Multiple sequence alignment - TraesCS4A01G070000

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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 TraesCS4A01G070000 chr4A 100.000 2723 0 0 1 2723 67586034 67583312 0 5029
1 TraesCS4A01G070000 chrUn 98.568 2723 33 2 2 2723 189394041 189396758 0 4807
2 TraesCS4A01G070000 chr7D 98.384 2723 38 2 2 2723 203554844 203552127 0 4780
3 TraesCS4A01G070000 chr5B 98.384 2722 38 2 2 2723 679660399 679663114 0 4778
4 TraesCS4A01G070000 chr7B 98.310 2722 40 2 2 2723 743087701 743090416 0 4767
5 TraesCS4A01G070000 chr5A 98.237 2722 42 2 2 2723 16601421 16598706 0 4756
6 TraesCS4A01G070000 chr5A 98.090 2723 45 3 2 2723 300074481 300077197 0 4734
7 TraesCS4A01G070000 chr5A 97.943 2723 53 3 2 2723 600278235 600275515 0 4715
8 TraesCS4A01G070000 chr6A 98.200 2722 43 3 2 2723 289130132 289132847 0 4750
9 TraesCS4A01G070000 chr4D 98.200 2722 41 2 2 2723 123414384 123417097 0 4748


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 TraesCS4A01G070000 chr4A 67583312 67586034 2722 True 5029 5029 100.000 1 2723 1 chr4A.!!$R1 2722
1 TraesCS4A01G070000 chrUn 189394041 189396758 2717 False 4807 4807 98.568 2 2723 1 chrUn.!!$F1 2721
2 TraesCS4A01G070000 chr7D 203552127 203554844 2717 True 4780 4780 98.384 2 2723 1 chr7D.!!$R1 2721
3 TraesCS4A01G070000 chr5B 679660399 679663114 2715 False 4778 4778 98.384 2 2723 1 chr5B.!!$F1 2721
4 TraesCS4A01G070000 chr7B 743087701 743090416 2715 False 4767 4767 98.310 2 2723 1 chr7B.!!$F1 2721
5 TraesCS4A01G070000 chr5A 16598706 16601421 2715 True 4756 4756 98.237 2 2723 1 chr5A.!!$R1 2721
6 TraesCS4A01G070000 chr5A 300074481 300077197 2716 False 4734 4734 98.090 2 2723 1 chr5A.!!$F1 2721
7 TraesCS4A01G070000 chr5A 600275515 600278235 2720 True 4715 4715 97.943 2 2723 1 chr5A.!!$R2 2721
8 TraesCS4A01G070000 chr6A 289130132 289132847 2715 False 4750 4750 98.200 2 2723 1 chr6A.!!$F1 2721
9 TraesCS4A01G070000 chr4D 123414384 123417097 2713 False 4748 4748 98.200 2 2723 1 chr4D.!!$F1 2721

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
579 580 1.302511 GCCGAGAACCTTCTTGCCA 60.303 57.895 0.0 0.0 37.73 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 1838 0.901827 TTAAGAGGCAGTGCATCCGA 59.098 50.0 25.1 11.39 40.43 4.55 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
342 343 6.168389 AGCCAGTTTCAATTCCAAATCATTC 58.832 36.000 0.00 0.00 0.00 2.67
496 497 7.621683 AGATCCACTCAACTAGGAAAGAAGTAT 59.378 37.037 0.00 0.00 34.62 2.12
520 521 4.558095 GCATTGCTGACTGACTGTTTGAAT 60.558 41.667 0.16 0.00 0.00 2.57
555 556 7.328277 ACTAGTAGCTAATCAAGTCAGAGTG 57.672 40.000 0.00 0.00 0.00 3.51
569 570 3.607370 GAGTGGGGTGGCCGAGAAC 62.607 68.421 0.00 0.00 0.00 3.01
579 580 1.302511 GCCGAGAACCTTCTTGCCA 60.303 57.895 0.00 0.00 37.73 4.92
827 828 5.221581 GGCCCGTATAGAAAGTCAATCCTTA 60.222 44.000 0.00 0.00 0.00 2.69
922 923 3.028850 CCTCATTCCATGGAAAGCATGT 58.971 45.455 30.28 10.74 37.69 3.21
1177 1179 9.908152 CTCGTATTTCATATGTACATGTTCCTA 57.092 33.333 18.81 0.00 0.00 2.94
1421 1424 0.112218 ATTTACCTGGGTGCACTGCA 59.888 50.000 17.98 0.00 35.60 4.41
1477 1480 2.678580 TCCGTGCTGGACCGATCA 60.679 61.111 0.00 0.00 43.74 2.92
1507 1510 6.884836 ACCAATAATAAAGTCTCCAGTCAACC 59.115 38.462 0.00 0.00 0.00 3.77
1508 1511 7.112779 CCAATAATAAAGTCTCCAGTCAACCT 58.887 38.462 0.00 0.00 0.00 3.50
1630 1633 4.401519 CCTTCTCTACCCGTATCTTGTTCA 59.598 45.833 0.00 0.00 0.00 3.18
1826 1829 5.820423 GCAAAATGGGTCAAAAAGTAGGTTT 59.180 36.000 0.00 0.00 0.00 3.27
1835 1838 6.040504 GGTCAAAAAGTAGGTTTGATTCCTGT 59.959 38.462 3.18 0.00 44.46 4.00
2087 2090 4.419282 TCAAAGGAAAGAAGGAATGGCAT 58.581 39.130 0.00 0.00 0.00 4.40
2184 2188 2.604912 ATTCACTTCCTTGGGGTTCC 57.395 50.000 0.00 0.00 0.00 3.62
2331 2336 9.932699 CTTTGATGATCTTCAACACATCTATTC 57.067 33.333 20.34 0.00 39.54 1.75
2597 2602 1.771255 GGAGTATGGCTGGAAGGTCAT 59.229 52.381 0.00 0.00 35.57 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
496 497 1.971481 AACAGTCAGTCAGCAATGCA 58.029 45.000 8.35 0.00 0.00 3.96
555 556 3.623703 GAAGGTTCTCGGCCACCCC 62.624 68.421 2.24 0.00 32.92 4.95
569 570 2.677875 GGGGCACTGGCAAGAAGG 60.678 66.667 4.78 0.00 43.71 3.46
579 580 2.043604 GCTTTGCTTTTGGGGGCACT 62.044 55.000 0.00 0.00 38.23 4.40
827 828 1.880027 GGAGCGGCATATCGGAAAAAT 59.120 47.619 1.45 0.00 0.00 1.82
870 871 0.796927 GCTTAGTTTTCGCTCCGCTT 59.203 50.000 0.00 0.00 0.00 4.68
1177 1179 2.273538 ACTATACTCATCCGAGCCGT 57.726 50.000 0.00 0.00 43.66 5.68
1213 1215 6.442541 TGGGAACAAGGAACTGTTTATAGA 57.557 37.500 0.00 0.00 40.86 1.98
1421 1424 5.281727 GTTCGACAGGAAGCTTTTGAAAAT 58.718 37.500 16.11 0.00 34.69 1.82
1507 1510 3.002656 GGTTGATGCGATGTATTCCACAG 59.997 47.826 0.00 0.00 41.51 3.66
1508 1511 2.942376 GGTTGATGCGATGTATTCCACA 59.058 45.455 0.00 0.00 42.69 4.17
1630 1633 3.771577 AGGAAGACGTGTTTCCAGAAT 57.228 42.857 23.28 6.64 45.28 2.40
1835 1838 0.901827 TTAAGAGGCAGTGCATCCGA 59.098 50.000 25.10 11.39 40.43 4.55
2087 2090 4.111255 TGATGTTCAATGGAGGGAAACA 57.889 40.909 0.00 0.00 0.00 2.83
2184 2188 7.451429 TCGTTTGTGTTCATGTTTTCAATTTG 58.549 30.769 0.00 0.00 0.00 2.32
2331 2336 1.002366 CTTCACTCGCAGGGAATTCG 58.998 55.000 0.00 0.00 36.96 3.34
2447 2452 1.417517 CCACATGCATGAGTAGGCCTA 59.582 52.381 32.75 8.91 31.29 3.93
2597 2602 3.632604 CCGATTGACAAGACTAGCTAGGA 59.367 47.826 24.35 1.07 0.00 2.94


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

AutoCloner maintained by Alex Coulton.