Multiple sequence alignment - TraesCS7A01G171200

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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 TraesCS7A01G171200 chr7A 100.000 3715 0 0 1 3715 126864055 126867769 0.000000e+00 6861.0
1 TraesCS7A01G171200 chr7A 89.815 108 10 1 1 107 704795007 704795114 1.800000e-28 137.0
2 TraesCS7A01G171200 chr7D 96.225 3152 102 7 581 3715 124298145 124301296 0.000000e+00 5145.0
3 TraesCS7A01G171200 chr7D 96.596 470 15 1 105 574 124296919 124297387 0.000000e+00 778.0
4 TraesCS7A01G171200 chr7D 86.957 115 8 3 1 108 69598757 69598643 5.040000e-24 122.0
5 TraesCS7A01G171200 chr7B 91.146 2496 121 28 181 2599 86138479 86140951 0.000000e+00 3293.0
6 TraesCS7A01G171200 chr7B 95.426 1115 49 2 2601 3715 86141034 86142146 0.000000e+00 1775.0
7 TraesCS7A01G171200 chr4D 78.933 1068 201 16 2612 3658 52468932 52469996 0.000000e+00 704.0
8 TraesCS7A01G171200 chr4D 79.592 490 83 12 953 1436 52467476 52467954 5.950000e-88 335.0
9 TraesCS7A01G171200 chr4B 79.502 1005 187 15 2612 3600 76814862 76815863 0.000000e+00 697.0
10 TraesCS7A01G171200 chr4B 79.010 505 86 14 953 1450 76813401 76813892 9.950000e-86 327.0
11 TraesCS7A01G171200 chr4A 78.611 1080 201 24 2612 3665 544202823 544201748 0.000000e+00 688.0
12 TraesCS7A01G171200 chr4A 87.931 116 7 1 1 109 567704717 567704602 3.010000e-26 130.0
13 TraesCS7A01G171200 chr5A 80.372 484 79 13 951 1430 561553278 561553749 1.640000e-93 353.0
14 TraesCS7A01G171200 chr5A 85.714 119 10 2 1 112 608948383 608948265 6.520000e-23 119.0
15 TraesCS7A01G171200 chr5D 80.591 474 76 13 957 1427 444710615 444711075 5.900000e-93 351.0
16 TraesCS7A01G171200 chr5B 80.169 474 77 14 957 1427 541498431 541498890 4.600000e-89 339.0
17 TraesCS7A01G171200 chr5B 80.000 350 58 8 954 1301 541527220 541527559 7.970000e-62 248.0
18 TraesCS7A01G171200 chr5B 97.143 35 1 0 596 630 595642454 595642420 4.010000e-05 60.2
19 TraesCS7A01G171200 chr3A 91.667 108 2 1 1 101 27756358 27756465 3.870000e-30 143.0
20 TraesCS7A01G171200 chr2A 90.351 114 4 4 1 107 582868976 582869089 3.870000e-30 143.0
21 TraesCS7A01G171200 chr2A 95.122 41 2 0 3342 3382 761176660 761176700 8.610000e-07 65.8
22 TraesCS7A01G171200 chr6A 88.696 115 6 5 1 108 94075649 94075763 2.330000e-27 134.0
23 TraesCS7A01G171200 chr2B 87.603 121 8 1 1 114 500705212 500705092 2.330000e-27 134.0
24 TraesCS7A01G171200 chr1A 88.034 117 7 1 1 110 65567200 65567316 8.370000e-27 132.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G171200 chr7A 126864055 126867769 3714 False 6861.0 6861 100.0000 1 3715 1 chr7A.!!$F1 3714
1 TraesCS7A01G171200 chr7D 124296919 124301296 4377 False 2961.5 5145 96.4105 105 3715 2 chr7D.!!$F1 3610
2 TraesCS7A01G171200 chr7B 86138479 86142146 3667 False 2534.0 3293 93.2860 181 3715 2 chr7B.!!$F1 3534
3 TraesCS7A01G171200 chr4D 52467476 52469996 2520 False 519.5 704 79.2625 953 3658 2 chr4D.!!$F1 2705
4 TraesCS7A01G171200 chr4B 76813401 76815863 2462 False 512.0 697 79.2560 953 3600 2 chr4B.!!$F1 2647
5 TraesCS7A01G171200 chr4A 544201748 544202823 1075 True 688.0 688 78.6110 2612 3665 1 chr4A.!!$R1 1053

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
51 52 0.175531 AATGCAATGCGCCCTAAACC 59.824 50.000 4.18 0.00 41.33 3.27 F
57 58 0.328258 ATGCGCCCTAAACCTTGTCT 59.672 50.000 4.18 0.00 0.00 3.41 F
58 59 0.978151 TGCGCCCTAAACCTTGTCTA 59.022 50.000 4.18 0.00 0.00 2.59 F
109 110 1.254026 CTGTGACGGAGGGAGTACAA 58.746 55.000 0.00 0.00 0.00 2.41 F
771 1527 1.377536 GCTTGGCTTCAGGTCTGATC 58.622 55.000 1.16 0.00 39.64 2.92 F
1344 2114 2.023041 GTAGACGCGTCGCTCTCC 59.977 66.667 31.56 14.03 34.09 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 2093 0.728466 AGAGCGACGCGTCTACAAAC 60.728 55.000 33.94 20.03 0.00 2.93 R
1344 2114 3.566130 CTGGAAGGAAGGCTTGAGG 57.434 57.895 3.46 0.00 0.00 3.86 R
1787 3062 4.590850 TCACGACCTTAGATCATCATGG 57.409 45.455 0.00 0.00 0.00 3.66 R
1975 3256 4.935205 TGAAAGTAGAACATCCGACCATTG 59.065 41.667 0.00 0.00 0.00 2.82 R
2688 4077 0.615850 ACTAGCAACTTCAGGAGCCC 59.384 55.000 0.00 0.00 0.00 5.19 R
2816 4205 2.634940 TCTCAGTCCAAAGTCCCTTGAG 59.365 50.000 0.00 0.00 33.63 3.02 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
42 43 6.662616 AGCTACTAGAAATAAATGCAATGCG 58.337 36.000 0.00 0.00 0.00 4.73
43 44 5.340667 GCTACTAGAAATAAATGCAATGCGC 59.659 40.000 0.00 0.00 42.89 6.09
44 45 4.610945 ACTAGAAATAAATGCAATGCGCC 58.389 39.130 4.18 0.00 41.33 6.53
45 46 2.825205 AGAAATAAATGCAATGCGCCC 58.175 42.857 4.18 0.00 41.33 6.13
46 47 2.431782 AGAAATAAATGCAATGCGCCCT 59.568 40.909 4.18 0.00 41.33 5.19
47 48 3.636300 AGAAATAAATGCAATGCGCCCTA 59.364 39.130 4.18 0.00 41.33 3.53
48 49 4.099266 AGAAATAAATGCAATGCGCCCTAA 59.901 37.500 4.18 0.00 41.33 2.69
49 50 4.399004 AATAAATGCAATGCGCCCTAAA 57.601 36.364 4.18 0.00 41.33 1.85
50 51 2.008752 AAATGCAATGCGCCCTAAAC 57.991 45.000 4.18 0.00 41.33 2.01
51 52 0.175531 AATGCAATGCGCCCTAAACC 59.824 50.000 4.18 0.00 41.33 3.27
52 53 0.684153 ATGCAATGCGCCCTAAACCT 60.684 50.000 4.18 0.00 41.33 3.50
53 54 0.897863 TGCAATGCGCCCTAAACCTT 60.898 50.000 4.18 0.00 41.33 3.50
54 55 0.458370 GCAATGCGCCCTAAACCTTG 60.458 55.000 4.18 0.00 32.94 3.61
55 56 0.887933 CAATGCGCCCTAAACCTTGT 59.112 50.000 4.18 0.00 0.00 3.16
56 57 1.135402 CAATGCGCCCTAAACCTTGTC 60.135 52.381 4.18 0.00 0.00 3.18
57 58 0.328258 ATGCGCCCTAAACCTTGTCT 59.672 50.000 4.18 0.00 0.00 3.41
58 59 0.978151 TGCGCCCTAAACCTTGTCTA 59.022 50.000 4.18 0.00 0.00 2.59
59 60 1.557832 TGCGCCCTAAACCTTGTCTAT 59.442 47.619 4.18 0.00 0.00 1.98
60 61 2.026636 TGCGCCCTAAACCTTGTCTATT 60.027 45.455 4.18 0.00 0.00 1.73
61 62 2.354821 GCGCCCTAAACCTTGTCTATTG 59.645 50.000 0.00 0.00 0.00 1.90
62 63 3.606687 CGCCCTAAACCTTGTCTATTGT 58.393 45.455 0.00 0.00 0.00 2.71
63 64 3.374058 CGCCCTAAACCTTGTCTATTGTG 59.626 47.826 0.00 0.00 0.00 3.33
64 65 4.585879 GCCCTAAACCTTGTCTATTGTGA 58.414 43.478 0.00 0.00 0.00 3.58
65 66 5.007682 GCCCTAAACCTTGTCTATTGTGAA 58.992 41.667 0.00 0.00 0.00 3.18
66 67 5.475564 GCCCTAAACCTTGTCTATTGTGAAA 59.524 40.000 0.00 0.00 0.00 2.69
67 68 6.349363 GCCCTAAACCTTGTCTATTGTGAAAG 60.349 42.308 0.00 0.00 0.00 2.62
68 69 6.349363 CCCTAAACCTTGTCTATTGTGAAAGC 60.349 42.308 0.00 0.00 0.00 3.51
69 70 4.749245 AACCTTGTCTATTGTGAAAGCG 57.251 40.909 0.00 0.00 0.00 4.68
70 71 2.484264 ACCTTGTCTATTGTGAAAGCGC 59.516 45.455 0.00 0.00 0.00 5.92
71 72 2.483877 CCTTGTCTATTGTGAAAGCGCA 59.516 45.455 11.47 0.00 0.00 6.09
72 73 3.127548 CCTTGTCTATTGTGAAAGCGCAT 59.872 43.478 11.47 0.00 33.94 4.73
73 74 3.745332 TGTCTATTGTGAAAGCGCATG 57.255 42.857 11.47 0.00 33.94 4.06
74 75 2.159531 TGTCTATTGTGAAAGCGCATGC 60.160 45.455 11.47 7.91 43.24 4.06
75 76 2.083002 TCTATTGTGAAAGCGCATGCA 58.917 42.857 19.57 0.00 46.23 3.96
76 77 2.487372 TCTATTGTGAAAGCGCATGCAA 59.513 40.909 19.57 7.75 46.23 4.08
77 78 2.151881 ATTGTGAAAGCGCATGCAAA 57.848 40.000 19.57 0.00 46.23 3.68
78 79 2.151881 TTGTGAAAGCGCATGCAAAT 57.848 40.000 19.57 0.00 46.23 2.32
79 80 2.151881 TGTGAAAGCGCATGCAAATT 57.848 40.000 19.57 8.54 46.23 1.82
80 81 2.481854 TGTGAAAGCGCATGCAAATTT 58.518 38.095 19.57 14.36 46.23 1.82
81 82 2.475864 TGTGAAAGCGCATGCAAATTTC 59.524 40.909 22.69 22.69 46.23 2.17
82 83 2.067766 TGAAAGCGCATGCAAATTTCC 58.932 42.857 24.79 14.13 46.23 3.13
83 84 2.288948 TGAAAGCGCATGCAAATTTCCT 60.289 40.909 24.79 7.30 46.23 3.36
84 85 2.460757 AAGCGCATGCAAATTTCCTT 57.539 40.000 19.57 4.98 46.23 3.36
85 86 2.000429 AGCGCATGCAAATTTCCTTC 58.000 45.000 19.57 0.00 46.23 3.46
86 87 1.547372 AGCGCATGCAAATTTCCTTCT 59.453 42.857 19.57 0.00 46.23 2.85
87 88 2.754552 AGCGCATGCAAATTTCCTTCTA 59.245 40.909 19.57 0.00 46.23 2.10
88 89 3.193267 AGCGCATGCAAATTTCCTTCTAA 59.807 39.130 19.57 0.00 46.23 2.10
89 90 3.925913 GCGCATGCAAATTTCCTTCTAAA 59.074 39.130 19.57 0.00 42.15 1.85
90 91 4.201618 GCGCATGCAAATTTCCTTCTAAAC 60.202 41.667 19.57 0.00 42.15 2.01
91 92 5.163513 CGCATGCAAATTTCCTTCTAAACT 58.836 37.500 19.57 0.00 0.00 2.66
92 93 5.061311 CGCATGCAAATTTCCTTCTAAACTG 59.939 40.000 19.57 0.00 0.00 3.16
93 94 5.928264 GCATGCAAATTTCCTTCTAAACTGT 59.072 36.000 14.21 0.00 0.00 3.55
94 95 6.128742 GCATGCAAATTTCCTTCTAAACTGTG 60.129 38.462 14.21 0.00 0.00 3.66
95 96 6.707440 TGCAAATTTCCTTCTAAACTGTGA 57.293 33.333 0.00 0.00 0.00 3.58
96 97 6.503524 TGCAAATTTCCTTCTAAACTGTGAC 58.496 36.000 0.00 0.00 0.00 3.67
97 98 5.625311 GCAAATTTCCTTCTAAACTGTGACG 59.375 40.000 0.00 0.00 0.00 4.35
98 99 5.941948 AATTTCCTTCTAAACTGTGACGG 57.058 39.130 0.00 0.00 0.00 4.79
99 100 4.675976 TTTCCTTCTAAACTGTGACGGA 57.324 40.909 0.00 0.00 0.00 4.69
100 101 3.936372 TCCTTCTAAACTGTGACGGAG 57.064 47.619 0.00 0.00 0.00 4.63
101 102 2.561419 TCCTTCTAAACTGTGACGGAGG 59.439 50.000 0.00 0.00 0.00 4.30
102 103 2.353803 CCTTCTAAACTGTGACGGAGGG 60.354 54.545 0.00 0.00 0.00 4.30
103 104 2.297698 TCTAAACTGTGACGGAGGGA 57.702 50.000 0.00 0.00 0.00 4.20
109 110 1.254026 CTGTGACGGAGGGAGTACAA 58.746 55.000 0.00 0.00 0.00 2.41
122 123 5.476091 GGGAGTACAATAGATCCCTGAAG 57.524 47.826 8.10 0.00 46.72 3.02
172 173 3.014623 CCCACCGTCTCCTTAAATTTCC 58.985 50.000 0.00 0.00 0.00 3.13
213 214 2.344592 TCTCCTCCAAAGGCAAGGTTA 58.655 47.619 0.00 0.00 43.02 2.85
304 305 9.305925 GAACCATATTCTGCTTTGGATTTTAAG 57.694 33.333 0.00 0.00 33.36 1.85
371 372 6.095440 GGCAGTGATGTAAATCCACTATGTTT 59.905 38.462 0.00 0.00 38.93 2.83
505 506 6.918022 GGAAACACCATACTTCTGAAACAAAG 59.082 38.462 0.00 0.00 38.79 2.77
576 607 8.781196 ACTTATGTTCTGTCATGCAATATCATC 58.219 33.333 0.00 0.00 0.00 2.92
655 1411 2.399396 AACACGATGCTTCCAAAACG 57.601 45.000 0.00 0.00 0.00 3.60
678 1434 3.545724 CCTAAAAGGTCACCCGTCC 57.454 57.895 0.00 0.00 35.12 4.79
771 1527 1.377536 GCTTGGCTTCAGGTCTGATC 58.622 55.000 1.16 0.00 39.64 2.92
786 1542 3.745975 GTCTGATCGAACCAAATGACACA 59.254 43.478 0.00 0.00 0.00 3.72
875 1631 3.569250 TCCAAAGATAAAAAGCCGTGC 57.431 42.857 0.00 0.00 0.00 5.34
908 1664 5.974108 TCAGGCACCTGTTAAATAGTACTC 58.026 41.667 16.12 0.00 43.96 2.59
1035 1791 2.362503 ACCGATGTCCGCCTCTCA 60.363 61.111 0.00 0.00 36.84 3.27
1248 2018 4.838486 GGACTCCACTCGCTCGCG 62.838 72.222 0.00 0.00 41.35 5.87
1251 2021 3.893763 CTCCACTCGCTCGCGGAT 61.894 66.667 6.13 0.00 40.25 4.18
1344 2114 2.023041 GTAGACGCGTCGCTCTCC 59.977 66.667 31.56 14.03 34.09 3.71
1425 2195 5.107065 CGTGGACTTCAAGAATAAGGTTGAC 60.107 44.000 0.00 0.00 32.40 3.18
1569 2426 7.014134 TGACATTCTGCTAAATCTTTTCACCAA 59.986 33.333 0.00 0.00 0.00 3.67
1591 2448 9.343539 ACCAATCTAGATCTTTAATTTACTGGC 57.656 33.333 5.51 0.00 0.00 4.85
1614 2880 5.583457 GCTTCCATGCAAATGCTTTTTAGAT 59.417 36.000 6.97 0.00 42.66 1.98
1723 2996 9.136952 CCTACTATTAAGTACAATTATGACGGC 57.863 37.037 0.00 0.00 37.15 5.68
1787 3062 5.878116 TGGCGGTGATATATTTAGGCATAAC 59.122 40.000 0.00 0.00 0.00 1.89
2161 3449 7.664731 ACTTTATCAGATCATTAGGAATGGCTG 59.335 37.037 12.67 12.67 40.16 4.85
2245 3533 2.363306 TGGTGAGAAGTTGTGCCATT 57.637 45.000 0.00 0.00 0.00 3.16
2388 3693 6.982141 TGTCATGACCATCTAACCGTTAATAC 59.018 38.462 22.85 0.00 0.00 1.89
2390 3695 8.355169 GTCATGACCATCTAACCGTTAATACTA 58.645 37.037 15.31 0.00 0.00 1.82
2469 3774 3.550678 GTCGATACACCGTCTTTGATTCC 59.449 47.826 0.00 0.00 0.00 3.01
2470 3775 3.446161 TCGATACACCGTCTTTGATTCCT 59.554 43.478 0.00 0.00 0.00 3.36
2688 4077 2.687425 TGATGTATTTTGCCATGGTCCG 59.313 45.455 14.67 0.00 0.00 4.79
2765 4154 4.246978 TCTCATCAGAGAGATCCTCCCTA 58.753 47.826 7.38 0.00 45.73 3.53
2816 4205 4.953579 TGGTTCTTGGTAATGCCCTTTATC 59.046 41.667 0.00 0.00 36.04 1.75
2888 4277 4.346709 ACAAGTTCCACCTTTTAAATGGGG 59.653 41.667 20.78 17.64 34.03 4.96
3085 4474 4.118410 GCACTGAATCAGAGTTCATCGAT 58.882 43.478 18.20 0.00 37.47 3.59
3241 4630 6.120905 CCTTTCAGAGATGGTGAATTCTCAT 58.879 40.000 7.05 10.30 40.69 2.90
3254 4643 4.079844 TGAATTCTCATGTGGGCCTATTCA 60.080 41.667 4.53 0.00 0.00 2.57
3263 4652 4.492646 TGTGGGCCTATTCATCTCATCTA 58.507 43.478 4.53 0.00 0.00 1.98
3460 4858 0.460284 CCAATCCCCTCGTGTCTTCG 60.460 60.000 0.00 0.00 0.00 3.79
3491 4889 4.040936 TGCCCTAAATATGTGTGTTGGT 57.959 40.909 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.282592 CGCATTGCATTTATTTCTAGTAGCTAA 58.717 33.333 9.69 0.00 0.00 3.09
17 18 7.571244 GCGCATTGCATTTATTTCTAGTAGCTA 60.571 37.037 9.69 0.00 45.45 3.32
18 19 6.662616 CGCATTGCATTTATTTCTAGTAGCT 58.337 36.000 9.69 0.00 0.00 3.32
19 20 5.340667 GCGCATTGCATTTATTTCTAGTAGC 59.659 40.000 9.69 0.00 45.45 3.58
20 21 6.901699 GCGCATTGCATTTATTTCTAGTAG 57.098 37.500 9.69 0.00 45.45 2.57
35 36 0.458370 CAAGGTTTAGGGCGCATTGC 60.458 55.000 10.83 0.00 45.38 3.56
36 37 0.887933 ACAAGGTTTAGGGCGCATTG 59.112 50.000 10.83 3.20 0.00 2.82
37 38 1.173913 GACAAGGTTTAGGGCGCATT 58.826 50.000 10.83 0.00 0.00 3.56
38 39 0.328258 AGACAAGGTTTAGGGCGCAT 59.672 50.000 10.83 0.00 0.00 4.73
39 40 0.978151 TAGACAAGGTTTAGGGCGCA 59.022 50.000 10.83 0.00 0.00 6.09
40 41 2.327200 ATAGACAAGGTTTAGGGCGC 57.673 50.000 0.00 0.00 0.00 6.53
41 42 3.374058 CACAATAGACAAGGTTTAGGGCG 59.626 47.826 0.00 0.00 0.00 6.13
42 43 4.585879 TCACAATAGACAAGGTTTAGGGC 58.414 43.478 0.00 0.00 0.00 5.19
43 44 6.349363 GCTTTCACAATAGACAAGGTTTAGGG 60.349 42.308 0.00 0.00 0.00 3.53
44 45 6.612306 GCTTTCACAATAGACAAGGTTTAGG 58.388 40.000 0.00 0.00 0.00 2.69
45 46 6.307155 CGCTTTCACAATAGACAAGGTTTAG 58.693 40.000 0.00 0.00 0.00 1.85
46 47 5.334569 GCGCTTTCACAATAGACAAGGTTTA 60.335 40.000 0.00 0.00 0.00 2.01
47 48 4.556699 GCGCTTTCACAATAGACAAGGTTT 60.557 41.667 0.00 0.00 0.00 3.27
48 49 3.058224 GCGCTTTCACAATAGACAAGGTT 60.058 43.478 0.00 0.00 0.00 3.50
49 50 2.484264 GCGCTTTCACAATAGACAAGGT 59.516 45.455 0.00 0.00 0.00 3.50
50 51 2.483877 TGCGCTTTCACAATAGACAAGG 59.516 45.455 9.73 0.00 0.00 3.61
51 52 3.811722 TGCGCTTTCACAATAGACAAG 57.188 42.857 9.73 0.00 0.00 3.16
52 53 3.670359 GCATGCGCTTTCACAATAGACAA 60.670 43.478 9.73 0.00 34.30 3.18
53 54 2.159531 GCATGCGCTTTCACAATAGACA 60.160 45.455 9.73 0.00 34.30 3.41
54 55 2.159531 TGCATGCGCTTTCACAATAGAC 60.160 45.455 14.09 0.00 39.64 2.59
55 56 2.083002 TGCATGCGCTTTCACAATAGA 58.917 42.857 14.09 0.00 39.64 1.98
56 57 2.547913 TGCATGCGCTTTCACAATAG 57.452 45.000 14.09 0.00 39.64 1.73
57 58 3.294816 TTTGCATGCGCTTTCACAATA 57.705 38.095 14.09 0.00 39.64 1.90
58 59 2.151881 TTTGCATGCGCTTTCACAAT 57.848 40.000 14.09 0.00 39.64 2.71
59 60 2.151881 ATTTGCATGCGCTTTCACAA 57.848 40.000 14.09 4.02 39.64 3.33
60 61 2.151881 AATTTGCATGCGCTTTCACA 57.848 40.000 14.09 0.00 39.64 3.58
61 62 2.159801 GGAAATTTGCATGCGCTTTCAC 60.160 45.455 26.78 18.12 39.64 3.18
62 63 2.067766 GGAAATTTGCATGCGCTTTCA 58.932 42.857 26.78 0.00 39.64 2.69
63 64 2.340337 AGGAAATTTGCATGCGCTTTC 58.660 42.857 21.75 21.75 39.64 2.62
64 65 2.460757 AGGAAATTTGCATGCGCTTT 57.539 40.000 14.09 12.01 39.64 3.51
65 66 2.028748 AGAAGGAAATTTGCATGCGCTT 60.029 40.909 14.09 0.00 39.64 4.68
66 67 1.547372 AGAAGGAAATTTGCATGCGCT 59.453 42.857 14.09 0.00 39.64 5.92
67 68 2.000429 AGAAGGAAATTTGCATGCGC 58.000 45.000 14.09 0.00 39.24 6.09
68 69 5.061311 CAGTTTAGAAGGAAATTTGCATGCG 59.939 40.000 14.09 0.00 0.00 4.73
69 70 5.928264 ACAGTTTAGAAGGAAATTTGCATGC 59.072 36.000 11.82 11.82 0.00 4.06
70 71 7.115378 GTCACAGTTTAGAAGGAAATTTGCATG 59.885 37.037 12.54 0.00 0.00 4.06
71 72 7.147976 GTCACAGTTTAGAAGGAAATTTGCAT 58.852 34.615 12.54 0.00 0.00 3.96
72 73 6.503524 GTCACAGTTTAGAAGGAAATTTGCA 58.496 36.000 12.54 0.00 0.00 4.08
73 74 5.625311 CGTCACAGTTTAGAAGGAAATTTGC 59.375 40.000 0.68 0.68 0.00 3.68
74 75 6.017440 TCCGTCACAGTTTAGAAGGAAATTTG 60.017 38.462 0.00 0.00 39.03 2.32
75 76 6.059484 TCCGTCACAGTTTAGAAGGAAATTT 58.941 36.000 0.00 0.00 39.03 1.82
76 77 5.617252 TCCGTCACAGTTTAGAAGGAAATT 58.383 37.500 0.00 0.00 39.03 1.82
77 78 5.223449 TCCGTCACAGTTTAGAAGGAAAT 57.777 39.130 0.00 0.00 39.03 2.17
78 79 4.502604 CCTCCGTCACAGTTTAGAAGGAAA 60.503 45.833 0.00 0.00 40.90 3.13
79 80 3.006537 CCTCCGTCACAGTTTAGAAGGAA 59.993 47.826 0.00 0.00 40.90 3.36
80 81 2.561419 CCTCCGTCACAGTTTAGAAGGA 59.439 50.000 0.00 0.00 39.55 3.36
81 82 2.353803 CCCTCCGTCACAGTTTAGAAGG 60.354 54.545 0.00 0.00 35.14 3.46
82 83 2.561419 TCCCTCCGTCACAGTTTAGAAG 59.439 50.000 0.00 0.00 0.00 2.85
83 84 2.561419 CTCCCTCCGTCACAGTTTAGAA 59.439 50.000 0.00 0.00 0.00 2.10
84 85 2.168496 CTCCCTCCGTCACAGTTTAGA 58.832 52.381 0.00 0.00 0.00 2.10
85 86 1.893801 ACTCCCTCCGTCACAGTTTAG 59.106 52.381 0.00 0.00 0.00 1.85
86 87 2.005370 ACTCCCTCCGTCACAGTTTA 57.995 50.000 0.00 0.00 0.00 2.01
87 88 1.617357 GTACTCCCTCCGTCACAGTTT 59.383 52.381 0.00 0.00 0.00 2.66
88 89 1.254954 GTACTCCCTCCGTCACAGTT 58.745 55.000 0.00 0.00 0.00 3.16
89 90 0.111832 TGTACTCCCTCCGTCACAGT 59.888 55.000 0.00 0.00 0.00 3.55
90 91 1.254026 TTGTACTCCCTCCGTCACAG 58.746 55.000 0.00 0.00 0.00 3.66
91 92 1.933021 ATTGTACTCCCTCCGTCACA 58.067 50.000 0.00 0.00 0.00 3.58
92 93 3.285484 TCTATTGTACTCCCTCCGTCAC 58.715 50.000 0.00 0.00 0.00 3.67
93 94 3.657398 TCTATTGTACTCCCTCCGTCA 57.343 47.619 0.00 0.00 0.00 4.35
94 95 3.506844 GGATCTATTGTACTCCCTCCGTC 59.493 52.174 0.00 0.00 0.00 4.79
95 96 3.498334 GGATCTATTGTACTCCCTCCGT 58.502 50.000 0.00 0.00 0.00 4.69
96 97 2.826725 GGGATCTATTGTACTCCCTCCG 59.173 54.545 8.10 0.00 43.45 4.63
100 101 4.902448 ACTTCAGGGATCTATTGTACTCCC 59.098 45.833 7.40 7.40 46.56 4.30
101 102 6.487299 AACTTCAGGGATCTATTGTACTCC 57.513 41.667 0.00 0.00 0.00 3.85
102 103 9.084533 AGATAACTTCAGGGATCTATTGTACTC 57.915 37.037 0.00 0.00 0.00 2.59
156 157 4.253685 TGCTCAGGAAATTTAAGGAGACG 58.746 43.478 13.63 0.00 0.00 4.18
157 158 5.882557 TCATGCTCAGGAAATTTAAGGAGAC 59.117 40.000 13.63 7.68 0.00 3.36
158 159 6.065976 TCATGCTCAGGAAATTTAAGGAGA 57.934 37.500 13.63 3.46 0.00 3.71
172 173 1.153005 GGGGCTTCCTCATGCTCAG 60.153 63.158 0.00 0.00 0.00 3.35
213 214 0.992695 GACTGGCCCTAGTTCCCTTT 59.007 55.000 0.00 0.00 0.00 3.11
304 305 3.421844 AGCTGGTGGTCCAATTAAAGTC 58.578 45.455 0.00 0.00 43.81 3.01
371 372 9.358406 AGATTTGCAGGATATATTTCATGACAA 57.642 29.630 11.31 11.03 29.04 3.18
525 526 8.157476 GTGGGATTTATGTGGAGATTACTACAT 58.843 37.037 0.00 0.00 42.71 2.29
576 607 9.853177 AAGTTTAAAGTAGGATGGAAGATATGG 57.147 33.333 0.00 0.00 0.00 2.74
674 1430 1.337728 TGTGGACATTGCTACAGGACG 60.338 52.381 0.00 0.00 0.00 4.79
678 1434 5.277490 CGGATTTATGTGGACATTGCTACAG 60.277 44.000 0.00 0.00 37.76 2.74
771 1527 2.772568 TTGCTGTGTCATTTGGTTCG 57.227 45.000 0.00 0.00 0.00 3.95
786 1542 4.706476 TGCTTAGTTCAATTAGGCATTGCT 59.294 37.500 8.82 0.00 42.06 3.91
875 1631 1.605710 CAGGTGCCTGAAGAAAGTGTG 59.394 52.381 12.66 0.00 46.30 3.82
908 1664 4.776349 TGCATGGGTGTTATGTAGTTAGG 58.224 43.478 0.00 0.00 0.00 2.69
1004 1760 2.366153 ATCGGTGGCAAGGGTGGTTT 62.366 55.000 0.00 0.00 0.00 3.27
1248 2018 3.679083 GCACTAACTGTACCACCTGATCC 60.679 52.174 0.00 0.00 0.00 3.36
1251 2021 2.605257 AGCACTAACTGTACCACCTGA 58.395 47.619 0.00 0.00 0.00 3.86
1323 2093 0.728466 AGAGCGACGCGTCTACAAAC 60.728 55.000 33.94 20.03 0.00 2.93
1344 2114 3.566130 CTGGAAGGAAGGCTTGAGG 57.434 57.895 3.46 0.00 0.00 3.86
1425 2195 4.652822 ACTAGCAGTAAAAAGGAAGGTGG 58.347 43.478 0.00 0.00 0.00 4.61
1569 2426 9.785982 GGAAGCCAGTAAATTAAAGATCTAGAT 57.214 33.333 4.47 4.47 0.00 1.98
1591 2448 6.814644 TGATCTAAAAAGCATTTGCATGGAAG 59.185 34.615 5.20 0.00 45.16 3.46
1720 2993 6.147821 CCTAAAATGTCATGATAGTTAGGCCG 59.852 42.308 21.64 8.03 0.00 6.13
1787 3062 4.590850 TCACGACCTTAGATCATCATGG 57.409 45.455 0.00 0.00 0.00 3.66
1975 3256 4.935205 TGAAAGTAGAACATCCGACCATTG 59.065 41.667 0.00 0.00 0.00 2.82
2161 3449 7.359181 GCATATTCAAATATACAAAAAGGCCGC 60.359 37.037 0.00 0.00 30.68 6.53
2245 3533 4.097012 GCAACGAAAACCACGTAAGAAAA 58.903 39.130 0.00 0.00 43.16 2.29
2388 3693 7.011763 CACATACCCAACTGATGACAGAAATAG 59.988 40.741 0.00 0.00 46.03 1.73
2390 3695 5.649395 CACATACCCAACTGATGACAGAAAT 59.351 40.000 0.00 0.00 46.03 2.17
2448 3753 3.446161 AGGAATCAAAGACGGTGTATCGA 59.554 43.478 0.00 0.00 0.00 3.59
2449 3754 3.782046 AGGAATCAAAGACGGTGTATCG 58.218 45.455 0.00 0.00 0.00 2.92
2451 3756 4.695455 CACAAGGAATCAAAGACGGTGTAT 59.305 41.667 0.00 0.00 0.00 2.29
2469 3774 4.692228 ACAAAAGGTAACAATGGCACAAG 58.308 39.130 0.00 0.00 41.54 3.16
2470 3775 4.744795 ACAAAAGGTAACAATGGCACAA 57.255 36.364 0.00 0.00 41.54 3.33
2521 3826 6.941857 ACCAAAGTTTTGACTAACCAAATGT 58.058 32.000 6.18 0.00 40.55 2.71
2525 3830 6.406400 CCATGACCAAAGTTTTGACTAACCAA 60.406 38.462 6.18 0.00 40.55 3.67
2688 4077 0.615850 ACTAGCAACTTCAGGAGCCC 59.384 55.000 0.00 0.00 0.00 5.19
2765 4154 4.844655 AGTGGTGTAGTCAATAGACCCTTT 59.155 41.667 0.00 0.00 45.35 3.11
2816 4205 2.634940 TCTCAGTCCAAAGTCCCTTGAG 59.365 50.000 0.00 0.00 33.63 3.02
2888 4277 4.630894 TGAATGGTGTTTGAACAGTGTC 57.369 40.909 0.00 0.00 40.05 3.67
2966 4355 5.429762 TGTCTCCACCTTTCTGATATGGAAT 59.570 40.000 0.00 0.00 38.95 3.01
3085 4474 6.229936 ACTTTCTCCGTTGGTATATGCTTA 57.770 37.500 0.00 0.00 0.00 3.09
3241 4630 3.321039 AGATGAGATGAATAGGCCCACA 58.679 45.455 0.00 0.00 0.00 4.17
3254 4643 9.471702 AAATGACTTGTGGAAAATAGATGAGAT 57.528 29.630 0.00 0.00 0.00 2.75
3460 4858 9.677567 CACACATATTTAGGGCAAACATATTAC 57.322 33.333 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.