Multiple sequence alignment - TraesCS1A01G269800

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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 TraesCS1A01G269800 chr1A 100.000 2507 0 0 1 2507 463958468 463960974 0.000000e+00 4630.0
1 TraesCS1A01G269800 chr1A 79.472 682 111 26 137 798 463923794 463924466 8.170000e-125 457.0
2 TraesCS1A01G269800 chr1B 94.796 1595 74 3 57 1642 488473826 488475420 0.000000e+00 2477.0
3 TraesCS1A01G269800 chr1B 79.762 168 23 7 1626 1785 500268464 500268628 7.330000e-21 111.0
4 TraesCS1A01G269800 chr1B 100.000 29 0 0 1842 1870 6390492 6390520 1.000000e-03 54.7
5 TraesCS1A01G269800 chr1D 93.731 1643 77 13 33 1650 365082092 365083733 0.000000e+00 2440.0
6 TraesCS1A01G269800 chr1D 76.573 461 60 26 1988 2435 365083886 365084311 2.530000e-50 209.0
7 TraesCS1A01G269800 chr1D 78.824 170 26 9 1622 1785 119295229 119295394 3.410000e-19 106.0
8 TraesCS1A01G269800 chr1D 96.875 32 0 1 4 34 78058078 78058047 5.000000e-03 52.8
9 TraesCS1A01G269800 chr3B 80.830 699 116 18 146 835 651427238 651426549 1.320000e-147 532.0
10 TraesCS1A01G269800 chr3B 85.030 334 39 9 1103 1432 651426305 651425979 1.860000e-86 329.0
11 TraesCS1A01G269800 chr3B 84.431 334 41 9 1103 1432 489350608 489350282 4.020000e-83 318.0
12 TraesCS1A01G269800 chr3B 80.120 166 24 7 1628 1786 26409414 26409577 5.670000e-22 115.0
13 TraesCS1A01G269800 chr3A 80.687 699 117 17 146 835 632041222 632040533 6.140000e-146 527.0
14 TraesCS1A01G269800 chr3A 77.609 594 105 23 167 743 632295260 632294678 4.000000e-88 335.0
15 TraesCS1A01G269800 chr3A 85.030 334 39 9 1103 1432 632040298 632039972 1.860000e-86 329.0
16 TraesCS1A01G269800 chr4B 80.321 686 119 16 158 835 46934226 46933549 2.880000e-139 505.0
17 TraesCS1A01G269800 chr4B 85.382 301 36 7 1103 1399 46933305 46933009 3.130000e-79 305.0
18 TraesCS1A01G269800 chr4B 89.655 58 6 0 147 204 672128282 672128339 9.620000e-10 75.0
19 TraesCS1A01G269800 chr3D 77.867 750 152 14 92 834 488902978 488903720 1.060000e-123 453.0
20 TraesCS1A01G269800 chr3D 77.778 621 110 23 140 743 488893876 488894485 8.530000e-95 357.0
21 TraesCS1A01G269800 chr3D 84.731 334 40 9 1103 1432 488951035 488951361 8.650000e-85 324.0
22 TraesCS1A01G269800 chr2B 85.030 334 39 9 1103 1432 254627112 254627438 1.860000e-86 329.0
23 TraesCS1A01G269800 chr2B 79.290 169 28 6 1626 1788 135092528 135092361 7.330000e-21 111.0
24 TraesCS1A01G269800 chr7D 85.284 299 40 3 1103 1399 89311902 89312198 3.130000e-79 305.0
25 TraesCS1A01G269800 chr7D 78.107 169 29 7 1624 1785 552634818 552634651 1.590000e-17 100.0
26 TraesCS1A01G269800 chr7D 100.000 32 0 0 1 32 177094343 177094312 2.690000e-05 60.2
27 TraesCS1A01G269800 chr5A 81.098 164 26 2 1628 1786 31211658 31211495 2.620000e-25 126.0
28 TraesCS1A01G269800 chr7B 80.117 171 27 6 1626 1790 437932158 437931989 1.220000e-23 121.0
29 TraesCS1A01G269800 chr7B 92.857 42 3 0 1831 1872 131741699 131741658 7.490000e-06 62.1
30 TraesCS1A01G269800 chr2D 80.226 177 22 10 1617 1784 552076776 552076604 1.220000e-23 121.0
31 TraesCS1A01G269800 chr5D 79.167 168 23 10 1628 1785 408752639 408752474 3.410000e-19 106.0
32 TraesCS1A01G269800 chr5B 90.698 43 4 0 1843 1885 541952404 541952362 9.690000e-05 58.4
33 TraesCS1A01G269800 chr6D 100.000 28 0 0 1845 1872 95724690 95724663 5.000000e-03 52.8


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 TraesCS1A01G269800 chr1A 463958468 463960974 2506 False 4630.0 4630 100.0000 1 2507 1 chr1A.!!$F2 2506
1 TraesCS1A01G269800 chr1A 463923794 463924466 672 False 457.0 457 79.4720 137 798 1 chr1A.!!$F1 661
2 TraesCS1A01G269800 chr1B 488473826 488475420 1594 False 2477.0 2477 94.7960 57 1642 1 chr1B.!!$F2 1585
3 TraesCS1A01G269800 chr1D 365082092 365084311 2219 False 1324.5 2440 85.1520 33 2435 2 chr1D.!!$F2 2402
4 TraesCS1A01G269800 chr3B 651425979 651427238 1259 True 430.5 532 82.9300 146 1432 2 chr3B.!!$R2 1286
5 TraesCS1A01G269800 chr3A 632039972 632041222 1250 True 428.0 527 82.8585 146 1432 2 chr3A.!!$R2 1286
6 TraesCS1A01G269800 chr3A 632294678 632295260 582 True 335.0 335 77.6090 167 743 1 chr3A.!!$R1 576
7 TraesCS1A01G269800 chr4B 46933009 46934226 1217 True 405.0 505 82.8515 158 1399 2 chr4B.!!$R1 1241
8 TraesCS1A01G269800 chr3D 488902978 488903720 742 False 453.0 453 77.8670 92 834 1 chr3D.!!$F2 742
9 TraesCS1A01G269800 chr3D 488893876 488894485 609 False 357.0 357 77.7780 140 743 1 chr3D.!!$F1 603

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
847 859 0.670546 CCGCGTTTCTGATCACCACT 60.671 55.0 4.92 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2446 0.968405 GGGCAAACCAGATGAAAGCA 59.032 50.0 0.0 0.0 39.85 3.91 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
21 22 3.684103 AGCTCGTCGACTGAGATTTAG 57.316 47.619 29.05 12.08 35.43 1.85
22 23 2.113289 GCTCGTCGACTGAGATTTAGC 58.887 52.381 29.05 16.38 35.43 3.09
23 24 2.478031 GCTCGTCGACTGAGATTTAGCA 60.478 50.000 29.05 2.11 35.43 3.49
24 25 3.358775 CTCGTCGACTGAGATTTAGCAG 58.641 50.000 23.94 2.46 35.43 4.24
26 27 3.190744 TCGTCGACTGAGATTTAGCAGTT 59.809 43.478 14.70 0.00 44.77 3.16
27 28 3.544285 CGTCGACTGAGATTTAGCAGTTC 59.456 47.826 14.70 0.00 44.77 3.01
28 29 3.860536 GTCGACTGAGATTTAGCAGTTCC 59.139 47.826 8.70 0.00 44.77 3.62
29 30 2.854777 CGACTGAGATTTAGCAGTTCCG 59.145 50.000 0.00 0.00 44.77 4.30
30 31 3.673594 CGACTGAGATTTAGCAGTTCCGT 60.674 47.826 0.00 0.00 44.77 4.69
31 32 4.246458 GACTGAGATTTAGCAGTTCCGTT 58.754 43.478 0.00 0.00 44.77 4.44
34 35 6.228258 ACTGAGATTTAGCAGTTCCGTTTAA 58.772 36.000 0.00 0.00 42.33 1.52
38 39 6.704310 AGATTTAGCAGTTCCGTTTAACCTA 58.296 36.000 0.00 0.00 0.00 3.08
47 48 3.036091 TCCGTTTAACCTATGCCTAGCT 58.964 45.455 0.00 0.00 0.00 3.32
78 79 3.007635 ACTGCTAATTCTAACCAACGGC 58.992 45.455 0.00 0.00 0.00 5.68
84 85 1.234615 TTCTAACCAACGGCAGCTGC 61.235 55.000 30.88 30.88 41.14 5.25
847 859 0.670546 CCGCGTTTCTGATCACCACT 60.671 55.000 4.92 0.00 0.00 4.00
856 868 1.267574 TGATCACCACTCCCTGCTCC 61.268 60.000 0.00 0.00 0.00 4.70
888 902 2.224113 CCTGAGCACTGCAAATTTTGGT 60.224 45.455 10.96 0.00 0.00 3.67
913 927 1.526887 GCATATCAATGTCCACGTCGG 59.473 52.381 0.00 0.00 35.38 4.79
944 970 1.733041 CATCGACCGAACACGCTGT 60.733 57.895 0.00 0.00 0.00 4.40
953 979 1.062002 CGAACACGCTGTCAAACACTT 59.938 47.619 0.00 0.00 0.00 3.16
954 980 2.705154 GAACACGCTGTCAAACACTTC 58.295 47.619 0.00 0.00 0.00 3.01
977 1007 1.332144 TTACCTGTATTCCGGCGCCT 61.332 55.000 26.68 8.22 0.00 5.52
978 1008 2.023414 TACCTGTATTCCGGCGCCTG 62.023 60.000 26.68 19.63 0.00 4.85
992 1022 3.041940 CCTGTGTTGCGGGTCGAC 61.042 66.667 7.13 7.13 38.84 4.20
994 1024 4.953868 TGTGTTGCGGGTCGACGG 62.954 66.667 9.92 5.12 31.43 4.79
1013 1043 0.530650 GCCTTCATGCGAATCGGAGA 60.531 55.000 4.35 0.00 45.75 3.71
1039 1069 3.745803 GGACTCGACTTCCGCCGT 61.746 66.667 0.00 0.00 38.37 5.68
1040 1070 2.202453 GACTCGACTTCCGCCGTC 60.202 66.667 0.00 0.00 38.37 4.79
1150 1378 1.080434 GAGCAAGAAGACGGCGAGT 60.080 57.895 16.62 0.00 0.00 4.18
1473 1701 0.458889 CTGCATTTGTGATTGCCGGG 60.459 55.000 2.18 0.00 38.08 5.73
1583 1819 3.678072 GTCTCGTGAATCAAACATCGGAA 59.322 43.478 0.00 0.00 0.00 4.30
1604 1840 6.514048 CGGAAAAAGAAGAGCAGAGTGAAATT 60.514 38.462 0.00 0.00 0.00 1.82
1605 1841 6.640092 GGAAAAAGAAGAGCAGAGTGAAATTG 59.360 38.462 0.00 0.00 0.00 2.32
1633 1869 6.906901 TCCTCCCAAAATTATACAGTACTCCT 59.093 38.462 0.00 0.00 0.00 3.69
1642 1878 7.598759 ATTATACAGTACTCCTTCCGTTCAT 57.401 36.000 0.00 0.00 0.00 2.57
1645 1881 5.326200 ACAGTACTCCTTCCGTTCATAAG 57.674 43.478 0.00 0.00 0.00 1.73
1646 1882 4.771054 ACAGTACTCCTTCCGTTCATAAGT 59.229 41.667 0.00 0.00 0.00 2.24
1647 1883 5.948162 ACAGTACTCCTTCCGTTCATAAGTA 59.052 40.000 0.00 0.00 0.00 2.24
1648 1884 6.606395 ACAGTACTCCTTCCGTTCATAAGTAT 59.394 38.462 0.00 0.00 0.00 2.12
1649 1885 7.776969 ACAGTACTCCTTCCGTTCATAAGTATA 59.223 37.037 0.00 0.00 0.00 1.47
1650 1886 8.074972 CAGTACTCCTTCCGTTCATAAGTATAC 58.925 40.741 0.00 0.00 0.00 1.47
1651 1887 7.776969 AGTACTCCTTCCGTTCATAAGTATACA 59.223 37.037 5.50 0.00 0.00 2.29
1652 1888 7.598759 ACTCCTTCCGTTCATAAGTATACAT 57.401 36.000 5.50 0.00 0.00 2.29
1653 1889 7.659186 ACTCCTTCCGTTCATAAGTATACATC 58.341 38.462 5.50 0.00 0.00 3.06
1654 1890 7.506261 ACTCCTTCCGTTCATAAGTATACATCT 59.494 37.037 5.50 0.00 0.00 2.90
1655 1891 8.246430 TCCTTCCGTTCATAAGTATACATCTT 57.754 34.615 5.50 0.00 0.00 2.40
1656 1892 8.701895 TCCTTCCGTTCATAAGTATACATCTTT 58.298 33.333 5.50 0.00 0.00 2.52
1657 1893 9.326413 CCTTCCGTTCATAAGTATACATCTTTT 57.674 33.333 5.50 0.00 0.00 2.27
1685 1921 6.665992 AATTCCAATATAGACTACGGAGCA 57.334 37.500 0.00 0.00 0.00 4.26
1686 1922 6.665992 ATTCCAATATAGACTACGGAGCAA 57.334 37.500 0.00 0.00 0.00 3.91
1687 1923 6.474140 TTCCAATATAGACTACGGAGCAAA 57.526 37.500 0.00 0.00 0.00 3.68
1688 1924 6.474140 TCCAATATAGACTACGGAGCAAAA 57.526 37.500 0.00 0.00 0.00 2.44
1689 1925 7.062749 TCCAATATAGACTACGGAGCAAAAT 57.937 36.000 0.00 0.00 0.00 1.82
1690 1926 8.185506 TCCAATATAGACTACGGAGCAAAATA 57.814 34.615 0.00 0.00 0.00 1.40
1691 1927 8.644216 TCCAATATAGACTACGGAGCAAAATAA 58.356 33.333 0.00 0.00 0.00 1.40
1692 1928 8.926710 CCAATATAGACTACGGAGCAAAATAAG 58.073 37.037 0.00 0.00 0.00 1.73
1693 1929 9.477484 CAATATAGACTACGGAGCAAAATAAGT 57.523 33.333 0.00 0.00 0.00 2.24
1694 1930 9.477484 AATATAGACTACGGAGCAAAATAAGTG 57.523 33.333 0.00 0.00 0.00 3.16
1695 1931 5.401531 AGACTACGGAGCAAAATAAGTGA 57.598 39.130 0.00 0.00 0.00 3.41
1696 1932 5.790593 AGACTACGGAGCAAAATAAGTGAA 58.209 37.500 0.00 0.00 0.00 3.18
1697 1933 6.407202 AGACTACGGAGCAAAATAAGTGAAT 58.593 36.000 0.00 0.00 0.00 2.57
1698 1934 6.535508 AGACTACGGAGCAAAATAAGTGAATC 59.464 38.462 0.00 0.00 0.00 2.52
1699 1935 6.407202 ACTACGGAGCAAAATAAGTGAATCT 58.593 36.000 0.00 0.00 0.00 2.40
1700 1936 7.553334 ACTACGGAGCAAAATAAGTGAATCTA 58.447 34.615 0.00 0.00 0.00 1.98
1701 1937 8.204836 ACTACGGAGCAAAATAAGTGAATCTAT 58.795 33.333 0.00 0.00 0.00 1.98
1702 1938 9.692749 CTACGGAGCAAAATAAGTGAATCTATA 57.307 33.333 0.00 0.00 0.00 1.31
1703 1939 8.366671 ACGGAGCAAAATAAGTGAATCTATAC 57.633 34.615 0.00 0.00 0.00 1.47
1704 1940 8.204836 ACGGAGCAAAATAAGTGAATCTATACT 58.795 33.333 0.00 0.00 0.00 2.12
1705 1941 9.046296 CGGAGCAAAATAAGTGAATCTATACTT 57.954 33.333 0.00 0.00 40.09 2.24
1758 1994 9.528018 GTAGTCTCTATTGAAATCTCTGAAAGG 57.472 37.037 0.00 0.00 0.00 3.11
1759 1995 8.144862 AGTCTCTATTGAAATCTCTGAAAGGT 57.855 34.615 0.00 0.00 0.00 3.50
1760 1996 8.257306 AGTCTCTATTGAAATCTCTGAAAGGTC 58.743 37.037 0.00 0.00 0.00 3.85
1761 1997 8.257306 GTCTCTATTGAAATCTCTGAAAGGTCT 58.743 37.037 0.00 0.00 0.00 3.85
1762 1998 9.480861 TCTCTATTGAAATCTCTGAAAGGTCTA 57.519 33.333 0.00 0.00 0.00 2.59
1781 2017 9.816787 AAGGTCTATATTTAGTAAGAGAGGGAG 57.183 37.037 0.00 0.00 0.00 4.30
1815 2069 7.911205 TGTTTATAGACAACAAACCGAAACAAG 59.089 33.333 0.00 0.00 32.88 3.16
1824 2078 5.290386 ACAAACCGAAACAAGTGAACAAAA 58.710 33.333 0.00 0.00 0.00 2.44
1827 2081 4.872664 ACCGAAACAAGTGAACAAAAACA 58.127 34.783 0.00 0.00 0.00 2.83
1828 2082 4.682401 ACCGAAACAAGTGAACAAAAACAC 59.318 37.500 0.00 0.00 37.30 3.32
1829 2083 4.681942 CCGAAACAAGTGAACAAAAACACA 59.318 37.500 0.00 0.00 39.18 3.72
1833 2087 7.109532 CGAAACAAGTGAACAAAAACACAAAAC 59.890 33.333 0.00 0.00 39.18 2.43
1847 2101 9.498176 AAAAACACAAAACCGTCTCTATATACT 57.502 29.630 0.00 0.00 0.00 2.12
1848 2102 8.699283 AAACACAAAACCGTCTCTATATACTC 57.301 34.615 0.00 0.00 0.00 2.59
1849 2103 6.803642 ACACAAAACCGTCTCTATATACTCC 58.196 40.000 0.00 0.00 0.00 3.85
1850 2104 6.183360 ACACAAAACCGTCTCTATATACTCCC 60.183 42.308 0.00 0.00 0.00 4.30
1851 2105 5.895534 ACAAAACCGTCTCTATATACTCCCA 59.104 40.000 0.00 0.00 0.00 4.37
1852 2106 6.183360 ACAAAACCGTCTCTATATACTCCCAC 60.183 42.308 0.00 0.00 0.00 4.61
1853 2107 4.031636 ACCGTCTCTATATACTCCCACC 57.968 50.000 0.00 0.00 0.00 4.61
1854 2108 3.008330 CCGTCTCTATATACTCCCACCG 58.992 54.545 0.00 0.00 0.00 4.94
1855 2109 3.558746 CCGTCTCTATATACTCCCACCGT 60.559 52.174 0.00 0.00 0.00 4.83
1856 2110 3.683822 CGTCTCTATATACTCCCACCGTC 59.316 52.174 0.00 0.00 0.00 4.79
1857 2111 4.009002 GTCTCTATATACTCCCACCGTCC 58.991 52.174 0.00 0.00 0.00 4.79
1858 2112 3.009916 TCTCTATATACTCCCACCGTCCC 59.990 52.174 0.00 0.00 0.00 4.46
1859 2113 2.718062 TCTATATACTCCCACCGTCCCA 59.282 50.000 0.00 0.00 0.00 4.37
1860 2114 2.715763 ATATACTCCCACCGTCCCAT 57.284 50.000 0.00 0.00 0.00 4.00
1861 2115 3.839323 ATATACTCCCACCGTCCCATA 57.161 47.619 0.00 0.00 0.00 2.74
1862 2116 2.482414 ATACTCCCACCGTCCCATAA 57.518 50.000 0.00 0.00 0.00 1.90
1863 2117 2.482414 TACTCCCACCGTCCCATAAT 57.518 50.000 0.00 0.00 0.00 1.28
1864 2118 2.482414 ACTCCCACCGTCCCATAATA 57.518 50.000 0.00 0.00 0.00 0.98
1865 2119 2.986050 ACTCCCACCGTCCCATAATAT 58.014 47.619 0.00 0.00 0.00 1.28
1866 2120 4.136341 ACTCCCACCGTCCCATAATATA 57.864 45.455 0.00 0.00 0.00 0.86
1867 2121 4.495565 ACTCCCACCGTCCCATAATATAA 58.504 43.478 0.00 0.00 0.00 0.98
1868 2122 4.530946 ACTCCCACCGTCCCATAATATAAG 59.469 45.833 0.00 0.00 0.00 1.73
1869 2123 4.754311 TCCCACCGTCCCATAATATAAGA 58.246 43.478 0.00 0.00 0.00 2.10
1870 2124 4.529377 TCCCACCGTCCCATAATATAAGAC 59.471 45.833 0.00 0.00 0.00 3.01
1877 2131 7.486802 CGTCCCATAATATAAGACGGTTTTT 57.513 36.000 13.30 0.00 44.86 1.94
1878 2132 7.349711 CGTCCCATAATATAAGACGGTTTTTG 58.650 38.462 13.30 0.00 44.86 2.44
1879 2133 7.136772 GTCCCATAATATAAGACGGTTTTTGC 58.863 38.462 0.00 0.00 0.00 3.68
1880 2134 6.263617 TCCCATAATATAAGACGGTTTTTGCC 59.736 38.462 0.00 0.00 0.00 4.52
1881 2135 6.039941 CCCATAATATAAGACGGTTTTTGCCA 59.960 38.462 0.00 0.00 0.00 4.92
1882 2136 6.915843 CCATAATATAAGACGGTTTTTGCCAC 59.084 38.462 0.00 0.00 0.00 5.01
1883 2137 7.201785 CCATAATATAAGACGGTTTTTGCCACT 60.202 37.037 0.00 0.00 0.00 4.00
1884 2138 8.832521 CATAATATAAGACGGTTTTTGCCACTA 58.167 33.333 0.00 0.00 0.00 2.74
1885 2139 6.673154 ATATAAGACGGTTTTTGCCACTAC 57.327 37.500 0.00 0.00 0.00 2.73
1886 2140 2.335316 AGACGGTTTTTGCCACTACA 57.665 45.000 0.00 0.00 0.00 2.74
1887 2141 1.944709 AGACGGTTTTTGCCACTACAC 59.055 47.619 0.00 0.00 0.00 2.90
1888 2142 1.944709 GACGGTTTTTGCCACTACACT 59.055 47.619 0.00 0.00 0.00 3.55
1889 2143 3.132925 GACGGTTTTTGCCACTACACTA 58.867 45.455 0.00 0.00 0.00 2.74
1890 2144 3.135994 ACGGTTTTTGCCACTACACTAG 58.864 45.455 0.00 0.00 0.00 2.57
1891 2145 2.095919 CGGTTTTTGCCACTACACTAGC 60.096 50.000 0.00 0.00 0.00 3.42
1892 2146 3.146847 GGTTTTTGCCACTACACTAGCT 58.853 45.455 0.00 0.00 0.00 3.32
1893 2147 4.320870 GGTTTTTGCCACTACACTAGCTA 58.679 43.478 0.00 0.00 0.00 3.32
1894 2148 4.392138 GGTTTTTGCCACTACACTAGCTAG 59.608 45.833 19.44 19.44 0.00 3.42
1895 2149 4.884668 TTTTGCCACTACACTAGCTAGT 57.115 40.909 20.95 20.95 36.90 2.57
1927 2181 9.739276 AAAACATTTTACACTATGAGATGGAGA 57.261 29.630 0.00 0.00 0.00 3.71
1928 2182 8.954950 AACATTTTACACTATGAGATGGAGAG 57.045 34.615 0.00 0.00 0.00 3.20
1929 2183 8.311395 ACATTTTACACTATGAGATGGAGAGA 57.689 34.615 0.00 0.00 0.00 3.10
1930 2184 8.200792 ACATTTTACACTATGAGATGGAGAGAC 58.799 37.037 0.00 0.00 0.00 3.36
1945 2199 8.223177 GATGGAGAGACATCAAATTCAAGAAT 57.777 34.615 0.00 0.00 45.11 2.40
1947 2201 8.728337 TGGAGAGACATCAAATTCAAGAATAG 57.272 34.615 0.00 0.00 0.00 1.73
1948 2202 8.324306 TGGAGAGACATCAAATTCAAGAATAGT 58.676 33.333 0.00 0.00 0.00 2.12
2018 2290 2.141517 CATGCCTCTTATCAAGCGAGG 58.858 52.381 0.00 0.00 45.59 4.63
2022 2294 1.539929 CCTCTTATCAAGCGAGGCCTG 60.540 57.143 12.00 3.42 38.05 4.85
2041 2314 4.030452 GCCGGTCAAGCACTGCAC 62.030 66.667 1.90 0.00 0.00 4.57
2045 2318 2.641559 GTCAAGCACTGCACCTGC 59.358 61.111 3.30 3.75 42.50 4.85
2047 2320 4.034258 CAAGCACTGCACCTGCCG 62.034 66.667 3.30 0.00 41.18 5.69
2101 2374 5.006261 CGGTATTCACTGTTTGCATCGATTA 59.994 40.000 0.00 0.00 0.00 1.75
2105 2378 5.940192 TCACTGTTTGCATCGATTACTTT 57.060 34.783 0.00 0.00 0.00 2.66
2116 2389 6.431543 TGCATCGATTACTTTGGGTCTTTTTA 59.568 34.615 0.00 0.00 0.00 1.52
2131 2404 9.594478 TGGGTCTTTTTATTTTTCTCTGTTTTC 57.406 29.630 0.00 0.00 0.00 2.29
2143 2416 9.902196 TTTTTCTCTGTTTTCTCGTTTTTACTT 57.098 25.926 0.00 0.00 0.00 2.24
2190 2463 3.254166 TCTTCTGCTTTCATCTGGTTTGC 59.746 43.478 0.00 0.00 0.00 3.68
2196 2469 3.494924 GCTTTCATCTGGTTTGCCCTTTT 60.495 43.478 0.00 0.00 0.00 2.27
2198 2471 5.741673 GCTTTCATCTGGTTTGCCCTTTTAA 60.742 40.000 0.00 0.00 0.00 1.52
2199 2472 5.878406 TTCATCTGGTTTGCCCTTTTAAA 57.122 34.783 0.00 0.00 0.00 1.52
2200 2473 5.878406 TCATCTGGTTTGCCCTTTTAAAA 57.122 34.783 0.00 0.00 0.00 1.52
2201 2474 6.240549 TCATCTGGTTTGCCCTTTTAAAAA 57.759 33.333 1.66 0.00 0.00 1.94
2202 2475 6.287525 TCATCTGGTTTGCCCTTTTAAAAAG 58.712 36.000 1.66 0.00 0.00 2.27
2203 2476 5.941555 TCTGGTTTGCCCTTTTAAAAAGA 57.058 34.783 1.66 0.00 0.00 2.52
2204 2477 6.493189 TCTGGTTTGCCCTTTTAAAAAGAT 57.507 33.333 1.66 0.00 0.00 2.40
2220 2493 2.936919 AGATCAACACAGGTCTGCAA 57.063 45.000 0.00 0.00 0.00 4.08
2225 2498 4.734398 TCAACACAGGTCTGCAATTTTT 57.266 36.364 0.00 0.00 0.00 1.94
2234 2507 6.183360 ACAGGTCTGCAATTTTTCATACACAA 60.183 34.615 0.00 0.00 0.00 3.33
2236 2509 6.869913 AGGTCTGCAATTTTTCATACACAATG 59.130 34.615 0.00 0.00 36.88 2.82
2501 2780 9.214957 TGTAAACTATCAGATTTTTCACATCGT 57.785 29.630 0.00 0.00 0.00 3.73
2505 2784 9.599866 AACTATCAGATTTTTCACATCGTATCA 57.400 29.630 0.00 0.00 0.00 2.15
2506 2785 9.599866 ACTATCAGATTTTTCACATCGTATCAA 57.400 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.002451 GCTAAATCTCAGTCGACGAGCTA 59.998 47.826 23.65 13.56 0.00 3.32
1 2 2.223386 GCTAAATCTCAGTCGACGAGCT 60.223 50.000 23.65 16.07 0.00 4.09
2 3 2.113289 GCTAAATCTCAGTCGACGAGC 58.887 52.381 23.65 14.12 0.00 5.03
3 4 3.181505 ACTGCTAAATCTCAGTCGACGAG 60.182 47.826 22.92 22.92 39.11 4.18
4 5 2.747989 ACTGCTAAATCTCAGTCGACGA 59.252 45.455 10.46 9.71 39.11 4.20
5 6 3.138205 ACTGCTAAATCTCAGTCGACG 57.862 47.619 10.46 5.48 39.11 5.12
6 7 3.860536 GGAACTGCTAAATCTCAGTCGAC 59.139 47.826 7.70 7.70 42.19 4.20
7 8 3.427638 CGGAACTGCTAAATCTCAGTCGA 60.428 47.826 0.00 0.00 42.19 4.20
8 9 2.854777 CGGAACTGCTAAATCTCAGTCG 59.145 50.000 0.00 0.00 42.19 4.18
9 10 3.851098 ACGGAACTGCTAAATCTCAGTC 58.149 45.455 0.00 0.00 42.19 3.51
10 11 3.963428 ACGGAACTGCTAAATCTCAGT 57.037 42.857 0.00 0.00 44.64 3.41
11 12 6.402226 GGTTAAACGGAACTGCTAAATCTCAG 60.402 42.308 0.00 0.00 36.45 3.35
12 13 5.410439 GGTTAAACGGAACTGCTAAATCTCA 59.590 40.000 0.00 0.00 0.00 3.27
13 14 5.642491 AGGTTAAACGGAACTGCTAAATCTC 59.358 40.000 0.00 0.00 0.00 2.75
14 15 5.557866 AGGTTAAACGGAACTGCTAAATCT 58.442 37.500 0.00 0.00 0.00 2.40
15 16 5.874895 AGGTTAAACGGAACTGCTAAATC 57.125 39.130 0.00 0.00 0.00 2.17
16 17 6.183360 GCATAGGTTAAACGGAACTGCTAAAT 60.183 38.462 0.00 0.00 29.81 1.40
17 18 5.122711 GCATAGGTTAAACGGAACTGCTAAA 59.877 40.000 0.00 0.00 29.81 1.85
18 19 4.632688 GCATAGGTTAAACGGAACTGCTAA 59.367 41.667 0.00 0.00 29.81 3.09
19 20 4.186159 GCATAGGTTAAACGGAACTGCTA 58.814 43.478 0.00 0.00 29.81 3.49
20 21 3.007635 GCATAGGTTAAACGGAACTGCT 58.992 45.455 0.00 0.00 29.81 4.24
21 22 2.096980 GGCATAGGTTAAACGGAACTGC 59.903 50.000 0.00 0.00 30.96 4.40
22 23 3.606687 AGGCATAGGTTAAACGGAACTG 58.393 45.455 0.00 0.00 0.00 3.16
23 24 3.994931 AGGCATAGGTTAAACGGAACT 57.005 42.857 0.00 0.00 0.00 3.01
24 25 3.558829 GCTAGGCATAGGTTAAACGGAAC 59.441 47.826 7.62 0.00 0.00 3.62
25 26 3.453353 AGCTAGGCATAGGTTAAACGGAA 59.547 43.478 3.90 0.00 36.31 4.30
26 27 3.036091 AGCTAGGCATAGGTTAAACGGA 58.964 45.455 3.90 0.00 36.31 4.69
27 28 3.391049 GAGCTAGGCATAGGTTAAACGG 58.609 50.000 11.85 0.00 39.82 4.44
28 29 3.050619 CGAGCTAGGCATAGGTTAAACG 58.949 50.000 11.85 6.78 39.82 3.60
29 30 4.202131 ACTCGAGCTAGGCATAGGTTAAAC 60.202 45.833 13.61 0.00 39.82 2.01
30 31 3.958798 ACTCGAGCTAGGCATAGGTTAAA 59.041 43.478 13.61 0.03 39.82 1.52
31 32 3.563223 ACTCGAGCTAGGCATAGGTTAA 58.437 45.455 13.61 2.45 39.82 2.01
34 35 2.953284 TACTCGAGCTAGGCATAGGT 57.047 50.000 13.61 10.27 42.40 3.08
38 39 4.336993 GCAGTATATACTCGAGCTAGGCAT 59.663 45.833 13.61 0.24 33.46 4.40
47 48 9.511272 TGGTTAGAATTAGCAGTATATACTCGA 57.489 33.333 12.62 2.44 33.46 4.04
84 85 1.079503 GTACAAGAAGAAGGCAGCGG 58.920 55.000 0.00 0.00 0.00 5.52
85 86 2.086054 AGTACAAGAAGAAGGCAGCG 57.914 50.000 0.00 0.00 0.00 5.18
112 113 0.311790 TGTACGTCTTCTTCGCCGTT 59.688 50.000 0.00 0.00 34.95 4.44
847 859 2.043852 GACGAGGAGGAGCAGGGA 60.044 66.667 0.00 0.00 0.00 4.20
856 868 2.041115 TGCTCAGGTCGACGAGGAG 61.041 63.158 18.36 18.91 0.00 3.69
888 902 4.260985 ACGTGGACATTGATATGCTTTCA 58.739 39.130 0.00 0.00 35.03 2.69
896 910 1.187974 ACCCGACGTGGACATTGATA 58.812 50.000 0.00 0.00 42.00 2.15
904 918 2.029964 GCAAGAACCCGACGTGGA 59.970 61.111 0.00 0.00 42.00 4.02
906 920 0.165944 GAATGCAAGAACCCGACGTG 59.834 55.000 0.00 0.00 0.00 4.49
913 927 1.401905 GGTCGATGGAATGCAAGAACC 59.598 52.381 0.00 0.00 0.00 3.62
944 970 7.118680 GGAATACAGGTAATTCGAAGTGTTTGA 59.881 37.037 8.63 0.00 0.00 2.69
953 979 2.544277 CGCCGGAATACAGGTAATTCGA 60.544 50.000 5.05 0.00 33.97 3.71
954 980 1.790623 CGCCGGAATACAGGTAATTCG 59.209 52.381 5.05 0.00 33.97 3.34
977 1007 4.953868 CCGTCGACCCGCAACACA 62.954 66.667 10.58 0.00 0.00 3.72
985 1015 2.511600 CATGAAGGCCGTCGACCC 60.512 66.667 14.24 6.34 0.00 4.46
992 1022 2.628106 CGATTCGCATGAAGGCCG 59.372 61.111 0.00 0.00 37.57 6.13
994 1024 0.530650 TCTCCGATTCGCATGAAGGC 60.531 55.000 0.00 0.00 37.57 4.35
995 1025 1.202463 AGTCTCCGATTCGCATGAAGG 60.202 52.381 0.00 0.00 37.57 3.46
1013 1043 1.122019 AAGTCGAGTCCCCTTGCAGT 61.122 55.000 0.00 0.00 0.00 4.40
1128 1356 3.181967 CCGTCTTCTTGCTCGGCG 61.182 66.667 0.00 0.00 36.68 6.46
1473 1701 1.066908 CTCTCTCGACATTGCTCTCCC 59.933 57.143 0.00 0.00 0.00 4.30
1583 1819 5.527033 GCAATTTCACTCTGCTCTTCTTTT 58.473 37.500 0.00 0.00 33.20 2.27
1604 1840 4.196193 CTGTATAATTTTGGGAGGACGCA 58.804 43.478 0.00 0.00 37.19 5.24
1605 1841 4.196971 ACTGTATAATTTTGGGAGGACGC 58.803 43.478 0.00 0.00 0.00 5.19
1659 1895 8.812972 TGCTCCGTAGTCTATATTGGAATTTAT 58.187 33.333 0.00 0.00 0.00 1.40
1660 1896 8.185506 TGCTCCGTAGTCTATATTGGAATTTA 57.814 34.615 0.00 0.00 0.00 1.40
1661 1897 7.062749 TGCTCCGTAGTCTATATTGGAATTT 57.937 36.000 0.00 0.00 0.00 1.82
1662 1898 6.665992 TGCTCCGTAGTCTATATTGGAATT 57.334 37.500 0.00 0.00 0.00 2.17
1663 1899 6.665992 TTGCTCCGTAGTCTATATTGGAAT 57.334 37.500 0.00 0.00 0.00 3.01
1664 1900 6.474140 TTTGCTCCGTAGTCTATATTGGAA 57.526 37.500 0.00 0.00 0.00 3.53
1665 1901 6.474140 TTTTGCTCCGTAGTCTATATTGGA 57.526 37.500 0.00 0.00 0.00 3.53
1666 1902 8.827177 TTATTTTGCTCCGTAGTCTATATTGG 57.173 34.615 0.00 0.00 0.00 3.16
1667 1903 9.477484 ACTTATTTTGCTCCGTAGTCTATATTG 57.523 33.333 0.00 0.00 0.00 1.90
1668 1904 9.477484 CACTTATTTTGCTCCGTAGTCTATATT 57.523 33.333 0.00 0.00 0.00 1.28
1669 1905 8.857098 TCACTTATTTTGCTCCGTAGTCTATAT 58.143 33.333 0.00 0.00 0.00 0.86
1670 1906 8.229253 TCACTTATTTTGCTCCGTAGTCTATA 57.771 34.615 0.00 0.00 0.00 1.31
1671 1907 7.108841 TCACTTATTTTGCTCCGTAGTCTAT 57.891 36.000 0.00 0.00 0.00 1.98
1672 1908 6.519679 TCACTTATTTTGCTCCGTAGTCTA 57.480 37.500 0.00 0.00 0.00 2.59
1673 1909 5.401531 TCACTTATTTTGCTCCGTAGTCT 57.598 39.130 0.00 0.00 0.00 3.24
1674 1910 6.535508 AGATTCACTTATTTTGCTCCGTAGTC 59.464 38.462 0.00 0.00 0.00 2.59
1675 1911 6.407202 AGATTCACTTATTTTGCTCCGTAGT 58.593 36.000 0.00 0.00 0.00 2.73
1676 1912 6.910536 AGATTCACTTATTTTGCTCCGTAG 57.089 37.500 0.00 0.00 0.00 3.51
1677 1913 9.472361 GTATAGATTCACTTATTTTGCTCCGTA 57.528 33.333 0.00 0.00 0.00 4.02
1678 1914 8.204836 AGTATAGATTCACTTATTTTGCTCCGT 58.795 33.333 0.00 0.00 0.00 4.69
1679 1915 8.594881 AGTATAGATTCACTTATTTTGCTCCG 57.405 34.615 0.00 0.00 0.00 4.63
1732 1968 9.528018 CCTTTCAGAGATTTCAATAGAGACTAC 57.472 37.037 0.00 0.00 0.00 2.73
1733 1969 9.261035 ACCTTTCAGAGATTTCAATAGAGACTA 57.739 33.333 0.00 0.00 0.00 2.59
1734 1970 8.144862 ACCTTTCAGAGATTTCAATAGAGACT 57.855 34.615 0.00 0.00 0.00 3.24
1735 1971 8.257306 AGACCTTTCAGAGATTTCAATAGAGAC 58.743 37.037 0.00 0.00 0.00 3.36
1736 1972 8.372877 AGACCTTTCAGAGATTTCAATAGAGA 57.627 34.615 0.00 0.00 0.00 3.10
1755 1991 9.816787 CTCCCTCTCTTACTAAATATAGACCTT 57.183 37.037 0.00 0.00 33.15 3.50
1756 1992 8.962205 ACTCCCTCTCTTACTAAATATAGACCT 58.038 37.037 0.00 0.00 33.15 3.85
1794 2030 5.587043 TCACTTGTTTCGGTTTGTTGTCTAT 59.413 36.000 0.00 0.00 0.00 1.98
1795 2031 4.936411 TCACTTGTTTCGGTTTGTTGTCTA 59.064 37.500 0.00 0.00 0.00 2.59
1797 2033 4.086199 TCACTTGTTTCGGTTTGTTGTC 57.914 40.909 0.00 0.00 0.00 3.18
1798 2034 4.231439 GTTCACTTGTTTCGGTTTGTTGT 58.769 39.130 0.00 0.00 0.00 3.32
1799 2035 4.230657 TGTTCACTTGTTTCGGTTTGTTG 58.769 39.130 0.00 0.00 0.00 3.33
1800 2036 4.506886 TGTTCACTTGTTTCGGTTTGTT 57.493 36.364 0.00 0.00 0.00 2.83
1801 2037 4.506886 TTGTTCACTTGTTTCGGTTTGT 57.493 36.364 0.00 0.00 0.00 2.83
1802 2038 5.830900 TTTTGTTCACTTGTTTCGGTTTG 57.169 34.783 0.00 0.00 0.00 2.93
1803 2039 5.753921 TGTTTTTGTTCACTTGTTTCGGTTT 59.246 32.000 0.00 0.00 0.00 3.27
1806 2042 4.681942 TGTGTTTTTGTTCACTTGTTTCGG 59.318 37.500 0.00 0.00 35.82 4.30
1807 2043 5.814314 TGTGTTTTTGTTCACTTGTTTCG 57.186 34.783 0.00 0.00 35.82 3.46
1808 2044 7.374754 GGTTTTGTGTTTTTGTTCACTTGTTTC 59.625 33.333 0.00 0.00 35.82 2.78
1815 2069 4.682401 AGACGGTTTTGTGTTTTTGTTCAC 59.318 37.500 0.00 0.00 35.43 3.18
1824 2078 7.263496 GGAGTATATAGAGACGGTTTTGTGTT 58.737 38.462 0.00 0.00 0.00 3.32
1827 2081 5.895534 TGGGAGTATATAGAGACGGTTTTGT 59.104 40.000 0.00 0.00 0.00 2.83
1828 2082 6.214399 GTGGGAGTATATAGAGACGGTTTTG 58.786 44.000 0.00 0.00 0.00 2.44
1829 2083 5.303845 GGTGGGAGTATATAGAGACGGTTTT 59.696 44.000 0.00 0.00 0.00 2.43
1833 2087 3.008330 CGGTGGGAGTATATAGAGACGG 58.992 54.545 0.00 0.00 0.00 4.79
1847 2101 4.529377 GTCTTATATTATGGGACGGTGGGA 59.471 45.833 0.00 0.00 0.00 4.37
1848 2102 4.619863 CGTCTTATATTATGGGACGGTGGG 60.620 50.000 17.59 0.46 43.69 4.61
1849 2103 4.491676 CGTCTTATATTATGGGACGGTGG 58.508 47.826 17.59 0.70 43.69 4.61
1853 2107 7.349711 CAAAAACCGTCTTATATTATGGGACG 58.650 38.462 18.04 18.04 45.92 4.79
1854 2108 7.136772 GCAAAAACCGTCTTATATTATGGGAC 58.863 38.462 0.00 0.00 0.00 4.46
1855 2109 6.263617 GGCAAAAACCGTCTTATATTATGGGA 59.736 38.462 0.00 0.00 0.00 4.37
1856 2110 6.039941 TGGCAAAAACCGTCTTATATTATGGG 59.960 38.462 0.00 0.00 0.00 4.00
1857 2111 6.915843 GTGGCAAAAACCGTCTTATATTATGG 59.084 38.462 0.00 0.00 0.00 2.74
1858 2112 7.703328 AGTGGCAAAAACCGTCTTATATTATG 58.297 34.615 0.00 0.00 0.00 1.90
1859 2113 7.875327 AGTGGCAAAAACCGTCTTATATTAT 57.125 32.000 0.00 0.00 0.00 1.28
1860 2114 7.823310 TGTAGTGGCAAAAACCGTCTTATATTA 59.177 33.333 0.00 0.00 0.00 0.98
1861 2115 6.655848 TGTAGTGGCAAAAACCGTCTTATATT 59.344 34.615 0.00 0.00 0.00 1.28
1862 2116 6.093082 GTGTAGTGGCAAAAACCGTCTTATAT 59.907 38.462 0.00 0.00 0.00 0.86
1863 2117 5.409214 GTGTAGTGGCAAAAACCGTCTTATA 59.591 40.000 0.00 0.00 0.00 0.98
1864 2118 4.214758 GTGTAGTGGCAAAAACCGTCTTAT 59.785 41.667 0.00 0.00 0.00 1.73
1865 2119 3.560896 GTGTAGTGGCAAAAACCGTCTTA 59.439 43.478 0.00 0.00 0.00 2.10
1866 2120 2.356695 GTGTAGTGGCAAAAACCGTCTT 59.643 45.455 0.00 0.00 0.00 3.01
1867 2121 1.944709 GTGTAGTGGCAAAAACCGTCT 59.055 47.619 0.00 0.00 0.00 4.18
1868 2122 1.944709 AGTGTAGTGGCAAAAACCGTC 59.055 47.619 0.00 0.00 0.00 4.79
1869 2123 2.047002 AGTGTAGTGGCAAAAACCGT 57.953 45.000 0.00 0.00 0.00 4.83
1870 2124 2.095919 GCTAGTGTAGTGGCAAAAACCG 60.096 50.000 0.00 0.00 0.00 4.44
1871 2125 3.146847 AGCTAGTGTAGTGGCAAAAACC 58.853 45.455 0.00 0.00 0.00 3.27
1872 2126 4.995487 ACTAGCTAGTGTAGTGGCAAAAAC 59.005 41.667 25.52 0.00 34.72 2.43
1873 2127 4.994852 CACTAGCTAGTGTAGTGGCAAAAA 59.005 41.667 35.77 0.00 46.51 1.94
1874 2128 4.566004 CACTAGCTAGTGTAGTGGCAAAA 58.434 43.478 35.77 0.00 46.51 2.44
1875 2129 4.188247 CACTAGCTAGTGTAGTGGCAAA 57.812 45.455 35.77 0.00 46.51 3.68
1876 2130 3.868757 CACTAGCTAGTGTAGTGGCAA 57.131 47.619 35.77 0.00 46.51 4.52
1901 2155 9.739276 TCTCCATCTCATAGTGTAAAATGTTTT 57.261 29.630 0.00 0.00 0.00 2.43
1902 2156 9.388506 CTCTCCATCTCATAGTGTAAAATGTTT 57.611 33.333 0.00 0.00 0.00 2.83
1903 2157 8.762645 TCTCTCCATCTCATAGTGTAAAATGTT 58.237 33.333 0.00 0.00 0.00 2.71
1904 2158 8.200792 GTCTCTCCATCTCATAGTGTAAAATGT 58.799 37.037 0.00 0.00 0.00 2.71
1905 2159 8.200120 TGTCTCTCCATCTCATAGTGTAAAATG 58.800 37.037 0.00 0.00 0.00 2.32
1906 2160 8.311395 TGTCTCTCCATCTCATAGTGTAAAAT 57.689 34.615 0.00 0.00 0.00 1.82
1907 2161 7.718334 TGTCTCTCCATCTCATAGTGTAAAA 57.282 36.000 0.00 0.00 0.00 1.52
1908 2162 7.561356 TGATGTCTCTCCATCTCATAGTGTAAA 59.439 37.037 0.00 0.00 41.47 2.01
1909 2163 7.062957 TGATGTCTCTCCATCTCATAGTGTAA 58.937 38.462 0.00 0.00 41.47 2.41
1910 2164 6.605119 TGATGTCTCTCCATCTCATAGTGTA 58.395 40.000 0.00 0.00 41.47 2.90
1911 2165 5.453158 TGATGTCTCTCCATCTCATAGTGT 58.547 41.667 0.00 0.00 41.47 3.55
1912 2166 6.402456 TTGATGTCTCTCCATCTCATAGTG 57.598 41.667 0.00 0.00 41.47 2.74
1913 2167 7.615039 ATTTGATGTCTCTCCATCTCATAGT 57.385 36.000 0.00 0.00 41.47 2.12
1914 2168 8.148999 TGAATTTGATGTCTCTCCATCTCATAG 58.851 37.037 0.00 0.00 41.47 2.23
1915 2169 8.026396 TGAATTTGATGTCTCTCCATCTCATA 57.974 34.615 0.00 0.00 41.47 2.15
1916 2170 6.896883 TGAATTTGATGTCTCTCCATCTCAT 58.103 36.000 0.00 0.00 41.47 2.90
1917 2171 6.303903 TGAATTTGATGTCTCTCCATCTCA 57.696 37.500 0.00 0.00 41.47 3.27
1918 2172 7.046652 TCTTGAATTTGATGTCTCTCCATCTC 58.953 38.462 0.00 0.00 41.47 2.75
1919 2173 6.955364 TCTTGAATTTGATGTCTCTCCATCT 58.045 36.000 0.00 0.00 41.47 2.90
1920 2174 7.621428 TTCTTGAATTTGATGTCTCTCCATC 57.379 36.000 0.00 0.00 41.32 3.51
1921 2175 9.339850 CTATTCTTGAATTTGATGTCTCTCCAT 57.660 33.333 0.95 0.00 0.00 3.41
1922 2176 8.324306 ACTATTCTTGAATTTGATGTCTCTCCA 58.676 33.333 0.95 0.00 0.00 3.86
1923 2177 8.729805 ACTATTCTTGAATTTGATGTCTCTCC 57.270 34.615 0.95 0.00 0.00 3.71
2029 2302 2.595463 GGCAGGTGCAGTGCTTGA 60.595 61.111 17.60 0.00 44.36 3.02
2039 2312 2.411290 AAAAACACGCGGCAGGTG 59.589 55.556 12.47 0.56 41.15 4.00
2059 2332 9.932207 TGAATACCGATAAGAAAACTACAAAGA 57.068 29.630 0.00 0.00 0.00 2.52
2060 2333 9.968743 GTGAATACCGATAAGAAAACTACAAAG 57.031 33.333 0.00 0.00 0.00 2.77
2062 2335 9.146984 CAGTGAATACCGATAAGAAAACTACAA 57.853 33.333 0.00 0.00 0.00 2.41
2063 2336 8.308931 ACAGTGAATACCGATAAGAAAACTACA 58.691 33.333 0.00 0.00 0.00 2.74
2064 2337 8.699283 ACAGTGAATACCGATAAGAAAACTAC 57.301 34.615 0.00 0.00 0.00 2.73
2066 2339 8.504005 CAAACAGTGAATACCGATAAGAAAACT 58.496 33.333 0.00 0.00 0.00 2.66
2067 2340 7.270579 GCAAACAGTGAATACCGATAAGAAAAC 59.729 37.037 0.00 0.00 0.00 2.43
2068 2341 7.041030 TGCAAACAGTGAATACCGATAAGAAAA 60.041 33.333 0.00 0.00 0.00 2.29
2069 2342 6.428465 TGCAAACAGTGAATACCGATAAGAAA 59.572 34.615 0.00 0.00 0.00 2.52
2070 2343 5.935206 TGCAAACAGTGAATACCGATAAGAA 59.065 36.000 0.00 0.00 0.00 2.52
2071 2344 5.483811 TGCAAACAGTGAATACCGATAAGA 58.516 37.500 0.00 0.00 0.00 2.10
2072 2345 5.794687 TGCAAACAGTGAATACCGATAAG 57.205 39.130 0.00 0.00 0.00 1.73
2077 2350 2.670905 TCGATGCAAACAGTGAATACCG 59.329 45.455 0.00 0.00 0.00 4.02
2081 2354 6.500684 AAGTAATCGATGCAAACAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
2101 2374 8.758829 ACAGAGAAAAATAAAAAGACCCAAAGT 58.241 29.630 0.00 0.00 0.00 2.66
2105 2378 9.594478 GAAAACAGAGAAAAATAAAAAGACCCA 57.406 29.630 0.00 0.00 0.00 4.51
2173 2446 0.968405 GGGCAAACCAGATGAAAGCA 59.032 50.000 0.00 0.00 39.85 3.91
2174 2447 1.260544 AGGGCAAACCAGATGAAAGC 58.739 50.000 0.00 0.00 43.89 3.51
2175 2448 4.341366 AAAAGGGCAAACCAGATGAAAG 57.659 40.909 0.00 0.00 43.89 2.62
2183 2456 6.240549 TGATCTTTTTAAAAGGGCAAACCA 57.759 33.333 16.21 0.00 43.89 3.67
2190 2463 6.816136 ACCTGTGTTGATCTTTTTAAAAGGG 58.184 36.000 16.21 9.14 0.00 3.95
2196 2469 5.129634 TGCAGACCTGTGTTGATCTTTTTA 58.870 37.500 0.00 0.00 0.00 1.52
2198 2471 3.554934 TGCAGACCTGTGTTGATCTTTT 58.445 40.909 0.00 0.00 0.00 2.27
2199 2472 3.213206 TGCAGACCTGTGTTGATCTTT 57.787 42.857 0.00 0.00 0.00 2.52
2200 2473 2.936919 TGCAGACCTGTGTTGATCTT 57.063 45.000 0.00 0.00 0.00 2.40
2201 2474 2.936919 TTGCAGACCTGTGTTGATCT 57.063 45.000 0.00 0.00 0.00 2.75
2202 2475 4.510038 AAATTGCAGACCTGTGTTGATC 57.490 40.909 0.00 0.00 0.00 2.92
2203 2476 4.942761 AAAATTGCAGACCTGTGTTGAT 57.057 36.364 0.00 0.00 0.00 2.57
2204 2477 4.159321 TGAAAAATTGCAGACCTGTGTTGA 59.841 37.500 0.00 0.00 0.00 3.18
2475 2754 9.214957 ACGATGTGAAAAATCTGATAGTTTACA 57.785 29.630 10.95 10.95 0.00 2.41
2479 2758 9.599866 TGATACGATGTGAAAAATCTGATAGTT 57.400 29.630 0.00 0.00 0.00 2.24
2480 2759 9.599866 TTGATACGATGTGAAAAATCTGATAGT 57.400 29.630 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.