Multiple sequence alignment - TraesCS6B01G190900

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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 TraesCS6B01G190900 chr6B 100.000 5535 0 0 1 5535 224252616 224258150 0.000000e+00 10222.0
1 TraesCS6B01G190900 chr6D 96.522 4831 123 14 104 4922 125985772 125990569 0.000000e+00 7949.0
2 TraesCS6B01G190900 chr6D 87.671 584 47 8 4955 5535 125990569 125991130 0.000000e+00 656.0
3 TraesCS6B01G190900 chr6D 97.546 163 3 1 1 162 125985612 125985774 1.520000e-70 278.0
4 TraesCS6B01G190900 chr6D 85.965 228 26 1 2764 2991 291716154 291715933 7.170000e-59 239.0
5 TraesCS6B01G190900 chr6A 93.113 3572 162 27 1978 5535 154040766 154037265 0.000000e+00 5156.0
6 TraesCS6B01G190900 chr6A 96.673 1052 33 2 929 1979 154041900 154040850 0.000000e+00 1748.0
7 TraesCS6B01G190900 chr6A 93.531 943 42 10 1 937 154042881 154041952 0.000000e+00 1386.0
8 TraesCS6B01G190900 chr1D 90.244 492 37 3 3490 3974 249618523 249619010 2.810000e-177 632.0
9 TraesCS6B01G190900 chr3A 87.755 490 51 4 3490 3974 434451098 434450613 1.040000e-156 564.0
10 TraesCS6B01G190900 chr7D 89.520 229 24 0 2763 2991 451621763 451621535 1.950000e-74 291.0
11 TraesCS6B01G190900 chr7D 84.649 228 29 1 2764 2991 23078052 23077831 7.220000e-54 222.0
12 TraesCS6B01G190900 chr1A 91.905 210 13 1 3768 3973 548308447 548308238 1.950000e-74 291.0
13 TraesCS6B01G190900 chr1A 87.879 231 28 0 2761 2991 466042077 466042307 7.070000e-69 272.0
14 TraesCS6B01G190900 chrUn 85.281 231 28 1 2761 2991 96527184 96527408 3.330000e-57 233.0
15 TraesCS6B01G190900 chr5D 85.281 231 28 1 2761 2991 178477709 178477933 3.330000e-57 233.0
16 TraesCS6B01G190900 chr4D 84.255 235 27 2 2761 2991 215190198 215190426 2.600000e-53 220.0
17 TraesCS6B01G190900 chr5A 78.547 289 55 7 4250 4535 36932641 36932925 3.410000e-42 183.0
18 TraesCS6B01G190900 chr2D 100.000 40 0 0 4885 4924 318561209 318561170 2.140000e-09 75.0
19 TraesCS6B01G190900 chr4A 97.143 35 1 0 4896 4930 429242589 429242555 5.990000e-05 60.2
20 TraesCS6B01G190900 chr2A 94.737 38 2 0 4888 4925 7528438 7528401 5.990000e-05 60.2


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 TraesCS6B01G190900 chr6B 224252616 224258150 5534 False 10222.000000 10222 100.000 1 5535 1 chr6B.!!$F1 5534
1 TraesCS6B01G190900 chr6D 125985612 125991130 5518 False 2961.000000 7949 93.913 1 5535 3 chr6D.!!$F1 5534
2 TraesCS6B01G190900 chr6A 154037265 154042881 5616 True 2763.333333 5156 94.439 1 5535 3 chr6A.!!$R1 5534

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
709 770 3.118592 GGCTGAAGTGGATAGTAGCACTT 60.119 47.826 0.0 0.0 40.16 3.16 F
2058 2268 1.526575 CCCTCTTTGCGGTGCATTGT 61.527 55.000 0.0 0.0 38.76 2.71 F
2797 3021 0.321034 ATGCAGCTTCAGAGTTCGCA 60.321 50.000 0.0 0.0 0.00 5.10 F
3993 4221 2.825086 ACGAGGTTCGCATAAATTGC 57.175 45.000 0.0 0.0 45.12 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 2427 0.445436 GGTTCTCAGCATGCAAGTCG 59.555 55.0 21.98 7.95 34.76 4.18 R
3993 4221 1.063806 CTTCAGCACTTTCGGTCTCG 58.936 55.0 0.00 0.00 37.82 4.04 R
4077 4308 0.603065 GAGAACCCGGCTGCATTTTT 59.397 50.0 0.50 0.00 0.00 1.94 R
5124 5392 0.108138 CCCGTCTAAGCCACCTCTTG 60.108 60.0 0.00 0.00 0.00 3.02 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
276 337 3.610040 TCAGTGTGAGCCGACAATATT 57.390 42.857 0.00 0.00 0.00 1.28
389 450 3.325870 TCTGCACCAATGAGACGTAAAG 58.674 45.455 0.00 0.00 0.00 1.85
709 770 3.118592 GGCTGAAGTGGATAGTAGCACTT 60.119 47.826 0.00 0.00 40.16 3.16
979 1103 5.935206 CCTTCTGCATATAGAGTCGAGTAGA 59.065 44.000 0.00 0.00 0.00 2.59
1104 1228 2.571757 CTACTGCCGTCGCTTGGA 59.428 61.111 0.00 0.00 35.36 3.53
1521 1645 4.621034 GCACCTGGTTCATAATTTGTTTCG 59.379 41.667 0.00 0.00 0.00 3.46
2058 2268 1.526575 CCCTCTTTGCGGTGCATTGT 61.527 55.000 0.00 0.00 38.76 2.71
2150 2360 5.364735 TGATGCCTACATTCAGATCAGAGAA 59.635 40.000 0.00 0.00 36.35 2.87
2217 2427 1.470098 CTGACAACAACAGGCTATGGC 59.530 52.381 0.00 0.00 37.82 4.40
2408 2632 9.494271 TCAATGTAGCTATTCATGTCCTTATTC 57.506 33.333 0.00 0.00 0.00 1.75
2409 2633 9.276590 CAATGTAGCTATTCATGTCCTTATTCA 57.723 33.333 0.00 0.00 0.00 2.57
2410 2634 8.839310 ATGTAGCTATTCATGTCCTTATTCAC 57.161 34.615 0.00 0.00 0.00 3.18
2413 2637 4.762251 GCTATTCATGTCCTTATTCACCCC 59.238 45.833 0.00 0.00 0.00 4.95
2414 2638 3.662759 TTCATGTCCTTATTCACCCCC 57.337 47.619 0.00 0.00 0.00 5.40
2535 2759 5.695816 CGACATGGTTGGAAAATGAAATGTT 59.304 36.000 0.00 0.00 0.00 2.71
2595 2819 0.821301 TCTTGCATGGACGCCACAAA 60.821 50.000 0.50 0.00 35.80 2.83
2797 3021 0.321034 ATGCAGCTTCAGAGTTCGCA 60.321 50.000 0.00 0.00 0.00 5.10
3018 3242 9.060347 CATTGCAGAACTGGTAATATAGTCAAT 57.940 33.333 3.99 0.00 0.00 2.57
3481 3706 4.799678 CTCTATGTAACATACCTCAGCCG 58.200 47.826 0.00 0.00 0.00 5.52
3570 3795 5.336213 CCATTCAAAATCACAGGGAAGACAG 60.336 44.000 0.00 0.00 0.00 3.51
3699 3927 4.948341 TGTACAGAAACTGAAGCTACCA 57.052 40.909 5.76 0.00 35.18 3.25
3707 3935 7.080724 CAGAAACTGAAGCTACCAGAAAATTC 58.919 38.462 19.27 15.84 35.69 2.17
3929 4157 3.325870 TCCATAACAAGTCGAACTGCAG 58.674 45.455 13.48 13.48 0.00 4.41
3952 4180 7.714377 GCAGGTATAGATTATCAGATGGAATGG 59.286 40.741 0.00 0.00 0.00 3.16
3993 4221 2.825086 ACGAGGTTCGCATAAATTGC 57.175 45.000 0.00 0.00 45.12 3.56
4005 4236 3.181510 GCATAAATTGCGAGACCGAAAGT 60.182 43.478 0.00 0.00 42.54 2.66
4025 4256 7.201393 CGAAAGTGCTGAAGAGTTCTGTATTAG 60.201 40.741 0.00 0.00 0.00 1.73
4077 4308 5.356882 GCAGTCAGCAAACAATACTTACA 57.643 39.130 0.00 0.00 44.79 2.41
4130 4361 4.780815 TCCGAAAACATATCAAGGAGCAT 58.219 39.130 0.00 0.00 0.00 3.79
4159 4390 8.696043 TCAAGATTATAGTGGCATAAAAGCAT 57.304 30.769 0.00 0.00 35.83 3.79
4254 4485 2.743928 CTGCCTGGTTCGCTGGAC 60.744 66.667 0.00 0.00 0.00 4.02
4283 4514 8.082242 ACTTATCAAAATTGGCAGTAAGTGAAC 58.918 33.333 0.00 0.00 31.76 3.18
4285 4516 6.214191 TCAAAATTGGCAGTAAGTGAACAA 57.786 33.333 0.00 0.00 0.00 2.83
4297 4528 8.073768 GCAGTAAGTGAACAAGTTTTTAGCATA 58.926 33.333 0.00 0.00 0.00 3.14
4322 4553 7.634671 TGACTCATTTTGATTCATGCTGTAT 57.365 32.000 0.00 0.00 32.21 2.29
4323 4554 8.735692 TGACTCATTTTGATTCATGCTGTATA 57.264 30.769 0.00 0.00 32.21 1.47
4324 4555 8.833493 TGACTCATTTTGATTCATGCTGTATAG 58.167 33.333 0.00 0.00 32.21 1.31
4426 4660 7.592885 AATATTTCTTTGCTATGCAGGACAT 57.407 32.000 0.00 0.00 40.61 3.06
4601 4835 8.748412 ACTCATAGAGATATAAGTGCTCCATTC 58.252 37.037 0.31 0.00 33.32 2.67
4602 4836 8.891985 TCATAGAGATATAAGTGCTCCATTCT 57.108 34.615 0.00 0.00 0.00 2.40
4603 4837 9.981460 TCATAGAGATATAAGTGCTCCATTCTA 57.019 33.333 0.00 0.00 0.00 2.10
4605 4839 7.169158 AGAGATATAAGTGCTCCATTCTAGC 57.831 40.000 0.00 0.00 40.50 3.42
4652 4886 4.600692 TTCCGACTGAAGATGTGAAGAA 57.399 40.909 0.00 0.00 0.00 2.52
4730 4964 9.613428 TTAAATGCTTCACTGTACAATATAGCT 57.387 29.630 16.06 0.00 0.00 3.32
4735 4969 5.276461 TCACTGTACAATATAGCTGGTGG 57.724 43.478 0.00 0.00 0.00 4.61
4739 4973 5.188948 ACTGTACAATATAGCTGGTGGACAA 59.811 40.000 0.00 0.00 34.48 3.18
4756 4990 3.375299 GGACAAAGTCATGTATGCCTGTC 59.625 47.826 0.00 0.31 33.68 3.51
4779 5013 4.321230 CGGCAAAAGCATTTCTTAGTTCCT 60.321 41.667 0.00 0.00 37.28 3.36
4800 5034 8.520351 GTTCCTTTTATAGCAGGTTATGTGTTT 58.480 33.333 0.00 0.00 0.00 2.83
4872 5106 4.162812 TGTTTGTTTTGACTGCTTCGAAC 58.837 39.130 0.00 0.00 0.00 3.95
4924 5158 2.776312 CATCACAATGATGCAGAGGC 57.224 50.000 5.90 0.00 46.37 4.70
4925 5159 1.337071 CATCACAATGATGCAGAGGCC 59.663 52.381 5.90 0.00 46.37 5.19
4926 5160 0.328926 TCACAATGATGCAGAGGCCA 59.671 50.000 5.01 0.00 40.13 5.36
4927 5161 0.738975 CACAATGATGCAGAGGCCAG 59.261 55.000 5.01 0.00 40.13 4.85
4928 5162 0.395311 ACAATGATGCAGAGGCCAGG 60.395 55.000 5.01 0.00 40.13 4.45
4929 5163 1.107538 CAATGATGCAGAGGCCAGGG 61.108 60.000 5.01 0.00 40.13 4.45
4930 5164 1.578215 AATGATGCAGAGGCCAGGGT 61.578 55.000 5.01 0.00 40.13 4.34
4931 5165 1.578215 ATGATGCAGAGGCCAGGGTT 61.578 55.000 5.01 0.00 40.13 4.11
4932 5166 0.913934 TGATGCAGAGGCCAGGGTTA 60.914 55.000 5.01 0.00 40.13 2.85
4933 5167 0.255890 GATGCAGAGGCCAGGGTTAA 59.744 55.000 5.01 0.00 40.13 2.01
4934 5168 0.704076 ATGCAGAGGCCAGGGTTAAA 59.296 50.000 5.01 0.00 40.13 1.52
4935 5169 0.251165 TGCAGAGGCCAGGGTTAAAC 60.251 55.000 5.01 0.00 40.13 2.01
4936 5170 0.965866 GCAGAGGCCAGGGTTAAACC 60.966 60.000 5.01 0.00 37.60 3.27
4937 5171 0.404040 CAGAGGCCAGGGTTAAACCA 59.596 55.000 13.24 0.00 41.02 3.67
4938 5172 1.005924 CAGAGGCCAGGGTTAAACCAT 59.994 52.381 13.24 0.00 41.02 3.55
4939 5173 1.716503 AGAGGCCAGGGTTAAACCATT 59.283 47.619 13.24 0.00 41.02 3.16
4940 5174 2.111792 AGAGGCCAGGGTTAAACCATTT 59.888 45.455 13.24 0.00 41.02 2.32
4941 5175 2.903784 GAGGCCAGGGTTAAACCATTTT 59.096 45.455 13.24 0.00 41.02 1.82
4942 5176 2.903784 AGGCCAGGGTTAAACCATTTTC 59.096 45.455 13.24 0.00 41.02 2.29
4943 5177 2.353307 GGCCAGGGTTAAACCATTTTCG 60.353 50.000 13.24 0.00 41.02 3.46
4944 5178 2.353307 GCCAGGGTTAAACCATTTTCGG 60.353 50.000 13.24 3.22 41.02 4.30
4945 5179 3.158676 CCAGGGTTAAACCATTTTCGGA 58.841 45.455 13.24 0.00 41.02 4.55
4946 5180 3.574826 CCAGGGTTAAACCATTTTCGGAA 59.425 43.478 13.24 0.00 41.02 4.30
4947 5181 4.039366 CCAGGGTTAAACCATTTTCGGAAA 59.961 41.667 13.24 0.00 41.02 3.13
4948 5182 5.453480 CCAGGGTTAAACCATTTTCGGAAAA 60.453 40.000 17.39 17.39 41.02 2.29
4949 5183 6.049790 CAGGGTTAAACCATTTTCGGAAAAA 58.950 36.000 18.78 4.26 41.02 1.94
4950 5184 6.708502 CAGGGTTAAACCATTTTCGGAAAAAT 59.291 34.615 18.78 6.16 44.12 1.82
4964 5231 3.068873 CGGAAAAATGTCAACCCCTTCAA 59.931 43.478 0.00 0.00 0.00 2.69
4984 5251 0.040067 CCGCTTCAACTGCAAACTCC 60.040 55.000 0.00 0.00 0.00 3.85
4992 5259 0.655733 ACTGCAAACTCCGAAACACG 59.344 50.000 0.00 0.00 42.18 4.49
4994 5261 1.531149 CTGCAAACTCCGAAACACGAT 59.469 47.619 0.00 0.00 45.77 3.73
5007 5274 2.851263 ACACGATGGCCTTACAAAGA 57.149 45.000 3.32 0.00 0.00 2.52
5054 5322 5.303333 GGATAAAAGAACAACCTGTTTGGGA 59.697 40.000 0.00 0.00 41.28 4.37
5094 5362 4.326826 TGTTCGATCAGGCTGAAGAAATT 58.673 39.130 28.32 12.01 32.07 1.82
5113 5381 9.807921 AAGAAATTAGAACCTTTATCCTTCACA 57.192 29.630 0.00 0.00 0.00 3.58
5114 5382 9.807921 AGAAATTAGAACCTTTATCCTTCACAA 57.192 29.630 0.00 0.00 0.00 3.33
5116 5384 9.807921 AAATTAGAACCTTTATCCTTCACAAGA 57.192 29.630 0.00 0.00 0.00 3.02
5117 5385 9.981460 AATTAGAACCTTTATCCTTCACAAGAT 57.019 29.630 0.00 0.00 0.00 2.40
5118 5386 9.620259 ATTAGAACCTTTATCCTTCACAAGATC 57.380 33.333 0.00 0.00 0.00 2.75
5119 5387 6.418946 AGAACCTTTATCCTTCACAAGATCC 58.581 40.000 0.00 0.00 0.00 3.36
5120 5388 6.216456 AGAACCTTTATCCTTCACAAGATCCT 59.784 38.462 0.00 0.00 0.00 3.24
5121 5389 6.394345 ACCTTTATCCTTCACAAGATCCTT 57.606 37.500 0.00 0.00 0.00 3.36
5122 5390 6.418946 ACCTTTATCCTTCACAAGATCCTTC 58.581 40.000 0.00 0.00 0.00 3.46
5123 5391 6.012508 ACCTTTATCCTTCACAAGATCCTTCA 60.013 38.462 0.00 0.00 0.00 3.02
5124 5392 6.317391 CCTTTATCCTTCACAAGATCCTTCAC 59.683 42.308 0.00 0.00 0.00 3.18
5125 5393 4.916041 ATCCTTCACAAGATCCTTCACA 57.084 40.909 0.00 0.00 0.00 3.58
5130 5398 4.277515 TCACAAGATCCTTCACAAGAGG 57.722 45.455 0.00 0.00 0.00 3.69
5153 5421 3.637229 TGGCTTAGACGGGAGATTAAGAG 59.363 47.826 0.00 0.00 34.01 2.85
5154 5422 3.890147 GGCTTAGACGGGAGATTAAGAGA 59.110 47.826 0.00 0.00 34.01 3.10
5158 5426 6.817140 GCTTAGACGGGAGATTAAGAGAAAAA 59.183 38.462 0.00 0.00 34.01 1.94
5207 5476 1.399791 CTTCTTGGCCTTTGCTCGATC 59.600 52.381 3.32 0.00 37.74 3.69
5229 5498 5.073428 TCGAGAGATGTATGGCTAGACAAT 58.927 41.667 0.13 0.00 30.87 2.71
5262 5531 1.133668 CCTGGCTTAATCTTGGGGAGG 60.134 57.143 0.00 0.00 0.00 4.30
5288 5557 6.538742 CGAACACCTCCTATTTTCACATACAT 59.461 38.462 0.00 0.00 0.00 2.29
5298 5567 0.620030 TCACATACATGCCAGCCACT 59.380 50.000 0.00 0.00 0.00 4.00
5299 5568 0.736636 CACATACATGCCAGCCACTG 59.263 55.000 0.00 0.00 0.00 3.66
5311 5580 1.005215 CAGCCACTGGAGGAGGAAAAT 59.995 52.381 0.00 0.00 0.00 1.82
5320 5589 5.014544 ACTGGAGGAGGAAAATCTTCATCAA 59.985 40.000 6.50 0.00 42.82 2.57
5336 5605 7.397221 TCTTCATCAATCAGCTTAAGGAGAAA 58.603 34.615 4.29 0.00 0.00 2.52
5342 5611 5.606348 ATCAGCTTAAGGAGAAAGATCGT 57.394 39.130 4.29 0.00 0.00 3.73
5353 5622 4.735822 GGAGAAAGATCGTATCGTGACAAG 59.264 45.833 0.00 0.00 0.00 3.16
5373 5642 4.590850 AGTCACAAAAATTTGGAGGAGC 57.409 40.909 10.38 0.00 42.34 4.70
5405 5674 2.100989 ACTTCGGTAAGAGAATCGGCT 58.899 47.619 0.00 0.00 42.67 5.52
5409 5678 1.405821 CGGTAAGAGAATCGGCTGACT 59.594 52.381 0.00 0.00 42.67 3.41
5410 5679 2.796383 CGGTAAGAGAATCGGCTGACTG 60.796 54.545 0.00 0.00 42.67 3.51
5478 5747 0.105593 TGATCTCAGCGGCCTTGATC 59.894 55.000 15.23 15.23 35.44 2.92
5482 5751 1.382557 TCAGCGGCCTTGATCCCTA 60.383 57.895 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.545965 ACTTCTTGGTACACTTATTGATCTTCG 59.454 37.037 0.00 0.00 39.29 3.79
276 337 3.804036 CCTACCATTTACTGCCATCGAA 58.196 45.455 0.00 0.00 0.00 3.71
389 450 4.065789 CTGGTGGTTCAAGTAAGACTTCC 58.934 47.826 0.00 0.00 36.03 3.46
832 896 7.571025 TCCTGTTTTATACCCTATGAGGAAAC 58.429 38.462 0.00 0.00 37.67 2.78
979 1103 4.605640 TGCTTGCCTTTGCTATTCTTTT 57.394 36.364 0.00 0.00 38.71 2.27
1077 1201 2.501128 GGCAGTAGCTCGATGGCA 59.499 61.111 12.59 0.00 41.70 4.92
1104 1228 2.969821 TGGAGTGGTTTATGGTTGCT 57.030 45.000 0.00 0.00 0.00 3.91
1521 1645 6.451064 CTCCAAATGTGGGGTTATTAAGAC 57.549 41.667 0.86 0.00 46.01 3.01
2058 2268 3.402110 CATATAGTTGAAGCATCCCGCA 58.598 45.455 0.00 0.00 46.13 5.69
2150 2360 7.242359 AGCAGTAACATATCTAGTCCATAGGT 58.758 38.462 0.00 0.00 31.83 3.08
2217 2427 0.445436 GGTTCTCAGCATGCAAGTCG 59.555 55.000 21.98 7.95 34.76 4.18
2363 2573 6.148480 ACATTGAATGCTCTGTGAGTAAGTTC 59.852 38.462 4.84 0.00 31.39 3.01
2535 2759 2.038863 TTTCTGAGTGGCTAGGGGAA 57.961 50.000 0.00 0.00 0.00 3.97
2595 2819 4.436079 AGGGGATACAAGAACTTGGTACT 58.564 43.478 17.05 5.47 44.45 2.73
2797 3021 1.002868 AGGCAGCTGATTTCGTGCT 60.003 52.632 20.43 0.00 36.15 4.40
3481 3706 1.871039 TCAGCTGTGCGGAAAGTAAAC 59.129 47.619 14.67 0.00 28.67 2.01
3531 3756 3.713003 TGAATGGCCTCTCTGAGTCTTA 58.287 45.455 3.32 0.00 0.00 2.10
3707 3935 1.949525 CTGGTTGGTTCACTTCAGGTG 59.050 52.381 0.00 0.00 46.60 4.00
3766 3994 1.464734 AGCATCCGTTCTTCTCGAGA 58.535 50.000 12.08 12.08 0.00 4.04
3900 4128 4.755411 TCGACTTGTTATGGATGTCTTCC 58.245 43.478 0.00 0.00 45.69 3.46
3929 4157 7.989741 CCACCATTCCATCTGATAATCTATACC 59.010 40.741 0.00 0.00 0.00 2.73
3952 4180 4.543590 TGAGATCCTCTTCTTTGTCCAC 57.456 45.455 0.00 0.00 0.00 4.02
3993 4221 1.063806 CTTCAGCACTTTCGGTCTCG 58.936 55.000 0.00 0.00 37.82 4.04
4000 4228 6.793492 AATACAGAACTCTTCAGCACTTTC 57.207 37.500 0.00 0.00 0.00 2.62
4025 4256 5.726963 GCGGTCTTGTCTTCGGATTTTATTC 60.727 44.000 0.00 0.00 0.00 1.75
4077 4308 0.603065 GAGAACCCGGCTGCATTTTT 59.397 50.000 0.50 0.00 0.00 1.94
4254 4485 7.271223 CACTTACTGCCAATTTTGATAAGTTCG 59.729 37.037 0.00 0.00 30.88 3.95
4322 4553 4.770531 TGGTCTCTGCTAAACACTAAGCTA 59.229 41.667 0.00 0.00 39.53 3.32
4323 4554 3.578716 TGGTCTCTGCTAAACACTAAGCT 59.421 43.478 0.00 0.00 39.53 3.74
4324 4555 3.926616 TGGTCTCTGCTAAACACTAAGC 58.073 45.455 0.00 0.00 39.25 3.09
4325 4556 5.392767 TCTGGTCTCTGCTAAACACTAAG 57.607 43.478 0.00 0.00 0.00 2.18
4326 4557 7.661536 ATATCTGGTCTCTGCTAAACACTAA 57.338 36.000 0.00 0.00 0.00 2.24
4327 4558 7.778382 TGTATATCTGGTCTCTGCTAAACACTA 59.222 37.037 0.00 0.00 0.00 2.74
4328 4559 6.607600 TGTATATCTGGTCTCTGCTAAACACT 59.392 38.462 0.00 0.00 0.00 3.55
4329 4560 6.697892 GTGTATATCTGGTCTCTGCTAAACAC 59.302 42.308 0.00 0.00 0.00 3.32
4330 4561 6.183360 GGTGTATATCTGGTCTCTGCTAAACA 60.183 42.308 0.00 0.00 0.00 2.83
4331 4562 6.217294 GGTGTATATCTGGTCTCTGCTAAAC 58.783 44.000 0.00 0.00 0.00 2.01
4332 4563 5.009710 CGGTGTATATCTGGTCTCTGCTAAA 59.990 44.000 0.00 0.00 0.00 1.85
4333 4564 4.519350 CGGTGTATATCTGGTCTCTGCTAA 59.481 45.833 0.00 0.00 0.00 3.09
4334 4565 4.072839 CGGTGTATATCTGGTCTCTGCTA 58.927 47.826 0.00 0.00 0.00 3.49
4335 4566 2.887783 CGGTGTATATCTGGTCTCTGCT 59.112 50.000 0.00 0.00 0.00 4.24
4412 4646 4.199310 GGAAACTTATGTCCTGCATAGCA 58.801 43.478 0.00 0.00 40.74 3.49
4426 4660 5.183228 GTCGGATGGAAATCTGGAAACTTA 58.817 41.667 0.00 0.00 0.00 2.24
4601 4835 3.871006 TGTGCATCCATTACTTTCGCTAG 59.129 43.478 0.00 0.00 0.00 3.42
4602 4836 3.867857 TGTGCATCCATTACTTTCGCTA 58.132 40.909 0.00 0.00 0.00 4.26
4603 4837 2.710377 TGTGCATCCATTACTTTCGCT 58.290 42.857 0.00 0.00 0.00 4.93
4604 4838 3.065233 TCATGTGCATCCATTACTTTCGC 59.935 43.478 0.00 0.00 0.00 4.70
4605 4839 4.591202 GTCATGTGCATCCATTACTTTCG 58.409 43.478 0.00 0.00 0.00 3.46
4652 4886 8.463930 TTGTAAGAATGTCAAAATGTCCTTCT 57.536 30.769 0.00 0.00 0.00 2.85
4730 4964 3.081061 GCATACATGACTTTGTCCACCA 58.919 45.455 0.00 0.00 0.00 4.17
4735 4969 3.062639 CGACAGGCATACATGACTTTGTC 59.937 47.826 0.00 7.17 45.98 3.18
4739 4973 2.315925 CCGACAGGCATACATGACTT 57.684 50.000 0.00 0.00 45.98 3.01
4756 4990 3.920412 GGAACTAAGAAATGCTTTTGCCG 59.080 43.478 1.76 0.00 46.87 5.69
4779 5013 8.630054 ACTCAAACACATAACCTGCTATAAAA 57.370 30.769 0.00 0.00 0.00 1.52
4800 5034 7.068962 TCGGTAATAAGATTACCACATGACTCA 59.931 37.037 22.20 0.00 43.48 3.41
4921 5155 2.713828 AAATGGTTTAACCCTGGCCT 57.286 45.000 12.02 0.00 37.50 5.19
4922 5156 2.353307 CGAAAATGGTTTAACCCTGGCC 60.353 50.000 12.02 0.00 37.50 5.36
4923 5157 2.353307 CCGAAAATGGTTTAACCCTGGC 60.353 50.000 12.02 0.00 37.50 4.85
4924 5158 3.158676 TCCGAAAATGGTTTAACCCTGG 58.841 45.455 12.02 4.64 37.50 4.45
4925 5159 4.857509 TTCCGAAAATGGTTTAACCCTG 57.142 40.909 12.02 0.00 37.50 4.45
4926 5160 5.873146 TTTTCCGAAAATGGTTTAACCCT 57.127 34.783 12.02 0.00 37.50 4.34
4937 5171 4.346709 AGGGGTTGACATTTTTCCGAAAAT 59.653 37.500 7.12 0.00 44.24 1.82
4938 5172 3.707102 AGGGGTTGACATTTTTCCGAAAA 59.293 39.130 2.01 2.01 38.96 2.29
4939 5173 3.301274 AGGGGTTGACATTTTTCCGAAA 58.699 40.909 0.00 0.00 0.00 3.46
4940 5174 2.952116 AGGGGTTGACATTTTTCCGAA 58.048 42.857 0.00 0.00 0.00 4.30
4941 5175 2.668144 AGGGGTTGACATTTTTCCGA 57.332 45.000 0.00 0.00 0.00 4.55
4942 5176 2.625790 TGAAGGGGTTGACATTTTTCCG 59.374 45.455 0.00 0.00 0.00 4.30
4943 5177 4.377021 GTTGAAGGGGTTGACATTTTTCC 58.623 43.478 0.00 0.00 0.00 3.13
4944 5178 4.377021 GGTTGAAGGGGTTGACATTTTTC 58.623 43.478 0.00 0.00 0.00 2.29
4945 5179 3.181470 CGGTTGAAGGGGTTGACATTTTT 60.181 43.478 0.00 0.00 0.00 1.94
4946 5180 2.364002 CGGTTGAAGGGGTTGACATTTT 59.636 45.455 0.00 0.00 0.00 1.82
4947 5181 1.960689 CGGTTGAAGGGGTTGACATTT 59.039 47.619 0.00 0.00 0.00 2.32
4948 5182 1.616159 CGGTTGAAGGGGTTGACATT 58.384 50.000 0.00 0.00 0.00 2.71
4949 5183 0.893727 GCGGTTGAAGGGGTTGACAT 60.894 55.000 0.00 0.00 0.00 3.06
4950 5184 1.527380 GCGGTTGAAGGGGTTGACA 60.527 57.895 0.00 0.00 0.00 3.58
4951 5185 0.822121 AAGCGGTTGAAGGGGTTGAC 60.822 55.000 0.00 0.00 0.00 3.18
4952 5186 0.536460 GAAGCGGTTGAAGGGGTTGA 60.536 55.000 3.70 0.00 0.00 3.18
4953 5187 0.821711 TGAAGCGGTTGAAGGGGTTG 60.822 55.000 3.70 0.00 0.00 3.77
4964 5231 0.663153 GAGTTTGCAGTTGAAGCGGT 59.337 50.000 0.00 0.00 33.85 5.68
4984 5251 1.434555 TGTAAGGCCATCGTGTTTCG 58.565 50.000 5.01 0.00 41.41 3.46
4992 5259 3.891049 ACTCCATCTTTGTAAGGCCATC 58.109 45.455 5.01 0.00 0.00 3.51
4994 5261 3.686016 GAACTCCATCTTTGTAAGGCCA 58.314 45.455 5.01 0.00 0.00 5.36
5007 5274 2.303022 TCCAAAGCTCTTCGAACTCCAT 59.697 45.455 0.00 0.00 0.00 3.41
5054 5322 7.209471 TCGAACAGGCTAATAATTGTTTTGT 57.791 32.000 0.00 0.00 34.18 2.83
5094 5362 7.403231 AGGATCTTGTGAAGGATAAAGGTTCTA 59.597 37.037 0.00 0.00 0.00 2.10
5122 5390 1.673033 CCGTCTAAGCCACCTCTTGTG 60.673 57.143 0.00 0.00 45.01 3.33
5123 5391 0.608640 CCGTCTAAGCCACCTCTTGT 59.391 55.000 0.00 0.00 0.00 3.16
5124 5392 0.108138 CCCGTCTAAGCCACCTCTTG 60.108 60.000 0.00 0.00 0.00 3.02
5125 5393 0.252103 TCCCGTCTAAGCCACCTCTT 60.252 55.000 0.00 0.00 0.00 2.85
5130 5398 3.383825 TCTTAATCTCCCGTCTAAGCCAC 59.616 47.826 0.00 0.00 0.00 5.01
5159 5427 5.491323 TTTTGTGGGGTGAAGAAGTTTTT 57.509 34.783 0.00 0.00 0.00 1.94
5160 5428 5.491323 TTTTTGTGGGGTGAAGAAGTTTT 57.509 34.783 0.00 0.00 0.00 2.43
5195 5464 2.223688 ACATCTCTCGATCGAGCAAAGG 60.224 50.000 34.92 25.30 41.71 3.11
5207 5476 4.837896 TTGTCTAGCCATACATCTCTCG 57.162 45.455 0.00 0.00 0.00 4.04
5262 5531 3.071479 TGTGAAAATAGGAGGTGTTCGC 58.929 45.455 0.00 0.00 0.00 4.70
5298 5567 5.519183 TTGATGAAGATTTTCCTCCTCCA 57.481 39.130 0.00 0.00 32.09 3.86
5299 5568 6.125029 TGATTGATGAAGATTTTCCTCCTCC 58.875 40.000 0.00 0.00 32.09 4.30
5300 5569 6.238703 GCTGATTGATGAAGATTTTCCTCCTC 60.239 42.308 0.00 0.00 32.09 3.71
5311 5580 6.550938 TCTCCTTAAGCTGATTGATGAAGA 57.449 37.500 0.00 0.00 0.00 2.87
5320 5589 5.606348 ACGATCTTTCTCCTTAAGCTGAT 57.394 39.130 0.00 0.00 0.00 2.90
5336 5605 3.439129 TGTGACTTGTCACGATACGATCT 59.561 43.478 23.37 0.00 43.12 2.75
5342 5611 6.915300 CCAAATTTTTGTGACTTGTCACGATA 59.085 34.615 23.37 16.32 43.12 2.92
5353 5622 4.550422 GAGCTCCTCCAAATTTTTGTGAC 58.450 43.478 0.87 0.00 36.45 3.67
5373 5642 6.927381 TCTCTTACCGAAGTGTTTAAAAGGAG 59.073 38.462 0.00 0.00 34.03 3.69
5405 5674 7.503566 TCTGTCATGTGATCTGTATATCAGTCA 59.496 37.037 0.00 0.00 43.97 3.41
5409 5678 6.779539 AGGTCTGTCATGTGATCTGTATATCA 59.220 38.462 0.00 0.00 33.48 2.15
5410 5679 7.225784 AGGTCTGTCATGTGATCTGTATATC 57.774 40.000 0.00 0.00 0.00 1.63
5429 5698 1.713078 AGGCCAAGGAAATCAAGGTCT 59.287 47.619 5.01 0.00 0.00 3.85
5478 5747 1.448365 GGCCGTAACACCGTTAGGG 60.448 63.158 17.26 17.26 43.47 3.53
5482 5751 2.031465 CTGGGCCGTAACACCGTT 59.969 61.111 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.