Multiple sequence alignment - TraesCS1A01G393200

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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 TraesCS1A01G393200 chr1A 100.000 2267 0 0 1 2267 559840717 559842983 0.000000e+00 4187.0
1 TraesCS1A01G393200 chr1A 97.414 696 18 0 1572 2267 513458192 513457497 0.000000e+00 1186.0
2 TraesCS1A01G393200 chr1A 77.225 1146 158 59 460 1553 559799886 559800980 1.950000e-160 575.0
3 TraesCS1A01G393200 chr1A 82.306 373 39 13 1189 1553 559830350 559830703 4.730000e-77 298.0
4 TraesCS1A01G393200 chr1B 88.423 1382 97 21 224 1553 645307291 645308661 0.000000e+00 1607.0
5 TraesCS1A01G393200 chr1B 87.692 130 8 3 117 239 645307139 645307267 6.530000e-31 145.0
6 TraesCS1A01G393200 chr1B 76.678 283 51 11 999 1275 645319903 645320176 2.350000e-30 143.0
7 TraesCS1A01G393200 chr1B 88.158 76 7 1 185 260 645269537 645269464 3.100000e-14 89.8
8 TraesCS1A01G393200 chr5A 97.414 696 18 0 1572 2267 3688615 3687920 0.000000e+00 1186.0
9 TraesCS1A01G393200 chr5A 97.274 697 19 0 1571 2267 682518066 682517370 0.000000e+00 1182.0
10 TraesCS1A01G393200 chr5A 96.624 711 21 2 1560 2267 648344880 648345590 0.000000e+00 1177.0
11 TraesCS1A01G393200 chr3A 97.414 696 18 0 1572 2267 26846774 26846079 0.000000e+00 1186.0
12 TraesCS1A01G393200 chr3A 97.159 704 17 3 1566 2267 691461751 691462453 0.000000e+00 1186.0
13 TraesCS1A01G393200 chr2A 97.278 698 19 0 1570 2267 71718769 71719466 0.000000e+00 1184.0
14 TraesCS1A01G393200 chr6A 97.274 697 19 0 1571 2267 573122900 573122204 0.000000e+00 1182.0
15 TraesCS1A01G393200 chr6A 97.009 702 21 0 1566 2267 8680928 8681629 0.000000e+00 1181.0
16 TraesCS1A01G393200 chr1D 87.382 634 32 16 376 979 467490551 467491166 0.000000e+00 684.0
17 TraesCS1A01G393200 chr1D 85.935 647 48 16 930 1567 467491167 467491779 0.000000e+00 651.0
18 TraesCS1A01G393200 chr1D 80.721 638 81 12 927 1553 467467284 467467890 2.050000e-125 459.0
19 TraesCS1A01G393200 chr1D 78.489 781 99 38 808 1553 467487334 467488080 4.440000e-122 448.0
20 TraesCS1A01G393200 chr1D 77.622 286 46 12 999 1275 467494683 467494959 8.380000e-35 158.0
21 TraesCS1A01G393200 chr1D 83.516 182 13 3 224 388 467490353 467490534 1.080000e-33 154.0
22 TraesCS1A01G393200 chr1D 84.071 113 7 3 809 921 467467149 467467250 5.150000e-17 99.0
23 TraesCS1A01G393200 chr5D 95.556 45 2 0 269 313 334903427 334903383 3.120000e-09 73.1


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 TraesCS1A01G393200 chr1A 559840717 559842983 2266 False 4187 4187 100.0000 1 2267 1 chr1A.!!$F3 2266
1 TraesCS1A01G393200 chr1A 513457497 513458192 695 True 1186 1186 97.4140 1572 2267 1 chr1A.!!$R1 695
2 TraesCS1A01G393200 chr1A 559799886 559800980 1094 False 575 575 77.2250 460 1553 1 chr1A.!!$F1 1093
3 TraesCS1A01G393200 chr1B 645307139 645308661 1522 False 876 1607 88.0575 117 1553 2 chr1B.!!$F2 1436
4 TraesCS1A01G393200 chr5A 3687920 3688615 695 True 1186 1186 97.4140 1572 2267 1 chr5A.!!$R1 695
5 TraesCS1A01G393200 chr5A 682517370 682518066 696 True 1182 1182 97.2740 1571 2267 1 chr5A.!!$R2 696
6 TraesCS1A01G393200 chr5A 648344880 648345590 710 False 1177 1177 96.6240 1560 2267 1 chr5A.!!$F1 707
7 TraesCS1A01G393200 chr3A 26846079 26846774 695 True 1186 1186 97.4140 1572 2267 1 chr3A.!!$R1 695
8 TraesCS1A01G393200 chr3A 691461751 691462453 702 False 1186 1186 97.1590 1566 2267 1 chr3A.!!$F1 701
9 TraesCS1A01G393200 chr2A 71718769 71719466 697 False 1184 1184 97.2780 1570 2267 1 chr2A.!!$F1 697
10 TraesCS1A01G393200 chr6A 573122204 573122900 696 True 1182 1182 97.2740 1571 2267 1 chr6A.!!$R1 696
11 TraesCS1A01G393200 chr6A 8680928 8681629 701 False 1181 1181 97.0090 1566 2267 1 chr6A.!!$F1 701
12 TraesCS1A01G393200 chr1D 467487334 467494959 7625 False 419 684 82.5888 224 1567 5 chr1D.!!$F2 1343
13 TraesCS1A01G393200 chr1D 467467149 467467890 741 False 279 459 82.3960 809 1553 2 chr1D.!!$F1 744

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
227 274 0.098905 CACGATCGACTGGACGTCAT 59.901 55.0 24.34 1.35 42.98 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 4446 1.000736 GCCGCGTCGCTTACTATACC 61.001 60.0 16.36 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
26 27 9.116067 GGTGCTACAATTACCATATAAAAGACA 57.884 33.333 0.00 0.00 34.61 3.41
32 33 9.959721 ACAATTACCATATAAAAGACAGACTGT 57.040 29.630 8.12 8.12 0.00 3.55
35 36 6.743575 ACCATATAAAAGACAGACTGTTGC 57.256 37.500 10.01 0.00 0.00 4.17
36 37 6.237901 ACCATATAAAAGACAGACTGTTGCA 58.762 36.000 10.01 0.00 0.00 4.08
37 38 6.886459 ACCATATAAAAGACAGACTGTTGCAT 59.114 34.615 10.01 2.52 0.00 3.96
38 39 8.046708 ACCATATAAAAGACAGACTGTTGCATA 58.953 33.333 10.01 4.54 0.00 3.14
40 41 4.732285 AAAAGACAGACTGTTGCATACG 57.268 40.909 10.01 0.00 0.00 3.06
41 42 2.370281 AGACAGACTGTTGCATACGG 57.630 50.000 10.01 0.00 39.17 4.02
43 44 1.726791 GACAGACTGTTGCATACGGTG 59.273 52.381 10.01 7.28 46.41 4.94
45 46 2.143122 CAGACTGTTGCATACGGTGTT 58.857 47.619 15.32 4.40 46.41 3.32
46 47 2.548057 CAGACTGTTGCATACGGTGTTT 59.452 45.455 15.32 2.54 46.41 2.83
47 48 3.003275 CAGACTGTTGCATACGGTGTTTT 59.997 43.478 15.32 0.69 46.41 2.43
48 49 3.630312 AGACTGTTGCATACGGTGTTTTT 59.370 39.130 15.32 0.00 46.41 1.94
49 50 4.817464 AGACTGTTGCATACGGTGTTTTTA 59.183 37.500 15.32 0.00 46.41 1.52
51 52 5.275494 ACTGTTGCATACGGTGTTTTTAAC 58.725 37.500 11.22 0.00 44.72 2.01
54 55 3.488363 TGCATACGGTGTTTTTAACCCT 58.512 40.909 0.00 0.00 33.88 4.34
55 56 3.253677 TGCATACGGTGTTTTTAACCCTG 59.746 43.478 0.00 0.00 33.88 4.45
56 57 3.253921 GCATACGGTGTTTTTAACCCTGT 59.746 43.478 0.00 0.00 33.88 4.00
57 58 4.614306 GCATACGGTGTTTTTAACCCTGTC 60.614 45.833 0.00 0.00 33.88 3.51
58 59 3.286329 ACGGTGTTTTTAACCCTGTCT 57.714 42.857 0.00 0.00 33.88 3.41
59 60 4.420522 ACGGTGTTTTTAACCCTGTCTA 57.579 40.909 0.00 0.00 33.88 2.59
61 62 6.112927 ACGGTGTTTTTAACCCTGTCTATA 57.887 37.500 0.00 0.00 33.88 1.31
62 63 6.168389 ACGGTGTTTTTAACCCTGTCTATAG 58.832 40.000 0.00 0.00 33.88 1.31
63 64 5.583457 CGGTGTTTTTAACCCTGTCTATAGG 59.417 44.000 0.00 0.00 37.59 2.57
64 65 6.479006 GGTGTTTTTAACCCTGTCTATAGGT 58.521 40.000 0.00 0.00 36.02 3.08
67 68 7.118825 GTGTTTTTAACCCTGTCTATAGGTGAC 59.881 40.741 0.00 0.00 36.02 3.67
68 69 5.587388 TTTAACCCTGTCTATAGGTGACG 57.413 43.478 0.00 0.00 37.26 4.35
70 71 2.376109 ACCCTGTCTATAGGTGACGTG 58.624 52.381 0.00 0.00 37.26 4.49
72 73 2.651455 CCTGTCTATAGGTGACGTGGA 58.349 52.381 0.00 0.00 37.26 4.02
73 74 3.223435 CCTGTCTATAGGTGACGTGGAT 58.777 50.000 0.00 0.00 37.26 3.41
74 75 3.004839 CCTGTCTATAGGTGACGTGGATG 59.995 52.174 0.00 0.00 37.26 3.51
75 76 2.956333 TGTCTATAGGTGACGTGGATGG 59.044 50.000 0.00 0.00 37.26 3.51
76 77 2.957006 GTCTATAGGTGACGTGGATGGT 59.043 50.000 0.00 0.00 0.00 3.55
77 78 3.383825 GTCTATAGGTGACGTGGATGGTT 59.616 47.826 0.00 0.00 0.00 3.67
78 79 4.581824 GTCTATAGGTGACGTGGATGGTTA 59.418 45.833 0.00 0.00 0.00 2.85
79 80 3.814005 ATAGGTGACGTGGATGGTTAC 57.186 47.619 0.00 0.00 0.00 2.50
80 81 1.640917 AGGTGACGTGGATGGTTACT 58.359 50.000 0.00 0.00 0.00 2.24
82 83 1.549170 GGTGACGTGGATGGTTACTCT 59.451 52.381 0.00 0.00 0.00 3.24
83 84 2.756760 GGTGACGTGGATGGTTACTCTA 59.243 50.000 0.00 0.00 0.00 2.43
84 85 3.181489 GGTGACGTGGATGGTTACTCTAG 60.181 52.174 0.00 0.00 0.00 2.43
85 86 3.693085 GTGACGTGGATGGTTACTCTAGA 59.307 47.826 0.00 0.00 0.00 2.43
87 88 5.530171 GTGACGTGGATGGTTACTCTAGATA 59.470 44.000 0.00 0.00 0.00 1.98
89 90 5.071370 ACGTGGATGGTTACTCTAGATAGG 58.929 45.833 0.00 0.00 0.00 2.57
90 91 4.082679 CGTGGATGGTTACTCTAGATAGGC 60.083 50.000 0.00 0.00 0.00 3.93
91 92 4.079970 TGGATGGTTACTCTAGATAGGCG 58.920 47.826 0.00 0.00 0.00 5.52
92 93 3.444388 GGATGGTTACTCTAGATAGGCGG 59.556 52.174 0.00 0.00 0.00 6.13
93 94 2.872732 TGGTTACTCTAGATAGGCGGG 58.127 52.381 0.00 0.00 0.00 6.13
94 95 2.176364 TGGTTACTCTAGATAGGCGGGT 59.824 50.000 0.00 0.00 0.00 5.28
95 96 2.557490 GGTTACTCTAGATAGGCGGGTG 59.443 54.545 0.00 0.00 0.00 4.61
96 97 3.220940 GTTACTCTAGATAGGCGGGTGT 58.779 50.000 0.00 0.00 0.00 4.16
98 99 1.495574 ACTCTAGATAGGCGGGTGTCT 59.504 52.381 0.00 0.00 0.00 3.41
99 100 2.091775 ACTCTAGATAGGCGGGTGTCTT 60.092 50.000 0.00 0.00 0.00 3.01
100 101 3.137913 ACTCTAGATAGGCGGGTGTCTTA 59.862 47.826 0.00 0.00 0.00 2.10
105 106 4.284178 AGATAGGCGGGTGTCTTAACTAA 58.716 43.478 0.00 0.00 0.00 2.24
106 107 4.900054 AGATAGGCGGGTGTCTTAACTAAT 59.100 41.667 0.00 0.00 0.00 1.73
107 108 3.261981 AGGCGGGTGTCTTAACTAATG 57.738 47.619 0.00 0.00 0.00 1.90
108 109 2.570302 AGGCGGGTGTCTTAACTAATGT 59.430 45.455 0.00 0.00 0.00 2.71
109 110 3.770933 AGGCGGGTGTCTTAACTAATGTA 59.229 43.478 0.00 0.00 0.00 2.29
111 112 4.497300 GCGGGTGTCTTAACTAATGTACA 58.503 43.478 0.00 0.00 0.00 2.90
112 113 5.114081 GCGGGTGTCTTAACTAATGTACAT 58.886 41.667 1.41 1.41 0.00 2.29
113 114 5.006358 GCGGGTGTCTTAACTAATGTACATG 59.994 44.000 9.63 0.00 0.00 3.21
115 116 5.296035 GGGTGTCTTAACTAATGTACATGCC 59.704 44.000 9.63 0.00 0.00 4.40
138 145 5.643777 CCCTGAGTAAATTGATGTCTCGTTT 59.356 40.000 0.00 0.00 0.00 3.60
161 168 2.781923 TGCAGTTTATTCAGCTGAGCA 58.218 42.857 17.43 17.53 32.39 4.26
162 169 3.148412 TGCAGTTTATTCAGCTGAGCAA 58.852 40.909 18.81 13.37 32.39 3.91
227 274 0.098905 CACGATCGACTGGACGTCAT 59.901 55.000 24.34 1.35 42.98 3.06
267 3064 3.742369 TGCACGCACTCACATGATATATG 59.258 43.478 0.00 0.00 0.00 1.78
354 3169 0.319211 TGCACGGACGAATTCGAACT 60.319 50.000 33.05 12.16 43.02 3.01
362 3177 2.991190 GACGAATTCGAACTGCTGGTTA 59.009 45.455 33.05 0.00 43.02 2.85
374 3189 6.238897 CGAACTGCTGGTTATAGAGATCTCTT 60.239 42.308 29.54 18.71 38.45 2.85
403 3248 3.791973 ATTGGCAAGTCAAACGACAAA 57.208 38.095 5.96 0.00 35.75 2.83
413 3258 1.088306 AAACGACAAAGGACGCACAA 58.912 45.000 0.00 0.00 35.61 3.33
416 3261 1.263217 ACGACAAAGGACGCACAAATC 59.737 47.619 0.00 0.00 35.61 2.17
424 3269 4.459331 CGCACAAATCCACCGCCG 62.459 66.667 0.00 0.00 0.00 6.46
476 3329 2.517959 CACATGGCTTTCCCTCAAAGA 58.482 47.619 0.00 0.00 44.02 2.52
523 3376 1.661480 CACACACCATGCAACCCAG 59.339 57.895 0.00 0.00 0.00 4.45
543 3403 4.994852 CCAGACCAAACATATACCATACCG 59.005 45.833 0.00 0.00 0.00 4.02
551 3411 4.820897 ACATATACCATACCGCATCAGTG 58.179 43.478 0.00 0.00 0.00 3.66
552 3412 4.283467 ACATATACCATACCGCATCAGTGT 59.717 41.667 0.00 0.00 0.00 3.55
568 3428 5.836821 TCAGTGTACTAGCTACTCCATTG 57.163 43.478 0.00 0.00 0.00 2.82
569 3429 5.506708 TCAGTGTACTAGCTACTCCATTGA 58.493 41.667 0.00 0.00 0.00 2.57
643 3525 1.270550 CATTTTGAAGTTCAGCGGCCT 59.729 47.619 5.56 0.00 0.00 5.19
671 3557 2.504032 CGGCCGGCCTTCTTATCA 59.496 61.111 41.01 0.00 0.00 2.15
750 3638 0.109689 GACAACTCAGAGACGACGGG 60.110 60.000 3.79 0.00 0.00 5.28
755 3643 2.432628 CAGAGACGACGGGGCAAC 60.433 66.667 0.00 0.00 0.00 4.17
974 3950 4.642437 CAGTTGCTGTAGAGTGGAGATAGA 59.358 45.833 0.00 0.00 0.00 1.98
1021 3997 1.298859 GGCCAAGGCTTGTGTACTCG 61.299 60.000 24.57 9.45 41.60 4.18
1202 4178 4.351938 CCAGGCGGACGACAACGA 62.352 66.667 0.00 0.00 42.66 3.85
1390 4377 5.119898 GCTGTCTTGAATCTTGATATAGCGG 59.880 44.000 0.00 0.00 0.00 5.52
1393 4380 7.445121 TGTCTTGAATCTTGATATAGCGGAAT 58.555 34.615 0.00 0.00 0.00 3.01
1448 4457 7.864379 ACATGTTACATACACGGTATAGTAAGC 59.136 37.037 0.00 0.00 40.19 3.09
1454 4463 0.041839 ACGGTATAGTAAGCGACGCG 60.042 55.000 15.18 3.53 42.76 6.01
1478 4487 4.376340 ACAAGCTTGTGGAAAAGAACAG 57.624 40.909 30.66 0.00 40.49 3.16
1489 4500 4.398044 TGGAAAAGAACAGAAGTTGTGACC 59.602 41.667 7.07 0.00 40.74 4.02
1490 4503 4.202020 GGAAAAGAACAGAAGTTGTGACCC 60.202 45.833 7.07 0.00 40.74 4.46
1503 4516 4.401202 AGTTGTGACCCGTTTTCTCAAAAT 59.599 37.500 0.00 0.00 30.50 1.82
1504 4517 4.300189 TGTGACCCGTTTTCTCAAAATG 57.700 40.909 0.00 0.00 37.18 2.32
1505 4518 3.948473 TGTGACCCGTTTTCTCAAAATGA 59.052 39.130 3.03 0.00 39.23 2.57
1506 4519 4.399618 TGTGACCCGTTTTCTCAAAATGAA 59.600 37.500 3.03 0.00 39.23 2.57
1507 4520 5.068460 TGTGACCCGTTTTCTCAAAATGAAT 59.932 36.000 3.03 0.00 39.23 2.57
1509 4522 7.142680 GTGACCCGTTTTCTCAAAATGAATAA 58.857 34.615 3.03 0.00 39.23 1.40
1553 4573 0.940991 CCCTTTGCGCAAGTTTCAGC 60.941 55.000 23.68 0.00 41.68 4.26
1558 4578 1.304254 TGCGCAAGTTTCAGCTGTTA 58.696 45.000 8.16 0.00 41.68 2.41
1567 4587 6.035975 GCAAGTTTCAGCTGTTATTGTTGTTT 59.964 34.615 14.67 0.00 0.00 2.83
1568 4588 7.221838 GCAAGTTTCAGCTGTTATTGTTGTTTA 59.778 33.333 14.67 0.00 0.00 2.01
1676 4990 2.203422 CCCGGTTTGTGAGCCCAA 60.203 61.111 0.00 0.00 0.00 4.12
1836 5974 1.478972 AGGCTCCCCTTTAGTCCCA 59.521 57.895 0.00 0.00 38.74 4.37
1898 7390 2.433145 CCTCGCGCAAGAGCAGAA 60.433 61.111 8.75 0.00 42.27 3.02
1948 7472 0.538287 GAGAGGGCTTTGTGGTGCTT 60.538 55.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.893727 GCAACAGTCTGTCTTTTATATGGTAAT 58.106 33.333 5.82 0.00 0.00 1.89
10 11 7.880713 TGCAACAGTCTGTCTTTTATATGGTAA 59.119 33.333 5.82 0.00 0.00 2.85
12 13 6.237901 TGCAACAGTCTGTCTTTTATATGGT 58.762 36.000 5.82 0.00 0.00 3.55
13 14 6.741992 TGCAACAGTCTGTCTTTTATATGG 57.258 37.500 5.82 0.00 0.00 2.74
14 15 8.058328 CGTATGCAACAGTCTGTCTTTTATATG 58.942 37.037 5.82 0.00 0.00 1.78
15 16 7.224753 CCGTATGCAACAGTCTGTCTTTTATAT 59.775 37.037 5.82 0.00 0.00 0.86
16 17 6.533723 CCGTATGCAACAGTCTGTCTTTTATA 59.466 38.462 5.82 0.00 0.00 0.98
17 18 5.351465 CCGTATGCAACAGTCTGTCTTTTAT 59.649 40.000 5.82 0.44 0.00 1.40
18 19 4.688879 CCGTATGCAACAGTCTGTCTTTTA 59.311 41.667 5.82 0.00 0.00 1.52
19 20 3.498397 CCGTATGCAACAGTCTGTCTTTT 59.502 43.478 5.82 0.00 0.00 2.27
20 21 3.067106 CCGTATGCAACAGTCTGTCTTT 58.933 45.455 5.82 0.00 0.00 2.52
21 22 2.037251 ACCGTATGCAACAGTCTGTCTT 59.963 45.455 5.82 0.00 0.00 3.01
22 23 1.618837 ACCGTATGCAACAGTCTGTCT 59.381 47.619 5.82 0.00 0.00 3.41
23 24 1.726791 CACCGTATGCAACAGTCTGTC 59.273 52.381 5.82 0.00 0.00 3.51
24 25 1.070134 ACACCGTATGCAACAGTCTGT 59.930 47.619 0.00 0.00 0.00 3.41
26 27 2.543777 AACACCGTATGCAACAGTCT 57.456 45.000 0.00 0.00 0.00 3.24
27 28 3.619233 AAAACACCGTATGCAACAGTC 57.381 42.857 0.00 0.00 0.00 3.51
28 29 5.275494 GTTAAAAACACCGTATGCAACAGT 58.725 37.500 0.00 0.00 0.00 3.55
29 30 4.677832 GGTTAAAAACACCGTATGCAACAG 59.322 41.667 0.00 0.00 0.00 3.16
30 31 4.499357 GGGTTAAAAACACCGTATGCAACA 60.499 41.667 0.00 0.00 34.79 3.33
32 33 3.890147 AGGGTTAAAAACACCGTATGCAA 59.110 39.130 0.00 0.00 34.56 4.08
33 34 3.253677 CAGGGTTAAAAACACCGTATGCA 59.746 43.478 0.00 0.00 34.56 3.96
34 35 3.253921 ACAGGGTTAAAAACACCGTATGC 59.746 43.478 0.00 0.00 34.56 3.14
35 36 4.758165 AGACAGGGTTAAAAACACCGTATG 59.242 41.667 0.00 0.00 34.56 2.39
36 37 4.976864 AGACAGGGTTAAAAACACCGTAT 58.023 39.130 0.00 0.00 34.56 3.06
37 38 4.420522 AGACAGGGTTAAAAACACCGTA 57.579 40.909 0.00 0.00 34.56 4.02
38 39 3.286329 AGACAGGGTTAAAAACACCGT 57.714 42.857 0.00 0.00 34.56 4.83
40 41 6.373495 CACCTATAGACAGGGTTAAAAACACC 59.627 42.308 0.00 0.00 40.29 4.16
41 42 7.118825 GTCACCTATAGACAGGGTTAAAAACAC 59.881 40.741 0.00 0.00 40.29 3.32
43 44 6.312180 CGTCACCTATAGACAGGGTTAAAAAC 59.688 42.308 0.00 0.00 40.29 2.43
45 46 5.481473 ACGTCACCTATAGACAGGGTTAAAA 59.519 40.000 0.00 0.00 40.29 1.52
46 47 5.018809 ACGTCACCTATAGACAGGGTTAAA 58.981 41.667 0.00 0.00 40.29 1.52
47 48 4.400251 CACGTCACCTATAGACAGGGTTAA 59.600 45.833 0.00 0.00 40.29 2.01
48 49 3.949754 CACGTCACCTATAGACAGGGTTA 59.050 47.826 0.00 0.00 40.29 2.85
49 50 2.758979 CACGTCACCTATAGACAGGGTT 59.241 50.000 0.00 0.00 40.29 4.11
51 52 1.681793 CCACGTCACCTATAGACAGGG 59.318 57.143 0.00 0.00 40.29 4.45
54 55 2.956333 CCATCCACGTCACCTATAGACA 59.044 50.000 0.00 0.00 35.77 3.41
55 56 2.957006 ACCATCCACGTCACCTATAGAC 59.043 50.000 0.00 0.00 0.00 2.59
56 57 3.308035 ACCATCCACGTCACCTATAGA 57.692 47.619 0.00 0.00 0.00 1.98
57 58 4.583489 AGTAACCATCCACGTCACCTATAG 59.417 45.833 0.00 0.00 0.00 1.31
58 59 4.539726 AGTAACCATCCACGTCACCTATA 58.460 43.478 0.00 0.00 0.00 1.31
59 60 3.371965 AGTAACCATCCACGTCACCTAT 58.628 45.455 0.00 0.00 0.00 2.57
61 62 1.549170 GAGTAACCATCCACGTCACCT 59.451 52.381 0.00 0.00 0.00 4.00
62 63 1.549170 AGAGTAACCATCCACGTCACC 59.451 52.381 0.00 0.00 0.00 4.02
63 64 3.693085 TCTAGAGTAACCATCCACGTCAC 59.307 47.826 0.00 0.00 0.00 3.67
64 65 3.959293 TCTAGAGTAACCATCCACGTCA 58.041 45.455 0.00 0.00 0.00 4.35
67 68 4.082679 GCCTATCTAGAGTAACCATCCACG 60.083 50.000 0.00 0.00 0.00 4.94
68 69 4.082679 CGCCTATCTAGAGTAACCATCCAC 60.083 50.000 0.00 0.00 0.00 4.02
70 71 3.444388 CCGCCTATCTAGAGTAACCATCC 59.556 52.174 0.00 0.00 0.00 3.51
72 73 3.181420 ACCCGCCTATCTAGAGTAACCAT 60.181 47.826 0.00 0.00 0.00 3.55
73 74 2.176364 ACCCGCCTATCTAGAGTAACCA 59.824 50.000 0.00 0.00 0.00 3.67
74 75 2.557490 CACCCGCCTATCTAGAGTAACC 59.443 54.545 0.00 0.00 0.00 2.85
75 76 3.220940 ACACCCGCCTATCTAGAGTAAC 58.779 50.000 0.00 0.00 0.00 2.50
76 77 3.137913 AGACACCCGCCTATCTAGAGTAA 59.862 47.826 0.00 0.00 0.00 2.24
77 78 2.709934 AGACACCCGCCTATCTAGAGTA 59.290 50.000 0.00 0.00 0.00 2.59
78 79 1.495574 AGACACCCGCCTATCTAGAGT 59.504 52.381 0.00 0.00 0.00 3.24
79 80 2.279935 AGACACCCGCCTATCTAGAG 57.720 55.000 0.00 0.00 0.00 2.43
80 81 2.750141 AAGACACCCGCCTATCTAGA 57.250 50.000 0.00 0.00 0.00 2.43
82 83 3.907221 AGTTAAGACACCCGCCTATCTA 58.093 45.455 0.00 0.00 0.00 1.98
83 84 2.748388 AGTTAAGACACCCGCCTATCT 58.252 47.619 0.00 0.00 0.00 1.98
84 85 4.660789 TTAGTTAAGACACCCGCCTATC 57.339 45.455 0.00 0.00 0.00 2.08
85 86 4.407945 ACATTAGTTAAGACACCCGCCTAT 59.592 41.667 0.00 0.00 0.00 2.57
87 88 2.570302 ACATTAGTTAAGACACCCGCCT 59.430 45.455 0.00 0.00 0.00 5.52
89 90 4.497300 TGTACATTAGTTAAGACACCCGC 58.503 43.478 0.00 0.00 0.00 6.13
90 91 5.006358 GCATGTACATTAGTTAAGACACCCG 59.994 44.000 5.37 0.00 0.00 5.28
91 92 5.296035 GGCATGTACATTAGTTAAGACACCC 59.704 44.000 5.37 0.00 0.00 4.61
92 93 5.296035 GGGCATGTACATTAGTTAAGACACC 59.704 44.000 5.37 0.00 0.00 4.16
93 94 6.037172 CAGGGCATGTACATTAGTTAAGACAC 59.963 42.308 5.37 0.00 0.00 3.67
94 95 6.070481 TCAGGGCATGTACATTAGTTAAGACA 60.070 38.462 5.37 0.00 0.00 3.41
95 96 6.346096 TCAGGGCATGTACATTAGTTAAGAC 58.654 40.000 5.37 0.00 0.00 3.01
96 97 6.156256 ACTCAGGGCATGTACATTAGTTAAGA 59.844 38.462 5.37 0.00 0.00 2.10
98 99 6.308015 ACTCAGGGCATGTACATTAGTTAA 57.692 37.500 5.37 0.00 0.00 2.01
99 100 5.950544 ACTCAGGGCATGTACATTAGTTA 57.049 39.130 5.37 0.00 0.00 2.24
100 101 4.844349 ACTCAGGGCATGTACATTAGTT 57.156 40.909 5.37 0.00 0.00 2.24
105 106 5.754782 TCAATTTACTCAGGGCATGTACAT 58.245 37.500 1.41 1.41 0.00 2.29
106 107 5.172687 TCAATTTACTCAGGGCATGTACA 57.827 39.130 0.00 0.00 0.00 2.90
107 108 5.590259 ACATCAATTTACTCAGGGCATGTAC 59.410 40.000 0.00 0.00 0.00 2.90
108 109 5.754782 ACATCAATTTACTCAGGGCATGTA 58.245 37.500 0.00 0.00 0.00 2.29
109 110 4.603131 ACATCAATTTACTCAGGGCATGT 58.397 39.130 0.00 0.00 0.00 3.21
111 112 5.121380 AGACATCAATTTACTCAGGGCAT 57.879 39.130 0.00 0.00 0.00 4.40
112 113 4.517285 GAGACATCAATTTACTCAGGGCA 58.483 43.478 0.00 0.00 0.00 5.36
113 114 3.557595 CGAGACATCAATTTACTCAGGGC 59.442 47.826 0.00 0.00 0.00 5.19
115 116 6.368791 TGAAACGAGACATCAATTTACTCAGG 59.631 38.462 0.00 0.00 0.00 3.86
138 145 3.376234 GCTCAGCTGAATAAACTGCATGA 59.624 43.478 18.85 0.00 37.23 3.07
227 274 4.512571 CGTGCATCATTGGATATGTTCTCA 59.487 41.667 0.00 0.00 30.87 3.27
326 3140 0.871722 TCGTCCGTGCATTTCCAAAG 59.128 50.000 0.00 0.00 0.00 2.77
354 3169 9.290988 CTAGTTAAGAGATCTCTATAACCAGCA 57.709 37.037 29.86 20.72 39.39 4.41
374 3189 6.930164 TCGTTTGACTTGCCAATTACTAGTTA 59.070 34.615 0.00 0.00 0.00 2.24
403 3248 1.671054 CGGTGGATTTGTGCGTCCT 60.671 57.895 0.00 0.00 35.49 3.85
413 3258 1.303091 GCAACTAACGGCGGTGGATT 61.303 55.000 17.29 2.58 0.00 3.01
416 3261 2.666862 TGCAACTAACGGCGGTGG 60.667 61.111 8.19 7.45 0.00 4.61
424 3269 1.918609 GACCTCGATCGTGCAACTAAC 59.081 52.381 15.94 0.00 31.75 2.34
469 3322 2.690778 CGCCGGCCCTTTCTTTGAG 61.691 63.158 23.46 0.00 0.00 3.02
523 3376 4.382291 TGCGGTATGGTATATGTTTGGTC 58.618 43.478 0.00 0.00 0.00 4.02
543 3403 3.632604 TGGAGTAGCTAGTACACTGATGC 59.367 47.826 9.60 0.00 33.55 3.91
551 3411 3.550436 GCCGTCAATGGAGTAGCTAGTAC 60.550 52.174 3.58 3.58 0.00 2.73
552 3412 2.621998 GCCGTCAATGGAGTAGCTAGTA 59.378 50.000 0.00 0.00 0.00 1.82
568 3428 1.789464 GAAGATCATGTCGATGCCGTC 59.211 52.381 0.00 0.00 33.17 4.79
569 3429 1.136891 TGAAGATCATGTCGATGCCGT 59.863 47.619 0.00 0.00 33.17 5.68
628 3510 2.669569 GCAGGCCGCTGAACTTCA 60.670 61.111 11.61 0.00 37.77 3.02
659 3541 1.369625 CGGTGTGTGATAAGAAGGCC 58.630 55.000 0.00 0.00 0.00 5.19
687 3573 2.708861 ACACTTCCACTACCACCAATCA 59.291 45.455 0.00 0.00 0.00 2.57
750 3638 3.292159 GGTTGGTGGTCGGTTGCC 61.292 66.667 0.00 0.00 0.00 4.52
755 3643 1.447838 CAGATCGGTTGGTGGTCGG 60.448 63.158 0.00 0.00 0.00 4.79
974 3950 2.393768 CGCGTGCAAGCTCAGGAAT 61.394 57.895 22.14 0.00 34.40 3.01
1014 3990 2.913578 ACCACACCGCCGAGTACA 60.914 61.111 0.00 0.00 0.00 2.90
1021 3997 3.055719 CACCATCACCACACCGCC 61.056 66.667 0.00 0.00 0.00 6.13
1051 4027 2.159310 CGAAAGAGGACGAGAGAAGCAT 60.159 50.000 0.00 0.00 0.00 3.79
1143 4119 3.568430 CCTTTCTTACAAAACGCCCTCTT 59.432 43.478 0.00 0.00 0.00 2.85
1275 4251 1.339097 ACTACACGCAAGGAGACCTT 58.661 50.000 0.00 0.00 45.88 3.50
1291 4267 2.758423 TGATGCCGCTGTAGAGAAACTA 59.242 45.455 0.00 0.00 0.00 2.24
1304 4281 2.009774 GTCCCATGTATATGATGCCGC 58.990 52.381 0.25 0.00 36.36 6.53
1437 4446 1.000736 GCCGCGTCGCTTACTATACC 61.001 60.000 16.36 0.00 0.00 2.73
1448 4457 4.724697 CAAGCTTGTGCCGCGTCG 62.725 66.667 18.65 0.00 40.80 5.12
1462 4471 5.801947 CACAACTTCTGTTCTTTTCCACAAG 59.198 40.000 0.00 0.00 35.47 3.16
1475 4484 2.413310 AAACGGGTCACAACTTCTGT 57.587 45.000 0.00 0.00 39.56 3.41
1478 4487 2.940410 TGAGAAAACGGGTCACAACTTC 59.060 45.455 0.00 0.00 0.00 3.01
1509 4522 4.518211 TGGCAAAATGCGGATGAAATTTTT 59.482 33.333 0.00 0.00 46.21 1.94
1567 4587 6.869206 AGCCCTGTTTTCTACTAGTGAATA 57.131 37.500 5.39 0.45 0.00 1.75
1568 4588 5.763876 AGCCCTGTTTTCTACTAGTGAAT 57.236 39.130 5.39 0.00 0.00 2.57
1836 5974 1.003355 CCGGTTGGTGACATGAGCT 60.003 57.895 0.00 0.00 42.32 4.09
1921 7413 3.254035 AAAGCCCTCTCCCCCTCGA 62.254 63.158 0.00 0.00 0.00 4.04
1948 7472 2.466846 TGTGCATAGGAGGTGAGCTAA 58.533 47.619 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.