Multiple sequence alignment - TraesCS1A01G014200

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 TraesCS1A01G014200 chr1A 100.000 2561 0 0 1 2561 7779045 7776485 0.000000e+00 4730.0
1 TraesCS1A01G014200 chr1A 85.803 1606 169 33 387 1956 7115256 7113674 0.000000e+00 1648.0
2 TraesCS1A01G014200 chr1A 85.833 1080 117 20 730 1791 7649106 7650167 0.000000e+00 1114.0
3 TraesCS1A01G014200 chr1A 88.489 278 31 1 1683 1959 7777081 7776804 4.080000e-88 335.0
4 TraesCS1A01G014200 chr1A 88.489 278 31 1 1965 2242 7777363 7777087 4.080000e-88 335.0
5 TraesCS1A01G014200 chr1D 88.769 1950 173 21 35 1956 6463487 6461556 0.000000e+00 2346.0
6 TraesCS1A01G014200 chr1D 90.138 507 34 5 1965 2459 6461830 6461328 0.000000e+00 645.0
7 TraesCS1A01G014200 chr1D 100.000 35 0 0 1 35 6463561 6463527 5.910000e-07 65.8
8 TraesCS1A01G014200 chr7B 88.223 1953 172 30 35 1954 452214536 452216463 0.000000e+00 2279.0
9 TraesCS1A01G014200 chr7B 90.507 611 39 6 1965 2561 452216192 452216797 0.000000e+00 789.0
10 TraesCS1A01G014200 chr2D 82.028 217 31 7 363 573 533165346 533165560 7.280000e-41 178.0
11 TraesCS1A01G014200 chr2D 81.057 227 35 7 353 573 533251763 533251987 9.420000e-40 174.0
12 TraesCS1A01G014200 chr2D 85.030 167 25 0 393 559 533658375 533658541 1.220000e-38 171.0
13 TraesCS1A01G014200 chr2D 81.034 116 18 3 831 944 533252276 533252389 3.510000e-14 89.8
14 TraesCS1A01G014200 chr2A 81.106 217 33 7 363 573 677546197 677546411 1.580000e-37 167.0
15 TraesCS1A01G014200 chr2B 82.955 176 29 1 384 559 633575447 633575621 9.490000e-35 158.0


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 TraesCS1A01G014200 chr1A 7776485 7779045 2560 True 1800.000000 4730 92.326 1 2561 3 chr1A.!!$R2 2560
1 TraesCS1A01G014200 chr1A 7113674 7115256 1582 True 1648.000000 1648 85.803 387 1956 1 chr1A.!!$R1 1569
2 TraesCS1A01G014200 chr1A 7649106 7650167 1061 False 1114.000000 1114 85.833 730 1791 1 chr1A.!!$F1 1061
3 TraesCS1A01G014200 chr1D 6461328 6463561 2233 True 1018.933333 2346 92.969 1 2459 3 chr1D.!!$R1 2458
4 TraesCS1A01G014200 chr7B 452214536 452216797 2261 False 1534.000000 2279 89.365 35 2561 2 chr7B.!!$F1 2526

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
728 790 0.037734 TCCTACAGACCAGACGCTGA 59.962 55.0 8.2 0.0 36.07 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2057 1.401905 GCCAAGAAAGCTGGATAACCG 59.598 52.381 0.0 0.0 39.42 4.44 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
229 283 2.347490 CAACGCCCTGCAGGTAGT 59.653 61.111 30.63 25.16 38.26 2.73
239 293 1.755008 GCAGGTAGTCCTCCTCGCT 60.755 63.158 0.00 0.00 43.07 4.93
381 441 0.739112 CAACTCTCTTGCGGAGGAGC 60.739 60.000 11.36 0.00 42.10 4.70
531 593 3.741476 CGCAAGAAGCTGCCCCAC 61.741 66.667 0.00 0.00 42.61 4.61
715 777 0.260230 CCTCCTCCTCTGCTCCTACA 59.740 60.000 0.00 0.00 0.00 2.74
716 778 1.691196 CTCCTCCTCTGCTCCTACAG 58.309 60.000 0.00 0.00 39.12 2.74
720 782 0.704664 TCCTCTGCTCCTACAGACCA 59.295 55.000 0.00 0.00 41.72 4.02
726 788 1.316706 GCTCCTACAGACCAGACGCT 61.317 60.000 0.00 0.00 0.00 5.07
728 790 0.037734 TCCTACAGACCAGACGCTGA 59.962 55.000 8.20 0.00 36.07 4.26
815 886 3.988525 GCGGCCAAACACATGCCA 61.989 61.111 2.24 0.00 45.63 4.92
817 888 2.854401 CGGCCAAACACATGCCACA 61.854 57.895 2.24 0.00 45.63 4.17
818 889 1.300853 GGCCAAACACATGCCACAC 60.301 57.895 0.00 0.00 44.70 3.82
819 890 1.661197 GCCAAACACATGCCACACG 60.661 57.895 0.00 0.00 0.00 4.49
820 891 1.007502 CCAAACACATGCCACACGG 60.008 57.895 0.00 0.00 0.00 4.94
823 900 1.795170 AAACACATGCCACACGGAGC 61.795 55.000 0.00 0.00 0.00 4.70
881 958 2.614520 TCCACGTTTTTGATTTCGAGCA 59.385 40.909 0.00 0.00 0.00 4.26
884 961 3.788694 CACGTTTTTGATTTCGAGCACAA 59.211 39.130 0.00 0.00 0.00 3.33
887 964 4.440758 CGTTTTTGATTTCGAGCACAATGT 59.559 37.500 0.00 0.00 0.00 2.71
892 969 3.058293 TGATTTCGAGCACAATGTCAACC 60.058 43.478 0.00 0.00 0.00 3.77
893 970 0.865111 TTCGAGCACAATGTCAACCG 59.135 50.000 0.00 0.00 0.00 4.44
898 975 1.497278 CACAATGTCAACCGGAGCG 59.503 57.895 9.46 0.00 0.00 5.03
911 988 1.522580 GGAGCGGAATCACAGGAGC 60.523 63.158 0.00 0.00 0.00 4.70
956 1033 2.124403 CTGGAGCCACAGGGATGC 60.124 66.667 0.00 0.00 41.93 3.91
957 1034 2.611800 TGGAGCCACAGGGATGCT 60.612 61.111 0.00 0.00 42.11 3.79
958 1035 2.124403 GGAGCCACAGGGATGCTG 60.124 66.667 0.00 0.00 38.00 4.41
975 1052 1.522668 CTGCTGGATTGGTTGACGAA 58.477 50.000 0.00 0.00 0.00 3.85
976 1053 1.879380 CTGCTGGATTGGTTGACGAAA 59.121 47.619 0.00 0.00 0.00 3.46
980 1057 4.520874 TGCTGGATTGGTTGACGAAATTTA 59.479 37.500 0.00 0.00 0.00 1.40
981 1058 5.184864 TGCTGGATTGGTTGACGAAATTTAT 59.815 36.000 0.00 0.00 0.00 1.40
1000 1077 0.753848 TCTGACCCGTCACAGTGTCA 60.754 55.000 0.00 0.00 35.46 3.58
1043 1120 4.619227 CGGCAACCTGTCGGTGGT 62.619 66.667 0.00 0.00 44.73 4.16
1063 1140 2.325082 GCCGACAGCAACGATTGGT 61.325 57.895 0.00 0.00 42.97 3.67
1065 1142 1.651987 CCGACAGCAACGATTGGTAT 58.348 50.000 0.00 0.00 39.79 2.73
1105 1182 1.380302 GTGGACATGGAGGGCAAGT 59.620 57.895 0.00 0.00 0.00 3.16
1146 1223 1.070786 ACGCGGCCAGTATTATGGG 59.929 57.895 12.47 0.00 40.97 4.00
1204 1281 2.682856 GCTATATCTCCAGCTCCTCTCG 59.317 54.545 0.00 0.00 34.86 4.04
1219 1296 2.678580 TCGCTGTCGGGGATGACA 60.679 61.111 0.00 0.00 46.15 3.58
1273 1350 2.496341 CGATCTGGCGCCTTGAGA 59.504 61.111 29.70 22.52 0.00 3.27
1281 1358 2.288666 TGGCGCCTTGAGAATTATGAC 58.711 47.619 29.70 0.00 0.00 3.06
1305 1382 2.964174 CAATGGGCGCTGAAGCAA 59.036 55.556 7.64 0.00 42.21 3.91
1330 1407 3.616956 TCAGAGTTGATAAGGTGCTGG 57.383 47.619 0.00 0.00 0.00 4.85
1342 1419 0.179070 GGTGCTGGACCTAGCTAAGC 60.179 60.000 11.48 7.32 44.01 3.09
1389 1466 1.337823 CCCGATCGTGACACCTTCTTT 60.338 52.381 15.09 0.00 0.00 2.52
1392 1469 3.363970 CCGATCGTGACACCTTCTTTTTG 60.364 47.826 15.09 0.00 0.00 2.44
1400 1477 2.689983 ACACCTTCTTTTTGGTCAGCAG 59.310 45.455 0.00 0.00 33.75 4.24
1401 1478 2.689983 CACCTTCTTTTTGGTCAGCAGT 59.310 45.455 0.00 0.00 33.75 4.40
1409 1486 3.569194 TTTGGTCAGCAGTGGTCTTTA 57.431 42.857 0.00 0.00 0.00 1.85
1412 1489 2.290260 TGGTCAGCAGTGGTCTTTATGG 60.290 50.000 0.00 0.00 0.00 2.74
1413 1490 1.740025 GTCAGCAGTGGTCTTTATGGC 59.260 52.381 0.00 0.00 0.00 4.40
1416 1493 0.392461 GCAGTGGTCTTTATGGCGGA 60.392 55.000 0.00 0.00 0.00 5.54
1418 1495 1.066143 CAGTGGTCTTTATGGCGGAGT 60.066 52.381 0.00 0.00 0.00 3.85
1423 1509 1.062525 CTTTATGGCGGAGTTGCGC 59.937 57.895 9.62 9.62 35.06 6.09
1476 1562 5.535043 GCCAAATTGGTGATTTCATTGAC 57.465 39.130 14.17 0.00 40.46 3.18
1483 1569 2.939103 GGTGATTTCATTGACCTCGAGG 59.061 50.000 30.11 30.11 42.17 4.63
1486 1572 4.331168 GTGATTTCATTGACCTCGAGGAAG 59.669 45.833 37.69 20.06 38.94 3.46
1493 1579 2.232298 GACCTCGAGGAAGGCAGTGG 62.232 65.000 37.69 8.57 40.34 4.00
1494 1580 2.581354 CTCGAGGAAGGCAGTGGG 59.419 66.667 3.91 0.00 0.00 4.61
1591 1677 1.980232 CATGCTTGGGCTTGCTCCA 60.980 57.895 0.00 0.00 36.94 3.86
1594 1680 1.217244 GCTTGGGCTTGCTCCAATG 59.783 57.895 13.19 9.89 42.63 2.82
1636 1722 6.104146 TGTGTACACCTGCACTTCTTAATA 57.896 37.500 22.91 0.00 36.63 0.98
1666 1752 4.893424 TTGTGTTAGCCAGTTTGTTCTC 57.107 40.909 0.00 0.00 0.00 2.87
1711 1802 1.395635 CAGCTTGCTTGGCCATGATA 58.604 50.000 22.21 7.31 0.00 2.15
1712 1803 1.961394 CAGCTTGCTTGGCCATGATAT 59.039 47.619 22.21 0.16 0.00 1.63
1713 1804 1.961394 AGCTTGCTTGGCCATGATATG 59.039 47.619 22.21 12.25 0.00 1.78
1714 1805 1.684983 GCTTGCTTGGCCATGATATGT 59.315 47.619 22.21 0.00 0.00 2.29
1715 1806 2.288030 GCTTGCTTGGCCATGATATGTC 60.288 50.000 22.21 3.96 0.00 3.06
1716 1807 2.732844 TGCTTGGCCATGATATGTCA 57.267 45.000 22.21 6.55 39.04 3.58
1717 1808 3.232720 TGCTTGGCCATGATATGTCAT 57.767 42.857 22.21 0.00 45.87 3.06
1733 1824 9.492973 TGATATGTCATGATTATGGTTGTACTG 57.507 33.333 0.00 0.00 34.97 2.74
1734 1825 9.710900 GATATGTCATGATTATGGTTGTACTGA 57.289 33.333 0.00 0.00 34.97 3.41
1736 1827 8.985315 ATGTCATGATTATGGTTGTACTGAAT 57.015 30.769 0.00 0.00 34.97 2.57
1737 1828 8.437360 TGTCATGATTATGGTTGTACTGAATC 57.563 34.615 0.00 0.00 34.97 2.52
1738 1829 7.498900 TGTCATGATTATGGTTGTACTGAATCC 59.501 37.037 0.00 0.00 34.97 3.01
1739 1830 7.716998 GTCATGATTATGGTTGTACTGAATCCT 59.283 37.037 0.00 0.00 34.97 3.24
1740 1831 8.933653 TCATGATTATGGTTGTACTGAATCCTA 58.066 33.333 0.00 0.00 34.97 2.94
1741 1832 9.212641 CATGATTATGGTTGTACTGAATCCTAG 57.787 37.037 0.00 0.00 0.00 3.02
1742 1833 8.319057 TGATTATGGTTGTACTGAATCCTAGT 57.681 34.615 0.00 0.00 0.00 2.57
1743 1834 9.429109 TGATTATGGTTGTACTGAATCCTAGTA 57.571 33.333 0.00 0.00 0.00 1.82
1748 1839 8.834004 TGGTTGTACTGAATCCTAGTATTAGT 57.166 34.615 0.00 0.00 33.60 2.24
1749 1840 8.692710 TGGTTGTACTGAATCCTAGTATTAGTG 58.307 37.037 0.00 0.00 33.60 2.74
1750 1841 8.910944 GGTTGTACTGAATCCTAGTATTAGTGA 58.089 37.037 0.00 0.00 33.60 3.41
1766 1857 9.998106 AGTATTAGTGATTGTTACTTGTGAACT 57.002 29.630 0.00 0.00 0.00 3.01
1769 1860 8.725405 TTAGTGATTGTTACTTGTGAACTTCA 57.275 30.769 0.00 0.00 0.00 3.02
1770 1861 7.807977 AGTGATTGTTACTTGTGAACTTCAT 57.192 32.000 0.00 0.00 0.00 2.57
1771 1862 8.225603 AGTGATTGTTACTTGTGAACTTCATT 57.774 30.769 0.00 0.00 0.00 2.57
1772 1863 8.686334 AGTGATTGTTACTTGTGAACTTCATTT 58.314 29.630 0.00 0.00 0.00 2.32
1773 1864 9.301153 GTGATTGTTACTTGTGAACTTCATTTT 57.699 29.630 0.00 0.00 0.00 1.82
1774 1865 9.299963 TGATTGTTACTTGTGAACTTCATTTTG 57.700 29.630 0.00 0.00 0.00 2.44
1775 1866 9.301153 GATTGTTACTTGTGAACTTCATTTTGT 57.699 29.630 0.00 0.00 0.00 2.83
1776 1867 9.651913 ATTGTTACTTGTGAACTTCATTTTGTT 57.348 25.926 0.00 0.00 0.00 2.83
1777 1868 8.682128 TGTTACTTGTGAACTTCATTTTGTTC 57.318 30.769 0.00 0.00 41.87 3.18
1778 1869 7.757624 TGTTACTTGTGAACTTCATTTTGTTCC 59.242 33.333 0.00 0.00 41.10 3.62
1779 1870 6.530019 ACTTGTGAACTTCATTTTGTTCCT 57.470 33.333 0.00 0.00 41.10 3.36
1780 1871 6.935167 ACTTGTGAACTTCATTTTGTTCCTT 58.065 32.000 0.00 0.00 41.10 3.36
1781 1872 7.386059 ACTTGTGAACTTCATTTTGTTCCTTT 58.614 30.769 0.00 0.00 41.10 3.11
1782 1873 7.877612 ACTTGTGAACTTCATTTTGTTCCTTTT 59.122 29.630 0.00 0.00 41.10 2.27
1783 1874 8.614469 TTGTGAACTTCATTTTGTTCCTTTTT 57.386 26.923 0.00 0.00 41.10 1.94
1784 1875 9.712305 TTGTGAACTTCATTTTGTTCCTTTTTA 57.288 25.926 0.00 0.00 41.10 1.52
1785 1876 9.364989 TGTGAACTTCATTTTGTTCCTTTTTAG 57.635 29.630 0.00 0.00 41.10 1.85
1786 1877 9.366216 GTGAACTTCATTTTGTTCCTTTTTAGT 57.634 29.630 0.00 0.00 41.10 2.24
1787 1878 9.936759 TGAACTTCATTTTGTTCCTTTTTAGTT 57.063 25.926 0.00 0.00 41.10 2.24
1809 1900 8.681486 AGTTATTATATGTTTGCTGATGCTCA 57.319 30.769 0.00 0.00 40.48 4.26
1810 1901 9.293404 AGTTATTATATGTTTGCTGATGCTCAT 57.707 29.630 0.00 0.00 40.48 2.90
1811 1902 9.338291 GTTATTATATGTTTGCTGATGCTCATG 57.662 33.333 0.00 0.00 40.48 3.07
1812 1903 7.754851 ATTATATGTTTGCTGATGCTCATGA 57.245 32.000 0.00 0.00 40.48 3.07
1813 1904 5.690997 ATATGTTTGCTGATGCTCATGAG 57.309 39.130 18.84 18.84 40.48 2.90
1814 1905 2.786777 TGTTTGCTGATGCTCATGAGT 58.213 42.857 23.38 4.98 40.48 3.41
1815 1906 3.151554 TGTTTGCTGATGCTCATGAGTT 58.848 40.909 23.38 11.88 40.48 3.01
1816 1907 3.189910 TGTTTGCTGATGCTCATGAGTTC 59.810 43.478 23.38 19.41 40.48 3.01
1817 1908 2.773993 TGCTGATGCTCATGAGTTCA 57.226 45.000 23.38 22.34 40.48 3.18
1818 1909 2.629051 TGCTGATGCTCATGAGTTCAG 58.371 47.619 32.22 32.22 40.53 3.02
1819 1910 2.027469 TGCTGATGCTCATGAGTTCAGT 60.027 45.455 33.97 17.42 40.12 3.41
1820 1911 2.608546 GCTGATGCTCATGAGTTCAGTC 59.391 50.000 33.97 27.50 40.12 3.51
1821 1912 3.679361 GCTGATGCTCATGAGTTCAGTCT 60.679 47.826 33.97 13.66 40.12 3.24
1822 1913 4.505808 CTGATGCTCATGAGTTCAGTCTT 58.494 43.478 30.25 13.49 36.72 3.01
1823 1914 4.251268 TGATGCTCATGAGTTCAGTCTTG 58.749 43.478 23.38 0.00 0.00 3.02
1824 1915 3.758755 TGCTCATGAGTTCAGTCTTGT 57.241 42.857 23.38 0.00 0.00 3.16
1825 1916 4.077300 TGCTCATGAGTTCAGTCTTGTT 57.923 40.909 23.38 0.00 0.00 2.83
1826 1917 4.454678 TGCTCATGAGTTCAGTCTTGTTT 58.545 39.130 23.38 0.00 0.00 2.83
1827 1918 5.610398 TGCTCATGAGTTCAGTCTTGTTTA 58.390 37.500 23.38 0.00 0.00 2.01
1828 1919 5.698089 TGCTCATGAGTTCAGTCTTGTTTAG 59.302 40.000 23.38 0.00 0.00 1.85
1829 1920 5.698545 GCTCATGAGTTCAGTCTTGTTTAGT 59.301 40.000 23.38 0.00 0.00 2.24
1830 1921 6.203723 GCTCATGAGTTCAGTCTTGTTTAGTT 59.796 38.462 23.38 0.00 0.00 2.24
1831 1922 7.482654 TCATGAGTTCAGTCTTGTTTAGTTG 57.517 36.000 0.00 0.00 0.00 3.16
1832 1923 7.272244 TCATGAGTTCAGTCTTGTTTAGTTGA 58.728 34.615 0.00 0.00 0.00 3.18
1833 1924 7.768582 TCATGAGTTCAGTCTTGTTTAGTTGAA 59.231 33.333 0.00 0.00 0.00 2.69
1834 1925 8.562892 CATGAGTTCAGTCTTGTTTAGTTGAAT 58.437 33.333 0.00 0.00 34.00 2.57
1835 1926 9.778741 ATGAGTTCAGTCTTGTTTAGTTGAATA 57.221 29.630 0.00 0.00 34.00 1.75
1836 1927 9.607988 TGAGTTCAGTCTTGTTTAGTTGAATAA 57.392 29.630 0.00 0.00 34.00 1.40
1839 1930 9.827411 GTTCAGTCTTGTTTAGTTGAATAATCC 57.173 33.333 0.00 0.00 34.00 3.01
1840 1931 8.251750 TCAGTCTTGTTTAGTTGAATAATCCG 57.748 34.615 0.00 0.00 0.00 4.18
1841 1932 7.333423 TCAGTCTTGTTTAGTTGAATAATCCGG 59.667 37.037 0.00 0.00 0.00 5.14
1842 1933 7.119262 CAGTCTTGTTTAGTTGAATAATCCGGT 59.881 37.037 0.00 0.00 0.00 5.28
1843 1934 7.333672 AGTCTTGTTTAGTTGAATAATCCGGTC 59.666 37.037 0.00 0.00 0.00 4.79
1844 1935 7.333672 GTCTTGTTTAGTTGAATAATCCGGTCT 59.666 37.037 0.00 0.00 0.00 3.85
1845 1936 7.881232 TCTTGTTTAGTTGAATAATCCGGTCTT 59.119 33.333 0.00 0.00 0.00 3.01
1846 1937 9.158233 CTTGTTTAGTTGAATAATCCGGTCTTA 57.842 33.333 0.00 1.15 0.00 2.10
1847 1938 9.675464 TTGTTTAGTTGAATAATCCGGTCTTAT 57.325 29.630 0.00 3.75 0.00 1.73
1848 1939 9.104965 TGTTTAGTTGAATAATCCGGTCTTATG 57.895 33.333 0.00 0.00 0.00 1.90
1849 1940 7.724305 TTAGTTGAATAATCCGGTCTTATGC 57.276 36.000 0.00 5.99 0.00 3.14
1850 1941 5.680619 AGTTGAATAATCCGGTCTTATGCA 58.319 37.500 13.15 13.15 0.00 3.96
1851 1942 5.760253 AGTTGAATAATCCGGTCTTATGCAG 59.240 40.000 15.34 0.00 28.27 4.41
1852 1943 5.290493 TGAATAATCCGGTCTTATGCAGT 57.710 39.130 13.15 0.80 0.00 4.40
1853 1944 5.680619 TGAATAATCCGGTCTTATGCAGTT 58.319 37.500 13.15 1.16 0.00 3.16
1854 1945 5.527214 TGAATAATCCGGTCTTATGCAGTTG 59.473 40.000 13.15 0.00 0.00 3.16
1855 1946 3.627395 AATCCGGTCTTATGCAGTTGA 57.373 42.857 0.00 0.00 0.00 3.18
1856 1947 2.380084 TCCGGTCTTATGCAGTTGAC 57.620 50.000 0.00 0.00 0.00 3.18
1857 1948 1.621317 TCCGGTCTTATGCAGTTGACA 59.379 47.619 0.00 0.00 0.00 3.58
1858 1949 2.037902 TCCGGTCTTATGCAGTTGACAA 59.962 45.455 0.00 0.00 0.00 3.18
1859 1950 2.416547 CCGGTCTTATGCAGTTGACAAG 59.583 50.000 14.68 9.37 0.00 3.16
1860 1951 2.416547 CGGTCTTATGCAGTTGACAAGG 59.583 50.000 14.68 3.56 0.00 3.61
1861 1952 2.162408 GGTCTTATGCAGTTGACAAGGC 59.838 50.000 14.68 5.10 0.00 4.35
1862 1953 2.813754 GTCTTATGCAGTTGACAAGGCA 59.186 45.455 14.72 14.72 41.00 4.75
1864 1955 3.441222 TCTTATGCAGTTGACAAGGCATG 59.559 43.478 26.10 16.15 45.74 4.06
1865 1956 1.913778 ATGCAGTTGACAAGGCATGA 58.086 45.000 20.62 1.05 44.64 3.07
1866 1957 1.689984 TGCAGTTGACAAGGCATGAA 58.310 45.000 9.72 0.00 0.00 2.57
1867 1958 2.241160 TGCAGTTGACAAGGCATGAAT 58.759 42.857 9.72 0.00 0.00 2.57
1868 1959 2.629137 TGCAGTTGACAAGGCATGAATT 59.371 40.909 9.72 0.00 0.00 2.17
1869 1960 3.825585 TGCAGTTGACAAGGCATGAATTA 59.174 39.130 9.72 0.00 0.00 1.40
1870 1961 4.280425 TGCAGTTGACAAGGCATGAATTAA 59.720 37.500 9.72 0.00 0.00 1.40
1871 1962 4.860907 GCAGTTGACAAGGCATGAATTAAG 59.139 41.667 0.00 0.00 0.00 1.85
1872 1963 5.565439 GCAGTTGACAAGGCATGAATTAAGT 60.565 40.000 0.00 0.00 0.00 2.24
1873 1964 5.860182 CAGTTGACAAGGCATGAATTAAGTG 59.140 40.000 0.00 0.00 0.00 3.16
1874 1965 4.439305 TGACAAGGCATGAATTAAGTGC 57.561 40.909 0.00 1.65 38.12 4.40
1875 1966 3.825585 TGACAAGGCATGAATTAAGTGCA 59.174 39.130 0.00 0.00 40.53 4.57
1876 1967 4.463539 TGACAAGGCATGAATTAAGTGCAT 59.536 37.500 0.00 2.03 40.53 3.96
1877 1968 5.651576 TGACAAGGCATGAATTAAGTGCATA 59.348 36.000 0.00 0.00 40.53 3.14
1878 1969 6.152492 TGACAAGGCATGAATTAAGTGCATAA 59.848 34.615 0.00 0.00 40.53 1.90
1879 1970 7.116075 ACAAGGCATGAATTAAGTGCATAAT 57.884 32.000 0.00 0.00 40.53 1.28
1880 1971 6.982141 ACAAGGCATGAATTAAGTGCATAATG 59.018 34.615 0.00 3.86 40.53 1.90
1881 1972 5.535333 AGGCATGAATTAAGTGCATAATGC 58.465 37.500 0.00 0.00 45.29 3.56
1906 1997 4.676546 ACTTTGCTGAGAAGTTTTCTTGC 58.323 39.130 9.33 9.33 40.87 4.01
1907 1998 4.400567 ACTTTGCTGAGAAGTTTTCTTGCT 59.599 37.500 14.22 0.00 40.87 3.91
1908 1999 4.989279 TTGCTGAGAAGTTTTCTTGCTT 57.011 36.364 14.22 0.00 40.87 3.91
1909 2000 4.989279 TGCTGAGAAGTTTTCTTGCTTT 57.011 36.364 14.22 0.00 40.87 3.51
1910 2001 4.675510 TGCTGAGAAGTTTTCTTGCTTTG 58.324 39.130 14.22 0.00 40.87 2.77
1911 2002 4.047142 GCTGAGAAGTTTTCTTGCTTTGG 58.953 43.478 9.12 0.00 40.87 3.28
1912 2003 4.440663 GCTGAGAAGTTTTCTTGCTTTGGT 60.441 41.667 9.12 0.00 40.87 3.67
1913 2004 4.997565 TGAGAAGTTTTCTTGCTTTGGTG 58.002 39.130 0.00 0.00 40.87 4.17
1914 2005 3.785486 AGAAGTTTTCTTGCTTTGGTGC 58.215 40.909 0.00 0.00 40.61 5.01
1915 2006 3.195396 AGAAGTTTTCTTGCTTTGGTGCA 59.805 39.130 0.00 0.00 40.61 4.57
1916 2007 3.825143 AGTTTTCTTGCTTTGGTGCAT 57.175 38.095 0.00 0.00 42.96 3.96
1917 2008 4.935352 AGTTTTCTTGCTTTGGTGCATA 57.065 36.364 0.00 0.00 42.96 3.14
1918 2009 5.473066 AGTTTTCTTGCTTTGGTGCATAT 57.527 34.783 0.00 0.00 42.96 1.78
1919 2010 5.232463 AGTTTTCTTGCTTTGGTGCATATG 58.768 37.500 0.00 0.00 42.96 1.78
1920 2011 4.870123 TTTCTTGCTTTGGTGCATATGT 57.130 36.364 4.29 0.00 42.96 2.29
1921 2012 3.853831 TCTTGCTTTGGTGCATATGTG 57.146 42.857 4.29 0.00 42.96 3.21
1937 2028 6.782298 CATATGTGCATTTGGTTTGTTTCA 57.218 33.333 0.00 0.00 0.00 2.69
1938 2029 6.592166 CATATGTGCATTTGGTTTGTTTCAC 58.408 36.000 0.00 0.00 0.00 3.18
1939 2030 4.199432 TGTGCATTTGGTTTGTTTCACT 57.801 36.364 0.00 0.00 0.00 3.41
1940 2031 5.330455 TGTGCATTTGGTTTGTTTCACTA 57.670 34.783 0.00 0.00 0.00 2.74
1941 2032 5.724328 TGTGCATTTGGTTTGTTTCACTAA 58.276 33.333 0.00 0.00 0.00 2.24
1942 2033 6.344500 TGTGCATTTGGTTTGTTTCACTAAT 58.656 32.000 0.00 0.00 0.00 1.73
1943 2034 6.820656 TGTGCATTTGGTTTGTTTCACTAATT 59.179 30.769 0.00 0.00 0.00 1.40
1944 2035 7.010923 TGTGCATTTGGTTTGTTTCACTAATTC 59.989 33.333 0.00 0.00 0.00 2.17
1945 2036 7.010923 GTGCATTTGGTTTGTTTCACTAATTCA 59.989 33.333 0.00 0.00 0.00 2.57
1946 2037 7.714377 TGCATTTGGTTTGTTTCACTAATTCAT 59.286 29.630 0.00 0.00 0.00 2.57
1947 2038 8.223100 GCATTTGGTTTGTTTCACTAATTCATC 58.777 33.333 0.00 0.00 0.00 2.92
1948 2039 9.258826 CATTTGGTTTGTTTCACTAATTCATCA 57.741 29.630 0.00 0.00 0.00 3.07
1949 2040 8.870160 TTTGGTTTGTTTCACTAATTCATCAG 57.130 30.769 0.00 0.00 0.00 2.90
1950 2041 6.980593 TGGTTTGTTTCACTAATTCATCAGG 58.019 36.000 0.00 0.00 0.00 3.86
1951 2042 6.549364 TGGTTTGTTTCACTAATTCATCAGGT 59.451 34.615 0.00 0.00 0.00 4.00
1952 2043 6.863126 GGTTTGTTTCACTAATTCATCAGGTG 59.137 38.462 0.00 0.00 0.00 4.00
1953 2044 7.255451 GGTTTGTTTCACTAATTCATCAGGTGA 60.255 37.037 0.00 0.00 35.51 4.02
1954 2045 8.299570 GTTTGTTTCACTAATTCATCAGGTGAT 58.700 33.333 0.00 0.00 36.90 3.06
1955 2046 9.513906 TTTGTTTCACTAATTCATCAGGTGATA 57.486 29.630 0.00 0.00 36.90 2.15
1956 2047 8.492673 TGTTTCACTAATTCATCAGGTGATAC 57.507 34.615 0.00 0.00 38.42 2.24
1957 2048 8.321353 TGTTTCACTAATTCATCAGGTGATACT 58.679 33.333 12.98 0.00 38.59 2.12
1958 2049 8.821894 GTTTCACTAATTCATCAGGTGATACTC 58.178 37.037 0.00 0.00 36.60 2.59
1959 2050 6.739112 TCACTAATTCATCAGGTGATACTCG 58.261 40.000 0.00 0.00 36.54 4.18
1960 2051 6.321435 TCACTAATTCATCAGGTGATACTCGT 59.679 38.462 0.00 0.00 36.54 4.18
1961 2052 6.419116 CACTAATTCATCAGGTGATACTCGTG 59.581 42.308 0.00 0.00 36.54 4.35
1962 2053 5.598416 AATTCATCAGGTGATACTCGTGA 57.402 39.130 0.00 0.00 36.54 4.35
1963 2054 5.798125 ATTCATCAGGTGATACTCGTGAT 57.202 39.130 0.00 0.00 39.79 3.06
1964 2055 5.598416 TTCATCAGGTGATACTCGTGATT 57.402 39.130 0.00 0.00 38.01 2.57
1965 2056 6.709018 TTCATCAGGTGATACTCGTGATTA 57.291 37.500 0.00 0.00 38.01 1.75
1966 2057 6.073327 TCATCAGGTGATACTCGTGATTAC 57.927 41.667 0.00 0.00 38.01 1.89
1967 2058 4.912187 CATCAGGTGATACTCGTGATTACG 59.088 45.833 3.19 3.19 41.29 3.18
1968 2059 4.023107 ATCAGGTGATACTCGTGATTACGG 60.023 45.833 10.37 3.77 40.79 4.02
1969 2060 6.438740 ATCAGGTGATACTCGTGATTACGGT 61.439 44.000 10.37 9.37 40.79 4.83
1970 2061 7.855881 ATCAGGTGATACTCGTGATTACGGTT 61.856 42.308 10.37 0.11 40.79 4.44
1971 2062 8.599979 ATCAGGTGATACTCGTGATTACGGTTA 61.600 40.741 10.37 2.41 40.79 2.85
1978 2069 3.093717 CGTGATTACGGTTATCCAGCT 57.906 47.619 1.39 0.00 46.23 4.24
1979 2070 3.454375 CGTGATTACGGTTATCCAGCTT 58.546 45.455 1.39 0.00 46.23 3.74
1980 2071 3.869246 CGTGATTACGGTTATCCAGCTTT 59.131 43.478 1.39 0.00 46.23 3.51
1981 2072 4.025979 CGTGATTACGGTTATCCAGCTTTC 60.026 45.833 1.39 0.00 46.23 2.62
1982 2073 5.116882 GTGATTACGGTTATCCAGCTTTCT 58.883 41.667 4.83 0.00 0.00 2.52
1983 2074 5.585047 GTGATTACGGTTATCCAGCTTTCTT 59.415 40.000 4.83 0.00 0.00 2.52
1984 2075 5.584649 TGATTACGGTTATCCAGCTTTCTTG 59.415 40.000 4.83 0.00 0.00 3.02
1985 2076 2.711542 ACGGTTATCCAGCTTTCTTGG 58.288 47.619 0.00 0.00 0.00 3.61
1986 2077 1.401905 CGGTTATCCAGCTTTCTTGGC 59.598 52.381 0.00 0.00 0.00 4.52
1987 2078 1.751351 GGTTATCCAGCTTTCTTGGCC 59.249 52.381 0.00 0.00 0.00 5.36
1988 2079 2.446435 GTTATCCAGCTTTCTTGGCCA 58.554 47.619 0.00 0.00 0.00 5.36
1989 2080 3.026694 GTTATCCAGCTTTCTTGGCCAT 58.973 45.455 6.09 0.00 0.00 4.40
1990 2081 2.242882 ATCCAGCTTTCTTGGCCATT 57.757 45.000 6.09 0.00 0.00 3.16
1991 2082 2.014010 TCCAGCTTTCTTGGCCATTT 57.986 45.000 6.09 0.00 0.00 2.32
2025 2116 4.451629 ACGGTTGTACTGAATCCTAGTG 57.548 45.455 0.00 0.00 0.00 2.74
2052 2143 3.876914 TGAGTGCTACTTGTGAACTTTGG 59.123 43.478 0.00 0.00 0.00 3.28
2066 2157 6.163476 GTGAACTTTGGTTTGTTCCTTTTCT 58.837 36.000 0.00 0.00 41.10 2.52
2105 2196 5.501574 GCTGATGCTTACGAATTCAGTCTTC 60.502 44.000 6.22 2.70 36.91 2.87
2128 2219 8.703604 TTCTTTAGTAGATGAATTCGGTCTTG 57.296 34.615 15.67 4.15 31.54 3.02
2135 2226 0.169009 GAATTCGGTCTTGTGCAGCC 59.831 55.000 0.00 0.00 0.00 4.85
2239 2334 9.685276 TTGTTTCACTTATTCATCAGGTGATAT 57.315 29.630 0.00 0.00 36.90 1.63
2240 2335 9.685276 TGTTTCACTTATTCATCAGGTGATATT 57.315 29.630 0.00 0.00 36.90 1.28
2387 2495 3.552132 TTGTACAGGTTGAAGCTGACA 57.448 42.857 28.68 22.77 45.98 3.58
2472 2580 5.146010 TGCCAATTTAACATGTTCCCTTC 57.854 39.130 15.85 0.71 0.00 3.46
2494 2602 0.843309 TTGAACTGCCTGAAGGTCCA 59.157 50.000 0.00 0.00 32.54 4.02
2496 2604 1.202806 TGAACTGCCTGAAGGTCCAAG 60.203 52.381 0.00 0.00 32.54 3.61
2500 2608 2.039084 ACTGCCTGAAGGTCCAAGTAAG 59.961 50.000 0.00 0.00 37.57 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 88 0.450184 CGTAATTCGGCCCAACCTTG 59.550 55.000 0.00 0.00 35.61 3.61
84 125 0.701303 CGCGACTGAACAAGTACGTC 59.299 55.000 0.00 0.00 40.07 4.34
239 293 1.658686 GGCGAAGAGGAAGAGCTCGA 61.659 60.000 8.37 0.00 0.00 4.04
311 365 1.203237 TCCTCCTCCTCCATAGCCATC 60.203 57.143 0.00 0.00 0.00 3.51
317 371 4.231658 CCAGATATCTCCTCCTCCTCCATA 59.768 50.000 1.03 0.00 0.00 2.74
715 777 0.753262 ACTGTTTCAGCGTCTGGTCT 59.247 50.000 6.95 0.00 34.37 3.85
716 778 1.140816 GACTGTTTCAGCGTCTGGTC 58.859 55.000 6.95 3.32 34.37 4.02
720 782 0.104304 AACGGACTGTTTCAGCGTCT 59.896 50.000 0.00 0.00 37.59 4.18
741 806 2.125512 GCGGGATTGCAGACGACT 60.126 61.111 0.00 0.00 34.15 4.18
815 886 3.023949 GCCAGATGGAGCTCCGTGT 62.024 63.158 32.31 25.47 39.43 4.49
817 888 1.557269 AAAGCCAGATGGAGCTCCGT 61.557 55.000 27.92 27.92 38.74 4.69
818 889 0.813210 GAAAGCCAGATGGAGCTCCG 60.813 60.000 27.43 13.92 38.74 4.63
819 890 0.813210 CGAAAGCCAGATGGAGCTCC 60.813 60.000 26.78 26.78 38.74 4.70
820 891 0.176680 TCGAAAGCCAGATGGAGCTC 59.823 55.000 4.71 4.71 38.74 4.09
823 900 1.139654 TGGATCGAAAGCCAGATGGAG 59.860 52.381 2.18 0.00 37.39 3.86
881 958 1.671054 CCGCTCCGGTTGACATTGT 60.671 57.895 0.00 0.00 42.73 2.71
892 969 1.227089 CTCCTGTGATTCCGCTCCG 60.227 63.158 0.00 0.00 0.00 4.63
893 970 1.522580 GCTCCTGTGATTCCGCTCC 60.523 63.158 0.00 0.00 0.00 4.70
898 975 0.179062 ATGCTCGCTCCTGTGATTCC 60.179 55.000 0.00 0.00 31.73 3.01
899 976 1.202510 AGATGCTCGCTCCTGTGATTC 60.203 52.381 0.00 0.00 31.73 2.52
900 977 0.829333 AGATGCTCGCTCCTGTGATT 59.171 50.000 0.00 0.00 31.73 2.57
948 1025 1.107538 CCAATCCAGCAGCATCCCTG 61.108 60.000 0.00 0.00 44.67 4.45
955 1032 0.955428 TCGTCAACCAATCCAGCAGC 60.955 55.000 0.00 0.00 0.00 5.25
956 1033 1.522668 TTCGTCAACCAATCCAGCAG 58.477 50.000 0.00 0.00 0.00 4.24
957 1034 1.974265 TTTCGTCAACCAATCCAGCA 58.026 45.000 0.00 0.00 0.00 4.41
958 1035 3.575965 AATTTCGTCAACCAATCCAGC 57.424 42.857 0.00 0.00 0.00 4.85
975 1052 4.253685 CACTGTGACGGGTCAGATAAATT 58.746 43.478 0.32 0.00 40.75 1.82
976 1053 3.260884 ACACTGTGACGGGTCAGATAAAT 59.739 43.478 15.86 0.00 40.75 1.40
980 1057 0.603569 GACACTGTGACGGGTCAGAT 59.396 55.000 15.86 0.00 40.75 2.90
981 1058 0.753848 TGACACTGTGACGGGTCAGA 60.754 55.000 15.86 0.00 40.75 3.27
1000 1077 2.120909 GCAGCATACCGCCAACCAT 61.121 57.895 0.00 0.00 44.04 3.55
1057 1134 4.093998 CAGCACAGTCTTGTCATACCAATC 59.906 45.833 0.00 0.00 34.62 2.67
1063 1140 2.289631 CCACCAGCACAGTCTTGTCATA 60.290 50.000 0.00 0.00 34.62 2.15
1065 1142 0.179048 CCACCAGCACAGTCTTGTCA 60.179 55.000 0.00 0.00 34.62 3.58
1146 1223 0.535102 CCTGTGACCACCCAACTGTC 60.535 60.000 0.00 0.00 0.00 3.51
1204 1281 2.100631 CGTTGTCATCCCCGACAGC 61.101 63.158 0.00 0.00 46.14 4.40
1219 1296 2.104111 TGTTGAGTGAACCCTCATCGTT 59.896 45.455 0.00 0.00 40.96 3.85
1296 1373 3.978718 ACTCTGAAACTTTGCTTCAGC 57.021 42.857 7.57 0.00 46.22 4.26
1305 1382 5.471456 CAGCACCTTATCAACTCTGAAACTT 59.529 40.000 0.00 0.00 34.49 2.66
1330 1407 1.687660 GTACCCCAGCTTAGCTAGGTC 59.312 57.143 25.25 15.84 41.54 3.85
1339 1416 1.380302 CCAGCTTGTACCCCAGCTT 59.620 57.895 8.26 0.00 35.17 3.74
1342 1419 0.609131 CCAACCAGCTTGTACCCCAG 60.609 60.000 0.00 0.00 0.00 4.45
1346 1423 1.244816 GAACCCAACCAGCTTGTACC 58.755 55.000 0.00 0.00 0.00 3.34
1351 1428 0.251787 GGATGGAACCCAACCAGCTT 60.252 55.000 7.33 0.00 44.54 3.74
1389 1466 2.435372 AAAGACCACTGCTGACCAAA 57.565 45.000 0.00 0.00 0.00 3.28
1392 1469 2.359900 CCATAAAGACCACTGCTGACC 58.640 52.381 0.00 0.00 0.00 4.02
1400 1477 1.737793 CAACTCCGCCATAAAGACCAC 59.262 52.381 0.00 0.00 0.00 4.16
1401 1478 1.948611 GCAACTCCGCCATAAAGACCA 60.949 52.381 0.00 0.00 0.00 4.02
1413 1490 1.135315 CAATGAAGGCGCAACTCCG 59.865 57.895 10.83 0.00 0.00 4.63
1416 1493 0.823356 ACACCAATGAAGGCGCAACT 60.823 50.000 10.83 0.00 0.00 3.16
1418 1495 1.851021 CGACACCAATGAAGGCGCAA 61.851 55.000 10.83 0.00 0.00 4.85
1423 1509 0.036164 TCCCACGACACCAATGAAGG 59.964 55.000 0.00 0.00 0.00 3.46
1449 1535 2.224495 AATCACCAATTTGGCGGCGG 62.224 55.000 15.49 0.68 42.67 6.13
1452 1538 2.739885 TGAAATCACCAATTTGGCGG 57.260 45.000 15.49 8.23 42.67 6.13
1459 1545 4.588899 TCGAGGTCAATGAAATCACCAAT 58.411 39.130 0.00 0.00 0.00 3.16
1461 1547 3.599343 CTCGAGGTCAATGAAATCACCA 58.401 45.455 3.91 0.00 0.00 4.17
1462 1548 2.939103 CCTCGAGGTCAATGAAATCACC 59.061 50.000 24.04 0.00 0.00 4.02
1463 1549 3.861840 TCCTCGAGGTCAATGAAATCAC 58.138 45.455 30.17 0.00 36.34 3.06
1465 1551 3.873952 CCTTCCTCGAGGTCAATGAAATC 59.126 47.826 30.17 0.00 36.34 2.17
1466 1552 3.878778 CCTTCCTCGAGGTCAATGAAAT 58.121 45.455 30.17 0.00 36.34 2.17
1468 1554 1.066143 GCCTTCCTCGAGGTCAATGAA 60.066 52.381 30.17 15.30 39.11 2.57
1471 1557 0.539051 CTGCCTTCCTCGAGGTCAAT 59.461 55.000 30.17 0.00 39.11 2.57
1476 1562 2.581354 CCACTGCCTTCCTCGAGG 59.419 66.667 26.32 26.32 39.93 4.63
1560 1646 2.158449 CCAAGCATGAGTCGAACTGAAC 59.842 50.000 0.00 0.00 0.00 3.18
1591 1677 7.286087 ACACATACATGACTATTCCATTGCATT 59.714 33.333 0.00 0.00 0.00 3.56
1594 1680 6.624352 ACACATACATGACTATTCCATTGC 57.376 37.500 0.00 0.00 0.00 3.56
1605 1691 3.370978 GTGCAGGTGTACACATACATGAC 59.629 47.826 26.51 6.31 43.21 3.06
1636 1722 6.655078 AACTGGCTAACACAATTCAAGAAT 57.345 33.333 0.00 0.00 0.00 2.40
1666 1752 9.654663 GGATAACAGTAGTATAATTTAGCCCAG 57.345 37.037 0.00 0.00 0.00 4.45
1711 1802 8.985315 ATTCAGTACAACCATAATCATGACAT 57.015 30.769 0.00 0.00 33.67 3.06
1712 1803 7.498900 GGATTCAGTACAACCATAATCATGACA 59.501 37.037 0.00 0.00 33.67 3.58
1713 1804 7.716998 AGGATTCAGTACAACCATAATCATGAC 59.283 37.037 0.00 0.00 33.67 3.06
1714 1805 7.805163 AGGATTCAGTACAACCATAATCATGA 58.195 34.615 0.00 0.00 33.67 3.07
1715 1806 9.212641 CTAGGATTCAGTACAACCATAATCATG 57.787 37.037 0.00 0.00 0.00 3.07
1716 1807 8.938883 ACTAGGATTCAGTACAACCATAATCAT 58.061 33.333 0.00 0.00 0.00 2.45
1717 1808 8.319057 ACTAGGATTCAGTACAACCATAATCA 57.681 34.615 0.00 0.00 0.00 2.57
1722 1813 9.435570 ACTAATACTAGGATTCAGTACAACCAT 57.564 33.333 2.60 0.00 31.53 3.55
1723 1814 8.692710 CACTAATACTAGGATTCAGTACAACCA 58.307 37.037 2.60 0.00 31.53 3.67
1724 1815 8.910944 TCACTAATACTAGGATTCAGTACAACC 58.089 37.037 2.60 0.00 31.53 3.77
1740 1831 9.998106 AGTTCACAAGTAACAATCACTAATACT 57.002 29.630 0.00 0.00 0.00 2.12
1743 1834 9.337396 TGAAGTTCACAAGTAACAATCACTAAT 57.663 29.630 0.08 0.00 0.00 1.73
1744 1835 8.725405 TGAAGTTCACAAGTAACAATCACTAA 57.275 30.769 0.08 0.00 0.00 2.24
1745 1836 8.902540 ATGAAGTTCACAAGTAACAATCACTA 57.097 30.769 7.96 0.00 31.85 2.74
1746 1837 7.807977 ATGAAGTTCACAAGTAACAATCACT 57.192 32.000 7.96 0.00 31.85 3.41
1747 1838 8.856490 AAATGAAGTTCACAAGTAACAATCAC 57.144 30.769 7.96 0.00 31.85 3.06
1748 1839 9.299963 CAAAATGAAGTTCACAAGTAACAATCA 57.700 29.630 7.96 0.00 32.86 2.57
1749 1840 9.301153 ACAAAATGAAGTTCACAAGTAACAATC 57.699 29.630 7.96 0.00 0.00 2.67
1750 1841 9.651913 AACAAAATGAAGTTCACAAGTAACAAT 57.348 25.926 7.96 0.00 0.00 2.71
1751 1842 9.134734 GAACAAAATGAAGTTCACAAGTAACAA 57.865 29.630 7.96 0.00 42.72 2.83
1752 1843 7.757624 GGAACAAAATGAAGTTCACAAGTAACA 59.242 33.333 7.96 0.00 44.46 2.41
1753 1844 7.973944 AGGAACAAAATGAAGTTCACAAGTAAC 59.026 33.333 7.96 2.47 44.46 2.50
1754 1845 8.062065 AGGAACAAAATGAAGTTCACAAGTAA 57.938 30.769 7.96 0.00 44.46 2.24
1755 1846 7.639113 AGGAACAAAATGAAGTTCACAAGTA 57.361 32.000 7.96 0.00 44.46 2.24
1756 1847 6.530019 AGGAACAAAATGAAGTTCACAAGT 57.470 33.333 7.96 2.13 44.46 3.16
1757 1848 7.832503 AAAGGAACAAAATGAAGTTCACAAG 57.167 32.000 7.96 1.49 44.46 3.16
1758 1849 8.614469 AAAAAGGAACAAAATGAAGTTCACAA 57.386 26.923 7.96 0.00 44.46 3.33
1759 1850 9.364989 CTAAAAAGGAACAAAATGAAGTTCACA 57.635 29.630 7.96 0.00 44.46 3.58
1760 1851 9.366216 ACTAAAAAGGAACAAAATGAAGTTCAC 57.634 29.630 7.96 0.00 44.46 3.18
1761 1852 9.936759 AACTAAAAAGGAACAAAATGAAGTTCA 57.063 25.926 8.27 8.27 44.46 3.18
1783 1874 9.777297 TGAGCATCAGCAAACATATAATAACTA 57.223 29.630 0.00 0.00 42.56 2.24
1784 1875 8.681486 TGAGCATCAGCAAACATATAATAACT 57.319 30.769 0.00 0.00 42.56 2.24
1802 1893 4.252073 ACAAGACTGAACTCATGAGCATC 58.748 43.478 22.83 19.95 0.00 3.91
1803 1894 4.283363 ACAAGACTGAACTCATGAGCAT 57.717 40.909 22.83 11.95 0.00 3.79
1804 1895 3.758755 ACAAGACTGAACTCATGAGCA 57.241 42.857 22.83 12.28 0.00 4.26
1805 1896 5.698545 ACTAAACAAGACTGAACTCATGAGC 59.301 40.000 22.83 7.99 0.00 4.26
1806 1897 7.439356 TCAACTAAACAAGACTGAACTCATGAG 59.561 37.037 21.37 21.37 0.00 2.90
1807 1898 7.272244 TCAACTAAACAAGACTGAACTCATGA 58.728 34.615 0.00 0.00 0.00 3.07
1808 1899 7.482654 TCAACTAAACAAGACTGAACTCATG 57.517 36.000 0.00 0.00 0.00 3.07
1809 1900 8.682936 ATTCAACTAAACAAGACTGAACTCAT 57.317 30.769 0.00 0.00 35.14 2.90
1810 1901 9.607988 TTATTCAACTAAACAAGACTGAACTCA 57.392 29.630 0.00 0.00 35.14 3.41
1813 1904 9.827411 GGATTATTCAACTAAACAAGACTGAAC 57.173 33.333 0.00 0.00 35.14 3.18
1814 1905 8.717821 CGGATTATTCAACTAAACAAGACTGAA 58.282 33.333 0.00 0.00 36.06 3.02
1815 1906 7.333423 CCGGATTATTCAACTAAACAAGACTGA 59.667 37.037 0.00 0.00 0.00 3.41
1816 1907 7.119262 ACCGGATTATTCAACTAAACAAGACTG 59.881 37.037 9.46 0.00 0.00 3.51
1817 1908 7.166167 ACCGGATTATTCAACTAAACAAGACT 58.834 34.615 9.46 0.00 0.00 3.24
1818 1909 7.333672 AGACCGGATTATTCAACTAAACAAGAC 59.666 37.037 9.46 0.00 0.00 3.01
1819 1910 7.391620 AGACCGGATTATTCAACTAAACAAGA 58.608 34.615 9.46 0.00 0.00 3.02
1820 1911 7.611213 AGACCGGATTATTCAACTAAACAAG 57.389 36.000 9.46 0.00 0.00 3.16
1821 1912 7.989416 AAGACCGGATTATTCAACTAAACAA 57.011 32.000 9.46 0.00 0.00 2.83
1822 1913 9.104965 CATAAGACCGGATTATTCAACTAAACA 57.895 33.333 9.46 0.00 0.00 2.83
1823 1914 8.068380 GCATAAGACCGGATTATTCAACTAAAC 58.932 37.037 9.46 0.00 0.00 2.01
1824 1915 7.771361 TGCATAAGACCGGATTATTCAACTAAA 59.229 33.333 9.46 0.00 0.00 1.85
1825 1916 7.276658 TGCATAAGACCGGATTATTCAACTAA 58.723 34.615 9.46 0.00 0.00 2.24
1826 1917 6.822442 TGCATAAGACCGGATTATTCAACTA 58.178 36.000 9.46 0.00 0.00 2.24
1827 1918 5.680619 TGCATAAGACCGGATTATTCAACT 58.319 37.500 9.46 0.00 0.00 3.16
1828 1919 5.527582 ACTGCATAAGACCGGATTATTCAAC 59.472 40.000 9.46 3.00 0.00 3.18
1829 1920 5.680619 ACTGCATAAGACCGGATTATTCAA 58.319 37.500 9.46 0.07 0.00 2.69
1830 1921 5.290493 ACTGCATAAGACCGGATTATTCA 57.710 39.130 9.46 11.82 0.00 2.57
1831 1922 5.758296 TCAACTGCATAAGACCGGATTATTC 59.242 40.000 9.46 7.62 0.00 1.75
1832 1923 5.527582 GTCAACTGCATAAGACCGGATTATT 59.472 40.000 9.46 0.00 0.00 1.40
1833 1924 5.057149 GTCAACTGCATAAGACCGGATTAT 58.943 41.667 9.46 9.72 0.00 1.28
1834 1925 4.081365 TGTCAACTGCATAAGACCGGATTA 60.081 41.667 9.46 7.47 0.00 1.75
1835 1926 3.270877 GTCAACTGCATAAGACCGGATT 58.729 45.455 9.46 4.99 0.00 3.01
1836 1927 2.236146 TGTCAACTGCATAAGACCGGAT 59.764 45.455 9.46 0.00 0.00 4.18
1837 1928 1.621317 TGTCAACTGCATAAGACCGGA 59.379 47.619 9.46 0.00 0.00 5.14
1838 1929 2.093306 TGTCAACTGCATAAGACCGG 57.907 50.000 0.00 0.00 0.00 5.28
1839 1930 2.416547 CCTTGTCAACTGCATAAGACCG 59.583 50.000 9.25 2.67 0.00 4.79
1840 1931 2.162408 GCCTTGTCAACTGCATAAGACC 59.838 50.000 9.25 0.00 0.00 3.85
1841 1932 2.813754 TGCCTTGTCAACTGCATAAGAC 59.186 45.455 5.81 5.81 0.00 3.01
1842 1933 3.138884 TGCCTTGTCAACTGCATAAGA 57.861 42.857 1.75 0.00 0.00 2.10
1843 1934 3.441222 TCATGCCTTGTCAACTGCATAAG 59.559 43.478 14.41 6.82 42.22 1.73
1844 1935 3.419943 TCATGCCTTGTCAACTGCATAA 58.580 40.909 14.41 1.97 42.22 1.90
1845 1936 3.070476 TCATGCCTTGTCAACTGCATA 57.930 42.857 14.41 4.86 42.22 3.14
1846 1937 1.913778 TCATGCCTTGTCAACTGCAT 58.086 45.000 10.61 10.61 44.79 3.96
1847 1938 1.689984 TTCATGCCTTGTCAACTGCA 58.310 45.000 7.32 7.32 38.23 4.41
1848 1939 3.308438 AATTCATGCCTTGTCAACTGC 57.692 42.857 0.00 0.00 0.00 4.40
1849 1940 5.860182 CACTTAATTCATGCCTTGTCAACTG 59.140 40.000 0.00 0.00 0.00 3.16
1850 1941 5.565439 GCACTTAATTCATGCCTTGTCAACT 60.565 40.000 0.00 0.00 33.06 3.16
1851 1942 4.622740 GCACTTAATTCATGCCTTGTCAAC 59.377 41.667 0.00 0.00 33.06 3.18
1852 1943 4.280425 TGCACTTAATTCATGCCTTGTCAA 59.720 37.500 6.15 0.00 38.63 3.18
1853 1944 3.825585 TGCACTTAATTCATGCCTTGTCA 59.174 39.130 6.15 0.00 38.63 3.58
1854 1945 4.439305 TGCACTTAATTCATGCCTTGTC 57.561 40.909 6.15 0.00 38.63 3.18
1855 1946 6.528537 TTATGCACTTAATTCATGCCTTGT 57.471 33.333 0.00 0.00 38.63 3.16
1856 1947 6.073980 GCATTATGCACTTAATTCATGCCTTG 60.074 38.462 12.80 1.65 44.26 3.61
1857 1948 5.987347 GCATTATGCACTTAATTCATGCCTT 59.013 36.000 12.80 0.00 44.26 4.35
1858 1949 5.535333 GCATTATGCACTTAATTCATGCCT 58.465 37.500 12.80 0.45 44.26 4.75
1859 1950 5.834239 GCATTATGCACTTAATTCATGCC 57.166 39.130 12.80 0.00 44.26 4.40
1883 1974 5.105063 GCAAGAAAACTTCTCAGCAAAGTT 58.895 37.500 8.20 0.00 46.22 2.66
1884 1975 4.400567 AGCAAGAAAACTTCTCAGCAAAGT 59.599 37.500 13.10 0.00 40.84 2.66
1885 1976 4.929781 AGCAAGAAAACTTCTCAGCAAAG 58.070 39.130 13.10 0.00 40.84 2.77
1886 1977 4.989279 AGCAAGAAAACTTCTCAGCAAA 57.011 36.364 13.10 0.00 40.84 3.68
1887 1978 4.989279 AAGCAAGAAAACTTCTCAGCAA 57.011 36.364 13.10 0.00 40.84 3.91
1888 1979 4.440525 CCAAAGCAAGAAAACTTCTCAGCA 60.441 41.667 13.10 0.00 40.84 4.41
1889 1980 4.047142 CCAAAGCAAGAAAACTTCTCAGC 58.953 43.478 5.95 5.95 39.61 4.26
1890 1981 5.039333 CACCAAAGCAAGAAAACTTCTCAG 58.961 41.667 0.00 0.00 39.61 3.35
1891 1982 4.677779 GCACCAAAGCAAGAAAACTTCTCA 60.678 41.667 0.00 0.00 39.61 3.27
1892 1983 3.798878 GCACCAAAGCAAGAAAACTTCTC 59.201 43.478 0.00 0.00 39.61 2.87
1893 1984 3.195396 TGCACCAAAGCAAGAAAACTTCT 59.805 39.130 0.00 0.00 42.46 2.85
1894 1985 3.520569 TGCACCAAAGCAAGAAAACTTC 58.479 40.909 0.00 0.00 42.46 3.01
1895 1986 3.608316 TGCACCAAAGCAAGAAAACTT 57.392 38.095 0.00 0.00 42.46 2.66
1913 2004 6.835356 GTGAAACAAACCAAATGCACATATGC 60.835 38.462 1.58 0.00 45.18 3.14
1914 2005 6.424509 AGTGAAACAAACCAAATGCACATATG 59.575 34.615 0.00 0.00 41.43 1.78
1915 2006 6.523840 AGTGAAACAAACCAAATGCACATAT 58.476 32.000 0.00 0.00 41.43 1.78
1916 2007 5.911752 AGTGAAACAAACCAAATGCACATA 58.088 33.333 0.00 0.00 41.43 2.29
1917 2008 4.768583 AGTGAAACAAACCAAATGCACAT 58.231 34.783 0.00 0.00 41.43 3.21
1918 2009 4.199432 AGTGAAACAAACCAAATGCACA 57.801 36.364 0.00 0.00 41.43 4.57
1919 2010 6.843069 ATTAGTGAAACAAACCAAATGCAC 57.157 33.333 0.00 0.00 41.43 4.57
1920 2011 7.044181 TGAATTAGTGAAACAAACCAAATGCA 58.956 30.769 0.00 0.00 41.43 3.96
1921 2012 7.475771 TGAATTAGTGAAACAAACCAAATGC 57.524 32.000 0.00 0.00 41.43 3.56
1922 2013 9.258826 TGATGAATTAGTGAAACAAACCAAATG 57.741 29.630 0.00 0.00 41.43 2.32
1923 2014 9.480053 CTGATGAATTAGTGAAACAAACCAAAT 57.520 29.630 0.00 0.00 41.43 2.32
1924 2015 7.925483 CCTGATGAATTAGTGAAACAAACCAAA 59.075 33.333 0.00 0.00 41.43 3.28
1925 2016 7.069331 ACCTGATGAATTAGTGAAACAAACCAA 59.931 33.333 0.00 0.00 41.43 3.67
1926 2017 6.549364 ACCTGATGAATTAGTGAAACAAACCA 59.451 34.615 0.00 0.00 41.43 3.67
1927 2018 6.863126 CACCTGATGAATTAGTGAAACAAACC 59.137 38.462 0.00 0.00 41.43 3.27
1928 2019 7.648142 TCACCTGATGAATTAGTGAAACAAAC 58.352 34.615 0.00 0.00 34.27 2.93
1929 2020 7.815840 TCACCTGATGAATTAGTGAAACAAA 57.184 32.000 0.00 0.00 34.27 2.83
1930 2021 8.946085 GTATCACCTGATGAATTAGTGAAACAA 58.054 33.333 0.00 0.00 41.93 2.83
1931 2022 8.321353 AGTATCACCTGATGAATTAGTGAAACA 58.679 33.333 0.00 0.00 41.93 2.83
1932 2023 8.723942 AGTATCACCTGATGAATTAGTGAAAC 57.276 34.615 0.00 0.00 41.93 2.78
1933 2024 7.706607 CGAGTATCACCTGATGAATTAGTGAAA 59.293 37.037 0.00 0.00 41.93 2.69
1934 2025 7.147897 ACGAGTATCACCTGATGAATTAGTGAA 60.148 37.037 0.00 0.00 41.93 3.18
1935 2026 6.321435 ACGAGTATCACCTGATGAATTAGTGA 59.679 38.462 0.00 0.00 41.93 3.41
1936 2027 6.419116 CACGAGTATCACCTGATGAATTAGTG 59.581 42.308 0.00 0.00 41.93 2.74
1937 2028 6.321435 TCACGAGTATCACCTGATGAATTAGT 59.679 38.462 0.00 0.00 41.93 2.24
1938 2029 6.739112 TCACGAGTATCACCTGATGAATTAG 58.261 40.000 0.00 0.00 41.93 1.73
1939 2030 6.709018 TCACGAGTATCACCTGATGAATTA 57.291 37.500 0.00 0.00 41.93 1.40
1940 2031 5.598416 TCACGAGTATCACCTGATGAATT 57.402 39.130 0.00 0.00 41.93 2.17
1941 2032 5.798125 ATCACGAGTATCACCTGATGAAT 57.202 39.130 0.00 0.00 41.93 2.57
1942 2033 5.598416 AATCACGAGTATCACCTGATGAA 57.402 39.130 0.00 0.00 41.93 2.57
1943 2034 6.073327 GTAATCACGAGTATCACCTGATGA 57.927 41.667 0.00 0.00 43.13 2.92
1959 2050 5.116882 AGAAAGCTGGATAACCGTAATCAC 58.883 41.667 0.00 0.00 39.42 3.06
1960 2051 5.353394 AGAAAGCTGGATAACCGTAATCA 57.647 39.130 0.00 0.00 39.42 2.57
1961 2052 5.007724 CCAAGAAAGCTGGATAACCGTAATC 59.992 44.000 0.00 0.00 39.42 1.75
1962 2053 4.881850 CCAAGAAAGCTGGATAACCGTAAT 59.118 41.667 0.00 0.00 39.42 1.89
1963 2054 4.258543 CCAAGAAAGCTGGATAACCGTAA 58.741 43.478 0.00 0.00 39.42 3.18
1964 2055 3.869065 CCAAGAAAGCTGGATAACCGTA 58.131 45.455 0.00 0.00 39.42 4.02
1965 2056 2.711542 CCAAGAAAGCTGGATAACCGT 58.288 47.619 0.00 0.00 39.42 4.83
1966 2057 1.401905 GCCAAGAAAGCTGGATAACCG 59.598 52.381 0.00 0.00 39.42 4.44
1967 2058 1.751351 GGCCAAGAAAGCTGGATAACC 59.249 52.381 0.00 0.00 0.00 2.85
1968 2059 2.446435 TGGCCAAGAAAGCTGGATAAC 58.554 47.619 0.61 0.00 0.00 1.89
1969 2060 2.897271 TGGCCAAGAAAGCTGGATAA 57.103 45.000 0.61 0.00 0.00 1.75
1970 2061 3.386932 AATGGCCAAGAAAGCTGGATA 57.613 42.857 10.96 0.00 0.00 2.59
1971 2062 2.242882 AATGGCCAAGAAAGCTGGAT 57.757 45.000 10.96 0.00 0.00 3.41
1972 2063 1.895131 GAAATGGCCAAGAAAGCTGGA 59.105 47.619 10.96 0.00 0.00 3.86
1973 2064 1.619827 TGAAATGGCCAAGAAAGCTGG 59.380 47.619 10.96 0.00 0.00 4.85
1974 2065 3.259064 CATGAAATGGCCAAGAAAGCTG 58.741 45.455 10.96 0.00 41.79 4.24
1975 2066 3.604875 CATGAAATGGCCAAGAAAGCT 57.395 42.857 10.96 0.00 41.79 3.74
2025 2116 5.290386 AGTTCACAAGTAGCACTCACTAAC 58.710 41.667 0.00 0.00 0.00 2.34
2105 2196 7.464710 GCACAAGACCGAATTCATCTACTAAAG 60.465 40.741 6.22 0.00 0.00 1.85
2128 2219 1.672356 ATGACCTTGTCGGCTGCAC 60.672 57.895 0.50 0.00 34.95 4.57
2135 2226 4.154015 TGCACTTATTTCATGACCTTGTCG 59.846 41.667 0.00 0.00 34.95 4.35
2387 2495 6.274200 ACTGGAGAGCAATCTTCCCAATATAT 59.726 38.462 0.00 0.00 0.00 0.86
2452 2560 7.930865 TCAAAAGAAGGGAACATGTTAAATTGG 59.069 33.333 11.95 0.00 0.00 3.16
2472 2580 2.294512 GGACCTTCAGGCAGTTCAAAAG 59.705 50.000 0.00 0.00 39.32 2.27
2527 2636 6.097554 ACATCCTCTTTCTCTCGACATAACAT 59.902 38.462 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.