Multiple sequence alignment - TraesCS4A01G154400

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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 TraesCS4A01G154400 chr4A 100.000 2590 0 0 1 2590 310733422 310736011 0.000000e+00 4783.0
1 TraesCS4A01G154400 chr4A 96.667 90 3 0 2353 2442 142270883 142270972 1.610000e-32 150.0
2 TraesCS4A01G154400 chr4A 96.226 53 2 0 2511 2563 605637282 605637230 1.280000e-13 87.9
3 TraesCS4A01G154400 chr5D 96.167 2609 79 9 1 2590 503284470 503281864 0.000000e+00 4244.0
4 TraesCS4A01G154400 chr5D 96.164 2607 81 9 1 2590 6183772 6186376 0.000000e+00 4242.0
5 TraesCS4A01G154400 chr5D 96.317 2471 70 9 1 2451 483806414 483808883 0.000000e+00 4039.0
6 TraesCS4A01G154400 chr6D 96.087 2607 82 11 1 2590 45514400 45517003 0.000000e+00 4231.0
7 TraesCS4A01G154400 chr2A 96.084 2605 86 10 1 2590 335833477 335836080 0.000000e+00 4231.0
8 TraesCS4A01G154400 chr1D 95.936 2608 77 12 1 2590 254403274 254400678 0.000000e+00 4202.0
9 TraesCS4A01G154400 chr1D 95.352 2603 100 15 1 2590 51880900 51883494 0.000000e+00 4117.0
10 TraesCS4A01G154400 chr3D 96.178 2407 69 10 5 2395 598875970 598873571 0.000000e+00 3914.0
11 TraesCS4A01G154400 chrUn 95.612 2256 82 10 77 2319 261572019 261574270 0.000000e+00 3602.0


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 TraesCS4A01G154400 chr4A 310733422 310736011 2589 False 4783 4783 100.000 1 2590 1 chr4A.!!$F2 2589
1 TraesCS4A01G154400 chr5D 503281864 503284470 2606 True 4244 4244 96.167 1 2590 1 chr5D.!!$R1 2589
2 TraesCS4A01G154400 chr5D 6183772 6186376 2604 False 4242 4242 96.164 1 2590 1 chr5D.!!$F1 2589
3 TraesCS4A01G154400 chr5D 483806414 483808883 2469 False 4039 4039 96.317 1 2451 1 chr5D.!!$F2 2450
4 TraesCS4A01G154400 chr6D 45514400 45517003 2603 False 4231 4231 96.087 1 2590 1 chr6D.!!$F1 2589
5 TraesCS4A01G154400 chr2A 335833477 335836080 2603 False 4231 4231 96.084 1 2590 1 chr2A.!!$F1 2589
6 TraesCS4A01G154400 chr1D 254400678 254403274 2596 True 4202 4202 95.936 1 2590 1 chr1D.!!$R1 2589
7 TraesCS4A01G154400 chr1D 51880900 51883494 2594 False 4117 4117 95.352 1 2590 1 chr1D.!!$F1 2589
8 TraesCS4A01G154400 chr3D 598873571 598875970 2399 True 3914 3914 96.178 5 2395 1 chr3D.!!$R1 2390
9 TraesCS4A01G154400 chrUn 261572019 261574270 2251 False 3602 3602 95.612 77 2319 1 chrUn.!!$F1 2242

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
295 298 2.356135 GTCAAAAGAGCGATTGGCCTA 58.644 47.619 3.32 0.0 45.17 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 1637 2.055579 TCCTATGAGGAGAGTAGCGGA 58.944 52.381 0.0 0.0 40.06 5.54 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
162 163 6.424032 GTTTTCCTATGAGTGGACCCTTTAT 58.576 40.000 0.00 0.0 32.65 1.40
245 248 5.698832 TGGATTGAATGTGTAAAAGAAGCG 58.301 37.500 0.00 0.0 0.00 4.68
263 266 7.304497 AGAAGCGGTATATTGATAAAGAGGT 57.696 36.000 0.00 0.0 0.00 3.85
265 268 7.873505 AGAAGCGGTATATTGATAAAGAGGTTC 59.126 37.037 0.00 0.0 34.04 3.62
295 298 2.356135 GTCAAAAGAGCGATTGGCCTA 58.644 47.619 3.32 0.0 45.17 3.93
761 765 6.424207 GGTTAATCATCCTAACCAAGATCGAC 59.576 42.308 6.84 0.0 45.21 4.20
766 770 7.361457 TCATCCTAACCAAGATCGACTATTT 57.639 36.000 0.00 0.0 0.00 1.40
877 882 6.152154 ACGGGAATTATTTTGTCCGAAAGAAT 59.848 34.615 6.57 0.0 40.53 2.40
1025 1030 4.506625 CCTGGTTCAACTCCTTCAATACCA 60.507 45.833 0.00 0.0 33.69 3.25
1056 1061 9.158233 CAAGATGTTCCATCTTTGCATTTATTT 57.842 29.630 15.01 0.0 36.32 1.40
1057 1062 9.729281 AAGATGTTCCATCTTTGCATTTATTTT 57.271 25.926 12.50 0.0 34.99 1.82
1249 1267 5.110814 TCTTCTGGAACTTTTCTGGAACA 57.889 39.130 0.00 0.0 0.00 3.18
1460 1488 0.816018 TTTTGGACTCAGCCGCGAAA 60.816 50.000 8.23 0.0 0.00 3.46
1664 1692 8.409358 AAAGCTCAATTTTGTACTGGATTAGT 57.591 30.769 0.00 0.0 43.56 2.24
1707 1735 7.286087 CCCATTTGGACAGATTTATCAGATTGA 59.714 37.037 0.00 0.0 37.39 2.57
1771 1800 8.607441 TTTTCATTATCATAGTGGATCTTCGG 57.393 34.615 0.00 0.0 0.00 4.30
1783 1812 2.671888 GGATCTTCGGAAAAACGGACTC 59.328 50.000 0.00 0.0 0.00 3.36
1789 1818 4.261578 TCGGAAAAACGGACTCTGTATT 57.738 40.909 0.00 0.0 0.00 1.89
1794 1823 5.107065 GGAAAAACGGACTCTGTATTGACTG 60.107 44.000 0.00 0.0 0.00 3.51
1834 1863 3.861840 TCATGCGCTAGAACTTTAGCTT 58.138 40.909 9.73 0.0 43.05 3.74
1855 1884 6.150474 AGCTTGTAAACATAAAAGCACGGTAT 59.850 34.615 12.04 0.0 45.89 2.73
1994 2024 5.360714 ACACTGAGCATATTTGGTATTTGGG 59.639 40.000 0.00 0.0 32.62 4.12
2021 2051 3.526931 ACGTATCAATGACCTGGTCAG 57.473 47.619 30.99 20.1 46.04 3.51
2022 2052 2.832129 ACGTATCAATGACCTGGTCAGT 59.168 45.455 30.99 27.2 46.04 3.41
2248 2282 1.255882 AATGCAAGCACGATTTGGGA 58.744 45.000 0.00 0.0 0.00 4.37
2266 2300 8.685257 ATTTGGGAAGGGATTTTTCTCTATTT 57.315 30.769 0.00 0.0 0.00 1.40
2337 2371 3.564225 CCCGAGCAACCCATATAGAAAAC 59.436 47.826 0.00 0.0 0.00 2.43
2338 2372 3.564225 CCGAGCAACCCATATAGAAAACC 59.436 47.826 0.00 0.0 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 266 4.695455 CGCTCTTTTGACCTTGGAATAGAA 59.305 41.667 0.00 0.00 0.00 2.10
265 268 4.253685 TCGCTCTTTTGACCTTGGAATAG 58.746 43.478 0.00 0.00 0.00 1.73
274 277 0.171231 GGCCAATCGCTCTTTTGACC 59.829 55.000 0.00 0.00 37.74 4.02
408 412 6.454795 ACAGGGTGTTGCATTTTTAATACAG 58.545 36.000 0.00 0.00 0.00 2.74
512 516 5.353123 TCTGAATACCCTTCGAATTTTTCCG 59.647 40.000 0.00 0.00 0.00 4.30
631 635 7.340999 ACAACTAACAACTATTTCCACAGGTTT 59.659 33.333 0.00 0.00 0.00 3.27
851 856 5.474189 TCTTTCGGACAAAATAATTCCCGTT 59.526 36.000 0.00 0.00 38.25 4.44
1249 1267 7.032598 TCCATCTTCCTAGAAAAGTGGATTT 57.967 36.000 16.21 0.00 33.21 2.17
1609 1637 2.055579 TCCTATGAGGAGAGTAGCGGA 58.944 52.381 0.00 0.00 40.06 5.54
1637 1665 9.696917 CTAATCCAGTACAAAATTGAGCTTTTT 57.303 29.630 0.00 0.00 0.00 1.94
1661 1689 7.626999 ATGGGTTTACTAATAGGATGCACTA 57.373 36.000 0.00 0.00 0.00 2.74
1664 1692 6.549364 CCAAATGGGTTTACTAATAGGATGCA 59.451 38.462 0.00 0.00 0.00 3.96
1771 1800 5.694910 TCAGTCAATACAGAGTCCGTTTTTC 59.305 40.000 0.00 0.00 0.00 2.29
1808 1837 5.390991 GCTAAAGTTCTAGCGCATGAAAGTT 60.391 40.000 11.47 12.33 35.31 2.66
1834 1863 7.173562 AGTTCATACCGTGCTTTTATGTTTACA 59.826 33.333 0.00 0.00 0.00 2.41
1855 1884 4.279671 ACCCAATCGTTGCATAAAAGTTCA 59.720 37.500 0.00 0.00 0.00 3.18
1994 2024 8.301720 TGACCAGGTCATTGATACGTATAATAC 58.698 37.037 19.21 3.15 37.67 1.89
2266 2300 8.209802 TGGAGTAGGTAATTCTTCCTTGTTAA 57.790 34.615 2.81 0.00 35.51 2.01
2319 2353 3.373767 GGGGGTTTTCTATATGGGTTGCT 60.374 47.826 0.00 0.00 0.00 3.91
2511 2545 0.179020 CAAGGACTCCCAAGCACACA 60.179 55.000 0.00 0.00 33.88 3.72


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

AutoCloner maintained by Alex Coulton.