGGC 59.078 38.462 0.00 0.00 43.30 4.40
1738 1944 8.133627 GTCCTTTGATTGTCTCAATGATAATGG 58.866 37.037 0.00 5.15 43.30 3.16
1739 1945 8.680001 TGTCCTTTGATTGTCTCAATGATAATG 58.320 33.333 0.00 0.00 43.30 1.90
1740 1946 8.812513 TGTCCTTTGATTGTCTCAATGATAAT 57.187 30.769 0.00 0.00 43.30 1.28
1741 1947 8.634335 TTGTCCTTTGATTGTCTCAATGATAA 57.366 30.769 0.00 0.25 43.30 1.75
1742 1948 7.884877 ACTTGTCCTTTGATTGTCTCAATGATA 59.115 33.333 0.00 0.00 43.30 2.15
1743 1949 6.718454 ACTTGTCCTTTGATTGTCTCAATGAT 59.282 34.615 0.00 0.00 43.30 2.45
1744 1950 6.064060 ACTTGTCCTTTGATTGTCTCAATGA 58.936 36.000 0.00 0.00 43.30 2.57
1745 1951 6.016860 TGACTTGTCCTTTGATTGTCTCAATG 60.017 38.462 0.00 0.00 43.30 2.82
1746 1952 6.064060 TGACTTGTCCTTTGATTGTCTCAAT 58.936 36.000 0.00 0.00 43.30 2.57
1747 1953 5.436175 TGACTTGTCCTTTGATTGTCTCAA 58.564 37.500 0.00 0.00 42.15 3.02
1748 1954 5.034852 TGACTTGTCCTTTGATTGTCTCA 57.965 39.130 0.00 0.00 0.00 3.27
1749 1955 5.123027 GGATGACTTGTCCTTTGATTGTCTC 59.877 44.000 0.00 0.00 32.85 3.36
1750 1956 5.006386 GGATGACTTGTCCTTTGATTGTCT 58.994 41.667 0.00 0.00 32.85 3.41
1751 1957 4.761739 TGGATGACTTGTCCTTTGATTGTC 59.238 41.667 0.00 0.00 36.68 3.18
1752 1958 4.728772 TGGATGACTTGTCCTTTGATTGT 58.271 39.130 0.00 0.00 36.68 2.71
1753 1959 5.464168 GTTGGATGACTTGTCCTTTGATTG 58.536 41.667 0.00 0.00 36.68 2.67
1754 1960 4.216257 CGTTGGATGACTTGTCCTTTGATT 59.784 41.667 0.00 0.00 36.68 2.57
1755 1961 3.753272 CGTTGGATGACTTGTCCTTTGAT 59.247 43.478 0.00 0.00 36.68 2.57
1756 1962 3.138304 CGTTGGATGACTTGTCCTTTGA 58.862 45.455 0.00 0.00 36.68 2.69
1757 1963 2.350772 GCGTTGGATGACTTGTCCTTTG 60.351 50.000 0.00 0.00 36.68 2.77
1758 1964 1.880027 GCGTTGGATGACTTGTCCTTT 59.120 47.619 0.00 0.00 36.68 3.11
1759 1965 1.523758 GCGTTGGATGACTTGTCCTT 58.476 50.000 0.00 0.00 36.68 3.36
1760 1966 0.321653 GGCGTTGGATGACTTGTCCT 60.322 55.000 0.00 0.00 36.68 3.85
1761 1967 0.321653 AGGCGTTGGATGACTTGTCC 60.322 55.000 0.00 0.00 36.26 4.02
1762 1968 1.197721 CAAGGCGTTGGATGACTTGTC 59.802 52.381 11.31 0.00 35.15 3.18
1763 1969 1.202758 TCAAGGCGTTGGATGACTTGT 60.203 47.619 18.38 0.00 39.49 3.16
1764 1970 1.522668 TCAAGGCGTTGGATGACTTG 58.477 50.000 18.38 9.03 39.76 3.16
1765 1971 2.270352 TTCAAGGCGTTGGATGACTT 57.730 45.000 18.38 0.00 34.09 3.01
1766 1972 2.270352 TTTCAAGGCGTTGGATGACT 57.730 45.000 18.38 0.00 34.09 3.41
1767 1973 3.363341 TTTTTCAAGGCGTTGGATGAC 57.637 42.857 18.38 0.00 34.09 3.06
1768 1974 4.157656 CCTATTTTTCAAGGCGTTGGATGA 59.842 41.667 18.38 2.84 34.09 2.92
1769 1975 4.423732 CCTATTTTTCAAGGCGTTGGATG 58.576 43.478 18.38 0.00 34.09 3.51
1770 1976 3.447229 CCCTATTTTTCAAGGCGTTGGAT 59.553 43.478 18.38 10.26 34.09 3.41
1771 1977 2.823154 CCCTATTTTTCAAGGCGTTGGA 59.177 45.455 18.38 7.73 34.09 3.53
1772 1978 2.673893 GCCCTATTTTTCAAGGCGTTGG 60.674 50.000 18.38 0.99 34.09 3.77
1773 1979 2.029470 TGCCCTATTTTTCAAGGCGTTG 60.029 45.455 12.91 12.91 46.92 4.10
1774 1980 2.243810 TGCCCTATTTTTCAAGGCGTT 58.756 42.857 0.00 0.00 46.92 4.84
1775 1981 1.917872 TGCCCTATTTTTCAAGGCGT 58.082 45.000 0.00 0.00 46.92 5.68
1776 1982 3.311486 TTTGCCCTATTTTTCAAGGCG 57.689 42.857 0.00 0.00 46.92 5.52
1777 1983 4.831107 TGATTTGCCCTATTTTTCAAGGC 58.169 39.130 0.00 0.00 44.13 4.35
1778 1984 6.051074 GGATGATTTGCCCTATTTTTCAAGG 58.949 40.000 0.00 0.00 0.00 3.61
1779 1985 6.642430 TGGATGATTTGCCCTATTTTTCAAG 58.358 36.000 0.00 0.00 0.00 3.02
1780 1986 6.617782 TGGATGATTTGCCCTATTTTTCAA 57.382 33.333 0.00 0.00 0.00 2.69
1781 1987 6.213195 AGTTGGATGATTTGCCCTATTTTTCA 59.787 34.615 0.00 0.00 0.00 2.69
1782 1988 6.643388 AGTTGGATGATTTGCCCTATTTTTC 58.357 36.000 0.00 0.00 0.00 2.29
1783 1989 6.625532 AGTTGGATGATTTGCCCTATTTTT 57.374 33.333 0.00 0.00 0.00 1.94
1784 1990 6.441604 AGAAGTTGGATGATTTGCCCTATTTT 59.558 34.615 0.00 0.00 0.00 1.82
1785 1991 5.960202 AGAAGTTGGATGATTTGCCCTATTT 59.040 36.000 0.00 0.00 0.00 1.40
1786 1992 5.522641 AGAAGTTGGATGATTTGCCCTATT 58.477 37.500 0.00 0.00 0.00 1.73
1787 1993 5.134725 AGAAGTTGGATGATTTGCCCTAT 57.865 39.130 0.00 0.00 0.00 2.57
1788 1994 4.591321 AGAAGTTGGATGATTTGCCCTA 57.409 40.909 0.00 0.00 0.00 3.53
1789 1995 3.463048 AGAAGTTGGATGATTTGCCCT 57.537 42.857 0.00 0.00 0.00 5.19
1790 1996 3.511146 TCAAGAAGTTGGATGATTTGCCC 59.489 43.478 0.00 0.00 34.09 5.36
1791 1997 4.789012 TCAAGAAGTTGGATGATTTGCC 57.211 40.909 0.00 0.00 34.09 4.52
1792 1998 7.542025 ACTAATCAAGAAGTTGGATGATTTGC 58.458 34.615 10.79 0.00 41.40 3.68
1793 1999 9.350357 CAACTAATCAAGAAGTTGGATGATTTG 57.650 33.333 10.79 11.08 45.68 2.32
1878 2084 4.584743 AGCAGATAACACGTAGGATCATCA 59.415 41.667 0.00 0.00 0.00 3.07
1905 2111 0.890683 CATTTTCACCCTGACTGCCC 59.109 55.000 0.00 0.00 0.00 5.36
1906 2112 1.270550 CACATTTTCACCCTGACTGCC 59.729 52.381 0.00 0.00 0.00 4.85
1907 2113 2.229792 TCACATTTTCACCCTGACTGC 58.770 47.619 0.00 0.00 0.00 4.40
1917 2123 5.335583 CCGCAGTCCTTAATTCACATTTTCA 60.336 40.000 0.00 0.00 0.00 2.69
1931 2137 2.120718 AGAGGGTCCGCAGTCCTT 59.879 61.111 0.00 0.00 0.00 3.36
1940 2146 1.153349 GACGATTGCCAGAGGGTCC 60.153 63.158 0.00 0.00 36.17 4.46
1958 2164 1.062587 GACTGATGGCAAATCGTTCGG 59.937 52.381 0.00 0.00 0.00 4.30
1959 2165 2.002586 AGACTGATGGCAAATCGTTCG 58.997 47.619 0.00 0.00 0.00 3.95
1960 2166 2.476854 GCAGACTGATGGCAAATCGTTC 60.477 50.000 6.65 0.00 0.00 3.95
1961 2167 1.470098 GCAGACTGATGGCAAATCGTT 59.530 47.619 6.65 0.00 0.00 3.85
1962 2168 1.089920 GCAGACTGATGGCAAATCGT 58.910 50.000 6.65 0.00 0.00 3.73
1963 2169 1.329906 GAGCAGACTGATGGCAAATCG 59.670 52.381 6.65 0.00 0.00 3.34
1964 2170 1.329906 CGAGCAGACTGATGGCAAATC 59.670 52.381 6.65 0.00 0.00 2.17
1965 2171 1.065926 TCGAGCAGACTGATGGCAAAT 60.066 47.619 6.65 0.00 0.00 2.32
1966 2172 0.321346 TCGAGCAGACTGATGGCAAA 59.679 50.000 6.65 0.00 0.00 3.68
1967 2173 0.390340 GTCGAGCAGACTGATGGCAA 60.390 55.000 6.65 0.00 46.13 4.52
1968 2174 1.216444 GTCGAGCAGACTGATGGCA 59.784 57.895 6.65 0.00 46.13 4.92
1969 2175 4.100981 GTCGAGCAGACTGATGGC 57.899 61.111 6.65 0.00 46.13 4.40
1976 2182 2.202324 GACGTCCGTCGAGCAGAC 60.202 66.667 3.51 2.66 46.16 3.51
1984 2190 2.129607 TGCTTAAAAGTGACGTCCGTC 58.870 47.619 14.12 12.66 44.77 4.79
1985 2191 2.228138 TGCTTAAAAGTGACGTCCGT 57.772 45.000 14.12 0.00 0.00 4.69
1986 2192 3.185594 TCATTGCTTAAAAGTGACGTCCG 59.814 43.478 14.12 0.00 0.00 4.79
1987 2193 4.378459 CCTCATTGCTTAAAAGTGACGTCC 60.378 45.833 14.12 4.42 0.00 4.79
1988 2194 4.378459 CCCTCATTGCTTAAAAGTGACGTC 60.378 45.833 9.11 9.11 0.00 4.34
1989 2195 3.502211 CCCTCATTGCTTAAAAGTGACGT 59.498 43.478 0.00 0.00 0.00 4.34
1990 2196 3.751175 TCCCTCATTGCTTAAAAGTGACG 59.249 43.478 0.00 0.00 0.00 4.35
1991 2197 4.762251 AGTCCCTCATTGCTTAAAAGTGAC 59.238 41.667 0.00 0.00 0.00 3.67
1992 2198 4.985538 AGTCCCTCATTGCTTAAAAGTGA 58.014 39.130 0.00 0.00 0.00 3.41
1993 2199 5.712152 AAGTCCCTCATTGCTTAAAAGTG 57.288 39.130 0.00 0.00 0.00 3.16
1994 2200 6.072673 CGTAAAGTCCCTCATTGCTTAAAAGT 60.073 38.462 0.00 0.00 0.00 2.66
1995 2201 6.314784 CGTAAAGTCCCTCATTGCTTAAAAG 58.685 40.000 0.00 0.00 0.00 2.27
1996 2202 5.182380 CCGTAAAGTCCCTCATTGCTTAAAA 59.818 40.000 0.00 0.00 0.00 1.52
1997 2203 4.698304 CCGTAAAGTCCCTCATTGCTTAAA 59.302 41.667 0.00 0.00 0.00 1.52
1998 2204 4.258543 CCGTAAAGTCCCTCATTGCTTAA 58.741 43.478 0.00 0.00 0.00 1.85
1999 2205 3.370103 CCCGTAAAGTCCCTCATTGCTTA 60.370 47.826 0.00 0.00 0.00 3.09
2000 2206 2.618045 CCCGTAAAGTCCCTCATTGCTT 60.618 50.000 0.00 0.00 0.00 3.91
2001 2207 1.065418 CCCGTAAAGTCCCTCATTGCT 60.065 52.381 0.00 0.00 0.00 3.91
2002 2208 1.379527 CCCGTAAAGTCCCTCATTGC 58.620 55.000 0.00 0.00 0.00 3.56
2003 2209 1.379527 GCCCGTAAAGTCCCTCATTG 58.620 55.000 0.00 0.00 0.00 2.82
2004 2210 0.107848 CGCCCGTAAAGTCCCTCATT 60.108 55.000 0.00 0.00 0.00 2.57
2005 2211 1.262640 ACGCCCGTAAAGTCCCTCAT 61.263 55.000 0.00 0.00 0.00 2.90
2006 2212 1.474332 AACGCCCGTAAAGTCCCTCA 61.474 55.000 0.00 0.00 0.00 3.86
2007 2213 0.738762 GAACGCCCGTAAAGTCCCTC 60.739 60.000 0.00 0.00 0.00 4.30
2008 2214 1.294459 GAACGCCCGTAAAGTCCCT 59.706 57.895 0.00 0.00 0.00 4.20
2009 2215 1.004679 TGAACGCCCGTAAAGTCCC 60.005 57.895 0.00 0.00 0.00 4.46
2010 2216 0.037975 TCTGAACGCCCGTAAAGTCC 60.038 55.000 0.00 0.00 0.00 3.85
2011 2217 1.066136 GTCTGAACGCCCGTAAAGTC 58.934 55.000 0.00 0.00 0.00 3.01
2012 2218 0.320160 GGTCTGAACGCCCGTAAAGT 60.320 55.000 0.00 0.00 0.00 2.66
2013 2219 1.349259 CGGTCTGAACGCCCGTAAAG 61.349 60.000 0.63 0.00 37.00 1.85
2014 2220 1.373246 CGGTCTGAACGCCCGTAAA 60.373 57.895 0.63 0.00 37.00 2.01
2015 2221 1.597797 ATCGGTCTGAACGCCCGTAA 61.598 55.000 10.84 0.00 42.30 3.18
2016 2222 2.048023 ATCGGTCTGAACGCCCGTA 61.048 57.895 10.84 0.00 42.30 4.02
2017 2223 3.379445 ATCGGTCTGAACGCCCGT 61.379 61.111 10.84 0.00 42.30 5.28
2018 2224 2.885644 CATCGGTCTGAACGCCCG 60.886 66.667 10.84 4.04 43.03 6.13
2019 2225 3.195698 GCATCGGTCTGAACGCCC 61.196 66.667 10.84 0.00 0.00 6.13
2020 2226 3.195698 GGCATCGGTCTGAACGCC 61.196 66.667 10.84 9.16 40.69 5.68
2021 2227 2.434185 TGGCATCGGTCTGAACGC 60.434 61.111 10.84 0.00 0.00 4.84
2022 2228 2.444624 CGTGGCATCGGTCTGAACG 61.445 63.158 9.20 9.20 0.00 3.95
2023 2229 2.740714 GCGTGGCATCGGTCTGAAC 61.741 63.158 10.56 0.00 0.00 3.18
2024 2230 2.434185 GCGTGGCATCGGTCTGAA 60.434 61.111 10.56 0.00 0.00 3.02
2025 2231 3.233259 TTGCGTGGCATCGGTCTGA 62.233 57.895 10.56 0.00 38.76 3.27
2026 2232 2.741985 TTGCGTGGCATCGGTCTG 60.742 61.111 10.56 0.00 38.76 3.51
2027 2233 2.434884 CTTGCGTGGCATCGGTCT 60.435 61.111 10.56 0.00 38.76 3.85
2028 2234 4.166011 GCTTGCGTGGCATCGGTC 62.166 66.667 10.56 0.00 38.76 4.79
2030 2236 3.511595 ATGCTTGCGTGGCATCGG 61.512 61.111 10.56 0.00 45.85 4.18
2034 2240 2.596923 TTGGATGCTTGCGTGGCA 60.597 55.556 0.85 0.85 44.05 4.92
2035 2241 1.865788 TTCTTGGATGCTTGCGTGGC 61.866 55.000 0.00 0.00 0.00 5.01
2036 2242 0.109597 GTTCTTGGATGCTTGCGTGG 60.110 55.000 0.00 0.00 0.00 4.94
2037 2243 0.109597 GGTTCTTGGATGCTTGCGTG 60.110 55.000 0.00 0.00 0.00 5.34
2038 2244 1.244019 GGGTTCTTGGATGCTTGCGT 61.244 55.000 0.00 0.00 0.00 5.24
2039 2245 0.962356 AGGGTTCTTGGATGCTTGCG 60.962 55.000 0.00 0.00 0.00 4.85
2040 2246 0.529378 CAGGGTTCTTGGATGCTTGC 59.471 55.000 0.00 0.00 0.00 4.01
2041 2247 1.180029 CCAGGGTTCTTGGATGCTTG 58.820 55.000 0.00 0.00 0.00 4.01
2042 2248 0.779997 ACCAGGGTTCTTGGATGCTT 59.220 50.000 3.03 0.00 0.00 3.91
2043 2249 0.038744 CACCAGGGTTCTTGGATGCT 59.961 55.000 3.03 0.00 0.00 3.79
2044 2250 0.251341 ACACCAGGGTTCTTGGATGC 60.251 55.000 3.03 0.00 0.00 3.91
2045 2251 1.826385 GACACCAGGGTTCTTGGATG 58.174 55.000 3.03 1.28 0.00 3.51
2046 2252 0.324943 CGACACCAGGGTTCTTGGAT 59.675 55.000 3.03 0.00 0.00 3.41
2047 2253 1.752198 CGACACCAGGGTTCTTGGA 59.248 57.895 3.03 0.00 0.00 3.53
2048 2254 1.302511 CCGACACCAGGGTTCTTGG 60.303 63.158 0.00 0.00 0.00 3.61
2049 2255 0.884704 CACCGACACCAGGGTTCTTG 60.885 60.000 0.00 0.00 33.23 3.02
2050 2256 1.342672 ACACCGACACCAGGGTTCTT 61.343 55.000 0.00 0.00 33.23 2.52
2051 2257 1.755393 GACACCGACACCAGGGTTCT 61.755 60.000 0.00 0.00 33.23 3.01
2052 2258 1.301479 GACACCGACACCAGGGTTC 60.301 63.158 0.00 0.00 33.23 3.62
2053 2259 1.628238 TTGACACCGACACCAGGGTT 61.628 55.000 0.00 0.00 33.23 4.11
2054 2260 1.628238 TTTGACACCGACACCAGGGT 61.628 55.000 0.00 0.00 36.87 4.34
2055 2261 0.464735 TTTTGACACCGACACCAGGG 60.465 55.000 0.00 0.00 0.00 4.45
2089 2295 1.159184 ACAGTTCGGGACCCCCTAA 59.841 57.895 4.46 0.00 42.67 2.69
2124 2330 2.070650 GTCCCCCGCCTCCTGTTAT 61.071 63.158 0.00 0.00 0.00 1.89
2262 2468 9.889388 ATCATAATCATAGGCTAGCTTATAGGA 57.111 33.333 18.03 12.90 0.00 2.94
2267 2473 9.440773 CAACAATCATAATCATAGGCTAGCTTA 57.559 33.333 15.72 12.40 0.00 3.09
2367 2573 7.410174 CAGTAAGGATATGTAGATCTCCTCCT 58.590 42.308 7.20 2.14 34.75 3.69
2538 2744 2.508526 GTCATTGAAGCCTGGTTCAGT 58.491 47.619 11.15 6.58 37.72 3.41
2574 2780 2.984562 TGCAATGCCGAAGACAATCTA 58.015 42.857 1.53 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.