Multiple sequence alignment - TraesCS6D01G175900

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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 TraesCS6D01G175900 chr6D 100.000 2594 0 0 1 2594 168755057 168757650 0 4791
1 TraesCS6D01G175900 chr6D 97.607 2591 54 1 1 2591 124517489 124520071 0 4434
2 TraesCS6D01G175900 chr6D 97.221 2591 63 2 1 2591 458898150 458900731 0 4377
3 TraesCS6D01G175900 chr7D 97.803 2594 51 3 1 2594 381973800 381971213 0 4470
4 TraesCS6D01G175900 chr7D 97.723 2591 51 1 1 2591 381923968 381926550 0 4451
5 TraesCS6D01G175900 chr7D 97.646 2591 53 1 1 2591 203499966 203502548 0 4440
6 TraesCS6D01G175900 chr7D 97.647 2592 52 2 1 2591 382050045 382052628 0 4440
7 TraesCS6D01G175900 chr5A 97.765 2595 49 2 1 2594 19248877 19246291 0 4462
8 TraesCS6D01G175900 chr7B 97.340 2594 55 3 1 2594 716878813 716876234 0 4396
9 TraesCS6D01G175900 chr4D 97.260 2591 61 3 1 2591 123335440 123338020 0 4383
10 TraesCS6D01G175900 chr4D 97.144 2591 60 2 1 2591 123549893 123552469 0 4362
11 TraesCS6D01G175900 chr1D 97.105 2591 65 4 1 2591 269406769 269409349 0 4361
12 TraesCS6D01G175900 chr7A 95.809 2434 97 4 1 2434 686715714 686713286 0 3925
13 TraesCS6D01G175900 chr7A 95.770 2435 92 6 1 2434 686650811 686648387 0 3916


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 TraesCS6D01G175900 chr6D 168755057 168757650 2593 False 4791 4791 100.000 1 2594 1 chr6D.!!$F2 2593
1 TraesCS6D01G175900 chr6D 124517489 124520071 2582 False 4434 4434 97.607 1 2591 1 chr6D.!!$F1 2590
2 TraesCS6D01G175900 chr6D 458898150 458900731 2581 False 4377 4377 97.221 1 2591 1 chr6D.!!$F3 2590
3 TraesCS6D01G175900 chr7D 381971213 381973800 2587 True 4470 4470 97.803 1 2594 1 chr7D.!!$R1 2593
4 TraesCS6D01G175900 chr7D 381923968 381926550 2582 False 4451 4451 97.723 1 2591 1 chr7D.!!$F2 2590
5 TraesCS6D01G175900 chr7D 203499966 203502548 2582 False 4440 4440 97.646 1 2591 1 chr7D.!!$F1 2590
6 TraesCS6D01G175900 chr7D 382050045 382052628 2583 False 4440 4440 97.647 1 2591 1 chr7D.!!$F3 2590
7 TraesCS6D01G175900 chr5A 19246291 19248877 2586 True 4462 4462 97.765 1 2594 1 chr5A.!!$R1 2593
8 TraesCS6D01G175900 chr7B 716876234 716878813 2579 True 4396 4396 97.340 1 2594 1 chr7B.!!$R1 2593
9 TraesCS6D01G175900 chr4D 123335440 123338020 2580 False 4383 4383 97.260 1 2591 1 chr4D.!!$F1 2590
10 TraesCS6D01G175900 chr4D 123549893 123552469 2576 False 4362 4362 97.144 1 2591 1 chr4D.!!$F2 2590
11 TraesCS6D01G175900 chr1D 269406769 269409349 2580 False 4361 4361 97.105 1 2591 1 chr1D.!!$F1 2590
12 TraesCS6D01G175900 chr7A 686713286 686715714 2428 True 3925 3925 95.809 1 2434 1 chr7A.!!$R2 2433
13 TraesCS6D01G175900 chr7A 686648387 686650811 2424 True 3916 3916 95.770 1 2434 1 chr7A.!!$R1 2433

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
281 282 0.178990 AACACAGGAAAGCACCCTCC 60.179 55.0 0.0 0.0 0.0 4.30 F
960 968 0.250727 CTCGAGCCCCAAGAAAACCA 60.251 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 1514 0.558712 AAGCCCCACAACCCAAAGTA 59.441 50.000 0.0 0.0 0.0 2.24 R
2500 2529 1.416401 GCCTGAGATGGGGATAACGAA 59.584 52.381 0.0 0.0 0.0 3.85 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
102 103 0.391130 CCGTTCCGAATGCTTCTCCA 60.391 55.000 0.00 0.00 0.00 3.86
184 185 5.380900 GCTTTGCTAATCTTCCCCTCTAAT 58.619 41.667 0.00 0.00 0.00 1.73
186 187 5.975988 TTGCTAATCTTCCCCTCTAATGT 57.024 39.130 0.00 0.00 0.00 2.71
281 282 0.178990 AACACAGGAAAGCACCCTCC 60.179 55.000 0.00 0.00 0.00 4.30
380 384 2.107378 TGTTTGAGCCTATGTTCACCCA 59.893 45.455 0.00 0.00 30.81 4.51
561 565 3.550431 GCCGAGGGGATAGCAGCA 61.550 66.667 0.00 0.00 34.06 4.41
568 572 1.855599 AGGGGATAGCAGCATTCCTTT 59.144 47.619 12.13 0.81 0.00 3.11
727 731 6.614906 AGAGAGAATCCACTTCAGATAACCAT 59.385 38.462 0.00 0.00 36.24 3.55
811 815 3.549423 CGAGAGTGGAGTTACGTGAACAA 60.549 47.826 0.00 0.00 40.86 2.83
903 907 3.304911 TTTGTGTGAATTCCCCAGTGA 57.695 42.857 2.27 0.00 0.00 3.41
904 908 3.304911 TTGTGTGAATTCCCCAGTGAA 57.695 42.857 2.27 0.00 0.00 3.18
908 912 3.253432 GTGTGAATTCCCCAGTGAAGAAC 59.747 47.826 2.27 0.00 0.00 3.01
960 968 0.250727 CTCGAGCCCCAAGAAAACCA 60.251 55.000 0.00 0.00 0.00 3.67
1079 1087 8.677148 TCTATTGCGCCTAAAATCTCTATTTT 57.323 30.769 4.18 0.00 45.21 1.82
1506 1514 6.259550 AGCAAATTCTATTTGTTCTTCGCT 57.740 33.333 12.26 0.00 0.00 4.93
1507 1515 7.377766 AGCAAATTCTATTTGTTCTTCGCTA 57.622 32.000 12.26 0.00 0.00 4.26
1664 1672 2.020720 ACCGAATCAGTTGCAACACAA 58.979 42.857 30.11 15.59 35.33 3.33
1713 1721 3.130516 GGTCGAGTCTGATACATCAACCA 59.869 47.826 0.00 0.00 36.18 3.67
1747 1755 3.513912 TCCTTGTACGAGTCCACAATCAT 59.486 43.478 9.32 0.00 34.34 2.45
1748 1756 4.707934 TCCTTGTACGAGTCCACAATCATA 59.292 41.667 9.32 0.00 34.34 2.15
1868 1876 2.733593 GTTGGAACGACGCGAGCT 60.734 61.111 15.93 0.00 0.00 4.09
2099 2108 3.756963 GGGCACGGAGAAATAAAGAAGTT 59.243 43.478 0.00 0.00 0.00 2.66
2300 2318 2.007608 CAAAGAACTACGCTTAGCCCC 58.992 52.381 0.00 0.00 0.00 5.80
2301 2319 0.540454 AAGAACTACGCTTAGCCCCC 59.460 55.000 0.00 0.00 0.00 5.40
2369 2393 1.140375 CCGTAGTACCCGAAGCACC 59.860 63.158 4.25 0.00 0.00 5.01
2387 2411 1.742768 CGGAGTGATCCAGTAGCCC 59.257 63.158 0.00 0.00 0.00 5.19
2460 2489 4.781087 ACACATTTACAGAGCTTACCCCTA 59.219 41.667 0.00 0.00 0.00 3.53
2490 2519 2.919494 GCAGAACGTTGGGGGCTTG 61.919 63.158 5.00 0.00 0.00 4.01
2500 2529 1.146263 GGGGGCTTGAATCGTCGAT 59.854 57.895 0.75 0.75 0.00 3.59
2519 2548 3.615110 CGATTCGTTATCCCCATCTCAGG 60.615 52.174 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 2.231478 TCTTCGCGAGAACTTCAGGATT 59.769 45.455 9.59 0.00 46.92 3.01
281 282 3.119352 GGAAGCTGCAGGGATTACAAAAG 60.119 47.826 17.12 0.00 0.00 2.27
333 337 3.603671 GGGGTCCTAGCTACGCCG 61.604 72.222 11.99 0.00 39.75 6.46
677 681 0.905357 AGTAGATGCCGAACCTGCTT 59.095 50.000 0.00 0.00 0.00 3.91
811 815 3.208747 AGTTGTTTTCCATCAGACGGT 57.791 42.857 0.00 0.00 0.00 4.83
903 907 2.956333 GCCCCACAAGTTGTTAGTTCTT 59.044 45.455 5.57 0.00 0.00 2.52
904 908 2.583143 GCCCCACAAGTTGTTAGTTCT 58.417 47.619 5.57 0.00 0.00 3.01
908 912 0.112412 AGGGCCCCACAAGTTGTTAG 59.888 55.000 21.43 0.54 0.00 2.34
960 968 1.801302 TTGAGTCCGAGGGAGAGGGT 61.801 60.000 0.00 0.00 29.39 4.34
1079 1087 5.431420 AGAAACACGTGACATATTTGCAA 57.569 34.783 25.01 0.00 0.00 4.08
1325 1333 3.866651 ACTATGGCGAATGCATCTATCC 58.133 45.455 0.00 0.00 45.35 2.59
1372 1380 3.242739 GCGCCCAAATCCGCTATATATTG 60.243 47.826 0.00 0.00 46.14 1.90
1506 1514 0.558712 AAGCCCCACAACCCAAAGTA 59.441 50.000 0.00 0.00 0.00 2.24
1507 1515 0.558712 TAAGCCCCACAACCCAAAGT 59.441 50.000 0.00 0.00 0.00 2.66
1664 1672 2.346766 TCGTAGCATGCATTCCCATT 57.653 45.000 21.98 0.00 0.00 3.16
1713 1721 4.395625 TCGTACAAGGATATGGAGTCGAT 58.604 43.478 0.00 0.00 0.00 3.59
1747 1755 2.253610 ACCCAGGTTCATCTCGTGTTA 58.746 47.619 0.00 0.00 0.00 2.41
1748 1756 1.056660 ACCCAGGTTCATCTCGTGTT 58.943 50.000 0.00 0.00 0.00 3.32
2099 2108 4.033776 CGGCTGCTTCTCCCCCAA 62.034 66.667 0.00 0.00 0.00 4.12
2216 2225 7.018150 AGATATCTGGATAGATGGATGGATCC 58.982 42.308 4.20 4.20 43.41 3.36
2303 2321 2.679342 TTTCATGAGCGGGGAGGGG 61.679 63.158 0.00 0.00 0.00 4.79
2304 2322 1.452108 GTTTCATGAGCGGGGAGGG 60.452 63.158 0.00 0.00 0.00 4.30
2305 2323 1.815421 CGTTTCATGAGCGGGGAGG 60.815 63.158 12.18 0.00 0.00 4.30
2306 2324 1.815421 CCGTTTCATGAGCGGGGAG 60.815 63.158 24.43 6.98 41.60 4.30
2307 2325 2.267642 CCGTTTCATGAGCGGGGA 59.732 61.111 24.43 0.00 41.60 4.81
2369 2393 1.742768 GGGCTACTGGATCACTCCG 59.257 63.158 0.00 0.00 45.37 4.63
2387 2411 1.522569 CACTTCTAGGCCCCTTCCG 59.477 63.158 0.00 0.00 0.00 4.30
2490 2519 2.985139 GGGGATAACGAATCGACGATTC 59.015 50.000 31.54 31.54 43.31 2.52
2500 2529 1.416401 GCCTGAGATGGGGATAACGAA 59.584 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.