Multiple sequence alignment - TraesCS7A01G491600

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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 TraesCS7A01G491600 chr7A 100.000 2279 0 0 1 2279 680405803 680408081 0.000000e+00 4209.0
1 TraesCS7A01G491600 chr7D 88.935 1916 105 54 1 1845 588679863 588677984 0.000000e+00 2265.0
2 TraesCS7A01G491600 chr7D 88.906 658 43 13 914 1564 346184933 346184299 0.000000e+00 784.0
3 TraesCS7A01G491600 chr7D 87.024 709 49 19 863 1564 354527428 354528100 0.000000e+00 760.0
4 TraesCS7A01G491600 chr7D 86.742 709 52 20 863 1564 195395647 195396320 0.000000e+00 750.0
5 TraesCS7A01G491600 chr7D 88.136 177 15 2 1578 1748 588841313 588841489 2.970000e-49 206.0
6 TraesCS7A01G491600 chr7B 89.385 1724 92 37 89 1755 663106913 663108602 0.000000e+00 2085.0
7 TraesCS7A01G491600 chr7B 85.992 721 55 19 863 1572 253264497 253263812 0.000000e+00 730.0
8 TraesCS7A01G491600 chr7B 83.562 146 11 4 1623 1755 663111898 663112043 8.550000e-25 124.0
9 TraesCS7A01G491600 chr7B 94.286 35 1 1 1818 1851 20161186 20161220 4.000000e-03 52.8
10 TraesCS7A01G491600 chr4B 85.596 722 57 21 862 1572 141080077 141080762 0.000000e+00 713.0
11 TraesCS7A01G491600 chr2B 85.097 718 67 19 863 1572 311334528 311335213 0.000000e+00 697.0
12 TraesCS7A01G491600 chr5A 77.959 245 39 14 2037 2277 423914419 423914652 3.050000e-29 139.0
13 TraesCS7A01G491600 chr2A 79.866 149 22 6 2126 2268 508115905 508115759 4.010000e-18 102.0
14 TraesCS7A01G491600 chr2A 92.500 40 3 0 1818 1857 214739846 214739885 8.790000e-05 58.4
15 TraesCS7A01G491600 chr2A 94.595 37 2 0 1821 1857 681934423 681934459 8.790000e-05 58.4
16 TraesCS7A01G491600 chr4D 100.000 28 0 0 1830 1857 342448813 342448786 4.000000e-03 52.8


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 TraesCS7A01G491600 chr7A 680405803 680408081 2278 False 4209.0 4209 100.0000 1 2279 1 chr7A.!!$F1 2278
1 TraesCS7A01G491600 chr7D 588677984 588679863 1879 True 2265.0 2265 88.9350 1 1845 1 chr7D.!!$R2 1844
2 TraesCS7A01G491600 chr7D 346184299 346184933 634 True 784.0 784 88.9060 914 1564 1 chr7D.!!$R1 650
3 TraesCS7A01G491600 chr7D 354527428 354528100 672 False 760.0 760 87.0240 863 1564 1 chr7D.!!$F2 701
4 TraesCS7A01G491600 chr7D 195395647 195396320 673 False 750.0 750 86.7420 863 1564 1 chr7D.!!$F1 701
5 TraesCS7A01G491600 chr7B 663106913 663112043 5130 False 1104.5 2085 86.4735 89 1755 2 chr7B.!!$F2 1666
6 TraesCS7A01G491600 chr7B 253263812 253264497 685 True 730.0 730 85.9920 863 1572 1 chr7B.!!$R1 709
7 TraesCS7A01G491600 chr4B 141080077 141080762 685 False 713.0 713 85.5960 862 1572 1 chr4B.!!$F1 710
8 TraesCS7A01G491600 chr2B 311334528 311335213 685 False 697.0 697 85.0970 863 1572 1 chr2B.!!$F1 709

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
328 348 0.10212 CTGCGCCAAAGAAACCACAA 59.898 50.0 4.18 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 1977 0.17668 CGGGTGTAGATGCTCTTGCT 59.823 55.0 0.0 0.0 40.48 3.91 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
31 32 9.440784 TCATGTTTAATCCGTTTTATTTATCGC 57.559 29.630 0.00 0.00 0.00 4.58
37 38 7.924103 AATCCGTTTTATTTATCGCATTTCC 57.076 32.000 0.00 0.00 0.00 3.13
38 39 5.823353 TCCGTTTTATTTATCGCATTTCCC 58.177 37.500 0.00 0.00 0.00 3.97
48 49 8.647143 ATTTATCGCATTTCCCAACTAATTTG 57.353 30.769 0.00 0.00 34.63 2.32
51 52 6.576662 TCGCATTTCCCAACTAATTTGTAA 57.423 33.333 0.00 0.00 32.71 2.41
52 53 6.616947 TCGCATTTCCCAACTAATTTGTAAG 58.383 36.000 0.00 0.00 32.71 2.34
53 54 6.207810 TCGCATTTCCCAACTAATTTGTAAGT 59.792 34.615 0.00 0.00 32.71 2.24
91 92 5.471797 TCAAATATTGAACAGAAGACGCCAA 59.528 36.000 0.00 0.00 36.59 4.52
142 155 2.087344 GCTTGTACGTAAGCCCAGC 58.913 57.895 11.27 2.42 45.62 4.85
178 194 3.337889 GCACGCACTCACGCTTCA 61.338 61.111 0.00 0.00 36.19 3.02
209 229 4.498241 CAGATACATACATGGATGGACGG 58.502 47.826 22.04 9.36 29.60 4.79
210 230 4.220602 CAGATACATACATGGATGGACGGA 59.779 45.833 22.04 2.38 29.60 4.69
211 231 2.910688 ACATACATGGATGGACGGAC 57.089 50.000 22.04 0.00 0.00 4.79
212 232 1.068588 ACATACATGGATGGACGGACG 59.931 52.381 22.04 0.00 0.00 4.79
328 348 0.102120 CTGCGCCAAAGAAACCACAA 59.898 50.000 4.18 0.00 0.00 3.33
331 351 1.526464 GCGCCAAAGAAACCACAAATG 59.474 47.619 0.00 0.00 0.00 2.32
340 360 1.314730 AACCACAAATGTCGGGACAC 58.685 50.000 3.22 0.00 45.05 3.67
380 400 2.514592 AGCCGGCCACATCATTCG 60.515 61.111 26.15 0.00 0.00 3.34
505 529 1.588824 CCGTGCACGTACCTACCTGA 61.589 60.000 34.81 0.00 37.74 3.86
573 604 2.125106 GGCACCGGTGGATCTCAC 60.125 66.667 34.58 16.46 45.34 3.51
782 822 1.647084 GTGTCAGTGAACCAACCGC 59.353 57.895 0.00 0.00 0.00 5.68
783 823 1.092921 GTGTCAGTGAACCAACCGCA 61.093 55.000 0.00 0.00 0.00 5.69
784 824 1.092921 TGTCAGTGAACCAACCGCAC 61.093 55.000 0.00 0.00 0.00 5.34
787 827 1.525995 AGTGAACCAACCGCACCAG 60.526 57.895 0.00 0.00 33.14 4.00
892 949 0.792640 CGCATATCCATCCGTCTTGC 59.207 55.000 0.00 0.00 0.00 4.01
955 1017 4.007644 CTCCTGACCAGCACCGCA 62.008 66.667 0.00 0.00 0.00 5.69
956 1018 4.314440 TCCTGACCAGCACCGCAC 62.314 66.667 0.00 0.00 0.00 5.34
1397 1462 0.652592 CGATGCCAGATCGAACAACC 59.347 55.000 0.00 0.00 43.59 3.77
1458 1523 1.705337 CGCGCGGATCTTGATTTGGT 61.705 55.000 24.84 0.00 0.00 3.67
1461 1526 2.286418 GCGCGGATCTTGATTTGGTTAG 60.286 50.000 8.83 0.00 0.00 2.34
1472 1537 6.658816 TCTTGATTTGGTTAGCTGCTTGATTA 59.341 34.615 7.79 0.00 0.00 1.75
1485 1550 7.263496 AGCTGCTTGATTATTTTCTTGATTCC 58.737 34.615 0.00 0.00 0.00 3.01
1487 1552 6.035843 TGCTTGATTATTTTCTTGATTCCGC 58.964 36.000 0.00 0.00 0.00 5.54
1488 1553 5.460091 GCTTGATTATTTTCTTGATTCCGCC 59.540 40.000 0.00 0.00 0.00 6.13
1489 1554 5.168526 TGATTATTTTCTTGATTCCGCCG 57.831 39.130 0.00 0.00 0.00 6.46
1490 1555 4.036262 TGATTATTTTCTTGATTCCGCCGG 59.964 41.667 0.00 0.00 0.00 6.13
1491 1556 2.122783 ATTTTCTTGATTCCGCCGGA 57.877 45.000 5.05 0.00 0.00 5.14
1492 1557 1.448985 TTTTCTTGATTCCGCCGGAG 58.551 50.000 5.05 0.00 31.21 4.63
1493 1558 1.024579 TTTCTTGATTCCGCCGGAGC 61.025 55.000 5.05 3.31 31.21 4.70
1494 1559 1.899437 TTCTTGATTCCGCCGGAGCT 61.899 55.000 5.05 0.00 36.60 4.09
1495 1560 1.040893 TCTTGATTCCGCCGGAGCTA 61.041 55.000 5.05 0.00 36.60 3.32
1496 1561 0.598680 CTTGATTCCGCCGGAGCTAG 60.599 60.000 5.05 5.58 36.60 3.42
1497 1562 1.040893 TTGATTCCGCCGGAGCTAGA 61.041 55.000 5.05 0.00 36.60 2.43
1498 1563 1.287503 GATTCCGCCGGAGCTAGAG 59.712 63.158 5.05 0.00 36.60 2.43
1499 1564 1.455959 ATTCCGCCGGAGCTAGAGT 60.456 57.895 5.05 0.00 36.60 3.24
1500 1565 0.178998 ATTCCGCCGGAGCTAGAGTA 60.179 55.000 5.05 0.00 36.60 2.59
1501 1566 0.818445 TTCCGCCGGAGCTAGAGTAG 60.818 60.000 5.05 0.00 36.60 2.57
1541 1623 2.724977 TCGTCTGGCTACAGTTCTTG 57.275 50.000 0.00 0.00 45.14 3.02
1566 1657 1.853114 GCTGCTGATGGATGATGCGG 61.853 60.000 0.00 0.00 0.00 5.69
1577 1668 0.465705 ATGATGCGGTACAGGAGTGG 59.534 55.000 0.00 0.00 0.00 4.00
1580 1671 1.961180 ATGCGGTACAGGAGTGGCTC 61.961 60.000 0.00 0.00 0.00 4.70
1588 1679 2.107141 GGAGTGGCTCCGAATCCG 59.893 66.667 0.00 0.00 41.08 4.18
1627 1733 1.815003 GGATGTGCCTTTTGACTCCTG 59.185 52.381 0.00 0.00 0.00 3.86
1628 1734 1.200948 GATGTGCCTTTTGACTCCTGC 59.799 52.381 0.00 0.00 0.00 4.85
1634 1742 1.221466 CTTTTGACTCCTGCGCGACA 61.221 55.000 12.10 6.68 0.00 4.35
1650 1758 3.236816 GCGACATGTCTGAAATGGTTTG 58.763 45.455 22.95 4.62 0.00 2.93
1657 1766 4.468713 TGTCTGAAATGGTTTGACATCCA 58.531 39.130 2.98 2.98 38.14 3.41
1661 1770 5.047872 TCTGAAATGGTTTGACATCCATGTG 60.048 40.000 11.72 0.00 42.73 3.21
1688 1797 3.917329 ATAGGAAATCTCGCGATCGAA 57.083 42.857 21.57 4.74 44.98 3.71
1823 1948 9.144298 ACCCTATTATGATTTTAGTCGAGAAGA 57.856 33.333 0.00 0.00 0.00 2.87
1839 1969 5.009710 TCGAGAAGAACAAGAGTAAGAGCAA 59.990 40.000 0.00 0.00 0.00 3.91
1840 1970 5.344665 CGAGAAGAACAAGAGTAAGAGCAAG 59.655 44.000 0.00 0.00 0.00 4.01
1841 1971 6.412362 AGAAGAACAAGAGTAAGAGCAAGA 57.588 37.500 0.00 0.00 0.00 3.02
1842 1972 6.454795 AGAAGAACAAGAGTAAGAGCAAGAG 58.545 40.000 0.00 0.00 0.00 2.85
1843 1973 4.565022 AGAACAAGAGTAAGAGCAAGAGC 58.435 43.478 0.00 0.00 42.56 4.09
1844 1974 4.039730 AGAACAAGAGTAAGAGCAAGAGCA 59.960 41.667 0.00 0.00 45.49 4.26
1845 1975 4.342862 ACAAGAGTAAGAGCAAGAGCAA 57.657 40.909 0.00 0.00 45.49 3.91
1846 1976 4.314121 ACAAGAGTAAGAGCAAGAGCAAG 58.686 43.478 0.00 0.00 45.49 4.01
1847 1977 4.039730 ACAAGAGTAAGAGCAAGAGCAAGA 59.960 41.667 0.00 0.00 45.49 3.02
1848 1978 4.454728 AGAGTAAGAGCAAGAGCAAGAG 57.545 45.455 0.00 0.00 45.49 2.85
1849 1979 2.929398 GAGTAAGAGCAAGAGCAAGAGC 59.071 50.000 0.00 0.00 45.49 4.09
1850 1980 2.301296 AGTAAGAGCAAGAGCAAGAGCA 59.699 45.455 0.00 0.00 45.49 4.26
1851 1981 2.267174 AAGAGCAAGAGCAAGAGCAA 57.733 45.000 0.00 0.00 45.49 3.91
1852 1982 1.810959 AGAGCAAGAGCAAGAGCAAG 58.189 50.000 0.00 0.00 45.49 4.01
1853 1983 1.347050 AGAGCAAGAGCAAGAGCAAGA 59.653 47.619 0.00 0.00 45.49 3.02
1854 1984 1.733360 GAGCAAGAGCAAGAGCAAGAG 59.267 52.381 0.00 0.00 45.49 2.85
1855 1985 0.168568 GCAAGAGCAAGAGCAAGAGC 59.831 55.000 0.00 0.00 45.49 4.09
1856 1986 1.520494 CAAGAGCAAGAGCAAGAGCA 58.480 50.000 0.00 0.00 45.49 4.26
1857 1987 2.085320 CAAGAGCAAGAGCAAGAGCAT 58.915 47.619 0.00 0.00 45.49 3.79
1858 1988 2.027003 AGAGCAAGAGCAAGAGCATC 57.973 50.000 0.00 0.00 45.49 3.91
1861 1991 2.865551 GAGCAAGAGCAAGAGCATCTAC 59.134 50.000 0.00 0.00 44.96 2.59
1863 1993 3.926359 AGCAAGAGCAAGAGCATCTACAC 60.926 47.826 0.00 0.00 44.96 2.90
1871 2001 2.513897 GCATCTACACCCGGGCAC 60.514 66.667 24.08 0.00 0.00 5.01
1886 2016 0.474614 GGCACCCTAAATCCCTCCTC 59.525 60.000 0.00 0.00 0.00 3.71
1893 2023 2.092914 CCTAAATCCCTCCTCAAACGCT 60.093 50.000 0.00 0.00 0.00 5.07
1894 2024 2.586648 AAATCCCTCCTCAAACGCTT 57.413 45.000 0.00 0.00 0.00 4.68
1897 2027 1.125093 TCCCTCCTCAAACGCTTGGA 61.125 55.000 0.00 0.00 33.01 3.53
1899 2029 1.291877 CCTCCTCAAACGCTTGGACG 61.292 60.000 0.00 0.00 39.50 4.79
1915 2045 4.969196 CGCGCATGCCCGGATACT 62.969 66.667 16.86 0.00 38.08 2.12
1916 2046 3.349006 GCGCATGCCCGGATACTG 61.349 66.667 13.15 0.00 33.98 2.74
1918 2048 1.956170 CGCATGCCCGGATACTGAC 60.956 63.158 13.15 0.00 0.00 3.51
1919 2049 1.598130 GCATGCCCGGATACTGACC 60.598 63.158 6.36 0.00 0.00 4.02
1921 2051 0.180171 CATGCCCGGATACTGACCAA 59.820 55.000 0.73 0.00 0.00 3.67
1923 2053 0.916086 TGCCCGGATACTGACCAATT 59.084 50.000 0.73 0.00 0.00 2.32
1924 2054 2.120312 TGCCCGGATACTGACCAATTA 58.880 47.619 0.73 0.00 0.00 1.40
1925 2055 2.506231 TGCCCGGATACTGACCAATTAA 59.494 45.455 0.73 0.00 0.00 1.40
1927 2057 3.564225 GCCCGGATACTGACCAATTAAAG 59.436 47.826 0.73 0.00 0.00 1.85
1928 2058 4.685030 GCCCGGATACTGACCAATTAAAGA 60.685 45.833 0.73 0.00 0.00 2.52
1929 2059 4.814771 CCCGGATACTGACCAATTAAAGAC 59.185 45.833 0.73 0.00 0.00 3.01
1930 2060 4.814771 CCGGATACTGACCAATTAAAGACC 59.185 45.833 0.00 0.00 0.00 3.85
1931 2061 5.424757 CGGATACTGACCAATTAAAGACCA 58.575 41.667 0.00 0.00 0.00 4.02
1932 2062 5.878116 CGGATACTGACCAATTAAAGACCAA 59.122 40.000 0.00 0.00 0.00 3.67
1933 2063 6.542370 CGGATACTGACCAATTAAAGACCAAT 59.458 38.462 0.00 0.00 0.00 3.16
1934 2064 7.067008 CGGATACTGACCAATTAAAGACCAATT 59.933 37.037 0.00 0.00 0.00 2.32
1961 2096 1.315690 AAATCGATCTAGACGGGCGA 58.684 50.000 0.00 11.36 35.32 5.54
1970 2105 4.477975 GACGGGCGACACTCCTCG 62.478 72.222 0.00 0.00 36.70 4.63
1974 2109 1.814527 GGGCGACACTCCTCGTATT 59.185 57.895 0.00 0.00 35.99 1.89
1978 2113 1.828832 CGACACTCCTCGTATTCAGC 58.171 55.000 0.00 0.00 0.00 4.26
1987 2123 3.901222 TCCTCGTATTCAGCCCAATATGA 59.099 43.478 6.87 6.87 34.48 2.15
1997 2133 2.292267 GCCCAATATGAGGCGGATATG 58.708 52.381 0.74 0.00 39.87 1.78
1999 2135 2.239654 CCCAATATGAGGCGGATATGGT 59.760 50.000 0.00 0.00 0.00 3.55
2000 2136 3.273434 CCAATATGAGGCGGATATGGTG 58.727 50.000 0.00 0.00 0.00 4.17
2005 2141 2.357517 GGCGGATATGGTGAGGCG 60.358 66.667 0.00 0.00 0.00 5.52
2006 2142 3.044305 GCGGATATGGTGAGGCGC 61.044 66.667 0.00 0.00 0.00 6.53
2008 2144 2.421739 GGATATGGTGAGGCGCGT 59.578 61.111 8.43 0.27 0.00 6.01
2009 2145 1.956170 GGATATGGTGAGGCGCGTG 60.956 63.158 7.63 0.00 0.00 5.34
2038 2174 1.448540 CCTGTCCGCCATGTCAGAC 60.449 63.158 0.00 0.00 0.00 3.51
2082 2218 2.265904 GCCCGGAAACCCAACAGTC 61.266 63.158 0.73 0.00 0.00 3.51
2086 2222 3.644861 GGAAACCCAACAGTCCGAT 57.355 52.632 0.00 0.00 0.00 4.18
2088 2224 1.271163 GGAAACCCAACAGTCCGATGA 60.271 52.381 0.00 0.00 0.00 2.92
2090 2226 1.348064 AACCCAACAGTCCGATGAGA 58.652 50.000 0.00 0.00 0.00 3.27
2100 2236 0.919710 TCCGATGAGAGTCTCCTCCA 59.080 55.000 17.57 0.00 38.58 3.86
2101 2237 1.133945 TCCGATGAGAGTCTCCTCCAG 60.134 57.143 17.57 10.02 38.58 3.86
2190 2327 4.176752 GGCGCCCTCCAACCCTAG 62.177 72.222 18.11 0.00 0.00 3.02
2197 2334 0.625849 CCTCCAACCCTAGCCACATT 59.374 55.000 0.00 0.00 0.00 2.71
2198 2335 1.408822 CCTCCAACCCTAGCCACATTC 60.409 57.143 0.00 0.00 0.00 2.67
2200 2337 1.922447 TCCAACCCTAGCCACATTCAT 59.078 47.619 0.00 0.00 0.00 2.57
2201 2338 2.092429 TCCAACCCTAGCCACATTCATC 60.092 50.000 0.00 0.00 0.00 2.92
2203 2340 3.624777 CAACCCTAGCCACATTCATCTT 58.375 45.455 0.00 0.00 0.00 2.40
2205 2342 3.118531 ACCCTAGCCACATTCATCTTCT 58.881 45.455 0.00 0.00 0.00 2.85
2208 2345 3.390639 CCTAGCCACATTCATCTTCTCCT 59.609 47.826 0.00 0.00 0.00 3.69
2214 2351 5.117584 CCACATTCATCTTCTCCTTCTCTG 58.882 45.833 0.00 0.00 0.00 3.35
2238 2375 1.683365 CCAACCCAAGCCCATCCAG 60.683 63.158 0.00 0.00 0.00 3.86
2247 2384 3.136750 CCCATCCAGCTCTCTCCG 58.863 66.667 0.00 0.00 0.00 4.63
2274 2411 3.691342 CTCTTCCCACGCCGTCCA 61.691 66.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.207810 ACTTACAAATTAGTTGGGAAATGCGA 59.792 34.615 0.00 0.00 41.97 5.10
29 30 6.386654 ACTTACAAATTAGTTGGGAAATGCG 58.613 36.000 0.00 0.00 41.97 4.73
76 77 1.860078 CCGTTGGCGTCTTCTGTTC 59.140 57.895 0.00 0.00 36.15 3.18
91 92 4.640855 CGTGTCTCGTGGTGCCGT 62.641 66.667 0.00 0.00 34.52 5.68
102 112 1.811266 GGCATCATCACGCGTGTCT 60.811 57.895 35.74 22.74 0.00 3.41
110 120 1.089920 ACAAGCTTCGGCATCATCAC 58.910 50.000 0.00 0.00 44.74 3.06
178 194 4.380550 CCATGTATGTATCTGGACGCGTAT 60.381 45.833 13.97 4.22 0.00 3.06
287 307 4.379174 GCTCTTGGCTTGTTCCGA 57.621 55.556 0.00 0.00 38.06 4.55
340 360 2.802667 CGAGAAACGCCTGCGGATG 61.803 63.158 16.63 0.00 44.69 3.51
480 504 2.367344 GGTACGTGCACGGTTCGTC 61.367 63.158 39.21 21.98 44.95 4.20
764 804 1.092921 TGCGGTTGGTTCACTGACAC 61.093 55.000 0.00 0.00 0.00 3.67
772 812 2.904866 TGCTGGTGCGGTTGGTTC 60.905 61.111 0.00 0.00 43.34 3.62
784 824 3.909258 CTTTTGCTGCCGCTGCTGG 62.909 63.158 21.13 1.93 38.71 4.85
907 964 4.355720 TCTTGGCTGGCTGGCTGG 62.356 66.667 18.27 10.94 42.34 4.85
908 965 2.750637 CTCTTGGCTGGCTGGCTG 60.751 66.667 18.27 11.29 42.34 4.85
953 1015 2.485122 CCGCAAATCGAAGGGTGC 59.515 61.111 0.00 0.00 41.67 5.01
954 1016 2.485122 GCCGCAAATCGAAGGGTG 59.515 61.111 0.00 0.00 41.67 4.61
955 1017 3.124921 CGCCGCAAATCGAAGGGT 61.125 61.111 0.00 0.00 41.67 4.34
956 1018 4.536687 GCGCCGCAAATCGAAGGG 62.537 66.667 3.15 0.00 41.67 3.95
957 1019 4.536687 GGCGCCGCAAATCGAAGG 62.537 66.667 12.58 0.00 41.67 3.46
985 1047 0.976073 TCCATGTCGACCCCTTCTCC 60.976 60.000 14.12 0.00 0.00 3.71
986 1048 0.461961 CTCCATGTCGACCCCTTCTC 59.538 60.000 14.12 0.00 0.00 2.87
1298 1360 9.197694 CGGAGAATGAAATACTAGTATGGAAAG 57.802 37.037 16.11 0.00 0.00 2.62
1365 1430 3.628942 TCTGGCATCGGATGAAAATCTTG 59.371 43.478 21.69 2.80 0.00 3.02
1397 1462 1.658717 GCACATCGATCGACCTCCG 60.659 63.158 22.06 9.19 40.25 4.63
1458 1523 9.793252 GAATCAAGAAAATAATCAAGCAGCTAA 57.207 29.630 0.00 0.00 0.00 3.09
1461 1526 6.197842 CGGAATCAAGAAAATAATCAAGCAGC 59.802 38.462 0.00 0.00 0.00 5.25
1472 1537 2.017049 CTCCGGCGGAATCAAGAAAAT 58.983 47.619 30.59 0.00 0.00 1.82
1493 1558 6.568869 AGAAACATGTAGCAAGCTACTCTAG 58.431 40.000 26.86 17.69 46.53 2.43
1494 1559 6.531503 AGAAACATGTAGCAAGCTACTCTA 57.468 37.500 26.86 12.16 46.53 2.43
1495 1560 5.413309 AGAAACATGTAGCAAGCTACTCT 57.587 39.130 26.86 19.37 46.53 3.24
1496 1561 4.266502 CGAGAAACATGTAGCAAGCTACTC 59.733 45.833 26.86 17.82 46.53 2.59
1497 1562 4.177026 CGAGAAACATGTAGCAAGCTACT 58.823 43.478 26.86 13.69 46.53 2.57
1498 1563 3.242123 GCGAGAAACATGTAGCAAGCTAC 60.242 47.826 21.98 21.98 46.56 3.58
1499 1564 2.930040 GCGAGAAACATGTAGCAAGCTA 59.070 45.455 0.00 0.00 0.00 3.32
1500 1565 1.734465 GCGAGAAACATGTAGCAAGCT 59.266 47.619 0.00 0.00 0.00 3.74
1501 1566 1.734465 AGCGAGAAACATGTAGCAAGC 59.266 47.619 0.00 2.98 0.00 4.01
1502 1567 3.482598 CGAAGCGAGAAACATGTAGCAAG 60.483 47.826 0.00 0.00 0.00 4.01
1503 1568 2.411748 CGAAGCGAGAAACATGTAGCAA 59.588 45.455 0.00 0.00 0.00 3.91
1504 1569 1.992667 CGAAGCGAGAAACATGTAGCA 59.007 47.619 0.00 0.00 0.00 3.49
1509 1574 1.391485 CCAGACGAAGCGAGAAACATG 59.609 52.381 0.00 0.00 0.00 3.21
1541 1623 2.910199 TCATCCATCAGCAGCAGTAAC 58.090 47.619 0.00 0.00 0.00 2.50
1581 1672 0.457853 ATCACACACGTCCGGATTCG 60.458 55.000 7.81 10.67 0.00 3.34
1584 1675 0.895530 AAGATCACACACGTCCGGAT 59.104 50.000 7.81 0.00 0.00 4.18
1585 1676 0.677288 AAAGATCACACACGTCCGGA 59.323 50.000 0.00 0.00 0.00 5.14
1586 1677 0.790207 CAAAGATCACACACGTCCGG 59.210 55.000 0.00 0.00 0.00 5.14
1587 1678 1.192312 CACAAAGATCACACACGTCCG 59.808 52.381 0.00 0.00 0.00 4.79
1588 1679 1.531149 CCACAAAGATCACACACGTCC 59.469 52.381 0.00 0.00 0.00 4.79
1627 1733 0.247814 CCATTTCAGACATGTCGCGC 60.248 55.000 19.85 0.00 34.09 6.86
1628 1734 1.078709 ACCATTTCAGACATGTCGCG 58.921 50.000 19.85 15.02 34.09 5.87
1657 1766 5.934625 GCGAGATTTCCTATAATGTCCACAT 59.065 40.000 0.00 0.00 38.41 3.21
1661 1770 4.806330 TCGCGAGATTTCCTATAATGTCC 58.194 43.478 3.71 0.00 33.31 4.02
1694 1803 2.666026 GCAATCAGCATCAGCATCATG 58.334 47.619 0.00 0.00 45.49 3.07
1816 1941 4.799678 TGCTCTTACTCTTGTTCTTCTCG 58.200 43.478 0.00 0.00 0.00 4.04
1823 1948 4.342862 TGCTCTTGCTCTTACTCTTGTT 57.657 40.909 0.00 0.00 40.48 2.83
1839 1969 1.555992 AGATGCTCTTGCTCTTGCTCT 59.444 47.619 0.00 0.00 40.48 4.09
1840 1970 2.027003 AGATGCTCTTGCTCTTGCTC 57.973 50.000 0.00 0.00 40.48 4.26
1841 1971 2.235650 TGTAGATGCTCTTGCTCTTGCT 59.764 45.455 0.00 0.00 40.48 3.91
1842 1972 2.351111 GTGTAGATGCTCTTGCTCTTGC 59.649 50.000 0.00 0.00 40.48 4.01
1843 1973 2.935201 GGTGTAGATGCTCTTGCTCTTG 59.065 50.000 0.00 0.00 40.48 3.02
1844 1974 2.093235 GGGTGTAGATGCTCTTGCTCTT 60.093 50.000 0.00 0.00 40.48 2.85
1845 1975 1.484240 GGGTGTAGATGCTCTTGCTCT 59.516 52.381 0.00 0.00 40.48 4.09
1846 1976 1.804372 CGGGTGTAGATGCTCTTGCTC 60.804 57.143 0.00 0.00 40.48 4.26
1847 1977 0.176680 CGGGTGTAGATGCTCTTGCT 59.823 55.000 0.00 0.00 40.48 3.91
1848 1978 0.811616 CCGGGTGTAGATGCTCTTGC 60.812 60.000 0.00 0.00 40.20 4.01
1849 1979 0.179073 CCCGGGTGTAGATGCTCTTG 60.179 60.000 14.18 0.00 0.00 3.02
1850 1980 1.972660 GCCCGGGTGTAGATGCTCTT 61.973 60.000 24.63 0.00 0.00 2.85
1851 1981 2.435693 GCCCGGGTGTAGATGCTCT 61.436 63.158 24.63 0.00 0.00 4.09
1852 1982 2.109181 GCCCGGGTGTAGATGCTC 59.891 66.667 24.63 0.00 0.00 4.26
1853 1983 2.687200 TGCCCGGGTGTAGATGCT 60.687 61.111 24.63 0.00 0.00 3.79
1854 1984 2.513897 GTGCCCGGGTGTAGATGC 60.514 66.667 24.63 5.07 0.00 3.91
1855 1985 2.189521 GGTGCCCGGGTGTAGATG 59.810 66.667 24.63 0.00 0.00 2.90
1856 1986 2.246513 TAGGGTGCCCGGGTGTAGAT 62.247 60.000 24.63 6.92 41.95 1.98
1857 1987 2.458969 TTAGGGTGCCCGGGTGTAGA 62.459 60.000 24.63 0.00 41.95 2.59
1858 1988 1.555477 TTTAGGGTGCCCGGGTGTAG 61.555 60.000 24.63 0.00 41.95 2.74
1861 1991 1.453197 GATTTAGGGTGCCCGGGTG 60.453 63.158 24.63 0.00 41.95 4.61
1863 1993 2.194868 GGATTTAGGGTGCCCGGG 59.805 66.667 19.09 19.09 41.95 5.73
1865 1995 1.148498 GAGGGATTTAGGGTGCCCG 59.852 63.158 0.98 0.00 45.40 6.13
1871 2001 2.919228 CGTTTGAGGAGGGATTTAGGG 58.081 52.381 0.00 0.00 0.00 3.53
1878 2008 1.125093 TCCAAGCGTTTGAGGAGGGA 61.125 55.000 14.10 0.00 36.36 4.20
1882 2012 1.959226 GCGTCCAAGCGTTTGAGGA 60.959 57.895 14.10 0.00 36.36 3.71
1899 2029 3.349006 CAGTATCCGGGCATGCGC 61.349 66.667 23.87 23.87 37.44 6.09
1901 2031 1.598130 GGTCAGTATCCGGGCATGC 60.598 63.158 9.90 9.90 0.00 4.06
1902 2032 0.180171 TTGGTCAGTATCCGGGCATG 59.820 55.000 0.00 0.00 0.00 4.06
1904 2034 0.916086 AATTGGTCAGTATCCGGGCA 59.084 50.000 0.00 0.00 0.00 5.36
1905 2035 2.922740 TAATTGGTCAGTATCCGGGC 57.077 50.000 0.00 0.00 0.00 6.13
1906 2036 4.814771 GTCTTTAATTGGTCAGTATCCGGG 59.185 45.833 0.00 0.00 0.00 5.73
1907 2037 4.814771 GGTCTTTAATTGGTCAGTATCCGG 59.185 45.833 0.00 0.00 0.00 5.14
1908 2038 5.424757 TGGTCTTTAATTGGTCAGTATCCG 58.575 41.667 0.00 0.00 0.00 4.18
1909 2039 7.881775 ATTGGTCTTTAATTGGTCAGTATCC 57.118 36.000 0.00 0.00 0.00 2.59
1940 2070 2.100252 TCGCCCGTCTAGATCGATTTTT 59.900 45.455 13.90 0.00 0.00 1.94
1941 2071 1.679680 TCGCCCGTCTAGATCGATTTT 59.320 47.619 13.90 0.00 0.00 1.82
1942 2072 1.001597 GTCGCCCGTCTAGATCGATTT 60.002 52.381 13.90 0.00 0.00 2.17
1943 2073 0.592148 GTCGCCCGTCTAGATCGATT 59.408 55.000 13.90 0.00 0.00 3.34
1944 2074 0.534427 TGTCGCCCGTCTAGATCGAT 60.534 55.000 13.90 0.00 0.00 3.59
1945 2075 1.153309 TGTCGCCCGTCTAGATCGA 60.153 57.895 13.90 9.72 0.00 3.59
1946 2076 1.009900 GTGTCGCCCGTCTAGATCG 60.010 63.158 0.00 1.64 0.00 3.69
1947 2077 0.308376 GAGTGTCGCCCGTCTAGATC 59.692 60.000 0.00 0.00 0.00 2.75
1949 2079 1.748122 GGAGTGTCGCCCGTCTAGA 60.748 63.158 0.00 0.00 0.00 2.43
1950 2080 1.716826 GAGGAGTGTCGCCCGTCTAG 61.717 65.000 0.00 0.00 0.00 2.43
1951 2081 1.748122 GAGGAGTGTCGCCCGTCTA 60.748 63.158 0.00 0.00 0.00 2.59
1952 2082 3.063084 GAGGAGTGTCGCCCGTCT 61.063 66.667 0.00 0.00 0.00 4.18
1953 2083 4.477975 CGAGGAGTGTCGCCCGTC 62.478 72.222 0.00 0.00 32.22 4.79
1954 2084 3.907260 TACGAGGAGTGTCGCCCGT 62.907 63.158 0.00 0.00 44.06 5.28
1958 2088 1.828832 CTGAATACGAGGAGTGTCGC 58.171 55.000 0.00 0.00 44.06 5.19
1961 2096 0.824759 GGGCTGAATACGAGGAGTGT 59.175 55.000 0.00 0.00 0.00 3.55
1970 2105 2.744202 CGCCTCATATTGGGCTGAATAC 59.256 50.000 12.24 0.00 45.57 1.89
1974 2109 1.053835 TCCGCCTCATATTGGGCTGA 61.054 55.000 12.24 9.09 45.57 4.26
1978 2113 2.239654 ACCATATCCGCCTCATATTGGG 59.760 50.000 0.00 0.00 0.00 4.12
1987 2123 2.872388 CGCCTCACCATATCCGCCT 61.872 63.158 0.00 0.00 0.00 5.52
2021 2157 0.738762 CAGTCTGACATGGCGGACAG 60.739 60.000 36.24 27.49 44.71 3.51
2047 2183 1.670674 GGGCGATTCCGTATGCGATTA 60.671 52.381 4.21 0.00 41.33 1.75
2048 2184 0.949105 GGGCGATTCCGTATGCGATT 60.949 55.000 4.21 0.00 41.33 3.34
2068 2204 1.165270 CATCGGACTGTTGGGTTTCC 58.835 55.000 0.00 0.00 0.00 3.13
2100 2236 3.484806 TGGCGTTCACACCCCACT 61.485 61.111 0.00 0.00 0.00 4.00
2101 2237 3.284449 GTGGCGTTCACACCCCAC 61.284 66.667 6.24 0.00 45.39 4.61
2176 2313 3.015145 TGGCTAGGGTTGGAGGGC 61.015 66.667 0.00 0.00 0.00 5.19
2177 2314 1.281925 ATGTGGCTAGGGTTGGAGGG 61.282 60.000 0.00 0.00 0.00 4.30
2180 2317 1.367346 TGAATGTGGCTAGGGTTGGA 58.633 50.000 0.00 0.00 0.00 3.53
2184 2321 3.118531 AGAAGATGAATGTGGCTAGGGT 58.881 45.455 0.00 0.00 0.00 4.34
2185 2322 3.495806 GGAGAAGATGAATGTGGCTAGGG 60.496 52.174 0.00 0.00 0.00 3.53
2190 2327 3.876320 GAGAAGGAGAAGATGAATGTGGC 59.124 47.826 0.00 0.00 0.00 5.01
2197 2334 1.135915 GCGCAGAGAAGGAGAAGATGA 59.864 52.381 0.30 0.00 0.00 2.92
2198 2335 1.569708 GCGCAGAGAAGGAGAAGATG 58.430 55.000 0.30 0.00 0.00 2.90
2200 2337 1.893786 GGCGCAGAGAAGGAGAAGA 59.106 57.895 10.83 0.00 0.00 2.87
2201 2338 1.518133 CGGCGCAGAGAAGGAGAAG 60.518 63.158 10.83 0.00 0.00 2.85
2203 2340 4.135153 GCGGCGCAGAGAAGGAGA 62.135 66.667 29.21 0.00 0.00 3.71
2223 2360 2.943265 AGCTGGATGGGCTTGGGT 60.943 61.111 0.00 0.00 36.56 4.51
2227 2364 1.344191 GGAGAGAGCTGGATGGGCTT 61.344 60.000 0.00 0.00 40.40 4.35
2257 2394 3.649277 CTGGACGGCGTGGGAAGAG 62.649 68.421 21.19 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.