Multiple sequence alignment - TraesCS4A01G155900

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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 TraesCS4A01G155900 chr4A 100.000 2372 0 0 1 2372 310783832 310781461 0 4381
1 TraesCS4A01G155900 chr3A 95.987 1844 70 1 1 1844 66004932 66003093 0 2992
2 TraesCS4A01G155900 chr3A 96.798 531 17 0 1842 2372 66003049 66002519 0 887
3 TraesCS4A01G155900 chr6D 95.879 1844 72 1 1 1844 389245621 389243782 0 2981
4 TraesCS4A01G155900 chr5D 95.824 1844 73 1 1 1844 503264575 503262736 0 2976
5 TraesCS4A01G155900 chr5D 95.770 1844 74 1 1 1844 503245473 503247312 0 2970
6 TraesCS4A01G155900 chr5D 96.610 531 18 0 1842 2372 503262692 503262162 0 881
7 TraesCS4A01G155900 chr2A 95.824 1844 73 1 1 1844 726906254 726904415 0 2976
8 TraesCS4A01G155900 chr2A 96.798 531 17 0 1842 2372 726904371 726903841 0 887
9 TraesCS4A01G155900 chr3D 95.770 1844 74 1 1 1844 589263325 589261486 0 2970
10 TraesCS4A01G155900 chr1D 95.770 1844 75 2 1 1844 254525806 254527646 0 2970
11 TraesCS4A01G155900 chr2D 95.716 1844 75 1 1 1844 591984810 591986649 0 2964
12 TraesCS4A01G155900 chr2D 96.798 531 17 0 1842 2372 591986693 591987223 0 887
13 TraesCS4A01G155900 chr2D 96.610 531 18 0 1842 2372 272810162 272809632 0 881
14 TraesCS4A01G155900 chr3B 95.716 1844 73 3 1 1844 201539723 201541560 0 2963
15 TraesCS4A01G155900 chr7D 96.798 531 17 0 1842 2372 231550894 231551424 0 887
16 TraesCS4A01G155900 chr7D 96.798 531 17 0 1842 2372 231607416 231606886 0 887
17 TraesCS4A01G155900 chr7D 96.798 531 16 1 1842 2372 231605833 231605304 0 885
18 TraesCS4A01G155900 chr7B 96.617 532 17 1 1842 2372 662728997 662729528 0 881


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 TraesCS4A01G155900 chr4A 310781461 310783832 2371 True 4381.0 4381 100.0000 1 2372 1 chr4A.!!$R1 2371
1 TraesCS4A01G155900 chr3A 66002519 66004932 2413 True 1939.5 2992 96.3925 1 2372 2 chr3A.!!$R1 2371
2 TraesCS4A01G155900 chr6D 389243782 389245621 1839 True 2981.0 2981 95.8790 1 1844 1 chr6D.!!$R1 1843
3 TraesCS4A01G155900 chr5D 503245473 503247312 1839 False 2970.0 2970 95.7700 1 1844 1 chr5D.!!$F1 1843
4 TraesCS4A01G155900 chr5D 503262162 503264575 2413 True 1928.5 2976 96.2170 1 2372 2 chr5D.!!$R1 2371
5 TraesCS4A01G155900 chr2A 726903841 726906254 2413 True 1931.5 2976 96.3110 1 2372 2 chr2A.!!$R1 2371
6 TraesCS4A01G155900 chr3D 589261486 589263325 1839 True 2970.0 2970 95.7700 1 1844 1 chr3D.!!$R1 1843
7 TraesCS4A01G155900 chr1D 254525806 254527646 1840 False 2970.0 2970 95.7700 1 1844 1 chr1D.!!$F1 1843
8 TraesCS4A01G155900 chr2D 591984810 591987223 2413 False 1925.5 2964 96.2570 1 2372 2 chr2D.!!$F1 2371
9 TraesCS4A01G155900 chr2D 272809632 272810162 530 True 881.0 881 96.6100 1842 2372 1 chr2D.!!$R1 530
10 TraesCS4A01G155900 chr3B 201539723 201541560 1837 False 2963.0 2963 95.7160 1 1844 1 chr3B.!!$F1 1843
11 TraesCS4A01G155900 chr7D 231550894 231551424 530 False 887.0 887 96.7980 1842 2372 1 chr7D.!!$F1 530
12 TraesCS4A01G155900 chr7D 231605304 231607416 2112 True 886.0 887 96.7980 1842 2372 2 chr7D.!!$R1 530
13 TraesCS4A01G155900 chr7B 662728997 662729528 531 False 881.0 881 96.6170 1842 2372 1 chr7B.!!$F1 530

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
214 217 0.038435 TCGTTGCGATTACGGGTTGA 60.038 50.0 0.0 0.0 39.38 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 1646 0.100146 CCCTCACGGTACTACTTCGC 59.9 60.0 0.0 0.0 0.0 4.7 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
33 34 1.202099 TTGGTTGGATCGTAGGGGCA 61.202 55.000 0.00 0.00 0.00 5.36
52 53 2.163412 GCAATGATTTACTTCACGGGCA 59.837 45.455 0.00 0.00 0.00 5.36
57 58 3.008157 TGATTTACTTCACGGGCAAGGTA 59.992 43.478 2.66 0.00 0.00 3.08
59 60 3.706600 TTACTTCACGGGCAAGGTATT 57.293 42.857 2.66 0.00 0.00 1.89
71 72 3.826729 GGCAAGGTATTTGGTTCAAGTCT 59.173 43.478 0.00 0.00 37.26 3.24
88 89 2.691996 TAGGATGGCCCAGCTGCA 60.692 61.111 8.66 0.81 37.41 4.41
214 217 0.038435 TCGTTGCGATTACGGGTTGA 60.038 50.000 0.00 0.00 39.38 3.18
261 264 7.914427 ATGATAGTATCTTGTACCTGAACCA 57.086 36.000 11.40 0.00 0.00 3.67
307 310 2.553028 GGGAAGAGGACTGAAACATGCA 60.553 50.000 0.00 0.00 0.00 3.96
310 313 2.508526 AGAGGACTGAAACATGCAACC 58.491 47.619 0.00 0.00 0.00 3.77
315 318 3.490078 GGACTGAAACATGCAACCGAAAA 60.490 43.478 0.00 0.00 0.00 2.29
349 352 5.070847 AGACAAAAAGATGGGCTGTCAAAAT 59.929 36.000 3.61 0.00 39.08 1.82
368 371 4.561254 AATGGTAGAGGAGGTAGGATGT 57.439 45.455 0.00 0.00 0.00 3.06
376 379 1.279271 GGAGGTAGGATGTGCAGTTGT 59.721 52.381 0.00 0.00 0.00 3.32
380 383 3.009473 AGGTAGGATGTGCAGTTGTTCAT 59.991 43.478 0.00 0.00 0.00 2.57
402 405 7.931275 TCATATCTAGTATGGATCGTACATGC 58.069 38.462 8.91 1.28 40.52 4.06
471 474 3.115390 CCCTGGGGAAGAAGATCAAGTA 58.885 50.000 4.27 0.00 37.50 2.24
474 477 4.033709 CTGGGGAAGAAGATCAAGTAGGA 58.966 47.826 0.00 0.00 0.00 2.94
519 522 2.701551 TCTCCCTTCAACCCTTTGAGA 58.298 47.619 0.00 0.00 42.79 3.27
554 557 2.654385 AGGAAGGAAAATCCATGGACCA 59.346 45.455 18.99 0.00 39.61 4.02
556 559 3.448660 GGAAGGAAAATCCATGGACCAAG 59.551 47.826 18.99 0.00 39.61 3.61
563 566 0.413037 TCCATGGACCAAGCCCATTT 59.587 50.000 11.44 0.00 42.18 2.32
625 628 3.681835 GGCGTCCAGGAGTCACGT 61.682 66.667 0.00 0.00 35.91 4.49
673 676 0.304705 GAACACATTAGCCATCCGCG 59.695 55.000 0.00 0.00 44.76 6.46
705 708 0.708802 AGTAAGGGTCGGAGAAGGGA 59.291 55.000 0.00 0.00 39.69 4.20
782 785 2.683933 GAGCTCCCCGTTCCTGGA 60.684 66.667 0.87 0.00 0.00 3.86
795 798 3.952323 CGTTCCTGGATCTCCTGTAACTA 59.048 47.826 0.00 0.00 33.65 2.24
811 814 1.497161 ACTAGATTCCCCGGAACCAG 58.503 55.000 0.73 0.00 36.91 4.00
916 919 6.449635 TGATGAAAGTTGTAAGCTGTGTTT 57.550 33.333 0.00 0.00 0.00 2.83
918 921 5.888691 TGAAAGTTGTAAGCTGTGTTTGA 57.111 34.783 0.00 0.00 0.00 2.69
1003 1006 1.029947 GTTTACCCTGTGGCGGATGG 61.030 60.000 0.00 0.00 33.59 3.51
1031 1034 1.134189 TCGAGTCCGCTTATCTCCAGA 60.134 52.381 0.00 0.00 35.37 3.86
1046 1049 0.038526 CCAGACCGTGAACTTAGCGT 60.039 55.000 0.00 0.00 0.00 5.07
1064 1067 9.322773 ACTTAGCGTATACTATGATAGCGATAA 57.677 33.333 0.00 4.00 0.00 1.75
1134 1137 4.960938 TGGACATTGATAAGATCCTTCCG 58.039 43.478 0.00 0.00 0.00 4.30
1227 1230 0.708209 TACCTAGGCACCCAGAGACA 59.292 55.000 9.30 0.00 0.00 3.41
1317 1320 8.226112 TCCCAAATAGGTCAACCTTTTAAACTA 58.774 33.333 7.07 0.00 46.09 2.24
1432 1435 1.582610 GGCGAACGAAATGGGAGCAA 61.583 55.000 0.00 0.00 0.00 3.91
1536 1539 2.211353 GCTAAAGTCCAGTAGCCGAG 57.789 55.000 0.00 0.00 37.37 4.63
1551 1554 1.850377 CCGAGAGCATCACTAGCTTG 58.150 55.000 0.00 0.00 43.58 4.01
1632 1635 5.368989 CCTTACAAGGCTAAATACTCCTGG 58.631 45.833 0.00 0.00 39.76 4.45
1633 1636 3.933861 ACAAGGCTAAATACTCCTGGG 57.066 47.619 0.00 0.00 0.00 4.45
1634 1637 3.190439 ACAAGGCTAAATACTCCTGGGT 58.810 45.455 0.00 0.00 0.00 4.51
1635 1638 3.054361 ACAAGGCTAAATACTCCTGGGTG 60.054 47.826 0.00 0.00 0.00 4.61
1636 1639 3.130734 AGGCTAAATACTCCTGGGTGA 57.869 47.619 0.00 0.00 0.00 4.02
1637 1640 2.772515 AGGCTAAATACTCCTGGGTGAC 59.227 50.000 0.00 0.00 0.00 3.67
1638 1641 2.504175 GGCTAAATACTCCTGGGTGACA 59.496 50.000 0.00 0.00 0.00 3.58
1639 1642 3.054655 GGCTAAATACTCCTGGGTGACAA 60.055 47.826 0.00 0.00 0.00 3.18
1640 1643 4.566907 GGCTAAATACTCCTGGGTGACAAA 60.567 45.833 0.00 0.00 0.00 2.83
1641 1644 5.193679 GCTAAATACTCCTGGGTGACAAAT 58.806 41.667 0.00 0.00 0.00 2.32
1642 1645 6.354130 GCTAAATACTCCTGGGTGACAAATA 58.646 40.000 0.00 0.00 0.00 1.40
1643 1646 6.483640 GCTAAATACTCCTGGGTGACAAATAG 59.516 42.308 0.00 0.00 0.00 1.73
1644 1647 2.789409 ACTCCTGGGTGACAAATAGC 57.211 50.000 0.00 0.00 0.00 2.97
1645 1648 1.066143 ACTCCTGGGTGACAAATAGCG 60.066 52.381 0.00 0.00 0.00 4.26
1646 1649 1.207089 CTCCTGGGTGACAAATAGCGA 59.793 52.381 0.00 0.00 0.00 4.93
1647 1650 1.626321 TCCTGGGTGACAAATAGCGAA 59.374 47.619 0.00 0.00 0.00 4.70
1648 1651 2.009774 CCTGGGTGACAAATAGCGAAG 58.990 52.381 0.00 0.00 0.00 3.79
1649 1652 2.615493 CCTGGGTGACAAATAGCGAAGT 60.615 50.000 0.00 0.00 0.00 3.01
1650 1653 3.369052 CCTGGGTGACAAATAGCGAAGTA 60.369 47.826 0.00 0.00 0.00 2.24
1651 1654 3.857052 TGGGTGACAAATAGCGAAGTAG 58.143 45.455 0.00 0.00 0.00 2.57
1652 1655 3.259876 TGGGTGACAAATAGCGAAGTAGT 59.740 43.478 0.00 0.00 0.00 2.73
1653 1656 4.463539 TGGGTGACAAATAGCGAAGTAGTA 59.536 41.667 0.00 0.00 0.00 1.82
1654 1657 4.802563 GGGTGACAAATAGCGAAGTAGTAC 59.197 45.833 0.00 0.00 0.00 2.73
1655 1658 4.802563 GGTGACAAATAGCGAAGTAGTACC 59.197 45.833 0.00 0.00 0.00 3.34
1656 1659 4.498323 GTGACAAATAGCGAAGTAGTACCG 59.502 45.833 0.00 0.00 0.00 4.02
1657 1660 4.156556 TGACAAATAGCGAAGTAGTACCGT 59.843 41.667 0.00 0.00 0.00 4.83
1658 1661 4.418392 ACAAATAGCGAAGTAGTACCGTG 58.582 43.478 0.00 0.00 0.00 4.94
1659 1662 4.156556 ACAAATAGCGAAGTAGTACCGTGA 59.843 41.667 0.00 0.00 0.00 4.35
1660 1663 4.548991 AATAGCGAAGTAGTACCGTGAG 57.451 45.455 0.00 0.00 0.00 3.51
1675 1678 2.846193 CGTGAGGGAAAGGTGAAAAGA 58.154 47.619 0.00 0.00 0.00 2.52
1676 1679 3.211045 CGTGAGGGAAAGGTGAAAAGAA 58.789 45.455 0.00 0.00 0.00 2.52
1677 1680 3.003378 CGTGAGGGAAAGGTGAAAAGAAC 59.997 47.826 0.00 0.00 0.00 3.01
1678 1681 3.318275 GTGAGGGAAAGGTGAAAAGAACC 59.682 47.826 0.00 0.00 38.03 3.62
1679 1682 2.891580 GAGGGAAAGGTGAAAAGAACCC 59.108 50.000 0.00 0.00 38.57 4.11
1680 1683 1.968493 GGGAAAGGTGAAAAGAACCCC 59.032 52.381 0.00 0.00 38.57 4.95
1681 1684 2.673258 GGAAAGGTGAAAAGAACCCCA 58.327 47.619 0.00 0.00 38.57 4.96
1682 1685 3.035363 GGAAAGGTGAAAAGAACCCCAA 58.965 45.455 0.00 0.00 38.57 4.12
1683 1686 3.069586 GGAAAGGTGAAAAGAACCCCAAG 59.930 47.826 0.00 0.00 38.57 3.61
1684 1687 3.398318 AAGGTGAAAAGAACCCCAAGT 57.602 42.857 0.00 0.00 38.57 3.16
1685 1688 2.666317 AGGTGAAAAGAACCCCAAGTG 58.334 47.619 0.00 0.00 38.57 3.16
1686 1689 1.686587 GGTGAAAAGAACCCCAAGTGG 59.313 52.381 0.00 0.00 0.00 4.00
1702 1705 4.630069 CCAAGTGGGTAGTGAAATAGAACG 59.370 45.833 0.00 0.00 0.00 3.95
1703 1706 5.235516 CAAGTGGGTAGTGAAATAGAACGT 58.764 41.667 0.00 0.00 0.00 3.99
1704 1707 4.817517 AGTGGGTAGTGAAATAGAACGTG 58.182 43.478 0.00 0.00 0.00 4.49
1705 1708 4.525487 AGTGGGTAGTGAAATAGAACGTGA 59.475 41.667 0.00 0.00 0.00 4.35
1706 1709 5.011329 AGTGGGTAGTGAAATAGAACGTGAA 59.989 40.000 0.00 0.00 0.00 3.18
1707 1710 5.697633 GTGGGTAGTGAAATAGAACGTGAAA 59.302 40.000 0.00 0.00 0.00 2.69
1708 1711 5.697633 TGGGTAGTGAAATAGAACGTGAAAC 59.302 40.000 0.00 0.00 0.00 2.78
1709 1712 5.121298 GGGTAGTGAAATAGAACGTGAAACC 59.879 44.000 0.00 0.00 0.00 3.27
1710 1713 4.985044 AGTGAAATAGAACGTGAAACCG 57.015 40.909 0.00 0.00 0.00 4.44
1711 1714 4.374399 AGTGAAATAGAACGTGAAACCGT 58.626 39.130 0.00 0.00 44.23 4.83
1712 1715 4.210537 AGTGAAATAGAACGTGAAACCGTG 59.789 41.667 0.00 0.00 41.65 4.94
1713 1716 3.059461 TGAAATAGAACGTGAAACCGTGC 60.059 43.478 0.00 0.00 41.65 5.34
1714 1717 4.848685 AGAACGTGAAACCGTGCT 57.151 50.000 0.00 0.00 41.90 4.40
1715 1718 1.493772 TAGAACGTGAAACCGTGCTG 58.506 50.000 4.52 0.00 46.09 4.41
1716 1719 0.179094 AGAACGTGAAACCGTGCTGA 60.179 50.000 0.00 0.00 44.94 4.26
1717 1720 0.232303 GAACGTGAAACCGTGCTGAG 59.768 55.000 0.00 0.00 41.65 3.35
1718 1721 1.772063 AACGTGAAACCGTGCTGAGC 61.772 55.000 0.00 0.00 41.65 4.26
1719 1722 1.956170 CGTGAAACCGTGCTGAGCT 60.956 57.895 5.83 0.00 0.00 4.09
1720 1723 1.862806 GTGAAACCGTGCTGAGCTC 59.137 57.895 6.82 6.82 0.00 4.09
1721 1724 1.301716 TGAAACCGTGCTGAGCTCC 60.302 57.895 12.15 0.00 0.00 4.70
1722 1725 2.032681 AAACCGTGCTGAGCTCCC 59.967 61.111 12.15 2.65 0.00 4.30
1723 1726 2.731691 GAAACCGTGCTGAGCTCCCA 62.732 60.000 12.15 5.62 0.00 4.37
1724 1727 2.337879 AAACCGTGCTGAGCTCCCAA 62.338 55.000 12.15 0.00 0.00 4.12
1725 1728 2.435586 CCGTGCTGAGCTCCCAAG 60.436 66.667 12.15 10.46 0.00 3.61
1738 1741 2.935481 CCAAGCAGTGGGAGGGGA 60.935 66.667 0.00 0.00 44.64 4.81
1739 1742 2.538141 CCAAGCAGTGGGAGGGGAA 61.538 63.158 0.00 0.00 44.64 3.97
1740 1743 1.460255 CAAGCAGTGGGAGGGGAAA 59.540 57.895 0.00 0.00 0.00 3.13
1741 1744 0.610232 CAAGCAGTGGGAGGGGAAAG 60.610 60.000 0.00 0.00 0.00 2.62
1742 1745 1.068352 AAGCAGTGGGAGGGGAAAGT 61.068 55.000 0.00 0.00 0.00 2.66
1743 1746 1.303643 GCAGTGGGAGGGGAAAGTG 60.304 63.158 0.00 0.00 0.00 3.16
1744 1747 1.779061 GCAGTGGGAGGGGAAAGTGA 61.779 60.000 0.00 0.00 0.00 3.41
1745 1748 0.995024 CAGTGGGAGGGGAAAGTGAT 59.005 55.000 0.00 0.00 0.00 3.06
1746 1749 1.065126 CAGTGGGAGGGGAAAGTGATC 60.065 57.143 0.00 0.00 0.00 2.92
1747 1750 1.203492 AGTGGGAGGGGAAAGTGATCT 60.203 52.381 0.00 0.00 0.00 2.75
1748 1751 1.210722 GTGGGAGGGGAAAGTGATCTC 59.789 57.143 0.00 0.00 0.00 2.75
1749 1752 1.081174 TGGGAGGGGAAAGTGATCTCT 59.919 52.381 0.00 0.00 0.00 3.10
1750 1753 1.488393 GGGAGGGGAAAGTGATCTCTG 59.512 57.143 0.00 0.00 0.00 3.35
1751 1754 2.472029 GGAGGGGAAAGTGATCTCTGA 58.528 52.381 0.00 0.00 0.00 3.27
1752 1755 2.169561 GGAGGGGAAAGTGATCTCTGAC 59.830 54.545 0.00 0.00 0.00 3.51
1753 1756 2.169561 GAGGGGAAAGTGATCTCTGACC 59.830 54.545 0.00 5.23 0.00 4.02
1754 1757 1.909302 GGGGAAAGTGATCTCTGACCA 59.091 52.381 16.72 0.00 0.00 4.02
1755 1758 2.355209 GGGGAAAGTGATCTCTGACCAC 60.355 54.545 16.72 12.20 0.00 4.16
1756 1759 2.611518 GGAAAGTGATCTCTGACCACG 58.388 52.381 12.58 0.00 36.06 4.94
1757 1760 2.028930 GGAAAGTGATCTCTGACCACGT 60.029 50.000 12.58 0.00 36.06 4.49
1758 1761 3.555168 GGAAAGTGATCTCTGACCACGTT 60.555 47.826 12.58 0.00 35.76 3.99
1759 1762 3.305398 AAGTGATCTCTGACCACGTTC 57.695 47.619 0.00 0.00 36.06 3.95
1760 1763 1.546476 AGTGATCTCTGACCACGTTCC 59.454 52.381 0.00 0.00 36.06 3.62
1761 1764 1.546476 GTGATCTCTGACCACGTTCCT 59.454 52.381 0.00 0.00 0.00 3.36
1762 1765 1.546029 TGATCTCTGACCACGTTCCTG 59.454 52.381 0.00 0.00 0.00 3.86
1763 1766 1.546476 GATCTCTGACCACGTTCCTGT 59.454 52.381 0.00 0.00 0.00 4.00
1764 1767 1.410004 TCTCTGACCACGTTCCTGTT 58.590 50.000 0.00 0.00 0.00 3.16
1765 1768 1.068588 TCTCTGACCACGTTCCTGTTG 59.931 52.381 0.00 0.00 0.00 3.33
1766 1769 1.068588 CTCTGACCACGTTCCTGTTGA 59.931 52.381 0.00 0.00 0.00 3.18
1767 1770 1.483004 TCTGACCACGTTCCTGTTGAA 59.517 47.619 0.00 0.00 0.00 2.69
1768 1771 1.867233 CTGACCACGTTCCTGTTGAAG 59.133 52.381 0.00 0.00 32.37 3.02
1769 1772 1.483004 TGACCACGTTCCTGTTGAAGA 59.517 47.619 0.00 0.00 32.37 2.87
1770 1773 2.093394 TGACCACGTTCCTGTTGAAGAA 60.093 45.455 0.00 0.00 32.37 2.52
1771 1774 3.139077 GACCACGTTCCTGTTGAAGAAT 58.861 45.455 0.00 0.00 32.37 2.40
1772 1775 2.878406 ACCACGTTCCTGTTGAAGAATG 59.122 45.455 0.00 0.00 35.54 2.67
1773 1776 3.138304 CCACGTTCCTGTTGAAGAATGA 58.862 45.455 0.00 0.00 33.96 2.57
1774 1777 3.187227 CCACGTTCCTGTTGAAGAATGAG 59.813 47.826 0.00 0.00 33.96 2.90
1775 1778 2.808543 ACGTTCCTGTTGAAGAATGAGC 59.191 45.455 0.00 0.00 33.96 4.26
1776 1779 2.160417 CGTTCCTGTTGAAGAATGAGCC 59.840 50.000 0.00 0.00 32.37 4.70
1777 1780 2.099141 TCCTGTTGAAGAATGAGCCG 57.901 50.000 0.00 0.00 0.00 5.52
1778 1781 1.089920 CCTGTTGAAGAATGAGCCGG 58.910 55.000 0.00 0.00 0.00 6.13
1779 1782 0.449388 CTGTTGAAGAATGAGCCGGC 59.551 55.000 21.89 21.89 0.00 6.13
1780 1783 1.298157 TGTTGAAGAATGAGCCGGCG 61.298 55.000 23.20 0.00 0.00 6.46
1781 1784 1.019278 GTTGAAGAATGAGCCGGCGA 61.019 55.000 23.20 12.86 0.00 5.54
1782 1785 1.019278 TTGAAGAATGAGCCGGCGAC 61.019 55.000 23.20 19.75 0.00 5.19
1783 1786 1.153549 GAAGAATGAGCCGGCGACT 60.154 57.895 23.20 13.92 0.00 4.18
1784 1787 1.148759 GAAGAATGAGCCGGCGACTC 61.149 60.000 23.20 16.65 34.62 3.36
1786 1789 1.447838 GAATGAGCCGGCGACTCAA 60.448 57.895 28.71 13.19 46.63 3.02
1787 1790 1.003839 AATGAGCCGGCGACTCAAA 60.004 52.632 28.71 7.89 46.63 2.69
1788 1791 1.021390 AATGAGCCGGCGACTCAAAG 61.021 55.000 28.71 0.87 46.63 2.77
1789 1792 2.815647 GAGCCGGCGACTCAAAGG 60.816 66.667 23.20 0.00 34.18 3.11
1790 1793 3.296709 GAGCCGGCGACTCAAAGGA 62.297 63.158 23.20 0.00 34.18 3.36
1791 1794 2.358247 GCCGGCGACTCAAAGGAA 60.358 61.111 12.58 0.00 0.00 3.36
1792 1795 2.391389 GCCGGCGACTCAAAGGAAG 61.391 63.158 12.58 0.00 0.00 3.46
1793 1796 1.004918 CCGGCGACTCAAAGGAAGT 60.005 57.895 9.30 0.00 0.00 3.01
1794 1797 0.602905 CCGGCGACTCAAAGGAAGTT 60.603 55.000 9.30 0.00 0.00 2.66
1795 1798 0.512952 CGGCGACTCAAAGGAAGTTG 59.487 55.000 0.00 0.00 0.00 3.16
1796 1799 0.238553 GGCGACTCAAAGGAAGTTGC 59.761 55.000 6.90 6.90 41.02 4.17
1797 1800 1.230324 GCGACTCAAAGGAAGTTGCT 58.770 50.000 7.99 0.00 39.25 3.91
1798 1801 1.604278 GCGACTCAAAGGAAGTTGCTT 59.396 47.619 3.44 3.44 39.25 3.91
1799 1802 2.603173 GCGACTCAAAGGAAGTTGCTTG 60.603 50.000 10.68 5.47 39.25 4.01
1800 1803 2.031682 CGACTCAAAGGAAGTTGCTTGG 60.032 50.000 10.68 7.83 0.00 3.61
1801 1804 2.952310 GACTCAAAGGAAGTTGCTTGGT 59.048 45.455 10.68 9.82 0.00 3.67
1802 1805 3.365472 ACTCAAAGGAAGTTGCTTGGTT 58.635 40.909 10.68 0.00 0.00 3.67
1803 1806 4.532834 ACTCAAAGGAAGTTGCTTGGTTA 58.467 39.130 10.68 0.00 0.00 2.85
1804 1807 4.953579 ACTCAAAGGAAGTTGCTTGGTTAA 59.046 37.500 10.68 0.00 0.00 2.01
1805 1808 5.067805 ACTCAAAGGAAGTTGCTTGGTTAAG 59.932 40.000 10.68 4.03 36.97 1.85
1806 1809 4.340950 TCAAAGGAAGTTGCTTGGTTAAGG 59.659 41.667 10.68 0.00 34.40 2.69
1807 1810 2.876581 AGGAAGTTGCTTGGTTAAGGG 58.123 47.619 0.00 0.00 34.40 3.95
1808 1811 2.445525 AGGAAGTTGCTTGGTTAAGGGA 59.554 45.455 0.00 0.00 34.40 4.20
1809 1812 3.117284 AGGAAGTTGCTTGGTTAAGGGAA 60.117 43.478 0.00 0.00 34.40 3.97
1810 1813 3.005472 GGAAGTTGCTTGGTTAAGGGAAC 59.995 47.826 0.00 0.00 37.31 3.62
1811 1814 3.306472 AGTTGCTTGGTTAAGGGAACA 57.694 42.857 0.00 0.00 40.09 3.18
1812 1815 3.222603 AGTTGCTTGGTTAAGGGAACAG 58.777 45.455 0.00 0.00 40.09 3.16
1813 1816 3.117663 AGTTGCTTGGTTAAGGGAACAGA 60.118 43.478 0.00 0.00 40.09 3.41
1814 1817 3.586470 TGCTTGGTTAAGGGAACAGAA 57.414 42.857 0.00 0.00 40.09 3.02
1815 1818 3.219281 TGCTTGGTTAAGGGAACAGAAC 58.781 45.455 0.00 0.00 40.09 3.01
1816 1819 2.557056 GCTTGGTTAAGGGAACAGAACC 59.443 50.000 0.00 0.00 43.83 3.62
1817 1820 2.963599 TGGTTAAGGGAACAGAACCC 57.036 50.000 0.00 0.00 43.25 4.11
1822 1825 2.033602 GGGAACAGAACCCACCGG 59.966 66.667 0.00 0.00 46.05 5.28
1823 1826 2.522367 GGGAACAGAACCCACCGGA 61.522 63.158 9.46 0.00 46.05 5.14
1824 1827 1.003718 GGAACAGAACCCACCGGAG 60.004 63.158 9.46 0.00 0.00 4.63
1825 1828 1.671379 GAACAGAACCCACCGGAGC 60.671 63.158 9.46 0.00 0.00 4.70
1826 1829 3.192103 AACAGAACCCACCGGAGCC 62.192 63.158 9.46 0.00 0.00 4.70
1827 1830 3.636231 CAGAACCCACCGGAGCCA 61.636 66.667 9.46 0.00 0.00 4.75
1828 1831 2.610859 AGAACCCACCGGAGCCAT 60.611 61.111 9.46 0.00 0.00 4.40
1829 1832 1.306654 AGAACCCACCGGAGCCATA 60.307 57.895 9.46 0.00 0.00 2.74
1830 1833 1.146263 GAACCCACCGGAGCCATAG 59.854 63.158 9.46 0.00 0.00 2.23
1831 1834 2.942648 GAACCCACCGGAGCCATAGC 62.943 65.000 9.46 0.00 40.32 2.97
1832 1835 4.609018 CCCACCGGAGCCATAGCG 62.609 72.222 9.46 0.00 46.67 4.26
1833 1836 3.536917 CCACCGGAGCCATAGCGA 61.537 66.667 9.46 0.00 46.67 4.93
1834 1837 2.499205 CACCGGAGCCATAGCGAA 59.501 61.111 9.46 0.00 46.67 4.70
1835 1838 1.153449 CACCGGAGCCATAGCGAAA 60.153 57.895 9.46 0.00 46.67 3.46
1836 1839 1.144057 ACCGGAGCCATAGCGAAAG 59.856 57.895 9.46 0.00 46.67 2.62
1879 1882 5.649831 GGATGAAGCTTGGATGAAACTAAGT 59.350 40.000 2.10 0.00 32.34 2.24
1892 3478 5.075493 TGAAACTAAGTAGAGGTCCGAACT 58.925 41.667 0.00 0.00 0.00 3.01
1947 3533 1.668826 TAGGGGTGAAATGCCACTCT 58.331 50.000 0.00 0.00 39.36 3.24
2021 3607 3.392616 CTGGACATCTAGGGGTAAAGCAT 59.607 47.826 0.00 0.00 0.00 3.79
2028 3614 5.249780 TCTAGGGGTAAAGCATTGTTTCA 57.750 39.130 0.00 0.00 0.00 2.69
2057 3643 1.807981 CGCGAGCGGTACCAAATCA 60.808 57.895 13.54 0.00 35.56 2.57
2143 3729 1.843851 TGGGGGATAAGCTTCATCGTT 59.156 47.619 0.00 0.00 0.00 3.85
2145 3731 2.222027 GGGGATAAGCTTCATCGTTGG 58.778 52.381 0.00 0.00 0.00 3.77
2156 3742 1.422024 TCATCGTTGGGAGGGAAACAA 59.578 47.619 0.00 0.00 0.00 2.83
2188 3774 2.173569 CAGCTAAGGCCCCTAAATGACT 59.826 50.000 0.00 0.00 39.73 3.41
2217 3804 1.497309 TAAAGGAGGTGGGGGTGCAG 61.497 60.000 0.00 0.00 0.00 4.41
2223 3810 2.829384 GGTGGGGGTGCAGAGACAA 61.829 63.158 0.00 0.00 0.00 3.18
2265 3852 1.144913 AGCCACCCTTTAAAGAGTGCA 59.855 47.619 20.99 0.00 33.89 4.57
2294 3881 4.081185 TGATCGAGCGCCCTTGCA 62.081 61.111 2.29 0.00 37.32 4.08
2362 3949 1.344953 AATGCATCGGTAGGGGAGCA 61.345 55.000 0.00 0.00 36.34 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.443681 CCTTGCCCGTGAAGTAAATCATT 59.556 43.478 0.00 0.00 0.00 2.57
52 53 6.697641 TCCTAGACTTGAACCAAATACCTT 57.302 37.500 0.00 0.00 0.00 3.50
57 58 4.273318 GCCATCCTAGACTTGAACCAAAT 58.727 43.478 0.00 0.00 0.00 2.32
59 60 2.026262 GGCCATCCTAGACTTGAACCAA 60.026 50.000 0.00 0.00 0.00 3.67
71 72 2.691996 TGCAGCTGGGCCATCCTA 60.692 61.111 17.12 0.00 36.20 2.94
88 89 5.222130 TGCTTCTTCTATTCTTTTCCCTGGT 60.222 40.000 0.00 0.00 0.00 4.00
152 155 1.508256 ACCAACTGAGCTATACCCCC 58.492 55.000 0.00 0.00 0.00 5.40
153 156 3.573695 TCTACCAACTGAGCTATACCCC 58.426 50.000 0.00 0.00 0.00 4.95
154 157 4.857509 CTCTACCAACTGAGCTATACCC 57.142 50.000 0.00 0.00 0.00 3.69
214 217 1.066143 CCGCCTGGACAATTAGACAGT 60.066 52.381 0.00 0.00 37.49 3.55
307 310 5.272283 TGTCTCAGTAGAGTTTTTCGGTT 57.728 39.130 0.00 0.00 42.66 4.44
310 313 7.906160 TCTTTTTGTCTCAGTAGAGTTTTTCG 58.094 34.615 0.00 0.00 42.66 3.46
315 318 6.234177 CCCATCTTTTTGTCTCAGTAGAGTT 58.766 40.000 0.00 0.00 42.66 3.01
349 352 2.690026 GCACATCCTACCTCCTCTACCA 60.690 54.545 0.00 0.00 0.00 3.25
368 371 7.360113 TCCATACTAGATATGAACAACTGCA 57.640 36.000 0.00 0.00 43.12 4.41
376 379 8.406297 GCATGTACGATCCATACTAGATATGAA 58.594 37.037 0.00 0.00 43.12 2.57
380 383 6.183360 CGTGCATGTACGATCCATACTAGATA 60.183 42.308 29.28 0.00 46.46 1.98
402 405 0.866061 CGCCGACTCCAACTATCGTG 60.866 60.000 0.00 0.00 34.02 4.35
471 474 3.695830 TCAAGTTATTCGCAAGGTCCT 57.304 42.857 0.00 0.00 38.47 3.85
474 477 3.081061 TGCATCAAGTTATTCGCAAGGT 58.919 40.909 0.00 0.00 38.47 3.50
519 522 6.976934 TTTCCTTCCTTTTGCTACATTTCT 57.023 33.333 0.00 0.00 0.00 2.52
554 557 0.252239 GGGGTGGAGAAAATGGGCTT 60.252 55.000 0.00 0.00 0.00 4.35
556 559 2.052104 CGGGGTGGAGAAAATGGGC 61.052 63.158 0.00 0.00 0.00 5.36
563 566 0.115745 AGTTCCTACGGGGTGGAGAA 59.884 55.000 0.00 0.00 36.25 2.87
625 628 2.291735 TGAACAGGGTCTATGGTCGGTA 60.292 50.000 0.00 0.00 37.18 4.02
673 676 1.745489 CTTACTGCCCAACCGGAGC 60.745 63.158 9.46 5.96 0.00 4.70
705 708 5.298276 TGCTGGTTTTAAGAACGAGTGATTT 59.702 36.000 0.00 0.00 0.00 2.17
782 785 4.153411 CGGGGAATCTAGTTACAGGAGAT 58.847 47.826 0.00 0.00 0.00 2.75
795 798 0.912486 CTTCTGGTTCCGGGGAATCT 59.088 55.000 11.74 0.00 36.30 2.40
842 845 9.154847 CTTCTCAAAATCTCAAAACAAAAGGTT 57.845 29.630 0.00 0.00 42.98 3.50
924 927 2.011947 GGCCAACGGTAGACAATAACC 58.988 52.381 0.00 0.00 0.00 2.85
936 939 1.410004 TCTACCATAGAGGCCAACGG 58.590 55.000 5.01 0.00 43.14 4.44
1031 1034 5.528690 TCATAGTATACGCTAAGTTCACGGT 59.471 40.000 0.00 0.00 0.00 4.83
1046 1049 8.496707 TTCGGTGTTATCGCTATCATAGTATA 57.503 34.615 0.00 0.00 0.00 1.47
1091 1094 7.994334 TGTCCATGAATGTGAAATCATAGATCA 59.006 33.333 0.00 2.51 34.61 2.92
1134 1137 4.127907 GCCATCCTAAGGTGCTACTAAAC 58.872 47.826 0.00 0.00 0.00 2.01
1227 1230 1.377333 GCTTGCTACGCCCTTCCTT 60.377 57.895 0.00 0.00 0.00 3.36
1317 1320 0.622136 TGCTCATGGATTCAGCAGGT 59.378 50.000 2.10 0.00 38.25 4.00
1418 1421 2.817844 GTTTAGGTTGCTCCCATTTCGT 59.182 45.455 0.00 0.00 36.75 3.85
1551 1554 2.409651 CTACTCGGGTCAGAGCGC 59.590 66.667 0.00 0.00 41.77 5.92
1578 1581 1.349357 TGATTCACACGGGATTCCACA 59.651 47.619 4.80 0.00 0.00 4.17
1613 1616 3.054361 CACCCAGGAGTATTTAGCCTTGT 60.054 47.826 0.00 0.00 0.00 3.16
1614 1617 3.199946 TCACCCAGGAGTATTTAGCCTTG 59.800 47.826 0.00 0.00 0.00 3.61
1615 1618 3.200165 GTCACCCAGGAGTATTTAGCCTT 59.800 47.826 0.00 0.00 0.00 4.35
1616 1619 2.772515 GTCACCCAGGAGTATTTAGCCT 59.227 50.000 0.00 0.00 0.00 4.58
1617 1620 2.504175 TGTCACCCAGGAGTATTTAGCC 59.496 50.000 0.00 0.00 0.00 3.93
1618 1621 3.906720 TGTCACCCAGGAGTATTTAGC 57.093 47.619 0.00 0.00 0.00 3.09
1619 1622 6.483640 GCTATTTGTCACCCAGGAGTATTTAG 59.516 42.308 0.00 0.00 0.00 1.85
1620 1623 6.354130 GCTATTTGTCACCCAGGAGTATTTA 58.646 40.000 0.00 0.00 0.00 1.40
1621 1624 5.193679 GCTATTTGTCACCCAGGAGTATTT 58.806 41.667 0.00 0.00 0.00 1.40
1622 1625 4.683400 CGCTATTTGTCACCCAGGAGTATT 60.683 45.833 0.00 0.00 0.00 1.89
1623 1626 3.181465 CGCTATTTGTCACCCAGGAGTAT 60.181 47.826 0.00 0.00 0.00 2.12
1624 1627 2.167693 CGCTATTTGTCACCCAGGAGTA 59.832 50.000 0.00 0.00 0.00 2.59
1625 1628 1.066143 CGCTATTTGTCACCCAGGAGT 60.066 52.381 0.00 0.00 0.00 3.85
1626 1629 1.207089 TCGCTATTTGTCACCCAGGAG 59.793 52.381 0.00 0.00 0.00 3.69
1627 1630 1.271856 TCGCTATTTGTCACCCAGGA 58.728 50.000 0.00 0.00 0.00 3.86
1628 1631 2.009774 CTTCGCTATTTGTCACCCAGG 58.990 52.381 0.00 0.00 0.00 4.45
1629 1632 2.699954 ACTTCGCTATTTGTCACCCAG 58.300 47.619 0.00 0.00 0.00 4.45
1630 1633 2.851263 ACTTCGCTATTTGTCACCCA 57.149 45.000 0.00 0.00 0.00 4.51
1631 1634 3.858247 ACTACTTCGCTATTTGTCACCC 58.142 45.455 0.00 0.00 0.00 4.61
1632 1635 4.802563 GGTACTACTTCGCTATTTGTCACC 59.197 45.833 0.00 0.00 0.00 4.02
1633 1636 4.498323 CGGTACTACTTCGCTATTTGTCAC 59.502 45.833 0.00 0.00 0.00 3.67
1634 1637 4.156556 ACGGTACTACTTCGCTATTTGTCA 59.843 41.667 0.00 0.00 0.00 3.58
1635 1638 4.498323 CACGGTACTACTTCGCTATTTGTC 59.502 45.833 0.00 0.00 0.00 3.18
1636 1639 4.156556 TCACGGTACTACTTCGCTATTTGT 59.843 41.667 0.00 0.00 0.00 2.83
1637 1640 4.665212 TCACGGTACTACTTCGCTATTTG 58.335 43.478 0.00 0.00 0.00 2.32
1638 1641 4.201990 CCTCACGGTACTACTTCGCTATTT 60.202 45.833 0.00 0.00 0.00 1.40
1639 1642 3.314635 CCTCACGGTACTACTTCGCTATT 59.685 47.826 0.00 0.00 0.00 1.73
1640 1643 2.877168 CCTCACGGTACTACTTCGCTAT 59.123 50.000 0.00 0.00 0.00 2.97
1641 1644 2.283298 CCTCACGGTACTACTTCGCTA 58.717 52.381 0.00 0.00 0.00 4.26
1642 1645 1.093159 CCTCACGGTACTACTTCGCT 58.907 55.000 0.00 0.00 0.00 4.93
1643 1646 0.100146 CCCTCACGGTACTACTTCGC 59.900 60.000 0.00 0.00 0.00 4.70
1644 1647 1.742761 TCCCTCACGGTACTACTTCG 58.257 55.000 0.00 0.00 0.00 3.79
1645 1648 3.119209 CCTTTCCCTCACGGTACTACTTC 60.119 52.174 0.00 0.00 0.00 3.01
1646 1649 2.830321 CCTTTCCCTCACGGTACTACTT 59.170 50.000 0.00 0.00 0.00 2.24
1647 1650 2.225217 ACCTTTCCCTCACGGTACTACT 60.225 50.000 0.00 0.00 0.00 2.57
1648 1651 2.094338 CACCTTTCCCTCACGGTACTAC 60.094 54.545 0.00 0.00 0.00 2.73
1649 1652 2.173519 CACCTTTCCCTCACGGTACTA 58.826 52.381 0.00 0.00 0.00 1.82
1650 1653 0.974383 CACCTTTCCCTCACGGTACT 59.026 55.000 0.00 0.00 0.00 2.73
1651 1654 0.971386 TCACCTTTCCCTCACGGTAC 59.029 55.000 0.00 0.00 0.00 3.34
1652 1655 1.719529 TTCACCTTTCCCTCACGGTA 58.280 50.000 0.00 0.00 0.00 4.02
1653 1656 0.841289 TTTCACCTTTCCCTCACGGT 59.159 50.000 0.00 0.00 0.00 4.83
1654 1657 1.880027 CTTTTCACCTTTCCCTCACGG 59.120 52.381 0.00 0.00 0.00 4.94
1655 1658 2.846193 TCTTTTCACCTTTCCCTCACG 58.154 47.619 0.00 0.00 0.00 4.35
1656 1659 3.318275 GGTTCTTTTCACCTTTCCCTCAC 59.682 47.826 0.00 0.00 0.00 3.51
1657 1660 3.562182 GGTTCTTTTCACCTTTCCCTCA 58.438 45.455 0.00 0.00 0.00 3.86
1658 1661 2.891580 GGGTTCTTTTCACCTTTCCCTC 59.108 50.000 0.00 0.00 34.36 4.30
1659 1662 2.425829 GGGGTTCTTTTCACCTTTCCCT 60.426 50.000 0.00 0.00 34.36 4.20
1660 1663 1.968493 GGGGTTCTTTTCACCTTTCCC 59.032 52.381 0.00 0.00 34.36 3.97
1661 1664 2.673258 TGGGGTTCTTTTCACCTTTCC 58.327 47.619 0.00 0.00 34.36 3.13
1662 1665 3.704566 ACTTGGGGTTCTTTTCACCTTTC 59.295 43.478 0.00 0.00 34.36 2.62
1663 1666 3.450817 CACTTGGGGTTCTTTTCACCTTT 59.549 43.478 0.00 0.00 34.36 3.11
1664 1667 3.031013 CACTTGGGGTTCTTTTCACCTT 58.969 45.455 0.00 0.00 34.36 3.50
1665 1668 2.666317 CACTTGGGGTTCTTTTCACCT 58.334 47.619 0.00 0.00 34.36 4.00
1666 1669 1.686587 CCACTTGGGGTTCTTTTCACC 59.313 52.381 0.00 0.00 0.00 4.02
1679 1682 4.630069 CGTTCTATTTCACTACCCACTTGG 59.370 45.833 0.00 0.00 41.37 3.61
1680 1683 5.120208 CACGTTCTATTTCACTACCCACTTG 59.880 44.000 0.00 0.00 0.00 3.16
1681 1684 5.011329 TCACGTTCTATTTCACTACCCACTT 59.989 40.000 0.00 0.00 0.00 3.16
1682 1685 4.525487 TCACGTTCTATTTCACTACCCACT 59.475 41.667 0.00 0.00 0.00 4.00
1683 1686 4.813027 TCACGTTCTATTTCACTACCCAC 58.187 43.478 0.00 0.00 0.00 4.61
1684 1687 5.471556 TTCACGTTCTATTTCACTACCCA 57.528 39.130 0.00 0.00 0.00 4.51
1685 1688 5.121298 GGTTTCACGTTCTATTTCACTACCC 59.879 44.000 0.00 0.00 0.00 3.69
1686 1689 5.164022 CGGTTTCACGTTCTATTTCACTACC 60.164 44.000 0.00 0.00 0.00 3.18
1687 1690 5.403466 ACGGTTTCACGTTCTATTTCACTAC 59.597 40.000 0.00 0.00 46.25 2.73
1688 1691 5.403166 CACGGTTTCACGTTCTATTTCACTA 59.597 40.000 0.00 0.00 46.25 2.74
1689 1692 4.210537 CACGGTTTCACGTTCTATTTCACT 59.789 41.667 0.00 0.00 46.25 3.41
1690 1693 4.451557 CACGGTTTCACGTTCTATTTCAC 58.548 43.478 0.00 0.00 46.25 3.18
1691 1694 3.059461 GCACGGTTTCACGTTCTATTTCA 60.059 43.478 0.00 0.00 46.25 2.69
1692 1695 3.185797 AGCACGGTTTCACGTTCTATTTC 59.814 43.478 0.00 0.00 46.25 2.17
1693 1696 3.059188 CAGCACGGTTTCACGTTCTATTT 60.059 43.478 0.00 0.00 46.25 1.40
1694 1697 2.478894 CAGCACGGTTTCACGTTCTATT 59.521 45.455 0.00 0.00 46.25 1.73
1695 1698 2.066262 CAGCACGGTTTCACGTTCTAT 58.934 47.619 0.00 0.00 46.25 1.98
1696 1699 1.067364 TCAGCACGGTTTCACGTTCTA 59.933 47.619 0.00 0.00 46.25 2.10
1697 1700 0.179094 TCAGCACGGTTTCACGTTCT 60.179 50.000 0.00 0.00 46.25 3.01
1698 1701 0.232303 CTCAGCACGGTTTCACGTTC 59.768 55.000 0.00 0.00 46.25 3.95
1699 1702 1.772063 GCTCAGCACGGTTTCACGTT 61.772 55.000 0.00 0.00 46.25 3.99
1701 1704 1.891060 GAGCTCAGCACGGTTTCACG 61.891 60.000 9.40 0.00 40.31 4.35
1702 1705 1.569479 GGAGCTCAGCACGGTTTCAC 61.569 60.000 17.19 0.00 0.00 3.18
1703 1706 1.301716 GGAGCTCAGCACGGTTTCA 60.302 57.895 17.19 0.00 0.00 2.69
1704 1707 2.035442 GGGAGCTCAGCACGGTTTC 61.035 63.158 17.19 0.00 0.00 2.78
1705 1708 2.032681 GGGAGCTCAGCACGGTTT 59.967 61.111 17.19 0.00 0.00 3.27
1706 1709 2.738213 CTTGGGAGCTCAGCACGGTT 62.738 60.000 17.19 0.00 0.00 4.44
1707 1710 3.241530 TTGGGAGCTCAGCACGGT 61.242 61.111 17.19 0.00 0.00 4.83
1708 1711 2.435586 CTTGGGAGCTCAGCACGG 60.436 66.667 17.19 0.00 0.00 4.94
1709 1712 3.123620 GCTTGGGAGCTCAGCACG 61.124 66.667 17.19 0.45 45.65 5.34
1721 1724 2.080336 TTTCCCCTCCCACTGCTTGG 62.080 60.000 0.00 0.00 46.47 3.61
1722 1725 0.610232 CTTTCCCCTCCCACTGCTTG 60.610 60.000 0.00 0.00 0.00 4.01
1723 1726 1.068352 ACTTTCCCCTCCCACTGCTT 61.068 55.000 0.00 0.00 0.00 3.91
1724 1727 1.464198 ACTTTCCCCTCCCACTGCT 60.464 57.895 0.00 0.00 0.00 4.24
1725 1728 1.303643 CACTTTCCCCTCCCACTGC 60.304 63.158 0.00 0.00 0.00 4.40
1726 1729 0.995024 ATCACTTTCCCCTCCCACTG 59.005 55.000 0.00 0.00 0.00 3.66
1727 1730 1.203492 AGATCACTTTCCCCTCCCACT 60.203 52.381 0.00 0.00 0.00 4.00
1728 1731 1.210722 GAGATCACTTTCCCCTCCCAC 59.789 57.143 0.00 0.00 0.00 4.61
1729 1732 1.081174 AGAGATCACTTTCCCCTCCCA 59.919 52.381 0.00 0.00 0.00 4.37
1730 1733 1.488393 CAGAGATCACTTTCCCCTCCC 59.512 57.143 0.00 0.00 0.00 4.30
1731 1734 2.169561 GTCAGAGATCACTTTCCCCTCC 59.830 54.545 0.00 0.00 0.00 4.30
1732 1735 2.169561 GGTCAGAGATCACTTTCCCCTC 59.830 54.545 0.00 0.00 0.00 4.30
1733 1736 2.192263 GGTCAGAGATCACTTTCCCCT 58.808 52.381 0.00 0.00 0.00 4.79
1734 1737 1.909302 TGGTCAGAGATCACTTTCCCC 59.091 52.381 0.00 0.00 0.00 4.81
1735 1738 2.675317 CGTGGTCAGAGATCACTTTCCC 60.675 54.545 8.58 0.00 41.08 3.97
1736 1739 2.028930 ACGTGGTCAGAGATCACTTTCC 60.029 50.000 8.58 0.00 41.08 3.13
1737 1740 3.305398 ACGTGGTCAGAGATCACTTTC 57.695 47.619 8.58 0.00 41.08 2.62
1738 1741 3.555168 GGAACGTGGTCAGAGATCACTTT 60.555 47.826 8.58 5.48 41.08 2.66
1739 1742 2.028930 GGAACGTGGTCAGAGATCACTT 60.029 50.000 8.58 0.00 41.08 3.16
1740 1743 1.546476 GGAACGTGGTCAGAGATCACT 59.454 52.381 8.58 0.00 41.08 3.41
1741 1744 1.546476 AGGAACGTGGTCAGAGATCAC 59.454 52.381 0.38 0.38 39.98 3.06
1742 1745 1.546029 CAGGAACGTGGTCAGAGATCA 59.454 52.381 0.00 0.00 0.00 2.92
1743 1746 1.546476 ACAGGAACGTGGTCAGAGATC 59.454 52.381 0.00 0.00 0.00 2.75
1744 1747 1.633774 ACAGGAACGTGGTCAGAGAT 58.366 50.000 0.00 0.00 0.00 2.75
1745 1748 1.068588 CAACAGGAACGTGGTCAGAGA 59.931 52.381 0.00 0.00 0.00 3.10
1746 1749 1.068588 TCAACAGGAACGTGGTCAGAG 59.931 52.381 0.00 0.00 0.00 3.35
1747 1750 1.116308 TCAACAGGAACGTGGTCAGA 58.884 50.000 0.00 0.00 0.00 3.27
1748 1751 1.867233 CTTCAACAGGAACGTGGTCAG 59.133 52.381 0.00 0.00 0.00 3.51
1749 1752 1.483004 TCTTCAACAGGAACGTGGTCA 59.517 47.619 0.00 0.00 0.00 4.02
1750 1753 2.234300 TCTTCAACAGGAACGTGGTC 57.766 50.000 0.00 0.00 0.00 4.02
1751 1754 2.702592 TTCTTCAACAGGAACGTGGT 57.297 45.000 0.00 0.00 0.00 4.16
1752 1755 3.138304 TCATTCTTCAACAGGAACGTGG 58.862 45.455 0.00 0.00 0.00 4.94
1753 1756 3.364366 GCTCATTCTTCAACAGGAACGTG 60.364 47.826 0.00 0.00 0.00 4.49
1754 1757 2.808543 GCTCATTCTTCAACAGGAACGT 59.191 45.455 0.00 0.00 0.00 3.99
1755 1758 2.160417 GGCTCATTCTTCAACAGGAACG 59.840 50.000 0.00 0.00 0.00 3.95
1756 1759 2.160417 CGGCTCATTCTTCAACAGGAAC 59.840 50.000 0.00 0.00 0.00 3.62
1757 1760 2.426522 CGGCTCATTCTTCAACAGGAA 58.573 47.619 0.00 0.00 0.00 3.36
1758 1761 1.339055 CCGGCTCATTCTTCAACAGGA 60.339 52.381 0.00 0.00 0.00 3.86
1759 1762 1.089920 CCGGCTCATTCTTCAACAGG 58.910 55.000 0.00 0.00 0.00 4.00
1760 1763 0.449388 GCCGGCTCATTCTTCAACAG 59.551 55.000 22.15 0.00 0.00 3.16
1761 1764 1.298157 CGCCGGCTCATTCTTCAACA 61.298 55.000 26.68 0.00 0.00 3.33
1762 1765 1.019278 TCGCCGGCTCATTCTTCAAC 61.019 55.000 26.68 0.00 0.00 3.18
1763 1766 1.019278 GTCGCCGGCTCATTCTTCAA 61.019 55.000 26.68 0.00 0.00 2.69
1764 1767 1.447838 GTCGCCGGCTCATTCTTCA 60.448 57.895 26.68 0.00 0.00 3.02
1765 1768 1.148759 GAGTCGCCGGCTCATTCTTC 61.149 60.000 26.68 8.42 33.45 2.87
1766 1769 1.153549 GAGTCGCCGGCTCATTCTT 60.154 57.895 26.68 2.26 33.45 2.52
1767 1770 1.888436 TTGAGTCGCCGGCTCATTCT 61.888 55.000 23.34 14.53 41.87 2.40
1768 1771 1.019278 TTTGAGTCGCCGGCTCATTC 61.019 55.000 23.34 16.95 41.87 2.67
1769 1772 1.003839 TTTGAGTCGCCGGCTCATT 60.004 52.632 23.34 7.50 41.87 2.57
1770 1773 1.448540 CTTTGAGTCGCCGGCTCAT 60.449 57.895 23.34 9.64 41.87 2.90
1771 1774 2.048222 CTTTGAGTCGCCGGCTCA 60.048 61.111 26.68 18.78 40.76 4.26
1772 1775 2.781595 TTCCTTTGAGTCGCCGGCTC 62.782 60.000 26.68 12.63 0.00 4.70
1773 1776 2.788191 CTTCCTTTGAGTCGCCGGCT 62.788 60.000 26.68 5.36 0.00 5.52
1774 1777 2.358247 TTCCTTTGAGTCGCCGGC 60.358 61.111 19.07 19.07 0.00 6.13
1775 1778 0.602905 AACTTCCTTTGAGTCGCCGG 60.603 55.000 0.00 0.00 0.00 6.13
1776 1779 0.512952 CAACTTCCTTTGAGTCGCCG 59.487 55.000 0.00 0.00 0.00 6.46
1777 1780 0.238553 GCAACTTCCTTTGAGTCGCC 59.761 55.000 0.00 0.00 0.00 5.54
1778 1781 1.230324 AGCAACTTCCTTTGAGTCGC 58.770 50.000 0.00 0.00 0.00 5.19
1779 1782 2.031682 CCAAGCAACTTCCTTTGAGTCG 60.032 50.000 0.00 0.00 0.00 4.18
1780 1783 2.952310 ACCAAGCAACTTCCTTTGAGTC 59.048 45.455 0.00 0.00 0.00 3.36
1781 1784 3.018423 ACCAAGCAACTTCCTTTGAGT 57.982 42.857 0.00 0.00 0.00 3.41
1782 1785 5.507985 CCTTAACCAAGCAACTTCCTTTGAG 60.508 44.000 0.00 0.00 0.00 3.02
1783 1786 4.340950 CCTTAACCAAGCAACTTCCTTTGA 59.659 41.667 0.00 0.00 0.00 2.69
1784 1787 4.501400 CCCTTAACCAAGCAACTTCCTTTG 60.501 45.833 0.00 0.00 0.00 2.77
1785 1788 3.641436 CCCTTAACCAAGCAACTTCCTTT 59.359 43.478 0.00 0.00 0.00 3.11
1786 1789 3.117284 TCCCTTAACCAAGCAACTTCCTT 60.117 43.478 0.00 0.00 0.00 3.36
1787 1790 2.445525 TCCCTTAACCAAGCAACTTCCT 59.554 45.455 0.00 0.00 0.00 3.36
1788 1791 2.871453 TCCCTTAACCAAGCAACTTCC 58.129 47.619 0.00 0.00 0.00 3.46
1789 1792 3.634910 TGTTCCCTTAACCAAGCAACTTC 59.365 43.478 0.00 0.00 37.27 3.01
1790 1793 3.636764 CTGTTCCCTTAACCAAGCAACTT 59.363 43.478 0.00 0.00 37.27 2.66
1791 1794 3.117663 TCTGTTCCCTTAACCAAGCAACT 60.118 43.478 0.00 0.00 37.27 3.16
1792 1795 3.219281 TCTGTTCCCTTAACCAAGCAAC 58.781 45.455 0.00 0.00 37.27 4.17
1793 1796 3.586470 TCTGTTCCCTTAACCAAGCAA 57.414 42.857 0.00 0.00 37.27 3.91
1794 1797 3.219281 GTTCTGTTCCCTTAACCAAGCA 58.781 45.455 0.00 0.00 37.27 3.91
1795 1798 2.557056 GGTTCTGTTCCCTTAACCAAGC 59.443 50.000 0.00 0.00 40.89 4.01
1796 1799 3.154710 GGGTTCTGTTCCCTTAACCAAG 58.845 50.000 0.00 0.00 42.61 3.61
1797 1800 2.514582 TGGGTTCTGTTCCCTTAACCAA 59.485 45.455 0.00 0.00 44.84 3.67
1798 1801 2.136863 TGGGTTCTGTTCCCTTAACCA 58.863 47.619 0.00 0.00 44.84 3.67
1799 1802 2.511659 GTGGGTTCTGTTCCCTTAACC 58.488 52.381 10.16 0.00 44.84 2.85
1800 1803 2.511659 GGTGGGTTCTGTTCCCTTAAC 58.488 52.381 10.16 0.00 44.84 2.01
1801 1804 1.072648 CGGTGGGTTCTGTTCCCTTAA 59.927 52.381 10.16 0.00 44.84 1.85
1802 1805 0.688487 CGGTGGGTTCTGTTCCCTTA 59.312 55.000 10.16 0.00 44.84 2.69
1803 1806 1.454539 CGGTGGGTTCTGTTCCCTT 59.545 57.895 10.16 0.00 44.84 3.95
1804 1807 2.526046 CCGGTGGGTTCTGTTCCCT 61.526 63.158 0.00 0.00 44.84 4.20
1805 1808 2.033602 CCGGTGGGTTCTGTTCCC 59.966 66.667 0.00 0.00 44.81 3.97
1806 1809 1.003718 CTCCGGTGGGTTCTGTTCC 60.004 63.158 0.00 0.00 33.83 3.62
1807 1810 1.671379 GCTCCGGTGGGTTCTGTTC 60.671 63.158 0.00 0.00 33.83 3.18
1808 1811 2.430367 GCTCCGGTGGGTTCTGTT 59.570 61.111 0.00 0.00 33.83 3.16
1809 1812 3.637273 GGCTCCGGTGGGTTCTGT 61.637 66.667 0.00 0.00 33.83 3.41
1810 1813 1.622607 TATGGCTCCGGTGGGTTCTG 61.623 60.000 0.00 0.00 33.83 3.02
1811 1814 1.306654 TATGGCTCCGGTGGGTTCT 60.307 57.895 0.00 0.00 33.83 3.01
1812 1815 1.146263 CTATGGCTCCGGTGGGTTC 59.854 63.158 0.00 0.00 33.83 3.62
1813 1816 3.043999 GCTATGGCTCCGGTGGGTT 62.044 63.158 0.00 0.00 35.22 4.11
1814 1817 3.480133 GCTATGGCTCCGGTGGGT 61.480 66.667 0.00 0.00 35.22 4.51
1815 1818 4.609018 CGCTATGGCTCCGGTGGG 62.609 72.222 0.00 0.00 36.09 4.61
1816 1819 2.587322 TTTCGCTATGGCTCCGGTGG 62.587 60.000 0.00 0.00 36.09 4.61
1817 1820 1.153449 TTTCGCTATGGCTCCGGTG 60.153 57.895 0.00 0.00 36.09 4.94
1818 1821 1.144057 CTTTCGCTATGGCTCCGGT 59.856 57.895 0.00 0.00 36.09 5.28
1819 1822 2.247437 GCTTTCGCTATGGCTCCGG 61.247 63.158 0.00 0.00 36.09 5.14
1820 1823 2.589492 CGCTTTCGCTATGGCTCCG 61.589 63.158 0.00 0.00 36.09 4.63
1821 1824 1.218230 CTCGCTTTCGCTATGGCTCC 61.218 60.000 0.00 0.00 36.09 4.70
1822 1825 0.528684 ACTCGCTTTCGCTATGGCTC 60.529 55.000 0.00 0.00 36.09 4.70
1823 1826 0.528684 GACTCGCTTTCGCTATGGCT 60.529 55.000 0.00 0.00 36.09 4.75
1824 1827 0.528684 AGACTCGCTTTCGCTATGGC 60.529 55.000 0.00 0.00 35.26 4.40
1825 1828 2.776312 TAGACTCGCTTTCGCTATGG 57.224 50.000 0.00 0.00 35.26 2.74
1826 1829 3.238441 GGATAGACTCGCTTTCGCTATG 58.762 50.000 0.00 0.00 35.26 2.23
1827 1830 2.885266 TGGATAGACTCGCTTTCGCTAT 59.115 45.455 0.00 0.00 35.26 2.97
1828 1831 2.294979 TGGATAGACTCGCTTTCGCTA 58.705 47.619 0.00 0.00 35.26 4.26
1829 1832 1.103803 TGGATAGACTCGCTTTCGCT 58.896 50.000 0.00 0.00 35.26 4.93
1830 1833 1.789464 CATGGATAGACTCGCTTTCGC 59.211 52.381 0.00 0.00 35.26 4.70
1831 1834 3.046390 GTCATGGATAGACTCGCTTTCG 58.954 50.000 0.00 0.00 33.29 3.46
1832 1835 3.181475 TGGTCATGGATAGACTCGCTTTC 60.181 47.826 0.00 0.00 36.29 2.62
1833 1836 2.766263 TGGTCATGGATAGACTCGCTTT 59.234 45.455 0.00 0.00 36.29 3.51
1834 1837 2.363680 CTGGTCATGGATAGACTCGCTT 59.636 50.000 0.00 0.00 36.29 4.68
1835 1838 1.959985 CTGGTCATGGATAGACTCGCT 59.040 52.381 0.00 0.00 36.29 4.93
1836 1839 1.000283 CCTGGTCATGGATAGACTCGC 60.000 57.143 0.00 0.00 36.29 5.03
1837 1840 2.587522 TCCTGGTCATGGATAGACTCG 58.412 52.381 0.00 0.00 36.29 4.18
1838 1841 4.155709 TCATCCTGGTCATGGATAGACTC 58.844 47.826 0.00 0.00 41.94 3.36
1839 1842 4.204792 TCATCCTGGTCATGGATAGACT 57.795 45.455 0.00 0.00 41.94 3.24
1840 1843 4.802248 GCTTCATCCTGGTCATGGATAGAC 60.802 50.000 0.00 0.00 41.94 2.59
1879 1882 2.873094 TCAGTCAGTTCGGACCTCTA 57.127 50.000 0.00 0.00 38.59 2.43
1913 3499 1.633432 CCCCTAACCACAACTCATCCA 59.367 52.381 0.00 0.00 0.00 3.41
2021 3607 2.844451 GCAGCCCGCACTGAAACAA 61.844 57.895 7.06 0.00 40.25 2.83
2057 3643 8.928448 TCATATCTAGTATTCAGAGTTTGCCTT 58.072 33.333 0.00 0.00 0.00 4.35
2143 3729 2.836187 CCGGGTTGTTTCCCTCCCA 61.836 63.158 0.00 0.00 44.95 4.37
2145 3731 0.393944 GATCCGGGTTGTTTCCCTCC 60.394 60.000 0.00 0.00 44.95 4.30
2188 3774 2.237143 CCACCTCCTTTATCACTGAGCA 59.763 50.000 0.00 0.00 0.00 4.26
2223 3810 1.630878 CTTCTAGGCAAACCTCCTGGT 59.369 52.381 0.00 0.00 46.34 4.00
2294 3881 1.568504 TAGCCCCGTTCATCTTCAGT 58.431 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.