Multiple sequence alignment - TraesCS2A01G242400

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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 TraesCS2A01G242400 chr2A 100.000 2545 0 0 1 2545 335847335 335849879 0 4700
1 TraesCS2A01G242400 chr2A 98.234 2548 42 2 1 2545 726906434 726903887 0 4453
2 TraesCS2A01G242400 chr3A 98.312 2548 40 2 1 2545 66005112 66002565 0 4464
3 TraesCS2A01G242400 chr6D 98.234 2548 42 2 1 2545 389245801 389243254 0 4453
4 TraesCS2A01G242400 chr3D 98.234 2548 41 3 1 2545 589263505 589260959 0 4453
5 TraesCS2A01G242400 chr5D 98.195 2548 43 2 1 2545 503264755 503262208 0 4447
6 TraesCS2A01G242400 chr5D 98.155 2548 44 2 1 2545 503245293 503247840 0 4442
7 TraesCS2A01G242400 chr2D 98.155 2548 44 2 1 2545 591984630 591987177 0 4442
8 TraesCS2A01G242400 chr7B 97.920 2548 50 2 1 2545 663099404 663096857 0 4409
9 TraesCS2A01G242400 chr3B 97.919 2547 50 3 1 2545 201539543 201542088 0 4407


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 TraesCS2A01G242400 chr2A 335847335 335849879 2544 False 4700 4700 100.000 1 2545 1 chr2A.!!$F1 2544
1 TraesCS2A01G242400 chr2A 726903887 726906434 2547 True 4453 4453 98.234 1 2545 1 chr2A.!!$R1 2544
2 TraesCS2A01G242400 chr3A 66002565 66005112 2547 True 4464 4464 98.312 1 2545 1 chr3A.!!$R1 2544
3 TraesCS2A01G242400 chr6D 389243254 389245801 2547 True 4453 4453 98.234 1 2545 1 chr6D.!!$R1 2544
4 TraesCS2A01G242400 chr3D 589260959 589263505 2546 True 4453 4453 98.234 1 2545 1 chr3D.!!$R1 2544
5 TraesCS2A01G242400 chr5D 503262208 503264755 2547 True 4447 4447 98.195 1 2545 1 chr5D.!!$R1 2544
6 TraesCS2A01G242400 chr5D 503245293 503247840 2547 False 4442 4442 98.155 1 2545 1 chr5D.!!$F1 2544
7 TraesCS2A01G242400 chr2D 591984630 591987177 2547 False 4442 4442 98.155 1 2545 1 chr2D.!!$F1 2544
8 TraesCS2A01G242400 chr7B 663096857 663099404 2547 True 4409 4409 97.920 1 2545 1 chr7B.!!$R1 2544
9 TraesCS2A01G242400 chr3B 201539543 201542088 2545 False 4407 4407 97.919 1 2545 1 chr3B.!!$F1 2544

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
964 966 0.616679 CCCCGTTCCTGGTTCTCCTA 60.617 60.0 0.0 0.0 34.23 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2448 1.279271 TGCTTCTAGGCAAACCTCCTC 59.721 52.381 0.0 0.0 46.34 3.71 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
372 374 1.243342 CCGCTCTTGCAATTGGGTCA 61.243 55.000 7.72 0.0 39.64 4.02
887 889 0.744771 GTCGGAGAAGGGCAATCACC 60.745 60.000 0.00 0.0 39.69 4.02
964 966 0.616679 CCCCGTTCCTGGTTCTCCTA 60.617 60.000 0.00 0.0 34.23 2.94
1084 1086 7.544622 AGCATAGTACGATGAAAGTTGTAAGA 58.455 34.615 18.86 0.0 0.00 2.10
1179 1183 1.195442 TACCCTGTGGCGGATGTCAA 61.195 55.000 0.00 0.0 33.59 3.18
1180 1184 1.077501 CCCTGTGGCGGATGTCAAT 60.078 57.895 0.00 0.0 0.00 2.57
1185 1189 0.887933 GTGGCGGATGTCAATGGTTT 59.112 50.000 0.00 0.0 0.00 3.27
1400 1404 0.708209 TACCTAGGCACCCAGAGACA 59.292 55.000 9.30 0.0 0.00 3.41
1585 1589 3.518590 CAAAAGCGATTCCCGTAGTAGT 58.481 45.455 0.00 0.0 41.15 2.73
1691 1695 2.364973 TGCCGCACCCTAGATGGA 60.365 61.111 0.00 0.0 38.35 3.41
1983 1987 2.807676 CAGTGGCTTGGTTAAGGGAAT 58.192 47.619 0.00 0.0 34.40 3.01
2352 2356 2.434336 CAGTGAGACGATGGGGGATAAA 59.566 50.000 0.00 0.0 0.00 1.40
2444 2448 3.365265 GGGGGTGCAAAGACAGCG 61.365 66.667 0.00 0.0 38.95 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
267 268 4.927267 TCTTCTATTCTTTTCCCTGGCA 57.073 40.909 0.00 0.00 0.00 4.92
372 374 0.393808 AGCCAACCCGTAATCGCAAT 60.394 50.000 0.00 0.00 35.54 3.56
435 437 4.164843 ACTTAGAAAAAGTGAGCCACCA 57.835 40.909 2.18 0.00 34.49 4.17
570 572 4.893524 TGACTCCAACTATCGTCCATGTAT 59.106 41.667 0.00 0.00 0.00 2.29
593 595 1.758906 GAAGCCTAGGAGAGCCGGT 60.759 63.158 14.75 0.00 39.96 5.28
594 596 2.503382 GGAAGCCTAGGAGAGCCGG 61.503 68.421 14.75 0.00 39.96 6.13
836 838 0.251832 ACCGGAGAGCGGATGGATAT 60.252 55.000 9.46 0.00 0.00 1.63
839 841 2.363795 AACCGGAGAGCGGATGGA 60.364 61.111 9.46 0.00 0.00 3.41
842 844 3.470888 CCCAACCGGAGAGCGGAT 61.471 66.667 9.46 0.00 0.00 4.18
887 889 4.766404 AGAATGCTGGTTTTAAGAACGG 57.234 40.909 0.00 0.00 0.00 4.44
964 966 1.493446 GGTTCCGGGGAATCCAGTTAT 59.507 52.381 0.00 0.00 36.45 1.89
1063 1065 8.301720 ACACATCTTACAACTTTCATCGTACTA 58.698 33.333 0.00 0.00 0.00 1.82
1179 1183 3.432326 GGAGATAAGCGGACTCAAACCAT 60.432 47.826 0.00 0.00 33.00 3.55
1180 1184 2.093658 GGAGATAAGCGGACTCAAACCA 60.094 50.000 0.00 0.00 33.00 3.67
1185 1189 0.747255 GCTGGAGATAAGCGGACTCA 59.253 55.000 0.00 0.00 33.00 3.41
1264 1268 7.172019 CGTCCATGAATGTGAAATCATAGATCA 59.828 37.037 0.00 2.51 34.61 2.92
1400 1404 1.377333 GCTTGCTACGCCCTTCCTT 60.377 57.895 0.00 0.00 0.00 3.36
1585 1589 2.125147 CTCCCATTTCGCTCGCCA 60.125 61.111 0.00 0.00 0.00 5.69
1691 1695 3.055385 TGCTTTCGGCTACTGGACTTTAT 60.055 43.478 0.00 0.00 42.39 1.40
1721 1725 1.741706 CTACTCGGGTCAGAGCGTAAA 59.258 52.381 0.00 0.00 41.77 2.01
2002 2006 2.795470 CCTATTAAGACTCGCTTTCGCC 59.205 50.000 0.00 0.00 38.05 5.54
2222 2226 4.625607 ATAGTGCTTTACCCCTAGATGC 57.374 45.455 0.00 0.00 0.00 3.91
2264 2268 1.471287 GTTTGCCTCGATTTGGTACCC 59.529 52.381 10.07 0.00 0.00 3.69
2352 2356 1.835494 TTCCCTCTCGACGATGAAGT 58.165 50.000 0.00 0.00 0.00 3.01
2444 2448 1.279271 TGCTTCTAGGCAAACCTCCTC 59.721 52.381 0.00 0.00 46.34 3.71


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

AutoCloner maintained by Alex Coulton.