Multiple sequence alignment - TraesCS1B01G430300

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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 TraesCS1B01G430300 chr1B 100.000 2449 0 0 1 2449 654687360 654684912 0 4523
1 TraesCS1B01G430300 chr5B 97.553 2452 57 2 1 2449 494655852 494658303 0 4193
2 TraesCS1B01G430300 chr5B 97.269 2453 63 3 1 2449 41406868 41404416 0 4156
3 TraesCS1B01G430300 chr5B 97.188 2454 63 5 1 2449 660354748 660352296 0 4145
4 TraesCS1B01G430300 chr5B 97.146 2453 64 5 1 2449 494664111 494661661 0 4137
5 TraesCS1B01G430300 chr2B 97.391 2453 60 3 1 2449 50469407 50471859 0 4172
6 TraesCS1B01G430300 chr2B 97.268 2452 63 4 1 2449 66032270 66029820 0 4154
7 TraesCS1B01G430300 chr6B 96.983 2453 70 3 1 2449 663151559 663149107 0 4117


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 TraesCS1B01G430300 chr1B 654684912 654687360 2448 True 4523 4523 100.000 1 2449 1 chr1B.!!$R1 2448
1 TraesCS1B01G430300 chr5B 494655852 494658303 2451 False 4193 4193 97.553 1 2449 1 chr5B.!!$F1 2448
2 TraesCS1B01G430300 chr5B 41404416 41406868 2452 True 4156 4156 97.269 1 2449 1 chr5B.!!$R1 2448
3 TraesCS1B01G430300 chr5B 660352296 660354748 2452 True 4145 4145 97.188 1 2449 1 chr5B.!!$R3 2448
4 TraesCS1B01G430300 chr5B 494661661 494664111 2450 True 4137 4137 97.146 1 2449 1 chr5B.!!$R2 2448
5 TraesCS1B01G430300 chr2B 50469407 50471859 2452 False 4172 4172 97.391 1 2449 1 chr2B.!!$F1 2448
6 TraesCS1B01G430300 chr2B 66029820 66032270 2450 True 4154 4154 97.268 1 2449 1 chr2B.!!$R1 2448
7 TraesCS1B01G430300 chr6B 663149107 663151559 2452 True 4117 4117 96.983 1 2449 1 chr6B.!!$R1 2448

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
262 264 0.967887 CCACTTCTCCTCCTCGCTCA 60.968 60.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2106 0.96738 AATGCAGCACTTGGTAGCCC 60.967 55.0 0.0 0.0 0.0 5.19 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
79 80 2.432628 CACCGAACCGACTCAGCC 60.433 66.667 0.00 0.0 0.00 4.85
109 110 2.758089 GCGCGGTCGTCTTCTCCTA 61.758 63.158 8.83 0.0 38.14 2.94
123 124 3.546543 CCTATTCCCCGAGCCGCA 61.547 66.667 0.00 0.0 0.00 5.69
262 264 0.967887 CCACTTCTCCTCCTCGCTCA 60.968 60.000 0.00 0.0 0.00 4.26
379 381 2.501723 TCGAGGAGCTAAGAATGCCTTT 59.498 45.455 0.00 0.0 36.34 3.11
566 568 1.988846 CTTTCCCTTGTCTCCCCTCTT 59.011 52.381 0.00 0.0 0.00 2.85
659 662 2.367202 GCTCCTCGGATTGACCCCA 61.367 63.158 0.00 0.0 34.64 4.96
719 722 2.048222 CGCTCTTCTTCCGCACCA 60.048 61.111 0.00 0.0 0.00 4.17
722 725 1.743252 CTCTTCTTCCGCACCAGCC 60.743 63.158 0.00 0.0 37.52 4.85
990 995 1.654954 CTGCTCTACCGCTGGTACGT 61.655 60.000 0.00 0.0 37.09 3.57
1174 1179 4.664688 AGGAGAGGTCACAATTGGAAAT 57.335 40.909 10.83 0.0 0.00 2.17
1306 1312 9.411801 GGAAAGTTAGGATTTTTGAACTGATTC 57.588 33.333 0.00 0.0 32.57 2.52
2039 2047 2.045885 ACTTGGAGGAGATTGAGGGGTA 59.954 50.000 0.00 0.0 0.00 3.69
2096 2106 6.308371 ACCGGACAAAAATAAACTGTACTG 57.692 37.500 9.46 0.0 0.00 2.74
2146 2156 2.350772 GCAGCGCAAATAACTTGACTGT 60.351 45.455 11.47 0.0 40.37 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.932261 GGCGAATCCCCTTTTACATCT 58.068 47.619 0.00 0.00 0.00 2.90
72 73 2.997897 GGGACTGGACGGCTGAGT 60.998 66.667 0.00 0.00 0.00 3.41
109 110 4.609018 CGATGCGGCTCGGGGAAT 62.609 66.667 12.08 0.00 35.03 3.01
123 124 1.448922 GAGCCCGTCTCAGTAGCGAT 61.449 60.000 0.00 0.00 41.51 4.58
368 370 3.412386 ACGAAGTAGCAAAGGCATTCTT 58.588 40.909 0.00 0.00 41.94 2.52
369 371 3.059352 ACGAAGTAGCAAAGGCATTCT 57.941 42.857 0.00 0.00 41.94 2.40
566 568 4.624024 CGAAATACCTAACGAGAGCAAACA 59.376 41.667 0.00 0.00 0.00 2.83
610 612 3.142162 CTGCAATGGCCATGGCGA 61.142 61.111 34.61 27.33 40.64 5.54
939 944 0.602905 GGAAGCAACACGCAGTAGGT 60.603 55.000 0.00 0.00 41.61 3.08
1145 1150 1.148027 TGTGACCTCTCCTTCCACTCT 59.852 52.381 0.00 0.00 0.00 3.24
1306 1312 5.988287 ACAATAAAACCCCATTTGCATAGG 58.012 37.500 0.00 0.00 0.00 2.57
1345 1351 1.001181 GTCACAAACGGGCAGGTACTA 59.999 52.381 0.00 0.00 36.02 1.82
1965 1973 8.980596 ACTTCCTTAAATTATGCCAATCAATCA 58.019 29.630 0.00 0.00 0.00 2.57
2009 2017 6.238648 TCAATCTCCTCCAAGTTCCTTAAAC 58.761 40.000 0.00 0.00 38.21 2.01
2031 2039 2.605535 CTAGCCAGCCCTACCCCTCA 62.606 65.000 0.00 0.00 0.00 3.86
2096 2106 0.967380 AATGCAGCACTTGGTAGCCC 60.967 55.000 0.00 0.00 0.00 5.19
2111 2121 1.531883 GCGCTGCAGTTTACCTAATGC 60.532 52.381 16.64 0.00 39.14 3.56
2129 2139 8.500837 TGAAAATTACAGTCAAGTTATTTGCG 57.499 30.769 0.00 0.00 31.71 4.85


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

AutoCloner maintained by Alex Coulton.