Multiple sequence alignment - TraesCS5A01G420200

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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 TraesCS5A01G420200 chr5A 100.000 3927 0 0 1 3927 606892553 606896479 0.000000e+00 7252.0
1 TraesCS5A01G420200 chr5A 95.921 662 13 3 3226 3887 706704400 706703753 0.000000e+00 1061.0
2 TraesCS5A01G420200 chr5A 100.000 42 0 0 3886 3927 706703786 706703745 1.170000e-10 78.7
3 TraesCS5A01G420200 chr5A 100.000 34 0 0 3886 3919 606896406 606896439 3.280000e-06 63.9
4 TraesCS5A01G420200 chr5D 93.236 2543 102 26 719 3226 486166913 486169420 0.000000e+00 3679.0
5 TraesCS5A01G420200 chr5D 84.679 731 60 23 9 716 486166168 486166869 0.000000e+00 682.0
6 TraesCS5A01G420200 chr5B 92.061 2557 126 30 719 3226 597218716 597221244 0.000000e+00 3526.0
7 TraesCS5A01G420200 chr5B 98.338 662 2 1 3226 3887 176624754 176624102 0.000000e+00 1153.0
8 TraesCS5A01G420200 chr5B 80.685 730 57 37 9 693 597217964 597218654 1.270000e-134 490.0
9 TraesCS5A01G420200 chr5B 100.000 42 0 0 3886 3927 176624135 176624094 1.170000e-10 78.7
10 TraesCS5A01G420200 chr1B 98.939 660 5 1 3228 3887 660660636 660661293 0.000000e+00 1179.0
11 TraesCS5A01G420200 chr1B 100.000 42 0 0 3886 3927 660661260 660661301 1.170000e-10 78.7
12 TraesCS5A01G420200 chr6B 97.121 660 8 1 3228 3887 696192658 696192010 0.000000e+00 1103.0
13 TraesCS5A01G420200 chr6B 95.921 662 15 1 3226 3887 337861069 337861718 0.000000e+00 1062.0
14 TraesCS5A01G420200 chr6B 95.770 662 15 2 3226 3887 315288890 315288242 0.000000e+00 1055.0
15 TraesCS5A01G420200 chr6B 93.475 659 30 5 3227 3884 129478840 129479486 0.000000e+00 966.0
16 TraesCS5A01G420200 chr6B 100.000 42 0 0 3886 3927 315288275 315288234 1.170000e-10 78.7
17 TraesCS5A01G420200 chr6B 100.000 42 0 0 3886 3927 337861685 337861726 1.170000e-10 78.7
18 TraesCS5A01G420200 chr6B 100.000 42 0 0 3886 3927 696192043 696192002 1.170000e-10 78.7
19 TraesCS5A01G420200 chr4B 95.166 662 19 2 3226 3887 404768903 404768255 0.000000e+00 1033.0
20 TraesCS5A01G420200 chr4B 86.538 520 57 7 2433 2941 582296939 582297456 9.530000e-156 560.0
21 TraesCS5A01G420200 chr4B 95.342 322 4 1 3226 3547 17194180 17193870 5.860000e-138 501.0
22 TraesCS5A01G420200 chr4B 100.000 42 0 0 3886 3927 404768288 404768247 1.170000e-10 78.7
23 TraesCS5A01G420200 chr3A 92.771 664 33 7 3224 3885 128069129 128069779 0.000000e+00 946.0
24 TraesCS5A01G420200 chr3B 87.048 664 56 11 3226 3887 52355640 52355005 0.000000e+00 723.0
25 TraesCS5A01G420200 chr3B 97.619 42 1 0 3886 3927 41802827 41802868 5.440000e-09 73.1
26 TraesCS5A01G420200 chr7D 89.578 403 38 3 2125 2523 578984495 578984897 3.500000e-140 508.0
27 TraesCS5A01G420200 chr7B 97.619 42 1 0 3886 3927 593014607 593014648 5.440000e-09 73.1
28 TraesCS5A01G420200 chr7B 97.059 34 1 0 3886 3919 644197550 644197583 1.520000e-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 TraesCS5A01G420200 chr5A 606892553 606896479 3926 False 3657.95 7252 100.0000 1 3927 2 chr5A.!!$F1 3926
1 TraesCS5A01G420200 chr5A 706703745 706704400 655 True 569.85 1061 97.9605 3226 3927 2 chr5A.!!$R1 701
2 TraesCS5A01G420200 chr5D 486166168 486169420 3252 False 2180.50 3679 88.9575 9 3226 2 chr5D.!!$F1 3217
3 TraesCS5A01G420200 chr5B 597217964 597221244 3280 False 2008.00 3526 86.3730 9 3226 2 chr5B.!!$F1 3217
4 TraesCS5A01G420200 chr5B 176624094 176624754 660 True 615.85 1153 99.1690 3226 3927 2 chr5B.!!$R1 701
5 TraesCS5A01G420200 chr1B 660660636 660661301 665 False 628.85 1179 99.4695 3228 3927 2 chr1B.!!$F1 699
6 TraesCS5A01G420200 chr6B 129478840 129479486 646 False 966.00 966 93.4750 3227 3884 1 chr6B.!!$F1 657
7 TraesCS5A01G420200 chr6B 696192002 696192658 656 True 590.85 1103 98.5605 3228 3927 2 chr6B.!!$R2 699
8 TraesCS5A01G420200 chr6B 337861069 337861726 657 False 570.35 1062 97.9605 3226 3927 2 chr6B.!!$F2 701
9 TraesCS5A01G420200 chr6B 315288234 315288890 656 True 566.85 1055 97.8850 3226 3927 2 chr6B.!!$R1 701
10 TraesCS5A01G420200 chr4B 582296939 582297456 517 False 560.00 560 86.5380 2433 2941 1 chr4B.!!$F1 508
11 TraesCS5A01G420200 chr4B 404768247 404768903 656 True 555.85 1033 97.5830 3226 3927 2 chr4B.!!$R2 701
12 TraesCS5A01G420200 chr3A 128069129 128069779 650 False 946.00 946 92.7710 3224 3885 1 chr3A.!!$F1 661
13 TraesCS5A01G420200 chr3B 52355005 52355640 635 True 723.00 723 87.0480 3226 3887 1 chr3B.!!$R1 661

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
119 123 0.034574 ACATCGCCAAGTTGCCCATA 60.035 50.0 0.00 0.0 0.0 2.74 F
1124 1244 0.033920 TCGGGCATCCATCGATTGAG 59.966 55.0 5.35 0.0 0.0 3.02 F
1125 1245 0.250038 CGGGCATCCATCGATTGAGT 60.250 55.0 5.35 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1953 0.173708 GCCTCGACGATTTGGTCTCT 59.826 55.000 0.0 0.0 34.75 3.10 R
2581 2732 0.743097 GTTCATTGCTGGAGATGGGC 59.257 55.000 0.0 0.0 0.00 5.36 R
3026 3189 3.754850 CAGTCAAAGAATGATCAGTGCCA 59.245 43.478 0.0 0.0 40.97 4.92 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
27 28 7.224297 TGAGGAATGCTTTCACCTAATATACC 58.776 38.462 13.72 0.00 33.23 2.73
32 33 9.952188 GAATGCTTTCACCTAATATACCTTTTC 57.048 33.333 7.43 0.00 0.00 2.29
35 36 8.956426 TGCTTTCACCTAATATACCTTTTCTTG 58.044 33.333 0.00 0.00 0.00 3.02
66 70 7.164233 AGTACCTAGTAGTCCACTGGATTAT 57.836 40.000 0.00 0.00 37.96 1.28
78 82 5.887598 TCCACTGGATTATGAAAGACCATTG 59.112 40.000 0.00 0.00 33.27 2.82
85 89 8.000709 TGGATTATGAAAGACCATTGAGCTAAT 58.999 33.333 0.00 0.00 0.00 1.73
99 103 2.124942 TAATCCGCGGCACATGCA 60.125 55.556 23.51 0.16 44.36 3.96
105 109 2.577644 GCGGCACATGCAACATCG 60.578 61.111 6.15 0.72 44.36 3.84
108 112 2.567569 GCACATGCAACATCGCCA 59.432 55.556 0.00 0.00 41.59 5.69
110 114 1.074319 GCACATGCAACATCGCCAAG 61.074 55.000 0.00 0.00 41.59 3.61
117 121 1.530419 AACATCGCCAAGTTGCCCA 60.530 52.632 0.00 0.00 0.00 5.36
119 123 0.034574 ACATCGCCAAGTTGCCCATA 60.035 50.000 0.00 0.00 0.00 2.74
120 124 1.321474 CATCGCCAAGTTGCCCATAT 58.679 50.000 0.00 0.00 0.00 1.78
135 139 3.565902 GCCCATATTAGTGGCAGAAGAAC 59.434 47.826 0.00 0.00 44.70 3.01
137 141 5.380043 CCCATATTAGTGGCAGAAGAACAT 58.620 41.667 0.00 0.00 37.96 2.71
139 143 5.178252 CCATATTAGTGGCAGAAGAACATCG 59.822 44.000 0.00 0.00 31.43 3.84
145 155 1.474077 GGCAGAAGAACATCGCCAAAT 59.526 47.619 0.00 0.00 38.23 2.32
159 169 2.601314 CGCCAAATGCATGAATGAAGTG 59.399 45.455 0.00 0.00 41.33 3.16
160 170 3.592059 GCCAAATGCATGAATGAAGTGT 58.408 40.909 0.00 0.00 40.77 3.55
161 171 3.369756 GCCAAATGCATGAATGAAGTGTG 59.630 43.478 0.00 0.00 40.77 3.82
162 172 4.811908 CCAAATGCATGAATGAAGTGTGA 58.188 39.130 0.00 0.00 0.00 3.58
165 175 2.506444 TGCATGAATGAAGTGTGAGCA 58.494 42.857 0.00 0.00 0.00 4.26
179 189 3.127721 GTGTGAGCATAAAGAAGGAAGGC 59.872 47.826 0.00 0.00 0.00 4.35
182 192 4.012374 TGAGCATAAAGAAGGAAGGCAAG 58.988 43.478 0.00 0.00 0.00 4.01
189 199 1.563410 AGAAGGAAGGCAAGGATCCAG 59.437 52.381 15.82 7.22 35.62 3.86
196 206 0.464373 GGCAAGGATCCAGCGAATCA 60.464 55.000 15.82 0.00 0.00 2.57
213 223 4.552365 AGGCGGTGCATCCATCGG 62.552 66.667 0.00 0.00 45.49 4.18
221 231 2.519302 CATCCATCGGGGGTTGGC 60.519 66.667 0.00 0.00 37.22 4.52
379 389 3.119849 CGTCGAGAAAAATCCAAGCCAAT 60.120 43.478 0.00 0.00 0.00 3.16
382 392 4.766891 TCGAGAAAAATCCAAGCCAATTCT 59.233 37.500 0.00 0.00 0.00 2.40
433 454 1.405105 CTCTGCTCCTCTTCTTCCTCG 59.595 57.143 0.00 0.00 0.00 4.63
434 455 0.179113 CTGCTCCTCTTCTTCCTCGC 60.179 60.000 0.00 0.00 0.00 5.03
435 456 1.142965 GCTCCTCTTCTTCCTCGCC 59.857 63.158 0.00 0.00 0.00 5.54
447 468 4.840005 CTCGCCCCCTTTCCGAGC 62.840 72.222 0.00 0.00 41.41 5.03
456 477 1.435515 CTTTCCGAGCGAGAGAGGG 59.564 63.158 0.00 0.00 0.00 4.30
458 479 2.494777 TTTCCGAGCGAGAGAGGGGA 62.495 60.000 0.00 0.00 0.00 4.81
494 529 1.107114 ATACCTCGACTCACTGCCTG 58.893 55.000 0.00 0.00 0.00 4.85
522 557 2.187424 CCTGCTCCTGCTCTGCTC 59.813 66.667 0.00 0.00 40.48 4.26
543 578 1.396996 CGGTTCGCCAAGAAATACAGG 59.603 52.381 0.00 0.00 41.10 4.00
545 580 2.678336 GGTTCGCCAAGAAATACAGGAG 59.322 50.000 0.00 0.00 41.10 3.69
546 581 3.596214 GTTCGCCAAGAAATACAGGAGA 58.404 45.455 0.00 0.00 41.10 3.71
580 617 4.303282 GAGACTTGTCTTGTCACTTCTCC 58.697 47.826 4.67 0.00 36.94 3.71
581 618 3.706594 AGACTTGTCTTGTCACTTCTCCA 59.293 43.478 0.00 0.00 36.94 3.86
582 619 4.054671 GACTTGTCTTGTCACTTCTCCAG 58.945 47.826 0.00 0.00 34.80 3.86
583 620 3.452627 ACTTGTCTTGTCACTTCTCCAGT 59.547 43.478 0.00 0.00 35.35 4.00
600 637 2.460918 CAGTGGTTCTTACTATCGGCG 58.539 52.381 0.00 0.00 0.00 6.46
632 685 1.374758 GAGCGGAGAACAGTGGTGG 60.375 63.158 0.00 0.00 0.00 4.61
636 689 1.837090 GGAGAACAGTGGTGGTGGT 59.163 57.895 0.00 0.00 0.00 4.16
637 690 0.535102 GGAGAACAGTGGTGGTGGTG 60.535 60.000 0.00 0.00 0.00 4.17
638 691 0.535102 GAGAACAGTGGTGGTGGTGG 60.535 60.000 0.00 0.00 0.00 4.61
673 726 0.188587 TCAGGTCAGTGGTCAGGAGT 59.811 55.000 0.00 0.00 0.00 3.85
675 728 1.051812 AGGTCAGTGGTCAGGAGTTG 58.948 55.000 0.00 0.00 0.00 3.16
693 746 0.325933 TGGGAGCAGTGGACTGATTG 59.674 55.000 11.06 0.00 43.41 2.67
694 747 0.326264 GGGAGCAGTGGACTGATTGT 59.674 55.000 11.06 0.00 43.41 2.71
695 748 1.677217 GGGAGCAGTGGACTGATTGTC 60.677 57.143 11.06 1.53 43.41 3.18
696 749 1.277557 GGAGCAGTGGACTGATTGTCT 59.722 52.381 11.06 0.00 43.41 3.41
704 757 3.070302 GTGGACTGATTGTCTATCTCCCC 59.930 52.174 0.00 0.00 44.74 4.81
710 763 2.366640 TTGTCTATCTCCCCCTCTCG 57.633 55.000 0.00 0.00 0.00 4.04
716 769 0.105913 ATCTCCCCCTCTCGTTCTCC 60.106 60.000 0.00 0.00 0.00 3.71
717 770 2.044252 TCCCCCTCTCGTTCTCCG 60.044 66.667 0.00 0.00 38.13 4.63
746 840 0.827368 GGAAGTGAAGCGATCCTCCT 59.173 55.000 0.00 0.00 0.00 3.69
747 841 1.202475 GGAAGTGAAGCGATCCTCCTC 60.202 57.143 0.00 0.00 0.00 3.71
748 842 0.827368 AAGTGAAGCGATCCTCCTCC 59.173 55.000 0.00 0.00 0.00 4.30
791 885 2.106566 CTGGAGCTAGAAGAAGGAGCA 58.893 52.381 0.00 0.00 38.73 4.26
963 1081 6.331042 TCTCTTGGATGAATGGATAATGGAGT 59.669 38.462 0.00 0.00 0.00 3.85
985 1103 0.250234 TGATCTTCCTTGCAGTCCCG 59.750 55.000 0.00 0.00 0.00 5.14
1103 1223 0.236449 CCCCCTTTTTCGTTCGTTCG 59.764 55.000 0.00 0.00 0.00 3.95
1124 1244 0.033920 TCGGGCATCCATCGATTGAG 59.966 55.000 5.35 0.00 0.00 3.02
1125 1245 0.250038 CGGGCATCCATCGATTGAGT 60.250 55.000 5.35 0.00 0.00 3.41
1681 1804 1.674057 CAGGGGCAAAGACGACTCT 59.326 57.895 0.00 0.00 0.00 3.24
1700 1823 3.432051 GATAGCCGCAGCGAGGTGT 62.432 63.158 18.75 10.37 46.67 4.16
1704 1827 3.414700 CCGCAGCGAGGTGTGTTC 61.415 66.667 18.75 0.00 0.00 3.18
1709 1832 1.071471 AGCGAGGTGTGTTCCTTGG 59.929 57.895 0.00 0.00 38.92 3.61
1724 1847 0.688487 CTTGGTCCGGTTTGTCCCTA 59.312 55.000 0.00 0.00 0.00 3.53
1728 1851 3.116959 TGGTCCGGTTTGTCCCTATATT 58.883 45.455 0.00 0.00 0.00 1.28
1730 1853 2.876550 GTCCGGTTTGTCCCTATATTGC 59.123 50.000 0.00 0.00 0.00 3.56
1772 1895 4.919754 CCTGTACAAAATTTGCTTGAGCTC 59.080 41.667 6.82 6.82 42.66 4.09
1824 1947 1.078143 GGATGTGGAGTGTGAGGCC 60.078 63.158 0.00 0.00 0.00 5.19
1830 1953 1.053835 TGGAGTGTGAGGCCACTGAA 61.054 55.000 5.01 0.00 45.46 3.02
1937 2060 3.070018 AGTCAGATGCTACTTGTGTTGC 58.930 45.455 0.00 0.00 43.39 4.17
1947 2076 5.385617 GCTACTTGTGTTGCAATCTTACAG 58.614 41.667 0.59 0.00 42.80 2.74
2086 2231 8.604890 GCAACAAGGTAAGAAATGAGTAGTATC 58.395 37.037 0.00 0.00 0.00 2.24
2116 2261 0.615331 TCTGATCAGGTGCAAGTCCC 59.385 55.000 22.42 0.00 0.00 4.46
2117 2262 0.617413 CTGATCAGGTGCAAGTCCCT 59.383 55.000 15.38 0.00 0.00 4.20
2119 2264 0.393537 GATCAGGTGCAAGTCCCTGG 60.394 60.000 18.23 3.54 46.75 4.45
2120 2265 0.842030 ATCAGGTGCAAGTCCCTGGA 60.842 55.000 18.23 8.02 46.75 3.86
2121 2266 1.059584 TCAGGTGCAAGTCCCTGGAA 61.060 55.000 18.23 0.70 46.75 3.53
2122 2267 0.607489 CAGGTGCAAGTCCCTGGAAG 60.607 60.000 12.25 0.00 43.74 3.46
2149 2294 6.028146 TGGATTCATTCATTTCTGTTGGTG 57.972 37.500 0.00 0.00 0.00 4.17
2155 2303 3.940209 TCATTTCTGTTGGTGAATGGC 57.060 42.857 0.00 0.00 0.00 4.40
2300 2449 6.289064 CAAGTTCAGGTTAGGAGTTTACTGT 58.711 40.000 0.00 0.00 0.00 3.55
2324 2473 1.550976 CTCTACCTGAACCCACAGACC 59.449 57.143 0.00 0.00 39.94 3.85
2333 2482 0.402272 ACCCACAGACCTAACCCCAA 60.402 55.000 0.00 0.00 0.00 4.12
2337 2486 2.446435 CACAGACCTAACCCCAAATGG 58.554 52.381 0.00 0.00 0.00 3.16
2343 2492 2.023113 ACCTAACCCCAAATGGCATCAT 60.023 45.455 0.00 0.00 34.56 2.45
2372 2521 4.313277 TGAGAGAGAAATACGGCATCAG 57.687 45.455 0.00 0.00 0.00 2.90
2381 2530 5.885912 AGAAATACGGCATCAGTTATTGGTT 59.114 36.000 0.00 0.00 0.00 3.67
2558 2709 4.080129 AGAGTGCCATACATGAACCATTCT 60.080 41.667 0.00 0.00 0.00 2.40
2581 2732 6.825213 TCTTTGTCAAATCACATCCCTATGAG 59.175 38.462 0.00 0.00 36.54 2.90
2642 2793 3.192844 AGATGCAAAACATTCAGCTGAGG 59.807 43.478 17.43 15.44 39.84 3.86
2877 3040 0.727398 GAAGTGCCGGATTGTACTGC 59.273 55.000 5.05 0.00 31.19 4.40
2957 3120 8.142551 ACCTTGAACTAGTAAGAAGTTGTACTG 58.857 37.037 6.93 1.22 37.31 2.74
3030 3193 1.679153 CTGCATATCAGCACATTGGCA 59.321 47.619 0.00 0.00 40.11 4.92
3085 3248 4.497291 TGGTAGCCACCCTACATAAAAG 57.503 45.455 0.00 0.00 46.73 2.27
3105 3269 4.600012 AGAAAACTCACCGATTTATGCG 57.400 40.909 0.00 0.00 0.00 4.73
3142 3306 4.406648 TGTATATGGAACCAGAGCTGTG 57.593 45.455 3.32 3.32 0.00 3.66
3146 3310 1.717032 TGGAACCAGAGCTGTGTACT 58.283 50.000 10.34 0.00 0.00 2.73
3885 4058 2.657237 GGACCTCCACACCAGACG 59.343 66.667 0.00 0.00 35.64 4.18
3886 4059 2.657237 GACCTCCACACCAGACGG 59.343 66.667 0.00 0.00 38.77 4.79
3887 4060 3.591254 GACCTCCACACCAGACGGC 62.591 68.421 0.00 0.00 34.57 5.68
3888 4061 4.394712 CCTCCACACCAGACGGCC 62.395 72.222 0.00 0.00 34.57 6.13
3889 4062 3.625897 CTCCACACCAGACGGCCA 61.626 66.667 2.24 0.00 34.57 5.36
3890 4063 2.927856 TCCACACCAGACGGCCAT 60.928 61.111 2.24 0.00 34.57 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.120538 GTATATTAGGTGAAAGCATTCCTCAAA 57.879 33.333 0.00 0.00 36.26 2.69
5 6 8.465273 AAAGGTATATTAGGTGAAAGCATTCC 57.535 34.615 0.00 0.00 36.26 3.01
6 7 9.952188 GAAAAGGTATATTAGGTGAAAGCATTC 57.048 33.333 0.00 0.00 36.26 2.67
7 8 9.700831 AGAAAAGGTATATTAGGTGAAAGCATT 57.299 29.630 0.00 0.00 36.26 3.56
15 16 9.667107 TCAGTTCAAGAAAAGGTATATTAGGTG 57.333 33.333 0.00 0.00 0.00 4.00
27 28 9.413048 CTACTAGGTACTTCAGTTCAAGAAAAG 57.587 37.037 0.00 0.00 41.75 2.27
32 33 6.433404 TGGACTACTAGGTACTTCAGTTCAAG 59.567 42.308 0.00 0.00 41.75 3.02
35 36 5.945191 AGTGGACTACTAGGTACTTCAGTTC 59.055 44.000 0.00 0.00 41.75 3.01
43 45 7.002879 TCATAATCCAGTGGACTACTAGGTAC 58.997 42.308 15.86 0.00 37.60 3.34
66 70 4.191544 CGGATTAGCTCAATGGTCTTTCA 58.808 43.478 0.00 0.00 0.00 2.69
78 82 1.595382 ATGTGCCGCGGATTAGCTC 60.595 57.895 33.48 14.36 34.40 4.09
99 103 0.899717 ATGGGCAACTTGGCGATGTT 60.900 50.000 11.38 0.00 44.78 2.71
105 109 2.362077 CCACTAATATGGGCAACTTGGC 59.638 50.000 6.79 6.79 42.88 4.52
117 121 4.752101 GCGATGTTCTTCTGCCACTAATAT 59.248 41.667 0.00 0.00 0.00 1.28
119 123 2.939103 GCGATGTTCTTCTGCCACTAAT 59.061 45.455 0.00 0.00 0.00 1.73
120 124 2.346803 GCGATGTTCTTCTGCCACTAA 58.653 47.619 0.00 0.00 0.00 2.24
139 143 3.369756 CACACTTCATTCATGCATTTGGC 59.630 43.478 0.00 0.00 45.13 4.52
145 155 2.506444 TGCTCACACTTCATTCATGCA 58.494 42.857 0.00 0.00 0.00 3.96
159 169 3.347216 TGCCTTCCTTCTTTATGCTCAC 58.653 45.455 0.00 0.00 0.00 3.51
160 170 3.719268 TGCCTTCCTTCTTTATGCTCA 57.281 42.857 0.00 0.00 0.00 4.26
161 171 3.379688 CCTTGCCTTCCTTCTTTATGCTC 59.620 47.826 0.00 0.00 0.00 4.26
162 172 3.010584 TCCTTGCCTTCCTTCTTTATGCT 59.989 43.478 0.00 0.00 0.00 3.79
165 175 4.230502 TGGATCCTTGCCTTCCTTCTTTAT 59.769 41.667 14.23 0.00 0.00 1.40
179 189 1.590932 CCTGATTCGCTGGATCCTTG 58.409 55.000 14.23 7.13 37.79 3.61
182 192 1.958205 CGCCTGATTCGCTGGATCC 60.958 63.158 4.20 4.20 37.79 3.36
189 199 3.173390 GATGCACCGCCTGATTCGC 62.173 63.158 0.00 0.00 0.00 4.70
196 206 4.552365 CCGATGGATGCACCGCCT 62.552 66.667 0.00 0.00 42.61 5.52
213 223 2.035783 GGACCAGAAGCCAACCCC 59.964 66.667 0.00 0.00 0.00 4.95
221 231 1.067495 GGACTCGAACTGGACCAGAAG 60.067 57.143 28.56 19.11 35.18 2.85
356 366 1.130561 GGCTTGGATTTTTCTCGACGG 59.869 52.381 0.00 0.00 0.00 4.79
359 369 4.766891 AGAATTGGCTTGGATTTTTCTCGA 59.233 37.500 0.00 0.00 0.00 4.04
364 374 3.909364 TGGGAGAATTGGCTTGGATTTTT 59.091 39.130 0.00 0.00 0.00 1.94
379 389 3.319198 GCAGGACCCGTGGGAGAA 61.319 66.667 13.01 0.00 38.96 2.87
433 454 4.840005 CTCGCTCGGAAAGGGGGC 62.840 72.222 0.00 0.00 38.45 5.80
434 455 3.075005 TCTCGCTCGGAAAGGGGG 61.075 66.667 0.00 0.00 39.78 5.40
435 456 2.010582 CTCTCTCGCTCGGAAAGGGG 62.011 65.000 0.00 0.00 38.45 4.79
447 468 2.492090 CGCTTGTCCCCTCTCTCG 59.508 66.667 0.00 0.00 0.00 4.04
456 477 0.101759 TATGTACGGAGCGCTTGTCC 59.898 55.000 13.26 7.91 0.00 4.02
458 479 2.288030 GGTATATGTACGGAGCGCTTGT 60.288 50.000 13.26 16.55 0.00 3.16
522 557 1.396996 CTGTATTTCTTGGCGAACCGG 59.603 52.381 0.00 0.00 39.70 5.28
543 578 0.397957 GTCTCCTCCCCTCCCTTCTC 60.398 65.000 0.00 0.00 0.00 2.87
545 580 0.043485 AAGTCTCCTCCCCTCCCTTC 59.957 60.000 0.00 0.00 0.00 3.46
546 581 0.252927 CAAGTCTCCTCCCCTCCCTT 60.253 60.000 0.00 0.00 0.00 3.95
580 617 2.460918 CGCCGATAGTAAGAACCACTG 58.539 52.381 0.00 0.00 0.00 3.66
581 618 1.202382 GCGCCGATAGTAAGAACCACT 60.202 52.381 0.00 0.00 0.00 4.00
582 619 1.206523 GCGCCGATAGTAAGAACCAC 58.793 55.000 0.00 0.00 0.00 4.16
583 620 0.248743 CGCGCCGATAGTAAGAACCA 60.249 55.000 0.00 0.00 0.00 3.67
590 627 3.973516 CCCAGCGCGCCGATAGTA 61.974 66.667 30.33 0.00 0.00 1.82
600 637 3.567797 GCTCGATCAACCCAGCGC 61.568 66.667 0.00 0.00 0.00 5.92
632 685 4.314440 TCGGCTGAGCACCACCAC 62.314 66.667 6.82 0.00 0.00 4.16
636 689 3.385384 CCTCTCGGCTGAGCACCA 61.385 66.667 18.28 0.00 42.26 4.17
637 690 3.363844 GACCTCTCGGCTGAGCACC 62.364 68.421 18.28 3.24 42.26 5.01
638 691 2.183046 GACCTCTCGGCTGAGCAC 59.817 66.667 18.28 5.17 42.26 4.40
658 711 0.035458 CCCAACTCCTGACCACTGAC 59.965 60.000 0.00 0.00 0.00 3.51
673 726 1.067295 AATCAGTCCACTGCTCCCAA 58.933 50.000 1.49 0.00 43.46 4.12
675 728 0.326264 ACAATCAGTCCACTGCTCCC 59.674 55.000 1.49 0.00 43.46 4.30
693 746 2.158579 AGAACGAGAGGGGGAGATAGAC 60.159 54.545 0.00 0.00 0.00 2.59
694 747 2.106857 GAGAACGAGAGGGGGAGATAGA 59.893 54.545 0.00 0.00 0.00 1.98
695 748 2.510613 GAGAACGAGAGGGGGAGATAG 58.489 57.143 0.00 0.00 0.00 2.08
696 749 1.145325 GGAGAACGAGAGGGGGAGATA 59.855 57.143 0.00 0.00 0.00 1.98
791 885 2.612115 AGCAAGGCAGGCTACCCT 60.612 61.111 0.00 0.00 44.25 4.34
802 900 0.036875 AGAAAGGGGAACGAGCAAGG 59.963 55.000 0.00 0.00 0.00 3.61
963 1081 2.553028 GGGACTGCAAGGAAGATCAACA 60.553 50.000 0.00 0.00 39.30 3.33
1099 1219 1.762222 CGATGGATGCCCGAACGAAC 61.762 60.000 0.00 0.00 34.29 3.95
1103 1223 0.588252 CAATCGATGGATGCCCGAAC 59.412 55.000 0.00 0.00 35.87 3.95
1124 1244 2.205152 GGATGCCATGGCCCATGAC 61.205 63.158 33.44 14.66 43.81 3.06
1125 1245 2.199257 GGATGCCATGGCCCATGA 59.801 61.111 33.44 15.55 43.81 3.07
1303 1423 2.126071 TTCCAGAGCTGCGCGTAC 60.126 61.111 8.43 0.00 0.00 3.67
1444 1567 4.451150 GTGGAGCCGATGTCGCCA 62.451 66.667 0.00 0.00 38.18 5.69
1663 1786 0.671781 CAGAGTCGTCTTTGCCCCTG 60.672 60.000 0.00 0.00 0.00 4.45
1681 1804 3.147595 ACCTCGCTGCGGCTATCA 61.148 61.111 23.03 0.00 36.09 2.15
1700 1823 0.256464 ACAAACCGGACCAAGGAACA 59.744 50.000 9.46 0.00 0.00 3.18
1704 1827 1.602605 GGGACAAACCGGACCAAGG 60.603 63.158 9.46 0.00 40.11 3.61
1709 1832 2.876550 GCAATATAGGGACAAACCGGAC 59.123 50.000 9.46 0.00 40.11 4.79
1747 1870 4.445385 GCTCAAGCAAATTTTGTACAGGTG 59.555 41.667 10.65 1.68 41.59 4.00
1772 1895 8.742777 TCCTCTTGAATTCCATTATTCAGTTTG 58.257 33.333 2.27 0.00 43.33 2.93
1824 1947 2.663602 CGACGATTTGGTCTCTTCAGTG 59.336 50.000 0.00 0.00 34.75 3.66
1827 1950 2.094700 CCTCGACGATTTGGTCTCTTCA 60.095 50.000 0.00 0.00 34.75 3.02
1830 1953 0.173708 GCCTCGACGATTTGGTCTCT 59.826 55.000 0.00 0.00 34.75 3.10
1937 2060 4.083110 CCACCTTGCTCAACTGTAAGATTG 60.083 45.833 0.00 0.00 37.43 2.67
1939 2062 3.679389 CCACCTTGCTCAACTGTAAGAT 58.321 45.455 0.00 0.00 37.43 2.40
1941 2064 1.537202 GCCACCTTGCTCAACTGTAAG 59.463 52.381 0.00 0.00 42.29 2.34
2086 2231 4.733815 GCACCTGATCAGAAAAGATGCATG 60.734 45.833 24.62 5.05 0.00 4.06
2116 2261 2.305009 GAATGAATCCAGGCCTTCCAG 58.695 52.381 0.00 0.00 33.74 3.86
2117 2262 1.640149 TGAATGAATCCAGGCCTTCCA 59.360 47.619 0.00 0.00 33.74 3.53
2118 2263 2.442236 TGAATGAATCCAGGCCTTCC 57.558 50.000 0.00 0.00 0.00 3.46
2119 2264 4.648307 AGAAATGAATGAATCCAGGCCTTC 59.352 41.667 0.00 0.00 0.00 3.46
2120 2265 4.404715 CAGAAATGAATGAATCCAGGCCTT 59.595 41.667 0.00 0.00 0.00 4.35
2121 2266 3.958798 CAGAAATGAATGAATCCAGGCCT 59.041 43.478 0.00 0.00 0.00 5.19
2122 2267 3.703052 ACAGAAATGAATGAATCCAGGCC 59.297 43.478 0.00 0.00 0.00 5.19
2123 2268 4.996788 ACAGAAATGAATGAATCCAGGC 57.003 40.909 0.00 0.00 0.00 4.85
2124 2269 5.186409 ACCAACAGAAATGAATGAATCCAGG 59.814 40.000 0.00 0.00 0.00 4.45
2125 2270 6.071784 TCACCAACAGAAATGAATGAATCCAG 60.072 38.462 0.00 0.00 0.00 3.86
2149 2294 6.870965 AGTGATAATTAGAGATGTCGCCATTC 59.129 38.462 0.00 0.00 0.00 2.67
2200 2349 9.638239 TTGTCAGCCTGAAATTCAATAATAAAC 57.362 29.630 0.00 0.00 0.00 2.01
2300 2449 2.637872 CTGTGGGTTCAGGTAGAGGAAA 59.362 50.000 0.00 0.00 0.00 3.13
2352 2501 4.314740 ACTGATGCCGTATTTCTCTCTC 57.685 45.455 0.00 0.00 0.00 3.20
2353 2502 4.744795 AACTGATGCCGTATTTCTCTCT 57.255 40.909 0.00 0.00 0.00 3.10
2372 2521 8.561738 TTCAGTCTCAATTAGGAACCAATAAC 57.438 34.615 0.00 0.00 0.00 1.89
2381 2530 7.619698 TGAGGTAGATTTCAGTCTCAATTAGGA 59.380 37.037 0.00 0.00 0.00 2.94
2558 2709 5.357878 GCTCATAGGGATGTGATTTGACAAA 59.642 40.000 2.48 2.48 34.41 2.83
2581 2732 0.743097 GTTCATTGCTGGAGATGGGC 59.257 55.000 0.00 0.00 0.00 5.36
2642 2793 4.522789 TGAAGGAAATGGTTACTTGCTTCC 59.477 41.667 12.05 6.38 44.71 3.46
2957 3120 7.703621 CCATTGAATAAGAAACATGTGTGGATC 59.296 37.037 0.00 0.00 0.00 3.36
3026 3189 3.754850 CAGTCAAAGAATGATCAGTGCCA 59.245 43.478 0.00 0.00 40.97 4.92
3030 3193 7.934855 AATAAGCAGTCAAAGAATGATCAGT 57.065 32.000 0.09 0.00 40.97 3.41
3073 3236 5.935789 TCGGTGAGTTTTCTTTTATGTAGGG 59.064 40.000 0.00 0.00 0.00 3.53
3085 3248 4.336532 ACGCATAAATCGGTGAGTTTTC 57.663 40.909 0.00 0.00 0.00 2.29
3172 3337 3.299503 TGCATACTGCTCATCCAGACTA 58.700 45.455 0.34 0.00 45.31 2.59
3174 3339 2.609427 TGCATACTGCTCATCCAGAC 57.391 50.000 0.34 0.00 45.31 3.51
3376 3548 7.601856 TGTGATGTTGTTGTTCTCTTCTTTTT 58.398 30.769 0.00 0.00 0.00 1.94
3377 3549 7.156876 TGTGATGTTGTTGTTCTCTTCTTTT 57.843 32.000 0.00 0.00 0.00 2.27
3866 4039 3.311110 TCTGGTGTGGAGGTCCGC 61.311 66.667 2.37 2.37 46.40 5.54
3867 4040 2.657237 GTCTGGTGTGGAGGTCCG 59.343 66.667 0.00 0.00 39.43 4.79
3887 4060 4.481112 GGTCCGCAAGCGCAATGG 62.481 66.667 11.47 5.84 38.40 3.16
3888 4061 3.386867 GAGGTCCGCAAGCGCAATG 62.387 63.158 11.47 9.81 38.40 2.82
3889 4062 3.127533 GAGGTCCGCAAGCGCAAT 61.128 61.111 11.47 0.00 38.40 3.56


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

AutoCloner maintained by Alex Coulton.