Multiple sequence alignment - TraesCS7D01G540400

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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 TraesCS7D01G540400 chr7D 100.000 2411 0 0 1 2411 630500666 630503076 0.000000e+00 4453
1 TraesCS7D01G540400 chr7D 90.524 496 27 6 1920 2411 630272562 630273041 2.610000e-179 638
2 TraesCS7D01G540400 chr7D 94.309 123 7 0 1608 1730 630270486 630270608 3.160000e-44 189
3 TraesCS7D01G540400 chr7D 86.957 138 13 2 1749 1881 630270600 630270737 1.490000e-32 150
4 TraesCS7D01G540400 chr7D 90.654 107 5 3 1454 1556 630270374 630270479 1.160000e-28 137
5 TraesCS7D01G540400 chr1D 97.026 1446 40 3 1 1446 422998685 422997243 0.000000e+00 2429
6 TraesCS7D01G540400 chr1D 96.676 1444 47 1 1 1444 423014373 423012931 0.000000e+00 2399
7 TraesCS7D01G540400 chr1D 87.500 104 11 2 1299 1402 461427014 461426913 4.210000e-23 119
8 TraesCS7D01G540400 chr7B 94.969 1451 64 3 1 1446 62395404 62393958 0.000000e+00 2266
9 TraesCS7D01G540400 chr7B 93.750 832 48 3 619 1446 605363632 605364463 0.000000e+00 1245
10 TraesCS7D01G540400 chr7B 94.586 628 31 2 1 626 605362690 605363316 0.000000e+00 968
11 TraesCS7D01G540400 chr7B 91.475 305 18 6 2107 2411 733080952 733081248 1.720000e-111 412
12 TraesCS7D01G540400 chr7B 89.455 275 17 6 1614 1879 733080296 733080567 1.070000e-88 337
13 TraesCS7D01G540400 chr7B 86.364 176 24 0 2236 2411 733296821 733296996 2.450000e-45 193
14 TraesCS7D01G540400 chrUn 97.399 1115 26 3 332 1446 94889386 94888275 0.000000e+00 1895
15 TraesCS7D01G540400 chrUn 96.654 538 16 2 910 1446 75322003 75322539 0.000000e+00 893
16 TraesCS7D01G540400 chrUn 96.654 538 16 2 910 1446 287805837 287806373 0.000000e+00 893
17 TraesCS7D01G540400 chr4D 95.270 740 34 1 705 1444 452673505 452674243 0.000000e+00 1171
18 TraesCS7D01G540400 chr7A 78.106 813 169 9 27 834 735512918 735512110 7.690000e-140 507
19 TraesCS7D01G540400 chr7A 86.747 166 20 2 2245 2409 726474679 726474843 1.470000e-42 183
20 TraesCS7D01G540400 chr3B 78.079 812 170 8 27 834 788218661 788219468 7.690000e-140 507
21 TraesCS7D01G540400 chr2B 77.924 838 168 15 4 835 534379731 534378905 7.690000e-140 507
22 TraesCS7D01G540400 chr1B 78.079 812 170 8 27 834 569877966 569878773 7.690000e-140 507
23 TraesCS7D01G540400 chr1B 89.326 178 19 0 2234 2411 361368702 361368879 8.670000e-55 224


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 TraesCS7D01G540400 chr7D 630500666 630503076 2410 False 4453.0 4453 100.000 1 2411 1 chr7D.!!$F1 2410
1 TraesCS7D01G540400 chr7D 630270374 630273041 2667 False 278.5 638 90.611 1454 2411 4 chr7D.!!$F2 957
2 TraesCS7D01G540400 chr1D 422997243 422998685 1442 True 2429.0 2429 97.026 1 1446 1 chr1D.!!$R1 1445
3 TraesCS7D01G540400 chr1D 423012931 423014373 1442 True 2399.0 2399 96.676 1 1444 1 chr1D.!!$R2 1443
4 TraesCS7D01G540400 chr7B 62393958 62395404 1446 True 2266.0 2266 94.969 1 1446 1 chr7B.!!$R1 1445
5 TraesCS7D01G540400 chr7B 605362690 605364463 1773 False 1106.5 1245 94.168 1 1446 2 chr7B.!!$F2 1445
6 TraesCS7D01G540400 chr7B 733080296 733081248 952 False 374.5 412 90.465 1614 2411 2 chr7B.!!$F3 797
7 TraesCS7D01G540400 chrUn 94888275 94889386 1111 True 1895.0 1895 97.399 332 1446 1 chrUn.!!$R1 1114
8 TraesCS7D01G540400 chrUn 75322003 75322539 536 False 893.0 893 96.654 910 1446 1 chrUn.!!$F1 536
9 TraesCS7D01G540400 chrUn 287805837 287806373 536 False 893.0 893 96.654 910 1446 1 chrUn.!!$F2 536
10 TraesCS7D01G540400 chr4D 452673505 452674243 738 False 1171.0 1171 95.270 705 1444 1 chr4D.!!$F1 739
11 TraesCS7D01G540400 chr7A 735512110 735512918 808 True 507.0 507 78.106 27 834 1 chr7A.!!$R1 807
12 TraesCS7D01G540400 chr3B 788218661 788219468 807 False 507.0 507 78.079 27 834 1 chr3B.!!$F1 807
13 TraesCS7D01G540400 chr2B 534378905 534379731 826 True 507.0 507 77.924 4 835 1 chr2B.!!$R1 831
14 TraesCS7D01G540400 chr1B 569877966 569878773 807 False 507.0 507 78.079 27 834 1 chr1B.!!$F2 807

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
61 62 0.264657 TGATAGGTGGCTGCCTAGGA 59.735 55.0 21.03 3.26 43.6 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1900 0.034896 GCGGGAAACTGACTCCAAGA 59.965 55.0 3.0 0.0 39.98 3.02 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
25 26 2.280592 GTGTTGGGAGCGGTCGTT 60.281 61.111 8.77 0.00 0.00 3.85
61 62 0.264657 TGATAGGTGGCTGCCTAGGA 59.735 55.000 21.03 3.26 43.60 2.94
204 205 1.099689 TCGACGTCATCACCAGCATA 58.900 50.000 17.16 0.00 0.00 3.14
793 1123 7.451566 GGTATATATCCTCCCTTTTGTGCATTT 59.548 37.037 0.00 0.00 0.00 2.32
860 1190 3.904800 TGACATGATGGGTCACGTATT 57.095 42.857 0.00 0.00 40.16 1.89
902 1232 2.719376 GTGACATGCACAAGGTGGT 58.281 52.632 13.27 0.00 46.91 4.16
962 1292 6.183360 GGCTGGCTTAAATTAAACGTAGATGT 60.183 38.462 0.00 0.00 0.00 3.06
963 1293 7.248437 GCTGGCTTAAATTAAACGTAGATGTT 58.752 34.615 0.00 0.00 0.00 2.71
1046 1377 8.236586 CGGTCAAATTATTTTCTCTTCATGTCA 58.763 33.333 0.00 0.00 0.00 3.58
1098 1429 1.498865 CGGAACTGCAAGCTTGTCGT 61.499 55.000 26.55 19.88 37.60 4.34
1366 1698 0.034863 GTTGAGGTCCGGCCCAAATA 60.035 55.000 3.37 0.00 38.26 1.40
1495 1830 3.064820 TGTCGAGTCTTTTGCCTTGTTTC 59.935 43.478 0.00 0.00 0.00 2.78
1556 1895 6.312918 TCTCTTGATTACATAGTTTTGACGCC 59.687 38.462 0.00 0.00 0.00 5.68
1558 1897 5.539582 TGATTACATAGTTTTGACGCCAC 57.460 39.130 0.00 0.00 0.00 5.01
1559 1898 4.393680 TGATTACATAGTTTTGACGCCACC 59.606 41.667 0.00 0.00 0.00 4.61
1560 1899 1.153353 ACATAGTTTTGACGCCACCG 58.847 50.000 0.00 0.00 41.14 4.94
1569 1908 3.231736 ACGCCACCGTCTTGGAGT 61.232 61.111 0.00 0.00 46.39 3.85
1570 1909 2.432628 CGCCACCGTCTTGGAGTC 60.433 66.667 0.00 0.00 42.00 3.36
1571 1910 2.741092 GCCACCGTCTTGGAGTCA 59.259 61.111 0.00 0.00 42.00 3.41
1572 1911 1.374758 GCCACCGTCTTGGAGTCAG 60.375 63.158 0.00 0.00 42.00 3.51
1573 1912 2.050269 CCACCGTCTTGGAGTCAGT 58.950 57.895 0.00 0.00 42.00 3.41
1574 1913 0.393077 CCACCGTCTTGGAGTCAGTT 59.607 55.000 0.00 0.00 42.00 3.16
1575 1914 1.202651 CCACCGTCTTGGAGTCAGTTT 60.203 52.381 0.00 0.00 42.00 2.66
1576 1915 2.135933 CACCGTCTTGGAGTCAGTTTC 58.864 52.381 0.00 0.00 42.00 2.78
1577 1916 1.070289 ACCGTCTTGGAGTCAGTTTCC 59.930 52.381 0.00 0.00 42.00 3.13
1578 1917 1.608283 CCGTCTTGGAGTCAGTTTCCC 60.608 57.143 0.00 0.00 42.00 3.97
1579 1918 1.797025 GTCTTGGAGTCAGTTTCCCG 58.203 55.000 0.00 0.00 33.62 5.14
1580 1919 0.034896 TCTTGGAGTCAGTTTCCCGC 59.965 55.000 0.00 0.00 33.62 6.13
1581 1920 0.250295 CTTGGAGTCAGTTTCCCGCA 60.250 55.000 0.00 0.00 33.62 5.69
1582 1921 0.400213 TTGGAGTCAGTTTCCCGCAT 59.600 50.000 0.00 0.00 33.62 4.73
1583 1922 0.321564 TGGAGTCAGTTTCCCGCATG 60.322 55.000 0.00 0.00 33.62 4.06
1584 1923 0.036388 GGAGTCAGTTTCCCGCATGA 60.036 55.000 0.00 0.00 0.00 3.07
1585 1924 1.363744 GAGTCAGTTTCCCGCATGAG 58.636 55.000 0.00 0.00 0.00 2.90
1586 1925 0.674895 AGTCAGTTTCCCGCATGAGC 60.675 55.000 0.00 0.00 37.42 4.26
1587 1926 0.674895 GTCAGTTTCCCGCATGAGCT 60.675 55.000 0.00 0.00 39.10 4.09
1588 1927 0.036732 TCAGTTTCCCGCATGAGCTT 59.963 50.000 0.00 0.00 39.10 3.74
1589 1928 0.449388 CAGTTTCCCGCATGAGCTTC 59.551 55.000 0.00 0.00 39.10 3.86
1590 1929 0.326264 AGTTTCCCGCATGAGCTTCT 59.674 50.000 0.00 0.00 39.10 2.85
1591 1930 0.449388 GTTTCCCGCATGAGCTTCTG 59.551 55.000 0.00 0.00 39.10 3.02
1592 1931 0.677731 TTTCCCGCATGAGCTTCTGG 60.678 55.000 0.00 0.00 39.10 3.86
1593 1932 1.552799 TTCCCGCATGAGCTTCTGGA 61.553 55.000 0.00 0.00 39.10 3.86
1594 1933 1.147824 CCCGCATGAGCTTCTGGAT 59.852 57.895 0.00 0.00 39.10 3.41
1595 1934 0.394192 CCCGCATGAGCTTCTGGATA 59.606 55.000 0.00 0.00 39.10 2.59
1596 1935 1.506493 CCGCATGAGCTTCTGGATAC 58.494 55.000 0.00 0.00 39.10 2.24
1597 1936 1.506493 CGCATGAGCTTCTGGATACC 58.494 55.000 0.00 0.00 39.10 2.73
1598 1937 1.875576 CGCATGAGCTTCTGGATACCC 60.876 57.143 0.00 0.00 39.10 3.69
1599 1938 1.141657 GCATGAGCTTCTGGATACCCA 59.858 52.381 0.00 0.00 37.75 4.51
1600 1939 2.843701 CATGAGCTTCTGGATACCCAC 58.156 52.381 0.00 0.00 37.58 4.61
1601 1940 1.204146 TGAGCTTCTGGATACCCACC 58.796 55.000 0.00 0.00 37.58 4.61
1602 1941 1.204146 GAGCTTCTGGATACCCACCA 58.796 55.000 0.00 0.00 37.58 4.17
1603 1942 1.771255 GAGCTTCTGGATACCCACCAT 59.229 52.381 0.00 0.00 37.58 3.55
1604 1943 1.771255 AGCTTCTGGATACCCACCATC 59.229 52.381 0.00 0.00 37.58 3.51
1605 1944 1.771255 GCTTCTGGATACCCACCATCT 59.229 52.381 0.00 0.00 37.58 2.90
1606 1945 2.224402 GCTTCTGGATACCCACCATCTC 60.224 54.545 0.00 0.00 37.58 2.75
1611 1950 2.093181 TGGATACCCACCATCTCGTTTG 60.093 50.000 0.00 0.00 37.58 2.93
1627 1966 1.098869 TTTGCTGGCGACAAGTTTCA 58.901 45.000 0.00 0.00 42.06 2.69
1639 1978 1.169661 AAGTTTCATCGGCGCCACAA 61.170 50.000 28.98 11.85 0.00 3.33
1670 2009 2.517166 GCGAGGCATTCCTTCCCC 60.517 66.667 0.00 0.00 44.46 4.81
1727 2101 1.001746 CTAGGATGCATGATGAGCGGT 59.998 52.381 2.46 0.00 33.85 5.68
1728 2102 0.250209 AGGATGCATGATGAGCGGTC 60.250 55.000 2.46 7.89 33.85 4.79
1729 2103 1.563435 GGATGCATGATGAGCGGTCG 61.563 60.000 2.46 0.00 33.85 4.79
1730 2104 0.877649 GATGCATGATGAGCGGTCGT 60.878 55.000 9.50 9.50 33.85 4.34
1731 2105 0.462581 ATGCATGATGAGCGGTCGTT 60.463 50.000 11.20 0.00 33.85 3.85
1732 2106 0.673333 TGCATGATGAGCGGTCGTTT 60.673 50.000 11.20 0.00 33.85 3.60
1733 2107 0.447801 GCATGATGAGCGGTCGTTTT 59.552 50.000 11.20 0.00 0.00 2.43
1734 2108 1.529826 GCATGATGAGCGGTCGTTTTC 60.530 52.381 11.20 5.38 0.00 2.29
1735 2109 2.002586 CATGATGAGCGGTCGTTTTCT 58.997 47.619 11.20 0.00 0.00 2.52
1736 2110 2.163818 TGATGAGCGGTCGTTTTCTT 57.836 45.000 11.20 0.00 0.00 2.52
1737 2111 2.066262 TGATGAGCGGTCGTTTTCTTC 58.934 47.619 11.20 0.00 0.00 2.87
1738 2112 2.288825 TGATGAGCGGTCGTTTTCTTCT 60.289 45.455 11.20 0.00 0.00 2.85
1739 2113 1.497991 TGAGCGGTCGTTTTCTTCTG 58.502 50.000 10.46 0.00 0.00 3.02
1740 2114 0.790814 GAGCGGTCGTTTTCTTCTGG 59.209 55.000 0.00 0.00 0.00 3.86
1741 2115 0.106149 AGCGGTCGTTTTCTTCTGGT 59.894 50.000 0.00 0.00 0.00 4.00
1742 2116 0.942252 GCGGTCGTTTTCTTCTGGTT 59.058 50.000 0.00 0.00 0.00 3.67
1743 2117 1.332686 GCGGTCGTTTTCTTCTGGTTT 59.667 47.619 0.00 0.00 0.00 3.27
1744 2118 2.601504 GCGGTCGTTTTCTTCTGGTTTC 60.602 50.000 0.00 0.00 0.00 2.78
1745 2119 2.032290 CGGTCGTTTTCTTCTGGTTTCC 60.032 50.000 0.00 0.00 0.00 3.13
1746 2120 3.211865 GGTCGTTTTCTTCTGGTTTCCT 58.788 45.455 0.00 0.00 0.00 3.36
1747 2121 4.383173 GGTCGTTTTCTTCTGGTTTCCTA 58.617 43.478 0.00 0.00 0.00 2.94
1748 2122 4.451435 GGTCGTTTTCTTCTGGTTTCCTAG 59.549 45.833 0.00 0.00 0.00 3.02
1749 2123 5.295152 GTCGTTTTCTTCTGGTTTCCTAGA 58.705 41.667 0.00 0.00 0.00 2.43
1750 2124 5.405873 GTCGTTTTCTTCTGGTTTCCTAGAG 59.594 44.000 0.00 0.00 0.00 2.43
1751 2125 4.152580 CGTTTTCTTCTGGTTTCCTAGAGC 59.847 45.833 0.00 0.00 0.00 4.09
1752 2126 5.309638 GTTTTCTTCTGGTTTCCTAGAGCT 58.690 41.667 0.00 0.00 0.00 4.09
1753 2127 6.465084 GTTTTCTTCTGGTTTCCTAGAGCTA 58.535 40.000 0.00 0.00 0.00 3.32
1764 2138 4.100279 TCCTAGAGCTATCGATCCAACA 57.900 45.455 0.00 0.00 0.00 3.33
1792 2166 5.986741 GCATTAATTCATTCACATGGCATCA 59.013 36.000 0.00 0.00 0.00 3.07
1840 2220 4.346730 TCTGGAATTCATGGCTCAATTGT 58.653 39.130 7.93 0.00 0.00 2.71
1845 2225 3.485947 TTCATGGCTCAATTGTAACGC 57.514 42.857 5.13 4.53 0.00 4.84
1881 2261 1.078848 CTCTCCTTCCTTGCACGGG 60.079 63.158 9.71 3.87 0.00 5.28
1894 4054 1.816863 GCACGGGACTGAGACTTGGA 61.817 60.000 0.00 0.00 0.00 3.53
1895 4055 0.038159 CACGGGACTGAGACTTGGAC 60.038 60.000 0.00 0.00 0.00 4.02
1896 4056 1.186267 ACGGGACTGAGACTTGGACC 61.186 60.000 0.00 0.00 0.00 4.46
1897 4057 1.592223 GGGACTGAGACTTGGACCG 59.408 63.158 0.00 0.00 0.00 4.79
1906 4080 3.447586 TGAGACTTGGACCGAGATTTAGG 59.552 47.826 16.24 0.00 0.00 2.69
1910 4084 3.055312 ACTTGGACCGAGATTTAGGAACC 60.055 47.826 16.24 0.00 0.00 3.62
1913 4087 0.828677 ACCGAGATTTAGGAACCCCG 59.171 55.000 0.00 0.00 37.58 5.73
1914 4088 0.828677 CCGAGATTTAGGAACCCCGT 59.171 55.000 0.00 0.00 37.58 5.28
1915 4089 1.208776 CCGAGATTTAGGAACCCCGTT 59.791 52.381 0.00 0.00 37.58 4.44
1916 4090 2.277084 CGAGATTTAGGAACCCCGTTG 58.723 52.381 0.00 0.00 37.58 4.10
1917 4091 2.640184 GAGATTTAGGAACCCCGTTGG 58.360 52.381 0.00 0.00 41.37 3.77
1918 4092 1.100510 GATTTAGGAACCCCGTTGGC 58.899 55.000 0.00 0.00 37.83 4.52
1919 4093 0.323999 ATTTAGGAACCCCGTTGGCC 60.324 55.000 0.00 0.00 37.83 5.36
1920 4094 2.429235 TTTAGGAACCCCGTTGGCCC 62.429 60.000 0.00 0.00 37.83 5.80
1968 4142 2.591715 CGATGGTTCATCCCGCCC 60.592 66.667 2.74 0.00 37.57 6.13
1974 4148 3.089874 TTCATCCCGCCCTCCCAG 61.090 66.667 0.00 0.00 0.00 4.45
1998 4172 5.717078 TGGTACACTAACTAACTGGTCAG 57.283 43.478 0.00 0.00 0.00 3.51
2067 4241 1.377725 CAGCCAGGCTTCCACGAAT 60.378 57.895 12.86 0.00 36.40 3.34
2094 4301 3.129287 CCATTCCCATCGTGAAGAAAAGG 59.871 47.826 0.00 0.00 0.00 3.11
2130 4365 0.251209 ACACCACGCTCCTCACTAGA 60.251 55.000 0.00 0.00 0.00 2.43
2139 4374 0.033991 TCCTCACTAGAGCCTCGCTT 60.034 55.000 0.00 0.00 39.88 4.68
2184 4419 1.066573 CAAACAAACACCACCAGGCAA 60.067 47.619 0.00 0.00 39.06 4.52
2187 4422 0.534412 CAAACACCACCAGGCAACAA 59.466 50.000 0.00 0.00 39.06 2.83
2320 4555 4.424626 GACGAGTACATGATGCTCAAGAA 58.575 43.478 0.00 0.00 39.91 2.52
2387 4622 2.179427 CAGATCCTGGTGGACACACTA 58.821 52.381 4.69 0.00 46.51 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 5.587043 ACCTATCACGCCAAATTCGAATTTA 59.413 36.000 30.14 17.32 36.52 1.40
204 205 1.617947 GGGCTCGTGGAGATGTCCTT 61.618 60.000 10.72 0.00 44.30 3.36
311 312 1.667191 GATGCGCTCGCTGATGGAT 60.667 57.895 9.73 0.00 42.51 3.41
318 319 3.193614 CTGCTTGATGCGCTCGCT 61.194 61.111 9.73 1.08 46.63 4.93
377 378 2.134630 CTTTGGAGGAGCAGGGCACT 62.135 60.000 0.00 0.00 0.00 4.40
793 1123 3.650281 ATCTGCATGTGGGTGATGTTA 57.350 42.857 0.00 0.00 0.00 2.41
795 1125 3.483421 CATATCTGCATGTGGGTGATGT 58.517 45.455 0.00 0.00 0.00 3.06
860 1190 3.731728 CCAGGCTGGCCTTGGCTA 61.732 66.667 22.68 4.43 45.70 3.93
902 1232 4.254709 AGTGCTCCAACGGCTGCA 62.255 61.111 0.50 0.00 31.92 4.41
917 1247 3.133365 GCAGGTGGTGGTTCCCAGT 62.133 63.158 0.00 0.00 34.43 4.00
1046 1377 5.345741 GCGTTATTGCATTTGAACAAGTGAT 59.654 36.000 12.81 2.98 30.67 3.06
1366 1698 5.129485 CCATCTCACATAGTTCTACAACCCT 59.871 44.000 0.00 0.00 32.22 4.34
1476 1811 3.691049 TGAAACAAGGCAAAAGACTCG 57.309 42.857 0.00 0.00 0.00 4.18
1504 1839 4.625607 AGGTCCTTCTTCGAACAGATTT 57.374 40.909 0.00 0.00 0.00 2.17
1505 1840 5.163395 GGATAGGTCCTTCTTCGAACAGATT 60.163 44.000 0.00 0.00 41.60 2.40
1506 1841 4.342665 GGATAGGTCCTTCTTCGAACAGAT 59.657 45.833 0.00 0.00 41.60 2.90
1507 1842 3.700038 GGATAGGTCCTTCTTCGAACAGA 59.300 47.826 0.00 0.00 41.60 3.41
1551 1890 2.432628 CTCCAAGACGGTGGCGTC 60.433 66.667 0.00 0.00 38.68 5.19
1556 1895 2.135933 GAAACTGACTCCAAGACGGTG 58.864 52.381 0.00 0.00 30.32 4.94
1558 1897 1.608283 GGGAAACTGACTCCAAGACGG 60.608 57.143 0.00 0.00 34.34 4.79
1559 1898 1.797025 GGGAAACTGACTCCAAGACG 58.203 55.000 3.00 0.00 34.34 4.18
1560 1899 1.797025 CGGGAAACTGACTCCAAGAC 58.203 55.000 3.00 0.00 39.98 3.01
1561 1900 0.034896 GCGGGAAACTGACTCCAAGA 59.965 55.000 3.00 0.00 39.98 3.02
1562 1901 0.250295 TGCGGGAAACTGACTCCAAG 60.250 55.000 3.00 0.00 39.98 3.61
1563 1902 0.400213 ATGCGGGAAACTGACTCCAA 59.600 50.000 3.00 0.00 39.98 3.53
1564 1903 0.321564 CATGCGGGAAACTGACTCCA 60.322 55.000 3.00 0.00 39.98 3.86
1565 1904 0.036388 TCATGCGGGAAACTGACTCC 60.036 55.000 0.00 0.00 39.98 3.85
1566 1905 1.363744 CTCATGCGGGAAACTGACTC 58.636 55.000 0.00 0.00 39.98 3.36
1567 1906 0.674895 GCTCATGCGGGAAACTGACT 60.675 55.000 0.00 0.00 39.98 3.41
1568 1907 0.674895 AGCTCATGCGGGAAACTGAC 60.675 55.000 0.00 0.00 45.42 3.51
1569 1908 0.036732 AAGCTCATGCGGGAAACTGA 59.963 50.000 0.00 0.00 45.42 3.41
1570 1909 0.449388 GAAGCTCATGCGGGAAACTG 59.551 55.000 0.00 0.00 45.42 3.16
1571 1910 0.326264 AGAAGCTCATGCGGGAAACT 59.674 50.000 0.00 0.00 45.42 2.66
1572 1911 0.449388 CAGAAGCTCATGCGGGAAAC 59.551 55.000 0.00 0.00 45.42 2.78
1573 1912 0.677731 CCAGAAGCTCATGCGGGAAA 60.678 55.000 0.00 0.00 45.42 3.13
1574 1913 1.078214 CCAGAAGCTCATGCGGGAA 60.078 57.895 0.00 0.00 45.42 3.97
1575 1914 1.340399 ATCCAGAAGCTCATGCGGGA 61.340 55.000 0.00 0.00 45.42 5.14
1576 1915 0.394192 TATCCAGAAGCTCATGCGGG 59.606 55.000 0.00 0.00 45.42 6.13
1577 1916 1.506493 GTATCCAGAAGCTCATGCGG 58.494 55.000 0.00 0.00 45.42 5.69
1578 1917 1.506493 GGTATCCAGAAGCTCATGCG 58.494 55.000 0.00 0.00 45.42 4.73
1579 1918 1.141657 TGGGTATCCAGAAGCTCATGC 59.858 52.381 0.00 0.00 38.32 4.06
1580 1919 2.486191 GGTGGGTATCCAGAAGCTCATG 60.486 54.545 0.00 0.00 45.05 3.07
1581 1920 1.771255 GGTGGGTATCCAGAAGCTCAT 59.229 52.381 0.00 0.00 45.05 2.90
1582 1921 1.204146 GGTGGGTATCCAGAAGCTCA 58.796 55.000 0.00 0.00 45.05 4.26
1583 1922 1.204146 TGGTGGGTATCCAGAAGCTC 58.796 55.000 0.00 0.00 45.05 4.09
1584 1923 1.771255 GATGGTGGGTATCCAGAAGCT 59.229 52.381 0.00 0.00 45.05 3.74
1585 1924 1.771255 AGATGGTGGGTATCCAGAAGC 59.229 52.381 0.00 0.00 45.05 3.86
1586 1925 2.036475 CGAGATGGTGGGTATCCAGAAG 59.964 54.545 0.00 0.00 45.05 2.85
1587 1926 2.039418 CGAGATGGTGGGTATCCAGAA 58.961 52.381 0.00 0.00 45.05 3.02
1588 1927 1.063190 ACGAGATGGTGGGTATCCAGA 60.063 52.381 0.00 0.00 45.05 3.86
1589 1928 1.414158 ACGAGATGGTGGGTATCCAG 58.586 55.000 0.00 0.00 45.05 3.86
1590 1929 1.874129 AACGAGATGGTGGGTATCCA 58.126 50.000 0.00 0.00 41.58 3.41
1591 1930 2.561569 CAAACGAGATGGTGGGTATCC 58.438 52.381 0.00 0.00 0.00 2.59
1592 1931 1.940613 GCAAACGAGATGGTGGGTATC 59.059 52.381 0.00 0.00 0.00 2.24
1593 1932 1.559682 AGCAAACGAGATGGTGGGTAT 59.440 47.619 0.00 0.00 0.00 2.73
1594 1933 0.981183 AGCAAACGAGATGGTGGGTA 59.019 50.000 0.00 0.00 0.00 3.69
1595 1934 0.606401 CAGCAAACGAGATGGTGGGT 60.606 55.000 9.89 0.00 41.38 4.51
1596 1935 2.174334 CAGCAAACGAGATGGTGGG 58.826 57.895 9.89 0.00 41.38 4.61
1598 1937 1.503542 GCCAGCAAACGAGATGGTG 59.496 57.895 11.73 11.11 46.53 4.17
1599 1938 2.034879 CGCCAGCAAACGAGATGGT 61.035 57.895 11.73 0.67 46.53 3.55
1601 1940 1.291184 TGTCGCCAGCAAACGAGATG 61.291 55.000 0.00 0.00 39.30 2.90
1602 1941 0.602638 TTGTCGCCAGCAAACGAGAT 60.603 50.000 0.00 0.00 39.30 2.75
1603 1942 1.221466 CTTGTCGCCAGCAAACGAGA 61.221 55.000 0.00 0.00 39.30 4.04
1604 1943 1.205064 CTTGTCGCCAGCAAACGAG 59.795 57.895 0.00 0.00 39.30 4.18
1605 1944 1.092921 AACTTGTCGCCAGCAAACGA 61.093 50.000 0.00 0.00 35.62 3.85
1606 1945 0.248458 AAACTTGTCGCCAGCAAACG 60.248 50.000 0.00 0.00 0.00 3.60
1611 1950 0.179215 CGATGAAACTTGTCGCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
1639 1978 2.915659 TCGCCGTCTCTTGTGGGT 60.916 61.111 0.00 0.00 0.00 4.51
1670 2009 4.355720 TGCCTTCCCTGCCTGCAG 62.356 66.667 12.17 12.17 43.26 4.41
1727 2101 5.539048 CTCTAGGAAACCAGAAGAAAACGA 58.461 41.667 0.00 0.00 0.00 3.85
1728 2102 4.152580 GCTCTAGGAAACCAGAAGAAAACG 59.847 45.833 0.00 0.00 0.00 3.60
1729 2103 5.309638 AGCTCTAGGAAACCAGAAGAAAAC 58.690 41.667 0.00 0.00 0.00 2.43
1730 2104 5.568620 AGCTCTAGGAAACCAGAAGAAAA 57.431 39.130 0.00 0.00 0.00 2.29
1731 2105 6.405953 CGATAGCTCTAGGAAACCAGAAGAAA 60.406 42.308 0.00 0.00 0.00 2.52
1732 2106 5.067936 CGATAGCTCTAGGAAACCAGAAGAA 59.932 44.000 0.00 0.00 0.00 2.52
1733 2107 4.580995 CGATAGCTCTAGGAAACCAGAAGA 59.419 45.833 0.00 0.00 0.00 2.87
1734 2108 4.580995 TCGATAGCTCTAGGAAACCAGAAG 59.419 45.833 0.00 0.00 0.00 2.85
1735 2109 4.533815 TCGATAGCTCTAGGAAACCAGAA 58.466 43.478 0.00 0.00 0.00 3.02
1736 2110 4.166246 TCGATAGCTCTAGGAAACCAGA 57.834 45.455 0.00 0.00 0.00 3.86
1737 2111 4.082463 GGATCGATAGCTCTAGGAAACCAG 60.082 50.000 0.00 0.00 0.00 4.00
1738 2112 3.827302 GGATCGATAGCTCTAGGAAACCA 59.173 47.826 0.00 0.00 0.00 3.67
1739 2113 3.827302 TGGATCGATAGCTCTAGGAAACC 59.173 47.826 0.00 0.00 0.00 3.27
1740 2114 5.221263 TGTTGGATCGATAGCTCTAGGAAAC 60.221 44.000 0.00 0.00 0.00 2.78
1741 2115 4.893524 TGTTGGATCGATAGCTCTAGGAAA 59.106 41.667 0.00 0.00 0.00 3.13
1742 2116 4.470602 TGTTGGATCGATAGCTCTAGGAA 58.529 43.478 0.00 0.00 0.00 3.36
1743 2117 4.100279 TGTTGGATCGATAGCTCTAGGA 57.900 45.455 0.00 0.00 0.00 2.94
1744 2118 4.551388 GTTGTTGGATCGATAGCTCTAGG 58.449 47.826 0.00 0.00 0.00 3.02
1745 2119 4.551388 GGTTGTTGGATCGATAGCTCTAG 58.449 47.826 0.00 0.00 0.00 2.43
1746 2120 3.004419 CGGTTGTTGGATCGATAGCTCTA 59.996 47.826 0.00 0.00 0.00 2.43
1747 2121 2.223829 CGGTTGTTGGATCGATAGCTCT 60.224 50.000 0.00 0.00 0.00 4.09
1748 2122 2.128035 CGGTTGTTGGATCGATAGCTC 58.872 52.381 0.00 0.00 0.00 4.09
1749 2123 1.806623 GCGGTTGTTGGATCGATAGCT 60.807 52.381 0.00 0.00 0.00 3.32
1750 2124 0.582005 GCGGTTGTTGGATCGATAGC 59.418 55.000 0.00 0.00 0.00 2.97
1751 2125 1.934589 TGCGGTTGTTGGATCGATAG 58.065 50.000 0.00 0.00 0.00 2.08
1752 2126 2.613026 ATGCGGTTGTTGGATCGATA 57.387 45.000 0.00 0.00 0.00 2.92
1753 2127 1.750193 AATGCGGTTGTTGGATCGAT 58.250 45.000 0.00 0.00 0.00 3.59
1764 2138 5.350633 CCATGTGAATGAATTAATGCGGTT 58.649 37.500 0.00 0.00 0.00 4.44
1792 2166 3.915437 AACCGATCAAGCGTTCAATTT 57.085 38.095 0.00 0.00 0.00 1.82
1840 2220 2.080693 ACCAATTCTTCATGCGCGTTA 58.919 42.857 8.43 0.00 0.00 3.18
1845 2225 0.813184 AGCCACCAATTCTTCATGCG 59.187 50.000 0.00 0.00 0.00 4.73
1881 2261 1.535833 TCTCGGTCCAAGTCTCAGTC 58.464 55.000 0.00 0.00 0.00 3.51
1894 4054 0.828677 CGGGGTTCCTAAATCTCGGT 59.171 55.000 0.00 0.00 35.77 4.69
1895 4055 0.828677 ACGGGGTTCCTAAATCTCGG 59.171 55.000 0.00 0.00 44.03 4.63
1896 4056 2.277084 CAACGGGGTTCCTAAATCTCG 58.723 52.381 0.00 0.00 45.29 4.04
1897 4057 2.640184 CCAACGGGGTTCCTAAATCTC 58.360 52.381 0.00 0.00 0.00 2.75
1906 4080 4.960866 AACGGGCCAACGGGGTTC 62.961 66.667 4.39 0.00 39.65 3.62
1910 4084 3.361977 CAAGAACGGGCCAACGGG 61.362 66.667 4.39 0.00 38.39 5.28
1913 4087 1.132453 GCTAATCAAGAACGGGCCAAC 59.868 52.381 4.39 0.00 0.00 3.77
1914 4088 1.271652 TGCTAATCAAGAACGGGCCAA 60.272 47.619 4.39 0.00 0.00 4.52
1915 4089 0.326595 TGCTAATCAAGAACGGGCCA 59.673 50.000 4.39 0.00 0.00 5.36
1916 4090 0.733150 GTGCTAATCAAGAACGGGCC 59.267 55.000 0.00 0.00 0.00 5.80
1917 4091 0.733150 GGTGCTAATCAAGAACGGGC 59.267 55.000 0.00 0.00 34.02 6.13
1918 4092 2.107950 TGGTGCTAATCAAGAACGGG 57.892 50.000 0.00 0.00 34.02 5.28
1919 4093 3.270027 TCATGGTGCTAATCAAGAACGG 58.730 45.455 0.00 0.00 34.02 4.44
1920 4094 4.944962 TTCATGGTGCTAATCAAGAACG 57.055 40.909 0.00 0.00 34.02 3.95
1921 4095 5.098211 GCTTTCATGGTGCTAATCAAGAAC 58.902 41.667 0.00 0.00 32.12 3.01
1968 4142 5.657302 AGTTAGTTAGTGTACCATCTGGGAG 59.343 44.000 0.54 0.00 41.15 4.30
1974 4148 6.276832 TGACCAGTTAGTTAGTGTACCATC 57.723 41.667 0.00 0.00 0.00 3.51
1984 4158 8.598916 TGAACAATTATCCTGACCAGTTAGTTA 58.401 33.333 0.00 0.00 0.00 2.24
2024 4198 3.964909 AGTAAAGCCGAGCAAACAAAAG 58.035 40.909 0.00 0.00 0.00 2.27
2028 4202 1.606668 CCAAGTAAAGCCGAGCAAACA 59.393 47.619 0.00 0.00 0.00 2.83
2054 4228 0.253327 GGGAAGATTCGTGGAAGCCT 59.747 55.000 0.00 0.00 0.00 4.58
2067 4241 1.578897 TCACGATGGGAATGGGAAGA 58.421 50.000 0.00 0.00 0.00 2.87
2094 4301 2.433491 TGTATGCGTGTGGACGGC 60.433 61.111 0.00 0.00 46.20 5.68
2130 4365 2.740055 CGTGAGCAAAGCGAGGCT 60.740 61.111 0.00 0.00 44.48 4.58
2139 4374 1.899814 AGGAGTAATGGTCGTGAGCAA 59.100 47.619 5.79 0.00 42.53 3.91
2184 4419 2.229792 CTACACAAGTGCCATGGTTGT 58.770 47.619 14.67 13.27 34.72 3.32
2187 4422 0.955428 CGCTACACAAGTGCCATGGT 60.955 55.000 14.67 0.00 0.00 3.55
2336 4571 2.989253 TCACGCTCGAGGAAGGCA 60.989 61.111 15.58 0.00 0.00 4.75
2387 4622 1.519719 GAGCTCTTCCATGTCCGCT 59.480 57.895 6.43 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.