Multiple sequence alignment - TraesCS1B01G411200

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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 TraesCS1B01G411200 chr1B 100.000 6776 0 0 1 6776 637607134 637613909 0 12514
1 TraesCS1B01G411200 chr7A 98.880 6788 60 10 1 6776 624766395 624759612 0 12100
2 TraesCS1B01G411200 chr7A 98.411 6797 81 12 1 6776 634123097 634129887 0 11928
3 TraesCS1B01G411200 chr6A 98.469 6794 80 16 1 6776 480630564 480637351 0 11948
4 TraesCS1B01G411200 chr6A 98.396 6794 88 13 1 6776 87933837 87940627 0 11923
5 TraesCS1B01G411200 chr6A 98.777 6624 62 11 169 6776 12700532 12693912 0 11766
6 TraesCS1B01G411200 chr7B 98.394 6789 93 12 1 6776 666533823 666527038 0 11919
7 TraesCS1B01G411200 chr7B 98.322 6794 85 22 1 6776 194120439 194127221 0 11888
8 TraesCS1B01G411200 chr6B 98.364 6783 78 15 1 6776 21371772 21365016 0 11880
9 TraesCS1B01G411200 chr5A 98.523 5415 61 10 1 5405 396395848 396401253 0 9539
10 TraesCS1B01G411200 chr4B 98.251 1944 21 9 1 1933 14719145 14717204 0 3389


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 TraesCS1B01G411200 chr1B 637607134 637613909 6775 False 12514 12514 100.000 1 6776 1 chr1B.!!$F1 6775
1 TraesCS1B01G411200 chr7A 624759612 624766395 6783 True 12100 12100 98.880 1 6776 1 chr7A.!!$R1 6775
2 TraesCS1B01G411200 chr7A 634123097 634129887 6790 False 11928 11928 98.411 1 6776 1 chr7A.!!$F1 6775
3 TraesCS1B01G411200 chr6A 480630564 480637351 6787 False 11948 11948 98.469 1 6776 1 chr6A.!!$F2 6775
4 TraesCS1B01G411200 chr6A 87933837 87940627 6790 False 11923 11923 98.396 1 6776 1 chr6A.!!$F1 6775
5 TraesCS1B01G411200 chr6A 12693912 12700532 6620 True 11766 11766 98.777 169 6776 1 chr6A.!!$R1 6607
6 TraesCS1B01G411200 chr7B 666527038 666533823 6785 True 11919 11919 98.394 1 6776 1 chr7B.!!$R1 6775
7 TraesCS1B01G411200 chr7B 194120439 194127221 6782 False 11888 11888 98.322 1 6776 1 chr7B.!!$F1 6775
8 TraesCS1B01G411200 chr6B 21365016 21371772 6756 True 11880 11880 98.364 1 6776 1 chr6B.!!$R1 6775
9 TraesCS1B01G411200 chr5A 396395848 396401253 5405 False 9539 9539 98.523 1 5405 1 chr5A.!!$F1 5404
10 TraesCS1B01G411200 chr4B 14717204 14719145 1941 True 3389 3389 98.251 1 1933 1 chr4B.!!$R1 1932

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
348 352 5.562298 AGGTGGTTGTCTATACTGTGTTT 57.438 39.130 0.00 0.00 0.00 2.83 F
1166 1187 2.317040 TCTGGAAGTCAACCTCTTCGT 58.683 47.619 0.00 0.00 41.26 3.85 F
1798 1845 9.602568 TTGCAATATCATTTCTTATTGTTGCAT 57.397 25.926 9.37 0.00 45.70 3.96 F
2164 2215 0.524862 GCTAGTTTCGAGGTCGGTCA 59.475 55.000 0.00 0.00 40.29 4.02 F
2377 2428 3.027412 GCCACTAGGAGATTCAGACAGA 58.973 50.000 0.00 0.00 36.89 3.41 F
3325 3382 6.019640 GTGGTTTCATTCAACACACAAATCTG 60.020 38.462 0.00 0.00 32.46 2.90 F
4171 4231 1.617850 GAGGAGACAGATGCGGATGAT 59.382 52.381 0.00 0.00 0.00 2.45 F
4598 4670 2.791613 TAGCACTCACGCCACCCCTA 62.792 60.000 0.00 0.00 0.00 3.53 F
5362 5435 0.469494 TTGCTGCCAACTCAGACTGA 59.531 50.000 4.78 4.78 36.19 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1208 1229 0.683973 CTCCCTGCTCAACACTCTGT 59.316 55.000 0.00 0.0 0.00 3.41 R
2141 2192 2.286872 CCGACCTCGAAACTAGCTCTA 58.713 52.381 0.00 0.0 43.02 2.43 R
3023 3080 2.373224 TGTTGTGCCAACTGATGACAA 58.627 42.857 15.91 0.0 0.00 3.18 R
3630 3688 5.843673 TCCAAAAGAACATGTGCAACTAA 57.156 34.783 6.60 0.0 38.04 2.24 R
4171 4231 1.433199 TCCTTGTCCTCCTCCTCTGAA 59.567 52.381 0.00 0.0 0.00 3.02 R
5310 5383 0.258774 GGCACCCCTACATCAATGGT 59.741 55.000 0.00 0.0 0.00 3.55 R
5320 5393 1.378762 GCAGAACTTGGCACCCCTA 59.621 57.895 0.00 0.0 0.00 3.53 R
5731 5804 2.507110 ATCGCAGAACCCGTCACCAG 62.507 60.000 0.00 0.0 43.58 4.00 R
6657 6744 5.714333 TCCCTTGCTGTAATTTTATCTGCAA 59.286 36.000 0.00 0.0 41.21 4.08 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
348 352 5.562298 AGGTGGTTGTCTATACTGTGTTT 57.438 39.130 0.00 0.00 0.00 2.83
1166 1187 2.317040 TCTGGAAGTCAACCTCTTCGT 58.683 47.619 0.00 0.00 41.26 3.85
1798 1845 9.602568 TTGCAATATCATTTCTTATTGTTGCAT 57.397 25.926 9.37 0.00 45.70 3.96
2141 2192 6.351456 GCCTCTCTAACTCCACTACAGAAATT 60.351 42.308 0.00 0.00 0.00 1.82
2164 2215 0.524862 GCTAGTTTCGAGGTCGGTCA 59.475 55.000 0.00 0.00 40.29 4.02
2377 2428 3.027412 GCCACTAGGAGATTCAGACAGA 58.973 50.000 0.00 0.00 36.89 3.41
3023 3080 7.553760 ACTCTTTTTGGAAATTGCACAGAAAAT 59.446 29.630 0.00 0.00 0.00 1.82
3325 3382 6.019640 GTGGTTTCATTCAACACACAAATCTG 60.020 38.462 0.00 0.00 32.46 2.90
3630 3688 7.721402 TGTTCAGTTGCACATATAAGGTTTTT 58.279 30.769 0.00 0.00 0.00 1.94
4171 4231 1.617850 GAGGAGACAGATGCGGATGAT 59.382 52.381 0.00 0.00 0.00 2.45
4598 4670 2.791613 TAGCACTCACGCCACCCCTA 62.792 60.000 0.00 0.00 0.00 3.53
4826 4898 6.003326 TGTGAGAAGATCAACTTTGCCATTA 58.997 36.000 0.00 0.00 40.43 1.90
4865 4937 8.725148 TCTTATCAACTGAAGCTGAAAAGAATC 58.275 33.333 0.00 0.00 0.00 2.52
5277 5350 3.069443 GGAACAGGCCACAAAAGATTTGA 59.931 43.478 5.01 0.00 0.00 2.69
5320 5393 1.647545 CGAGCCGCAACCATTGATGT 61.648 55.000 0.00 0.00 0.00 3.06
5362 5435 0.469494 TTGCTGCCAACTCAGACTGA 59.531 50.000 4.78 4.78 36.19 3.41
5373 5446 3.672808 ACTCAGACTGAAAAGATGCCAG 58.327 45.455 6.61 0.00 0.00 4.85
5452 5525 2.061220 CCACAGCTGGTCAGGAAGA 58.939 57.895 19.93 0.00 32.03 2.87
5518 5591 3.870419 GCTTCAATGCCAAACACAAAAGA 59.130 39.130 0.00 0.00 0.00 2.52
5542 5615 4.018960 AGGTGATCCAACTATCAAAGTGCT 60.019 41.667 0.00 0.00 38.88 4.40
5657 5730 2.076100 CTATTGCGAACCAAGTCAGCA 58.924 47.619 0.00 0.00 36.76 4.41
5731 5804 6.702282 CCCTTACGAAGATCAAACTCTTATCC 59.298 42.308 0.00 0.00 35.63 2.59
5862 5947 2.037251 GAGTGTGAGTTAGACCCAGCAA 59.963 50.000 0.00 0.00 0.00 3.91
5957 6042 0.550914 ATTGCCACACCCCGATATGT 59.449 50.000 0.00 0.00 0.00 2.29
6361 6446 9.030301 GCTAACTTGTCTTTTTATTGCTTTCAA 57.970 29.630 0.00 0.00 36.51 2.69
6657 6744 9.860898 GAGTTTTGAGCCATGTTTTATAATCTT 57.139 29.630 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1166 1187 1.970114 AGGACGCTTCGAGTTCCGA 60.970 57.895 0.00 0.00 46.94 4.55
1208 1229 0.683973 CTCCCTGCTCAACACTCTGT 59.316 55.000 0.00 0.00 0.00 3.41
1798 1845 7.548075 GGCAGCTACAAAAAGTTCTAGTGTATA 59.452 37.037 0.00 0.00 0.00 1.47
2141 2192 2.286872 CCGACCTCGAAACTAGCTCTA 58.713 52.381 0.00 0.00 43.02 2.43
2164 2215 4.103311 GTCTGATAAGTTCAATAGCCCCCT 59.897 45.833 0.00 0.00 32.78 4.79
2377 2428 8.463930 TGAGAATTTCCAGTTATGTTGAAAGT 57.536 30.769 0.00 0.00 30.96 2.66
3023 3080 2.373224 TGTTGTGCCAACTGATGACAA 58.627 42.857 15.91 0.00 0.00 3.18
3053 3110 9.793252 CAAACTTAAAGCTATAATCTGTGCAAT 57.207 29.630 0.00 0.00 0.00 3.56
3244 3301 6.180472 ACTGGGGTAGACAAATTCAACTATG 58.820 40.000 0.00 0.00 0.00 2.23
3630 3688 5.843673 TCCAAAAGAACATGTGCAACTAA 57.156 34.783 6.60 0.00 38.04 2.24
3984 4044 7.575155 GCTGCTGTACGTAAGGATCAATATCTA 60.575 40.741 0.00 0.00 46.39 1.98
4171 4231 1.433199 TCCTTGTCCTCCTCCTCTGAA 59.567 52.381 0.00 0.00 0.00 3.02
4598 4670 1.135489 CAATGAATTGCTGCTGCTCGT 60.135 47.619 17.00 4.79 40.48 4.18
4826 4898 5.471456 CAGTTGATAAGAACAGGCTCTTGTT 59.529 40.000 0.00 0.00 43.61 2.83
4865 4937 2.827322 TGCTTCCTCCATGTCAATTTGG 59.173 45.455 0.00 0.00 0.00 3.28
5277 5350 2.939640 GCTCTCTCTCGTCTCTGAACCT 60.940 54.545 0.00 0.00 0.00 3.50
5310 5383 0.258774 GGCACCCCTACATCAATGGT 59.741 55.000 0.00 0.00 0.00 3.55
5320 5393 1.378762 GCAGAACTTGGCACCCCTA 59.621 57.895 0.00 0.00 0.00 3.53
5362 5435 5.815581 TGGTATCTGTAACTGGCATCTTTT 58.184 37.500 0.00 0.00 0.00 2.27
5373 5446 3.328382 TGGCACACTGGTATCTGTAAC 57.672 47.619 0.00 0.00 0.00 2.50
5518 5591 4.702131 GCACTTTGATAGTTGGATCACCTT 59.298 41.667 0.00 0.00 35.56 3.50
5542 5615 2.507886 TGAAAGACAACTCTTGGGGACA 59.492 45.455 0.00 0.00 36.80 4.02
5657 5730 3.666274 CACAAACATGGGTGCATCATTT 58.334 40.909 0.00 0.00 0.00 2.32
5731 5804 2.507110 ATCGCAGAACCCGTCACCAG 62.507 60.000 0.00 0.00 43.58 4.00
5862 5947 3.693085 GCATCACATCCTTCATTCACAGT 59.307 43.478 0.00 0.00 0.00 3.55
6657 6744 5.714333 TCCCTTGCTGTAATTTTATCTGCAA 59.286 36.000 0.00 0.00 41.21 4.08


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

AutoCloner maintained by Alex Coulton.