Multiple sequence alignment - TraesCS6A01G161000

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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 TraesCS6A01G161000 chr6A 100.000 3530 0 0 1 3530 155855307 155858836 0.000000e+00 6519
1 TraesCS6A01G161000 chr6A 96.999 3532 103 3 1 3530 375862753 375859223 0.000000e+00 5932
2 TraesCS6A01G161000 chr3B 97.225 3531 94 4 1 3530 483331221 483334748 0.000000e+00 5975
3 TraesCS6A01G161000 chr3B 96.857 3532 109 2 1 3530 575841735 575838204 0.000000e+00 5906
4 TraesCS6A01G161000 chr2A 98.455 3300 50 1 1 3299 755478556 755481855 0.000000e+00 5810
5 TraesCS6A01G161000 chr7B 98.365 3302 54 0 1 3302 742950730 742947429 0.000000e+00 5799
6 TraesCS6A01G161000 chr7A 98.274 3302 57 0 1 3302 60170759 60167458 0.000000e+00 5782
7 TraesCS6A01G161000 chr4A 96.176 3530 133 2 1 3530 350170250 350173777 0.000000e+00 5770
8 TraesCS6A01G161000 chr5A 98.212 3299 58 1 1 3299 420183711 420187008 0.000000e+00 5764
9 TraesCS6A01G161000 chr4B 97.496 3355 84 0 176 3530 209240740 209244094 0.000000e+00 5731
10 TraesCS6A01G161000 chrUn 97.929 338 7 0 3193 3530 186164019 186164356 1.410000e-163 586
11 TraesCS6A01G161000 chrUn 97.929 338 7 0 3193 3530 404775285 404774948 1.410000e-163 586
12 TraesCS6A01G161000 chrUn 97.633 338 8 0 3193 3530 45101032 45101369 6.570000e-162 580


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 TraesCS6A01G161000 chr6A 155855307 155858836 3529 False 6519 6519 100.000 1 3530 1 chr6A.!!$F1 3529
1 TraesCS6A01G161000 chr6A 375859223 375862753 3530 True 5932 5932 96.999 1 3530 1 chr6A.!!$R1 3529
2 TraesCS6A01G161000 chr3B 483331221 483334748 3527 False 5975 5975 97.225 1 3530 1 chr3B.!!$F1 3529
3 TraesCS6A01G161000 chr3B 575838204 575841735 3531 True 5906 5906 96.857 1 3530 1 chr3B.!!$R1 3529
4 TraesCS6A01G161000 chr2A 755478556 755481855 3299 False 5810 5810 98.455 1 3299 1 chr2A.!!$F1 3298
5 TraesCS6A01G161000 chr7B 742947429 742950730 3301 True 5799 5799 98.365 1 3302 1 chr7B.!!$R1 3301
6 TraesCS6A01G161000 chr7A 60167458 60170759 3301 True 5782 5782 98.274 1 3302 1 chr7A.!!$R1 3301
7 TraesCS6A01G161000 chr4A 350170250 350173777 3527 False 5770 5770 96.176 1 3530 1 chr4A.!!$F1 3529
8 TraesCS6A01G161000 chr5A 420183711 420187008 3297 False 5764 5764 98.212 1 3299 1 chr5A.!!$F1 3298
9 TraesCS6A01G161000 chr4B 209240740 209244094 3354 False 5731 5731 97.496 176 3530 1 chr4B.!!$F1 3354

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
366 367 4.303282 GCTATCCGAAAGAGGAGATCAAC 58.697 47.826 0.0 0.0 44.55 3.18 F
1408 1411 0.181587 TGTCGAAGTGAAAGCCCCAA 59.818 50.000 0.0 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 1862 1.562575 CTGGTGGTCGGCGTAACAAC 61.563 60.000 6.85 6.11 0.0 3.32 R
2715 2720 1.468405 TGGGGTTGGGTGGGGTATT 60.468 57.895 0.00 0.00 0.0 1.89 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
63 64 4.788100 CGTAATTGATTGAAAAGTGCTCGG 59.212 41.667 0.00 0.00 0.00 4.63
234 235 6.891361 TGAAAGCAATGGGAAATGAGATTCTA 59.109 34.615 0.00 0.00 0.00 2.10
366 367 4.303282 GCTATCCGAAAGAGGAGATCAAC 58.697 47.826 0.00 0.00 44.55 3.18
647 650 6.088173 CAGTTGCTCAATTCATTCGATTTCA 58.912 36.000 0.00 0.00 0.00 2.69
654 657 9.507280 GCTCAATTCATTCGATTTCAAAATAGA 57.493 29.630 0.00 0.00 0.00 1.98
1054 1057 8.622157 TCACGACTCTATTAGAAAGTAGAATGG 58.378 37.037 0.00 0.00 0.00 3.16
1160 1163 3.594134 ACGAGATTCAAGCAGGAGAAAG 58.406 45.455 0.00 0.00 0.00 2.62
1292 1295 1.586422 CGCACTGGATCTATTGTGGG 58.414 55.000 2.52 2.34 37.12 4.61
1408 1411 0.181587 TGTCGAAGTGAAAGCCCCAA 59.818 50.000 0.00 0.00 0.00 4.12
1600 1604 1.457346 GGGCACAAATGAGAGTGAGG 58.543 55.000 0.00 0.00 37.97 3.86
1857 1862 4.971830 GTGGCATATCGACAAATGTCATTG 59.028 41.667 13.51 6.14 44.99 2.82
1945 1950 4.909200 TCTTAGAAAGAGCCGCTAAACGAC 60.909 45.833 0.00 0.00 37.14 4.34
2096 2101 4.745620 GCTCTTTTATCGCGGAATTAGACT 59.254 41.667 6.13 0.00 0.00 3.24
2138 2143 4.039357 CAGTCGCGTCGGGTCTGT 62.039 66.667 22.19 0.37 0.00 3.41
2169 2174 6.543831 AGTTGAAAGCTATGAAACAAGTCTGT 59.456 34.615 0.00 0.00 37.39 3.41
2463 2468 9.816354 CAAAAATCTTTCTTAGAAAAAGGTGGA 57.184 29.630 8.82 2.18 36.22 4.02
2498 2503 4.015084 AGAAAGATGGAACCAGATGCTTG 58.985 43.478 0.00 0.00 0.00 4.01
2700 2705 2.860971 AGCCACAAGGGGGAGCTT 60.861 61.111 0.00 0.00 37.04 3.74
2750 2755 0.112218 CCACAAGGGTTGATGGACCA 59.888 55.000 0.00 0.00 41.65 4.02
2949 2954 7.835822 TCAACAAGAAATCCAAGAAAGAACAA 58.164 30.769 0.00 0.00 0.00 2.83
2951 2956 7.169158 ACAAGAAATCCAAGAAAGAACAACA 57.831 32.000 0.00 0.00 0.00 3.33
3099 3104 4.773674 AGTTCTTTGATTCATTCCATGGCA 59.226 37.500 6.96 0.00 0.00 4.92
3102 3107 1.391577 TGATTCATTCCATGGCACGG 58.608 50.000 6.96 0.00 0.00 4.94
3268 3274 9.561069 AAAGAAATGTGAGAATGTAGTTACAGT 57.439 29.630 0.00 0.00 39.92 3.55
3310 3316 4.278310 TCGTTCTCTTGGTCCATAGATGA 58.722 43.478 5.51 4.87 0.00 2.92
3314 3320 2.702478 CTCTTGGTCCATAGATGAGGCA 59.298 50.000 0.00 0.00 0.00 4.75
3350 3356 1.686052 GAATGAGGAGCCTCTGTCGAT 59.314 52.381 16.87 0.00 43.12 3.59
3416 3422 2.151202 GTCGGTGATTCAAGCCAAGAA 58.849 47.619 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.573434 TCGCTTCTCTGATCTTTAATAAGCA 58.427 36.000 14.09 0.00 38.34 3.91
63 64 0.878086 GCATCTGCCGGAACTAGAGC 60.878 60.000 5.05 5.11 34.31 4.09
234 235 6.831868 ACTTGTTTGTACCAGTAATCAAACCT 59.168 34.615 15.69 3.07 44.78 3.50
366 367 6.375455 GCCTACCCATATTGATAGTGGAATTG 59.625 42.308 0.00 0.00 34.94 2.32
517 518 1.643832 GCCGTGAGAATGATTCCGC 59.356 57.895 0.75 0.00 0.00 5.54
654 657 9.846248 GTGAAATTGCAAGAATCACTTTATACT 57.154 29.630 23.91 0.00 37.87 2.12
1054 1057 6.254804 ACTTGAAAATTCGTGTAAAAGTTGGC 59.745 34.615 0.00 0.00 0.00 4.52
1160 1163 2.573340 CGCTGGCAAATTCCACCC 59.427 61.111 0.00 0.00 31.74 4.61
1335 1338 6.395780 TTTCCATCAATAGGTACTCCCAAA 57.604 37.500 0.00 0.00 41.75 3.28
1408 1411 6.597672 TGCACAGATTTACGTTCAATAATCCT 59.402 34.615 0.00 0.00 0.00 3.24
1600 1604 4.730042 CGCAACATAGACACAATACAATGC 59.270 41.667 0.00 0.00 0.00 3.56
1857 1862 1.562575 CTGGTGGTCGGCGTAACAAC 61.563 60.000 6.85 6.11 0.00 3.32
2096 2101 5.221303 ACGGATAAGCCAACGTTAATAGCTA 60.221 40.000 12.78 0.00 35.90 3.32
2138 2143 3.592898 TCATAGCTTTCAACTGAGCGA 57.407 42.857 0.00 0.00 43.53 4.93
2169 2174 4.038642 GCCAATTCCAGTTTTGAACTACCA 59.961 41.667 0.00 0.00 40.46 3.25
2463 2468 8.727910 GGTTCCATCTTTCTTTCGTTAGTTAAT 58.272 33.333 0.00 0.00 0.00 1.40
2498 2503 6.662414 AAGGCAAAGTGCTTTCTTTTAAAC 57.338 33.333 0.00 0.00 38.32 2.01
2700 2705 4.264668 TGGGGTATTCTGAACTACTGGAGA 60.265 45.833 0.00 0.00 0.00 3.71
2715 2720 1.468405 TGGGGTTGGGTGGGGTATT 60.468 57.895 0.00 0.00 0.00 1.89
2750 2755 7.842260 TCATCAGGTATAGGTATAGGTAGGT 57.158 40.000 0.00 0.00 0.00 3.08
2949 2954 7.877612 ACTTTTCTTGTCATGTTTTTCCTTTGT 59.122 29.630 0.00 0.00 0.00 2.83
2951 2956 7.877612 ACACTTTTCTTGTCATGTTTTTCCTTT 59.122 29.630 0.00 0.00 0.00 3.11
3099 3104 3.576078 TTAGCCAATGATGGATTCCGT 57.424 42.857 0.00 0.00 44.90 4.69
3102 3107 6.808829 TGATTGTTTAGCCAATGATGGATTC 58.191 36.000 0.00 0.00 44.90 2.52
3310 3316 2.260639 ATCCATCGGATAGGATGCCT 57.739 50.000 16.26 0.00 41.16 4.75
3314 3320 4.408270 CCTCATTCATCCATCGGATAGGAT 59.592 45.833 13.06 13.06 40.98 3.24
3350 3356 9.466497 AAAAGCAGAATCCTATCATTTCACTAA 57.534 29.630 0.00 0.00 0.00 2.24
3401 3407 1.473677 CCGCATTCTTGGCTTGAATCA 59.526 47.619 3.31 0.00 32.47 2.57
3416 3422 1.452108 GCTCTTAAGGTGCCCGCAT 60.452 57.895 1.85 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.