Multiple sequence alignment - TraesCS6B01G453600

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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 TraesCS6B01G453600 chr6B 100.000 3112 0 0 1 3112 711728116 711731227 0.000000e+00 5747
1 TraesCS6B01G453600 chr1A 98.883 2597 26 3 518 3112 489163580 489160985 0.000000e+00 4632
2 TraesCS6B01G453600 chr1A 97.239 507 13 1 15 520 489164125 489163619 0.000000e+00 857
3 TraesCS6B01G453600 chr1A 93.895 475 17 4 12 484 24356268 24356732 0.000000e+00 706
4 TraesCS6B01G453600 chr1A 93.856 472 17 4 15 484 24380722 24381183 0.000000e+00 701
5 TraesCS6B01G453600 chr4D 98.806 2596 30 1 518 3112 399431283 399428688 0.000000e+00 4621
6 TraesCS6B01G453600 chr4D 94.632 503 18 2 15 517 399431818 399431325 0.000000e+00 771
7 TraesCS6B01G453600 chr6A 98.613 2596 33 2 518 3112 587882837 587880244 0.000000e+00 4591
8 TraesCS6B01G453600 chr6A 97.217 503 14 0 15 517 587883381 587882879 0.000000e+00 852
9 TraesCS6B01G453600 chr6A 97.949 195 4 0 15 209 587878284 587878090 3.840000e-89 339
10 TraesCS6B01G453600 chr7A 98.344 2596 33 2 518 3112 56102523 56105109 0.000000e+00 4547
11 TraesCS6B01G453600 chr7A 97.222 504 14 0 14 517 56101978 56102481 0.000000e+00 854
12 TraesCS6B01G453600 chr5B 97.305 2597 63 5 518 3112 594223950 594221359 0.000000e+00 4401
13 TraesCS6B01G453600 chr5B 94.235 503 19 2 15 517 594224484 594223992 0.000000e+00 760
14 TraesCS6B01G453600 chr2A 92.918 2598 169 11 518 3112 735407329 735409914 0.000000e+00 3764
15 TraesCS6B01G453600 chr2A 91.834 2596 181 10 518 3112 759034094 759036659 0.000000e+00 3591
16 TraesCS6B01G453600 chr2A 92.841 2165 151 4 950 3112 716472121 716469959 0.000000e+00 3136
17 TraesCS6B01G453600 chr2B 92.580 2601 173 11 521 3112 9119658 9117069 0.000000e+00 3716
18 TraesCS6B01G453600 chr3B 92.364 2593 178 10 521 3112 771430007 771427434 0.000000e+00 3674
19 TraesCS6B01G453600 chr3B 84.553 369 46 8 15 379 771430518 771430157 3.820000e-94 355
20 TraesCS6B01G453600 chr4B 88.842 2608 254 20 518 3112 390295538 390298121 0.000000e+00 3169


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 TraesCS6B01G453600 chr6B 711728116 711731227 3111 False 5747.000000 5747 100.000000 1 3112 1 chr6B.!!$F1 3111
1 TraesCS6B01G453600 chr1A 489160985 489164125 3140 True 2744.500000 4632 98.061000 15 3112 2 chr1A.!!$R1 3097
2 TraesCS6B01G453600 chr4D 399428688 399431818 3130 True 2696.000000 4621 96.719000 15 3112 2 chr4D.!!$R1 3097
3 TraesCS6B01G453600 chr6A 587878090 587883381 5291 True 1927.333333 4591 97.926333 15 3112 3 chr6A.!!$R1 3097
4 TraesCS6B01G453600 chr7A 56101978 56105109 3131 False 2700.500000 4547 97.783000 14 3112 2 chr7A.!!$F1 3098
5 TraesCS6B01G453600 chr5B 594221359 594224484 3125 True 2580.500000 4401 95.770000 15 3112 2 chr5B.!!$R1 3097
6 TraesCS6B01G453600 chr2A 735407329 735409914 2585 False 3764.000000 3764 92.918000 518 3112 1 chr2A.!!$F1 2594
7 TraesCS6B01G453600 chr2A 759034094 759036659 2565 False 3591.000000 3591 91.834000 518 3112 1 chr2A.!!$F2 2594
8 TraesCS6B01G453600 chr2A 716469959 716472121 2162 True 3136.000000 3136 92.841000 950 3112 1 chr2A.!!$R1 2162
9 TraesCS6B01G453600 chr2B 9117069 9119658 2589 True 3716.000000 3716 92.580000 521 3112 1 chr2B.!!$R1 2591
10 TraesCS6B01G453600 chr3B 771427434 771430518 3084 True 2014.500000 3674 88.458500 15 3112 2 chr3B.!!$R1 3097
11 TraesCS6B01G453600 chr4B 390295538 390298121 2583 False 3169.000000 3169 88.842000 518 3112 1 chr4B.!!$F1 2594

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
982 1041 2.171448 GGAAGCATGGATCCAGTAGTGT 59.829 50.0 21.33 0.0 35.71 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 2273 4.188462 CGGTGATGCAACAATAACTCCTA 58.812 43.478 0.0 0.0 0.0 2.94 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
43 44 8.977412 TGGTGTGAGTTGAGATTTATGTATCTA 58.023 33.333 0.00 0.0 35.06 1.98
135 140 4.945411 TCCAGAAAATTCCCCATTCATCA 58.055 39.130 0.00 0.0 0.00 3.07
982 1041 2.171448 GGAAGCATGGATCCAGTAGTGT 59.829 50.000 21.33 0.0 35.71 3.55
1061 1120 6.354039 GCAATTTGCTGGGAAATCAAATAG 57.646 37.500 14.11 0.0 40.96 1.73
1420 1479 1.752501 CGACCGTGCGGCTTTATCTG 61.753 60.000 10.87 0.0 39.32 2.90
1596 1655 5.186021 GGGAGTTCAGAGTGTGAATAGAAGA 59.814 44.000 5.94 0.0 46.99 2.87
1599 1658 7.238486 AGTTCAGAGTGTGAATAGAAGACAT 57.762 36.000 5.94 0.0 46.99 3.06
1809 1868 9.801873 AAATCAAAACCTTGGATTATTGATACG 57.198 29.630 0.00 0.0 36.72 3.06
2031 2109 7.973388 AGCTCTATCGATAAATCTCATAACTGC 59.027 37.037 6.58 0.0 0.00 4.40
2172 2269 4.320714 GCTCTTGCATCATGTTTGTCTTCA 60.321 41.667 0.00 0.0 39.41 3.02
2176 2273 5.456548 TGCATCATGTTTGTCTTCATGTT 57.543 34.783 0.00 0.0 41.22 2.71
2612 2710 7.742151 AGTTTGAATTGTTTCTTGCTTTGAAC 58.258 30.769 0.00 0.0 32.78 3.18
2713 2812 3.542712 AGTTGCACGTTCATTGATGTC 57.457 42.857 0.00 0.0 0.00 3.06
2752 2851 0.469144 TTCCTTTGGGGTGAGGCAAC 60.469 55.000 0.00 0.0 36.25 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.065374 TCACACCAACAATAGTGTATTGGTT 58.935 36.000 15.25 6.52 43.45 3.67
1 2 5.626142 TCACACCAACAATAGTGTATTGGT 58.374 37.500 12.72 12.72 45.74 3.67
3 4 6.801539 ACTCACACCAACAATAGTGTATTG 57.198 37.500 0.00 5.33 45.20 1.90
4 5 6.995686 TCAACTCACACCAACAATAGTGTATT 59.004 34.615 0.00 0.00 45.20 1.89
5 6 6.530120 TCAACTCACACCAACAATAGTGTAT 58.470 36.000 0.00 0.00 45.20 2.29
6 7 5.919755 TCAACTCACACCAACAATAGTGTA 58.080 37.500 0.00 0.00 45.20 2.90
8 9 5.056480 TCTCAACTCACACCAACAATAGTG 58.944 41.667 0.00 0.00 39.93 2.74
9 10 5.290493 TCTCAACTCACACCAACAATAGT 57.710 39.130 0.00 0.00 0.00 2.12
10 11 6.808008 AATCTCAACTCACACCAACAATAG 57.192 37.500 0.00 0.00 0.00 1.73
11 12 8.729756 CATAAATCTCAACTCACACCAACAATA 58.270 33.333 0.00 0.00 0.00 1.90
12 13 7.231317 ACATAAATCTCAACTCACACCAACAAT 59.769 33.333 0.00 0.00 0.00 2.71
43 44 1.729586 TTACACTTGAGCCCTCTGGT 58.270 50.000 0.00 0.00 0.00 4.00
135 140 0.033208 CAGAGAGAGAGGGCAGAGGT 60.033 60.000 0.00 0.00 0.00 3.85
195 201 3.130633 TCCGATGCCATATTGAGTTTCG 58.869 45.455 0.00 0.00 0.00 3.46
982 1041 6.852858 TGACATTATTTCGACTTGTTGTCA 57.147 33.333 12.91 12.91 45.60 3.58
1059 1118 4.635769 CGGGTTGCCTGCATTCTA 57.364 55.556 0.00 0.00 0.00 2.10
1420 1479 1.226746 GGAGTATGGCGGTATTGCAC 58.773 55.000 0.00 0.00 36.28 4.57
1596 1655 2.727544 GCGGTGTGGTTTGCATGT 59.272 55.556 0.00 0.00 0.00 3.21
1599 1658 3.578272 GACGCGGTGTGGTTTGCA 61.578 61.111 12.47 0.00 0.00 4.08
1809 1868 4.999950 CCTGTCATATGATTTGTAGCTCCC 59.000 45.833 9.02 0.00 0.00 4.30
2031 2109 5.765182 ACAAGTAGGATCAAACCAACTTCTG 59.235 40.000 0.00 0.00 0.00 3.02
2172 2269 6.095440 GGTGATGCAACAATAACTCCTAACAT 59.905 38.462 0.00 0.00 0.00 2.71
2176 2273 4.188462 CGGTGATGCAACAATAACTCCTA 58.812 43.478 0.00 0.00 0.00 2.94
2506 2604 4.798387 GCTGATTTTTAATAAGGGCACACG 59.202 41.667 0.00 0.00 0.00 4.49
2612 2710 5.525012 ACATGATGTCTGATGTTCAATACCG 59.475 40.000 0.00 0.00 27.94 4.02
2713 2812 5.105228 AGGAATTTGGGCACATTCATTGTAG 60.105 40.000 4.76 0.00 36.57 2.74


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

AutoCloner maintained by Alex Coulton.