Multiple sequence alignment - TraesCS2D01G551900

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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 TraesCS2D01G551900 chr2D 100.000 4232 0 0 1 4232 627239691 627235460 0.000000e+00 7816.0
1 TraesCS2D01G551900 chr2D 88.263 639 61 5 1937 2567 630120871 630121503 0.000000e+00 752.0
2 TraesCS2D01G551900 chr2D 88.272 324 28 4 2932 3245 630121551 630121874 3.090000e-101 379.0
3 TraesCS2D01G551900 chr2D 89.100 211 22 1 1514 1724 630120455 630120664 1.170000e-65 261.0
4 TraesCS2D01G551900 chr2D 76.453 327 55 17 3763 4069 627171281 627170957 1.580000e-34 158.0
5 TraesCS2D01G551900 chr2B 93.869 4029 213 14 223 4232 769052811 769048798 0.000000e+00 6041.0
6 TraesCS2D01G551900 chr2B 95.761 401 17 0 2696 3096 768778744 768778344 0.000000e+00 647.0
7 TraesCS2D01G551900 chr2B 94.295 298 10 2 2412 2702 768791142 768790845 2.320000e-122 449.0
8 TraesCS2D01G551900 chr2B 94.485 272 11 1 2435 2702 768873662 768873391 2.350000e-112 416.0
9 TraesCS2D01G551900 chr2B 88.252 349 33 6 3859 4205 768778333 768777991 1.100000e-110 411.0
10 TraesCS2D01G551900 chr2B 94.118 272 11 2 2435 2702 768850372 768850102 3.940000e-110 409.0
11 TraesCS2D01G551900 chr2B 93.846 65 3 1 2435 2499 768906313 768906250 3.480000e-16 97.1
12 TraesCS2D01G551900 chr2B 81.553 103 15 3 3968 4069 768617842 768617743 9.750000e-12 82.4
13 TraesCS2D01G551900 chr2A 91.076 4202 295 38 25 4205 757937689 757933547 0.000000e+00 5609.0
14 TraesCS2D01G551900 chr4D 77.108 332 66 9 195 519 25504872 25505200 2.600000e-42 183.0
15 TraesCS2D01G551900 chr7B 72.861 339 78 13 215 545 710565566 710565898 2.080000e-18 104.0
16 TraesCS2D01G551900 chr7B 72.566 339 79 13 215 545 710632426 710632758 9.680000e-17 99.0
17 TraesCS2D01G551900 chr7B 78.676 136 27 2 235 368 710255287 710255422 5.830000e-14 89.8
18 TraesCS2D01G551900 chr6A 79.487 117 19 5 323 436 23328363 23328477 1.260000e-10 78.7
19 TraesCS2D01G551900 chr6D 80.682 88 15 2 350 436 24913204 24913118 2.730000e-07 67.6


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 TraesCS2D01G551900 chr2D 627235460 627239691 4231 True 7816 7816 100.0000 1 4232 1 chr2D.!!$R2 4231
1 TraesCS2D01G551900 chr2D 630120455 630121874 1419 False 464 752 88.5450 1514 3245 3 chr2D.!!$F1 1731
2 TraesCS2D01G551900 chr2B 769048798 769052811 4013 True 6041 6041 93.8690 223 4232 1 chr2B.!!$R6 4009
3 TraesCS2D01G551900 chr2B 768777991 768778744 753 True 529 647 92.0065 2696 4205 2 chr2B.!!$R7 1509
4 TraesCS2D01G551900 chr2A 757933547 757937689 4142 True 5609 5609 91.0760 25 4205 1 chr2A.!!$R1 4180

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
655 667 0.106708 GCATCGCCTCCACAATAGGA 59.893 55.0 0.0 0.0 36.08 2.94 F
1347 1370 0.388649 CCTTCAACACCGTCCTCTCG 60.389 60.0 0.0 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 1978 0.988063 TCCATGACACCAAATCGGGA 59.012 50.0 0.0 0.0 40.22 5.14 R
3333 3401 0.601046 TGCAGAGAAGACAAGCACCG 60.601 55.0 0.0 0.0 0.00 4.94 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
34 35 1.132036 AGGGAGGGGGAGTTTTCTTCT 60.132 52.381 0.00 0.00 0.00 2.85
41 42 1.271434 GGGAGTTTTCTTCTTCCCGCT 60.271 52.381 0.00 0.00 0.00 5.52
42 43 2.077627 GGAGTTTTCTTCTTCCCGCTC 58.922 52.381 0.00 0.00 0.00 5.03
80 82 1.001406 AGCATAGCTCAATACCGCCTC 59.999 52.381 0.00 0.00 30.62 4.70
81 83 1.941668 GCATAGCTCAATACCGCCTCC 60.942 57.143 0.00 0.00 0.00 4.30
82 84 0.603569 ATAGCTCAATACCGCCTCCG 59.396 55.000 0.00 0.00 0.00 4.63
151 153 0.746923 AGAAAATCGCTAACGGCCCC 60.747 55.000 0.00 0.00 40.63 5.80
152 154 2.043676 GAAAATCGCTAACGGCCCCG 62.044 60.000 4.96 4.96 46.03 5.73
153 155 2.524951 AAAATCGCTAACGGCCCCGA 62.525 55.000 14.44 0.00 42.83 5.14
154 156 2.319890 AAATCGCTAACGGCCCCGAT 62.320 55.000 14.44 3.99 41.63 4.18
155 157 1.466025 AATCGCTAACGGCCCCGATA 61.466 55.000 14.44 5.08 39.25 2.92
156 158 1.255667 ATCGCTAACGGCCCCGATAT 61.256 55.000 14.44 1.98 42.83 1.63
157 159 1.736645 CGCTAACGGCCCCGATATG 60.737 63.158 14.44 2.10 42.83 1.78
158 160 1.370064 GCTAACGGCCCCGATATGT 59.630 57.895 14.44 0.00 42.83 2.29
159 161 0.949105 GCTAACGGCCCCGATATGTG 60.949 60.000 14.44 0.00 42.83 3.21
160 162 0.677288 CTAACGGCCCCGATATGTGA 59.323 55.000 14.44 0.00 42.83 3.58
161 163 1.069513 CTAACGGCCCCGATATGTGAA 59.930 52.381 14.44 0.00 42.83 3.18
162 164 0.179056 AACGGCCCCGATATGTGAAG 60.179 55.000 14.44 0.00 42.83 3.02
167 170 1.748493 GCCCCGATATGTGAAGCAAAA 59.252 47.619 0.00 0.00 0.00 2.44
173 176 0.109964 TATGTGAAGCAAAACGCCGC 60.110 50.000 0.00 0.00 44.04 6.53
177 180 3.896863 GAAGCAAAACGCCGCCCAG 62.897 63.158 0.00 0.00 44.04 4.45
183 186 1.515521 AAAACGCCGCCCAGAGAAAG 61.516 55.000 0.00 0.00 0.00 2.62
185 188 2.047274 CGCCGCCCAGAGAAAGAA 60.047 61.111 0.00 0.00 0.00 2.52
191 194 0.790814 GCCCAGAGAAAGAAACGACG 59.209 55.000 0.00 0.00 0.00 5.12
193 196 2.059541 CCCAGAGAAAGAAACGACGAC 58.940 52.381 0.00 0.00 0.00 4.34
197 200 3.182572 CAGAGAAAGAAACGACGACAAGG 59.817 47.826 0.00 0.00 0.00 3.61
198 201 3.121544 GAGAAAGAAACGACGACAAGGT 58.878 45.455 0.00 0.00 0.00 3.50
214 217 3.133362 ACAAGGTCGTGTAGAAACCTCAA 59.867 43.478 0.00 0.00 42.58 3.02
219 222 4.501058 GGTCGTGTAGAAACCTCAAAGACT 60.501 45.833 0.00 0.00 0.00 3.24
237 240 7.231317 TCAAAGACTATGAAAGCTGGTCAAATT 59.769 33.333 4.58 0.00 0.00 1.82
277 280 3.231818 ACCTAAACCGATCGGATCTCAT 58.768 45.455 39.55 15.98 38.96 2.90
285 288 2.031069 CGATCGGATCTCATAACACCGT 60.031 50.000 15.50 0.00 43.36 4.83
286 289 3.187842 CGATCGGATCTCATAACACCGTA 59.812 47.826 15.50 0.00 43.36 4.02
324 327 1.106285 GCCCTCTGCCGATGAAAAAT 58.894 50.000 0.00 0.00 0.00 1.82
345 349 2.193127 ACACCAATGGAACGGGATAGA 58.807 47.619 6.16 0.00 0.00 1.98
368 372 6.380274 AGAACGAGGAGAACATTATTCCTACA 59.620 38.462 0.00 0.00 41.32 2.74
384 388 0.746063 TACACTGGGACAACGTCGTT 59.254 50.000 4.40 4.40 38.70 3.85
400 404 1.339610 TCGTTGTTTTGCCATCCCAAG 59.660 47.619 0.00 0.00 0.00 3.61
420 424 2.689983 AGCCAAACACAAAGACTCCTTG 59.310 45.455 0.00 0.00 31.91 3.61
431 436 6.542370 CACAAAGACTCCTTGAAGAAAACCTA 59.458 38.462 0.00 0.00 31.91 3.08
455 460 3.454371 AGATCACCTATGCCGTTGTAC 57.546 47.619 0.00 0.00 0.00 2.90
482 487 1.827344 TCCATGTCTGATGTCGAGCTT 59.173 47.619 0.00 0.00 0.00 3.74
505 510 1.399215 CGTCGTACAAAACCATGCACC 60.399 52.381 0.00 0.00 0.00 5.01
519 524 1.371558 GCACCGACACCCTCTTCTT 59.628 57.895 0.00 0.00 0.00 2.52
612 624 2.047274 CGTCGCACACCTCCCAAT 60.047 61.111 0.00 0.00 0.00 3.16
622 634 1.228510 CCTCCCAATGAAGGCCTCC 59.771 63.158 5.23 0.00 0.00 4.30
636 648 4.504916 CTCCGCTCGAGCACCCTG 62.505 72.222 34.69 18.93 42.21 4.45
651 663 1.452651 CCTGCATCGCCTCCACAAT 60.453 57.895 0.00 0.00 0.00 2.71
653 665 1.224075 CTGCATCGCCTCCACAATAG 58.776 55.000 0.00 0.00 0.00 1.73
655 667 0.106708 GCATCGCCTCCACAATAGGA 59.893 55.000 0.00 0.00 36.08 2.94
675 691 2.370849 GACTCCTCGATCTAGACCTCCT 59.629 54.545 0.00 0.00 0.00 3.69
767 783 1.269723 GTGGCTGCTAGGGTTTTTCAC 59.730 52.381 0.00 0.00 0.00 3.18
772 788 1.960689 TGCTAGGGTTTTTCACTTGCC 59.039 47.619 0.00 0.00 45.15 4.52
775 791 1.413118 AGGGTTTTTCACTTGCCTGG 58.587 50.000 0.00 0.00 0.00 4.45
776 792 1.119684 GGGTTTTTCACTTGCCTGGT 58.880 50.000 0.00 0.00 0.00 4.00
784 800 3.726517 CTTGCCTGGTTGGTCGCG 61.727 66.667 0.00 0.00 38.35 5.87
853 873 4.039004 ACTTGGTCATGCTTGTATGCAAAA 59.961 37.500 0.00 0.00 46.61 2.44
854 874 4.597404 TGGTCATGCTTGTATGCAAAAA 57.403 36.364 0.00 0.00 46.61 1.94
873 893 9.123709 TGCAAAAATTGAATACGCTAAAACTAG 57.876 29.630 0.00 0.00 0.00 2.57
979 999 2.869897 CTGCAGTCGAGTAGAACTTCC 58.130 52.381 5.25 0.00 0.00 3.46
1203 1226 2.766400 GCTCCTCGTGGTCTCCTCG 61.766 68.421 2.99 4.23 41.16 4.63
1347 1370 0.388649 CCTTCAACACCGTCCTCTCG 60.389 60.000 0.00 0.00 0.00 4.04
1572 1595 0.538584 CCCTGCTGCAGATGTACTCA 59.461 55.000 30.10 2.50 32.44 3.41
1743 1792 4.008933 GCACCCACCGAGAGCACT 62.009 66.667 0.00 0.00 0.00 4.40
1829 1878 2.663196 GGTGGTGAAGTCGGAGGG 59.337 66.667 0.00 0.00 0.00 4.30
1834 1883 1.079057 GTGAAGTCGGAGGGGCTTC 60.079 63.158 1.31 1.31 39.09 3.86
1878 1927 1.142748 GCTGCTCGGCATGTACTCT 59.857 57.895 0.00 0.00 38.13 3.24
1917 1966 1.133982 ACTGCGTTGCATGTGTTTGAA 59.866 42.857 0.00 0.00 38.13 2.69
1929 1978 5.278660 GCATGTGTTTGAAAGGATTGAGACT 60.279 40.000 0.00 0.00 0.00 3.24
1932 1981 4.216472 GTGTTTGAAAGGATTGAGACTCCC 59.784 45.833 0.00 0.00 32.89 4.30
1935 1984 3.107601 TGAAAGGATTGAGACTCCCGAT 58.892 45.455 0.00 0.00 32.89 4.18
1968 2017 3.879892 GGAATACTCTGATTGCTGGGTTC 59.120 47.826 0.00 0.00 0.00 3.62
2105 2154 0.244450 GCTGCTTTACCTGCAATGCA 59.756 50.000 7.99 7.99 40.13 3.96
2206 2255 7.830201 TCAATATGTATTTTACAAACGGGGAGT 59.170 33.333 0.00 0.00 42.76 3.85
2556 2613 4.839121 ACACCATACCAAAGCGAGATTTA 58.161 39.130 0.00 0.00 0.00 1.40
2895 2952 3.625313 GGAGAATTCTGCTAAGTTCCTGC 59.375 47.826 18.82 0.00 0.00 4.85
3656 3726 5.458779 GTCAAACTGCATCAAACAAGTTACC 59.541 40.000 0.00 0.00 0.00 2.85
3777 3849 3.868077 ACAATTGCTCGAGTCTGCTTATC 59.132 43.478 15.13 0.00 0.00 1.75
3801 3873 1.905894 AGGGAGAGAGAAGTTTGAGCC 59.094 52.381 0.00 0.00 0.00 4.70
3863 3937 5.884771 TCTGTTTCAGTCTATCTGTGATCG 58.115 41.667 0.00 0.00 43.97 3.69
4022 4097 5.627499 TTAATCATTTGTCAGGTGTGCTC 57.373 39.130 0.00 0.00 0.00 4.26
4126 4201 9.434559 GTTCTAACAGAAGACAAAAATGTACAC 57.565 33.333 0.00 0.00 34.42 2.90
4191 4268 2.043526 AGTCAAGCCCTTCCCAATCATT 59.956 45.455 0.00 0.00 0.00 2.57
4211 4288 7.435068 TCATTTAAGCTTCCTGAGTTTACAC 57.565 36.000 0.00 0.00 31.75 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.773541 ACTCCCCCTCCCTCATTTTT 58.226 50.000 0.00 0.00 0.00 1.94
8 9 1.773541 AACTCCCCCTCCCTCATTTT 58.226 50.000 0.00 0.00 0.00 1.82
9 10 1.773541 AAACTCCCCCTCCCTCATTT 58.226 50.000 0.00 0.00 0.00 2.32
10 11 1.641192 GAAAACTCCCCCTCCCTCATT 59.359 52.381 0.00 0.00 0.00 2.57
11 12 1.203622 AGAAAACTCCCCCTCCCTCAT 60.204 52.381 0.00 0.00 0.00 2.90
12 13 0.196118 AGAAAACTCCCCCTCCCTCA 59.804 55.000 0.00 0.00 0.00 3.86
13 14 1.282447 GAAGAAAACTCCCCCTCCCTC 59.718 57.143 0.00 0.00 0.00 4.30
14 15 1.132036 AGAAGAAAACTCCCCCTCCCT 60.132 52.381 0.00 0.00 0.00 4.20
15 16 1.373536 AGAAGAAAACTCCCCCTCCC 58.626 55.000 0.00 0.00 0.00 4.30
16 17 2.291024 GGAAGAAGAAAACTCCCCCTCC 60.291 54.545 0.00 0.00 0.00 4.30
17 18 2.291024 GGGAAGAAGAAAACTCCCCCTC 60.291 54.545 0.00 0.00 31.80 4.30
18 19 1.711375 GGGAAGAAGAAAACTCCCCCT 59.289 52.381 0.00 0.00 31.80 4.79
19 20 1.613520 CGGGAAGAAGAAAACTCCCCC 60.614 57.143 0.41 0.00 34.05 5.40
20 21 1.822506 CGGGAAGAAGAAAACTCCCC 58.177 55.000 0.41 0.00 34.05 4.81
21 22 1.166129 GCGGGAAGAAGAAAACTCCC 58.834 55.000 0.00 0.00 0.00 4.30
22 23 2.077627 GAGCGGGAAGAAGAAAACTCC 58.922 52.381 0.00 0.00 0.00 3.85
23 24 2.077627 GGAGCGGGAAGAAGAAAACTC 58.922 52.381 0.00 0.00 0.00 3.01
61 63 1.433534 GAGGCGGTATTGAGCTATGC 58.566 55.000 0.00 0.00 0.00 3.14
65 67 2.797278 CCGGAGGCGGTATTGAGCT 61.797 63.158 0.00 0.00 46.14 4.09
82 84 4.899239 CCGCTGATGCCGAGGACC 62.899 72.222 0.00 0.00 35.36 4.46
84 86 3.531207 CTCCGCTGATGCCGAGGA 61.531 66.667 0.00 0.00 39.65 3.71
88 90 1.996786 AATTTGCTCCGCTGATGCCG 61.997 55.000 0.00 0.00 35.36 5.69
110 112 3.167485 TCTACGAGCTCCTGGGTTTTAA 58.833 45.455 8.47 0.00 0.00 1.52
121 123 3.440228 AGCGATTTTCTTCTACGAGCTC 58.560 45.455 2.73 2.73 0.00 4.09
122 124 3.512033 AGCGATTTTCTTCTACGAGCT 57.488 42.857 0.00 0.00 0.00 4.09
151 153 2.440501 GGCGTTTTGCTTCACATATCG 58.559 47.619 0.00 0.00 45.43 2.92
152 154 2.440501 CGGCGTTTTGCTTCACATATC 58.559 47.619 0.00 0.00 45.43 1.63
153 155 1.467374 GCGGCGTTTTGCTTCACATAT 60.467 47.619 9.37 0.00 45.43 1.78
154 156 0.109964 GCGGCGTTTTGCTTCACATA 60.110 50.000 9.37 0.00 45.43 2.29
155 157 1.371635 GCGGCGTTTTGCTTCACAT 60.372 52.632 9.37 0.00 45.43 3.21
156 158 2.025441 GCGGCGTTTTGCTTCACA 59.975 55.556 9.37 0.00 45.43 3.58
157 159 2.729491 GGCGGCGTTTTGCTTCAC 60.729 61.111 9.37 0.00 45.43 3.18
158 160 3.972276 GGGCGGCGTTTTGCTTCA 61.972 61.111 9.37 0.00 45.43 3.02
159 161 3.896863 CTGGGCGGCGTTTTGCTTC 62.897 63.158 9.37 0.00 45.43 3.86
160 162 3.977244 CTGGGCGGCGTTTTGCTT 61.977 61.111 9.37 0.00 45.43 3.91
161 163 4.947147 TCTGGGCGGCGTTTTGCT 62.947 61.111 9.37 0.00 45.43 3.91
162 164 4.404654 CTCTGGGCGGCGTTTTGC 62.405 66.667 9.37 0.00 45.38 3.68
167 170 2.391724 TTTCTTTCTCTGGGCGGCGT 62.392 55.000 9.37 0.00 0.00 5.68
173 176 2.059541 GTCGTCGTTTCTTTCTCTGGG 58.940 52.381 0.00 0.00 0.00 4.45
177 180 3.121544 ACCTTGTCGTCGTTTCTTTCTC 58.878 45.455 0.00 0.00 0.00 2.87
191 194 3.243636 TGAGGTTTCTACACGACCTTGTC 60.244 47.826 0.00 0.00 43.59 3.18
193 196 3.380479 TGAGGTTTCTACACGACCTTG 57.620 47.619 0.00 0.00 43.59 3.61
197 200 4.618965 AGTCTTTGAGGTTTCTACACGAC 58.381 43.478 0.00 0.00 0.00 4.34
198 201 4.931661 AGTCTTTGAGGTTTCTACACGA 57.068 40.909 0.00 0.00 0.00 4.35
200 203 8.603242 TTTCATAGTCTTTGAGGTTTCTACAC 57.397 34.615 0.00 0.00 0.00 2.90
210 213 5.240891 TGACCAGCTTTCATAGTCTTTGAG 58.759 41.667 0.00 0.00 0.00 3.02
214 217 6.716628 TGAATTTGACCAGCTTTCATAGTCTT 59.283 34.615 11.64 0.00 0.00 3.01
219 222 5.122239 CGTCTGAATTTGACCAGCTTTCATA 59.878 40.000 6.87 0.00 0.00 2.15
277 280 4.197750 GAGATGTCTCTCCTACGGTGTTA 58.802 47.826 2.80 0.00 41.86 2.41
316 319 5.337169 CCCGTTCCATTGGTGTATTTTTCAT 60.337 40.000 1.86 0.00 0.00 2.57
324 327 3.376636 TCTATCCCGTTCCATTGGTGTA 58.623 45.455 1.86 0.00 0.00 2.90
345 349 6.154706 AGTGTAGGAATAATGTTCTCCTCGTT 59.845 38.462 0.00 0.00 40.20 3.85
368 372 4.431035 CAACGACGTTGTCCCAGT 57.569 55.556 28.28 0.00 38.56 4.00
384 388 0.762082 TGGCTTGGGATGGCAAAACA 60.762 50.000 0.00 0.00 37.05 2.83
389 393 1.152376 TGTTTGGCTTGGGATGGCA 60.152 52.632 0.00 0.00 38.22 4.92
400 404 2.687935 TCAAGGAGTCTTTGTGTTTGGC 59.312 45.455 14.03 0.00 0.00 4.52
420 424 9.103861 CATAGGTGATCTTTCTAGGTTTTCTTC 57.896 37.037 0.00 0.00 0.00 2.87
431 436 3.055094 ACAACGGCATAGGTGATCTTTCT 60.055 43.478 0.00 0.00 32.17 2.52
455 460 1.205655 ACATCAGACATGGACCAGTCG 59.794 52.381 14.54 11.17 39.67 4.18
482 487 1.527736 GCATGGTTTTGTACGACGACA 59.472 47.619 0.00 0.00 0.00 4.35
505 510 1.472878 TCATCGAAGAAGAGGGTGTCG 59.527 52.381 0.00 0.00 43.58 4.35
606 618 2.998097 CGGAGGCCTTCATTGGGA 59.002 61.111 12.82 0.00 0.00 4.37
612 624 3.452786 CTCGAGCGGAGGCCTTCA 61.453 66.667 12.82 0.00 41.24 3.02
622 634 4.827087 ATGCAGGGTGCTCGAGCG 62.827 66.667 30.75 17.84 45.31 5.03
636 648 0.106708 TCCTATTGTGGAGGCGATGC 59.893 55.000 0.00 0.00 33.73 3.91
651 663 3.579586 GAGGTCTAGATCGAGGAGTCCTA 59.420 52.174 12.99 0.00 31.76 2.94
653 665 2.551504 GGAGGTCTAGATCGAGGAGTCC 60.552 59.091 0.00 0.00 0.00 3.85
655 667 2.370849 GAGGAGGTCTAGATCGAGGAGT 59.629 54.545 2.78 0.00 0.00 3.85
767 783 3.726517 CGCGACCAACCAGGCAAG 61.727 66.667 0.00 0.00 43.14 4.01
772 788 1.659098 GAAGAATACGCGACCAACCAG 59.341 52.381 15.93 0.00 0.00 4.00
775 791 2.602878 TGAGAAGAATACGCGACCAAC 58.397 47.619 15.93 0.00 0.00 3.77
776 792 3.119280 TCATGAGAAGAATACGCGACCAA 60.119 43.478 15.93 0.00 0.00 3.67
784 800 7.895870 TCGAATCGTTTTCATGAGAAGAATAC 58.104 34.615 1.52 0.00 34.71 1.89
873 893 7.650504 GGTGTGGTTCCTAACTTAAATTCAAAC 59.349 37.037 0.00 0.00 0.00 2.93
1221 1244 3.310860 GACGATGAAGGTGCCGGGT 62.311 63.158 2.18 0.00 0.00 5.28
1743 1792 1.302591 ACTGAGCACCGACGAGAGA 60.303 57.895 0.00 0.00 0.00 3.10
1834 1883 3.190849 CAGCGGCGTGTCAGGATG 61.191 66.667 9.37 0.00 37.54 3.51
1878 1927 3.002583 TCCAGATCACCGCAGCCA 61.003 61.111 0.00 0.00 0.00 4.75
1917 1966 3.370953 CCAAATCGGGAGTCTCAATCCTT 60.371 47.826 1.47 0.00 37.01 3.36
1929 1978 0.988063 TCCATGACACCAAATCGGGA 59.012 50.000 0.00 0.00 40.22 5.14
1932 1981 5.007039 CAGAGTATTCCATGACACCAAATCG 59.993 44.000 0.00 0.00 0.00 3.34
1935 1984 5.497464 TCAGAGTATTCCATGACACCAAA 57.503 39.130 0.00 0.00 0.00 3.28
1968 2017 1.696336 CATCCATCCCCAGTACCAGAG 59.304 57.143 0.00 0.00 0.00 3.35
2206 2255 1.536766 CAAAATTCGTGCTGAGCCTGA 59.463 47.619 0.23 0.00 0.00 3.86
2895 2952 7.218773 CCAACAGACAAATCATTTAATGCTACG 59.781 37.037 0.00 0.00 0.00 3.51
2916 2973 1.093972 CAGCGGCATGAATACCAACA 58.906 50.000 1.45 0.00 0.00 3.33
3333 3401 0.601046 TGCAGAGAAGACAAGCACCG 60.601 55.000 0.00 0.00 0.00 4.94
3656 3726 2.814280 ACTGTGTTACTTCCACCTCG 57.186 50.000 0.00 0.00 31.71 4.63
3777 3849 4.215185 GCTCAAACTTCTCTCTCCCTTTTG 59.785 45.833 0.00 0.00 0.00 2.44
3801 3873 3.325870 TGTAAGAGACACCAAAGCATCG 58.674 45.455 0.00 0.00 31.20 3.84
3863 3937 5.505173 TTATAGCTCAAAATTCTGCTGGC 57.495 39.130 0.00 0.00 37.02 4.85
4022 4097 1.996191 GTGTCTTTCCTAGAAGCAGCG 59.004 52.381 0.00 0.00 33.81 5.18
4076 4151 7.456725 ACAATTCCAGTATAATCTCTGGGATG 58.543 38.462 10.64 9.57 46.03 3.51
4191 4268 8.911918 TTAATGTGTAAACTCAGGAAGCTTAA 57.088 30.769 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.