Multiple sequence alignment - TraesCS6B01G105500

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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 TraesCS6B01G105500 chr6B 100.000 3433 0 0 1 3433 85662842 85666274 0 6340
1 TraesCS6B01G105500 chr7B 97.063 3439 93 6 1 3433 300041533 300044969 0 5784
2 TraesCS6B01G105500 chr2B 96.830 3438 98 7 1 3433 317055746 317052315 0 5734
3 TraesCS6B01G105500 chr3B 96.423 3439 116 7 1 3433 151826086 151822649 0 5662
4 TraesCS6B01G105500 chr3B 96.193 3441 113 17 1 3433 545972554 545969124 0 5613
5 TraesCS6B01G105500 chr2A 95.499 3444 130 19 1 3433 384174888 384171459 0 5478
6 TraesCS6B01G105500 chr2A 95.238 3444 142 18 1 3433 685104320 685100888 0 5432
7 TraesCS6B01G105500 chr3A 95.411 3443 136 18 1 3433 662010406 662006976 0 5463
8 TraesCS6B01G105500 chr5A 95.562 3425 127 19 19 3433 465654136 465657545 0 5459
9 TraesCS6B01G105500 chr5A 95.325 3444 137 17 1 3433 141902098 141905528 0 5446


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 TraesCS6B01G105500 chr6B 85662842 85666274 3432 False 6340 6340 100.000 1 3433 1 chr6B.!!$F1 3432
1 TraesCS6B01G105500 chr7B 300041533 300044969 3436 False 5784 5784 97.063 1 3433 1 chr7B.!!$F1 3432
2 TraesCS6B01G105500 chr2B 317052315 317055746 3431 True 5734 5734 96.830 1 3433 1 chr2B.!!$R1 3432
3 TraesCS6B01G105500 chr3B 151822649 151826086 3437 True 5662 5662 96.423 1 3433 1 chr3B.!!$R1 3432
4 TraesCS6B01G105500 chr3B 545969124 545972554 3430 True 5613 5613 96.193 1 3433 1 chr3B.!!$R2 3432
5 TraesCS6B01G105500 chr2A 384171459 384174888 3429 True 5478 5478 95.499 1 3433 1 chr2A.!!$R1 3432
6 TraesCS6B01G105500 chr2A 685100888 685104320 3432 True 5432 5432 95.238 1 3433 1 chr2A.!!$R2 3432
7 TraesCS6B01G105500 chr3A 662006976 662010406 3430 True 5463 5463 95.411 1 3433 1 chr3A.!!$R1 3432
8 TraesCS6B01G105500 chr5A 465654136 465657545 3409 False 5459 5459 95.562 19 3433 1 chr5A.!!$F2 3414
9 TraesCS6B01G105500 chr5A 141902098 141905528 3430 False 5446 5446 95.325 1 3433 1 chr5A.!!$F1 3432

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
986 1003 1.774254 TCTCTCCAAAGCCCAAAGTCA 59.226 47.619 0.0 0.0 0.0 3.41 F
1230 1247 0.743345 GCGGCAGGTTTCGTAGGATT 60.743 55.000 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2296 2319 1.264557 CTACTCCTGCGTACTCGATGG 59.735 57.143 0.0 0.0 39.71 3.51 R
3183 3213 0.804544 GCGCTTATACACGGTGCTCA 60.805 55.000 8.3 0.0 34.21 4.26 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
616 631 6.208988 AGTACAGCTTGACTATTCGAATCA 57.791 37.500 15.25 4.73 0.00 2.57
623 638 4.406648 TGACTATTCGAATCAGTGCCAT 57.593 40.909 15.25 0.00 0.00 4.40
743 758 7.292713 ACCATTTAAATTGGACGGTTAGTTT 57.707 32.000 18.02 0.00 0.00 2.66
986 1003 1.774254 TCTCTCCAAAGCCCAAAGTCA 59.226 47.619 0.00 0.00 0.00 3.41
1168 1185 1.891919 GTCTGCACCAGCGAACCAA 60.892 57.895 0.00 0.00 46.23 3.67
1180 1197 1.440938 CGAACCAAACAAGGCCGACA 61.441 55.000 0.00 0.00 32.10 4.35
1230 1247 0.743345 GCGGCAGGTTTCGTAGGATT 60.743 55.000 0.00 0.00 0.00 3.01
1367 1384 4.922206 TGGTGAGCAATCCTACTCATTTT 58.078 39.130 0.00 0.00 44.29 1.82
2101 2124 4.034510 CGACAAAGAGAAGCTGAAGTTGTT 59.965 41.667 0.00 0.00 0.00 2.83
2296 2319 2.743928 CGAGCTGCCAGACAACCC 60.744 66.667 0.00 0.00 0.00 4.11
2471 2494 2.152016 GCCTGCCTTCGTTTTACTTCT 58.848 47.619 0.00 0.00 0.00 2.85
2494 2517 4.522405 TGCTTGTGCTTGCCTTTTATCTTA 59.478 37.500 0.00 0.00 40.48 2.10
2846 2872 4.867047 GCGCTACTATGAATGCACTATCAT 59.133 41.667 13.92 13.92 39.50 2.45
3183 3213 2.524306 CCACAGGTCAAGAGAGAGAGT 58.476 52.381 0.00 0.00 0.00 3.24
3228 3258 2.821991 AAGTGTTCAGAGGAGTTCGG 57.178 50.000 0.00 0.00 0.00 4.30
3236 3266 0.832135 AGAGGAGTTCGGCTGGTGAA 60.832 55.000 0.00 0.00 0.00 3.18
3262 3292 2.280628 GCTGCGCTTATAAACAGGTCT 58.719 47.619 9.73 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
502 517 4.221924 TCATACTCGGACTGGTGATTGAAA 59.778 41.667 0.00 0.0 0.00 2.69
616 631 7.013655 GTGATGATGGAATTTTACTATGGCACT 59.986 37.037 0.00 0.0 0.00 4.40
623 638 5.820423 CGGTGGTGATGATGGAATTTTACTA 59.180 40.000 0.00 0.0 0.00 1.82
673 688 4.202245 TGTCAAGCTGTACTTATGACCC 57.798 45.455 9.37 0.0 36.04 4.46
812 829 1.937899 GTGTGTGTAGTGGGTGTTGTC 59.062 52.381 0.00 0.0 0.00 3.18
986 1003 3.411517 CCATGGCCTTCCTCCGGT 61.412 66.667 3.32 0.0 0.00 5.28
1168 1185 0.110486 ATCACCTTGTCGGCCTTGTT 59.890 50.000 0.00 0.0 35.61 2.83
1180 1197 1.202330 CAGAGCCTGGAGATCACCTT 58.798 55.000 10.73 0.0 0.00 3.50
1230 1247 4.840005 TGCACACCAACGCCGACA 62.840 61.111 0.00 0.0 0.00 4.35
1300 1317 0.603569 ACCAAGCAGAGTTCGTCGAT 59.396 50.000 0.00 0.0 0.00 3.59
2101 2124 1.343580 TGGGGTTGATCTCCATACCGA 60.344 52.381 9.12 0.0 42.62 4.69
2296 2319 1.264557 CTACTCCTGCGTACTCGATGG 59.735 57.143 0.00 0.0 39.71 3.51
2356 2379 1.737838 TTCCGAACCATCTGTGATGC 58.262 50.000 2.30 0.0 0.00 3.91
2440 2463 2.297315 CGAAGGCAGGCTCTGATGTATA 59.703 50.000 0.00 0.0 32.44 1.47
2471 2494 2.892852 AGATAAAAGGCAAGCACAAGCA 59.107 40.909 0.00 0.0 45.49 3.91
2494 2517 9.822185 AAGAGCAAACTTCTAATTTGAAACAAT 57.178 25.926 3.95 0.0 39.01 2.71
2846 2872 3.994204 TGCGTGTAGACTGAGTTGTAA 57.006 42.857 0.00 0.0 0.00 2.41
2962 2991 5.580691 TCTTGTCAGTTTTGTGTGAGTGTAG 59.419 40.000 0.00 0.0 0.00 2.74
3004 3033 4.202641 TGACTCCTCCAGTAACTTGGACTA 60.203 45.833 0.00 0.0 42.24 2.59
3122 3152 1.134907 CGTTGTGCGGATTACTAGGGT 60.135 52.381 0.00 0.0 36.85 4.34
3183 3213 0.804544 GCGCTTATACACGGTGCTCA 60.805 55.000 8.30 0.0 34.21 4.26
3262 3292 2.279073 CTAGTCGAGGGGGCTCCA 59.721 66.667 5.99 0.0 38.24 3.86


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

AutoCloner maintained by Alex Coulton.