Multiple sequence alignment - TraesCS7A01G366200

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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 TraesCS7A01G366200 chr7A 100.000 5484 0 0 1 5484 539852010 539857493 0.000000e+00 10128
1 TraesCS7A01G366200 chr7A 87.357 4097 475 19 1019 5085 540202848 540206931 0.000000e+00 4656
2 TraesCS7A01G366200 chr7A 79.036 1598 291 40 3059 4629 540757522 540759102 0.000000e+00 1055
3 TraesCS7A01G366200 chr7A 79.684 1457 260 25 3057 4491 540284390 540285832 0.000000e+00 1018
4 TraesCS7A01G366200 chr7A 84.628 618 78 10 828 1428 540755559 540756176 2.830000e-167 599
5 TraesCS7A01G366200 chr7A 83.548 620 85 14 822 1428 540771448 540772063 1.030000e-156 564
6 TraesCS7A01G366200 chr7A 83.173 208 22 9 46 243 540201893 540202097 1.570000e-40 178
7 TraesCS7A01G366200 chr7D 96.415 3738 127 4 819 4553 459746860 459743127 0.000000e+00 6154
8 TraesCS7A01G366200 chr7D 80.997 3552 609 57 1032 4546 459474555 459471033 0.000000e+00 2760
9 TraesCS7A01G366200 chr7D 93.617 846 30 10 1 824 459747732 459746889 0.000000e+00 1242
10 TraesCS7A01G366200 chr7D 80.000 1460 251 29 3057 4491 459464437 459462994 0.000000e+00 1040
11 TraesCS7A01G366200 chr7D 79.644 1459 258 28 3057 4491 459431609 459430166 0.000000e+00 1013
12 TraesCS7A01G366200 chr7D 87.619 105 7 4 141 245 459450884 459450786 3.470000e-22 117
13 TraesCS7A01G366200 chr7B 90.029 4453 376 29 1035 5428 481668832 481664389 0.000000e+00 5701
14 TraesCS7A01G366200 chr7B 80.260 1459 249 25 3057 4491 481616062 481614619 0.000000e+00 1062
15 TraesCS7A01G366200 chr7B 87.435 191 10 10 62 243 481814525 481814340 2.000000e-49 207
16 TraesCS7A01G366200 chr7B 81.500 200 20 7 630 824 481618277 481618090 1.230000e-31 148
17 TraesCS7A01G366200 chr7B 91.398 93 5 1 46 138 481843809 481843720 2.070000e-24 124
18 TraesCS7A01G366200 chr5A 82.806 3600 549 43 1019 4570 680981209 680984786 0.000000e+00 3155
19 TraesCS7A01G366200 chr5A 82.435 3524 559 39 1019 4492 680921300 680924813 0.000000e+00 3024
20 TraesCS7A01G366200 chr4D 82.396 3681 566 51 943 4570 500300901 500304552 0.000000e+00 3133
21 TraesCS7A01G366200 chr4D 82.391 3589 552 49 1019 4546 500197214 500200783 0.000000e+00 3053
22 TraesCS7A01G366200 chr4B 82.616 3624 549 50 1000 4569 643629115 643632711 0.000000e+00 3127
23 TraesCS7A01G366200 chr4B 81.602 3582 593 43 1019 4546 643528201 643531770 0.000000e+00 2904
24 TraesCS7A01G366200 chrUn 82.796 3441 535 38 1103 4497 60417104 60413675 0.000000e+00 3022
25 TraesCS7A01G366200 chrUn 83.187 2623 378 37 1973 4546 60473870 60471262 0.000000e+00 2342
26 TraesCS7A01G366200 chr6B 87.692 65 7 1 5022 5085 497239054 497238990 2.120000e-09 75


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 TraesCS7A01G366200 chr7A 539852010 539857493 5483 False 10128 10128 100.000 1 5484 1 chr7A.!!$F1 5483
1 TraesCS7A01G366200 chr7A 540201893 540206931 5038 False 2417 4656 85.265 46 5085 2 chr7A.!!$F4 5039
2 TraesCS7A01G366200 chr7A 540284390 540285832 1442 False 1018 1018 79.684 3057 4491 1 chr7A.!!$F2 1434
3 TraesCS7A01G366200 chr7A 540755559 540759102 3543 False 827 1055 81.832 828 4629 2 chr7A.!!$F5 3801
4 TraesCS7A01G366200 chr7A 540771448 540772063 615 False 564 564 83.548 822 1428 1 chr7A.!!$F3 606
5 TraesCS7A01G366200 chr7D 459743127 459747732 4605 True 3698 6154 95.016 1 4553 2 chr7D.!!$R5 4552
6 TraesCS7A01G366200 chr7D 459471033 459474555 3522 True 2760 2760 80.997 1032 4546 1 chr7D.!!$R4 3514
7 TraesCS7A01G366200 chr7D 459462994 459464437 1443 True 1040 1040 80.000 3057 4491 1 chr7D.!!$R3 1434
8 TraesCS7A01G366200 chr7D 459430166 459431609 1443 True 1013 1013 79.644 3057 4491 1 chr7D.!!$R1 1434
9 TraesCS7A01G366200 chr7B 481664389 481668832 4443 True 5701 5701 90.029 1035 5428 1 chr7B.!!$R1 4393
10 TraesCS7A01G366200 chr7B 481614619 481618277 3658 True 605 1062 80.880 630 4491 2 chr7B.!!$R4 3861
11 TraesCS7A01G366200 chr5A 680981209 680984786 3577 False 3155 3155 82.806 1019 4570 1 chr5A.!!$F2 3551
12 TraesCS7A01G366200 chr5A 680921300 680924813 3513 False 3024 3024 82.435 1019 4492 1 chr5A.!!$F1 3473
13 TraesCS7A01G366200 chr4D 500300901 500304552 3651 False 3133 3133 82.396 943 4570 1 chr4D.!!$F2 3627
14 TraesCS7A01G366200 chr4D 500197214 500200783 3569 False 3053 3053 82.391 1019 4546 1 chr4D.!!$F1 3527
15 TraesCS7A01G366200 chr4B 643629115 643632711 3596 False 3127 3127 82.616 1000 4569 1 chr4B.!!$F2 3569
16 TraesCS7A01G366200 chr4B 643528201 643531770 3569 False 2904 2904 81.602 1019 4546 1 chr4B.!!$F1 3527
17 TraesCS7A01G366200 chrUn 60413675 60417104 3429 True 3022 3022 82.796 1103 4497 1 chrUn.!!$R1 3394
18 TraesCS7A01G366200 chrUn 60471262 60473870 2608 True 2342 2342 83.187 1973 4546 1 chrUn.!!$R2 2573

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
891 1139 0.028505 CCGTATCGATCGTTGACCGT 59.971 55.000 15.94 0.0 37.94 4.83 F
1072 1395 0.467844 TGCCTTCTTTTGCTGCCTGA 60.468 50.000 0.00 0.0 0.00 3.86 F
1252 1584 2.109126 GTGATTGCGCTGGACCTCC 61.109 63.158 9.73 0.0 0.00 4.30 F
3598 3988 0.461548 TGGAGCACATAGGAGCTTCG 59.538 55.000 0.00 0.0 41.23 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 2578 0.323302 TCCAGGTGAAGCATGCGTAA 59.677 50.00 13.01 0.0 0.00 3.18 R
3383 3725 4.258543 CAAATGGAGATTGGCTTGCATTT 58.741 39.13 0.00 0.0 43.27 2.32 R
3601 3991 0.318441 CGAAGGGCTTCACACTCTGA 59.682 55.00 0.00 0.0 39.46 3.27 R
5154 5596 0.107165 GCGAAATAGGCTGGGGTCTT 60.107 55.00 0.00 0.0 0.00 3.01 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 0.318699 TCGCAAGTCACAGGAACTCG 60.319 55.000 0.00 0.00 35.01 4.18
112 117 2.108566 CAGGATCAGCAGCCGGAG 59.891 66.667 5.05 0.00 0.00 4.63
253 264 4.586235 GTGCCATCCCCATCCCCG 62.586 72.222 0.00 0.00 0.00 5.73
259 270 2.154074 ATCCCCATCCCCGTTAGCC 61.154 63.158 0.00 0.00 0.00 3.93
336 347 2.549563 CGATCTGTGATATGGCTGCCTT 60.550 50.000 21.03 16.33 0.00 4.35
374 385 3.106827 AGGGGGTTTTATGCATTTGGAG 58.893 45.455 3.54 0.00 0.00 3.86
390 401 6.971184 GCATTTGGAGATCAGAAATGTTGTAG 59.029 38.462 18.06 1.87 38.69 2.74
476 516 7.979444 TCAAAGGTAGGAAAGTAAATGACAG 57.021 36.000 0.00 0.00 0.00 3.51
490 531 7.241628 AGTAAATGACAGAAAAAGGGGAAGAT 58.758 34.615 0.00 0.00 0.00 2.40
515 579 2.860735 CGTTCATACTTCAGCCAGCTAC 59.139 50.000 0.00 0.00 0.00 3.58
526 670 1.221840 CCAGCTACCATGCCGTTCT 59.778 57.895 0.00 0.00 0.00 3.01
528 672 0.108186 CAGCTACCATGCCGTTCTGA 60.108 55.000 0.00 0.00 0.00 3.27
544 688 4.327357 CGTTCTGACTAAGTTGCCTGTATG 59.673 45.833 0.00 0.00 0.00 2.39
545 689 4.471904 TCTGACTAAGTTGCCTGTATGG 57.528 45.455 0.00 0.00 39.35 2.74
548 692 3.270877 GACTAAGTTGCCTGTATGGGTG 58.729 50.000 0.00 0.00 36.00 4.61
592 745 1.754803 TGTCAAATCTCGCCGAGGTAT 59.245 47.619 15.08 0.00 0.00 2.73
718 876 2.896044 TGGGACAATTGCAATGTAAGCA 59.104 40.909 13.82 0.00 35.94 3.91
719 877 3.056678 TGGGACAATTGCAATGTAAGCAG 60.057 43.478 13.82 0.33 38.44 4.24
722 880 4.418392 GACAATTGCAATGTAAGCAGAGG 58.582 43.478 13.82 0.00 43.75 3.69
762 922 0.687354 GGCTGTCCCTGTCTGAGAAA 59.313 55.000 0.00 0.00 0.00 2.52
810 977 5.050634 CCAAATGCATGCACACAATATTAGC 60.051 40.000 25.37 0.00 0.00 3.09
847 1083 4.503643 CCAAAATCTGGTCCAAAAGCATGT 60.504 41.667 0.00 0.00 40.78 3.21
891 1139 0.028505 CCGTATCGATCGTTGACCGT 59.971 55.000 15.94 0.00 37.94 4.83
892 1140 1.110085 CGTATCGATCGTTGACCGTG 58.890 55.000 15.94 0.00 37.94 4.94
1011 1331 3.740044 ACAATAACAATGGCGTCTTCG 57.260 42.857 0.00 0.00 40.37 3.79
1072 1395 0.467844 TGCCTTCTTTTGCTGCCTGA 60.468 50.000 0.00 0.00 0.00 3.86
1122 1448 5.983333 ATGATAGACAATCCCTCCTTTGT 57.017 39.130 0.00 0.00 38.71 2.83
1252 1584 2.109126 GTGATTGCGCTGGACCTCC 61.109 63.158 9.73 0.00 0.00 4.30
1338 1670 5.514204 GCTGCAACTGTCAAATAATAGCTTG 59.486 40.000 0.00 0.00 0.00 4.01
1375 1707 4.093291 AGCTTGGCCTCCTGAGCG 62.093 66.667 3.32 0.00 38.03 5.03
1554 1886 3.915437 AACCTTCGCAACAATAACCTG 57.085 42.857 0.00 0.00 0.00 4.00
1591 1923 4.927267 TCTGCTTTTGGAAATCTCCCTA 57.073 40.909 0.00 0.00 41.64 3.53
1628 1960 2.656002 TCTCGCTAGCACTGGACTTAT 58.344 47.619 16.45 0.00 0.00 1.73
1859 2192 8.068892 AACAGTTTTGTTGGTTCAATACCTTA 57.931 30.769 0.00 0.00 45.54 2.69
1941 2274 6.997942 GGAATAATACCTTCCTCACTAGGT 57.002 41.667 0.00 0.00 46.28 3.08
2177 2510 2.791158 GCCACACGCTTCCAAATATTCG 60.791 50.000 0.00 0.00 0.00 3.34
2904 3243 2.868583 CGTCGGCAATCTGATTCATCTT 59.131 45.455 0.00 0.00 0.00 2.40
3459 3849 6.603237 TCATATGAAGACATTGTAAAGGCG 57.397 37.500 1.98 0.00 37.87 5.52
3598 3988 0.461548 TGGAGCACATAGGAGCTTCG 59.538 55.000 0.00 0.00 41.23 3.79
3601 3991 2.297597 GGAGCACATAGGAGCTTCGTAT 59.702 50.000 0.00 0.00 41.23 3.06
3773 4163 5.585390 GATGGATCATGAACATGGTGAAAC 58.415 41.667 17.81 2.19 39.24 2.78
3933 4323 2.222953 GGTTGCATACGTCACCGATTTC 60.223 50.000 0.00 0.00 37.88 2.17
4159 4568 3.881688 GCATGAGCCAACAGATATCAACT 59.118 43.478 5.32 0.00 33.58 3.16
4199 4608 5.594317 AGTTTTGGAGTGCTTCTGTTACAAT 59.406 36.000 0.00 0.00 0.00 2.71
4238 4647 7.469456 GCAGTCCAACTGGTGAAAAATTTAGTA 60.469 37.037 9.01 0.00 46.01 1.82
4285 4694 9.677567 TTTGTTGATAGAGCATTTACAAAGAAC 57.322 29.630 0.00 0.00 31.76 3.01
4297 4706 7.274250 GCATTTACAAAGAACATTCATGAGGTC 59.726 37.037 0.00 0.00 0.00 3.85
4312 4721 2.835156 TGAGGTCGTTGATCCCACAATA 59.165 45.455 0.00 0.00 32.36 1.90
4335 4744 2.719739 ACAAGATGACAGGAATGCAGG 58.280 47.619 0.00 0.00 0.00 4.85
4336 4745 1.404391 CAAGATGACAGGAATGCAGGC 59.596 52.381 0.00 0.00 0.00 4.85
4371 4780 9.125026 GAAGAATTGTGTTATCCCACTGATTAT 57.875 33.333 0.00 0.00 36.30 1.28
4480 4891 1.671979 CCTCACACATGTATGCCAGG 58.328 55.000 0.00 0.00 0.00 4.45
4498 4909 3.305608 CCAGGTGAAGCAAAGATTTGGAC 60.306 47.826 7.38 0.00 38.57 4.02
4504 4916 1.153353 GCAAAGATTTGGACGACGGA 58.847 50.000 7.38 0.00 38.57 4.69
4513 4925 2.170273 GACGACGGAAACTTGCGC 59.830 61.111 0.00 0.00 46.36 6.09
4593 5006 3.065371 GGATTCAGTTACTGGCATTTCCG 59.935 47.826 12.79 0.00 37.80 4.30
4719 5135 9.512435 CTCAAATGTCCAATCAGATTGATTTAC 57.488 33.333 22.78 14.85 44.03 2.01
4824 5255 2.297701 GAACAAGTGCACTTTCAGGGA 58.702 47.619 29.23 0.00 33.11 4.20
4981 5421 9.181805 GCTGTAGTTTTCTTTATTTTCAGTTCC 57.818 33.333 0.00 0.00 0.00 3.62
4996 5436 6.975196 TTCAGTTCCTTTCATTTTCATCCA 57.025 33.333 0.00 0.00 0.00 3.41
5009 5449 9.650714 TTCATTTTCATCCATGATCTTAGGATT 57.349 29.630 10.26 0.00 40.07 3.01
5015 5455 3.324846 TCCATGATCTTAGGATTCCCACG 59.675 47.826 0.00 0.00 33.88 4.94
5045 5485 0.652592 CCGTTGCTTCCTGCTAATCG 59.347 55.000 0.00 0.00 43.37 3.34
5046 5486 0.026803 CGTTGCTTCCTGCTAATCGC 59.973 55.000 0.00 0.00 43.37 4.58
5052 5492 2.564771 CTTCCTGCTAATCGCCAATCA 58.435 47.619 0.00 0.00 38.05 2.57
5106 5548 3.890756 AGGTCTGCACATGAAATCAACAA 59.109 39.130 0.00 0.00 0.00 2.83
5107 5549 4.022589 AGGTCTGCACATGAAATCAACAAG 60.023 41.667 0.00 0.00 0.00 3.16
5112 5554 7.170320 GTCTGCACATGAAATCAACAAGAAAAT 59.830 33.333 0.00 0.00 0.00 1.82
5113 5555 8.358895 TCTGCACATGAAATCAACAAGAAAATA 58.641 29.630 0.00 0.00 0.00 1.40
5128 5570 8.581253 ACAAGAAAATAAAATCCCCTACAGAG 57.419 34.615 0.00 0.00 0.00 3.35
5154 5596 3.335579 TCGAACTGAGTCGAGATTCTCA 58.664 45.455 13.88 3.72 44.76 3.27
5156 5598 4.094911 CGAACTGAGTCGAGATTCTCAAG 58.905 47.826 13.88 5.43 43.86 3.02
5160 5602 2.755655 TGAGTCGAGATTCTCAAGACCC 59.244 50.000 13.88 5.59 37.69 4.46
5164 5606 1.472376 CGAGATTCTCAAGACCCCAGC 60.472 57.143 13.88 0.00 0.00 4.85
5166 5608 0.915364 GATTCTCAAGACCCCAGCCT 59.085 55.000 0.00 0.00 0.00 4.58
5184 5642 0.179029 CTATTTCGCCCAATCCCCGT 60.179 55.000 0.00 0.00 0.00 5.28
5193 5651 0.546122 CCAATCCCCGTGGAAGATCA 59.454 55.000 0.00 0.00 45.98 2.92
5196 5654 1.345715 ATCCCCGTGGAAGATCACCC 61.346 60.000 0.00 0.00 45.98 4.61
5428 5890 1.144276 TTGTCTCACGGGCGAAACA 59.856 52.632 0.00 0.00 0.00 2.83
5429 5891 0.878523 TTGTCTCACGGGCGAAACAG 60.879 55.000 0.00 0.00 0.00 3.16
5430 5892 2.357034 TCTCACGGGCGAAACAGC 60.357 61.111 0.00 0.00 0.00 4.40
5431 5893 2.357517 CTCACGGGCGAAACAGCT 60.358 61.111 0.00 0.00 37.29 4.24
5432 5894 2.664851 TCACGGGCGAAACAGCTG 60.665 61.111 13.48 13.48 37.29 4.24
5433 5895 2.972505 CACGGGCGAAACAGCTGT 60.973 61.111 15.25 15.25 37.29 4.40
5434 5896 2.972505 ACGGGCGAAACAGCTGTG 60.973 61.111 22.49 9.41 37.29 3.66
5435 5897 2.972505 CGGGCGAAACAGCTGTGT 60.973 61.111 22.49 16.52 39.19 3.72
5436 5898 2.639286 GGGCGAAACAGCTGTGTG 59.361 61.111 22.49 14.20 36.84 3.82
5437 5899 2.186826 GGGCGAAACAGCTGTGTGT 61.187 57.895 22.49 9.05 36.84 3.72
5438 5900 1.724582 GGGCGAAACAGCTGTGTGTT 61.725 55.000 22.49 11.45 42.62 3.32
5439 5901 0.592247 GGCGAAACAGCTGTGTGTTG 60.592 55.000 22.49 13.57 39.82 3.33
5440 5902 0.376852 GCGAAACAGCTGTGTGTTGA 59.623 50.000 22.49 0.00 39.82 3.18
5441 5903 1.002468 GCGAAACAGCTGTGTGTTGAT 60.002 47.619 22.49 0.00 39.82 2.57
5442 5904 2.541588 GCGAAACAGCTGTGTGTTGATT 60.542 45.455 22.49 8.94 39.82 2.57
5443 5905 3.694734 CGAAACAGCTGTGTGTTGATTT 58.305 40.909 22.49 8.10 39.82 2.17
5444 5906 3.725740 CGAAACAGCTGTGTGTTGATTTC 59.274 43.478 22.49 15.94 39.82 2.17
5445 5907 4.496341 CGAAACAGCTGTGTGTTGATTTCT 60.496 41.667 22.49 0.00 39.82 2.52
5446 5908 5.277297 CGAAACAGCTGTGTGTTGATTTCTA 60.277 40.000 22.49 0.00 39.82 2.10
5447 5909 5.424121 AACAGCTGTGTGTTGATTTCTAC 57.576 39.130 22.49 0.00 39.25 2.59
5448 5910 3.494626 ACAGCTGTGTGTTGATTTCTACG 59.505 43.478 20.97 0.00 34.75 3.51
5449 5911 2.480419 AGCTGTGTGTTGATTTCTACGC 59.520 45.455 0.00 0.00 33.79 4.42
5450 5912 2.223144 GCTGTGTGTTGATTTCTACGCA 59.777 45.455 4.64 4.64 39.13 5.24
5451 5913 3.120199 GCTGTGTGTTGATTTCTACGCAT 60.120 43.478 10.65 0.00 42.13 4.73
5452 5914 4.092821 GCTGTGTGTTGATTTCTACGCATA 59.907 41.667 10.65 7.91 42.13 3.14
5453 5915 5.524511 TGTGTGTTGATTTCTACGCATAC 57.475 39.130 10.65 1.98 42.13 2.39
5454 5916 4.090786 TGTGTGTTGATTTCTACGCATACG 59.909 41.667 10.65 0.00 42.13 3.06
5455 5917 4.325204 GTGTGTTGATTTCTACGCATACGA 59.675 41.667 10.65 0.00 42.13 3.43
5456 5918 5.005394 GTGTGTTGATTTCTACGCATACGAT 59.995 40.000 10.65 0.00 42.13 3.73
5457 5919 6.197655 GTGTGTTGATTTCTACGCATACGATA 59.802 38.462 10.65 0.00 42.13 2.92
5458 5920 6.416750 TGTGTTGATTTCTACGCATACGATAG 59.583 38.462 4.64 0.00 43.93 2.08
5459 5921 6.417044 GTGTTGATTTCTACGCATACGATAGT 59.583 38.462 0.00 0.00 43.93 2.12
5460 5922 7.043590 GTGTTGATTTCTACGCATACGATAGTT 60.044 37.037 0.00 0.00 43.93 2.24
5473 5935 3.597377 CGATAGTTGTACGATGACCGA 57.403 47.619 0.00 0.00 41.76 4.69
5474 5936 4.143194 CGATAGTTGTACGATGACCGAT 57.857 45.455 0.00 0.00 41.76 4.18
5475 5937 4.534168 CGATAGTTGTACGATGACCGATT 58.466 43.478 0.00 0.00 41.76 3.34
5476 5938 4.611782 CGATAGTTGTACGATGACCGATTC 59.388 45.833 0.00 0.00 41.76 2.52
5477 5939 3.861276 AGTTGTACGATGACCGATTCA 57.139 42.857 0.00 0.00 41.76 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.320247 CTGTGACTTGCGAGCCTTCT 60.320 55.000 0.00 0.00 0.00 2.85
29 30 7.007725 CGCACTCAATTGTGATTTCTAAACATC 59.992 37.037 14.16 0.00 40.12 3.06
253 264 1.478105 CCATTCCTTTGCCTGGCTAAC 59.522 52.381 21.03 0.00 0.00 2.34
259 270 1.467920 GGTCTCCATTCCTTTGCCTG 58.532 55.000 0.00 0.00 0.00 4.85
336 347 4.617520 TGCAAGCGGCTGGTTCGA 62.618 61.111 7.09 0.00 45.15 3.71
358 369 8.814235 CATTTCTGATCTCCAAATGCATAAAAC 58.186 33.333 0.00 0.00 32.33 2.43
390 401 2.202756 CTAGGCGCCTCGTTGACC 60.203 66.667 36.73 0.00 0.00 4.02
476 516 1.886542 ACGCACATCTTCCCCTTTTTC 59.113 47.619 0.00 0.00 0.00 2.29
490 531 1.270571 TGGCTGAAGTATGAACGCACA 60.271 47.619 0.00 0.00 0.00 4.57
515 579 2.386661 ACTTAGTCAGAACGGCATGG 57.613 50.000 0.00 0.00 0.00 3.66
544 688 1.392589 ATCGGAATGCATGAACACCC 58.607 50.000 0.00 0.00 0.00 4.61
545 689 3.814842 TGATATCGGAATGCATGAACACC 59.185 43.478 0.00 0.00 0.00 4.16
548 692 4.318332 TCCTGATATCGGAATGCATGAAC 58.682 43.478 13.42 0.00 0.00 3.18
718 876 1.617947 GGACGATGCCTCCAACCTCT 61.618 60.000 0.00 0.00 0.00 3.69
719 877 1.153349 GGACGATGCCTCCAACCTC 60.153 63.158 0.00 0.00 0.00 3.85
722 880 2.109126 GCAGGACGATGCCTCCAAC 61.109 63.158 0.00 0.00 40.43 3.77
762 922 5.003804 ACGCTAACAGATTTGACCTTTCAT 58.996 37.500 0.00 0.00 0.00 2.57
847 1083 3.136443 GGAACTGGGATGATACATGACCA 59.864 47.826 0.00 0.00 0.00 4.02
855 1091 1.128200 CGGTGGGAACTGGGATGATA 58.872 55.000 0.00 0.00 0.00 2.15
891 1139 1.276421 GCCCTCTAGACAGCAACTTCA 59.724 52.381 4.68 0.00 0.00 3.02
892 1140 1.552792 AGCCCTCTAGACAGCAACTTC 59.447 52.381 10.96 0.00 0.00 3.01
1011 1331 2.067365 AACCTGGAAACAAGACACCC 57.933 50.000 0.00 0.00 42.06 4.61
1088 1414 6.967199 GGATTGTCTATCATTTTCGGTTTCAC 59.033 38.462 0.00 0.00 34.77 3.18
1122 1448 0.321671 CCGAGAGCCAGGACTTGAAA 59.678 55.000 0.00 0.00 0.00 2.69
1252 1584 0.464870 CCTGAGATGCCTCCTGACTG 59.535 60.000 0.00 0.00 38.66 3.51
1259 1591 1.001860 GTATGGAGCCTGAGATGCCTC 59.998 57.143 0.00 0.00 39.86 4.70
1554 1886 1.101331 CAGAAGGGATGCTTCCTTGC 58.899 55.000 17.48 9.49 43.98 4.01
1628 1960 0.968901 AGACGGAGGTATGTTGCCGA 60.969 55.000 7.16 0.00 46.29 5.54
1859 2192 1.212935 GGGGAGATGTGGCAGTAACAT 59.787 52.381 0.00 0.00 40.93 2.71
1941 2274 1.132657 TGAACCAGGGAGGACAGGTTA 60.133 52.381 0.00 0.00 43.94 2.85
2245 2578 0.323302 TCCAGGTGAAGCATGCGTAA 59.677 50.000 13.01 0.00 0.00 3.18
3383 3725 4.258543 CAAATGGAGATTGGCTTGCATTT 58.741 39.130 0.00 0.00 43.27 2.32
3598 3988 3.526534 GAAGGGCTTCACACTCTGATAC 58.473 50.000 0.00 0.00 39.31 2.24
3601 3991 0.318441 CGAAGGGCTTCACACTCTGA 59.682 55.000 0.00 0.00 39.46 3.27
3752 4142 4.405548 TGTTTCACCATGTTCATGATCCA 58.594 39.130 13.51 0.00 0.00 3.41
3773 4163 7.121168 TCCTTTGGCTTAATGACAGAGTATTTG 59.879 37.037 0.00 0.00 34.35 2.32
3933 4323 2.029838 ACAGAAATCTTGCTAGGCCG 57.970 50.000 0.00 0.00 0.00 6.13
4145 4554 7.050377 ACATCACCCTTAGTTGATATCTGTTG 58.950 38.462 3.98 0.00 0.00 3.33
4159 4568 5.308497 TCCAAAACTGTAGACATCACCCTTA 59.692 40.000 0.00 0.00 0.00 2.69
4199 4608 1.702401 TGGACTGCACCCTGTTATCAA 59.298 47.619 2.45 0.00 0.00 2.57
4238 4647 8.310122 ACAAATTCATGAAGGCTTATACCATT 57.690 30.769 14.54 0.00 0.00 3.16
4285 4694 2.874701 GGGATCAACGACCTCATGAATG 59.125 50.000 0.00 0.00 0.00 2.67
4297 4706 5.416083 TCTTGTAGTATTGTGGGATCAACG 58.584 41.667 0.00 0.00 0.00 4.10
4312 4721 4.511527 CTGCATTCCTGTCATCTTGTAGT 58.488 43.478 0.00 0.00 0.00 2.73
4335 4744 2.744202 ACACAATTCTTCATCAGGTCGC 59.256 45.455 0.00 0.00 0.00 5.19
4336 4745 6.238211 GGATAACACAATTCTTCATCAGGTCG 60.238 42.308 0.00 0.00 0.00 4.79
4371 4780 0.753262 GGAGCAAGAGAGGCCGATTA 59.247 55.000 0.00 0.00 0.00 1.75
4480 4891 3.555518 GTCGTCCAAATCTTTGCTTCAC 58.444 45.455 0.00 0.00 36.86 3.18
4498 4909 3.295228 CTGGCGCAAGTTTCCGTCG 62.295 63.158 10.83 0.00 41.68 5.12
4513 4925 3.525537 TCTTCTTTAGATGCGCTTCTGG 58.474 45.455 30.03 20.46 0.00 3.86
4593 5006 6.668541 TGCAGCAAGAGAATATTACTGTTC 57.331 37.500 0.00 0.00 0.00 3.18
4656 5072 3.187700 GGATGGTGCTTACAGAGTTACG 58.812 50.000 0.00 0.00 0.00 3.18
4719 5135 7.367285 TCCGAAATCACCTTCTAAAAACATTG 58.633 34.615 0.00 0.00 0.00 2.82
4741 5157 1.528586 GTGCATTCTCATTCGGATCCG 59.471 52.381 28.62 28.62 41.35 4.18
4824 5255 2.125512 GTGCGGAGGCGATCTTGT 60.126 61.111 0.00 0.00 44.10 3.16
4889 5328 5.799827 CCAAAGGGGTCTCAACAAATTTA 57.200 39.130 0.00 0.00 0.00 1.40
4913 5353 6.821616 ATTAACAGTCTCTCATGGAGGATT 57.178 37.500 10.23 4.49 42.10 3.01
4915 5355 5.960811 AGAATTAACAGTCTCTCATGGAGGA 59.039 40.000 10.23 0.00 42.10 3.71
4981 5421 9.128404 TCCTAAGATCATGGATGAAAATGAAAG 57.872 33.333 0.00 0.00 40.69 2.62
4986 5426 7.673082 GGGAATCCTAAGATCATGGATGAAAAT 59.327 37.037 12.74 0.65 40.15 1.82
4996 5436 5.832539 AATCGTGGGAATCCTAAGATCAT 57.167 39.130 13.62 0.00 0.00 2.45
5009 5449 3.899052 ACGGAAGATAAAATCGTGGGA 57.101 42.857 0.00 0.00 32.60 4.37
5015 5455 5.573146 CAGGAAGCAACGGAAGATAAAATC 58.427 41.667 0.00 0.00 0.00 2.17
5045 5485 2.103537 AATTGCTGGCTTTGATTGGC 57.896 45.000 0.00 0.00 0.00 4.52
5046 5486 2.160813 GCAAATTGCTGGCTTTGATTGG 59.839 45.455 11.19 0.00 40.96 3.16
5085 5525 3.921119 TGTTGATTTCATGTGCAGACC 57.079 42.857 0.00 0.00 0.00 3.85
5086 5526 5.112220 TCTTGTTGATTTCATGTGCAGAC 57.888 39.130 0.00 0.00 0.00 3.51
5096 5538 9.725019 AGGGGATTTTATTTTCTTGTTGATTTC 57.275 29.630 0.00 0.00 0.00 2.17
5099 5541 9.320295 TGTAGGGGATTTTATTTTCTTGTTGAT 57.680 29.630 0.00 0.00 0.00 2.57
5106 5548 9.682465 GTTACTCTGTAGGGGATTTTATTTTCT 57.318 33.333 0.00 0.00 0.00 2.52
5107 5549 9.682465 AGTTACTCTGTAGGGGATTTTATTTTC 57.318 33.333 0.00 0.00 0.00 2.29
5112 5554 6.189859 TCGAGTTACTCTGTAGGGGATTTTA 58.810 40.000 10.83 0.00 0.00 1.52
5113 5555 5.021458 TCGAGTTACTCTGTAGGGGATTTT 58.979 41.667 10.83 0.00 0.00 1.82
5146 5588 0.915364 GGCTGGGGTCTTGAGAATCT 59.085 55.000 0.00 0.00 34.92 2.40
5148 5590 2.270434 TAGGCTGGGGTCTTGAGAAT 57.730 50.000 0.00 0.00 0.00 2.40
5149 5591 2.270434 ATAGGCTGGGGTCTTGAGAA 57.730 50.000 0.00 0.00 0.00 2.87
5154 5596 0.107165 GCGAAATAGGCTGGGGTCTT 60.107 55.000 0.00 0.00 0.00 3.01
5156 5598 1.526225 GGCGAAATAGGCTGGGGTC 60.526 63.158 0.00 0.00 0.00 4.46
5160 5602 0.954452 GATTGGGCGAAATAGGCTGG 59.046 55.000 0.00 0.00 36.85 4.85
5164 5606 0.889186 CGGGGATTGGGCGAAATAGG 60.889 60.000 0.00 0.00 0.00 2.57
5166 5608 0.464735 CACGGGGATTGGGCGAAATA 60.465 55.000 0.00 0.00 0.00 1.40
5184 5642 2.268796 TGATCTGGGGTGATCTTCCA 57.731 50.000 9.12 6.11 42.30 3.53
5193 5651 0.617413 CTGTCTGCTTGATCTGGGGT 59.383 55.000 0.00 0.00 0.00 4.95
5196 5654 2.756840 TGTCTGTCTGCTTGATCTGG 57.243 50.000 0.00 0.00 0.00 3.86
5316 5774 2.825836 CGAGGACAGGGCCAATGC 60.826 66.667 6.18 0.00 0.00 3.56
5404 5866 3.148084 CCCGTGAGACAACAGGGT 58.852 61.111 0.00 0.00 42.16 4.34
5405 5867 2.358737 GCCCGTGAGACAACAGGG 60.359 66.667 0.00 0.00 44.72 4.45
5414 5876 2.357517 AGCTGTTTCGCCCGTGAG 60.358 61.111 0.00 0.00 0.00 3.51
5428 5890 2.480419 GCGTAGAAATCAACACACAGCT 59.520 45.455 0.00 0.00 0.00 4.24
5429 5891 2.223144 TGCGTAGAAATCAACACACAGC 59.777 45.455 0.00 0.00 0.00 4.40
5430 5892 4.668576 ATGCGTAGAAATCAACACACAG 57.331 40.909 0.00 0.00 0.00 3.66
5431 5893 4.090786 CGTATGCGTAGAAATCAACACACA 59.909 41.667 0.00 0.00 0.00 3.72
5432 5894 4.325204 TCGTATGCGTAGAAATCAACACAC 59.675 41.667 2.37 0.00 39.49 3.82
5433 5895 4.487019 TCGTATGCGTAGAAATCAACACA 58.513 39.130 2.37 0.00 39.49 3.72
5434 5896 5.637104 ATCGTATGCGTAGAAATCAACAC 57.363 39.130 2.37 0.00 39.49 3.32
5435 5897 6.500910 ACTATCGTATGCGTAGAAATCAACA 58.499 36.000 15.54 0.00 39.49 3.33
5436 5898 6.988109 ACTATCGTATGCGTAGAAATCAAC 57.012 37.500 15.54 0.00 39.49 3.18
5437 5899 6.976349 ACAACTATCGTATGCGTAGAAATCAA 59.024 34.615 15.54 0.00 39.49 2.57
5438 5900 6.500910 ACAACTATCGTATGCGTAGAAATCA 58.499 36.000 15.54 0.00 39.49 2.57
5439 5901 6.988109 ACAACTATCGTATGCGTAGAAATC 57.012 37.500 15.54 0.00 39.49 2.17
5440 5902 6.576313 CGTACAACTATCGTATGCGTAGAAAT 59.424 38.462 15.54 0.92 39.49 2.17
5441 5903 5.903530 CGTACAACTATCGTATGCGTAGAAA 59.096 40.000 15.54 0.00 39.49 2.52
5442 5904 5.234116 TCGTACAACTATCGTATGCGTAGAA 59.766 40.000 15.54 0.00 39.49 2.10
5443 5905 4.744631 TCGTACAACTATCGTATGCGTAGA 59.255 41.667 15.54 0.00 39.49 2.59
5444 5906 5.010249 TCGTACAACTATCGTATGCGTAG 57.990 43.478 2.37 7.11 39.49 3.51
5445 5907 5.177327 TCATCGTACAACTATCGTATGCGTA 59.823 40.000 2.37 0.00 39.49 4.42
5446 5908 3.950087 TCGTACAACTATCGTATGCGT 57.050 42.857 2.37 0.00 39.49 5.24
5447 5909 4.317551 GTCATCGTACAACTATCGTATGCG 59.682 45.833 0.00 0.00 39.92 4.73
5448 5910 4.615961 GGTCATCGTACAACTATCGTATGC 59.384 45.833 0.00 0.00 0.00 3.14
5449 5911 4.844522 CGGTCATCGTACAACTATCGTATG 59.155 45.833 0.00 0.00 0.00 2.39
5450 5912 4.751600 TCGGTCATCGTACAACTATCGTAT 59.248 41.667 0.00 0.00 40.32 3.06
5451 5913 4.119136 TCGGTCATCGTACAACTATCGTA 58.881 43.478 0.00 0.00 40.32 3.43
5452 5914 2.938451 TCGGTCATCGTACAACTATCGT 59.062 45.455 0.00 0.00 40.32 3.73
5453 5915 3.597377 TCGGTCATCGTACAACTATCG 57.403 47.619 0.00 0.00 40.32 2.92
5454 5916 5.516996 TGAATCGGTCATCGTACAACTATC 58.483 41.667 0.00 0.00 40.32 2.08
5455 5917 5.509716 TGAATCGGTCATCGTACAACTAT 57.490 39.130 0.00 0.00 40.32 2.12
5456 5918 4.968812 TGAATCGGTCATCGTACAACTA 57.031 40.909 0.00 0.00 40.32 2.24
5457 5919 3.861276 TGAATCGGTCATCGTACAACT 57.139 42.857 0.00 0.00 40.32 3.16


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

AutoCloner maintained by Alex Coulton.