Multiple sequence alignment - TraesCS3A01G317000

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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 TraesCS3A01G317000 chr3A 100.000 2645 0 0 1 2645 557423595 557420951 0.000000e+00 4885
1 TraesCS3A01G317000 chr3D 91.361 2593 134 25 99 2638 428240063 428242618 0.000000e+00 3465
2 TraesCS3A01G317000 chr3D 92.480 625 34 8 1631 2243 428242783 428243406 0.000000e+00 881
3 TraesCS3A01G317000 chr3B 93.935 2160 82 24 506 2645 559876868 559878998 0.000000e+00 3217
4 TraesCS3A01G317000 chr3B 90.796 402 36 1 99 500 559876043 559876443 1.080000e-148 536
5 TraesCS3A01G317000 chr3B 92.174 115 5 4 1 115 481747292 481747182 2.730000e-35 159
6 TraesCS3A01G317000 chr6D 96.970 99 3 0 1 99 445922969 445923067 1.630000e-37 167
7 TraesCS3A01G317000 chr4D 93.636 110 7 0 1 110 369365889 369365780 5.860000e-37 165
8 TraesCS3A01G317000 chr4D 94.231 104 5 1 1 103 468678158 468678261 9.800000e-35 158
9 TraesCS3A01G317000 chr2A 95.192 104 5 0 1 104 745863719 745863822 5.860000e-37 165
10 TraesCS3A01G317000 chr1A 94.393 107 6 0 1 107 374234682 374234788 5.860000e-37 165
11 TraesCS3A01G317000 chr1A 92.241 116 6 3 1 115 408692131 408692244 7.580000e-36 161
12 TraesCS3A01G317000 chr4A 90.678 118 9 2 1 118 300498995 300499110 3.530000e-34 156
13 TraesCS3A01G317000 chr2B 89.167 120 10 2 1 120 157308993 157309109 2.120000e-31 147


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 TraesCS3A01G317000 chr3A 557420951 557423595 2644 True 4885.0 4885 100.0000 1 2645 1 chr3A.!!$R1 2644
1 TraesCS3A01G317000 chr3D 428240063 428243406 3343 False 2173.0 3465 91.9205 99 2638 2 chr3D.!!$F1 2539
2 TraesCS3A01G317000 chr3B 559876043 559878998 2955 False 1876.5 3217 92.3655 99 2645 2 chr3B.!!$F1 2546

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
398 399 0.184692 TGGCCCAGTGACAATGTCAA 59.815 50.0 18.48 0.0 44.49 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 2071 0.250513 ACTCAGAACCAAGCCGATCC 59.749 55.0 0.0 0.0 0.0 3.36 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
37 38 7.964604 ATTTGTTCTACTTTTAGCTCTTCGT 57.035 32.000 0.00 0.00 0.00 3.85
38 39 7.781548 TTTGTTCTACTTTTAGCTCTTCGTT 57.218 32.000 0.00 0.00 0.00 3.85
39 40 6.764877 TGTTCTACTTTTAGCTCTTCGTTG 57.235 37.500 0.00 0.00 0.00 4.10
40 41 5.694910 TGTTCTACTTTTAGCTCTTCGTTGG 59.305 40.000 0.00 0.00 0.00 3.77
41 42 4.817517 TCTACTTTTAGCTCTTCGTTGGG 58.182 43.478 0.00 0.00 0.00 4.12
42 43 3.487120 ACTTTTAGCTCTTCGTTGGGT 57.513 42.857 0.00 0.00 0.00 4.51
43 44 3.816994 ACTTTTAGCTCTTCGTTGGGTT 58.183 40.909 0.00 0.00 0.00 4.11
44 45 3.813724 ACTTTTAGCTCTTCGTTGGGTTC 59.186 43.478 0.00 0.00 0.00 3.62
45 46 2.074547 TTAGCTCTTCGTTGGGTTCG 57.925 50.000 0.00 0.00 0.00 3.95
46 47 1.250328 TAGCTCTTCGTTGGGTTCGA 58.750 50.000 0.00 0.00 35.50 3.71
47 48 0.319641 AGCTCTTCGTTGGGTTCGAC 60.320 55.000 0.00 0.00 37.05 4.20
48 49 0.599204 GCTCTTCGTTGGGTTCGACA 60.599 55.000 0.00 0.00 37.05 4.35
49 50 1.137513 CTCTTCGTTGGGTTCGACAC 58.862 55.000 0.00 0.00 37.05 3.67
50 51 0.748450 TCTTCGTTGGGTTCGACACT 59.252 50.000 0.00 0.00 37.05 3.55
51 52 1.137513 CTTCGTTGGGTTCGACACTC 58.862 55.000 0.00 0.00 37.05 3.51
52 53 0.748450 TTCGTTGGGTTCGACACTCT 59.252 50.000 0.00 0.00 37.05 3.24
53 54 0.748450 TCGTTGGGTTCGACACTCTT 59.252 50.000 0.00 0.00 32.30 2.85
54 55 1.955778 TCGTTGGGTTCGACACTCTTA 59.044 47.619 0.00 0.00 32.30 2.10
55 56 2.056577 CGTTGGGTTCGACACTCTTAC 58.943 52.381 0.00 0.00 0.00 2.34
56 57 2.288030 CGTTGGGTTCGACACTCTTACT 60.288 50.000 0.00 0.00 0.00 2.24
57 58 3.725490 GTTGGGTTCGACACTCTTACTT 58.275 45.455 0.00 0.00 0.00 2.24
58 59 4.557296 CGTTGGGTTCGACACTCTTACTTA 60.557 45.833 0.00 0.00 0.00 2.24
59 60 5.476614 GTTGGGTTCGACACTCTTACTTAT 58.523 41.667 0.00 0.00 0.00 1.73
60 61 5.320549 TGGGTTCGACACTCTTACTTATC 57.679 43.478 0.00 0.00 0.00 1.75
61 62 4.142534 TGGGTTCGACACTCTTACTTATCG 60.143 45.833 0.00 0.00 0.00 2.92
62 63 4.095483 GGGTTCGACACTCTTACTTATCGA 59.905 45.833 0.00 0.00 36.85 3.59
63 64 5.392380 GGGTTCGACACTCTTACTTATCGAA 60.392 44.000 2.99 2.99 43.90 3.71
64 65 6.088824 GGTTCGACACTCTTACTTATCGAAA 58.911 40.000 8.30 0.00 46.48 3.46
65 66 6.583806 GGTTCGACACTCTTACTTATCGAAAA 59.416 38.462 8.30 0.00 46.48 2.29
66 67 7.410193 GGTTCGACACTCTTACTTATCGAAAAC 60.410 40.741 8.30 2.36 46.48 2.43
67 68 6.906659 TCGACACTCTTACTTATCGAAAACT 58.093 36.000 0.00 0.00 35.80 2.66
68 69 6.800408 TCGACACTCTTACTTATCGAAAACTG 59.200 38.462 0.00 0.00 35.80 3.16
69 70 6.581542 CGACACTCTTACTTATCGAAAACTGT 59.418 38.462 0.00 0.00 0.00 3.55
70 71 7.114529 CGACACTCTTACTTATCGAAAACTGTT 59.885 37.037 0.00 0.00 0.00 3.16
71 72 8.073355 ACACTCTTACTTATCGAAAACTGTTG 57.927 34.615 0.00 0.00 0.00 3.33
72 73 7.709613 ACACTCTTACTTATCGAAAACTGTTGT 59.290 33.333 0.00 0.00 0.00 3.32
73 74 8.004344 CACTCTTACTTATCGAAAACTGTTGTG 58.996 37.037 0.00 0.00 0.00 3.33
74 75 7.924412 ACTCTTACTTATCGAAAACTGTTGTGA 59.076 33.333 0.00 0.00 0.00 3.58
75 76 8.827177 TCTTACTTATCGAAAACTGTTGTGAT 57.173 30.769 0.00 1.08 0.00 3.06
76 77 8.922676 TCTTACTTATCGAAAACTGTTGTGATC 58.077 33.333 0.00 0.00 0.00 2.92
77 78 8.827177 TTACTTATCGAAAACTGTTGTGATCT 57.173 30.769 0.00 0.00 0.00 2.75
78 79 7.352719 ACTTATCGAAAACTGTTGTGATCTC 57.647 36.000 0.00 0.00 0.00 2.75
79 80 6.369065 ACTTATCGAAAACTGTTGTGATCTCC 59.631 38.462 0.00 0.00 0.00 3.71
80 81 4.336889 TCGAAAACTGTTGTGATCTCCT 57.663 40.909 0.00 0.00 0.00 3.69
81 82 5.462530 TCGAAAACTGTTGTGATCTCCTA 57.537 39.130 0.00 0.00 0.00 2.94
82 83 6.037786 TCGAAAACTGTTGTGATCTCCTAT 57.962 37.500 0.00 0.00 0.00 2.57
83 84 7.165460 TCGAAAACTGTTGTGATCTCCTATA 57.835 36.000 0.00 0.00 0.00 1.31
84 85 7.033791 TCGAAAACTGTTGTGATCTCCTATAC 58.966 38.462 0.00 0.00 0.00 1.47
85 86 7.036220 CGAAAACTGTTGTGATCTCCTATACT 58.964 38.462 0.00 0.00 0.00 2.12
86 87 7.545965 CGAAAACTGTTGTGATCTCCTATACTT 59.454 37.037 0.00 0.00 0.00 2.24
87 88 8.553459 AAAACTGTTGTGATCTCCTATACTTG 57.447 34.615 0.00 0.00 0.00 3.16
88 89 6.859112 ACTGTTGTGATCTCCTATACTTGT 57.141 37.500 0.00 0.00 0.00 3.16
89 90 6.634805 ACTGTTGTGATCTCCTATACTTGTG 58.365 40.000 0.00 0.00 0.00 3.33
90 91 5.977635 TGTTGTGATCTCCTATACTTGTGG 58.022 41.667 0.00 0.00 0.00 4.17
91 92 5.104941 TGTTGTGATCTCCTATACTTGTGGG 60.105 44.000 0.00 0.00 0.00 4.61
92 93 4.620723 TGTGATCTCCTATACTTGTGGGT 58.379 43.478 0.00 0.00 0.00 4.51
93 94 5.030147 TGTGATCTCCTATACTTGTGGGTT 58.970 41.667 0.00 0.00 0.00 4.11
94 95 6.199376 TGTGATCTCCTATACTTGTGGGTTA 58.801 40.000 0.00 0.00 0.00 2.85
95 96 6.844388 TGTGATCTCCTATACTTGTGGGTTAT 59.156 38.462 0.00 0.00 0.00 1.89
96 97 7.015292 TGTGATCTCCTATACTTGTGGGTTATC 59.985 40.741 0.00 0.00 0.00 1.75
97 98 7.015292 GTGATCTCCTATACTTGTGGGTTATCA 59.985 40.741 0.00 0.00 0.00 2.15
181 182 0.980231 GAGTCATCTGCCCACTCCCT 60.980 60.000 0.00 0.00 31.93 4.20
189 190 0.548926 TGCCCACTCCCTATTCACCA 60.549 55.000 0.00 0.00 0.00 4.17
230 231 1.304052 CCATTCCTCGCCAAACCCA 60.304 57.895 0.00 0.00 0.00 4.51
232 233 1.678970 ATTCCTCGCCAAACCCAGC 60.679 57.895 0.00 0.00 0.00 4.85
273 274 1.591703 GAGCCACCTCGATGTGTCA 59.408 57.895 17.87 0.00 34.35 3.58
280 281 0.321671 CCTCGATGTGTCACCAACCT 59.678 55.000 0.00 0.00 0.00 3.50
357 358 2.277404 GAGCGGGAGAGAGGGAGT 59.723 66.667 0.00 0.00 0.00 3.85
360 361 1.682684 GCGGGAGAGAGGGAGTGAA 60.683 63.158 0.00 0.00 0.00 3.18
386 387 8.558973 TGACAAAAATAAATTTATTGGCCCAG 57.441 30.769 21.23 12.02 33.85 4.45
398 399 0.184692 TGGCCCAGTGACAATGTCAA 59.815 50.000 18.48 0.00 44.49 3.18
399 400 0.883833 GGCCCAGTGACAATGTCAAG 59.116 55.000 18.48 13.17 44.49 3.02
408 409 7.080099 CCAGTGACAATGTCAAGAATTTACTG 58.920 38.462 18.48 16.44 44.49 2.74
442 443 6.422701 CGAAAGCATCCCGTACATATTTCTAA 59.577 38.462 0.00 0.00 0.00 2.10
469 470 8.664669 AAAACCATTGAGACAACCCTAATAAT 57.335 30.769 0.00 0.00 0.00 1.28
503 526 8.915036 TGAAGAGATGATTTACTAGTAACCTCC 58.085 37.037 14.96 5.53 0.00 4.30
528 946 8.446273 CCTCTTAGTGTGTTATTCACTCATTTG 58.554 37.037 1.82 0.00 46.27 2.32
534 952 7.041780 AGTGTGTTATTCACTCATTTGTGTCTC 60.042 37.037 0.00 0.00 46.27 3.36
535 953 6.204688 TGTGTTATTCACTCATTTGTGTCTCC 59.795 38.462 0.00 0.00 46.27 3.71
539 957 3.076621 TCACTCATTTGTGTCTCCATGC 58.923 45.455 0.00 0.00 38.90 4.06
585 1003 4.704057 ACATCTTCCTTTCATCTTTGCCTC 59.296 41.667 0.00 0.00 0.00 4.70
596 1014 2.259917 TCTTTGCCTCACAGGAGATGA 58.740 47.619 0.00 0.00 44.26 2.92
605 1023 5.537188 CCTCACAGGAGATGATTTACTAGC 58.463 45.833 0.00 0.00 44.26 3.42
625 1043 5.108385 AGCAACCGTTGAAGATTGTAAAG 57.892 39.130 15.63 0.00 0.00 1.85
646 1064 2.290960 GGAAGGGAGCAGTAAACCACAT 60.291 50.000 0.00 0.00 0.00 3.21
712 1131 2.167861 GCCGACTAGCAGCGAAAGG 61.168 63.158 2.27 0.00 0.00 3.11
738 1160 4.097589 GCTTCAGAAGAAAGGCAGCATAAT 59.902 41.667 14.86 0.00 32.35 1.28
739 1161 5.297776 GCTTCAGAAGAAAGGCAGCATAATA 59.702 40.000 14.86 0.00 32.35 0.98
740 1162 6.183360 GCTTCAGAAGAAAGGCAGCATAATAA 60.183 38.462 14.86 0.00 32.35 1.40
741 1163 7.629222 GCTTCAGAAGAAAGGCAGCATAATAAA 60.629 37.037 14.86 0.00 32.35 1.40
742 1164 7.088589 TCAGAAGAAAGGCAGCATAATAAAC 57.911 36.000 0.00 0.00 0.00 2.01
743 1165 5.967674 CAGAAGAAAGGCAGCATAATAAACG 59.032 40.000 0.00 0.00 0.00 3.60
744 1166 4.292977 AGAAAGGCAGCATAATAAACGC 57.707 40.909 0.00 0.00 0.00 4.84
745 1167 2.755836 AAGGCAGCATAATAAACGCG 57.244 45.000 3.53 3.53 0.00 6.01
746 1168 0.944386 AGGCAGCATAATAAACGCGG 59.056 50.000 12.47 0.00 0.00 6.46
747 1169 0.661020 GGCAGCATAATAAACGCGGT 59.339 50.000 12.47 0.00 0.00 5.68
748 1170 1.596954 GGCAGCATAATAAACGCGGTG 60.597 52.381 12.47 0.00 0.00 4.94
749 1171 1.741993 CAGCATAATAAACGCGGTGC 58.258 50.000 12.47 1.43 0.00 5.01
750 1172 1.063321 CAGCATAATAAACGCGGTGCA 59.937 47.619 12.47 0.00 35.17 4.57
751 1173 1.063469 AGCATAATAAACGCGGTGCAC 59.937 47.619 12.47 8.80 35.17 4.57
752 1174 1.202087 GCATAATAAACGCGGTGCACA 60.202 47.619 20.43 0.00 33.09 4.57
768 1190 3.767230 CACGACAGAGCGTTGCGG 61.767 66.667 0.00 0.00 43.59 5.69
811 1233 2.233676 TGCGGAGAAGCATCAAAGACTA 59.766 45.455 0.00 0.00 42.92 2.59
1167 1589 2.026449 CCTCAAGCTCATCTCCCAGTTT 60.026 50.000 0.00 0.00 0.00 2.66
1649 2071 0.820891 ACTGCTGGCCTGTGAACAAG 60.821 55.000 11.69 0.00 0.00 3.16
1664 2086 0.693049 ACAAGGATCGGCTTGGTTCT 59.307 50.000 14.00 0.00 35.10 3.01
1671 2093 0.756294 TCGGCTTGGTTCTGAGTTGA 59.244 50.000 0.00 0.00 0.00 3.18
1750 2173 6.603237 TTGGCTCAATCTATATCGTTTGTG 57.397 37.500 0.00 0.00 0.00 3.33
1751 2174 5.670485 TGGCTCAATCTATATCGTTTGTGT 58.330 37.500 0.00 0.00 0.00 3.72
1781 2204 4.088634 TGCCAATCTTATGGAAAGTTGCT 58.911 39.130 0.00 0.00 43.54 3.91
1808 2232 6.980978 CCTACAGATCGATTGTTTCATACTGT 59.019 38.462 15.21 14.16 39.03 3.55
1888 2319 3.248363 GCTGTTCAAAGGATTGGTTTTGC 59.752 43.478 0.00 0.00 37.15 3.68
1901 2332 2.225467 GGTTTTGCTCTGAGCTGTTCT 58.775 47.619 28.04 0.00 42.97 3.01
1909 2340 4.453478 TGCTCTGAGCTGTTCTTATGTTTG 59.547 41.667 28.04 0.00 42.97 2.93
2010 2441 7.428282 TGTTGATAACAGAGCGAATTTTACA 57.572 32.000 0.00 0.00 36.25 2.41
2056 2487 9.345517 CTGTTGCATAATTATTATATGTGGTGC 57.654 33.333 0.00 0.00 34.06 5.01
2316 2748 9.334947 AGATACATGGATGTTCAGTTATGAAAG 57.665 33.333 0.00 0.00 46.75 2.62
2342 2774 6.291377 ACAAGTCATGATGTGTCTACACTTT 58.709 36.000 13.95 2.40 46.55 2.66
2464 2901 7.930217 TCTGAATTGTTCCTTTCTTTGTACTG 58.070 34.615 0.00 0.00 0.00 2.74
2481 2918 1.270305 ACTGTGTGGTCGTTGGATCAG 60.270 52.381 0.00 0.00 32.89 2.90
2547 2984 7.160633 GTTGTTTGTCAACGATAAAAATGCT 57.839 32.000 0.00 0.00 45.23 3.79
2548 2985 8.276060 GTTGTTTGTCAACGATAAAAATGCTA 57.724 30.769 0.00 0.00 45.23 3.49
2590 3041 7.121611 TGGATTCTGTTGCATATTGGCTATATG 59.878 37.037 20.16 20.16 45.95 1.78
2606 3057 5.120208 GGCTATATGCGGTACAATTGTACAG 59.880 44.000 36.91 34.45 45.02 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.654663 ACGAAGAGCTAAAAGTAGAACAAATAT 57.345 29.630 0.00 0.00 0.00 1.28
12 13 9.485206 AACGAAGAGCTAAAAGTAGAACAAATA 57.515 29.630 0.00 0.00 0.00 1.40
13 14 7.964604 ACGAAGAGCTAAAAGTAGAACAAAT 57.035 32.000 0.00 0.00 0.00 2.32
14 15 7.254658 CCAACGAAGAGCTAAAAGTAGAACAAA 60.255 37.037 0.00 0.00 0.00 2.83
15 16 6.202188 CCAACGAAGAGCTAAAAGTAGAACAA 59.798 38.462 0.00 0.00 0.00 2.83
16 17 5.694910 CCAACGAAGAGCTAAAAGTAGAACA 59.305 40.000 0.00 0.00 0.00 3.18
17 18 5.120363 CCCAACGAAGAGCTAAAAGTAGAAC 59.880 44.000 0.00 0.00 0.00 3.01
18 19 5.221581 ACCCAACGAAGAGCTAAAAGTAGAA 60.222 40.000 0.00 0.00 0.00 2.10
19 20 4.282703 ACCCAACGAAGAGCTAAAAGTAGA 59.717 41.667 0.00 0.00 0.00 2.59
20 21 4.566987 ACCCAACGAAGAGCTAAAAGTAG 58.433 43.478 0.00 0.00 0.00 2.57
21 22 4.612264 ACCCAACGAAGAGCTAAAAGTA 57.388 40.909 0.00 0.00 0.00 2.24
22 23 3.487120 ACCCAACGAAGAGCTAAAAGT 57.513 42.857 0.00 0.00 0.00 2.66
23 24 3.120649 CGAACCCAACGAAGAGCTAAAAG 60.121 47.826 0.00 0.00 0.00 2.27
24 25 2.803956 CGAACCCAACGAAGAGCTAAAA 59.196 45.455 0.00 0.00 0.00 1.52
25 26 2.036217 TCGAACCCAACGAAGAGCTAAA 59.964 45.455 0.00 0.00 36.84 1.85
26 27 1.614903 TCGAACCCAACGAAGAGCTAA 59.385 47.619 0.00 0.00 36.84 3.09
27 28 1.068055 GTCGAACCCAACGAAGAGCTA 60.068 52.381 0.00 0.00 41.31 3.32
28 29 0.319641 GTCGAACCCAACGAAGAGCT 60.320 55.000 0.00 0.00 41.31 4.09
29 30 0.599204 TGTCGAACCCAACGAAGAGC 60.599 55.000 0.00 0.00 41.31 4.09
30 31 1.137513 GTGTCGAACCCAACGAAGAG 58.862 55.000 0.00 0.00 41.31 2.85
31 32 0.748450 AGTGTCGAACCCAACGAAGA 59.252 50.000 0.00 0.00 41.31 2.87
32 33 1.137513 GAGTGTCGAACCCAACGAAG 58.862 55.000 0.00 0.00 41.31 3.79
33 34 0.748450 AGAGTGTCGAACCCAACGAA 59.252 50.000 0.00 0.00 41.31 3.85
34 35 0.748450 AAGAGTGTCGAACCCAACGA 59.252 50.000 0.00 0.00 37.43 3.85
35 36 2.056577 GTAAGAGTGTCGAACCCAACG 58.943 52.381 0.00 0.00 0.00 4.10
36 37 3.382048 AGTAAGAGTGTCGAACCCAAC 57.618 47.619 0.00 0.00 0.00 3.77
37 38 5.620654 CGATAAGTAAGAGTGTCGAACCCAA 60.621 44.000 0.00 0.00 0.00 4.12
38 39 4.142534 CGATAAGTAAGAGTGTCGAACCCA 60.143 45.833 0.00 0.00 0.00 4.51
39 40 4.095483 TCGATAAGTAAGAGTGTCGAACCC 59.905 45.833 0.00 0.00 35.48 4.11
40 41 5.227238 TCGATAAGTAAGAGTGTCGAACC 57.773 43.478 0.00 0.00 35.48 3.62
41 42 7.325579 AGTTTTCGATAAGTAAGAGTGTCGAAC 59.674 37.037 7.42 0.00 44.53 3.95
42 43 7.325338 CAGTTTTCGATAAGTAAGAGTGTCGAA 59.675 37.037 4.17 4.17 43.60 3.71
43 44 6.800408 CAGTTTTCGATAAGTAAGAGTGTCGA 59.200 38.462 0.00 0.00 36.46 4.20
44 45 6.581542 ACAGTTTTCGATAAGTAAGAGTGTCG 59.418 38.462 0.00 0.00 0.00 4.35
45 46 7.870588 ACAGTTTTCGATAAGTAAGAGTGTC 57.129 36.000 0.00 0.00 0.00 3.67
46 47 7.709613 ACAACAGTTTTCGATAAGTAAGAGTGT 59.290 33.333 0.00 0.00 0.00 3.55
47 48 8.004344 CACAACAGTTTTCGATAAGTAAGAGTG 58.996 37.037 0.00 1.00 0.00 3.51
48 49 7.924412 TCACAACAGTTTTCGATAAGTAAGAGT 59.076 33.333 0.00 0.00 0.00 3.24
49 50 8.294341 TCACAACAGTTTTCGATAAGTAAGAG 57.706 34.615 0.00 0.00 0.00 2.85
50 51 8.827177 ATCACAACAGTTTTCGATAAGTAAGA 57.173 30.769 0.00 0.00 0.00 2.10
51 52 8.926710 AGATCACAACAGTTTTCGATAAGTAAG 58.073 33.333 0.00 0.00 0.00 2.34
52 53 8.827177 AGATCACAACAGTTTTCGATAAGTAA 57.173 30.769 0.00 0.00 0.00 2.24
53 54 7.544566 GGAGATCACAACAGTTTTCGATAAGTA 59.455 37.037 0.00 0.00 0.00 2.24
54 55 6.369065 GGAGATCACAACAGTTTTCGATAAGT 59.631 38.462 0.00 0.00 0.00 2.24
55 56 6.591834 AGGAGATCACAACAGTTTTCGATAAG 59.408 38.462 0.00 0.00 0.00 1.73
56 57 6.464222 AGGAGATCACAACAGTTTTCGATAA 58.536 36.000 0.00 0.00 0.00 1.75
57 58 6.037786 AGGAGATCACAACAGTTTTCGATA 57.962 37.500 0.00 0.00 0.00 2.92
58 59 4.899502 AGGAGATCACAACAGTTTTCGAT 58.100 39.130 0.00 0.00 0.00 3.59
59 60 4.336889 AGGAGATCACAACAGTTTTCGA 57.663 40.909 0.00 0.00 0.00 3.71
60 61 7.036220 AGTATAGGAGATCACAACAGTTTTCG 58.964 38.462 0.00 0.00 0.00 3.46
61 62 8.660373 CAAGTATAGGAGATCACAACAGTTTTC 58.340 37.037 0.00 0.00 0.00 2.29
62 63 8.157476 ACAAGTATAGGAGATCACAACAGTTTT 58.843 33.333 0.00 0.00 0.00 2.43
63 64 7.604164 CACAAGTATAGGAGATCACAACAGTTT 59.396 37.037 0.00 0.00 0.00 2.66
64 65 7.099764 CACAAGTATAGGAGATCACAACAGTT 58.900 38.462 0.00 0.00 0.00 3.16
65 66 6.351371 CCACAAGTATAGGAGATCACAACAGT 60.351 42.308 0.00 0.00 0.00 3.55
66 67 6.045318 CCACAAGTATAGGAGATCACAACAG 58.955 44.000 0.00 0.00 0.00 3.16
67 68 5.104941 CCCACAAGTATAGGAGATCACAACA 60.105 44.000 0.00 0.00 0.00 3.33
68 69 5.104900 ACCCACAAGTATAGGAGATCACAAC 60.105 44.000 0.00 0.00 0.00 3.32
69 70 5.030147 ACCCACAAGTATAGGAGATCACAA 58.970 41.667 0.00 0.00 0.00 3.33
70 71 4.620723 ACCCACAAGTATAGGAGATCACA 58.379 43.478 0.00 0.00 0.00 3.58
71 72 5.615925 AACCCACAAGTATAGGAGATCAC 57.384 43.478 0.00 0.00 0.00 3.06
72 73 7.073208 TGATAACCCACAAGTATAGGAGATCA 58.927 38.462 0.00 0.00 0.00 2.92
73 74 7.451877 TCTGATAACCCACAAGTATAGGAGATC 59.548 40.741 0.00 0.00 0.00 2.75
74 75 7.306013 TCTGATAACCCACAAGTATAGGAGAT 58.694 38.462 0.00 0.00 0.00 2.75
75 76 6.679542 TCTGATAACCCACAAGTATAGGAGA 58.320 40.000 0.00 0.00 0.00 3.71
76 77 6.978674 TCTGATAACCCACAAGTATAGGAG 57.021 41.667 0.00 0.00 0.00 3.69
77 78 6.497259 GGATCTGATAACCCACAAGTATAGGA 59.503 42.308 0.00 0.00 0.00 2.94
78 79 6.295916 GGGATCTGATAACCCACAAGTATAGG 60.296 46.154 9.05 0.00 42.81 2.57
79 80 6.295916 GGGGATCTGATAACCCACAAGTATAG 60.296 46.154 19.65 0.00 44.87 1.31
80 81 5.546499 GGGGATCTGATAACCCACAAGTATA 59.454 44.000 19.65 0.00 44.87 1.47
81 82 4.351111 GGGGATCTGATAACCCACAAGTAT 59.649 45.833 19.65 0.00 44.87 2.12
82 83 3.714798 GGGGATCTGATAACCCACAAGTA 59.285 47.826 19.65 0.00 44.87 2.24
83 84 2.509964 GGGGATCTGATAACCCACAAGT 59.490 50.000 19.65 0.00 44.87 3.16
84 85 3.214696 GGGGATCTGATAACCCACAAG 57.785 52.381 19.65 0.00 44.87 3.16
89 90 0.250338 GCGTGGGGATCTGATAACCC 60.250 60.000 18.37 18.37 43.64 4.11
90 91 0.250338 GGCGTGGGGATCTGATAACC 60.250 60.000 0.00 0.00 0.00 2.85
91 92 0.250338 GGGCGTGGGGATCTGATAAC 60.250 60.000 0.00 0.00 0.00 1.89
92 93 1.754380 CGGGCGTGGGGATCTGATAA 61.754 60.000 0.00 0.00 0.00 1.75
93 94 2.207229 CGGGCGTGGGGATCTGATA 61.207 63.158 0.00 0.00 0.00 2.15
94 95 3.550431 CGGGCGTGGGGATCTGAT 61.550 66.667 0.00 0.00 0.00 2.90
181 182 2.910319 AGTAGGGTTGTGCTGGTGAATA 59.090 45.455 0.00 0.00 0.00 1.75
189 190 2.031495 AGAAGGAGTAGGGTTGTGCT 57.969 50.000 0.00 0.00 0.00 4.40
244 245 3.106407 GTGGCTCGAGTGACACGC 61.106 66.667 15.13 0.00 0.00 5.34
269 270 1.069090 GAGTGCGAGGTTGGTGACA 59.931 57.895 0.00 0.00 39.83 3.58
273 274 4.681978 GCGGAGTGCGAGGTTGGT 62.682 66.667 8.74 0.00 0.00 3.67
300 301 2.697761 GGCACGACGAGGTAGCTCA 61.698 63.158 21.17 0.00 0.00 4.26
328 329 2.050350 CCCGCTCTCTTACCCGTCA 61.050 63.158 0.00 0.00 0.00 4.35
360 361 9.176460 CTGGGCCAATAAATTTATTTTTGTCAT 57.824 29.630 18.72 0.00 31.28 3.06
386 387 6.381801 CCCAGTAAATTCTTGACATTGTCAC 58.618 40.000 18.84 5.45 42.60 3.67
398 399 2.304761 TCGCAACTCCCCAGTAAATTCT 59.695 45.455 0.00 0.00 30.14 2.40
399 400 2.706890 TCGCAACTCCCCAGTAAATTC 58.293 47.619 0.00 0.00 30.14 2.17
448 449 6.715264 GGGTATTATTAGGGTTGTCTCAATGG 59.285 42.308 0.00 0.00 0.00 3.16
571 989 3.072915 TCTCCTGTGAGGCAAAGATGAAA 59.927 43.478 0.00 0.00 39.23 2.69
585 1003 5.525378 GGTTGCTAGTAAATCATCTCCTGTG 59.475 44.000 0.00 0.00 0.00 3.66
596 1014 6.430000 ACAATCTTCAACGGTTGCTAGTAAAT 59.570 34.615 15.89 3.63 0.00 1.40
605 1023 5.682943 TCCTTTACAATCTTCAACGGTTG 57.317 39.130 14.62 14.62 0.00 3.77
625 1043 1.073284 TGTGGTTTACTGCTCCCTTCC 59.927 52.381 0.00 0.00 0.00 3.46
661 1079 4.487948 CAAAGATGAATGGAATTGCACGT 58.512 39.130 0.12 0.00 36.07 4.49
712 1131 2.095314 GCTGCCTTTCTTCTGAAGCTTC 60.095 50.000 19.89 19.89 33.28 3.86
738 1160 2.279318 TCGTGTGCACCGCGTTTA 60.279 55.556 23.63 8.24 46.91 2.01
739 1161 3.932313 GTCGTGTGCACCGCGTTT 61.932 61.111 23.63 0.00 46.91 3.60
743 1165 3.406361 CTCTGTCGTGTGCACCGC 61.406 66.667 15.69 13.18 0.00 5.68
744 1166 3.406361 GCTCTGTCGTGTGCACCG 61.406 66.667 15.69 17.12 0.00 4.94
745 1167 3.406361 CGCTCTGTCGTGTGCACC 61.406 66.667 15.69 4.74 0.00 5.01
746 1168 2.237751 AACGCTCTGTCGTGTGCAC 61.238 57.895 10.75 10.75 42.46 4.57
747 1169 2.106131 AACGCTCTGTCGTGTGCA 59.894 55.556 0.00 0.00 42.46 4.57
748 1170 2.546321 CAACGCTCTGTCGTGTGC 59.454 61.111 0.00 0.00 42.46 4.57
749 1171 2.546321 GCAACGCTCTGTCGTGTG 59.454 61.111 0.00 0.00 42.46 3.82
750 1172 3.030308 CGCAACGCTCTGTCGTGT 61.030 61.111 0.00 0.00 42.46 4.49
751 1173 3.767230 CCGCAACGCTCTGTCGTG 61.767 66.667 0.00 0.00 42.46 4.35
752 1174 4.280494 ACCGCAACGCTCTGTCGT 62.280 61.111 0.00 0.00 45.58 4.34
811 1233 2.092807 AGGGGTTTCGTGTAAAGTGTGT 60.093 45.455 0.00 0.00 0.00 3.72
919 1341 1.485124 GATTTGGGGGCTAGGGTTTG 58.515 55.000 0.00 0.00 0.00 2.93
1056 1478 0.384309 TGATGATCGCGTACAGGTCC 59.616 55.000 5.77 0.45 0.00 4.46
1167 1589 0.935194 GGGAGGAGGAGAGGGAGTTA 59.065 60.000 0.00 0.00 0.00 2.24
1344 1766 4.552365 CACTGGGCGATGGCGGAT 62.552 66.667 0.00 0.00 41.24 4.18
1524 1946 1.613836 CCCCCATCTTATGCAGCTTC 58.386 55.000 0.00 0.00 0.00 3.86
1557 1979 0.826715 GTCTGGCCTGCTGATCTGTA 59.173 55.000 3.32 0.00 0.00 2.74
1649 2071 0.250513 ACTCAGAACCAAGCCGATCC 59.749 55.000 0.00 0.00 0.00 3.36
1664 2086 8.055279 ACAAAACAGAAAGAAGAATCAACTCA 57.945 30.769 0.00 0.00 0.00 3.41
1671 2093 7.014038 AGAGCATGACAAAACAGAAAGAAGAAT 59.986 33.333 0.00 0.00 0.00 2.40
1750 2173 6.449635 TCCATAAGATTGGCATTGTTGTAC 57.550 37.500 2.41 0.00 36.66 2.90
1751 2174 7.178274 ACTTTCCATAAGATTGGCATTGTTGTA 59.822 33.333 2.41 0.00 36.66 2.41
1781 2204 5.614324 ATGAAACAATCGATCTGTAGGGA 57.386 39.130 0.00 0.00 0.00 4.20
1808 2232 8.108378 TGAATACAATCAAGGGTCCCTATAAA 57.892 34.615 12.06 0.00 31.13 1.40
1888 2319 6.870965 AGTACAAACATAAGAACAGCTCAGAG 59.129 38.462 0.00 0.00 0.00 3.35
1909 2340 9.562583 TCAAAAGACAACATTGTAACAAAGTAC 57.437 29.630 0.00 0.00 42.43 2.73
1921 2352 5.885912 ACAGTAGTGGTCAAAAGACAACATT 59.114 36.000 1.92 0.00 31.57 2.71
1978 2409 7.899178 TCGCTCTGTTATCAACAAAGAATAA 57.101 32.000 0.00 0.00 41.61 1.40
2032 2463 8.233868 TCGCACCACATATAATAATTATGCAAC 58.766 33.333 0.00 0.00 0.00 4.17
2056 2487 1.927174 GGACATCACGGAGAAACATCG 59.073 52.381 0.00 0.00 0.00 3.84
2217 2649 3.636153 AGTTCCAACTGCCCTAGATTC 57.364 47.619 0.00 0.00 37.98 2.52
2316 2748 6.633668 GTGTAGACACATCATGACTTGTAC 57.366 41.667 10.33 7.47 45.75 2.90
2342 2774 8.441608 CAAATCAATGATGCCATTTCGTTAAAA 58.558 29.630 0.00 0.00 40.81 1.52
2349 2783 8.882415 AACTATCAAATCAATGATGCCATTTC 57.118 30.769 0.00 0.00 40.81 2.17
2354 2788 9.754382 ATACAAAACTATCAAATCAATGATGCC 57.246 29.630 0.00 0.00 40.21 4.40
2386 2820 7.210718 TCGAGAAGTACAGAGTTGAATACAA 57.789 36.000 0.00 0.00 0.00 2.41
2398 2833 6.980978 ACCATTATTGACATCGAGAAGTACAG 59.019 38.462 0.00 0.00 0.00 2.74
2464 2901 2.029290 AGTACTGATCCAACGACCACAC 60.029 50.000 0.00 0.00 0.00 3.82
2481 2918 2.620251 TATGGATGGCACTGCAGTAC 57.380 50.000 21.20 14.70 0.00 2.73
2559 2996 5.334646 CCAATATGCAACAGAATCCATCGAG 60.335 44.000 0.00 0.00 0.00 4.04
2606 3057 4.202101 TGAATGGACATCACAAACCAACAC 60.202 41.667 0.00 0.00 36.00 3.32
2611 3062 5.138125 ACATTGAATGGACATCACAAACC 57.862 39.130 10.27 0.00 33.60 3.27


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

AutoCloner maintained by Alex Coulton.