Multiple sequence alignment - TraesCS5B01G380600

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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 TraesCS5B01G380600 chr5B 100.000 4916 0 0 1 4916 558421880 558416965 0.000000e+00 9079.0
1 TraesCS5B01G380600 chr5B 86.328 256 35 0 1505 1760 558408165 558407910 3.750000e-71 279.0
2 TraesCS5B01G380600 chr5A 93.231 4683 191 60 1 4630 574492621 574488012 0.000000e+00 6776.0
3 TraesCS5B01G380600 chr5A 94.340 477 26 1 426 902 568231525 568231050 0.000000e+00 730.0
4 TraesCS5B01G380600 chr5A 85.556 270 36 3 1493 1760 574485304 574485036 3.750000e-71 279.0
5 TraesCS5B01G380600 chr5D 93.468 3016 130 31 1 2967 456629075 456626078 0.000000e+00 4416.0
6 TraesCS5B01G380600 chr5D 87.443 1983 146 37 2950 4849 456625906 456623944 0.000000e+00 2187.0
7 TraesCS5B01G380600 chr5D 89.341 910 59 18 1 902 399709944 399709065 0.000000e+00 1109.0
8 TraesCS5B01G380600 chr5D 85.240 271 37 3 1492 1760 456622169 456621900 4.850000e-70 276.0
9 TraesCS5B01G380600 chr7B 85.636 912 68 28 1 902 62054597 62055455 0.000000e+00 900.0
10 TraesCS5B01G380600 chr3B 85.526 912 69 35 1 902 40891429 40892287 0.000000e+00 894.0
11 TraesCS5B01G380600 chr2B 85.197 912 70 32 1 902 311738443 311739299 0.000000e+00 876.0
12 TraesCS5B01G380600 chr2A 94.549 477 22 3 426 902 387014727 387015199 0.000000e+00 734.0
13 TraesCS5B01G380600 chr4A 94.526 475 22 3 426 900 416574866 416574396 0.000000e+00 730.0
14 TraesCS5B01G380600 chr4A 88.372 86 9 1 4530 4615 143701111 143701195 8.710000e-18 102.0
15 TraesCS5B01G380600 chr4A 92.424 66 5 0 4530 4595 452348702 452348767 1.460000e-15 95.3
16 TraesCS5B01G380600 chr3A 94.340 477 26 1 426 902 11775391 11774916 0.000000e+00 730.0
17 TraesCS5B01G380600 chr4D 92.424 66 5 0 4530 4595 120884368 120884433 1.460000e-15 95.3


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 TraesCS5B01G380600 chr5B 558416965 558421880 4915 True 9079.0 9079 100.0000 1 4916 1 chr5B.!!$R2 4915
1 TraesCS5B01G380600 chr5A 574485036 574492621 7585 True 3527.5 6776 89.3935 1 4630 2 chr5A.!!$R2 4629
2 TraesCS5B01G380600 chr5D 456621900 456629075 7175 True 2293.0 4416 88.7170 1 4849 3 chr5D.!!$R2 4848
3 TraesCS5B01G380600 chr5D 399709065 399709944 879 True 1109.0 1109 89.3410 1 902 1 chr5D.!!$R1 901
4 TraesCS5B01G380600 chr7B 62054597 62055455 858 False 900.0 900 85.6360 1 902 1 chr7B.!!$F1 901
5 TraesCS5B01G380600 chr3B 40891429 40892287 858 False 894.0 894 85.5260 1 902 1 chr3B.!!$F1 901
6 TraesCS5B01G380600 chr2B 311738443 311739299 856 False 876.0 876 85.1970 1 902 1 chr2B.!!$F1 901

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
968 1015 0.036875 AGTTTGCTACAGACTGGCCC 59.963 55.000 7.51 0.0 27.56 5.80 F
1396 1461 1.299089 GCAACTTTGGCACGTCCAC 60.299 57.895 6.27 0.0 46.55 4.02 F
2131 2197 4.261072 GGAATGCACAGATGATGATGTCAC 60.261 45.833 0.00 0.0 40.28 3.67 F
3294 3582 2.167900 ACCCTAGCATCGTGTAGGTTTC 59.832 50.000 0.00 0.0 34.96 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 2237 0.793861 TACGCAATTTCCGTGACAGC 59.206 50.000 10.3 0.0 39.54 4.40 R
2284 2350 1.076192 AGCCCAGATGCACAGCTTT 59.924 52.632 0.0 0.0 0.00 3.51 R
3759 4050 3.312697 GGCAAATAATTCCACCGACTCTC 59.687 47.826 0.0 0.0 0.00 3.20 R
4402 4709 0.033796 AGGACCGGGTGTCGAATAGA 60.034 55.000 3.3 0.0 45.46 1.98 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
48 56 1.356398 GGTCCTGGATGGTTTGGGTAA 59.644 52.381 0.00 0.00 37.07 2.85
49 57 2.443416 GTCCTGGATGGTTTGGGTAAC 58.557 52.381 0.00 0.00 37.07 2.50
66 74 4.261909 GGGTAACGACCTGTATCTGTATGG 60.262 50.000 0.00 0.00 46.09 2.74
86 94 1.478510 GAGCGACAGATCCAGGAGAAA 59.521 52.381 0.00 0.00 0.00 2.52
87 95 1.205893 AGCGACAGATCCAGGAGAAAC 59.794 52.381 0.00 0.00 0.00 2.78
96 104 3.771577 TCCAGGAGAAACTTTCTGTCC 57.228 47.619 8.83 5.38 40.87 4.02
112 120 7.713942 ACTTTCTGTCCGATTAGTTTTACAGTT 59.286 33.333 0.00 0.00 36.56 3.16
188 210 1.139058 AGGAATGTCTGCCGTACCATC 59.861 52.381 0.00 0.00 0.00 3.51
227 255 7.792364 TCTTCTTCTTGACTACCATTAAGGA 57.208 36.000 0.00 0.00 41.22 3.36
228 256 8.202461 TCTTCTTCTTGACTACCATTAAGGAA 57.798 34.615 0.00 0.00 41.22 3.36
229 257 8.656806 TCTTCTTCTTGACTACCATTAAGGAAA 58.343 33.333 0.00 0.00 41.22 3.13
230 258 9.284968 CTTCTTCTTGACTACCATTAAGGAAAA 57.715 33.333 0.00 0.00 41.22 2.29
313 353 5.669164 AGGAAACTGTTCAGATCTACTCC 57.331 43.478 6.83 0.00 41.13 3.85
448 492 2.235898 GCCACTTCAGATTCTCACCTCT 59.764 50.000 0.00 0.00 0.00 3.69
451 495 4.222588 CCACTTCAGATTCTCACCTCTTCT 59.777 45.833 0.00 0.00 0.00 2.85
453 497 5.868801 CACTTCAGATTCTCACCTCTTCTTC 59.131 44.000 0.00 0.00 0.00 2.87
455 499 4.682563 TCAGATTCTCACCTCTTCTTCCT 58.317 43.478 0.00 0.00 0.00 3.36
623 668 4.295870 TCGATATAACATCCAGTGCGTTC 58.704 43.478 0.00 0.00 0.00 3.95
819 865 7.646548 ACTCTAGGGGCAAATTTATCTTTTC 57.353 36.000 0.00 0.00 0.00 2.29
968 1015 0.036875 AGTTTGCTACAGACTGGCCC 59.963 55.000 7.51 0.00 27.56 5.80
982 1029 3.686760 GCCCTTCCTTGGCTGAAC 58.313 61.111 0.00 0.00 45.70 3.18
1122 1169 1.937191 TGGAGGTCATGCTACTGTCA 58.063 50.000 0.00 0.00 0.00 3.58
1135 1182 3.058224 GCTACTGTCATTTGTTGGACCAC 60.058 47.826 0.00 0.00 33.09 4.16
1143 1190 2.920724 TTGTTGGACCACTGATTCGA 57.079 45.000 0.00 0.00 0.00 3.71
1173 1220 4.019174 GGAAAATCTCTGCCCAAGATGAA 58.981 43.478 0.00 0.00 33.78 2.57
1275 1322 5.005107 GCGAAGGTAAGGATTTACTTGTACG 59.995 44.000 0.00 0.00 39.30 3.67
1300 1347 4.274865 CACTTCTGTGTTTCGCTTTTCTC 58.725 43.478 0.00 0.00 39.24 2.87
1396 1461 1.299089 GCAACTTTGGCACGTCCAC 60.299 57.895 6.27 0.00 46.55 4.02
2131 2197 4.261072 GGAATGCACAGATGATGATGTCAC 60.261 45.833 0.00 0.00 40.28 3.67
2284 2350 3.244156 CGCAACTGAGCAATGCAAATAA 58.756 40.909 8.35 0.00 40.04 1.40
2291 2357 4.885413 TGAGCAATGCAAATAAAAGCTGT 58.115 34.783 8.35 0.00 0.00 4.40
2394 2460 4.397417 GCATTCAGTAGCCTGTTTCTTCAT 59.603 41.667 0.00 0.00 39.82 2.57
2696 2762 4.386652 GGCATGCAGTAAATGTGTTTCTTG 59.613 41.667 21.36 0.00 0.00 3.02
2705 2771 5.913137 AAATGTGTTTCTTGGTGACTTGA 57.087 34.783 0.00 0.00 0.00 3.02
3294 3582 2.167900 ACCCTAGCATCGTGTAGGTTTC 59.832 50.000 0.00 0.00 34.96 2.78
3295 3583 2.431057 CCCTAGCATCGTGTAGGTTTCT 59.569 50.000 0.00 0.00 34.96 2.52
3440 3730 3.142951 TGTAAACAAACGGACATCCTGG 58.857 45.455 0.00 0.00 0.00 4.45
3471 3762 7.921214 CAGATAACTCGGCTAAATGAAGTCTAA 59.079 37.037 0.00 0.00 0.00 2.10
3495 3786 4.877823 CGATTCTGATCCATTTTCCTGACA 59.122 41.667 0.00 0.00 0.00 3.58
3560 3851 5.425539 AGGGTCTTGTTTATGCTCTTAGCTA 59.574 40.000 0.03 0.00 42.97 3.32
3585 3876 6.653320 AGGAACGCTTAGAATGTTATGACAAA 59.347 34.615 0.00 0.00 39.66 2.83
3587 3878 7.148474 GGAACGCTTAGAATGTTATGACAAAGA 60.148 37.037 0.00 0.00 39.66 2.52
3604 3895 6.005583 ACAAAGATACATCAGTTGTTGCAG 57.994 37.500 5.80 0.00 39.87 4.41
3657 3948 5.292101 GCAGTTGTCAGTAGATATTTCGCTT 59.708 40.000 0.00 0.00 0.00 4.68
3666 3957 8.136165 TCAGTAGATATTTCGCTTAAGGAGTTC 58.864 37.037 4.29 0.00 0.00 3.01
3974 4265 4.158394 ACCATAAAATTCGTCATGCTGCTT 59.842 37.500 0.00 0.00 0.00 3.91
4104 4395 7.741785 TCATTTTGTAAAGTCCTCACTCCTTA 58.258 34.615 0.00 0.00 29.93 2.69
4228 4534 4.387026 TTCTCATGTTGATTTGGTCCCT 57.613 40.909 0.00 0.00 0.00 4.20
4264 4570 5.198207 AGTTGCAAGTTGTAACCCTAGTTT 58.802 37.500 26.87 9.31 42.72 2.66
4315 4621 4.097741 GGTTGCTTGCATCATACATGGTTA 59.902 41.667 0.00 0.00 0.00 2.85
4401 4708 9.685828 TTTGAAATAAAATTTCTTACCAGTCGG 57.314 29.630 12.25 0.00 38.77 4.79
4403 4710 8.508875 TGAAATAAAATTTCTTACCAGTCGGTC 58.491 33.333 12.25 0.00 44.71 4.79
4404 4711 8.631480 AAATAAAATTTCTTACCAGTCGGTCT 57.369 30.769 0.00 0.00 44.71 3.85
4405 4712 9.729281 AAATAAAATTTCTTACCAGTCGGTCTA 57.271 29.630 0.00 0.00 44.71 2.59
4430 4755 0.533308 CACCCGGTCCTTGAAACGAA 60.533 55.000 0.00 0.00 0.00 3.85
4435 4760 1.609580 CGGTCCTTGAAACGAATGGGA 60.610 52.381 0.00 0.00 0.00 4.37
4452 4777 8.635328 ACGAATGGGATTTTGTTTAAACTACTT 58.365 29.630 18.72 2.15 0.00 2.24
4492 4817 8.859517 TTTTAAGACGTTTTTGGGTATTTCAG 57.140 30.769 0.00 0.00 0.00 3.02
4498 4823 7.551617 AGACGTTTTTGGGTATTTCAGTATAGG 59.448 37.037 0.00 0.00 0.00 2.57
4508 4833 6.750963 GGTATTTCAGTATAGGCTACATACGC 59.249 42.308 0.00 0.00 34.66 4.42
4513 4838 2.440539 ATAGGCTACATACGCACTGC 57.559 50.000 0.00 0.00 0.00 4.40
4517 4842 1.003545 GGCTACATACGCACTGCAATG 60.004 52.381 10.45 10.45 0.00 2.82
4546 4871 4.396166 ACAAATGGAAGAGGATTTGTAGCG 59.604 41.667 8.04 0.00 46.20 4.26
4554 4879 1.144496 GATTTGTAGCGCCGGGGTA 59.856 57.895 20.83 8.98 0.00 3.69
4600 4928 9.760660 CATTAAGTTCAAAAGAATACCGAGAAG 57.239 33.333 0.00 0.00 0.00 2.85
4603 4931 8.897872 AAGTTCAAAAGAATACCGAGAAGTTA 57.102 30.769 0.00 0.00 0.00 2.24
4606 4934 8.648968 GTTCAAAAGAATACCGAGAAGTTAGAG 58.351 37.037 0.00 0.00 0.00 2.43
4681 5113 7.552687 TGTATTTCCTTCACCACTGATATGTTC 59.447 37.037 0.00 0.00 0.00 3.18
4683 5115 4.104086 TCCTTCACCACTGATATGTTCCT 58.896 43.478 0.00 0.00 0.00 3.36
4689 5121 5.249622 TCACCACTGATATGTTCCTTGGTAA 59.750 40.000 0.00 0.00 36.70 2.85
4697 5129 9.573133 CTGATATGTTCCTTGGTAATTTTTCAC 57.427 33.333 0.00 0.00 0.00 3.18
4707 5139 7.651704 CCTTGGTAATTTTTCACGAAACTTCAT 59.348 33.333 0.00 0.00 0.00 2.57
4709 5141 9.453325 TTGGTAATTTTTCACGAAACTTCATAC 57.547 29.630 0.00 0.00 0.00 2.39
4710 5142 8.622157 TGGTAATTTTTCACGAAACTTCATACA 58.378 29.630 0.00 0.00 0.00 2.29
4732 5164 2.093447 GGAGTAGATTGGACACCCACTG 60.093 54.545 0.00 0.00 43.41 3.66
4750 5182 7.557719 CACCCACTGTTGATATCCTTAAATTCT 59.442 37.037 0.00 0.00 0.00 2.40
4805 5248 0.603975 GAGCACCCATAATCTCCCGC 60.604 60.000 0.00 0.00 0.00 6.13
4814 5257 0.971386 TAATCTCCCGCGTAATCCCC 59.029 55.000 4.92 0.00 0.00 4.81
4834 5277 5.470777 TCCCCGTGAACAAATACACTAAAAG 59.529 40.000 0.00 0.00 35.23 2.27
4857 5390 9.886132 AAAGTGTCTACCTACATTACATTTAGG 57.114 33.333 0.00 0.00 38.73 2.69
4882 5415 9.634163 GGAAAAGTTACAACATTTTATAGGTGG 57.366 33.333 0.00 0.00 30.87 4.61
4883 5416 9.135843 GAAAAGTTACAACATTTTATAGGTGGC 57.864 33.333 0.00 0.00 30.87 5.01
4884 5417 8.417273 AAAGTTACAACATTTTATAGGTGGCT 57.583 30.769 0.00 0.00 0.00 4.75
4886 5419 4.718940 ACAACATTTTATAGGTGGCTGC 57.281 40.909 0.00 0.00 0.00 5.25
4887 5420 4.344104 ACAACATTTTATAGGTGGCTGCT 58.656 39.130 0.00 0.00 0.00 4.24
4888 5421 5.505780 ACAACATTTTATAGGTGGCTGCTA 58.494 37.500 0.00 0.00 0.00 3.49
4891 5424 5.505780 ACATTTTATAGGTGGCTGCTACAA 58.494 37.500 18.00 5.72 0.00 2.41
4892 5425 5.949354 ACATTTTATAGGTGGCTGCTACAAA 59.051 36.000 18.00 9.37 0.00 2.83
4894 5427 6.693315 TTTTATAGGTGGCTGCTACAAATC 57.307 37.500 18.00 0.34 0.00 2.17
4895 5428 3.931907 ATAGGTGGCTGCTACAAATCA 57.068 42.857 18.00 0.00 0.00 2.57
4898 5431 0.811281 GTGGCTGCTACAAATCACCC 59.189 55.000 11.52 0.00 0.00 4.61
4899 5432 0.676466 TGGCTGCTACAAATCACCCG 60.676 55.000 0.00 0.00 0.00 5.28
4900 5433 1.376609 GGCTGCTACAAATCACCCGG 61.377 60.000 0.00 0.00 0.00 5.73
4901 5434 0.392461 GCTGCTACAAATCACCCGGA 60.392 55.000 0.73 0.00 0.00 5.14
4903 5436 1.942657 CTGCTACAAATCACCCGGATG 59.057 52.381 0.73 0.00 36.02 3.51
4905 5438 2.172505 TGCTACAAATCACCCGGATGAT 59.827 45.455 5.10 5.10 41.20 2.45
4912 5445 2.418368 TCACCCGGATGATTTTCTGG 57.582 50.000 0.73 0.00 41.19 3.86
4913 5446 1.633432 TCACCCGGATGATTTTCTGGT 59.367 47.619 0.73 0.00 40.08 4.00
4915 5448 1.633432 ACCCGGATGATTTTCTGGTGA 59.367 47.619 0.73 0.00 40.08 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 56 2.623889 GCTCCATACAGATACAGGTCGT 59.376 50.000 0.00 0.00 0.00 4.34
49 57 2.350868 CGCTCCATACAGATACAGGTCG 60.351 54.545 0.00 0.00 0.00 4.79
66 74 1.107114 TTCTCCTGGATCTGTCGCTC 58.893 55.000 0.00 0.00 0.00 5.03
86 94 7.215085 ACTGTAAAACTAATCGGACAGAAAGT 58.785 34.615 6.83 0.00 38.12 2.66
87 95 7.653767 ACTGTAAAACTAATCGGACAGAAAG 57.346 36.000 6.83 0.00 38.12 2.62
112 120 9.667107 ATCTTAAACTCGGTCATCTGAAAATTA 57.333 29.630 0.00 0.00 0.00 1.40
233 261 8.184848 TGCGCTATTTATGTAAACAAATAAGCA 58.815 29.630 9.73 3.63 37.64 3.91
234 262 8.555166 TGCGCTATTTATGTAAACAAATAAGC 57.445 30.769 9.73 0.00 34.43 3.09
236 264 8.184848 TGCTGCGCTATTTATGTAAACAAATAA 58.815 29.630 9.73 0.00 0.00 1.40
242 271 5.403897 TCTGCTGCGCTATTTATGTAAAC 57.596 39.130 9.73 0.00 0.00 2.01
266 295 2.479566 ATACTCCACACCAGCAACTG 57.520 50.000 0.00 0.00 0.00 3.16
311 351 5.831525 GGTTTTTCTCTTACCCTCTTTTGGA 59.168 40.000 0.00 0.00 0.00 3.53
312 352 5.596772 TGGTTTTTCTCTTACCCTCTTTTGG 59.403 40.000 0.00 0.00 0.00 3.28
313 353 6.709018 TGGTTTTTCTCTTACCCTCTTTTG 57.291 37.500 0.00 0.00 0.00 2.44
623 668 3.311871 GCATGTCAGATGAGCCTAAACAG 59.688 47.826 0.00 0.00 0.00 3.16
968 1015 2.335712 GCCGGTTCAGCCAAGGAAG 61.336 63.158 1.90 0.00 36.97 3.46
982 1029 0.605319 ATGTTGGTAGTGTGTGCCGG 60.605 55.000 0.00 0.00 32.27 6.13
1122 1169 3.750371 TCGAATCAGTGGTCCAACAAAT 58.250 40.909 0.00 0.00 0.00 2.32
1135 1182 6.054295 AGATTTTCCATTCCTCTCGAATCAG 58.946 40.000 0.00 0.00 39.28 2.90
1143 1190 3.372458 GGGCAGAGATTTTCCATTCCTCT 60.372 47.826 0.00 0.00 34.83 3.69
1173 1220 8.788325 AAAACACTACACTTGAGAGTAAACTT 57.212 30.769 0.00 0.00 33.90 2.66
1332 1394 9.605275 ATGAAATTCGAATTCATAACAGAGAGA 57.395 29.630 22.93 0.00 43.73 3.10
1349 1414 7.637709 TCGTACATCAGGAATATGAAATTCG 57.362 36.000 0.00 0.00 31.76 3.34
1439 1505 7.717875 TGTAAGTTTGCAACTATAAACCTGTCT 59.282 33.333 0.00 0.00 41.91 3.41
1468 1534 7.867921 TGTTCAGGGATTATATTTGGTACACT 58.132 34.615 0.00 0.00 39.29 3.55
2171 2237 0.793861 TACGCAATTTCCGTGACAGC 59.206 50.000 10.30 0.00 39.54 4.40
2284 2350 1.076192 AGCCCAGATGCACAGCTTT 59.924 52.632 0.00 0.00 0.00 3.51
2291 2357 2.953648 CACATATTTCAGCCCAGATGCA 59.046 45.455 0.00 0.00 0.00 3.96
2696 2762 2.550830 ACTGTGATGGTCAAGTCACC 57.449 50.000 3.38 0.00 43.09 4.02
2705 2771 8.540388 ACATTAAACTCACTATACTGTGATGGT 58.460 33.333 0.00 0.00 44.66 3.55
3047 3314 7.792374 TGTGGAGATCATAGATACAAAAAGC 57.208 36.000 0.00 0.00 0.00 3.51
3440 3730 3.795623 TTAGCCGAGTTATCTGTGGAC 57.204 47.619 0.00 0.00 0.00 4.02
3445 3735 6.276847 AGACTTCATTTAGCCGAGTTATCTG 58.723 40.000 0.00 0.00 0.00 2.90
3454 3745 5.749109 AGAATCGTTAGACTTCATTTAGCCG 59.251 40.000 0.00 0.00 0.00 5.52
3471 3762 4.878397 GTCAGGAAAATGGATCAGAATCGT 59.122 41.667 0.00 0.00 32.24 3.73
3560 3851 5.730550 TGTCATAACATTCTAAGCGTTCCT 58.269 37.500 0.00 0.00 0.00 3.36
3585 3876 3.678289 TGCTGCAACAACTGATGTATCT 58.322 40.909 0.00 0.00 42.99 1.98
3587 3878 4.852134 TTTGCTGCAACAACTGATGTAT 57.148 36.364 15.72 0.00 42.99 2.29
3598 3889 5.163713 TGTTTTGGGTAAAATTTGCTGCAAC 60.164 36.000 15.72 2.71 38.01 4.17
3604 3895 6.315144 ACAAGACTGTTTTGGGTAAAATTTGC 59.685 34.615 14.55 0.00 38.01 3.68
3657 3948 7.974504 AGTTCATAGGAAAACAGAACTCCTTA 58.025 34.615 0.00 0.00 43.80 2.69
3759 4050 3.312697 GGCAAATAATTCCACCGACTCTC 59.687 47.826 0.00 0.00 0.00 3.20
3828 4119 3.960102 ACACCACCTCAAACACAATGATT 59.040 39.130 0.00 0.00 0.00 2.57
3974 4265 5.572511 AGTTTGTATATAAACGTTCACGCGA 59.427 36.000 15.93 0.00 43.51 5.87
4104 4395 8.915036 CCATAACATACTCCTACTTACAGTCTT 58.085 37.037 0.00 0.00 0.00 3.01
4228 4534 5.449107 ACTTGCAACTCTAACTTCGACTA 57.551 39.130 0.00 0.00 0.00 2.59
4264 4570 2.937519 TCCATAACCACAACACAAGCA 58.062 42.857 0.00 0.00 0.00 3.91
4402 4709 0.033796 AGGACCGGGTGTCGAATAGA 60.034 55.000 3.30 0.00 45.46 1.98
4403 4710 0.822164 AAGGACCGGGTGTCGAATAG 59.178 55.000 3.30 0.00 45.46 1.73
4404 4711 0.533491 CAAGGACCGGGTGTCGAATA 59.467 55.000 3.30 0.00 45.46 1.75
4405 4712 1.189524 TCAAGGACCGGGTGTCGAAT 61.190 55.000 3.30 0.00 45.46 3.34
4430 4755 8.721133 AGGAAGTAGTTTAAACAAAATCCCAT 57.279 30.769 20.06 5.47 0.00 4.00
4435 4760 7.812690 ACGGAGGAAGTAGTTTAAACAAAAT 57.187 32.000 20.06 4.64 0.00 1.82
4452 4777 5.563475 CGTCTTAAAAGTAGTGAACGGAGGA 60.563 44.000 0.00 0.00 0.00 3.71
4492 4817 3.243336 GCAGTGCGTATGTAGCCTATAC 58.757 50.000 0.00 0.00 0.00 1.47
4498 4823 1.933181 TCATTGCAGTGCGTATGTAGC 59.067 47.619 22.11 0.00 0.00 3.58
4508 4833 3.985279 CCATTTGTTCACTCATTGCAGTG 59.015 43.478 2.16 2.16 44.61 3.66
4513 4838 5.474532 TCCTCTTCCATTTGTTCACTCATTG 59.525 40.000 0.00 0.00 0.00 2.82
4517 4842 6.015940 ACAAATCCTCTTCCATTTGTTCACTC 60.016 38.462 4.55 0.00 46.42 3.51
4681 5113 6.975772 TGAAGTTTCGTGAAAAATTACCAAGG 59.024 34.615 0.00 0.00 35.43 3.61
4683 5115 9.453325 GTATGAAGTTTCGTGAAAAATTACCAA 57.547 29.630 0.00 0.00 35.43 3.67
4689 5121 7.228706 ACTCCTGTATGAAGTTTCGTGAAAAAT 59.771 33.333 0.00 0.00 31.33 1.82
4697 5129 6.477033 CCAATCTACTCCTGTATGAAGTTTCG 59.523 42.308 0.00 0.00 0.00 3.46
4707 5139 3.245839 TGGGTGTCCAATCTACTCCTGTA 60.246 47.826 0.00 0.00 40.73 2.74
4709 5141 2.093447 GTGGGTGTCCAATCTACTCCTG 60.093 54.545 0.00 0.00 46.04 3.86
4710 5142 2.188817 GTGGGTGTCCAATCTACTCCT 58.811 52.381 0.00 0.00 46.04 3.69
4761 5193 8.783903 TCCACACCCCTAAACAAATACTTATAT 58.216 33.333 0.00 0.00 0.00 0.86
4762 5194 8.160434 TCCACACCCCTAAACAAATACTTATA 57.840 34.615 0.00 0.00 0.00 0.98
4763 5195 7.034967 TCCACACCCCTAAACAAATACTTAT 57.965 36.000 0.00 0.00 0.00 1.73
4766 5198 4.809691 GCTCCACACCCCTAAACAAATACT 60.810 45.833 0.00 0.00 0.00 2.12
4767 5199 3.442625 GCTCCACACCCCTAAACAAATAC 59.557 47.826 0.00 0.00 0.00 1.89
4805 5248 3.933955 TGTATTTGTTCACGGGGATTACG 59.066 43.478 0.00 0.00 37.36 3.18
4857 5390 9.135843 GCCACCTATAAAATGTTGTAACTTTTC 57.864 33.333 8.47 0.00 35.87 2.29
4862 5395 6.033966 GCAGCCACCTATAAAATGTTGTAAC 58.966 40.000 0.00 0.00 0.00 2.50
4866 5399 4.989279 AGCAGCCACCTATAAAATGTTG 57.011 40.909 0.00 0.00 0.00 3.33
4872 5405 5.588648 GTGATTTGTAGCAGCCACCTATAAA 59.411 40.000 0.00 0.00 32.80 1.40
4878 5411 0.811281 GGTGATTTGTAGCAGCCACC 59.189 55.000 0.00 0.00 37.50 4.61
4882 5415 0.392461 TCCGGGTGATTTGTAGCAGC 60.392 55.000 0.00 0.00 37.44 5.25
4883 5416 1.942657 CATCCGGGTGATTTGTAGCAG 59.057 52.381 9.89 0.00 0.00 4.24
4884 5417 1.557371 TCATCCGGGTGATTTGTAGCA 59.443 47.619 15.09 0.00 0.00 3.49
4892 5425 2.242196 ACCAGAAAATCATCCGGGTGAT 59.758 45.455 24.95 24.95 40.44 3.06
4894 5427 1.745087 CACCAGAAAATCATCCGGGTG 59.255 52.381 8.97 8.97 38.28 4.61
4895 5428 1.633432 TCACCAGAAAATCATCCGGGT 59.367 47.619 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.