Multiple sequence alignment - TraesCS6D01G154700

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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 TraesCS6D01G154700 chr6D 100.000 7879 0 0 1 7879 129791892 129784014 0.000000e+00 14550.0
1 TraesCS6D01G154700 chr6B 95.431 4137 130 27 522 4629 228249855 228245749 0.000000e+00 6538.0
2 TraesCS6D01G154700 chr6B 96.847 3267 95 6 4615 7879 228245736 228242476 0.000000e+00 5456.0
3 TraesCS6D01G154700 chr6A 93.976 2822 113 23 5083 7879 168120929 168118140 0.000000e+00 4217.0
4 TraesCS6D01G154700 chr6A 96.053 2103 56 8 521 2600 168125858 168123760 0.000000e+00 3398.0
5 TraesCS6D01G154700 chr6A 98.015 1763 25 4 2599 4352 168123636 168121875 0.000000e+00 3053.0
6 TraesCS6D01G154700 chr6A 97.411 734 18 1 4352 5085 168121775 168121043 0.000000e+00 1249.0
7 TraesCS6D01G154700 chr6A 84.808 520 57 8 1 517 168126635 168126135 3.280000e-138 503.0
8 TraesCS6D01G154700 chr6A 96.296 54 2 0 7490 7543 168118502 168118449 1.090000e-13 89.8
9 TraesCS6D01G154700 chr5D 90.909 44 3 1 7695 7737 458094790 458094833 3.070000e-04 58.4
10 TraesCS6D01G154700 chr5D 100.000 30 0 0 7695 7724 458180054 458180083 1.000000e-03 56.5
11 TraesCS6D01G154700 chr5B 90.909 44 3 1 7695 7737 560441440 560441483 3.070000e-04 58.4
12 TraesCS6D01G154700 chr5B 89.362 47 3 2 7692 7737 561061782 561061827 3.070000e-04 58.4
13 TraesCS6D01G154700 chr5A 90.909 44 3 1 7695 7737 575706039 575706082 3.070000e-04 58.4
14 TraesCS6D01G154700 chr5A 90.909 44 3 1 7695 7737 576084877 576084920 3.070000e-04 58.4
15 TraesCS6D01G154700 chr5A 90.909 44 3 1 7695 7737 576272554 576272511 3.070000e-04 58.4


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 TraesCS6D01G154700 chr6D 129784014 129791892 7878 True 14550.000000 14550 100.0000 1 7879 1 chr6D.!!$R1 7878
1 TraesCS6D01G154700 chr6B 228242476 228249855 7379 True 5997.000000 6538 96.1390 522 7879 2 chr6B.!!$R1 7357
2 TraesCS6D01G154700 chr6A 168118140 168126635 8495 True 2084.966667 4217 94.4265 1 7879 6 chr6A.!!$R1 7878

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
239 243 0.243636 GGGCTGGAAAATCAACACGG 59.756 55.000 0.00 0.00 0.00 4.94 F
714 1014 0.251077 CCAAAGCACAGAAGCCTCCT 60.251 55.000 0.00 0.00 34.23 3.69 F
1248 1557 1.011131 GGTTTGTATAGCAGCGCGC 60.011 57.895 26.66 26.66 42.91 6.86 F
1625 1934 1.409412 CACTATATCGCGCACTGGAC 58.591 55.000 8.75 0.00 0.00 4.02 F
1747 2056 2.102588 GTGTCGTGGCTATGTAATCCCT 59.897 50.000 0.00 0.00 0.00 4.20 F
3470 3907 1.382522 CATTCATTCACCTCCACCCG 58.617 55.000 0.00 0.00 0.00 5.28 F
5343 6036 1.235724 GGTCAGTGCTTGGTAACCAC 58.764 55.000 0.00 0.00 30.78 4.16 F
6468 7171 1.697284 TACCAAGCATGTGCCAAACA 58.303 45.000 0.57 0.00 44.79 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1089 1390 0.101399 CGTCGGAGGGATCAGTGAAG 59.899 60.000 0.00 0.00 0.00 3.02 R
1625 1934 0.809385 CAGAAAGCTGCCATGGTGAG 59.191 55.000 14.67 10.93 34.95 3.51 R
2884 3321 1.338769 CCCTGAAAACGTCGAGGGAAT 60.339 52.381 9.83 0.00 42.77 3.01 R
3470 3907 0.249657 GGAGGTCGAGGATGATGTGC 60.250 60.000 0.00 0.00 0.00 4.57 R
4412 4962 6.706295 AGAAGTCAACTCTTGGGAATCTAAG 58.294 40.000 0.00 0.00 33.42 2.18 R
5777 6480 1.553690 TAGCACCACTGAGGGCTTCC 61.554 60.000 11.03 0.00 41.96 3.46 R
6513 7216 0.602638 TGTCAGTTGTCCGATGCACC 60.603 55.000 0.00 0.00 0.00 5.01 R
7675 8416 1.215423 GAATGTGGCCCCAGGATAAGT 59.785 52.381 0.00 0.00 0.00 2.24 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
17 18 4.051167 TAGGCACCTCCGGTCCGA 62.051 66.667 14.39 0.00 40.77 4.55
64 65 1.019278 TCGTCGAAAATGCAGGAGGC 61.019 55.000 0.00 0.00 45.13 4.70
103 104 1.477295 GAAGTCTCCGGATCCGACTTT 59.523 52.381 35.42 19.90 45.18 2.66
104 105 0.818296 AGTCTCCGGATCCGACTTTG 59.182 55.000 35.42 17.97 42.83 2.77
117 118 2.351726 CCGACTTTGAAACGATGGGATC 59.648 50.000 0.00 0.00 0.00 3.36
122 123 2.293677 TGAAACGATGGGATCAGACG 57.706 50.000 0.00 0.00 34.57 4.18
127 128 0.318529 CGATGGGATCAGACGCTCAG 60.319 60.000 0.00 0.00 0.00 3.35
159 160 2.668212 CATGGTGTCGTTGGCGGT 60.668 61.111 0.00 0.00 38.89 5.68
198 199 1.990799 CATTCAACGACGAGGCTACA 58.009 50.000 0.00 0.00 0.00 2.74
201 202 0.669619 TCAACGACGAGGCTACAACA 59.330 50.000 0.00 0.00 0.00 3.33
206 210 2.223876 ACGACGAGGCTACAACAAAGAA 60.224 45.455 0.00 0.00 0.00 2.52
219 223 1.336240 ACAAAGAAGAAGCGGCAATGC 60.336 47.619 1.45 0.00 0.00 3.56
231 235 1.218854 GCAATGCGGGCTGGAAAAT 59.781 52.632 0.00 0.00 0.00 1.82
237 241 0.388520 GCGGGCTGGAAAATCAACAC 60.389 55.000 0.00 0.00 0.00 3.32
239 243 0.243636 GGGCTGGAAAATCAACACGG 59.756 55.000 0.00 0.00 0.00 4.94
265 269 3.417185 GAAATGTCTTTCGCGTCAATCC 58.583 45.455 5.77 0.00 32.04 3.01
266 270 1.369625 ATGTCTTTCGCGTCAATCCC 58.630 50.000 5.77 0.00 0.00 3.85
283 287 4.934797 ATCCCTTTTTCAGATGGAGTGA 57.065 40.909 0.00 0.00 0.00 3.41
284 288 4.292186 TCCCTTTTTCAGATGGAGTGAG 57.708 45.455 0.00 0.00 0.00 3.51
305 309 2.167662 CTCCAAATACACCCCCACAAC 58.832 52.381 0.00 0.00 0.00 3.32
306 310 1.203075 TCCAAATACACCCCCACAACC 60.203 52.381 0.00 0.00 0.00 3.77
309 313 0.479378 AATACACCCCCACAACCGTT 59.521 50.000 0.00 0.00 0.00 4.44
311 315 1.135094 TACACCCCCACAACCGTTAA 58.865 50.000 0.00 0.00 0.00 2.01
316 320 3.764972 CACCCCCACAACCGTTAAATATT 59.235 43.478 0.00 0.00 0.00 1.28
345 349 4.101585 TCAAGGATGAAATGGCGACTCTAT 59.898 41.667 0.00 0.00 30.99 1.98
346 350 4.264460 AGGATGAAATGGCGACTCTATC 57.736 45.455 0.00 0.00 0.00 2.08
357 361 3.804873 GGCGACTCTATCATGACCTTTTC 59.195 47.826 0.00 0.00 0.00 2.29
361 365 6.037610 GCGACTCTATCATGACCTTTTCAATT 59.962 38.462 0.00 0.00 37.92 2.32
400 404 6.864560 TCTGTTATTACAACAATCGAGTCG 57.135 37.500 6.09 6.09 32.92 4.18
401 405 6.614160 TCTGTTATTACAACAATCGAGTCGA 58.386 36.000 19.06 19.06 35.34 4.20
402 406 7.255569 TCTGTTATTACAACAATCGAGTCGAT 58.744 34.615 22.14 22.14 40.10 3.59
403 407 8.400186 TCTGTTATTACAACAATCGAGTCGATA 58.600 33.333 27.27 11.15 38.60 2.92
404 408 9.181805 CTGTTATTACAACAATCGAGTCGATAT 57.818 33.333 27.27 17.10 38.60 1.63
405 409 8.964150 TGTTATTACAACAATCGAGTCGATATG 58.036 33.333 27.27 24.95 46.30 1.78
406 410 9.177304 GTTATTACAACAATCGAGTCGATATGA 57.823 33.333 27.27 10.01 46.30 2.15
407 411 7.624706 ATTACAACAATCGAGTCGATATGAC 57.375 36.000 27.27 0.00 46.30 3.06
453 457 9.243637 GAAAAACATATGACAACACTGCTAAAA 57.756 29.630 10.38 0.00 0.00 1.52
459 463 4.609947 TGACAACACTGCTAAAATTGCTG 58.390 39.130 0.00 0.00 35.85 4.41
464 468 6.642131 ACAACACTGCTAAAATTGCTGTTATG 59.358 34.615 0.00 0.00 39.86 1.90
466 470 5.162794 CACTGCTAAAATTGCTGTTATGCA 58.837 37.500 0.00 0.00 39.86 3.96
480 484 9.920133 TTGCTGTTATGCAATTTAAGTGAATAA 57.080 25.926 2.09 2.09 46.43 1.40
500 504 1.065709 ACGAAAGATATGGCCACGGTT 60.066 47.619 8.16 0.00 0.00 4.44
538 818 2.613506 GGGACCCACGCTGTTTTCG 61.614 63.158 5.33 0.00 0.00 3.46
539 819 2.251371 GACCCACGCTGTTTTCGC 59.749 61.111 0.00 0.00 0.00 4.70
544 824 0.384725 CCACGCTGTTTTCGCTTCTG 60.385 55.000 0.00 0.00 0.00 3.02
671 953 2.777692 TCTCTTCCTCCTCTCTCTCTCC 59.222 54.545 0.00 0.00 0.00 3.71
714 1014 0.251077 CCAAAGCACAGAAGCCTCCT 60.251 55.000 0.00 0.00 34.23 3.69
794 1094 2.587194 CTCTGCGGGCGATTCCTG 60.587 66.667 0.00 0.00 44.43 3.86
945 1246 3.321497 CTTCTAGAACATCCTATGCCGC 58.679 50.000 0.00 0.00 0.00 6.53
946 1247 2.598565 TCTAGAACATCCTATGCCGCT 58.401 47.619 0.00 0.00 0.00 5.52
1248 1557 1.011131 GGTTTGTATAGCAGCGCGC 60.011 57.895 26.66 26.66 42.91 6.86
1324 1633 2.181777 CGCTTCTGCTCGTGCCTA 59.818 61.111 7.05 0.00 38.71 3.93
1355 1664 3.879295 CGCATAAACATTCAGATCTGGGT 59.121 43.478 22.42 14.90 0.00 4.51
1483 1792 5.402270 GGCATGTTTTTGTGCTTGTAAGTAG 59.598 40.000 0.00 0.00 41.04 2.57
1625 1934 1.409412 CACTATATCGCGCACTGGAC 58.591 55.000 8.75 0.00 0.00 4.02
1747 2056 2.102588 GTGTCGTGGCTATGTAATCCCT 59.897 50.000 0.00 0.00 0.00 4.20
2422 2731 8.892723 CATGGAAAGCTTAGTTACAATGTATGA 58.107 33.333 0.00 0.00 0.00 2.15
2759 3194 2.867287 TGGAACAAACACATGCACAG 57.133 45.000 0.00 0.00 31.92 3.66
2896 3333 5.535406 AGACTCATATTTATTCCCTCGACGT 59.465 40.000 0.00 0.00 0.00 4.34
3276 3713 5.059161 TGAGTTCATTTCTGAGTTGAGGTG 58.941 41.667 0.00 0.00 31.68 4.00
3470 3907 1.382522 CATTCATTCACCTCCACCCG 58.617 55.000 0.00 0.00 0.00 5.28
3831 4274 7.699391 GTGGTAGTTGATTGTCAATTGATCATG 59.301 37.037 12.12 0.00 38.79 3.07
3852 4295 8.883954 TCATGCAAATATTTCTGTTTGTTTCA 57.116 26.923 0.00 0.00 36.26 2.69
4412 4962 9.587772 TCAAGTCTAATTTCTGTAGCTTGTATC 57.412 33.333 0.00 0.00 35.93 2.24
4422 4972 7.291411 TCTGTAGCTTGTATCTTAGATTCCC 57.709 40.000 0.00 0.00 0.00 3.97
4425 4975 7.500992 TGTAGCTTGTATCTTAGATTCCCAAG 58.499 38.462 17.17 17.17 0.00 3.61
4500 5050 2.356069 TCCTCATCGACAAGACATCTCG 59.644 50.000 0.00 0.00 0.00 4.04
4644 5221 7.444487 AGCGGTTTATTAGATACTCATTTTCCC 59.556 37.037 0.00 0.00 0.00 3.97
4869 5446 2.235016 GTGGAGTTTGGGCATTGTGTA 58.765 47.619 0.00 0.00 0.00 2.90
4974 5551 2.961741 AGCTCGGATGAAGATTGCTCTA 59.038 45.455 0.00 0.00 0.00 2.43
4977 5554 3.566351 TCGGATGAAGATTGCTCTAGGA 58.434 45.455 0.00 0.00 0.00 2.94
5017 5594 7.038659 AGAGTAAGTACATTCTGTCTCATTGC 58.961 38.462 0.00 0.00 0.00 3.56
5076 5653 5.588648 TGCTGCAGAGTAATTAATTACACCC 59.411 40.000 30.54 21.32 43.83 4.61
5109 5802 8.649810 ATTATTTTTCGTAGTTTAGTTGCACG 57.350 30.769 0.00 0.00 0.00 5.34
5334 6027 2.233271 CCACAAGAATGGTCAGTGCTT 58.767 47.619 0.00 0.00 34.77 3.91
5343 6036 1.235724 GGTCAGTGCTTGGTAACCAC 58.764 55.000 0.00 0.00 30.78 4.16
5448 6141 6.726490 ATGATCTGGGATTCAAATTTGAGG 57.274 37.500 19.64 8.41 38.61 3.86
5449 6142 4.403432 TGATCTGGGATTCAAATTTGAGGC 59.597 41.667 19.64 15.20 38.61 4.70
5491 6184 8.035984 AGAACCTAAAACATAGAACTGCTCTAC 58.964 37.037 0.00 0.00 39.52 2.59
5505 6198 3.626930 TGCTCTACCTCTCTTTCTCTCC 58.373 50.000 0.00 0.00 0.00 3.71
5514 6207 6.133356 ACCTCTCTTTCTCTCCGATTAGAAT 58.867 40.000 0.00 0.00 32.05 2.40
5525 6218 9.102757 TCTCTCCGATTAGAATTTTTCTCATTG 57.897 33.333 0.00 0.00 41.14 2.82
5555 6249 6.546403 TCAAGCTAGATTACCGAACACTCTAT 59.454 38.462 0.00 0.00 0.00 1.98
5777 6480 2.357009 CTCATTTGGGAAGCAGGATTCG 59.643 50.000 0.00 0.00 0.00 3.34
5961 6664 2.972713 AGCAGTCTGGTTTACTGAAGGA 59.027 45.455 7.39 0.00 45.89 3.36
6059 6762 8.164057 ACCTTAATTCTCTGGGAAGAATAACT 57.836 34.615 0.00 0.00 43.53 2.24
6145 6848 4.475944 CTTTGCATCAAGGTAGTTTTCCG 58.524 43.478 0.00 0.00 0.00 4.30
6147 6850 3.071479 TGCATCAAGGTAGTTTTCCGTC 58.929 45.455 0.00 0.00 0.00 4.79
6151 6854 2.301009 TCAAGGTAGTTTTCCGTCCTCC 59.699 50.000 0.00 0.00 0.00 4.30
6163 6866 1.831736 CCGTCCTCCTTTCTGGTACAT 59.168 52.381 0.00 0.00 38.20 2.29
6468 7171 1.697284 TACCAAGCATGTGCCAAACA 58.303 45.000 0.57 0.00 44.79 2.83
6519 7222 8.752187 AGAAACAAAAGATATTACATGGTGCAT 58.248 29.630 0.00 0.00 0.00 3.96
6571 7274 0.896923 TATTAAGTGACCGCACCCGT 59.103 50.000 0.00 0.00 46.32 5.28
6572 7275 0.672401 ATTAAGTGACCGCACCCGTG 60.672 55.000 0.00 0.00 46.32 4.94
6781 7484 1.342174 TCCACCGGTAACTCACTTGAC 59.658 52.381 6.87 0.00 0.00 3.18
6804 7507 6.234177 ACAGTGCAGCTTCTTTCTTATACTT 58.766 36.000 0.00 0.00 0.00 2.24
7005 7708 1.666888 GCCAATTGACGACAGCCAAAG 60.667 52.381 7.12 0.00 0.00 2.77
7055 7758 4.340666 AGAAGACACTATGTGATGCTCGAT 59.659 41.667 4.61 0.00 36.96 3.59
7090 7795 2.437413 CAAAGTAAACTCTGCTCCCCC 58.563 52.381 0.00 0.00 0.00 5.40
7146 7851 6.724263 TGGCAATCAGTATTATTAGCGTTTG 58.276 36.000 0.00 0.00 0.00 2.93
7260 7965 5.287226 CACGTATACCCATTCTCCACTTAC 58.713 45.833 0.00 0.00 0.00 2.34
7489 8195 5.755409 TGTAGATGCCCACTCTTTCTTAA 57.245 39.130 0.00 0.00 0.00 1.85
7588 8325 3.053245 ACACACTAGTAGATGCCTCTCCT 60.053 47.826 3.59 0.00 32.66 3.69
7693 8434 1.308877 AACTTATCCTGGGGCCACAT 58.691 50.000 8.98 0.00 0.00 3.21
7844 8585 2.671682 GTGCCCTCCACCTCCTTC 59.328 66.667 0.00 0.00 38.55 3.46
7847 8588 1.920835 GCCCTCCACCTCCTTCAGT 60.921 63.158 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.440250 CCTCGATCCTGTCAACGAATAGTT 60.440 45.833 0.00 0.00 45.45 2.24
45 46 1.019278 GCCTCCTGCATTTTCGACGA 61.019 55.000 0.00 0.00 40.77 4.20
49 50 0.652592 CTACGCCTCCTGCATTTTCG 59.347 55.000 0.00 0.00 41.33 3.46
64 65 0.453950 CAACGGTCGTGTCTCCTACG 60.454 60.000 0.00 0.00 42.56 3.51
67 68 0.314302 CTTCAACGGTCGTGTCTCCT 59.686 55.000 0.00 0.00 0.00 3.69
103 104 1.739035 GCGTCTGATCCCATCGTTTCA 60.739 52.381 0.00 0.00 0.00 2.69
104 105 0.931005 GCGTCTGATCCCATCGTTTC 59.069 55.000 0.00 0.00 0.00 2.78
117 118 1.987704 CTCCTCGACCTGAGCGTCTG 61.988 65.000 0.00 0.00 43.82 3.51
122 123 4.200283 CGCCTCCTCGACCTGAGC 62.200 72.222 0.00 0.00 43.82 4.26
165 166 0.035152 TGAATGCTTCATGCCGTCCT 60.035 50.000 0.00 0.00 42.00 3.85
173 174 2.002586 CCTCGTCGTTGAATGCTTCAT 58.997 47.619 0.00 0.00 39.84 2.57
180 181 2.288579 TGTTGTAGCCTCGTCGTTGAAT 60.289 45.455 0.00 0.00 0.00 2.57
189 190 3.120511 GCTTCTTCTTTGTTGTAGCCTCG 60.121 47.826 0.00 0.00 0.00 4.63
192 193 2.095718 CCGCTTCTTCTTTGTTGTAGCC 60.096 50.000 0.00 0.00 0.00 3.93
198 199 2.863704 GCATTGCCGCTTCTTCTTTGTT 60.864 45.455 0.00 0.00 0.00 2.83
201 202 0.109597 CGCATTGCCGCTTCTTCTTT 60.110 50.000 2.41 0.00 0.00 2.52
219 223 0.109781 CGTGTTGATTTTCCAGCCCG 60.110 55.000 0.00 0.00 0.00 6.13
223 227 1.812571 CCCTCCGTGTTGATTTTCCAG 59.187 52.381 0.00 0.00 0.00 3.86
231 235 0.768622 ACATTTCCCCTCCGTGTTGA 59.231 50.000 0.00 0.00 0.00 3.18
237 241 1.369625 CGAAAGACATTTCCCCTCCG 58.630 55.000 0.00 0.00 41.56 4.63
239 243 0.727398 CGCGAAAGACATTTCCCCTC 59.273 55.000 0.00 0.00 41.56 4.30
257 261 4.009675 TCCATCTGAAAAAGGGATTGACG 58.990 43.478 0.00 0.00 0.00 4.35
259 263 5.012239 CACTCCATCTGAAAAAGGGATTGA 58.988 41.667 0.00 0.00 31.98 2.57
265 269 3.683802 AGCTCACTCCATCTGAAAAAGG 58.316 45.455 0.00 0.00 0.00 3.11
266 270 4.943142 GAGCTCACTCCATCTGAAAAAG 57.057 45.455 9.40 0.00 36.90 2.27
283 287 0.331616 GTGGGGGTGTATTTGGAGCT 59.668 55.000 0.00 0.00 0.00 4.09
284 288 0.039035 TGTGGGGGTGTATTTGGAGC 59.961 55.000 0.00 0.00 0.00 4.70
305 309 8.673711 TCATCCTTGAAACTCAATATTTAACGG 58.326 33.333 0.00 0.00 35.59 4.44
378 382 6.864560 TCGACTCGATTGTTGTAATAACAG 57.135 37.500 0.00 0.00 36.83 3.16
379 383 8.964150 CATATCGACTCGATTGTTGTAATAACA 58.036 33.333 18.74 0.00 44.59 2.41
385 389 5.969435 GTGTCATATCGACTCGATTGTTGTA 59.031 40.000 18.74 0.67 44.59 2.41
386 390 4.798907 GTGTCATATCGACTCGATTGTTGT 59.201 41.667 18.74 0.00 44.59 3.32
387 391 5.037385 AGTGTCATATCGACTCGATTGTTG 58.963 41.667 18.74 13.68 44.59 3.33
389 393 4.902443 AGTGTCATATCGACTCGATTGT 57.098 40.909 18.74 6.27 44.59 2.71
390 394 5.516696 ACAAAGTGTCATATCGACTCGATTG 59.483 40.000 18.74 15.39 44.59 2.67
394 398 5.763444 AAACAAAGTGTCATATCGACTCG 57.237 39.130 0.00 0.00 45.60 4.18
422 426 7.845622 GCAGTGTTGTCATATGTTTTTCAAAAC 59.154 33.333 8.02 8.02 46.40 2.43
441 445 5.634859 GCATAACAGCAATTTTAGCAGTGTT 59.365 36.000 0.00 0.00 35.45 3.32
468 472 8.617809 GGCCATATCTTTCGTTATTCACTTAAA 58.382 33.333 0.00 0.00 0.00 1.52
479 483 1.065709 ACCGTGGCCATATCTTTCGTT 60.066 47.619 9.72 0.00 0.00 3.85
480 484 0.539986 ACCGTGGCCATATCTTTCGT 59.460 50.000 9.72 0.00 0.00 3.85
490 494 0.180642 TCTACACAAAACCGTGGCCA 59.819 50.000 0.00 0.00 41.38 5.36
491 495 0.589708 GTCTACACAAAACCGTGGCC 59.410 55.000 0.00 0.00 41.38 5.36
500 504 1.667151 CCGTCCCGGTCTACACAAA 59.333 57.895 0.00 0.00 42.73 2.83
519 523 2.593436 AAAACAGCGTGGGTCCCG 60.593 61.111 2.65 0.00 0.00 5.14
520 524 2.613506 CGAAAACAGCGTGGGTCCC 61.614 63.158 0.00 0.00 0.00 4.46
538 818 0.037447 AAGGAGAAGGGTGCAGAAGC 59.963 55.000 0.00 0.00 42.57 3.86
539 819 1.339535 GGAAGGAGAAGGGTGCAGAAG 60.340 57.143 0.00 0.00 0.00 2.85
544 824 2.269241 CGGGAAGGAGAAGGGTGC 59.731 66.667 0.00 0.00 0.00 5.01
671 953 2.437651 GGGAAGAGGAAGGATGAAGAGG 59.562 54.545 0.00 0.00 0.00 3.69
714 1014 4.345547 GGGTTTAGGGTTTTGAAATGGACA 59.654 41.667 0.00 0.00 0.00 4.02
862 1163 1.641677 CCCAAATCCGCGACGATTC 59.358 57.895 8.23 0.00 31.14 2.52
1089 1390 0.101399 CGTCGGAGGGATCAGTGAAG 59.899 60.000 0.00 0.00 0.00 3.02
1162 1463 2.580867 CGTGCGCAGAGTAGAGGC 60.581 66.667 12.22 0.00 0.00 4.70
1267 1576 2.960512 GCACACACGCGCACCAATA 61.961 57.895 5.73 0.00 0.00 1.90
1324 1633 1.497991 ATGTTTATGCGAGCGCGTAT 58.502 45.000 17.99 17.99 44.90 3.06
1355 1664 5.762711 CCATCACGTAACCATATCCAATGAA 59.237 40.000 0.00 0.00 0.00 2.57
1450 1759 4.739137 GCACAAAAACATGCCCACTCTTTA 60.739 41.667 0.00 0.00 35.73 1.85
1483 1792 0.681175 AGCCATTGCACAAAGGGAAC 59.319 50.000 6.76 0.00 42.62 3.62
1625 1934 0.809385 CAGAAAGCTGCCATGGTGAG 59.191 55.000 14.67 10.93 34.95 3.51
1677 1986 1.152649 GATCCATGTTCCCCATCCCT 58.847 55.000 0.00 0.00 0.00 4.20
1809 2118 6.738114 TGGAAGTAACATCAGAAAAAGCAAG 58.262 36.000 0.00 0.00 0.00 4.01
1819 2128 5.885230 TTTCTGCATGGAAGTAACATCAG 57.115 39.130 0.00 0.00 0.00 2.90
1949 2258 7.329962 GTGTCAAAAATTGCAGAATCATGATCA 59.670 33.333 9.06 0.00 0.00 2.92
2334 2643 2.104451 AGCTGAGATTCCTGCAATCGAT 59.896 45.455 0.00 0.00 45.20 3.59
2759 3194 9.516314 AAAAGTACTTTAGCTTCAAAATGTGTC 57.484 29.630 20.83 0.00 31.63 3.67
2790 3227 3.276857 GGATCAGAGCAAGAAAGATGCA 58.723 45.455 0.00 0.00 46.22 3.96
2884 3321 1.338769 CCCTGAAAACGTCGAGGGAAT 60.339 52.381 9.83 0.00 42.77 3.01
2896 3333 5.200483 AGTTGAATGACAAGTCCCTGAAAA 58.800 37.500 0.00 0.00 37.58 2.29
3276 3713 6.234177 AGGGCAATATATAACAGAGTTCAGC 58.766 40.000 0.00 0.00 0.00 4.26
3470 3907 0.249657 GGAGGTCGAGGATGATGTGC 60.250 60.000 0.00 0.00 0.00 4.57
4412 4962 6.706295 AGAAGTCAACTCTTGGGAATCTAAG 58.294 40.000 0.00 0.00 33.42 2.18
4422 4972 7.736447 AACCAGATAAAGAAGTCAACTCTTG 57.264 36.000 0.00 0.00 0.00 3.02
4500 5050 2.205074 CGGTCCTCAATACTGCATGAC 58.795 52.381 0.00 0.00 0.00 3.06
4634 5211 3.375299 CCTTCGCTACTTGGGAAAATGAG 59.625 47.826 0.00 0.00 45.05 2.90
4644 5221 6.842163 ACAAATTTGATACCTTCGCTACTTG 58.158 36.000 24.64 0.00 0.00 3.16
5017 5594 2.373540 TAGACGATTTGGTGGGAACG 57.626 50.000 0.00 0.00 0.00 3.95
5334 6027 3.707611 AGCAATACTATCCGTGGTTACCA 59.292 43.478 0.00 0.00 0.00 3.25
5343 6036 9.862371 AAGATCATAAAGTAGCAATACTATCCG 57.138 33.333 0.00 0.00 32.15 4.18
5448 6141 2.555757 GTTCTAATGCATCCATCCCTGC 59.444 50.000 0.00 0.00 38.87 4.85
5449 6142 3.152341 GGTTCTAATGCATCCATCCCTG 58.848 50.000 0.00 0.00 0.00 4.45
5491 6184 6.648879 ATTCTAATCGGAGAGAAAGAGAGG 57.351 41.667 8.65 0.00 43.63 3.69
5505 6198 9.483062 GACACTCAATGAGAAAAATTCTAATCG 57.517 33.333 18.20 0.00 40.87 3.34
5514 6207 6.992123 TCTAGCTTGACACTCAATGAGAAAAA 59.008 34.615 18.20 4.99 35.59 1.94
5525 6218 4.634184 TCGGTAATCTAGCTTGACACTC 57.366 45.455 0.00 0.00 0.00 3.51
5555 6249 7.857456 ACCTCAGAATTACCACATGTTACATA 58.143 34.615 0.00 0.00 0.00 2.29
5578 6272 3.971245 TGCAAATATCACCCCAAAACC 57.029 42.857 0.00 0.00 0.00 3.27
5777 6480 1.553690 TAGCACCACTGAGGGCTTCC 61.554 60.000 11.03 0.00 41.96 3.46
5961 6664 7.609532 CCCTCTTGAACTGAAGAAGACAATAAT 59.390 37.037 0.00 0.00 31.52 1.28
6059 6762 2.766263 AGAGCCACGTATTCTTGGATCA 59.234 45.455 14.12 0.00 46.33 2.92
6145 6848 5.070685 ACAAAATGTACCAGAAAGGAGGAC 58.929 41.667 0.00 0.00 41.22 3.85
6147 6850 5.770162 AGAACAAAATGTACCAGAAAGGAGG 59.230 40.000 0.00 0.00 41.22 4.30
6151 6854 8.154649 ACTACAGAACAAAATGTACCAGAAAG 57.845 34.615 0.00 0.00 0.00 2.62
6163 6866 8.349983 GCAAGGATAAGAAACTACAGAACAAAA 58.650 33.333 0.00 0.00 0.00 2.44
6449 7152 1.612950 CTGTTTGGCACATGCTTGGTA 59.387 47.619 3.48 0.00 39.30 3.25
6513 7216 0.602638 TGTCAGTTGTCCGATGCACC 60.603 55.000 0.00 0.00 0.00 5.01
6519 7222 1.170290 TCGAGCTGTCAGTTGTCCGA 61.170 55.000 0.93 0.00 0.00 4.55
6571 7274 1.532523 TTGCTCGAAACATGGATGCA 58.467 45.000 0.00 0.00 0.00 3.96
6572 7275 2.857592 ATTGCTCGAAACATGGATGC 57.142 45.000 0.00 0.00 0.00 3.91
6781 7484 6.734104 AAGTATAAGAAAGAAGCTGCACTG 57.266 37.500 1.02 0.00 0.00 3.66
6804 7507 9.695526 CAATCAAATTAAGACCAAGATGTGAAA 57.304 29.630 0.00 0.00 0.00 2.69
6815 7518 7.066766 ACTGATCAGAGCAATCAAATTAAGACC 59.933 37.037 29.27 0.00 32.96 3.85
7027 7730 2.964740 TCACATAGTGTCTTCTGCAGC 58.035 47.619 9.47 0.00 34.79 5.25
7055 7758 3.775261 ACTTTGCTTACTTCCCCGTAA 57.225 42.857 0.00 0.00 0.00 3.18
7090 7795 2.614057 ACTTTTCAACCAGAGTGAAGCG 59.386 45.455 0.00 0.00 0.00 4.68
7146 7851 3.129287 CCAACCAAGCAATACATGAGACC 59.871 47.826 0.00 0.00 0.00 3.85
7260 7965 3.827302 AGGGGCATATAGACAGAACTACG 59.173 47.826 0.00 0.00 0.00 3.51
7489 8195 5.839063 TGACCTCATCGAATCCTAATTAGGT 59.161 40.000 27.14 12.32 44.02 3.08
7539 8276 4.666655 CGCTATTGTATGCCGTGAATTAGC 60.667 45.833 0.00 0.00 0.00 3.09
7588 8325 4.720902 CGTGCATGACAGGGGCCA 62.721 66.667 4.39 0.00 0.00 5.36
7675 8416 1.215423 GAATGTGGCCCCAGGATAAGT 59.785 52.381 0.00 0.00 0.00 2.24
7693 8434 2.356432 CCCAACAGCATCTCCATCTGAA 60.356 50.000 0.00 0.00 0.00 3.02
7847 8588 1.328279 TCGAGAAGTTCAGTGGCAGA 58.672 50.000 5.50 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.