Multiple sequence alignment - TraesCS2B01G251700

Loading Multiple Alignment...

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 TraesCS2B01G251700 chr2B 100.000 5236 0 0 684 5919 265215556 265220791 0.000000e+00 9670.0
1 TraesCS2B01G251700 chr2B 100.000 187 0 0 1 187 265214873 265215059 4.390000e-91 346.0
2 TraesCS2B01G251700 chr2D 94.680 4474 129 53 686 5118 209506879 209511284 0.000000e+00 6842.0
3 TraesCS2B01G251700 chr2D 93.531 742 29 8 5196 5919 209511426 209512166 0.000000e+00 1086.0
4 TraesCS2B01G251700 chr2D 94.565 184 4 1 1 184 209506588 209506765 4.520000e-71 279.0
5 TraesCS2B01G251700 chr2A 94.863 4380 116 45 684 5011 262573088 262577410 0.000000e+00 6741.0
6 TraesCS2B01G251700 chr2A 92.943 751 25 10 5196 5919 262577852 262578601 0.000000e+00 1068.0
7 TraesCS2B01G251700 chr2A 92.982 57 2 2 124 180 262572923 262572977 1.370000e-11 82.4
8 TraesCS2B01G251700 chr1B 93.023 43 3 0 4273 4315 491040049 491040007 4.950000e-06 63.9
9 TraesCS2B01G251700 chr1B 100.000 29 0 0 4280 4308 104465483 104465511 3.000000e-03 54.7
10 TraesCS2B01G251700 chr1D 100.000 29 0 0 4280 4308 63634623 63634651 3.000000e-03 54.7
11 TraesCS2B01G251700 chr1A 100.000 29 0 0 4280 4308 62612470 62612498 3.000000e-03 54.7


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 TraesCS2B01G251700 chr2B 265214873 265220791 5918 False 5008.000000 9670 100.000000 1 5919 2 chr2B.!!$F1 5918
1 TraesCS2B01G251700 chr2D 209506588 209512166 5578 False 2735.666667 6842 94.258667 1 5919 3 chr2D.!!$F1 5918
2 TraesCS2B01G251700 chr2A 262572923 262578601 5678 False 2630.466667 6741 93.596000 124 5919 3 chr2A.!!$F1 5795

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
727 728 0.109873 CCGAGCAGAGCAAAGCAAAG 60.110 55.0 0.0 0.0 0.00 2.77 F
729 730 0.313043 GAGCAGAGCAAAGCAAAGCA 59.687 50.0 0.0 0.0 0.00 3.91 F
730 731 0.748450 AGCAGAGCAAAGCAAAGCAA 59.252 45.0 0.0 0.0 0.00 3.91 F
2651 2667 0.869454 CTCGAATCGCTCCAGCAGTC 60.869 60.0 0.0 0.0 42.21 3.51 F
4504 4568 0.396139 CATGCACATAGGCCCCAGTT 60.396 55.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1918 0.038618 CGGACAGGTCAATCGTGTGA 60.039 55.000 1.41 0.00 43.80 3.58 R
2651 2667 1.135972 GCGAGTTGTTGTACAGCATGG 60.136 52.381 13.51 2.34 43.62 3.66 R
2780 2796 1.226603 GCGTCGAACGATAGCAGGT 60.227 57.895 17.27 0.00 46.05 4.00 R
4526 4590 0.107312 GCAGGCAGATGGTCAGTGAT 60.107 55.000 0.00 0.00 0.00 3.06 R
5358 5710 2.292103 TTGCAGTTTGCTTTGGTCAC 57.708 45.000 2.48 0.00 45.31 3.67 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
27 28 0.467290 AAGCTTTCGACCCAAGCCAA 60.467 50.000 15.02 0.00 46.76 4.52
80 81 4.705337 TTTGCTTTCGTACCAACAAGTT 57.295 36.364 0.00 0.00 0.00 2.66
93 94 3.005367 CCAACAAGTTAAAATCCACGGCT 59.995 43.478 0.00 0.00 0.00 5.52
184 185 3.244700 CCATCCTCCTCTCTCTCTCTCTC 60.245 56.522 0.00 0.00 0.00 3.20
185 186 3.421394 TCCTCCTCTCTCTCTCTCTCT 57.579 52.381 0.00 0.00 0.00 3.10
703 704 3.051940 AGCTCCTCCATTAGTCCATCA 57.948 47.619 0.00 0.00 0.00 3.07
704 705 3.596101 AGCTCCTCCATTAGTCCATCAT 58.404 45.455 0.00 0.00 0.00 2.45
707 708 4.202398 GCTCCTCCATTAGTCCATCATTCA 60.202 45.833 0.00 0.00 0.00 2.57
720 721 0.321346 TCATTCACCGAGCAGAGCAA 59.679 50.000 0.00 0.00 0.00 3.91
726 727 0.819259 ACCGAGCAGAGCAAAGCAAA 60.819 50.000 0.00 0.00 0.00 3.68
727 728 0.109873 CCGAGCAGAGCAAAGCAAAG 60.110 55.000 0.00 0.00 0.00 2.77
728 729 0.728466 CGAGCAGAGCAAAGCAAAGC 60.728 55.000 0.00 0.00 0.00 3.51
729 730 0.313043 GAGCAGAGCAAAGCAAAGCA 59.687 50.000 0.00 0.00 0.00 3.91
730 731 0.748450 AGCAGAGCAAAGCAAAGCAA 59.252 45.000 0.00 0.00 0.00 3.91
936 938 4.293626 GTGTGCGTGCGTGTGTCC 62.294 66.667 0.00 0.00 0.00 4.02
1120 1136 1.602237 GGTGATGATGGGGACGTGT 59.398 57.895 0.00 0.00 0.00 4.49
1526 1542 2.186903 GATCCCCAAAGCGCTCGA 59.813 61.111 12.06 1.58 0.00 4.04
1635 1651 1.856265 CGGCCTTGAACCTGCAAGAC 61.856 60.000 0.00 0.00 46.31 3.01
1725 1741 1.359459 GGAATCAACTCACCGGCGAC 61.359 60.000 9.30 0.00 0.00 5.19
2278 2294 3.738590 GCCGGAGATCTTTAACCTCACTC 60.739 52.174 5.05 0.00 0.00 3.51
2651 2667 0.869454 CTCGAATCGCTCCAGCAGTC 60.869 60.000 0.00 0.00 42.21 3.51
3103 3119 1.999051 CTCTCCGCCAACGAATTCG 59.001 57.895 25.64 25.64 43.93 3.34
3242 3258 1.699656 CTGAATCTGGCGCAGAACCG 61.700 60.000 10.83 2.82 44.04 4.44
3256 3272 3.881019 AACCGGCTCTCAGGTCCGA 62.881 63.158 0.00 0.00 45.53 4.55
3411 3427 1.898574 GGTGGGCATAATCCCTGCG 60.899 63.158 0.12 0.00 46.67 5.18
3549 3565 1.056700 ATCGGCTGGATGGTAGGCTT 61.057 55.000 0.00 0.00 38.46 4.35
3804 3820 2.022129 CTGCACGGTGTTCTCGTCC 61.022 63.158 10.24 0.00 38.94 4.79
4146 4162 5.561919 GCTCATCTACGAGTACATGGAGAAG 60.562 48.000 3.68 0.40 35.33 2.85
4203 4237 4.463879 CGGGTGCTGAGCTGGGAG 62.464 72.222 5.83 0.00 0.00 4.30
4447 4481 3.721969 TACATGGCACCAGGTAGGA 57.278 52.632 10.00 0.00 41.39 2.94
4449 4483 0.547712 ACATGGCACCAGGTAGGAGT 60.548 55.000 4.94 0.00 39.28 3.85
4450 4484 1.273609 ACATGGCACCAGGTAGGAGTA 60.274 52.381 4.94 0.00 39.28 2.59
4452 4486 2.263895 TGGCACCAGGTAGGAGTAAT 57.736 50.000 0.00 0.00 41.22 1.89
4453 4487 3.408157 TGGCACCAGGTAGGAGTAATA 57.592 47.619 0.00 0.00 41.22 0.98
4456 4490 3.646637 GGCACCAGGTAGGAGTAATACAT 59.353 47.826 0.00 0.00 41.22 2.29
4458 4492 5.306160 GGCACCAGGTAGGAGTAATACATAA 59.694 44.000 0.00 0.00 41.22 1.90
4459 4493 6.183361 GGCACCAGGTAGGAGTAATACATAAA 60.183 42.308 0.00 0.00 41.22 1.40
4460 4494 7.450903 GCACCAGGTAGGAGTAATACATAAAT 58.549 38.462 0.00 0.00 41.22 1.40
4461 4495 7.603024 GCACCAGGTAGGAGTAATACATAAATC 59.397 40.741 0.00 0.00 41.22 2.17
4483 4547 3.055530 CCTGACACTCAAATAGGTCTGCT 60.056 47.826 0.00 0.00 0.00 4.24
4484 4548 3.930336 TGACACTCAAATAGGTCTGCTG 58.070 45.455 0.00 0.00 0.00 4.41
4485 4549 2.675348 GACACTCAAATAGGTCTGCTGC 59.325 50.000 0.00 0.00 0.00 5.25
4486 4550 2.038952 ACACTCAAATAGGTCTGCTGCA 59.961 45.455 0.88 0.88 0.00 4.41
4487 4551 3.276857 CACTCAAATAGGTCTGCTGCAT 58.723 45.455 1.31 0.00 0.00 3.96
4488 4552 3.064958 CACTCAAATAGGTCTGCTGCATG 59.935 47.826 1.31 0.00 0.00 4.06
4489 4553 2.019249 TCAAATAGGTCTGCTGCATGC 58.981 47.619 11.82 11.82 43.25 4.06
4504 4568 0.396139 CATGCACATAGGCCCCAGTT 60.396 55.000 0.00 0.00 0.00 3.16
4508 4572 2.371841 TGCACATAGGCCCCAGTTATAG 59.628 50.000 0.00 0.00 0.00 1.31
4509 4573 2.372172 GCACATAGGCCCCAGTTATAGT 59.628 50.000 0.00 0.00 0.00 2.12
4510 4574 3.581332 GCACATAGGCCCCAGTTATAGTA 59.419 47.826 0.00 0.00 0.00 1.82
4513 4577 4.591924 ACATAGGCCCCAGTTATAGTACAC 59.408 45.833 0.00 0.00 0.00 2.90
4516 4580 3.208234 AGGCCCCAGTTATAGTACACCTA 59.792 47.826 0.00 0.00 0.00 3.08
4517 4581 3.323115 GGCCCCAGTTATAGTACACCTAC 59.677 52.174 0.00 0.00 0.00 3.18
4518 4582 3.005155 GCCCCAGTTATAGTACACCTACG 59.995 52.174 0.00 0.00 0.00 3.51
4519 4583 4.210331 CCCCAGTTATAGTACACCTACGT 58.790 47.826 0.00 0.00 0.00 3.57
4520 4584 5.376625 CCCCAGTTATAGTACACCTACGTA 58.623 45.833 0.00 0.00 0.00 3.57
4521 4585 5.239525 CCCCAGTTATAGTACACCTACGTAC 59.760 48.000 0.00 0.00 41.75 3.67
4522 4586 5.050091 CCCAGTTATAGTACACCTACGTACG 60.050 48.000 15.01 15.01 45.25 3.67
4523 4587 5.523916 CCAGTTATAGTACACCTACGTACGT 59.476 44.000 25.98 25.98 45.25 3.57
4524 4588 6.700081 CCAGTTATAGTACACCTACGTACGTA 59.300 42.308 25.41 25.41 45.25 3.57
4525 4589 7.385205 CCAGTTATAGTACACCTACGTACGTAT 59.615 40.741 26.98 15.44 45.25 3.06
4526 4590 9.406828 CAGTTATAGTACACCTACGTACGTATA 57.593 37.037 26.98 15.35 45.25 1.47
4546 4610 1.196766 TCACTGACCATCTGCCTGCT 61.197 55.000 0.00 0.00 0.00 4.24
4547 4611 0.743701 CACTGACCATCTGCCTGCTC 60.744 60.000 0.00 0.00 0.00 4.26
4548 4612 0.908656 ACTGACCATCTGCCTGCTCT 60.909 55.000 0.00 0.00 0.00 4.09
4549 4613 0.462225 CTGACCATCTGCCTGCTCTG 60.462 60.000 0.00 0.00 0.00 3.35
4550 4614 1.818785 GACCATCTGCCTGCTCTGC 60.819 63.158 0.00 0.00 0.00 4.26
4555 4619 0.464013 ATCTGCCTGCTCTGCATGTC 60.464 55.000 0.00 0.00 38.13 3.06
4642 4706 3.461773 ATGGAGCTCGTCACCGGG 61.462 66.667 6.32 0.00 37.72 5.73
4825 4889 3.790437 CTCCGATGCACCAGGCCT 61.790 66.667 0.00 0.00 43.89 5.19
4924 4988 1.645997 GCAGAAGCGCTAGGAATGC 59.354 57.895 12.05 13.25 0.00 3.56
4925 4989 1.091771 GCAGAAGCGCTAGGAATGCA 61.092 55.000 12.05 0.00 32.58 3.96
4956 5020 9.450807 CTATTTACCAACTGTTTCTTGTTTCAG 57.549 33.333 0.00 0.00 0.00 3.02
4964 5028 8.872845 CAACTGTTTCTTGTTTCAGCTAATTTT 58.127 29.630 0.00 0.00 0.00 1.82
4967 5031 6.760770 TGTTTCTTGTTTCAGCTAATTTTGGG 59.239 34.615 0.00 0.00 0.00 4.12
5054 5131 5.659971 AGAAGAATCCCCTTGAATTGGATTG 59.340 40.000 10.79 0.00 46.28 2.67
5091 5379 2.206576 ATTTGACTGGGCTTGGAGAC 57.793 50.000 0.00 0.00 0.00 3.36
5118 5406 5.119931 TGTACAAGCGATGCAAATTTCTT 57.880 34.783 0.00 0.00 0.00 2.52
5119 5407 4.916831 TGTACAAGCGATGCAAATTTCTTG 59.083 37.500 11.47 11.47 37.51 3.02
5123 5454 4.978083 AGCGATGCAAATTTCTTGAGAT 57.022 36.364 0.00 0.00 0.00 2.75
5142 5473 0.907486 TCCCTGAGGAACATCTGCAG 59.093 55.000 7.63 7.63 40.08 4.41
5166 5499 2.879233 TTCTGTCAGCGACCCCCAC 61.879 63.158 0.00 0.00 0.00 4.61
5174 5507 3.157680 CGACCCCCACAAGGAAGT 58.842 61.111 0.00 0.00 38.24 3.01
5175 5508 1.003718 CGACCCCCACAAGGAAGTC 60.004 63.158 0.00 0.00 38.24 3.01
5176 5509 1.764571 CGACCCCCACAAGGAAGTCA 61.765 60.000 0.00 0.00 36.87 3.41
5177 5510 0.476771 GACCCCCACAAGGAAGTCAA 59.523 55.000 0.00 0.00 38.24 3.18
5178 5511 1.075536 GACCCCCACAAGGAAGTCAAT 59.924 52.381 0.00 0.00 38.24 2.57
5179 5512 1.075536 ACCCCCACAAGGAAGTCAATC 59.924 52.381 0.00 0.00 38.24 2.67
5180 5513 1.075374 CCCCCACAAGGAAGTCAATCA 59.925 52.381 0.00 0.00 38.24 2.57
5181 5514 2.490718 CCCCCACAAGGAAGTCAATCAA 60.491 50.000 0.00 0.00 38.24 2.57
5182 5515 2.558359 CCCCACAAGGAAGTCAATCAAC 59.442 50.000 0.00 0.00 38.24 3.18
5183 5516 3.221771 CCCACAAGGAAGTCAATCAACA 58.778 45.455 0.00 0.00 38.24 3.33
5184 5517 3.254166 CCCACAAGGAAGTCAATCAACAG 59.746 47.826 0.00 0.00 38.24 3.16
5185 5518 3.254166 CCACAAGGAAGTCAATCAACAGG 59.746 47.826 0.00 0.00 36.89 4.00
5186 5519 3.254166 CACAAGGAAGTCAATCAACAGGG 59.746 47.826 0.00 0.00 0.00 4.45
5188 5521 4.202609 ACAAGGAAGTCAATCAACAGGGAT 60.203 41.667 0.00 0.00 0.00 3.85
5189 5522 5.014123 ACAAGGAAGTCAATCAACAGGGATA 59.986 40.000 0.00 0.00 0.00 2.59
5193 5526 6.069440 AGGAAGTCAATCAACAGGGATATGAA 60.069 38.462 0.00 0.00 0.00 2.57
5194 5527 6.774656 GGAAGTCAATCAACAGGGATATGAAT 59.225 38.462 0.00 0.00 0.00 2.57
5197 5549 7.524290 AGTCAATCAACAGGGATATGAATCAT 58.476 34.615 0.00 0.00 33.41 2.45
5210 5562 8.321353 GGGATATGAATCATGTACCATAAGTCA 58.679 37.037 15.37 0.00 36.21 3.41
5223 5575 8.946085 TGTACCATAAGTCAATCATTTGAACTC 58.054 33.333 0.00 0.00 43.29 3.01
5231 5583 7.752695 AGTCAATCATTTGAACTCGAATAACC 58.247 34.615 0.00 0.00 43.29 2.85
5237 5589 4.944962 TTGAACTCGAATAACCATGCTG 57.055 40.909 0.00 0.00 0.00 4.41
5425 5777 3.242518 TGAACAGCTAATCGTCGTCTTG 58.757 45.455 0.00 0.00 0.00 3.02
5467 5819 6.441274 ACAAAAGTCTATGAGCACAACAATG 58.559 36.000 0.00 0.00 0.00 2.82
5493 5857 8.562892 GTCATATAAGTAGCTTTTGATGTGCAT 58.437 33.333 0.00 0.00 0.00 3.96
5592 5956 5.682943 TTCAGCATTACAACTGTTGGTAC 57.317 39.130 23.15 8.85 35.37 3.34
5599 5963 5.564048 TTACAACTGTTGGTACCAAACAC 57.436 39.130 28.67 17.83 37.70 3.32
5603 5967 4.911514 ACTGTTGGTACCAAACACATTC 57.088 40.909 28.67 14.72 37.70 2.67
5666 6034 5.891551 TCAGGCAGTTTTAAGAAGAAAACCT 59.108 36.000 7.87 0.00 46.15 3.50
5828 6196 8.763049 ATGCACTACATATATGTCATGTGTAC 57.237 34.615 27.90 20.05 41.97 2.90
5875 6252 1.942657 GTCATATCACGTGCAGCCATT 59.057 47.619 11.67 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 1.588674 CGCCATAGCCGTGGATTTTA 58.411 50.000 9.05 0.00 42.02 1.52
93 94 1.745890 CGGTTCAGGATCCGCCATA 59.254 57.895 5.98 0.00 40.28 2.74
117 118 0.668535 GTCCCTTTTATGGGCGATGC 59.331 55.000 0.00 0.00 46.67 3.91
119 120 0.818040 GCGTCCCTTTTATGGGCGAT 60.818 55.000 7.58 0.00 46.67 4.58
120 121 1.450669 GCGTCCCTTTTATGGGCGA 60.451 57.895 7.58 0.00 46.67 5.54
121 122 2.478033 GGCGTCCCTTTTATGGGCG 61.478 63.158 0.00 0.00 46.67 6.13
122 123 0.968393 TTGGCGTCCCTTTTATGGGC 60.968 55.000 0.00 0.00 46.67 5.36
124 125 0.815095 GGTTGGCGTCCCTTTTATGG 59.185 55.000 0.00 0.00 0.00 2.74
125 126 1.201414 GTGGTTGGCGTCCCTTTTATG 59.799 52.381 0.00 0.00 0.00 1.90
126 127 1.074889 AGTGGTTGGCGTCCCTTTTAT 59.925 47.619 0.00 0.00 0.00 1.40
127 128 0.475044 AGTGGTTGGCGTCCCTTTTA 59.525 50.000 0.00 0.00 0.00 1.52
128 129 0.822121 GAGTGGTTGGCGTCCCTTTT 60.822 55.000 0.00 0.00 0.00 2.27
702 703 1.129998 CTTTGCTCTGCTCGGTGAATG 59.870 52.381 0.00 0.00 0.00 2.67
703 704 1.446907 CTTTGCTCTGCTCGGTGAAT 58.553 50.000 0.00 0.00 0.00 2.57
704 705 1.230635 GCTTTGCTCTGCTCGGTGAA 61.231 55.000 0.00 0.00 0.00 3.18
707 708 0.819259 TTTGCTTTGCTCTGCTCGGT 60.819 50.000 0.00 0.00 0.00 4.69
720 721 0.459934 TTGTTGCGCTTGCTTTGCTT 60.460 45.000 9.73 0.00 40.12 3.91
726 727 1.103398 AAGGAGTTGTTGCGCTTGCT 61.103 50.000 9.73 0.00 40.12 3.91
727 728 0.661483 GAAGGAGTTGTTGCGCTTGC 60.661 55.000 9.73 0.00 39.78 4.01
728 729 0.947244 AGAAGGAGTTGTTGCGCTTG 59.053 50.000 9.73 0.00 0.00 4.01
729 730 2.037251 TCTAGAAGGAGTTGTTGCGCTT 59.963 45.455 9.73 0.00 0.00 4.68
730 731 1.618837 TCTAGAAGGAGTTGTTGCGCT 59.381 47.619 9.73 0.00 0.00 5.92
919 921 4.293626 GGACACACGCACGCACAC 62.294 66.667 0.00 0.00 0.00 3.82
920 922 4.821589 TGGACACACGCACGCACA 62.822 61.111 0.00 0.00 0.00 4.57
921 923 3.506312 CTTGGACACACGCACGCAC 62.506 63.158 0.00 0.00 0.00 5.34
922 924 3.268603 CTTGGACACACGCACGCA 61.269 61.111 0.00 0.00 0.00 5.24
923 925 4.012895 CCTTGGACACACGCACGC 62.013 66.667 0.00 0.00 0.00 5.34
924 926 4.012895 GCCTTGGACACACGCACG 62.013 66.667 0.00 0.00 0.00 5.34
945 947 1.055040 AACTTGTGAGGAGAGCAGCT 58.945 50.000 0.00 0.00 0.00 4.24
951 964 0.033504 GGCGTCAACTTGTGAGGAGA 59.966 55.000 0.49 0.00 43.50 3.71
956 969 1.270094 CCACTAGGCGTCAACTTGTGA 60.270 52.381 8.23 0.00 41.90 3.58
997 1010 3.376935 CTCCTGCGCCCGTCATCTT 62.377 63.158 4.18 0.00 0.00 2.40
1113 1129 0.179067 TCACCTCCAACAACACGTCC 60.179 55.000 0.00 0.00 0.00 4.79
1120 1136 0.884704 GCGCTCTTCACCTCCAACAA 60.885 55.000 0.00 0.00 0.00 2.83
1149 1165 1.758592 CAAAACTCCCTCCGGGTCA 59.241 57.895 0.00 0.00 44.74 4.02
1338 1354 2.029964 GTGAGGCGGTTGGACGAA 59.970 61.111 0.00 0.00 35.47 3.85
1375 1391 4.489771 CCTTTGGAGGCGCCCGAT 62.490 66.667 26.15 3.93 35.94 4.18
1387 1403 1.743958 CATGAGAAGCTGGAGCCTTTG 59.256 52.381 0.00 0.00 43.38 2.77
1388 1404 1.954258 GCATGAGAAGCTGGAGCCTTT 60.954 52.381 0.00 0.00 43.38 3.11
1509 1525 1.884926 CTCGAGCGCTTTGGGGATC 60.885 63.158 13.26 0.00 37.44 3.36
1563 1579 2.671177 CGCTCCGGTGAAGTTGCAG 61.671 63.158 7.92 0.00 0.00 4.41
1570 1586 2.802792 CGGTATCGCTCCGGTGAA 59.197 61.111 7.92 0.00 43.68 3.18
1725 1741 2.588877 CCAAGCTCCGGCGGTATG 60.589 66.667 27.32 18.82 44.37 2.39
1902 1918 0.038618 CGGACAGGTCAATCGTGTGA 60.039 55.000 1.41 0.00 43.80 3.58
2388 2404 2.562876 GGTCTCCGGTATCTCGCCC 61.563 68.421 0.00 0.00 0.00 6.13
2535 2551 2.759973 AGCTCCGGCGGAATCAGA 60.760 61.111 30.59 6.30 44.37 3.27
2651 2667 1.135972 GCGAGTTGTTGTACAGCATGG 60.136 52.381 13.51 2.34 43.62 3.66
2780 2796 1.226603 GCGTCGAACGATAGCAGGT 60.227 57.895 17.27 0.00 46.05 4.00
3242 3258 2.042800 GGTATCGGACCTGAGAGCC 58.957 63.158 0.58 0.00 45.89 4.70
3411 3427 3.604582 CTTGGAGAGAGACCCAATTGAC 58.395 50.000 7.12 0.00 41.16 3.18
3647 3663 3.755628 TAGACCGGCCACGTCTGC 61.756 66.667 25.73 0.00 38.78 4.26
3648 3664 2.181021 GTAGACCGGCCACGTCTG 59.819 66.667 25.73 0.00 38.78 3.51
3649 3665 3.437795 CGTAGACCGGCCACGTCT 61.438 66.667 22.41 22.41 38.78 4.18
3650 3666 2.768492 ATCGTAGACCGGCCACGTC 61.768 63.158 18.84 11.52 42.51 4.34
3651 3667 2.753043 ATCGTAGACCGGCCACGT 60.753 61.111 18.84 2.16 42.51 4.49
3663 3679 2.101575 GACGCGGAGTGCATCGTA 59.898 61.111 12.47 0.00 46.97 3.43
3707 3723 3.128764 CACTAGGAGCACAATCGTCAGTA 59.871 47.826 0.00 0.00 0.00 2.74
3804 3820 2.203280 TTCGTGTTGCCCTGGGTG 60.203 61.111 15.56 0.00 0.00 4.61
4146 4162 2.125512 CAGTCGTACAGGCTGCCC 60.126 66.667 16.57 4.00 46.47 5.36
4445 4479 8.421784 TGAGTGTCAGGATTTATGTATTACTCC 58.578 37.037 0.00 0.00 31.27 3.85
4446 4480 9.817809 TTGAGTGTCAGGATTTATGTATTACTC 57.182 33.333 0.00 0.00 0.00 2.59
4452 4486 8.768397 ACCTATTTGAGTGTCAGGATTTATGTA 58.232 33.333 0.00 0.00 0.00 2.29
4453 4487 7.633789 ACCTATTTGAGTGTCAGGATTTATGT 58.366 34.615 0.00 0.00 0.00 2.29
4456 4490 7.331026 CAGACCTATTTGAGTGTCAGGATTTA 58.669 38.462 0.00 0.00 31.35 1.40
4458 4492 5.738909 CAGACCTATTTGAGTGTCAGGATT 58.261 41.667 0.00 0.00 31.35 3.01
4459 4493 4.383552 GCAGACCTATTTGAGTGTCAGGAT 60.384 45.833 0.00 0.00 31.35 3.24
4460 4494 3.055819 GCAGACCTATTTGAGTGTCAGGA 60.056 47.826 0.00 0.00 31.35 3.86
4461 4495 3.055530 AGCAGACCTATTTGAGTGTCAGG 60.056 47.826 0.00 0.00 31.35 3.86
4483 4547 2.123769 GGGGCCTATGTGCATGCA 60.124 61.111 18.46 18.46 0.00 3.96
4484 4548 2.123769 TGGGGCCTATGTGCATGC 60.124 61.111 11.82 11.82 0.00 4.06
4485 4549 0.396139 AACTGGGGCCTATGTGCATG 60.396 55.000 0.84 0.00 0.00 4.06
4486 4550 1.221635 TAACTGGGGCCTATGTGCAT 58.778 50.000 0.84 0.00 0.00 3.96
4487 4551 1.221635 ATAACTGGGGCCTATGTGCA 58.778 50.000 0.84 0.00 0.00 4.57
4488 4552 2.372172 ACTATAACTGGGGCCTATGTGC 59.628 50.000 0.84 0.00 0.00 4.57
4489 4553 4.591498 TGTACTATAACTGGGGCCTATGTG 59.409 45.833 0.84 0.00 0.00 3.21
4504 4568 9.569167 GTGATATACGTACGTAGGTGTACTATA 57.431 37.037 29.65 16.84 42.00 1.31
4508 4572 6.420903 TCAGTGATATACGTACGTAGGTGTAC 59.579 42.308 29.65 22.59 41.01 2.90
4509 4573 6.420903 GTCAGTGATATACGTACGTAGGTGTA 59.579 42.308 29.65 24.03 33.77 2.90
4510 4574 5.235186 GTCAGTGATATACGTACGTAGGTGT 59.765 44.000 29.65 22.83 33.77 4.16
4513 4577 4.751600 TGGTCAGTGATATACGTACGTAGG 59.248 45.833 29.65 13.47 33.77 3.18
4516 4580 5.049612 CAGATGGTCAGTGATATACGTACGT 60.050 44.000 25.98 25.98 0.00 3.57
4517 4581 5.383130 CAGATGGTCAGTGATATACGTACG 58.617 45.833 15.01 15.01 0.00 3.67
4518 4582 5.154932 GCAGATGGTCAGTGATATACGTAC 58.845 45.833 0.00 0.00 0.00 3.67
4519 4583 4.217767 GGCAGATGGTCAGTGATATACGTA 59.782 45.833 0.00 0.00 0.00 3.57
4520 4584 3.005897 GGCAGATGGTCAGTGATATACGT 59.994 47.826 0.00 0.00 0.00 3.57
4521 4585 3.256879 AGGCAGATGGTCAGTGATATACG 59.743 47.826 0.00 0.00 0.00 3.06
4522 4586 4.564041 CAGGCAGATGGTCAGTGATATAC 58.436 47.826 0.00 0.00 0.00 1.47
4523 4587 3.007290 GCAGGCAGATGGTCAGTGATATA 59.993 47.826 0.00 0.00 0.00 0.86
4524 4588 2.224475 GCAGGCAGATGGTCAGTGATAT 60.224 50.000 0.00 0.00 0.00 1.63
4525 4589 1.139654 GCAGGCAGATGGTCAGTGATA 59.860 52.381 0.00 0.00 0.00 2.15
4526 4590 0.107312 GCAGGCAGATGGTCAGTGAT 60.107 55.000 0.00 0.00 0.00 3.06
4527 4591 1.196766 AGCAGGCAGATGGTCAGTGA 61.197 55.000 0.00 0.00 0.00 3.41
4528 4592 0.743701 GAGCAGGCAGATGGTCAGTG 60.744 60.000 9.35 0.00 45.03 3.66
4529 4593 1.601171 GAGCAGGCAGATGGTCAGT 59.399 57.895 9.35 0.00 45.03 3.41
4549 4613 0.179181 CACATTCTGCACGGACATGC 60.179 55.000 0.00 0.00 46.32 4.06
4550 4614 0.179181 GCACATTCTGCACGGACATG 60.179 55.000 0.00 0.00 46.29 3.21
4642 4706 4.329545 TTGTCCGTGGGCAGGAGC 62.330 66.667 0.00 0.00 38.65 4.70
4783 4847 3.144120 CTCGAGGACCTCCGCCATG 62.144 68.421 16.13 0.66 42.08 3.66
4861 4925 0.179137 TAACGTGGAGCAGCAGATCG 60.179 55.000 0.00 0.00 0.00 3.69
4922 4986 4.929479 ACAGTTGGTAAATAGGGAATGCA 58.071 39.130 0.00 0.00 0.00 3.96
4923 4987 5.914898 AACAGTTGGTAAATAGGGAATGC 57.085 39.130 0.00 0.00 0.00 3.56
4924 4988 7.703058 AGAAACAGTTGGTAAATAGGGAATG 57.297 36.000 0.00 0.00 0.00 2.67
4925 4989 7.728532 ACAAGAAACAGTTGGTAAATAGGGAAT 59.271 33.333 0.00 0.00 0.00 3.01
4929 4993 8.410141 TGAAACAAGAAACAGTTGGTAAATAGG 58.590 33.333 0.00 0.00 0.00 2.57
4930 4994 9.450807 CTGAAACAAGAAACAGTTGGTAAATAG 57.549 33.333 0.00 0.00 0.00 1.73
4932 4996 6.756542 GCTGAAACAAGAAACAGTTGGTAAAT 59.243 34.615 0.00 0.00 33.57 1.40
4937 5001 4.376340 AGCTGAAACAAGAAACAGTTGG 57.624 40.909 0.00 0.00 33.57 3.77
4956 5020 3.608316 TTCATGCCACCCAAAATTAGC 57.392 42.857 0.00 0.00 0.00 3.09
4964 5028 0.899717 GCCTCTTTTCATGCCACCCA 60.900 55.000 0.00 0.00 0.00 4.51
4967 5031 1.340889 TGTTGCCTCTTTTCATGCCAC 59.659 47.619 0.00 0.00 0.00 5.01
5048 5125 6.985653 TGAAAGTTAAACAATCCCAATCCA 57.014 33.333 0.00 0.00 0.00 3.41
5054 5131 8.764287 CAGTCAAATTGAAAGTTAAACAATCCC 58.236 33.333 0.00 0.00 33.90 3.85
5091 5379 2.967459 TGCATCGCTTGTACAAACAG 57.033 45.000 10.03 4.21 36.83 3.16
5118 5406 3.036819 CAGATGTTCCTCAGGGATCTCA 58.963 50.000 0.00 0.00 41.87 3.27
5119 5407 2.224257 GCAGATGTTCCTCAGGGATCTC 60.224 54.545 0.00 0.00 41.87 2.75
5123 5454 0.907486 CTGCAGATGTTCCTCAGGGA 59.093 55.000 8.42 0.00 40.36 4.20
5142 5473 2.541556 GGGTCGCTGACAGAACTTATC 58.458 52.381 6.65 0.00 33.68 1.75
5166 5499 3.754965 TCCCTGTTGATTGACTTCCTTG 58.245 45.455 0.00 0.00 0.00 3.61
5174 5507 7.292319 ACATGATTCATATCCCTGTTGATTGA 58.708 34.615 0.00 0.00 0.00 2.57
5175 5508 7.520451 ACATGATTCATATCCCTGTTGATTG 57.480 36.000 0.00 0.00 0.00 2.67
5176 5509 7.667219 GGTACATGATTCATATCCCTGTTGATT 59.333 37.037 0.00 0.00 31.75 2.57
5177 5510 7.170965 GGTACATGATTCATATCCCTGTTGAT 58.829 38.462 0.00 0.00 31.75 2.57
5178 5511 6.101005 TGGTACATGATTCATATCCCTGTTGA 59.899 38.462 0.00 0.00 31.75 3.18
5179 5512 6.298361 TGGTACATGATTCATATCCCTGTTG 58.702 40.000 0.00 0.00 31.75 3.33
5180 5513 6.514012 TGGTACATGATTCATATCCCTGTT 57.486 37.500 0.00 0.00 31.75 3.16
5193 5526 9.631257 TCAAATGATTGACTTATGGTACATGAT 57.369 29.630 0.00 0.00 41.56 2.45
5194 5527 9.460019 TTCAAATGATTGACTTATGGTACATGA 57.540 29.630 0.00 0.00 44.48 3.07
5197 5549 8.862325 AGTTCAAATGATTGACTTATGGTACA 57.138 30.769 0.00 0.00 45.01 2.90
5210 5562 6.974622 GCATGGTTATTCGAGTTCAAATGATT 59.025 34.615 0.00 0.00 0.00 2.57
5223 5575 2.009051 TGTCTGCAGCATGGTTATTCG 58.991 47.619 9.47 0.00 35.86 3.34
5231 5583 3.011818 TGATTACCTTGTCTGCAGCATG 58.988 45.455 9.47 12.11 40.87 4.06
5237 5589 6.317140 TGAATCTGATTGATTACCTTGTCTGC 59.683 38.462 7.78 0.00 44.70 4.26
5358 5710 2.292103 TTGCAGTTTGCTTTGGTCAC 57.708 45.000 2.48 0.00 45.31 3.67
5425 5777 8.926715 ACTTTTGTTCAAATTTTCTACAGACC 57.073 30.769 0.00 0.00 0.00 3.85
5467 5819 7.919690 TGCACATCAAAAGCTACTTATATGAC 58.080 34.615 0.00 0.00 0.00 3.06
5592 5956 3.551454 CCAGAGCAGTTGAATGTGTTTGG 60.551 47.826 0.00 0.00 0.00 3.28
5599 5963 4.458295 AGAAATGACCAGAGCAGTTGAATG 59.542 41.667 0.00 0.00 0.00 2.67
5603 5967 4.318332 TGTAGAAATGACCAGAGCAGTTG 58.682 43.478 0.00 0.00 0.00 3.16
5828 6196 5.784177 TCTCCAGTTGTAGCTTTACTGAAG 58.216 41.667 18.63 11.44 41.33 3.02
5875 6252 4.020662 GCAAAGAGGGAGAAAGAGAGAGAA 60.021 45.833 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.