Multiple sequence alignment - TraesCS7D01G412600

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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 TraesCS7D01G412600 chr7D 100.000 4929 0 0 1 4929 530923346 530928274 0.000000e+00 9103.0
1 TraesCS7D01G412600 chr7D 90.103 485 34 3 2443 2927 611010910 611011380 7.010000e-173 617.0
2 TraesCS7D01G412600 chr7D 87.952 498 38 13 3554 4035 611011383 611011874 7.160000e-158 568.0
3 TraesCS7D01G412600 chr7D 89.855 276 23 4 4588 4861 611011901 611012173 2.820000e-92 350.0
4 TraesCS7D01G412600 chr7D 81.375 349 50 8 175 509 529038293 529038640 2.260000e-68 270.0
5 TraesCS7D01G412600 chr7D 94.186 172 6 2 2237 2404 611008921 611009092 4.890000e-65 259.0
6 TraesCS7D01G412600 chr7D 91.270 126 8 2 4410 4532 611008127 611008252 8.490000e-38 169.0
7 TraesCS7D01G412600 chr7D 84.615 143 19 1 4108 4250 611007989 611008128 6.650000e-29 139.0
8 TraesCS7D01G412600 chr7A 95.818 2678 98 8 1865 4532 611467567 611470240 0.000000e+00 4313.0
9 TraesCS7D01G412600 chr7A 95.147 1154 43 9 689 1840 611466357 611467499 0.000000e+00 1808.0
10 TraesCS7D01G412600 chr7A 91.528 720 49 7 2456 3168 700977473 700978187 0.000000e+00 981.0
11 TraesCS7D01G412600 chr7A 97.481 397 9 1 4534 4929 611470671 611471067 0.000000e+00 676.0
12 TraesCS7D01G412600 chr7A 88.265 392 28 9 13 390 611465967 611466354 2.090000e-123 453.0
13 TraesCS7D01G412600 chr7A 89.347 291 20 7 3618 3898 700978182 700978471 6.070000e-94 355.0
14 TraesCS7D01G412600 chr7A 89.003 291 21 7 3618 3898 700941637 700941926 2.820000e-92 350.0
15 TraesCS7D01G412600 chr7A 94.444 216 12 0 2953 3168 700941427 700941642 2.840000e-87 333.0
16 TraesCS7D01G412600 chr7A 92.576 229 14 2 4545 4772 700942050 700942276 4.760000e-85 326.0
17 TraesCS7D01G412600 chr7A 92.576 229 14 2 4545 4772 700978595 700978821 4.760000e-85 326.0
18 TraesCS7D01G412600 chr7A 91.919 198 15 1 2264 2461 700976397 700976593 4.860000e-70 276.0
19 TraesCS7D01G412600 chr7A 90.964 166 14 1 4246 4411 494786993 494786829 6.420000e-54 222.0
20 TraesCS7D01G412600 chr7A 90.152 132 13 0 4730 4861 700942269 700942400 6.560000e-39 172.0
21 TraesCS7D01G412600 chr7A 90.152 132 13 0 4730 4861 700978814 700978945 6.560000e-39 172.0
22 TraesCS7D01G412600 chr7B 96.446 2279 68 8 1835 4103 571257369 571259644 0.000000e+00 3747.0
23 TraesCS7D01G412600 chr7B 95.022 1125 49 5 717 1840 571256204 571257322 0.000000e+00 1760.0
24 TraesCS7D01G412600 chr7B 93.989 183 11 0 4571 4753 571260438 571260620 1.350000e-70 278.0
25 TraesCS7D01G412600 chr7B 91.925 161 12 1 4246 4406 176002828 176002987 1.790000e-54 224.0
26 TraesCS7D01G412600 chr7B 98.246 57 1 0 4194 4250 571259639 571259695 3.140000e-17 100.0
27 TraesCS7D01G412600 chr7B 93.478 46 3 0 4534 4579 571260220 571260265 8.850000e-08 69.4
28 TraesCS7D01G412600 chr2D 80.287 558 71 30 175 704 590039070 590038524 7.740000e-103 385.0
29 TraesCS7D01G412600 chr2D 79.114 158 32 1 13 170 535289757 535289601 1.880000e-19 108.0
30 TraesCS7D01G412600 chr2B 84.746 354 35 13 175 511 714486260 714485909 2.200000e-88 337.0
31 TraesCS7D01G412600 chrUn 92.576 229 14 2 4545 4772 83255731 83255505 4.760000e-85 326.0
32 TraesCS7D01G412600 chrUn 92.576 229 14 2 4545 4772 406969716 406969490 4.760000e-85 326.0
33 TraesCS7D01G412600 chrUn 90.152 132 13 0 4730 4861 83255512 83255381 6.560000e-39 172.0
34 TraesCS7D01G412600 chrUn 90.152 132 13 0 4730 4861 406969497 406969366 6.560000e-39 172.0
35 TraesCS7D01G412600 chr2A 78.383 569 75 26 175 704 724364327 724363768 4.760000e-85 326.0
36 TraesCS7D01G412600 chr2A 88.827 179 18 2 4247 4424 161773053 161772876 8.310000e-53 219.0
37 TraesCS7D01G412600 chr2A 83.505 97 8 6 4418 4511 65648776 65648867 3.160000e-12 84.2
38 TraesCS7D01G412600 chr4B 84.249 273 31 9 4241 4508 532434994 532435259 6.330000e-64 255.0
39 TraesCS7D01G412600 chr5D 76.157 562 84 31 175 700 207818336 207817789 2.950000e-62 250.0
40 TraesCS7D01G412600 chr5D 87.023 131 13 3 4410 4537 515243803 515243674 1.430000e-30 145.0
41 TraesCS7D01G412600 chr6D 91.071 168 13 2 4242 4408 467802263 467802429 4.960000e-55 226.0
42 TraesCS7D01G412600 chr3D 91.071 168 14 1 4244 4411 375693995 375693829 4.960000e-55 226.0
43 TraesCS7D01G412600 chr3D 89.535 172 17 1 4243 4414 454156356 454156526 2.990000e-52 217.0
44 TraesCS7D01G412600 chr3B 91.071 168 12 3 4241 4408 529407783 529407947 1.790000e-54 224.0
45 TraesCS7D01G412600 chr6B 75.269 558 85 32 175 701 465156711 465156176 2.990000e-52 217.0
46 TraesCS7D01G412600 chr3A 81.229 293 33 15 222 492 194832929 194833221 2.990000e-52 217.0
47 TraesCS7D01G412600 chr3A 88.889 126 9 4 4410 4532 293591468 293591591 3.070000e-32 150.0


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 TraesCS7D01G412600 chr7D 530923346 530928274 4928 False 9103.000000 9103 100.00000 1 4929 1 chr7D.!!$F2 4928
1 TraesCS7D01G412600 chr7D 611007989 611012173 4184 False 350.333333 617 89.66350 2237 4861 6 chr7D.!!$F3 2624
2 TraesCS7D01G412600 chr7A 611465967 611471067 5100 False 1812.500000 4313 94.17775 13 4929 4 chr7A.!!$F1 4916
3 TraesCS7D01G412600 chr7A 700976397 700978945 2548 False 422.000000 981 91.10440 2264 4861 5 chr7A.!!$F3 2597
4 TraesCS7D01G412600 chr7A 700941427 700942400 973 False 295.250000 350 91.54375 2953 4861 4 chr7A.!!$F2 1908
5 TraesCS7D01G412600 chr7B 571256204 571260620 4416 False 1190.880000 3747 95.43620 717 4753 5 chr7B.!!$F2 4036
6 TraesCS7D01G412600 chr2D 590038524 590039070 546 True 385.000000 385 80.28700 175 704 1 chr2D.!!$R2 529
7 TraesCS7D01G412600 chr2A 724363768 724364327 559 True 326.000000 326 78.38300 175 704 1 chr2A.!!$R2 529
8 TraesCS7D01G412600 chr5D 207817789 207818336 547 True 250.000000 250 76.15700 175 700 1 chr5D.!!$R1 525
9 TraesCS7D01G412600 chr6B 465156176 465156711 535 True 217.000000 217 75.26900 175 701 1 chr6B.!!$R1 526

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
798 861 0.310854 GTTGAGCCGTTGACCCAAAG 59.689 55.0 0.00 0.00 0.0 2.77 F
818 881 0.526662 CCTCAGTACGACGGCTTTCT 59.473 55.0 0.00 0.00 0.0 2.52 F
1611 1674 0.830648 TCATAGGCTTTGGAGGGTCG 59.169 55.0 5.10 0.00 0.0 4.79 F
3322 6113 0.597568 TGGTTTCATCGCTTGGCAAG 59.402 50.0 22.75 22.75 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2738 5529 1.339711 CGGCAAACTTTATGCTGTGC 58.660 50.000 0.0 0.0 43.60 4.57 R
2753 5544 1.400846 GTAGTCAATCGAGAGTCGGCA 59.599 52.381 0.0 0.0 40.88 5.69 R
3565 6356 0.389166 GTGAGGAGTTCAGCGTCAGG 60.389 60.000 0.0 0.0 36.21 3.86 R
4715 8148 0.167470 CAACAGCAGCAATCCACTCG 59.833 55.000 0.0 0.0 0.00 4.18 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
29 30 0.461870 ATGAAGCGTCGCCATTGCTA 60.462 50.000 14.86 0.00 38.17 3.49
62 63 2.290071 ACAGACATAGGTTTTCACCCGG 60.290 50.000 0.00 0.00 45.63 5.73
69 70 1.971695 GTTTTCACCCGGAGCCCTG 60.972 63.158 0.73 0.00 0.00 4.45
120 121 1.101049 AAGCAAACGACACCCACAGG 61.101 55.000 0.00 0.00 40.04 4.00
172 173 0.514691 CTTTTGCTCGGACACTCAGC 59.485 55.000 0.00 0.00 0.00 4.26
184 185 4.429108 GGACACTCAGCAATAGTCTTCTC 58.571 47.826 0.00 0.00 0.00 2.87
413 444 8.746052 TCTGAAAATTAATACCATTCCATCGT 57.254 30.769 0.00 0.00 0.00 3.73
414 445 8.620416 TCTGAAAATTAATACCATTCCATCGTG 58.380 33.333 0.00 0.00 0.00 4.35
498 533 5.175856 GTCGAGGTATACATGCTGAAATGTC 59.824 44.000 5.01 0.00 41.09 3.06
553 614 0.981183 ATGTAAGGTGGCCGAGACAA 59.019 50.000 0.00 0.00 0.00 3.18
554 615 0.981183 TGTAAGGTGGCCGAGACAAT 59.019 50.000 0.00 0.00 0.00 2.71
566 627 5.888724 TGGCCGAGACAATTAATTTTATCCA 59.111 36.000 0.00 0.00 0.00 3.41
591 652 4.520179 GGTATTACCCAACACCTGGTTAG 58.480 47.826 0.00 0.00 44.76 2.34
612 673 4.205587 AGGTAGTACTGGTATGAGAACGG 58.794 47.826 5.39 0.00 0.00 4.44
616 677 6.095440 GGTAGTACTGGTATGAGAACGGTTTA 59.905 42.308 5.39 0.00 0.00 2.01
619 680 7.095270 AGTACTGGTATGAGAACGGTTTAAAG 58.905 38.462 0.00 0.00 0.00 1.85
644 705 1.466025 GGTGCGGGTACGGATATGGA 61.466 60.000 0.00 0.00 43.94 3.41
648 709 2.105134 TGCGGGTACGGATATGGATTTT 59.895 45.455 0.00 0.00 41.36 1.82
650 711 3.804411 GCGGGTACGGATATGGATTTTGA 60.804 47.826 0.00 0.00 41.36 2.69
651 712 3.994392 CGGGTACGGATATGGATTTTGAG 59.006 47.826 0.00 0.00 36.18 3.02
652 713 4.262292 CGGGTACGGATATGGATTTTGAGA 60.262 45.833 0.00 0.00 36.18 3.27
700 761 4.294523 GCGACCATTAGCCACACA 57.705 55.556 0.00 0.00 0.00 3.72
702 763 0.673644 GCGACCATTAGCCACACACT 60.674 55.000 0.00 0.00 0.00 3.55
703 764 1.359848 CGACCATTAGCCACACACTC 58.640 55.000 0.00 0.00 0.00 3.51
705 766 2.350522 GACCATTAGCCACACACTCTG 58.649 52.381 0.00 0.00 0.00 3.35
706 767 1.003580 ACCATTAGCCACACACTCTGG 59.996 52.381 0.00 0.00 0.00 3.86
720 781 0.387202 CTCTGGACCCACTCGCATAG 59.613 60.000 0.00 0.00 0.00 2.23
784 847 1.278172 CGATATCCTGCCGCGTTGAG 61.278 60.000 4.92 0.00 0.00 3.02
794 857 3.723348 GCGTTGAGCCGTTGACCC 61.723 66.667 0.00 0.00 40.81 4.46
795 858 2.280524 CGTTGAGCCGTTGACCCA 60.281 61.111 0.00 0.00 0.00 4.51
798 861 0.310854 GTTGAGCCGTTGACCCAAAG 59.689 55.000 0.00 0.00 0.00 2.77
799 862 1.452145 TTGAGCCGTTGACCCAAAGC 61.452 55.000 0.00 0.00 0.00 3.51
800 863 2.597510 AGCCGTTGACCCAAAGCC 60.598 61.111 0.00 0.00 0.00 4.35
818 881 0.526662 CCTCAGTACGACGGCTTTCT 59.473 55.000 0.00 0.00 0.00 2.52
822 885 1.153686 GTACGACGGCTTTCTCCCC 60.154 63.158 0.00 0.00 0.00 4.81
823 886 2.353610 TACGACGGCTTTCTCCCCC 61.354 63.158 0.00 0.00 0.00 5.40
855 918 1.478288 CCTCCTCTCATCCCATTTGCC 60.478 57.143 0.00 0.00 0.00 4.52
887 950 3.312890 TCTCCAGATCCATTTCCTCCTC 58.687 50.000 0.00 0.00 0.00 3.71
927 990 4.011517 GGCGGGTTCGGTTGGAGA 62.012 66.667 0.00 0.00 36.79 3.71
1071 1134 3.068691 AAGCTCGCCGCACTCCTA 61.069 61.111 0.00 0.00 42.61 2.94
1188 1251 3.749064 GCGGAGGCTCTCGACACA 61.749 66.667 23.46 0.00 35.83 3.72
1307 1370 3.813596 GCCTAACGCTGTCATGGG 58.186 61.111 0.00 0.00 0.00 4.00
1611 1674 0.830648 TCATAGGCTTTGGAGGGTCG 59.169 55.000 5.10 0.00 0.00 4.79
1751 1814 7.606073 GCTCTCTCAAATAAGAAAGGAAGACTT 59.394 37.037 0.00 0.00 42.52 3.01
1909 2024 9.731819 TCTATCGATTTACTAGATGTGTGAAAC 57.268 33.333 1.71 0.00 37.35 2.78
2038 2154 1.661112 GCGTGGAAGACTATCAAGTGC 59.339 52.381 0.00 0.00 35.56 4.40
2330 2450 3.295093 TCAGATAGCAGAGAAGACTGGG 58.705 50.000 0.00 0.00 38.22 4.45
2508 5292 3.526899 TGGAAGATTTGGTGAGGAGGTA 58.473 45.455 0.00 0.00 0.00 3.08
2569 5353 7.728847 AAATTTATTTGACACAGGAAAAGGC 57.271 32.000 0.00 0.00 0.00 4.35
2687 5478 6.128445 CCGTGATCTCATTATATCAAAGGCAC 60.128 42.308 0.00 0.00 34.06 5.01
2738 5529 3.684305 TCATCAAACACATAGCTTGGTCG 59.316 43.478 0.00 0.00 0.00 4.79
2753 5544 2.226330 TGGTCGCACAGCATAAAGTTT 58.774 42.857 0.00 0.00 0.00 2.66
2853 5644 1.338674 TGGCGTCTTTGGATGTACTGG 60.339 52.381 0.00 0.00 0.00 4.00
3082 5873 6.715347 ATAAGGGAATTGCCAACAAGTATC 57.285 37.500 19.16 0.00 39.69 2.24
3158 5949 0.609151 CATTGGGAACATGCAAGGCA 59.391 50.000 0.00 0.00 44.86 4.75
3218 6009 3.276857 TCAATCAATCTCTTGCAGGAGC 58.723 45.455 20.42 0.00 42.57 4.70
3283 6074 2.741759 TGAGCGCACATAAGACAAGA 57.258 45.000 11.47 0.00 0.00 3.02
3322 6113 0.597568 TGGTTTCATCGCTTGGCAAG 59.402 50.000 22.75 22.75 0.00 4.01
3378 6169 1.448985 ACGGATGGTCGTTTGATTGG 58.551 50.000 0.00 0.00 40.85 3.16
3435 6226 2.042464 CCTGCAGGAGCTAATCACCTA 58.958 52.381 29.88 0.00 42.74 3.08
3513 6304 2.849502 GCCTTCAAATCGGCGTTAATCG 60.850 50.000 6.85 0.00 43.12 3.34
3565 6356 2.492088 GGGTTTGCCTGTCTTGTTATCC 59.508 50.000 0.00 0.00 34.45 2.59
3806 6608 1.145819 GCCCTGAGTGATCTCTGCC 59.854 63.158 1.15 0.00 40.98 4.85
3864 6666 0.315568 GTTCACGAGCTGGAGTCTGT 59.684 55.000 1.44 0.00 0.00 3.41
3945 6747 1.186200 TGAGGTGGAGATGAGAACGG 58.814 55.000 0.00 0.00 0.00 4.44
3994 6799 9.421806 CAGATTGTCTGGATCTATTATCACTTC 57.578 37.037 0.00 0.00 40.71 3.01
4045 6863 4.362677 TCCAAGAAGCTATCTAGGGTTGT 58.637 43.478 0.00 0.00 37.42 3.32
4263 7081 5.482878 TCAATAATATACTCCCTCCGTTCCC 59.517 44.000 0.00 0.00 0.00 3.97
4316 7134 5.794687 TGGACTACATACGAAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
4318 7136 5.935206 TGGACTACATACGAAGCAAAATGAA 59.065 36.000 0.00 0.00 0.00 2.57
4328 7146 7.144722 ACGAAGCAAAATGAATGAATCTACA 57.855 32.000 0.00 0.00 0.00 2.74
4359 7177 9.512435 AAAATACGTCTATATACATCCGTATGC 57.488 33.333 0.00 0.00 40.25 3.14
4418 7236 4.101119 AGGAACGGAGGGACTATATTTGTG 59.899 45.833 0.00 0.00 41.55 3.33
4428 7247 9.099454 GAGGGACTATATTTGTGTGACTTAAAG 57.901 37.037 0.00 0.00 41.55 1.85
4516 7335 6.326323 ACATTTGGTTGGTCTAATTTCTGGTT 59.674 34.615 0.00 0.00 0.00 3.67
4522 7341 7.229907 TGGTTGGTCTAATTTCTGGTTAAAGTC 59.770 37.037 0.00 0.00 0.00 3.01
4532 7351 6.945938 TTCTGGTTAAAGTCGAATTTTGGA 57.054 33.333 16.73 5.46 0.00 3.53
4703 8136 4.790810 GTGATGTGCACAGTGATCTATG 57.209 45.455 25.84 0.00 46.91 2.23
4715 8148 7.678218 GCACAGTGATCTATGAAAATCAGGTTC 60.678 40.741 4.15 0.00 32.76 3.62
4822 8293 5.902613 TCCTTAGTGATGCTTGGATTTTG 57.097 39.130 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.417592 CGACGCTTCATGCTGTCAC 59.582 57.895 0.00 0.00 41.60 3.67
3 4 2.382746 GCGACGCTTCATGCTGTCA 61.383 57.895 13.73 0.00 41.60 3.58
4 5 2.397252 GCGACGCTTCATGCTGTC 59.603 61.111 13.73 0.00 39.75 3.51
6 7 1.985447 AATGGCGACGCTTCATGCTG 61.985 55.000 20.77 0.00 40.11 4.41
8 9 1.584483 CAATGGCGACGCTTCATGC 60.584 57.895 20.77 1.85 38.57 4.06
9 10 1.584483 GCAATGGCGACGCTTCATG 60.584 57.895 20.77 14.21 0.00 3.07
10 11 2.793946 GCAATGGCGACGCTTCAT 59.206 55.556 20.77 12.64 0.00 2.57
20 21 1.176527 TGCTTGGACTTAGCAATGGC 58.823 50.000 0.00 0.00 45.05 4.40
29 30 4.074970 CCTATGTCTGTTTGCTTGGACTT 58.925 43.478 0.00 0.00 0.00 3.01
86 87 1.865865 TGCTTCTTGGAGTTGTCGTC 58.134 50.000 0.00 0.00 0.00 4.20
131 132 1.017177 TCGTGCTATTTGGTGTCGGC 61.017 55.000 0.00 0.00 0.00 5.54
157 158 0.894835 TATTGCTGAGTGTCCGAGCA 59.105 50.000 0.00 0.00 40.94 4.26
172 173 8.404000 CAAAGGATCAAATGGAGAAGACTATTG 58.596 37.037 0.00 0.00 0.00 1.90
184 185 4.646492 CCCTACTTCCAAAGGATCAAATGG 59.354 45.833 0.00 0.00 34.58 3.16
239 241 4.145052 ACAAGAGGGACACAATTTTCTCC 58.855 43.478 0.00 0.00 0.00 3.71
287 309 9.567848 GTGAACTTCTTAAAGAAACATTCACAA 57.432 29.630 18.98 0.00 42.99 3.33
413 444 7.173047 AGCACATATATATCGTGATTTGTTGCA 59.827 33.333 20.34 0.00 32.23 4.08
414 445 7.479603 CAGCACATATATATCGTGATTTGTTGC 59.520 37.037 20.34 8.99 32.23 4.17
514 559 8.883954 TTACATGACATTTTTCAGCATTTTCA 57.116 26.923 0.00 0.00 0.00 2.69
531 576 0.535335 TCTCGGCCACCTTACATGAC 59.465 55.000 2.24 0.00 0.00 3.06
532 577 0.535335 GTCTCGGCCACCTTACATGA 59.465 55.000 2.24 0.00 0.00 3.07
533 578 0.249120 TGTCTCGGCCACCTTACATG 59.751 55.000 2.24 0.00 0.00 3.21
535 580 0.981183 ATTGTCTCGGCCACCTTACA 59.019 50.000 2.24 0.00 0.00 2.41
585 646 6.331577 TCTCATACCAGTACTACCTAACCA 57.668 41.667 0.00 0.00 0.00 3.67
586 647 6.238593 CGTTCTCATACCAGTACTACCTAACC 60.239 46.154 0.00 0.00 0.00 2.85
587 648 6.238593 CCGTTCTCATACCAGTACTACCTAAC 60.239 46.154 0.00 0.00 0.00 2.34
591 652 3.950395 ACCGTTCTCATACCAGTACTACC 59.050 47.826 0.00 0.00 0.00 3.18
593 654 7.701539 TTAAACCGTTCTCATACCAGTACTA 57.298 36.000 0.00 0.00 0.00 1.82
594 655 6.594788 TTAAACCGTTCTCATACCAGTACT 57.405 37.500 0.00 0.00 0.00 2.73
612 673 1.500396 CGCACCTCGGGCTTTAAAC 59.500 57.895 0.00 0.00 33.78 2.01
693 754 2.032681 GGGTCCAGAGTGTGTGGC 59.967 66.667 0.00 0.00 34.77 5.01
700 761 0.324368 TATGCGAGTGGGTCCAGAGT 60.324 55.000 0.00 0.00 0.00 3.24
702 763 0.324368 ACTATGCGAGTGGGTCCAGA 60.324 55.000 0.00 0.00 36.87 3.86
703 764 0.103208 GACTATGCGAGTGGGTCCAG 59.897 60.000 0.00 0.00 39.06 3.86
705 766 1.065928 CGACTATGCGAGTGGGTCC 59.934 63.158 0.00 0.00 39.06 4.46
706 767 1.589196 GCGACTATGCGAGTGGGTC 60.589 63.158 0.00 0.00 39.06 4.46
720 781 2.750237 GTGGGGTGGGAATGCGAC 60.750 66.667 0.00 0.00 0.00 5.19
758 821 1.299541 CGGCAGGATATCGCAAACTT 58.700 50.000 5.18 0.00 0.00 2.66
784 847 2.597510 AGGCTTTGGGTCAACGGC 60.598 61.111 3.20 3.20 38.18 5.68
787 850 2.152016 GTACTGAGGCTTTGGGTCAAC 58.848 52.381 0.00 0.00 0.00 3.18
788 851 1.270625 CGTACTGAGGCTTTGGGTCAA 60.271 52.381 0.00 0.00 0.00 3.18
789 852 0.320374 CGTACTGAGGCTTTGGGTCA 59.680 55.000 0.00 0.00 0.00 4.02
791 854 0.320697 GTCGTACTGAGGCTTTGGGT 59.679 55.000 0.00 0.00 0.00 4.51
794 857 1.352156 GCCGTCGTACTGAGGCTTTG 61.352 60.000 13.01 0.00 45.67 2.77
795 858 1.080025 GCCGTCGTACTGAGGCTTT 60.080 57.895 13.01 0.00 45.67 3.51
799 862 0.526662 AGAAAGCCGTCGTACTGAGG 59.473 55.000 0.00 0.00 0.00 3.86
800 863 1.467713 GGAGAAAGCCGTCGTACTGAG 60.468 57.143 0.00 0.00 0.00 3.35
822 885 2.696504 GGAGGGAAGGGGGAAGGG 60.697 72.222 0.00 0.00 0.00 3.95
823 886 1.694525 GAGGAGGGAAGGGGGAAGG 60.695 68.421 0.00 0.00 0.00 3.46
855 918 8.517062 AAATGGATCTGGAGAAGTTTTATCAG 57.483 34.615 0.00 0.00 0.00 2.90
927 990 2.210711 GCGGCCTCACCCTAGCTAT 61.211 63.158 0.00 0.00 33.26 2.97
1071 1134 1.273838 TGCATCTTGTACTCCCCCTCT 60.274 52.381 0.00 0.00 0.00 3.69
1085 1148 1.302285 CTCAGGCCCTTGTGCATCT 59.698 57.895 0.00 0.00 0.00 2.90
1146 1209 1.141449 CAGCTTCTCCAGGAGAGCG 59.859 63.158 24.09 18.51 42.90 5.03
1188 1251 1.611851 CCTCCACTCCCTGAGCTGT 60.612 63.158 0.00 0.00 32.04 4.40
1307 1370 1.587043 GACGCCCTTCCAAAAGAGCC 61.587 60.000 0.00 0.00 32.94 4.70
1415 1478 2.681976 GCATCAAGCCTGTACCTGTCAT 60.682 50.000 0.00 0.00 37.23 3.06
1473 1536 4.329545 GCAGGCAACCGAGGGTCA 62.330 66.667 0.00 0.00 33.12 4.02
1611 1674 3.418684 TTAGCAAGAGTTGTCTTCCCC 57.581 47.619 0.00 0.00 41.40 4.81
1648 1711 2.162408 GGCAATTGAACAGTCTACCAGC 59.838 50.000 10.34 0.00 0.00 4.85
1655 1718 3.375782 AAGCTTGGCAATTGAACAGTC 57.624 42.857 10.34 3.37 0.00 3.51
1751 1814 2.758423 TCACTCGATCGAGAAATGGGAA 59.242 45.455 42.97 18.04 44.53 3.97
1909 2024 8.613060 ACAGTCAAGGCATAATATGATAAGTG 57.387 34.615 4.14 0.86 0.00 3.16
2038 2154 2.288395 ACAGGAATTTTCAAGCAAGGCG 60.288 45.455 0.00 0.00 0.00 5.52
2272 2388 4.989279 ACTACCAATTGTGATGATTGCC 57.011 40.909 4.43 0.00 34.05 4.52
2508 5292 8.734386 CAACCTTAACAAATCTTTCTGCTATCT 58.266 33.333 0.00 0.00 0.00 1.98
2680 5471 7.657354 GTGATAAAATTTTCTTCCAGTGCCTTT 59.343 33.333 6.72 0.00 0.00 3.11
2738 5529 1.339711 CGGCAAACTTTATGCTGTGC 58.660 50.000 0.00 0.00 43.60 4.57
2753 5544 1.400846 GTAGTCAATCGAGAGTCGGCA 59.599 52.381 0.00 0.00 40.88 5.69
2853 5644 2.381725 CGAAAGGGGAGGTACTTGAC 57.618 55.000 0.00 0.00 41.55 3.18
2941 5732 6.183360 ACCTCAACAGACACAACTTTGTTATG 60.183 38.462 0.00 0.00 39.91 1.90
3082 5873 1.082300 CAGTTGCAGCAGCTGAACG 60.082 57.895 30.06 16.78 43.65 3.95
3158 5949 5.615289 GGTTATGCATGACAGTTCCTCTAT 58.385 41.667 21.65 0.00 0.00 1.98
3218 6009 4.467795 TCTCATTCTAGTCAAACCTCCCAG 59.532 45.833 0.00 0.00 0.00 4.45
3378 6169 3.588955 GACCAAGAACCAAATGGAATGC 58.411 45.455 6.42 0.00 37.66 3.56
3435 6226 6.155910 AGGTATCTGACAGAGACACAAATCAT 59.844 38.462 26.80 2.76 38.15 2.45
3513 6304 1.536943 AAGGGTCTCCTGCGTCACTC 61.537 60.000 0.00 0.00 44.07 3.51
3565 6356 0.389166 GTGAGGAGTTCAGCGTCAGG 60.389 60.000 0.00 0.00 36.21 3.86
3864 6666 0.819259 GCTGGCCGCAATCCTGATTA 60.819 55.000 13.61 0.00 38.92 1.75
3988 6793 7.050377 CCAGCTTGATAAAATAGGAGAAGTGA 58.950 38.462 0.00 0.00 0.00 3.41
3989 6794 6.261826 CCCAGCTTGATAAAATAGGAGAAGTG 59.738 42.308 0.00 0.00 0.00 3.16
3991 6796 6.360618 ACCCAGCTTGATAAAATAGGAGAAG 58.639 40.000 0.00 0.00 0.00 2.85
3992 6797 6.158695 AGACCCAGCTTGATAAAATAGGAGAA 59.841 38.462 0.00 0.00 0.00 2.87
3994 6799 5.762218 CAGACCCAGCTTGATAAAATAGGAG 59.238 44.000 0.00 0.00 0.00 3.69
4091 6909 4.370364 TTTTCTGAATTTAGGGCGATGC 57.630 40.909 0.00 0.00 0.00 3.91
4130 6948 3.261897 TCAGCTCTTACCTTTTCCTCTGG 59.738 47.826 0.00 0.00 0.00 3.86
4170 6988 3.810310 ACCCTGTTGCGATTTCAAAAA 57.190 38.095 0.00 0.00 0.00 1.94
4171 6989 3.810310 AACCCTGTTGCGATTTCAAAA 57.190 38.095 0.00 0.00 0.00 2.44
4172 6990 3.491792 GGAAACCCTGTTGCGATTTCAAA 60.492 43.478 0.00 0.00 32.13 2.69
4188 7006 7.824779 GTGATATAGTGAGGGATTATGGAAACC 59.175 40.741 0.00 0.00 0.00 3.27
4286 7104 8.812147 TGCTTCGTATGTAGTCCATATTAAAG 57.188 34.615 0.00 0.00 38.29 1.85
4288 7106 9.602568 TTTTGCTTCGTATGTAGTCCATATTAA 57.397 29.630 0.00 0.00 38.29 1.40
4394 7212 4.720273 ACAAATATAGTCCCTCCGTTCCTT 59.280 41.667 0.00 0.00 0.00 3.36
4396 7214 4.141779 ACACAAATATAGTCCCTCCGTTCC 60.142 45.833 0.00 0.00 0.00 3.62
4402 7220 9.099454 CTTTAAGTCACACAAATATAGTCCCTC 57.901 37.037 0.00 0.00 0.00 4.30
4418 7236 9.874215 GTTTTCAGTGGTATAACTTTAAGTCAC 57.126 33.333 0.00 2.03 0.00 3.67
4516 7335 5.475220 TCCAGCATTCCAAAATTCGACTTTA 59.525 36.000 0.76 0.00 0.00 1.85
4522 7341 3.191162 TGTCTCCAGCATTCCAAAATTCG 59.809 43.478 0.00 0.00 0.00 3.34
4532 7351 3.489355 TCACAAATGTGTCTCCAGCATT 58.511 40.909 12.87 0.00 45.76 3.56
4561 7812 5.464722 CGTGCAGATAAAGATTACAGCTGAT 59.535 40.000 23.35 3.68 0.00 2.90
4703 8136 4.672801 GCAATCCACTCGAACCTGATTTTC 60.673 45.833 0.00 0.00 0.00 2.29
4715 8148 0.167470 CAACAGCAGCAATCCACTCG 59.833 55.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.