Multiple sequence alignment - TraesCS6A01G267000

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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 TraesCS6A01G267000 chr6A 100.000 2195 0 0 1 2195 492707405 492705211 0.000000e+00 4054.0
1 TraesCS6A01G267000 chr6A 82.500 80 10 3 88 164 417623073 417623151 1.410000e-07 67.6
2 TraesCS6A01G267000 chr6D 97.428 1983 39 11 220 2195 351112130 351114107 0.000000e+00 3369.0
3 TraesCS6A01G267000 chr6D 98.000 100 2 0 1 100 351111543 351111642 8.060000e-40 174.0
4 TraesCS6A01G267000 chr6B 97.215 1616 37 3 586 2195 528622262 528620649 0.000000e+00 2728.0
5 TraesCS6A01G267000 chr6B 92.973 370 13 5 221 588 528622723 528622365 5.370000e-146 527.0
6 TraesCS6A01G267000 chr6B 92.308 65 5 0 3 67 528622873 528622809 2.320000e-15 93.5
7 TraesCS6A01G267000 chr3B 88.889 72 8 0 88 159 43181512 43181583 3.000000e-14 89.8
8 TraesCS6A01G267000 chr3B 90.000 60 6 0 82 141 128758835 128758776 6.500000e-11 78.7
9 TraesCS6A01G267000 chr3B 88.710 62 7 0 80 141 252934666 252934605 2.340000e-10 76.8
10 TraesCS6A01G267000 chr3B 82.759 87 9 6 93 176 72722966 72722883 3.020000e-09 73.1
11 TraesCS6A01G267000 chr7D 88.060 67 6 2 76 141 514348287 514348222 6.500000e-11 78.7
12 TraesCS6A01G267000 chr4D 86.301 73 8 1 85 157 424579604 424579674 6.500000e-11 78.7
13 TraesCS6A01G267000 chr2B 91.228 57 5 0 85 141 493852652 493852708 6.500000e-11 78.7
14 TraesCS6A01G267000 chr4A 83.117 77 11 2 67 141 595811978 595812054 3.910000e-08 69.4
15 TraesCS6A01G267000 chr1D 92.500 40 2 1 155 193 442376636 442376675 3.040000e-04 56.5


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 TraesCS6A01G267000 chr6A 492705211 492707405 2194 True 4054.000000 4054 100.000000 1 2195 1 chr6A.!!$R1 2194
1 TraesCS6A01G267000 chr6D 351111543 351114107 2564 False 1771.500000 3369 97.714000 1 2195 2 chr6D.!!$F1 2194
2 TraesCS6A01G267000 chr6B 528620649 528622873 2224 True 1116.166667 2728 94.165333 3 2195 3 chr6B.!!$R1 2192

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
283 667 1.048724 TAAGGAGGGGAGATGGTGCG 61.049 60.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2495 2.108168 CGAGGGAAGTATCCTTGGTCA 58.892 52.381 0.0 0.0 45.77 4.02 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
81 82 6.270927 ACTGCTGCTATGATCCTTCCTTATAA 59.729 38.462 0.00 0.00 0.00 0.98
114 115 9.495572 ACTGCCTCTGTAAATTAATATAAGAGC 57.504 33.333 9.98 7.62 0.00 4.09
269 653 9.474313 ACTAAAATGCCTTATGATGTTTAAGGA 57.526 29.630 12.50 0.56 45.76 3.36
270 654 9.956720 CTAAAATGCCTTATGATGTTTAAGGAG 57.043 33.333 12.50 0.00 45.76 3.69
279 663 3.459598 TGATGTTTAAGGAGGGGAGATGG 59.540 47.826 0.00 0.00 0.00 3.51
283 667 1.048724 TAAGGAGGGGAGATGGTGCG 61.049 60.000 0.00 0.00 0.00 5.34
285 669 3.866582 GAGGGGAGATGGTGCGGG 61.867 72.222 0.00 0.00 0.00 6.13
348 734 4.649218 TCCCTTCACAAAAGAAAAAGGAGG 59.351 41.667 1.10 0.00 39.05 4.30
582 968 3.398406 AGTGCATCATGTTCACGTTGTA 58.602 40.909 0.00 0.00 35.97 2.41
621 1112 3.628646 ATTCCGCCCAGGTGTCAGC 62.629 63.158 0.00 0.00 41.99 4.26
708 1200 3.325135 ACTCTCTCCCGAACTGAACATTT 59.675 43.478 0.00 0.00 0.00 2.32
861 1353 2.510012 CTCGCCATCAGCTTCGCA 60.510 61.111 0.00 0.00 40.39 5.10
873 1365 1.552337 AGCTTCGCAATCTCTCTTCCA 59.448 47.619 0.00 0.00 0.00 3.53
1065 1557 3.099171 CCAGGCAGGGGGAATTCA 58.901 61.111 7.93 0.00 0.00 2.57
1115 1607 2.358737 GTCAAGGTCACCAGGCCG 60.359 66.667 0.00 0.00 0.00 6.13
1260 1754 0.675083 TCAAATGCTGCAGTTGGGTG 59.325 50.000 33.59 16.23 39.46 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 8.535690 ACGCTCTTATATTAATTTACAGAGGC 57.464 34.615 16.85 12.16 0.00 4.70
196 511 6.342111 GGAGAACTAAAATACTCCCTCTGTG 58.658 44.000 0.00 0.00 41.89 3.66
209 524 5.950758 TTTTATGCAGCGGAGAACTAAAA 57.049 34.783 0.00 0.00 0.00 1.52
267 651 3.866582 CCGCACCATCTCCCCTCC 61.867 72.222 0.00 0.00 0.00 4.30
269 653 4.741239 ACCCGCACCATCTCCCCT 62.741 66.667 0.00 0.00 0.00 4.79
270 654 4.176752 GACCCGCACCATCTCCCC 62.177 72.222 0.00 0.00 0.00 4.81
283 667 3.127533 GATGCACACAGCCGACCC 61.128 66.667 0.00 0.00 44.83 4.46
285 669 4.152625 GCGATGCACACAGCCGAC 62.153 66.667 0.00 0.00 44.83 4.79
486 872 5.005094 CCTTTGGTGGCATGATTTGATTTT 58.995 37.500 0.00 0.00 0.00 1.82
515 901 6.417191 TTTCTGTTCTATTTGTCCGCATAC 57.583 37.500 0.00 0.00 0.00 2.39
582 968 6.547510 GGAATTTTGGAGGCTTACATGTATCT 59.452 38.462 6.36 5.10 0.00 1.98
621 1112 7.305820 CGCTGATTCTTTTTGCTTTGCTATATG 60.306 37.037 0.00 0.00 0.00 1.78
873 1365 1.587054 CAAGACCGACGGCTTCTCT 59.413 57.895 15.39 6.34 0.00 3.10
1065 1557 3.021695 TGACCGTATCGATGAGGTTCTT 58.978 45.455 22.10 5.19 37.07 2.52
1260 1754 7.375053 TCTTGTTGGTAATATGTTTTGCCTTC 58.625 34.615 0.00 0.00 33.04 3.46
1371 1865 3.587506 AGTAGAAGGGGTAGCAATGTTGT 59.412 43.478 0.00 0.00 0.00 3.32
1372 1866 3.941483 CAGTAGAAGGGGTAGCAATGTTG 59.059 47.826 0.00 0.00 0.00 3.33
1373 1867 3.622455 GCAGTAGAAGGGGTAGCAATGTT 60.622 47.826 0.00 0.00 0.00 2.71
1433 1928 8.114290 GTGATTTTGCAGCATTTGATATTTCAG 58.886 33.333 0.00 0.00 32.27 3.02
1898 2399 5.458041 AAGGTTTTGGTGATGTCATTCTG 57.542 39.130 0.00 0.00 0.00 3.02
1904 2405 2.962421 TGGGAAAGGTTTTGGTGATGTC 59.038 45.455 0.00 0.00 0.00 3.06
1994 2495 2.108168 CGAGGGAAGTATCCTTGGTCA 58.892 52.381 0.00 0.00 45.77 4.02


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

AutoCloner maintained by Alex Coulton.