Multiple sequence alignment - TraesCS6A01G214400

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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 TraesCS6A01G214400 chr6A 100.000 3884 0 0 1 3884 392196603 392192720 0.000000e+00 7173
1 TraesCS6A01G214400 chr6D 97.900 3333 46 4 574 3884 273924798 273921468 0.000000e+00 5746
2 TraesCS6A01G214400 chr6D 98.230 452 8 0 3 454 273925591 273925140 0.000000e+00 791
3 TraesCS6A01G214400 chr6B 93.018 3896 173 44 3 3847 435835280 435831433 0.000000e+00 5596
4 TraesCS6A01G214400 chr2A 84.848 231 35 0 2652 2882 585212583 585212353 2.330000e-57 233
5 TraesCS6A01G214400 chr2D 84.416 231 36 0 2652 2882 441574416 441574186 1.090000e-55 228
6 TraesCS6A01G214400 chr2B 84.416 231 36 0 2652 2882 519185105 519184875 1.090000e-55 228
7 TraesCS6A01G214400 chr5B 82.407 216 38 0 2667 2882 19790652 19790437 5.120000e-44 189
8 TraesCS6A01G214400 chr5B 89.873 79 8 0 1980 2058 19791257 19791179 6.870000e-18 102


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 TraesCS6A01G214400 chr6A 392192720 392196603 3883 True 7173.0 7173 100.000 1 3884 1 chr6A.!!$R1 3883
1 TraesCS6A01G214400 chr6D 273921468 273925591 4123 True 3268.5 5746 98.065 3 3884 2 chr6D.!!$R1 3881
2 TraesCS6A01G214400 chr6B 435831433 435835280 3847 True 5596.0 5596 93.018 3 3847 1 chr6B.!!$R1 3844

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
520 524 0.472471 GGGAGACTCACCCAAACACA 59.528 55.000 6.67 0.0 46.05 3.72 F
1352 1581 3.214328 AGTGTGTCAGGTCACCATTTTC 58.786 45.455 0.00 0.0 37.51 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1766 2.213499 GCTGGTATATGTGCTGACACC 58.787 52.381 0.0 0.0 46.86 4.16 R
2908 3173 4.344679 TCAATTCACCCTCATTTTTGCAGT 59.655 37.500 0.0 0.0 0.00 4.40 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
486 490 3.864789 AGACATAATACAAGGCAGGGG 57.135 47.619 0.00 0.00 0.00 4.79
488 492 2.174854 GACATAATACAAGGCAGGGGGT 59.825 50.000 0.00 0.00 0.00 4.95
491 495 1.874299 AATACAAGGCAGGGGGTGGG 61.874 60.000 0.00 0.00 0.00 4.61
520 524 0.472471 GGGAGACTCACCCAAACACA 59.528 55.000 6.67 0.00 46.05 3.72
545 552 8.672815 CAAAGCTTAAATGTTTGAAGGGAAAAA 58.327 29.630 0.00 0.00 33.78 1.94
1352 1581 3.214328 AGTGTGTCAGGTCACCATTTTC 58.786 45.455 0.00 0.00 37.51 2.29
1557 1808 1.067364 CCTTTGCATGCAGACACACAA 59.933 47.619 21.50 9.45 0.00 3.33
1799 2062 8.220755 TCCTAACCATCAAATTATACAAGCAC 57.779 34.615 0.00 0.00 0.00 4.40
1961 2225 7.551262 TCCAGTTTATATGCTTGTAACACGAAT 59.449 33.333 0.00 0.00 0.00 3.34
2129 2393 0.250081 TGCGCATGTCACACAGGTTA 60.250 50.000 5.66 0.00 31.66 2.85
2445 2710 7.121168 CAGCTTATATTTTTCTGACCTCCACAA 59.879 37.037 0.00 0.00 0.00 3.33
2908 3173 3.245229 ACTGGGATAACTGCATTCCAACA 60.245 43.478 0.00 0.00 32.92 3.33
2978 3243 2.696759 GGTGGGCGTTGTGTATGGC 61.697 63.158 0.00 0.00 37.59 4.40
3491 3760 2.435805 GTCCTGGTCAGATTATGCTCCA 59.564 50.000 0.00 0.00 33.66 3.86
3561 3830 2.762535 TGGTAGACAGGCTTAGCAAC 57.237 50.000 6.53 0.00 0.00 4.17
3643 3912 0.527565 CCCGGCTTTGAATGAAGTGG 59.472 55.000 0.00 0.00 0.00 4.00
3800 4069 0.585357 CACACACTGCTTGTCAGAGC 59.415 55.000 0.00 0.00 45.72 4.09
3881 4150 1.302832 CTCAGCTGGTGAACCCCAC 60.303 63.158 15.13 0.00 44.95 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.622811 CCACTGAAACTGCCTCTCTCT 59.377 52.381 0.00 0.00 0.00 3.10
1 2 1.943507 GCCACTGAAACTGCCTCTCTC 60.944 57.143 0.00 0.00 0.00 3.20
210 212 3.243002 GCACTTCTAATGCTTGAGATGCC 60.243 47.826 2.42 0.00 40.08 4.40
456 460 9.688091 TGCCTTGTATTATGTCTAAATGGTAAA 57.312 29.630 0.00 0.00 0.00 2.01
459 463 6.772716 CCTGCCTTGTATTATGTCTAAATGGT 59.227 38.462 0.00 0.00 0.00 3.55
460 464 6.207417 CCCTGCCTTGTATTATGTCTAAATGG 59.793 42.308 0.00 0.00 0.00 3.16
461 465 6.207417 CCCCTGCCTTGTATTATGTCTAAATG 59.793 42.308 0.00 0.00 0.00 2.32
462 466 6.306987 CCCCTGCCTTGTATTATGTCTAAAT 58.693 40.000 0.00 0.00 0.00 1.40
463 467 5.398581 CCCCCTGCCTTGTATTATGTCTAAA 60.399 44.000 0.00 0.00 0.00 1.85
466 470 2.443255 CCCCCTGCCTTGTATTATGTCT 59.557 50.000 0.00 0.00 0.00 3.41
472 476 1.697297 CCACCCCCTGCCTTGTATT 59.303 57.895 0.00 0.00 0.00 1.89
473 477 2.316586 CCCACCCCCTGCCTTGTAT 61.317 63.158 0.00 0.00 0.00 2.29
499 503 1.379146 GTTTGGGTGAGTCTCCCCC 59.621 63.158 24.38 13.29 44.00 5.40
504 508 2.024414 GCTTTGTGTTTGGGTGAGTCT 58.976 47.619 0.00 0.00 0.00 3.24
520 524 8.800370 TTTTTCCCTTCAAACATTTAAGCTTT 57.200 26.923 3.20 0.00 0.00 3.51
545 552 3.798515 TCCCACCCTCTTTATGTACACT 58.201 45.455 0.00 0.00 0.00 3.55
764 990 6.518493 CCGTCACTTGTAATATTTAGGGCTA 58.482 40.000 0.00 0.00 0.00 3.93
1330 1559 2.550830 AATGGTGACCTGACACACTC 57.449 50.000 2.11 0.00 41.88 3.51
1352 1581 5.493133 ACAGCGTGATACTTTAGAGAGAG 57.507 43.478 0.00 0.00 0.00 3.20
1515 1766 2.213499 GCTGGTATATGTGCTGACACC 58.787 52.381 0.00 0.00 46.86 4.16
2088 2352 7.352739 CGCACAACTGTAAGAAAGAGTTTATT 58.647 34.615 0.00 0.00 39.57 1.40
2096 2360 3.228749 CATGCGCACAACTGTAAGAAAG 58.771 45.455 14.90 0.00 37.43 2.62
2129 2393 2.567169 TGATTCCGGAATGTCTGTCACT 59.433 45.455 33.84 6.89 0.00 3.41
2908 3173 4.344679 TCAATTCACCCTCATTTTTGCAGT 59.655 37.500 0.00 0.00 0.00 4.40
2978 3243 5.006358 AGGAATTAAACTACATTACGCTGCG 59.994 40.000 21.91 21.91 0.00 5.18
3158 3425 9.950680 CATTTATTGGCGTCAAATCTAATAGTT 57.049 29.630 6.51 0.00 36.36 2.24
3451 3720 1.699634 ACTGCACTAACATGTCAGGGT 59.300 47.619 14.07 2.71 31.81 4.34
3491 3760 9.136323 ACTAATTTGGTTTTCTTGATCAGTTCT 57.864 29.630 0.00 0.00 0.00 3.01
3561 3830 0.622665 ACCTGATTCCCTTCCTGCTG 59.377 55.000 0.00 0.00 0.00 4.41
3643 3912 5.613142 GCAAAAGCAGATGCATTTTGTGTAC 60.613 40.000 25.56 15.24 43.16 2.90
3689 3958 7.309377 CCTTGAAAATTGGAAACAGATAGCTCA 60.309 37.037 0.00 0.00 44.54 4.26
3852 4121 4.787280 AGCTGAGCCCGGGTAGCT 62.787 66.667 30.85 30.85 45.23 3.32


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

AutoCloner maintained by Alex Coulton.