Multiple sequence alignment - TraesCS4D01G204100

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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 TraesCS4D01G204100 chr4D 100.000 3697 0 0 1 3697 351470890 351467194 0.000000e+00 6828
1 TraesCS4D01G204100 chr4A 94.076 1418 63 9 1817 3224 113851512 113852918 0.000000e+00 2134
2 TraesCS4D01G204100 chr4A 87.961 1030 49 19 699 1671 113850501 113851512 0.000000e+00 1146
3 TraesCS4D01G204100 chr4A 92.553 470 19 3 3244 3697 113853031 113853500 0.000000e+00 660
4 TraesCS4D01G204100 chr4A 88.539 349 23 7 2879 3216 120453618 120453276 1.240000e-109 407
5 TraesCS4D01G204100 chr4A 96.815 157 5 0 3240 3396 120413660 120413504 2.830000e-66 263
6 TraesCS4D01G204100 chr4A 83.688 141 19 3 1674 1813 84537358 84537495 3.000000e-26 130
7 TraesCS4D01G204100 chr4B 94.557 1378 53 11 1857 3224 434471746 434470381 0.000000e+00 2109
8 TraesCS4D01G204100 chr4B 89.222 835 41 15 819 1606 434472836 434472004 0.000000e+00 998
9 TraesCS4D01G204100 chr4B 93.407 455 10 3 3244 3685 434470265 434469818 0.000000e+00 656
10 TraesCS4D01G204100 chr4B 93.421 76 4 1 1596 1671 434471921 434471847 1.090000e-20 111
11 TraesCS4D01G204100 chr4B 89.888 89 5 2 699 787 434472896 434472812 1.090000e-20 111
12 TraesCS4D01G204100 chr2B 90.308 681 64 2 1 681 722024132 722024810 0.000000e+00 891
13 TraesCS4D01G204100 chr2B 89.831 354 30 6 340 693 517374531 517374878 2.020000e-122 449
14 TraesCS4D01G204100 chr2D 90.047 633 62 1 1 633 594532945 594533576 0.000000e+00 819
15 TraesCS4D01G204100 chr2D 87.407 135 10 6 1683 1813 133769421 133769552 8.270000e-32 148
16 TraesCS4D01G204100 chr2D 83.582 134 14 8 1684 1813 627964982 627964853 6.490000e-23 119
17 TraesCS4D01G204100 chr5B 87.243 682 84 3 1 681 655412472 655413151 0.000000e+00 774
18 TraesCS4D01G204100 chr5B 81.379 145 17 8 1674 1813 70557887 70557748 3.900000e-20 110
19 TraesCS4D01G204100 chr3A 86.087 690 91 4 1 689 657383427 657384112 0.000000e+00 737
20 TraesCS4D01G204100 chr5A 83.994 681 105 4 1 681 553332468 553333144 0.000000e+00 651
21 TraesCS4D01G204100 chr7B 88.732 213 21 3 470 681 105503486 105503276 1.320000e-64 257
22 TraesCS4D01G204100 chr7B 86.567 134 7 7 1683 1816 48465615 48465493 1.790000e-28 137
23 TraesCS4D01G204100 chr3D 75.378 463 113 1 1 463 170184821 170185282 4.810000e-54 222
24 TraesCS4D01G204100 chr7A 86.567 134 7 7 1683 1816 97882768 97882646 1.790000e-28 137
25 TraesCS4D01G204100 chr5D 83.333 156 12 11 1669 1813 233044599 233044447 8.330000e-27 132
26 TraesCS4D01G204100 chr7D 82.209 163 15 10 1661 1813 34756855 34757013 1.080000e-25 128
27 TraesCS4D01G204100 chr1D 81.548 168 18 9 1656 1813 341037505 341037341 3.880000e-25 126
28 TraesCS4D01G204100 chr6B 81.022 137 17 6 1686 1813 50125664 50125528 2.350000e-17 100


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 TraesCS4D01G204100 chr4D 351467194 351470890 3696 True 6828.000000 6828 100.000 1 3697 1 chr4D.!!$R1 3696
1 TraesCS4D01G204100 chr4A 113850501 113853500 2999 False 1313.333333 2134 91.530 699 3697 3 chr4A.!!$F2 2998
2 TraesCS4D01G204100 chr4B 434469818 434472896 3078 True 797.000000 2109 92.099 699 3685 5 chr4B.!!$R1 2986
3 TraesCS4D01G204100 chr2B 722024132 722024810 678 False 891.000000 891 90.308 1 681 1 chr2B.!!$F2 680
4 TraesCS4D01G204100 chr2D 594532945 594533576 631 False 819.000000 819 90.047 1 633 1 chr2D.!!$F2 632
5 TraesCS4D01G204100 chr5B 655412472 655413151 679 False 774.000000 774 87.243 1 681 1 chr5B.!!$F1 680
6 TraesCS4D01G204100 chr3A 657383427 657384112 685 False 737.000000 737 86.087 1 689 1 chr3A.!!$F1 688
7 TraesCS4D01G204100 chr5A 553332468 553333144 676 False 651.000000 651 83.994 1 681 1 chr5A.!!$F1 680

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
713 714 0.035458 CCCTTCTGAAACTCGCACCT 59.965 55.0 0.00 0.00 0.0 4.00 F
1507 1562 0.042967 GGTCGCGCGATGAAAGAATC 60.043 55.0 37.03 18.95 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2609 2829 0.103208 CCTCTAGGTGGTCATCGTGC 59.897 60.0 0.0 0.0 0.0 5.34 R
3010 3234 0.253327 GAGGCCCCGAGTTCTGAATT 59.747 55.0 0.0 0.0 0.0 2.17 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
118 119 1.202818 AGCTGAACTGTGGAGGGTTTC 60.203 52.381 0.00 0.00 0.00 2.78
129 130 2.176798 TGGAGGGTTTCACAAGTCCATT 59.823 45.455 0.00 0.00 0.00 3.16
166 167 1.153449 CGCATCGCCCCTAAAGTGA 60.153 57.895 0.00 0.00 0.00 3.41
193 194 0.322997 CGTCCTGGGTGACTCTCTCT 60.323 60.000 0.00 0.00 32.97 3.10
235 236 0.250597 GGGCGGTGTAAAGGTTGTCT 60.251 55.000 0.00 0.00 0.00 3.41
259 260 6.916360 TCCAATGGCTTGAATTTTACTTCT 57.084 33.333 0.00 0.00 34.04 2.85
448 449 3.618351 CATCAGCTTTTCCACATCCTCT 58.382 45.455 0.00 0.00 0.00 3.69
521 522 4.226394 TCCTGAACCCTATTCCGATGAAAA 59.774 41.667 0.00 0.00 33.32 2.29
535 536 1.559368 TGAAAACCGATCGGACCCTA 58.441 50.000 39.55 19.33 38.96 3.53
572 573 3.148279 CCGCCGTCCTAGCCTCTT 61.148 66.667 0.00 0.00 0.00 2.85
580 581 1.477295 GTCCTAGCCTCTTTAGTGCGT 59.523 52.381 0.00 0.00 0.00 5.24
602 603 1.228124 CACGGGTCAAGGAAGGCAA 60.228 57.895 0.00 0.00 0.00 4.52
616 617 0.838987 AGGCAAAACGGAGGTAGGGA 60.839 55.000 0.00 0.00 0.00 4.20
688 689 3.808834 CCTAACAAGAGGGGGAAAACT 57.191 47.619 0.00 0.00 32.39 2.66
689 690 4.921644 CCTAACAAGAGGGGGAAAACTA 57.078 45.455 0.00 0.00 32.39 2.24
690 691 5.452341 CCTAACAAGAGGGGGAAAACTAT 57.548 43.478 0.00 0.00 32.39 2.12
691 692 5.193679 CCTAACAAGAGGGGGAAAACTATG 58.806 45.833 0.00 0.00 32.39 2.23
692 693 4.741928 AACAAGAGGGGGAAAACTATGT 57.258 40.909 0.00 0.00 0.00 2.29
693 694 4.034285 ACAAGAGGGGGAAAACTATGTG 57.966 45.455 0.00 0.00 0.00 3.21
694 695 2.755103 CAAGAGGGGGAAAACTATGTGC 59.245 50.000 0.00 0.00 0.00 4.57
695 696 1.285078 AGAGGGGGAAAACTATGTGCC 59.715 52.381 0.00 0.00 0.00 5.01
696 697 0.335019 AGGGGGAAAACTATGTGCCC 59.665 55.000 0.00 0.00 44.46 5.36
697 698 0.335019 GGGGGAAAACTATGTGCCCT 59.665 55.000 0.00 0.00 44.58 5.19
713 714 0.035458 CCCTTCTGAAACTCGCACCT 59.965 55.000 0.00 0.00 0.00 4.00
754 755 2.266055 CCGGTCAGAGAACCCTGC 59.734 66.667 0.00 0.00 35.79 4.85
755 756 2.266055 CGGTCAGAGAACCCTGCC 59.734 66.667 0.00 0.00 35.79 4.85
756 757 2.286523 CGGTCAGAGAACCCTGCCT 61.287 63.158 0.00 0.00 35.79 4.75
757 758 1.298014 GGTCAGAGAACCCTGCCTG 59.702 63.158 0.00 0.00 34.28 4.85
762 763 0.617249 AGAGAACCCTGCCTGAGAGG 60.617 60.000 0.00 0.00 38.80 3.69
782 783 4.641645 CGCACAAGTCCCAGCCCA 62.642 66.667 0.00 0.00 0.00 5.36
787 788 1.383799 CAAGTCCCAGCCCAATCCA 59.616 57.895 0.00 0.00 0.00 3.41
788 789 0.682209 CAAGTCCCAGCCCAATCCAG 60.682 60.000 0.00 0.00 0.00 3.86
789 790 0.846427 AAGTCCCAGCCCAATCCAGA 60.846 55.000 0.00 0.00 0.00 3.86
790 791 1.225704 GTCCCAGCCCAATCCAGAG 59.774 63.158 0.00 0.00 0.00 3.35
791 792 1.229951 TCCCAGCCCAATCCAGAGT 60.230 57.895 0.00 0.00 0.00 3.24
792 793 1.225704 CCCAGCCCAATCCAGAGTC 59.774 63.158 0.00 0.00 0.00 3.36
793 794 1.225704 CCAGCCCAATCCAGAGTCC 59.774 63.158 0.00 0.00 0.00 3.85
810 811 1.111116 TCCAGACACGGAACCGAACT 61.111 55.000 20.14 11.80 42.83 3.01
821 822 0.535102 AACCGAACTGAGCCCAACTG 60.535 55.000 0.00 0.00 0.00 3.16
843 844 4.779733 AGTCCCAGCCCGATCCGT 62.780 66.667 0.00 0.00 0.00 4.69
959 980 3.665675 GACCGCATCGCCTTCCACT 62.666 63.158 0.00 0.00 0.00 4.00
1316 1361 4.996122 CAGGGAATTTGCATTTTGTTAGCA 59.004 37.500 0.00 0.00 36.32 3.49
1340 1385 8.606040 CAAGGATTGTGAAATTGGTATGTTTT 57.394 30.769 0.00 0.00 42.34 2.43
1352 1397 2.677836 GGTATGTTTTCGCTCAGATGCA 59.322 45.455 0.00 0.00 0.00 3.96
1368 1413 1.517039 GCAGTGCGGGCTTAAATGC 60.517 57.895 0.00 0.00 0.00 3.56
1411 1464 1.971695 GGTTCCTCGGCTTGTTGGG 60.972 63.158 0.00 0.00 0.00 4.12
1412 1465 1.971695 GTTCCTCGGCTTGTTGGGG 60.972 63.158 0.00 0.00 0.00 4.96
1416 1469 0.958876 CCTCGGCTTGTTGGGGTTAC 60.959 60.000 0.00 0.00 0.00 2.50
1442 1495 2.671070 GCTTGCCATTTTCCTTGGTACG 60.671 50.000 0.00 0.00 36.57 3.67
1453 1506 2.758979 TCCTTGGTACGATGAGAACTCC 59.241 50.000 0.00 0.00 0.00 3.85
1465 1518 1.732809 GAGAACTCCTTTTAGCACGGC 59.267 52.381 0.00 0.00 0.00 5.68
1507 1562 0.042967 GGTCGCGCGATGAAAGAATC 60.043 55.000 37.03 18.95 0.00 2.52
1513 1568 2.544685 CGCGATGAAAGAATCTGAGGT 58.455 47.619 0.00 0.00 0.00 3.85
1553 1609 1.185315 GGATGGGTGTTTGTCATGGG 58.815 55.000 0.00 0.00 0.00 4.00
1583 1639 4.554960 TTGGATCGGTGGTGTTATGTTA 57.445 40.909 0.00 0.00 0.00 2.41
1585 1641 3.200483 GGATCGGTGGTGTTATGTTACC 58.800 50.000 0.00 0.00 37.48 2.85
1593 1649 6.101997 GGTGGTGTTATGTTACCAGTACTAC 58.898 44.000 0.00 0.00 46.87 2.73
1630 1781 6.261826 CGAGCTTATCCCTGAATTTCAAGATT 59.738 38.462 13.77 1.01 0.00 2.40
1634 1785 9.521503 GCTTATCCCTGAATTTCAAGATTAAAC 57.478 33.333 13.77 3.10 0.00 2.01
1636 1787 6.509418 TCCCTGAATTTCAAGATTAAACGG 57.491 37.500 0.01 0.00 0.00 4.44
1667 1818 9.202273 GCTTCATCATTGGATTTCTACTAGTAG 57.798 37.037 21.87 21.87 34.56 2.57
1677 1828 9.352191 TGGATTTCTACTAGTAGTATGAACTCC 57.648 37.037 26.91 26.91 37.67 3.85
1678 1829 9.577222 GGATTTCTACTAGTAGTATGAACTCCT 57.423 37.037 26.69 14.23 36.37 3.69
1681 1832 8.659925 TTCTACTAGTAGTATGAACTCCTTCG 57.340 38.462 25.58 0.00 37.15 3.79
1682 1833 7.215789 TCTACTAGTAGTATGAACTCCTTCGG 58.784 42.308 25.58 0.00 37.15 4.30
1683 1834 5.753716 ACTAGTAGTATGAACTCCTTCGGT 58.246 41.667 0.00 0.00 37.15 4.69
1684 1835 6.186234 ACTAGTAGTATGAACTCCTTCGGTT 58.814 40.000 0.00 0.00 37.15 4.44
1685 1836 5.579564 AGTAGTATGAACTCCTTCGGTTC 57.420 43.478 0.00 0.00 42.17 3.62
1689 1840 2.992124 TGAACTCCTTCGGTTCACAA 57.008 45.000 5.35 0.00 45.14 3.33
1690 1841 3.269538 TGAACTCCTTCGGTTCACAAA 57.730 42.857 5.35 0.00 45.14 2.83
1691 1842 3.815809 TGAACTCCTTCGGTTCACAAAT 58.184 40.909 5.35 0.00 45.14 2.32
1692 1843 4.963373 TGAACTCCTTCGGTTCACAAATA 58.037 39.130 5.35 0.00 45.14 1.40
1693 1844 5.556915 TGAACTCCTTCGGTTCACAAATAT 58.443 37.500 5.35 0.00 45.14 1.28
1694 1845 6.703319 TGAACTCCTTCGGTTCACAAATATA 58.297 36.000 5.35 0.00 45.14 0.86
1695 1846 7.162761 TGAACTCCTTCGGTTCACAAATATAA 58.837 34.615 5.35 0.00 45.14 0.98
1696 1847 7.333423 TGAACTCCTTCGGTTCACAAATATAAG 59.667 37.037 5.35 0.00 45.14 1.73
1697 1848 6.708285 ACTCCTTCGGTTCACAAATATAAGT 58.292 36.000 0.00 0.00 0.00 2.24
1698 1849 7.166167 ACTCCTTCGGTTCACAAATATAAGTT 58.834 34.615 0.00 0.00 0.00 2.66
1699 1850 7.119262 ACTCCTTCGGTTCACAAATATAAGTTG 59.881 37.037 0.00 0.00 0.00 3.16
1700 1851 6.938030 TCCTTCGGTTCACAAATATAAGTTGT 59.062 34.615 0.48 0.48 39.79 3.32
1701 1852 7.446013 TCCTTCGGTTCACAAATATAAGTTGTT 59.554 33.333 3.11 0.00 37.09 2.83
1702 1853 8.079809 CCTTCGGTTCACAAATATAAGTTGTTT 58.920 33.333 3.11 0.00 37.09 2.83
1703 1854 9.458374 CTTCGGTTCACAAATATAAGTTGTTTT 57.542 29.630 3.11 0.00 37.09 2.43
1704 1855 8.789881 TCGGTTCACAAATATAAGTTGTTTTG 57.210 30.769 3.11 0.00 37.09 2.44
1705 1856 7.863375 TCGGTTCACAAATATAAGTTGTTTTGG 59.137 33.333 3.11 0.00 37.09 3.28
1706 1857 7.863375 CGGTTCACAAATATAAGTTGTTTTGGA 59.137 33.333 3.11 0.00 37.09 3.53
1707 1858 9.705290 GGTTCACAAATATAAGTTGTTTTGGAT 57.295 29.630 3.11 0.00 37.09 3.41
1738 1889 8.645814 ATTAATATGGACTACATACGGACTGA 57.354 34.615 0.00 0.00 44.41 3.41
1739 1890 6.971726 AATATGGACTACATACGGACTGAA 57.028 37.500 0.00 0.00 44.41 3.02
1740 1891 6.971726 ATATGGACTACATACGGACTGAAA 57.028 37.500 0.00 0.00 44.41 2.69
1741 1892 5.871396 ATGGACTACATACGGACTGAAAT 57.129 39.130 0.00 0.00 38.26 2.17
1742 1893 5.006153 TGGACTACATACGGACTGAAATG 57.994 43.478 0.00 0.00 0.00 2.32
1743 1894 4.707934 TGGACTACATACGGACTGAAATGA 59.292 41.667 7.93 0.00 0.00 2.57
1744 1895 5.163550 TGGACTACATACGGACTGAAATGAG 60.164 44.000 7.93 4.83 0.00 2.90
1745 1896 5.163540 GGACTACATACGGACTGAAATGAGT 60.164 44.000 7.93 7.04 0.00 3.41
1746 1897 5.651530 ACTACATACGGACTGAAATGAGTG 58.348 41.667 7.93 0.00 0.00 3.51
1747 1898 4.801330 ACATACGGACTGAAATGAGTGA 57.199 40.909 7.93 0.00 0.00 3.41
1748 1899 5.147330 ACATACGGACTGAAATGAGTGAA 57.853 39.130 7.93 0.00 0.00 3.18
1749 1900 4.929808 ACATACGGACTGAAATGAGTGAAC 59.070 41.667 7.93 0.00 0.00 3.18
1750 1901 3.469008 ACGGACTGAAATGAGTGAACA 57.531 42.857 0.00 0.00 0.00 3.18
1751 1902 3.804036 ACGGACTGAAATGAGTGAACAA 58.196 40.909 0.00 0.00 0.00 2.83
1752 1903 4.196193 ACGGACTGAAATGAGTGAACAAA 58.804 39.130 0.00 0.00 0.00 2.83
1753 1904 4.035208 ACGGACTGAAATGAGTGAACAAAC 59.965 41.667 0.00 0.00 0.00 2.93
1754 1905 4.035091 CGGACTGAAATGAGTGAACAAACA 59.965 41.667 0.00 0.00 0.00 2.83
1755 1906 5.273944 GGACTGAAATGAGTGAACAAACAC 58.726 41.667 0.00 0.00 40.60 3.32
1756 1907 5.163663 GGACTGAAATGAGTGAACAAACACA 60.164 40.000 0.00 0.00 42.45 3.72
1757 1908 5.640732 ACTGAAATGAGTGAACAAACACAC 58.359 37.500 0.00 0.00 42.45 3.82
1759 1910 6.597672 ACTGAAATGAGTGAACAAACACACTA 59.402 34.615 0.00 0.00 45.54 2.74
1760 1911 7.120579 ACTGAAATGAGTGAACAAACACACTAA 59.879 33.333 0.00 0.00 45.54 2.24
1761 1912 7.821652 TGAAATGAGTGAACAAACACACTAAA 58.178 30.769 0.00 0.00 45.54 1.85
1762 1913 7.967854 TGAAATGAGTGAACAAACACACTAAAG 59.032 33.333 0.00 0.00 45.54 1.85
1763 1914 5.229921 TGAGTGAACAAACACACTAAAGC 57.770 39.130 0.00 0.00 45.54 3.51
1764 1915 4.941263 TGAGTGAACAAACACACTAAAGCT 59.059 37.500 0.00 0.00 45.54 3.74
1765 1916 5.414454 TGAGTGAACAAACACACTAAAGCTT 59.586 36.000 0.00 0.00 45.54 3.74
1766 1917 5.880341 AGTGAACAAACACACTAAAGCTTC 58.120 37.500 0.00 0.00 44.06 3.86
1767 1918 4.728608 GTGAACAAACACACTAAAGCTTCG 59.271 41.667 0.00 0.00 40.11 3.79
1768 1919 4.632251 TGAACAAACACACTAAAGCTTCGA 59.368 37.500 0.00 0.00 0.00 3.71
1769 1920 5.295787 TGAACAAACACACTAAAGCTTCGAT 59.704 36.000 0.00 0.00 0.00 3.59
1770 1921 5.751243 ACAAACACACTAAAGCTTCGATT 57.249 34.783 0.00 0.00 0.00 3.34
1771 1922 5.748592 ACAAACACACTAAAGCTTCGATTC 58.251 37.500 0.00 0.00 0.00 2.52
1772 1923 5.295787 ACAAACACACTAAAGCTTCGATTCA 59.704 36.000 0.00 0.00 0.00 2.57
1773 1924 5.597813 AACACACTAAAGCTTCGATTCAG 57.402 39.130 0.00 0.00 0.00 3.02
1774 1925 4.883083 ACACACTAAAGCTTCGATTCAGA 58.117 39.130 0.00 0.00 0.00 3.27
1775 1926 5.297547 ACACACTAAAGCTTCGATTCAGAA 58.702 37.500 0.00 0.00 0.00 3.02
1776 1927 5.758296 ACACACTAAAGCTTCGATTCAGAAA 59.242 36.000 0.00 0.00 0.00 2.52
1777 1928 6.260050 ACACACTAAAGCTTCGATTCAGAAAA 59.740 34.615 0.00 0.00 0.00 2.29
1778 1929 7.132213 CACACTAAAGCTTCGATTCAGAAAAA 58.868 34.615 0.00 0.00 0.00 1.94
1809 1960 9.864034 GTTAGAACATCATATATTTGTGAACGG 57.136 33.333 0.03 0.00 0.00 4.44
1810 1961 9.825109 TTAGAACATCATATATTTGTGAACGGA 57.175 29.630 0.03 0.00 0.00 4.69
1811 1962 8.370493 AGAACATCATATATTTGTGAACGGAG 57.630 34.615 0.03 0.00 0.00 4.63
1812 1963 7.442364 AGAACATCATATATTTGTGAACGGAGG 59.558 37.037 0.03 0.00 0.00 4.30
1813 1964 6.826668 ACATCATATATTTGTGAACGGAGGA 58.173 36.000 0.00 0.00 0.00 3.71
1814 1965 6.931281 ACATCATATATTTGTGAACGGAGGAG 59.069 38.462 0.00 0.00 0.00 3.69
1815 1966 5.853936 TCATATATTTGTGAACGGAGGAGG 58.146 41.667 0.00 0.00 0.00 4.30
1824 1992 4.159135 TGTGAACGGAGGAGGTAGTAAATC 59.841 45.833 0.00 0.00 0.00 2.17
1829 1997 5.703310 ACGGAGGAGGTAGTAAATCAGTAT 58.297 41.667 0.00 0.00 0.00 2.12
1844 2012 9.754382 GTAAATCAGTATAGTTTCGGTATCCAA 57.246 33.333 0.00 0.00 0.00 3.53
1851 2019 9.193806 AGTATAGTTTCGGTATCCAAAAGACTA 57.806 33.333 0.00 0.00 0.00 2.59
1852 2020 9.242477 GTATAGTTTCGGTATCCAAAAGACTAC 57.758 37.037 0.00 0.00 0.00 2.73
1854 2022 5.047802 AGTTTCGGTATCCAAAAGACTACGA 60.048 40.000 0.00 0.00 0.00 3.43
1855 2023 4.361451 TCGGTATCCAAAAGACTACGAC 57.639 45.455 0.00 0.00 0.00 4.34
1865 2077 3.393426 AAGACTACGACCTTCCCCATA 57.607 47.619 0.00 0.00 0.00 2.74
1866 2078 3.614568 AGACTACGACCTTCCCCATAT 57.385 47.619 0.00 0.00 0.00 1.78
1968 2180 7.803279 ATTGCTATAGTTGCCCTTAAGTTAC 57.197 36.000 0.97 0.00 0.00 2.50
1971 2183 5.990386 GCTATAGTTGCCCTTAAGTTACCTC 59.010 44.000 0.97 0.00 0.00 3.85
1987 2203 5.897250 AGTTACCTCCTTGTTCAACCAAATT 59.103 36.000 0.00 0.00 0.00 1.82
2003 2223 6.212888 ACCAAATTGTATGGATTTCTGAGC 57.787 37.500 1.57 0.00 40.56 4.26
2096 2316 2.036236 GCTGGTGCTGCAAAAGTCT 58.964 52.632 2.77 0.00 36.03 3.24
2138 2358 2.026542 TCAGCAGAATCATGGAGCAGTT 60.027 45.455 0.00 0.00 0.00 3.16
2144 2364 1.002069 ATCATGGAGCAGTTCCCCAA 58.998 50.000 0.00 0.00 46.19 4.12
2159 2379 3.239449 TCCCCAATACTATGATCGCAGT 58.761 45.455 4.61 4.61 0.00 4.40
2429 2649 0.995024 AAAGCTACATCTGCCCCAGT 59.005 50.000 0.00 0.00 32.61 4.00
2462 2682 3.476552 TCTCACAAACACAATGTCCCTC 58.523 45.455 0.00 0.00 0.00 4.30
2517 2737 0.784778 GAAGTGCTCGGACAAGTTCG 59.215 55.000 0.00 0.00 0.00 3.95
2548 2768 5.500234 AGATAAGGTCTGCTTAATGTGCAA 58.500 37.500 0.00 0.00 40.13 4.08
2603 2823 2.442126 AGAGAAAGGAGGAACGGGTTTT 59.558 45.455 0.00 0.00 0.00 2.43
2609 2829 4.693525 GGAACGGGTTTTGCCGCG 62.694 66.667 0.00 0.00 38.44 6.46
2630 2850 0.033011 ACGATGACCACCTAGAGGCT 60.033 55.000 0.00 0.00 39.32 4.58
2643 2863 5.046950 CACCTAGAGGCTAAGAACTTCAAGT 60.047 44.000 0.00 0.00 39.32 3.16
2692 2912 0.905357 GTGAAGCCTGCTCCTAAGGA 59.095 55.000 0.00 0.00 36.91 3.36
2741 2961 7.262048 TGTTGTATAATGCTGTCAGTTATCGA 58.738 34.615 0.93 0.00 0.00 3.59
2742 2962 7.222031 TGTTGTATAATGCTGTCAGTTATCGAC 59.778 37.037 0.93 4.70 0.00 4.20
2743 2963 7.039313 TGTATAATGCTGTCAGTTATCGACT 57.961 36.000 0.93 0.00 39.89 4.18
2744 2964 7.489160 TGTATAATGCTGTCAGTTATCGACTT 58.511 34.615 0.93 0.00 36.10 3.01
2745 2965 8.626526 TGTATAATGCTGTCAGTTATCGACTTA 58.373 33.333 0.93 0.00 36.10 2.24
2746 2966 9.627395 GTATAATGCTGTCAGTTATCGACTTAT 57.373 33.333 0.93 0.00 36.10 1.73
2747 2967 8.749841 ATAATGCTGTCAGTTATCGACTTATC 57.250 34.615 0.93 0.00 36.10 1.75
2862 3083 3.419943 TCCAAGTGATAATGTGCTTGCA 58.580 40.909 0.00 0.00 37.56 4.08
2886 3107 3.371102 TTGCTCCGATGCAGTATCTAC 57.629 47.619 0.00 0.00 44.27 2.59
2907 3128 1.269448 GGATTTCTTTGGCGCTTGACA 59.731 47.619 7.64 0.00 0.00 3.58
2914 3135 0.592637 TTGGCGCTTGACATGTCTTG 59.407 50.000 25.55 18.18 0.00 3.02
2923 3144 3.988379 TGACATGTCTTGCCAGTTTTC 57.012 42.857 25.55 0.00 0.00 2.29
2989 3210 6.757010 TGTAAGAGCAGATATTCGTTTTCCTC 59.243 38.462 0.00 0.00 0.00 3.71
2996 3220 5.231568 CAGATATTCGTTTTCCTCGTACCAC 59.768 44.000 0.00 0.00 0.00 4.16
3006 3230 1.338674 CCTCGTACCACCATGCTTTGA 60.339 52.381 0.00 0.00 0.00 2.69
3010 3234 2.746904 CGTACCACCATGCTTTGATCAA 59.253 45.455 3.38 3.38 0.00 2.57
3021 3245 6.530534 CCATGCTTTGATCAAATTCAGAACTC 59.469 38.462 20.76 3.78 0.00 3.01
3045 3269 2.431454 GCCTCTTTGGAACTTCTGGAG 58.569 52.381 0.00 0.00 38.35 3.86
3096 3321 4.337836 GTCCCTAGTGGTAAGCAGTACTAC 59.662 50.000 0.00 6.10 42.88 2.73
3200 3425 9.237187 TCTACAGATTATGTCTCCATCTATGTC 57.763 37.037 0.00 0.00 42.70 3.06
3219 3444 2.865551 GTCGTTAAACCACAGGAAACGA 59.134 45.455 15.86 15.86 46.67 3.85
3239 3493 4.275936 ACGAAGAAAATCACCACAGGAAAG 59.724 41.667 0.00 0.00 0.00 2.62
3240 3494 4.515191 CGAAGAAAATCACCACAGGAAAGA 59.485 41.667 0.00 0.00 0.00 2.52
3241 3495 5.334414 CGAAGAAAATCACCACAGGAAAGAG 60.334 44.000 0.00 0.00 0.00 2.85
3242 3496 4.401925 AGAAAATCACCACAGGAAAGAGG 58.598 43.478 0.00 0.00 0.00 3.69
3347 3668 5.123820 TGAAAAGGATAATGGAAACGCTGAG 59.876 40.000 0.00 0.00 0.00 3.35
3500 3837 3.571401 AGAGCTTGATTTCCAAACAGGTG 59.429 43.478 0.00 0.00 39.02 4.00
3595 3933 0.319986 TGATTGCGCCGAACTGTACA 60.320 50.000 4.18 0.00 0.00 2.90
3604 3942 1.067846 CCGAACTGTACAGCTACTGCA 60.068 52.381 22.90 0.00 42.74 4.41
3625 3963 2.507944 CTGAATGGGGCTCCTCCG 59.492 66.667 3.07 0.00 34.94 4.63
3691 4029 5.140747 AGAGTAATTCTCGTCTGCTGTTT 57.859 39.130 0.00 0.00 46.86 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.340658 CACGACGTTCCAGATCTGTG 58.659 55.000 21.11 12.59 0.00 3.66
118 119 8.837788 TCATCAAGCTATATAATGGACTTGTG 57.162 34.615 0.00 0.00 36.69 3.33
129 130 5.659440 TGCGGTGATCATCAAGCTATATA 57.341 39.130 15.06 0.00 34.68 0.86
193 194 1.266178 TCTCGTGCTTGGGAGATTGA 58.734 50.000 0.00 0.00 34.52 2.57
235 236 7.301868 AGAAGTAAAATTCAAGCCATTGGAA 57.698 32.000 6.95 0.00 37.02 3.53
259 260 2.417257 GGCATGGGATCTTGCGCAA 61.417 57.895 23.48 23.48 42.75 4.85
315 316 4.761739 TGATTAGGGTTCACTCAAGCAAAG 59.238 41.667 0.00 0.00 33.79 2.77
448 449 1.219124 GACGGATCAAGCAGAGGCA 59.781 57.895 0.00 0.00 44.61 4.75
521 522 0.185416 ATCAGTAGGGTCCGATCGGT 59.815 55.000 32.15 16.68 36.47 4.69
535 536 2.197465 GAGGGTTAGGGTTCCATCAGT 58.803 52.381 0.00 0.00 35.06 3.41
580 581 4.243008 TTCCTTGACCCGTGCGCA 62.243 61.111 5.66 5.66 0.00 6.09
602 603 1.274447 CGTCTTTCCCTACCTCCGTTT 59.726 52.381 0.00 0.00 0.00 3.60
616 617 1.226323 CGCCGTCGAGATCGTCTTT 60.226 57.895 1.70 0.00 40.80 2.52
681 682 3.686016 TCAGAAGGGCACATAGTTTTCC 58.314 45.455 0.00 0.00 0.00 3.13
682 683 5.241728 AGTTTCAGAAGGGCACATAGTTTTC 59.758 40.000 0.00 0.00 0.00 2.29
685 686 4.327680 GAGTTTCAGAAGGGCACATAGTT 58.672 43.478 0.00 0.00 0.00 2.24
686 687 3.617531 CGAGTTTCAGAAGGGCACATAGT 60.618 47.826 0.00 0.00 0.00 2.12
687 688 2.932614 CGAGTTTCAGAAGGGCACATAG 59.067 50.000 0.00 0.00 0.00 2.23
688 689 2.935238 GCGAGTTTCAGAAGGGCACATA 60.935 50.000 0.00 0.00 0.00 2.29
689 690 1.813513 CGAGTTTCAGAAGGGCACAT 58.186 50.000 0.00 0.00 0.00 3.21
690 691 0.884704 GCGAGTTTCAGAAGGGCACA 60.885 55.000 0.00 0.00 0.00 4.57
691 692 0.884704 TGCGAGTTTCAGAAGGGCAC 60.885 55.000 0.00 0.00 0.00 5.01
692 693 0.884704 GTGCGAGTTTCAGAAGGGCA 60.885 55.000 0.00 0.00 0.00 5.36
693 694 1.578206 GGTGCGAGTTTCAGAAGGGC 61.578 60.000 0.00 0.00 0.00 5.19
694 695 0.035458 AGGTGCGAGTTTCAGAAGGG 59.965 55.000 0.00 0.00 0.00 3.95
695 696 1.151668 CAGGTGCGAGTTTCAGAAGG 58.848 55.000 0.00 0.00 0.00 3.46
696 697 0.514691 GCAGGTGCGAGTTTCAGAAG 59.485 55.000 0.00 0.00 0.00 2.85
697 698 0.884704 GGCAGGTGCGAGTTTCAGAA 60.885 55.000 0.00 0.00 43.26 3.02
713 714 2.746904 CGTGTCATTTGACTTATGGGCA 59.253 45.455 11.67 0.00 44.99 5.36
754 755 1.447489 CTTGTGCGAGCCTCTCAGG 60.447 63.158 0.00 0.00 38.80 3.86
755 756 0.735632 GACTTGTGCGAGCCTCTCAG 60.736 60.000 0.00 0.00 0.00 3.35
756 757 1.290324 GACTTGTGCGAGCCTCTCA 59.710 57.895 0.00 0.00 0.00 3.27
757 758 1.446966 GGACTTGTGCGAGCCTCTC 60.447 63.158 0.00 0.00 0.00 3.20
762 763 3.426568 GCTGGGACTTGTGCGAGC 61.427 66.667 12.48 12.48 0.00 5.03
782 783 0.898320 CCGTGTCTGGACTCTGGATT 59.102 55.000 2.38 0.00 0.00 3.01
787 788 1.524863 CGGTTCCGTGTCTGGACTCT 61.525 60.000 2.82 0.00 37.89 3.24
788 789 1.080705 CGGTTCCGTGTCTGGACTC 60.081 63.158 2.82 0.00 37.89 3.36
789 790 1.111116 TTCGGTTCCGTGTCTGGACT 61.111 55.000 11.04 0.00 37.89 3.85
790 791 0.942884 GTTCGGTTCCGTGTCTGGAC 60.943 60.000 11.04 0.00 37.89 4.02
791 792 1.111116 AGTTCGGTTCCGTGTCTGGA 61.111 55.000 11.04 0.00 35.83 3.86
792 793 0.944311 CAGTTCGGTTCCGTGTCTGG 60.944 60.000 11.04 0.00 0.00 3.86
793 794 0.031585 TCAGTTCGGTTCCGTGTCTG 59.968 55.000 11.04 15.42 0.00 3.51
810 811 2.115910 CTTGGGCAGTTGGGCTCA 59.884 61.111 0.00 0.00 43.97 4.26
843 844 0.898789 GGTGGAGTGGAGACGAAGGA 60.899 60.000 0.00 0.00 0.00 3.36
1316 1361 7.598493 CGAAAACATACCAATTTCACAATCCTT 59.402 33.333 0.00 0.00 33.68 3.36
1352 1397 3.051392 GCGCATTTAAGCCCGCACT 62.051 57.895 0.30 0.00 45.21 4.40
1368 1413 2.127839 TCCTAGGAGCAGGAATGCG 58.872 57.895 7.62 0.00 41.88 4.73
1411 1464 1.746470 AATGGCAAGCTACGGTAACC 58.254 50.000 0.00 0.00 0.00 2.85
1412 1465 3.427098 GGAAAATGGCAAGCTACGGTAAC 60.427 47.826 0.00 0.00 0.00 2.50
1416 1469 1.463674 AGGAAAATGGCAAGCTACGG 58.536 50.000 0.00 0.00 0.00 4.02
1442 1495 3.619038 CCGTGCTAAAAGGAGTTCTCATC 59.381 47.826 2.24 0.00 0.00 2.92
1453 1506 3.531262 ACTAAAACGCCGTGCTAAAAG 57.469 42.857 0.00 0.00 0.00 2.27
1465 1518 3.112580 CCAGTGCCACAAAACTAAAACG 58.887 45.455 0.00 0.00 0.00 3.60
1507 1562 5.220739 GGATCGAATTTGATTGTCACCTCAG 60.221 44.000 9.62 0.00 0.00 3.35
1513 1568 3.947196 CCCAGGATCGAATTTGATTGTCA 59.053 43.478 9.62 0.00 0.00 3.58
1553 1609 2.073816 CCACCGATCCAAACACTGTAC 58.926 52.381 0.00 0.00 0.00 2.90
1583 1639 7.011857 GCTCGTACAATACTAAGTAGTACTGGT 59.988 40.741 5.39 8.72 39.56 4.00
1585 1641 8.140677 AGCTCGTACAATACTAAGTAGTACTG 57.859 38.462 5.39 5.61 41.18 2.74
1593 1649 7.040617 TCAGGGATAAGCTCGTACAATACTAAG 60.041 40.741 0.00 0.00 0.00 2.18
1605 1756 5.118990 TCTTGAAATTCAGGGATAAGCTCG 58.881 41.667 5.27 0.00 0.00 5.03
1630 1781 4.155826 CCAATGATGAAGCAAGACCGTTTA 59.844 41.667 0.00 0.00 0.00 2.01
1634 1785 2.358957 TCCAATGATGAAGCAAGACCG 58.641 47.619 0.00 0.00 0.00 4.79
1636 1787 6.205101 AGAAATCCAATGATGAAGCAAGAC 57.795 37.500 0.00 0.00 0.00 3.01
1674 1825 7.119262 ACAACTTATATTTGTGAACCGAAGGAG 59.881 37.037 0.00 0.00 43.05 3.69
1675 1826 6.938030 ACAACTTATATTTGTGAACCGAAGGA 59.062 34.615 0.00 0.00 43.05 3.36
1676 1827 7.141100 ACAACTTATATTTGTGAACCGAAGG 57.859 36.000 0.55 0.00 44.86 3.46
1677 1828 9.458374 AAAACAACTTATATTTGTGAACCGAAG 57.542 29.630 1.94 0.00 37.26 3.79
1678 1829 9.239002 CAAAACAACTTATATTTGTGAACCGAA 57.761 29.630 1.94 0.00 37.26 4.30
1679 1830 7.863375 CCAAAACAACTTATATTTGTGAACCGA 59.137 33.333 1.94 0.00 37.26 4.69
1680 1831 7.863375 TCCAAAACAACTTATATTTGTGAACCG 59.137 33.333 1.94 0.00 37.26 4.44
1681 1832 9.705290 ATCCAAAACAACTTATATTTGTGAACC 57.295 29.630 1.94 0.00 37.26 3.62
1712 1863 9.743581 TCAGTCCGTATGTAGTCCATATTAATA 57.256 33.333 0.00 0.00 38.29 0.98
1713 1864 8.645814 TCAGTCCGTATGTAGTCCATATTAAT 57.354 34.615 0.00 0.00 38.29 1.40
1714 1865 8.467963 TTCAGTCCGTATGTAGTCCATATTAA 57.532 34.615 0.00 0.00 38.29 1.40
1715 1866 8.467963 TTTCAGTCCGTATGTAGTCCATATTA 57.532 34.615 0.00 0.00 38.29 0.98
1716 1867 6.971726 TTCAGTCCGTATGTAGTCCATATT 57.028 37.500 0.00 0.00 38.29 1.28
1717 1868 6.971726 TTTCAGTCCGTATGTAGTCCATAT 57.028 37.500 0.00 0.00 38.29 1.78
1718 1869 6.548251 TCATTTCAGTCCGTATGTAGTCCATA 59.452 38.462 0.00 0.00 34.86 2.74
1719 1870 5.362717 TCATTTCAGTCCGTATGTAGTCCAT 59.637 40.000 0.00 0.00 37.58 3.41
1720 1871 4.707934 TCATTTCAGTCCGTATGTAGTCCA 59.292 41.667 0.00 0.00 0.00 4.02
1721 1872 5.163540 ACTCATTTCAGTCCGTATGTAGTCC 60.164 44.000 0.00 0.00 0.00 3.85
1722 1873 5.744345 CACTCATTTCAGTCCGTATGTAGTC 59.256 44.000 0.00 0.00 0.00 2.59
1723 1874 5.417894 TCACTCATTTCAGTCCGTATGTAGT 59.582 40.000 0.00 0.00 0.00 2.73
1724 1875 5.891451 TCACTCATTTCAGTCCGTATGTAG 58.109 41.667 0.00 0.00 0.00 2.74
1725 1876 5.907866 TCACTCATTTCAGTCCGTATGTA 57.092 39.130 0.00 0.00 0.00 2.29
1726 1877 4.801330 TCACTCATTTCAGTCCGTATGT 57.199 40.909 0.00 0.00 0.00 2.29
1727 1878 4.929211 TGTTCACTCATTTCAGTCCGTATG 59.071 41.667 0.00 0.00 0.00 2.39
1728 1879 5.147330 TGTTCACTCATTTCAGTCCGTAT 57.853 39.130 0.00 0.00 0.00 3.06
1729 1880 4.594123 TGTTCACTCATTTCAGTCCGTA 57.406 40.909 0.00 0.00 0.00 4.02
1730 1881 3.469008 TGTTCACTCATTTCAGTCCGT 57.531 42.857 0.00 0.00 0.00 4.69
1731 1882 4.035091 TGTTTGTTCACTCATTTCAGTCCG 59.965 41.667 0.00 0.00 0.00 4.79
1732 1883 5.163663 TGTGTTTGTTCACTCATTTCAGTCC 60.164 40.000 0.00 0.00 38.90 3.85
1733 1884 5.739161 GTGTGTTTGTTCACTCATTTCAGTC 59.261 40.000 0.00 0.00 38.90 3.51
1734 1885 5.415701 AGTGTGTTTGTTCACTCATTTCAGT 59.584 36.000 0.00 0.00 40.28 3.41
1735 1886 5.883661 AGTGTGTTTGTTCACTCATTTCAG 58.116 37.500 0.00 0.00 40.28 3.02
1736 1887 5.895636 AGTGTGTTTGTTCACTCATTTCA 57.104 34.783 0.00 0.00 40.28 2.69
1737 1888 7.044052 GCTTTAGTGTGTTTGTTCACTCATTTC 60.044 37.037 1.08 0.00 42.77 2.17
1738 1889 6.751888 GCTTTAGTGTGTTTGTTCACTCATTT 59.248 34.615 1.08 0.00 42.77 2.32
1739 1890 6.095440 AGCTTTAGTGTGTTTGTTCACTCATT 59.905 34.615 1.08 0.00 42.77 2.57
1740 1891 5.590259 AGCTTTAGTGTGTTTGTTCACTCAT 59.410 36.000 1.08 0.00 42.77 2.90
1741 1892 4.941263 AGCTTTAGTGTGTTTGTTCACTCA 59.059 37.500 1.08 0.00 42.77 3.41
1742 1893 5.485662 AGCTTTAGTGTGTTTGTTCACTC 57.514 39.130 1.08 0.00 42.77 3.51
1743 1894 5.447279 CGAAGCTTTAGTGTGTTTGTTCACT 60.447 40.000 0.00 0.00 45.21 3.41
1744 1895 4.728608 CGAAGCTTTAGTGTGTTTGTTCAC 59.271 41.667 0.00 0.00 38.63 3.18
1745 1896 4.632251 TCGAAGCTTTAGTGTGTTTGTTCA 59.368 37.500 0.00 0.00 0.00 3.18
1746 1897 5.151632 TCGAAGCTTTAGTGTGTTTGTTC 57.848 39.130 0.00 0.00 0.00 3.18
1747 1898 5.751243 ATCGAAGCTTTAGTGTGTTTGTT 57.249 34.783 0.00 0.00 0.00 2.83
1748 1899 5.295787 TGAATCGAAGCTTTAGTGTGTTTGT 59.704 36.000 0.00 0.00 0.00 2.83
1749 1900 5.747565 TGAATCGAAGCTTTAGTGTGTTTG 58.252 37.500 0.00 0.00 0.00 2.93
1750 1901 5.758296 TCTGAATCGAAGCTTTAGTGTGTTT 59.242 36.000 0.00 0.00 0.00 2.83
1751 1902 5.297547 TCTGAATCGAAGCTTTAGTGTGTT 58.702 37.500 0.00 0.00 0.00 3.32
1752 1903 4.883083 TCTGAATCGAAGCTTTAGTGTGT 58.117 39.130 0.00 0.00 0.00 3.72
1753 1904 5.845985 TTCTGAATCGAAGCTTTAGTGTG 57.154 39.130 0.00 0.00 0.00 3.82
1754 1905 6.861065 TTTTCTGAATCGAAGCTTTAGTGT 57.139 33.333 0.00 0.00 0.00 3.55
1783 1934 9.864034 CCGTTCACAAATATATGATGTTCTAAC 57.136 33.333 2.48 6.59 0.00 2.34
1784 1935 9.825109 TCCGTTCACAAATATATGATGTTCTAA 57.175 29.630 2.48 0.00 0.00 2.10
1785 1936 9.476202 CTCCGTTCACAAATATATGATGTTCTA 57.524 33.333 2.48 0.00 0.00 2.10
1786 1937 7.442364 CCTCCGTTCACAAATATATGATGTTCT 59.558 37.037 2.48 0.00 0.00 3.01
1787 1938 7.441157 TCCTCCGTTCACAAATATATGATGTTC 59.559 37.037 2.48 0.00 0.00 3.18
1788 1939 7.279615 TCCTCCGTTCACAAATATATGATGTT 58.720 34.615 2.48 0.00 0.00 2.71
1789 1940 6.826668 TCCTCCGTTCACAAATATATGATGT 58.173 36.000 0.00 0.00 0.00 3.06
1790 1941 6.369890 CCTCCTCCGTTCACAAATATATGATG 59.630 42.308 0.00 0.00 0.00 3.07
1791 1942 6.043243 ACCTCCTCCGTTCACAAATATATGAT 59.957 38.462 0.00 0.00 0.00 2.45
1792 1943 5.365605 ACCTCCTCCGTTCACAAATATATGA 59.634 40.000 0.00 0.00 0.00 2.15
1793 1944 5.611374 ACCTCCTCCGTTCACAAATATATG 58.389 41.667 0.00 0.00 0.00 1.78
1794 1945 5.888982 ACCTCCTCCGTTCACAAATATAT 57.111 39.130 0.00 0.00 0.00 0.86
1795 1946 5.895534 ACTACCTCCTCCGTTCACAAATATA 59.104 40.000 0.00 0.00 0.00 0.86
1796 1947 4.715297 ACTACCTCCTCCGTTCACAAATAT 59.285 41.667 0.00 0.00 0.00 1.28
1797 1948 4.091549 ACTACCTCCTCCGTTCACAAATA 58.908 43.478 0.00 0.00 0.00 1.40
1798 1949 2.904434 ACTACCTCCTCCGTTCACAAAT 59.096 45.455 0.00 0.00 0.00 2.32
1799 1950 2.322658 ACTACCTCCTCCGTTCACAAA 58.677 47.619 0.00 0.00 0.00 2.83
1800 1951 2.005370 ACTACCTCCTCCGTTCACAA 57.995 50.000 0.00 0.00 0.00 3.33
1801 1952 2.885135 TACTACCTCCTCCGTTCACA 57.115 50.000 0.00 0.00 0.00 3.58
1802 1953 4.159135 TGATTTACTACCTCCTCCGTTCAC 59.841 45.833 0.00 0.00 0.00 3.18
1803 1954 4.346730 TGATTTACTACCTCCTCCGTTCA 58.653 43.478 0.00 0.00 0.00 3.18
1804 1955 4.401837 ACTGATTTACTACCTCCTCCGTTC 59.598 45.833 0.00 0.00 0.00 3.95
1805 1956 4.351127 ACTGATTTACTACCTCCTCCGTT 58.649 43.478 0.00 0.00 0.00 4.44
1806 1957 3.978610 ACTGATTTACTACCTCCTCCGT 58.021 45.455 0.00 0.00 0.00 4.69
1807 1958 6.941436 ACTATACTGATTTACTACCTCCTCCG 59.059 42.308 0.00 0.00 0.00 4.63
1808 1959 8.709272 AACTATACTGATTTACTACCTCCTCC 57.291 38.462 0.00 0.00 0.00 4.30
1810 1961 8.848182 CGAAACTATACTGATTTACTACCTCCT 58.152 37.037 0.00 0.00 0.00 3.69
1811 1962 8.081025 CCGAAACTATACTGATTTACTACCTCC 58.919 40.741 0.00 0.00 0.00 4.30
1812 1963 8.628280 ACCGAAACTATACTGATTTACTACCTC 58.372 37.037 0.00 0.00 0.00 3.85
1813 1964 8.530804 ACCGAAACTATACTGATTTACTACCT 57.469 34.615 0.00 0.00 0.00 3.08
1824 1992 7.980099 AGTCTTTTGGATACCGAAACTATACTG 59.020 37.037 0.00 0.00 33.73 2.74
1829 1997 6.150976 TCGTAGTCTTTTGGATACCGAAACTA 59.849 38.462 0.00 0.00 33.73 2.24
1844 2012 2.019807 TGGGGAAGGTCGTAGTCTTT 57.980 50.000 0.00 0.00 0.00 2.52
1851 2019 3.202151 ACAAATGATATGGGGAAGGTCGT 59.798 43.478 0.00 0.00 0.00 4.34
1852 2020 3.815401 GACAAATGATATGGGGAAGGTCG 59.185 47.826 0.00 0.00 0.00 4.79
1854 2022 4.879295 TGACAAATGATATGGGGAAGGT 57.121 40.909 0.00 0.00 0.00 3.50
1855 2023 5.387788 TGATGACAAATGATATGGGGAAGG 58.612 41.667 0.00 0.00 0.00 3.46
1865 2077 6.693466 TGCTGAAATGTTGATGACAAATGAT 58.307 32.000 0.00 0.00 42.62 2.45
1866 2078 6.086785 TGCTGAAATGTTGATGACAAATGA 57.913 33.333 0.00 0.00 42.62 2.57
1968 2180 4.670896 ACAATTTGGTTGAACAAGGAGG 57.329 40.909 0.00 0.00 40.37 4.30
1971 2183 6.095432 TCCATACAATTTGGTTGAACAAGG 57.905 37.500 0.00 0.00 40.37 3.61
1987 2203 5.106317 GGAAAAACGCTCAGAAATCCATACA 60.106 40.000 0.00 0.00 0.00 2.29
2003 2223 3.632189 CTTGCTGGAAGAAGGAAAAACG 58.368 45.455 2.37 0.00 34.07 3.60
2096 2316 5.569355 TGATCAAAAGCATCCAACTCCTTA 58.431 37.500 0.00 0.00 0.00 2.69
2138 2358 3.006859 CACTGCGATCATAGTATTGGGGA 59.993 47.826 0.00 0.00 0.00 4.81
2144 2364 4.258702 GGAACCACTGCGATCATAGTAT 57.741 45.455 0.00 0.00 0.00 2.12
2429 2649 3.698539 TGTTTGTGAGATTGGACTTGCAA 59.301 39.130 0.00 0.00 0.00 4.08
2462 2682 2.102438 ACATGTGCTGATCGCCACG 61.102 57.895 0.00 3.21 38.05 4.94
2477 2697 1.340088 TGCAGAAAACATGGCCACAT 58.660 45.000 8.16 0.00 37.99 3.21
2548 2768 1.134220 TCCTCTCTTTGCACGGTTTGT 60.134 47.619 0.00 0.00 0.00 2.83
2609 2829 0.103208 CCTCTAGGTGGTCATCGTGC 59.897 60.000 0.00 0.00 0.00 5.34
2630 2850 8.319146 CCACTCCCTAAATACTTGAAGTTCTTA 58.681 37.037 1.97 1.20 0.00 2.10
2643 2863 2.508300 GCCCAGAACCACTCCCTAAATA 59.492 50.000 0.00 0.00 0.00 1.40
2692 2912 9.243105 ACAACAGTTACATAATTGAAGGCTATT 57.757 29.630 1.58 0.00 0.00 1.73
2741 2961 3.898380 TCGTGCCACAACGATAAGT 57.102 47.368 0.00 0.00 46.99 2.24
2747 2967 5.428770 GTTACATATATTCGTGCCACAACG 58.571 41.667 0.00 0.00 44.92 4.10
2748 2968 5.526111 AGGTTACATATATTCGTGCCACAAC 59.474 40.000 0.00 0.00 0.00 3.32
2862 3083 2.472695 TACTGCATCGGAGCAAAACT 57.527 45.000 4.37 0.00 45.13 2.66
2886 3107 0.521291 TCAAGCGCCAAAGAAATCCG 59.479 50.000 2.29 0.00 0.00 4.18
2907 3128 5.536161 ACAACATAGAAAACTGGCAAGACAT 59.464 36.000 0.00 0.00 0.00 3.06
2914 3135 4.275936 AGTGTGACAACATAGAAAACTGGC 59.724 41.667 0.00 0.00 38.92 4.85
2923 3144 5.579904 CAGAATCTCCAGTGTGACAACATAG 59.420 44.000 0.00 0.00 38.92 2.23
2989 3210 2.355197 TGATCAAAGCATGGTGGTACG 58.645 47.619 0.00 0.00 0.00 3.67
2996 3220 6.395629 AGTTCTGAATTTGATCAAAGCATGG 58.604 36.000 24.17 14.03 33.32 3.66
3006 3230 2.369394 GCCCCGAGTTCTGAATTTGAT 58.631 47.619 1.99 0.00 0.00 2.57
3010 3234 0.253327 GAGGCCCCGAGTTCTGAATT 59.747 55.000 0.00 0.00 0.00 2.17
3021 3245 0.960861 GAAGTTCCAAAGAGGCCCCG 60.961 60.000 0.00 0.00 37.29 5.73
3057 3281 1.065709 GGGACTCTTTGGATTGCCGTA 60.066 52.381 0.00 0.00 36.79 4.02
3060 3284 2.239907 ACTAGGGACTCTTTGGATTGCC 59.760 50.000 0.00 0.00 41.75 4.52
3096 3321 5.647658 TGCAAAGGGATATGTTACAGACTTG 59.352 40.000 0.00 0.00 0.00 3.16
3200 3425 3.556775 TCTTCGTTTCCTGTGGTTTAACG 59.443 43.478 0.00 0.00 41.95 3.18
3219 3444 4.829492 CCTCTTTCCTGTGGTGATTTTCTT 59.171 41.667 0.00 0.00 0.00 2.52
3239 3493 5.712917 CCCTTCTGATGGATAGTACTACCTC 59.287 48.000 4.31 0.00 0.00 3.85
3240 3494 5.375956 TCCCTTCTGATGGATAGTACTACCT 59.624 44.000 4.31 0.00 0.00 3.08
3241 3495 5.642165 TCCCTTCTGATGGATAGTACTACC 58.358 45.833 4.31 9.33 0.00 3.18
3242 3496 7.451877 TCATTCCCTTCTGATGGATAGTACTAC 59.548 40.741 4.31 0.00 0.00 2.73
3500 3837 1.956477 ACAGGGTTCATTCAAGCACAC 59.044 47.619 0.00 0.00 33.79 3.82
3595 3933 1.681166 CCATTCAGCCTTGCAGTAGCT 60.681 52.381 1.71 1.71 42.74 3.32
3604 3942 1.931007 GAGGAGCCCCATTCAGCCTT 61.931 60.000 0.00 0.00 33.88 4.35
3625 3963 3.103911 CTCGCGTTCACCACCGAC 61.104 66.667 5.77 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.