Multiple sequence alignment - TraesCS2A01G330700

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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 TraesCS2A01G330700 chr2A 100.000 4405 0 0 1 4405 563256642 563261046 0 8135
1 TraesCS2A01G330700 chr1B 99.001 4406 43 1 1 4405 683734142 683729737 0 7891
2 TraesCS2A01G330700 chr1B 98.231 4409 72 3 1 4405 583536771 583532365 0 7705
3 TraesCS2A01G330700 chr1B 97.914 4410 85 5 1 4405 338892817 338897224 0 7627
4 TraesCS2A01G330700 chr7B 98.820 4407 50 1 1 4405 698140160 698144566 0 7849
5 TraesCS2A01G330700 chrUn 98.571 4408 59 3 1 4405 40085859 40090265 0 7788
6 TraesCS2A01G330700 chr5B 98.570 4406 61 2 1 4405 713082218 713077814 0 7786
7 TraesCS2A01G330700 chr5B 98.162 4407 75 6 1 4405 713126499 713130901 0 7685
8 TraesCS2A01G330700 chr3B 98.435 4409 62 4 1 4405 92261856 92266261 0 7753
9 TraesCS2A01G330700 chr3B 98.367 4408 67 3 1 4405 92142924 92147329 0 7736


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 TraesCS2A01G330700 chr2A 563256642 563261046 4404 False 8135 8135 100.000 1 4405 1 chr2A.!!$F1 4404
1 TraesCS2A01G330700 chr1B 683729737 683734142 4405 True 7891 7891 99.001 1 4405 1 chr1B.!!$R2 4404
2 TraesCS2A01G330700 chr1B 583532365 583536771 4406 True 7705 7705 98.231 1 4405 1 chr1B.!!$R1 4404
3 TraesCS2A01G330700 chr1B 338892817 338897224 4407 False 7627 7627 97.914 1 4405 1 chr1B.!!$F1 4404
4 TraesCS2A01G330700 chr7B 698140160 698144566 4406 False 7849 7849 98.820 1 4405 1 chr7B.!!$F1 4404
5 TraesCS2A01G330700 chrUn 40085859 40090265 4406 False 7788 7788 98.571 1 4405 1 chrUn.!!$F1 4404
6 TraesCS2A01G330700 chr5B 713077814 713082218 4404 True 7786 7786 98.570 1 4405 1 chr5B.!!$R1 4404
7 TraesCS2A01G330700 chr5B 713126499 713130901 4402 False 7685 7685 98.162 1 4405 1 chr5B.!!$F1 4404
8 TraesCS2A01G330700 chr3B 92261856 92266261 4405 False 7753 7753 98.435 1 4405 1 chr3B.!!$F2 4404
9 TraesCS2A01G330700 chr3B 92142924 92147329 4405 False 7736 7736 98.367 1 4405 1 chr3B.!!$F1 4404

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
884 887 1.920325 CCCCTGCTCCTGGTCTTCA 60.920 63.158 0.0 0.0 0.0 3.02 F
1863 1873 1.227823 TATTCAATCCCGCCGCTGG 60.228 57.895 0.0 0.0 0.0 4.85 F
2396 2407 1.758592 GGGCACAAGTGGTCTGGTA 59.241 57.895 2.0 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2246 0.469917 CATTCTATGCTGACCCGGGT 59.530 55.000 30.81 30.81 0.00 5.28 R
2781 2793 1.464997 GGGCAATCGTTGAGTGAACTC 59.535 52.381 3.41 3.41 43.15 3.01 R
3949 3964 0.700564 ACCAGCATTGATGAGTGGGT 59.299 50.000 2.89 0.00 37.60 4.51 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
136 137 4.655762 TCATCGTCCAATCTTCTCGATT 57.344 40.909 0.00 0.00 43.03 3.34
282 283 6.348950 CCTTTTGAATGTAGCGGATAACAACA 60.349 38.462 0.00 0.00 0.00 3.33
415 416 3.703556 TGCCTCTAGAAAGATCAGACAGG 59.296 47.826 0.00 0.00 0.00 4.00
529 530 6.611236 TCAAGAAGGAAATCCAAAAGGAACTT 59.389 34.615 1.67 0.00 46.07 2.66
884 887 1.920325 CCCCTGCTCCTGGTCTTCA 60.920 63.158 0.00 0.00 0.00 3.02
1151 1154 9.417561 TGGTACTATAATTCCTATTCCTATCCG 57.582 37.037 0.00 0.00 0.00 4.18
1281 1285 5.045724 AGACAAAATGGAGAGAAGCTCATCT 60.046 40.000 0.43 0.43 45.81 2.90
1395 1399 6.510317 GCGGTCTGCTCTATTTACAATTCTTC 60.510 42.308 0.00 0.00 41.73 2.87
1603 1613 2.841988 TGGTGCTTGTTTGGGGGC 60.842 61.111 0.00 0.00 0.00 5.80
1647 1657 1.810030 GCTCTCGCCTTACCAACGG 60.810 63.158 0.00 0.00 0.00 4.44
1863 1873 1.227823 TATTCAATCCCGCCGCTGG 60.228 57.895 0.00 0.00 0.00 4.85
2111 2121 2.520465 TACGTCCGTACCGCTCCTCA 62.520 60.000 0.00 0.00 0.00 3.86
2236 2246 2.671619 CCAAAAAGCGAGCCCCGA 60.672 61.111 0.00 0.00 41.76 5.14
2396 2407 1.758592 GGGCACAAGTGGTCTGGTA 59.241 57.895 2.00 0.00 0.00 3.25
2719 2731 1.855213 CTCGTCCCACGTACGGTTCA 61.855 60.000 21.06 0.00 43.14 3.18
2998 3011 5.242393 CCATAAACTTTCCTGCCTCATATGG 59.758 44.000 2.13 0.00 33.52 2.74
3688 3703 6.537301 AGAAGTAATCACAACGTCACTTTTCA 59.463 34.615 0.00 0.00 0.00 2.69
3707 3722 2.158957 TCACCGGAGATTTCATGGTAGC 60.159 50.000 9.46 0.00 33.38 3.58
3949 3964 1.250154 GGCTATTGTTGTGCCAGGCA 61.250 55.000 11.22 11.22 45.46 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 9.685276 AAAGGAGTATTGATGTCAATATGTTCA 57.315 29.630 16.08 0.00 46.63 3.18
282 283 2.398588 TCAATTCGATAGCCCCACTCT 58.601 47.619 0.00 0.00 0.00 3.24
415 416 5.451662 CGTACAATTACAGCTCGTCTTACTC 59.548 44.000 0.00 0.00 0.00 2.59
529 530 0.237235 GCGATCGCACCAAAAACTCA 59.763 50.000 33.89 0.00 41.49 3.41
884 887 4.839121 TGCCGACCATTAATGACTAGTTT 58.161 39.130 17.23 0.00 0.00 2.66
1395 1399 4.437121 CGTGGTAAAGAGAAGAGAGTACGG 60.437 50.000 0.00 0.00 0.00 4.02
1441 1445 1.218316 CTTTACTTCGGAGCGCCCT 59.782 57.895 2.29 0.00 0.00 5.19
1603 1613 2.620112 CCGCTTTCTGGTGGCACAG 61.620 63.158 20.82 14.45 41.80 3.66
1647 1657 4.479993 AGCCATCAGCAGTCGGCC 62.480 66.667 7.68 0.00 46.08 6.13
1863 1873 0.540923 AAGGAGTCAGCTGAGCATCC 59.459 55.000 25.17 25.17 0.00 3.51
1873 1883 6.381420 TCTTCCTATCAAGGTTAAGGAGTCAG 59.619 42.308 0.00 0.00 44.09 3.51
2111 2121 1.270907 GGATGCGGGATCTACTCCAT 58.729 55.000 9.42 0.00 46.98 3.41
2201 2211 4.324991 GAAGCCCGTTCCCACCGT 62.325 66.667 0.00 0.00 0.00 4.83
2236 2246 0.469917 CATTCTATGCTGACCCGGGT 59.530 55.000 30.81 30.81 0.00 5.28
2265 2276 1.884497 CGGCCAACACAACATTAGGGA 60.884 52.381 2.24 0.00 0.00 4.20
2396 2407 1.043116 TCTGACCAATCGGCTCGGAT 61.043 55.000 0.00 0.00 34.57 4.18
2781 2793 1.464997 GGGCAATCGTTGAGTGAACTC 59.535 52.381 3.41 3.41 43.15 3.01
2998 3011 6.870439 CAGAAAATCTTCCAGTTTTCCATTCC 59.130 38.462 6.89 0.00 42.45 3.01
3688 3703 2.119495 AGCTACCATGAAATCTCCGGT 58.881 47.619 0.00 0.00 32.55 5.28
3949 3964 0.700564 ACCAGCATTGATGAGTGGGT 59.299 50.000 2.89 0.00 37.60 4.51


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

AutoCloner maintained by Alex Coulton.