Multiple sequence alignment - TraesCS1A01G233900

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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 TraesCS1A01G233900 chr1A 100.000 3075 0 0 1 3075 409609158 409612232 0 5679
1 TraesCS1A01G233900 chr2A 98.667 3075 36 4 1 3075 374483602 374486671 0 5446
2 TraesCS1A01G233900 chr2A 98.635 3076 38 4 1 3075 628569730 628572802 0 5445
3 TraesCS1A01G233900 chr2A 98.602 3075 41 2 1 3075 628648288 628645216 0 5439
4 TraesCS1A01G233900 chr2A 98.341 3075 43 4 1 3075 161526796 161529862 0 5389
5 TraesCS1A01G233900 chr1B 98.179 3075 50 4 1 3075 95491967 95495035 0 5363
6 TraesCS1A01G233900 chr1B 98.146 3075 54 2 1 3075 530764198 530761127 0 5360
7 TraesCS1A01G233900 chr2B 97.693 3077 63 5 1 3075 424685091 424682021 0 5282
8 TraesCS1A01G233900 chr7D 97.453 2709 62 4 367 3075 474677238 474679939 0 4614
9 TraesCS1A01G233900 chr5A 95.809 2744 105 6 1 2743 272284647 272287381 0 4421


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 TraesCS1A01G233900 chr1A 409609158 409612232 3074 False 5679 5679 100.000 1 3075 1 chr1A.!!$F1 3074
1 TraesCS1A01G233900 chr2A 374483602 374486671 3069 False 5446 5446 98.667 1 3075 1 chr2A.!!$F2 3074
2 TraesCS1A01G233900 chr2A 628569730 628572802 3072 False 5445 5445 98.635 1 3075 1 chr2A.!!$F3 3074
3 TraesCS1A01G233900 chr2A 628645216 628648288 3072 True 5439 5439 98.602 1 3075 1 chr2A.!!$R1 3074
4 TraesCS1A01G233900 chr2A 161526796 161529862 3066 False 5389 5389 98.341 1 3075 1 chr2A.!!$F1 3074
5 TraesCS1A01G233900 chr1B 95491967 95495035 3068 False 5363 5363 98.179 1 3075 1 chr1B.!!$F1 3074
6 TraesCS1A01G233900 chr1B 530761127 530764198 3071 True 5360 5360 98.146 1 3075 1 chr1B.!!$R1 3074
7 TraesCS1A01G233900 chr2B 424682021 424685091 3070 True 5282 5282 97.693 1 3075 1 chr2B.!!$R1 3074
8 TraesCS1A01G233900 chr7D 474677238 474679939 2701 False 4614 4614 97.453 367 3075 1 chr7D.!!$F1 2708
9 TraesCS1A01G233900 chr5A 272284647 272287381 2734 False 4421 4421 95.809 1 2743 1 chr5A.!!$F1 2742

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
988 990 2.046892 CAAGCTACCAGCAGCGGT 60.047 61.111 12.63 12.63 45.56 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2823 2839 2.128771 AGCACTTGTCAACCTGTGTT 57.871 45.0 5.6 0.0 34.14 3.32 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
699 701 2.450609 TGCTAAAGTTCTCCGGTCAC 57.549 50.000 0.00 0.00 0.00 3.67
988 990 2.046892 CAAGCTACCAGCAGCGGT 60.047 61.111 12.63 12.63 45.56 5.68
1002 1004 1.064505 CAGCGGTGGCAATCTTACATG 59.935 52.381 6.74 0.00 43.41 3.21
1041 1043 3.695830 AAGGAGATGAGCGTTGGTTAA 57.304 42.857 0.00 0.00 0.00 2.01
1113 1115 7.505258 TGACGGTGATATTCCTCAAAATCATA 58.495 34.615 0.00 0.00 31.49 2.15
1114 1116 7.990314 TGACGGTGATATTCCTCAAAATCATAA 59.010 33.333 0.00 0.00 31.49 1.90
1169 1171 2.498481 CCATTGCTCATCAAATGTGGGT 59.502 45.455 0.00 0.00 38.34 4.51
1300 1305 2.360483 CACTATGATGACTGCTCGAGGT 59.640 50.000 15.58 4.04 0.00 3.85
1301 1306 3.565902 CACTATGATGACTGCTCGAGGTA 59.434 47.826 15.58 0.00 0.00 3.08
1668 1673 6.722129 AGAATCCTTATGCTAGGTACGAGAAT 59.278 38.462 0.00 0.00 36.63 2.40
1741 1746 5.316167 TCAAAGAGATAAGGAAGCAAAGCA 58.684 37.500 0.00 0.00 0.00 3.91
1761 1766 1.080366 CGTTTCATGGGACGACCGA 60.080 57.895 14.06 0.00 44.64 4.69
2072 2077 2.292828 ACTTGTAGGCCAAACTGCAT 57.707 45.000 5.01 0.00 33.12 3.96
2213 2218 1.556911 GAGGAGAAAGGGTGCAGATCA 59.443 52.381 0.00 0.00 0.00 2.92
2823 2839 9.708092 TTTTTCAAATGATTGCTTGATGTATCA 57.292 25.926 0.00 0.00 36.45 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
307 308 6.752335 TGTCAAAGAAATTCTTCATTTGCG 57.248 33.333 8.86 0.00 35.27 4.85
988 990 4.823442 GGATGATGTCATGTAAGATTGCCA 59.177 41.667 0.00 0.00 36.57 4.92
1002 1004 5.118990 TCCTTTTTCAGATCGGATGATGTC 58.881 41.667 0.00 0.00 34.09 3.06
1041 1043 8.658840 ACAGGTATATTGTTTGGTTGGTTATT 57.341 30.769 0.00 0.00 0.00 1.40
1113 1115 3.320541 TGTCGCCTTCATGGTTGATTTTT 59.679 39.130 0.00 0.00 38.35 1.94
1114 1116 2.890311 TGTCGCCTTCATGGTTGATTTT 59.110 40.909 0.00 0.00 38.35 1.82
1169 1171 7.279758 TGACAAGTTATGCATGTCGATAATCAA 59.720 33.333 10.16 0.00 45.70 2.57
1741 1746 1.375523 GGTCGTCCCATGAAACGCT 60.376 57.895 13.08 0.00 38.72 5.07
1761 1766 0.176680 CCGCTAGAATCCTGCACTGT 59.823 55.000 0.00 0.00 0.00 3.55
1850 1855 9.524106 CAAGAAAATGATATTAGAGCATGCAAA 57.476 29.630 21.98 11.43 33.38 3.68
2072 2077 9.310449 GATAGAGGTGAAGTTATATGTCCCTTA 57.690 37.037 0.00 0.00 0.00 2.69
2213 2218 5.643777 CGTAAACCTCCTCAACATCTTCATT 59.356 40.000 0.00 0.00 0.00 2.57
2823 2839 2.128771 AGCACTTGTCAACCTGTGTT 57.871 45.000 5.60 0.00 34.14 3.32


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

AutoCloner maintained by Alex Coulton.