Multiple sequence alignment - TraesCS4A01G096700

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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 TraesCS4A01G096700 chr4A 100.000 5473 0 0 1 5473 105596581 105602053 0.000000 10107.0
1 TraesCS4A01G096700 chr4D 96.948 5374 129 16 1 5364 359420780 359415432 0.000000 8983.0
2 TraesCS4A01G096700 chr4B 95.527 5522 169 31 1 5473 443818795 443813303 0.000000 8757.0
3 TraesCS4A01G096700 chr4B 97.222 36 1 0 3074 3109 443820979 443820944 0.000017 62.1
4 TraesCS4A01G096700 chr2B 83.629 1014 109 27 3095 4079 519684847 519685832 0.000000 900.0


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 TraesCS4A01G096700 chr4A 105596581 105602053 5472 False 10107.00 10107 100.0000 1 5473 1 chr4A.!!$F1 5472
1 TraesCS4A01G096700 chr4D 359415432 359420780 5348 True 8983.00 8983 96.9480 1 5364 1 chr4D.!!$R1 5363
2 TraesCS4A01G096700 chr4B 443813303 443820979 7676 True 4409.55 8757 96.3745 1 5473 2 chr4B.!!$R1 5472
3 TraesCS4A01G096700 chr2B 519684847 519685832 985 False 900.00 900 83.6290 3095 4079 1 chr2B.!!$F1 984

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
569 2755 0.388006 CGGCGAAACCATTTCAACCC 60.388 55.000 0.00 0.0 39.63 4.11 F
1443 3637 0.253044 TGGACCAGGATAGCTGCAAC 59.747 55.000 1.02 0.0 0.00 4.17 F
1709 3903 0.240411 GCAGCAGCCTTCAACAAGAG 59.760 55.000 0.00 0.0 33.58 2.85 F
1998 4195 0.320771 TGAAGAAGTTCCTCGCCTGC 60.321 55.000 0.00 0.0 0.00 4.85 F
2371 4568 1.013596 GGTTTGTTTTGCTTGCACCC 58.986 50.000 0.00 0.0 0.00 4.61 F
3893 6120 1.066454 GGAAAACCAACCTTGTGTCCG 59.934 52.381 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 3652 0.684535 TCTGAGACGCAATGTGGGAA 59.315 50.000 0.00 0.0 34.12 3.97 R
3169 5366 0.252479 CAAGCTCCTGTGAGGCATCT 59.748 55.000 0.00 0.0 39.14 2.90 R
3630 5831 9.658799 TGATCTAATTAGACAGGAAAAGACTTG 57.341 33.333 17.35 0.0 34.72 3.16 R
3893 6120 6.109359 ACAGCACTAACTGAATCATAAGGAC 58.891 40.000 0.00 0.0 40.25 3.85 R
4110 6339 0.890996 AAGTTGCCTACAGGTGCTGC 60.891 55.000 0.00 0.0 34.37 5.25 R
5292 7563 3.071874 TGAACACTGCTATTTCTGGGG 57.928 47.619 0.00 0.0 0.00 4.96 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
54 2239 1.023513 GCTGAATTGCGAGCCTCTGT 61.024 55.000 0.00 0.00 0.00 3.41
193 2378 2.511600 CTGTGATCGGCGGGTTCC 60.512 66.667 7.21 0.00 0.00 3.62
220 2405 1.209504 GGTCATGGTGAGAATTCGGGA 59.790 52.381 0.00 0.00 0.00 5.14
363 2548 5.591099 TGAGAATTCTTGCTTGGTTTTCAC 58.409 37.500 9.87 0.00 0.00 3.18
491 2677 2.087646 AGGCTTTTCTCTTTGATCGCC 58.912 47.619 0.00 0.00 34.16 5.54
508 2694 2.906897 CTGGCGTGCTGGTTTGGT 60.907 61.111 0.00 0.00 0.00 3.67
524 2710 0.894184 TGGTTTGCCCGGCGAATTTA 60.894 50.000 15.43 2.62 34.24 1.40
569 2755 0.388006 CGGCGAAACCATTTCAACCC 60.388 55.000 0.00 0.00 39.63 4.11
712 2898 1.149174 ATCATTTCGGGCGCTCCAT 59.851 52.632 7.64 0.00 34.36 3.41
745 2931 1.368374 CTCCTGGGGTTTTGGGACTA 58.632 55.000 0.00 0.00 0.00 2.59
830 3019 7.171678 GGTTTATCCGAGATTTATCCTGACTTG 59.828 40.741 0.00 0.00 0.00 3.16
948 3142 2.001812 CAGATCTGTGTTCTGGGACG 57.998 55.000 14.95 0.00 37.53 4.79
1064 3258 2.711922 GGAGATGGAGTCGTGCGGT 61.712 63.158 0.00 0.00 0.00 5.68
1177 3371 3.573772 TTGGCGAGTCTGACAGCGG 62.574 63.158 19.54 4.68 0.00 5.52
1443 3637 0.253044 TGGACCAGGATAGCTGCAAC 59.747 55.000 1.02 0.00 0.00 4.17
1506 3700 0.839946 ATCACCATTCTCGGAAGGGG 59.160 55.000 17.61 11.58 0.00 4.79
1687 3881 1.404449 CGGCAAATGTGATGGCATTGT 60.404 47.619 0.00 0.00 43.00 2.71
1709 3903 0.240411 GCAGCAGCCTTCAACAAGAG 59.760 55.000 0.00 0.00 33.58 2.85
1886 4083 9.739276 AGAGTATTCTGTAGATAGAGAGAATGG 57.261 37.037 0.00 0.00 36.18 3.16
1998 4195 0.320771 TGAAGAAGTTCCTCGCCTGC 60.321 55.000 0.00 0.00 0.00 4.85
2019 4216 3.476552 CAAGTACAGGAAAGTTGCTCCA 58.523 45.455 0.00 0.00 35.20 3.86
2371 4568 1.013596 GGTTTGTTTTGCTTGCACCC 58.986 50.000 0.00 0.00 0.00 4.61
2429 4626 4.291783 TGTAACTTATTTTGGCGCAACAC 58.708 39.130 10.83 0.00 0.00 3.32
2671 4868 6.655003 TCACTGAAGGTATTTTCCAGACATTC 59.345 38.462 0.00 0.00 35.13 2.67
2714 4911 7.686438 ACTTGTTCATGCACATAAATAGACA 57.314 32.000 0.00 0.00 0.00 3.41
2908 5105 5.014858 GCTGGGATTGGTCATGATGATATT 58.985 41.667 0.00 0.00 0.00 1.28
2935 5132 4.074970 ACAACATAGGCTTTTCACTGGAG 58.925 43.478 0.00 0.00 0.00 3.86
3169 5366 1.154093 CTCGAAGCACGGCGAAGTA 60.154 57.895 16.62 0.00 42.82 2.24
3563 5764 6.199393 AGATGTTAAACTTCGTGCTTTTGAC 58.801 36.000 0.00 0.00 0.00 3.18
3630 5831 9.760660 CTGTCATATACTTTACTTTGACTTTGC 57.239 33.333 0.00 0.00 35.63 3.68
3646 5849 4.273318 ACTTTGCAAGTCTTTTCCTGTCT 58.727 39.130 0.00 0.00 37.02 3.41
3893 6120 1.066454 GGAAAACCAACCTTGTGTCCG 59.934 52.381 0.00 0.00 0.00 4.79
4104 6333 1.500844 CAGAAGCTTCTTGGCTGCG 59.499 57.895 26.44 9.66 42.45 5.18
4105 6334 2.177778 GAAGCTTCTTGGCTGCGC 59.822 61.111 19.44 0.00 42.24 6.09
4106 6335 2.595463 AAGCTTCTTGGCTGCGCA 60.595 55.556 10.98 10.98 42.24 6.09
4107 6336 2.524636 GAAGCTTCTTGGCTGCGCAG 62.525 60.000 32.83 32.83 42.24 5.18
4108 6337 4.112341 GCTTCTTGGCTGCGCAGG 62.112 66.667 36.47 21.02 0.00 4.85
4174 6408 7.277098 GGTCAAATTTGATGAATGAAGATGGTG 59.723 37.037 23.05 0.00 39.73 4.17
4419 6653 5.529289 TCACCTAATAACTCCCATCTCAGT 58.471 41.667 0.00 0.00 0.00 3.41
5027 7270 3.890756 TGTCTCTGGCATGTGATTTTGTT 59.109 39.130 0.00 0.00 0.00 2.83
5028 7271 5.069318 TGTCTCTGGCATGTGATTTTGTTA 58.931 37.500 0.00 0.00 0.00 2.41
5029 7272 5.048782 TGTCTCTGGCATGTGATTTTGTTAC 60.049 40.000 0.00 0.00 0.00 2.50
5030 7273 5.182001 GTCTCTGGCATGTGATTTTGTTACT 59.818 40.000 0.00 0.00 0.00 2.24
5031 7274 5.181811 TCTCTGGCATGTGATTTTGTTACTG 59.818 40.000 0.00 0.00 0.00 2.74
5037 7280 7.090173 GGCATGTGATTTTGTTACTGTATTGT 58.910 34.615 0.00 0.00 0.00 2.71
5230 7474 5.277683 CCAATGCTGATTGTACTACATGAGC 60.278 44.000 0.00 0.00 37.82 4.26
5245 7489 7.503521 CTACATGAGCAGTAGTTAGATCTCA 57.496 40.000 0.00 0.00 35.39 3.27
5295 7566 5.635120 AGATCTTAACTTGCCATAATCCCC 58.365 41.667 0.00 0.00 0.00 4.81
5312 7583 2.642311 TCCCCAGAAATAGCAGTGTTCA 59.358 45.455 0.00 0.00 0.00 3.18
5314 7585 4.019174 CCCCAGAAATAGCAGTGTTCAAT 58.981 43.478 0.00 0.00 0.00 2.57
5315 7586 4.463891 CCCCAGAAATAGCAGTGTTCAATT 59.536 41.667 0.00 0.00 0.00 2.32
5316 7587 5.047092 CCCCAGAAATAGCAGTGTTCAATTT 60.047 40.000 0.00 0.00 0.00 1.82
5384 7655 7.013529 CACTACCAATACTTTTTGAAGTACGC 58.986 38.462 1.48 0.00 38.01 4.42
5440 7711 7.534723 AGTTAACTACACTTGTGGTCATCTA 57.465 36.000 6.26 0.00 38.86 1.98
5466 7737 1.887198 TCGAGAGGGTGAGAGTTGTTC 59.113 52.381 0.00 0.00 0.00 3.18
5468 7739 2.608261 CGAGAGGGTGAGAGTTGTTCAC 60.608 54.545 0.00 0.00 43.25 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 2257 1.055849 ATTCCCCAAACCCAAGCAAC 58.944 50.000 0.00 0.00 0.00 4.17
141 2326 0.612732 TCAGGCAGAAATGGGCTTGG 60.613 55.000 0.00 0.00 39.39 3.61
144 2329 3.772096 TTTCAGGCAGAAATGGGCT 57.228 47.368 0.44 0.00 41.17 5.19
193 2378 4.429212 TCACCATGACCGGCGTCG 62.429 66.667 0.29 0.29 42.37 5.12
202 2387 3.712016 TTTCCCGAATTCTCACCATGA 57.288 42.857 3.52 0.00 0.00 3.07
208 2393 3.443681 GCTCCAAATTTCCCGAATTCTCA 59.556 43.478 3.52 0.00 36.96 3.27
220 2405 1.682344 GGCCTCCCGCTCCAAATTT 60.682 57.895 0.00 0.00 37.74 1.82
397 2582 3.105157 GCGGACGCGTCGGTTAAA 61.105 61.111 36.58 0.00 33.17 1.52
491 2677 2.015227 AAACCAAACCAGCACGCCAG 62.015 55.000 0.00 0.00 0.00 4.85
504 2690 1.749334 AAATTCGCCGGGCAAACCAA 61.749 50.000 20.71 3.40 40.22 3.67
508 2694 3.320673 AAATTAAATTCGCCGGGCAAA 57.679 38.095 20.71 7.50 0.00 3.68
524 2710 6.816140 CCGTATTAAATGCACCCAAGAAAATT 59.184 34.615 0.00 0.00 0.00 1.82
569 2755 4.932200 AGTAAGCGGAGAGAACAATCTTTG 59.068 41.667 0.00 0.00 35.54 2.77
719 2905 1.215423 CAAAACCCCAGGAGGATAGGG 59.785 57.143 1.11 0.00 45.75 3.53
948 3142 1.154150 GTTGCGCTGCTCATGGTTC 60.154 57.895 9.73 0.00 0.00 3.62
1177 3371 2.484889 AGAAACAAGAAGAGACGCCAC 58.515 47.619 0.00 0.00 0.00 5.01
1443 3637 1.345176 GGAAATCAACGCGCTCTCG 59.655 57.895 5.73 0.00 39.07 4.04
1458 3652 0.684535 TCTGAGACGCAATGTGGGAA 59.315 50.000 0.00 0.00 34.12 3.97
1506 3700 2.774234 TGGAACCTCATTCAGATCCTCC 59.226 50.000 0.00 0.00 39.30 4.30
1687 3881 2.669569 GTTGAAGGCTGCTGCGGA 60.670 61.111 13.72 0.00 40.82 5.54
1709 3903 0.748005 ATTGTACATGTCAGGGGCGC 60.748 55.000 0.00 0.00 0.00 6.53
1801 3995 6.567050 ACTTGTGAATTTTGCAGCCATATAG 58.433 36.000 0.00 0.00 0.00 1.31
1809 4003 3.003689 AGACGGACTTGTGAATTTTGCAG 59.996 43.478 0.00 0.00 0.00 4.41
1810 4004 2.948979 AGACGGACTTGTGAATTTTGCA 59.051 40.909 0.00 0.00 0.00 4.08
1886 4083 6.093219 CCCGGAAGATTTATCATCATCATCAC 59.907 42.308 0.73 0.00 0.00 3.06
1998 4195 3.476552 TGGAGCAACTTTCCTGTACTTG 58.523 45.455 0.00 0.00 35.67 3.16
2019 4216 1.074405 TCTCCTTTGTGCATTCTGGCT 59.926 47.619 0.00 0.00 34.04 4.75
2371 4568 2.969443 AAATTGAAGAGGAACGCACG 57.031 45.000 0.00 0.00 0.00 5.34
2419 4616 1.785041 GCAGAAGAAGTGTTGCGCCA 61.785 55.000 4.18 0.00 0.00 5.69
2429 4626 3.428589 GCCCTTATTTGCTGCAGAAGAAG 60.429 47.826 20.43 15.78 0.00 2.85
2749 4946 4.477302 AAGTACACATTAAACCACACGC 57.523 40.909 0.00 0.00 0.00 5.34
2908 5105 4.072131 GTGAAAAGCCTATGTTGTCCAGA 58.928 43.478 0.00 0.00 0.00 3.86
2935 5132 1.241315 AATGCCGTGTACAGTTGGGC 61.241 55.000 16.30 16.30 44.00 5.36
3080 5277 4.761975 ACTCAGGTTACAAACGTTGAAGA 58.238 39.130 0.00 0.00 0.00 2.87
3169 5366 0.252479 CAAGCTCCTGTGAGGCATCT 59.748 55.000 0.00 0.00 39.14 2.90
3630 5831 9.658799 TGATCTAATTAGACAGGAAAAGACTTG 57.341 33.333 17.35 0.00 34.72 3.16
3893 6120 6.109359 ACAGCACTAACTGAATCATAAGGAC 58.891 40.000 0.00 0.00 40.25 3.85
4106 6335 4.087892 CCTACAGGTGCTGCGCCT 62.088 66.667 28.18 28.18 46.26 5.52
4109 6338 2.358615 TTGCCTACAGGTGCTGCG 60.359 61.111 0.00 0.00 34.37 5.18
4110 6339 0.890996 AAGTTGCCTACAGGTGCTGC 60.891 55.000 0.00 0.00 34.37 5.25
5002 7243 5.356190 ACAAAATCACATGCCAGAGACATAG 59.644 40.000 0.00 0.00 0.00 2.23
5292 7563 3.071874 TGAACACTGCTATTTCTGGGG 57.928 47.619 0.00 0.00 0.00 4.96
5316 7587 6.263617 ACGATGTTTAGCTTAACAGGGAAAAA 59.736 34.615 21.44 0.00 40.99 1.94
5384 7655 8.347035 ACGTCCCCATCAAAAATAATAATAACG 58.653 33.333 0.00 0.00 0.00 3.18
5398 7669 3.992943 ACTTCATAACGTCCCCATCAA 57.007 42.857 0.00 0.00 0.00 2.57
5440 7711 3.904717 ACTCTCACCCTCTCGATACAAT 58.095 45.455 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.