Multiple sequence alignment - TraesCS3A01G415500

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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 TraesCS3A01G415500 chr3A 100.000 2423 0 0 381 2803 658722262 658724684 0.000000e+00 4475.0
1 TraesCS3A01G415500 chr3A 100.000 76 0 0 1 76 658721882 658721957 1.050000e-29 141.0
2 TraesCS3A01G415500 chr3D 88.493 1573 95 26 383 1900 523833130 523834671 0.000000e+00 1823.0
3 TraesCS3A01G415500 chr3D 91.353 532 41 5 1900 2427 523834624 523835154 0.000000e+00 723.0
4 TraesCS3A01G415500 chr3D 90.256 390 35 3 2413 2801 523837210 523837597 8.960000e-140 507.0
5 TraesCS3A01G415500 chr3B 90.468 1112 49 12 616 1706 691343097 691344172 0.000000e+00 1413.0
6 TraesCS3A01G415500 chr3B 91.667 876 65 8 1929 2801 691344385 691345255 0.000000e+00 1206.0
7 TraesCS3A01G415500 chr3B 89.894 188 17 1 381 566 691322254 691322441 1.000000e-59 241.0
8 TraesCS3A01G415500 chr3B 97.059 34 1 0 1862 1895 691344438 691344471 1.080000e-04 58.4
9 TraesCS3A01G415500 chr3B 100.000 29 0 0 1617 1645 688230978 688230950 1.000000e-03 54.7
10 TraesCS3A01G415500 chr3B 100.000 29 0 0 1617 1645 688290654 688290626 1.000000e-03 54.7
11 TraesCS3A01G415500 chr5D 94.872 39 2 0 27 65 292765696 292765734 8.380000e-06 62.1
12 TraesCS3A01G415500 chr4B 92.683 41 3 0 1605 1645 59598602 59598642 3.020000e-05 60.2
13 TraesCS3A01G415500 chr7D 100.000 29 0 0 1617 1645 22988808 22988836 1.000000e-03 54.7


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 TraesCS3A01G415500 chr3A 658721882 658724684 2802 False 2308.000000 4475 100.000000 1 2803 2 chr3A.!!$F1 2802
1 TraesCS3A01G415500 chr3D 523833130 523837597 4467 False 1017.666667 1823 90.034000 383 2801 3 chr3D.!!$F1 2418
2 TraesCS3A01G415500 chr3B 691343097 691345255 2158 False 892.466667 1413 93.064667 616 2801 3 chr3B.!!$F2 2185

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
56 57 0.037734 AGGGAATCGCCGGAGTTTTT 59.962 50.0 5.05 0.0 37.63 1.94 F
984 1030 0.182775 AGCTTCTTTTCCCCGTGTGT 59.817 50.0 0.00 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1039 1085 0.036732 TTGCAGTGAGCTGGTTAGGG 59.963 55.0 0.0 0.0 45.94 3.53 R
2036 2139 0.389166 CTTGGAGTCAGAGTCGCACC 60.389 60.0 0.0 0.0 0.00 5.01 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
28 29 7.072263 CAATCCCATTGTCTATCTTAGAGGT 57.928 40.000 0.00 0.00 35.04 3.85
29 30 6.678568 ATCCCATTGTCTATCTTAGAGGTG 57.321 41.667 0.00 0.00 35.04 4.00
30 31 4.901849 TCCCATTGTCTATCTTAGAGGTGG 59.098 45.833 0.00 0.00 35.04 4.61
31 32 4.040952 CCCATTGTCTATCTTAGAGGTGGG 59.959 50.000 11.42 11.42 41.50 4.61
32 33 4.040952 CCATTGTCTATCTTAGAGGTGGGG 59.959 50.000 0.00 0.00 35.04 4.96
33 34 3.330126 TGTCTATCTTAGAGGTGGGGG 57.670 52.381 0.00 0.00 35.04 5.40
34 35 2.590611 TGTCTATCTTAGAGGTGGGGGT 59.409 50.000 0.00 0.00 35.04 4.95
35 36 2.966516 GTCTATCTTAGAGGTGGGGGTG 59.033 54.545 0.00 0.00 35.04 4.61
36 37 1.694696 CTATCTTAGAGGTGGGGGTGC 59.305 57.143 0.00 0.00 0.00 5.01
37 38 0.253160 ATCTTAGAGGTGGGGGTGCA 60.253 55.000 0.00 0.00 0.00 4.57
38 39 0.909610 TCTTAGAGGTGGGGGTGCAG 60.910 60.000 0.00 0.00 0.00 4.41
39 40 1.915078 CTTAGAGGTGGGGGTGCAGG 61.915 65.000 0.00 0.00 0.00 4.85
40 41 3.943137 TAGAGGTGGGGGTGCAGGG 62.943 68.421 0.00 0.00 0.00 4.45
42 43 4.938756 AGGTGGGGGTGCAGGGAA 62.939 66.667 0.00 0.00 0.00 3.97
43 44 3.672503 GGTGGGGGTGCAGGGAAT 61.673 66.667 0.00 0.00 0.00 3.01
44 45 2.043953 GTGGGGGTGCAGGGAATC 60.044 66.667 0.00 0.00 0.00 2.52
45 46 3.727258 TGGGGGTGCAGGGAATCG 61.727 66.667 0.00 0.00 0.00 3.34
50 51 4.467084 GTGCAGGGAATCGCCGGA 62.467 66.667 5.05 0.00 37.63 5.14
51 52 4.161295 TGCAGGGAATCGCCGGAG 62.161 66.667 5.05 0.00 37.63 4.63
52 53 4.162690 GCAGGGAATCGCCGGAGT 62.163 66.667 5.05 0.00 37.63 3.85
53 54 2.584608 CAGGGAATCGCCGGAGTT 59.415 61.111 5.05 0.00 37.63 3.01
54 55 1.078426 CAGGGAATCGCCGGAGTTT 60.078 57.895 5.05 2.46 37.63 2.66
55 56 0.676782 CAGGGAATCGCCGGAGTTTT 60.677 55.000 5.05 0.00 37.63 2.43
56 57 0.037734 AGGGAATCGCCGGAGTTTTT 59.962 50.000 5.05 0.00 37.63 1.94
57 58 0.450583 GGGAATCGCCGGAGTTTTTC 59.549 55.000 5.05 7.66 37.63 2.29
58 59 1.161843 GGAATCGCCGGAGTTTTTCA 58.838 50.000 5.05 0.00 0.00 2.69
59 60 1.135774 GGAATCGCCGGAGTTTTTCAC 60.136 52.381 5.05 0.00 0.00 3.18
60 61 0.879090 AATCGCCGGAGTTTTTCACC 59.121 50.000 5.05 0.00 0.00 4.02
61 62 1.296056 ATCGCCGGAGTTTTTCACCG 61.296 55.000 5.05 0.00 46.86 4.94
65 66 1.946267 CGGAGTTTTTCACCGGTGG 59.054 57.895 33.40 15.70 44.36 4.61
66 67 0.816421 CGGAGTTTTTCACCGGTGGT 60.816 55.000 33.40 11.95 44.36 4.16
485 487 3.779183 AGATCATGCTTGAGAGGAGGAAA 59.221 43.478 8.40 0.00 37.57 3.13
486 488 3.623906 TCATGCTTGAGAGGAGGAAAG 57.376 47.619 0.00 0.00 30.92 2.62
500 502 3.181433 GGAGGAAAGAAGGTTGGGAGAAA 60.181 47.826 0.00 0.00 0.00 2.52
517 519 6.936900 TGGGAGAAAGAAGATTAAGTGTGAAG 59.063 38.462 0.00 0.00 0.00 3.02
533 535 5.251700 AGTGTGAAGGGTTGGATTTAGATCT 59.748 40.000 0.00 0.00 32.66 2.75
534 536 6.443849 AGTGTGAAGGGTTGGATTTAGATCTA 59.556 38.462 0.00 0.00 32.66 1.98
535 537 7.037586 AGTGTGAAGGGTTGGATTTAGATCTAA 60.038 37.037 11.24 11.24 31.23 2.10
536 538 7.065923 GTGTGAAGGGTTGGATTTAGATCTAAC 59.934 40.741 14.85 12.45 46.90 2.34
548 550 7.764901 GGATTTAGATCTAACGAACAGGAAACT 59.235 37.037 14.85 0.00 34.85 2.66
551 553 9.985730 TTTAGATCTAACGAACAGGAAACTAAA 57.014 29.630 14.85 0.00 40.21 1.85
561 563 5.886960 ACAGGAAACTAAATGACTGATGC 57.113 39.130 0.00 0.00 40.21 3.91
566 568 5.863935 GGAAACTAAATGACTGATGCCAAAC 59.136 40.000 0.00 0.00 0.00 2.93
567 569 6.403866 AAACTAAATGACTGATGCCAAACA 57.596 33.333 0.00 0.00 0.00 2.83
599 601 2.180276 ACCTGACATTTAGACGCTCCT 58.820 47.619 0.00 0.00 0.00 3.69
676 696 5.311016 CGGTTTACGTATGCATCAAGTAG 57.689 43.478 0.19 0.00 37.93 2.57
677 697 4.208460 CGGTTTACGTATGCATCAAGTAGG 59.792 45.833 0.19 0.00 37.93 3.18
678 698 5.114081 GGTTTACGTATGCATCAAGTAGGT 58.886 41.667 0.19 0.00 0.00 3.08
812 844 1.909302 TGTTGATCCCTTCCTCCTGAC 59.091 52.381 0.00 0.00 0.00 3.51
860 892 9.809096 TCATTTAAAGAGCTCTGACTAACTATG 57.191 33.333 19.06 14.99 0.00 2.23
875 907 2.126417 CTATGTACCCCGACTCGGCG 62.126 65.000 12.37 6.26 46.86 6.46
895 927 2.562635 GAAATTAGACCCCTTCCTCGC 58.437 52.381 0.00 0.00 0.00 5.03
909 941 1.078759 CCTCGCTCGTCAACATCACC 61.079 60.000 0.00 0.00 0.00 4.02
973 1019 0.610232 AGGCCGCATGAAGCTTCTTT 60.610 50.000 26.09 11.83 42.61 2.52
983 1029 1.266989 GAAGCTTCTTTTCCCCGTGTG 59.733 52.381 19.44 0.00 0.00 3.82
984 1030 0.182775 AGCTTCTTTTCCCCGTGTGT 59.817 50.000 0.00 0.00 0.00 3.72
987 1033 2.418976 GCTTCTTTTCCCCGTGTGTATC 59.581 50.000 0.00 0.00 0.00 2.24
1028 1074 2.742372 ACCGTTGCACTGCGATCC 60.742 61.111 6.14 0.00 0.00 3.36
1039 1085 1.604755 ACTGCGATCCTCGTACTCATC 59.395 52.381 0.00 0.00 42.81 2.92
1070 1116 3.264947 CTCACTGCAATCTCCATCGAAA 58.735 45.455 0.00 0.00 0.00 3.46
1095 1141 0.329596 ACACCCATCAGCCCTTTCTC 59.670 55.000 0.00 0.00 0.00 2.87
1112 1158 1.200483 CTCGCGCTTACATACACAGG 58.800 55.000 5.56 0.00 0.00 4.00
1154 1201 3.432890 GGCTATGTGGAGAAAGAAGGAGG 60.433 52.174 0.00 0.00 0.00 4.30
1478 1525 0.040351 AGCACACTAGGAGAGAGCCA 59.960 55.000 0.00 0.00 0.00 4.75
1494 1541 0.865111 GCCAACGGCCACAATTTTTC 59.135 50.000 2.24 0.00 44.06 2.29
1525 1576 3.653664 TTTCGCGGGGAATGGCCAT 62.654 57.895 14.09 14.09 38.95 4.40
1565 1616 2.126467 CGTTGAATTGCCTTTGTGGTG 58.874 47.619 0.00 0.00 38.35 4.17
1600 1651 8.680001 TCTTTCTTTGTTACTCCCTTTGTAAAC 58.320 33.333 0.00 0.00 32.58 2.01
1601 1652 8.584063 TTTCTTTGTTACTCCCTTTGTAAACT 57.416 30.769 0.00 0.00 32.58 2.66
1602 1653 8.584063 TTCTTTGTTACTCCCTTTGTAAACTT 57.416 30.769 0.00 0.00 32.58 2.66
1603 1654 8.584063 TCTTTGTTACTCCCTTTGTAAACTTT 57.416 30.769 0.00 0.00 32.58 2.66
1604 1655 9.027202 TCTTTGTTACTCCCTTTGTAAACTTTT 57.973 29.630 0.00 0.00 32.58 2.27
1605 1656 9.297586 CTTTGTTACTCCCTTTGTAAACTTTTC 57.702 33.333 0.00 0.00 32.58 2.29
1606 1657 8.584063 TTGTTACTCCCTTTGTAAACTTTTCT 57.416 30.769 0.00 0.00 32.58 2.52
1607 1658 7.992008 TGTTACTCCCTTTGTAAACTTTTCTG 58.008 34.615 0.00 0.00 32.58 3.02
1608 1659 7.612633 TGTTACTCCCTTTGTAAACTTTTCTGT 59.387 33.333 0.00 0.00 32.58 3.41
1609 1660 9.112725 GTTACTCCCTTTGTAAACTTTTCTGTA 57.887 33.333 0.00 0.00 32.58 2.74
1610 1661 9.683870 TTACTCCCTTTGTAAACTTTTCTGTAA 57.316 29.630 0.00 0.00 0.00 2.41
1611 1662 8.762481 ACTCCCTTTGTAAACTTTTCTGTAAT 57.238 30.769 0.00 0.00 0.00 1.89
1723 1825 8.193250 ACACGGTCTTTCAATTGTGTATATAC 57.807 34.615 5.13 5.89 38.65 1.47
1848 1951 5.741011 ACAATAGCTATGAAACGGAGGAAA 58.259 37.500 7.09 0.00 0.00 3.13
1853 1956 9.654663 AATAGCTATGAAACGGAGGAAATATAC 57.345 33.333 7.09 0.00 0.00 1.47
1854 1957 7.062749 AGCTATGAAACGGAGGAAATATACA 57.937 36.000 0.00 0.00 0.00 2.29
1855 1958 7.506114 AGCTATGAAACGGAGGAAATATACAA 58.494 34.615 0.00 0.00 0.00 2.41
1856 1959 7.441458 AGCTATGAAACGGAGGAAATATACAAC 59.559 37.037 0.00 0.00 0.00 3.32
1857 1960 7.441458 GCTATGAAACGGAGGAAATATACAACT 59.559 37.037 0.00 0.00 0.00 3.16
1858 1961 9.976511 CTATGAAACGGAGGAAATATACAACTA 57.023 33.333 0.00 0.00 0.00 2.24
1888 1991 6.140786 GGTGAACGAGGTTTCTTCAAAATAC 58.859 40.000 0.00 0.00 0.00 1.89
1889 1992 6.140786 GTGAACGAGGTTTCTTCAAAATACC 58.859 40.000 0.00 0.00 0.00 2.73
1896 1999 7.064253 CGAGGTTTCTTCAAAATACCGAAGTAT 59.936 37.037 0.00 0.00 41.09 2.12
1912 2015 8.882415 ACCGAAGTATACAACTATAAATGGTG 57.118 34.615 5.50 0.00 37.50 4.17
1913 2016 8.698210 ACCGAAGTATACAACTATAAATGGTGA 58.302 33.333 5.50 0.00 37.50 4.02
1914 2017 9.537192 CCGAAGTATACAACTATAAATGGTGAA 57.463 33.333 5.50 0.00 37.50 3.18
1964 2067 4.906618 ACATTCAACCGTTCCACTAGATT 58.093 39.130 0.00 0.00 0.00 2.40
1999 2102 5.805728 AGAGATAATGGTGAACGAGGTTTT 58.194 37.500 0.00 0.00 0.00 2.43
2036 2139 3.061322 TGTGGTTATCGTCTTTTCCACG 58.939 45.455 0.00 0.00 45.43 4.94
2039 2142 2.414138 GGTTATCGTCTTTTCCACGGTG 59.586 50.000 0.00 0.00 37.85 4.94
2062 2165 4.621991 CGACTCTGACTCCAAGAGAAAAA 58.378 43.478 7.42 0.00 33.32 1.94
2115 2220 7.218228 TCAATTTGTATCAACTCATTGCACT 57.782 32.000 0.00 0.00 35.63 4.40
2184 2291 6.003950 TGATATTTAACCTGCCTTATGCTCC 58.996 40.000 0.00 0.00 42.00 4.70
2325 2432 0.615331 ATGCCATGTCGGTGAACTCT 59.385 50.000 0.00 0.00 36.97 3.24
2458 4634 9.744468 AAAAATTATATCGTAAACCAGATTGGC 57.256 29.630 0.00 0.00 42.67 4.52
2508 4685 4.750098 ACTGTTGGAGACTGAAATTACACG 59.250 41.667 0.00 0.00 0.00 4.49
2517 4694 1.801771 TGAAATTACACGGAACCAGCG 59.198 47.619 0.00 0.00 0.00 5.18
2543 4720 4.610605 TGGAAACAGATACCTCGAAACA 57.389 40.909 0.00 0.00 35.01 2.83
2609 4786 7.497595 TGCCACTACAAACGAGATCTAATAAT 58.502 34.615 0.00 0.00 0.00 1.28
2675 4852 4.955450 ACTTGTAATCCATTGCAGGCATTA 59.045 37.500 0.00 0.00 33.88 1.90
2682 4859 3.117776 TCCATTGCAGGCATTAGAGATGT 60.118 43.478 0.00 0.00 0.00 3.06
2691 4868 6.264067 GCAGGCATTAGAGATGTCCTTATTTT 59.736 38.462 0.00 0.00 0.00 1.82
2717 4894 9.639563 TGAAAAATTATGAGGGCATTATGAGTA 57.360 29.630 0.00 0.00 35.94 2.59
2777 4954 7.720515 TCCTCAACTCTACCTTAATACTCTAGC 59.279 40.741 0.00 0.00 0.00 3.42
2785 4962 8.090831 TCTACCTTAATACTCTAGCGTTATCGA 58.909 37.037 0.00 0.00 39.71 3.59
2801 4978 1.185618 TCGAAGGGTGTGTCTCCAGG 61.186 60.000 0.00 0.00 0.00 4.45
2802 4979 1.679898 GAAGGGTGTGTCTCCAGGG 59.320 63.158 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.933521 CACCTCTAAGATAGACAATGGGATTG 59.066 42.308 0.00 0.00 45.59 2.67
5 6 6.043706 CCACCTCTAAGATAGACAATGGGATT 59.956 42.308 0.00 0.00 0.00 3.01
6 7 5.545723 CCACCTCTAAGATAGACAATGGGAT 59.454 44.000 0.00 0.00 0.00 3.85
7 8 4.901849 CCACCTCTAAGATAGACAATGGGA 59.098 45.833 0.00 0.00 0.00 4.37
8 9 4.040952 CCCACCTCTAAGATAGACAATGGG 59.959 50.000 9.69 9.69 38.64 4.00
9 10 4.040952 CCCCACCTCTAAGATAGACAATGG 59.959 50.000 0.00 0.00 0.00 3.16
10 11 4.040952 CCCCCACCTCTAAGATAGACAATG 59.959 50.000 0.00 0.00 0.00 2.82
11 12 4.235372 CCCCCACCTCTAAGATAGACAAT 58.765 47.826 0.00 0.00 0.00 2.71
12 13 3.013648 ACCCCCACCTCTAAGATAGACAA 59.986 47.826 0.00 0.00 0.00 3.18
13 14 2.590611 ACCCCCACCTCTAAGATAGACA 59.409 50.000 0.00 0.00 0.00 3.41
14 15 2.966516 CACCCCCACCTCTAAGATAGAC 59.033 54.545 0.00 0.00 0.00 2.59
15 16 2.693074 GCACCCCCACCTCTAAGATAGA 60.693 54.545 0.00 0.00 0.00 1.98
16 17 1.694696 GCACCCCCACCTCTAAGATAG 59.305 57.143 0.00 0.00 0.00 2.08
17 18 1.009060 TGCACCCCCACCTCTAAGATA 59.991 52.381 0.00 0.00 0.00 1.98
18 19 0.253160 TGCACCCCCACCTCTAAGAT 60.253 55.000 0.00 0.00 0.00 2.40
19 20 0.909610 CTGCACCCCCACCTCTAAGA 60.910 60.000 0.00 0.00 0.00 2.10
20 21 1.604378 CTGCACCCCCACCTCTAAG 59.396 63.158 0.00 0.00 0.00 2.18
21 22 1.923395 CCTGCACCCCCACCTCTAA 60.923 63.158 0.00 0.00 0.00 2.10
22 23 2.285368 CCTGCACCCCCACCTCTA 60.285 66.667 0.00 0.00 0.00 2.43
25 26 4.938756 TTCCCTGCACCCCCACCT 62.939 66.667 0.00 0.00 0.00 4.00
26 27 3.662117 GATTCCCTGCACCCCCACC 62.662 68.421 0.00 0.00 0.00 4.61
27 28 2.043953 GATTCCCTGCACCCCCAC 60.044 66.667 0.00 0.00 0.00 4.61
28 29 3.727258 CGATTCCCTGCACCCCCA 61.727 66.667 0.00 0.00 0.00 4.96
33 34 4.467084 TCCGGCGATTCCCTGCAC 62.467 66.667 9.30 0.00 0.00 4.57
34 35 4.161295 CTCCGGCGATTCCCTGCA 62.161 66.667 9.30 0.00 0.00 4.41
35 36 3.682292 AACTCCGGCGATTCCCTGC 62.682 63.158 9.30 0.00 0.00 4.85
36 37 0.676782 AAAACTCCGGCGATTCCCTG 60.677 55.000 9.30 0.00 0.00 4.45
37 38 0.037734 AAAAACTCCGGCGATTCCCT 59.962 50.000 9.30 0.00 0.00 4.20
38 39 0.450583 GAAAAACTCCGGCGATTCCC 59.549 55.000 9.30 0.00 0.00 3.97
39 40 1.135774 GTGAAAAACTCCGGCGATTCC 60.136 52.381 9.30 0.00 0.00 3.01
40 41 1.135774 GGTGAAAAACTCCGGCGATTC 60.136 52.381 9.30 3.66 0.00 2.52
41 42 0.879090 GGTGAAAAACTCCGGCGATT 59.121 50.000 9.30 0.00 0.00 3.34
42 43 2.551644 GGTGAAAAACTCCGGCGAT 58.448 52.632 9.30 0.00 0.00 4.58
43 44 4.052519 GGTGAAAAACTCCGGCGA 57.947 55.556 9.30 0.00 0.00 5.54
48 49 3.105187 ACCACCGGTGAAAAACTCC 57.895 52.632 36.07 0.00 32.98 3.85
408 409 4.100084 CATCCGCCTGCCTCCACA 62.100 66.667 0.00 0.00 0.00 4.17
432 434 4.849310 TGCAACCGCCGGCCTATC 62.849 66.667 23.46 7.15 37.32 2.08
452 454 6.327365 TCTCAAGCATGATCTAATCCACCTTA 59.673 38.462 0.00 0.00 34.37 2.69
464 466 3.834489 TTCCTCCTCTCAAGCATGATC 57.166 47.619 0.00 0.00 34.37 2.92
485 487 5.590976 AATCTTCTTTCTCCCAACCTTCT 57.409 39.130 0.00 0.00 0.00 2.85
486 488 6.943146 ACTTAATCTTCTTTCTCCCAACCTTC 59.057 38.462 0.00 0.00 0.00 3.46
500 502 5.073144 TCCAACCCTTCACACTTAATCTTCT 59.927 40.000 0.00 0.00 0.00 2.85
517 519 6.110707 TGTTCGTTAGATCTAAATCCAACCC 58.889 40.000 16.73 1.53 31.99 4.11
533 535 7.211573 TCAGTCATTTAGTTTCCTGTTCGTTA 58.788 34.615 0.00 0.00 0.00 3.18
534 536 6.053005 TCAGTCATTTAGTTTCCTGTTCGTT 58.947 36.000 0.00 0.00 0.00 3.85
535 537 5.607477 TCAGTCATTTAGTTTCCTGTTCGT 58.393 37.500 0.00 0.00 0.00 3.85
536 538 6.537566 CATCAGTCATTTAGTTTCCTGTTCG 58.462 40.000 0.00 0.00 0.00 3.95
538 540 5.183904 GGCATCAGTCATTTAGTTTCCTGTT 59.816 40.000 0.00 0.00 0.00 3.16
542 544 5.643379 TTGGCATCAGTCATTTAGTTTCC 57.357 39.130 0.00 0.00 0.00 3.13
576 578 3.130693 GGAGCGTCTAAATGTCAGGTACT 59.869 47.826 0.00 0.00 43.88 2.73
577 579 3.130693 AGGAGCGTCTAAATGTCAGGTAC 59.869 47.826 0.00 0.00 0.00 3.34
578 580 3.362706 AGGAGCGTCTAAATGTCAGGTA 58.637 45.455 0.00 0.00 0.00 3.08
673 693 2.805194 AGTCAGTGGACCTACACCTAC 58.195 52.381 0.00 0.00 45.48 3.18
674 694 3.162666 CAAGTCAGTGGACCTACACCTA 58.837 50.000 0.00 0.00 45.48 3.08
675 695 1.971357 CAAGTCAGTGGACCTACACCT 59.029 52.381 0.00 0.00 45.48 4.00
676 696 1.608283 GCAAGTCAGTGGACCTACACC 60.608 57.143 0.00 0.00 45.48 4.16
677 697 1.608283 GGCAAGTCAGTGGACCTACAC 60.608 57.143 0.00 0.00 45.48 2.90
678 698 0.685097 GGCAAGTCAGTGGACCTACA 59.315 55.000 0.00 0.00 45.48 2.74
736 756 1.939255 GTAGCTTCTGCAGATTGGAGC 59.061 52.381 24.40 24.40 42.74 4.70
875 907 2.170817 AGCGAGGAAGGGGTCTAATTTC 59.829 50.000 0.00 0.00 0.00 2.17
895 927 2.977914 AGGAATGGTGATGTTGACGAG 58.022 47.619 0.00 0.00 0.00 4.18
909 941 7.391554 TCAAGGATTAGTGTTTGAGAAGGAATG 59.608 37.037 0.00 0.00 0.00 2.67
973 1019 4.480115 AGATATCAGATACACACGGGGAA 58.520 43.478 5.32 0.00 0.00 3.97
987 1033 9.308000 GGTGGATTATATAGGAGGAGATATCAG 57.692 40.741 5.32 0.00 0.00 2.90
1010 1056 2.476051 GATCGCAGTGCAACGGTG 59.524 61.111 16.83 0.00 45.86 4.94
1028 1074 2.034812 GCTGGTTAGGGATGAGTACGAG 59.965 54.545 0.00 0.00 0.00 4.18
1039 1085 0.036732 TTGCAGTGAGCTGGTTAGGG 59.963 55.000 0.00 0.00 45.94 3.53
1070 1116 2.138542 AGGGCTGATGGGTGTATGATT 58.861 47.619 0.00 0.00 0.00 2.57
1095 1141 1.081556 TGCCTGTGTATGTAAGCGCG 61.082 55.000 0.00 0.00 0.00 6.86
1112 1158 1.129251 CATGGCCATATCGATCGTTGC 59.871 52.381 20.30 11.09 0.00 4.17
1478 1525 5.826601 AAAATTGAAAAATTGTGGCCGTT 57.173 30.435 0.00 0.00 0.00 4.44
1512 1563 1.264045 AAAACCATGGCCATTCCCCG 61.264 55.000 17.92 3.95 0.00 5.73
1565 1616 9.841880 GGGAGTAACAAAGAAAGAAATATTGAC 57.158 33.333 0.00 0.00 0.00 3.18
1723 1825 9.976511 ATTGTTAATGAAAGCCTCATATTCATG 57.023 29.630 1.41 0.00 44.43 3.07
1750 1852 7.875041 CGATGAGAGATTACTATGGTTTTGGAT 59.125 37.037 0.00 0.00 0.00 3.41
1751 1853 7.147724 ACGATGAGAGATTACTATGGTTTTGGA 60.148 37.037 0.00 0.00 0.00 3.53
1762 1864 5.482908 ACTTTTGCACGATGAGAGATTACT 58.517 37.500 0.00 0.00 0.00 2.24
1768 1870 2.670414 GGAGACTTTTGCACGATGAGAG 59.330 50.000 0.00 0.00 0.00 3.20
1771 1873 2.542020 TGGAGACTTTTGCACGATGA 57.458 45.000 0.00 0.00 0.00 2.92
1772 1874 2.096496 GGATGGAGACTTTTGCACGATG 59.904 50.000 0.00 0.00 0.00 3.84
1811 1914 9.461312 TCATAGCTATTGTCATGGTTTTAGTTT 57.539 29.630 2.64 0.00 0.00 2.66
1823 1926 4.404394 TCCTCCGTTTCATAGCTATTGTCA 59.596 41.667 2.64 0.00 0.00 3.58
1831 1934 7.441458 AGTTGTATATTTCCTCCGTTTCATAGC 59.559 37.037 0.00 0.00 0.00 2.97
1848 1951 9.706691 CCTCGTTCACCATTTATAGTTGTATAT 57.293 33.333 0.00 0.00 0.00 0.86
1853 1956 6.737254 AACCTCGTTCACCATTTATAGTTG 57.263 37.500 0.00 0.00 0.00 3.16
1854 1957 7.166167 AGAAACCTCGTTCACCATTTATAGTT 58.834 34.615 0.00 0.00 0.00 2.24
1855 1958 6.708285 AGAAACCTCGTTCACCATTTATAGT 58.292 36.000 0.00 0.00 0.00 2.12
1856 1959 7.333423 TGAAGAAACCTCGTTCACCATTTATAG 59.667 37.037 0.00 0.00 0.00 1.31
1857 1960 7.162761 TGAAGAAACCTCGTTCACCATTTATA 58.837 34.615 0.00 0.00 0.00 0.98
1858 1961 6.001460 TGAAGAAACCTCGTTCACCATTTAT 58.999 36.000 0.00 0.00 0.00 1.40
1859 1962 5.369833 TGAAGAAACCTCGTTCACCATTTA 58.630 37.500 0.00 0.00 0.00 1.40
1871 1974 6.555812 ACTTCGGTATTTTGAAGAAACCTC 57.444 37.500 8.79 0.00 43.34 3.85
1888 1991 9.537192 TTCACCATTTATAGTTGTATACTTCGG 57.463 33.333 4.17 0.00 38.33 4.30
1930 2033 9.316730 GGAACGGTTGAATGTATTACTATGTTA 57.683 33.333 0.00 0.00 0.00 2.41
1931 2034 7.825270 TGGAACGGTTGAATGTATTACTATGTT 59.175 33.333 0.00 0.00 0.00 2.71
1934 2037 7.562135 AGTGGAACGGTTGAATGTATTACTAT 58.438 34.615 0.00 0.00 45.86 2.12
1964 2067 8.026396 TCACCATTATCTCTTTGATCATCTCA 57.974 34.615 0.00 0.00 36.65 3.27
1999 2102 5.838531 AACCACACTTCGGTATTTTGAAA 57.161 34.783 0.00 0.00 34.99 2.69
2036 2139 0.389166 CTTGGAGTCAGAGTCGCACC 60.389 60.000 0.00 0.00 0.00 5.01
2039 2142 1.169577 TCTCTTGGAGTCAGAGTCGC 58.830 55.000 7.23 0.00 0.00 5.19
2087 2190 8.089597 TGCAATGAGTTGATACAAATTGATGTT 58.910 29.630 0.00 0.00 37.53 2.71
2103 2206 3.710209 AGCTAGGAAGTGCAATGAGTT 57.290 42.857 0.00 0.00 0.00 3.01
2115 2220 3.643320 CTCACCATGGTCATAGCTAGGAA 59.357 47.826 16.53 0.00 0.00 3.36
2184 2291 5.095691 AGGCATATGTAAAAATCGCTTCG 57.904 39.130 4.29 0.00 0.00 3.79
2325 2432 0.894835 TCTGCGTGATGCCTTCTGTA 59.105 50.000 0.00 0.00 45.60 2.74
2458 4634 2.947852 ACACTCGAATGAAGAAGACGG 58.052 47.619 0.00 0.00 0.00 4.79
2495 4671 2.812011 GCTGGTTCCGTGTAATTTCAGT 59.188 45.455 0.00 0.00 0.00 3.41
2496 4672 2.159707 CGCTGGTTCCGTGTAATTTCAG 60.160 50.000 0.00 0.00 0.00 3.02
2508 4685 3.013921 TGTTTCCATTATCGCTGGTTCC 58.986 45.455 0.00 0.00 35.19 3.62
2517 4694 7.494625 TGTTTCGAGGTATCTGTTTCCATTATC 59.505 37.037 0.00 0.00 0.00 1.75
2532 4709 2.531771 TGATGAGGGTGTTTCGAGGTA 58.468 47.619 0.00 0.00 0.00 3.08
2543 4720 5.191722 TCAAAAGCCTAAGTATGATGAGGGT 59.808 40.000 0.00 0.00 0.00 4.34
2578 4755 3.067106 CTCGTTTGTAGTGGCAAGTGAT 58.933 45.455 0.00 0.00 0.00 3.06
2585 4762 7.569591 GCATTATTAGATCTCGTTTGTAGTGGC 60.570 40.741 0.00 0.00 0.00 5.01
2609 4786 4.997395 GTCCTAACAGATGTTTCTTCAGCA 59.003 41.667 3.14 0.00 39.31 4.41
2682 4859 8.820831 TGCCCTCATAATTTTTCAAAATAAGGA 58.179 29.630 12.68 5.46 37.62 3.36
2691 4868 8.537728 ACTCATAATGCCCTCATAATTTTTCA 57.462 30.769 0.00 0.00 31.46 2.69
2697 4874 7.559335 TGTCTACTCATAATGCCCTCATAAT 57.441 36.000 0.00 0.00 31.46 1.28
2699 4876 7.559335 AATGTCTACTCATAATGCCCTCATA 57.441 36.000 0.00 0.00 31.46 2.15
2700 4877 6.445451 AATGTCTACTCATAATGCCCTCAT 57.555 37.500 0.00 0.00 33.53 2.90
2701 4878 5.894298 AATGTCTACTCATAATGCCCTCA 57.106 39.130 0.00 0.00 0.00 3.86
2702 4879 8.677148 TTTTAATGTCTACTCATAATGCCCTC 57.323 34.615 0.00 0.00 0.00 4.30
2777 4954 2.527100 GAGACACACCCTTCGATAACG 58.473 52.381 0.00 0.00 41.26 3.18
2785 4962 3.906980 CCCTGGAGACACACCCTT 58.093 61.111 0.00 0.00 35.60 3.95


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

AutoCloner maintained by Alex Coulton.