Multiple sequence alignment - TraesCS3B01G423900

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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 TraesCS3B01G423900 chr3B 100.000 2549 0 0 1 2549 661407227 661409775 0 4708
1 TraesCS3B01G423900 chr3B 97.980 1980 36 3 570 2549 702857655 702855680 0 3432
2 TraesCS3B01G423900 chr6A 98.131 1980 33 3 571 2549 617222869 617220893 0 3448
3 TraesCS3B01G423900 chr6A 98.031 1981 35 3 570 2549 533982323 533980346 0 3439
4 TraesCS3B01G423900 chr6B 98.031 1981 38 1 569 2549 8435751 8437730 0 3441
5 TraesCS3B01G423900 chr6B 96.120 567 22 0 4 570 685255419 685254853 0 926
6 TraesCS3B01G423900 chr4A 98.032 1982 36 2 569 2549 36562911 36564890 0 3441
7 TraesCS3B01G423900 chr1B 97.938 1988 37 3 563 2549 42162347 42160363 0 3441
8 TraesCS3B01G423900 chr3A 98.031 1981 35 3 569 2549 54951916 54953892 0 3439
9 TraesCS3B01G423900 chr3A 95.246 568 27 0 3 570 455473367 455473934 0 900
10 TraesCS3B01G423900 chr2B 97.981 1981 35 4 570 2549 776222961 776224937 0 3432
11 TraesCS3B01G423900 chr2B 97.981 1981 35 4 570 2549 781094240 781096216 0 3432
12 TraesCS3B01G423900 chr5D 96.303 568 21 0 3 570 54996993 54996426 0 933
13 TraesCS3B01G423900 chr5D 96.303 568 21 0 3 570 427018407 427017840 0 933
14 TraesCS3B01G423900 chr5D 96.303 568 21 0 3 570 427086105 427085538 0 933
15 TraesCS3B01G423900 chr3D 96.303 568 21 0 3 570 103339663 103339096 0 933
16 TraesCS3B01G423900 chr3D 94.718 568 30 0 3 570 158513086 158513653 0 883
17 TraesCS3B01G423900 chr1D 96.303 568 21 0 3 570 237452043 237452610 0 933
18 TraesCS3B01G423900 chr1A 95.567 564 25 0 3 566 570884330 570883767 0 904


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 TraesCS3B01G423900 chr3B 661407227 661409775 2548 False 4708 4708 100.000 1 2549 1 chr3B.!!$F1 2548
1 TraesCS3B01G423900 chr3B 702855680 702857655 1975 True 3432 3432 97.980 570 2549 1 chr3B.!!$R1 1979
2 TraesCS3B01G423900 chr6A 617220893 617222869 1976 True 3448 3448 98.131 571 2549 1 chr6A.!!$R2 1978
3 TraesCS3B01G423900 chr6A 533980346 533982323 1977 True 3439 3439 98.031 570 2549 1 chr6A.!!$R1 1979
4 TraesCS3B01G423900 chr6B 8435751 8437730 1979 False 3441 3441 98.031 569 2549 1 chr6B.!!$F1 1980
5 TraesCS3B01G423900 chr6B 685254853 685255419 566 True 926 926 96.120 4 570 1 chr6B.!!$R1 566
6 TraesCS3B01G423900 chr4A 36562911 36564890 1979 False 3441 3441 98.032 569 2549 1 chr4A.!!$F1 1980
7 TraesCS3B01G423900 chr1B 42160363 42162347 1984 True 3441 3441 97.938 563 2549 1 chr1B.!!$R1 1986
8 TraesCS3B01G423900 chr3A 54951916 54953892 1976 False 3439 3439 98.031 569 2549 1 chr3A.!!$F1 1980
9 TraesCS3B01G423900 chr3A 455473367 455473934 567 False 900 900 95.246 3 570 1 chr3A.!!$F2 567
10 TraesCS3B01G423900 chr2B 776222961 776224937 1976 False 3432 3432 97.981 570 2549 1 chr2B.!!$F1 1979
11 TraesCS3B01G423900 chr2B 781094240 781096216 1976 False 3432 3432 97.981 570 2549 1 chr2B.!!$F2 1979
12 TraesCS3B01G423900 chr5D 54996426 54996993 567 True 933 933 96.303 3 570 1 chr5D.!!$R1 567
13 TraesCS3B01G423900 chr5D 427017840 427018407 567 True 933 933 96.303 3 570 1 chr5D.!!$R2 567
14 TraesCS3B01G423900 chr5D 427085538 427086105 567 True 933 933 96.303 3 570 1 chr5D.!!$R3 567
15 TraesCS3B01G423900 chr3D 103339096 103339663 567 True 933 933 96.303 3 570 1 chr3D.!!$R1 567
16 TraesCS3B01G423900 chr3D 158513086 158513653 567 False 883 883 94.718 3 570 1 chr3D.!!$F1 567
17 TraesCS3B01G423900 chr1D 237452043 237452610 567 False 933 933 96.303 3 570 1 chr1D.!!$F1 567
18 TraesCS3B01G423900 chr1A 570883767 570884330 563 True 904 904 95.567 3 566 1 chr1A.!!$R1 563

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
461 462 0.898326 TTCAGCGGTGTGAGGAGCTA 60.898 55.0 15.22 0.0 37.94 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 2246 1.139058 CTTCCTTCCCTACCCATGTCG 59.861 57.143 0.0 0.0 0.0 4.35 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
37 38 7.221838 TCAACCTTCTTTAATTGCTCAAAAACG 59.778 33.333 0.00 0.00 0.00 3.60
79 80 6.365839 CACACTAAGCATTGTGTAAGTTGAG 58.634 40.000 8.75 0.00 44.43 3.02
101 102 6.071334 TGAGTTCCACCTAGTCTTACAATCAG 60.071 42.308 0.00 0.00 0.00 2.90
192 193 3.448660 GGTGAGGCAATCCAAAAAGCTAT 59.551 43.478 0.00 0.00 33.74 2.97
222 223 7.596494 TCTCTAATCTTTTCAATTGCTGGTTG 58.404 34.615 0.00 0.00 0.00 3.77
314 315 2.605338 CCTTGCAACATGAGTTTGTCCG 60.605 50.000 0.00 0.00 35.28 4.79
374 375 7.980662 TGTCATTTGAAGAACAATTGTCAACAT 59.019 29.630 12.39 0.00 39.43 2.71
440 441 8.654230 TGATTCATGAAGTTCTTCAGCTATAC 57.346 34.615 14.54 9.85 34.02 1.47
461 462 0.898326 TTCAGCGGTGTGAGGAGCTA 60.898 55.000 15.22 0.00 37.94 3.32
545 546 9.877178 TGAAAACAACACCAAACAATTTACTAT 57.123 25.926 0.00 0.00 0.00 2.12
936 937 4.537433 GCTAGCTGTGGAGGGCGG 62.537 72.222 7.70 0.00 0.00 6.13
1078 1079 1.957562 CCTGTCTTCGTCTGTCCGT 59.042 57.895 0.00 0.00 0.00 4.69
1116 1117 2.233922 TGATCGAAGGGTTTCTCAGACC 59.766 50.000 0.00 0.00 36.41 3.85
1133 1134 1.909302 GACCCTGAGGAACCAGAATCA 59.091 52.381 0.00 0.00 36.29 2.57
1159 1160 1.741145 TCTACGTGTGCAGCGAGAATA 59.259 47.619 16.16 0.00 0.00 1.75
1237 1238 4.037923 GGTTGATCTGTTTGGTGTTCATGT 59.962 41.667 0.00 0.00 0.00 3.21
1305 1306 6.178324 TCTGATGAATGAACTGCAAGAAGAT 58.822 36.000 0.00 0.00 37.43 2.40
1360 1361 3.872603 TGGCCACACCACGAGCTT 61.873 61.111 0.00 0.00 46.36 3.74
1379 1380 2.898729 TCGGAAGAAGAGATGGATGC 57.101 50.000 0.00 0.00 37.03 3.91
1552 1553 7.549842 TGAAAATGTATGGAAAGGCATGAATTG 59.450 33.333 0.00 0.00 0.00 2.32
2081 2083 3.925913 CCAGGTGCCAAAATAAATGAACG 59.074 43.478 0.00 0.00 0.00 3.95
2244 2246 2.777832 AGGACAGATGGCAAGACTTC 57.222 50.000 0.00 0.00 0.00 3.01
2346 2349 0.104304 ACGCGTGAGAGTGGTTTTCT 59.896 50.000 12.93 0.00 44.38 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.959639 TTGAGCAATTAAAGAAGGTTGAGT 57.040 33.333 0.00 0.0 0.00 3.41
26 27 5.250200 ACCATATAAGGTCGTTTTTGAGCA 58.750 37.500 0.00 0.0 37.28 4.26
79 80 5.046520 ACCTGATTGTAAGACTAGGTGGAAC 60.047 44.000 0.00 0.0 37.17 3.62
222 223 4.758674 TCAAAGATGGCTTAGATGCTATGC 59.241 41.667 0.00 0.0 34.31 3.14
314 315 2.838202 TGTTGGTGAAGAGGATAGGGAC 59.162 50.000 0.00 0.0 0.00 4.46
374 375 3.953712 TGAGAAGCTATCAACGGTGAA 57.046 42.857 7.51 0.0 37.30 3.18
440 441 1.079543 CTCCTCACACCGCTGAAGG 60.080 63.158 0.00 0.0 37.30 3.46
461 462 7.835822 TGCATTTGTAGGTTTATTTATGTGCT 58.164 30.769 0.00 0.0 0.00 4.40
545 546 7.384660 CCTTGTTTTTATCAACATTTGCTGCTA 59.615 33.333 0.00 0.0 36.54 3.49
816 817 0.837272 ATATAGCACACCCGCCAACT 59.163 50.000 0.00 0.0 0.00 3.16
936 937 4.858680 GCTAGCTTCCCACCGCCC 62.859 72.222 7.70 0.0 0.00 6.13
967 968 0.902531 GAAGGGGATCTCAACACCGA 59.097 55.000 0.00 0.0 35.74 4.69
1116 1117 2.484417 CGGATGATTCTGGTTCCTCAGG 60.484 54.545 0.00 0.0 35.58 3.86
1159 1160 1.222567 ATTGCCCCGATTCTTACCCT 58.777 50.000 0.00 0.0 0.00 4.34
1237 1238 4.761739 CCAAAGAAAGAAGCATGTCACCTA 59.238 41.667 0.00 0.0 0.00 3.08
1305 1306 1.532523 TGCGCAACCATTCTTCATGA 58.467 45.000 8.16 0.0 34.31 3.07
1360 1361 1.414181 GGCATCCATCTCTTCTTCCGA 59.586 52.381 0.00 0.0 0.00 4.55
1379 1380 2.661537 TGTCAGTGCGTGCTTCGG 60.662 61.111 4.36 0.0 40.26 4.30
2191 2193 1.410882 GCAGCCCTAAACACCACAAAA 59.589 47.619 0.00 0.0 0.00 2.44
2244 2246 1.139058 CTTCCTTCCCTACCCATGTCG 59.861 57.143 0.00 0.0 0.00 4.35
2346 2349 8.239998 CCTCCAAAATTTAAGTGCAAAACAAAA 58.760 29.630 0.00 0.0 0.00 2.44


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

AutoCloner maintained by Alex Coulton.