Multiple sequence alignment - TraesCS3D01G238400

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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 TraesCS3D01G238400 chr3D 100.000 6197 0 0 1 6197 329698266 329692070 0.000000e+00 11444.0
1 TraesCS3D01G238400 chr3D 98.013 604 12 0 5594 6197 46551688 46551085 0.000000e+00 1050.0
2 TraesCS3D01G238400 chr3B 98.531 5311 61 6 241 5538 427321398 427316092 0.000000e+00 9359.0
3 TraesCS3D01G238400 chr3B 97.260 292 5 2 1 289 427321708 427321417 5.580000e-135 492.0
4 TraesCS3D01G238400 chr3B 94.574 129 3 1 467 591 201492583 201492711 4.900000e-46 196.0
5 TraesCS3D01G238400 chr3B 94.915 59 3 0 5535 5593 427316068 427316010 6.610000e-15 93.5
6 TraesCS3D01G238400 chr3A 94.911 4736 203 13 855 5563 444725544 444720820 0.000000e+00 7376.0
7 TraesCS3D01G238400 chr3A 95.475 221 8 2 67 287 444726027 444725809 9.880000e-93 351.0
8 TraesCS3D01G238400 chr3A 89.300 243 10 4 241 467 444725823 444725581 2.190000e-74 291.0
9 TraesCS3D01G238400 chr6D 98.510 604 9 0 5594 6197 473243495 473242892 0.000000e+00 1066.0
10 TraesCS3D01G238400 chr6D 98.023 607 12 0 5591 6197 210876247 210876853 0.000000e+00 1055.0
11 TraesCS3D01G238400 chr6D 97.865 609 10 1 5592 6197 147412659 147413267 0.000000e+00 1050.0
12 TraesCS3D01G238400 chr6D 97.865 609 10 1 5592 6197 158211769 158211161 0.000000e+00 1050.0
13 TraesCS3D01G238400 chr5D 98.510 604 9 0 5594 6197 99334156 99334759 0.000000e+00 1066.0
14 TraesCS3D01G238400 chr5D 95.276 127 4 1 467 591 6236319 6236193 3.790000e-47 200.0
15 TraesCS3D01G238400 chr2D 98.510 604 9 0 5594 6197 125441392 125441995 0.000000e+00 1066.0
16 TraesCS3D01G238400 chr2D 94.531 128 4 1 467 591 648663723 648663596 1.760000e-45 195.0
17 TraesCS3D01G238400 chr1D 98.350 606 10 0 5592 6197 194925007 194924402 0.000000e+00 1064.0
18 TraesCS3D01G238400 chr1D 98.020 606 12 0 5592 6197 236087853 236087248 0.000000e+00 1053.0
19 TraesCS3D01G238400 chr1D 94.531 128 4 1 467 591 254476578 254476705 1.760000e-45 195.0
20 TraesCS3D01G238400 chrUn 94.531 128 4 1 467 591 426380805 426380678 1.760000e-45 195.0
21 TraesCS3D01G238400 chr7D 94.531 128 4 1 467 591 231565875 231566002 1.760000e-45 195.0
22 TraesCS3D01G238400 chr7D 94.531 128 4 1 467 591 231581480 231581607 1.760000e-45 195.0
23 TraesCS3D01G238400 chr1A 94.531 128 4 1 467 591 554448365 554448238 1.760000e-45 195.0


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 TraesCS3D01G238400 chr3D 329692070 329698266 6196 True 11444.000000 11444 100.000000 1 6197 1 chr3D.!!$R2 6196
1 TraesCS3D01G238400 chr3D 46551085 46551688 603 True 1050.000000 1050 98.013000 5594 6197 1 chr3D.!!$R1 603
2 TraesCS3D01G238400 chr3B 427316010 427321708 5698 True 3314.833333 9359 96.902000 1 5593 3 chr3B.!!$R1 5592
3 TraesCS3D01G238400 chr3A 444720820 444726027 5207 True 2672.666667 7376 93.228667 67 5563 3 chr3A.!!$R1 5496
4 TraesCS3D01G238400 chr6D 473242892 473243495 603 True 1066.000000 1066 98.510000 5594 6197 1 chr6D.!!$R2 603
5 TraesCS3D01G238400 chr6D 210876247 210876853 606 False 1055.000000 1055 98.023000 5591 6197 1 chr6D.!!$F2 606
6 TraesCS3D01G238400 chr6D 147412659 147413267 608 False 1050.000000 1050 97.865000 5592 6197 1 chr6D.!!$F1 605
7 TraesCS3D01G238400 chr6D 158211161 158211769 608 True 1050.000000 1050 97.865000 5592 6197 1 chr6D.!!$R1 605
8 TraesCS3D01G238400 chr5D 99334156 99334759 603 False 1066.000000 1066 98.510000 5594 6197 1 chr5D.!!$F1 603
9 TraesCS3D01G238400 chr2D 125441392 125441995 603 False 1066.000000 1066 98.510000 5594 6197 1 chr2D.!!$F1 603
10 TraesCS3D01G238400 chr1D 194924402 194925007 605 True 1064.000000 1064 98.350000 5592 6197 1 chr1D.!!$R1 605
11 TraesCS3D01G238400 chr1D 236087248 236087853 605 True 1053.000000 1053 98.020000 5592 6197 1 chr1D.!!$R2 605

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
63 64 1.458827 GTGCGCAGAGAAGAGAAACTG 59.541 52.381 12.22 0.0 0.00 3.16 F
450 537 2.200373 AGTTTGTGCCCTATGTCACC 57.800 50.000 0.00 0.0 32.51 4.02 F
2010 2114 1.214175 TCACAACTTGAGAAGGCCCAA 59.786 47.619 0.00 0.0 0.00 4.12 F
2476 2580 0.536724 TGCGGCATCAGAGCTAAAGA 59.463 50.000 0.00 0.0 34.17 2.52 F
3019 3123 1.694696 ACACTTCAGTCAAGACCCTCC 59.305 52.381 0.00 0.0 35.82 4.30 F
3806 3910 4.041444 AGCTTCTGTGAGGAACTTTGAGAT 59.959 41.667 0.00 0.0 41.55 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 1921 4.321718 CATGTCTGTTGATGTCTTCAGGT 58.678 43.478 0.0 0.0 35.27 4.00 R
2220 2324 4.505742 CCATCTATCTCCACCCCTAAAAGC 60.506 50.000 0.0 0.0 0.00 3.51 R
3019 3123 1.783284 TGCTGCTCTAACTCACGTTG 58.217 50.000 0.0 0.0 34.59 4.10 R
4365 4469 3.117491 TGGAGTCTCTGAAAGTTGCTG 57.883 47.619 0.0 0.0 33.76 4.41 R
4760 4864 0.827925 AGAGACCACTGACTTGGCGA 60.828 55.000 0.0 0.0 40.77 5.54 R
5412 5521 0.833287 TGCCTCTTGAGCCTCCATAC 59.167 55.000 0.0 0.0 0.00 2.39 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
63 64 1.458827 GTGCGCAGAGAAGAGAAACTG 59.541 52.381 12.22 0.00 0.00 3.16
450 537 2.200373 AGTTTGTGCCCTATGTCACC 57.800 50.000 0.00 0.00 32.51 4.02
476 563 9.282247 CACTGCTTAATGAATGAATAACAGAAC 57.718 33.333 0.00 0.00 0.00 3.01
775 862 3.386768 AAGATGGGGTAATCATCGACG 57.613 47.619 0.00 0.00 44.04 5.12
1314 1406 4.074259 CAGGTGTTGATGAGAATGTGGAA 58.926 43.478 0.00 0.00 0.00 3.53
1817 1921 3.681034 GCAGAGAAGAAGGCAGCAGAATA 60.681 47.826 0.00 0.00 0.00 1.75
1841 1945 3.678289 TGAAGACATCAACAGACATGGG 58.322 45.455 0.00 0.00 34.30 4.00
2010 2114 1.214175 TCACAACTTGAGAAGGCCCAA 59.786 47.619 0.00 0.00 0.00 4.12
2105 2209 5.707298 CAGTGGAATGTGATAACCTGAAAGT 59.293 40.000 0.00 0.00 0.00 2.66
2220 2324 4.276926 AGTTTACTGGAAAGCAAGCTTCAG 59.723 41.667 17.10 17.10 35.38 3.02
2476 2580 0.536724 TGCGGCATCAGAGCTAAAGA 59.463 50.000 0.00 0.00 34.17 2.52
3019 3123 1.694696 ACACTTCAGTCAAGACCCTCC 59.305 52.381 0.00 0.00 35.82 4.30
3243 3347 4.158764 AGAACTGAGTTAGATCAAGGACGG 59.841 45.833 0.00 0.00 31.07 4.79
3629 3733 6.992063 TTCTATCAAGAACCTTGAATCTGC 57.008 37.500 12.64 0.00 36.80 4.26
3806 3910 4.041444 AGCTTCTGTGAGGAACTTTGAGAT 59.959 41.667 0.00 0.00 41.55 2.75
4873 4977 1.608055 TGCATGTGGTGGAGAGTTTG 58.392 50.000 0.00 0.00 0.00 2.93
4914 5018 7.656412 TGTTAAACAATTATCTTGCTGAGCAA 58.344 30.769 19.84 19.84 46.80 3.91
5179 5283 4.612412 GTCACAACCGTCCCCGCA 62.612 66.667 0.00 0.00 0.00 5.69
5225 5329 8.006298 TGATTACCAAAAGTTCATTGTCAGTT 57.994 30.769 0.00 0.00 0.00 3.16
5364 5469 5.822519 GGCCTGTGTATTCTATTGTCATTGA 59.177 40.000 0.00 0.00 0.00 2.57
5412 5521 8.660435 TCCTTAGATTTTACCATCCTATTCCAG 58.340 37.037 0.00 0.00 0.00 3.86
5469 5583 9.699410 TTTGGTGGTCTGAATCATATTCTAATT 57.301 29.630 1.70 0.00 0.00 1.40
5514 5628 6.068010 TGCTCTTGTTCTCCTTTTCCATTTA 58.932 36.000 0.00 0.00 0.00 1.40
5515 5629 6.549364 TGCTCTTGTTCTCCTTTTCCATTTAA 59.451 34.615 0.00 0.00 0.00 1.52
5564 5705 4.846779 TCCCTCTTTGTTTTGCATGTAC 57.153 40.909 0.00 0.00 0.00 2.90
5587 5728 6.692486 ACCCTTGATAATATGTCGTCTGATC 58.308 40.000 0.00 0.00 0.00 2.92
5588 5729 6.267699 ACCCTTGATAATATGTCGTCTGATCA 59.732 38.462 0.00 0.00 0.00 2.92
5603 5744 8.079203 GTCGTCTGATCATCATTGTTAGAGTAT 58.921 37.037 0.00 0.00 0.00 2.12
5605 5746 9.254133 CGTCTGATCATCATTGTTAGAGTATTT 57.746 33.333 0.00 0.00 0.00 1.40
5641 5782 6.040166 ACGACTTCTAGTCCAAGTCAGTTTTA 59.960 38.462 18.00 0.00 46.99 1.52
5650 5791 6.677076 AGTCCAAGTCAGTTTTATACCCCTAT 59.323 38.462 0.00 0.00 0.00 2.57
5694 5835 7.170393 TCTTATATACTCTTGTATGCCGCAT 57.830 36.000 11.38 11.38 39.49 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.009033 TGATTGTTGTACCTCTCCCCTTG 59.991 47.826 0.00 0.00 0.00 3.61
11 12 1.066430 TCCGCCTGATTGTTGTACCTC 60.066 52.381 0.00 0.00 0.00 3.85
63 64 1.888512 TGCTTTTGTGGCTCCATTCTC 59.111 47.619 0.00 0.00 0.00 2.87
450 537 9.282247 GTTCTGTTATTCATTCATTAAGCAGTG 57.718 33.333 0.00 0.00 0.00 3.66
745 832 2.814805 ACCCCATCTTTGTGGATGAG 57.185 50.000 6.10 0.93 44.01 2.90
775 862 1.006805 CCTCTCCGATCCATCACGC 60.007 63.158 0.00 0.00 0.00 5.34
1314 1406 5.185454 TCTCCTATCATTCGCAAAATGTGT 58.815 37.500 8.26 3.11 0.00 3.72
1370 1462 8.110860 TGATTTCTTCAAGGTATTTCCAGAAC 57.889 34.615 0.00 0.00 39.02 3.01
1817 1921 4.321718 CATGTCTGTTGATGTCTTCAGGT 58.678 43.478 0.00 0.00 35.27 4.00
1841 1945 5.694006 CCAGATAACGTCTTCATCTCATTCC 59.306 44.000 0.00 0.00 34.00 3.01
2010 2114 4.934602 GTCTGCACTTCTTTCTCAGCTAAT 59.065 41.667 0.00 0.00 0.00 1.73
2061 2165 5.583457 CACTGACAGCATCATGTTCTCATTA 59.417 40.000 1.25 0.00 36.48 1.90
2220 2324 4.505742 CCATCTATCTCCACCCCTAAAAGC 60.506 50.000 0.00 0.00 0.00 3.51
2457 2561 0.536724 TCTTTAGCTCTGATGCCGCA 59.463 50.000 0.00 0.00 0.00 5.69
3019 3123 1.783284 TGCTGCTCTAACTCACGTTG 58.217 50.000 0.00 0.00 34.59 4.10
3243 3347 3.492421 TGCAAGATCGAAATTTGCTCC 57.508 42.857 23.38 5.35 45.53 4.70
3629 3733 4.920640 TCCTCCTTTAACTGAGCTATCG 57.079 45.455 0.00 0.00 0.00 2.92
4365 4469 3.117491 TGGAGTCTCTGAAAGTTGCTG 57.883 47.619 0.00 0.00 33.76 4.41
4443 4547 3.708403 TGGCCTATCTGCTCAATATGG 57.292 47.619 3.32 0.00 0.00 2.74
4760 4864 0.827925 AGAGACCACTGACTTGGCGA 60.828 55.000 0.00 0.00 40.77 5.54
4914 5018 4.398044 TCGTTTTCCTTGAGCAGTTCTTTT 59.602 37.500 0.00 0.00 0.00 2.27
5412 5521 0.833287 TGCCTCTTGAGCCTCCATAC 59.167 55.000 0.00 0.00 0.00 2.39
5436 5549 3.924114 TTCAGACCACCAAACTCAGAA 57.076 42.857 0.00 0.00 0.00 3.02
5469 5583 4.157656 GCATCACAAAAGCCACATTACCTA 59.842 41.667 0.00 0.00 0.00 3.08
5564 5705 6.691508 TGATCAGACGACATATTATCAAGGG 58.308 40.000 0.00 0.00 0.00 3.95
5605 5746 9.797642 TTGGACTAGAAGTCGTATACCATAATA 57.202 33.333 0.00 0.00 45.96 0.98
5641 5782 1.222298 ACCGACTTGGGATAGGGGTAT 59.778 52.381 0.00 0.00 44.64 2.73
6046 6190 2.430367 GCGGGGAAGACAGTTGGT 59.570 61.111 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.