Multiple sequence alignment - TraesCS5A01G421200

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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 TraesCS5A01G421200 chr5A 100.000 3086 0 0 1 3086 607275659 607272574 0.000000e+00 5699
1 TraesCS5A01G421200 chr3D 97.409 3088 72 7 1 3086 589278285 589281366 0.000000e+00 5252
2 TraesCS5A01G421200 chr5D 97.378 3089 75 6 1 3086 6190200 6187115 0.000000e+00 5251
3 TraesCS5A01G421200 chr5D 97.311 3087 78 5 2 3086 503276967 503280050 0.000000e+00 5236
4 TraesCS5A01G421200 chr5D 96.275 3087 107 8 3 3086 432402239 432405320 0.000000e+00 5057
5 TraesCS5A01G421200 chr5D 97.713 2711 58 4 1 2709 503219478 503216770 0.000000e+00 4660
6 TraesCS5A01G421200 chr1D 97.151 3089 82 6 1 3086 254396850 254399935 0.000000e+00 5212
7 TraesCS5A01G421200 chr2A 95.986 3089 99 8 1 3086 335839889 335836823 0.000000e+00 4994
8 TraesCS5A01G421200 chr4A 95.475 3094 129 8 2 3086 309516389 309513298 0.000000e+00 4927
9 TraesCS5A01G421200 chr4B 95.310 3092 122 11 1 3086 308697731 308694657 0.000000e+00 4885
10 TraesCS5A01G421200 chr6D 97.603 2712 60 5 1 2709 168256186 168253477 0.000000e+00 4643
11 TraesCS5A01G421200 chr3B 97.529 2712 61 6 1 2709 201528284 201525576 0.000000e+00 4632
12 TraesCS5A01G421200 chr7B 87.350 751 71 13 2343 3086 719442374 719441641 0.000000e+00 839
13 TraesCS5A01G421200 chr7D 95.205 146 7 0 2644 2789 204018405 204018550 6.660000e-57 231


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 TraesCS5A01G421200 chr5A 607272574 607275659 3085 True 5699 5699 100.000 1 3086 1 chr5A.!!$R1 3085
1 TraesCS5A01G421200 chr3D 589278285 589281366 3081 False 5252 5252 97.409 1 3086 1 chr3D.!!$F1 3085
2 TraesCS5A01G421200 chr5D 6187115 6190200 3085 True 5251 5251 97.378 1 3086 1 chr5D.!!$R1 3085
3 TraesCS5A01G421200 chr5D 503276967 503280050 3083 False 5236 5236 97.311 2 3086 1 chr5D.!!$F2 3084
4 TraesCS5A01G421200 chr5D 432402239 432405320 3081 False 5057 5057 96.275 3 3086 1 chr5D.!!$F1 3083
5 TraesCS5A01G421200 chr5D 503216770 503219478 2708 True 4660 4660 97.713 1 2709 1 chr5D.!!$R2 2708
6 TraesCS5A01G421200 chr1D 254396850 254399935 3085 False 5212 5212 97.151 1 3086 1 chr1D.!!$F1 3085
7 TraesCS5A01G421200 chr2A 335836823 335839889 3066 True 4994 4994 95.986 1 3086 1 chr2A.!!$R1 3085
8 TraesCS5A01G421200 chr4A 309513298 309516389 3091 True 4927 4927 95.475 2 3086 1 chr4A.!!$R1 3084
9 TraesCS5A01G421200 chr4B 308694657 308697731 3074 True 4885 4885 95.310 1 3086 1 chr4B.!!$R1 3085
10 TraesCS5A01G421200 chr6D 168253477 168256186 2709 True 4643 4643 97.603 1 2709 1 chr6D.!!$R1 2708
11 TraesCS5A01G421200 chr3B 201525576 201528284 2708 True 4632 4632 97.529 1 2709 1 chr3B.!!$R1 2708
12 TraesCS5A01G421200 chr7B 719441641 719442374 733 True 839 839 87.350 2343 3086 1 chr7B.!!$R1 743

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
672 677 1.066858 ACACCTATCTTGAGCACACGG 60.067 52.381 0.0 0.0 0.0 4.94 F
1885 1892 1.544246 GACAAGTGGGTAATGTTGGGC 59.456 52.381 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2047 0.326595 TTCCAAGCGCAGGATAACCA 59.673 50.0 20.31 4.53 38.94 3.67 R
3016 3043 1.092345 GCTGCTTGGCCTGTAGTAGC 61.092 60.0 20.48 20.48 41.62 3.58 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
165 166 3.654201 GCTGGATGCACACGAACA 58.346 55.556 0.00 0.00 42.31 3.18
245 246 9.739276 ATCATCCATACATAACGAATTGGTATT 57.261 29.630 0.00 0.00 0.00 1.89
432 435 2.961526 TCGGGATTCACTAAGACAGC 57.038 50.000 0.00 0.00 0.00 4.40
479 482 3.868619 TTGGTGTTAAGGTGGTAGCTT 57.131 42.857 0.00 0.00 39.52 3.74
491 494 3.954258 GGTGGTAGCTTTGAATAGCCATT 59.046 43.478 0.00 0.00 42.20 3.16
575 579 2.574369 TGATCATTACCCTTCAACCGGT 59.426 45.455 0.00 0.00 36.08 5.28
604 609 8.927675 TTCTATTCCACTTCTAGATAGAGGAC 57.072 38.462 15.45 0.00 34.00 3.85
672 677 1.066858 ACACCTATCTTGAGCACACGG 60.067 52.381 0.00 0.00 0.00 4.94
827 832 8.770828 GCGCCTATACTGTAAAATAGATTTTCA 58.229 33.333 0.00 2.75 40.24 2.69
951 957 7.856415 AGAGATATATTTTACATCCCAGAGGC 58.144 38.462 0.00 0.00 0.00 4.70
1025 1031 3.561313 GGAAATGCCCTACCTTTGAGTGA 60.561 47.826 0.00 0.00 0.00 3.41
1121 1127 5.655090 TGATCCAATTTGACTACCTCTACGA 59.345 40.000 0.00 0.00 0.00 3.43
1287 1293 4.444876 CCTTGTTTCAAAGAGAGGAGGACA 60.445 45.833 0.00 0.00 0.00 4.02
1288 1294 4.982241 TGTTTCAAAGAGAGGAGGACAT 57.018 40.909 0.00 0.00 0.00 3.06
1319 1325 7.174413 TCACATTTAATTTGATGGTCAGAGGA 58.826 34.615 5.92 0.00 0.00 3.71
1459 1465 5.252547 TGCTACATGAAGAACATAAGCCAA 58.747 37.500 0.00 0.00 41.98 4.52
1469 1475 4.949856 AGAACATAAGCCAAATGACGGAAT 59.050 37.500 0.00 0.00 0.00 3.01
1597 1603 5.630121 AGATCCATCTGTCTAGAGATCGTT 58.370 41.667 10.21 0.00 38.60 3.85
1885 1892 1.544246 GACAAGTGGGTAATGTTGGGC 59.456 52.381 0.00 0.00 0.00 5.36
2004 2011 2.282180 GGCGGTGAAGGGAAAGCA 60.282 61.111 0.00 0.00 0.00 3.91
2037 2047 1.959710 AAAAACCCACAACCCCTTGT 58.040 45.000 0.00 0.00 41.61 3.16
2078 2088 7.837187 TGGAAGAAGAACTAGGAAAAGGAAAAA 59.163 33.333 0.00 0.00 0.00 1.94
2324 2337 3.877559 TCTAACCTCCGTACTTCGATCA 58.122 45.455 0.00 0.00 42.86 2.92
2333 2346 6.387041 TCCGTACTTCGATCAAGATATTGT 57.613 37.500 10.61 0.00 42.86 2.71
2480 2498 5.479124 AGAAACAATAGTAACGTGGTCCT 57.521 39.130 0.00 0.00 0.00 3.85
2548 2566 7.752239 GCGATTCATAATGGAAAGGAACATATG 59.248 37.037 0.00 0.00 0.00 1.78
3055 3082 5.048434 GCAGCCAAGAAGAAGTGTAAAGAAT 60.048 40.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
290 291 3.701542 TGCTCTGAGTTCCAGTATCGATT 59.298 43.478 1.71 0.00 43.38 3.34
432 435 4.396166 AGAGTTCGACCCAATGCTTTATTG 59.604 41.667 0.00 0.00 44.67 1.90
479 482 4.473196 TCCAGGTAGTCAATGGCTATTCAA 59.527 41.667 0.00 0.00 33.92 2.69
661 666 0.534203 GTTCCCTTCCGTGTGCTCAA 60.534 55.000 0.00 0.00 0.00 3.02
662 667 1.070786 GTTCCCTTCCGTGTGCTCA 59.929 57.895 0.00 0.00 0.00 4.26
672 677 0.108281 GCCTGTCTACGGTTCCCTTC 60.108 60.000 0.00 0.00 0.00 3.46
776 781 0.949582 ACCTCCCCCTCTATGCCTTA 59.050 55.000 0.00 0.00 0.00 2.69
827 832 6.659242 ACCAGATATGTCTTTTTGATTCCGTT 59.341 34.615 0.00 0.00 30.42 4.44
1319 1325 5.535753 ACCACTGCTTAGCTTTCAATTTT 57.464 34.783 5.60 0.00 0.00 1.82
1459 1465 1.556911 AGGTCTCTGCATTCCGTCATT 59.443 47.619 0.00 0.00 0.00 2.57
1469 1475 3.953542 TCTACATCCTAGGTCTCTGCA 57.046 47.619 9.08 0.00 0.00 4.41
1762 1769 5.491070 TGCAATGAGTTTCACTATAGCACT 58.509 37.500 0.00 0.00 0.00 4.40
1772 1779 3.960102 ACCCTCTTTTGCAATGAGTTTCA 59.040 39.130 21.02 0.00 32.43 2.69
2037 2047 0.326595 TTCCAAGCGCAGGATAACCA 59.673 50.000 20.31 4.53 38.94 3.67
2306 2319 3.087031 TCTTGATCGAAGTACGGAGGTT 58.913 45.455 0.00 0.00 42.82 3.50
2324 2337 8.256356 AGAGTGGCTTCTATGTACAATATCTT 57.744 34.615 0.00 0.00 0.00 2.40
2333 2346 8.380099 TCCTTTTTAAAGAGTGGCTTCTATGTA 58.620 33.333 5.15 0.00 38.28 2.29
2480 2498 1.699634 GGGTAGAATGCTAGATGCCCA 59.300 52.381 0.00 0.00 42.00 5.36
2548 2566 9.297037 ACCATAGGATTTGTTATGTAAATAGGC 57.703 33.333 0.00 0.00 0.00 3.93
2803 2822 7.828717 TGCTGTTGAAGTTCCATCTATTAATGA 59.171 33.333 0.00 0.00 0.00 2.57
3016 3043 1.092345 GCTGCTTGGCCTGTAGTAGC 61.092 60.000 20.48 20.48 41.62 3.58
3055 3082 7.119699 CCAATATGCTAGTTTCAACAACTCTCA 59.880 37.037 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.