Multiple sequence alignment - TraesCS5B01G282100

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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 TraesCS5B01G282100 chr5B 100.000 3380 0 0 1 3380 466972656 466976035 0.000000e+00 6242.0
1 TraesCS5B01G282100 chr5B 84.043 188 27 2 185 369 280458560 280458373 9.640000e-41 178.0
2 TraesCS5B01G282100 chr5A 89.881 1591 135 15 1 1586 491521228 491522797 0.000000e+00 2023.0
3 TraesCS5B01G282100 chr5A 93.380 1148 53 7 1600 2731 491369480 491370620 0.000000e+00 1677.0
4 TraesCS5B01G282100 chr5A 87.453 1339 95 26 247 1577 491368279 491369552 0.000000e+00 1474.0
5 TraesCS5B01G282100 chr5A 88.527 1168 107 13 1579 2731 491522695 491523850 0.000000e+00 1389.0
6 TraesCS5B01G282100 chr5A 87.210 1079 105 23 1573 2645 491318688 491317637 0.000000e+00 1197.0
7 TraesCS5B01G282100 chr5A 95.633 687 24 3 904 1586 491319265 491318581 0.000000e+00 1098.0
8 TraesCS5B01G282100 chr5A 95.480 354 13 1 2822 3175 491370619 491370969 2.280000e-156 562.0
9 TraesCS5B01G282100 chr5A 98.276 58 1 0 3187 3244 491374013 491374070 5.970000e-18 102.0
10 TraesCS5B01G282100 chr6D 89.050 1589 110 39 3 1586 106891064 106892593 0.000000e+00 1912.0
11 TraesCS5B01G282100 chr6D 89.429 1173 93 11 1574 2731 106892487 106893643 0.000000e+00 1450.0
12 TraesCS5B01G282100 chr6A 87.539 1589 128 34 3 1586 130404832 130406355 0.000000e+00 1773.0
13 TraesCS5B01G282100 chr6A 88.832 1173 103 15 1574 2731 130406249 130407408 0.000000e+00 1415.0
14 TraesCS5B01G282100 chr5D 89.499 1438 96 26 154 1586 388588317 388589704 0.000000e+00 1768.0
15 TraesCS5B01G282100 chr5D 93.713 1177 49 9 1573 2731 388331882 388333051 0.000000e+00 1740.0
16 TraesCS5B01G282100 chr5D 90.051 1166 86 14 1577 2731 388589601 388590747 0.000000e+00 1483.0
17 TraesCS5B01G282100 chr5D 92.323 1016 66 7 579 1586 388330979 388331990 0.000000e+00 1434.0
18 TraesCS5B01G282100 chr5D 95.342 687 27 2 904 1586 388423605 388422920 0.000000e+00 1086.0
19 TraesCS5B01G282100 chr5D 89.345 779 58 12 1573 2346 388423028 388422270 0.000000e+00 955.0
20 TraesCS5B01G282100 chr5D 96.056 355 13 1 2822 3175 388333050 388333404 8.130000e-161 577.0
21 TraesCS5B01G282100 chr5D 95.177 311 11 3 275 583 388330725 388331033 3.920000e-134 488.0
22 TraesCS5B01G282100 chr5D 95.307 277 13 0 1 277 388330289 388330565 1.110000e-119 440.0
23 TraesCS5B01G282100 chr5D 98.611 144 2 0 3237 3380 426433814 426433671 4.330000e-64 255.0
24 TraesCS5B01G282100 chr5D 87.283 173 13 3 1 164 388539185 388539357 4.450000e-44 189.0
25 TraesCS5B01G282100 chr5D 98.276 58 1 0 3187 3244 388336898 388336955 5.970000e-18 102.0
26 TraesCS5B01G282100 chr3B 99.296 142 1 0 3239 3380 407495556 407495415 1.200000e-64 257.0
27 TraesCS5B01G282100 chr3B 98.611 144 2 0 3237 3380 204484227 204484370 4.330000e-64 255.0
28 TraesCS5B01G282100 chr3B 99.296 142 0 1 3239 3380 780346477 780346617 4.330000e-64 255.0
29 TraesCS5B01G282100 chr3B 98.601 143 2 0 3238 3380 410571365 410571507 1.560000e-63 254.0
30 TraesCS5B01G282100 chr7D 97.973 148 2 1 3234 3380 576537427 576537574 4.330000e-64 255.0
31 TraesCS5B01G282100 chr7D 100.000 29 0 0 723 751 22263061 22263033 2.000000e-03 54.7
32 TraesCS5B01G282100 chr2D 98.601 143 2 0 3238 3380 154119804 154119946 1.560000e-63 254.0
33 TraesCS5B01G282100 chr2B 97.945 146 2 1 3235 3380 165257476 165257620 5.600000e-63 252.0
34 TraesCS5B01G282100 chr1D 97.945 146 2 1 3236 3380 231414817 231414672 5.600000e-63 252.0
35 TraesCS5B01G282100 chr6B 85.635 181 23 2 185 362 678297353 678297533 1.600000e-43 187.0
36 TraesCS5B01G282100 chr3D 84.043 188 27 2 185 369 605343356 605343543 9.640000e-41 178.0
37 TraesCS5B01G282100 chr7A 92.500 40 3 0 717 756 256013712 256013751 1.310000e-04 58.4
38 TraesCS5B01G282100 chr3A 100.000 30 0 0 723 752 697272163 697272134 4.710000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G282100 chr5B 466972656 466976035 3379 False 6242.000000 6242 100.00000 1 3380 1 chr5B.!!$F1 3379
1 TraesCS5B01G282100 chr5A 491521228 491523850 2622 False 1706.000000 2023 89.20400 1 2731 2 chr5A.!!$F2 2730
2 TraesCS5B01G282100 chr5A 491317637 491319265 1628 True 1147.500000 1197 91.42150 904 2645 2 chr5A.!!$R1 1741
3 TraesCS5B01G282100 chr5A 491368279 491374070 5791 False 953.750000 1677 93.64725 247 3244 4 chr5A.!!$F1 2997
4 TraesCS5B01G282100 chr6D 106891064 106893643 2579 False 1681.000000 1912 89.23950 3 2731 2 chr6D.!!$F1 2728
5 TraesCS5B01G282100 chr6A 130404832 130407408 2576 False 1594.000000 1773 88.18550 3 2731 2 chr6A.!!$F1 2728
6 TraesCS5B01G282100 chr5D 388588317 388590747 2430 False 1625.500000 1768 89.77500 154 2731 2 chr5D.!!$F3 2577
7 TraesCS5B01G282100 chr5D 388422270 388423605 1335 True 1020.500000 1086 92.34350 904 2346 2 chr5D.!!$R2 1442
8 TraesCS5B01G282100 chr5D 388330289 388336955 6666 False 796.833333 1740 95.14200 1 3244 6 chr5D.!!$F2 3243

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
962 1161 0.600057 GGCTGCCAAAGGAAAGAGTG 59.4 55.0 15.17 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2743 2975 1.201647 CCCTTTCTCACTTCTACGCGA 59.798 52.381 15.93 0.0 0.0 5.87 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
52 53 7.675619 AGAAGGATTGTGGTAAAAGATTGGATT 59.324 33.333 0.00 0.00 0.00 3.01
89 90 0.610174 GGGCTCAGATATGGATGCGA 59.390 55.000 0.00 0.00 0.00 5.10
96 97 4.563061 TCAGATATGGATGCGACTGATTG 58.437 43.478 0.00 0.00 31.02 2.67
105 106 4.096984 GGATGCGACTGATTGAAAGGAAAT 59.903 41.667 0.00 0.00 0.00 2.17
133 134 3.250040 GTCTTAAACGCATGTGACAAGGT 59.750 43.478 14.43 0.00 0.00 3.50
483 649 5.835113 TTTCTTCCACCAGTTTTTCTCTG 57.165 39.130 0.00 0.00 0.00 3.35
689 883 7.463961 TCTTTCTTCGTCCATACCTATATCC 57.536 40.000 0.00 0.00 0.00 2.59
798 992 4.622740 GTGCCAAGATTCAAAGCAACATAC 59.377 41.667 0.00 0.00 34.79 2.39
803 997 5.490139 AGATTCAAAGCAACATACATCGG 57.510 39.130 0.00 0.00 0.00 4.18
805 999 4.678509 TTCAAAGCAACATACATCGGTC 57.321 40.909 0.00 0.00 0.00 4.79
813 1007 1.070108 ACATACATCGGTCGATCGACG 60.070 52.381 34.69 29.09 45.41 5.12
817 1011 1.816679 ATCGGTCGATCGACGTGGA 60.817 57.895 34.69 30.15 45.41 4.02
820 1014 1.944676 GGTCGATCGACGTGGATGC 60.945 63.158 34.69 19.47 45.41 3.91
834 1028 1.040646 GGATGCACGGGTCAGATCTA 58.959 55.000 0.00 0.00 0.00 1.98
851 1045 8.420222 GTCAGATCTATTGGATGTAGATATGGG 58.580 40.741 14.26 0.00 43.23 4.00
852 1046 7.070447 TCAGATCTATTGGATGTAGATATGGGC 59.930 40.741 14.26 0.00 43.23 5.36
862 1061 8.651389 TGGATGTAGATATGGGCTTATATTAGC 58.349 37.037 5.12 5.12 40.48 3.09
962 1161 0.600057 GGCTGCCAAAGGAAAGAGTG 59.400 55.000 15.17 0.00 0.00 3.51
964 1163 1.321474 CTGCCAAAGGAAAGAGTGCA 58.679 50.000 0.00 0.00 0.00 4.57
1279 1478 1.668101 GGACGAGATCCTTGAGGCGT 61.668 60.000 0.00 0.00 45.22 5.68
1342 1541 2.106074 GGCAATGTGATCGACGGCA 61.106 57.895 0.00 0.00 0.00 5.69
1346 1545 1.869132 CAATGTGATCGACGGCATCAT 59.131 47.619 6.66 3.06 32.86 2.45
1519 1723 4.082463 TGTTGCCCTCGGTGATTTAAAATC 60.082 41.667 0.00 0.00 0.00 2.17
1575 1781 2.783379 ATCTGCAGGGATCTCCTACA 57.217 50.000 15.13 3.38 46.12 2.74
1576 1782 1.781786 TCTGCAGGGATCTCCTACAC 58.218 55.000 15.13 0.00 46.12 2.90
1577 1783 0.387202 CTGCAGGGATCTCCTACACG 59.613 60.000 5.57 0.00 46.12 4.49
1578 1784 0.033503 TGCAGGGATCTCCTACACGA 60.034 55.000 2.78 0.00 46.12 4.35
1579 1785 1.333177 GCAGGGATCTCCTACACGAT 58.667 55.000 2.78 0.00 46.12 3.73
1580 1786 1.271102 GCAGGGATCTCCTACACGATC 59.729 57.143 2.78 0.00 46.12 3.69
1581 1787 2.870175 CAGGGATCTCCTACACGATCT 58.130 52.381 2.78 0.00 46.12 2.75
1582 1788 3.811098 GCAGGGATCTCCTACACGATCTA 60.811 52.174 2.78 0.00 46.12 1.98
1583 1789 3.754323 CAGGGATCTCCTACACGATCTAC 59.246 52.174 2.78 0.00 46.12 2.59
1584 1790 3.394940 AGGGATCTCCTACACGATCTACA 59.605 47.826 1.23 0.00 45.98 2.74
1585 1791 3.502979 GGGATCTCCTACACGATCTACAC 59.497 52.174 0.00 0.00 36.97 2.90
1586 1792 4.135306 GGATCTCCTACACGATCTACACA 58.865 47.826 0.00 0.00 36.97 3.72
1587 1793 4.762765 GGATCTCCTACACGATCTACACAT 59.237 45.833 0.00 0.00 36.97 3.21
1588 1794 5.938710 GGATCTCCTACACGATCTACACATA 59.061 44.000 0.00 0.00 36.97 2.29
1589 1795 6.430308 GGATCTCCTACACGATCTACACATAA 59.570 42.308 0.00 0.00 36.97 1.90
1590 1796 7.040617 GGATCTCCTACACGATCTACACATAAA 60.041 40.741 0.00 0.00 36.97 1.40
1591 1797 7.818997 TCTCCTACACGATCTACACATAAAT 57.181 36.000 0.00 0.00 0.00 1.40
1592 1798 8.234136 TCTCCTACACGATCTACACATAAATT 57.766 34.615 0.00 0.00 0.00 1.82
1593 1799 8.135529 TCTCCTACACGATCTACACATAAATTG 58.864 37.037 0.00 0.00 0.00 2.32
1594 1800 7.778083 TCCTACACGATCTACACATAAATTGT 58.222 34.615 0.00 0.00 39.91 2.71
1595 1801 8.255206 TCCTACACGATCTACACATAAATTGTT 58.745 33.333 0.00 0.00 36.00 2.83
1596 1802 8.328146 CCTACACGATCTACACATAAATTGTTG 58.672 37.037 0.00 0.00 36.00 3.33
1597 1803 6.542852 ACACGATCTACACATAAATTGTTGC 58.457 36.000 0.00 0.00 36.00 4.17
1598 1804 6.371548 ACACGATCTACACATAAATTGTTGCT 59.628 34.615 0.00 0.00 36.00 3.91
1599 1805 6.901887 CACGATCTACACATAAATTGTTGCTC 59.098 38.462 0.00 0.00 36.00 4.26
1600 1806 6.818644 ACGATCTACACATAAATTGTTGCTCT 59.181 34.615 0.00 0.00 36.00 4.09
1601 1807 7.010552 ACGATCTACACATAAATTGTTGCTCTC 59.989 37.037 0.00 0.00 36.00 3.20
1602 1808 7.010460 CGATCTACACATAAATTGTTGCTCTCA 59.990 37.037 0.00 0.00 36.00 3.27
1603 1809 7.977789 TCTACACATAAATTGTTGCTCTCAA 57.022 32.000 0.00 0.00 36.00 3.02
1613 1819 3.896648 GTTGCTCTCAACGATTGGAAA 57.103 42.857 0.00 0.00 42.55 3.13
1614 1820 4.425577 GTTGCTCTCAACGATTGGAAAT 57.574 40.909 0.00 0.00 42.55 2.17
1615 1821 4.406943 GTTGCTCTCAACGATTGGAAATC 58.593 43.478 0.00 0.00 42.55 2.17
1616 1822 3.942829 TGCTCTCAACGATTGGAAATCT 58.057 40.909 0.00 0.00 0.00 2.40
1617 1823 4.326826 TGCTCTCAACGATTGGAAATCTT 58.673 39.130 0.00 0.00 0.00 2.40
1618 1824 4.761739 TGCTCTCAACGATTGGAAATCTTT 59.238 37.500 0.00 0.00 0.00 2.52
1619 1825 5.106555 TGCTCTCAACGATTGGAAATCTTTC 60.107 40.000 0.00 0.00 36.46 2.62
1620 1826 5.123027 GCTCTCAACGATTGGAAATCTTTCT 59.877 40.000 0.00 0.00 37.35 2.52
1621 1827 6.348868 GCTCTCAACGATTGGAAATCTTTCTT 60.349 38.462 0.00 0.00 37.35 2.52
1622 1828 7.510549 TCTCAACGATTGGAAATCTTTCTTT 57.489 32.000 0.00 0.00 37.35 2.52
1623 1829 7.940850 TCTCAACGATTGGAAATCTTTCTTTT 58.059 30.769 0.00 0.00 37.35 2.27
1624 1830 7.862372 TCTCAACGATTGGAAATCTTTCTTTTG 59.138 33.333 0.00 0.00 37.35 2.44
1625 1831 7.488322 TCAACGATTGGAAATCTTTCTTTTGT 58.512 30.769 0.00 0.00 37.35 2.83
1626 1832 7.434897 TCAACGATTGGAAATCTTTCTTTTGTG 59.565 33.333 0.00 0.00 37.35 3.33
1627 1833 6.805713 ACGATTGGAAATCTTTCTTTTGTGT 58.194 32.000 0.00 0.00 37.35 3.72
1628 1834 6.697019 ACGATTGGAAATCTTTCTTTTGTGTG 59.303 34.615 0.00 0.00 37.35 3.82
1629 1835 6.346040 CGATTGGAAATCTTTCTTTTGTGTGC 60.346 38.462 2.93 0.00 37.35 4.57
1630 1836 5.336150 TGGAAATCTTTCTTTTGTGTGCA 57.664 34.783 2.93 0.00 37.35 4.57
1631 1837 5.916318 TGGAAATCTTTCTTTTGTGTGCAT 58.084 33.333 0.00 0.00 37.35 3.96
1632 1838 6.347696 TGGAAATCTTTCTTTTGTGTGCATT 58.652 32.000 0.00 0.00 37.35 3.56
1633 1839 6.822676 TGGAAATCTTTCTTTTGTGTGCATTT 59.177 30.769 0.00 0.00 37.35 2.32
1634 1840 7.984050 TGGAAATCTTTCTTTTGTGTGCATTTA 59.016 29.630 0.00 0.00 37.35 1.40
1635 1841 8.992073 GGAAATCTTTCTTTTGTGTGCATTTAT 58.008 29.630 0.00 0.00 37.35 1.40
1639 1845 8.894409 TCTTTCTTTTGTGTGCATTTATATCG 57.106 30.769 0.00 0.00 0.00 2.92
1640 1846 7.967854 TCTTTCTTTTGTGTGCATTTATATCGG 59.032 33.333 0.00 0.00 0.00 4.18
1641 1847 6.993786 TCTTTTGTGTGCATTTATATCGGA 57.006 33.333 0.00 0.00 0.00 4.55
1642 1848 7.015226 TCTTTTGTGTGCATTTATATCGGAG 57.985 36.000 0.00 0.00 0.00 4.63
1643 1849 6.821160 TCTTTTGTGTGCATTTATATCGGAGA 59.179 34.615 0.00 0.00 45.75 3.71
1644 1850 7.498900 TCTTTTGTGTGCATTTATATCGGAGAT 59.501 33.333 0.00 0.00 45.12 2.75
1645 1851 6.785488 TTGTGTGCATTTATATCGGAGATC 57.215 37.500 0.00 0.00 45.12 2.75
1646 1852 5.852827 TGTGTGCATTTATATCGGAGATCA 58.147 37.500 0.00 0.00 45.12 2.92
1647 1853 6.466812 TGTGTGCATTTATATCGGAGATCAT 58.533 36.000 0.00 0.00 45.12 2.45
1648 1854 7.610865 TGTGTGCATTTATATCGGAGATCATA 58.389 34.615 0.00 0.00 45.12 2.15
1649 1855 8.260114 TGTGTGCATTTATATCGGAGATCATAT 58.740 33.333 0.00 0.00 45.12 1.78
1650 1856 9.750125 GTGTGCATTTATATCGGAGATCATATA 57.250 33.333 0.00 0.00 45.12 0.86
1651 1857 9.750125 TGTGCATTTATATCGGAGATCATATAC 57.250 33.333 0.00 0.00 45.12 1.47
1652 1858 9.750125 GTGCATTTATATCGGAGATCATATACA 57.250 33.333 0.00 0.00 45.12 2.29
1663 1869 8.506437 TCGGAGATCATATACAATTCAATTTGC 58.494 33.333 0.00 0.00 0.00 3.68
1664 1870 8.291740 CGGAGATCATATACAATTCAATTTGCA 58.708 33.333 0.00 0.00 0.00 4.08
1665 1871 9.622004 GGAGATCATATACAATTCAATTTGCAG 57.378 33.333 0.00 0.00 0.00 4.41
1666 1872 9.622004 GAGATCATATACAATTCAATTTGCAGG 57.378 33.333 0.00 0.00 0.00 4.85
1667 1873 8.582437 AGATCATATACAATTCAATTTGCAGGG 58.418 33.333 0.00 0.00 0.00 4.45
1668 1874 7.894753 TCATATACAATTCAATTTGCAGGGA 57.105 32.000 0.00 0.00 0.00 4.20
1669 1875 8.481492 TCATATACAATTCAATTTGCAGGGAT 57.519 30.769 0.00 0.00 0.00 3.85
1670 1876 8.579006 TCATATACAATTCAATTTGCAGGGATC 58.421 33.333 0.00 0.00 0.00 3.36
1671 1877 4.476628 ACAATTCAATTTGCAGGGATCC 57.523 40.909 1.92 1.92 0.00 3.36
1828 2034 3.976490 CTACCCTCCCTGCCCACGA 62.976 68.421 0.00 0.00 0.00 4.35
2030 2236 7.226720 ACACACACAATTACTTAAGGACTTCTG 59.773 37.037 7.53 0.00 0.00 3.02
2032 2238 5.408604 ACACAATTACTTAAGGACTTCTGCG 59.591 40.000 7.53 0.00 0.00 5.18
2496 2724 9.540538 TGATCACCTCCCTGAAATAAAATAAAA 57.459 29.630 0.00 0.00 0.00 1.52
2540 2768 7.687941 ACTTAAACTTGACCGAAATGATCAT 57.312 32.000 1.18 1.18 0.00 2.45
2569 2798 0.598065 AAAACTTGCGGCTCACATCC 59.402 50.000 0.00 0.00 0.00 3.51
2603 2832 4.506654 CGTGGTAATACAGTGCTAATCACC 59.493 45.833 0.00 0.00 46.81 4.02
2609 2838 3.573491 GTGCTAATCACCGCCGGC 61.573 66.667 19.07 19.07 39.79 6.13
2746 2978 9.370126 GTTGTCTAATAATTATTGATGTGTCGC 57.630 33.333 18.98 4.13 0.00 5.19
2747 2979 7.783209 TGTCTAATAATTATTGATGTGTCGCG 58.217 34.615 18.98 0.00 0.00 5.87
2748 2980 7.436970 TGTCTAATAATTATTGATGTGTCGCGT 59.563 33.333 18.98 0.00 0.00 6.01
2749 2981 8.908678 GTCTAATAATTATTGATGTGTCGCGTA 58.091 33.333 18.98 0.00 0.00 4.42
2750 2982 9.124807 TCTAATAATTATTGATGTGTCGCGTAG 57.875 33.333 18.98 5.46 0.00 3.51
2751 2983 7.940178 AATAATTATTGATGTGTCGCGTAGA 57.060 32.000 9.93 0.00 0.00 2.59
2752 2984 7.940178 ATAATTATTGATGTGTCGCGTAGAA 57.060 32.000 5.77 0.00 0.00 2.10
2753 2985 5.890110 ATTATTGATGTGTCGCGTAGAAG 57.110 39.130 5.77 0.00 0.00 2.85
2754 2986 2.717580 TTGATGTGTCGCGTAGAAGT 57.282 45.000 5.77 0.00 0.00 3.01
2755 2987 1.977188 TGATGTGTCGCGTAGAAGTG 58.023 50.000 5.77 0.00 0.00 3.16
2756 2988 1.538075 TGATGTGTCGCGTAGAAGTGA 59.462 47.619 5.77 0.00 0.00 3.41
2757 2989 2.177977 GATGTGTCGCGTAGAAGTGAG 58.822 52.381 5.77 0.00 0.00 3.51
2758 2990 1.232119 TGTGTCGCGTAGAAGTGAGA 58.768 50.000 5.77 0.00 0.00 3.27
2759 2991 1.605232 TGTGTCGCGTAGAAGTGAGAA 59.395 47.619 5.77 0.00 0.00 2.87
2760 2992 2.033675 TGTGTCGCGTAGAAGTGAGAAA 59.966 45.455 5.77 0.00 0.00 2.52
2761 2993 2.657372 GTGTCGCGTAGAAGTGAGAAAG 59.343 50.000 5.77 0.00 0.00 2.62
2762 2994 2.251893 GTCGCGTAGAAGTGAGAAAGG 58.748 52.381 5.77 0.00 0.00 3.11
2763 2995 1.201647 TCGCGTAGAAGTGAGAAAGGG 59.798 52.381 5.77 0.00 0.00 3.95
2764 2996 1.201647 CGCGTAGAAGTGAGAAAGGGA 59.798 52.381 0.00 0.00 0.00 4.20
2765 2997 2.352421 CGCGTAGAAGTGAGAAAGGGAA 60.352 50.000 0.00 0.00 0.00 3.97
2766 2998 3.254892 GCGTAGAAGTGAGAAAGGGAAG 58.745 50.000 0.00 0.00 0.00 3.46
2767 2999 3.056749 GCGTAGAAGTGAGAAAGGGAAGA 60.057 47.826 0.00 0.00 0.00 2.87
2768 3000 4.382147 GCGTAGAAGTGAGAAAGGGAAGAT 60.382 45.833 0.00 0.00 0.00 2.40
2769 3001 5.725362 CGTAGAAGTGAGAAAGGGAAGATT 58.275 41.667 0.00 0.00 0.00 2.40
2770 3002 5.808030 CGTAGAAGTGAGAAAGGGAAGATTC 59.192 44.000 0.00 0.00 0.00 2.52
2771 3003 4.826556 AGAAGTGAGAAAGGGAAGATTCG 58.173 43.478 0.00 0.00 0.00 3.34
2772 3004 4.528596 AGAAGTGAGAAAGGGAAGATTCGA 59.471 41.667 0.00 0.00 0.00 3.71
2773 3005 5.188751 AGAAGTGAGAAAGGGAAGATTCGAT 59.811 40.000 0.00 0.00 0.00 3.59
2774 3006 5.428184 AGTGAGAAAGGGAAGATTCGATT 57.572 39.130 0.00 0.00 0.00 3.34
2775 3007 5.181748 AGTGAGAAAGGGAAGATTCGATTG 58.818 41.667 0.00 0.00 0.00 2.67
2776 3008 4.938226 GTGAGAAAGGGAAGATTCGATTGT 59.062 41.667 0.00 0.00 0.00 2.71
2777 3009 6.070767 AGTGAGAAAGGGAAGATTCGATTGTA 60.071 38.462 0.00 0.00 0.00 2.41
2778 3010 6.256757 GTGAGAAAGGGAAGATTCGATTGTAG 59.743 42.308 0.00 0.00 0.00 2.74
2779 3011 5.675538 AGAAAGGGAAGATTCGATTGTAGG 58.324 41.667 0.00 0.00 0.00 3.18
2780 3012 4.423625 AAGGGAAGATTCGATTGTAGGG 57.576 45.455 0.00 0.00 0.00 3.53
2781 3013 3.654273 AGGGAAGATTCGATTGTAGGGA 58.346 45.455 0.00 0.00 0.00 4.20
2782 3014 3.643792 AGGGAAGATTCGATTGTAGGGAG 59.356 47.826 0.00 0.00 0.00 4.30
2783 3015 3.641906 GGGAAGATTCGATTGTAGGGAGA 59.358 47.826 0.00 0.00 0.00 3.71
2784 3016 4.262249 GGGAAGATTCGATTGTAGGGAGAG 60.262 50.000 0.00 0.00 0.00 3.20
2785 3017 4.585162 GGAAGATTCGATTGTAGGGAGAGA 59.415 45.833 0.00 0.00 0.00 3.10
2786 3018 5.069251 GGAAGATTCGATTGTAGGGAGAGAA 59.931 44.000 0.00 0.00 0.00 2.87
2787 3019 6.407074 GGAAGATTCGATTGTAGGGAGAGAAA 60.407 42.308 0.00 0.00 0.00 2.52
2788 3020 5.908341 AGATTCGATTGTAGGGAGAGAAAC 58.092 41.667 0.00 0.00 0.00 2.78
2789 3021 3.777465 TCGATTGTAGGGAGAGAAACG 57.223 47.619 0.00 0.00 0.00 3.60
2790 3022 3.349927 TCGATTGTAGGGAGAGAAACGA 58.650 45.455 0.00 0.00 0.00 3.85
2791 3023 3.760151 TCGATTGTAGGGAGAGAAACGAA 59.240 43.478 0.00 0.00 0.00 3.85
2792 3024 3.858238 CGATTGTAGGGAGAGAAACGAAC 59.142 47.826 0.00 0.00 0.00 3.95
2793 3025 3.672767 TTGTAGGGAGAGAAACGAACC 57.327 47.619 0.00 0.00 0.00 3.62
2794 3026 2.600790 TGTAGGGAGAGAAACGAACCA 58.399 47.619 0.00 0.00 0.00 3.67
2795 3027 2.967201 TGTAGGGAGAGAAACGAACCAA 59.033 45.455 0.00 0.00 0.00 3.67
2796 3028 3.388676 TGTAGGGAGAGAAACGAACCAAA 59.611 43.478 0.00 0.00 0.00 3.28
2797 3029 3.127425 AGGGAGAGAAACGAACCAAAG 57.873 47.619 0.00 0.00 0.00 2.77
2798 3030 1.535896 GGGAGAGAAACGAACCAAAGC 59.464 52.381 0.00 0.00 0.00 3.51
2799 3031 2.218603 GGAGAGAAACGAACCAAAGCA 58.781 47.619 0.00 0.00 0.00 3.91
2800 3032 2.616842 GGAGAGAAACGAACCAAAGCAA 59.383 45.455 0.00 0.00 0.00 3.91
2801 3033 3.253432 GGAGAGAAACGAACCAAAGCAAT 59.747 43.478 0.00 0.00 0.00 3.56
2802 3034 4.467735 GAGAGAAACGAACCAAAGCAATC 58.532 43.478 0.00 0.00 0.00 2.67
2803 3035 4.137543 AGAGAAACGAACCAAAGCAATCT 58.862 39.130 0.00 0.00 0.00 2.40
2804 3036 4.214332 AGAGAAACGAACCAAAGCAATCTC 59.786 41.667 0.00 0.00 0.00 2.75
2805 3037 4.137543 AGAAACGAACCAAAGCAATCTCT 58.862 39.130 0.00 0.00 0.00 3.10
2806 3038 4.214332 AGAAACGAACCAAAGCAATCTCTC 59.786 41.667 0.00 0.00 0.00 3.20
2807 3039 3.409026 ACGAACCAAAGCAATCTCTCT 57.591 42.857 0.00 0.00 0.00 3.10
2808 3040 3.330267 ACGAACCAAAGCAATCTCTCTC 58.670 45.455 0.00 0.00 0.00 3.20
2809 3041 3.007398 ACGAACCAAAGCAATCTCTCTCT 59.993 43.478 0.00 0.00 0.00 3.10
2810 3042 3.616379 CGAACCAAAGCAATCTCTCTCTC 59.384 47.826 0.00 0.00 0.00 3.20
2811 3043 4.620332 CGAACCAAAGCAATCTCTCTCTCT 60.620 45.833 0.00 0.00 0.00 3.10
2812 3044 4.470334 ACCAAAGCAATCTCTCTCTCTC 57.530 45.455 0.00 0.00 0.00 3.20
2813 3045 4.095946 ACCAAAGCAATCTCTCTCTCTCT 58.904 43.478 0.00 0.00 0.00 3.10
2814 3046 4.160252 ACCAAAGCAATCTCTCTCTCTCTC 59.840 45.833 0.00 0.00 0.00 3.20
2815 3047 4.403432 CCAAAGCAATCTCTCTCTCTCTCT 59.597 45.833 0.00 0.00 0.00 3.10
2816 3048 5.450965 CCAAAGCAATCTCTCTCTCTCTCTC 60.451 48.000 0.00 0.00 0.00 3.20
2817 3049 4.785346 AGCAATCTCTCTCTCTCTCTCT 57.215 45.455 0.00 0.00 0.00 3.10
2818 3050 4.712476 AGCAATCTCTCTCTCTCTCTCTC 58.288 47.826 0.00 0.00 0.00 3.20
2819 3051 4.164796 AGCAATCTCTCTCTCTCTCTCTCA 59.835 45.833 0.00 0.00 0.00 3.27
2820 3052 5.068636 GCAATCTCTCTCTCTCTCTCTCAT 58.931 45.833 0.00 0.00 0.00 2.90
2821 3053 5.533903 GCAATCTCTCTCTCTCTCTCTCATT 59.466 44.000 0.00 0.00 0.00 2.57
2822 3054 6.712095 GCAATCTCTCTCTCTCTCTCTCATTA 59.288 42.308 0.00 0.00 0.00 1.90
2830 3062 8.218423 TCTCTCTCTCTCTCATTATGGATACT 57.782 38.462 0.00 0.00 37.61 2.12
2907 3139 1.019805 GCCTGCCACTTAACCGAGAC 61.020 60.000 0.00 0.00 0.00 3.36
3108 3341 1.613061 GGTCCGACCCATTTCCCAT 59.387 57.895 6.25 0.00 30.04 4.00
3185 3418 8.490311 AGTAATAAAATTCAAGGAGAGGAGAGG 58.510 37.037 0.00 0.00 0.00 3.69
3192 6930 1.221213 AGGAGAGGAGAGGGCTCACT 61.221 60.000 0.00 0.00 43.14 3.41
3244 6982 3.762823 CTCGTCTAAGTCTACAACCCCTT 59.237 47.826 0.00 0.00 0.00 3.95
3245 6983 3.508793 TCGTCTAAGTCTACAACCCCTTG 59.491 47.826 0.00 0.00 0.00 3.61
3246 6984 3.508793 CGTCTAAGTCTACAACCCCTTGA 59.491 47.826 0.00 0.00 0.00 3.02
3247 6985 4.021719 CGTCTAAGTCTACAACCCCTTGAA 60.022 45.833 0.00 0.00 0.00 2.69
3248 6986 5.480205 GTCTAAGTCTACAACCCCTTGAAG 58.520 45.833 0.00 0.00 0.00 3.02
3249 6987 3.790089 AAGTCTACAACCCCTTGAAGG 57.210 47.619 3.69 3.69 34.30 3.46
3250 6988 2.986050 AGTCTACAACCCCTTGAAGGA 58.014 47.619 13.97 0.00 37.67 3.36
3251 6989 3.323775 AGTCTACAACCCCTTGAAGGAA 58.676 45.455 13.97 0.00 37.67 3.36
3252 6990 3.720002 AGTCTACAACCCCTTGAAGGAAA 59.280 43.478 13.97 0.00 37.67 3.13
3253 6991 4.354087 AGTCTACAACCCCTTGAAGGAAAT 59.646 41.667 13.97 0.00 37.67 2.17
3254 6992 5.550403 AGTCTACAACCCCTTGAAGGAAATA 59.450 40.000 13.97 0.00 37.67 1.40
3255 6993 6.217693 AGTCTACAACCCCTTGAAGGAAATAT 59.782 38.462 13.97 0.00 37.67 1.28
3256 6994 6.318900 GTCTACAACCCCTTGAAGGAAATATG 59.681 42.308 13.97 6.83 37.67 1.78
3257 6995 3.769300 ACAACCCCTTGAAGGAAATATGC 59.231 43.478 13.97 0.00 37.67 3.14
3258 6996 3.032265 ACCCCTTGAAGGAAATATGCC 57.968 47.619 13.97 0.00 37.67 4.40
3259 6997 2.319844 CCCCTTGAAGGAAATATGCCC 58.680 52.381 13.97 0.00 37.67 5.36
3260 6998 2.091111 CCCCTTGAAGGAAATATGCCCT 60.091 50.000 13.97 0.00 37.67 5.19
3261 6999 3.140144 CCCCTTGAAGGAAATATGCCCTA 59.860 47.826 13.97 0.00 37.67 3.53
3262 7000 4.401925 CCCTTGAAGGAAATATGCCCTAG 58.598 47.826 13.97 0.00 37.67 3.02
3263 7001 4.104738 CCCTTGAAGGAAATATGCCCTAGA 59.895 45.833 13.97 0.00 37.67 2.43
3264 7002 5.312079 CCTTGAAGGAAATATGCCCTAGAG 58.688 45.833 4.95 0.00 37.67 2.43
3265 7003 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
3340 7078 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
3341 7079 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
3342 7080 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
3343 7081 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
3344 7082 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
3345 7083 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
3346 7084 7.554835 TGCTAGAATTGTATTAACCGGAAACAT 59.445 33.333 9.46 0.00 0.00 2.71
3347 7085 7.855904 GCTAGAATTGTATTAACCGGAAACATG 59.144 37.037 9.46 0.00 0.00 3.21
3348 7086 7.931578 AGAATTGTATTAACCGGAAACATGA 57.068 32.000 9.46 0.00 0.00 3.07
3349 7087 8.519799 AGAATTGTATTAACCGGAAACATGAT 57.480 30.769 9.46 0.00 0.00 2.45
3350 7088 9.621629 AGAATTGTATTAACCGGAAACATGATA 57.378 29.630 9.46 0.00 0.00 2.15
3351 7089 9.659830 GAATTGTATTAACCGGAAACATGATAC 57.340 33.333 9.46 7.13 0.00 2.24
3352 7090 8.740123 ATTGTATTAACCGGAAACATGATACA 57.260 30.769 9.46 9.57 0.00 2.29
3353 7091 8.740123 TTGTATTAACCGGAAACATGATACAT 57.260 30.769 9.46 0.00 31.27 2.29
3354 7092 8.148807 TGTATTAACCGGAAACATGATACATG 57.851 34.615 9.46 9.72 0.00 3.21
3355 7093 7.771361 TGTATTAACCGGAAACATGATACATGT 59.229 33.333 9.46 10.94 0.00 3.21
3356 7094 4.963276 AACCGGAAACATGATACATGTG 57.037 40.909 9.46 7.59 31.80 3.21
3357 7095 3.950397 ACCGGAAACATGATACATGTGT 58.050 40.909 9.46 11.88 31.80 3.72
3358 7096 3.689161 ACCGGAAACATGATACATGTGTG 59.311 43.478 9.46 4.81 31.80 3.82
3359 7097 3.938334 CCGGAAACATGATACATGTGTGA 59.062 43.478 16.29 0.00 31.80 3.58
3360 7098 4.394610 CCGGAAACATGATACATGTGTGAA 59.605 41.667 16.29 0.00 31.80 3.18
3361 7099 5.066375 CCGGAAACATGATACATGTGTGAAT 59.934 40.000 16.29 0.00 31.80 2.57
3362 7100 6.259829 CCGGAAACATGATACATGTGTGAATA 59.740 38.462 16.29 0.00 31.80 1.75
3363 7101 7.125755 CGGAAACATGATACATGTGTGAATAC 58.874 38.462 16.29 1.40 31.80 1.89
3364 7102 7.201600 CGGAAACATGATACATGTGTGAATACA 60.202 37.037 16.29 0.00 34.63 2.29
3365 7103 8.623903 GGAAACATGATACATGTGTGAATACAT 58.376 33.333 16.29 0.00 41.77 2.29
3369 7107 9.481340 ACATGATACATGTGTGAATACATAGAC 57.519 33.333 15.11 0.00 39.17 2.59
3370 7108 9.480053 CATGATACATGTGTGAATACATAGACA 57.520 33.333 9.11 0.00 39.17 3.41
3372 7110 9.883142 TGATACATGTGTGAATACATAGACAAA 57.117 29.630 9.11 0.00 39.17 2.83
3374 7112 7.977789 ACATGTGTGAATACATAGACAAACA 57.022 32.000 0.00 0.00 39.17 2.83
3375 7113 8.565896 ACATGTGTGAATACATAGACAAACAT 57.434 30.769 0.00 0.00 40.42 2.71
3376 7114 9.665719 ACATGTGTGAATACATAGACAAACATA 57.334 29.630 0.00 0.00 38.58 2.29
3378 7116 9.890629 ATGTGTGAATACATAGACAAACATAGT 57.109 29.630 0.00 0.00 38.77 2.12
3379 7117 9.150348 TGTGTGAATACATAGACAAACATAGTG 57.850 33.333 0.00 0.00 39.39 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.600484 TGAGCCCACAATCTTTCCTTTAAAA 59.400 36.000 0.00 0.00 0.00 1.52
96 97 9.997482 TGCGTTTAAGACATAATATTTCCTTTC 57.003 29.630 0.00 0.00 0.00 2.62
105 106 7.835634 TGTCACATGCGTTTAAGACATAATA 57.164 32.000 0.00 0.00 31.72 0.98
133 134 4.095932 ACGTGATACTCTCATTACGAGCAA 59.904 41.667 7.31 0.00 39.49 3.91
363 526 1.421268 CCACTATGGGCAGCCTAATGA 59.579 52.381 12.43 0.00 32.67 2.57
483 649 0.949397 GGGACGGTTGAGGTGTTTTC 59.051 55.000 0.00 0.00 0.00 2.29
741 935 5.889853 TGCCTTAGGTTCTTCGTATCTAGAA 59.110 40.000 0.00 0.00 0.00 2.10
803 997 1.226575 TGCATCCACGTCGATCGAC 60.227 57.895 33.22 33.22 42.86 4.20
805 999 3.299585 GTGCATCCACGTCGATCG 58.700 61.111 9.36 9.36 46.00 3.69
813 1007 0.811616 GATCTGACCCGTGCATCCAC 60.812 60.000 0.00 0.00 38.62 4.02
817 1011 2.224378 CCAATAGATCTGACCCGTGCAT 60.224 50.000 5.18 0.00 0.00 3.96
820 1014 3.070159 ACATCCAATAGATCTGACCCGTG 59.930 47.826 5.18 0.70 30.59 4.94
827 1021 7.070946 AGCCCATATCTACATCCAATAGATCTG 59.929 40.741 5.18 0.35 39.55 2.90
862 1061 4.012374 GCCACTGGGTTATCATATCCATG 58.988 47.826 0.00 0.00 36.17 3.66
879 1078 5.716979 TCTATCTAGTATTTGGAGGCCACT 58.283 41.667 5.01 0.00 30.78 4.00
944 1143 0.038801 GCACTCTTTCCTTTGGCAGC 60.039 55.000 0.00 0.00 0.00 5.25
962 1161 3.366374 GGTCTTCTAAACCAAGTGCATGC 60.366 47.826 11.82 11.82 36.75 4.06
964 1163 4.373156 AGGTCTTCTAAACCAAGTGCAT 57.627 40.909 0.00 0.00 39.39 3.96
1163 1362 0.467384 CTCCTCAACATCATCGGGCT 59.533 55.000 0.00 0.00 0.00 5.19
1272 1471 0.894184 AGAACTTCCTCGACGCCTCA 60.894 55.000 0.00 0.00 0.00 3.86
1342 1541 4.598036 ACCCTTCATTCTGGAACATGAT 57.402 40.909 0.00 0.00 38.20 2.45
1346 1545 2.027561 CCGTACCCTTCATTCTGGAACA 60.028 50.000 0.00 0.00 0.00 3.18
1575 1781 6.818644 AGAGCAACAATTTATGTGTAGATCGT 59.181 34.615 0.00 0.00 42.99 3.73
1576 1782 7.010460 TGAGAGCAACAATTTATGTGTAGATCG 59.990 37.037 0.00 0.00 42.99 3.69
1577 1783 8.201554 TGAGAGCAACAATTTATGTGTAGATC 57.798 34.615 0.00 0.00 42.99 2.75
1578 1784 8.565896 TTGAGAGCAACAATTTATGTGTAGAT 57.434 30.769 0.00 0.00 42.99 1.98
1579 1785 7.977789 TTGAGAGCAACAATTTATGTGTAGA 57.022 32.000 0.00 0.00 42.99 2.59
1594 1800 4.326826 AGATTTCCAATCGTTGAGAGCAA 58.673 39.130 0.00 0.00 0.00 3.91
1595 1801 3.942829 AGATTTCCAATCGTTGAGAGCA 58.057 40.909 0.00 0.00 0.00 4.26
1596 1802 4.954092 AAGATTTCCAATCGTTGAGAGC 57.046 40.909 0.15 0.00 0.00 4.09
1597 1803 6.734104 AGAAAGATTTCCAATCGTTGAGAG 57.266 37.500 2.88 0.00 37.92 3.20
1598 1804 7.510549 AAAGAAAGATTTCCAATCGTTGAGA 57.489 32.000 2.88 0.00 37.92 3.27
1599 1805 7.649306 ACAAAAGAAAGATTTCCAATCGTTGAG 59.351 33.333 2.88 0.00 37.92 3.02
1600 1806 7.434897 CACAAAAGAAAGATTTCCAATCGTTGA 59.565 33.333 2.88 0.00 37.92 3.18
1601 1807 7.222611 ACACAAAAGAAAGATTTCCAATCGTTG 59.777 33.333 2.88 1.78 37.92 4.10
1602 1808 7.222611 CACACAAAAGAAAGATTTCCAATCGTT 59.777 33.333 1.73 0.00 37.92 3.85
1603 1809 6.697019 CACACAAAAGAAAGATTTCCAATCGT 59.303 34.615 1.73 0.00 37.92 3.73
1604 1810 6.346040 GCACACAAAAGAAAGATTTCCAATCG 60.346 38.462 1.73 0.00 37.92 3.34
1605 1811 6.479660 TGCACACAAAAGAAAGATTTCCAATC 59.520 34.615 1.73 0.00 37.92 2.67
1606 1812 6.347696 TGCACACAAAAGAAAGATTTCCAAT 58.652 32.000 1.73 0.00 37.92 3.16
1607 1813 5.728471 TGCACACAAAAGAAAGATTTCCAA 58.272 33.333 1.73 0.00 37.92 3.53
1608 1814 5.336150 TGCACACAAAAGAAAGATTTCCA 57.664 34.783 1.73 0.00 37.92 3.53
1609 1815 6.849588 AATGCACACAAAAGAAAGATTTCC 57.150 33.333 0.00 0.00 37.92 3.13
1613 1819 9.507280 CGATATAAATGCACACAAAAGAAAGAT 57.493 29.630 0.00 0.00 0.00 2.40
1614 1820 7.967854 CCGATATAAATGCACACAAAAGAAAGA 59.032 33.333 0.00 0.00 0.00 2.52
1615 1821 7.967854 TCCGATATAAATGCACACAAAAGAAAG 59.032 33.333 0.00 0.00 0.00 2.62
1616 1822 7.821652 TCCGATATAAATGCACACAAAAGAAA 58.178 30.769 0.00 0.00 0.00 2.52
1617 1823 7.335673 TCTCCGATATAAATGCACACAAAAGAA 59.664 33.333 0.00 0.00 0.00 2.52
1618 1824 6.821160 TCTCCGATATAAATGCACACAAAAGA 59.179 34.615 0.00 0.00 0.00 2.52
1619 1825 7.015226 TCTCCGATATAAATGCACACAAAAG 57.985 36.000 0.00 0.00 0.00 2.27
1620 1826 6.993786 TCTCCGATATAAATGCACACAAAA 57.006 33.333 0.00 0.00 0.00 2.44
1621 1827 6.765512 TGATCTCCGATATAAATGCACACAAA 59.234 34.615 0.00 0.00 0.00 2.83
1622 1828 6.287525 TGATCTCCGATATAAATGCACACAA 58.712 36.000 0.00 0.00 0.00 3.33
1623 1829 5.852827 TGATCTCCGATATAAATGCACACA 58.147 37.500 0.00 0.00 0.00 3.72
1624 1830 6.974932 ATGATCTCCGATATAAATGCACAC 57.025 37.500 0.00 0.00 0.00 3.82
1625 1831 9.750125 GTATATGATCTCCGATATAAATGCACA 57.250 33.333 0.00 0.00 0.00 4.57
1626 1832 9.750125 TGTATATGATCTCCGATATAAATGCAC 57.250 33.333 0.00 0.00 0.00 4.57
1637 1843 8.506437 GCAAATTGAATTGTATATGATCTCCGA 58.494 33.333 0.00 0.00 32.80 4.55
1638 1844 8.291740 TGCAAATTGAATTGTATATGATCTCCG 58.708 33.333 0.00 0.00 32.80 4.63
1639 1845 9.622004 CTGCAAATTGAATTGTATATGATCTCC 57.378 33.333 0.00 0.00 32.80 3.71
1640 1846 9.622004 CCTGCAAATTGAATTGTATATGATCTC 57.378 33.333 0.00 0.00 32.80 2.75
1641 1847 8.582437 CCCTGCAAATTGAATTGTATATGATCT 58.418 33.333 0.00 0.00 32.80 2.75
1642 1848 8.579006 TCCCTGCAAATTGAATTGTATATGATC 58.421 33.333 0.00 0.00 32.80 2.92
1643 1849 8.481492 TCCCTGCAAATTGAATTGTATATGAT 57.519 30.769 0.00 0.00 32.80 2.45
1644 1850 7.894753 TCCCTGCAAATTGAATTGTATATGA 57.105 32.000 0.00 0.00 32.80 2.15
1645 1851 7.816031 GGATCCCTGCAAATTGAATTGTATATG 59.184 37.037 0.00 0.00 32.80 1.78
1646 1852 7.038799 GGGATCCCTGCAAATTGAATTGTATAT 60.039 37.037 24.69 0.00 32.80 0.86
1647 1853 6.267471 GGGATCCCTGCAAATTGAATTGTATA 59.733 38.462 24.69 0.00 32.80 1.47
1648 1854 5.070847 GGGATCCCTGCAAATTGAATTGTAT 59.929 40.000 24.69 0.00 32.80 2.29
1649 1855 4.405358 GGGATCCCTGCAAATTGAATTGTA 59.595 41.667 24.69 0.00 32.80 2.41
1650 1856 3.198417 GGGATCCCTGCAAATTGAATTGT 59.802 43.478 24.69 0.00 32.80 2.71
1651 1857 3.432608 GGGGATCCCTGCAAATTGAATTG 60.433 47.826 30.08 0.00 41.34 2.32
1652 1858 2.773661 GGGGATCCCTGCAAATTGAATT 59.226 45.455 30.08 0.00 41.34 2.17
1653 1859 2.401568 GGGGATCCCTGCAAATTGAAT 58.598 47.619 30.08 0.00 41.34 2.57
1654 1860 1.864669 GGGGATCCCTGCAAATTGAA 58.135 50.000 30.08 0.00 41.34 2.69
1655 1861 3.613661 GGGGATCCCTGCAAATTGA 57.386 52.632 30.08 0.00 41.34 2.57
1665 1871 1.326328 GTACTCGTGTAGGGGATCCC 58.674 60.000 23.95 23.95 45.90 3.85
1666 1872 1.680207 GTGTACTCGTGTAGGGGATCC 59.320 57.143 1.92 1.92 0.00 3.36
1667 1873 1.680207 GGTGTACTCGTGTAGGGGATC 59.320 57.143 0.00 0.00 0.00 3.36
1668 1874 1.287146 AGGTGTACTCGTGTAGGGGAT 59.713 52.381 0.00 0.00 0.00 3.85
1669 1875 0.700564 AGGTGTACTCGTGTAGGGGA 59.299 55.000 0.00 0.00 0.00 4.81
1670 1876 1.553706 AAGGTGTACTCGTGTAGGGG 58.446 55.000 0.00 0.00 0.00 4.79
1671 1877 3.614092 TCTAAGGTGTACTCGTGTAGGG 58.386 50.000 0.00 0.00 0.00 3.53
1828 2034 3.677648 CCGTTCACGAGGTCCGGT 61.678 66.667 0.00 0.00 43.93 5.28
2030 2236 6.398205 CGTTCATGATCAATGCAAATAATCGC 60.398 38.462 0.00 0.00 36.11 4.58
2032 2238 8.071967 TCTCGTTCATGATCAATGCAAATAATC 58.928 33.333 0.00 0.00 36.11 1.75
2136 2364 1.561643 CCAGTGACAGCCTCTCCTTA 58.438 55.000 0.00 0.00 0.00 2.69
2540 2768 5.759273 TGAGCCGCAAGTTTTAGTACTAAAA 59.241 36.000 28.77 28.77 41.23 1.52
2569 2798 4.740268 TGTATTACCACGCTCACTAGTTG 58.260 43.478 0.00 0.00 0.00 3.16
2603 2832 1.636340 CTTGATTTCGTAGCCGGCG 59.364 57.895 23.20 7.22 33.95 6.46
2609 2838 4.985409 GCCTAGTCATCCTTGATTTCGTAG 59.015 45.833 0.00 0.00 33.56 3.51
2731 2963 5.232202 CACTTCTACGCGACACATCAATAAT 59.768 40.000 15.93 0.00 0.00 1.28
2732 2964 4.561213 CACTTCTACGCGACACATCAATAA 59.439 41.667 15.93 0.00 0.00 1.40
2733 2965 4.102649 CACTTCTACGCGACACATCAATA 58.897 43.478 15.93 0.00 0.00 1.90
2734 2966 2.923655 CACTTCTACGCGACACATCAAT 59.076 45.455 15.93 0.00 0.00 2.57
2735 2967 2.030628 TCACTTCTACGCGACACATCAA 60.031 45.455 15.93 0.00 0.00 2.57
2736 2968 1.538075 TCACTTCTACGCGACACATCA 59.462 47.619 15.93 0.00 0.00 3.07
2737 2969 2.159558 TCTCACTTCTACGCGACACATC 60.160 50.000 15.93 0.00 0.00 3.06
2738 2970 1.810755 TCTCACTTCTACGCGACACAT 59.189 47.619 15.93 0.00 0.00 3.21
2739 2971 1.232119 TCTCACTTCTACGCGACACA 58.768 50.000 15.93 0.00 0.00 3.72
2740 2972 2.327081 TTCTCACTTCTACGCGACAC 57.673 50.000 15.93 0.00 0.00 3.67
2741 2973 2.351447 CCTTTCTCACTTCTACGCGACA 60.351 50.000 15.93 0.00 0.00 4.35
2742 2974 2.251893 CCTTTCTCACTTCTACGCGAC 58.748 52.381 15.93 0.00 0.00 5.19
2743 2975 1.201647 CCCTTTCTCACTTCTACGCGA 59.798 52.381 15.93 0.00 0.00 5.87
2744 2976 1.201647 TCCCTTTCTCACTTCTACGCG 59.798 52.381 3.53 3.53 0.00 6.01
2745 2977 3.056749 TCTTCCCTTTCTCACTTCTACGC 60.057 47.826 0.00 0.00 0.00 4.42
2746 2978 4.785511 TCTTCCCTTTCTCACTTCTACG 57.214 45.455 0.00 0.00 0.00 3.51
2747 2979 5.808030 CGAATCTTCCCTTTCTCACTTCTAC 59.192 44.000 0.00 0.00 0.00 2.59
2748 2980 5.715279 TCGAATCTTCCCTTTCTCACTTCTA 59.285 40.000 0.00 0.00 0.00 2.10
2749 2981 4.528596 TCGAATCTTCCCTTTCTCACTTCT 59.471 41.667 0.00 0.00 0.00 2.85
2750 2982 4.822026 TCGAATCTTCCCTTTCTCACTTC 58.178 43.478 0.00 0.00 0.00 3.01
2751 2983 4.891992 TCGAATCTTCCCTTTCTCACTT 57.108 40.909 0.00 0.00 0.00 3.16
2752 2984 5.181748 CAATCGAATCTTCCCTTTCTCACT 58.818 41.667 0.00 0.00 0.00 3.41
2753 2985 4.938226 ACAATCGAATCTTCCCTTTCTCAC 59.062 41.667 0.00 0.00 0.00 3.51
2754 2986 5.165961 ACAATCGAATCTTCCCTTTCTCA 57.834 39.130 0.00 0.00 0.00 3.27
2755 2987 5.755861 CCTACAATCGAATCTTCCCTTTCTC 59.244 44.000 0.00 0.00 0.00 2.87
2756 2988 5.396884 CCCTACAATCGAATCTTCCCTTTCT 60.397 44.000 0.00 0.00 0.00 2.52
2757 2989 4.816925 CCCTACAATCGAATCTTCCCTTTC 59.183 45.833 0.00 0.00 0.00 2.62
2758 2990 4.473559 TCCCTACAATCGAATCTTCCCTTT 59.526 41.667 0.00 0.00 0.00 3.11
2759 2991 4.037927 TCCCTACAATCGAATCTTCCCTT 58.962 43.478 0.00 0.00 0.00 3.95
2760 2992 3.643792 CTCCCTACAATCGAATCTTCCCT 59.356 47.826 0.00 0.00 0.00 4.20
2761 2993 3.641906 TCTCCCTACAATCGAATCTTCCC 59.358 47.826 0.00 0.00 0.00 3.97
2762 2994 4.585162 TCTCTCCCTACAATCGAATCTTCC 59.415 45.833 0.00 0.00 0.00 3.46
2763 2995 5.776173 TCTCTCCCTACAATCGAATCTTC 57.224 43.478 0.00 0.00 0.00 2.87
2764 2996 6.342111 GTTTCTCTCCCTACAATCGAATCTT 58.658 40.000 0.00 0.00 0.00 2.40
2765 2997 5.450688 CGTTTCTCTCCCTACAATCGAATCT 60.451 44.000 0.00 0.00 0.00 2.40
2766 2998 4.740695 CGTTTCTCTCCCTACAATCGAATC 59.259 45.833 0.00 0.00 0.00 2.52
2767 2999 4.401519 TCGTTTCTCTCCCTACAATCGAAT 59.598 41.667 0.00 0.00 0.00 3.34
2768 3000 3.760151 TCGTTTCTCTCCCTACAATCGAA 59.240 43.478 0.00 0.00 0.00 3.71
2769 3001 3.349927 TCGTTTCTCTCCCTACAATCGA 58.650 45.455 0.00 0.00 0.00 3.59
2770 3002 3.777465 TCGTTTCTCTCCCTACAATCG 57.223 47.619 0.00 0.00 0.00 3.34
2771 3003 4.182339 GGTTCGTTTCTCTCCCTACAATC 58.818 47.826 0.00 0.00 0.00 2.67
2772 3004 3.581332 TGGTTCGTTTCTCTCCCTACAAT 59.419 43.478 0.00 0.00 0.00 2.71
2773 3005 2.967201 TGGTTCGTTTCTCTCCCTACAA 59.033 45.455 0.00 0.00 0.00 2.41
2774 3006 2.600790 TGGTTCGTTTCTCTCCCTACA 58.399 47.619 0.00 0.00 0.00 2.74
2775 3007 3.672767 TTGGTTCGTTTCTCTCCCTAC 57.327 47.619 0.00 0.00 0.00 3.18
2776 3008 3.556423 GCTTTGGTTCGTTTCTCTCCCTA 60.556 47.826 0.00 0.00 0.00 3.53
2777 3009 2.810767 GCTTTGGTTCGTTTCTCTCCCT 60.811 50.000 0.00 0.00 0.00 4.20
2778 3010 1.535896 GCTTTGGTTCGTTTCTCTCCC 59.464 52.381 0.00 0.00 0.00 4.30
2779 3011 2.218603 TGCTTTGGTTCGTTTCTCTCC 58.781 47.619 0.00 0.00 0.00 3.71
2780 3012 3.963383 TTGCTTTGGTTCGTTTCTCTC 57.037 42.857 0.00 0.00 0.00 3.20
2781 3013 4.137543 AGATTGCTTTGGTTCGTTTCTCT 58.862 39.130 0.00 0.00 0.00 3.10
2782 3014 4.214332 AGAGATTGCTTTGGTTCGTTTCTC 59.786 41.667 0.00 0.00 0.00 2.87
2783 3015 4.137543 AGAGATTGCTTTGGTTCGTTTCT 58.862 39.130 0.00 0.00 0.00 2.52
2784 3016 4.214332 AGAGAGATTGCTTTGGTTCGTTTC 59.786 41.667 0.00 0.00 0.00 2.78
2785 3017 4.137543 AGAGAGATTGCTTTGGTTCGTTT 58.862 39.130 0.00 0.00 0.00 3.60
2786 3018 3.744660 AGAGAGATTGCTTTGGTTCGTT 58.255 40.909 0.00 0.00 0.00 3.85
2787 3019 3.007398 AGAGAGAGATTGCTTTGGTTCGT 59.993 43.478 0.00 0.00 0.00 3.85
2788 3020 3.594134 AGAGAGAGATTGCTTTGGTTCG 58.406 45.455 0.00 0.00 0.00 3.95
2789 3021 4.831107 AGAGAGAGAGATTGCTTTGGTTC 58.169 43.478 0.00 0.00 0.00 3.62
2790 3022 4.531732 AGAGAGAGAGAGATTGCTTTGGTT 59.468 41.667 0.00 0.00 0.00 3.67
2791 3023 4.095946 AGAGAGAGAGAGATTGCTTTGGT 58.904 43.478 0.00 0.00 0.00 3.67
2792 3024 4.403432 AGAGAGAGAGAGAGATTGCTTTGG 59.597 45.833 0.00 0.00 0.00 3.28
2793 3025 5.359009 AGAGAGAGAGAGAGAGATTGCTTTG 59.641 44.000 0.00 0.00 0.00 2.77
2794 3026 5.513233 AGAGAGAGAGAGAGAGATTGCTTT 58.487 41.667 0.00 0.00 0.00 3.51
2795 3027 5.121380 AGAGAGAGAGAGAGAGATTGCTT 57.879 43.478 0.00 0.00 0.00 3.91
2796 3028 4.164796 TGAGAGAGAGAGAGAGAGATTGCT 59.835 45.833 0.00 0.00 0.00 3.91
2797 3029 4.454678 TGAGAGAGAGAGAGAGAGATTGC 58.545 47.826 0.00 0.00 0.00 3.56
2798 3030 8.727910 CATAATGAGAGAGAGAGAGAGAGATTG 58.272 40.741 0.00 0.00 0.00 2.67
2799 3031 7.886970 CCATAATGAGAGAGAGAGAGAGAGATT 59.113 40.741 0.00 0.00 0.00 2.40
2800 3032 7.238305 TCCATAATGAGAGAGAGAGAGAGAGAT 59.762 40.741 0.00 0.00 0.00 2.75
2801 3033 6.558394 TCCATAATGAGAGAGAGAGAGAGAGA 59.442 42.308 0.00 0.00 0.00 3.10
2802 3034 6.772605 TCCATAATGAGAGAGAGAGAGAGAG 58.227 44.000 0.00 0.00 0.00 3.20
2803 3035 6.762077 TCCATAATGAGAGAGAGAGAGAGA 57.238 41.667 0.00 0.00 0.00 3.10
2804 3036 8.324306 AGTATCCATAATGAGAGAGAGAGAGAG 58.676 40.741 0.00 0.00 0.00 3.20
2805 3037 8.102676 CAGTATCCATAATGAGAGAGAGAGAGA 58.897 40.741 0.00 0.00 30.46 3.10
2806 3038 7.148188 GCAGTATCCATAATGAGAGAGAGAGAG 60.148 44.444 0.00 0.00 30.46 3.20
2807 3039 6.658816 GCAGTATCCATAATGAGAGAGAGAGA 59.341 42.308 0.00 0.00 30.46 3.10
2808 3040 6.660521 AGCAGTATCCATAATGAGAGAGAGAG 59.339 42.308 0.00 0.00 30.46 3.20
2809 3041 6.551085 AGCAGTATCCATAATGAGAGAGAGA 58.449 40.000 0.00 0.00 30.46 3.10
2810 3042 6.839124 AGCAGTATCCATAATGAGAGAGAG 57.161 41.667 0.00 0.00 30.46 3.20
2811 3043 7.009550 AGAAGCAGTATCCATAATGAGAGAGA 58.990 38.462 0.00 0.00 30.46 3.10
2812 3044 7.230849 AGAAGCAGTATCCATAATGAGAGAG 57.769 40.000 0.00 0.00 30.46 3.20
2813 3045 7.609097 AAGAAGCAGTATCCATAATGAGAGA 57.391 36.000 0.00 0.00 30.46 3.10
2814 3046 9.941325 ATAAAGAAGCAGTATCCATAATGAGAG 57.059 33.333 0.00 0.00 30.46 3.20
2830 3062 8.262601 TCACTCCATAAGGATATAAAGAAGCA 57.737 34.615 0.00 0.00 44.70 3.91
2882 3114 1.269723 GGTTAAGTGGCAGGCTTTCAC 59.730 52.381 8.46 8.46 0.00 3.18
3175 3408 1.111277 GAAGTGAGCCCTCTCCTCTC 58.889 60.000 0.00 0.00 38.58 3.20
3176 3409 0.325203 GGAAGTGAGCCCTCTCCTCT 60.325 60.000 0.00 0.00 38.58 3.69
3177 3410 0.616111 TGGAAGTGAGCCCTCTCCTC 60.616 60.000 0.00 0.00 38.58 3.71
3178 3411 0.907230 GTGGAAGTGAGCCCTCTCCT 60.907 60.000 0.00 0.00 38.58 3.69
3179 3412 1.599576 GTGGAAGTGAGCCCTCTCC 59.400 63.158 0.00 0.00 38.58 3.71
3180 3413 1.599576 GGTGGAAGTGAGCCCTCTC 59.400 63.158 0.00 0.00 39.78 3.20
3181 3414 2.286523 CGGTGGAAGTGAGCCCTCT 61.287 63.158 0.00 0.00 0.00 3.69
3182 3415 2.266055 CGGTGGAAGTGAGCCCTC 59.734 66.667 0.00 0.00 0.00 4.30
3183 3416 2.203788 TCGGTGGAAGTGAGCCCT 60.204 61.111 0.00 0.00 0.00 5.19
3184 3417 2.047179 GTCGGTGGAAGTGAGCCC 60.047 66.667 0.00 0.00 0.00 5.19
3185 3418 2.047179 GGTCGGTGGAAGTGAGCC 60.047 66.667 0.00 0.00 0.00 4.70
3244 6982 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
3256 6994 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
3314 7052 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
3315 7053 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
3316 7054 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
3317 7055 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
3318 7056 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
3319 7057 7.554835 TGTTTCCGGTTAATACAATTCTAGCAT 59.445 33.333 0.00 0.00 0.00 3.79
3320 7058 6.879993 TGTTTCCGGTTAATACAATTCTAGCA 59.120 34.615 0.00 0.00 0.00 3.49
3321 7059 7.311364 TGTTTCCGGTTAATACAATTCTAGC 57.689 36.000 0.00 0.00 0.00 3.42
3322 7060 9.104965 TCATGTTTCCGGTTAATACAATTCTAG 57.895 33.333 0.00 0.00 0.00 2.43
3323 7061 9.621629 ATCATGTTTCCGGTTAATACAATTCTA 57.378 29.630 0.00 0.00 0.00 2.10
3324 7062 7.931578 TCATGTTTCCGGTTAATACAATTCT 57.068 32.000 0.00 0.00 0.00 2.40
3325 7063 9.659830 GTATCATGTTTCCGGTTAATACAATTC 57.340 33.333 0.00 0.00 0.00 2.17
3326 7064 9.179909 TGTATCATGTTTCCGGTTAATACAATT 57.820 29.630 0.00 0.00 0.00 2.32
3327 7065 8.740123 TGTATCATGTTTCCGGTTAATACAAT 57.260 30.769 0.00 0.00 0.00 2.71
3328 7066 8.616942 CATGTATCATGTTTCCGGTTAATACAA 58.383 33.333 0.00 0.00 33.52 2.41
3329 7067 7.771361 ACATGTATCATGTTTCCGGTTAATACA 59.229 33.333 0.00 7.97 34.10 2.29
3330 7068 8.067784 CACATGTATCATGTTTCCGGTTAATAC 58.932 37.037 11.89 2.60 0.00 1.89
3331 7069 7.771361 ACACATGTATCATGTTTCCGGTTAATA 59.229 33.333 11.89 0.00 0.00 0.98
3332 7070 6.601613 ACACATGTATCATGTTTCCGGTTAAT 59.398 34.615 11.89 0.00 0.00 1.40
3333 7071 5.941058 ACACATGTATCATGTTTCCGGTTAA 59.059 36.000 11.89 0.00 0.00 2.01
3334 7072 5.352846 CACACATGTATCATGTTTCCGGTTA 59.647 40.000 11.89 0.00 0.00 2.85
3335 7073 4.155826 CACACATGTATCATGTTTCCGGTT 59.844 41.667 11.89 0.00 0.00 4.44
3336 7074 3.689161 CACACATGTATCATGTTTCCGGT 59.311 43.478 11.89 5.17 0.00 5.28
3337 7075 3.938334 TCACACATGTATCATGTTTCCGG 59.062 43.478 11.89 0.00 0.00 5.14
3338 7076 5.544136 TTCACACATGTATCATGTTTCCG 57.456 39.130 11.89 4.94 0.00 4.30
3339 7077 7.984391 TGTATTCACACATGTATCATGTTTCC 58.016 34.615 11.89 0.00 0.00 3.13
3343 7081 9.481340 GTCTATGTATTCACACATGTATCATGT 57.519 33.333 9.21 9.21 39.46 3.21
3344 7082 9.480053 TGTCTATGTATTCACACATGTATCATG 57.520 33.333 0.00 7.99 39.46 3.07
3346 7084 9.883142 TTTGTCTATGTATTCACACATGTATCA 57.117 29.630 0.00 0.00 39.46 2.15
3348 7086 9.665719 TGTTTGTCTATGTATTCACACATGTAT 57.334 29.630 0.00 0.00 39.46 2.29
3349 7087 9.665719 ATGTTTGTCTATGTATTCACACATGTA 57.334 29.630 0.00 0.00 39.46 2.29
3350 7088 7.977789 TGTTTGTCTATGTATTCACACATGT 57.022 32.000 0.00 0.00 39.46 3.21
3352 7090 9.890629 ACTATGTTTGTCTATGTATTCACACAT 57.109 29.630 0.00 0.00 41.88 3.21
3353 7091 9.150348 CACTATGTTTGTCTATGTATTCACACA 57.850 33.333 0.00 0.00 37.54 3.72


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

AutoCloner maintained by Alex Coulton.