Multiple sequence alignment - TraesCS4A01G024800

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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 TraesCS4A01G024800 chr4A 100.000 2255 0 0 1 2255 17099601 17097347 0 4165
1 TraesCS4A01G024800 chr6D 97.473 2256 56 1 1 2255 389255237 389252982 0 3849
2 TraesCS4A01G024800 chr6D 97.385 2256 58 1 1 2255 389250442 389248187 0 3838
3 TraesCS4A01G024800 chr5D 97.385 2256 57 2 1 2255 503239094 503236840 0 3838
4 TraesCS4A01G024800 chr5D 97.296 2256 57 2 1 2255 503229313 503227061 0 3825
5 TraesCS4A01G024800 chr5D 97.296 2256 56 3 1 2255 503243340 503241089 0 3823
6 TraesCS4A01G024800 chr3A 97.340 2256 58 2 1 2255 66007064 66009318 0 3832
7 TraesCS4A01G024800 chr3A 97.074 2256 65 1 1 2255 672899453 672901708 0 3799
8 TraesCS4A01G024800 chr3D 97.207 2256 61 2 1 2255 589265455 589267709 0 3816
9 TraesCS4A01G024800 chr7B 97.119 2256 64 1 1 2255 662724472 662722217 0 3805


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 TraesCS4A01G024800 chr4A 17097347 17099601 2254 True 4165.0 4165 100.0000 1 2255 1 chr4A.!!$R1 2254
1 TraesCS4A01G024800 chr6D 389248187 389255237 7050 True 3843.5 3849 97.4290 1 2255 2 chr6D.!!$R1 2254
2 TraesCS4A01G024800 chr5D 503236840 503243340 6500 True 3830.5 3838 97.3405 1 2255 2 chr5D.!!$R2 2254
3 TraesCS4A01G024800 chr5D 503227061 503229313 2252 True 3825.0 3825 97.2960 1 2255 1 chr5D.!!$R1 2254
4 TraesCS4A01G024800 chr3A 66007064 66009318 2254 False 3832.0 3832 97.3400 1 2255 1 chr3A.!!$F1 2254
5 TraesCS4A01G024800 chr3A 672899453 672901708 2255 False 3799.0 3799 97.0740 1 2255 1 chr3A.!!$F2 2254
6 TraesCS4A01G024800 chr3D 589265455 589267709 2254 False 3816.0 3816 97.2070 1 2255 1 chr3D.!!$F1 2254
7 TraesCS4A01G024800 chr7B 662722217 662724472 2255 True 3805.0 3805 97.1190 1 2255 1 chr7B.!!$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
775 5028 0.029474 TATCCCTTCCCCGTCCCATT 60.029 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 5997 0.538118 AAGACCCGCGGTAGCAATAA 59.462 50.0 26.12 0.0 45.49 1.4 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
29 30 4.322349 GCCGATGCTTATTCCTCAGATACT 60.322 45.833 0.00 0.00 33.53 2.12
45 46 7.605691 CCTCAGATACTGTCATTGTTTCTTCTT 59.394 37.037 0.00 0.00 32.61 2.52
48 49 7.116948 CAGATACTGTCATTGTTTCTTCTTCGT 59.883 37.037 0.00 0.00 0.00 3.85
131 132 0.901124 CCCATTGCGGAAAATTCCCA 59.099 50.000 6.61 3.42 44.67 4.37
166 167 0.472734 AGGAGTCTGGGCTGTGTCTT 60.473 55.000 0.00 0.00 0.00 3.01
192 193 0.835941 AGTGTGGCTGATCATCCTCC 59.164 55.000 16.28 7.80 0.00 4.30
288 289 1.135286 GGCGGATTTCTCCTTTTGCTG 60.135 52.381 0.00 0.00 39.65 4.41
377 381 0.608856 TACTCACCCGTTCGCCACTA 60.609 55.000 0.00 0.00 0.00 2.74
408 412 0.250124 TCCCGTTCGACTTGCATGTT 60.250 50.000 6.70 0.00 0.00 2.71
435 439 1.227147 GCCGCCAGCGTTCATACTA 60.227 57.895 11.55 0.00 37.81 1.82
642 646 4.821532 AGCCTCTTATCCATTCCCATTT 57.178 40.909 0.00 0.00 0.00 2.32
643 647 5.148225 AGCCTCTTATCCATTCCCATTTT 57.852 39.130 0.00 0.00 0.00 1.82
775 5028 0.029474 TATCCCTTCCCCGTCCCATT 60.029 55.000 0.00 0.00 0.00 3.16
778 5031 1.688811 CCTTCCCCGTCCCATTGAA 59.311 57.895 0.00 0.00 0.00 2.69
811 5064 1.064685 CGAATCCTAAGGCAAAGGGGT 60.065 52.381 5.43 0.00 34.66 4.95
837 5090 3.252554 ACTCAAGGTCACTCTTCCTCT 57.747 47.619 0.00 0.00 33.09 3.69
932 5185 5.531122 TCGAAAGTAGGATTGACTATGGG 57.469 43.478 0.00 0.00 0.00 4.00
965 5218 6.993786 TCGCACATGGTTTCATAAAATCTA 57.006 33.333 0.00 0.00 31.33 1.98
968 5221 9.283768 TCGCACATGGTTTCATAAAATCTATAT 57.716 29.630 0.00 0.00 31.33 0.86
1038 5291 7.712797 TGTTCAGCATGTTCTATTCGATACTA 58.287 34.615 0.00 0.00 37.40 1.82
1111 5364 4.474651 ACCAAGTCAAGATGATATGGGTCA 59.525 41.667 14.76 0.00 38.50 4.02
1146 5399 3.378427 GCGCCAAAGATCTTACCATTTCT 59.622 43.478 8.75 0.00 0.00 2.52
1279 5532 9.533831 AGGAACACATACAAGAAAAAGGATAAT 57.466 29.630 0.00 0.00 0.00 1.28
1424 5678 7.038729 ACCTCTGTAGAAAGACTGATTCATTCA 60.039 37.037 6.76 0.00 34.86 2.57
1444 5698 4.420206 TCAGATCGATATGAGGACCCAAT 58.580 43.478 18.40 0.00 0.00 3.16
1448 5702 3.313791 TCGATATGAGGACCCAATTCCA 58.686 45.455 0.00 0.00 38.25 3.53
1494 5748 2.871096 ATTTGAAGCGGGTTGACCTA 57.129 45.000 0.00 0.00 36.97 3.08
1546 5800 0.911525 CTGAGCCCCCTTTCTCCTCA 60.912 60.000 0.00 0.00 0.00 3.86
1553 5807 0.247736 CCCTTTCTCCTCAGTCCACG 59.752 60.000 0.00 0.00 0.00 4.94
1554 5808 1.257743 CCTTTCTCCTCAGTCCACGA 58.742 55.000 0.00 0.00 0.00 4.35
1591 5845 0.324614 TGGTGCCGACAGTTCATCAT 59.675 50.000 0.00 0.00 0.00 2.45
1613 5867 3.389329 TGGAAGAAAGAACTCACAGAGCT 59.611 43.478 0.00 0.00 32.04 4.09
1619 5873 3.107402 AGAACTCACAGAGCTGGGATA 57.893 47.619 2.45 0.00 42.88 2.59
1742 5997 6.536447 TCTTTTCTGTATACTTTCCCCGTTT 58.464 36.000 4.17 0.00 0.00 3.60
2020 11070 4.579869 AGGTTCTCTATTGATGCAAACGT 58.420 39.130 0.00 0.00 0.00 3.99
2115 11165 6.969993 AATAAGTCGAAGATAGAAGAGCCT 57.030 37.500 0.00 0.00 40.67 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.429791 TTTCACGAAGAAGAAACAATGACA 57.570 33.333 0.00 0.00 37.57 3.58
45 46 2.861935 GGTCGTCAACTTCTTTTCACGA 59.138 45.455 0.00 0.00 34.08 4.35
48 49 3.269538 TGGGTCGTCAACTTCTTTTCA 57.730 42.857 0.00 0.00 0.00 2.69
131 132 2.660064 CCTACGGGAGGCAGCAGTT 61.660 63.158 0.00 0.00 38.96 3.16
159 160 1.691976 CCACACTGGGACTAAGACACA 59.308 52.381 0.00 0.00 32.67 3.72
192 193 1.000283 GATGATCAGTAGCTGGTCCGG 60.000 57.143 0.09 0.00 40.58 5.14
377 381 1.808891 CGAACGGGAAGTGGTGTTTCT 60.809 52.381 0.00 0.00 0.00 2.52
408 412 2.884367 GCTGGCGGCATGCTTAAA 59.116 55.556 18.92 0.49 45.43 1.52
432 436 2.691011 GAGAGTTCGATCCTGGCTTAGT 59.309 50.000 0.00 0.00 0.00 2.24
435 439 0.827368 GGAGAGTTCGATCCTGGCTT 59.173 55.000 0.00 0.00 32.51 4.35
493 497 6.204688 ACAATTTCGAATCTGCTTTGTCTACA 59.795 34.615 0.00 0.00 0.00 2.74
642 646 0.178926 TTACTCCCCCACCACGAGAA 60.179 55.000 0.00 0.00 0.00 2.87
643 647 0.613853 CTTACTCCCCCACCACGAGA 60.614 60.000 0.00 0.00 0.00 4.04
778 5031 7.610305 TGCCTTAGGATTCGTTAATTCTCTTTT 59.390 33.333 0.69 0.00 32.81 2.27
811 5064 4.202264 GGAAGAGTGACCTTGAGTTTCTCA 60.202 45.833 0.00 0.00 38.87 3.27
837 5090 0.398696 TAGTGCGGAAAGAAAGCCCA 59.601 50.000 0.00 0.00 0.00 5.36
993 5246 7.000472 TGAACAAGATCTTCTTCATGGAAACT 59.000 34.615 18.79 0.00 33.78 2.66
1038 5291 2.725637 GAGTCGGGTTCTTCTCCTACT 58.274 52.381 0.00 0.00 0.00 2.57
1111 5364 2.034221 GGCGCAAGAAGAAGGGGT 59.966 61.111 10.83 0.00 43.02 4.95
1146 5399 1.668826 ATGTAGCCCCAGTTCCTTCA 58.331 50.000 0.00 0.00 0.00 3.02
1199 5452 2.558359 CTCAAGAAAAGGGCGTGGAAAT 59.442 45.455 0.00 0.00 0.00 2.17
1242 5495 9.256228 TCTTGTATGTGTTCCTAAGAGAAGTAT 57.744 33.333 0.00 0.00 0.00 2.12
1424 5678 4.223923 GGAATTGGGTCCTCATATCGATCT 59.776 45.833 0.00 0.00 34.56 2.75
1444 5698 2.168936 GGATTCTGGCAATGCAATGGAA 59.831 45.455 7.79 5.78 0.00 3.53
1448 5702 2.769663 ACATGGATTCTGGCAATGCAAT 59.230 40.909 7.79 0.00 31.88 3.56
1494 5748 4.558226 TTGTACCATGAGAGAAGCACAT 57.442 40.909 0.00 0.00 0.00 3.21
1591 5845 3.389329 AGCTCTGTGAGTTCTTTCTTCCA 59.611 43.478 0.00 0.00 31.39 3.53
1717 5972 6.309389 ACGGGGAAAGTATACAGAAAAGAT 57.691 37.500 5.50 0.00 0.00 2.40
1742 5997 0.538118 AAGACCCGCGGTAGCAATAA 59.462 50.000 26.12 0.00 45.49 1.40
2020 11070 6.217900 CCTCTATCCCTATCCTCTAGGTACAA 59.782 46.154 0.00 0.00 36.34 2.41
2115 11165 9.312904 AGTTTCCATTTCTTCATTTGGAATCTA 57.687 29.630 10.77 0.00 45.14 1.98


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

AutoCloner maintained by Alex Coulton.