Multiple sequence alignment - TraesCS2B01G252600

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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 TraesCS2B01G252600 chr2B 100.000 2255 0 0 1 2255 272612216 272614470 0 4165
1 TraesCS2B01G252600 chr6D 97.339 2255 60 0 1 2255 389255237 389252983 0 3832
2 TraesCS2B01G252600 chr6D 97.251 2255 62 0 1 2255 389250442 389248188 0 3821
3 TraesCS2B01G252600 chr3A 97.206 2255 62 1 1 2255 66007064 66009317 0 3814
4 TraesCS2B01G252600 chr5D 97.162 2255 63 1 1 2255 503239094 503236841 0 3808
5 TraesCS2B01G252600 chr5D 97.118 2255 61 2 1 2255 503243340 503241090 0 3801
6 TraesCS2B01G252600 chr3D 97.162 2255 63 1 1 2255 589265455 589267708 0 3808
7 TraesCS2B01G252600 chr7B 97.073 2255 66 0 1 2255 662724472 662722218 0 3799


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 TraesCS2B01G252600 chr2B 272612216 272614470 2254 False 4165.0 4165 100.000 1 2255 1 chr2B.!!$F1 2254
1 TraesCS2B01G252600 chr6D 389248188 389255237 7049 True 3826.5 3832 97.295 1 2255 2 chr6D.!!$R1 2254
2 TraesCS2B01G252600 chr3A 66007064 66009317 2253 False 3814.0 3814 97.206 1 2255 1 chr3A.!!$F1 2254
3 TraesCS2B01G252600 chr5D 503236841 503243340 6499 True 3804.5 3808 97.140 1 2255 2 chr5D.!!$R1 2254
4 TraesCS2B01G252600 chr3D 589265455 589267708 2253 False 3808.0 3808 97.162 1 2255 1 chr3D.!!$F1 2254
5 TraesCS2B01G252600 chr7B 662722218 662724472 2254 True 3799.0 3799 97.073 1 2255 1 chr7B.!!$R1 2254

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
773 774 0.251922 TATATCCCTTCCCCGTCCCG 60.252 60.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 5999 1.32474 TGCATAAGACCCGCGGTAGT 61.325 55.0 26.12 16.35 35.25 2.73 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
47 48 3.485463 ACCGTCATTGTTTCTTCTCCA 57.515 42.857 0.00 0.00 0.00 3.86
65 66 5.424757 TCTCCAAGAAAAGAAGTTGACGAA 58.575 37.500 0.00 0.00 0.00 3.85
144 145 4.664267 TCCCCACTGCTGCCTCCT 62.664 66.667 0.00 0.00 0.00 3.69
173 174 2.567049 GGTCGTGTCTCAGTCCCG 59.433 66.667 0.00 0.00 0.00 5.14
314 315 1.764134 CCTACGGGGTATTAGCAACCA 59.236 52.381 0.00 0.00 38.87 3.67
375 376 1.012486 GTTACTCACCCGTTCGCCAG 61.012 60.000 0.00 0.00 0.00 4.85
439 440 1.220206 CCAGCGTTCATCCTGAGCT 59.780 57.895 0.00 0.00 38.90 4.09
511 512 6.535150 CCTTATTCGTAGACAAAGCAGATTCA 59.465 38.462 0.00 0.00 34.32 2.57
575 576 6.560003 TTCAGATTATTAGCCTGGAGTTCA 57.440 37.500 0.00 0.00 0.00 3.18
583 584 2.056906 GCCTGGAGTTCACCACCAGT 62.057 60.000 15.27 0.00 46.61 4.00
609 610 1.209621 GCCAACCCTACCCTATCACA 58.790 55.000 0.00 0.00 0.00 3.58
632 633 3.523157 TCAATCCCACAAGCCTCTTATCA 59.477 43.478 0.00 0.00 0.00 2.15
637 638 4.228210 TCCCACAAGCCTCTTATCAATTCT 59.772 41.667 0.00 0.00 0.00 2.40
704 705 7.629157 TCACATTGTGTTTAGGGATAATCAGA 58.371 34.615 16.06 0.00 34.79 3.27
727 728 4.651503 ACTCGAACTGATATCTTCCACCAT 59.348 41.667 3.98 0.00 0.00 3.55
773 774 0.251922 TATATCCCTTCCCCGTCCCG 60.252 60.000 0.00 0.00 0.00 5.14
791 792 5.349809 GTCCCGTCGAGAAAGAGAATTAAT 58.650 41.667 0.00 0.00 0.00 1.40
818 819 3.771978 GGCAAAGGGGCGAGAAAA 58.228 55.556 0.00 0.00 33.57 2.29
825 826 0.698818 AGGGGCGAGAAAATCAAGGT 59.301 50.000 0.00 0.00 0.00 3.50
1048 5297 7.558807 TGTTCTATTCGATACTGGTAGGAGAAA 59.441 37.037 0.00 0.00 0.00 2.52
1059 5308 2.301009 GGTAGGAGAAAAACCCGACTCA 59.699 50.000 0.00 0.00 0.00 3.41
1111 5360 4.474651 ACCAAGTCAAGATGATATGGGTCA 59.525 41.667 14.76 0.00 38.50 4.02
1126 5375 0.110486 GGTCACCCCTTCTTCTTGCA 59.890 55.000 0.00 0.00 0.00 4.08
1145 5394 6.267471 TCTTGCACCAAAGATCTTACCATTTT 59.733 34.615 8.75 0.00 31.19 1.82
1176 5425 4.280929 ACTGGGGCTACATTTCTTTTCAAC 59.719 41.667 0.00 0.00 0.00 3.18
1312 5562 8.624776 CCTCCCATTAACTACTTCATTTTCATC 58.375 37.037 0.00 0.00 0.00 2.92
1353 5603 5.983333 AGAAATCCATGTCCTACCAAGAT 57.017 39.130 0.00 0.00 0.00 2.40
1529 5779 3.719871 TGGTACAATCCTCTTCCTGCTA 58.280 45.455 0.00 0.00 31.92 3.49
1814 6065 5.003160 CCTTCAACACAACATAGGTCATCA 58.997 41.667 0.00 0.00 0.00 3.07
1815 6066 5.122869 CCTTCAACACAACATAGGTCATCAG 59.877 44.000 0.00 0.00 0.00 2.90
1844 6095 0.531974 GGACGACTCACCAAAGCACA 60.532 55.000 0.00 0.00 0.00 4.57
1889 6140 4.534500 TCCTATTTGAAGAGTGCCTAACCA 59.466 41.667 0.00 0.00 0.00 3.67
1955 11001 4.560716 CGGGATTTTTCTTGGGAAGTTTCC 60.561 45.833 2.17 2.17 46.82 3.13
2021 11067 4.579869 AGGTTCTCTATTGATGCAAACGT 58.420 39.130 0.00 0.00 0.00 3.99
2029 11075 3.617540 TTGATGCAAACGTTGTACCTG 57.382 42.857 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.937079 ACGGTTCGTCAACTTCTTTTCTT 59.063 39.130 0.00 0.00 33.69 2.52
65 66 1.988406 GAGGTGGAAGGCCTACGGT 60.988 63.158 5.16 0.00 36.29 4.83
144 145 1.822990 GACACGACCCAGAATCCTACA 59.177 52.381 0.00 0.00 0.00 2.74
151 152 0.959553 GACTGAGACACGACCCAGAA 59.040 55.000 0.00 0.00 0.00 3.02
158 159 2.114625 ACCGGGACTGAGACACGA 59.885 61.111 8.36 0.00 36.15 4.35
173 174 0.835941 AGAGGATGATCAGCCACACC 59.164 55.000 30.59 16.30 39.89 4.16
314 315 3.230976 GAGGGGAACAACAACTGGAAAT 58.769 45.455 0.00 0.00 0.00 2.17
439 440 4.439253 TCTCATGGAGAGTTCGATCCTA 57.561 45.455 4.50 0.00 44.98 2.94
549 550 4.410228 ACTCCAGGCTAATAATCTGAAGCA 59.590 41.667 1.24 0.00 36.68 3.91
575 576 2.770232 GGTTGGCTATACTACTGGTGGT 59.230 50.000 0.00 0.00 0.00 4.16
583 584 5.316722 TGATAGGGTAGGGTTGGCTATACTA 59.683 44.000 0.00 0.00 0.00 1.82
609 610 4.166725 TGATAAGAGGCTTGTGGGATTGAT 59.833 41.667 0.00 0.00 0.00 2.57
632 633 1.352156 GCCACGAGCGAACGAGAATT 61.352 55.000 8.50 0.00 37.03 2.17
687 688 6.380274 AGTTCGAGTCTGATTATCCCTAAACA 59.620 38.462 0.00 0.00 0.00 2.83
704 705 4.023980 TGGTGGAAGATATCAGTTCGAGT 58.976 43.478 5.32 0.00 0.00 4.18
742 743 4.282703 GGAAGGGATATAACTCAGCGGTAA 59.717 45.833 0.00 0.00 0.00 2.85
773 774 8.655651 AGGATTCATTAATTCTCTTTCTCGAC 57.344 34.615 0.00 0.00 0.00 4.20
791 792 1.341976 GCCCCTTTGCCTTAGGATTCA 60.342 52.381 0.69 0.00 34.56 2.57
818 819 1.827969 CGGAGGAAGAGTGACCTTGAT 59.172 52.381 0.00 0.00 36.57 2.57
1111 5360 0.555769 TTGGTGCAAGAAGAAGGGGT 59.444 50.000 0.00 0.00 0.00 4.95
1126 5375 6.151144 CCTTCGAAAATGGTAAGATCTTTGGT 59.849 38.462 14.36 0.00 0.00 3.67
1145 5394 0.543410 TGTAGCCCCAGTTCCTTCGA 60.543 55.000 0.00 0.00 0.00 3.71
1176 5425 8.558973 AACAGATAGAAACTCTTGAATGGAAG 57.441 34.615 0.00 0.00 0.00 3.46
1353 5603 9.823647 CAAGAGGATAGCAAGTTCTAAATTCTA 57.176 33.333 0.00 0.00 0.00 2.10
1397 5647 6.672266 TGAATCAGTCTTTCTACAGAGGTT 57.328 37.500 0.00 0.00 0.00 3.50
1529 5779 2.301738 CCGAGGAGAAAGGGGGCTT 61.302 63.158 0.00 0.00 0.00 4.35
1577 5827 1.883926 TCTTCCGTGATGAACTGTCGA 59.116 47.619 0.00 0.00 0.00 4.20
1718 5968 8.560903 AGAATGGGGAAAGTATACAGAAAAGAT 58.439 33.333 5.50 0.00 0.00 2.40
1748 5999 1.324740 TGCATAAGACCCGCGGTAGT 61.325 55.000 26.12 16.35 35.25 2.73
1814 6065 2.420722 GTGAGTCGTCCGAGATCTTTCT 59.579 50.000 0.00 0.00 33.88 2.52
1815 6066 2.478200 GGTGAGTCGTCCGAGATCTTTC 60.478 54.545 0.00 0.00 0.00 2.62
1844 6095 6.498303 AGGAATCCATTTTCTAACTGGCTTTT 59.502 34.615 0.61 0.00 0.00 2.27
1889 6140 5.133221 GGGTTAATGTGAGCTTATCCATGT 58.867 41.667 0.00 0.00 0.00 3.21
2021 11067 4.673132 TCTATCCCTATCCTCCAGGTACAA 59.327 45.833 0.00 0.00 36.34 2.41
2029 11075 4.325816 CCTCTTCCTCTATCCCTATCCTCC 60.326 54.167 0.00 0.00 0.00 4.30
2092 11138 7.155328 TGGGCTCTTCTATCTTCGATTTATTC 58.845 38.462 0.00 0.00 0.00 1.75
2098 11144 3.838565 TCTGGGCTCTTCTATCTTCGAT 58.161 45.455 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.