Multiple sequence alignment - TraesCS4D01G119800

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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 TraesCS4D01G119800 chr4D 100.000 5204 0 0 1 5204 101014096 101008893 0.000000e+00 9611
1 TraesCS4D01G119800 chr4D 100.000 132 0 0 4440 4571 101009509 101009378 1.450000e-60 244
2 TraesCS4D01G119800 chr4D 100.000 132 0 0 4588 4719 101009657 101009526 1.450000e-60 244
3 TraesCS4D01G119800 chr4B 97.463 4573 95 11 5 4571 144684480 144679923 0.000000e+00 7782
4 TraesCS4D01G119800 chr4B 97.083 617 18 0 4588 5204 144680054 144679438 0.000000e+00 1040
5 TraesCS4D01G119800 chr4B 88.095 126 15 0 2242 2367 144682374 144682249 3.250000e-32 150
6 TraesCS4D01G119800 chr4A 97.618 4283 70 7 294 4571 474931708 474935963 0.000000e+00 7315
7 TraesCS4D01G119800 chr4A 97.078 616 17 1 4590 5204 474935834 474936449 0.000000e+00 1037
8 TraesCS4D01G119800 chr4A 97.934 242 2 3 36 275 474931142 474931382 2.900000e-112 416
9 TraesCS4D01G119800 chr4A 88.095 126 15 0 2242 2367 474933515 474933640 3.250000e-32 150


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 TraesCS4D01G119800 chr4D 101008893 101014096 5203 True 9611.000000 9611 100.000000 1 5204 1 chr4D.!!$R1 5203
1 TraesCS4D01G119800 chr4B 144679438 144684480 5042 True 2990.666667 7782 94.213667 5 5204 3 chr4B.!!$R1 5199
2 TraesCS4D01G119800 chr4A 474931142 474936449 5307 False 2229.500000 7315 95.181250 36 5204 4 chr4A.!!$F1 5168

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
553 864 0.690762 TGTTCTTTTCTCCCTCCCGG 59.309 55.0 0.00 0.00 0.0 5.73 F
1882 2201 0.033991 TCGGAGAGAGGAGAGGTTGG 60.034 60.0 0.00 0.00 0.0 3.77 F
2303 2622 0.387878 GCAGACACAGACACTCGAGG 60.388 60.0 18.41 8.36 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2352 1.128200 GCCCCCTGACAAAAACCTTT 58.872 50.000 0.0 0.0 0.00 3.11 R
3846 4165 1.061421 GCATTTGCATTGGCGTGATTG 59.939 47.619 0.0 0.0 45.35 2.67 R
4256 4575 0.377203 GGAAAGCTGCCCGTTTATCG 59.623 55.000 0.0 0.0 39.52 2.92 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
238 241 1.812113 TTTCCTCCCCCTCGTCTCCT 61.812 60.000 0.00 0.00 0.00 3.69
385 696 1.210155 CCCTTTCGCTTTTGCTCCG 59.790 57.895 0.00 0.00 44.80 4.63
548 859 2.438392 AGGTTCGTGTTCTTTTCTCCCT 59.562 45.455 0.00 0.00 0.00 4.20
553 864 0.690762 TGTTCTTTTCTCCCTCCCGG 59.309 55.000 0.00 0.00 0.00 5.73
555 866 0.981943 TTCTTTTCTCCCTCCCGGTC 59.018 55.000 0.00 0.00 0.00 4.79
557 868 0.910088 CTTTTCTCCCTCCCGGTCCT 60.910 60.000 0.00 0.00 0.00 3.85
1494 1813 2.716217 GGTGAGGAGAATTGTTCCCTG 58.284 52.381 2.65 0.00 35.20 4.45
1882 2201 0.033991 TCGGAGAGAGGAGAGGTTGG 60.034 60.000 0.00 0.00 0.00 3.77
2033 2352 5.199723 TCTGCATAATCAAATTGGTAGCCA 58.800 37.500 0.00 0.00 0.00 4.75
2178 2497 4.818534 TGCAGACAAAGACATTCAAGAC 57.181 40.909 0.00 0.00 0.00 3.01
2225 2544 5.379706 AAGGATCCTCAATTCCTGGTTAG 57.620 43.478 16.52 0.00 41.58 2.34
2228 2547 4.080299 GGATCCTCAATTCCTGGTTAGTGT 60.080 45.833 3.84 0.00 0.00 3.55
2238 2557 4.385825 TCCTGGTTAGTGTAAGTGCAAAG 58.614 43.478 0.00 0.00 0.00 2.77
2252 2571 1.614903 TGCAAAGGCTTTCAGTGATGG 59.385 47.619 10.08 0.00 41.91 3.51
2303 2622 0.387878 GCAGACACAGACACTCGAGG 60.388 60.000 18.41 8.36 0.00 4.63
2637 2956 1.001974 TCCTTTGGTGACGGACATCTG 59.998 52.381 0.00 0.00 0.00 2.90
2652 2971 4.142513 GGACATCTGAAATCTGGACAAAGC 60.143 45.833 0.00 0.00 0.00 3.51
2728 3047 9.855361 GTTGTATTGAAGATGACAATAAGATCG 57.145 33.333 0.00 0.00 40.36 3.69
3846 4165 3.664107 TGTATTGTCTGTTCCTGCTGTC 58.336 45.455 0.00 0.00 0.00 3.51
3942 4261 2.741145 ACGGAGAGTGCTTCTTATCCT 58.259 47.619 0.00 0.00 35.87 3.24
3992 4311 6.293626 GCATCTTTCACAAGAAGCTTGTCTAA 60.294 38.462 2.10 5.45 46.08 2.10
4057 4376 2.808543 GTTTCAGACTCGGCACTTCATT 59.191 45.455 0.00 0.00 0.00 2.57
4175 4494 2.034066 AATGGTGCCGGTGTCCAG 59.966 61.111 16.58 0.00 34.62 3.86
4205 4524 6.650807 GTGTCCAGAAGAAAGAACATGTGATA 59.349 38.462 0.00 0.00 0.00 2.15
4256 4575 5.504173 GCTTCTTACAGGTCACAGTTTTGAC 60.504 44.000 0.00 0.00 44.53 3.18
4540 4860 5.551760 CTGCGTCTTGAAACAGGATTATT 57.448 39.130 0.00 0.00 0.00 1.40
4561 4881 5.627499 TTAATTCCTGACATGACAAGTGC 57.373 39.130 0.00 0.00 0.00 4.40
4562 4882 2.936919 TTCCTGACATGACAAGTGCT 57.063 45.000 0.00 0.00 0.00 4.40
4563 4883 4.558226 ATTCCTGACATGACAAGTGCTA 57.442 40.909 0.00 0.00 0.00 3.49
4564 4884 4.558226 TTCCTGACATGACAAGTGCTAT 57.442 40.909 0.00 0.00 0.00 2.97
4565 4885 5.675684 TTCCTGACATGACAAGTGCTATA 57.324 39.130 0.00 0.00 0.00 1.31
4566 4886 5.675684 TCCTGACATGACAAGTGCTATAA 57.324 39.130 0.00 0.00 0.00 0.98
4567 4887 5.664457 TCCTGACATGACAAGTGCTATAAG 58.336 41.667 0.00 0.00 0.00 1.73
4568 4888 4.813161 CCTGACATGACAAGTGCTATAAGG 59.187 45.833 0.00 0.00 0.00 2.69
4569 4889 5.420725 TGACATGACAAGTGCTATAAGGT 57.579 39.130 0.00 0.00 0.00 3.50
4570 4890 5.804639 TGACATGACAAGTGCTATAAGGTT 58.195 37.500 0.00 0.00 0.00 3.50
4571 4891 6.237901 TGACATGACAAGTGCTATAAGGTTT 58.762 36.000 0.00 0.00 0.00 3.27
4572 4892 6.371548 TGACATGACAAGTGCTATAAGGTTTC 59.628 38.462 0.00 0.00 0.00 2.78
4573 4893 6.237901 ACATGACAAGTGCTATAAGGTTTCA 58.762 36.000 0.00 0.00 0.00 2.69
4574 4894 6.372659 ACATGACAAGTGCTATAAGGTTTCAG 59.627 38.462 0.00 0.00 0.00 3.02
4575 4895 6.109156 TGACAAGTGCTATAAGGTTTCAGA 57.891 37.500 0.00 0.00 0.00 3.27
4576 4896 5.932303 TGACAAGTGCTATAAGGTTTCAGAC 59.068 40.000 0.00 0.00 0.00 3.51
4577 4897 6.115448 ACAAGTGCTATAAGGTTTCAGACT 57.885 37.500 0.00 0.00 0.00 3.24
4578 4898 6.166982 ACAAGTGCTATAAGGTTTCAGACTC 58.833 40.000 0.00 0.00 0.00 3.36
4579 4899 5.000012 AGTGCTATAAGGTTTCAGACTCG 58.000 43.478 0.00 0.00 0.00 4.18
4580 4900 4.113354 GTGCTATAAGGTTTCAGACTCGG 58.887 47.826 0.00 0.00 0.00 4.63
4581 4901 3.124560 GCTATAAGGTTTCAGACTCGGC 58.875 50.000 0.00 0.00 0.00 5.54
4582 4902 3.430374 GCTATAAGGTTTCAGACTCGGCA 60.430 47.826 0.00 0.00 0.00 5.69
4583 4903 2.450609 TAAGGTTTCAGACTCGGCAC 57.549 50.000 0.00 0.00 0.00 5.01
4584 4904 0.759346 AAGGTTTCAGACTCGGCACT 59.241 50.000 0.00 0.00 0.00 4.40
4585 4905 0.759346 AGGTTTCAGACTCGGCACTT 59.241 50.000 0.00 0.00 0.00 3.16
4586 4906 1.149148 GGTTTCAGACTCGGCACTTC 58.851 55.000 0.00 0.00 0.00 3.01
4587 4907 1.270358 GGTTTCAGACTCGGCACTTCT 60.270 52.381 0.00 0.00 0.00 2.85
4588 4908 2.484889 GTTTCAGACTCGGCACTTCTT 58.515 47.619 0.00 0.00 0.00 2.52
4589 4909 3.554337 GGTTTCAGACTCGGCACTTCTTA 60.554 47.826 0.00 0.00 0.00 2.10
4590 4910 4.246458 GTTTCAGACTCGGCACTTCTTAT 58.754 43.478 0.00 0.00 0.00 1.73
4591 4911 3.510388 TCAGACTCGGCACTTCTTATG 57.490 47.619 0.00 0.00 0.00 1.90
4592 4912 2.826128 TCAGACTCGGCACTTCTTATGT 59.174 45.455 0.00 0.00 0.00 2.29
4593 4913 3.258372 TCAGACTCGGCACTTCTTATGTT 59.742 43.478 0.00 0.00 0.00 2.71
4594 4914 4.461431 TCAGACTCGGCACTTCTTATGTTA 59.539 41.667 0.00 0.00 0.00 2.41
4595 4915 4.563184 CAGACTCGGCACTTCTTATGTTAC 59.437 45.833 0.00 0.00 0.00 2.50
4596 4916 4.219944 AGACTCGGCACTTCTTATGTTACA 59.780 41.667 0.00 0.00 0.00 2.41
4597 4917 4.243270 ACTCGGCACTTCTTATGTTACAC 58.757 43.478 0.00 0.00 0.00 2.90
4598 4918 4.021368 ACTCGGCACTTCTTATGTTACACT 60.021 41.667 0.00 0.00 0.00 3.55
4599 4919 4.491676 TCGGCACTTCTTATGTTACACTC 58.508 43.478 0.00 0.00 0.00 3.51
4600 4920 3.303495 CGGCACTTCTTATGTTACACTCG 59.697 47.826 0.00 0.00 0.00 4.18
4601 4921 4.243270 GGCACTTCTTATGTTACACTCGT 58.757 43.478 0.00 0.00 0.00 4.18
4602 4922 4.326548 GGCACTTCTTATGTTACACTCGTC 59.673 45.833 0.00 0.00 0.00 4.20
4603 4923 4.326548 GCACTTCTTATGTTACACTCGTCC 59.673 45.833 0.00 0.00 0.00 4.79
4604 4924 5.466819 CACTTCTTATGTTACACTCGTCCA 58.533 41.667 0.00 0.00 0.00 4.02
4605 4925 5.345202 CACTTCTTATGTTACACTCGTCCAC 59.655 44.000 0.00 0.00 0.00 4.02
4606 4926 5.010314 ACTTCTTATGTTACACTCGTCCACA 59.990 40.000 0.00 0.00 0.00 4.17
4607 4927 4.801891 TCTTATGTTACACTCGTCCACAC 58.198 43.478 0.00 0.00 0.00 3.82
4608 4928 4.521639 TCTTATGTTACACTCGTCCACACT 59.478 41.667 0.00 0.00 0.00 3.55
4609 4929 5.706833 TCTTATGTTACACTCGTCCACACTA 59.293 40.000 0.00 0.00 0.00 2.74
4610 4930 3.909776 TGTTACACTCGTCCACACTAG 57.090 47.619 0.00 0.00 0.00 2.57
4611 4931 3.216800 TGTTACACTCGTCCACACTAGT 58.783 45.455 0.00 0.00 0.00 2.57
4612 4932 4.388485 TGTTACACTCGTCCACACTAGTA 58.612 43.478 0.00 0.00 27.64 1.82
4613 4933 5.005740 TGTTACACTCGTCCACACTAGTAT 58.994 41.667 0.00 0.00 27.64 2.12
4614 4934 5.474532 TGTTACACTCGTCCACACTAGTATT 59.525 40.000 0.00 0.00 27.64 1.89
4615 4935 6.016024 TGTTACACTCGTCCACACTAGTATTT 60.016 38.462 0.00 0.00 27.64 1.40
4616 4936 5.056894 ACACTCGTCCACACTAGTATTTC 57.943 43.478 0.00 0.00 27.64 2.17
4617 4937 4.521639 ACACTCGTCCACACTAGTATTTCA 59.478 41.667 0.00 0.00 27.64 2.69
4618 4938 5.096169 CACTCGTCCACACTAGTATTTCAG 58.904 45.833 0.00 0.00 27.64 3.02
4619 4939 4.765856 ACTCGTCCACACTAGTATTTCAGT 59.234 41.667 0.00 0.00 26.82 3.41
4620 4940 5.243283 ACTCGTCCACACTAGTATTTCAGTT 59.757 40.000 0.00 0.00 26.82 3.16
4621 4941 5.706916 TCGTCCACACTAGTATTTCAGTTC 58.293 41.667 0.00 0.00 0.00 3.01
4622 4942 5.242171 TCGTCCACACTAGTATTTCAGTTCA 59.758 40.000 0.00 0.00 0.00 3.18
4623 4943 5.573282 CGTCCACACTAGTATTTCAGTTCAG 59.427 44.000 0.00 0.00 0.00 3.02
4624 4944 5.869888 GTCCACACTAGTATTTCAGTTCAGG 59.130 44.000 0.00 0.00 0.00 3.86
4625 4945 5.778241 TCCACACTAGTATTTCAGTTCAGGA 59.222 40.000 0.00 0.00 0.00 3.86
4626 4946 6.071334 TCCACACTAGTATTTCAGTTCAGGAG 60.071 42.308 0.00 0.00 0.00 3.69
4627 4947 6.071334 CCACACTAGTATTTCAGTTCAGGAGA 60.071 42.308 0.00 0.00 0.00 3.71
4628 4948 7.364232 CCACACTAGTATTTCAGTTCAGGAGAT 60.364 40.741 0.00 0.00 0.00 2.75
4629 4949 8.037758 CACACTAGTATTTCAGTTCAGGAGATT 58.962 37.037 0.00 0.00 0.00 2.40
4630 4950 9.256228 ACACTAGTATTTCAGTTCAGGAGATTA 57.744 33.333 0.00 0.00 0.00 1.75
4641 4961 9.060347 TCAGTTCAGGAGATTATCATTTATTGC 57.940 33.333 0.00 0.00 0.00 3.56
4642 4962 9.064706 CAGTTCAGGAGATTATCATTTATTGCT 57.935 33.333 0.00 0.00 0.00 3.91
4643 4963 9.282569 AGTTCAGGAGATTATCATTTATTGCTC 57.717 33.333 0.00 0.00 0.00 4.26
4644 4964 9.060347 GTTCAGGAGATTATCATTTATTGCTCA 57.940 33.333 0.00 0.00 0.00 4.26
4645 4965 9.631257 TTCAGGAGATTATCATTTATTGCTCAA 57.369 29.630 0.00 0.00 0.00 3.02
4646 4966 9.281371 TCAGGAGATTATCATTTATTGCTCAAG 57.719 33.333 0.00 0.00 0.00 3.02
4647 4967 9.064706 CAGGAGATTATCATTTATTGCTCAAGT 57.935 33.333 0.00 0.00 0.00 3.16
4665 4985 9.973450 TGCTCAAGTAGAAAGATATGATAACTC 57.027 33.333 0.00 0.00 0.00 3.01
4666 4986 9.418045 GCTCAAGTAGAAAGATATGATAACTCC 57.582 37.037 0.00 0.00 0.00 3.85
4669 4989 9.202273 CAAGTAGAAAGATATGATAACTCCTGC 57.798 37.037 0.00 0.00 0.00 4.85
4670 4990 7.598278 AGTAGAAAGATATGATAACTCCTGCG 58.402 38.462 0.00 0.00 0.00 5.18
4671 4991 6.412362 AGAAAGATATGATAACTCCTGCGT 57.588 37.500 0.00 0.00 0.00 5.24
4672 4992 6.451393 AGAAAGATATGATAACTCCTGCGTC 58.549 40.000 0.00 0.00 0.00 5.19
4673 4993 6.266558 AGAAAGATATGATAACTCCTGCGTCT 59.733 38.462 0.00 0.00 0.00 4.18
4674 4994 6.412362 AAGATATGATAACTCCTGCGTCTT 57.588 37.500 0.00 0.00 0.00 3.01
4675 4995 5.777802 AGATATGATAACTCCTGCGTCTTG 58.222 41.667 0.00 0.00 0.00 3.02
4676 4996 5.536538 AGATATGATAACTCCTGCGTCTTGA 59.463 40.000 0.00 0.00 0.00 3.02
4677 4997 3.953712 TGATAACTCCTGCGTCTTGAA 57.046 42.857 0.00 0.00 0.00 2.69
4678 4998 4.265904 TGATAACTCCTGCGTCTTGAAA 57.734 40.909 0.00 0.00 0.00 2.69
4679 4999 3.994392 TGATAACTCCTGCGTCTTGAAAC 59.006 43.478 0.00 0.00 0.00 2.78
4680 5000 2.325583 AACTCCTGCGTCTTGAAACA 57.674 45.000 0.00 0.00 0.00 2.83
4681 5001 1.871080 ACTCCTGCGTCTTGAAACAG 58.129 50.000 0.00 0.00 0.00 3.16
4688 5008 5.551760 CTGCGTCTTGAAACAGGATTATT 57.448 39.130 0.00 0.00 0.00 1.40
4689 5009 6.662414 CTGCGTCTTGAAACAGGATTATTA 57.338 37.500 0.00 0.00 0.00 0.98
4690 5010 7.072177 CTGCGTCTTGAAACAGGATTATTAA 57.928 36.000 0.00 0.00 0.00 1.40
4691 5011 7.624360 TGCGTCTTGAAACAGGATTATTAAT 57.376 32.000 0.00 0.00 0.00 1.40
4692 5012 8.050778 TGCGTCTTGAAACAGGATTATTAATT 57.949 30.769 0.00 0.00 0.00 1.40
4693 5013 8.181573 TGCGTCTTGAAACAGGATTATTAATTC 58.818 33.333 0.00 0.00 0.00 2.17
4694 5014 7.644157 GCGTCTTGAAACAGGATTATTAATTCC 59.356 37.037 0.00 0.00 0.00 3.01
4695 5015 8.893727 CGTCTTGAAACAGGATTATTAATTCCT 58.106 33.333 3.22 3.22 0.00 3.36
4706 5026 9.347240 AGGATTATTAATTCCTGACATGACAAG 57.653 33.333 7.74 0.00 0.00 3.16
4712 5032 4.558226 TTCCTGACATGACAAGTGCTAT 57.442 40.909 0.00 0.00 0.00 2.97
4751 5071 9.358406 TGTCAAATTATTCCTATTGATGCTCAT 57.642 29.630 0.00 0.00 34.62 2.90
4771 5091 7.704899 TGCTCATCTCTTTTCATATTGCAATTG 59.295 33.333 18.75 14.92 0.00 2.32
4787 5107 8.962884 ATTGCAATTGTTCTTTTCTTTTACCT 57.037 26.923 5.99 0.00 0.00 3.08
4794 5114 7.769272 TGTTCTTTTCTTTTACCTGCAATTG 57.231 32.000 0.00 0.00 0.00 2.32
5185 5506 3.835395 ACTAATCATAGGCTAGAGGCACC 59.165 47.826 5.83 0.00 44.01 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.349365 TGGACTAATTTGGCCTTTTAGGG 58.651 43.478 13.21 2.90 35.37 3.53
2 3 6.544928 AATGGACTAATTTGGCCTTTTAGG 57.455 37.500 13.21 0.00 38.80 2.69
3 4 9.586435 CTTTAATGGACTAATTTGGCCTTTTAG 57.414 33.333 16.12 10.93 0.00 1.85
385 696 0.750182 CCACGGAGGAGGAGAGAGAC 60.750 65.000 0.00 0.00 41.22 3.36
548 859 2.488771 TACGCAAGAGAGGACCGGGA 62.489 60.000 6.32 0.00 43.62 5.14
553 864 1.516603 GCCGTACGCAAGAGAGGAC 60.517 63.158 10.49 0.00 43.62 3.85
555 866 1.226717 GAGCCGTACGCAAGAGAGG 60.227 63.158 10.49 0.00 41.38 3.69
557 868 1.015109 CTAGAGCCGTACGCAAGAGA 58.985 55.000 10.49 0.00 41.38 3.10
762 1081 6.627087 TCCCAGAAAAATAGACATCAGACT 57.373 37.500 0.00 0.00 0.00 3.24
867 1186 4.701651 CCACTCTCTGGCATCAAAACAATA 59.298 41.667 0.00 0.00 31.36 1.90
1247 1566 4.503741 AAATTGTTCTGTTCACCGGATG 57.496 40.909 9.46 2.48 0.00 3.51
1882 2201 6.155393 TCAAAACATAAACCCCCATATGGTTC 59.845 38.462 20.46 0.00 45.23 3.62
1887 2206 8.622572 AAGATTCAAAACATAAACCCCCATAT 57.377 30.769 0.00 0.00 0.00 1.78
2033 2352 1.128200 GCCCCCTGACAAAAACCTTT 58.872 50.000 0.00 0.00 0.00 3.11
2225 2544 3.066760 ACTGAAAGCCTTTGCACTTACAC 59.933 43.478 0.00 0.00 41.13 2.90
2228 2547 3.550820 TCACTGAAAGCCTTTGCACTTA 58.449 40.909 0.00 0.00 41.13 2.24
2238 2557 3.272574 TCATCTCCATCACTGAAAGCC 57.727 47.619 0.00 0.00 37.60 4.35
2252 2571 8.549548 CAATATGATGTTCTGACAGTTCATCTC 58.450 37.037 26.16 14.38 39.58 2.75
2303 2622 4.789012 TGCTCCTTCACATGAATTTTCC 57.211 40.909 0.00 0.00 33.01 3.13
2438 2757 5.952347 GTCCAACCCTCTTCCAATTCTTTAT 59.048 40.000 0.00 0.00 0.00 1.40
2637 2956 4.037923 TGTTGGAAGCTTTGTCCAGATTTC 59.962 41.667 0.00 0.00 45.79 2.17
2652 2971 4.545823 TGTTAGCTCGTTTTGTTGGAAG 57.454 40.909 0.00 0.00 0.00 3.46
2728 3047 2.790468 GCTCATTCGCATGAAAGCAGTC 60.790 50.000 0.00 0.00 39.04 3.51
3846 4165 1.061421 GCATTTGCATTGGCGTGATTG 59.939 47.619 0.00 0.00 45.35 2.67
3924 4243 3.449018 TGACAGGATAAGAAGCACTCTCC 59.551 47.826 0.00 0.00 31.02 3.71
3942 4261 7.239763 TCCATATTCTTCACTTACACTGACA 57.760 36.000 0.00 0.00 0.00 3.58
3992 4311 0.692419 AAGGGATGGTCCAGCTCGAT 60.692 55.000 7.15 0.00 38.64 3.59
4057 4376 4.411869 TGCTGAATCATACCCCATGAGTAA 59.588 41.667 0.00 0.00 46.76 2.24
4175 4494 1.000955 TCTTTCTTCTGGACACTCGGC 59.999 52.381 0.00 0.00 0.00 5.54
4205 4524 3.056607 GGCTTGACATACCAGTGCAAAAT 60.057 43.478 0.00 0.00 0.00 1.82
4235 4554 4.116961 CGTCAAAACTGTGACCTGTAAGA 58.883 43.478 0.01 0.00 44.23 2.10
4256 4575 0.377203 GGAAAGCTGCCCGTTTATCG 59.623 55.000 0.00 0.00 39.52 2.92
4322 4642 7.873739 AGAATTTCGACAAACCAAATGATTC 57.126 32.000 0.00 0.00 0.00 2.52
4436 4756 6.050432 AGTGTGGACGAGTGTAACATAAAAA 58.950 36.000 0.00 0.00 41.43 1.94
4437 4757 5.603596 AGTGTGGACGAGTGTAACATAAAA 58.396 37.500 0.00 0.00 41.43 1.52
4540 4860 4.910195 AGCACTTGTCATGTCAGGAATTA 58.090 39.130 8.94 0.00 0.00 1.40
4561 4881 4.113354 GTGCCGAGTCTGAAACCTTATAG 58.887 47.826 0.00 0.00 0.00 1.31
4562 4882 3.767673 AGTGCCGAGTCTGAAACCTTATA 59.232 43.478 0.00 0.00 0.00 0.98
4563 4883 2.567615 AGTGCCGAGTCTGAAACCTTAT 59.432 45.455 0.00 0.00 0.00 1.73
4564 4884 1.968493 AGTGCCGAGTCTGAAACCTTA 59.032 47.619 0.00 0.00 0.00 2.69
4565 4885 0.759346 AGTGCCGAGTCTGAAACCTT 59.241 50.000 0.00 0.00 0.00 3.50
4566 4886 0.759346 AAGTGCCGAGTCTGAAACCT 59.241 50.000 0.00 0.00 0.00 3.50
4567 4887 1.149148 GAAGTGCCGAGTCTGAAACC 58.851 55.000 0.00 0.00 0.00 3.27
4568 4888 2.156343 AGAAGTGCCGAGTCTGAAAC 57.844 50.000 0.00 0.00 0.00 2.78
4569 4889 2.910688 AAGAAGTGCCGAGTCTGAAA 57.089 45.000 0.00 0.00 0.00 2.69
4570 4890 3.258372 ACATAAGAAGTGCCGAGTCTGAA 59.742 43.478 0.00 0.00 0.00 3.02
4571 4891 2.826128 ACATAAGAAGTGCCGAGTCTGA 59.174 45.455 0.00 0.00 0.00 3.27
4572 4892 3.238108 ACATAAGAAGTGCCGAGTCTG 57.762 47.619 0.00 0.00 0.00 3.51
4573 4893 3.963428 AACATAAGAAGTGCCGAGTCT 57.037 42.857 0.00 0.00 0.00 3.24
4574 4894 4.326548 GTGTAACATAAGAAGTGCCGAGTC 59.673 45.833 0.00 0.00 36.32 3.36
4575 4895 4.021368 AGTGTAACATAAGAAGTGCCGAGT 60.021 41.667 0.00 0.00 41.43 4.18
4576 4896 4.495422 AGTGTAACATAAGAAGTGCCGAG 58.505 43.478 0.00 0.00 41.43 4.63
4577 4897 4.491676 GAGTGTAACATAAGAAGTGCCGA 58.508 43.478 0.00 0.00 41.43 5.54
4578 4898 3.303495 CGAGTGTAACATAAGAAGTGCCG 59.697 47.826 0.00 0.00 41.43 5.69
4579 4899 4.243270 ACGAGTGTAACATAAGAAGTGCC 58.757 43.478 0.00 0.00 41.43 5.01
4580 4900 4.326548 GGACGAGTGTAACATAAGAAGTGC 59.673 45.833 0.00 0.00 41.43 4.40
4581 4901 5.345202 GTGGACGAGTGTAACATAAGAAGTG 59.655 44.000 0.00 0.00 41.43 3.16
4582 4902 5.010314 TGTGGACGAGTGTAACATAAGAAGT 59.990 40.000 0.00 0.00 41.43 3.01
4583 4903 5.345202 GTGTGGACGAGTGTAACATAAGAAG 59.655 44.000 0.00 0.00 41.43 2.85
4584 4904 5.010314 AGTGTGGACGAGTGTAACATAAGAA 59.990 40.000 0.00 0.00 41.43 2.52
4585 4905 4.521639 AGTGTGGACGAGTGTAACATAAGA 59.478 41.667 0.00 0.00 41.43 2.10
4586 4906 4.806330 AGTGTGGACGAGTGTAACATAAG 58.194 43.478 0.00 0.00 41.43 1.73
4587 4907 4.859304 AGTGTGGACGAGTGTAACATAA 57.141 40.909 0.00 0.00 41.43 1.90
4588 4908 5.005740 ACTAGTGTGGACGAGTGTAACATA 58.994 41.667 0.00 0.00 41.43 2.29
4589 4909 3.825014 ACTAGTGTGGACGAGTGTAACAT 59.175 43.478 0.00 0.00 41.43 2.71
4590 4910 3.216800 ACTAGTGTGGACGAGTGTAACA 58.783 45.455 0.00 0.00 41.43 2.41
4591 4911 3.911661 ACTAGTGTGGACGAGTGTAAC 57.088 47.619 0.00 0.00 36.75 2.50
4592 4912 6.207221 TGAAATACTAGTGTGGACGAGTGTAA 59.793 38.462 5.39 0.00 38.39 2.41
4593 4913 5.706833 TGAAATACTAGTGTGGACGAGTGTA 59.293 40.000 5.39 0.00 38.39 2.90
4594 4914 4.521639 TGAAATACTAGTGTGGACGAGTGT 59.478 41.667 5.39 0.00 38.39 3.55
4595 4915 5.055642 TGAAATACTAGTGTGGACGAGTG 57.944 43.478 5.39 0.00 38.39 3.51
4596 4916 4.765856 ACTGAAATACTAGTGTGGACGAGT 59.234 41.667 5.39 0.00 40.70 4.18
4597 4917 5.312120 ACTGAAATACTAGTGTGGACGAG 57.688 43.478 5.39 0.00 0.00 4.18
4598 4918 5.242171 TGAACTGAAATACTAGTGTGGACGA 59.758 40.000 5.39 0.00 0.00 4.20
4599 4919 5.466819 TGAACTGAAATACTAGTGTGGACG 58.533 41.667 5.39 0.00 0.00 4.79
4600 4920 5.869888 CCTGAACTGAAATACTAGTGTGGAC 59.130 44.000 5.39 0.00 0.00 4.02
4601 4921 5.778241 TCCTGAACTGAAATACTAGTGTGGA 59.222 40.000 5.39 0.00 0.00 4.02
4602 4922 6.037786 TCCTGAACTGAAATACTAGTGTGG 57.962 41.667 5.39 0.00 0.00 4.17
4603 4923 6.925211 TCTCCTGAACTGAAATACTAGTGTG 58.075 40.000 5.39 0.00 0.00 3.82
4604 4924 7.726033 ATCTCCTGAACTGAAATACTAGTGT 57.274 36.000 5.39 0.00 0.00 3.55
4615 4935 9.060347 GCAATAAATGATAATCTCCTGAACTGA 57.940 33.333 0.00 0.00 0.00 3.41
4616 4936 9.064706 AGCAATAAATGATAATCTCCTGAACTG 57.935 33.333 0.00 0.00 0.00 3.16
4617 4937 9.282569 GAGCAATAAATGATAATCTCCTGAACT 57.717 33.333 0.00 0.00 0.00 3.01
4618 4938 9.060347 TGAGCAATAAATGATAATCTCCTGAAC 57.940 33.333 0.00 0.00 0.00 3.18
4619 4939 9.631257 TTGAGCAATAAATGATAATCTCCTGAA 57.369 29.630 0.00 0.00 0.00 3.02
4620 4940 9.281371 CTTGAGCAATAAATGATAATCTCCTGA 57.719 33.333 0.00 0.00 0.00 3.86
4621 4941 9.064706 ACTTGAGCAATAAATGATAATCTCCTG 57.935 33.333 0.00 0.00 0.00 3.86
4639 4959 9.973450 GAGTTATCATATCTTTCTACTTGAGCA 57.027 33.333 0.00 0.00 0.00 4.26
4640 4960 9.418045 GGAGTTATCATATCTTTCTACTTGAGC 57.582 37.037 0.00 0.00 0.00 4.26
4643 4963 9.202273 GCAGGAGTTATCATATCTTTCTACTTG 57.798 37.037 0.00 0.00 0.00 3.16
4644 4964 8.085296 CGCAGGAGTTATCATATCTTTCTACTT 58.915 37.037 0.00 0.00 0.00 2.24
4645 4965 7.231722 ACGCAGGAGTTATCATATCTTTCTACT 59.768 37.037 0.00 0.00 0.00 2.57
4646 4966 7.371936 ACGCAGGAGTTATCATATCTTTCTAC 58.628 38.462 0.00 0.00 0.00 2.59
4647 4967 7.448777 AGACGCAGGAGTTATCATATCTTTCTA 59.551 37.037 0.00 0.00 0.00 2.10
4648 4968 6.266558 AGACGCAGGAGTTATCATATCTTTCT 59.733 38.462 0.00 0.00 0.00 2.52
4649 4969 6.451393 AGACGCAGGAGTTATCATATCTTTC 58.549 40.000 0.00 0.00 0.00 2.62
4650 4970 6.412362 AGACGCAGGAGTTATCATATCTTT 57.588 37.500 0.00 0.00 0.00 2.52
4651 4971 6.040955 TCAAGACGCAGGAGTTATCATATCTT 59.959 38.462 0.00 0.00 0.00 2.40
4652 4972 5.536538 TCAAGACGCAGGAGTTATCATATCT 59.463 40.000 0.00 0.00 0.00 1.98
4653 4973 5.773575 TCAAGACGCAGGAGTTATCATATC 58.226 41.667 0.00 0.00 0.00 1.63
4654 4974 5.791336 TCAAGACGCAGGAGTTATCATAT 57.209 39.130 0.00 0.00 0.00 1.78
4655 4975 5.592104 TTCAAGACGCAGGAGTTATCATA 57.408 39.130 0.00 0.00 0.00 2.15
4656 4976 4.471904 TTCAAGACGCAGGAGTTATCAT 57.528 40.909 0.00 0.00 0.00 2.45
4657 4977 3.953712 TTCAAGACGCAGGAGTTATCA 57.046 42.857 0.00 0.00 0.00 2.15
4658 4978 3.994392 TGTTTCAAGACGCAGGAGTTATC 59.006 43.478 0.00 0.00 0.00 1.75
4659 4979 3.997021 CTGTTTCAAGACGCAGGAGTTAT 59.003 43.478 0.00 0.00 0.00 1.89
4660 4980 3.390135 CTGTTTCAAGACGCAGGAGTTA 58.610 45.455 0.00 0.00 0.00 2.24
4661 4981 2.213499 CTGTTTCAAGACGCAGGAGTT 58.787 47.619 0.00 0.00 0.00 3.01
4662 4982 1.871080 CTGTTTCAAGACGCAGGAGT 58.129 50.000 0.00 0.00 0.00 3.85
4666 4986 5.551760 AATAATCCTGTTTCAAGACGCAG 57.448 39.130 0.00 0.00 0.00 5.18
4667 4987 7.624360 ATTAATAATCCTGTTTCAAGACGCA 57.376 32.000 0.00 0.00 0.00 5.24
4668 4988 7.644157 GGAATTAATAATCCTGTTTCAAGACGC 59.356 37.037 0.00 0.00 32.75 5.19
4669 4989 8.893727 AGGAATTAATAATCCTGTTTCAAGACG 58.106 33.333 7.74 0.00 44.38 4.18
4681 5001 9.125026 ACTTGTCATGTCAGGAATTAATAATCC 57.875 33.333 8.94 0.00 35.88 3.01
4682 5002 9.941664 CACTTGTCATGTCAGGAATTAATAATC 57.058 33.333 8.94 0.00 0.00 1.75
4683 5003 8.408601 GCACTTGTCATGTCAGGAATTAATAAT 58.591 33.333 8.94 0.00 0.00 1.28
4684 5004 7.611467 AGCACTTGTCATGTCAGGAATTAATAA 59.389 33.333 8.94 0.00 0.00 1.40
4685 5005 7.112122 AGCACTTGTCATGTCAGGAATTAATA 58.888 34.615 8.94 0.00 0.00 0.98
4686 5006 5.948162 AGCACTTGTCATGTCAGGAATTAAT 59.052 36.000 8.94 0.00 0.00 1.40
4687 5007 5.316167 AGCACTTGTCATGTCAGGAATTAA 58.684 37.500 8.94 0.00 0.00 1.40
4688 5008 4.910195 AGCACTTGTCATGTCAGGAATTA 58.090 39.130 8.94 0.00 0.00 1.40
4689 5009 3.759581 AGCACTTGTCATGTCAGGAATT 58.240 40.909 8.94 0.00 0.00 2.17
4690 5010 3.430042 AGCACTTGTCATGTCAGGAAT 57.570 42.857 8.94 0.00 0.00 3.01
4691 5011 2.936919 AGCACTTGTCATGTCAGGAA 57.063 45.000 8.94 0.00 0.00 3.36
4692 5012 5.395657 CCTTATAGCACTTGTCATGTCAGGA 60.396 44.000 8.94 0.00 0.00 3.86
4693 5013 4.813161 CCTTATAGCACTTGTCATGTCAGG 59.187 45.833 0.65 0.65 0.00 3.86
4694 5014 5.423015 ACCTTATAGCACTTGTCATGTCAG 58.577 41.667 0.00 0.00 0.00 3.51
4695 5015 5.420725 ACCTTATAGCACTTGTCATGTCA 57.579 39.130 0.00 0.00 0.00 3.58
4696 5016 5.874810 TCAACCTTATAGCACTTGTCATGTC 59.125 40.000 0.00 0.00 0.00 3.06
4697 5017 5.643777 GTCAACCTTATAGCACTTGTCATGT 59.356 40.000 0.00 0.00 0.00 3.21
4698 5018 5.643348 TGTCAACCTTATAGCACTTGTCATG 59.357 40.000 0.00 0.00 0.00 3.07
4699 5019 5.804639 TGTCAACCTTATAGCACTTGTCAT 58.195 37.500 0.00 0.00 0.00 3.06
4700 5020 5.222079 TGTCAACCTTATAGCACTTGTCA 57.778 39.130 0.00 0.00 0.00 3.58
4701 5021 6.743575 AATGTCAACCTTATAGCACTTGTC 57.256 37.500 0.00 0.00 0.00 3.18
4702 5022 6.490040 ACAAATGTCAACCTTATAGCACTTGT 59.510 34.615 0.00 0.00 0.00 3.16
4703 5023 6.913170 ACAAATGTCAACCTTATAGCACTTG 58.087 36.000 0.00 0.00 0.00 3.16
4704 5024 7.145932 GACAAATGTCAACCTTATAGCACTT 57.854 36.000 8.63 0.00 44.18 3.16
4705 5025 6.743575 GACAAATGTCAACCTTATAGCACT 57.256 37.500 8.63 0.00 44.18 4.40
4751 5071 9.985730 AAAGAACAATTGCAATATGAAAAGAGA 57.014 25.926 13.39 0.00 0.00 3.10
4771 5091 6.479990 AGCAATTGCAGGTAAAAGAAAAGAAC 59.520 34.615 30.89 0.00 45.16 3.01
4787 5107 5.123502 TGCAGAAAAAGAAAAAGCAATTGCA 59.876 32.000 30.89 2.81 45.16 4.08


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

AutoCloner maintained by Alex Coulton.