Multiple sequence alignment - TraesCS3A01G183300

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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 TraesCS3A01G183300 chr3A 100.000 6974 0 0 1 6974 212705091 212712064 0 12879
1 TraesCS3A01G183300 chr2A 98.739 6980 77 10 1 6974 742784336 742791310 0 12392
2 TraesCS3A01G183300 chr2A 98.609 6975 88 8 1 6974 306618786 306625752 0 12334
3 TraesCS3A01G183300 chr7A 98.725 6978 82 6 1 6974 549409743 549402769 0 12386
4 TraesCS3A01G183300 chr3B 98.569 6986 79 10 1 6974 798422227 798429203 0 12327
5 TraesCS3A01G183300 chr3B 97.985 6054 84 15 1 6028 642076066 642082107 0 10469
6 TraesCS3A01G183300 chr7B 98.567 6979 86 12 1 6974 147706497 147713466 0 12321
7 TraesCS3A01G183300 chr6A 98.443 7002 75 16 1 6974 90756944 90763939 0 12296
8 TraesCS3A01G183300 chr1A 98.201 7002 88 15 1 6974 531033312 531040303 0 12198
9 TraesCS3A01G183300 chr1A 98.057 7000 95 18 1 6974 521305227 521312211 0 12135
10 TraesCS3A01G183300 chr5A 98.101 7005 98 11 1 6974 687730712 687723712 0 12166
11 TraesCS3A01G183300 chr1B 98.028 6998 94 19 1 6974 65600595 65593618 0 12118
12 TraesCS3A01G183300 chr6B 97.411 5949 90 15 3 5942 69680196 69686089 0 10074


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 TraesCS3A01G183300 chr3A 212705091 212712064 6973 False 12879 12879 100.000 1 6974 1 chr3A.!!$F1 6973
1 TraesCS3A01G183300 chr2A 742784336 742791310 6974 False 12392 12392 98.739 1 6974 1 chr2A.!!$F2 6973
2 TraesCS3A01G183300 chr2A 306618786 306625752 6966 False 12334 12334 98.609 1 6974 1 chr2A.!!$F1 6973
3 TraesCS3A01G183300 chr7A 549402769 549409743 6974 True 12386 12386 98.725 1 6974 1 chr7A.!!$R1 6973
4 TraesCS3A01G183300 chr3B 798422227 798429203 6976 False 12327 12327 98.569 1 6974 1 chr3B.!!$F2 6973
5 TraesCS3A01G183300 chr3B 642076066 642082107 6041 False 10469 10469 97.985 1 6028 1 chr3B.!!$F1 6027
6 TraesCS3A01G183300 chr7B 147706497 147713466 6969 False 12321 12321 98.567 1 6974 1 chr7B.!!$F1 6973
7 TraesCS3A01G183300 chr6A 90756944 90763939 6995 False 12296 12296 98.443 1 6974 1 chr6A.!!$F1 6973
8 TraesCS3A01G183300 chr1A 531033312 531040303 6991 False 12198 12198 98.201 1 6974 1 chr1A.!!$F2 6973
9 TraesCS3A01G183300 chr1A 521305227 521312211 6984 False 12135 12135 98.057 1 6974 1 chr1A.!!$F1 6973
10 TraesCS3A01G183300 chr5A 687723712 687730712 7000 True 12166 12166 98.101 1 6974 1 chr5A.!!$R1 6973
11 TraesCS3A01G183300 chr1B 65593618 65600595 6977 True 12118 12118 98.028 1 6974 1 chr1B.!!$R1 6973
12 TraesCS3A01G183300 chr6B 69680196 69686089 5893 False 10074 10074 97.411 3 5942 1 chr6B.!!$F1 5939

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
784 806 0.586319 CATCGAGTTGGCGTGTTTGT 59.414 50.0 0.00 0.00 0.00 2.83 F
1428 1452 0.402887 TATACGATCCCGCCTCCAGA 59.597 55.0 0.00 0.00 39.95 3.86 F
1442 1466 2.697751 CCTCCAGAGAATTCGTGATCCT 59.302 50.0 11.29 0.00 0.00 3.24 F
4113 4180 2.490903 GGGTGAAGAAGACTACTACGCA 59.509 50.0 0.00 0.00 0.00 5.24 F
4692 4761 0.468226 GACATACCCAATGCTCCGGA 59.532 55.0 2.93 2.93 39.39 5.14 F
5375 5446 0.475632 TGGGGGTCCTCACTTGTGAT 60.476 55.0 3.79 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3282 3339 8.729805 AAAAACAAGTGCAAAAGAAATGGATA 57.270 26.923 0.0 0.0 0.0 2.59 R
4113 4180 1.149174 CTGATATGCTTGGCCCCGT 59.851 57.895 0.0 0.0 0.0 5.28 R
4278 4345 3.260632 TGTTGTTCTAGCCTGCACATCTA 59.739 43.478 0.0 0.0 0.0 1.98 R
5865 5938 2.041701 GGGGTGGCTGCAATGAATATT 58.958 47.619 0.5 0.0 0.0 1.28 R
5971 6045 3.193267 GCAGGCACATTGGAACTTGATTA 59.807 43.478 0.0 0.0 0.0 1.75 R
6206 6281 5.992829 AGAGCAAGCAAGATGAGAGATTATG 59.007 40.000 0.0 0.0 0.0 1.90 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
259 262 4.651994 GAAAATGACTGTCATAGTTGCCG 58.348 43.478 22.53 0.00 40.53 5.69
296 309 6.294731 GGTGGCAACTAATTTCATTGAACTCT 60.295 38.462 0.00 0.00 37.61 3.24
398 412 3.976793 ATATGCTTTCTGAATGTGGCG 57.023 42.857 5.36 0.00 0.00 5.69
467 481 5.767665 ACTACATGAACAAATGTGGCAGTTA 59.232 36.000 0.00 0.00 41.36 2.24
784 806 0.586319 CATCGAGTTGGCGTGTTTGT 59.414 50.000 0.00 0.00 0.00 2.83
959 983 4.815269 TGCTTACCCATTGCATTTTACAC 58.185 39.130 0.00 0.00 0.00 2.90
1387 1411 1.039068 TACGAACCTTGTCAACCCGA 58.961 50.000 0.00 0.00 0.00 5.14
1428 1452 0.402887 TATACGATCCCGCCTCCAGA 59.597 55.000 0.00 0.00 39.95 3.86
1442 1466 2.697751 CCTCCAGAGAATTCGTGATCCT 59.302 50.000 11.29 0.00 0.00 3.24
4113 4180 2.490903 GGGTGAAGAAGACTACTACGCA 59.509 50.000 0.00 0.00 0.00 5.24
4407 4474 2.042639 GAGCCATGCCACCCCATT 60.043 61.111 0.00 0.00 0.00 3.16
4432 4499 1.513158 CGTCGAAGTGGATGCTCCT 59.487 57.895 0.00 0.00 37.46 3.69
4554 4623 3.382546 GCACTTCACAAGGATATGCCATT 59.617 43.478 0.00 0.00 40.02 3.16
4684 4753 4.603131 AGCAATCAACAGACATACCCAAT 58.397 39.130 0.00 0.00 0.00 3.16
4692 4761 0.468226 GACATACCCAATGCTCCGGA 59.532 55.000 2.93 2.93 39.39 5.14
4913 4982 2.679716 GCACTTCCAGGCTCCCAT 59.320 61.111 0.00 0.00 0.00 4.00
4952 5021 5.770162 CCCTACAGTCCAAACAAGAAGATTT 59.230 40.000 0.00 0.00 0.00 2.17
5375 5446 0.475632 TGGGGGTCCTCACTTGTGAT 60.476 55.000 3.79 0.00 0.00 3.06
5971 6045 3.322466 CCTCACGAGGGCAAGGGT 61.322 66.667 5.08 0.00 44.87 4.34
6051 6126 2.401699 CTGGTCCTGTGAGGCAGCAA 62.402 60.000 0.00 0.00 43.71 3.91
6206 6281 3.497103 AGCGTAAATTACCATACCCCC 57.503 47.619 0.00 0.00 0.00 5.40
6801 6881 7.831690 TGGCAACTTGATAGTAAAATACATGGA 59.168 33.333 0.00 0.00 33.17 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 115 0.463654 TCGCCACAGTCTGCAGTTTT 60.464 50.000 14.67 0.0 0.00 2.43
259 262 3.680786 GCCACCTCGTTTTGGGGC 61.681 66.667 0.00 0.0 35.13 5.80
398 412 3.381949 GTTCGGTCATACTGCCATAGTC 58.618 50.000 0.00 0.0 40.89 2.59
467 481 3.817647 GCAGAAGAGAACAGATTTGTGGT 59.182 43.478 0.00 0.0 37.67 4.16
476 490 0.514691 GTTGCCGCAGAAGAGAACAG 59.485 55.000 0.00 0.0 0.00 3.16
959 983 6.018343 ACAAACCAAATTGTTAATGGCGAAAG 60.018 34.615 0.00 0.0 40.52 2.62
1241 1265 4.084223 TGTTGCGAATACGTTTCTTCTTCC 60.084 41.667 0.00 0.0 41.98 3.46
1387 1411 0.541392 TCACCAAGCCAGTCGCATAT 59.459 50.000 0.00 0.0 41.38 1.78
1428 1452 1.137086 CGTCCCAGGATCACGAATTCT 59.863 52.381 3.52 0.0 35.49 2.40
1442 1466 1.916777 GGAAGTCTTCCCCGTCCCA 60.917 63.158 19.59 0.0 44.30 4.37
3282 3339 8.729805 AAAAACAAGTGCAAAAGAAATGGATA 57.270 26.923 0.00 0.0 0.00 2.59
4113 4180 1.149174 CTGATATGCTTGGCCCCGT 59.851 57.895 0.00 0.0 0.00 5.28
4278 4345 3.260632 TGTTGTTCTAGCCTGCACATCTA 59.739 43.478 0.00 0.0 0.00 1.98
4407 4474 0.530744 ATCCACTTCGACGCTTGCTA 59.469 50.000 0.00 0.0 0.00 3.49
4432 4499 0.984230 CCTTGCCTAGGTTGGTCTCA 59.016 55.000 11.31 0.0 39.39 3.27
4554 4623 1.282738 TGCCAGGATTCTCATCTGCAA 59.717 47.619 0.00 0.0 30.55 4.08
4595 4664 1.683917 CGCCTTAGCAGTATCTCCACT 59.316 52.381 0.00 0.0 39.83 4.00
4684 4753 0.185175 TCCTAGCTACATCCGGAGCA 59.815 55.000 11.34 0.0 41.36 4.26
4692 4761 2.445145 TCTCTCCTGCTCCTAGCTACAT 59.555 50.000 0.03 0.0 42.97 2.29
4913 4982 1.276989 GTAGGGGACACCGACATTGAA 59.723 52.381 1.52 0.0 46.96 2.69
5514 5586 4.582240 TGAACTGTATTTGCCATGTGACAA 59.418 37.500 0.00 0.0 0.00 3.18
5865 5938 2.041701 GGGGTGGCTGCAATGAATATT 58.958 47.619 0.50 0.0 0.00 1.28
5971 6045 3.193267 GCAGGCACATTGGAACTTGATTA 59.807 43.478 0.00 0.0 0.00 1.75
6206 6281 5.992829 AGAGCAAGCAAGATGAGAGATTATG 59.007 40.000 0.00 0.0 0.00 1.90


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

AutoCloner maintained by Alex Coulton.