Multiple sequence alignment - TraesCS5D01G326900

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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 TraesCS5D01G326900 chr5D 100.000 2417 0 0 1 2417 419365812 419363396 0.000000e+00 4464
1 TraesCS5D01G326900 chr5D 98.525 1017 14 1 1402 2417 419462593 419461577 0.000000e+00 1794
2 TraesCS5D01G326900 chr5D 99.102 668 6 0 732 1399 329121315 329121982 0.000000e+00 1201
3 TraesCS5D01G326900 chr5D 98.952 668 6 1 732 1399 503217009 503216343 0.000000e+00 1194
4 TraesCS5D01G326900 chr5D 94.531 384 5 7 350 732 419462962 419462594 1.610000e-161 579
5 TraesCS5D01G326900 chrUn 99.404 671 4 0 732 1402 93410839 93411509 0.000000e+00 1218
6 TraesCS5D01G326900 chrUn 93.103 145 9 1 1682 1826 279331511 279331368 6.770000e-51 211
7 TraesCS5D01G326900 chrUn 93.103 145 9 1 1682 1826 326755741 326755884 6.770000e-51 211
8 TraesCS5D01G326900 chrUn 93.103 145 9 1 1682 1826 349543314 349543457 6.770000e-51 211
9 TraesCS5D01G326900 chrUn 93.103 145 9 1 1682 1826 386695312 386695455 6.770000e-51 211
10 TraesCS5D01G326900 chr2D 99.401 668 4 0 732 1399 272795102 272795769 0.000000e+00 1212
11 TraesCS5D01G326900 chr6D 99.255 671 4 1 732 1402 168250331 168249662 0.000000e+00 1210
12 TraesCS5D01G326900 chr7D 99.106 671 6 0 732 1402 231547384 231546714 0.000000e+00 1206
13 TraesCS5D01G326900 chr7D 94.231 572 32 1 1847 2417 612677905 612678476 0.000000e+00 872
14 TraesCS5D01G326900 chr7D 94.087 575 27 2 1843 2417 475459751 475459184 0.000000e+00 867
15 TraesCS5D01G326900 chr7D 93.531 572 36 1 1847 2417 66542487 66541916 0.000000e+00 850
16 TraesCS5D01G326900 chr3A 98.361 671 10 1 732 1402 672911218 672911887 0.000000e+00 1177
17 TraesCS5D01G326900 chr3A 87.455 279 27 4 171 449 724868031 724868301 5.020000e-82 315
18 TraesCS5D01G326900 chr3A 92.019 213 15 2 212 424 625722564 625722354 5.050000e-77 298
19 TraesCS5D01G326900 chr3A 91.057 123 10 1 1448 1569 625722034 625721912 5.350000e-37 165
20 TraesCS5D01G326900 chr3B 98.353 668 10 1 732 1399 201525815 201525149 0.000000e+00 1171
21 TraesCS5D01G326900 chr2A 97.754 668 12 2 732 1399 335829686 335829022 0.000000e+00 1147
22 TraesCS5D01G326900 chr2A 93.170 571 18 9 171 732 279494189 279494747 0.000000e+00 819
23 TraesCS5D01G326900 chr2A 92.774 429 26 4 1424 1848 279494763 279495190 1.230000e-172 616
24 TraesCS5D01G326900 chr2A 89.655 232 18 5 211 442 460724045 460724270 8.450000e-75 291
25 TraesCS5D01G326900 chr2A 91.160 181 15 1 266 446 19241079 19241258 6.670000e-61 244
26 TraesCS5D01G326900 chr2A 83.600 250 31 7 1402 1649 460724624 460724865 2.420000e-55 226
27 TraesCS5D01G326900 chr3D 94.066 573 32 2 1847 2417 37176399 37175827 0.000000e+00 869
28 TraesCS5D01G326900 chr3D 89.344 244 14 5 210 453 342810927 342810696 1.820000e-76 296
29 TraesCS5D01G326900 chr3D 89.516 124 12 1 205 328 346957009 346957131 3.220000e-34 156
30 TraesCS5D01G326900 chr3D 97.260 73 2 0 1499 1571 342810523 342810451 9.070000e-25 124
31 TraesCS5D01G326900 chr7B 90.334 569 55 0 1849 2417 354241941 354242509 0.000000e+00 747
32 TraesCS5D01G326900 chr4B 88.991 545 60 0 1873 2417 67350865 67350321 0.000000e+00 675
33 TraesCS5D01G326900 chr2B 88.510 557 63 1 1847 2403 261103676 261104231 0.000000e+00 673
34 TraesCS5D01G326900 chr2B 87.097 558 66 5 1847 2401 796382136 796382690 5.670000e-176 627
35 TraesCS5D01G326900 chr4D 91.632 239 18 2 211 449 445760835 445761071 1.790000e-86 329
36 TraesCS5D01G326900 chr4D 84.646 254 29 7 1402 1653 445761466 445761711 6.670000e-61 244
37 TraesCS5D01G326900 chr7A 93.103 145 9 1 1682 1826 734190183 734190040 6.770000e-51 211
38 TraesCS5D01G326900 chr5A 86.842 152 11 4 2 149 534989139 534989285 6.920000e-36 161
39 TraesCS5D01G326900 chr5A 96.203 79 3 0 1770 1848 219242751 219242673 1.950000e-26 130
40 TraesCS5D01G326900 chr4A 97.143 70 2 0 1779 1848 374327087 374327018 4.220000e-23 119


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 TraesCS5D01G326900 chr5D 419363396 419365812 2416 True 4464.0 4464 100.0000 1 2417 1 chr5D.!!$R1 2416
1 TraesCS5D01G326900 chr5D 329121315 329121982 667 False 1201.0 1201 99.1020 732 1399 1 chr5D.!!$F1 667
2 TraesCS5D01G326900 chr5D 503216343 503217009 666 True 1194.0 1194 98.9520 732 1399 1 chr5D.!!$R2 667
3 TraesCS5D01G326900 chr5D 419461577 419462962 1385 True 1186.5 1794 96.5280 350 2417 2 chr5D.!!$R3 2067
4 TraesCS5D01G326900 chrUn 93410839 93411509 670 False 1218.0 1218 99.4040 732 1402 1 chrUn.!!$F1 670
5 TraesCS5D01G326900 chr2D 272795102 272795769 667 False 1212.0 1212 99.4010 732 1399 1 chr2D.!!$F1 667
6 TraesCS5D01G326900 chr6D 168249662 168250331 669 True 1210.0 1210 99.2550 732 1402 1 chr6D.!!$R1 670
7 TraesCS5D01G326900 chr7D 231546714 231547384 670 True 1206.0 1206 99.1060 732 1402 1 chr7D.!!$R2 670
8 TraesCS5D01G326900 chr7D 612677905 612678476 571 False 872.0 872 94.2310 1847 2417 1 chr7D.!!$F1 570
9 TraesCS5D01G326900 chr7D 475459184 475459751 567 True 867.0 867 94.0870 1843 2417 1 chr7D.!!$R3 574
10 TraesCS5D01G326900 chr7D 66541916 66542487 571 True 850.0 850 93.5310 1847 2417 1 chr7D.!!$R1 570
11 TraesCS5D01G326900 chr3A 672911218 672911887 669 False 1177.0 1177 98.3610 732 1402 1 chr3A.!!$F1 670
12 TraesCS5D01G326900 chr3A 625721912 625722564 652 True 231.5 298 91.5380 212 1569 2 chr3A.!!$R1 1357
13 TraesCS5D01G326900 chr3B 201525149 201525815 666 True 1171.0 1171 98.3530 732 1399 1 chr3B.!!$R1 667
14 TraesCS5D01G326900 chr2A 335829022 335829686 664 True 1147.0 1147 97.7540 732 1399 1 chr2A.!!$R1 667
15 TraesCS5D01G326900 chr2A 279494189 279495190 1001 False 717.5 819 92.9720 171 1848 2 chr2A.!!$F2 1677
16 TraesCS5D01G326900 chr2A 460724045 460724865 820 False 258.5 291 86.6275 211 1649 2 chr2A.!!$F3 1438
17 TraesCS5D01G326900 chr3D 37175827 37176399 572 True 869.0 869 94.0660 1847 2417 1 chr3D.!!$R1 570
18 TraesCS5D01G326900 chr7B 354241941 354242509 568 False 747.0 747 90.3340 1849 2417 1 chr7B.!!$F1 568
19 TraesCS5D01G326900 chr4B 67350321 67350865 544 True 675.0 675 88.9910 1873 2417 1 chr4B.!!$R1 544
20 TraesCS5D01G326900 chr2B 261103676 261104231 555 False 673.0 673 88.5100 1847 2403 1 chr2B.!!$F1 556
21 TraesCS5D01G326900 chr2B 796382136 796382690 554 False 627.0 627 87.0970 1847 2401 1 chr2B.!!$F2 554
22 TraesCS5D01G326900 chr4D 445760835 445761711 876 False 286.5 329 88.1390 211 1653 2 chr4D.!!$F1 1442

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
686 722 1.616921 CATGCCCACTCCTTCCCAT 59.383 57.895 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 2569 1.270305 TGAATTCGGATGGAGCGATCC 60.27 52.381 14.17 14.17 38.93 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
31 32 9.522193 TGGTAGGATATATGGTACTAGAGATCT 57.478 37.037 8.15 0.00 0.00 2.75
32 33 9.787435 GGTAGGATATATGGTACTAGAGATCTG 57.213 40.741 0.00 0.00 0.00 2.90
35 36 9.693739 AGGATATATGGTACTAGAGATCTGTTG 57.306 37.037 0.00 0.00 0.00 3.33
36 37 9.469097 GGATATATGGTACTAGAGATCTGTTGT 57.531 37.037 11.43 11.43 0.00 3.32
38 39 9.815306 ATATATGGTACTAGAGATCTGTTGTGT 57.185 33.333 15.53 7.43 0.00 3.72
39 40 5.899120 TGGTACTAGAGATCTGTTGTGTC 57.101 43.478 15.53 9.18 0.00 3.67
40 41 5.571285 TGGTACTAGAGATCTGTTGTGTCT 58.429 41.667 15.53 0.95 0.00 3.41
41 42 6.718294 TGGTACTAGAGATCTGTTGTGTCTA 58.282 40.000 15.53 5.63 0.00 2.59
42 43 6.598457 TGGTACTAGAGATCTGTTGTGTCTAC 59.402 42.308 15.53 6.83 0.00 2.59
43 44 6.038492 GGTACTAGAGATCTGTTGTGTCTACC 59.962 46.154 15.53 11.40 0.00 3.18
44 45 4.951094 ACTAGAGATCTGTTGTGTCTACCC 59.049 45.833 0.00 0.00 0.00 3.69
45 46 3.100671 AGAGATCTGTTGTGTCTACCCC 58.899 50.000 0.00 0.00 0.00 4.95
46 47 3.100671 GAGATCTGTTGTGTCTACCCCT 58.899 50.000 0.00 0.00 0.00 4.79
47 48 3.515901 GAGATCTGTTGTGTCTACCCCTT 59.484 47.826 0.00 0.00 0.00 3.95
48 49 3.910627 AGATCTGTTGTGTCTACCCCTTT 59.089 43.478 0.00 0.00 0.00 3.11
49 50 3.485463 TCTGTTGTGTCTACCCCTTTG 57.515 47.619 0.00 0.00 0.00 2.77
50 51 2.105821 TCTGTTGTGTCTACCCCTTTGG 59.894 50.000 0.00 0.00 41.37 3.28
64 65 4.053469 CCCTTTGGGCGTTTTAATATGG 57.947 45.455 0.00 0.00 35.35 2.74
65 66 3.449377 CCCTTTGGGCGTTTTAATATGGT 59.551 43.478 0.00 0.00 35.35 3.55
66 67 4.645588 CCCTTTGGGCGTTTTAATATGGTA 59.354 41.667 0.00 0.00 35.35 3.25
67 68 5.303333 CCCTTTGGGCGTTTTAATATGGTAT 59.697 40.000 0.00 0.00 35.35 2.73
68 69 6.490721 CCCTTTGGGCGTTTTAATATGGTATA 59.509 38.462 0.00 0.00 35.35 1.47
69 70 7.177744 CCCTTTGGGCGTTTTAATATGGTATAT 59.822 37.037 0.00 0.00 35.35 0.86
70 71 9.233649 CCTTTGGGCGTTTTAATATGGTATATA 57.766 33.333 0.00 0.00 0.00 0.86
105 106 8.824756 ACCAAGATATAGACAGAGTGTAGAAA 57.175 34.615 0.00 0.00 0.00 2.52
106 107 8.688151 ACCAAGATATAGACAGAGTGTAGAAAC 58.312 37.037 0.00 0.00 0.00 2.78
107 108 8.908903 CCAAGATATAGACAGAGTGTAGAAACT 58.091 37.037 0.00 0.00 0.00 2.66
108 109 9.729023 CAAGATATAGACAGAGTGTAGAAACTG 57.271 37.037 0.00 0.00 36.58 3.16
109 110 7.936584 AGATATAGACAGAGTGTAGAAACTGC 58.063 38.462 0.00 0.00 34.25 4.40
110 111 3.669251 AGACAGAGTGTAGAAACTGCC 57.331 47.619 0.00 0.00 34.25 4.85
111 112 3.235200 AGACAGAGTGTAGAAACTGCCT 58.765 45.455 0.00 0.00 34.25 4.75
112 113 3.006323 AGACAGAGTGTAGAAACTGCCTG 59.994 47.826 0.00 0.00 34.25 4.85
113 114 2.965831 ACAGAGTGTAGAAACTGCCTGA 59.034 45.455 0.00 0.00 34.25 3.86
114 115 3.388024 ACAGAGTGTAGAAACTGCCTGAA 59.612 43.478 0.00 0.00 34.25 3.02
115 116 3.743396 CAGAGTGTAGAAACTGCCTGAAC 59.257 47.826 0.00 0.00 0.00 3.18
116 117 3.067833 GAGTGTAGAAACTGCCTGAACC 58.932 50.000 0.00 0.00 0.00 3.62
117 118 2.438021 AGTGTAGAAACTGCCTGAACCA 59.562 45.455 0.00 0.00 0.00 3.67
118 119 2.548480 GTGTAGAAACTGCCTGAACCAC 59.452 50.000 0.00 0.00 0.00 4.16
119 120 2.438021 TGTAGAAACTGCCTGAACCACT 59.562 45.455 0.00 0.00 0.00 4.00
120 121 2.736670 AGAAACTGCCTGAACCACTT 57.263 45.000 0.00 0.00 0.00 3.16
121 122 2.301346 AGAAACTGCCTGAACCACTTG 58.699 47.619 0.00 0.00 0.00 3.16
122 123 2.092429 AGAAACTGCCTGAACCACTTGA 60.092 45.455 0.00 0.00 0.00 3.02
123 124 2.435372 AACTGCCTGAACCACTTGAA 57.565 45.000 0.00 0.00 0.00 2.69
124 125 2.664402 ACTGCCTGAACCACTTGAAT 57.336 45.000 0.00 0.00 0.00 2.57
125 126 2.949447 ACTGCCTGAACCACTTGAATT 58.051 42.857 0.00 0.00 0.00 2.17
126 127 3.299503 ACTGCCTGAACCACTTGAATTT 58.700 40.909 0.00 0.00 0.00 1.82
127 128 3.706086 ACTGCCTGAACCACTTGAATTTT 59.294 39.130 0.00 0.00 0.00 1.82
128 129 4.892934 ACTGCCTGAACCACTTGAATTTTA 59.107 37.500 0.00 0.00 0.00 1.52
129 130 5.362430 ACTGCCTGAACCACTTGAATTTTAA 59.638 36.000 0.00 0.00 0.00 1.52
130 131 6.041979 ACTGCCTGAACCACTTGAATTTTAAT 59.958 34.615 0.00 0.00 0.00 1.40
131 132 6.825610 TGCCTGAACCACTTGAATTTTAATT 58.174 32.000 0.00 0.00 0.00 1.40
132 133 7.278875 TGCCTGAACCACTTGAATTTTAATTT 58.721 30.769 0.00 0.00 0.00 1.82
133 134 7.226325 TGCCTGAACCACTTGAATTTTAATTTG 59.774 33.333 0.00 0.00 0.00 2.32
134 135 7.307930 GCCTGAACCACTTGAATTTTAATTTGG 60.308 37.037 3.30 3.30 31.79 3.28
135 136 7.714813 CCTGAACCACTTGAATTTTAATTTGGT 59.285 33.333 4.29 4.29 37.37 3.67
136 137 8.430801 TGAACCACTTGAATTTTAATTTGGTG 57.569 30.769 9.06 8.52 36.45 4.17
137 138 6.859420 ACCACTTGAATTTTAATTTGGTGC 57.141 33.333 7.97 0.00 35.53 5.01
138 139 6.352516 ACCACTTGAATTTTAATTTGGTGCA 58.647 32.000 7.97 0.00 35.53 4.57
139 140 6.482973 ACCACTTGAATTTTAATTTGGTGCAG 59.517 34.615 7.97 2.33 35.53 4.41
140 141 6.482973 CCACTTGAATTTTAATTTGGTGCAGT 59.517 34.615 0.00 0.00 0.00 4.40
141 142 7.012232 CCACTTGAATTTTAATTTGGTGCAGTT 59.988 33.333 0.00 0.00 0.00 3.16
142 143 8.397148 CACTTGAATTTTAATTTGGTGCAGTTT 58.603 29.630 0.00 0.00 0.00 2.66
143 144 8.955388 ACTTGAATTTTAATTTGGTGCAGTTTT 58.045 25.926 0.00 0.00 0.00 2.43
144 145 9.786105 CTTGAATTTTAATTTGGTGCAGTTTTT 57.214 25.926 0.00 0.00 0.00 1.94
145 146 9.565213 TTGAATTTTAATTTGGTGCAGTTTTTG 57.435 25.926 0.00 0.00 0.00 2.44
162 163 8.992287 CAGTTTTTGCAATTTTAATCTGAACC 57.008 30.769 0.00 0.00 0.00 3.62
163 164 8.610896 CAGTTTTTGCAATTTTAATCTGAACCA 58.389 29.630 0.00 0.00 0.00 3.67
164 165 9.171877 AGTTTTTGCAATTTTAATCTGAACCAA 57.828 25.926 0.00 0.00 0.00 3.67
165 166 9.780413 GTTTTTGCAATTTTAATCTGAACCAAA 57.220 25.926 0.00 0.00 0.00 3.28
167 168 9.947669 TTTTGCAATTTTAATCTGAACCAAATG 57.052 25.926 0.00 0.00 0.00 2.32
168 169 8.899427 TTGCAATTTTAATCTGAACCAAATGA 57.101 26.923 0.00 0.00 0.00 2.57
169 170 8.899427 TGCAATTTTAATCTGAACCAAATGAA 57.101 26.923 0.00 0.00 0.00 2.57
195 196 6.859508 CCATATGCACAACACATCATATTGTC 59.140 38.462 0.00 0.00 34.36 3.18
341 342 9.683069 GAATCTTAACATCACAAACTGAAACAT 57.317 29.630 0.00 0.00 30.60 2.71
488 515 9.691362 ACTCTTATTTTTGCGACATATGTTTTT 57.309 25.926 10.30 0.00 0.00 1.94
594 623 4.890988 TCACTTATGGAAGGGATACTCCA 58.109 43.478 0.00 0.00 40.32 3.86
683 719 2.048603 GTGCATGCCCACTCCTTCC 61.049 63.158 16.68 0.00 33.02 3.46
684 720 2.440980 GCATGCCCACTCCTTCCC 60.441 66.667 6.36 0.00 0.00 3.97
685 721 3.089838 CATGCCCACTCCTTCCCA 58.910 61.111 0.00 0.00 0.00 4.37
686 722 1.616921 CATGCCCACTCCTTCCCAT 59.383 57.895 0.00 0.00 0.00 4.00
702 738 9.171877 CTCCTTCCCATATTATAATCTCTTTGC 57.828 37.037 0.00 0.00 0.00 3.68
713 749 3.883744 CTCTTTGCGCCACGGTCCT 62.884 63.158 4.18 0.00 0.00 3.85
727 763 4.384208 CCACGGTCCTTCTTCCTTCATTAT 60.384 45.833 0.00 0.00 0.00 1.28
728 764 5.163343 CCACGGTCCTTCTTCCTTCATTATA 60.163 44.000 0.00 0.00 0.00 0.98
729 765 6.464465 CCACGGTCCTTCTTCCTTCATTATAT 60.464 42.308 0.00 0.00 0.00 0.86
730 766 6.647067 CACGGTCCTTCTTCCTTCATTATATC 59.353 42.308 0.00 0.00 0.00 1.63
1774 2021 1.445582 GGGAGGTGCACGTACGAAG 60.446 63.158 24.41 14.85 0.00 3.79
1957 2206 6.315642 GGAACTTCTAGCCAAACCTTACATAC 59.684 42.308 0.00 0.00 0.00 2.39
2073 2322 6.314917 AGGATGGTTTTGATTTCTTGTACCT 58.685 36.000 0.00 0.00 0.00 3.08
2209 2458 6.638021 ACCCCTTTTACAAGCTAGTATCTT 57.362 37.500 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.787435 CAGATCTCTAGTACCATATATCCTACC 57.213 40.741 0.00 0.00 0.00 3.18
9 10 9.693739 CAACAGATCTCTAGTACCATATATCCT 57.306 37.037 0.00 0.00 0.00 3.24
10 11 9.469097 ACAACAGATCTCTAGTACCATATATCC 57.531 37.037 0.00 0.00 0.00 2.59
12 13 9.815306 ACACAACAGATCTCTAGTACCATATAT 57.185 33.333 0.00 0.00 0.00 0.86
13 14 9.286170 GACACAACAGATCTCTAGTACCATATA 57.714 37.037 0.00 0.00 0.00 0.86
14 15 8.001875 AGACACAACAGATCTCTAGTACCATAT 58.998 37.037 0.00 0.00 0.00 1.78
15 16 7.347252 AGACACAACAGATCTCTAGTACCATA 58.653 38.462 0.00 0.00 0.00 2.74
16 17 6.191315 AGACACAACAGATCTCTAGTACCAT 58.809 40.000 0.00 0.00 0.00 3.55
17 18 5.571285 AGACACAACAGATCTCTAGTACCA 58.429 41.667 0.00 0.00 0.00 3.25
18 19 6.038492 GGTAGACACAACAGATCTCTAGTACC 59.962 46.154 0.00 0.00 0.00 3.34
19 20 6.038492 GGGTAGACACAACAGATCTCTAGTAC 59.962 46.154 0.00 0.00 0.00 2.73
20 21 6.120905 GGGTAGACACAACAGATCTCTAGTA 58.879 44.000 0.00 0.00 0.00 1.82
21 22 4.951094 GGGTAGACACAACAGATCTCTAGT 59.049 45.833 0.00 0.00 0.00 2.57
22 23 4.339814 GGGGTAGACACAACAGATCTCTAG 59.660 50.000 0.00 0.00 0.00 2.43
23 24 4.017407 AGGGGTAGACACAACAGATCTCTA 60.017 45.833 0.00 0.00 0.00 2.43
24 25 3.100671 GGGGTAGACACAACAGATCTCT 58.899 50.000 0.00 0.00 0.00 3.10
25 26 3.100671 AGGGGTAGACACAACAGATCTC 58.899 50.000 0.00 0.00 0.00 2.75
26 27 3.191888 AGGGGTAGACACAACAGATCT 57.808 47.619 0.00 0.00 0.00 2.75
27 28 3.983044 AAGGGGTAGACACAACAGATC 57.017 47.619 0.00 0.00 0.00 2.75
28 29 3.244911 CCAAAGGGGTAGACACAACAGAT 60.245 47.826 0.00 0.00 0.00 2.90
29 30 2.105821 CCAAAGGGGTAGACACAACAGA 59.894 50.000 0.00 0.00 0.00 3.41
30 31 2.504367 CCAAAGGGGTAGACACAACAG 58.496 52.381 0.00 0.00 0.00 3.16
31 32 2.649531 CCAAAGGGGTAGACACAACA 57.350 50.000 0.00 0.00 0.00 3.33
44 45 4.729227 ACCATATTAAAACGCCCAAAGG 57.271 40.909 0.00 0.00 0.00 3.11
79 80 9.916360 TTTCTACACTCTGTCTATATCTTGGTA 57.084 33.333 0.00 0.00 0.00 3.25
80 81 8.688151 GTTTCTACACTCTGTCTATATCTTGGT 58.312 37.037 0.00 0.00 0.00 3.67
81 82 8.908903 AGTTTCTACACTCTGTCTATATCTTGG 58.091 37.037 0.00 0.00 0.00 3.61
82 83 9.729023 CAGTTTCTACACTCTGTCTATATCTTG 57.271 37.037 0.00 0.00 0.00 3.02
83 84 8.410141 GCAGTTTCTACACTCTGTCTATATCTT 58.590 37.037 0.00 0.00 0.00 2.40
84 85 7.013846 GGCAGTTTCTACACTCTGTCTATATCT 59.986 40.741 0.00 0.00 31.03 1.98
85 86 7.013846 AGGCAGTTTCTACACTCTGTCTATATC 59.986 40.741 0.00 0.00 40.38 1.63
86 87 6.836527 AGGCAGTTTCTACACTCTGTCTATAT 59.163 38.462 0.00 0.00 40.38 0.86
87 88 6.095580 CAGGCAGTTTCTACACTCTGTCTATA 59.904 42.308 0.00 0.00 40.23 1.31
88 89 5.020132 AGGCAGTTTCTACACTCTGTCTAT 58.980 41.667 0.00 0.00 40.38 1.98
89 90 4.218635 CAGGCAGTTTCTACACTCTGTCTA 59.781 45.833 0.00 0.00 40.23 2.59
90 91 3.006323 CAGGCAGTTTCTACACTCTGTCT 59.994 47.826 0.00 0.00 42.44 3.41
91 92 3.005897 TCAGGCAGTTTCTACACTCTGTC 59.994 47.826 0.00 0.00 33.43 3.51
92 93 2.965831 TCAGGCAGTTTCTACACTCTGT 59.034 45.455 0.00 0.00 0.00 3.41
93 94 3.667497 TCAGGCAGTTTCTACACTCTG 57.333 47.619 0.00 0.00 0.00 3.35
94 95 3.244249 GGTTCAGGCAGTTTCTACACTCT 60.244 47.826 0.00 0.00 0.00 3.24
95 96 3.067833 GGTTCAGGCAGTTTCTACACTC 58.932 50.000 0.00 0.00 0.00 3.51
96 97 2.438021 TGGTTCAGGCAGTTTCTACACT 59.562 45.455 0.00 0.00 0.00 3.55
97 98 2.548480 GTGGTTCAGGCAGTTTCTACAC 59.452 50.000 0.00 0.00 0.00 2.90
98 99 2.438021 AGTGGTTCAGGCAGTTTCTACA 59.562 45.455 0.00 0.00 0.00 2.74
99 100 3.127425 AGTGGTTCAGGCAGTTTCTAC 57.873 47.619 0.00 0.00 0.00 2.59
100 101 3.135712 TCAAGTGGTTCAGGCAGTTTCTA 59.864 43.478 0.00 0.00 0.00 2.10
101 102 2.092429 TCAAGTGGTTCAGGCAGTTTCT 60.092 45.455 0.00 0.00 0.00 2.52
102 103 2.297701 TCAAGTGGTTCAGGCAGTTTC 58.702 47.619 0.00 0.00 0.00 2.78
103 104 2.435372 TCAAGTGGTTCAGGCAGTTT 57.565 45.000 0.00 0.00 0.00 2.66
104 105 2.435372 TTCAAGTGGTTCAGGCAGTT 57.565 45.000 0.00 0.00 0.00 3.16
105 106 2.664402 ATTCAAGTGGTTCAGGCAGT 57.336 45.000 0.00 0.00 0.00 4.40
106 107 4.326504 AAAATTCAAGTGGTTCAGGCAG 57.673 40.909 0.00 0.00 0.00 4.85
107 108 5.860941 TTAAAATTCAAGTGGTTCAGGCA 57.139 34.783 0.00 0.00 0.00 4.75
108 109 7.307930 CCAAATTAAAATTCAAGTGGTTCAGGC 60.308 37.037 0.00 0.00 0.00 4.85
109 110 7.714813 ACCAAATTAAAATTCAAGTGGTTCAGG 59.285 33.333 4.43 0.00 33.99 3.86
110 111 8.550376 CACCAAATTAAAATTCAAGTGGTTCAG 58.450 33.333 6.74 0.00 34.96 3.02
111 112 7.011857 GCACCAAATTAAAATTCAAGTGGTTCA 59.988 33.333 6.74 0.00 34.96 3.18
112 113 7.011857 TGCACCAAATTAAAATTCAAGTGGTTC 59.988 33.333 6.74 4.21 34.96 3.62
113 114 6.825721 TGCACCAAATTAAAATTCAAGTGGTT 59.174 30.769 6.74 0.00 34.96 3.67
114 115 6.352516 TGCACCAAATTAAAATTCAAGTGGT 58.647 32.000 4.43 4.43 36.64 4.16
115 116 6.482973 ACTGCACCAAATTAAAATTCAAGTGG 59.517 34.615 11.32 7.83 31.79 4.00
116 117 7.481275 ACTGCACCAAATTAAAATTCAAGTG 57.519 32.000 0.00 7.53 0.00 3.16
117 118 8.504812 AAACTGCACCAAATTAAAATTCAAGT 57.495 26.923 0.00 0.00 0.00 3.16
118 119 9.786105 AAAAACTGCACCAAATTAAAATTCAAG 57.214 25.926 0.00 0.00 0.00 3.02
119 120 9.565213 CAAAAACTGCACCAAATTAAAATTCAA 57.435 25.926 0.00 0.00 0.00 2.69
137 138 8.610896 TGGTTCAGATTAAAATTGCAAAAACTG 58.389 29.630 1.71 7.83 0.00 3.16
138 139 8.729805 TGGTTCAGATTAAAATTGCAAAAACT 57.270 26.923 1.71 0.00 0.00 2.66
139 140 9.780413 TTTGGTTCAGATTAAAATTGCAAAAAC 57.220 25.926 1.71 0.00 0.00 2.43
141 142 9.947669 CATTTGGTTCAGATTAAAATTGCAAAA 57.052 25.926 1.71 0.00 0.00 2.44
142 143 9.334947 TCATTTGGTTCAGATTAAAATTGCAAA 57.665 25.926 1.71 0.00 0.00 3.68
143 144 8.899427 TCATTTGGTTCAGATTAAAATTGCAA 57.101 26.923 0.00 0.00 0.00 4.08
144 145 8.772705 GTTCATTTGGTTCAGATTAAAATTGCA 58.227 29.630 0.00 0.00 0.00 4.08
145 146 8.229811 GGTTCATTTGGTTCAGATTAAAATTGC 58.770 33.333 0.00 0.00 0.00 3.56
146 147 9.270640 TGGTTCATTTGGTTCAGATTAAAATTG 57.729 29.630 0.00 0.00 0.00 2.32
151 152 8.196771 GCATATGGTTCATTTGGTTCAGATTAA 58.803 33.333 4.56 0.00 0.00 1.40
152 153 7.341512 TGCATATGGTTCATTTGGTTCAGATTA 59.658 33.333 4.56 0.00 0.00 1.75
153 154 6.154877 TGCATATGGTTCATTTGGTTCAGATT 59.845 34.615 4.56 0.00 0.00 2.40
154 155 5.657745 TGCATATGGTTCATTTGGTTCAGAT 59.342 36.000 4.56 0.00 0.00 2.90
155 156 5.015515 TGCATATGGTTCATTTGGTTCAGA 58.984 37.500 4.56 0.00 0.00 3.27
156 157 5.104374 GTGCATATGGTTCATTTGGTTCAG 58.896 41.667 4.56 0.00 0.00 3.02
157 158 4.525874 TGTGCATATGGTTCATTTGGTTCA 59.474 37.500 4.56 0.00 0.00 3.18
158 159 5.070770 TGTGCATATGGTTCATTTGGTTC 57.929 39.130 4.56 0.00 0.00 3.62
159 160 5.221601 TGTTGTGCATATGGTTCATTTGGTT 60.222 36.000 4.56 0.00 0.00 3.67
160 161 4.282957 TGTTGTGCATATGGTTCATTTGGT 59.717 37.500 4.56 0.00 0.00 3.67
161 162 4.626604 GTGTTGTGCATATGGTTCATTTGG 59.373 41.667 4.56 0.00 0.00 3.28
162 163 5.228665 TGTGTTGTGCATATGGTTCATTTG 58.771 37.500 4.56 0.00 0.00 2.32
163 164 5.465532 TGTGTTGTGCATATGGTTCATTT 57.534 34.783 4.56 0.00 0.00 2.32
164 165 5.185442 TGATGTGTTGTGCATATGGTTCATT 59.815 36.000 4.56 0.00 0.00 2.57
165 166 4.705991 TGATGTGTTGTGCATATGGTTCAT 59.294 37.500 4.56 0.00 0.00 2.57
166 167 4.077822 TGATGTGTTGTGCATATGGTTCA 58.922 39.130 4.56 0.00 0.00 3.18
167 168 4.700268 TGATGTGTTGTGCATATGGTTC 57.300 40.909 4.56 0.00 0.00 3.62
168 169 6.964807 ATATGATGTGTTGTGCATATGGTT 57.035 33.333 4.56 0.00 33.86 3.67
169 170 6.321945 ACAATATGATGTGTTGTGCATATGGT 59.678 34.615 4.56 0.00 40.18 3.55
212 213 7.913297 CCACACGAAGAAGAGTGATTTTAAAAA 59.087 33.333 4.44 0.00 40.56 1.94
213 214 7.414436 CCACACGAAGAAGAGTGATTTTAAAA 58.586 34.615 2.51 2.51 40.56 1.52
214 215 6.512741 GCCACACGAAGAAGAGTGATTTTAAA 60.513 38.462 2.42 0.00 40.56 1.52
215 216 5.049680 GCCACACGAAGAAGAGTGATTTTAA 60.050 40.000 2.42 0.00 40.56 1.52
216 217 4.451096 GCCACACGAAGAAGAGTGATTTTA 59.549 41.667 2.42 0.00 40.56 1.52
341 342 3.881688 CACACCAAAATCAAATGCCCAAA 59.118 39.130 0.00 0.00 0.00 3.28
468 495 7.721286 TTCCAAAAACATATGTCGCAAAAAT 57.279 28.000 9.23 0.00 0.00 1.82
488 515 7.805163 ACTGATGATATGAGTGGTAAATTCCA 58.195 34.615 0.00 0.00 34.85 3.53
663 699 3.925630 AAGGAGTGGGCATGCACGG 62.926 63.158 21.36 0.00 0.00 4.94
683 719 6.546395 GTGGCGCAAAGAGATTATAATATGG 58.454 40.000 10.83 0.00 0.00 2.74
684 720 6.243551 CGTGGCGCAAAGAGATTATAATATG 58.756 40.000 10.83 0.00 0.00 1.78
685 721 5.351465 CCGTGGCGCAAAGAGATTATAATAT 59.649 40.000 10.83 0.00 0.00 1.28
686 722 4.688879 CCGTGGCGCAAAGAGATTATAATA 59.311 41.667 10.83 0.00 0.00 0.98
702 738 2.434359 GGAAGAAGGACCGTGGCG 60.434 66.667 0.00 0.00 0.00 5.69
713 749 8.701895 ACCACGTTAGATATAATGAAGGAAGAA 58.298 33.333 16.74 0.00 0.00 2.52
727 763 1.394266 GCCCGGGACCACGTTAGATA 61.394 60.000 29.31 0.00 0.00 1.98
728 764 2.728435 GCCCGGGACCACGTTAGAT 61.728 63.158 29.31 0.00 0.00 1.98
729 765 3.384532 GCCCGGGACCACGTTAGA 61.385 66.667 29.31 0.00 0.00 2.10
730 766 2.918230 GATGCCCGGGACCACGTTAG 62.918 65.000 29.31 0.00 0.00 2.34
976 1013 0.466963 AAGGTTATTCCCCGCCTACG 59.533 55.000 0.00 0.00 36.75 3.51
1957 2206 3.621682 AGGTAGGGGTAGGAGATGAAG 57.378 52.381 0.00 0.00 0.00 3.02
2209 2458 2.687935 GTTGTCAAACCAGAAGCCTCAA 59.312 45.455 0.00 0.00 0.00 3.02
2320 2569 1.270305 TGAATTCGGATGGAGCGATCC 60.270 52.381 14.17 14.17 38.93 3.36


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

AutoCloner maintained by Alex Coulton.