Multiple sequence alignment - TraesCS4D01G330100

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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 TraesCS4D01G330100 chr4D 100.000 2468 0 0 1 2468 488495133 488497600 0 4558
1 TraesCS4D01G330100 chr5A 90.394 1624 69 39 893 2468 670250906 670252490 0 2054
2 TraesCS4D01G330100 chr5A 93.635 597 27 8 175 765 670250145 670250736 0 881
3 TraesCS4D01G330100 chr4B 89.908 1635 82 36 900 2468 625118679 625120296 0 2028
4 TraesCS4D01G330100 chr4B 86.239 763 50 19 133 872 624871108 624871838 0 776


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 TraesCS4D01G330100 chr4D 488495133 488497600 2467 False 4558.0 4558 100.0000 1 2468 1 chr4D.!!$F1 2467
1 TraesCS4D01G330100 chr5A 670250145 670252490 2345 False 1467.5 2054 92.0145 175 2468 2 chr5A.!!$F1 2293
2 TraesCS4D01G330100 chr4B 625118679 625120296 1617 False 2028.0 2028 89.9080 900 2468 1 chr4B.!!$F2 1568
3 TraesCS4D01G330100 chr4B 624871108 624871838 730 False 776.0 776 86.2390 133 872 1 chr4B.!!$F1 739

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
86 87 0.249741 CACGTTCTCCCGGTTGACTT 60.25 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 2027 1.900498 GCAGGGCTTGTCTTGCTGT 60.9 57.895 2.06 0.0 0.0 4.4 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
19 20 2.112475 GATCGATCAGACGTCTGTGG 57.888 55.000 37.21 27.66 44.12 4.17
20 21 1.402259 GATCGATCAGACGTCTGTGGT 59.598 52.381 37.21 26.54 44.12 4.16
21 22 1.244816 TCGATCAGACGTCTGTGGTT 58.755 50.000 37.21 23.50 44.12 3.67
22 23 1.611977 TCGATCAGACGTCTGTGGTTT 59.388 47.619 37.21 21.39 44.12 3.27
23 24 2.035449 TCGATCAGACGTCTGTGGTTTT 59.965 45.455 37.21 19.89 44.12 2.43
24 25 3.253921 TCGATCAGACGTCTGTGGTTTTA 59.746 43.478 37.21 21.49 44.12 1.52
25 26 3.364023 CGATCAGACGTCTGTGGTTTTAC 59.636 47.826 37.21 21.04 44.12 2.01
26 27 2.734670 TCAGACGTCTGTGGTTTTACG 58.265 47.619 37.21 14.50 44.12 3.18
27 28 2.358582 TCAGACGTCTGTGGTTTTACGA 59.641 45.455 37.21 17.03 44.12 3.43
28 29 2.724690 CAGACGTCTGTGGTTTTACGAG 59.275 50.000 32.77 6.84 39.09 4.18
29 30 2.360165 AGACGTCTGTGGTTTTACGAGT 59.640 45.455 19.30 0.00 38.64 4.18
30 31 2.723143 GACGTCTGTGGTTTTACGAGTC 59.277 50.000 8.70 0.00 38.64 3.36
31 32 2.360165 ACGTCTGTGGTTTTACGAGTCT 59.640 45.455 0.00 0.00 38.64 3.24
32 33 2.978489 CGTCTGTGGTTTTACGAGTCTC 59.022 50.000 0.00 0.00 37.53 3.36
33 34 2.978489 GTCTGTGGTTTTACGAGTCTCG 59.022 50.000 20.57 20.57 46.93 4.04
42 43 3.351450 CGAGTCTCGTGGTGTGGA 58.649 61.111 14.27 0.00 34.72 4.02
43 44 1.081376 CGAGTCTCGTGGTGTGGAC 60.081 63.158 14.27 0.00 34.72 4.02
44 45 1.516365 CGAGTCTCGTGGTGTGGACT 61.516 60.000 14.27 0.00 41.05 3.85
45 46 0.674534 GAGTCTCGTGGTGTGGACTT 59.325 55.000 0.00 0.00 38.87 3.01
46 47 0.674534 AGTCTCGTGGTGTGGACTTC 59.325 55.000 0.00 0.00 35.82 3.01
47 48 0.674534 GTCTCGTGGTGTGGACTTCT 59.325 55.000 0.00 0.00 0.00 2.85
48 49 0.673985 TCTCGTGGTGTGGACTTCTG 59.326 55.000 0.00 0.00 0.00 3.02
49 50 0.673985 CTCGTGGTGTGGACTTCTGA 59.326 55.000 0.00 0.00 0.00 3.27
50 51 0.673985 TCGTGGTGTGGACTTCTGAG 59.326 55.000 0.00 0.00 0.00 3.35
51 52 0.389391 CGTGGTGTGGACTTCTGAGT 59.611 55.000 0.00 0.00 39.32 3.41
61 62 1.527311 GACTTCTGAGTCGGTGTTTGC 59.473 52.381 0.00 0.00 42.60 3.68
62 63 0.508641 CTTCTGAGTCGGTGTTTGCG 59.491 55.000 0.00 0.00 0.00 4.85
63 64 1.495584 TTCTGAGTCGGTGTTTGCGC 61.496 55.000 0.00 0.00 0.00 6.09
64 65 3.281751 CTGAGTCGGTGTTTGCGCG 62.282 63.158 0.00 0.00 0.00 6.86
65 66 4.719616 GAGTCGGTGTTTGCGCGC 62.720 66.667 27.26 27.26 0.00 6.86
81 82 4.324991 GCCCACGTTCTCCCGGTT 62.325 66.667 0.00 0.00 0.00 4.44
82 83 2.358247 CCCACGTTCTCCCGGTTG 60.358 66.667 0.00 0.00 0.00 3.77
83 84 2.738480 CCACGTTCTCCCGGTTGA 59.262 61.111 0.00 0.00 0.00 3.18
84 85 1.666872 CCACGTTCTCCCGGTTGAC 60.667 63.158 0.00 0.00 0.00 3.18
85 86 1.366366 CACGTTCTCCCGGTTGACT 59.634 57.895 0.00 0.00 0.00 3.41
86 87 0.249741 CACGTTCTCCCGGTTGACTT 60.250 55.000 0.00 0.00 0.00 3.01
87 88 0.466963 ACGTTCTCCCGGTTGACTTT 59.533 50.000 0.00 0.00 0.00 2.66
88 89 1.688197 ACGTTCTCCCGGTTGACTTTA 59.312 47.619 0.00 0.00 0.00 1.85
89 90 2.102925 ACGTTCTCCCGGTTGACTTTAA 59.897 45.455 0.00 0.00 0.00 1.52
90 91 2.477754 CGTTCTCCCGGTTGACTTTAAC 59.522 50.000 0.00 0.00 0.00 2.01
91 92 2.810274 GTTCTCCCGGTTGACTTTAACC 59.190 50.000 0.00 0.00 45.28 2.85
101 102 5.488645 GTTGACTTTAACCAAAGACCGAA 57.511 39.130 4.23 0.00 43.32 4.30
102 103 5.268544 GTTGACTTTAACCAAAGACCGAAC 58.731 41.667 4.23 0.00 43.32 3.95
103 104 4.515361 TGACTTTAACCAAAGACCGAACA 58.485 39.130 4.23 0.00 43.32 3.18
104 105 4.573201 TGACTTTAACCAAAGACCGAACAG 59.427 41.667 4.23 0.00 43.32 3.16
105 106 4.773013 ACTTTAACCAAAGACCGAACAGA 58.227 39.130 4.23 0.00 43.32 3.41
106 107 5.187687 ACTTTAACCAAAGACCGAACAGAA 58.812 37.500 4.23 0.00 43.32 3.02
107 108 5.296035 ACTTTAACCAAAGACCGAACAGAAG 59.704 40.000 4.23 0.00 43.32 2.85
108 109 1.594331 ACCAAAGACCGAACAGAAGC 58.406 50.000 0.00 0.00 0.00 3.86
109 110 1.141053 ACCAAAGACCGAACAGAAGCT 59.859 47.619 0.00 0.00 0.00 3.74
110 111 2.222027 CCAAAGACCGAACAGAAGCTT 58.778 47.619 0.00 0.00 0.00 3.74
111 112 2.224314 CCAAAGACCGAACAGAAGCTTC 59.776 50.000 19.11 19.11 0.00 3.86
112 113 3.134458 CAAAGACCGAACAGAAGCTTCT 58.866 45.455 23.49 23.49 38.25 2.85
113 114 2.734276 AGACCGAACAGAAGCTTCTC 57.266 50.000 26.18 14.39 34.74 2.87
114 115 1.964223 AGACCGAACAGAAGCTTCTCA 59.036 47.619 26.18 0.00 34.74 3.27
115 116 2.365617 AGACCGAACAGAAGCTTCTCAA 59.634 45.455 26.18 0.00 34.74 3.02
116 117 3.131396 GACCGAACAGAAGCTTCTCAAA 58.869 45.455 26.18 0.00 34.74 2.69
117 118 2.872858 ACCGAACAGAAGCTTCTCAAAC 59.127 45.455 26.18 15.59 34.74 2.93
118 119 2.096713 CCGAACAGAAGCTTCTCAAACG 60.097 50.000 26.18 24.18 34.74 3.60
119 120 2.660362 CGAACAGAAGCTTCTCAAACGC 60.660 50.000 26.18 11.19 34.74 4.84
120 121 1.230324 ACAGAAGCTTCTCAAACGCC 58.770 50.000 26.18 0.00 34.74 5.68
121 122 0.519077 CAGAAGCTTCTCAAACGCCC 59.481 55.000 26.18 0.00 34.74 6.13
122 123 0.951040 AGAAGCTTCTCAAACGCCCG 60.951 55.000 23.49 0.00 29.94 6.13
123 124 1.912371 GAAGCTTCTCAAACGCCCGG 61.912 60.000 19.44 0.00 0.00 5.73
124 125 2.668550 GCTTCTCAAACGCCCGGT 60.669 61.111 0.00 0.00 0.00 5.28
125 126 2.677979 GCTTCTCAAACGCCCGGTC 61.678 63.158 0.00 0.00 0.00 4.79
126 127 2.356553 TTCTCAAACGCCCGGTCG 60.357 61.111 1.92 1.92 0.00 4.79
127 128 3.154584 TTCTCAAACGCCCGGTCGT 62.155 57.895 3.85 3.85 45.58 4.34
128 129 3.110178 CTCAAACGCCCGGTCGTC 61.110 66.667 12.48 0.00 42.46 4.20
129 130 4.668118 TCAAACGCCCGGTCGTCC 62.668 66.667 12.48 0.00 42.46 4.79
130 131 4.675029 CAAACGCCCGGTCGTCCT 62.675 66.667 12.48 0.00 42.46 3.85
131 132 3.932483 AAACGCCCGGTCGTCCTT 61.932 61.111 12.48 0.00 42.46 3.36
170 175 4.783155 TCCTTCACCCCCAAGGAA 57.217 55.556 0.00 0.00 45.40 3.36
203 218 1.418334 CAAATCCCCCACACCAAACA 58.582 50.000 0.00 0.00 0.00 2.83
204 219 1.765314 CAAATCCCCCACACCAAACAA 59.235 47.619 0.00 0.00 0.00 2.83
205 220 1.419381 AATCCCCCACACCAAACAAC 58.581 50.000 0.00 0.00 0.00 3.32
215 230 2.834549 ACACCAAACAACCATCCAAACA 59.165 40.909 0.00 0.00 0.00 2.83
228 243 1.652012 CAAACAACACGGCCACGAT 59.348 52.632 2.24 0.00 44.60 3.73
319 334 2.525629 TGAACCTGTCGGCCTCCA 60.526 61.111 0.00 0.00 0.00 3.86
531 546 4.527157 GTCTACGACGACGGGCCG 62.527 72.222 27.06 27.06 44.46 6.13
680 701 1.507141 CCGCCGAGTTGTGAAGCTTT 61.507 55.000 0.00 0.00 0.00 3.51
692 713 1.745087 TGAAGCTTTGATTCATCCCGC 59.255 47.619 0.00 0.00 31.86 6.13
738 759 3.126001 TGTGTTTCCTTCCTGCTGTAG 57.874 47.619 0.00 0.00 0.00 2.74
767 791 8.959058 CAGCACTACTACTAGATGTAAAAATCG 58.041 37.037 0.00 0.00 0.00 3.34
772 796 9.798994 CTACTACTAGATGTAAAAATCGTTGGT 57.201 33.333 0.00 0.00 0.00 3.67
776 800 4.472286 AGATGTAAAAATCGTTGGTTGCG 58.528 39.130 0.00 0.00 0.00 4.85
781 805 4.707210 AAAAATCGTTGGTTGCGAAATG 57.293 36.364 0.00 0.00 41.84 2.32
788 812 3.443976 GTTGGTTGCGAAATGAACTTGT 58.556 40.909 0.00 0.00 0.00 3.16
792 816 3.059461 GGTTGCGAAATGAACTTGTACGA 60.059 43.478 0.00 0.00 0.00 3.43
796 820 3.427528 GCGAAATGAACTTGTACGAGTGA 59.572 43.478 16.68 7.07 0.00 3.41
807 831 5.756347 ACTTGTACGAGTGAAATTTGCTGTA 59.244 36.000 15.25 0.00 0.00 2.74
819 844 8.057742 GTGAAATTTGCTGTAAATTGTGTGAAG 58.942 33.333 15.53 0.00 45.74 3.02
830 855 2.347697 TGTGTGAAGATCGAAGACGG 57.652 50.000 0.00 0.00 42.51 4.79
843 868 2.673893 CGAAGACGGTGTGATCCATCAA 60.674 50.000 0.00 0.00 35.74 2.57
846 871 0.984230 ACGGTGTGATCCATCAACCT 59.016 50.000 14.05 4.62 38.75 3.50
853 878 4.023193 GTGTGATCCATCAACCTTCGTTTT 60.023 41.667 0.00 0.00 38.75 2.43
855 880 5.765677 TGTGATCCATCAACCTTCGTTTTAA 59.234 36.000 0.00 0.00 38.75 1.52
856 881 6.084277 GTGATCCATCAACCTTCGTTTTAAC 58.916 40.000 0.00 0.00 38.75 2.01
857 882 6.001460 TGATCCATCAACCTTCGTTTTAACT 58.999 36.000 0.00 0.00 33.08 2.24
858 883 5.682943 TCCATCAACCTTCGTTTTAACTG 57.317 39.130 0.00 0.00 0.00 3.16
859 884 5.127491 TCCATCAACCTTCGTTTTAACTGT 58.873 37.500 0.00 0.00 0.00 3.55
860 885 5.591067 TCCATCAACCTTCGTTTTAACTGTT 59.409 36.000 0.00 0.00 0.00 3.16
861 886 5.912955 CCATCAACCTTCGTTTTAACTGTTC 59.087 40.000 0.00 0.00 0.00 3.18
862 887 6.238648 CCATCAACCTTCGTTTTAACTGTTCT 60.239 38.462 0.00 0.00 0.00 3.01
863 888 6.114221 TCAACCTTCGTTTTAACTGTTCTG 57.886 37.500 0.00 0.00 0.00 3.02
864 889 5.875910 TCAACCTTCGTTTTAACTGTTCTGA 59.124 36.000 0.00 0.00 0.00 3.27
865 890 6.372103 TCAACCTTCGTTTTAACTGTTCTGAA 59.628 34.615 0.00 0.00 0.00 3.02
866 891 6.937436 ACCTTCGTTTTAACTGTTCTGAAT 57.063 33.333 0.00 0.00 0.00 2.57
892 917 7.926674 TCTGATCTGATTTGCTGTGAAAATA 57.073 32.000 0.00 0.00 0.00 1.40
894 919 6.558009 TGATCTGATTTGCTGTGAAAATAGC 58.442 36.000 0.00 0.00 40.29 2.97
970 1098 3.162858 AACCCAACCGACGACCCA 61.163 61.111 0.00 0.00 0.00 4.51
975 1103 4.303993 AACCGACGACCCAACCCG 62.304 66.667 0.00 0.00 0.00 5.28
977 1105 4.729856 CCGACGACCCAACCCGAC 62.730 72.222 0.00 0.00 0.00 4.79
978 1106 4.729856 CGACGACCCAACCCGACC 62.730 72.222 0.00 0.00 0.00 4.79
979 1107 4.383861 GACGACCCAACCCGACCC 62.384 72.222 0.00 0.00 0.00 4.46
982 1110 4.383861 GACCCAACCCGACCCGAC 62.384 72.222 0.00 0.00 0.00 4.79
986 1114 2.681064 CAACCCGACCCGACCCTA 60.681 66.667 0.00 0.00 0.00 3.53
987 1115 2.363406 AACCCGACCCGACCCTAG 60.363 66.667 0.00 0.00 0.00 3.02
997 1125 3.450115 GACCCTAGCGACGCACCT 61.450 66.667 23.70 3.65 0.00 4.00
999 1127 3.449227 CCCTAGCGACGCACCTCA 61.449 66.667 23.70 0.26 0.00 3.86
1006 1134 2.359850 GACGCACCTCAATGGCCA 60.360 61.111 8.56 8.56 40.22 5.36
1554 1703 6.705381 TGCTGCTGCTTATGTTTGTTAATTTT 59.295 30.769 17.00 0.00 40.48 1.82
1555 1704 7.226325 TGCTGCTGCTTATGTTTGTTAATTTTT 59.774 29.630 17.00 0.00 40.48 1.94
1617 1796 2.494870 GCATTTCTTCCTTGTCATGCCT 59.505 45.455 0.00 0.00 32.53 4.75
1666 1845 7.706179 GTGACAGGAAATCAACTTTCATTTTGA 59.294 33.333 0.71 0.00 44.29 2.69
1794 1980 5.646606 TGTCAGTTACAAAAGTCAAAAGGC 58.353 37.500 0.00 0.00 34.29 4.35
1795 1981 4.733405 GTCAGTTACAAAAGTCAAAAGGCG 59.267 41.667 0.00 0.00 0.00 5.52
1797 1983 2.785713 TACAAAAGTCAAAAGGCGGC 57.214 45.000 0.00 0.00 0.00 6.53
1798 1984 0.820871 ACAAAAGTCAAAAGGCGGCA 59.179 45.000 13.08 0.00 0.00 5.69
1799 1985 1.208259 CAAAAGTCAAAAGGCGGCAC 58.792 50.000 13.08 0.00 0.00 5.01
1800 1986 0.820871 AAAAGTCAAAAGGCGGCACA 59.179 45.000 13.08 0.00 0.00 4.57
1801 1987 0.385390 AAAGTCAAAAGGCGGCACAG 59.615 50.000 13.08 0.00 0.00 3.66
1802 1988 2.050077 GTCAAAAGGCGGCACAGC 60.050 61.111 13.08 0.00 0.00 4.40
1825 2011 3.146066 GGCACTTGTTCCAATCAGTGTA 58.854 45.455 0.00 0.00 0.00 2.90
1834 2020 6.280643 TGTTCCAATCAGTGTATAATCTCCG 58.719 40.000 0.00 0.00 0.00 4.63
1841 2027 4.081365 TCAGTGTATAATCTCCGTTGCCAA 60.081 41.667 0.00 0.00 0.00 4.52
1859 2045 1.458639 AACAGCAAGACAAGCCCTGC 61.459 55.000 0.00 0.00 0.00 4.85
1862 2048 1.303155 GCAAGACAAGCCCTGCTCT 60.303 57.895 0.00 0.00 38.25 4.09
1867 2053 0.107945 GACAAGCCCTGCTCTTCGAT 60.108 55.000 0.00 0.00 38.25 3.59
1891 2083 0.459899 ATGCGGCGAGTACATGAGAA 59.540 50.000 12.98 0.00 0.00 2.87
1892 2084 0.457853 TGCGGCGAGTACATGAGAAC 60.458 55.000 12.98 0.00 0.00 3.01
1911 2103 6.070021 TGAGAACTGATCCCTCATGTATGTTT 60.070 38.462 0.00 0.00 32.57 2.83
1940 2132 0.620030 TGTACTGGTGCTGGCATCAT 59.380 50.000 9.04 3.12 36.37 2.45
1941 2133 1.303309 GTACTGGTGCTGGCATCATC 58.697 55.000 9.04 0.00 36.37 2.92
1942 2134 0.911053 TACTGGTGCTGGCATCATCA 59.089 50.000 9.04 4.01 36.37 3.07
1943 2135 0.393944 ACTGGTGCTGGCATCATCAG 60.394 55.000 25.57 25.57 45.58 2.90
1958 2151 6.750963 GGCATCATCAGAATTCAGAAGTTTTC 59.249 38.462 8.44 0.00 0.00 2.29
1976 2169 5.594317 AGTTTTCTTTAGAGCAAAGGAGCAA 59.406 36.000 0.00 0.00 43.37 3.91
2001 2194 3.498774 ATTCAGAAGCTGTGTGAGGTT 57.501 42.857 0.00 0.00 45.32 3.50
2011 2204 3.058639 GCTGTGTGAGGTTTGAATCTGTC 60.059 47.826 0.00 0.00 0.00 3.51
2017 2211 6.372659 GTGTGAGGTTTGAATCTGTCACATAT 59.627 38.462 6.28 0.00 44.36 1.78
2026 2220 5.069516 TGAATCTGTCACATATAGCTGCAGA 59.930 40.000 20.43 0.00 36.21 4.26
2055 2249 1.204146 AACCATATCTGCGTCCTGGT 58.796 50.000 0.00 0.00 41.89 4.00
2146 2341 0.958876 CACAGCAGCAAGAGCCATCA 60.959 55.000 0.00 0.00 43.56 3.07
2266 2461 4.458708 GCACGTTCTTCTTGACAAGAATC 58.541 43.478 26.66 18.92 45.75 2.52
2281 2476 2.610532 GAATCGGGGTTCTGGCCTCC 62.611 65.000 3.32 0.99 0.00 4.30
2290 2485 2.832129 GGTTCTGGCCTCCGATGATATA 59.168 50.000 3.32 0.00 0.00 0.86
2314 2509 0.886490 CAAAGACGACAGCCAGCCTT 60.886 55.000 0.00 0.00 0.00 4.35
2389 2584 3.753272 CAGATTGATTCGTTGGGTCAACT 59.247 43.478 8.80 0.00 41.62 3.16
2428 2623 4.191544 CTGACAGAAAGTTGGACACTTCA 58.808 43.478 0.00 0.00 45.77 3.02
2453 2648 0.035725 CATCTTGCTCTGAGGGTGCA 60.036 55.000 6.83 0.00 41.80 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.402259 ACCACAGACGTCTGATCGATC 59.598 52.381 43.55 18.72 46.59 3.69
1 2 1.464734 ACCACAGACGTCTGATCGAT 58.535 50.000 43.55 23.71 46.59 3.59
2 3 1.244816 AACCACAGACGTCTGATCGA 58.755 50.000 43.55 0.00 46.59 3.59
4 5 3.364023 CGTAAAACCACAGACGTCTGATC 59.636 47.826 43.55 23.56 46.59 2.92
6 7 2.358582 TCGTAAAACCACAGACGTCTGA 59.641 45.455 43.55 22.31 46.59 3.27
10 11 2.360165 AGACTCGTAAAACCACAGACGT 59.640 45.455 0.00 0.00 36.69 4.34
11 12 2.978489 GAGACTCGTAAAACCACAGACG 59.022 50.000 0.00 0.00 36.66 4.18
12 13 2.978489 CGAGACTCGTAAAACCACAGAC 59.022 50.000 16.83 0.00 34.72 3.51
13 14 3.278367 CGAGACTCGTAAAACCACAGA 57.722 47.619 16.83 0.00 34.72 3.41
25 26 1.081376 GTCCACACCACGAGACTCG 60.081 63.158 22.97 22.97 46.93 4.18
26 27 0.674534 AAGTCCACACCACGAGACTC 59.325 55.000 0.00 0.00 38.61 3.36
27 28 0.674534 GAAGTCCACACCACGAGACT 59.325 55.000 0.00 0.00 41.25 3.24
28 29 0.674534 AGAAGTCCACACCACGAGAC 59.325 55.000 0.00 0.00 0.00 3.36
29 30 0.673985 CAGAAGTCCACACCACGAGA 59.326 55.000 0.00 0.00 0.00 4.04
30 31 0.673985 TCAGAAGTCCACACCACGAG 59.326 55.000 0.00 0.00 0.00 4.18
31 32 0.673985 CTCAGAAGTCCACACCACGA 59.326 55.000 0.00 0.00 0.00 4.35
32 33 0.389391 ACTCAGAAGTCCACACCACG 59.611 55.000 0.00 0.00 0.00 4.94
33 34 2.156343 GACTCAGAAGTCCACACCAC 57.844 55.000 0.00 0.00 45.26 4.16
42 43 1.583054 GCAAACACCGACTCAGAAGT 58.417 50.000 0.00 0.00 38.88 3.01
43 44 0.508641 CGCAAACACCGACTCAGAAG 59.491 55.000 0.00 0.00 0.00 2.85
44 45 1.495584 GCGCAAACACCGACTCAGAA 61.496 55.000 0.30 0.00 0.00 3.02
45 46 1.954146 GCGCAAACACCGACTCAGA 60.954 57.895 0.30 0.00 0.00 3.27
46 47 2.551270 GCGCAAACACCGACTCAG 59.449 61.111 0.30 0.00 0.00 3.35
47 48 3.334751 CGCGCAAACACCGACTCA 61.335 61.111 8.75 0.00 0.00 3.41
48 49 4.719616 GCGCGCAAACACCGACTC 62.720 66.667 29.10 0.00 0.00 3.36
64 65 4.324991 AACCGGGAGAACGTGGGC 62.325 66.667 6.32 0.00 0.00 5.36
65 66 2.358247 CAACCGGGAGAACGTGGG 60.358 66.667 6.32 0.00 0.00 4.61
66 67 1.666872 GTCAACCGGGAGAACGTGG 60.667 63.158 6.32 0.00 0.00 4.94
67 68 0.249741 AAGTCAACCGGGAGAACGTG 60.250 55.000 6.32 0.00 0.00 4.49
68 69 0.466963 AAAGTCAACCGGGAGAACGT 59.533 50.000 6.32 0.00 0.00 3.99
69 70 2.443887 TAAAGTCAACCGGGAGAACG 57.556 50.000 6.32 0.00 0.00 3.95
70 71 2.810274 GGTTAAAGTCAACCGGGAGAAC 59.190 50.000 6.32 0.00 38.74 3.01
71 72 3.130280 GGTTAAAGTCAACCGGGAGAA 57.870 47.619 6.32 0.00 38.74 2.87
72 73 2.845363 GGTTAAAGTCAACCGGGAGA 57.155 50.000 6.32 0.00 38.74 3.71
78 79 3.878699 TCGGTCTTTGGTTAAAGTCAACC 59.121 43.478 0.00 0.00 46.90 3.77
79 80 5.163733 TGTTCGGTCTTTGGTTAAAGTCAAC 60.164 40.000 0.00 0.00 43.04 3.18
80 81 4.942483 TGTTCGGTCTTTGGTTAAAGTCAA 59.058 37.500 0.00 0.00 43.04 3.18
81 82 4.515361 TGTTCGGTCTTTGGTTAAAGTCA 58.485 39.130 0.00 0.00 43.04 3.41
82 83 4.812626 TCTGTTCGGTCTTTGGTTAAAGTC 59.187 41.667 0.00 0.00 43.04 3.01
83 84 4.773013 TCTGTTCGGTCTTTGGTTAAAGT 58.227 39.130 0.00 0.00 43.04 2.66
84 85 5.744666 TTCTGTTCGGTCTTTGGTTAAAG 57.255 39.130 0.00 0.00 43.72 1.85
85 86 4.035909 GCTTCTGTTCGGTCTTTGGTTAAA 59.964 41.667 0.00 0.00 0.00 1.52
86 87 3.562557 GCTTCTGTTCGGTCTTTGGTTAA 59.437 43.478 0.00 0.00 0.00 2.01
87 88 3.135994 GCTTCTGTTCGGTCTTTGGTTA 58.864 45.455 0.00 0.00 0.00 2.85
88 89 1.947456 GCTTCTGTTCGGTCTTTGGTT 59.053 47.619 0.00 0.00 0.00 3.67
89 90 1.141053 AGCTTCTGTTCGGTCTTTGGT 59.859 47.619 0.00 0.00 0.00 3.67
90 91 1.884235 AGCTTCTGTTCGGTCTTTGG 58.116 50.000 0.00 0.00 0.00 3.28
91 92 3.134458 AGAAGCTTCTGTTCGGTCTTTG 58.866 45.455 27.96 0.00 35.89 2.77
92 93 3.181465 TGAGAAGCTTCTGTTCGGTCTTT 60.181 43.478 33.07 4.83 37.73 2.52
93 94 2.365617 TGAGAAGCTTCTGTTCGGTCTT 59.634 45.455 33.07 5.41 37.73 3.01
94 95 1.964223 TGAGAAGCTTCTGTTCGGTCT 59.036 47.619 33.07 6.04 37.73 3.85
95 96 2.440539 TGAGAAGCTTCTGTTCGGTC 57.559 50.000 33.07 16.96 37.73 4.79
96 97 2.872858 GTTTGAGAAGCTTCTGTTCGGT 59.127 45.455 33.07 7.84 37.73 4.69
97 98 2.096713 CGTTTGAGAAGCTTCTGTTCGG 60.097 50.000 33.07 15.08 37.73 4.30
98 99 2.660362 GCGTTTGAGAAGCTTCTGTTCG 60.660 50.000 33.07 26.93 37.73 3.95
99 100 2.349912 GGCGTTTGAGAAGCTTCTGTTC 60.350 50.000 33.07 19.10 37.73 3.18
100 101 1.604278 GGCGTTTGAGAAGCTTCTGTT 59.396 47.619 33.07 10.30 37.73 3.16
101 102 1.230324 GGCGTTTGAGAAGCTTCTGT 58.770 50.000 33.07 11.13 37.73 3.41
102 103 0.519077 GGGCGTTTGAGAAGCTTCTG 59.481 55.000 33.07 18.72 37.73 3.02
103 104 0.951040 CGGGCGTTTGAGAAGCTTCT 60.951 55.000 28.83 28.83 41.00 2.85
104 105 1.497722 CGGGCGTTTGAGAAGCTTC 59.502 57.895 19.11 19.11 0.00 3.86
105 106 1.966451 CCGGGCGTTTGAGAAGCTT 60.966 57.895 0.00 0.00 0.00 3.74
106 107 2.358737 CCGGGCGTTTGAGAAGCT 60.359 61.111 0.00 0.00 0.00 3.74
107 108 2.668550 ACCGGGCGTTTGAGAAGC 60.669 61.111 6.32 0.00 0.00 3.86
108 109 2.380410 CGACCGGGCGTTTGAGAAG 61.380 63.158 25.18 0.00 0.00 2.85
109 110 2.356553 CGACCGGGCGTTTGAGAA 60.357 61.111 25.18 0.00 0.00 2.87
110 111 3.562779 GACGACCGGGCGTTTGAGA 62.563 63.158 39.68 0.00 45.72 3.27
111 112 3.110178 GACGACCGGGCGTTTGAG 61.110 66.667 39.68 6.39 45.72 3.02
112 113 4.668118 GGACGACCGGGCGTTTGA 62.668 66.667 39.68 0.00 45.72 2.69
113 114 4.675029 AGGACGACCGGGCGTTTG 62.675 66.667 39.68 7.82 45.72 2.93
114 115 3.871248 GAAGGACGACCGGGCGTTT 62.871 63.158 39.68 29.06 45.72 3.60
115 116 4.368543 GAAGGACGACCGGGCGTT 62.369 66.667 39.68 23.26 45.72 4.84
117 118 3.869473 TTTGAAGGACGACCGGGCG 62.869 63.158 32.33 32.33 41.83 6.13
118 119 2.031465 TTTGAAGGACGACCGGGC 59.969 61.111 6.32 0.00 41.83 6.13
119 120 2.033194 GCTTTGAAGGACGACCGGG 61.033 63.158 6.32 0.00 41.83 5.73
120 121 1.004918 AGCTTTGAAGGACGACCGG 60.005 57.895 0.00 0.00 41.83 5.28
121 122 1.901650 GCAGCTTTGAAGGACGACCG 61.902 60.000 0.00 0.00 41.83 4.79
122 123 1.578206 GGCAGCTTTGAAGGACGACC 61.578 60.000 0.00 0.00 0.00 4.79
123 124 1.869690 GGCAGCTTTGAAGGACGAC 59.130 57.895 0.00 0.00 0.00 4.34
124 125 1.667830 CGGCAGCTTTGAAGGACGA 60.668 57.895 0.00 0.00 0.00 4.20
125 126 1.961277 ACGGCAGCTTTGAAGGACG 60.961 57.895 0.00 0.00 0.00 4.79
126 127 1.576421 CACGGCAGCTTTGAAGGAC 59.424 57.895 0.00 0.00 0.00 3.85
127 128 2.260869 GCACGGCAGCTTTGAAGGA 61.261 57.895 0.00 0.00 0.00 3.36
128 129 2.256461 GCACGGCAGCTTTGAAGG 59.744 61.111 0.00 0.00 0.00 3.46
129 130 2.256461 GGCACGGCAGCTTTGAAG 59.744 61.111 0.00 0.00 34.17 3.02
150 151 2.221299 CCTTGGGGGTGAAGGACGA 61.221 63.158 0.00 0.00 42.44 4.20
170 175 0.037734 GATTTGGAGGGGTGGTTCGT 59.962 55.000 0.00 0.00 0.00 3.85
203 218 0.387565 GCCGTGTTGTTTGGATGGTT 59.612 50.000 0.00 0.00 0.00 3.67
204 219 1.460273 GGCCGTGTTGTTTGGATGGT 61.460 55.000 0.00 0.00 0.00 3.55
205 220 1.288752 GGCCGTGTTGTTTGGATGG 59.711 57.895 0.00 0.00 0.00 3.51
215 230 2.431942 GTCGATCGTGGCCGTGTT 60.432 61.111 15.94 0.00 35.01 3.32
426 441 1.517475 GAGCGTCTCGAAGAAGGGC 60.517 63.158 0.00 0.00 34.09 5.19
665 686 4.472691 TGAATCAAAGCTTCACAACTCG 57.527 40.909 0.00 0.00 0.00 4.18
672 693 1.745087 GCGGGATGAATCAAAGCTTCA 59.255 47.619 0.00 0.00 37.06 3.02
680 701 3.163832 ATCGCCGCGGGATGAATCA 62.164 57.895 29.38 0.00 33.98 2.57
707 728 2.423577 AGGAAACACATCTGTAACCGC 58.576 47.619 0.00 0.00 33.48 5.68
709 730 4.455877 CAGGAAGGAAACACATCTGTAACC 59.544 45.833 0.00 0.00 0.00 2.85
767 791 3.443976 ACAAGTTCATTTCGCAACCAAC 58.556 40.909 0.00 0.00 0.00 3.77
772 796 3.805422 ACTCGTACAAGTTCATTTCGCAA 59.195 39.130 0.00 0.00 0.00 4.85
776 800 8.682016 CAAATTTCACTCGTACAAGTTCATTTC 58.318 33.333 0.00 0.00 0.00 2.17
781 805 5.621228 CAGCAAATTTCACTCGTACAAGTTC 59.379 40.000 0.00 0.00 0.00 3.01
788 812 7.589587 CACAATTTACAGCAAATTTCACTCGTA 59.410 33.333 0.00 0.00 42.93 3.43
792 816 7.264221 TCACACAATTTACAGCAAATTTCACT 58.736 30.769 0.00 0.00 42.93 3.41
796 820 8.891671 ATCTTCACACAATTTACAGCAAATTT 57.108 26.923 0.00 0.00 42.93 1.82
807 831 4.152402 CCGTCTTCGATCTTCACACAATTT 59.848 41.667 0.00 0.00 39.71 1.82
819 844 1.134367 TGGATCACACCGTCTTCGATC 59.866 52.381 0.00 0.00 39.71 3.69
830 855 2.699954 ACGAAGGTTGATGGATCACAC 58.300 47.619 0.00 0.00 36.36 3.82
843 868 6.937436 ATTCAGAACAGTTAAAACGAAGGT 57.063 33.333 0.00 0.00 0.00 3.50
846 871 8.670135 TCAGAAATTCAGAACAGTTAAAACGAA 58.330 29.630 0.00 0.00 0.00 3.85
853 878 9.730705 AATCAGATCAGAAATTCAGAACAGTTA 57.269 29.630 0.00 0.00 0.00 2.24
855 880 8.512956 CAAATCAGATCAGAAATTCAGAACAGT 58.487 33.333 0.00 0.00 0.00 3.55
856 881 7.485277 GCAAATCAGATCAGAAATTCAGAACAG 59.515 37.037 0.00 0.00 0.00 3.16
857 882 7.176165 AGCAAATCAGATCAGAAATTCAGAACA 59.824 33.333 0.00 0.00 0.00 3.18
858 883 7.485277 CAGCAAATCAGATCAGAAATTCAGAAC 59.515 37.037 0.00 0.00 0.00 3.01
859 884 7.176165 ACAGCAAATCAGATCAGAAATTCAGAA 59.824 33.333 0.00 0.00 0.00 3.02
860 885 6.657966 ACAGCAAATCAGATCAGAAATTCAGA 59.342 34.615 0.00 0.00 0.00 3.27
861 886 6.747739 CACAGCAAATCAGATCAGAAATTCAG 59.252 38.462 0.00 0.00 0.00 3.02
862 887 6.431852 TCACAGCAAATCAGATCAGAAATTCA 59.568 34.615 0.00 0.00 0.00 2.57
863 888 6.849502 TCACAGCAAATCAGATCAGAAATTC 58.150 36.000 0.00 0.00 0.00 2.17
864 889 6.829229 TCACAGCAAATCAGATCAGAAATT 57.171 33.333 0.00 0.00 0.00 1.82
865 890 6.829229 TTCACAGCAAATCAGATCAGAAAT 57.171 33.333 0.00 0.00 0.00 2.17
866 891 6.638096 TTTCACAGCAAATCAGATCAGAAA 57.362 33.333 0.00 0.00 0.00 2.52
892 917 4.974721 CCTGGTTGGGTTGCGGCT 62.975 66.667 0.00 0.00 0.00 5.52
894 919 2.983592 GACCTGGTTGGGTTGCGG 60.984 66.667 0.00 0.00 40.06 5.69
970 1098 2.363406 CTAGGGTCGGGTCGGGTT 60.363 66.667 0.00 0.00 0.00 4.11
975 1103 3.885521 CGTCGCTAGGGTCGGGTC 61.886 72.222 16.54 0.00 0.00 4.46
978 1106 4.849329 GTGCGTCGCTAGGGTCGG 62.849 72.222 23.24 8.77 0.00 4.79
979 1107 4.849329 GGTGCGTCGCTAGGGTCG 62.849 72.222 19.50 19.23 0.00 4.79
980 1108 3.412879 GAGGTGCGTCGCTAGGGTC 62.413 68.421 19.50 4.49 0.00 4.46
981 1109 3.450115 GAGGTGCGTCGCTAGGGT 61.450 66.667 19.50 0.00 0.00 4.34
982 1110 2.298158 ATTGAGGTGCGTCGCTAGGG 62.298 60.000 19.50 0.00 0.00 3.53
983 1111 1.141881 ATTGAGGTGCGTCGCTAGG 59.858 57.895 19.50 0.00 0.00 3.02
984 1112 1.148157 CCATTGAGGTGCGTCGCTAG 61.148 60.000 19.50 0.00 0.00 3.42
985 1113 1.153647 CCATTGAGGTGCGTCGCTA 60.154 57.895 19.50 1.76 0.00 4.26
986 1114 2.434884 CCATTGAGGTGCGTCGCT 60.435 61.111 19.50 0.00 0.00 4.93
987 1115 4.166011 GCCATTGAGGTGCGTCGC 62.166 66.667 11.10 11.10 40.61 5.19
1617 1796 7.882791 TCACATTTCTTGGCAAAGATAGAACTA 59.117 33.333 3.86 0.00 42.04 2.24
1666 1845 9.358406 ACACATACATCATACATGGATGAAATT 57.642 29.630 24.30 13.43 41.69 1.82
1671 1853 7.500720 AACACACATACATCATACATGGATG 57.499 36.000 12.09 12.09 44.04 3.51
1797 1983 2.639286 GAACAAGTGCCGGCTGTG 59.361 61.111 29.70 23.38 0.00 3.66
1798 1984 2.594592 GGAACAAGTGCCGGCTGT 60.595 61.111 29.70 21.17 0.00 4.40
1799 1985 2.594303 TGGAACAAGTGCCGGCTG 60.594 61.111 29.70 20.43 31.92 4.85
1811 1997 6.281405 ACGGAGATTATACACTGATTGGAAC 58.719 40.000 0.00 0.00 0.00 3.62
1825 2011 2.017049 GCTGTTGGCAACGGAGATTAT 58.983 47.619 36.61 0.00 40.26 1.28
1841 2027 1.900498 GCAGGGCTTGTCTTGCTGT 60.900 57.895 2.06 0.00 0.00 4.40
1877 2063 3.376540 GGATCAGTTCTCATGTACTCGC 58.623 50.000 0.00 0.00 0.00 5.03
1891 2083 4.723789 AGGAAACATACATGAGGGATCAGT 59.276 41.667 0.00 0.00 0.00 3.41
1892 2084 5.061853 CAGGAAACATACATGAGGGATCAG 58.938 45.833 0.00 0.00 0.00 2.90
1911 2103 2.906389 AGCACCAGTACAATCTTCAGGA 59.094 45.455 0.00 0.00 0.00 3.86
1940 2132 8.778358 GCTCTAAAGAAAACTTCTGAATTCTGA 58.222 33.333 10.68 10.68 40.59 3.27
1941 2133 8.562892 TGCTCTAAAGAAAACTTCTGAATTCTG 58.437 33.333 7.05 6.50 40.59 3.02
1942 2134 8.682936 TGCTCTAAAGAAAACTTCTGAATTCT 57.317 30.769 7.05 0.13 40.59 2.40
1943 2135 9.736023 TTTGCTCTAAAGAAAACTTCTGAATTC 57.264 29.630 0.00 0.00 40.59 2.17
1958 2151 4.067896 TCTGTTGCTCCTTTGCTCTAAAG 58.932 43.478 0.00 0.00 44.35 1.85
1976 2169 4.063689 CTCACACAGCTTCTGAATTCTGT 58.936 43.478 15.35 15.35 40.08 3.41
2001 2194 5.673514 TGCAGCTATATGTGACAGATTCAA 58.326 37.500 0.00 0.00 35.39 2.69
2011 2204 5.699458 TCATGACAATCTGCAGCTATATGTG 59.301 40.000 9.47 3.57 0.00 3.21
2017 2211 3.691118 GGTTTCATGACAATCTGCAGCTA 59.309 43.478 9.47 0.00 0.00 3.32
2026 2220 4.883585 ACGCAGATATGGTTTCATGACAAT 59.116 37.500 0.00 0.00 34.96 2.71
2055 2249 1.971481 TCAGCAAAAGCAAGAGAGCA 58.029 45.000 0.00 0.00 36.85 4.26
2146 2341 9.553064 GACACAAATATCTATCACCAATTCTCT 57.447 33.333 0.00 0.00 0.00 3.10
2281 2476 6.206498 TGTCGTCTTTGGTCTTATATCATCG 58.794 40.000 0.00 0.00 0.00 3.84
2290 2485 0.468226 TGGCTGTCGTCTTTGGTCTT 59.532 50.000 0.00 0.00 0.00 3.01
2314 2509 4.466370 ACAGAGCCTAACAAGCATAGTGTA 59.534 41.667 0.00 0.00 0.00 2.90
2389 2584 7.257790 TCTGTCAGGAAAGATTGGAGAAATA 57.742 36.000 0.00 0.00 0.00 1.40
2428 2623 3.458857 ACCCTCAGAGCAAGATGATTCAT 59.541 43.478 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.