Multiple sequence alignment - TraesCS1B01G240600

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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 TraesCS1B01G240600 chr1B 100.000 2462 0 0 1 2462 428535037 428537498 0.000000e+00 4547
1 TraesCS1B01G240600 chr1D 94.454 2362 96 22 83 2416 316204506 316206860 0.000000e+00 3603
2 TraesCS1B01G240600 chr1D 92.308 91 7 0 1 91 316172500 316172590 1.990000e-26 130
3 TraesCS1B01G240600 chr1A 93.292 2415 119 22 83 2462 397052310 397054716 0.000000e+00 3522


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 TraesCS1B01G240600 chr1B 428535037 428537498 2461 False 4547 4547 100.000 1 2462 1 chr1B.!!$F1 2461
1 TraesCS1B01G240600 chr1D 316204506 316206860 2354 False 3603 3603 94.454 83 2416 1 chr1D.!!$F2 2333
2 TraesCS1B01G240600 chr1A 397052310 397054716 2406 False 3522 3522 93.292 83 2462 1 chr1A.!!$F1 2379

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
48 49 0.044855 AGAGCCCCAACCTCTACCAT 59.955 55.0 0.0 0.0 37.88 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 1659 0.949105 ATTCACACCCGTCGCAAGTC 60.949 55.0 0.0 0.0 39.48 3.01 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
19 20 1.609208 ACCATTGTGTTCCTGTCAGC 58.391 50.000 0.00 0.00 0.00 4.26
20 21 1.143684 ACCATTGTGTTCCTGTCAGCT 59.856 47.619 0.00 0.00 0.00 4.24
21 22 2.371841 ACCATTGTGTTCCTGTCAGCTA 59.628 45.455 0.00 0.00 0.00 3.32
22 23 3.181445 ACCATTGTGTTCCTGTCAGCTAA 60.181 43.478 0.00 0.00 0.00 3.09
23 24 4.012374 CCATTGTGTTCCTGTCAGCTAAT 58.988 43.478 0.00 0.00 0.00 1.73
24 25 5.185454 CCATTGTGTTCCTGTCAGCTAATA 58.815 41.667 0.00 0.00 0.00 0.98
25 26 5.824624 CCATTGTGTTCCTGTCAGCTAATAT 59.175 40.000 0.00 0.00 0.00 1.28
26 27 6.319658 CCATTGTGTTCCTGTCAGCTAATATT 59.680 38.462 0.00 0.00 0.00 1.28
27 28 7.148018 CCATTGTGTTCCTGTCAGCTAATATTT 60.148 37.037 0.00 0.00 0.00 1.40
28 29 6.985188 TGTGTTCCTGTCAGCTAATATTTC 57.015 37.500 0.00 0.00 0.00 2.17
29 30 6.472016 TGTGTTCCTGTCAGCTAATATTTCA 58.528 36.000 0.00 0.00 0.00 2.69
30 31 6.595326 TGTGTTCCTGTCAGCTAATATTTCAG 59.405 38.462 0.00 0.00 0.00 3.02
31 32 6.818644 GTGTTCCTGTCAGCTAATATTTCAGA 59.181 38.462 0.00 0.00 0.00 3.27
32 33 7.010923 GTGTTCCTGTCAGCTAATATTTCAGAG 59.989 40.741 0.00 0.00 0.00 3.35
33 34 5.605534 TCCTGTCAGCTAATATTTCAGAGC 58.394 41.667 0.00 0.00 35.07 4.09
34 35 4.754114 CCTGTCAGCTAATATTTCAGAGCC 59.246 45.833 4.64 0.00 35.45 4.70
35 36 4.708177 TGTCAGCTAATATTTCAGAGCCC 58.292 43.478 4.64 0.00 35.45 5.19
36 37 4.068599 GTCAGCTAATATTTCAGAGCCCC 58.931 47.826 4.64 0.00 35.45 5.80
37 38 3.716353 TCAGCTAATATTTCAGAGCCCCA 59.284 43.478 4.64 0.00 35.45 4.96
38 39 4.165950 TCAGCTAATATTTCAGAGCCCCAA 59.834 41.667 4.64 0.00 35.45 4.12
39 40 4.276926 CAGCTAATATTTCAGAGCCCCAAC 59.723 45.833 4.64 0.00 35.45 3.77
40 41 3.570125 GCTAATATTTCAGAGCCCCAACC 59.430 47.826 0.00 0.00 0.00 3.77
41 42 4.689983 GCTAATATTTCAGAGCCCCAACCT 60.690 45.833 0.00 0.00 0.00 3.50
42 43 3.584733 ATATTTCAGAGCCCCAACCTC 57.415 47.619 0.00 0.00 0.00 3.85
43 44 1.376649 ATTTCAGAGCCCCAACCTCT 58.623 50.000 0.00 0.00 40.17 3.69
44 45 2.038863 TTTCAGAGCCCCAACCTCTA 57.961 50.000 0.00 0.00 37.57 2.43
45 46 1.276622 TTCAGAGCCCCAACCTCTAC 58.723 55.000 0.00 0.00 37.57 2.59
46 47 0.617820 TCAGAGCCCCAACCTCTACC 60.618 60.000 0.00 0.00 37.57 3.18
47 48 0.909610 CAGAGCCCCAACCTCTACCA 60.910 60.000 0.00 0.00 37.57 3.25
48 49 0.044855 AGAGCCCCAACCTCTACCAT 59.955 55.000 0.00 0.00 37.88 3.55
49 50 0.919710 GAGCCCCAACCTCTACCATT 59.080 55.000 0.00 0.00 0.00 3.16
50 51 0.625849 AGCCCCAACCTCTACCATTG 59.374 55.000 0.00 0.00 0.00 2.82
51 52 0.331616 GCCCCAACCTCTACCATTGT 59.668 55.000 0.00 0.00 0.00 2.71
52 53 1.682087 GCCCCAACCTCTACCATTGTC 60.682 57.143 0.00 0.00 0.00 3.18
53 54 1.916181 CCCCAACCTCTACCATTGTCT 59.084 52.381 0.00 0.00 0.00 3.41
54 55 2.308866 CCCCAACCTCTACCATTGTCTT 59.691 50.000 0.00 0.00 0.00 3.01
55 56 3.521937 CCCCAACCTCTACCATTGTCTTA 59.478 47.826 0.00 0.00 0.00 2.10
56 57 4.018779 CCCCAACCTCTACCATTGTCTTAA 60.019 45.833 0.00 0.00 0.00 1.85
57 58 5.515886 CCCCAACCTCTACCATTGTCTTAAA 60.516 44.000 0.00 0.00 0.00 1.52
58 59 6.187682 CCCAACCTCTACCATTGTCTTAAAT 58.812 40.000 0.00 0.00 0.00 1.40
59 60 6.663523 CCCAACCTCTACCATTGTCTTAAATT 59.336 38.462 0.00 0.00 0.00 1.82
60 61 7.178451 CCCAACCTCTACCATTGTCTTAAATTT 59.822 37.037 0.00 0.00 0.00 1.82
61 62 8.028938 CCAACCTCTACCATTGTCTTAAATTTG 58.971 37.037 0.00 0.00 0.00 2.32
62 63 8.576442 CAACCTCTACCATTGTCTTAAATTTGT 58.424 33.333 0.00 0.00 0.00 2.83
63 64 8.706322 ACCTCTACCATTGTCTTAAATTTGTT 57.294 30.769 0.00 0.00 0.00 2.83
64 65 8.793592 ACCTCTACCATTGTCTTAAATTTGTTC 58.206 33.333 0.00 0.00 0.00 3.18
65 66 8.792633 CCTCTACCATTGTCTTAAATTTGTTCA 58.207 33.333 0.00 0.00 0.00 3.18
66 67 9.612620 CTCTACCATTGTCTTAAATTTGTTCAC 57.387 33.333 0.00 0.00 0.00 3.18
67 68 9.126151 TCTACCATTGTCTTAAATTTGTTCACA 57.874 29.630 0.00 0.00 0.00 3.58
68 69 9.743057 CTACCATTGTCTTAAATTTGTTCACAA 57.257 29.630 0.00 5.30 0.00 3.33
89 90 8.533657 TCACAAATTTTAGATTGCCATCTTCAT 58.466 29.630 5.50 0.00 40.53 2.57
96 97 8.668510 TTTAGATTGCCATCTTCATAGTTCTC 57.331 34.615 5.50 0.00 40.53 2.87
97 98 6.244552 AGATTGCCATCTTCATAGTTCTCA 57.755 37.500 0.00 0.00 36.18 3.27
100 101 5.016051 TGCCATCTTCATAGTTCTCACTC 57.984 43.478 0.00 0.00 34.06 3.51
110 111 6.556212 TCATAGTTCTCACTCTCTTTAAGCG 58.444 40.000 0.00 0.00 34.06 4.68
115 116 1.540267 TCACTCTCTTTAAGCGCGAGT 59.460 47.619 12.10 3.61 35.49 4.18
143 144 1.225855 GTTCTCGGTTGCACACATGA 58.774 50.000 0.00 0.00 0.00 3.07
165 166 6.258354 TGAACTAGGTCTTCATGGTTAGGTA 58.742 40.000 9.68 0.00 29.97 3.08
172 173 3.055385 TCTTCATGGTTAGGTAGTGTGCC 60.055 47.826 0.00 0.00 0.00 5.01
175 176 2.320681 TGGTTAGGTAGTGTGCCTCT 57.679 50.000 0.00 0.00 37.54 3.69
178 179 3.512724 TGGTTAGGTAGTGTGCCTCTAAC 59.487 47.826 0.00 0.00 39.09 2.34
183 184 2.678336 GGTAGTGTGCCTCTAACATTGC 59.322 50.000 0.00 0.00 0.00 3.56
186 187 0.323302 TGTGCCTCTAACATTGCCGA 59.677 50.000 0.00 0.00 0.00 5.54
239 240 3.597377 AATGCATGTCGATTCATGTCG 57.403 42.857 15.15 0.00 44.68 4.35
242 243 2.138320 GCATGTCGATTCATGTCGGAT 58.862 47.619 15.15 0.00 44.68 4.18
247 248 3.129638 TGTCGATTCATGTCGGATGTACA 59.870 43.478 0.00 0.00 41.74 2.90
261 262 3.131577 GGATGTACAATGTAGTCGGGTCA 59.868 47.826 0.00 0.00 0.00 4.02
275 276 4.003648 GTCGGGTCATCAAAGTTGATCTT 58.996 43.478 3.51 0.00 45.62 2.40
311 312 3.825014 GGAGTGTTTCCCCTTTAAAGACC 59.175 47.826 16.98 1.63 40.37 3.85
312 313 3.483421 AGTGTTTCCCCTTTAAAGACCG 58.517 45.455 16.98 3.59 32.18 4.79
350 351 9.503427 GTGCATATCACCAAACTAAAATTCTAC 57.497 33.333 0.00 0.00 39.79 2.59
351 352 9.461312 TGCATATCACCAAACTAAAATTCTACT 57.539 29.630 0.00 0.00 0.00 2.57
380 383 3.506398 TGCCGAGGGATTGATATACAGA 58.494 45.455 0.00 0.00 0.00 3.41
424 427 4.065088 GGGAAGGAAACCAAAATTCTTGC 58.935 43.478 0.00 0.00 0.00 4.01
425 428 3.740832 GGAAGGAAACCAAAATTCTTGCG 59.259 43.478 0.00 0.00 0.00 4.85
431 434 1.963515 ACCAAAATTCTTGCGGCTTCT 59.036 42.857 0.00 0.00 0.00 2.85
441 444 2.831685 TGCGGCTTCTACTTCTTTCA 57.168 45.000 0.00 0.00 0.00 2.69
442 445 2.688507 TGCGGCTTCTACTTCTTTCAG 58.311 47.619 0.00 0.00 0.00 3.02
470 473 4.901250 TCATGCATACTCTCATGTCCCTTA 59.099 41.667 0.00 0.00 40.54 2.69
480 483 3.492337 TCATGTCCCTTACAACAAACCC 58.508 45.455 0.00 0.00 42.70 4.11
481 484 2.368311 TGTCCCTTACAACAAACCCC 57.632 50.000 0.00 0.00 34.29 4.95
505 508 2.127651 TTGGAACCCCACCTTCTACT 57.872 50.000 0.00 0.00 43.41 2.57
509 512 4.962839 TGGAACCCCACCTTCTACTAATA 58.037 43.478 0.00 0.00 37.58 0.98
630 649 9.809096 GAGATTGACTTAGTGACTGATTATCAA 57.191 33.333 0.00 0.00 0.00 2.57
685 704 2.159612 TGAGTCGTCAAAGTCGATACCG 60.160 50.000 0.00 0.00 39.45 4.02
757 776 8.157476 AGGTTTATATCACCAAGCCACTATTAG 58.843 37.037 6.74 0.00 36.67 1.73
763 782 4.530553 TCACCAAGCCACTATTAGAACTGA 59.469 41.667 0.00 0.00 0.00 3.41
769 788 6.360370 AGCCACTATTAGAACTGAGACAAA 57.640 37.500 0.00 0.00 0.00 2.83
833 859 7.722949 TTGCTGAGGGATTGAAATAAGAAAT 57.277 32.000 0.00 0.00 0.00 2.17
835 861 8.225603 TGCTGAGGGATTGAAATAAGAAATAC 57.774 34.615 0.00 0.00 0.00 1.89
849 876 5.880054 AAGAAATACAAACTCCACATCCG 57.120 39.130 0.00 0.00 0.00 4.18
872 900 6.919721 CGGAAGGAAATGAAAATTCTTGGTA 58.080 36.000 0.00 0.00 0.00 3.25
968 996 1.011293 TCCATTTCCTCCCCATCTCCT 59.989 52.381 0.00 0.00 0.00 3.69
1630 1659 2.301583 GAGCTAATGGAGGCTTAGAGGG 59.698 54.545 0.00 0.00 39.05 4.30
1657 1686 2.677836 CGACGGGTGTGAATTCATGAAT 59.322 45.455 15.36 15.36 0.00 2.57
1705 1734 5.104776 ACCTCTGTAGATTTATCTGCAAGCA 60.105 40.000 10.93 0.00 46.34 3.91
1899 1932 6.083098 TGAATTGTCAGTGGTACCATTTTG 57.917 37.500 19.72 16.49 0.00 2.44
1920 1953 2.362077 GTCTTGTGGTTTGAATGGCTGT 59.638 45.455 0.00 0.00 0.00 4.40
1997 2030 9.985730 ATTGAAGTGCAATAAATTCTTTCAGAA 57.014 25.926 0.00 0.00 45.16 3.02
2156 2189 5.124457 GGTAGTCTGATAACTAACGTCACCA 59.876 44.000 0.00 0.00 33.68 4.17
2442 2476 5.849475 TCATATCAGCCCTTTGGTCCTTATA 59.151 40.000 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.143684 AGCTGACAGGAACACAATGGT 59.856 47.619 4.26 0.00 0.00 3.55
1 2 1.901591 AGCTGACAGGAACACAATGG 58.098 50.000 4.26 0.00 0.00 3.16
2 3 6.932356 ATATTAGCTGACAGGAACACAATG 57.068 37.500 4.26 0.00 0.00 2.82
3 4 7.611467 TGAAATATTAGCTGACAGGAACACAAT 59.389 33.333 4.26 0.00 0.00 2.71
4 5 6.939730 TGAAATATTAGCTGACAGGAACACAA 59.060 34.615 4.26 0.00 0.00 3.33
5 6 6.472016 TGAAATATTAGCTGACAGGAACACA 58.528 36.000 4.26 0.00 0.00 3.72
6 7 6.818644 TCTGAAATATTAGCTGACAGGAACAC 59.181 38.462 4.26 0.00 0.00 3.32
7 8 6.946340 TCTGAAATATTAGCTGACAGGAACA 58.054 36.000 4.26 0.00 0.00 3.18
8 9 6.018343 GCTCTGAAATATTAGCTGACAGGAAC 60.018 42.308 4.26 0.00 32.18 3.62
9 10 6.051717 GCTCTGAAATATTAGCTGACAGGAA 58.948 40.000 4.26 0.00 32.18 3.36
10 11 5.453903 GGCTCTGAAATATTAGCTGACAGGA 60.454 44.000 4.26 0.00 35.30 3.86
11 12 4.754114 GGCTCTGAAATATTAGCTGACAGG 59.246 45.833 4.26 0.00 35.30 4.00
12 13 4.754114 GGGCTCTGAAATATTAGCTGACAG 59.246 45.833 0.00 0.00 35.30 3.51
13 14 4.444876 GGGGCTCTGAAATATTAGCTGACA 60.445 45.833 0.00 0.00 35.30 3.58
14 15 4.068599 GGGGCTCTGAAATATTAGCTGAC 58.931 47.826 0.00 0.71 35.30 3.51
15 16 3.716353 TGGGGCTCTGAAATATTAGCTGA 59.284 43.478 0.00 0.00 35.30 4.26
16 17 4.090761 TGGGGCTCTGAAATATTAGCTG 57.909 45.455 0.00 0.00 35.30 4.24
17 18 4.464947 GTTGGGGCTCTGAAATATTAGCT 58.535 43.478 7.66 0.00 35.30 3.32
18 19 3.570125 GGTTGGGGCTCTGAAATATTAGC 59.430 47.826 0.09 0.09 0.00 3.09
19 20 5.053978 AGGTTGGGGCTCTGAAATATTAG 57.946 43.478 0.00 0.00 0.00 1.73
20 21 4.726825 AGAGGTTGGGGCTCTGAAATATTA 59.273 41.667 0.00 0.00 0.00 0.98
21 22 3.529319 AGAGGTTGGGGCTCTGAAATATT 59.471 43.478 0.00 0.00 0.00 1.28
22 23 3.126453 AGAGGTTGGGGCTCTGAAATAT 58.874 45.455 0.00 0.00 0.00 1.28
23 24 2.562296 AGAGGTTGGGGCTCTGAAATA 58.438 47.619 0.00 0.00 0.00 1.40
24 25 1.376649 AGAGGTTGGGGCTCTGAAAT 58.623 50.000 0.00 0.00 0.00 2.17
25 26 1.628846 GTAGAGGTTGGGGCTCTGAAA 59.371 52.381 0.00 0.00 0.00 2.69
26 27 1.276622 GTAGAGGTTGGGGCTCTGAA 58.723 55.000 0.00 0.00 0.00 3.02
27 28 0.617820 GGTAGAGGTTGGGGCTCTGA 60.618 60.000 0.00 0.00 0.00 3.27
28 29 0.909610 TGGTAGAGGTTGGGGCTCTG 60.910 60.000 0.00 0.00 0.00 3.35
29 30 0.044855 ATGGTAGAGGTTGGGGCTCT 59.955 55.000 0.00 0.00 0.00 4.09
30 31 0.919710 AATGGTAGAGGTTGGGGCTC 59.080 55.000 0.00 0.00 0.00 4.70
31 32 0.625849 CAATGGTAGAGGTTGGGGCT 59.374 55.000 0.00 0.00 0.00 5.19
32 33 0.331616 ACAATGGTAGAGGTTGGGGC 59.668 55.000 0.00 0.00 0.00 5.80
33 34 1.916181 AGACAATGGTAGAGGTTGGGG 59.084 52.381 0.00 0.00 0.00 4.96
34 35 3.721087 AAGACAATGGTAGAGGTTGGG 57.279 47.619 0.00 0.00 0.00 4.12
35 36 7.703058 AATTTAAGACAATGGTAGAGGTTGG 57.297 36.000 0.00 0.00 0.00 3.77
36 37 8.576442 ACAAATTTAAGACAATGGTAGAGGTTG 58.424 33.333 0.00 0.00 0.00 3.77
37 38 8.706322 ACAAATTTAAGACAATGGTAGAGGTT 57.294 30.769 0.00 0.00 0.00 3.50
38 39 8.706322 AACAAATTTAAGACAATGGTAGAGGT 57.294 30.769 0.00 0.00 0.00 3.85
39 40 8.792633 TGAACAAATTTAAGACAATGGTAGAGG 58.207 33.333 0.00 0.00 0.00 3.69
40 41 9.612620 GTGAACAAATTTAAGACAATGGTAGAG 57.387 33.333 0.00 0.00 0.00 2.43
41 42 9.126151 TGTGAACAAATTTAAGACAATGGTAGA 57.874 29.630 0.00 0.00 0.00 2.59
42 43 9.743057 TTGTGAACAAATTTAAGACAATGGTAG 57.257 29.630 0.00 0.00 32.11 3.18
59 60 8.149647 AGATGGCAATCTAAAATTTGTGAACAA 58.850 29.630 0.21 0.00 41.57 2.83
60 61 7.669427 AGATGGCAATCTAAAATTTGTGAACA 58.331 30.769 0.21 0.00 41.57 3.18
61 62 8.538409 AAGATGGCAATCTAAAATTTGTGAAC 57.462 30.769 3.37 0.00 42.60 3.18
62 63 8.366401 TGAAGATGGCAATCTAAAATTTGTGAA 58.634 29.630 3.37 0.00 42.60 3.18
63 64 7.894708 TGAAGATGGCAATCTAAAATTTGTGA 58.105 30.769 3.37 0.00 42.60 3.58
64 65 8.712285 ATGAAGATGGCAATCTAAAATTTGTG 57.288 30.769 3.37 0.00 42.60 3.33
69 70 9.638176 AGAACTATGAAGATGGCAATCTAAAAT 57.362 29.630 3.37 1.46 42.60 1.82
70 71 9.113838 GAGAACTATGAAGATGGCAATCTAAAA 57.886 33.333 3.37 0.00 42.60 1.52
71 72 8.267183 TGAGAACTATGAAGATGGCAATCTAAA 58.733 33.333 3.37 0.00 42.60 1.85
72 73 7.712639 GTGAGAACTATGAAGATGGCAATCTAA 59.287 37.037 3.37 0.00 42.60 2.10
73 74 7.070447 AGTGAGAACTATGAAGATGGCAATCTA 59.930 37.037 3.37 0.00 42.60 1.98
74 75 6.054295 GTGAGAACTATGAAGATGGCAATCT 58.946 40.000 0.00 0.00 45.48 2.40
75 76 6.054295 AGTGAGAACTATGAAGATGGCAATC 58.946 40.000 0.00 0.00 0.00 2.67
76 77 5.999044 AGTGAGAACTATGAAGATGGCAAT 58.001 37.500 0.00 0.00 0.00 3.56
77 78 5.188555 AGAGTGAGAACTATGAAGATGGCAA 59.811 40.000 0.00 0.00 0.00 4.52
78 79 4.713814 AGAGTGAGAACTATGAAGATGGCA 59.286 41.667 0.00 0.00 0.00 4.92
79 80 5.068987 AGAGAGTGAGAACTATGAAGATGGC 59.931 44.000 0.00 0.00 0.00 4.40
80 81 6.713762 AGAGAGTGAGAACTATGAAGATGG 57.286 41.667 0.00 0.00 0.00 3.51
89 90 4.672024 CGCGCTTAAAGAGAGTGAGAACTA 60.672 45.833 5.56 0.00 37.83 2.24
96 97 1.983972 ACTCGCGCTTAAAGAGAGTG 58.016 50.000 14.93 0.00 44.77 3.51
100 101 4.167268 AGTAAGAACTCGCGCTTAAAGAG 58.833 43.478 5.56 6.78 37.96 2.85
110 111 2.662156 CCGAGAACAAGTAAGAACTCGC 59.338 50.000 0.00 0.00 43.42 5.03
115 116 3.558418 GTGCAACCGAGAACAAGTAAGAA 59.442 43.478 0.00 0.00 0.00 2.52
143 144 6.154706 CACTACCTAACCATGAAGACCTAGTT 59.845 42.308 0.00 0.00 0.00 2.24
165 166 1.826385 GGCAATGTTAGAGGCACACT 58.174 50.000 0.00 0.00 0.00 3.55
172 173 7.280205 ACTTAAAGGTTATCGGCAATGTTAGAG 59.720 37.037 0.00 0.00 0.00 2.43
175 176 6.879993 TCACTTAAAGGTTATCGGCAATGTTA 59.120 34.615 0.00 0.00 0.00 2.41
178 179 5.811399 TCACTTAAAGGTTATCGGCAATG 57.189 39.130 0.00 0.00 0.00 2.82
183 184 5.357032 AGCCATTTCACTTAAAGGTTATCGG 59.643 40.000 0.00 0.00 0.00 4.18
186 187 6.496911 ACCAAGCCATTTCACTTAAAGGTTAT 59.503 34.615 0.00 0.00 0.00 1.89
224 225 3.459232 ACATCCGACATGAATCGACAT 57.541 42.857 7.25 0.00 45.13 3.06
230 231 6.582636 ACTACATTGTACATCCGACATGAAT 58.417 36.000 9.40 0.00 0.00 2.57
231 232 5.972935 ACTACATTGTACATCCGACATGAA 58.027 37.500 9.40 0.00 0.00 2.57
239 240 3.131577 TGACCCGACTACATTGTACATCC 59.868 47.826 0.00 0.00 0.00 3.51
242 243 3.764972 TGATGACCCGACTACATTGTACA 59.235 43.478 0.00 0.00 0.00 2.90
247 248 4.553330 ACTTTGATGACCCGACTACATT 57.447 40.909 0.00 0.00 0.00 2.71
275 276 3.159213 ACACTCCTTTGCATTGGATGA 57.841 42.857 8.39 0.00 0.00 2.92
301 302 3.396260 TGAGTGTCCCGGTCTTTAAAG 57.604 47.619 9.04 9.04 0.00 1.85
304 305 1.621814 CCTTGAGTGTCCCGGTCTTTA 59.378 52.381 0.00 0.00 0.00 1.85
307 308 1.152312 ACCTTGAGTGTCCCGGTCT 60.152 57.895 0.00 0.00 0.00 3.85
360 363 4.537135 TTCTGTATATCAATCCCTCGGC 57.463 45.455 0.00 0.00 0.00 5.54
389 392 1.760613 TCCTTCCCCGTATGTGACATC 59.239 52.381 0.00 0.00 0.00 3.06
390 393 1.874129 TCCTTCCCCGTATGTGACAT 58.126 50.000 2.65 2.65 0.00 3.06
391 394 1.646912 TTCCTTCCCCGTATGTGACA 58.353 50.000 0.00 0.00 0.00 3.58
392 395 2.353323 GTTTCCTTCCCCGTATGTGAC 58.647 52.381 0.00 0.00 0.00 3.67
394 397 1.003812 TGGTTTCCTTCCCCGTATGTG 59.996 52.381 0.00 0.00 0.00 3.21
395 398 1.364269 TGGTTTCCTTCCCCGTATGT 58.636 50.000 0.00 0.00 0.00 2.29
396 399 2.500392 TTGGTTTCCTTCCCCGTATG 57.500 50.000 0.00 0.00 0.00 2.39
397 400 3.529216 TTTTGGTTTCCTTCCCCGTAT 57.471 42.857 0.00 0.00 0.00 3.06
398 401 3.529216 ATTTTGGTTTCCTTCCCCGTA 57.471 42.857 0.00 0.00 0.00 4.02
399 402 2.391926 ATTTTGGTTTCCTTCCCCGT 57.608 45.000 0.00 0.00 0.00 5.28
400 403 2.897326 AGAATTTTGGTTTCCTTCCCCG 59.103 45.455 0.00 0.00 0.00 5.73
401 404 4.641396 CAAGAATTTTGGTTTCCTTCCCC 58.359 43.478 0.00 0.00 0.00 4.81
424 427 4.991687 AGAAACTGAAAGAAGTAGAAGCCG 59.008 41.667 0.00 0.00 37.43 5.52
425 428 5.992217 TGAGAAACTGAAAGAAGTAGAAGCC 59.008 40.000 0.00 0.00 37.43 4.35
431 434 8.097038 AGTATGCATGAGAAACTGAAAGAAGTA 58.903 33.333 10.16 0.00 37.43 2.24
441 444 5.987098 ACATGAGAGTATGCATGAGAAACT 58.013 37.500 10.16 3.80 43.43 2.66
442 445 5.236047 GGACATGAGAGTATGCATGAGAAAC 59.764 44.000 10.16 0.00 43.43 2.78
556 560 0.309922 CATGCATGCAATCGAGGACC 59.690 55.000 26.68 0.00 0.00 4.46
630 649 6.360370 ACATTGGACAGTAGACAACACTAT 57.640 37.500 0.00 0.00 0.00 2.12
685 704 3.064900 AGCACTCCTTCAAGTTGGATC 57.935 47.619 2.34 0.00 0.00 3.36
833 859 2.027561 CCTTCCGGATGTGGAGTTTGTA 60.028 50.000 4.15 0.00 39.72 2.41
835 861 1.003118 TCCTTCCGGATGTGGAGTTTG 59.997 52.381 4.15 0.00 39.72 2.93
849 876 8.314021 ACATACCAAGAATTTTCATTTCCTTCC 58.686 33.333 0.00 0.00 0.00 3.46
872 900 4.018870 GGAGAAAGGGAAAGAAGAGGACAT 60.019 45.833 0.00 0.00 0.00 3.06
1059 1087 1.553690 CGTGGAAGATGGTGGGGTCT 61.554 60.000 0.00 0.00 0.00 3.85
1630 1659 0.949105 ATTCACACCCGTCGCAAGTC 60.949 55.000 0.00 0.00 39.48 3.01
1657 1686 4.609559 GCGAATACGACACATCACAAACAA 60.610 41.667 0.00 0.00 42.66 2.83
1705 1734 4.640771 AACATGACTAATCACCACCACT 57.359 40.909 0.00 0.00 37.79 4.00
1899 1932 2.362077 ACAGCCATTCAAACCACAAGAC 59.638 45.455 0.00 0.00 0.00 3.01
1920 1953 5.776208 TGGATAGTAGTACCACACACTTCAA 59.224 40.000 0.00 0.00 0.00 2.69
1997 2030 7.788026 TCATCAATGTACCTAATCCGTACTTT 58.212 34.615 0.00 0.00 37.55 2.66
2074 2107 4.084223 GCAACAATTTTGAGCCAATCAGTG 60.084 41.667 0.00 0.00 39.68 3.66
2156 2189 6.976934 ACTGGACCAAACTATGTTCAAATT 57.023 33.333 0.00 0.00 0.00 1.82
2241 2274 9.480053 AACATAATCAAGCCAATAATAATGTGC 57.520 29.630 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.