Multiple sequence alignment - TraesCS6A01G086100

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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 TraesCS6A01G086100 chr6A 100.000 2042 0 0 352 2393 54479144 54481185 0.000000e+00 3771.0
1 TraesCS6A01G086100 chr6A 100.000 90 0 0 1 90 54478793 54478882 1.470000e-37 167.0
2 TraesCS6A01G086100 chr6B 89.138 1915 128 44 513 2393 101555187 101553319 0.000000e+00 2311.0
3 TraesCS6A01G086100 chrUn 90.212 1512 69 42 555 2034 69887968 69886504 0.000000e+00 1899.0
4 TraesCS6A01G086100 chrUn 94.751 381 15 2 2018 2393 69886488 69886108 2.650000e-164 588.0
5 TraesCS6A01G086100 chrUn 86.905 168 15 4 352 513 69888255 69888089 5.250000e-42 182.0
6 TraesCS6A01G086100 chrUn 98.305 59 1 0 507 565 69888045 69887987 1.170000e-18 104.0
7 TraesCS6A01G086100 chr5A 94.545 55 3 0 686 740 608659371 608659317 4.240000e-13 86.1


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 TraesCS6A01G086100 chr6A 54478793 54481185 2392 False 1969.00 3771 100.00000 1 2393 2 chr6A.!!$F1 2392
1 TraesCS6A01G086100 chr6B 101553319 101555187 1868 True 2311.00 2311 89.13800 513 2393 1 chr6B.!!$R1 1880
2 TraesCS6A01G086100 chrUn 69886108 69888255 2147 True 693.25 1899 92.54325 352 2393 4 chrUn.!!$R1 2041

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
89 90 0.105778 GGAAAGATGGAGAGGCGAGG 59.894 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 1661 0.530744 TCTGAACCTGAAGCGCGTAT 59.469 50.0 8.43 0.0 0.0 3.06 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
43 44 2.819595 CAACGTCGGGCCATGGAG 60.820 66.667 18.40 5.90 0.00 3.86
44 45 4.096003 AACGTCGGGCCATGGAGG 62.096 66.667 18.40 6.96 41.84 4.30
46 47 3.781307 CGTCGGGCCATGGAGGAA 61.781 66.667 18.40 0.00 41.22 3.36
47 48 2.190578 GTCGGGCCATGGAGGAAG 59.809 66.667 18.40 1.08 41.22 3.46
48 49 3.797353 TCGGGCCATGGAGGAAGC 61.797 66.667 18.40 0.00 41.22 3.86
50 51 4.883354 GGGCCATGGAGGAAGCGG 62.883 72.222 18.40 0.00 41.22 5.52
51 52 3.797353 GGCCATGGAGGAAGCGGA 61.797 66.667 18.40 0.00 41.22 5.54
52 53 2.512896 GCCATGGAGGAAGCGGAT 59.487 61.111 18.40 0.00 41.22 4.18
53 54 1.895707 GCCATGGAGGAAGCGGATG 60.896 63.158 18.40 0.00 41.22 3.51
54 55 1.895707 CCATGGAGGAAGCGGATGC 60.896 63.158 5.56 0.00 41.22 3.91
55 56 1.153107 CATGGAGGAAGCGGATGCA 60.153 57.895 0.00 0.00 46.23 3.96
56 57 1.147824 ATGGAGGAAGCGGATGCAG 59.852 57.895 0.00 0.00 46.23 4.41
57 58 1.340399 ATGGAGGAAGCGGATGCAGA 61.340 55.000 0.00 0.00 46.23 4.26
58 59 1.227497 GGAGGAAGCGGATGCAGAG 60.227 63.158 0.00 0.00 46.23 3.35
59 60 1.680522 GGAGGAAGCGGATGCAGAGA 61.681 60.000 0.00 0.00 46.23 3.10
60 61 0.176680 GAGGAAGCGGATGCAGAGAA 59.823 55.000 0.00 0.00 46.23 2.87
61 62 0.615331 AGGAAGCGGATGCAGAGAAA 59.385 50.000 0.00 0.00 46.23 2.52
62 63 1.012841 GGAAGCGGATGCAGAGAAAG 58.987 55.000 0.00 0.00 46.23 2.62
63 64 1.406069 GGAAGCGGATGCAGAGAAAGA 60.406 52.381 0.00 0.00 46.23 2.52
64 65 1.932511 GAAGCGGATGCAGAGAAAGAG 59.067 52.381 0.00 0.00 46.23 2.85
65 66 1.189752 AGCGGATGCAGAGAAAGAGA 58.810 50.000 0.00 0.00 46.23 3.10
66 67 1.552337 AGCGGATGCAGAGAAAGAGAA 59.448 47.619 0.00 0.00 46.23 2.87
67 68 2.027745 AGCGGATGCAGAGAAAGAGAAA 60.028 45.455 0.00 0.00 46.23 2.52
68 69 2.351111 GCGGATGCAGAGAAAGAGAAAG 59.649 50.000 0.00 0.00 42.15 2.62
69 70 3.854666 CGGATGCAGAGAAAGAGAAAGA 58.145 45.455 0.00 0.00 0.00 2.52
70 71 3.864583 CGGATGCAGAGAAAGAGAAAGAG 59.135 47.826 0.00 0.00 0.00 2.85
71 72 4.190772 GGATGCAGAGAAAGAGAAAGAGG 58.809 47.826 0.00 0.00 0.00 3.69
72 73 4.081198 GGATGCAGAGAAAGAGAAAGAGGA 60.081 45.833 0.00 0.00 0.00 3.71
73 74 4.963318 TGCAGAGAAAGAGAAAGAGGAA 57.037 40.909 0.00 0.00 0.00 3.36
74 75 5.296151 TGCAGAGAAAGAGAAAGAGGAAA 57.704 39.130 0.00 0.00 0.00 3.13
75 76 5.303971 TGCAGAGAAAGAGAAAGAGGAAAG 58.696 41.667 0.00 0.00 0.00 2.62
76 77 5.070981 TGCAGAGAAAGAGAAAGAGGAAAGA 59.929 40.000 0.00 0.00 0.00 2.52
77 78 6.172630 GCAGAGAAAGAGAAAGAGGAAAGAT 58.827 40.000 0.00 0.00 0.00 2.40
78 79 6.092533 GCAGAGAAAGAGAAAGAGGAAAGATG 59.907 42.308 0.00 0.00 0.00 2.90
79 80 6.594937 CAGAGAAAGAGAAAGAGGAAAGATGG 59.405 42.308 0.00 0.00 0.00 3.51
80 81 6.500049 AGAGAAAGAGAAAGAGGAAAGATGGA 59.500 38.462 0.00 0.00 0.00 3.41
81 82 6.710278 AGAAAGAGAAAGAGGAAAGATGGAG 58.290 40.000 0.00 0.00 0.00 3.86
82 83 6.500049 AGAAAGAGAAAGAGGAAAGATGGAGA 59.500 38.462 0.00 0.00 0.00 3.71
83 84 5.937975 AGAGAAAGAGGAAAGATGGAGAG 57.062 43.478 0.00 0.00 0.00 3.20
84 85 4.716287 AGAGAAAGAGGAAAGATGGAGAGG 59.284 45.833 0.00 0.00 0.00 3.69
85 86 3.199727 AGAAAGAGGAAAGATGGAGAGGC 59.800 47.826 0.00 0.00 0.00 4.70
86 87 1.118838 AGAGGAAAGATGGAGAGGCG 58.881 55.000 0.00 0.00 0.00 5.52
87 88 1.115467 GAGGAAAGATGGAGAGGCGA 58.885 55.000 0.00 0.00 0.00 5.54
88 89 1.068434 GAGGAAAGATGGAGAGGCGAG 59.932 57.143 0.00 0.00 0.00 5.03
89 90 0.105778 GGAAAGATGGAGAGGCGAGG 59.894 60.000 0.00 0.00 0.00 4.63
378 379 2.003301 GCTTTGCGGGAAAACAAACAA 58.997 42.857 0.00 0.00 32.60 2.83
401 402 2.851195 GACTGGTCCACAAACTCATGT 58.149 47.619 0.00 0.00 0.00 3.21
413 414 1.581934 ACTCATGTGTGACGGTGTTG 58.418 50.000 0.00 0.00 0.00 3.33
425 426 4.214545 GTGACGGTGTTGGATGACAAATTA 59.785 41.667 0.00 0.00 41.58 1.40
427 428 3.187637 ACGGTGTTGGATGACAAATTACG 59.812 43.478 0.00 0.00 41.58 3.18
466 472 0.608035 TGTGGGCGATTTGAGGGTTC 60.608 55.000 0.00 0.00 0.00 3.62
473 479 1.327764 CGATTTGAGGGTTCGCTTAGC 59.672 52.381 0.00 0.00 0.00 3.09
607 696 0.955428 TTGTGGGCGCTTCAGCTAAG 60.955 55.000 7.64 0.00 39.32 2.18
635 739 5.970140 TTGACTAATTTTCACACGAACGA 57.030 34.783 0.14 0.00 0.00 3.85
724 828 1.443407 CAAGCGACCGGAGATGGAT 59.557 57.895 9.46 0.00 0.00 3.41
897 1002 4.634443 CCCATTAAAAGACGACCGAGAAAT 59.366 41.667 0.00 0.00 0.00 2.17
928 1043 5.425630 AGAGAAGACACTTTTACACCGTTT 58.574 37.500 0.00 0.00 0.00 3.60
929 1044 5.293569 AGAGAAGACACTTTTACACCGTTTG 59.706 40.000 0.00 0.00 0.00 2.93
930 1045 3.685836 AGACACTTTTACACCGTTTGC 57.314 42.857 0.00 0.00 0.00 3.68
931 1046 3.011119 AGACACTTTTACACCGTTTGCA 58.989 40.909 0.00 0.00 0.00 4.08
932 1047 3.103007 GACACTTTTACACCGTTTGCAC 58.897 45.455 0.00 0.00 0.00 4.57
933 1048 2.159352 ACACTTTTACACCGTTTGCACC 60.159 45.455 0.00 0.00 0.00 5.01
934 1049 1.064357 ACTTTTACACCGTTTGCACCG 59.936 47.619 0.00 0.00 0.00 4.94
935 1050 1.064357 CTTTTACACCGTTTGCACCGT 59.936 47.619 4.46 0.00 0.00 4.83
936 1051 1.093159 TTTACACCGTTTGCACCGTT 58.907 45.000 4.46 0.00 0.00 4.44
937 1052 0.377554 TTACACCGTTTGCACCGTTG 59.622 50.000 4.46 3.03 0.00 4.10
1020 1135 2.048127 GCGTCGCCTTCACCTTCT 60.048 61.111 5.75 0.00 0.00 2.85
1044 1159 1.762460 CCTCCAGCTGGTCCGGTAT 60.762 63.158 31.58 0.00 36.34 2.73
1222 1337 0.841961 CATCCATGAGGCTTCTCCCA 59.158 55.000 0.00 0.00 36.72 4.37
1226 1341 0.841961 CATGAGGCTTCTCCCATCCA 59.158 55.000 0.00 0.00 36.72 3.41
1235 1350 0.262876 TCTCCCATCCAGCTAGAGCA 59.737 55.000 4.01 0.00 45.16 4.26
1317 1432 0.535102 CACCCATGGCCGGACTTATC 60.535 60.000 9.82 0.00 0.00 1.75
1467 1587 9.748100 GAAGAACAAGAAAATCGAGATTAGTTC 57.252 33.333 0.00 8.54 33.71 3.01
1588 1708 1.078708 TGAATTTCGCCGGGAGTCC 60.079 57.895 2.18 0.00 0.00 3.85
1600 1720 3.150767 CCGGGAGTCCTAGAATCTACAG 58.849 54.545 9.58 0.00 0.00 2.74
1601 1721 3.150767 CGGGAGTCCTAGAATCTACAGG 58.849 54.545 9.58 0.00 0.00 4.00
1611 1731 3.079578 AGAATCTACAGGTCGACGTCAA 58.920 45.455 17.16 0.00 0.00 3.18
1612 1732 3.504906 AGAATCTACAGGTCGACGTCAAA 59.495 43.478 17.16 0.00 0.00 2.69
1613 1733 3.928727 ATCTACAGGTCGACGTCAAAA 57.071 42.857 17.16 0.00 0.00 2.44
1614 1734 3.004024 TCTACAGGTCGACGTCAAAAC 57.996 47.619 17.16 10.05 0.00 2.43
1615 1735 2.358582 TCTACAGGTCGACGTCAAAACA 59.641 45.455 17.16 0.00 0.00 2.83
1616 1736 2.234300 ACAGGTCGACGTCAAAACAT 57.766 45.000 17.16 5.23 0.00 2.71
1617 1737 2.132762 ACAGGTCGACGTCAAAACATC 58.867 47.619 17.16 0.00 0.00 3.06
1618 1738 2.223971 ACAGGTCGACGTCAAAACATCT 60.224 45.455 17.16 1.63 0.00 2.90
1619 1739 2.408704 CAGGTCGACGTCAAAACATCTC 59.591 50.000 17.16 0.00 0.00 2.75
1620 1740 2.035449 AGGTCGACGTCAAAACATCTCA 59.965 45.455 17.16 0.00 0.00 3.27
1621 1741 2.408704 GGTCGACGTCAAAACATCTCAG 59.591 50.000 17.16 0.00 0.00 3.35
1622 1742 3.050619 GTCGACGTCAAAACATCTCAGT 58.949 45.455 17.16 0.00 0.00 3.41
1623 1743 4.224433 GTCGACGTCAAAACATCTCAGTA 58.776 43.478 17.16 0.00 0.00 2.74
1624 1744 4.857588 GTCGACGTCAAAACATCTCAGTAT 59.142 41.667 17.16 0.00 0.00 2.12
1625 1745 5.345202 GTCGACGTCAAAACATCTCAGTATT 59.655 40.000 17.16 0.00 0.00 1.89
1626 1746 6.525628 GTCGACGTCAAAACATCTCAGTATTA 59.474 38.462 17.16 0.00 0.00 0.98
1627 1747 7.220300 GTCGACGTCAAAACATCTCAGTATTAT 59.780 37.037 17.16 0.00 0.00 1.28
1628 1748 7.431376 TCGACGTCAAAACATCTCAGTATTATC 59.569 37.037 17.16 0.00 0.00 1.75
1629 1749 7.432545 CGACGTCAAAACATCTCAGTATTATCT 59.567 37.037 17.16 0.00 0.00 1.98
1630 1750 9.731819 GACGTCAAAACATCTCAGTATTATCTA 57.268 33.333 11.55 0.00 0.00 1.98
1650 1770 9.760926 TTATCTATTATGCTCACTAGATGACCT 57.239 33.333 0.00 0.00 33.93 3.85
1655 1775 2.275318 GCTCACTAGATGACCTGTTGC 58.725 52.381 0.00 0.00 32.37 4.17
1657 1777 1.893137 TCACTAGATGACCTGTTGCGT 59.107 47.619 0.00 0.00 29.99 5.24
1661 1781 1.512926 AGATGACCTGTTGCGTCAAC 58.487 50.000 13.54 13.54 43.16 3.18
1664 1784 0.176910 TGACCTGTTGCGTCAACTGA 59.823 50.000 21.80 6.79 43.85 3.41
1668 1788 1.831389 CTGTTGCGTCAACTGACCCG 61.831 60.000 18.81 0.00 43.85 5.28
1679 1799 3.056821 TCAACTGACCCGTGAGACATAAG 60.057 47.826 0.00 0.00 0.00 1.73
1688 1808 3.247442 CGTGAGACATAAGTTGGCGTTA 58.753 45.455 0.00 0.00 38.94 3.18
1693 1813 5.178623 TGAGACATAAGTTGGCGTTAAAGTG 59.821 40.000 0.00 0.00 38.94 3.16
1719 1839 5.073428 TGCCAAATAATGTGGTGTTACTCA 58.927 37.500 0.00 0.00 38.50 3.41
1720 1840 5.182950 TGCCAAATAATGTGGTGTTACTCAG 59.817 40.000 0.00 0.00 38.50 3.35
1722 1842 6.622896 GCCAAATAATGTGGTGTTACTCAGAC 60.623 42.308 0.00 0.00 38.50 3.51
1723 1843 6.655003 CCAAATAATGTGGTGTTACTCAGACT 59.345 38.462 0.00 0.00 0.00 3.24
1724 1844 7.822334 CCAAATAATGTGGTGTTACTCAGACTA 59.178 37.037 0.00 0.00 0.00 2.59
1725 1845 8.656849 CAAATAATGTGGTGTTACTCAGACTAC 58.343 37.037 0.00 0.00 0.00 2.73
1726 1846 4.803098 ATGTGGTGTTACTCAGACTACC 57.197 45.455 0.00 0.00 0.00 3.18
1727 1847 3.840991 TGTGGTGTTACTCAGACTACCT 58.159 45.455 0.00 0.00 0.00 3.08
1728 1848 4.220724 TGTGGTGTTACTCAGACTACCTT 58.779 43.478 0.00 0.00 0.00 3.50
1729 1849 4.038763 TGTGGTGTTACTCAGACTACCTTG 59.961 45.833 0.00 0.00 0.00 3.61
1730 1850 3.576982 TGGTGTTACTCAGACTACCTTGG 59.423 47.826 0.00 0.00 0.00 3.61
1731 1851 3.577415 GGTGTTACTCAGACTACCTTGGT 59.423 47.826 0.00 0.00 0.00 3.67
1736 1856 7.712205 GTGTTACTCAGACTACCTTGGTTTTTA 59.288 37.037 0.00 0.00 0.00 1.52
1808 1928 5.815233 ATATGCTGTCATAGTTAGGCTGT 57.185 39.130 0.00 0.00 38.46 4.40
1941 2091 2.922740 ACGAACTAAACCCAAGCTCA 57.077 45.000 0.00 0.00 0.00 4.26
2008 2158 8.843885 TCTATGATGATGCTTAAGAGAAATGG 57.156 34.615 6.67 0.00 0.00 3.16
2093 2276 5.295950 CCTGCATGGACAAATTAACAAACA 58.704 37.500 0.00 0.00 38.35 2.83
2115 2298 2.169978 TGATGCATTGGGAGACTGAGAG 59.830 50.000 0.00 0.00 0.00 3.20
2137 2320 8.603242 AGAGACTCGCAAAAGAAGTAAAAATA 57.397 30.769 0.00 0.00 0.00 1.40
2340 2527 8.477419 AAGAAGTAATCTTGAATCAAACCCAA 57.523 30.769 0.00 0.00 46.71 4.12
2355 2542 8.934023 ATCAAACCCAACTCTTGTCTTTATTA 57.066 30.769 0.00 0.00 0.00 0.98
2382 2569 2.160219 GCAAGAGAAACATCGTCATGCA 59.840 45.455 0.00 0.00 32.57 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.729856 ACGTTGCCGTCCTACCGC 62.730 66.667 0.00 0.00 46.28 5.68
26 27 2.819595 CTCCATGGCCCGACGTTG 60.820 66.667 6.96 0.00 0.00 4.10
27 28 4.096003 CCTCCATGGCCCGACGTT 62.096 66.667 6.96 0.00 0.00 3.99
29 30 3.740128 CTTCCTCCATGGCCCGACG 62.740 68.421 6.96 0.00 35.26 5.12
30 31 2.190578 CTTCCTCCATGGCCCGAC 59.809 66.667 6.96 0.00 35.26 4.79
31 32 3.797353 GCTTCCTCCATGGCCCGA 61.797 66.667 6.96 0.00 35.26 5.14
33 34 4.883354 CCGCTTCCTCCATGGCCC 62.883 72.222 6.96 0.00 35.26 5.80
34 35 3.125376 ATCCGCTTCCTCCATGGCC 62.125 63.158 6.96 0.00 35.26 5.36
35 36 1.895707 CATCCGCTTCCTCCATGGC 60.896 63.158 6.96 0.00 35.26 4.40
36 37 1.895707 GCATCCGCTTCCTCCATGG 60.896 63.158 4.97 4.97 34.30 3.66
37 38 1.153107 TGCATCCGCTTCCTCCATG 60.153 57.895 0.00 0.00 39.64 3.66
38 39 1.147824 CTGCATCCGCTTCCTCCAT 59.852 57.895 0.00 0.00 39.64 3.41
39 40 1.964608 CTCTGCATCCGCTTCCTCCA 61.965 60.000 0.00 0.00 39.64 3.86
40 41 1.227497 CTCTGCATCCGCTTCCTCC 60.227 63.158 0.00 0.00 39.64 4.30
41 42 0.176680 TTCTCTGCATCCGCTTCCTC 59.823 55.000 0.00 0.00 39.64 3.71
42 43 0.615331 TTTCTCTGCATCCGCTTCCT 59.385 50.000 0.00 0.00 39.64 3.36
43 44 1.012841 CTTTCTCTGCATCCGCTTCC 58.987 55.000 0.00 0.00 39.64 3.46
44 45 1.932511 CTCTTTCTCTGCATCCGCTTC 59.067 52.381 0.00 0.00 39.64 3.86
45 46 1.552337 TCTCTTTCTCTGCATCCGCTT 59.448 47.619 0.00 0.00 39.64 4.68
46 47 1.189752 TCTCTTTCTCTGCATCCGCT 58.810 50.000 0.00 0.00 39.64 5.52
47 48 2.015736 TTCTCTTTCTCTGCATCCGC 57.984 50.000 0.00 0.00 39.24 5.54
48 49 3.854666 TCTTTCTCTTTCTCTGCATCCG 58.145 45.455 0.00 0.00 0.00 4.18
49 50 4.081198 TCCTCTTTCTCTTTCTCTGCATCC 60.081 45.833 0.00 0.00 0.00 3.51
50 51 5.083533 TCCTCTTTCTCTTTCTCTGCATC 57.916 43.478 0.00 0.00 0.00 3.91
51 52 5.495926 TTCCTCTTTCTCTTTCTCTGCAT 57.504 39.130 0.00 0.00 0.00 3.96
52 53 4.963318 TTCCTCTTTCTCTTTCTCTGCA 57.037 40.909 0.00 0.00 0.00 4.41
53 54 5.546526 TCTTTCCTCTTTCTCTTTCTCTGC 58.453 41.667 0.00 0.00 0.00 4.26
54 55 6.594937 CCATCTTTCCTCTTTCTCTTTCTCTG 59.405 42.308 0.00 0.00 0.00 3.35
55 56 6.500049 TCCATCTTTCCTCTTTCTCTTTCTCT 59.500 38.462 0.00 0.00 0.00 3.10
56 57 6.706295 TCCATCTTTCCTCTTTCTCTTTCTC 58.294 40.000 0.00 0.00 0.00 2.87
57 58 6.500049 TCTCCATCTTTCCTCTTTCTCTTTCT 59.500 38.462 0.00 0.00 0.00 2.52
58 59 6.706295 TCTCCATCTTTCCTCTTTCTCTTTC 58.294 40.000 0.00 0.00 0.00 2.62
59 60 6.296374 CCTCTCCATCTTTCCTCTTTCTCTTT 60.296 42.308 0.00 0.00 0.00 2.52
60 61 5.189539 CCTCTCCATCTTTCCTCTTTCTCTT 59.810 44.000 0.00 0.00 0.00 2.85
61 62 4.716287 CCTCTCCATCTTTCCTCTTTCTCT 59.284 45.833 0.00 0.00 0.00 3.10
62 63 4.683129 GCCTCTCCATCTTTCCTCTTTCTC 60.683 50.000 0.00 0.00 0.00 2.87
63 64 3.199727 GCCTCTCCATCTTTCCTCTTTCT 59.800 47.826 0.00 0.00 0.00 2.52
64 65 3.540617 GCCTCTCCATCTTTCCTCTTTC 58.459 50.000 0.00 0.00 0.00 2.62
65 66 2.093235 CGCCTCTCCATCTTTCCTCTTT 60.093 50.000 0.00 0.00 0.00 2.52
66 67 1.484240 CGCCTCTCCATCTTTCCTCTT 59.516 52.381 0.00 0.00 0.00 2.85
67 68 1.118838 CGCCTCTCCATCTTTCCTCT 58.881 55.000 0.00 0.00 0.00 3.69
68 69 1.068434 CTCGCCTCTCCATCTTTCCTC 59.932 57.143 0.00 0.00 0.00 3.71
69 70 1.118838 CTCGCCTCTCCATCTTTCCT 58.881 55.000 0.00 0.00 0.00 3.36
70 71 0.105778 CCTCGCCTCTCCATCTTTCC 59.894 60.000 0.00 0.00 0.00 3.13
71 72 3.677002 CCTCGCCTCTCCATCTTTC 57.323 57.895 0.00 0.00 0.00 2.62
367 368 3.431856 GACCAGTCCGTTGTTTGTTTTC 58.568 45.455 0.00 0.00 0.00 2.29
371 372 3.089788 GGACCAGTCCGTTGTTTGT 57.910 52.632 0.05 0.00 40.36 2.83
396 397 0.466124 TCCAACACCGTCACACATGA 59.534 50.000 0.00 0.00 0.00 3.07
397 398 1.197492 CATCCAACACCGTCACACATG 59.803 52.381 0.00 0.00 0.00 3.21
401 402 0.466124 TGTCATCCAACACCGTCACA 59.534 50.000 0.00 0.00 0.00 3.58
402 403 1.588674 TTGTCATCCAACACCGTCAC 58.411 50.000 0.00 0.00 0.00 3.67
425 426 0.169672 CGTCCGAACCACTATGACGT 59.830 55.000 0.00 0.00 42.68 4.34
427 428 0.813184 TCCGTCCGAACCACTATGAC 59.187 55.000 0.00 0.00 0.00 3.06
431 432 0.528924 CACATCCGTCCGAACCACTA 59.471 55.000 0.00 0.00 0.00 2.74
433 434 1.740296 CCACATCCGTCCGAACCAC 60.740 63.158 0.00 0.00 0.00 4.16
466 472 1.802960 CATTAGGGCATCAGCTAAGCG 59.197 52.381 0.00 0.00 41.70 4.68
471 477 0.822532 GCTGCATTAGGGCATCAGCT 60.823 55.000 3.65 0.00 44.71 4.24
473 479 1.947013 CGCTGCATTAGGGCATCAG 59.053 57.895 0.00 0.00 43.97 2.90
509 515 1.543802 GCGGGAAATGGTCATGTTGAA 59.456 47.619 0.00 0.00 0.00 2.69
565 653 1.582968 CACATGCACTCAACTGCCC 59.417 57.895 0.00 0.00 36.21 5.36
607 696 3.608073 GTGTGAAAATTAGTCAATGGCGC 59.392 43.478 0.00 0.00 0.00 6.53
635 739 2.519377 TCAGTTCAACGACGTGGATT 57.481 45.000 5.78 0.00 0.00 3.01
897 1002 7.280205 GTGTAAAAGTGTCTTCTCTTCTTTCCA 59.720 37.037 0.00 0.00 0.00 3.53
930 1045 3.673484 CTGGCCCTTGCAACGGTG 61.673 66.667 14.83 0.00 40.13 4.94
931 1046 3.884774 TCTGGCCCTTGCAACGGT 61.885 61.111 14.83 0.00 40.13 4.83
932 1047 3.365265 GTCTGGCCCTTGCAACGG 61.365 66.667 9.87 9.87 40.13 4.44
933 1048 3.365265 GGTCTGGCCCTTGCAACG 61.365 66.667 0.00 0.00 40.13 4.10
934 1049 3.365265 CGGTCTGGCCCTTGCAAC 61.365 66.667 0.00 0.00 40.13 4.17
935 1050 4.659172 CCGGTCTGGCCCTTGCAA 62.659 66.667 0.00 0.00 40.13 4.08
938 1053 3.636231 TGACCGGTCTGGCCCTTG 61.636 66.667 33.39 0.00 43.94 3.61
939 1054 3.637273 GTGACCGGTCTGGCCCTT 61.637 66.667 33.39 0.00 43.94 3.95
1020 1135 1.201429 GGACCAGCTGGAGGAGGAAA 61.201 60.000 39.19 0.00 38.94 3.13
1044 1159 2.675423 CTCGGGAGGGACGACACA 60.675 66.667 0.00 0.00 36.25 3.72
1222 1337 1.421480 TGCATCTGCTCTAGCTGGAT 58.579 50.000 0.00 7.00 42.66 3.41
1226 1341 1.202663 CCACATGCATCTGCTCTAGCT 60.203 52.381 0.00 0.00 42.66 3.32
1235 1350 2.361483 TTGCCGCCACATGCATCT 60.361 55.556 0.00 0.00 41.33 2.90
1304 1419 3.857038 GCCCGATAAGTCCGGCCA 61.857 66.667 2.24 0.00 45.24 5.36
1467 1587 8.574196 AAATCGATGAACCTGTAAAAACTTTG 57.426 30.769 0.00 0.00 0.00 2.77
1474 1594 8.786826 AATCAGTAAATCGATGAACCTGTAAA 57.213 30.769 0.00 0.00 0.00 2.01
1541 1661 0.530744 TCTGAACCTGAAGCGCGTAT 59.469 50.000 8.43 0.00 0.00 3.06
1588 1708 3.869832 TGACGTCGACCTGTAGATTCTAG 59.130 47.826 10.58 0.00 0.00 2.43
1600 1720 2.400399 TGAGATGTTTTGACGTCGACC 58.600 47.619 10.58 2.93 0.00 4.79
1601 1721 3.050619 ACTGAGATGTTTTGACGTCGAC 58.949 45.455 11.62 5.18 0.00 4.20
1636 1756 2.094494 ACGCAACAGGTCATCTAGTGAG 60.094 50.000 0.00 0.00 37.56 3.51
1646 1766 0.582005 GTCAGTTGACGCAACAGGTC 59.418 55.000 19.82 9.28 45.66 3.85
1655 1775 0.663568 GTCTCACGGGTCAGTTGACG 60.664 60.000 6.21 0.00 45.65 4.35
1657 1777 1.338107 ATGTCTCACGGGTCAGTTGA 58.662 50.000 0.00 0.00 0.00 3.18
1661 1781 3.254060 CAACTTATGTCTCACGGGTCAG 58.746 50.000 0.00 0.00 0.00 3.51
1664 1784 1.338769 GCCAACTTATGTCTCACGGGT 60.339 52.381 0.00 0.00 0.00 5.28
1668 1788 5.178809 ACTTTAACGCCAACTTATGTCTCAC 59.821 40.000 0.00 0.00 0.00 3.51
1679 1799 2.226912 TGGCATACACTTTAACGCCAAC 59.773 45.455 0.00 0.00 46.04 3.77
1688 1808 6.014669 ACACCACATTATTTGGCATACACTTT 60.015 34.615 0.00 0.00 37.69 2.66
1693 1813 7.095695 AGTAACACCACATTATTTGGCATAC 57.904 36.000 0.00 0.00 37.69 2.39
1722 1842 9.274206 GCCTCTTAGATATAAAAACCAAGGTAG 57.726 37.037 0.00 0.00 0.00 3.18
1723 1843 8.774183 TGCCTCTTAGATATAAAAACCAAGGTA 58.226 33.333 0.00 0.00 0.00 3.08
1724 1844 7.639378 TGCCTCTTAGATATAAAAACCAAGGT 58.361 34.615 0.00 0.00 0.00 3.50
1725 1845 8.519799 TTGCCTCTTAGATATAAAAACCAAGG 57.480 34.615 0.00 0.00 0.00 3.61
1726 1846 9.396022 TCTTGCCTCTTAGATATAAAAACCAAG 57.604 33.333 0.00 0.00 0.00 3.61
1727 1847 9.396022 CTCTTGCCTCTTAGATATAAAAACCAA 57.604 33.333 0.00 0.00 0.00 3.67
1728 1848 8.548877 ACTCTTGCCTCTTAGATATAAAAACCA 58.451 33.333 0.00 0.00 0.00 3.67
1729 1849 8.966069 ACTCTTGCCTCTTAGATATAAAAACC 57.034 34.615 0.00 0.00 0.00 3.27
1906 2056 5.347620 AGTTCGTATGGTTGGTAGCAATA 57.652 39.130 11.06 3.91 35.04 1.90
1941 2091 6.936968 CCTATCATTAGGGTTAAGGCTACT 57.063 41.667 0.00 0.00 41.31 2.57
1985 2135 6.148315 CGCCATTTCTCTTAAGCATCATCATA 59.852 38.462 0.00 0.00 0.00 2.15
2008 2158 4.120331 GAAGCCCACCATGTGCGC 62.120 66.667 0.00 0.00 37.58 6.09
2052 2234 3.370527 GCAGGCATTCTGGGTTTAGACTA 60.371 47.826 0.00 0.00 43.54 2.59
2061 2244 1.076559 TCCATGCAGGCATTCTGGG 60.077 57.895 3.57 3.11 43.54 4.45
2093 2276 2.775960 TCTCAGTCTCCCAATGCATCAT 59.224 45.455 0.00 0.00 0.00 2.45
2115 2298 9.447040 ACTTTATTTTTACTTCTTTTGCGAGTC 57.553 29.630 0.00 0.00 0.00 3.36
2137 2320 7.452880 TGCTATATTGTTTTCTGAGCACTTT 57.547 32.000 0.00 0.00 33.73 2.66
2159 2342 5.749620 TGTTTGAAATGTCATTTGCATTGC 58.250 33.333 15.52 0.46 36.75 3.56
2257 2444 6.635755 AGTCTTTGCTACTCTAATCTGAACC 58.364 40.000 0.00 0.00 0.00 3.62
2355 2542 7.307632 GCATGACGATGTTTCTCTTGCTATTAT 60.308 37.037 0.00 0.00 33.05 1.28


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

AutoCloner maintained by Alex Coulton.