Multiple sequence alignment - TraesCS1D01G105900

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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 TraesCS1D01G105900 chr1D 100.000 4027 0 0 857 4883 97917507 97913481 0.000000e+00 7437
1 TraesCS1D01G105900 chr1D 100.000 674 0 0 1 674 97918363 97917690 0.000000e+00 1245
2 TraesCS1D01G105900 chr1A 96.791 2337 54 8 870 3188 93397401 93395068 0.000000e+00 3880
3 TraesCS1D01G105900 chr1A 93.828 1604 62 14 3309 4883 93395068 93393473 0.000000e+00 2379
4 TraesCS1D01G105900 chr1A 91.604 667 23 12 39 674 93398100 93397436 0.000000e+00 891
5 TraesCS1D01G105900 chr1B 96.307 1787 49 6 2643 4420 155424426 155426204 0.000000e+00 2918
6 TraesCS1D01G105900 chr1B 95.017 1806 58 8 866 2648 155411714 155413510 0.000000e+00 2808
7 TraesCS1D01G105900 chr1B 88.358 670 37 14 39 674 155410688 155411350 0.000000e+00 767
8 TraesCS1D01G105900 chr1B 86.042 480 26 17 4418 4883 155429437 155429889 1.230000e-130 477


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 TraesCS1D01G105900 chr1D 97913481 97918363 4882 True 4341.000000 7437 100.000000 1 4883 2 chr1D.!!$R1 4882
1 TraesCS1D01G105900 chr1A 93393473 93398100 4627 True 2383.333333 3880 94.074333 39 4883 3 chr1A.!!$R1 4844
2 TraesCS1D01G105900 chr1B 155410688 155413510 2822 False 1787.500000 2808 91.687500 39 2648 2 chr1B.!!$F1 2609
3 TraesCS1D01G105900 chr1B 155424426 155429889 5463 False 1697.500000 2918 91.174500 2643 4883 2 chr1B.!!$F2 2240

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
117 119 0.390735 ATGAAACCGACCTACCACGC 60.391 55.0 0.00 0.0 0.00 5.34 F
507 528 0.826256 GACTTCCTTTTGGGCCGGTT 60.826 55.0 1.90 0.0 40.87 4.44 F
1587 1810 0.940833 GCTCAGCGCCTATTTTCTCC 59.059 55.0 2.29 0.0 0.00 3.71 F
1897 2120 0.459489 TGGCCAAGCACAAGTGTTTC 59.541 50.0 0.61 0.0 31.58 2.78 F
2749 2982 0.620556 GTGGATCCATGGGTGAGTGT 59.379 55.0 19.62 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1657 1.494960 AAACACACCAACCAGCCATT 58.505 45.0 0.00 0.0 0.00 3.16 R
1614 1837 1.758783 GGTGCTTCTTTCGCAACAAG 58.241 50.0 0.00 0.0 44.29 3.16 R
3382 3618 0.320374 TGTCGGACCAATCCTGTCAC 59.680 55.0 5.55 0.0 43.73 3.67 R
3704 3940 5.243060 ACCTGGGAAGTTTGTAATTGTTAGC 59.757 40.0 0.00 0.0 0.00 3.09 R
4311 4557 0.040958 GCTGCGTCTTTGGTGACTTG 60.041 55.0 0.00 0.0 35.00 3.16 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
24 25 6.825610 AGCCCATTTCAAAAGAAAATGTACA 58.174 32.000 0.00 0.00 40.77 2.90
25 26 7.278875 AGCCCATTTCAAAAGAAAATGTACAA 58.721 30.769 0.00 0.00 40.77 2.41
26 27 7.938490 AGCCCATTTCAAAAGAAAATGTACAAT 59.062 29.630 0.00 0.00 40.77 2.71
27 28 9.213799 GCCCATTTCAAAAGAAAATGTACAATA 57.786 29.630 0.00 0.00 40.77 1.90
49 50 2.026641 AGTTGAGTGTGCAATGCAAGT 58.973 42.857 10.44 3.39 41.47 3.16
51 52 3.822735 AGTTGAGTGTGCAATGCAAGTAT 59.177 39.130 10.44 0.00 41.47 2.12
52 53 4.083110 AGTTGAGTGTGCAATGCAAGTATC 60.083 41.667 10.44 6.76 41.47 2.24
53 54 3.410508 TGAGTGTGCAATGCAAGTATCA 58.589 40.909 10.44 9.41 41.47 2.15
54 55 3.189080 TGAGTGTGCAATGCAAGTATCAC 59.811 43.478 10.44 13.50 41.47 3.06
117 119 0.390735 ATGAAACCGACCTACCACGC 60.391 55.000 0.00 0.00 0.00 5.34
147 149 3.105187 TCGCTAGCCGACCATAGAA 57.895 52.632 9.66 0.00 41.89 2.10
172 174 1.613317 ATCTCCACGCGTCCAATCCA 61.613 55.000 9.86 0.00 0.00 3.41
461 482 3.365472 GCTCTTCTCTTCCTCTTCCTCT 58.635 50.000 0.00 0.00 0.00 3.69
507 528 0.826256 GACTTCCTTTTGGGCCGGTT 60.826 55.000 1.90 0.00 40.87 4.44
532 553 4.955925 AGATTCTCGGCTCGTATATGAG 57.044 45.455 16.38 16.38 39.05 2.90
545 566 1.428869 ATATGAGCTGGACCCTGGTC 58.571 55.000 15.35 15.35 43.87 4.02
630 651 2.355837 GAGCGGTTCTCGTGTGCA 60.356 61.111 0.00 0.00 41.72 4.57
967 1175 3.196040 GCCCATCAGCCATCTTTCA 57.804 52.632 0.00 0.00 0.00 2.69
1073 1294 1.068474 CCTCGCAAGGTTAGTGTTCG 58.932 55.000 0.00 0.00 37.94 3.95
1078 1299 2.286772 CGCAAGGTTAGTGTTCGCTTTT 60.287 45.455 0.00 0.00 0.00 2.27
1128 1349 7.010552 TGTTTCAATTTGATGGTTACGGTTTTG 59.989 33.333 0.00 0.00 0.00 2.44
1268 1489 9.174166 TCCAGTTATTTAAGGTTTTCTAGATGC 57.826 33.333 0.00 0.00 0.00 3.91
1392 1615 4.141937 TGAAGACATCACAGGTGCCTATAC 60.142 45.833 0.00 0.00 31.50 1.47
1434 1657 7.261325 TGTTGTATCTGCAAGCTTTTTGTTTA 58.739 30.769 0.00 0.00 0.00 2.01
1442 1665 4.319694 GCAAGCTTTTTGTTTAATGGCTGG 60.320 41.667 0.00 0.00 0.00 4.85
1465 1688 9.751542 CTGGTTGGTGTGTTTTATATTTTGTTA 57.248 29.630 0.00 0.00 0.00 2.41
1587 1810 0.940833 GCTCAGCGCCTATTTTCTCC 59.059 55.000 2.29 0.00 0.00 3.71
1725 1948 4.683781 GTCGCATCTAATTCCTCATCACTC 59.316 45.833 0.00 0.00 0.00 3.51
1739 1962 3.431912 TCATCACTCGACAAAATTGACCG 59.568 43.478 0.00 3.68 0.00 4.79
1783 2006 7.922811 GTCATGGACTTCTTTGAACAATTTCTT 59.077 33.333 0.00 0.00 32.36 2.52
1842 2065 6.770785 ACACAATGTTGTTCTACCAATACACT 59.229 34.615 0.00 0.00 39.91 3.55
1897 2120 0.459489 TGGCCAAGCACAAGTGTTTC 59.541 50.000 0.61 0.00 31.58 2.78
1950 2173 7.383361 GTGAAAACATATTGCGAATAACTTGC 58.617 34.615 0.00 0.00 0.00 4.01
2050 2273 8.798859 AATCTTGTTCTCTTGCATAGTGTAAT 57.201 30.769 0.00 0.00 0.00 1.89
2062 2285 5.176774 TGCATAGTGTAATATTACTGCACGC 59.823 40.000 24.98 20.54 36.68 5.34
2576 2809 5.163343 ACCTTGCACTCTTGTAGTTGTTAGA 60.163 40.000 0.00 0.00 35.76 2.10
2638 2871 7.040201 ACAGAGATCATGCAACACTGTTTTAAT 60.040 33.333 0.00 0.00 33.30 1.40
2749 2982 0.620556 GTGGATCCATGGGTGAGTGT 59.379 55.000 19.62 0.00 0.00 3.55
2910 3143 6.689561 TCCTGGTATTCTATTGGTCCTTCTA 58.310 40.000 0.00 0.00 0.00 2.10
3219 3452 5.109500 TGGTATTGCAGTGGATTGTGATA 57.891 39.130 0.00 0.00 0.00 2.15
3252 3485 4.222810 GCCCCACCAGATTTTGTCTATTTT 59.777 41.667 0.00 0.00 34.69 1.82
3253 3486 5.420739 GCCCCACCAGATTTTGTCTATTTTA 59.579 40.000 0.00 0.00 34.69 1.52
3269 3502 9.005777 TGTCTATTTTAGTGTTATTTCACCCAC 57.994 33.333 0.00 0.00 38.91 4.61
3289 3522 5.699458 CCCACGTTTTTGTACTTCTATGACT 59.301 40.000 0.00 0.00 0.00 3.41
3320 3556 7.667557 TGTACAGAAGACTAAATAAGCACAGT 58.332 34.615 0.00 0.00 0.00 3.55
3382 3618 6.308766 GCTGCTTTTTATATTGACTGTTGTGG 59.691 38.462 0.00 0.00 0.00 4.17
3840 4076 1.368579 CGCGGTTATTACCCCGGAT 59.631 57.895 0.73 0.00 41.06 4.18
3844 4080 2.224257 GCGGTTATTACCCCGGATGTTA 60.224 50.000 0.73 0.00 44.36 2.41
4180 4424 7.286087 TCTCGGTAAAGTGAAGGTGCTTATATA 59.714 37.037 0.00 0.00 0.00 0.86
4190 4434 9.219603 GTGAAGGTGCTTATATATGCAAATCTA 57.780 33.333 21.16 8.68 41.10 1.98
4230 4476 3.531538 CCATGCGTGGTAGAATAAGTGT 58.468 45.455 17.42 0.00 40.83 3.55
4311 4557 4.024218 GCTAACAGATGTGCATCTCCATTC 60.024 45.833 11.38 0.00 45.78 2.67
4312 4558 3.639672 ACAGATGTGCATCTCCATTCA 57.360 42.857 11.38 0.00 45.78 2.57
4326 4572 3.138304 TCCATTCAAGTCACCAAAGACG 58.862 45.455 0.00 0.00 43.24 4.18
4378 4629 1.418637 TCCTCACCACGTTAGGCTTTT 59.581 47.619 0.00 0.00 27.94 2.27
4423 7908 2.352561 TCCTCACCCATTCCCTGTAA 57.647 50.000 0.00 0.00 0.00 2.41
4502 7987 3.489355 TCCCAGCATGCACCTATTAATG 58.511 45.455 21.98 5.61 31.97 1.90
4512 7997 3.751893 GCACCTATTAATGCCACCCATCT 60.752 47.826 0.00 0.00 35.73 2.90
4514 7999 4.895297 CACCTATTAATGCCACCCATCTTT 59.105 41.667 0.00 0.00 31.43 2.52
4517 8002 5.776716 CCTATTAATGCCACCCATCTTTCAT 59.223 40.000 0.00 0.00 31.43 2.57
4528 8013 3.069586 CCCATCTTTCATCATGCAGCAAT 59.930 43.478 0.00 0.00 0.00 3.56
4532 8017 7.251281 CCATCTTTCATCATGCAGCAATATAG 58.749 38.462 0.00 0.00 0.00 1.31
4544 8029 7.880160 TGCAGCAATATAGGAGTTATGTTTT 57.120 32.000 0.00 0.00 0.00 2.43
4547 8032 8.836413 GCAGCAATATAGGAGTTATGTTTTACA 58.164 33.333 0.00 0.00 0.00 2.41
4625 8110 6.166279 TCAAGTACAGAAGGATCACACATTC 58.834 40.000 0.00 0.00 0.00 2.67
4670 8155 4.833380 AGTACCACTCACTAGAAAGCAGAA 59.167 41.667 0.00 0.00 0.00 3.02
4695 8180 7.099266 TCAGTTTCATTCAGAAGCAAAAGAA 57.901 32.000 0.00 0.00 39.64 2.52
4723 8208 3.130340 GTCCAGACCATGTTCTCTCTCTC 59.870 52.174 0.00 0.00 0.00 3.20
4724 8209 3.011144 TCCAGACCATGTTCTCTCTCTCT 59.989 47.826 0.00 0.00 0.00 3.10
4771 8256 6.100404 ACTGGCAAAGAATTTTGAATAGCA 57.900 33.333 4.33 0.00 45.21 3.49
4772 8257 6.704310 ACTGGCAAAGAATTTTGAATAGCAT 58.296 32.000 4.33 0.00 45.21 3.79
4773 8258 6.815142 ACTGGCAAAGAATTTTGAATAGCATC 59.185 34.615 4.33 0.00 45.21 3.91
4774 8259 6.938507 TGGCAAAGAATTTTGAATAGCATCT 58.061 32.000 4.33 0.00 45.21 2.90
4776 8261 6.238022 GGCAAAGAATTTTGAATAGCATCTGC 60.238 38.462 4.33 0.00 45.21 4.26
4777 8262 6.311935 GCAAAGAATTTTGAATAGCATCTGCA 59.688 34.615 4.79 0.00 45.21 4.41
4778 8263 7.464178 GCAAAGAATTTTGAATAGCATCTGCAG 60.464 37.037 7.63 7.63 45.21 4.41
4822 8321 9.376075 TCAATGAGCACAACAATTTAAGAAAAA 57.624 25.926 0.00 0.00 0.00 1.94
4825 8324 8.939201 TGAGCACAACAATTTAAGAAAAATCA 57.061 26.923 0.00 0.00 0.00 2.57
4826 8325 9.376075 TGAGCACAACAATTTAAGAAAAATCAA 57.624 25.926 0.00 0.00 0.00 2.57
4827 8326 9.853921 GAGCACAACAATTTAAGAAAAATCAAG 57.146 29.630 0.00 0.00 0.00 3.02
4828 8327 8.337532 AGCACAACAATTTAAGAAAAATCAAGC 58.662 29.630 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.825610 TGTACATTTTCTTTTGAAATGGGCT 58.174 32.000 12.51 0.00 46.43 5.19
1 2 7.489574 TTGTACATTTTCTTTTGAAATGGGC 57.510 32.000 12.51 6.60 46.43 5.36
13 14 9.950680 CACACTCAACTTTATTGTACATTTTCT 57.049 29.630 0.00 0.00 0.00 2.52
14 15 8.690840 GCACACTCAACTTTATTGTACATTTTC 58.309 33.333 0.00 0.00 0.00 2.29
15 16 8.194104 TGCACACTCAACTTTATTGTACATTTT 58.806 29.630 0.00 0.00 0.00 1.82
16 17 7.711846 TGCACACTCAACTTTATTGTACATTT 58.288 30.769 0.00 0.00 0.00 2.32
17 18 7.270757 TGCACACTCAACTTTATTGTACATT 57.729 32.000 0.00 0.00 0.00 2.71
18 19 6.875948 TGCACACTCAACTTTATTGTACAT 57.124 33.333 0.00 0.00 0.00 2.29
19 20 6.685527 TTGCACACTCAACTTTATTGTACA 57.314 33.333 0.00 0.00 0.00 2.90
20 21 6.088085 GCATTGCACACTCAACTTTATTGTAC 59.912 38.462 3.15 0.00 0.00 2.90
21 22 6.148948 GCATTGCACACTCAACTTTATTGTA 58.851 36.000 3.15 0.00 0.00 2.41
22 23 4.984161 GCATTGCACACTCAACTTTATTGT 59.016 37.500 3.15 0.00 0.00 2.71
23 24 4.983538 TGCATTGCACACTCAACTTTATTG 59.016 37.500 7.38 0.00 31.71 1.90
24 25 5.199024 TGCATTGCACACTCAACTTTATT 57.801 34.783 7.38 0.00 31.71 1.40
25 26 4.852134 TGCATTGCACACTCAACTTTAT 57.148 36.364 7.38 0.00 31.71 1.40
26 27 4.097741 ACTTGCATTGCACACTCAACTTTA 59.902 37.500 11.66 0.00 38.71 1.85
27 28 3.119029 ACTTGCATTGCACACTCAACTTT 60.119 39.130 11.66 0.00 38.71 2.66
28 29 2.428171 ACTTGCATTGCACACTCAACTT 59.572 40.909 11.66 0.00 38.71 2.66
29 30 2.026641 ACTTGCATTGCACACTCAACT 58.973 42.857 11.66 0.00 38.71 3.16
30 31 2.497107 ACTTGCATTGCACACTCAAC 57.503 45.000 11.66 0.00 38.71 3.18
31 32 3.819902 TGATACTTGCATTGCACACTCAA 59.180 39.130 11.66 0.00 38.71 3.02
32 33 3.189080 GTGATACTTGCATTGCACACTCA 59.811 43.478 11.66 9.22 38.71 3.41
33 34 3.189080 TGTGATACTTGCATTGCACACTC 59.811 43.478 22.22 13.52 38.71 3.51
34 35 3.148412 TGTGATACTTGCATTGCACACT 58.852 40.909 22.22 8.39 38.71 3.55
35 36 3.189080 TCTGTGATACTTGCATTGCACAC 59.811 43.478 11.66 15.44 38.71 3.82
36 37 3.410508 TCTGTGATACTTGCATTGCACA 58.589 40.909 11.66 2.60 38.71 4.57
37 38 4.161333 GTTCTGTGATACTTGCATTGCAC 58.839 43.478 11.66 0.00 38.71 4.57
49 50 4.558226 AGGTCAGCAATGTTCTGTGATA 57.442 40.909 0.00 0.00 33.48 2.15
51 52 2.936919 AGGTCAGCAATGTTCTGTGA 57.063 45.000 0.00 0.00 33.48 3.58
52 53 3.402110 TGTAGGTCAGCAATGTTCTGTG 58.598 45.455 0.00 0.00 33.48 3.66
53 54 3.769739 TGTAGGTCAGCAATGTTCTGT 57.230 42.857 0.00 0.00 33.48 3.41
54 55 4.611355 CGTTTGTAGGTCAGCAATGTTCTG 60.611 45.833 0.00 0.00 0.00 3.02
96 98 1.636988 GTGGTAGGTCGGTTTCATCG 58.363 55.000 0.00 0.00 0.00 3.84
99 101 1.005867 GCGTGGTAGGTCGGTTTCA 60.006 57.895 0.00 0.00 0.00 2.69
120 122 2.934553 GGTCGGCTAGCGAATTAGTTTT 59.065 45.455 9.00 0.00 0.00 2.43
142 144 3.181475 ACGCGTGGAGATGTGAATTCTAT 60.181 43.478 12.93 1.30 0.00 1.98
145 147 1.324736 GACGCGTGGAGATGTGAATTC 59.675 52.381 20.70 0.00 0.00 2.17
147 149 0.460284 GGACGCGTGGAGATGTGAAT 60.460 55.000 20.70 0.00 0.00 2.57
172 174 0.387202 CTCTGCGAGGTCGGATTCAT 59.613 55.000 0.89 0.00 39.39 2.57
461 482 1.919240 TGTGAGCCGACCTAGAAGAA 58.081 50.000 0.00 0.00 0.00 2.52
507 528 6.171213 TCATATACGAGCCGAGAATCTTAGA 58.829 40.000 1.50 0.00 0.00 2.10
1073 1294 9.516314 GGAATATACATTAGGAACAACAAAAGC 57.484 33.333 0.00 0.00 0.00 3.51
1078 1299 9.693739 ACAATGGAATATACATTAGGAACAACA 57.306 29.630 5.52 0.00 36.47 3.33
1128 1349 3.118992 CCTCCCTTAAAATGCAAGAAGCC 60.119 47.826 0.00 0.00 44.83 4.35
1268 1489 2.246739 CCATGATACCGTGCCTGCG 61.247 63.158 0.00 0.00 0.00 5.18
1392 1615 1.878953 ACAAACGGCCAACAGACTAG 58.121 50.000 2.24 0.00 0.00 2.57
1434 1657 1.494960 AAACACACCAACCAGCCATT 58.505 45.000 0.00 0.00 0.00 3.16
1465 1688 2.234908 GGGATCAGTGCTCTACAGTTGT 59.765 50.000 0.00 0.00 0.00 3.32
1468 1691 2.541233 AGGGATCAGTGCTCTACAGT 57.459 50.000 0.00 0.00 0.00 3.55
1587 1810 2.167693 ACTGATGAGCCAATGCAAATGG 59.832 45.455 15.67 15.67 41.13 3.16
1614 1837 1.758783 GGTGCTTCTTTCGCAACAAG 58.241 50.000 0.00 0.00 44.29 3.16
1725 1948 4.404507 AGTTGATCGGTCAATTTTGTCG 57.595 40.909 15.35 0.00 45.46 4.35
1739 1962 6.659242 TCCATGACTTAAAAGGGAAGTTGATC 59.341 38.462 0.00 0.00 37.27 2.92
1783 2006 7.169645 GGACGAAACACACATAAACTAGTAACA 59.830 37.037 0.00 0.00 0.00 2.41
1842 2065 3.287222 CACAGTTTTCTTTCCAGGACCA 58.713 45.455 0.00 0.00 0.00 4.02
1897 2120 3.135994 AGGCCAACAAAACTACAGTACG 58.864 45.455 5.01 0.00 0.00 3.67
1950 2173 3.432252 CCTTGTAAGTTACAGTTGCCTCG 59.568 47.826 15.06 0.16 40.24 4.63
2369 2594 8.550376 GTGGAACGTTTAACTAAACATAGAACA 58.450 33.333 0.46 1.98 44.29 3.18
2441 2674 4.754322 CCAACAAACTACCAAAAAGCACT 58.246 39.130 0.00 0.00 0.00 4.40
2536 2769 5.048083 GTGCAAGGTCTTCATCCAAATACAA 60.048 40.000 0.00 0.00 0.00 2.41
2576 2809 4.035441 GTGAAACAAAATTGCAATGCCAGT 59.965 37.500 13.82 6.95 36.32 4.00
2615 2848 7.596248 ACAATTAAAACAGTGTTGCATGATCTC 59.404 33.333 9.79 0.00 0.00 2.75
2638 2871 6.828273 AGCTCCAAATACAGCAATATGTACAA 59.172 34.615 0.00 0.00 38.43 2.41
2749 2982 3.472283 TTGGTTCGCACTTGGTAACTA 57.528 42.857 0.00 0.00 37.61 2.24
2945 3178 5.517904 ACGTACGTAGGAGAGAAATAATGC 58.482 41.667 21.41 0.00 0.00 3.56
3219 3452 2.283604 GGTGGGGCAAACGGGATT 60.284 61.111 0.00 0.00 0.00 3.01
3252 3485 6.095160 ACAAAAACGTGGGTGAAATAACACTA 59.905 34.615 0.00 0.00 40.22 2.74
3253 3486 5.105675 ACAAAAACGTGGGTGAAATAACACT 60.106 36.000 0.00 0.00 40.22 3.55
3320 3556 6.641169 TTGTGGTTGCTGAATTGTATTGTA 57.359 33.333 0.00 0.00 0.00 2.41
3382 3618 0.320374 TGTCGGACCAATCCTGTCAC 59.680 55.000 5.55 0.00 43.73 3.67
3704 3940 5.243060 ACCTGGGAAGTTTGTAATTGTTAGC 59.757 40.000 0.00 0.00 0.00 3.09
4143 4387 6.285224 TCACTTTACCGAGAAAACTTGATCA 58.715 36.000 0.00 0.00 0.00 2.92
4311 4557 0.040958 GCTGCGTCTTTGGTGACTTG 60.041 55.000 0.00 0.00 35.00 3.16
4312 4558 1.166531 GGCTGCGTCTTTGGTGACTT 61.167 55.000 0.00 0.00 35.00 3.01
4326 4572 6.075762 TGTGATCACATTATAATTGGCTGC 57.924 37.500 24.56 0.00 36.21 5.25
4378 4629 2.500229 GGATCACCAGACAAACCGAAA 58.500 47.619 0.00 0.00 35.97 3.46
4423 7908 6.903534 TGAGGAGAATTTAGAGGTGTAATCCT 59.096 38.462 0.00 0.00 40.97 3.24
4502 7987 1.068127 GCATGATGAAAGATGGGTGGC 59.932 52.381 0.00 0.00 0.00 5.01
4512 7997 6.301486 ACTCCTATATTGCTGCATGATGAAA 58.699 36.000 1.84 0.00 0.00 2.69
4514 7999 5.494390 ACTCCTATATTGCTGCATGATGA 57.506 39.130 1.84 0.00 0.00 2.92
4517 8002 6.772605 ACATAACTCCTATATTGCTGCATGA 58.227 36.000 1.84 0.00 0.00 3.07
4532 8017 7.667043 TGATGACACTGTAAAACATAACTCC 57.333 36.000 0.00 0.00 0.00 3.85
4544 8029 6.765512 TGTTCAGTTCAAATGATGACACTGTA 59.234 34.615 10.94 2.13 42.04 2.74
4547 8032 6.698008 TTGTTCAGTTCAAATGATGACACT 57.302 33.333 0.00 0.00 37.92 3.55
4656 8141 6.791887 TGAAACTGATTCTGCTTTCTAGTG 57.208 37.500 13.86 0.00 38.92 2.74
4670 8155 7.281040 TCTTTTGCTTCTGAATGAAACTGAT 57.719 32.000 0.00 0.00 33.79 2.90
4695 8180 3.964031 GAGAACATGGTCTGGACTATCCT 59.036 47.826 20.40 0.00 37.46 3.24
4723 8208 1.410153 AGGCAGTTTGCTTTGGTCAAG 59.590 47.619 0.67 0.00 44.28 3.02
4724 8209 1.484038 AGGCAGTTTGCTTTGGTCAA 58.516 45.000 0.67 0.00 44.28 3.18
4817 8316 7.183580 AGCTACAGATATCGCTTGATTTTTC 57.816 36.000 0.00 0.00 33.40 2.29
4822 8321 7.163001 TCAATAGCTACAGATATCGCTTGAT 57.837 36.000 7.95 0.00 34.14 2.57
4823 8322 6.575162 TCAATAGCTACAGATATCGCTTGA 57.425 37.500 7.95 4.89 34.14 3.02
4824 8323 9.179552 GATATCAATAGCTACAGATATCGCTTG 57.820 37.037 25.88 12.82 39.35 4.01
4825 8324 8.907885 TGATATCAATAGCTACAGATATCGCTT 58.092 33.333 29.51 14.46 46.19 4.68
4826 8325 8.349245 GTGATATCAATAGCTACAGATATCGCT 58.651 37.037 33.14 17.46 46.81 4.93
4827 8326 8.500837 GTGATATCAATAGCTACAGATATCGC 57.499 38.462 30.60 30.60 46.19 4.58
4828 8327 9.662545 CAGTGATATCAATAGCTACAGATATCG 57.337 37.037 29.51 20.86 46.19 2.92


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

AutoCloner maintained by Alex Coulton.