Multiple sequence alignment - TraesCS6B01G357500

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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 TraesCS6B01G357500 chr6B 100.000 2300 0 0 1 2300 625653464 625651165 0 4248
1 TraesCS6B01G357500 chr6B 95.871 2301 94 1 1 2300 128916648 128914348 0 3722
2 TraesCS6B01G357500 chr1B 96.654 2301 74 3 1 2300 49802949 49800651 0 3819
3 TraesCS6B01G357500 chr1B 96.089 2301 89 1 1 2300 683729610 683731910 0 3749
4 TraesCS6B01G357500 chr1B 95.613 2302 97 4 1 2300 338897351 338895052 0 3688
5 TraesCS6B01G357500 chr7B 95.920 2304 88 4 1 2300 47200211 47202512 0 3729
6 TraesCS6B01G357500 chr7B 95.741 2301 97 1 1 2300 698144693 698142393 0 3705
7 TraesCS6B01G357500 chr2A 95.741 2301 97 1 1 2300 563261173 563258873 0 3705
8 TraesCS6B01G357500 chr3B 95.611 2301 100 1 1 2300 92266388 92264088 0 3688
9 TraesCS6B01G357500 chr3B 95.569 2302 100 2 1 2300 5082608 5084909 0 3685


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 TraesCS6B01G357500 chr6B 625651165 625653464 2299 True 4248 4248 100.000 1 2300 1 chr6B.!!$R2 2299
1 TraesCS6B01G357500 chr6B 128914348 128916648 2300 True 3722 3722 95.871 1 2300 1 chr6B.!!$R1 2299
2 TraesCS6B01G357500 chr1B 49800651 49802949 2298 True 3819 3819 96.654 1 2300 1 chr1B.!!$R1 2299
3 TraesCS6B01G357500 chr1B 683729610 683731910 2300 False 3749 3749 96.089 1 2300 1 chr1B.!!$F1 2299
4 TraesCS6B01G357500 chr1B 338895052 338897351 2299 True 3688 3688 95.613 1 2300 1 chr1B.!!$R2 2299
5 TraesCS6B01G357500 chr7B 47200211 47202512 2301 False 3729 3729 95.920 1 2300 1 chr7B.!!$F1 2299
6 TraesCS6B01G357500 chr7B 698142393 698144693 2300 True 3705 3705 95.741 1 2300 1 chr7B.!!$R1 2299
7 TraesCS6B01G357500 chr2A 563258873 563261173 2300 True 3705 3705 95.741 1 2300 1 chr2A.!!$R1 2299
8 TraesCS6B01G357500 chr3B 92264088 92266388 2300 True 3688 3688 95.611 1 2300 1 chr3B.!!$R1 2299
9 TraesCS6B01G357500 chr3B 5082608 5084909 2301 False 3685 3685 95.569 1 2300 1 chr3B.!!$F1 2299

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
584 585 1.02833 CAGCATTGATGAGTGGGCGT 61.028 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 2134 0.179045 GCACAAGTGGTCTGGTGTCT 60.179 55.0 2.0 0.0 44.91 3.41 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
100 101 4.530553 TGAAGCTAGAAGGACATTGGTGTA 59.469 41.667 0.00 0.0 39.09 2.90
239 240 5.648092 CGAATGAGGAATTTGGAGGTTAGTT 59.352 40.000 0.00 0.0 0.00 2.24
298 299 2.174639 AGATATGCGAAATCACCCCCAA 59.825 45.455 0.00 0.0 0.00 4.12
349 350 7.228108 CCATAGACGTGGAGTAGAAACATAGTA 59.772 40.741 0.00 0.0 42.02 1.82
375 376 4.836825 ACTATGACTCAAATCCACACAGG 58.163 43.478 0.00 0.0 39.47 4.00
397 398 6.833933 CAGGCTATTTTATCTACACCCCTTTT 59.166 38.462 0.00 0.0 0.00 2.27
407 408 2.007636 ACACCCCTTTTACCATCCCAT 58.992 47.619 0.00 0.0 0.00 4.00
584 585 1.028330 CAGCATTGATGAGTGGGCGT 61.028 55.000 0.00 0.0 0.00 5.68
649 650 5.534278 TGAAATGTTCCTGCAAAGTCATACA 59.466 36.000 0.00 0.0 0.00 2.29
752 753 1.478916 TCGATTGATGCGGGTAAGACA 59.521 47.619 0.00 0.0 0.00 3.41
853 854 4.651778 TGAAATCTCCGGTGAAAAGTGAT 58.348 39.130 10.77 0.0 0.00 3.06
874 875 8.976353 AGTGATGTTGTGATTACTTCTAGATCT 58.024 33.333 0.00 0.0 0.00 2.75
1568 1570 2.969821 AGTTTATGGGCAACAGGTCA 57.030 45.000 0.00 0.0 39.74 4.02
1665 1667 3.828451 ACAAATGGAATGAGAAGTGGGTG 59.172 43.478 0.00 0.0 0.00 4.61
1748 1750 2.489329 CAAGGGCAATCGTTGAGTGAAT 59.511 45.455 0.00 0.0 42.11 2.57
1757 1759 6.684555 GCAATCGTTGAGTGAATTGTATCTTC 59.315 38.462 0.00 0.0 28.30 2.87
1761 1763 7.151976 TCGTTGAGTGAATTGTATCTTCTTCA 58.848 34.615 0.00 0.0 0.00 3.02
1845 1847 2.103263 GGGACGAGTTTCTGCCTCATAT 59.897 50.000 0.00 0.0 0.00 1.78
1879 1881 0.252742 ACCGGGGAAGTTGAGGAGAT 60.253 55.000 6.32 0.0 0.00 2.75
1890 1892 3.208692 AGTTGAGGAGATATGGGGAGACT 59.791 47.826 0.00 0.0 0.00 3.24
1941 1943 1.702022 GGGGCGGGGATAAGCTTGTA 61.702 60.000 9.86 0.0 0.00 2.41
1999 2002 2.158726 ACCGACCCAGCAAGAAAAGTAA 60.159 45.455 0.00 0.0 0.00 2.24
2131 2134 1.215382 CGTCTGACCAATCGGCTCA 59.785 57.895 1.55 0.0 34.57 4.26
2212 2215 4.082523 CGATGTGCCCTGACCCGT 62.083 66.667 0.00 0.0 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.189859 TCAAATTCTGGACATCTTAAGGCAT 58.810 36.000 1.85 0.0 0.00 4.40
72 73 3.402628 TGTCCTTCTAGCTTCAACACC 57.597 47.619 0.00 0.0 0.00 4.16
100 101 7.458397 TGAAGGTGTTCTTTATACAAGATGGT 58.542 34.615 0.00 0.0 35.50 3.55
239 240 5.198207 TCTCTCCCGATATATAATGCCGAA 58.802 41.667 0.00 0.0 0.00 4.30
349 350 7.418368 CCTGTGTGGATTTGAGTCATAGTATCT 60.418 40.741 0.00 0.0 38.35 1.98
375 376 7.776500 TGGTAAAAGGGGTGTAGATAAAATAGC 59.224 37.037 0.00 0.0 0.00 2.97
397 398 2.963101 CACGAGGAGTTATGGGATGGTA 59.037 50.000 0.00 0.0 0.00 3.25
407 408 2.298163 GGTGAGTTTCCACGAGGAGTTA 59.702 50.000 0.78 0.0 46.74 2.24
500 501 7.737972 TGTACTACTTTTGAAAGCATTAGCA 57.262 32.000 3.48 0.0 45.49 3.49
584 585 3.010138 AGCTTGGGTATTTAAGTGCCAGA 59.990 43.478 7.38 0.0 0.00 3.86
649 650 8.571345 ACAAAACCTATAAATATGGTAGGGGTT 58.429 33.333 11.10 0.0 39.42 4.11
752 753 0.105453 ATATGTGGAGAGAGCGGGGT 60.105 55.000 0.00 0.0 0.00 4.95
996 997 8.941995 ATAGGACTCTTGCTAGTATCATAACA 57.058 34.615 0.00 0.0 0.00 2.41
1305 1306 5.343307 ACCACCATAATGAAATTGCCTTC 57.657 39.130 0.00 0.0 36.99 3.46
1568 1570 3.603532 ACATGATGAATCACTTCGTGCT 58.396 40.909 0.00 0.0 40.83 4.40
1665 1667 4.981389 GAGGTCTCGATCATTTACATGC 57.019 45.455 0.00 0.0 0.00 4.06
1757 1759 5.177696 GCGGCTTAGGTCAACTAATATGAAG 59.822 44.000 0.00 0.0 40.71 3.02
1761 1763 4.377897 GTGCGGCTTAGGTCAACTAATAT 58.622 43.478 0.00 0.0 40.71 1.28
1821 1823 1.070786 GGCAGAAACTCGTCCCACA 59.929 57.895 0.00 0.0 0.00 4.17
1845 1847 3.145551 GGTCTTCGGCCCGAGCTA 61.146 66.667 5.73 0.0 37.14 3.32
1879 1881 1.833630 CAGCAGTTGAGTCTCCCCATA 59.166 52.381 0.00 0.0 0.00 2.74
1890 1892 4.680237 CCGACCGGCAGCAGTTGA 62.680 66.667 0.00 0.0 0.00 3.18
1941 1943 2.567169 GGGGCAATAAGGTTGCTTCTTT 59.433 45.455 11.92 0.0 44.36 2.52
1951 1953 2.282106 GGGGGTGGGGCAATAAGG 59.718 66.667 0.00 0.0 0.00 2.69
2131 2134 0.179045 GCACAAGTGGTCTGGTGTCT 60.179 55.000 2.00 0.0 44.91 3.41
2212 2215 1.756408 TAAAAGCGGACGTGGGGACA 61.756 55.000 0.00 0.0 38.70 4.02


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

AutoCloner maintained by Alex Coulton.