Multiple sequence alignment - TraesCS5D01G441800

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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 TraesCS5D01G441800 chr5D 100.000 2561 0 0 1 2561 494188061 494190621 0.000000e+00 4730.0
1 TraesCS5D01G441800 chr5D 98.065 672 13 0 1 672 374625289 374624618 0.000000e+00 1170.0
2 TraesCS5D01G441800 chr5D 93.810 420 21 4 2145 2561 521224974 521224557 6.020000e-176 627.0
3 TraesCS5D01G441800 chr5D 91.250 400 29 6 1709 2106 179084264 179084659 8.060000e-150 540.0
4 TraesCS5D01G441800 chr5D 90.000 400 38 2 1709 2106 7892471 7892870 1.360000e-142 516.0
5 TraesCS5D01G441800 chr5B 93.160 1038 56 7 665 1702 610300678 610301700 0.000000e+00 1509.0
6 TraesCS5D01G441800 chr5B 93.587 421 24 1 1050 1470 655432286 655432703 2.160000e-175 625.0
7 TraesCS5D01G441800 chr5B 90.250 400 37 2 1709 2106 596507311 596506912 2.920000e-144 521.0
8 TraesCS5D01G441800 chr5B 90.254 236 17 5 1466 1700 655438150 655438380 1.150000e-78 303.0
9 TraesCS5D01G441800 chr5B 95.652 46 1 1 2097 2142 295650107 295650151 3.530000e-09 73.1
10 TraesCS5D01G441800 chr5A 93.159 994 50 9 674 1661 617204148 617205129 0.000000e+00 1443.0
11 TraesCS5D01G441800 chr5A 93.041 388 22 4 981 1368 617187420 617187802 1.720000e-156 562.0
12 TraesCS5D01G441800 chr2D 98.368 674 11 0 1 674 351066768 351066095 0.000000e+00 1184.0
13 TraesCS5D01G441800 chr2D 90.750 400 34 3 1709 2106 31474468 31474866 4.850000e-147 531.0
14 TraesCS5D01G441800 chr2D 90.074 403 37 3 1705 2105 506464630 506465031 1.050000e-143 520.0
15 TraesCS5D01G441800 chr7D 98.361 671 11 0 1 671 55778176 55777506 0.000000e+00 1179.0
16 TraesCS5D01G441800 chr7D 97.917 672 13 1 1 672 529615287 529614617 0.000000e+00 1162.0
17 TraesCS5D01G441800 chr1D 98.214 672 12 0 1 672 418015634 418016305 0.000000e+00 1175.0
18 TraesCS5D01G441800 chr3D 97.612 670 13 1 1 670 351118354 351117688 0.000000e+00 1146.0
19 TraesCS5D01G441800 chr3D 90.500 400 35 3 1709 2106 17116367 17116765 2.260000e-145 525.0
20 TraesCS5D01G441800 chr3D 90.274 401 34 4 1709 2106 573156160 573155762 1.050000e-143 520.0
21 TraesCS5D01G441800 chr6D 95.970 670 27 0 1 670 221623636 221624305 0.000000e+00 1088.0
22 TraesCS5D01G441800 chr6D 92.388 670 49 2 2 670 456549985 456550653 0.000000e+00 953.0
23 TraesCS5D01G441800 chr6D 90.226 399 34 2 1709 2106 397666745 397666351 1.360000e-142 516.0
24 TraesCS5D01G441800 chr6A 93.769 674 39 3 1 671 53996669 53995996 0.000000e+00 1009.0
25 TraesCS5D01G441800 chr6A 92.995 414 25 3 2151 2561 177805205 177804793 3.650000e-168 601.0
26 TraesCS5D01G441800 chr2A 93.095 420 25 3 2145 2561 745067745 745068163 1.680000e-171 612.0
27 TraesCS5D01G441800 chr2A 100.000 37 0 0 2106 2142 745067627 745067663 4.570000e-08 69.4
28 TraesCS5D01G441800 chr2A 97.368 38 1 0 2104 2141 602719689 602719726 5.910000e-07 65.8
29 TraesCS5D01G441800 chr3B 92.619 420 25 5 2145 2561 24045769 24045353 1.310000e-167 599.0
30 TraesCS5D01G441800 chr4A 91.905 420 27 4 2145 2561 5747637 5748052 4.750000e-162 580.0
31 TraesCS5D01G441800 chr4A 90.692 419 34 4 2145 2559 708512864 708512447 1.040000e-153 553.0
32 TraesCS5D01G441800 chr4A 89.268 410 39 5 1700 2106 563836973 563837380 2.270000e-140 508.0
33 TraesCS5D01G441800 chr4A 100.000 37 0 0 2106 2142 5747519 5747555 4.570000e-08 69.4
34 TraesCS5D01G441800 chr1B 91.429 420 32 3 2145 2561 656124027 656123609 7.950000e-160 573.0
35 TraesCS5D01G441800 chr1B 90.909 418 32 5 2147 2561 374862061 374862475 8.000000e-155 556.0
36 TraesCS5D01G441800 chr1B 91.774 389 27 4 2176 2561 499924155 499924541 1.040000e-148 536.0
37 TraesCS5D01G441800 chr1B 97.778 45 1 0 2098 2142 656124150 656124106 7.600000e-11 78.7
38 TraesCS5D01G441800 chr4B 76.991 226 44 8 1308 1528 13297746 13297968 3.460000e-24 122.0
39 TraesCS5D01G441800 chr2B 97.619 42 0 1 2101 2142 672611094 672611054 1.270000e-08 71.3
40 TraesCS5D01G441800 chr7B 100.000 35 0 0 2107 2141 92964543 92964577 5.910000e-07 65.8
41 TraesCS5D01G441800 chr7B 95.122 41 2 0 2102 2142 684290894 684290934 5.910000e-07 65.8
42 TraesCS5D01G441800 chr4D 97.297 37 1 0 2106 2142 385696647 385696683 2.130000e-06 63.9


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 TraesCS5D01G441800 chr5D 494188061 494190621 2560 False 4730.00 4730 100.0000 1 2561 1 chr5D.!!$F3 2560
1 TraesCS5D01G441800 chr5D 374624618 374625289 671 True 1170.00 1170 98.0650 1 672 1 chr5D.!!$R1 671
2 TraesCS5D01G441800 chr5B 610300678 610301700 1022 False 1509.00 1509 93.1600 665 1702 1 chr5B.!!$F2 1037
3 TraesCS5D01G441800 chr5A 617204148 617205129 981 False 1443.00 1443 93.1590 674 1661 1 chr5A.!!$F2 987
4 TraesCS5D01G441800 chr2D 351066095 351066768 673 True 1184.00 1184 98.3680 1 674 1 chr2D.!!$R1 673
5 TraesCS5D01G441800 chr7D 55777506 55778176 670 True 1179.00 1179 98.3610 1 671 1 chr7D.!!$R1 670
6 TraesCS5D01G441800 chr7D 529614617 529615287 670 True 1162.00 1162 97.9170 1 672 1 chr7D.!!$R2 671
7 TraesCS5D01G441800 chr1D 418015634 418016305 671 False 1175.00 1175 98.2140 1 672 1 chr1D.!!$F1 671
8 TraesCS5D01G441800 chr3D 351117688 351118354 666 True 1146.00 1146 97.6120 1 670 1 chr3D.!!$R1 669
9 TraesCS5D01G441800 chr6D 221623636 221624305 669 False 1088.00 1088 95.9700 1 670 1 chr6D.!!$F1 669
10 TraesCS5D01G441800 chr6D 456549985 456550653 668 False 953.00 953 92.3880 2 670 1 chr6D.!!$F2 668
11 TraesCS5D01G441800 chr6A 53995996 53996669 673 True 1009.00 1009 93.7690 1 671 1 chr6A.!!$R1 670
12 TraesCS5D01G441800 chr2A 745067627 745068163 536 False 340.70 612 96.5475 2106 2561 2 chr2A.!!$F2 455
13 TraesCS5D01G441800 chr4A 5747519 5748052 533 False 324.70 580 95.9525 2106 2561 2 chr4A.!!$F2 455
14 TraesCS5D01G441800 chr1B 656123609 656124150 541 True 325.85 573 94.6035 2098 2561 2 chr1B.!!$R1 463

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
706 713 0.036732 GGCTGACCATTGACTCCACA 59.963 55.0 0.0 0.0 35.26 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1829 0.104855 ACAAGCTGAGCACGAGTCAA 59.895 50.0 7.39 0.0 0.0 3.18 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
113 114 1.600023 CTGGCCACGAACTTTTACCA 58.400 50.000 0.00 0.00 0.00 3.25
388 389 6.456988 CGGTTGCAATACTTTCCAGATAGAAC 60.457 42.308 0.59 0.00 0.00 3.01
464 468 8.097038 ACAAGATTCAGCTACTGTATTTGAAGA 58.903 33.333 15.00 0.66 32.00 2.87
706 713 0.036732 GGCTGACCATTGACTCCACA 59.963 55.000 0.00 0.00 35.26 4.17
707 714 1.545428 GGCTGACCATTGACTCCACAA 60.545 52.381 0.00 0.00 35.26 3.33
708 715 2.440409 GCTGACCATTGACTCCACAAT 58.560 47.619 0.00 0.00 40.50 2.71
709 716 2.821969 GCTGACCATTGACTCCACAATT 59.178 45.455 0.00 0.00 38.25 2.32
710 717 3.366679 GCTGACCATTGACTCCACAATTG 60.367 47.826 3.24 3.24 38.25 2.32
711 718 4.074259 CTGACCATTGACTCCACAATTGA 58.926 43.478 13.59 0.00 38.25 2.57
790 797 1.238439 CCATTGACACTTGCGGACTT 58.762 50.000 0.00 0.00 0.00 3.01
791 798 1.069022 CCATTGACACTTGCGGACTTG 60.069 52.381 0.00 0.00 0.00 3.16
831 838 5.689383 TTCTCTGAATTTTCCAAGAACGG 57.311 39.130 0.00 0.00 0.00 4.44
863 871 1.021202 CTTCACGGCAAACTTGGTCA 58.979 50.000 0.00 0.00 0.00 4.02
879 887 4.751028 CTTGGTCATCAAGGTTCCTTCCTT 60.751 45.833 0.60 0.00 46.81 3.36
895 908 9.444600 GTTCCTTCCTTACTCACAATTTGTATA 57.555 33.333 0.86 0.00 0.00 1.47
896 909 9.444600 TTCCTTCCTTACTCACAATTTGTATAC 57.555 33.333 0.86 0.00 0.00 1.47
939 952 2.857152 CGCTTGCTCTGACAGATTCTAC 59.143 50.000 5.42 0.00 0.00 2.59
1014 1027 1.678970 GAAAATGGAGCAGGCCGGT 60.679 57.895 1.90 1.36 0.00 5.28
1178 1191 2.586245 CCTGCTCGCCTTCATCCA 59.414 61.111 0.00 0.00 0.00 3.41
1554 1567 2.108976 ACCGACACTGTGCTGGTG 59.891 61.111 19.90 3.46 40.19 4.17
1573 1586 3.689649 GGTGGACTGATTGGTGTGATAAC 59.310 47.826 0.00 0.00 0.00 1.89
1581 1594 4.696877 TGATTGGTGTGATAACTCAGCTTG 59.303 41.667 5.95 0.00 38.36 4.01
1596 1609 2.738846 CAGCTTGATGTATATCCACGCC 59.261 50.000 0.00 0.00 32.09 5.68
1669 1682 3.572642 TGTTCAGTCAAGTAGTCCTCCA 58.427 45.455 0.00 0.00 0.00 3.86
1676 1689 2.758979 TCAAGTAGTCCTCCATCCGTTC 59.241 50.000 0.00 0.00 0.00 3.95
1689 1702 0.736053 TCCGTTCACAAAGGCAACAC 59.264 50.000 0.00 0.00 41.41 3.32
1695 1708 2.907634 TCACAAAGGCAACACGTTCTA 58.092 42.857 0.00 0.00 41.41 2.10
1721 1734 4.932268 TTTTAATCGGGCTACAAACGAG 57.068 40.909 0.00 0.00 40.21 4.18
1722 1735 3.598019 TTAATCGGGCTACAAACGAGT 57.402 42.857 0.00 0.00 40.21 4.18
1723 1736 2.005971 AATCGGGCTACAAACGAGTC 57.994 50.000 0.00 0.00 40.21 3.36
1724 1737 0.179145 ATCGGGCTACAAACGAGTCG 60.179 55.000 11.85 11.85 40.21 4.18
1725 1738 1.210931 CGGGCTACAAACGAGTCGA 59.789 57.895 21.50 0.00 0.00 4.20
1726 1739 0.797249 CGGGCTACAAACGAGTCGAG 60.797 60.000 21.50 10.97 0.00 4.04
1727 1740 1.077089 GGGCTACAAACGAGTCGAGC 61.077 60.000 21.50 16.66 0.00 5.03
1728 1741 0.109226 GGCTACAAACGAGTCGAGCT 60.109 55.000 21.50 0.00 0.00 4.09
1729 1742 1.261097 GCTACAAACGAGTCGAGCTC 58.739 55.000 21.50 2.73 40.77 4.09
1730 1743 1.401148 GCTACAAACGAGTCGAGCTCA 60.401 52.381 21.50 0.00 44.33 4.26
1731 1744 2.921069 GCTACAAACGAGTCGAGCTCAA 60.921 50.000 21.50 0.00 44.33 3.02
1732 1745 2.218953 ACAAACGAGTCGAGCTCAAA 57.781 45.000 21.50 0.00 44.33 2.69
1733 1746 1.859080 ACAAACGAGTCGAGCTCAAAC 59.141 47.619 21.50 11.21 44.33 2.93
1734 1747 1.129326 AAACGAGTCGAGCTCAAACG 58.871 50.000 21.50 14.94 44.33 3.60
1735 1748 0.309922 AACGAGTCGAGCTCAAACGA 59.690 50.000 21.50 2.36 44.33 3.85
1736 1749 0.110147 ACGAGTCGAGCTCAAACGAG 60.110 55.000 21.50 12.16 44.33 4.18
1737 1750 0.110147 CGAGTCGAGCTCAAACGAGT 60.110 55.000 15.40 8.60 44.33 4.18
1738 1751 1.663445 CGAGTCGAGCTCAAACGAGTT 60.663 52.381 15.40 0.00 44.33 3.01
1739 1752 1.716581 GAGTCGAGCTCAAACGAGTTG 59.283 52.381 15.40 0.00 43.58 3.16
1740 1753 0.784778 GTCGAGCTCAAACGAGTTGG 59.215 55.000 15.40 0.00 39.16 3.77
1741 1754 0.671796 TCGAGCTCAAACGAGTTGGA 59.328 50.000 15.40 0.00 37.85 3.53
1742 1755 1.063806 CGAGCTCAAACGAGTTGGAG 58.936 55.000 15.40 14.38 42.25 3.86
1743 1756 1.603172 CGAGCTCAAACGAGTTGGAGT 60.603 52.381 18.45 8.17 41.57 3.85
1744 1757 2.484889 GAGCTCAAACGAGTTGGAGTT 58.515 47.619 18.45 14.09 41.57 3.01
1745 1758 2.213499 AGCTCAAACGAGTTGGAGTTG 58.787 47.619 18.45 1.17 41.57 3.16
1746 1759 1.264288 GCTCAAACGAGTTGGAGTTGG 59.736 52.381 18.45 0.00 41.57 3.77
1747 1760 1.264288 CTCAAACGAGTTGGAGTTGGC 59.736 52.381 11.27 0.00 36.20 4.52
1748 1761 1.134220 TCAAACGAGTTGGAGTTGGCT 60.134 47.619 0.00 0.00 37.85 4.75
1749 1762 1.264288 CAAACGAGTTGGAGTTGGCTC 59.736 52.381 0.00 0.00 40.93 4.70
1750 1763 0.468226 AACGAGTTGGAGTTGGCTCA 59.532 50.000 0.00 0.00 43.37 4.26
1751 1764 0.468226 ACGAGTTGGAGTTGGCTCAA 59.532 50.000 0.00 0.00 43.37 3.02
1752 1765 0.868406 CGAGTTGGAGTTGGCTCAAC 59.132 55.000 9.31 9.31 43.37 3.18
1763 1776 4.574599 GTTGGCTCAACTCAACTCAAAT 57.425 40.909 9.89 0.00 40.73 2.32
1764 1777 4.293415 GTTGGCTCAACTCAACTCAAATG 58.707 43.478 9.89 0.00 40.73 2.32
1765 1778 3.819368 TGGCTCAACTCAACTCAAATGA 58.181 40.909 0.00 0.00 0.00 2.57
1766 1779 4.206375 TGGCTCAACTCAACTCAAATGAA 58.794 39.130 0.00 0.00 0.00 2.57
1767 1780 4.644234 TGGCTCAACTCAACTCAAATGAAA 59.356 37.500 0.00 0.00 0.00 2.69
1768 1781 5.126869 TGGCTCAACTCAACTCAAATGAAAA 59.873 36.000 0.00 0.00 0.00 2.29
1769 1782 6.183360 TGGCTCAACTCAACTCAAATGAAAAT 60.183 34.615 0.00 0.00 0.00 1.82
1770 1783 6.703165 GGCTCAACTCAACTCAAATGAAAATT 59.297 34.615 0.00 0.00 0.00 1.82
1771 1784 7.095899 GGCTCAACTCAACTCAAATGAAAATTC 60.096 37.037 0.00 0.00 0.00 2.17
1772 1785 7.357859 GCTCAACTCAACTCAAATGAAAATTCG 60.358 37.037 0.00 0.00 0.00 3.34
1773 1786 7.702386 TCAACTCAACTCAAATGAAAATTCGA 58.298 30.769 0.00 0.00 0.00 3.71
1774 1787 7.857389 TCAACTCAACTCAAATGAAAATTCGAG 59.143 33.333 0.00 0.00 0.00 4.04
1775 1788 6.145535 ACTCAACTCAAATGAAAATTCGAGC 58.854 36.000 0.00 0.00 0.00 5.03
1776 1789 5.146460 TCAACTCAAATGAAAATTCGAGCG 58.854 37.500 0.00 0.00 0.00 5.03
1777 1790 5.049749 TCAACTCAAATGAAAATTCGAGCGA 60.050 36.000 0.00 0.00 0.00 4.93
1778 1791 4.962693 ACTCAAATGAAAATTCGAGCGAG 58.037 39.130 0.00 0.00 0.00 5.03
1779 1792 4.452455 ACTCAAATGAAAATTCGAGCGAGT 59.548 37.500 0.00 0.00 0.00 4.18
1780 1793 5.049405 ACTCAAATGAAAATTCGAGCGAGTT 60.049 36.000 0.00 0.00 0.00 3.01
1781 1794 5.382303 TCAAATGAAAATTCGAGCGAGTTC 58.618 37.500 1.18 4.20 0.00 3.01
1782 1795 5.049749 TCAAATGAAAATTCGAGCGAGTTCA 60.050 36.000 13.96 13.96 0.00 3.18
1783 1796 5.356882 AATGAAAATTCGAGCGAGTTCAA 57.643 34.783 14.94 1.82 30.68 2.69
1784 1797 4.804608 TGAAAATTCGAGCGAGTTCAAA 57.195 36.364 10.98 0.00 0.00 2.69
1785 1798 4.523813 TGAAAATTCGAGCGAGTTCAAAC 58.476 39.130 10.98 0.00 0.00 2.93
1786 1799 4.272504 TGAAAATTCGAGCGAGTTCAAACT 59.727 37.500 10.98 0.00 43.16 2.66
1787 1800 3.795561 AATTCGAGCGAGTTCAAACTG 57.204 42.857 0.00 0.00 39.88 3.16
1788 1801 2.502213 TTCGAGCGAGTTCAAACTGA 57.498 45.000 0.00 0.00 39.88 3.41
1789 1802 2.051879 TCGAGCGAGTTCAAACTGAG 57.948 50.000 0.00 0.00 39.88 3.35
1790 1803 1.337071 TCGAGCGAGTTCAAACTGAGT 59.663 47.619 0.00 0.00 39.88 3.41
1791 1804 1.453524 CGAGCGAGTTCAAACTGAGTG 59.546 52.381 0.00 0.00 39.88 3.51
1792 1805 2.743938 GAGCGAGTTCAAACTGAGTGA 58.256 47.619 0.00 0.00 39.88 3.41
1793 1806 3.123804 GAGCGAGTTCAAACTGAGTGAA 58.876 45.455 0.00 0.00 39.88 3.18
1794 1807 3.126831 AGCGAGTTCAAACTGAGTGAAG 58.873 45.455 0.00 0.00 39.88 3.02
1795 1808 2.348966 GCGAGTTCAAACTGAGTGAAGC 60.349 50.000 0.00 0.00 39.88 3.86
1796 1809 3.126831 CGAGTTCAAACTGAGTGAAGCT 58.873 45.455 0.00 0.00 39.88 3.74
1797 1810 3.557595 CGAGTTCAAACTGAGTGAAGCTT 59.442 43.478 0.00 0.00 39.88 3.74
1798 1811 4.745125 CGAGTTCAAACTGAGTGAAGCTTA 59.255 41.667 0.00 0.00 39.88 3.09
1799 1812 5.406780 CGAGTTCAAACTGAGTGAAGCTTAT 59.593 40.000 0.00 0.00 39.88 1.73
1800 1813 6.551385 AGTTCAAACTGAGTGAAGCTTATG 57.449 37.500 0.00 0.00 37.98 1.90
1801 1814 6.291377 AGTTCAAACTGAGTGAAGCTTATGA 58.709 36.000 0.00 0.00 37.98 2.15
1802 1815 6.939163 AGTTCAAACTGAGTGAAGCTTATGAT 59.061 34.615 0.00 0.00 37.98 2.45
1803 1816 6.974932 TCAAACTGAGTGAAGCTTATGATC 57.025 37.500 0.00 0.00 0.00 2.92
1804 1817 5.578336 TCAAACTGAGTGAAGCTTATGATCG 59.422 40.000 0.00 0.00 0.00 3.69
1805 1818 4.991153 ACTGAGTGAAGCTTATGATCGA 57.009 40.909 0.00 0.00 0.00 3.59
1806 1819 4.930963 ACTGAGTGAAGCTTATGATCGAG 58.069 43.478 0.00 0.00 0.00 4.04
1807 1820 3.711086 TGAGTGAAGCTTATGATCGAGC 58.289 45.455 0.00 0.00 39.17 5.03
1815 1828 4.865776 AGCTTATGATCGAGCTGTAGAAC 58.134 43.478 14.86 0.00 46.82 3.01
1816 1829 4.582656 AGCTTATGATCGAGCTGTAGAACT 59.417 41.667 14.86 0.00 46.82 3.01
1817 1830 5.068460 AGCTTATGATCGAGCTGTAGAACTT 59.932 40.000 14.86 0.00 46.82 2.66
1818 1831 5.174761 GCTTATGATCGAGCTGTAGAACTTG 59.825 44.000 0.90 0.00 36.01 3.16
1819 1832 4.991153 ATGATCGAGCTGTAGAACTTGA 57.009 40.909 0.90 0.00 0.00 3.02
1820 1833 4.098055 TGATCGAGCTGTAGAACTTGAC 57.902 45.455 0.90 0.00 0.00 3.18
1821 1834 3.759086 TGATCGAGCTGTAGAACTTGACT 59.241 43.478 0.90 0.00 0.00 3.41
1822 1835 3.833545 TCGAGCTGTAGAACTTGACTC 57.166 47.619 0.00 0.00 0.00 3.36
1823 1836 2.159824 TCGAGCTGTAGAACTTGACTCG 59.840 50.000 0.00 0.00 45.02 4.18
1824 1837 2.095668 CGAGCTGTAGAACTTGACTCGT 60.096 50.000 0.00 0.00 40.33 4.18
1825 1838 3.238441 GAGCTGTAGAACTTGACTCGTG 58.762 50.000 0.00 0.00 0.00 4.35
1826 1839 1.721926 GCTGTAGAACTTGACTCGTGC 59.278 52.381 0.00 0.00 0.00 5.34
1827 1840 2.608261 GCTGTAGAACTTGACTCGTGCT 60.608 50.000 0.00 0.00 0.00 4.40
1828 1841 3.238441 CTGTAGAACTTGACTCGTGCTC 58.762 50.000 0.00 0.00 0.00 4.26
1829 1842 2.621526 TGTAGAACTTGACTCGTGCTCA 59.378 45.455 0.00 0.00 0.00 4.26
1830 1843 2.430546 AGAACTTGACTCGTGCTCAG 57.569 50.000 0.00 0.00 0.00 3.35
1831 1844 0.787183 GAACTTGACTCGTGCTCAGC 59.213 55.000 0.00 0.00 0.00 4.26
1832 1845 0.390860 AACTTGACTCGTGCTCAGCT 59.609 50.000 0.00 0.00 0.00 4.24
1833 1846 0.390860 ACTTGACTCGTGCTCAGCTT 59.609 50.000 0.00 0.00 0.00 3.74
1834 1847 0.788995 CTTGACTCGTGCTCAGCTTG 59.211 55.000 0.00 0.00 0.00 4.01
1835 1848 0.104855 TTGACTCGTGCTCAGCTTGT 59.895 50.000 0.00 0.00 0.00 3.16
1836 1849 0.958822 TGACTCGTGCTCAGCTTGTA 59.041 50.000 0.00 0.00 0.00 2.41
1837 1850 1.339929 TGACTCGTGCTCAGCTTGTAA 59.660 47.619 0.00 0.00 0.00 2.41
1838 1851 1.721926 GACTCGTGCTCAGCTTGTAAC 59.278 52.381 0.00 0.00 0.00 2.50
1839 1852 1.068588 ACTCGTGCTCAGCTTGTAACA 59.931 47.619 0.00 0.00 0.00 2.41
1840 1853 2.135139 CTCGTGCTCAGCTTGTAACAA 58.865 47.619 0.00 0.00 0.00 2.83
1841 1854 2.738846 CTCGTGCTCAGCTTGTAACAAT 59.261 45.455 0.00 0.00 0.00 2.71
1842 1855 3.138304 TCGTGCTCAGCTTGTAACAATT 58.862 40.909 0.00 0.00 0.00 2.32
1843 1856 3.563808 TCGTGCTCAGCTTGTAACAATTT 59.436 39.130 0.00 0.00 0.00 1.82
1844 1857 3.908382 CGTGCTCAGCTTGTAACAATTTC 59.092 43.478 0.00 0.00 0.00 2.17
1845 1858 4.319766 CGTGCTCAGCTTGTAACAATTTCT 60.320 41.667 0.00 0.00 0.00 2.52
1846 1859 5.107104 CGTGCTCAGCTTGTAACAATTTCTA 60.107 40.000 0.00 0.00 0.00 2.10
1847 1860 6.310197 GTGCTCAGCTTGTAACAATTTCTAG 58.690 40.000 0.00 0.00 0.00 2.43
1848 1861 5.997746 TGCTCAGCTTGTAACAATTTCTAGT 59.002 36.000 0.00 0.00 0.00 2.57
1849 1862 6.147821 TGCTCAGCTTGTAACAATTTCTAGTC 59.852 38.462 0.00 0.00 0.00 2.59
1850 1863 6.147821 GCTCAGCTTGTAACAATTTCTAGTCA 59.852 38.462 0.00 0.00 0.00 3.41
1851 1864 7.307989 GCTCAGCTTGTAACAATTTCTAGTCAA 60.308 37.037 0.00 0.00 0.00 3.18
1852 1865 8.621532 TCAGCTTGTAACAATTTCTAGTCAAT 57.378 30.769 0.00 0.00 0.00 2.57
1853 1866 8.721478 TCAGCTTGTAACAATTTCTAGTCAATC 58.279 33.333 0.00 0.00 0.00 2.67
1854 1867 8.725148 CAGCTTGTAACAATTTCTAGTCAATCT 58.275 33.333 0.00 0.00 0.00 2.40
1855 1868 8.940952 AGCTTGTAACAATTTCTAGTCAATCTC 58.059 33.333 0.00 0.00 0.00 2.75
1856 1869 7.900352 GCTTGTAACAATTTCTAGTCAATCTCG 59.100 37.037 0.00 0.00 0.00 4.04
1857 1870 9.140286 CTTGTAACAATTTCTAGTCAATCTCGA 57.860 33.333 0.00 0.00 0.00 4.04
1858 1871 8.689251 TGTAACAATTTCTAGTCAATCTCGAG 57.311 34.615 5.93 5.93 0.00 4.04
1859 1872 6.654793 AACAATTTCTAGTCAATCTCGAGC 57.345 37.500 7.81 0.00 0.00 5.03
1860 1873 5.971763 ACAATTTCTAGTCAATCTCGAGCT 58.028 37.500 7.81 0.71 0.00 4.09
1861 1874 7.101652 ACAATTTCTAGTCAATCTCGAGCTA 57.898 36.000 7.81 2.00 0.00 3.32
1862 1875 7.199766 ACAATTTCTAGTCAATCTCGAGCTAG 58.800 38.462 7.81 12.08 0.00 3.42
1863 1876 6.952773 ATTTCTAGTCAATCTCGAGCTAGT 57.047 37.500 17.96 6.40 33.08 2.57
1864 1877 6.761099 TTTCTAGTCAATCTCGAGCTAGTT 57.239 37.500 17.96 5.51 33.08 2.24
1865 1878 6.761099 TTCTAGTCAATCTCGAGCTAGTTT 57.239 37.500 17.96 3.67 33.08 2.66
1866 1879 6.366315 TCTAGTCAATCTCGAGCTAGTTTC 57.634 41.667 17.96 3.86 33.08 2.78
1867 1880 4.022464 AGTCAATCTCGAGCTAGTTTCG 57.978 45.455 7.81 11.15 39.33 3.46
1868 1881 3.690139 AGTCAATCTCGAGCTAGTTTCGA 59.310 43.478 7.81 16.82 44.05 3.71
1877 1890 5.946298 TCGAGCTAGTTTCGAGTTAAATGA 58.054 37.500 14.71 0.00 41.68 2.57
1878 1891 6.028368 TCGAGCTAGTTTCGAGTTAAATGAG 58.972 40.000 14.71 0.00 41.68 2.90
1879 1892 6.028368 CGAGCTAGTTTCGAGTTAAATGAGA 58.972 40.000 11.77 0.00 40.36 3.27
1880 1893 6.693545 CGAGCTAGTTTCGAGTTAAATGAGAT 59.306 38.462 11.77 0.00 40.36 2.75
1881 1894 7.305705 CGAGCTAGTTTCGAGTTAAATGAGATG 60.306 40.741 11.77 0.00 40.36 2.90
1882 1895 6.758886 AGCTAGTTTCGAGTTAAATGAGATGG 59.241 38.462 0.00 0.00 0.00 3.51
1883 1896 6.535508 GCTAGTTTCGAGTTAAATGAGATGGT 59.464 38.462 0.00 0.00 0.00 3.55
1884 1897 7.705325 GCTAGTTTCGAGTTAAATGAGATGGTA 59.295 37.037 0.00 0.00 0.00 3.25
1885 1898 9.582431 CTAGTTTCGAGTTAAATGAGATGGTAA 57.418 33.333 0.00 0.00 0.00 2.85
1886 1899 8.842358 AGTTTCGAGTTAAATGAGATGGTAAA 57.158 30.769 0.00 0.00 0.00 2.01
1887 1900 9.280174 AGTTTCGAGTTAAATGAGATGGTAAAA 57.720 29.630 0.00 0.00 0.00 1.52
1888 1901 9.887406 GTTTCGAGTTAAATGAGATGGTAAAAA 57.113 29.630 0.00 0.00 0.00 1.94
1939 1952 7.801716 AAAAATTGACGCTATATGCTAGGAA 57.198 32.000 0.00 0.00 40.11 3.36
1940 1953 6.787085 AAATTGACGCTATATGCTAGGAAC 57.213 37.500 0.00 0.00 40.11 3.62
1941 1954 3.936372 TGACGCTATATGCTAGGAACC 57.064 47.619 0.00 0.00 40.11 3.62
1942 1955 3.497332 TGACGCTATATGCTAGGAACCT 58.503 45.455 0.00 0.00 40.11 3.50
1943 1956 4.659115 TGACGCTATATGCTAGGAACCTA 58.341 43.478 0.50 0.50 40.11 3.08
1944 1957 4.700692 TGACGCTATATGCTAGGAACCTAG 59.299 45.833 19.97 19.97 46.41 3.02
1978 1991 9.924650 ATTAGGATATTTAACACATAGTCGACC 57.075 33.333 13.01 0.00 0.00 4.79
1979 1992 7.356089 AGGATATTTAACACATAGTCGACCA 57.644 36.000 13.01 0.00 0.00 4.02
1980 1993 7.208080 AGGATATTTAACACATAGTCGACCAC 58.792 38.462 13.01 0.00 0.00 4.16
1981 1994 6.143438 GGATATTTAACACATAGTCGACCACG 59.857 42.308 13.01 2.84 41.26 4.94
1982 1995 3.921119 TTAACACATAGTCGACCACGT 57.079 42.857 13.01 3.55 40.69 4.49
1983 1996 2.060326 AACACATAGTCGACCACGTG 57.940 50.000 20.88 20.88 40.69 4.49
1984 1997 0.956633 ACACATAGTCGACCACGTGT 59.043 50.000 21.90 21.90 40.69 4.49
1985 1998 1.068748 ACACATAGTCGACCACGTGTC 60.069 52.381 21.90 11.01 40.81 3.67
1986 1999 1.068816 CACATAGTCGACCACGTGTCA 60.069 52.381 15.65 1.39 44.71 3.58
1987 2000 1.816835 ACATAGTCGACCACGTGTCAT 59.183 47.619 15.65 0.00 44.71 3.06
1988 2001 3.011818 ACATAGTCGACCACGTGTCATA 58.988 45.455 15.65 6.11 44.71 2.15
1989 2002 3.441222 ACATAGTCGACCACGTGTCATAA 59.559 43.478 15.65 0.00 44.71 1.90
1990 2003 4.097437 ACATAGTCGACCACGTGTCATAAT 59.903 41.667 15.65 5.49 44.71 1.28
1991 2004 3.587797 AGTCGACCACGTGTCATAATT 57.412 42.857 15.65 0.00 44.71 1.40
1992 2005 4.707030 AGTCGACCACGTGTCATAATTA 57.293 40.909 15.65 0.00 44.71 1.40
1993 2006 4.669318 AGTCGACCACGTGTCATAATTAG 58.331 43.478 15.65 0.00 44.71 1.73
1994 2007 3.795101 GTCGACCACGTGTCATAATTAGG 59.205 47.826 15.65 0.00 44.71 2.69
1995 2008 2.538449 CGACCACGTGTCATAATTAGGC 59.462 50.000 15.65 0.00 44.71 3.93
1996 2009 2.870411 GACCACGTGTCATAATTAGGCC 59.130 50.000 15.65 0.00 43.85 5.19
1997 2010 2.504175 ACCACGTGTCATAATTAGGCCT 59.496 45.455 11.78 11.78 0.00 5.19
1998 2011 3.707611 ACCACGTGTCATAATTAGGCCTA 59.292 43.478 15.65 8.91 0.00 3.93
1999 2012 4.162698 ACCACGTGTCATAATTAGGCCTAA 59.837 41.667 27.11 27.11 0.00 2.69
2000 2013 5.120399 CCACGTGTCATAATTAGGCCTAAA 58.880 41.667 28.50 14.21 0.00 1.85
2001 2014 5.763204 CCACGTGTCATAATTAGGCCTAAAT 59.237 40.000 28.50 22.64 0.00 1.40
2002 2015 6.073222 CCACGTGTCATAATTAGGCCTAAATC 60.073 42.308 28.50 14.75 0.00 2.17
2003 2016 6.706270 CACGTGTCATAATTAGGCCTAAATCT 59.294 38.462 28.50 17.68 0.00 2.40
2004 2017 7.226720 CACGTGTCATAATTAGGCCTAAATCTT 59.773 37.037 28.50 19.95 0.00 2.40
2005 2018 8.426489 ACGTGTCATAATTAGGCCTAAATCTTA 58.574 33.333 28.50 21.34 0.00 2.10
2006 2019 9.436957 CGTGTCATAATTAGGCCTAAATCTTAT 57.563 33.333 28.50 22.46 0.00 1.73
2010 2023 9.672673 TCATAATTAGGCCTAAATCTTATCTGC 57.327 33.333 28.50 0.00 0.00 4.26
2011 2024 9.453572 CATAATTAGGCCTAAATCTTATCTGCA 57.546 33.333 28.50 2.90 0.00 4.41
2012 2025 7.751768 AATTAGGCCTAAATCTTATCTGCAC 57.248 36.000 28.50 0.00 0.00 4.57
2013 2026 6.500589 TTAGGCCTAAATCTTATCTGCACT 57.499 37.500 23.21 0.00 0.00 4.40
2014 2027 5.379706 AGGCCTAAATCTTATCTGCACTT 57.620 39.130 1.29 0.00 0.00 3.16
2015 2028 6.500589 AGGCCTAAATCTTATCTGCACTTA 57.499 37.500 1.29 0.00 0.00 2.24
2016 2029 6.900194 AGGCCTAAATCTTATCTGCACTTAA 58.100 36.000 1.29 0.00 0.00 1.85
2017 2030 7.521669 AGGCCTAAATCTTATCTGCACTTAAT 58.478 34.615 1.29 0.00 0.00 1.40
2018 2031 8.001292 AGGCCTAAATCTTATCTGCACTTAATT 58.999 33.333 1.29 0.00 0.00 1.40
2019 2032 9.284968 GGCCTAAATCTTATCTGCACTTAATTA 57.715 33.333 0.00 0.00 0.00 1.40
2034 2047 9.593134 TGCACTTAATTAAGTTTTCATGTTTGT 57.407 25.926 24.99 0.74 43.57 2.83
2155 2248 2.676016 TTTGCAGCGCGGTTTGGAAG 62.676 55.000 8.73 0.00 0.00 3.46
2210 2303 0.963962 CTACCACCACACCACTACGT 59.036 55.000 0.00 0.00 0.00 3.57
2354 2448 3.125146 TCGCTTCTTCCATTTGATTGTCG 59.875 43.478 0.00 0.00 0.00 4.35
2438 2532 6.966021 TCAAGTGCCAATGTTAGTACTTTTC 58.034 36.000 0.00 0.00 36.89 2.29
2482 2576 5.046663 TGCCACAGTTTCCTTTTCTTTTCTT 60.047 36.000 0.00 0.00 0.00 2.52
2538 2634 0.758685 CTTGCTCTCCTCCCGATCCT 60.759 60.000 0.00 0.00 0.00 3.24
2539 2635 0.325671 TTGCTCTCCTCCCGATCCTT 60.326 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
259 260 0.594602 GCTGCAGCAATGAACTCACA 59.405 50.000 33.36 0.00 41.59 3.58
388 389 2.744202 GGACCGCATTATAGCAATCAGG 59.256 50.000 0.00 0.00 0.00 3.86
464 468 6.494835 AGCAACATCTAATCCCAACTCTTTTT 59.505 34.615 0.00 0.00 0.00 1.94
706 713 1.134491 GCGGCTACACCCTACTCAATT 60.134 52.381 0.00 0.00 33.26 2.32
707 714 0.464452 GCGGCTACACCCTACTCAAT 59.536 55.000 0.00 0.00 33.26 2.57
708 715 1.610554 GGCGGCTACACCCTACTCAA 61.611 60.000 0.00 0.00 33.26 3.02
709 716 2.056223 GGCGGCTACACCCTACTCA 61.056 63.158 0.00 0.00 33.26 3.41
710 717 2.794028 GGGCGGCTACACCCTACTC 61.794 68.421 9.56 0.00 43.36 2.59
711 718 2.762875 GGGCGGCTACACCCTACT 60.763 66.667 9.56 0.00 43.36 2.57
791 798 3.875510 AAAGGACAGGCAGGCAGGC 62.876 63.158 0.00 0.00 44.61 4.85
831 838 0.165944 CGTGAAGTGAAACGATGGGC 59.834 55.000 0.00 0.00 45.86 5.36
879 887 5.460748 CCGCATCGTATACAAATTGTGAGTA 59.539 40.000 9.15 0.00 0.00 2.59
895 908 1.291877 GCTCTGTTTGACCGCATCGT 61.292 55.000 0.00 0.00 0.00 3.73
896 909 1.421485 GCTCTGTTTGACCGCATCG 59.579 57.895 0.00 0.00 0.00 3.84
939 952 2.505819 AGAGGTGGCCTGTGTTTATAGG 59.494 50.000 3.32 0.00 38.17 2.57
986 999 4.235360 CTGCTCCATTTTCTTTTGAGCTG 58.765 43.478 10.69 6.80 46.56 4.24
1014 1027 2.669569 GTTGGCTGCGCTCCTTGA 60.670 61.111 9.73 0.00 0.00 3.02
1554 1567 4.832248 TGAGTTATCACACCAATCAGTCC 58.168 43.478 0.00 0.00 0.00 3.85
1573 1586 3.677121 GCGTGGATATACATCAAGCTGAG 59.323 47.826 0.00 0.00 32.32 3.35
1581 1594 6.371809 TTTCTTTTGGCGTGGATATACATC 57.628 37.500 0.00 0.00 0.00 3.06
1664 1677 1.453155 CCTTTGTGAACGGATGGAGG 58.547 55.000 0.00 0.00 0.00 4.30
1669 1682 1.336755 GTGTTGCCTTTGTGAACGGAT 59.663 47.619 0.00 0.00 0.00 4.18
1676 1689 3.896648 ATAGAACGTGTTGCCTTTGTG 57.103 42.857 0.00 0.00 0.00 3.33
1702 1715 3.514645 GACTCGTTTGTAGCCCGATTAA 58.485 45.455 0.00 0.00 0.00 1.40
1703 1716 2.478370 CGACTCGTTTGTAGCCCGATTA 60.478 50.000 0.00 0.00 0.00 1.75
1704 1717 1.734707 CGACTCGTTTGTAGCCCGATT 60.735 52.381 0.00 0.00 0.00 3.34
1705 1718 0.179145 CGACTCGTTTGTAGCCCGAT 60.179 55.000 0.00 0.00 0.00 4.18
1706 1719 1.210931 CGACTCGTTTGTAGCCCGA 59.789 57.895 0.00 0.00 0.00 5.14
1707 1720 0.797249 CTCGACTCGTTTGTAGCCCG 60.797 60.000 0.00 0.00 0.00 6.13
1708 1721 1.077089 GCTCGACTCGTTTGTAGCCC 61.077 60.000 0.00 0.00 0.00 5.19
1709 1722 0.109226 AGCTCGACTCGTTTGTAGCC 60.109 55.000 5.67 0.00 0.00 3.93
1710 1723 1.261097 GAGCTCGACTCGTTTGTAGC 58.739 55.000 0.00 0.00 35.18 3.58
1719 1732 1.716581 CAACTCGTTTGAGCTCGACTC 59.283 52.381 9.64 2.40 46.69 3.36
1720 1733 1.603172 CCAACTCGTTTGAGCTCGACT 60.603 52.381 9.64 0.00 46.69 4.18
1721 1734 0.784778 CCAACTCGTTTGAGCTCGAC 59.215 55.000 9.64 9.49 46.69 4.20
1722 1735 0.671796 TCCAACTCGTTTGAGCTCGA 59.328 50.000 9.64 3.88 46.69 4.04
1723 1736 1.063806 CTCCAACTCGTTTGAGCTCG 58.936 55.000 9.64 0.00 46.69 5.03
1724 1737 2.156343 ACTCCAACTCGTTTGAGCTC 57.844 50.000 6.82 6.82 46.69 4.09
1725 1738 2.213499 CAACTCCAACTCGTTTGAGCT 58.787 47.619 9.91 0.00 46.69 4.09
1726 1739 1.264288 CCAACTCCAACTCGTTTGAGC 59.736 52.381 9.91 0.00 46.69 4.26
1727 1740 4.894983 GAGCCAACTCCAACTCGTTTGAG 61.895 52.174 8.76 8.76 41.52 3.02
1728 1741 1.134220 AGCCAACTCCAACTCGTTTGA 60.134 47.619 1.70 0.00 37.39 2.69
1729 1742 1.264288 GAGCCAACTCCAACTCGTTTG 59.736 52.381 0.00 0.00 36.90 2.93
1730 1743 1.134220 TGAGCCAACTCCAACTCGTTT 60.134 47.619 0.00 0.00 42.74 3.60
1731 1744 0.468226 TGAGCCAACTCCAACTCGTT 59.532 50.000 0.00 0.00 42.74 3.85
1732 1745 0.468226 TTGAGCCAACTCCAACTCGT 59.532 50.000 0.00 0.00 42.74 4.18
1733 1746 0.868406 GTTGAGCCAACTCCAACTCG 59.132 55.000 9.89 0.00 42.74 4.18
1742 1755 4.036734 TCATTTGAGTTGAGTTGAGCCAAC 59.963 41.667 9.31 9.31 43.83 3.77
1743 1756 4.206375 TCATTTGAGTTGAGTTGAGCCAA 58.794 39.130 0.00 0.00 0.00 4.52
1744 1757 3.819368 TCATTTGAGTTGAGTTGAGCCA 58.181 40.909 0.00 0.00 0.00 4.75
1745 1758 4.836125 TTCATTTGAGTTGAGTTGAGCC 57.164 40.909 0.00 0.00 0.00 4.70
1746 1759 7.357859 CGAATTTTCATTTGAGTTGAGTTGAGC 60.358 37.037 0.00 0.00 0.00 4.26
1747 1760 7.857389 TCGAATTTTCATTTGAGTTGAGTTGAG 59.143 33.333 0.00 0.00 30.31 3.02
1748 1761 7.702386 TCGAATTTTCATTTGAGTTGAGTTGA 58.298 30.769 0.00 0.00 30.31 3.18
1749 1762 7.357859 GCTCGAATTTTCATTTGAGTTGAGTTG 60.358 37.037 11.99 0.00 46.80 3.16
1750 1763 6.638468 GCTCGAATTTTCATTTGAGTTGAGTT 59.362 34.615 11.99 0.00 46.80 3.01
1751 1764 6.145535 GCTCGAATTTTCATTTGAGTTGAGT 58.854 36.000 11.99 0.00 46.80 3.41
1752 1765 5.282310 CGCTCGAATTTTCATTTGAGTTGAG 59.718 40.000 11.99 0.00 46.80 3.02
1753 1766 5.049749 TCGCTCGAATTTTCATTTGAGTTGA 60.050 36.000 11.99 8.63 46.80 3.18
1754 1767 5.146460 TCGCTCGAATTTTCATTTGAGTTG 58.854 37.500 11.99 6.98 46.80 3.16
1755 1768 5.049405 ACTCGCTCGAATTTTCATTTGAGTT 60.049 36.000 11.99 0.00 46.80 3.01
1756 1769 4.452455 ACTCGCTCGAATTTTCATTTGAGT 59.548 37.500 11.99 0.00 46.80 3.41
1758 1771 5.049749 TGAACTCGCTCGAATTTTCATTTGA 60.050 36.000 6.56 0.00 32.58 2.69
1759 1772 5.146460 TGAACTCGCTCGAATTTTCATTTG 58.854 37.500 6.56 0.00 0.00 2.32
1760 1773 5.356882 TGAACTCGCTCGAATTTTCATTT 57.643 34.783 6.56 0.00 0.00 2.32
1761 1774 5.356882 TTGAACTCGCTCGAATTTTCATT 57.643 34.783 9.80 0.00 0.00 2.57
1762 1775 5.049405 AGTTTGAACTCGCTCGAATTTTCAT 60.049 36.000 9.80 0.00 32.86 2.57
1763 1776 4.272504 AGTTTGAACTCGCTCGAATTTTCA 59.727 37.500 6.56 6.56 32.86 2.69
1764 1777 4.608882 CAGTTTGAACTCGCTCGAATTTTC 59.391 41.667 0.00 0.00 37.08 2.29
1765 1778 4.272504 TCAGTTTGAACTCGCTCGAATTTT 59.727 37.500 0.00 0.00 37.08 1.82
1766 1779 3.807622 TCAGTTTGAACTCGCTCGAATTT 59.192 39.130 0.00 0.00 37.08 1.82
1767 1780 3.390135 TCAGTTTGAACTCGCTCGAATT 58.610 40.909 0.00 0.00 37.08 2.17
1768 1781 2.989840 CTCAGTTTGAACTCGCTCGAAT 59.010 45.455 0.00 0.00 37.08 3.34
1769 1782 2.223735 ACTCAGTTTGAACTCGCTCGAA 60.224 45.455 0.00 0.00 37.08 3.71
1770 1783 1.337071 ACTCAGTTTGAACTCGCTCGA 59.663 47.619 0.00 0.00 37.08 4.04
1771 1784 1.453524 CACTCAGTTTGAACTCGCTCG 59.546 52.381 0.00 0.00 37.08 5.03
1772 1785 2.743938 TCACTCAGTTTGAACTCGCTC 58.256 47.619 0.00 0.00 37.08 5.03
1773 1786 2.890808 TCACTCAGTTTGAACTCGCT 57.109 45.000 0.00 0.00 37.08 4.93
1774 1787 2.348966 GCTTCACTCAGTTTGAACTCGC 60.349 50.000 0.00 0.00 37.08 5.03
1775 1788 3.126831 AGCTTCACTCAGTTTGAACTCG 58.873 45.455 0.00 0.00 37.08 4.18
1776 1789 6.425114 TCATAAGCTTCACTCAGTTTGAACTC 59.575 38.462 0.00 0.00 37.08 3.01
1777 1790 6.291377 TCATAAGCTTCACTCAGTTTGAACT 58.709 36.000 0.00 0.00 40.60 3.01
1778 1791 6.545504 TCATAAGCTTCACTCAGTTTGAAC 57.454 37.500 0.00 0.00 0.00 3.18
1779 1792 6.091305 CGATCATAAGCTTCACTCAGTTTGAA 59.909 38.462 0.00 0.00 0.00 2.69
1780 1793 5.578336 CGATCATAAGCTTCACTCAGTTTGA 59.422 40.000 0.00 0.00 0.00 2.69
1781 1794 5.578336 TCGATCATAAGCTTCACTCAGTTTG 59.422 40.000 0.00 0.00 0.00 2.93
1782 1795 5.724328 TCGATCATAAGCTTCACTCAGTTT 58.276 37.500 0.00 0.00 0.00 2.66
1783 1796 5.330455 TCGATCATAAGCTTCACTCAGTT 57.670 39.130 0.00 0.00 0.00 3.16
1784 1797 4.736168 GCTCGATCATAAGCTTCACTCAGT 60.736 45.833 0.00 0.00 35.60 3.41
1785 1798 3.735240 GCTCGATCATAAGCTTCACTCAG 59.265 47.826 0.00 0.00 35.60 3.35
1786 1799 3.382865 AGCTCGATCATAAGCTTCACTCA 59.617 43.478 0.00 0.00 46.49 3.41
1787 1800 3.735240 CAGCTCGATCATAAGCTTCACTC 59.265 47.826 0.00 0.00 46.49 3.51
1788 1801 3.131933 ACAGCTCGATCATAAGCTTCACT 59.868 43.478 0.00 0.00 46.49 3.41
1789 1802 3.452474 ACAGCTCGATCATAAGCTTCAC 58.548 45.455 0.00 0.00 46.49 3.18
1790 1803 3.808466 ACAGCTCGATCATAAGCTTCA 57.192 42.857 0.00 0.00 46.49 3.02
1791 1804 5.114785 TCTACAGCTCGATCATAAGCTTC 57.885 43.478 0.00 0.00 46.49 3.86
1792 1805 5.068460 AGTTCTACAGCTCGATCATAAGCTT 59.932 40.000 3.48 3.48 46.49 3.74
1794 1807 4.865776 AGTTCTACAGCTCGATCATAAGC 58.134 43.478 4.06 4.06 38.84 3.09
1795 1808 6.416455 GTCAAGTTCTACAGCTCGATCATAAG 59.584 42.308 0.00 0.00 0.00 1.73
1796 1809 6.095580 AGTCAAGTTCTACAGCTCGATCATAA 59.904 38.462 0.00 0.00 0.00 1.90
1797 1810 5.590663 AGTCAAGTTCTACAGCTCGATCATA 59.409 40.000 0.00 0.00 0.00 2.15
1798 1811 4.400884 AGTCAAGTTCTACAGCTCGATCAT 59.599 41.667 0.00 0.00 0.00 2.45
1799 1812 3.759086 AGTCAAGTTCTACAGCTCGATCA 59.241 43.478 0.00 0.00 0.00 2.92
1800 1813 4.347813 GAGTCAAGTTCTACAGCTCGATC 58.652 47.826 0.00 0.00 0.00 3.69
1801 1814 3.181505 CGAGTCAAGTTCTACAGCTCGAT 60.182 47.826 5.28 0.00 44.58 3.59
1802 1815 2.159824 CGAGTCAAGTTCTACAGCTCGA 59.840 50.000 5.28 0.00 44.58 4.04
1803 1816 2.095668 ACGAGTCAAGTTCTACAGCTCG 60.096 50.000 9.10 9.10 46.37 5.03
1804 1817 3.238441 CACGAGTCAAGTTCTACAGCTC 58.762 50.000 0.00 0.00 0.00 4.09
1805 1818 2.608261 GCACGAGTCAAGTTCTACAGCT 60.608 50.000 0.00 0.00 0.00 4.24
1806 1819 1.721926 GCACGAGTCAAGTTCTACAGC 59.278 52.381 0.00 0.00 0.00 4.40
1807 1820 3.238441 GAGCACGAGTCAAGTTCTACAG 58.762 50.000 0.00 0.00 0.00 2.74
1808 1821 2.621526 TGAGCACGAGTCAAGTTCTACA 59.378 45.455 0.00 0.00 0.00 2.74
1809 1822 3.238441 CTGAGCACGAGTCAAGTTCTAC 58.762 50.000 0.00 0.00 0.00 2.59
1810 1823 2.351835 GCTGAGCACGAGTCAAGTTCTA 60.352 50.000 0.00 0.00 0.00 2.10
1811 1824 1.604185 GCTGAGCACGAGTCAAGTTCT 60.604 52.381 0.00 0.00 0.00 3.01
1812 1825 0.787183 GCTGAGCACGAGTCAAGTTC 59.213 55.000 0.00 0.00 0.00 3.01
1813 1826 0.390860 AGCTGAGCACGAGTCAAGTT 59.609 50.000 7.39 0.00 0.00 2.66
1814 1827 0.390860 AAGCTGAGCACGAGTCAAGT 59.609 50.000 7.39 0.00 0.00 3.16
1815 1828 0.788995 CAAGCTGAGCACGAGTCAAG 59.211 55.000 7.39 0.00 0.00 3.02
1816 1829 0.104855 ACAAGCTGAGCACGAGTCAA 59.895 50.000 7.39 0.00 0.00 3.18
1817 1830 0.958822 TACAAGCTGAGCACGAGTCA 59.041 50.000 7.39 0.00 0.00 3.41
1818 1831 1.721926 GTTACAAGCTGAGCACGAGTC 59.278 52.381 7.39 0.00 0.00 3.36
1819 1832 1.068588 TGTTACAAGCTGAGCACGAGT 59.931 47.619 7.39 1.63 0.00 4.18
1820 1833 1.783284 TGTTACAAGCTGAGCACGAG 58.217 50.000 7.39 0.00 0.00 4.18
1821 1834 2.232756 TTGTTACAAGCTGAGCACGA 57.767 45.000 7.39 0.00 0.00 4.35
1822 1835 3.542712 AATTGTTACAAGCTGAGCACG 57.457 42.857 7.39 0.00 0.00 5.34
1823 1836 5.113502 AGAAATTGTTACAAGCTGAGCAC 57.886 39.130 7.39 0.00 0.00 4.40
1824 1837 5.997746 ACTAGAAATTGTTACAAGCTGAGCA 59.002 36.000 7.39 0.00 0.00 4.26
1825 1838 6.147821 TGACTAGAAATTGTTACAAGCTGAGC 59.852 38.462 3.63 0.00 0.00 4.26
1826 1839 7.658179 TGACTAGAAATTGTTACAAGCTGAG 57.342 36.000 3.63 0.36 0.00 3.35
1827 1840 8.621532 ATTGACTAGAAATTGTTACAAGCTGA 57.378 30.769 3.63 0.00 0.00 4.26
1828 1841 8.725148 AGATTGACTAGAAATTGTTACAAGCTG 58.275 33.333 3.63 0.41 32.89 4.24
1829 1842 8.854614 AGATTGACTAGAAATTGTTACAAGCT 57.145 30.769 3.63 3.86 0.00 3.74
1830 1843 7.900352 CGAGATTGACTAGAAATTGTTACAAGC 59.100 37.037 3.63 0.00 0.00 4.01
1831 1844 9.140286 TCGAGATTGACTAGAAATTGTTACAAG 57.860 33.333 3.63 0.00 0.00 3.16
1832 1845 9.140286 CTCGAGATTGACTAGAAATTGTTACAA 57.860 33.333 6.58 0.00 30.48 2.41
1833 1846 7.275779 GCTCGAGATTGACTAGAAATTGTTACA 59.724 37.037 18.75 0.00 30.48 2.41
1834 1847 7.489757 AGCTCGAGATTGACTAGAAATTGTTAC 59.510 37.037 18.75 0.00 30.48 2.50
1835 1848 7.548097 AGCTCGAGATTGACTAGAAATTGTTA 58.452 34.615 18.75 0.00 30.48 2.41
1836 1849 6.402222 AGCTCGAGATTGACTAGAAATTGTT 58.598 36.000 18.75 0.00 30.48 2.83
1837 1850 5.971763 AGCTCGAGATTGACTAGAAATTGT 58.028 37.500 18.75 0.00 30.48 2.71
1838 1851 7.199766 ACTAGCTCGAGATTGACTAGAAATTG 58.800 38.462 22.90 4.83 35.42 2.32
1839 1852 7.341445 ACTAGCTCGAGATTGACTAGAAATT 57.659 36.000 22.90 5.49 35.42 1.82
1840 1853 6.952773 ACTAGCTCGAGATTGACTAGAAAT 57.047 37.500 22.90 5.76 35.42 2.17
1841 1854 6.761099 AACTAGCTCGAGATTGACTAGAAA 57.239 37.500 22.90 0.00 35.42 2.52
1842 1855 6.457122 CGAAACTAGCTCGAGATTGACTAGAA 60.457 42.308 22.90 0.00 38.61 2.10
1843 1856 5.006844 CGAAACTAGCTCGAGATTGACTAGA 59.993 44.000 22.90 0.00 38.61 2.43
1844 1857 5.006844 TCGAAACTAGCTCGAGATTGACTAG 59.993 44.000 18.75 17.91 40.25 2.57
1845 1858 4.874396 TCGAAACTAGCTCGAGATTGACTA 59.126 41.667 18.75 6.58 40.25 2.59
1846 1859 3.690139 TCGAAACTAGCTCGAGATTGACT 59.310 43.478 18.75 5.62 40.25 3.41
1847 1860 4.017380 TCGAAACTAGCTCGAGATTGAC 57.983 45.455 18.75 7.51 40.25 3.18
1854 1867 5.946298 TCATTTAACTCGAAACTAGCTCGA 58.054 37.500 14.72 14.72 42.75 4.04
1855 1868 6.028368 TCTCATTTAACTCGAAACTAGCTCG 58.972 40.000 8.22 8.22 37.66 5.03
1856 1869 7.043059 CCATCTCATTTAACTCGAAACTAGCTC 60.043 40.741 0.00 0.00 0.00 4.09
1857 1870 6.758886 CCATCTCATTTAACTCGAAACTAGCT 59.241 38.462 0.00 0.00 0.00 3.32
1858 1871 6.535508 ACCATCTCATTTAACTCGAAACTAGC 59.464 38.462 0.00 0.00 0.00 3.42
1859 1872 9.582431 TTACCATCTCATTTAACTCGAAACTAG 57.418 33.333 0.00 0.00 0.00 2.57
1860 1873 9.932207 TTTACCATCTCATTTAACTCGAAACTA 57.068 29.630 0.00 0.00 0.00 2.24
1861 1874 8.842358 TTTACCATCTCATTTAACTCGAAACT 57.158 30.769 0.00 0.00 0.00 2.66
1862 1875 9.887406 TTTTTACCATCTCATTTAACTCGAAAC 57.113 29.630 0.00 0.00 0.00 2.78
1952 1965 9.924650 GGTCGACTATGTGTTAAATATCCTAAT 57.075 33.333 16.46 0.00 0.00 1.73
1953 1966 8.916062 TGGTCGACTATGTGTTAAATATCCTAA 58.084 33.333 16.46 0.00 0.00 2.69
1954 1967 8.355169 GTGGTCGACTATGTGTTAAATATCCTA 58.645 37.037 16.46 0.00 0.00 2.94
1955 1968 7.208080 GTGGTCGACTATGTGTTAAATATCCT 58.792 38.462 16.46 0.00 0.00 3.24
1956 1969 6.143438 CGTGGTCGACTATGTGTTAAATATCC 59.857 42.308 16.46 0.00 39.71 2.59
1957 1970 6.694411 ACGTGGTCGACTATGTGTTAAATATC 59.306 38.462 23.98 0.00 40.62 1.63
1958 1971 6.474427 CACGTGGTCGACTATGTGTTAAATAT 59.526 38.462 33.81 7.51 38.87 1.28
1959 1972 5.801444 CACGTGGTCGACTATGTGTTAAATA 59.199 40.000 33.81 0.00 38.87 1.40
1960 1973 4.624024 CACGTGGTCGACTATGTGTTAAAT 59.376 41.667 33.81 8.79 38.87 1.40
1961 1974 3.982701 CACGTGGTCGACTATGTGTTAAA 59.017 43.478 33.81 1.75 38.87 1.52
1962 1975 3.567530 CACGTGGTCGACTATGTGTTAA 58.432 45.455 33.81 3.09 38.87 2.01
1963 1976 3.206034 CACGTGGTCGACTATGTGTTA 57.794 47.619 33.81 4.67 38.87 2.41
1964 1977 2.060326 CACGTGGTCGACTATGTGTT 57.940 50.000 33.81 10.74 38.87 3.32
1965 1978 3.786809 CACGTGGTCGACTATGTGT 57.213 52.632 33.81 18.54 38.87 3.72
1966 1979 1.614385 GACACGTGGTCGACTATGTG 58.386 55.000 37.64 37.64 45.95 3.21
1976 1989 2.504175 AGGCCTAATTATGACACGTGGT 59.496 45.455 21.57 8.03 0.00 4.16
1977 1990 3.194005 AGGCCTAATTATGACACGTGG 57.806 47.619 21.57 1.66 0.00 4.94
1978 1991 6.706270 AGATTTAGGCCTAATTATGACACGTG 59.294 38.462 25.70 15.48 0.00 4.49
1979 1992 6.827727 AGATTTAGGCCTAATTATGACACGT 58.172 36.000 25.70 0.00 0.00 4.49
1980 1993 7.730364 AAGATTTAGGCCTAATTATGACACG 57.270 36.000 25.70 0.00 0.00 4.49
1984 1997 9.672673 GCAGATAAGATTTAGGCCTAATTATGA 57.327 33.333 25.70 13.17 0.00 2.15
1985 1998 9.453572 TGCAGATAAGATTTAGGCCTAATTATG 57.546 33.333 25.70 16.48 0.00 1.90
1986 1999 9.454859 GTGCAGATAAGATTTAGGCCTAATTAT 57.545 33.333 25.70 23.39 0.00 1.28
1987 2000 8.660435 AGTGCAGATAAGATTTAGGCCTAATTA 58.340 33.333 25.70 20.09 0.00 1.40
1988 2001 7.521669 AGTGCAGATAAGATTTAGGCCTAATT 58.478 34.615 25.70 21.47 0.00 1.40
1989 2002 7.084268 AGTGCAGATAAGATTTAGGCCTAAT 57.916 36.000 25.70 15.37 0.00 1.73
1990 2003 6.500589 AGTGCAGATAAGATTTAGGCCTAA 57.499 37.500 21.68 21.68 0.00 2.69
1991 2004 6.500589 AAGTGCAGATAAGATTTAGGCCTA 57.499 37.500 8.91 8.91 0.00 3.93
1992 2005 5.379706 AAGTGCAGATAAGATTTAGGCCT 57.620 39.130 11.78 11.78 0.00 5.19
1993 2006 7.751768 ATTAAGTGCAGATAAGATTTAGGCC 57.248 36.000 0.00 0.00 0.00 5.19
2008 2021 9.593134 ACAAACATGAAAACTTAATTAAGTGCA 57.407 25.926 27.29 23.76 45.17 4.57
2098 2111 9.888878 CTGGTCGTTAGATTTCTCGTATATTAA 57.111 33.333 0.00 0.00 0.00 1.40
2099 2112 9.060347 ACTGGTCGTTAGATTTCTCGTATATTA 57.940 33.333 0.00 0.00 0.00 0.98
2100 2113 7.938715 ACTGGTCGTTAGATTTCTCGTATATT 58.061 34.615 0.00 0.00 0.00 1.28
2101 2114 7.507733 ACTGGTCGTTAGATTTCTCGTATAT 57.492 36.000 0.00 0.00 0.00 0.86
2102 2115 6.292542 CGACTGGTCGTTAGATTTCTCGTATA 60.293 42.308 14.05 0.00 46.99 1.47
2103 2116 5.503683 CGACTGGTCGTTAGATTTCTCGTAT 60.504 44.000 14.05 0.00 46.99 3.06
2104 2117 4.201753 CGACTGGTCGTTAGATTTCTCGTA 60.202 45.833 14.05 0.00 46.99 3.43
2142 2155 4.020378 TTCGCTTCCAAACCGCGC 62.020 61.111 0.00 0.00 45.87 6.86
2155 2248 1.446272 CTTGGAGACCTCGGTTCGC 60.446 63.158 0.00 0.00 0.00 4.70
2161 2254 1.474879 GGTCTTCTCTTGGAGACCTCG 59.525 57.143 14.49 0.00 45.28 4.63
2252 2346 3.819564 AATTATGCTGACGTGGCTCTA 57.180 42.857 0.00 0.00 0.00 2.43
2354 2448 1.484038 TTAAATGGGATGGCTGCACC 58.516 50.000 0.50 1.45 39.84 5.01
2438 2532 6.638468 GTGGCACTAAAAATGAACAGAGAAAG 59.362 38.462 11.13 0.00 0.00 2.62
2448 2542 4.892934 AGGAAACTGTGGCACTAAAAATGA 59.107 37.500 19.83 0.00 41.13 2.57


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

AutoCloner maintained by Alex Coulton.