Multiple sequence alignment - TraesCS6A01G090200

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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 TraesCS6A01G090200 chr6A 100.000 4287 0 0 1 4287 58054863 58059149 0.000000e+00 7917
1 TraesCS6A01G090200 chr2D 93.228 3662 168 43 114 3725 458542164 458538533 0.000000e+00 5315
2 TraesCS6A01G090200 chr2D 91.787 1449 82 27 2310 3725 458521988 458523432 0.000000e+00 1982
3 TraesCS6A01G090200 chr2D 93.440 564 25 7 3724 4287 458533143 458533694 0.000000e+00 826
4 TraesCS6A01G090200 chr2D 93.177 513 30 4 3723 4235 458538506 458537999 0.000000e+00 749
5 TraesCS6A01G090200 chr2D 95.444 439 19 1 3168 3606 458525344 458525781 0.000000e+00 699
6 TraesCS6A01G090200 chr2D 94.393 321 14 4 1 320 458521645 458521962 1.390000e-134 490
7 TraesCS6A01G090200 chr2D 91.327 196 14 3 3723 3917 458523459 458523652 9.140000e-67 265
8 TraesCS6A01G090200 chr2D 92.188 128 9 1 3599 3725 458532988 458533115 3.410000e-41 180
9 TraesCS6A01G090200 chr5A 92.407 3424 184 32 1 3371 401445024 401448424 0.000000e+00 4813
10 TraesCS6A01G090200 chr5A 91.667 312 16 5 3976 4285 401448668 401448971 1.430000e-114 424
11 TraesCS6A01G090200 chr2A 97.210 2796 53 8 1 2780 654661212 654663998 0.000000e+00 4708
12 TraesCS6A01G090200 chr2A 98.138 1504 25 3 2785 4287 654664033 654665534 0.000000e+00 2619
13 TraesCS6A01G090200 chr7B 86.112 2837 286 56 2 2780 125137927 125135141 0.000000e+00 2957
14 TraesCS6A01G090200 chr7B 85.982 1548 154 44 2785 4287 125135107 125133578 0.000000e+00 1598
15 TraesCS6A01G090200 chr5B 85.543 2836 296 60 2 2780 50096597 50099375 0.000000e+00 2861
16 TraesCS6A01G090200 chr5B 87.158 1534 142 30 2785 4287 50099409 50100918 0.000000e+00 1690
17 TraesCS6A01G090200 chr7D 92.121 1853 83 33 1922 3725 51501216 51503054 0.000000e+00 2555
18 TraesCS6A01G090200 chr7D 93.977 1212 56 12 109 1319 51468498 51469693 0.000000e+00 1818
19 TraesCS6A01G090200 chr7D 91.869 578 31 11 3712 4287 51503071 51503634 0.000000e+00 793
20 TraesCS6A01G090200 chr7D 97.248 109 3 0 1 109 51466828 51466936 7.320000e-43 185
21 TraesCS6A01G090200 chr4B 88.047 1966 158 27 1718 3636 374741009 374739074 0.000000e+00 2257
22 TraesCS6A01G090200 chr4B 84.965 2115 214 44 1522 3574 625197598 625195526 0.000000e+00 2049
23 TraesCS6A01G090200 chr4B 85.880 517 41 13 3723 4227 374739055 374738559 4.910000e-144 521
24 TraesCS6A01G090200 chr4B 83.304 569 50 19 3723 4287 625195375 625194848 2.320000e-132 483
25 TraesCS6A01G090200 chr4B 80.674 564 85 17 2 555 625215833 625215284 2.380000e-112 416
26 TraesCS6A01G090200 chr6B 78.531 885 142 29 3 859 176403215 176404079 4.880000e-149 538


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 TraesCS6A01G090200 chr6A 58054863 58059149 4286 False 7917.0 7917 100.00000 1 4287 1 chr6A.!!$F1 4286
1 TraesCS6A01G090200 chr2D 458537999 458542164 4165 True 3032.0 5315 93.20250 114 4235 2 chr2D.!!$R1 4121
2 TraesCS6A01G090200 chr2D 458521645 458525781 4136 False 859.0 1982 93.23775 1 3917 4 chr2D.!!$F1 3916
3 TraesCS6A01G090200 chr2D 458532988 458533694 706 False 503.0 826 92.81400 3599 4287 2 chr2D.!!$F2 688
4 TraesCS6A01G090200 chr5A 401445024 401448971 3947 False 2618.5 4813 92.03700 1 4285 2 chr5A.!!$F1 4284
5 TraesCS6A01G090200 chr2A 654661212 654665534 4322 False 3663.5 4708 97.67400 1 4287 2 chr2A.!!$F1 4286
6 TraesCS6A01G090200 chr7B 125133578 125137927 4349 True 2277.5 2957 86.04700 2 4287 2 chr7B.!!$R1 4285
7 TraesCS6A01G090200 chr5B 50096597 50100918 4321 False 2275.5 2861 86.35050 2 4287 2 chr5B.!!$F1 4285
8 TraesCS6A01G090200 chr7D 51501216 51503634 2418 False 1674.0 2555 91.99500 1922 4287 2 chr7D.!!$F2 2365
9 TraesCS6A01G090200 chr7D 51466828 51469693 2865 False 1001.5 1818 95.61250 1 1319 2 chr7D.!!$F1 1318
10 TraesCS6A01G090200 chr4B 374738559 374741009 2450 True 1389.0 2257 86.96350 1718 4227 2 chr4B.!!$R2 2509
11 TraesCS6A01G090200 chr4B 625194848 625197598 2750 True 1266.0 2049 84.13450 1522 4287 2 chr4B.!!$R3 2765
12 TraesCS6A01G090200 chr4B 625215284 625215833 549 True 416.0 416 80.67400 2 555 1 chr4B.!!$R1 553
13 TraesCS6A01G090200 chr6B 176403215 176404079 864 False 538.0 538 78.53100 3 859 1 chr6B.!!$F1 856

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
172 1738 0.893447 ATTTCCTGGCTGCTGCTTTC 59.107 50.0 15.64 0.0 39.59 2.62 F
1165 2778 1.679139 CAAGGCACAGGTGTCTGAAA 58.321 50.0 7.38 0.0 46.11 2.69 F
1276 2889 0.601046 CACAGCACAAGAAGCCGAGA 60.601 55.0 0.00 0.0 0.00 4.04 F
2075 3719 0.445436 GTGCTCATGTGAAGAAGGCG 59.555 55.0 0.00 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1186 2799 0.038526 GCTCTTGCTGCATTGCTTGT 60.039 50.000 10.49 0.00 36.03 3.16 R
2075 3719 2.228103 CTGGGCCGTTCTTTTCTTAACC 59.772 50.000 0.00 0.00 0.00 2.85 R
3026 4727 3.035363 TGGCAATCTGATTGGATGCAAT 58.965 40.909 26.67 12.76 40.57 3.56 R
3694 5418 1.308998 CAACAAGAGGGTTTGCGTCT 58.691 50.000 0.00 0.00 0.00 4.18 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
26 27 6.481313 CAGATGATCGTGATGTAGTTTCCATT 59.519 38.462 0.00 0.00 0.00 3.16
172 1738 0.893447 ATTTCCTGGCTGCTGCTTTC 59.107 50.000 15.64 0.00 39.59 2.62
232 1798 4.565444 GGGAAAAGTGGATTTTGGATTGGG 60.565 45.833 0.00 0.00 41.24 4.12
241 1807 3.905493 TTTTGGATTGGGGGTTGTCTA 57.095 42.857 0.00 0.00 0.00 2.59
360 1928 3.998341 GCTCACAATGGCATTTTGATTGT 59.002 39.130 24.66 12.00 40.20 2.71
391 1964 7.758495 AGGTAATTTACATGGATTTTGTCGAC 58.242 34.615 9.11 9.11 0.00 4.20
505 2078 7.880059 AGAAATTGATAAAAACAAGCTCAGC 57.120 32.000 0.00 0.00 0.00 4.26
506 2079 7.664758 AGAAATTGATAAAAACAAGCTCAGCT 58.335 30.769 0.00 0.00 42.56 4.24
507 2080 7.811713 AGAAATTGATAAAAACAAGCTCAGCTC 59.188 33.333 0.00 0.00 38.25 4.09
508 2081 6.579666 ATTGATAAAAACAAGCTCAGCTCA 57.420 33.333 0.00 0.00 38.25 4.26
509 2082 5.618056 TGATAAAAACAAGCTCAGCTCAG 57.382 39.130 0.00 0.00 38.25 3.35
557 2130 7.611213 AACGGAATGTAATACCTCTTTTCTG 57.389 36.000 0.00 0.00 0.00 3.02
558 2131 6.942976 ACGGAATGTAATACCTCTTTTCTGA 58.057 36.000 0.00 0.00 0.00 3.27
559 2132 7.391620 ACGGAATGTAATACCTCTTTTCTGAA 58.608 34.615 0.00 0.00 0.00 3.02
732 2334 2.225522 TGTGGATGGAGTTAGTGGAGGA 60.226 50.000 0.00 0.00 0.00 3.71
823 2428 1.755959 CTCTAGATGAGTGGCTGCAGT 59.244 52.381 16.64 0.00 37.99 4.40
1165 2778 1.679139 CAAGGCACAGGTGTCTGAAA 58.321 50.000 7.38 0.00 46.11 2.69
1241 2854 1.222567 CCACCCCAAACTAGCCCTAT 58.777 55.000 0.00 0.00 0.00 2.57
1276 2889 0.601046 CACAGCACAAGAAGCCGAGA 60.601 55.000 0.00 0.00 0.00 4.04
1473 3086 4.908601 AGTCCCATGTGTTACTGATGAA 57.091 40.909 0.00 0.00 0.00 2.57
1477 3090 4.012374 CCCATGTGTTACTGATGAAGCTT 58.988 43.478 0.00 0.00 0.00 3.74
2075 3719 0.445436 GTGCTCATGTGAAGAAGGCG 59.555 55.000 0.00 0.00 0.00 5.52
2780 4446 9.643693 CCTTATTTTTCTGAAGCATGTTATGTT 57.356 29.630 0.00 0.00 0.00 2.71
3284 4993 6.015180 TGGCTTCTATGCAATTCTTTTCTTGT 60.015 34.615 0.00 0.00 34.04 3.16
3357 5068 5.567138 ATCCCTTTCTACAAATTGAAGCG 57.433 39.130 0.00 0.00 0.00 4.68
3650 5374 6.592994 GTCCTTAACTATCTTGTGGGTTGTAC 59.407 42.308 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.336372 GCATAAAAGCACCCAAGTCATGTTA 60.336 40.000 0.00 0.00 0.00 2.41
172 1738 4.351874 TTGGTACTTCTTCACCTCCTTG 57.648 45.455 0.00 0.00 35.73 3.61
241 1807 0.461339 GACATACCGCGAACATGGGT 60.461 55.000 8.23 0.00 37.84 4.51
505 2078 7.067859 TCCAAATTCAATTCTATCAAGGCTGAG 59.932 37.037 0.00 0.00 34.23 3.35
506 2079 6.891361 TCCAAATTCAATTCTATCAAGGCTGA 59.109 34.615 0.00 0.00 35.56 4.26
507 2080 7.104043 TCCAAATTCAATTCTATCAAGGCTG 57.896 36.000 0.00 0.00 0.00 4.85
508 2081 7.722949 TTCCAAATTCAATTCTATCAAGGCT 57.277 32.000 0.00 0.00 0.00 4.58
509 2082 8.659491 GTTTTCCAAATTCAATTCTATCAAGGC 58.341 33.333 0.00 0.00 0.00 4.35
823 2428 2.492484 GGTCTTGACTAGAAGGAAGCGA 59.508 50.000 0.00 0.00 33.81 4.93
969 2581 5.776716 TGGGATCTGCTTCAAAGAGAAAAAT 59.223 36.000 0.00 0.00 35.40 1.82
1165 2778 6.767524 TGTTGGAACATCAAAAGTAACACT 57.232 33.333 0.00 0.00 39.30 3.55
1186 2799 0.038526 GCTCTTGCTGCATTGCTTGT 60.039 50.000 10.49 0.00 36.03 3.16
1241 2854 0.767998 TGTGGCACCCATGTGAACTA 59.232 50.000 16.26 0.00 45.76 2.24
1276 2889 1.284198 ACCTGCAGCTTCCATCTCAAT 59.716 47.619 8.66 0.00 0.00 2.57
1473 3086 2.024414 GATAAAATCACCCGCCAAGCT 58.976 47.619 0.00 0.00 0.00 3.74
1704 3320 1.959042 CAAGCACTGGACTGTTGTCT 58.041 50.000 0.00 0.00 42.54 3.41
1771 3390 1.191489 TCAGTGTCGAAGCATGGGGA 61.191 55.000 0.00 0.00 0.00 4.81
2075 3719 2.228103 CTGGGCCGTTCTTTTCTTAACC 59.772 50.000 0.00 0.00 0.00 2.85
2783 4449 7.386573 TGCTTATTCTGAACGACACTAATGAAA 59.613 33.333 0.00 0.00 0.00 2.69
3026 4727 3.035363 TGGCAATCTGATTGGATGCAAT 58.965 40.909 26.67 12.76 40.57 3.56
3186 4889 4.767928 ACTAACCGCCCACAAATTCAAATA 59.232 37.500 0.00 0.00 0.00 1.40
3202 4905 7.142680 ACAACCAAATCAATAAACACTAACCG 58.857 34.615 0.00 0.00 0.00 4.44
3284 4993 5.760743 TCATGACAACACCATCGAAGTTTTA 59.239 36.000 0.00 0.00 0.00 1.52
3353 5064 5.242393 TCCTAAGTAGAACAACAGTACGCTT 59.758 40.000 0.00 0.00 0.00 4.68
3357 5068 6.270156 AGCTCCTAAGTAGAACAACAGTAC 57.730 41.667 0.00 0.00 0.00 2.73
3473 5190 3.080319 GGGATGCTTGATAAGATCTGCC 58.920 50.000 0.00 0.00 0.00 4.85
3671 5395 9.209175 GTCTGTTACATTGAGTCTACATTCTTT 57.791 33.333 0.00 0.00 0.00 2.52
3694 5418 1.308998 CAACAAGAGGGTTTGCGTCT 58.691 50.000 0.00 0.00 0.00 4.18
3830 5591 5.233957 CATATGTTGCATTCGGAGTTCAA 57.766 39.130 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.