Multiple sequence alignment - TraesCS7A01G528900

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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 TraesCS7A01G528900 chr7A 100.000 2684 0 0 1 2684 709120834 709123517 0.000000e+00 4957.0
1 TraesCS7A01G528900 chr7A 82.570 1245 127 44 690 1887 708912875 708914076 0.000000e+00 1014.0
2 TraesCS7A01G528900 chr7A 90.769 650 50 7 9 649 709128498 709129146 0.000000e+00 859.0
3 TraesCS7A01G528900 chr7A 90.630 651 53 6 854 1500 709129342 709129988 0.000000e+00 857.0
4 TraesCS7A01G528900 chr7A 77.506 449 69 20 1949 2371 708920858 708921300 9.600000e-60 241.0
5 TraesCS7A01G528900 chr7A 96.667 60 2 0 1619 1678 709029241 709029300 1.700000e-17 100.0
6 TraesCS7A01G528900 chr7A 83.621 116 10 5 1619 1733 709130156 709130263 1.700000e-17 100.0
7 TraesCS7A01G528900 chr7A 85.714 70 9 1 743 811 708919214 708919283 3.710000e-09 73.1
8 TraesCS7A01G528900 chr7D 91.727 689 44 5 46 721 616133409 616134097 0.000000e+00 944.0
9 TraesCS7A01G528900 chr7D 89.253 763 45 14 745 1501 616134092 616134823 0.000000e+00 920.0
10 TraesCS7A01G528900 chr7D 85.788 774 78 18 1922 2682 616058364 616059118 0.000000e+00 791.0
11 TraesCS7A01G528900 chr7D 80.939 1086 130 45 577 1621 616102637 616103686 0.000000e+00 787.0
12 TraesCS7A01G528900 chr7D 80.851 1081 134 46 577 1623 616067689 616068730 0.000000e+00 782.0
13 TraesCS7A01G528900 chr7D 82.217 911 122 23 725 1621 616055249 616056133 0.000000e+00 749.0
14 TraesCS7A01G528900 chr7D 78.049 451 65 22 1949 2371 616069628 616070072 1.230000e-63 254.0
15 TraesCS7A01G528900 chr7D 84.158 202 17 6 1619 1807 616174792 616174991 5.900000e-42 182.0
16 TraesCS7A01G528900 chr7B 84.598 896 102 15 743 1621 709322942 709323818 0.000000e+00 857.0
17 TraesCS7A01G528900 chr7B 86.822 774 80 12 769 1533 709377869 709378629 0.000000e+00 845.0
18 TraesCS7A01G528900 chr7B 84.518 872 104 16 690 1557 709258252 709259096 0.000000e+00 833.0
19 TraesCS7A01G528900 chr7B 89.567 508 42 6 30 529 709377042 709377546 3.770000e-178 634.0
20 TraesCS7A01G528900 chr7B 89.416 274 16 5 1619 1891 709323856 709324117 1.540000e-87 333.0
21 TraesCS7A01G528900 chr7B 85.932 263 19 9 2131 2388 709324530 709324779 5.700000e-67 265.0
22 TraesCS7A01G528900 chr7B 81.191 319 44 11 2370 2676 709369097 709369411 2.670000e-60 243.0
23 TraesCS7A01G528900 chr7B 95.902 122 5 0 528 649 709377576 709377697 5.860000e-47 198.0
24 TraesCS7A01G528900 chr7B 84.921 126 13 5 526 649 709258037 709258158 3.630000e-24 122.0
25 TraesCS7A01G528900 chr7B 87.654 81 9 1 616 695 709377741 709377821 2.850000e-15 93.5
26 TraesCS7A01G528900 chr3D 88.497 539 40 8 963 1501 422409363 422409879 1.360000e-177 632.0


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 TraesCS7A01G528900 chr7A 709120834 709123517 2683 False 4957.000000 4957 100.000000 1 2684 1 chr7A.!!$F3 2683
1 TraesCS7A01G528900 chr7A 708912875 708914076 1201 False 1014.000000 1014 82.570000 690 1887 1 chr7A.!!$F1 1197
2 TraesCS7A01G528900 chr7A 709128498 709130263 1765 False 605.333333 859 88.340000 9 1733 3 chr7A.!!$F5 1724
3 TraesCS7A01G528900 chr7D 616133409 616134823 1414 False 932.000000 944 90.490000 46 1501 2 chr7D.!!$F5 1455
4 TraesCS7A01G528900 chr7D 616102637 616103686 1049 False 787.000000 787 80.939000 577 1621 1 chr7D.!!$F1 1044
5 TraesCS7A01G528900 chr7D 616055249 616059118 3869 False 770.000000 791 84.002500 725 2682 2 chr7D.!!$F3 1957
6 TraesCS7A01G528900 chr7D 616067689 616070072 2383 False 518.000000 782 79.450000 577 2371 2 chr7D.!!$F4 1794
7 TraesCS7A01G528900 chr7B 709322942 709324779 1837 False 485.000000 857 86.648667 743 2388 3 chr7B.!!$F3 1645
8 TraesCS7A01G528900 chr7B 709258037 709259096 1059 False 477.500000 833 84.719500 526 1557 2 chr7B.!!$F2 1031
9 TraesCS7A01G528900 chr7B 709377042 709378629 1587 False 442.625000 845 89.986250 30 1533 4 chr7B.!!$F4 1503
10 TraesCS7A01G528900 chr3D 422409363 422409879 516 False 632.000000 632 88.497000 963 1501 1 chr3D.!!$F1 538

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
814 1054 0.98989 GGTGTCACGATAGCAACGTC 59.01 55.0 0.0 0.0 42.07 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 5916 0.174845 TGCTTGCCTAATCGCGTAGT 59.825 50.0 5.77 0.0 0.0 2.73 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
24 25 3.291584 TCCAAAATGGTAAGTGTGTGCA 58.708 40.909 0.00 0.00 39.03 4.57
125 126 5.380900 TCATATTGAAACCACAGTCCACAA 58.619 37.500 0.00 0.00 0.00 3.33
193 194 1.202463 ACGCAATCGATTAGCTCAGCT 60.202 47.619 21.77 3.60 39.93 4.24
270 274 5.781818 ACCCAGGAAAATGTCATGAATTCTT 59.218 36.000 7.05 0.00 40.61 2.52
275 280 9.865321 CAGGAAAATGTCATGAATTCTTGTAAT 57.135 29.630 17.97 11.46 40.61 1.89
371 378 3.517602 TCGAATGTTCCTGATAACCACG 58.482 45.455 0.00 0.00 0.00 4.94
379 386 2.756760 TCCTGATAACCACGGACACTAC 59.243 50.000 0.00 0.00 0.00 2.73
402 415 2.125512 CAAGCTCCCCGGAAGTCG 60.126 66.667 0.73 0.00 38.88 4.18
427 440 2.224079 CCATGAAAGAATATCGCCACCG 59.776 50.000 0.00 0.00 0.00 4.94
443 456 3.456663 CCGTCTATCGATGTCACGG 57.543 57.895 22.41 22.41 43.71 4.94
467 482 6.783482 GGGACTAGTTAAGGGAGACTGATAAT 59.217 42.308 0.00 0.00 0.00 1.28
471 486 6.567602 AGTTAAGGGAGACTGATAATGCTT 57.432 37.500 0.00 0.00 0.00 3.91
688 844 1.759299 ATGCCATGCCATGTGGACC 60.759 57.895 3.63 0.00 39.12 4.46
809 1049 2.741517 CACAATTGGTGTCACGATAGCA 59.258 45.455 10.83 0.00 42.75 3.49
812 1052 1.424403 TTGGTGTCACGATAGCAACG 58.576 50.000 4.56 0.00 35.53 4.10
814 1054 0.989890 GGTGTCACGATAGCAACGTC 59.010 55.000 0.00 0.00 42.07 4.34
835 1075 2.032681 GGAGGCCGACAAGCAACT 59.967 61.111 0.00 0.00 0.00 3.16
837 1077 2.357517 AGGCCGACAAGCAACTCG 60.358 61.111 0.00 0.00 0.00 4.18
838 1078 4.090057 GGCCGACAAGCAACTCGC 62.090 66.667 0.00 0.00 42.91 5.03
839 1079 3.345808 GCCGACAAGCAACTCGCA 61.346 61.111 0.00 0.00 46.13 5.10
840 1080 2.551270 CCGACAAGCAACTCGCAC 59.449 61.111 0.00 0.00 46.13 5.34
841 1081 1.956170 CCGACAAGCAACTCGCACT 60.956 57.895 0.00 0.00 46.13 4.40
842 1082 1.202568 CGACAAGCAACTCGCACTG 59.797 57.895 0.00 0.00 46.13 3.66
843 1083 1.082496 GACAAGCAACTCGCACTGC 60.082 57.895 0.00 0.00 46.13 4.40
908 1177 4.278419 TCTTCGCTTCGATGGATAAGATCA 59.722 41.667 0.00 0.00 35.23 2.92
937 1209 1.733041 CGTACGTGCCACCACAGAG 60.733 63.158 7.22 0.00 42.17 3.35
948 1220 1.606601 CCACAGAGTCCTCCGTCCA 60.607 63.158 0.00 0.00 0.00 4.02
984 1270 2.552743 GCCTTTATAAATCCACCGGAGC 59.447 50.000 9.46 0.00 34.05 4.70
1071 1359 2.751166 ACTCAAGAACACAGATCGGG 57.249 50.000 0.00 0.00 0.00 5.14
1267 1565 2.586792 GCAGGGGCGAGATCAAGT 59.413 61.111 0.00 0.00 0.00 3.16
1269 1567 1.965754 GCAGGGGCGAGATCAAGTCT 61.966 60.000 0.00 0.00 40.81 3.24
1591 1919 1.275291 GGATTGGACGTCCTCAAGACA 59.725 52.381 33.39 10.38 46.69 3.41
1779 2220 3.808174 GGAATTAGTTACCTCCATGTCGC 59.192 47.826 0.00 0.00 0.00 5.19
1794 2235 1.259507 TGTCGCTCGTTTCTTTTTCGG 59.740 47.619 0.00 0.00 0.00 4.30
1799 4211 3.182972 CGCTCGTTTCTTTTTCGGAAGTA 59.817 43.478 0.00 0.00 0.00 2.24
1822 4234 4.212214 AGTCTCTTTGATTCTGCACGAAAC 59.788 41.667 0.00 2.14 34.79 2.78
1833 4245 2.396601 TGCACGAAACTAAGTACCACG 58.603 47.619 0.00 0.00 0.00 4.94
1861 4273 5.392703 CCACAATCCATGTCAGTCATTTCTG 60.393 44.000 0.00 0.00 41.46 3.02
1891 4865 4.022849 GCCATGTCATAGTTTTGGATAGGC 60.023 45.833 0.00 0.00 0.00 3.93
1893 4867 5.771666 CCATGTCATAGTTTTGGATAGGCAT 59.228 40.000 0.00 0.00 0.00 4.40
1895 4869 5.754782 TGTCATAGTTTTGGATAGGCATGT 58.245 37.500 0.00 0.00 0.00 3.21
1896 4870 5.822519 TGTCATAGTTTTGGATAGGCATGTC 59.177 40.000 0.00 0.00 0.00 3.06
1897 4871 5.822519 GTCATAGTTTTGGATAGGCATGTCA 59.177 40.000 0.00 0.00 0.00 3.58
1898 4872 6.017605 GTCATAGTTTTGGATAGGCATGTCAG 60.018 42.308 0.00 0.00 0.00 3.51
1899 4873 4.307032 AGTTTTGGATAGGCATGTCAGT 57.693 40.909 0.00 0.00 0.00 3.41
1900 4874 4.666512 AGTTTTGGATAGGCATGTCAGTT 58.333 39.130 0.00 0.00 0.00 3.16
1901 4875 5.815581 AGTTTTGGATAGGCATGTCAGTTA 58.184 37.500 0.00 0.00 0.00 2.24
1902 4876 6.426587 AGTTTTGGATAGGCATGTCAGTTAT 58.573 36.000 0.00 0.00 0.00 1.89
1903 4877 6.891908 AGTTTTGGATAGGCATGTCAGTTATT 59.108 34.615 0.00 0.00 0.00 1.40
1904 4878 7.397192 AGTTTTGGATAGGCATGTCAGTTATTT 59.603 33.333 0.00 0.00 0.00 1.40
1905 4879 6.942532 TTGGATAGGCATGTCAGTTATTTC 57.057 37.500 0.00 0.00 0.00 2.17
1906 4880 6.252599 TGGATAGGCATGTCAGTTATTTCT 57.747 37.500 0.00 0.00 0.00 2.52
1907 4881 6.662755 TGGATAGGCATGTCAGTTATTTCTT 58.337 36.000 0.00 0.00 0.00 2.52
1908 4882 7.801104 TGGATAGGCATGTCAGTTATTTCTTA 58.199 34.615 0.00 0.00 0.00 2.10
1909 4883 8.271458 TGGATAGGCATGTCAGTTATTTCTTAA 58.729 33.333 0.00 0.00 0.00 1.85
1910 4884 8.778358 GGATAGGCATGTCAGTTATTTCTTAAG 58.222 37.037 0.00 0.00 0.00 1.85
1911 4885 8.682936 ATAGGCATGTCAGTTATTTCTTAAGG 57.317 34.615 0.00 0.00 0.00 2.69
1912 4886 6.721318 AGGCATGTCAGTTATTTCTTAAGGA 58.279 36.000 0.00 0.00 0.00 3.36
1913 4887 7.349598 AGGCATGTCAGTTATTTCTTAAGGAT 58.650 34.615 0.00 0.35 0.00 3.24
1914 4888 7.284034 AGGCATGTCAGTTATTTCTTAAGGATG 59.716 37.037 0.00 0.00 0.00 3.51
1915 4889 6.914757 GCATGTCAGTTATTTCTTAAGGATGC 59.085 38.462 1.85 0.00 0.00 3.91
1916 4890 7.420800 CATGTCAGTTATTTCTTAAGGATGCC 58.579 38.462 1.85 0.00 0.00 4.40
1917 4891 6.480763 TGTCAGTTATTTCTTAAGGATGCCA 58.519 36.000 1.85 0.00 0.00 4.92
1918 4892 7.118723 TGTCAGTTATTTCTTAAGGATGCCAT 58.881 34.615 1.85 0.00 0.00 4.40
1919 4893 7.067372 TGTCAGTTATTTCTTAAGGATGCCATG 59.933 37.037 1.85 0.00 0.00 3.66
1920 4894 7.067494 GTCAGTTATTTCTTAAGGATGCCATGT 59.933 37.037 1.85 0.00 0.00 3.21
1921 4895 8.271458 TCAGTTATTTCTTAAGGATGCCATGTA 58.729 33.333 1.85 0.00 0.00 2.29
1922 4896 8.902806 CAGTTATTTCTTAAGGATGCCATGTAA 58.097 33.333 1.85 0.00 0.00 2.41
1923 4897 9.646522 AGTTATTTCTTAAGGATGCCATGTAAT 57.353 29.630 1.85 0.00 0.00 1.89
1927 4901 9.646522 ATTTCTTAAGGATGCCATGTAATAGTT 57.353 29.630 1.85 0.00 0.00 2.24
1928 4902 9.474313 TTTCTTAAGGATGCCATGTAATAGTTT 57.526 29.630 1.85 0.00 0.00 2.66
1929 4903 9.474313 TTCTTAAGGATGCCATGTAATAGTTTT 57.526 29.630 1.85 0.00 0.00 2.43
1934 4908 9.646522 AAGGATGCCATGTAATAGTTTTATCTT 57.353 29.630 0.00 0.00 0.00 2.40
1935 4909 9.646522 AGGATGCCATGTAATAGTTTTATCTTT 57.353 29.630 0.00 0.00 0.00 2.52
1938 4912 8.925161 TGCCATGTAATAGTTTTATCTTTTGC 57.075 30.769 0.00 0.00 0.00 3.68
1939 4913 7.700234 TGCCATGTAATAGTTTTATCTTTTGCG 59.300 33.333 0.00 0.00 0.00 4.85
1940 4914 7.913297 GCCATGTAATAGTTTTATCTTTTGCGA 59.087 33.333 0.00 0.00 0.00 5.10
1941 4915 9.781834 CCATGTAATAGTTTTATCTTTTGCGAA 57.218 29.630 0.00 0.00 0.00 4.70
1956 4930 2.231215 GCGAAGAGCCATGTCATAGT 57.769 50.000 0.00 0.00 40.81 2.12
1957 4931 2.555199 GCGAAGAGCCATGTCATAGTT 58.445 47.619 0.00 0.00 40.81 2.24
1958 4932 2.939103 GCGAAGAGCCATGTCATAGTTT 59.061 45.455 0.00 0.00 40.81 2.66
1959 4933 3.375299 GCGAAGAGCCATGTCATAGTTTT 59.625 43.478 0.00 0.00 40.81 2.43
1960 4934 4.728882 GCGAAGAGCCATGTCATAGTTTTG 60.729 45.833 0.00 0.00 40.81 2.44
1961 4935 4.201851 CGAAGAGCCATGTCATAGTTTTGG 60.202 45.833 0.00 0.00 0.00 3.28
1962 4936 4.574674 AGAGCCATGTCATAGTTTTGGA 57.425 40.909 0.00 0.00 0.00 3.53
1963 4937 5.121380 AGAGCCATGTCATAGTTTTGGAT 57.879 39.130 0.00 0.00 0.00 3.41
1964 4938 6.252599 AGAGCCATGTCATAGTTTTGGATA 57.747 37.500 0.00 0.00 0.00 2.59
1965 4939 6.294473 AGAGCCATGTCATAGTTTTGGATAG 58.706 40.000 0.00 0.00 0.00 2.08
1966 4940 5.380043 AGCCATGTCATAGTTTTGGATAGG 58.620 41.667 0.00 0.00 0.00 2.57
1967 4941 5.103940 AGCCATGTCATAGTTTTGGATAGGT 60.104 40.000 0.00 0.00 0.00 3.08
1968 4942 6.101150 AGCCATGTCATAGTTTTGGATAGGTA 59.899 38.462 0.00 0.00 0.00 3.08
1969 4943 6.428159 GCCATGTCATAGTTTTGGATAGGTAG 59.572 42.308 0.00 0.00 0.00 3.18
2001 4975 2.700897 GTGAGGACATATAGCCACAGGT 59.299 50.000 0.00 0.00 0.00 4.00
2004 4978 1.140852 GGACATATAGCCACAGGTGCA 59.859 52.381 0.00 0.00 0.00 4.57
2009 4983 1.538047 ATAGCCACAGGTGCAAAGTG 58.462 50.000 7.29 7.29 0.00 3.16
2014 4988 0.947244 CACAGGTGCAAAGTGAGGAC 59.053 55.000 8.32 0.00 35.33 3.85
2019 4993 3.820467 CAGGTGCAAAGTGAGGACAAATA 59.180 43.478 0.00 0.00 0.00 1.40
2080 5301 9.677567 TTTATGTCTTCAATTTAACAAGCTGAC 57.322 29.630 0.00 0.00 0.00 3.51
2081 5302 6.942532 TGTCTTCAATTTAACAAGCTGACT 57.057 33.333 0.00 0.00 0.00 3.41
2095 5316 7.864108 ACAAGCTGACTATATGTTATTTGCA 57.136 32.000 0.00 0.00 0.00 4.08
2146 5404 7.064609 TGTTCGAATGAAGGTTCTGAACATATC 59.935 37.037 21.01 15.11 41.22 1.63
2176 5447 9.751542 TTATGGTGTATTTTACCTGTTTTGTTG 57.248 29.630 0.00 0.00 39.01 3.33
2224 5495 5.489792 TGGCTGACTTATATTCCCATCTC 57.510 43.478 0.00 0.00 0.00 2.75
2240 5511 3.491964 CCATCTCGCGGGAGTAATAACAA 60.492 47.826 26.49 7.48 41.26 2.83
2266 5537 5.063880 GCCTCGAGGTATTTCATTATTGGT 58.936 41.667 31.43 0.00 37.57 3.67
2321 5601 0.036952 AGGCACCGACATCAGTTGAG 60.037 55.000 0.00 0.00 0.00 3.02
2323 5603 0.320771 GCACCGACATCAGTTGAGGT 60.321 55.000 0.00 0.00 42.23 3.85
2347 5627 5.104569 TCAGCCATACATTGTAGATTCACCA 60.105 40.000 2.53 0.00 0.00 4.17
2388 5671 7.882179 TCTTAAGGAGCAAGAAACCAAATTAC 58.118 34.615 1.85 0.00 0.00 1.89
2401 5684 9.753674 AGAAACCAAATTACTTCCATTAGATCA 57.246 29.630 0.00 0.00 0.00 2.92
2456 5739 4.661125 TGATGTTTGAAATATCAGCGTGC 58.339 39.130 12.44 0.00 34.61 5.34
2470 5753 2.225019 CAGCGTGCTTTTCTTCAGATGT 59.775 45.455 0.00 0.00 0.00 3.06
2544 5827 7.775053 TTAATAGTTTCCTCCACAAAGCAAT 57.225 32.000 0.00 0.00 0.00 3.56
2552 5835 3.508793 CCTCCACAAAGCAATCACAAGAT 59.491 43.478 0.00 0.00 35.53 2.40
2556 5839 7.230849 TCCACAAAGCAATCACAAGATAAAT 57.769 32.000 0.00 0.00 33.08 1.40
2559 5842 8.863049 CCACAAAGCAATCACAAGATAAATAAC 58.137 33.333 0.00 0.00 33.08 1.89
2608 5899 6.645790 TCTTCGTTTTACTCCTCTTGTACT 57.354 37.500 0.00 0.00 0.00 2.73
2625 5916 9.101325 CTCTTGTACTCCCAAGGGATTTATATA 57.899 37.037 8.58 0.00 44.20 0.86
2629 5920 9.317827 TGTACTCCCAAGGGATTTATATACTAC 57.682 37.037 8.58 0.00 44.24 2.73
2643 5934 2.129823 TACTACGCGATTAGGCAAGC 57.870 50.000 15.93 0.00 0.00 4.01
2648 5939 1.867233 ACGCGATTAGGCAAGCAATAG 59.133 47.619 15.93 0.00 0.00 1.73
2654 5945 5.277974 GCGATTAGGCAAGCAATAGAATCAA 60.278 40.000 0.00 0.00 0.00 2.57
2673 5964 0.534877 AGCCAGCACAATCACACGAA 60.535 50.000 0.00 0.00 0.00 3.85
2682 5973 2.031191 ACAATCACACGAACCGTTCAAC 59.969 45.455 11.74 0.00 38.32 3.18
2683 5974 1.942677 ATCACACGAACCGTTCAACA 58.057 45.000 11.74 0.00 38.32 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.923281 GCACACACTTACCATTTTGGATTC 59.077 41.667 0.00 0.00 40.96 2.52
2 3 3.894427 TGCACACACTTACCATTTTGGAT 59.106 39.130 0.00 0.00 40.96 3.41
3 4 3.067461 GTGCACACACTTACCATTTTGGA 59.933 43.478 13.17 0.00 43.85 3.53
4 5 3.380142 GTGCACACACTTACCATTTTGG 58.620 45.455 13.17 0.00 43.85 3.28
5 6 3.042189 CGTGCACACACTTACCATTTTG 58.958 45.455 18.64 0.00 45.10 2.44
6 7 2.946329 TCGTGCACACACTTACCATTTT 59.054 40.909 18.64 0.00 45.10 1.82
9 10 1.795768 CTCGTGCACACACTTACCAT 58.204 50.000 18.64 0.00 45.10 3.55
11 12 1.860078 GCTCGTGCACACACTTACC 59.140 57.895 18.64 0.00 45.10 2.85
12 13 1.487231 CGCTCGTGCACACACTTAC 59.513 57.895 18.64 0.00 45.10 2.34
13 14 2.307309 GCGCTCGTGCACACACTTA 61.307 57.895 18.64 0.00 45.10 2.24
14 15 3.640000 GCGCTCGTGCACACACTT 61.640 61.111 18.64 0.00 45.10 3.16
21 22 1.872234 GACTATTCGCGCTCGTGCA 60.872 57.895 5.56 0.00 39.64 4.57
24 25 1.136308 CGATAGACTATTCGCGCTCGT 60.136 52.381 5.56 0.00 35.81 4.18
125 126 3.211865 CACTCATTCATATGCAGGTGCT 58.788 45.455 3.18 0.00 42.66 4.40
238 242 0.482446 ATTTTCCTGGGTGCTCCACA 59.518 50.000 7.20 1.73 41.46 4.17
338 345 7.338710 TCAGGAACATTCGAATTTCTTATCCT 58.661 34.615 21.52 16.04 34.01 3.24
339 346 7.553881 TCAGGAACATTCGAATTTCTTATCC 57.446 36.000 21.52 14.60 0.00 2.59
344 351 6.884295 TGGTTATCAGGAACATTCGAATTTCT 59.116 34.615 21.52 8.93 0.00 2.52
371 378 3.939592 GGGAGCTTGTTATTGTAGTGTCC 59.060 47.826 0.00 0.00 0.00 4.02
379 386 2.017049 CTTCCGGGGAGCTTGTTATTG 58.983 52.381 0.00 0.00 0.00 1.90
402 415 3.876914 TGGCGATATTCTTTCATGGTGTC 59.123 43.478 0.00 0.00 0.00 3.67
427 440 1.948145 AGTCCCGTGACATCGATAGAC 59.052 52.381 0.00 0.00 43.78 2.59
443 456 7.662897 CATTATCAGTCTCCCTTAACTAGTCC 58.337 42.308 0.00 0.00 0.00 3.85
688 844 5.306532 GCTTTGTAGCATCCCATATGATG 57.693 43.478 3.65 2.05 46.95 3.07
805 1045 1.295423 GCCTCCTTGGACGTTGCTA 59.705 57.895 0.00 0.00 38.35 3.49
812 1052 1.376037 CTTGTCGGCCTCCTTGGAC 60.376 63.158 0.00 0.00 41.70 4.02
814 1054 2.747855 GCTTGTCGGCCTCCTTGG 60.748 66.667 0.00 0.00 39.35 3.61
844 1084 3.909086 GAGTCAGCCACCCAGTGCC 62.909 68.421 0.00 0.00 31.34 5.01
870 1110 5.330455 AGCGAAGAAGATTATGTGTGAGA 57.670 39.130 0.00 0.00 0.00 3.27
908 1177 4.052229 ACGTACGCGCCAGCTCTT 62.052 61.111 16.72 0.00 42.83 2.85
937 1209 3.703127 GGGGTGTGGACGGAGGAC 61.703 72.222 0.00 0.00 0.00 3.85
984 1270 0.455410 CGTTGAGGAGAGAGCTGAGG 59.545 60.000 0.00 0.00 0.00 3.86
1071 1359 0.229753 CGAACGTAGCCATCGATTGC 59.770 55.000 13.35 13.35 38.82 3.56
1417 1715 2.427320 CCGCATCATCATCCCCGT 59.573 61.111 0.00 0.00 0.00 5.28
1472 1776 2.200370 ACTGGTCGGTCTCCCACA 59.800 61.111 0.00 0.00 0.00 4.17
1634 2003 2.854777 CGGACGCACAAGAGATCTTTAG 59.145 50.000 0.00 0.00 33.11 1.85
1686 2056 9.555727 TTACAGTAGCTAGCTAATTAATTTGGG 57.444 33.333 25.74 12.35 0.00 4.12
1695 2065 9.262358 GCTGTTAATTTACAGTAGCTAGCTAAT 57.738 33.333 25.74 22.17 45.76 1.73
1699 2069 5.815740 TGGCTGTTAATTTACAGTAGCTAGC 59.184 40.000 21.90 6.62 45.76 3.42
1700 2070 7.843490 TTGGCTGTTAATTTACAGTAGCTAG 57.157 36.000 21.90 0.92 45.76 3.42
1703 2073 7.141100 TCTTTGGCTGTTAATTTACAGTAGC 57.859 36.000 21.90 11.37 45.76 3.58
1779 2220 5.690857 AGACTACTTCCGAAAAAGAAACGAG 59.309 40.000 0.00 0.00 0.00 4.18
1794 2235 5.061560 CGTGCAGAATCAAAGAGACTACTTC 59.938 44.000 0.00 0.00 0.00 3.01
1799 4211 3.667497 TCGTGCAGAATCAAAGAGACT 57.333 42.857 0.00 0.00 0.00 3.24
1833 4245 3.270877 GACTGACATGGATTGTGGTACC 58.729 50.000 4.43 4.43 39.18 3.34
1839 4251 5.563592 TCAGAAATGACTGACATGGATTGT 58.436 37.500 0.00 0.00 41.21 2.71
1861 4273 5.450965 CCAAAACTATGACATGGCATCCTTC 60.451 44.000 19.78 0.00 0.00 3.46
1891 4865 7.067372 TGGCATCCTTAAGAAATAACTGACATG 59.933 37.037 3.36 0.00 0.00 3.21
1893 4867 6.480763 TGGCATCCTTAAGAAATAACTGACA 58.519 36.000 3.36 0.00 0.00 3.58
1895 4869 7.118723 ACATGGCATCCTTAAGAAATAACTGA 58.881 34.615 3.36 0.00 0.00 3.41
1896 4870 7.338800 ACATGGCATCCTTAAGAAATAACTG 57.661 36.000 3.36 0.00 0.00 3.16
1897 4871 9.646522 ATTACATGGCATCCTTAAGAAATAACT 57.353 29.630 3.36 0.00 0.00 2.24
1901 4875 9.646522 AACTATTACATGGCATCCTTAAGAAAT 57.353 29.630 3.36 0.00 0.00 2.17
1902 4876 9.474313 AAACTATTACATGGCATCCTTAAGAAA 57.526 29.630 3.36 0.00 0.00 2.52
1903 4877 9.474313 AAAACTATTACATGGCATCCTTAAGAA 57.526 29.630 3.36 0.00 0.00 2.52
1908 4882 9.646522 AAGATAAAACTATTACATGGCATCCTT 57.353 29.630 0.00 0.00 0.00 3.36
1909 4883 9.646522 AAAGATAAAACTATTACATGGCATCCT 57.353 29.630 0.00 0.00 0.00 3.24
1912 4886 9.533253 GCAAAAGATAAAACTATTACATGGCAT 57.467 29.630 0.00 0.00 0.00 4.40
1913 4887 7.700234 CGCAAAAGATAAAACTATTACATGGCA 59.300 33.333 0.00 0.00 0.00 4.92
1914 4888 7.913297 TCGCAAAAGATAAAACTATTACATGGC 59.087 33.333 0.00 0.00 0.00 4.40
1915 4889 9.781834 TTCGCAAAAGATAAAACTATTACATGG 57.218 29.630 0.00 0.00 0.00 3.66
1919 4893 9.211556 GCTCTTCGCAAAAGATAAAACTATTAC 57.788 33.333 0.00 0.00 38.92 1.89
1920 4894 8.395633 GGCTCTTCGCAAAAGATAAAACTATTA 58.604 33.333 0.00 0.00 41.67 0.98
1921 4895 7.094377 TGGCTCTTCGCAAAAGATAAAACTATT 60.094 33.333 0.00 0.00 41.67 1.73
1922 4896 6.374333 TGGCTCTTCGCAAAAGATAAAACTAT 59.626 34.615 0.00 0.00 41.67 2.12
1923 4897 5.703592 TGGCTCTTCGCAAAAGATAAAACTA 59.296 36.000 0.00 0.00 41.67 2.24
1924 4898 4.518970 TGGCTCTTCGCAAAAGATAAAACT 59.481 37.500 0.00 0.00 41.67 2.66
1925 4899 4.794169 TGGCTCTTCGCAAAAGATAAAAC 58.206 39.130 0.00 0.00 41.67 2.43
1926 4900 5.048083 ACATGGCTCTTCGCAAAAGATAAAA 60.048 36.000 0.00 0.00 41.67 1.52
1927 4901 4.458989 ACATGGCTCTTCGCAAAAGATAAA 59.541 37.500 0.00 0.00 41.67 1.40
1928 4902 4.009675 ACATGGCTCTTCGCAAAAGATAA 58.990 39.130 0.00 0.00 41.67 1.75
1929 4903 3.609853 ACATGGCTCTTCGCAAAAGATA 58.390 40.909 0.00 0.00 41.67 1.98
1930 4904 2.421424 GACATGGCTCTTCGCAAAAGAT 59.579 45.455 0.00 0.00 41.67 2.40
1931 4905 1.806542 GACATGGCTCTTCGCAAAAGA 59.193 47.619 0.00 0.00 41.67 2.52
1932 4906 1.536766 TGACATGGCTCTTCGCAAAAG 59.463 47.619 0.00 0.00 41.67 2.27
1933 4907 1.603456 TGACATGGCTCTTCGCAAAA 58.397 45.000 0.00 0.00 41.67 2.44
1934 4908 1.825090 ATGACATGGCTCTTCGCAAA 58.175 45.000 0.00 0.00 41.67 3.68
1935 4909 2.093500 ACTATGACATGGCTCTTCGCAA 60.093 45.455 0.00 0.00 41.67 4.85
1936 4910 1.482182 ACTATGACATGGCTCTTCGCA 59.518 47.619 0.00 0.00 41.67 5.10
1937 4911 2.231215 ACTATGACATGGCTCTTCGC 57.769 50.000 0.00 0.00 38.13 4.70
1938 4912 4.201851 CCAAAACTATGACATGGCTCTTCG 60.202 45.833 0.00 0.00 0.00 3.79
1939 4913 4.943705 TCCAAAACTATGACATGGCTCTTC 59.056 41.667 0.00 0.00 0.00 2.87
1940 4914 4.922206 TCCAAAACTATGACATGGCTCTT 58.078 39.130 0.00 0.00 0.00 2.85
1941 4915 4.574674 TCCAAAACTATGACATGGCTCT 57.425 40.909 0.00 0.00 0.00 4.09
1942 4916 5.471456 CCTATCCAAAACTATGACATGGCTC 59.529 44.000 0.00 0.00 0.00 4.70
1943 4917 5.103940 ACCTATCCAAAACTATGACATGGCT 60.104 40.000 0.00 0.00 0.00 4.75
1944 4918 5.133221 ACCTATCCAAAACTATGACATGGC 58.867 41.667 0.00 0.00 0.00 4.40
1945 4919 7.735917 TCTACCTATCCAAAACTATGACATGG 58.264 38.462 0.00 0.00 0.00 3.66
1946 4920 9.613428 TTTCTACCTATCCAAAACTATGACATG 57.387 33.333 0.00 0.00 0.00 3.21
1977 4951 4.384098 CCTGTGGCTATATGTCCTCACAAA 60.384 45.833 0.00 0.00 35.64 2.83
1978 4952 3.134623 CCTGTGGCTATATGTCCTCACAA 59.865 47.826 0.00 0.00 35.64 3.33
2001 4975 4.515191 GTGACTATTTGTCCTCACTTTGCA 59.485 41.667 0.00 0.00 44.75 4.08
2004 4978 6.260936 CACAAGTGACTATTTGTCCTCACTTT 59.739 38.462 8.77 0.66 44.75 2.66
2009 4983 5.297547 TGACACAAGTGACTATTTGTCCTC 58.702 41.667 14.74 2.56 44.75 3.71
2019 4993 9.026121 AGAGTAGTAATATTGACACAAGTGACT 57.974 33.333 7.28 0.16 0.00 3.41
2026 5000 8.749354 ACACATGAGAGTAGTAATATTGACACA 58.251 33.333 0.00 0.00 0.00 3.72
2027 5003 9.587772 AACACATGAGAGTAGTAATATTGACAC 57.412 33.333 0.00 0.00 0.00 3.67
2073 5294 6.828273 TGGTGCAAATAACATATAGTCAGCTT 59.172 34.615 0.00 0.00 0.00 3.74
2119 5342 4.878971 TGTTCAGAACCTTCATTCGAACAA 59.121 37.500 10.93 0.00 42.35 2.83
2122 5345 7.331026 AGATATGTTCAGAACCTTCATTCGAA 58.669 34.615 10.93 0.00 33.57 3.71
2166 5437 9.533253 AGATCTTCAATTTAACCAACAAAACAG 57.467 29.630 0.00 0.00 0.00 3.16
2197 5468 8.270744 AGATGGGAATATAAGTCAGCCATTATC 58.729 37.037 0.00 0.00 0.00 1.75
2198 5469 8.167691 AGATGGGAATATAAGTCAGCCATTAT 57.832 34.615 0.00 0.00 0.00 1.28
2199 5470 7.574021 AGATGGGAATATAAGTCAGCCATTA 57.426 36.000 0.00 0.00 0.00 1.90
2200 5471 6.460103 AGATGGGAATATAAGTCAGCCATT 57.540 37.500 0.00 0.00 0.00 3.16
2204 5475 3.929610 GCGAGATGGGAATATAAGTCAGC 59.070 47.826 0.00 0.00 0.00 4.26
2224 5495 2.735134 GGCTATTGTTATTACTCCCGCG 59.265 50.000 0.00 0.00 0.00 6.46
2240 5511 7.106239 CCAATAATGAAATACCTCGAGGCTAT 58.894 38.462 31.56 22.48 39.32 2.97
2266 5537 6.146837 CGCATAACCCAAAAATGAAAATGACA 59.853 34.615 0.00 0.00 0.00 3.58
2321 5601 5.237344 GTGAATCTACAATGTATGGCTGACC 59.763 44.000 0.00 0.00 0.00 4.02
2323 5603 5.104569 TGGTGAATCTACAATGTATGGCTGA 60.105 40.000 0.00 0.00 0.00 4.26
2347 5627 7.148103 GCTCCTTAAGAAATGATTTTGCTCTCT 60.148 37.037 3.36 0.00 0.00 3.10
2442 5725 5.631026 TGAAGAAAAGCACGCTGATATTTC 58.369 37.500 6.01 6.01 0.00 2.17
2453 5736 3.251729 TGAGCACATCTGAAGAAAAGCAC 59.748 43.478 0.00 0.00 0.00 4.40
2456 5739 6.069684 ACTTTGAGCACATCTGAAGAAAAG 57.930 37.500 1.06 0.00 0.00 2.27
2516 5799 7.094377 TGCTTTGTGGAGGAAACTATTAATCAC 60.094 37.037 0.00 0.00 44.43 3.06
2518 5801 7.391148 TGCTTTGTGGAGGAAACTATTAATC 57.609 36.000 0.00 0.00 44.43 1.75
2575 5858 7.848128 AGGAGTAAAACGAAGAATATCTCCAA 58.152 34.615 0.00 0.00 40.65 3.53
2576 5859 7.342284 AGAGGAGTAAAACGAAGAATATCTCCA 59.658 37.037 0.00 0.00 40.65 3.86
2577 5860 7.718525 AGAGGAGTAAAACGAAGAATATCTCC 58.281 38.462 0.00 0.00 39.12 3.71
2578 5861 9.026074 CAAGAGGAGTAAAACGAAGAATATCTC 57.974 37.037 0.00 0.00 0.00 2.75
2580 5863 8.705048 ACAAGAGGAGTAAAACGAAGAATATC 57.295 34.615 0.00 0.00 0.00 1.63
2581 5864 9.583765 GTACAAGAGGAGTAAAACGAAGAATAT 57.416 33.333 0.00 0.00 0.00 1.28
2582 5865 8.800332 AGTACAAGAGGAGTAAAACGAAGAATA 58.200 33.333 0.00 0.00 0.00 1.75
2590 5881 5.479124 TGGGAGTACAAGAGGAGTAAAAC 57.521 43.478 0.00 0.00 0.00 2.43
2608 5899 5.105635 CGCGTAGTATATAAATCCCTTGGGA 60.106 44.000 11.22 11.22 0.00 4.37
2625 5916 0.174845 TGCTTGCCTAATCGCGTAGT 59.825 50.000 5.77 0.00 0.00 2.73
2629 5920 2.135139 TCTATTGCTTGCCTAATCGCG 58.865 47.619 0.00 0.00 0.00 5.87
2643 5934 4.707030 TTGTGCTGGCTTGATTCTATTG 57.293 40.909 0.00 0.00 0.00 1.90
2648 5939 2.229543 TGTGATTGTGCTGGCTTGATTC 59.770 45.455 0.00 0.00 0.00 2.52
2654 5945 0.534877 TTCGTGTGATTGTGCTGGCT 60.535 50.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.