Multiple sequence alignment - TraesCS1B01G189200

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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 TraesCS1B01G189200 chr1B 100.000 2720 0 0 1 2720 338950910 338953629 0 5024
1 TraesCS1B01G189200 chr1B 98.092 2725 47 2 1 2720 683732399 683729675 0 4739
2 TraesCS1B01G189200 chr1B 97.762 2726 53 5 1 2720 338894563 338897286 0 4689
3 TraesCS1B01G189200 chr7B 97.688 2725 58 2 1 2720 698141904 698144628 0 4678
4 TraesCS1B01G189200 chr3B 97.616 2726 59 3 1 2720 5085398 5082673 0 4669
5 TraesCS1B01G189200 chr3B 97.321 2725 67 3 1 2720 92263600 92266323 0 4623
6 TraesCS1B01G189200 chr3B 97.211 2725 70 3 1 2720 92144668 92147391 0 4606
7 TraesCS1B01G189200 chr3B 96.917 2725 76 5 1 2720 575738088 575735367 0 4560
8 TraesCS1B01G189200 chr2A 97.541 2725 62 2 1 2720 563258384 563261108 0 4656
9 TraesCS1B01G189200 chr5B 97.469 2726 62 4 1 2720 713080476 713077752 0 4645


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 TraesCS1B01G189200 chr1B 338950910 338953629 2719 False 5024 5024 100.000 1 2720 1 chr1B.!!$F2 2719
1 TraesCS1B01G189200 chr1B 683729675 683732399 2724 True 4739 4739 98.092 1 2720 1 chr1B.!!$R1 2719
2 TraesCS1B01G189200 chr1B 338894563 338897286 2723 False 4689 4689 97.762 1 2720 1 chr1B.!!$F1 2719
3 TraesCS1B01G189200 chr7B 698141904 698144628 2724 False 4678 4678 97.688 1 2720 1 chr7B.!!$F1 2719
4 TraesCS1B01G189200 chr3B 5082673 5085398 2725 True 4669 4669 97.616 1 2720 1 chr3B.!!$R1 2719
5 TraesCS1B01G189200 chr3B 92263600 92266323 2723 False 4623 4623 97.321 1 2720 1 chr3B.!!$F2 2719
6 TraesCS1B01G189200 chr3B 92144668 92147391 2723 False 4606 4606 97.211 1 2720 1 chr3B.!!$F1 2719
7 TraesCS1B01G189200 chr3B 575735367 575738088 2721 True 4560 4560 96.917 1 2720 1 chr3B.!!$R2 2719
8 TraesCS1B01G189200 chr2A 563258384 563261108 2724 False 4656 4656 97.541 1 2720 1 chr2A.!!$F1 2719
9 TraesCS1B01G189200 chr5B 713077752 713080476 2724 True 4645 4645 97.469 1 2720 1 chr5B.!!$R1 2719

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
821 826 0.53109 GGTCGGTTTGTTTTTGGGGC 60.531 55.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2251 4.000331 CATCTATTGGAAGAGATGGCGT 58.0 45.455 13.84 0.0 46.01 5.68 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
821 826 0.531090 GGTCGGTTTGTTTTTGGGGC 60.531 55.000 0.00 0.0 0.00 5.80
851 856 5.159209 CAATAAGCTTGCTTCTTCACAAGG 58.841 41.667 9.86 0.0 42.82 3.61
883 889 1.614241 CCTTTCCTGTCCGTCCCGAT 61.614 60.000 0.00 0.0 0.00 4.18
1347 1355 6.183360 GCATGTTCCCAGAAAGAAGATACTTC 60.183 42.308 0.00 0.0 0.00 3.01
1358 1367 9.799106 AGAAAGAAGATACTTCTTTTCCATTCA 57.201 29.630 28.10 0.0 45.59 2.57
1433 1442 4.832823 TCTATATGCTCCGATTGGAACTGA 59.167 41.667 2.51 0.0 45.87 3.41
1690 1699 3.846588 GCCTTCCCCAATGGATCTCTATA 59.153 47.826 0.00 0.0 44.66 1.31
1728 1737 3.791320 AGAAGTTCACTGACCATCCCTA 58.209 45.455 5.50 0.0 0.00 3.53
1751 1760 4.913784 TCAAACATAACCCAAGGTAGGAC 58.086 43.478 0.00 0.0 33.12 3.85
1753 1762 2.923908 ACATAACCCAAGGTAGGACCA 58.076 47.619 0.00 0.0 41.95 4.02
1992 2003 9.527157 TGGAAACTTATTGATTAATGAGGTCAA 57.473 29.630 6.89 0.0 35.00 3.18
2422 2434 7.913674 AGAGAAAATAGTCTGTGTGGATTTC 57.086 36.000 0.00 0.0 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.095228 CGCACATAAGCCATCGGGTT 61.095 55.000 2.65 2.65 45.82 4.11
291 295 1.173913 GGGATGCTTAACGCCACTTT 58.826 50.000 0.00 0.00 38.05 2.66
406 410 2.541466 AGTGGGAATTCTCTCGTTCCT 58.459 47.619 6.92 0.00 42.76 3.36
413 417 1.482593 CAGCGGTAGTGGGAATTCTCT 59.517 52.381 6.92 5.41 0.00 3.10
576 581 1.078426 GTTATGCTGTGCCCCGACT 60.078 57.895 0.00 0.00 0.00 4.18
590 595 8.160106 CCTAAATGGAATGGCTCTCTTAGTTAT 58.840 37.037 0.00 0.00 38.35 1.89
821 826 1.139520 GCAAGCTTATTGCCCCACG 59.860 57.895 0.00 0.00 44.23 4.94
851 856 1.152819 GAAAGGGGGCGGGGATAAC 60.153 63.158 0.00 0.00 0.00 1.89
883 889 1.671742 GAGACCCAACTGCTTCCGA 59.328 57.895 0.00 0.00 0.00 4.55
1347 1355 5.689383 TCCTCGTTTCTTGAATGGAAAAG 57.311 39.130 0.00 0.00 34.97 2.27
1358 1367 0.674534 AGTCGTGCTCCTCGTTTCTT 59.325 50.000 0.00 0.00 0.00 2.52
1690 1699 7.013369 GTGAACTTCTATTGGTTTCAAAGGAGT 59.987 37.037 0.00 0.00 34.42 3.85
1728 1737 5.506708 GTCCTACCTTGGGTTATGTTTGAT 58.493 41.667 0.00 0.00 37.09 2.57
1751 1760 5.208121 AGAGTCCTATTCTTCTCCTCTTGG 58.792 45.833 0.00 0.00 0.00 3.61
1753 1762 5.128663 GCAAGAGTCCTATTCTTCTCCTCTT 59.871 44.000 0.00 0.00 38.08 2.85
2240 2251 4.000331 CATCTATTGGAAGAGATGGCGT 58.000 45.455 13.84 0.00 46.01 5.68
2422 2434 6.982852 AGAAACATACCGGATACTATGACTG 58.017 40.000 9.46 0.00 31.14 3.51
2650 2662 4.373156 AAGAACACCTTCATACTGGCTT 57.627 40.909 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.