Multiple sequence alignment - TraesCS7D01G248400

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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 TraesCS7D01G248400 chr7D 100.000 2675 0 0 1 2675 219917658 219914984 0.000000e+00 4940
1 TraesCS7D01G248400 chr7D 98.179 659 11 1 2018 2675 136193203 136193861 0.000000e+00 1149
2 TraesCS7D01G248400 chr7D 97.594 665 14 2 2012 2675 534867219 534866556 0.000000e+00 1138
3 TraesCS7D01G248400 chr7D 92.126 127 10 0 584 710 599881271 599881397 2.120000e-41 180
4 TraesCS7D01G248400 chr7D 82.812 128 20 2 584 710 394186232 394186358 2.180000e-21 113
5 TraesCS7D01G248400 chr7A 94.582 1329 49 8 707 2014 232529016 232527690 0.000000e+00 2034
6 TraesCS7D01G248400 chr7A 88.889 234 18 6 306 538 232532421 232532195 5.640000e-72 281
7 TraesCS7D01G248400 chr7A 90.551 127 12 0 584 710 627115796 627115922 4.580000e-38 169
8 TraesCS7D01G248400 chr7B 94.625 1321 54 6 709 2014 179533436 179534754 0.000000e+00 2030
9 TraesCS7D01G248400 chr3A 89.406 1331 89 23 718 2014 202828609 202827297 0.000000e+00 1629
10 TraesCS7D01G248400 chr3A 93.463 872 54 1 1143 2014 205709725 205710593 0.000000e+00 1291
11 TraesCS7D01G248400 chr3A 85.149 404 27 10 718 1091 205703648 205704048 1.500000e-102 383
12 TraesCS7D01G248400 chr3A 79.808 312 50 11 24 327 687060359 687060053 5.800000e-52 215
13 TraesCS7D01G248400 chr3D 92.143 1120 61 6 873 1983 167034596 167035697 0.000000e+00 1555
14 TraesCS7D01G248400 chr3D 89.601 952 66 11 717 1642 166930319 166931263 0.000000e+00 1179
15 TraesCS7D01G248400 chr3D 92.838 377 27 0 1638 2014 166937625 166938001 5.030000e-152 547
16 TraesCS7D01G248400 chr3D 91.473 129 11 0 583 711 5563958 5563830 7.610000e-41 178
17 TraesCS7D01G248400 chr3D 86.047 129 16 2 583 710 225859716 225859589 1.290000e-28 137
18 TraesCS7D01G248400 chr3B 91.549 1065 58 6 951 2014 242461027 242462060 0.000000e+00 1439
19 TraesCS7D01G248400 chr3B 91.073 1053 62 6 951 2002 242548820 242549841 0.000000e+00 1395
20 TraesCS7D01G248400 chr3B 77.972 1085 193 26 958 2013 166685445 166684378 2.900000e-179 638
21 TraesCS7D01G248400 chr3B 82.267 547 70 18 1 535 242460286 242460817 5.250000e-122 448
22 TraesCS7D01G248400 chr3B 91.489 94 6 2 826 919 242460937 242461028 7.770000e-26 128
23 TraesCS7D01G248400 chr3B 91.489 94 6 2 826 919 242548730 242548821 7.770000e-26 128
24 TraesCS7D01G248400 chr3B 96.721 61 2 0 717 777 242548659 242548719 4.710000e-18 102
25 TraesCS7D01G248400 chr3B 96.610 59 2 0 717 775 242460873 242460931 6.090000e-17 99
26 TraesCS7D01G248400 chr1D 98.630 657 8 1 2020 2675 14571144 14570488 0.000000e+00 1162
27 TraesCS7D01G248400 chr1D 98.326 657 10 1 2020 2675 112416508 112417164 0.000000e+00 1151
28 TraesCS7D01G248400 chr1D 98.174 657 10 2 2020 2675 14519568 14520223 0.000000e+00 1146
29 TraesCS7D01G248400 chr1D 80.831 313 41 17 38 341 440925101 440925403 7.450000e-56 228
30 TraesCS7D01G248400 chr1D 91.406 128 11 0 584 711 324396830 324396703 2.740000e-40 176
31 TraesCS7D01G248400 chr1D 92.562 121 9 0 590 710 482898524 482898404 9.840000e-40 174
32 TraesCS7D01G248400 chr2D 98.182 660 10 2 2017 2675 625509097 625509755 0.000000e+00 1151
33 TraesCS7D01G248400 chr2D 80.906 309 44 13 38 341 458545102 458545400 2.070000e-56 230
34 TraesCS7D01G248400 chr5D 98.182 660 9 3 2019 2675 265671465 265672124 0.000000e+00 1149
35 TraesCS7D01G248400 chr5D 81.759 307 42 10 45 341 478730040 478730342 7.400000e-61 244
36 TraesCS7D01G248400 chr4D 98.174 657 10 2 2021 2675 21731158 21730502 0.000000e+00 1146
37 TraesCS7D01G248400 chr4D 79.487 312 52 9 27 332 354979849 354980154 7.500000e-51 211
38 TraesCS7D01G248400 chr6D 98.018 656 12 1 2021 2675 365439673 365439018 0.000000e+00 1138
39 TraesCS7D01G248400 chr6D 91.093 494 44 0 1528 2021 123025540 123026033 0.000000e+00 669
40 TraesCS7D01G248400 chr6D 93.701 127 8 0 584 710 62116261 62116135 9.770000e-45 191
41 TraesCS7D01G248400 chrUn 90.448 335 15 5 951 1284 477602057 477602375 2.460000e-115 425
42 TraesCS7D01G248400 chrUn 80.892 314 39 17 38 341 11222486 11222788 7.450000e-56 228
43 TraesCS7D01G248400 chrUn 91.489 94 6 2 826 919 477601967 477602058 7.770000e-26 128
44 TraesCS7D01G248400 chr2B 83.214 280 35 11 57 332 66552948 66552677 2.060000e-61 246
45 TraesCS7D01G248400 chr1A 79.245 318 53 9 27 341 442618122 442618429 2.700000e-50 209
46 TraesCS7D01G248400 chr6A 91.406 128 11 0 583 710 617825216 617825343 2.740000e-40 176


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 TraesCS7D01G248400 chr7D 219914984 219917658 2674 True 4940.000000 4940 100.000000 1 2675 1 chr7D.!!$R1 2674
1 TraesCS7D01G248400 chr7D 136193203 136193861 658 False 1149.000000 1149 98.179000 2018 2675 1 chr7D.!!$F1 657
2 TraesCS7D01G248400 chr7D 534866556 534867219 663 True 1138.000000 1138 97.594000 2012 2675 1 chr7D.!!$R2 663
3 TraesCS7D01G248400 chr7A 232527690 232532421 4731 True 1157.500000 2034 91.735500 306 2014 2 chr7A.!!$R1 1708
4 TraesCS7D01G248400 chr7B 179533436 179534754 1318 False 2030.000000 2030 94.625000 709 2014 1 chr7B.!!$F1 1305
5 TraesCS7D01G248400 chr3A 202827297 202828609 1312 True 1629.000000 1629 89.406000 718 2014 1 chr3A.!!$R1 1296
6 TraesCS7D01G248400 chr3A 205709725 205710593 868 False 1291.000000 1291 93.463000 1143 2014 1 chr3A.!!$F2 871
7 TraesCS7D01G248400 chr3D 167034596 167035697 1101 False 1555.000000 1555 92.143000 873 1983 1 chr3D.!!$F3 1110
8 TraesCS7D01G248400 chr3D 166930319 166931263 944 False 1179.000000 1179 89.601000 717 1642 1 chr3D.!!$F1 925
9 TraesCS7D01G248400 chr3B 166684378 166685445 1067 True 638.000000 638 77.972000 958 2013 1 chr3B.!!$R1 1055
10 TraesCS7D01G248400 chr3B 242548659 242549841 1182 False 541.666667 1395 93.094333 717 2002 3 chr3B.!!$F2 1285
11 TraesCS7D01G248400 chr3B 242460286 242462060 1774 False 528.500000 1439 90.478750 1 2014 4 chr3B.!!$F1 2013
12 TraesCS7D01G248400 chr1D 14570488 14571144 656 True 1162.000000 1162 98.630000 2020 2675 1 chr1D.!!$R1 655
13 TraesCS7D01G248400 chr1D 112416508 112417164 656 False 1151.000000 1151 98.326000 2020 2675 1 chr1D.!!$F2 655
14 TraesCS7D01G248400 chr1D 14519568 14520223 655 False 1146.000000 1146 98.174000 2020 2675 1 chr1D.!!$F1 655
15 TraesCS7D01G248400 chr2D 625509097 625509755 658 False 1151.000000 1151 98.182000 2017 2675 1 chr2D.!!$F2 658
16 TraesCS7D01G248400 chr5D 265671465 265672124 659 False 1149.000000 1149 98.182000 2019 2675 1 chr5D.!!$F1 656
17 TraesCS7D01G248400 chr4D 21730502 21731158 656 True 1146.000000 1146 98.174000 2021 2675 1 chr4D.!!$R1 654
18 TraesCS7D01G248400 chr6D 365439018 365439673 655 True 1138.000000 1138 98.018000 2021 2675 1 chr6D.!!$R2 654

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
910 3989 0.663153 GATGTATTTGCCCCTCGTGC 59.337 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 5111 0.534412 GCAGCAGTAGGAGCAGAAGA 59.466 55.0 0.0 0.0 0.0 2.87 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 8.750298 TCAAAGTTAGAAGTAGATCGAGGAAAT 58.250 33.333 0.00 0.00 0.00 2.17
70 71 1.734465 CTCAAATGAGCTCGGGTGAAC 59.266 52.381 9.64 0.00 35.13 3.18
71 72 1.071542 TCAAATGAGCTCGGGTGAACA 59.928 47.619 9.64 0.00 0.00 3.18
88 89 7.463515 CGGGTGAACAGTAAAATCAAAACAAAC 60.464 37.037 0.00 0.00 0.00 2.93
143 144 5.185668 TGTGTGACAAACATTGAGGAATG 57.814 39.130 0.00 0.00 41.97 2.67
155 156 6.506500 CATTGAGGAATGTTCTAAGTGCTT 57.493 37.500 0.00 0.00 35.19 3.91
159 160 4.338879 AGGAATGTTCTAAGTGCTTGCAT 58.661 39.130 0.00 0.00 0.00 3.96
174 175 6.044046 GTGCTTGCATAATTTCATCATGGAA 58.956 36.000 0.00 0.00 0.00 3.53
177 178 6.926826 GCTTGCATAATTTCATCATGGAATCA 59.073 34.615 0.00 0.00 30.96 2.57
186 187 6.459670 TTCATCATGGAATCACATTCTTGG 57.540 37.500 0.00 0.00 39.24 3.61
192 193 3.091545 GGAATCACATTCTTGGAAGGCA 58.908 45.455 0.00 0.00 39.24 4.75
201 202 2.045524 TCTTGGAAGGCATGGCAAAAA 58.954 42.857 22.64 9.01 0.00 1.94
202 203 2.037511 TCTTGGAAGGCATGGCAAAAAG 59.962 45.455 22.64 17.42 0.00 2.27
207 208 3.882288 GGAAGGCATGGCAAAAAGAAAAA 59.118 39.130 22.64 0.00 0.00 1.94
208 209 4.023792 GGAAGGCATGGCAAAAAGAAAAAG 60.024 41.667 22.64 0.00 0.00 2.27
209 210 4.155063 AGGCATGGCAAAAAGAAAAAGT 57.845 36.364 22.64 0.00 0.00 2.66
211 212 5.056480 AGGCATGGCAAAAAGAAAAAGTAC 58.944 37.500 22.64 0.00 0.00 2.73
212 213 5.056480 GGCATGGCAAAAAGAAAAAGTACT 58.944 37.500 15.47 0.00 0.00 2.73
213 214 5.050159 GGCATGGCAAAAAGAAAAAGTACTG 60.050 40.000 15.47 0.00 0.00 2.74
214 215 5.558844 GCATGGCAAAAAGAAAAAGTACTGC 60.559 40.000 0.00 0.00 0.00 4.40
221 224 7.962373 GCAAAAAGAAAAAGTACTGCAAAATGT 59.038 29.630 0.00 0.00 0.00 2.71
230 233 8.419076 AAAGTACTGCAAAATGTTTTCGAAAT 57.581 26.923 12.12 0.00 0.00 2.17
250 253 7.042725 TCGAAATTAGCATTTTCAGAGTATCGG 60.043 37.037 6.78 0.00 34.38 4.18
255 258 5.942872 AGCATTTTCAGAGTATCGGTTTTG 58.057 37.500 0.00 0.00 42.67 2.44
257 260 6.016276 AGCATTTTCAGAGTATCGGTTTTGTT 60.016 34.615 0.00 0.00 42.67 2.83
258 261 6.640907 GCATTTTCAGAGTATCGGTTTTGTTT 59.359 34.615 0.00 0.00 42.67 2.83
259 262 7.169140 GCATTTTCAGAGTATCGGTTTTGTTTT 59.831 33.333 0.00 0.00 42.67 2.43
260 263 8.690840 CATTTTCAGAGTATCGGTTTTGTTTTC 58.309 33.333 0.00 0.00 42.67 2.29
263 266 7.186021 TCAGAGTATCGGTTTTGTTTTCTTC 57.814 36.000 0.00 0.00 42.67 2.87
267 270 1.743958 TCGGTTTTGTTTTCTTCGCCA 59.256 42.857 0.00 0.00 0.00 5.69
268 271 2.359531 TCGGTTTTGTTTTCTTCGCCAT 59.640 40.909 0.00 0.00 0.00 4.40
274 277 1.269448 TGTTTTCTTCGCCATGCCTTC 59.731 47.619 0.00 0.00 0.00 3.46
275 278 1.541588 GTTTTCTTCGCCATGCCTTCT 59.458 47.619 0.00 0.00 0.00 2.85
277 280 2.315925 TTCTTCGCCATGCCTTCTAG 57.684 50.000 0.00 0.00 0.00 2.43
278 281 1.485124 TCTTCGCCATGCCTTCTAGA 58.515 50.000 0.00 0.00 0.00 2.43
284 287 2.032550 CGCCATGCCTTCTAGAAATGTG 59.967 50.000 6.63 3.68 0.00 3.21
288 291 5.163478 GCCATGCCTTCTAGAAATGTGATTT 60.163 40.000 6.63 0.00 34.64 2.17
391 394 2.100879 AACTGTCCACCCGAGCTCAC 62.101 60.000 15.40 3.47 0.00 3.51
405 410 1.690893 AGCTCACTGAGAAACTCTGCA 59.309 47.619 10.45 0.00 33.65 4.41
475 484 3.573967 TGAAAGAAAAGGCATGTTCCCTC 59.426 43.478 0.00 0.00 0.00 4.30
477 486 1.428912 AGAAAAGGCATGTTCCCTCCA 59.571 47.619 0.00 0.00 0.00 3.86
480 489 1.142688 AAGGCATGTTCCCTCCACCT 61.143 55.000 0.00 0.00 0.00 4.00
528 537 7.104290 ACCAGTCAATTACTTCTAGCTAAACC 58.896 38.462 0.00 0.00 35.76 3.27
529 538 6.539103 CCAGTCAATTACTTCTAGCTAAACCC 59.461 42.308 0.00 0.00 35.76 4.11
537 546 9.682465 ATTACTTCTAGCTAAACCCTTTTTAGG 57.318 33.333 0.00 0.00 33.72 2.69
538 547 5.944599 ACTTCTAGCTAAACCCTTTTTAGGC 59.055 40.000 0.00 0.00 33.72 3.93
539 548 5.508280 TCTAGCTAAACCCTTTTTAGGCA 57.492 39.130 0.00 0.00 33.72 4.75
540 549 5.250982 TCTAGCTAAACCCTTTTTAGGCAC 58.749 41.667 0.00 0.00 33.72 5.01
542 551 4.480115 AGCTAAACCCTTTTTAGGCACTT 58.520 39.130 6.04 0.00 41.75 3.16
544 553 6.072649 AGCTAAACCCTTTTTAGGCACTTAA 58.927 36.000 6.04 0.00 41.75 1.85
545 554 6.551975 AGCTAAACCCTTTTTAGGCACTTAAA 59.448 34.615 6.04 0.00 41.75 1.52
546 555 7.070198 AGCTAAACCCTTTTTAGGCACTTAAAA 59.930 33.333 6.04 0.00 43.31 1.52
547 556 7.711772 GCTAAACCCTTTTTAGGCACTTAAAAA 59.288 33.333 9.28 9.28 44.52 1.94
588 597 9.418045 GATGATTTCTAGCTAAACTGATACTCC 57.582 37.037 0.00 0.00 0.00 3.85
594 603 2.694109 GCTAAACTGATACTCCCTCCGT 59.306 50.000 0.00 0.00 0.00 4.69
595 604 3.132467 GCTAAACTGATACTCCCTCCGTT 59.868 47.826 0.00 0.00 0.00 4.44
600 609 2.500098 CTGATACTCCCTCCGTTCCAAA 59.500 50.000 0.00 0.00 0.00 3.28
601 610 3.112263 TGATACTCCCTCCGTTCCAAAT 58.888 45.455 0.00 0.00 0.00 2.32
604 613 3.629142 ACTCCCTCCGTTCCAAATTAG 57.371 47.619 0.00 0.00 0.00 1.73
605 614 2.910977 ACTCCCTCCGTTCCAAATTAGT 59.089 45.455 0.00 0.00 0.00 2.24
606 615 3.329814 ACTCCCTCCGTTCCAAATTAGTT 59.670 43.478 0.00 0.00 0.00 2.24
607 616 3.681593 TCCCTCCGTTCCAAATTAGTTG 58.318 45.455 0.00 0.00 36.94 3.16
608 617 3.328343 TCCCTCCGTTCCAAATTAGTTGA 59.672 43.478 0.00 0.00 39.87 3.18
609 618 4.018779 TCCCTCCGTTCCAAATTAGTTGAT 60.019 41.667 0.00 0.00 39.87 2.57
610 619 4.335594 CCCTCCGTTCCAAATTAGTTGATC 59.664 45.833 0.00 0.00 39.87 2.92
704 2915 9.685828 TTTAAGTCAATTAATTTGAAACGGAGG 57.314 29.630 0.00 0.00 45.71 4.30
705 2916 6.267496 AGTCAATTAATTTGAAACGGAGGG 57.733 37.500 0.00 0.00 45.71 4.30
715 3759 0.981183 AAACGGAGGGAGTATGTGCA 59.019 50.000 0.00 0.00 0.00 4.57
819 3884 1.073768 AACAAAACGCGTTGGCACAC 61.074 50.000 27.34 0.00 39.29 3.82
820 3885 1.226547 CAAAACGCGTTGGCACACT 60.227 52.632 27.34 4.48 39.29 3.55
889 3968 4.397382 CCGTGTCGGTGTATATATACGTG 58.603 47.826 16.29 9.56 42.73 4.49
903 3982 1.292061 TACGTGCGATGTATTTGCCC 58.708 50.000 0.00 0.00 33.31 5.36
909 3988 0.937304 CGATGTATTTGCCCCTCGTG 59.063 55.000 0.00 0.00 0.00 4.35
910 3989 0.663153 GATGTATTTGCCCCTCGTGC 59.337 55.000 0.00 0.00 0.00 5.34
920 3999 2.579201 CCTCGTGCCCATCTCGTT 59.421 61.111 0.00 0.00 33.77 3.85
981 4066 2.416566 CCTGTCTCCGTCATCTCTGTTG 60.417 54.545 0.00 0.00 0.00 3.33
1107 4199 3.165875 CATCGGGACCACCTATGACTAT 58.834 50.000 0.00 0.00 36.97 2.12
1126 4218 2.203640 ACCAGGAGTCGTGCCTCA 60.204 61.111 7.33 0.00 32.12 3.86
1285 4397 2.507102 CGCACATCGTCGGCTTCT 60.507 61.111 0.00 0.00 0.00 2.85
1290 4402 3.760035 ATCGTCGGCTTCTGCGGT 61.760 61.111 0.00 0.00 40.82 5.68
1425 4537 0.038892 GCACCTTCATGTGGCAACTG 60.039 55.000 7.28 0.00 36.73 3.16
1450 4562 2.787249 CCGCCAAGAAGATGCACG 59.213 61.111 0.00 0.00 0.00 5.34
1468 4580 2.347490 GGTGCCACATCGTCCACT 59.653 61.111 0.00 0.00 0.00 4.00
1509 4621 3.148279 CTCGTCGGAGGGGAAGGG 61.148 72.222 0.00 0.00 36.61 3.95
1611 4723 4.424867 ATGGGGGAGTACCGGGCA 62.425 66.667 6.32 0.00 41.60 5.36
1674 4786 1.347707 GACACATGGTCTCTTGGGTGA 59.652 52.381 0.00 0.00 43.46 4.02
1698 4810 1.196766 TGGCAGAGATGCTCACAGGT 61.197 55.000 0.00 0.00 32.06 4.00
1701 4813 2.006056 GCAGAGATGCTCACAGGTGAC 61.006 57.143 0.00 0.00 35.46 3.67
1993 5111 3.755628 CTGCTGCAAATGCCCGCT 61.756 61.111 3.02 0.00 41.18 5.52
2014 5132 1.753649 CTTCTGCTCCTACTGCTGCTA 59.246 52.381 0.00 0.00 0.00 3.49
2015 5133 1.852633 TCTGCTCCTACTGCTGCTAA 58.147 50.000 0.00 0.00 0.00 3.09
2016 5134 1.753649 TCTGCTCCTACTGCTGCTAAG 59.246 52.381 0.00 0.00 0.00 2.18
2153 5271 2.819595 CAACGGTGCAGCGCCTAT 60.820 61.111 35.78 18.13 0.00 2.57
2292 5410 1.905215 ACTGTGACTTAGATGCCAGCT 59.095 47.619 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.941555 AGGTGAATTTCCTCGATCTACTT 57.058 39.130 0.00 0.00 0.00 2.24
19 20 4.467795 TGAGAAGGTGAATTTCCTCGATCT 59.532 41.667 4.06 4.14 33.76 2.75
22 23 3.617531 GCTGAGAAGGTGAATTTCCTCGA 60.618 47.826 4.06 0.00 33.76 4.04
23 24 2.675348 GCTGAGAAGGTGAATTTCCTCG 59.325 50.000 4.06 0.00 33.76 4.63
31 32 4.208426 TCGGGCTGAGAAGGTGAA 57.792 55.556 0.00 0.00 0.00 3.18
63 64 7.547722 AGTTTGTTTTGATTTTACTGTTCACCC 59.452 33.333 0.00 0.00 0.00 4.61
138 139 4.708726 ATGCAAGCACTTAGAACATTCC 57.291 40.909 0.00 0.00 0.00 3.01
139 140 8.693542 AAATTATGCAAGCACTTAGAACATTC 57.306 30.769 0.00 0.00 0.00 2.67
143 144 7.970061 TGATGAAATTATGCAAGCACTTAGAAC 59.030 33.333 0.00 0.00 0.00 3.01
155 156 7.349412 TGTGATTCCATGATGAAATTATGCA 57.651 32.000 0.00 0.00 38.84 3.96
174 175 3.028850 CCATGCCTTCCAAGAATGTGAT 58.971 45.455 0.00 0.00 0.00 3.06
177 178 1.188863 GCCATGCCTTCCAAGAATGT 58.811 50.000 0.00 0.00 0.00 2.71
183 184 2.045524 TCTTTTTGCCATGCCTTCCAA 58.954 42.857 0.00 0.00 0.00 3.53
186 187 4.576053 ACTTTTTCTTTTTGCCATGCCTTC 59.424 37.500 0.00 0.00 0.00 3.46
192 193 5.669477 TGCAGTACTTTTTCTTTTTGCCAT 58.331 33.333 0.00 0.00 0.00 4.40
201 202 7.757624 TCGAAAACATTTTGCAGTACTTTTTCT 59.242 29.630 16.91 0.00 32.17 2.52
202 203 7.890763 TCGAAAACATTTTGCAGTACTTTTTC 58.109 30.769 12.18 12.18 0.00 2.29
207 208 9.180678 CTAATTTCGAAAACATTTTGCAGTACT 57.819 29.630 15.66 0.00 0.00 2.73
208 209 7.944649 GCTAATTTCGAAAACATTTTGCAGTAC 59.055 33.333 15.66 0.00 0.00 2.73
209 210 7.649705 TGCTAATTTCGAAAACATTTTGCAGTA 59.350 29.630 19.75 5.44 0.00 2.74
211 212 6.875753 TGCTAATTTCGAAAACATTTTGCAG 58.124 32.000 19.75 6.73 0.00 4.41
212 213 6.834959 TGCTAATTTCGAAAACATTTTGCA 57.165 29.167 19.75 19.75 0.00 4.08
213 214 8.712341 AAATGCTAATTTCGAAAACATTTTGC 57.288 26.923 23.99 20.51 33.70 3.68
230 233 7.174253 ACAAAACCGATACTCTGAAAATGCTAA 59.826 33.333 0.00 0.00 0.00 3.09
240 243 6.071463 CGAAGAAAACAAAACCGATACTCTG 58.929 40.000 0.00 0.00 0.00 3.35
250 253 2.220824 GGCATGGCGAAGAAAACAAAAC 59.779 45.455 2.41 0.00 0.00 2.43
255 258 1.541588 AGAAGGCATGGCGAAGAAAAC 59.458 47.619 14.30 0.97 0.00 2.43
257 260 2.236146 TCTAGAAGGCATGGCGAAGAAA 59.764 45.455 14.30 0.00 0.00 2.52
258 261 1.831106 TCTAGAAGGCATGGCGAAGAA 59.169 47.619 14.30 0.00 0.00 2.52
259 262 1.485124 TCTAGAAGGCATGGCGAAGA 58.515 50.000 14.30 11.93 0.00 2.87
260 263 2.315925 TTCTAGAAGGCATGGCGAAG 57.684 50.000 14.30 9.84 0.00 3.79
263 266 2.032550 CACATTTCTAGAAGGCATGGCG 59.967 50.000 14.30 0.00 0.00 5.69
267 270 7.893124 ATGAAATCACATTTCTAGAAGGCAT 57.107 32.000 5.12 0.00 46.71 4.40
268 271 8.806429 TTATGAAATCACATTTCTAGAAGGCA 57.194 30.769 5.12 0.00 46.71 4.75
356 359 7.065204 GGTGGACAGTTAAAAAGAAAATGCAAA 59.935 33.333 0.00 0.00 0.00 3.68
357 360 6.536941 GGTGGACAGTTAAAAAGAAAATGCAA 59.463 34.615 0.00 0.00 0.00 4.08
358 361 6.045955 GGTGGACAGTTAAAAAGAAAATGCA 58.954 36.000 0.00 0.00 0.00 3.96
359 362 5.465390 GGGTGGACAGTTAAAAAGAAAATGC 59.535 40.000 0.00 0.00 0.00 3.56
360 363 5.689961 CGGGTGGACAGTTAAAAAGAAAATG 59.310 40.000 0.00 0.00 0.00 2.32
391 394 2.266554 GGACGATGCAGAGTTTCTCAG 58.733 52.381 0.00 0.00 32.06 3.35
448 455 5.335504 GGAACATGCCTTTTCTTTCAGAGAG 60.336 44.000 0.00 0.00 35.37 3.20
475 484 2.190578 GGGCTGATTCGGAGGTGG 59.809 66.667 0.00 0.00 0.00 4.61
477 486 0.625849 ATTTGGGCTGATTCGGAGGT 59.374 50.000 0.00 0.00 0.00 3.85
480 489 2.806945 AGAATTTGGGCTGATTCGGA 57.193 45.000 0.00 0.00 37.35 4.55
554 563 9.520515 AGTTTAGCTAGAAATCATCCTCAAAAA 57.479 29.630 0.00 0.00 0.00 1.94
555 564 8.950210 CAGTTTAGCTAGAAATCATCCTCAAAA 58.050 33.333 0.00 0.00 0.00 2.44
556 565 8.321353 TCAGTTTAGCTAGAAATCATCCTCAAA 58.679 33.333 0.00 0.00 0.00 2.69
557 566 7.851228 TCAGTTTAGCTAGAAATCATCCTCAA 58.149 34.615 0.00 0.00 0.00 3.02
558 567 7.423844 TCAGTTTAGCTAGAAATCATCCTCA 57.576 36.000 0.00 0.00 0.00 3.86
559 568 9.418045 GTATCAGTTTAGCTAGAAATCATCCTC 57.582 37.037 0.00 0.00 0.00 3.71
565 574 7.958088 AGGGAGTATCAGTTTAGCTAGAAATC 58.042 38.462 0.00 0.00 36.25 2.17
588 597 4.335594 GGATCAACTAATTTGGAACGGAGG 59.664 45.833 0.00 0.00 35.69 4.30
685 2896 6.267496 ACTCCCTCCGTTTCAAATTAATTG 57.733 37.500 0.39 0.00 40.58 2.32
686 2897 7.614192 ACATACTCCCTCCGTTTCAAATTAATT 59.386 33.333 0.00 0.00 0.00 1.40
687 2898 7.067008 CACATACTCCCTCCGTTTCAAATTAAT 59.933 37.037 0.00 0.00 0.00 1.40
688 2899 6.373216 CACATACTCCCTCCGTTTCAAATTAA 59.627 38.462 0.00 0.00 0.00 1.40
689 2900 5.878116 CACATACTCCCTCCGTTTCAAATTA 59.122 40.000 0.00 0.00 0.00 1.40
690 2901 4.700213 CACATACTCCCTCCGTTTCAAATT 59.300 41.667 0.00 0.00 0.00 1.82
691 2902 4.261801 CACATACTCCCTCCGTTTCAAAT 58.738 43.478 0.00 0.00 0.00 2.32
692 2903 3.670625 CACATACTCCCTCCGTTTCAAA 58.329 45.455 0.00 0.00 0.00 2.69
693 2904 2.614481 GCACATACTCCCTCCGTTTCAA 60.614 50.000 0.00 0.00 0.00 2.69
694 2905 1.066430 GCACATACTCCCTCCGTTTCA 60.066 52.381 0.00 0.00 0.00 2.69
695 2906 1.066430 TGCACATACTCCCTCCGTTTC 60.066 52.381 0.00 0.00 0.00 2.78
696 2907 0.981183 TGCACATACTCCCTCCGTTT 59.019 50.000 0.00 0.00 0.00 3.60
697 2908 0.981183 TTGCACATACTCCCTCCGTT 59.019 50.000 0.00 0.00 0.00 4.44
699 2910 2.365617 AGTATTGCACATACTCCCTCCG 59.634 50.000 12.81 0.00 29.47 4.63
700 2911 4.130118 CAAGTATTGCACATACTCCCTCC 58.870 47.826 16.68 0.00 40.39 4.30
715 3759 3.508840 GCAGGCGGCGCAAGTATT 61.509 61.111 34.36 8.30 41.68 1.89
744 3788 2.772077 TGTTCCAATCCGATTCCGAA 57.228 45.000 0.00 0.00 38.22 4.30
856 3935 1.226974 CGACACGGCTTGGATCGAT 60.227 57.895 0.00 0.00 34.77 3.59
889 3968 0.814010 ACGAGGGGCAAATACATCGC 60.814 55.000 0.00 0.00 33.67 4.58
903 3982 1.811266 CAACGAGATGGGCACGAGG 60.811 63.158 0.00 0.00 34.56 4.63
991 4076 1.226859 TGAACGCCATCGGATCGAC 60.227 57.895 6.14 1.72 39.18 4.20
1107 4199 2.203640 AGGCACGACTCCTGGTCA 60.204 61.111 0.00 0.00 44.70 4.02
1126 4218 2.359230 GCCGAACTTGCCTCTGCT 60.359 61.111 0.00 0.00 38.71 4.24
1290 4402 1.136252 GTTACGTAGTCGAGCGTGACA 60.136 52.381 19.48 2.13 43.73 3.58
1450 4562 2.746277 GTGGACGATGTGGCACCC 60.746 66.667 16.26 9.07 0.00 4.61
1468 4580 2.279741 GTTAGCAGGATTGATGTCGCA 58.720 47.619 0.00 0.00 0.00 5.10
1508 4620 4.468689 CGAACCCTCTTCCGGCCC 62.469 72.222 0.00 0.00 0.00 5.80
1509 4621 3.660732 GACGAACCCTCTTCCGGCC 62.661 68.421 0.00 0.00 0.00 6.13
1611 4723 3.790437 CCCAGCAGCATCTCGGGT 61.790 66.667 0.00 0.00 31.80 5.28
1698 4810 1.001393 GGCCCGGAAAATCCTGTCA 60.001 57.895 0.73 0.00 33.30 3.58
1701 4813 3.518068 GCGGCCCGGAAAATCCTG 61.518 66.667 4.77 0.00 33.30 3.86
1844 4959 1.219124 GGGAACAGATCTCGCAGCA 59.781 57.895 0.00 0.00 0.00 4.41
1986 5104 4.087892 GGAGCAGAAGAGCGGGCA 62.088 66.667 0.00 0.00 40.15 5.36
1993 5111 0.534412 GCAGCAGTAGGAGCAGAAGA 59.466 55.000 0.00 0.00 0.00 2.87
2014 5132 6.705381 TCAAAATTGTCAAATTTGCCGATCTT 59.295 30.769 17.69 0.00 43.63 2.40
2015 5133 6.146021 GTCAAAATTGTCAAATTTGCCGATCT 59.854 34.615 17.69 0.00 43.63 2.75
2016 5134 6.298853 GTCAAAATTGTCAAATTTGCCGATC 58.701 36.000 17.69 2.54 43.63 3.69
2153 5271 3.240134 GAGTGCAACGCCCCAGAGA 62.240 63.158 0.00 0.00 45.86 3.10


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

AutoCloner maintained by Alex Coulton.