Multiple sequence alignment - TraesCS4D01G090700

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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 TraesCS4D01G090700 chr4D 100.000 5677 0 0 1 5677 65876199 65870523 0 10484
1 TraesCS4D01G090700 chr2D 97.372 5708 93 11 1 5677 536208779 536214460 0 9657
2 TraesCS4D01G090700 chr1D 96.484 5716 130 26 1 5677 10804018 10798335 0 9376
3 TraesCS4D01G090700 chr1D 97.069 3890 82 10 1 3858 108798298 108794409 0 6523
4 TraesCS4D01G090700 chr1D 97.277 3820 77 4 1 3794 58485281 58481463 0 6453
5 TraesCS4D01G090700 chr3D 96.251 5708 166 18 1 5677 175421988 175416298 0 9311
6 TraesCS4D01G090700 chrUn 95.638 5708 179 20 1 5677 52473564 52479232 0 9097
7 TraesCS4D01G090700 chr4B 95.436 5719 190 25 1 5677 539963814 539958125 0 9049
8 TraesCS4D01G090700 chr6A 93.602 5736 284 52 1 5677 494425529 494431240 0 8482
9 TraesCS4D01G090700 chr6A 93.414 4692 228 41 1055 5677 184604852 184600173 0 6878
10 TraesCS4D01G090700 chr3B 92.718 5754 333 51 1 5677 694806662 694800918 0 8226
11 TraesCS4D01G090700 chr3B 95.411 4053 155 13 1654 5677 177748105 177752155 0 6425
12 TraesCS4D01G090700 chr3B 94.747 4055 171 19 1654 5677 756008049 756004006 0 6270
13 TraesCS4D01G090700 chr3B 95.603 2047 61 9 1 2018 691342004 691339958 0 3254
14 TraesCS4D01G090700 chr7D 92.483 5734 319 69 1 5677 135379638 135385316 0 8098
15 TraesCS4D01G090700 chr7D 97.398 4766 89 11 1 4735 30313040 30317801 0 8082
16 TraesCS4D01G090700 chr7B 94.502 4056 184 19 1654 5677 99710133 99706085 0 6218
17 TraesCS4D01G090700 chr5B 96.709 3737 115 7 1944 5677 12558308 12562039 0 6213
18 TraesCS4D01G090700 chr6B 96.569 1953 55 8 1 1945 680526001 680524053 0 3225


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 TraesCS4D01G090700 chr4D 65870523 65876199 5676 True 10484 10484 100.000 1 5677 1 chr4D.!!$R1 5676
1 TraesCS4D01G090700 chr2D 536208779 536214460 5681 False 9657 9657 97.372 1 5677 1 chr2D.!!$F1 5676
2 TraesCS4D01G090700 chr1D 10798335 10804018 5683 True 9376 9376 96.484 1 5677 1 chr1D.!!$R1 5676
3 TraesCS4D01G090700 chr1D 108794409 108798298 3889 True 6523 6523 97.069 1 3858 1 chr1D.!!$R3 3857
4 TraesCS4D01G090700 chr1D 58481463 58485281 3818 True 6453 6453 97.277 1 3794 1 chr1D.!!$R2 3793
5 TraesCS4D01G090700 chr3D 175416298 175421988 5690 True 9311 9311 96.251 1 5677 1 chr3D.!!$R1 5676
6 TraesCS4D01G090700 chrUn 52473564 52479232 5668 False 9097 9097 95.638 1 5677 1 chrUn.!!$F1 5676
7 TraesCS4D01G090700 chr4B 539958125 539963814 5689 True 9049 9049 95.436 1 5677 1 chr4B.!!$R1 5676
8 TraesCS4D01G090700 chr6A 494425529 494431240 5711 False 8482 8482 93.602 1 5677 1 chr6A.!!$F1 5676
9 TraesCS4D01G090700 chr6A 184600173 184604852 4679 True 6878 6878 93.414 1055 5677 1 chr6A.!!$R1 4622
10 TraesCS4D01G090700 chr3B 694800918 694806662 5744 True 8226 8226 92.718 1 5677 1 chr3B.!!$R2 5676
11 TraesCS4D01G090700 chr3B 177748105 177752155 4050 False 6425 6425 95.411 1654 5677 1 chr3B.!!$F1 4023
12 TraesCS4D01G090700 chr3B 756004006 756008049 4043 True 6270 6270 94.747 1654 5677 1 chr3B.!!$R3 4023
13 TraesCS4D01G090700 chr3B 691339958 691342004 2046 True 3254 3254 95.603 1 2018 1 chr3B.!!$R1 2017
14 TraesCS4D01G090700 chr7D 135379638 135385316 5678 False 8098 8098 92.483 1 5677 1 chr7D.!!$F2 5676
15 TraesCS4D01G090700 chr7D 30313040 30317801 4761 False 8082 8082 97.398 1 4735 1 chr7D.!!$F1 4734
16 TraesCS4D01G090700 chr7B 99706085 99710133 4048 True 6218 6218 94.502 1654 5677 1 chr7B.!!$R1 4023
17 TraesCS4D01G090700 chr5B 12558308 12562039 3731 False 6213 6213 96.709 1944 5677 1 chr5B.!!$F1 3733
18 TraesCS4D01G090700 chr6B 680524053 680526001 1948 True 3225 3225 96.569 1 1945 1 chr6B.!!$R1 1944

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
842 905 1.746615 AGCAGCAACCCAGCATACG 60.747 57.895 0.00 0.0 36.85 3.06 F
1513 1581 1.021968 GGAGGTGACGCACTTTGTTT 58.978 50.000 9.31 0.0 34.40 2.83 F
3237 3374 0.462047 CCCGCTAAGATGGTGGACAC 60.462 60.000 0.00 0.0 36.54 3.67 F
3751 3918 0.698818 ATGTCAACCCTCAAGGACCC 59.301 55.000 0.00 0.0 39.89 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 1828 0.814457 GTTGGACACCAGTTGCACAA 59.186 50.000 0.00 0.0 33.81 3.33 R
3239 3376 0.454600 GCGCACTAGGTACAGCAGTA 59.545 55.000 0.30 0.0 0.00 2.74 R
4354 4539 1.946768 GCTGTGCAACTAACTGGTTGA 59.053 47.619 9.84 0.0 46.55 3.18 R
5371 5600 2.610694 CCAGTTGCAGAGTGGCACG 61.611 63.158 12.71 0.0 44.86 5.34 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
182 203 5.324409 ACTTTTGTCCATGGCTAATGAAGA 58.676 37.500 6.96 0.00 38.72 2.87
701 755 5.123227 TCTTTTCTGTGGTTACCAACAGAG 58.877 41.667 24.38 17.86 40.16 3.35
842 905 1.746615 AGCAGCAACCCAGCATACG 60.747 57.895 0.00 0.00 36.85 3.06
1170 1237 5.483685 TTGCTAAGGATCACTACAACAGT 57.516 39.130 0.00 0.00 38.32 3.55
1346 1413 8.844244 CCCTATTCTAGATCCAAAATCTGTTTG 58.156 37.037 0.00 0.00 0.00 2.93
1513 1581 1.021968 GGAGGTGACGCACTTTGTTT 58.978 50.000 9.31 0.00 34.40 2.83
1734 1828 6.639632 ACTGTGCAACTGAAATGACTTAAT 57.360 33.333 0.00 0.00 39.30 1.40
1900 1999 5.066505 GTGTCCATTTCCTGCGATTATCTTT 59.933 40.000 0.00 0.00 0.00 2.52
2231 2360 2.938956 AAGCTTATGCGGAGGCTTAT 57.061 45.000 11.47 0.00 42.23 1.73
2378 2507 2.112380 TGGCATCGAGCTTTGATTGA 57.888 45.000 6.78 0.00 44.79 2.57
2581 2711 4.161189 TCCAGGACTCTCTGATGATTTCAC 59.839 45.833 0.00 0.00 36.93 3.18
2692 2827 5.374898 GCACTTTGAGAAGTTGTACGAATC 58.625 41.667 0.00 0.00 43.48 2.52
3079 3216 6.610075 ATTTGTTGCCAAATATGGTTCTCT 57.390 33.333 0.00 0.00 46.80 3.10
3150 3287 5.815581 AGTGCTATAAAATGGACAAGGACA 58.184 37.500 0.00 0.00 0.00 4.02
3236 3373 0.907704 ACCCGCTAAGATGGTGGACA 60.908 55.000 0.00 0.00 36.54 4.02
3237 3374 0.462047 CCCGCTAAGATGGTGGACAC 60.462 60.000 0.00 0.00 36.54 3.67
3317 3479 5.587844 TCCTCAATCAAAGAAGCAGATAAGC 59.412 40.000 0.00 0.00 0.00 3.09
3751 3918 0.698818 ATGTCAACCCTCAAGGACCC 59.301 55.000 0.00 0.00 39.89 4.46
3889 4060 4.348020 ACTCCCCATCAAACTAGGTCTA 57.652 45.455 0.00 0.00 0.00 2.59
3912 4083 2.430465 ACTCCAGTTGCACACATCATC 58.570 47.619 0.00 0.00 0.00 2.92
4332 4516 3.135994 CCGTGCTACTACAGGTGTTTTT 58.864 45.455 0.00 0.00 0.00 1.94
4672 4861 0.037232 GTGTGTCCACTCAGGCTACC 60.037 60.000 0.00 0.00 38.61 3.18
4776 4969 7.227314 GTGGACACATTCAGCATCTATGATTTA 59.773 37.037 0.00 0.00 0.00 1.40
5103 5306 2.746142 CGCTGGTGACCCAATCATATGT 60.746 50.000 0.00 0.00 41.27 2.29
5361 5590 2.977914 ACTGCTTATGTGCCAGTGTAG 58.022 47.619 0.00 0.00 0.00 2.74
5371 5600 5.130292 TGTGCCAGTGTAGAACTACTTAC 57.870 43.478 12.25 4.49 36.83 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 174 6.945435 TCATTAGCCATGGACAAAAGTTCTTA 59.055 34.615 18.40 0.00 33.07 2.10
182 203 7.913297 GCGTGAATATGTTAATATGGTTTGTGT 59.087 33.333 0.00 0.00 0.00 3.72
237 260 1.806542 CTTTGCAATAGGTGTGCGACT 59.193 47.619 0.00 0.00 45.27 4.18
842 905 5.928264 CCATTTTCTGTCCATTTTCCTTGTC 59.072 40.000 0.00 0.00 0.00 3.18
1001 1065 0.178975 AACATTTGCCTCGGTTCCCA 60.179 50.000 0.00 0.00 0.00 4.37
1170 1237 0.896923 AACCCATCCGTAGTGCGTAA 59.103 50.000 0.00 0.00 39.32 3.18
1346 1413 2.433604 TCTTCCATCTCCTCATCACTGC 59.566 50.000 0.00 0.00 0.00 4.40
1513 1581 0.324614 AGCGGATGATTGTGGTCACA 59.675 50.000 0.00 0.00 39.98 3.58
1681 1752 1.889105 AGTTGCACACTGGACTGCG 60.889 57.895 0.00 0.00 36.08 5.18
1734 1828 0.814457 GTTGGACACCAGTTGCACAA 59.186 50.000 0.00 0.00 33.81 3.33
2284 2413 2.577059 CTAGGAAGGGCGCGAACA 59.423 61.111 12.10 0.00 0.00 3.18
2298 2427 3.139077 GGCCATGTCGGTTTATTCCTAG 58.861 50.000 0.00 0.00 36.97 3.02
2378 2507 3.454082 CCTCTAGGAATGCTCCAAAGACT 59.546 47.826 0.00 0.00 45.24 3.24
2581 2711 2.292267 AGCTGAAGTCAACACACTTGG 58.708 47.619 0.00 0.00 36.71 3.61
2692 2827 1.903404 GGCACCCAAGTTGACCTGG 60.903 63.158 3.87 0.00 0.00 4.45
3079 3216 2.940994 TGCCTGCACCAAGTAGTTTA 57.059 45.000 0.00 0.00 0.00 2.01
3236 3373 2.100989 GCACTAGGTACAGCAGTAGGT 58.899 52.381 0.00 0.00 0.00 3.08
3237 3374 1.065701 CGCACTAGGTACAGCAGTAGG 59.934 57.143 0.00 0.00 0.00 3.18
3238 3375 1.534175 GCGCACTAGGTACAGCAGTAG 60.534 57.143 0.30 0.00 0.00 2.57
3239 3376 0.454600 GCGCACTAGGTACAGCAGTA 59.545 55.000 0.30 0.00 0.00 2.74
3240 3377 1.215647 GCGCACTAGGTACAGCAGT 59.784 57.895 0.30 0.00 0.00 4.40
3241 3378 1.519455 GGCGCACTAGGTACAGCAG 60.519 63.158 10.83 0.00 0.00 4.24
3242 3379 2.225791 CTGGCGCACTAGGTACAGCA 62.226 60.000 10.83 0.00 0.00 4.41
3243 3380 1.519455 CTGGCGCACTAGGTACAGC 60.519 63.158 10.83 0.00 0.00 4.40
3244 3381 1.141881 CCTGGCGCACTAGGTACAG 59.858 63.158 10.83 4.21 0.00 2.74
3245 3382 2.355986 CCCTGGCGCACTAGGTACA 61.356 63.158 19.15 1.78 31.99 2.90
3246 3383 2.056223 TCCCTGGCGCACTAGGTAC 61.056 63.158 19.15 0.00 31.99 3.34
3247 3384 2.056223 GTCCCTGGCGCACTAGGTA 61.056 63.158 19.15 5.08 31.99 3.08
3317 3479 7.201274 CGAAAATCGTATATCATGTTCCTCTCG 60.201 40.741 0.00 0.00 34.72 4.04
3558 3721 4.016479 ACCTAGTTAGATCAGGAGTTGGGA 60.016 45.833 3.16 0.00 33.44 4.37
3889 4060 4.019792 TGATGTGTGCAACTGGAGTTAT 57.980 40.909 0.00 0.00 38.04 1.89
4332 4516 6.625362 TGATGTGTGCAAGTTAAGTTGAAAA 58.375 32.000 24.16 8.45 0.00 2.29
4354 4539 1.946768 GCTGTGCAACTAACTGGTTGA 59.053 47.619 9.84 0.00 46.55 3.18
4672 4861 4.772434 ACAAACGATGAAACAGAATCACG 58.228 39.130 0.00 0.00 0.00 4.35
5103 5306 3.326006 ACTCAACATCAGGAAGAAGCTGA 59.674 43.478 0.00 0.00 0.00 4.26
5371 5600 2.610694 CCAGTTGCAGAGTGGCACG 61.611 63.158 12.71 0.00 44.86 5.34


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

AutoCloner maintained by Alex Coulton.