Multiple sequence alignment - TraesCS3B01G169500

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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 TraesCS3B01G169500 chr3B 100.000 2743 0 0 1 2743 169653990 169656732 0.000000e+00 5066.0
1 TraesCS3B01G169500 chr3B 84.787 986 134 15 1 977 349293528 349292550 0.000000e+00 976.0
2 TraesCS3B01G169500 chr3B 98.899 454 5 0 524 977 169648947 169649400 0.000000e+00 811.0
3 TraesCS3B01G169500 chr3B 92.593 162 11 1 2413 2573 674990134 674989973 5.910000e-57 231.0
4 TraesCS3B01G169500 chr3B 84.270 178 23 4 2570 2743 426003969 426004145 4.700000e-38 169.0
5 TraesCS3B01G169500 chr5B 96.531 980 29 5 1 977 100046215 100047192 0.000000e+00 1616.0
6 TraesCS3B01G169500 chr5B 95.184 976 45 2 1 975 10162801 10161827 0.000000e+00 1541.0
7 TraesCS3B01G169500 chr5B 85.340 648 60 21 976 1617 50644440 50645058 2.980000e-179 638.0
8 TraesCS3B01G169500 chr5B 87.410 556 46 13 976 1525 50932128 50931591 3.880000e-173 617.0
9 TraesCS3B01G169500 chr5B 87.230 556 47 13 976 1525 38355914 38356451 1.810000e-171 612.0
10 TraesCS3B01G169500 chr5B 92.593 162 11 1 2413 2573 411972027 411971866 5.910000e-57 231.0
11 TraesCS3B01G169500 chr5B 88.462 104 6 3 2246 2345 38798253 38798354 1.330000e-23 121.0
12 TraesCS3B01G169500 chr5B 94.737 57 2 1 2357 2413 606546834 606546889 1.350000e-13 87.9
13 TraesCS3B01G169500 chr4B 94.990 978 47 2 1 977 429456378 429457354 0.000000e+00 1533.0
14 TraesCS3B01G169500 chr4B 83.789 987 142 18 1 978 80976221 80977198 0.000000e+00 920.0
15 TraesCS3B01G169500 chr4B 92.593 162 11 1 2413 2573 499224663 499224502 5.910000e-57 231.0
16 TraesCS3B01G169500 chr4B 92.593 162 11 1 2413 2573 549841917 549841756 5.910000e-57 231.0
17 TraesCS3B01G169500 chr4B 88.947 190 16 5 2393 2580 532434983 532435169 2.120000e-56 230.0
18 TraesCS3B01G169500 chr3D 89.492 885 55 20 977 1845 116077197 116078059 0.000000e+00 1085.0
19 TraesCS3B01G169500 chr3D 86.077 984 108 20 3 978 15037538 15036576 0.000000e+00 1031.0
20 TraesCS3B01G169500 chr3D 93.884 327 14 3 1958 2283 116078290 116078611 3.170000e-134 488.0
21 TraesCS3B01G169500 chr3D 87.640 178 11 6 2570 2743 116078639 116078809 2.150000e-46 196.0
22 TraesCS3B01G169500 chr3D 87.387 111 10 4 2573 2680 313282295 313282186 1.030000e-24 124.0
23 TraesCS3B01G169500 chr4D 86.451 989 111 19 1 978 32024942 32023966 0.000000e+00 1062.0
24 TraesCS3B01G169500 chr7B 84.467 985 140 13 1 977 60072300 60071321 0.000000e+00 959.0
25 TraesCS3B01G169500 chr7B 90.395 177 16 1 2398 2573 736726791 736726967 5.910000e-57 231.0
26 TraesCS3B01G169500 chr5A 81.029 991 161 26 1 978 608614346 608613370 0.000000e+00 763.0
27 TraesCS3B01G169500 chr5A 85.823 656 57 22 984 1622 38016803 38016167 0.000000e+00 664.0
28 TraesCS3B01G169500 chr5A 86.879 564 49 13 972 1525 31219138 31218590 2.340000e-170 608.0
29 TraesCS3B01G169500 chr5A 86.879 564 49 13 972 1525 31267809 31268357 2.340000e-170 608.0
30 TraesCS3B01G169500 chr5A 85.714 140 16 3 2172 2307 31216693 31216554 7.920000e-31 145.0
31 TraesCS3B01G169500 chr5A 86.131 137 15 3 2172 2304 31270254 31270390 7.920000e-31 145.0
32 TraesCS3B01G169500 chr5A 94.737 57 3 0 2357 2413 613931111 613931167 3.760000e-14 89.8
33 TraesCS3B01G169500 chr5D 85.909 660 59 20 976 1619 48450284 48450925 0.000000e+00 673.0
34 TraesCS3B01G169500 chr5D 85.714 665 59 21 976 1622 48048025 48047379 0.000000e+00 669.0
35 TraesCS3B01G169500 chr5D 85.849 106 7 6 2246 2344 42961757 42961861 3.740000e-19 106.0
36 TraesCS3B01G169500 chr7D 95.062 162 5 3 2414 2573 205540857 205540697 4.530000e-63 252.0
37 TraesCS3B01G169500 chr2B 90.395 177 16 1 2398 2573 206593543 206593719 5.910000e-57 231.0
38 TraesCS3B01G169500 chrUn 91.975 162 12 1 2413 2573 86671478 86671317 2.750000e-55 226.0
39 TraesCS3B01G169500 chr6B 83.516 182 21 6 2570 2743 127042152 127042332 7.860000e-36 161.0


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 TraesCS3B01G169500 chr3B 169653990 169656732 2742 False 5066.000000 5066 100.000000 1 2743 1 chr3B.!!$F2 2742
1 TraesCS3B01G169500 chr3B 349292550 349293528 978 True 976.000000 976 84.787000 1 977 1 chr3B.!!$R1 976
2 TraesCS3B01G169500 chr5B 100046215 100047192 977 False 1616.000000 1616 96.531000 1 977 1 chr5B.!!$F4 976
3 TraesCS3B01G169500 chr5B 10161827 10162801 974 True 1541.000000 1541 95.184000 1 975 1 chr5B.!!$R1 974
4 TraesCS3B01G169500 chr5B 50644440 50645058 618 False 638.000000 638 85.340000 976 1617 1 chr5B.!!$F3 641
5 TraesCS3B01G169500 chr5B 50931591 50932128 537 True 617.000000 617 87.410000 976 1525 1 chr5B.!!$R2 549
6 TraesCS3B01G169500 chr5B 38355914 38356451 537 False 612.000000 612 87.230000 976 1525 1 chr5B.!!$F1 549
7 TraesCS3B01G169500 chr4B 429456378 429457354 976 False 1533.000000 1533 94.990000 1 977 1 chr4B.!!$F2 976
8 TraesCS3B01G169500 chr4B 80976221 80977198 977 False 920.000000 920 83.789000 1 978 1 chr4B.!!$F1 977
9 TraesCS3B01G169500 chr3D 15036576 15037538 962 True 1031.000000 1031 86.077000 3 978 1 chr3D.!!$R1 975
10 TraesCS3B01G169500 chr3D 116077197 116078809 1612 False 589.666667 1085 90.338667 977 2743 3 chr3D.!!$F1 1766
11 TraesCS3B01G169500 chr4D 32023966 32024942 976 True 1062.000000 1062 86.451000 1 978 1 chr4D.!!$R1 977
12 TraesCS3B01G169500 chr7B 60071321 60072300 979 True 959.000000 959 84.467000 1 977 1 chr7B.!!$R1 976
13 TraesCS3B01G169500 chr5A 608613370 608614346 976 True 763.000000 763 81.029000 1 978 1 chr5A.!!$R2 977
14 TraesCS3B01G169500 chr5A 38016167 38016803 636 True 664.000000 664 85.823000 984 1622 1 chr5A.!!$R1 638
15 TraesCS3B01G169500 chr5A 31216554 31219138 2584 True 376.500000 608 86.296500 972 2307 2 chr5A.!!$R3 1335
16 TraesCS3B01G169500 chr5A 31267809 31270390 2581 False 376.500000 608 86.505000 972 2304 2 chr5A.!!$F2 1332
17 TraesCS3B01G169500 chr5D 48450284 48450925 641 False 673.000000 673 85.909000 976 1619 1 chr5D.!!$F2 643
18 TraesCS3B01G169500 chr5D 48047379 48048025 646 True 669.000000 669 85.714000 976 1622 1 chr5D.!!$R1 646

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
658 661 1.301874 CGCCGTTTAAGGGTGTCCA 60.302 57.895 8.86 0.0 34.83 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1864 0.689055 ACATGAACAGAGGCAGAGCA 59.311 50.0 0.0 0.0 0.0 4.26 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
658 661 1.301874 CGCCGTTTAAGGGTGTCCA 60.302 57.895 8.86 0.00 34.83 4.02
956 967 5.575606 CCAATTGTGTGCAAATTCAGAGATC 59.424 40.000 4.43 0.00 38.21 2.75
1309 1327 4.728102 CCGCGTCGGCCTACAACA 62.728 66.667 8.31 0.00 41.17 3.33
1310 1331 2.508439 CGCGTCGGCCTACAACAT 60.508 61.111 8.31 0.00 35.02 2.71
1402 1423 1.153229 GTCTACATGCCGTTCCCCC 60.153 63.158 0.00 0.00 0.00 5.40
1403 1424 2.203015 CTACATGCCGTTCCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
1404 1425 2.684294 TACATGCCGTTCCCCCGA 60.684 61.111 0.00 0.00 0.00 5.14
1405 1426 2.918230 CTACATGCCGTTCCCCCGAC 62.918 65.000 0.00 0.00 0.00 4.79
1474 1498 2.848679 TCCAGACCAGCACCTGCA 60.849 61.111 0.00 0.00 45.16 4.41
1518 1542 1.760086 CCCCTCCTCAGCGATGACT 60.760 63.158 0.00 0.00 0.00 3.41
1584 1622 7.117523 AGTCTTCTCGATCATTTTGTTCTTCTG 59.882 37.037 0.00 0.00 0.00 3.02
1607 1647 5.183713 TGTGTTTCTAGCCATGAAGGATTTG 59.816 40.000 0.00 0.00 41.22 2.32
1610 1650 5.372343 TTCTAGCCATGAAGGATTTGCTA 57.628 39.130 0.00 0.00 41.22 3.49
1624 1664 6.562518 AGGATTTGCTACTAGTAGTTCGAAC 58.437 40.000 26.76 20.71 35.65 3.95
1633 1673 5.960113 ACTAGTAGTTCGAACGAGAGACTA 58.040 41.667 21.87 20.28 0.00 2.59
1635 1675 5.070770 AGTAGTTCGAACGAGAGACTAGA 57.929 43.478 21.87 0.00 0.00 2.43
1661 1701 2.350484 CGTATCGTGCCGTGATGAGTAT 60.350 50.000 0.00 0.00 0.00 2.12
1662 1702 2.140065 ATCGTGCCGTGATGAGTATG 57.860 50.000 0.00 0.00 0.00 2.39
1664 1704 2.018515 TCGTGCCGTGATGAGTATGTA 58.981 47.619 0.00 0.00 0.00 2.29
1666 1706 3.067601 TCGTGCCGTGATGAGTATGTAAT 59.932 43.478 0.00 0.00 0.00 1.89
1667 1707 3.182372 CGTGCCGTGATGAGTATGTAATG 59.818 47.826 0.00 0.00 0.00 1.90
1668 1708 4.119862 GTGCCGTGATGAGTATGTAATGT 58.880 43.478 0.00 0.00 0.00 2.71
1669 1709 4.025730 GTGCCGTGATGAGTATGTAATGTG 60.026 45.833 0.00 0.00 0.00 3.21
1672 1712 5.276868 GCCGTGATGAGTATGTAATGTGTTC 60.277 44.000 0.00 0.00 0.00 3.18
1673 1713 6.042777 CCGTGATGAGTATGTAATGTGTTCT 58.957 40.000 0.00 0.00 0.00 3.01
1674 1714 7.200455 CCGTGATGAGTATGTAATGTGTTCTA 58.800 38.462 0.00 0.00 0.00 2.10
1676 1716 7.915923 CGTGATGAGTATGTAATGTGTTCTACT 59.084 37.037 0.00 0.00 0.00 2.57
1677 1717 9.239002 GTGATGAGTATGTAATGTGTTCTACTC 57.761 37.037 0.00 0.00 36.96 2.59
1678 1718 8.414003 TGATGAGTATGTAATGTGTTCTACTCC 58.586 37.037 0.00 0.00 36.06 3.85
1679 1719 7.956328 TGAGTATGTAATGTGTTCTACTCCT 57.044 36.000 0.00 0.00 36.06 3.69
1681 1721 7.113658 AGTATGTAATGTGTTCTACTCCTGG 57.886 40.000 0.00 0.00 0.00 4.45
1682 1722 6.668283 AGTATGTAATGTGTTCTACTCCTGGT 59.332 38.462 0.00 0.00 0.00 4.00
1683 1723 5.401531 TGTAATGTGTTCTACTCCTGGTC 57.598 43.478 0.00 0.00 0.00 4.02
1684 1724 4.836175 TGTAATGTGTTCTACTCCTGGTCA 59.164 41.667 0.00 0.00 0.00 4.02
1685 1725 3.963428 ATGTGTTCTACTCCTGGTCAC 57.037 47.619 0.00 0.00 0.00 3.67
1686 1726 1.611977 TGTGTTCTACTCCTGGTCACG 59.388 52.381 0.00 0.00 0.00 4.35
1691 1731 2.022195 TCTACTCCTGGTCACGTATGC 58.978 52.381 0.00 0.00 0.00 3.14
1739 1835 5.389859 TTTGTCCAGTATTGCTTGAATGG 57.610 39.130 0.00 0.00 0.00 3.16
1749 1845 8.199449 CAGTATTGCTTGAATGGATTTTGGTAT 58.801 33.333 0.00 0.00 0.00 2.73
1766 1862 9.826574 ATTTTGGTATGAATTTGATTGATCTGG 57.173 29.630 0.00 0.00 0.00 3.86
1768 1864 7.959658 TGGTATGAATTTGATTGATCTGGTT 57.040 32.000 0.00 0.00 0.00 3.67
1770 1866 6.698766 GGTATGAATTTGATTGATCTGGTTGC 59.301 38.462 0.00 0.00 0.00 4.17
1792 1899 1.462283 CTGCCTCTGTTCATGTTCGTG 59.538 52.381 0.00 0.00 0.00 4.35
1855 1963 2.484264 GCTTGTGCTAATTTCGTCCTGT 59.516 45.455 0.00 0.00 36.03 4.00
1863 1971 4.511454 GCTAATTTCGTCCTGTATGCATCA 59.489 41.667 0.19 0.10 0.00 3.07
1865 1973 3.885724 TTTCGTCCTGTATGCATCAGA 57.114 42.857 20.83 5.93 35.20 3.27
1869 1977 3.255888 TCGTCCTGTATGCATCAGATACC 59.744 47.826 20.83 9.30 35.20 2.73
1870 1978 3.005791 CGTCCTGTATGCATCAGATACCA 59.994 47.826 20.83 2.76 35.20 3.25
1875 1983 7.826252 GTCCTGTATGCATCAGATACCATTTAT 59.174 37.037 20.83 0.00 35.20 1.40
1876 1984 8.385491 TCCTGTATGCATCAGATACCATTTATT 58.615 33.333 20.83 0.00 35.20 1.40
1877 1985 9.671279 CCTGTATGCATCAGATACCATTTATTA 57.329 33.333 20.83 0.00 35.20 0.98
1893 2001 9.146586 ACCATTTATTAATATGCATGGTTCACT 57.853 29.630 19.57 6.16 41.33 3.41
1894 2002 9.985730 CCATTTATTAATATGCATGGTTCACTT 57.014 29.630 10.16 0.00 0.00 3.16
1897 2005 8.870160 TTATTAATATGCATGGTTCACTTTGC 57.130 30.769 10.16 0.00 35.67 3.68
1898 2006 6.528537 TTAATATGCATGGTTCACTTTGCT 57.471 33.333 10.16 0.00 36.10 3.91
1899 2007 5.410355 AATATGCATGGTTCACTTTGCTT 57.590 34.783 10.16 0.00 36.10 3.91
1900 2008 2.798976 TGCATGGTTCACTTTGCTTC 57.201 45.000 0.00 0.00 36.10 3.86
1901 2009 1.340889 TGCATGGTTCACTTTGCTTCC 59.659 47.619 0.00 0.00 36.10 3.46
1902 2010 1.340889 GCATGGTTCACTTTGCTTCCA 59.659 47.619 0.00 0.00 32.41 3.53
1903 2011 2.608752 GCATGGTTCACTTTGCTTCCAG 60.609 50.000 0.00 0.00 32.41 3.86
1904 2012 2.727123 TGGTTCACTTTGCTTCCAGA 57.273 45.000 0.00 0.00 0.00 3.86
1905 2013 3.228188 TGGTTCACTTTGCTTCCAGAT 57.772 42.857 0.00 0.00 0.00 2.90
1906 2014 3.565307 TGGTTCACTTTGCTTCCAGATT 58.435 40.909 0.00 0.00 0.00 2.40
1908 2016 5.324409 TGGTTCACTTTGCTTCCAGATTAT 58.676 37.500 0.00 0.00 0.00 1.28
1915 2023 6.587608 CACTTTGCTTCCAGATTATTTCCAAC 59.412 38.462 0.00 0.00 0.00 3.77
1918 2026 6.271488 TGCTTCCAGATTATTTCCAACTTG 57.729 37.500 0.00 0.00 0.00 3.16
1924 2032 7.110155 TCCAGATTATTTCCAACTTGTACTCC 58.890 38.462 0.00 0.00 0.00 3.85
1928 2036 8.047310 AGATTATTTCCAACTTGTACTCCGAAT 58.953 33.333 0.00 0.00 0.00 3.34
1929 2037 7.605410 TTATTTCCAACTTGTACTCCGAATC 57.395 36.000 0.00 0.00 0.00 2.52
1930 2038 4.884668 TTCCAACTTGTACTCCGAATCT 57.115 40.909 0.00 0.00 0.00 2.40
1935 2043 5.107065 CCAACTTGTACTCCGAATCTTGAAC 60.107 44.000 0.00 0.00 0.00 3.18
1936 2044 5.470047 ACTTGTACTCCGAATCTTGAACT 57.530 39.130 0.00 0.00 0.00 3.01
1937 2045 5.230942 ACTTGTACTCCGAATCTTGAACTG 58.769 41.667 0.00 0.00 0.00 3.16
1938 2046 3.585862 TGTACTCCGAATCTTGAACTGC 58.414 45.455 0.00 0.00 0.00 4.40
1939 2047 2.839486 ACTCCGAATCTTGAACTGCA 57.161 45.000 0.00 0.00 0.00 4.41
1940 2048 3.340814 ACTCCGAATCTTGAACTGCAT 57.659 42.857 0.00 0.00 0.00 3.96
1941 2049 3.005554 ACTCCGAATCTTGAACTGCATG 58.994 45.455 0.00 0.00 0.00 4.06
1942 2050 3.005554 CTCCGAATCTTGAACTGCATGT 58.994 45.455 0.00 0.00 0.00 3.21
1943 2051 4.183865 CTCCGAATCTTGAACTGCATGTA 58.816 43.478 0.00 0.00 0.00 2.29
1944 2052 4.574892 TCCGAATCTTGAACTGCATGTAA 58.425 39.130 0.00 0.00 0.00 2.41
1945 2053 5.185454 TCCGAATCTTGAACTGCATGTAAT 58.815 37.500 0.00 0.00 0.00 1.89
2033 2830 6.509418 TTTTGTGCTAGTTTCTGTGAAGTT 57.491 33.333 0.00 0.00 0.00 2.66
2037 2834 7.046292 TGTGCTAGTTTCTGTGAAGTTACTA 57.954 36.000 0.00 0.00 0.00 1.82
2048 2845 8.503458 TCTGTGAAGTTACTATGTAGGAGTAC 57.497 38.462 0.00 0.00 0.00 2.73
2123 3534 1.408969 AAATTGTCGTGGGGCAAGTT 58.591 45.000 0.00 0.00 0.00 2.66
2140 3551 4.515567 GCAAGTTTCTGCCAAGTTACTAGT 59.484 41.667 0.00 0.00 36.25 2.57
2214 3667 7.861630 TGCAATTTACAGTTAGTCAAGTTCTC 58.138 34.615 0.00 0.00 0.00 2.87
2285 3742 0.729116 GCTCGCTTACATGCATGTGT 59.271 50.000 36.72 19.43 41.89 3.72
2289 3746 4.229096 CTCGCTTACATGCATGTGTTTTT 58.771 39.130 36.72 15.60 41.89 1.94
2290 3747 4.225984 TCGCTTACATGCATGTGTTTTTC 58.774 39.130 36.72 19.73 41.89 2.29
2295 3752 4.566545 ACATGCATGTGTTTTTCGAGAA 57.433 36.364 30.92 0.00 40.03 2.87
2304 3761 4.574828 TGTGTTTTTCGAGAAGAGGAAAGG 59.425 41.667 0.00 0.00 34.03 3.11
2307 3764 5.527582 TGTTTTTCGAGAAGAGGAAAGGAAG 59.472 40.000 0.00 0.00 34.03 3.46
2308 3765 4.957684 TTTCGAGAAGAGGAAAGGAAGT 57.042 40.909 0.00 0.00 0.00 3.01
2309 3766 3.944055 TCGAGAAGAGGAAAGGAAGTG 57.056 47.619 0.00 0.00 0.00 3.16
2310 3767 2.028930 TCGAGAAGAGGAAAGGAAGTGC 60.029 50.000 0.00 0.00 0.00 4.40
2311 3768 2.289072 CGAGAAGAGGAAAGGAAGTGCA 60.289 50.000 0.00 0.00 0.00 4.57
2312 3769 3.333804 GAGAAGAGGAAAGGAAGTGCAG 58.666 50.000 0.00 0.00 0.00 4.41
2313 3770 2.975489 AGAAGAGGAAAGGAAGTGCAGA 59.025 45.455 0.00 0.00 0.00 4.26
2314 3771 3.007831 AGAAGAGGAAAGGAAGTGCAGAG 59.992 47.826 0.00 0.00 0.00 3.35
2315 3772 2.614259 AGAGGAAAGGAAGTGCAGAGA 58.386 47.619 0.00 0.00 0.00 3.10
2316 3773 2.975489 AGAGGAAAGGAAGTGCAGAGAA 59.025 45.455 0.00 0.00 0.00 2.87
2317 3774 3.392616 AGAGGAAAGGAAGTGCAGAGAAA 59.607 43.478 0.00 0.00 0.00 2.52
2318 3775 4.137543 GAGGAAAGGAAGTGCAGAGAAAA 58.862 43.478 0.00 0.00 0.00 2.29
2319 3776 4.536765 AGGAAAGGAAGTGCAGAGAAAAA 58.463 39.130 0.00 0.00 0.00 1.94
2320 3777 5.143369 AGGAAAGGAAGTGCAGAGAAAAAT 58.857 37.500 0.00 0.00 0.00 1.82
2321 3778 5.010415 AGGAAAGGAAGTGCAGAGAAAAATG 59.990 40.000 0.00 0.00 0.00 2.32
2322 3779 5.221322 GGAAAGGAAGTGCAGAGAAAAATGT 60.221 40.000 0.00 0.00 0.00 2.71
2323 3780 5.859205 AAGGAAGTGCAGAGAAAAATGTT 57.141 34.783 0.00 0.00 0.00 2.71
2324 3781 5.444663 AGGAAGTGCAGAGAAAAATGTTC 57.555 39.130 0.00 0.00 0.00 3.18
2325 3782 4.889409 AGGAAGTGCAGAGAAAAATGTTCA 59.111 37.500 0.00 0.00 0.00 3.18
2326 3783 5.009410 AGGAAGTGCAGAGAAAAATGTTCAG 59.991 40.000 0.00 0.00 0.00 3.02
2327 3784 5.009010 GGAAGTGCAGAGAAAAATGTTCAGA 59.991 40.000 0.00 0.00 0.00 3.27
2328 3785 6.294397 GGAAGTGCAGAGAAAAATGTTCAGAT 60.294 38.462 0.00 0.00 0.00 2.90
2329 3786 6.645790 AGTGCAGAGAAAAATGTTCAGATT 57.354 33.333 0.00 0.00 0.00 2.40
2330 3787 7.750229 AGTGCAGAGAAAAATGTTCAGATTA 57.250 32.000 0.00 0.00 0.00 1.75
2331 3788 7.588512 AGTGCAGAGAAAAATGTTCAGATTAC 58.411 34.615 0.00 0.00 0.00 1.89
2332 3789 7.229306 AGTGCAGAGAAAAATGTTCAGATTACA 59.771 33.333 0.00 0.00 0.00 2.41
2333 3790 8.025445 GTGCAGAGAAAAATGTTCAGATTACAT 58.975 33.333 0.00 0.00 37.82 2.29
2334 3791 8.024865 TGCAGAGAAAAATGTTCAGATTACATG 58.975 33.333 0.00 0.00 36.41 3.21
2335 3792 8.239314 GCAGAGAAAAATGTTCAGATTACATGA 58.761 33.333 0.00 0.00 36.41 3.07
2339 3796 9.865321 AGAAAAATGTTCAGATTACATGAATGG 57.135 29.630 0.00 0.00 38.81 3.16
2340 3797 9.859427 GAAAAATGTTCAGATTACATGAATGGA 57.141 29.630 0.00 0.00 38.81 3.41
2341 3798 9.643693 AAAAATGTTCAGATTACATGAATGGAC 57.356 29.630 0.00 0.00 38.81 4.02
2342 3799 7.943079 AATGTTCAGATTACATGAATGGACA 57.057 32.000 0.00 1.98 38.81 4.02
2343 3800 6.741992 TGTTCAGATTACATGAATGGACAC 57.258 37.500 0.00 0.00 38.81 3.67
2344 3801 6.237154 TGTTCAGATTACATGAATGGACACA 58.763 36.000 0.00 0.00 38.81 3.72
2345 3802 6.714356 TGTTCAGATTACATGAATGGACACAA 59.286 34.615 0.00 0.00 38.81 3.33
2346 3803 6.990341 TCAGATTACATGAATGGACACAAG 57.010 37.500 0.00 0.00 0.00 3.16
2347 3804 5.882000 TCAGATTACATGAATGGACACAAGG 59.118 40.000 0.00 0.00 0.00 3.61
2348 3805 5.882000 CAGATTACATGAATGGACACAAGGA 59.118 40.000 0.00 0.00 0.00 3.36
2349 3806 6.375174 CAGATTACATGAATGGACACAAGGAA 59.625 38.462 0.00 0.00 0.00 3.36
2350 3807 6.947733 AGATTACATGAATGGACACAAGGAAA 59.052 34.615 0.00 0.00 0.00 3.13
2351 3808 6.968263 TTACATGAATGGACACAAGGAAAA 57.032 33.333 0.00 0.00 0.00 2.29
2352 3809 7.537596 TTACATGAATGGACACAAGGAAAAT 57.462 32.000 0.00 0.00 0.00 1.82
2353 3810 8.642935 TTACATGAATGGACACAAGGAAAATA 57.357 30.769 0.00 0.00 0.00 1.40
2354 3811 7.722949 ACATGAATGGACACAAGGAAAATAT 57.277 32.000 0.00 0.00 0.00 1.28
2355 3812 7.549839 ACATGAATGGACACAAGGAAAATATG 58.450 34.615 0.00 0.00 0.00 1.78
2356 3813 5.964758 TGAATGGACACAAGGAAAATATGC 58.035 37.500 0.00 0.00 0.00 3.14
2357 3814 5.716228 TGAATGGACACAAGGAAAATATGCT 59.284 36.000 0.00 0.00 0.00 3.79
2358 3815 6.211184 TGAATGGACACAAGGAAAATATGCTT 59.789 34.615 0.00 0.00 40.83 3.91
2359 3816 6.610075 ATGGACACAAGGAAAATATGCTTT 57.390 33.333 0.00 0.00 37.65 3.51
2360 3817 5.782047 TGGACACAAGGAAAATATGCTTTG 58.218 37.500 0.00 0.00 37.65 2.77
2361 3818 5.170748 GGACACAAGGAAAATATGCTTTGG 58.829 41.667 0.00 0.00 37.65 3.28
2362 3819 5.047377 GGACACAAGGAAAATATGCTTTGGA 60.047 40.000 0.00 0.00 37.65 3.53
2363 3820 6.418057 ACACAAGGAAAATATGCTTTGGAA 57.582 33.333 0.00 0.00 37.65 3.53
2364 3821 6.223120 ACACAAGGAAAATATGCTTTGGAAC 58.777 36.000 0.00 0.00 37.65 3.62
2365 3822 6.183360 ACACAAGGAAAATATGCTTTGGAACA 60.183 34.615 0.00 0.00 37.65 3.18
2366 3823 6.875195 CACAAGGAAAATATGCTTTGGAACAT 59.125 34.615 0.00 0.00 37.65 2.71
2367 3824 6.875195 ACAAGGAAAATATGCTTTGGAACATG 59.125 34.615 0.00 0.00 37.65 3.21
2368 3825 5.981174 AGGAAAATATGCTTTGGAACATGG 58.019 37.500 0.00 0.00 39.30 3.66
2369 3826 5.484998 AGGAAAATATGCTTTGGAACATGGT 59.515 36.000 0.00 0.00 39.30 3.55
2370 3827 5.581874 GGAAAATATGCTTTGGAACATGGTG 59.418 40.000 0.00 0.00 39.30 4.17
2371 3828 4.741321 AATATGCTTTGGAACATGGTGG 57.259 40.909 0.00 0.00 39.30 4.61
2372 3829 2.014010 ATGCTTTGGAACATGGTGGT 57.986 45.000 0.00 0.00 39.30 4.16
2373 3830 2.666272 TGCTTTGGAACATGGTGGTA 57.334 45.000 0.00 0.00 39.30 3.25
2374 3831 2.950781 TGCTTTGGAACATGGTGGTAA 58.049 42.857 0.00 0.00 39.30 2.85
2375 3832 3.505386 TGCTTTGGAACATGGTGGTAAT 58.495 40.909 0.00 0.00 39.30 1.89
2376 3833 3.900601 TGCTTTGGAACATGGTGGTAATT 59.099 39.130 0.00 0.00 39.30 1.40
2377 3834 5.080337 TGCTTTGGAACATGGTGGTAATTA 58.920 37.500 0.00 0.00 39.30 1.40
2378 3835 5.047660 TGCTTTGGAACATGGTGGTAATTAC 60.048 40.000 7.09 7.09 39.30 1.89
2379 3836 5.047660 GCTTTGGAACATGGTGGTAATTACA 60.048 40.000 17.16 1.24 39.30 2.41
2380 3837 5.968528 TTGGAACATGGTGGTAATTACAC 57.031 39.130 17.16 12.33 39.30 2.90
2381 3838 4.986783 TGGAACATGGTGGTAATTACACA 58.013 39.130 17.16 12.43 40.54 3.72
2382 3839 5.575157 TGGAACATGGTGGTAATTACACAT 58.425 37.500 17.16 13.95 40.54 3.21
2383 3840 5.417266 TGGAACATGGTGGTAATTACACATG 59.583 40.000 27.59 27.59 40.54 3.21
2426 3883 7.845066 AAAATATTCAGTACTTCCTCCGTTC 57.155 36.000 0.00 0.00 0.00 3.95
2427 3884 3.889520 ATTCAGTACTTCCTCCGTTCC 57.110 47.619 0.00 0.00 0.00 3.62
2428 3885 2.599408 TCAGTACTTCCTCCGTTCCT 57.401 50.000 0.00 0.00 0.00 3.36
2429 3886 3.726557 TCAGTACTTCCTCCGTTCCTA 57.273 47.619 0.00 0.00 0.00 2.94
2430 3887 4.038271 TCAGTACTTCCTCCGTTCCTAA 57.962 45.455 0.00 0.00 0.00 2.69
2431 3888 4.410099 TCAGTACTTCCTCCGTTCCTAAA 58.590 43.478 0.00 0.00 0.00 1.85
2432 3889 5.021458 TCAGTACTTCCTCCGTTCCTAAAT 58.979 41.667 0.00 0.00 0.00 1.40
2433 3890 6.189859 TCAGTACTTCCTCCGTTCCTAAATA 58.810 40.000 0.00 0.00 0.00 1.40
2434 3891 6.837568 TCAGTACTTCCTCCGTTCCTAAATAT 59.162 38.462 0.00 0.00 0.00 1.28
2435 3892 8.000709 TCAGTACTTCCTCCGTTCCTAAATATA 58.999 37.037 0.00 0.00 0.00 0.86
2436 3893 8.636213 CAGTACTTCCTCCGTTCCTAAATATAA 58.364 37.037 0.00 0.00 0.00 0.98
2437 3894 8.858094 AGTACTTCCTCCGTTCCTAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
2438 3895 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2439 3896 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2440 3897 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2441 3898 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
2442 3899 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
2443 3900 8.765517 TCCTCCGTTCCTAAATATAAGTCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
2444 3901 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2505 3962 8.764524 AGTGAATCAACACTCTAAACTATGTC 57.235 34.615 0.00 0.00 46.36 3.06
2506 3963 8.589338 AGTGAATCAACACTCTAAACTATGTCT 58.411 33.333 0.00 0.00 46.36 3.41
2507 3964 9.856488 GTGAATCAACACTCTAAACTATGTCTA 57.144 33.333 0.00 0.00 37.73 2.59
2537 3994 9.778741 ACATCCGTATGTAGTCAATATTGAAAT 57.221 29.630 19.55 13.50 44.66 2.17
2540 3997 9.476202 TCCGTATGTAGTCAATATTGAAATCTG 57.524 33.333 19.55 5.66 39.21 2.90
2541 3998 9.261180 CCGTATGTAGTCAATATTGAAATCTGT 57.739 33.333 19.55 7.53 39.21 3.41
2567 4024 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2568 4025 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2584 4041 4.131596 CGGAGGGAGTAAAAGTCAAAACA 58.868 43.478 0.00 0.00 0.00 2.83
2593 4050 8.926715 GAGTAAAAGTCAAAACACTCCAAATT 57.073 30.769 0.00 0.00 0.00 1.82
2594 4051 8.926715 AGTAAAAGTCAAAACACTCCAAATTC 57.073 30.769 0.00 0.00 0.00 2.17
2595 4052 8.749354 AGTAAAAGTCAAAACACTCCAAATTCT 58.251 29.630 0.00 0.00 0.00 2.40
2614 4071 9.853921 CAAATTCTATTTTCAACAAACTTGAGC 57.146 29.630 0.00 0.00 0.00 4.26
2615 4072 9.822185 AAATTCTATTTTCAACAAACTTGAGCT 57.178 25.926 0.00 0.00 0.00 4.09
2620 4077 2.627945 TCAACAAACTTGAGCTGTCGT 58.372 42.857 0.00 0.00 0.00 4.34
2630 4088 2.739292 TGAGCTGTCGTTTCTGTGTAC 58.261 47.619 0.00 0.00 0.00 2.90
2648 4106 8.714179 TCTGTGTACAAAAATATTCTGTAACGG 58.286 33.333 0.00 13.37 0.00 4.44
2683 4141 9.270576 CTGACAAAAATGACAAATATTCTCTCG 57.729 33.333 0.00 0.00 0.00 4.04
2687 4145 9.079833 CAAAAATGACAAATATTCTCTCGCAAT 57.920 29.630 0.00 0.00 0.00 3.56
2689 4147 9.941664 AAAATGACAAATATTCTCTCGCAATAG 57.058 29.630 0.00 0.00 0.00 1.73
2690 4148 6.530913 TGACAAATATTCTCTCGCAATAGC 57.469 37.500 0.00 0.00 37.42 2.97
2691 4149 6.048509 TGACAAATATTCTCTCGCAATAGCA 58.951 36.000 0.00 0.00 42.27 3.49
2698 4156 4.063998 TCTCTCGCAATAGCATGAACAT 57.936 40.909 0.00 0.00 42.27 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 2.615493 GCTAGTGTGCCTGTATGGTTGT 60.615 50.000 0.00 0.00 38.35 3.32
113 114 7.711846 AGCTTCAGATGTCTGTGTATACTTAG 58.288 38.462 9.65 2.81 44.12 2.18
542 543 4.965814 TGTGGATTATCAGATGAGCTTCC 58.034 43.478 0.00 0.00 0.00 3.46
547 548 4.750598 CAGCACTGTGGATTATCAGATGAG 59.249 45.833 10.21 0.00 35.84 2.90
1232 1247 3.083349 CCAGCGTGGGGAGGATCA 61.083 66.667 0.00 0.00 36.25 2.92
1296 1314 1.138047 CGTCGATGTTGTAGGCCGAC 61.138 60.000 9.38 9.38 44.06 4.79
1309 1327 2.163613 TGTAGTTGATGCTGACGTCGAT 59.836 45.455 11.62 2.51 34.28 3.59
1310 1331 1.538075 TGTAGTTGATGCTGACGTCGA 59.462 47.619 11.62 0.00 34.28 4.20
1402 1423 4.452733 GAGGTTGAGGCGGGGTCG 62.453 72.222 0.00 0.00 39.81 4.79
1403 1424 4.452733 CGAGGTTGAGGCGGGGTC 62.453 72.222 0.00 0.00 0.00 4.46
1407 1428 4.697756 TTGGCGAGGTTGAGGCGG 62.698 66.667 0.00 0.00 35.52 6.13
1414 1435 4.699522 GGCGAGGTTGGCGAGGTT 62.700 66.667 0.00 0.00 0.00 3.50
1449 1470 4.436998 CTGGTCTGGACGGCGGAC 62.437 72.222 13.24 8.75 0.00 4.79
1518 1542 1.279271 GCTACTTGCCTCTTGGGAGAA 59.721 52.381 0.00 0.00 41.86 2.87
1584 1622 5.644644 CAAATCCTTCATGGCTAGAAACAC 58.355 41.667 0.00 0.00 35.26 3.32
1607 1647 4.803088 TCTCTCGTTCGAACTACTAGTAGC 59.197 45.833 26.54 12.55 36.66 3.58
1610 1650 4.819769 AGTCTCTCGTTCGAACTACTAGT 58.180 43.478 24.80 0.00 0.00 2.57
1661 1701 4.836175 TGACCAGGAGTAGAACACATTACA 59.164 41.667 0.00 0.00 0.00 2.41
1662 1702 5.169295 GTGACCAGGAGTAGAACACATTAC 58.831 45.833 0.00 0.00 0.00 1.89
1664 1704 3.306088 CGTGACCAGGAGTAGAACACATT 60.306 47.826 0.00 0.00 0.00 2.71
1666 1706 1.611977 CGTGACCAGGAGTAGAACACA 59.388 52.381 0.00 0.00 0.00 3.72
1667 1707 1.612463 ACGTGACCAGGAGTAGAACAC 59.388 52.381 0.00 0.00 0.00 3.32
1668 1708 1.991121 ACGTGACCAGGAGTAGAACA 58.009 50.000 0.00 0.00 0.00 3.18
1669 1709 3.734293 GCATACGTGACCAGGAGTAGAAC 60.734 52.174 0.00 0.00 0.00 3.01
1672 1712 1.749063 TGCATACGTGACCAGGAGTAG 59.251 52.381 0.00 0.00 0.00 2.57
1673 1713 1.842052 TGCATACGTGACCAGGAGTA 58.158 50.000 0.00 0.00 0.00 2.59
1674 1714 0.973632 TTGCATACGTGACCAGGAGT 59.026 50.000 0.00 0.00 0.00 3.85
1676 1716 1.277842 ACATTGCATACGTGACCAGGA 59.722 47.619 0.00 0.00 0.00 3.86
1677 1717 1.398041 CACATTGCATACGTGACCAGG 59.602 52.381 0.00 0.00 32.23 4.45
1678 1718 2.076100 ACACATTGCATACGTGACCAG 58.924 47.619 15.24 0.00 34.69 4.00
1679 1719 2.177394 ACACATTGCATACGTGACCA 57.823 45.000 15.24 0.00 34.69 4.02
1681 1721 4.625742 AGTAGAACACATTGCATACGTGAC 59.374 41.667 15.24 9.64 34.69 3.67
1682 1722 4.816392 AGTAGAACACATTGCATACGTGA 58.184 39.130 15.24 0.00 34.69 4.35
1683 1723 5.348724 AGAAGTAGAACACATTGCATACGTG 59.651 40.000 0.00 8.62 36.70 4.49
1684 1724 5.348724 CAGAAGTAGAACACATTGCATACGT 59.651 40.000 0.00 0.00 0.00 3.57
1685 1725 5.220472 CCAGAAGTAGAACACATTGCATACG 60.220 44.000 0.00 0.00 0.00 3.06
1686 1726 5.643777 ACCAGAAGTAGAACACATTGCATAC 59.356 40.000 0.00 0.00 0.00 2.39
1691 1731 5.056480 TGTGACCAGAAGTAGAACACATTG 58.944 41.667 0.00 0.00 33.04 2.82
1749 1845 5.713389 AGAGCAACCAGATCAATCAAATTCA 59.287 36.000 0.00 0.00 34.30 2.57
1766 1862 1.467734 CATGAACAGAGGCAGAGCAAC 59.532 52.381 0.00 0.00 0.00 4.17
1768 1864 0.689055 ACATGAACAGAGGCAGAGCA 59.311 50.000 0.00 0.00 0.00 4.26
1770 1866 1.998315 CGAACATGAACAGAGGCAGAG 59.002 52.381 0.00 0.00 0.00 3.35
1848 1955 3.005791 TGGTATCTGATGCATACAGGACG 59.994 47.826 19.47 0.00 36.22 4.79
1875 1983 6.528537 AGCAAAGTGAACCATGCATATTAA 57.471 33.333 0.00 0.00 41.18 1.40
1876 1984 6.405731 GGAAGCAAAGTGAACCATGCATATTA 60.406 38.462 0.00 0.00 41.18 0.98
1877 1985 5.410355 AAGCAAAGTGAACCATGCATATT 57.590 34.783 0.00 0.00 41.18 1.28
1878 1986 4.142093 GGAAGCAAAGTGAACCATGCATAT 60.142 41.667 0.00 0.00 41.18 1.78
1879 1987 3.193267 GGAAGCAAAGTGAACCATGCATA 59.807 43.478 0.00 0.00 41.18 3.14
1882 1990 1.340889 TGGAAGCAAAGTGAACCATGC 59.659 47.619 0.00 1.01 39.06 4.06
1883 1991 2.886523 TCTGGAAGCAAAGTGAACCATG 59.113 45.455 0.00 0.00 0.00 3.66
1884 1992 3.228188 TCTGGAAGCAAAGTGAACCAT 57.772 42.857 0.00 0.00 0.00 3.55
1886 1994 5.904362 ATAATCTGGAAGCAAAGTGAACC 57.096 39.130 0.00 0.00 0.00 3.62
1887 1995 6.808704 GGAAATAATCTGGAAGCAAAGTGAAC 59.191 38.462 0.00 0.00 0.00 3.18
1888 1996 6.493115 TGGAAATAATCTGGAAGCAAAGTGAA 59.507 34.615 0.00 0.00 0.00 3.18
1890 1998 6.271488 TGGAAATAATCTGGAAGCAAAGTG 57.729 37.500 0.00 0.00 0.00 3.16
1891 1999 6.494835 AGTTGGAAATAATCTGGAAGCAAAGT 59.505 34.615 0.00 0.00 0.00 2.66
1892 2000 6.928520 AGTTGGAAATAATCTGGAAGCAAAG 58.071 36.000 0.00 0.00 0.00 2.77
1893 2001 6.916360 AGTTGGAAATAATCTGGAAGCAAA 57.084 33.333 0.00 0.00 0.00 3.68
1894 2002 6.267471 ACAAGTTGGAAATAATCTGGAAGCAA 59.733 34.615 7.96 0.00 0.00 3.91
1895 2003 5.774690 ACAAGTTGGAAATAATCTGGAAGCA 59.225 36.000 7.96 0.00 0.00 3.91
1896 2004 6.272822 ACAAGTTGGAAATAATCTGGAAGC 57.727 37.500 7.96 0.00 0.00 3.86
1897 2005 8.567285 AGTACAAGTTGGAAATAATCTGGAAG 57.433 34.615 7.96 0.00 0.00 3.46
1898 2006 7.610305 GGAGTACAAGTTGGAAATAATCTGGAA 59.390 37.037 7.96 0.00 0.00 3.53
1899 2007 7.110155 GGAGTACAAGTTGGAAATAATCTGGA 58.890 38.462 7.96 0.00 0.00 3.86
1900 2008 6.037172 CGGAGTACAAGTTGGAAATAATCTGG 59.963 42.308 7.96 0.00 0.00 3.86
1901 2009 6.816640 TCGGAGTACAAGTTGGAAATAATCTG 59.183 38.462 7.96 4.74 0.00 2.90
1902 2010 6.942976 TCGGAGTACAAGTTGGAAATAATCT 58.057 36.000 7.96 0.00 0.00 2.40
1903 2011 7.605410 TTCGGAGTACAAGTTGGAAATAATC 57.395 36.000 7.96 0.00 0.00 1.75
1904 2012 8.047310 AGATTCGGAGTACAAGTTGGAAATAAT 58.953 33.333 7.96 0.00 0.00 1.28
1905 2013 7.391620 AGATTCGGAGTACAAGTTGGAAATAA 58.608 34.615 7.96 0.00 0.00 1.40
1906 2014 6.942976 AGATTCGGAGTACAAGTTGGAAATA 58.057 36.000 7.96 0.00 0.00 1.40
1908 2016 5.223449 AGATTCGGAGTACAAGTTGGAAA 57.777 39.130 7.96 0.00 0.00 3.13
1915 2023 4.092091 GCAGTTCAAGATTCGGAGTACAAG 59.908 45.833 0.00 0.00 0.00 3.16
1918 2026 3.585862 TGCAGTTCAAGATTCGGAGTAC 58.414 45.455 0.00 0.00 0.00 2.73
1924 2032 6.110543 TCATTACATGCAGTTCAAGATTCG 57.889 37.500 0.00 0.00 0.00 3.34
1928 2036 4.571984 CGGATCATTACATGCAGTTCAAGA 59.428 41.667 0.00 0.00 0.00 3.02
1929 2037 4.571984 TCGGATCATTACATGCAGTTCAAG 59.428 41.667 0.00 0.00 0.00 3.02
1930 2038 4.512484 TCGGATCATTACATGCAGTTCAA 58.488 39.130 0.00 0.00 0.00 2.69
1935 2043 4.563061 TGAGATCGGATCATTACATGCAG 58.437 43.478 19.47 0.00 0.00 4.41
1936 2044 4.605640 TGAGATCGGATCATTACATGCA 57.394 40.909 19.47 0.00 0.00 3.96
1937 2045 4.934001 ACATGAGATCGGATCATTACATGC 59.066 41.667 26.83 9.96 35.20 4.06
1938 2046 8.538409 TTAACATGAGATCGGATCATTACATG 57.462 34.615 26.12 26.12 35.20 3.21
1939 2047 8.588472 TCTTAACATGAGATCGGATCATTACAT 58.412 33.333 19.47 14.61 35.20 2.29
1940 2048 7.951591 TCTTAACATGAGATCGGATCATTACA 58.048 34.615 19.47 13.22 35.20 2.41
1941 2049 8.867935 CATCTTAACATGAGATCGGATCATTAC 58.132 37.037 19.47 8.64 35.20 1.89
1942 2050 8.588472 ACATCTTAACATGAGATCGGATCATTA 58.412 33.333 19.47 6.11 35.20 1.90
1943 2051 7.387122 CACATCTTAACATGAGATCGGATCATT 59.613 37.037 19.47 8.26 35.20 2.57
1944 2052 6.872547 CACATCTTAACATGAGATCGGATCAT 59.127 38.462 19.47 4.60 37.90 2.45
1945 2053 6.040842 TCACATCTTAACATGAGATCGGATCA 59.959 38.462 19.47 2.19 31.66 2.92
1946 2054 6.450545 TCACATCTTAACATGAGATCGGATC 58.549 40.000 10.02 10.02 31.66 3.36
1947 2055 6.410942 TCACATCTTAACATGAGATCGGAT 57.589 37.500 0.00 0.00 31.66 4.18
1948 2056 5.852282 TCACATCTTAACATGAGATCGGA 57.148 39.130 0.00 0.00 31.66 4.55
1950 2058 8.131731 TCTACTTCACATCTTAACATGAGATCG 58.868 37.037 0.00 0.00 31.66 3.69
1951 2059 9.979578 ATCTACTTCACATCTTAACATGAGATC 57.020 33.333 0.00 0.00 31.66 2.75
1953 2061 9.591792 CAATCTACTTCACATCTTAACATGAGA 57.408 33.333 0.00 0.00 0.00 3.27
1954 2062 8.824781 CCAATCTACTTCACATCTTAACATGAG 58.175 37.037 0.00 0.00 0.00 2.90
1955 2063 8.539544 TCCAATCTACTTCACATCTTAACATGA 58.460 33.333 0.00 0.00 0.00 3.07
1956 2064 8.722480 TCCAATCTACTTCACATCTTAACATG 57.278 34.615 0.00 0.00 0.00 3.21
2048 2845 8.553459 AATCAGACACAATTGTAGGAAACTAG 57.447 34.615 11.53 0.00 45.49 2.57
2096 3507 2.615493 CCCCACGACAATTTAGAGCAGT 60.615 50.000 0.00 0.00 0.00 4.40
2109 3520 1.949257 CAGAAACTTGCCCCACGAC 59.051 57.895 0.00 0.00 0.00 4.34
2123 3534 6.932960 GGAAACTAACTAGTAACTTGGCAGAA 59.067 38.462 0.00 0.00 34.99 3.02
2183 3636 5.163864 TGACTAACTGTAAATTGCATCAGCG 60.164 40.000 0.00 0.00 46.23 5.18
2214 3667 7.490402 GGGAAGTTCATCAATGCAGAATTTTAG 59.510 37.037 5.01 0.00 0.00 1.85
2285 3742 5.527582 CACTTCCTTTCCTCTTCTCGAAAAA 59.472 40.000 0.00 0.00 0.00 1.94
2289 3746 2.028930 GCACTTCCTTTCCTCTTCTCGA 60.029 50.000 0.00 0.00 0.00 4.04
2290 3747 2.289072 TGCACTTCCTTTCCTCTTCTCG 60.289 50.000 0.00 0.00 0.00 4.04
2295 3752 2.614259 TCTCTGCACTTCCTTTCCTCT 58.386 47.619 0.00 0.00 0.00 3.69
2304 3761 6.064846 TCTGAACATTTTTCTCTGCACTTC 57.935 37.500 0.00 0.00 0.00 3.01
2307 3764 7.362662 TGTAATCTGAACATTTTTCTCTGCAC 58.637 34.615 0.00 0.00 0.00 4.57
2308 3765 7.509141 TGTAATCTGAACATTTTTCTCTGCA 57.491 32.000 0.00 0.00 0.00 4.41
2309 3766 8.239314 TCATGTAATCTGAACATTTTTCTCTGC 58.761 33.333 0.00 0.00 35.39 4.26
2313 3770 9.865321 CCATTCATGTAATCTGAACATTTTTCT 57.135 29.630 0.00 0.00 35.39 2.52
2314 3771 9.859427 TCCATTCATGTAATCTGAACATTTTTC 57.141 29.630 0.00 0.00 35.39 2.29
2315 3772 9.643693 GTCCATTCATGTAATCTGAACATTTTT 57.356 29.630 0.00 0.00 35.39 1.94
2316 3773 8.805175 TGTCCATTCATGTAATCTGAACATTTT 58.195 29.630 0.00 0.00 35.39 1.82
2317 3774 8.246180 GTGTCCATTCATGTAATCTGAACATTT 58.754 33.333 0.00 0.00 35.39 2.32
2318 3775 7.394077 TGTGTCCATTCATGTAATCTGAACATT 59.606 33.333 0.00 0.00 35.39 2.71
2319 3776 6.885918 TGTGTCCATTCATGTAATCTGAACAT 59.114 34.615 0.00 0.00 38.08 2.71
2320 3777 6.237154 TGTGTCCATTCATGTAATCTGAACA 58.763 36.000 0.00 0.00 35.57 3.18
2321 3778 6.741992 TGTGTCCATTCATGTAATCTGAAC 57.258 37.500 0.00 0.00 35.57 3.18
2322 3779 6.375174 CCTTGTGTCCATTCATGTAATCTGAA 59.625 38.462 0.00 0.00 37.06 3.02
2323 3780 5.882000 CCTTGTGTCCATTCATGTAATCTGA 59.118 40.000 0.00 0.00 0.00 3.27
2324 3781 5.882000 TCCTTGTGTCCATTCATGTAATCTG 59.118 40.000 0.00 0.00 0.00 2.90
2325 3782 6.065976 TCCTTGTGTCCATTCATGTAATCT 57.934 37.500 0.00 0.00 0.00 2.40
2326 3783 6.757897 TTCCTTGTGTCCATTCATGTAATC 57.242 37.500 0.00 0.00 0.00 1.75
2327 3784 7.537596 TTTTCCTTGTGTCCATTCATGTAAT 57.462 32.000 0.00 0.00 0.00 1.89
2328 3785 6.968263 TTTTCCTTGTGTCCATTCATGTAA 57.032 33.333 0.00 0.00 0.00 2.41
2329 3786 8.685427 CATATTTTCCTTGTGTCCATTCATGTA 58.315 33.333 0.00 0.00 0.00 2.29
2330 3787 7.549839 CATATTTTCCTTGTGTCCATTCATGT 58.450 34.615 0.00 0.00 0.00 3.21
2331 3788 6.477688 GCATATTTTCCTTGTGTCCATTCATG 59.522 38.462 0.00 0.00 0.00 3.07
2332 3789 6.381994 AGCATATTTTCCTTGTGTCCATTCAT 59.618 34.615 0.00 0.00 0.00 2.57
2333 3790 5.716228 AGCATATTTTCCTTGTGTCCATTCA 59.284 36.000 0.00 0.00 0.00 2.57
2334 3791 6.212888 AGCATATTTTCCTTGTGTCCATTC 57.787 37.500 0.00 0.00 0.00 2.67
2335 3792 6.610075 AAGCATATTTTCCTTGTGTCCATT 57.390 33.333 0.00 0.00 0.00 3.16
2336 3793 6.400568 CAAAGCATATTTTCCTTGTGTCCAT 58.599 36.000 0.00 0.00 0.00 3.41
2337 3794 5.279406 CCAAAGCATATTTTCCTTGTGTCCA 60.279 40.000 0.00 0.00 0.00 4.02
2338 3795 5.047377 TCCAAAGCATATTTTCCTTGTGTCC 60.047 40.000 0.00 0.00 0.00 4.02
2339 3796 6.024552 TCCAAAGCATATTTTCCTTGTGTC 57.975 37.500 0.00 0.00 0.00 3.67
2340 3797 6.183360 TGTTCCAAAGCATATTTTCCTTGTGT 60.183 34.615 0.00 0.00 0.00 3.72
2341 3798 6.222389 TGTTCCAAAGCATATTTTCCTTGTG 58.778 36.000 0.00 0.00 0.00 3.33
2342 3799 6.418057 TGTTCCAAAGCATATTTTCCTTGT 57.582 33.333 0.00 0.00 0.00 3.16
2343 3800 6.314400 CCATGTTCCAAAGCATATTTTCCTTG 59.686 38.462 0.00 0.00 0.00 3.61
2344 3801 6.013466 ACCATGTTCCAAAGCATATTTTCCTT 60.013 34.615 0.00 0.00 0.00 3.36
2345 3802 5.484998 ACCATGTTCCAAAGCATATTTTCCT 59.515 36.000 0.00 0.00 0.00 3.36
2346 3803 5.581874 CACCATGTTCCAAAGCATATTTTCC 59.418 40.000 0.00 0.00 0.00 3.13
2347 3804 5.581874 CCACCATGTTCCAAAGCATATTTTC 59.418 40.000 0.00 0.00 0.00 2.29
2348 3805 5.012975 ACCACCATGTTCCAAAGCATATTTT 59.987 36.000 0.00 0.00 0.00 1.82
2349 3806 4.531732 ACCACCATGTTCCAAAGCATATTT 59.468 37.500 0.00 0.00 0.00 1.40
2350 3807 4.095946 ACCACCATGTTCCAAAGCATATT 58.904 39.130 0.00 0.00 0.00 1.28
2351 3808 3.711863 ACCACCATGTTCCAAAGCATAT 58.288 40.909 0.00 0.00 0.00 1.78
2352 3809 3.168035 ACCACCATGTTCCAAAGCATA 57.832 42.857 0.00 0.00 0.00 3.14
2353 3810 2.014010 ACCACCATGTTCCAAAGCAT 57.986 45.000 0.00 0.00 0.00 3.79
2354 3811 2.666272 TACCACCATGTTCCAAAGCA 57.334 45.000 0.00 0.00 0.00 3.91
2355 3812 4.535526 AATTACCACCATGTTCCAAAGC 57.464 40.909 0.00 0.00 0.00 3.51
2356 3813 6.015856 TGTGTAATTACCACCATGTTCCAAAG 60.016 38.462 13.01 0.00 0.00 2.77
2357 3814 5.833667 TGTGTAATTACCACCATGTTCCAAA 59.166 36.000 13.01 0.00 0.00 3.28
2358 3815 5.386060 TGTGTAATTACCACCATGTTCCAA 58.614 37.500 13.01 0.00 0.00 3.53
2359 3816 4.986783 TGTGTAATTACCACCATGTTCCA 58.013 39.130 13.01 0.00 0.00 3.53
2360 3817 5.650266 TCATGTGTAATTACCACCATGTTCC 59.350 40.000 24.37 0.00 32.44 3.62
2361 3818 6.751514 TCATGTGTAATTACCACCATGTTC 57.248 37.500 24.37 6.18 32.44 3.18
2362 3819 8.682710 GTTATCATGTGTAATTACCACCATGTT 58.317 33.333 24.37 21.12 32.44 2.71
2363 3820 8.052748 AGTTATCATGTGTAATTACCACCATGT 58.947 33.333 24.37 18.48 32.44 3.21
2364 3821 8.344831 CAGTTATCATGTGTAATTACCACCATG 58.655 37.037 21.96 21.96 32.13 3.66
2365 3822 8.271458 TCAGTTATCATGTGTAATTACCACCAT 58.729 33.333 13.01 9.33 0.00 3.55
2366 3823 7.625469 TCAGTTATCATGTGTAATTACCACCA 58.375 34.615 13.01 7.52 0.00 4.17
2367 3824 8.677148 ATCAGTTATCATGTGTAATTACCACC 57.323 34.615 13.01 2.14 0.00 4.61
2401 3858 7.336176 GGAACGGAGGAAGTACTGAATATTTTT 59.664 37.037 0.00 0.00 0.00 1.94
2406 3863 4.607239 AGGAACGGAGGAAGTACTGAATA 58.393 43.478 0.00 0.00 0.00 1.75
2411 3868 8.773033 TTATATTTAGGAACGGAGGAAGTACT 57.227 34.615 0.00 0.00 0.00 2.73
2412 3869 8.637099 ACTTATATTTAGGAACGGAGGAAGTAC 58.363 37.037 0.00 0.00 0.00 2.73
2413 3870 8.773033 ACTTATATTTAGGAACGGAGGAAGTA 57.227 34.615 0.00 0.00 0.00 2.24
2414 3871 7.564292 AGACTTATATTTAGGAACGGAGGAAGT 59.436 37.037 0.00 0.00 0.00 3.01
2415 3872 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
2416 3873 7.909485 AGACTTATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
2417 3874 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
2418 3875 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2473 3930 9.788960 GTTTAGAGTGTTGATTCACTTCTTTTT 57.211 29.630 0.98 0.00 46.81 1.94
2474 3931 9.178758 AGTTTAGAGTGTTGATTCACTTCTTTT 57.821 29.630 0.98 0.00 46.81 2.27
2475 3932 8.738645 AGTTTAGAGTGTTGATTCACTTCTTT 57.261 30.769 0.98 0.00 46.81 2.52
2477 3934 9.429359 CATAGTTTAGAGTGTTGATTCACTTCT 57.571 33.333 0.98 3.43 46.81 2.85
2478 3935 9.209175 ACATAGTTTAGAGTGTTGATTCACTTC 57.791 33.333 0.98 0.00 46.81 3.01
2479 3936 9.209175 GACATAGTTTAGAGTGTTGATTCACTT 57.791 33.333 0.98 0.00 46.81 3.16
2481 3938 8.764524 AGACATAGTTTAGAGTGTTGATTCAC 57.235 34.615 0.00 0.00 38.46 3.18
2501 3958 9.901172 TGACTACATACGGATGTATATAGACAT 57.099 33.333 20.64 12.70 45.42 3.06
2502 3959 9.729281 TTGACTACATACGGATGTATATAGACA 57.271 33.333 20.64 13.92 45.42 3.41
2511 3968 9.778741 ATTTCAATATTGACTACATACGGATGT 57.221 29.630 19.12 19.12 42.14 3.06
2514 3971 9.476202 CAGATTTCAATATTGACTACATACGGA 57.524 33.333 17.76 0.00 36.83 4.69
2515 3972 9.261180 ACAGATTTCAATATTGACTACATACGG 57.739 33.333 17.76 8.47 36.83 4.02
2542 3999 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2543 4000 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2544 4001 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2545 4002 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2546 4003 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2547 4004 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2548 4005 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2549 4006 8.551682 TTTACTCCCTCCGTTCCTAAATATAA 57.448 34.615 0.00 0.00 0.00 0.98
2550 4007 8.551682 TTTTACTCCCTCCGTTCCTAAATATA 57.448 34.615 0.00 0.00 0.00 0.86
2551 4008 7.126879 ACTTTTACTCCCTCCGTTCCTAAATAT 59.873 37.037 0.00 0.00 0.00 1.28
2552 4009 6.441604 ACTTTTACTCCCTCCGTTCCTAAATA 59.558 38.462 0.00 0.00 0.00 1.40
2553 4010 5.250082 ACTTTTACTCCCTCCGTTCCTAAAT 59.750 40.000 0.00 0.00 0.00 1.40
2554 4011 4.594491 ACTTTTACTCCCTCCGTTCCTAAA 59.406 41.667 0.00 0.00 0.00 1.85
2555 4012 4.162651 ACTTTTACTCCCTCCGTTCCTAA 58.837 43.478 0.00 0.00 0.00 2.69
2556 4013 3.766051 GACTTTTACTCCCTCCGTTCCTA 59.234 47.826 0.00 0.00 0.00 2.94
2557 4014 2.566279 GACTTTTACTCCCTCCGTTCCT 59.434 50.000 0.00 0.00 0.00 3.36
2558 4015 2.301009 TGACTTTTACTCCCTCCGTTCC 59.699 50.000 0.00 0.00 0.00 3.62
2559 4016 3.672767 TGACTTTTACTCCCTCCGTTC 57.327 47.619 0.00 0.00 0.00 3.95
2560 4017 4.426736 TTTGACTTTTACTCCCTCCGTT 57.573 40.909 0.00 0.00 0.00 4.44
2561 4018 4.132336 GTTTTGACTTTTACTCCCTCCGT 58.868 43.478 0.00 0.00 0.00 4.69
2562 4019 4.024302 GTGTTTTGACTTTTACTCCCTCCG 60.024 45.833 0.00 0.00 0.00 4.63
2563 4020 5.131067 AGTGTTTTGACTTTTACTCCCTCC 58.869 41.667 0.00 0.00 0.00 4.30
2564 4021 5.238868 GGAGTGTTTTGACTTTTACTCCCTC 59.761 44.000 9.49 0.00 45.23 4.30
2565 4022 5.131067 GGAGTGTTTTGACTTTTACTCCCT 58.869 41.667 9.49 0.00 45.23 4.20
2566 4023 5.434352 GGAGTGTTTTGACTTTTACTCCC 57.566 43.478 9.49 0.00 45.23 4.30
2568 4025 8.926715 AATTTGGAGTGTTTTGACTTTTACTC 57.073 30.769 0.00 0.00 35.13 2.59
2592 4049 7.771183 ACAGCTCAAGTTTGTTGAAAATAGAA 58.229 30.769 0.00 0.00 0.00 2.10
2593 4050 7.333528 ACAGCTCAAGTTTGTTGAAAATAGA 57.666 32.000 0.00 0.00 0.00 1.98
2594 4051 6.358030 CGACAGCTCAAGTTTGTTGAAAATAG 59.642 38.462 0.00 0.00 0.00 1.73
2595 4052 6.183360 ACGACAGCTCAAGTTTGTTGAAAATA 60.183 34.615 0.00 0.00 31.96 1.40
2596 4053 5.036737 CGACAGCTCAAGTTTGTTGAAAAT 58.963 37.500 0.00 0.00 0.00 1.82
2600 4057 2.627945 ACGACAGCTCAAGTTTGTTGA 58.372 42.857 0.00 0.00 31.96 3.18
2614 4071 9.103048 GAATATTTTTGTACACAGAAACGACAG 57.897 33.333 0.00 0.00 33.63 3.51
2615 4072 8.832521 AGAATATTTTTGTACACAGAAACGACA 58.167 29.630 0.00 0.00 33.63 4.35
2657 4115 9.270576 CGAGAGAATATTTGTCATTTTTGTCAG 57.729 33.333 0.00 0.00 0.00 3.51
2682 4140 4.609113 CGAGGTAATGTTCATGCTATTGCG 60.609 45.833 0.00 0.00 43.34 4.85
2683 4141 4.273480 ACGAGGTAATGTTCATGCTATTGC 59.727 41.667 0.00 0.00 40.20 3.56
2687 4145 9.239551 ACTATATACGAGGTAATGTTCATGCTA 57.760 33.333 0.00 0.00 0.00 3.49
2688 4146 8.029522 CACTATATACGAGGTAATGTTCATGCT 58.970 37.037 0.00 0.00 0.00 3.79
2689 4147 8.027189 TCACTATATACGAGGTAATGTTCATGC 58.973 37.037 0.00 0.00 0.00 4.06
2690 4148 9.343103 GTCACTATATACGAGGTAATGTTCATG 57.657 37.037 0.00 0.00 0.00 3.07
2691 4149 9.074576 TGTCACTATATACGAGGTAATGTTCAT 57.925 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.