Multiple sequence alignment - TraesCS2B01G283500

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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 TraesCS2B01G283500 chr2B 100.000 3086 0 0 1 3086 391150411 391153496 0.000000e+00 5699.0
1 TraesCS2B01G283500 chr2B 98.025 3088 59 1 1 3086 391219635 391216548 0.000000e+00 5363.0
2 TraesCS2B01G283500 chr6B 98.478 3089 44 1 1 3086 596596249 596593161 0.000000e+00 5441.0
3 TraesCS2B01G283500 chr1D 98.187 3089 52 2 1 3086 212442251 212439164 0.000000e+00 5391.0
4 TraesCS2B01G283500 chrUn 98.122 3088 56 1 1 3086 171013895 171016982 0.000000e+00 5380.0
5 TraesCS2B01G283500 chr5B 97.895 3088 62 2 1 3086 567285580 567288666 0.000000e+00 5339.0
6 TraesCS2B01G283500 chr3B 97.575 3093 67 3 1 3086 759910398 759913489 0.000000e+00 5289.0
7 TraesCS2B01G283500 chr3B 96.889 3086 94 2 2 3086 173951981 173955065 0.000000e+00 5166.0
8 TraesCS2B01G283500 chr3B 94.722 1743 80 8 1348 3086 730154243 730152509 0.000000e+00 2699.0
9 TraesCS2B01G283500 chr3B 98.033 305 6 0 1 305 797545227 797544923 5.860000e-147 531.0
10 TraesCS2B01G283500 chr3B 96.085 281 11 0 573 853 730158459 730158179 2.800000e-125 459.0
11 TraesCS2B01G283500 chr3B 93.929 280 14 3 847 1124 730154519 730154241 1.320000e-113 420.0
12 TraesCS2B01G283500 chr3B 97.143 35 1 0 1248 1282 6013618 6013584 3.320000e-05 60.2


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 TraesCS2B01G283500 chr2B 391150411 391153496 3085 False 5699.000000 5699 100.000 1 3086 1 chr2B.!!$F1 3085
1 TraesCS2B01G283500 chr2B 391216548 391219635 3087 True 5363.000000 5363 98.025 1 3086 1 chr2B.!!$R1 3085
2 TraesCS2B01G283500 chr6B 596593161 596596249 3088 True 5441.000000 5441 98.478 1 3086 1 chr6B.!!$R1 3085
3 TraesCS2B01G283500 chr1D 212439164 212442251 3087 True 5391.000000 5391 98.187 1 3086 1 chr1D.!!$R1 3085
4 TraesCS2B01G283500 chrUn 171013895 171016982 3087 False 5380.000000 5380 98.122 1 3086 1 chrUn.!!$F1 3085
5 TraesCS2B01G283500 chr5B 567285580 567288666 3086 False 5339.000000 5339 97.895 1 3086 1 chr5B.!!$F1 3085
6 TraesCS2B01G283500 chr3B 759910398 759913489 3091 False 5289.000000 5289 97.575 1 3086 1 chr3B.!!$F2 3085
7 TraesCS2B01G283500 chr3B 173951981 173955065 3084 False 5166.000000 5166 96.889 2 3086 1 chr3B.!!$F1 3084
8 TraesCS2B01G283500 chr3B 730152509 730158459 5950 True 1192.666667 2699 94.912 573 3086 3 chr3B.!!$R3 2513

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
795 796 1.20271 TCCGCTTGCTTTCAACCACTA 60.203 47.619 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2666 6341 0.381089 GCGCCAGTCACTCGTACTAT 59.619 55.0 0.0 0.0 0.0 2.12 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
197 198 5.795870 AGCTAGGGAATAATTGGGGCTTATA 59.204 40.000 0.00 0.00 0.00 0.98
245 246 4.594675 AGAGGTCTTCCTAGCTGACTTA 57.405 45.455 0.00 0.00 45.24 2.24
294 295 4.592942 TCTCTATGGCTTGTGAATTGCTT 58.407 39.130 0.00 0.00 0.00 3.91
437 438 7.334171 ACATTGTTTGGGAAAGAAAGTGAAAAG 59.666 33.333 0.00 0.00 26.74 2.27
523 524 2.031807 CGGACGAGTCGATGTCAATAGT 59.968 50.000 21.50 0.00 36.83 2.12
707 708 7.518731 TCAAAGTGAAACGATTTTCCTTTTG 57.481 32.000 13.11 13.11 45.86 2.44
746 747 7.286546 TGAATTGGATTTTCTTTCACCACTACA 59.713 33.333 0.00 0.00 0.00 2.74
781 782 5.067283 ACAGAAAACACTAACATTTCCGCTT 59.933 36.000 0.00 0.00 34.39 4.68
795 796 1.202710 TCCGCTTGCTTTCAACCACTA 60.203 47.619 0.00 0.00 0.00 2.74
1021 4690 2.108970 TGAAATATGCCATGCCAGCAA 58.891 42.857 0.00 0.00 44.83 3.91
1245 4914 2.101249 GGAGATGCACAGAGGAAGAGAG 59.899 54.545 0.00 0.00 0.00 3.20
1293 4962 6.176183 ACTCAATCAAGAAACAAGATCGGAT 58.824 36.000 0.00 0.00 0.00 4.18
1358 5027 1.418334 AGGCAGCCGATAAGTCATCT 58.582 50.000 5.55 0.00 0.00 2.90
1469 5138 3.508402 AGAACCCGCGGTTTTGAAATAAT 59.492 39.130 26.12 0.00 46.95 1.28
1846 5516 9.152595 GAAATCTTCCTACTCGAACAATAAGTT 57.847 33.333 0.00 0.00 44.93 2.66
2019 5689 4.594920 CCTAACATAGGTCACATCCCTCAT 59.405 45.833 0.00 0.00 41.18 2.90
2434 6105 1.198094 TCTCTCGGGAAACATGGCCA 61.198 55.000 8.56 8.56 0.00 5.36
2663 6338 1.990160 TTGCCGGTGACCTTTGTCCT 61.990 55.000 1.90 0.00 41.01 3.85
2666 6341 1.263356 CCGGTGACCTTTGTCCTCTA 58.737 55.000 0.00 0.00 41.01 2.43
2766 6445 5.016245 AGTGATTTCCCCTTTATTTCCCTCA 59.984 40.000 0.00 0.00 0.00 3.86
2847 6526 4.524714 GCCTATTATCAGTGGTCAGCTCTA 59.475 45.833 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
245 246 7.652507 ACGAAACTCGAAAGAAGATCTAGTTTT 59.347 33.333 15.29 8.3 43.74 2.43
261 262 2.753452 AGCCATAGAGAACGAAACTCGA 59.247 45.455 2.59 0.0 43.74 4.04
294 295 4.345257 AGAAGAGAGTGAAACAGGCAGTAA 59.655 41.667 0.00 0.0 41.43 2.24
707 708 7.992180 AAATCCAATTCAAATATCTCAACGC 57.008 32.000 0.00 0.0 0.00 4.84
746 747 3.558418 AGTGTTTTCTGTGCGTTACGATT 59.442 39.130 9.62 0.0 0.00 3.34
781 782 3.290948 AAGTGGTAGTGGTTGAAAGCA 57.709 42.857 0.00 0.0 0.00 3.91
795 796 1.768870 ACAGTGCTCAGGTAAAGTGGT 59.231 47.619 0.00 0.0 0.00 4.16
1021 4690 8.976986 AGTAGACGACACGTTTTAAATCTTAT 57.023 30.769 0.00 0.0 41.37 1.73
1293 4962 0.245539 GGAGACGAACCGGAATCACA 59.754 55.000 9.46 0.0 0.00 3.58
1358 5027 7.039363 CCAGTCCATTATTCAAACAAACCCTTA 60.039 37.037 0.00 0.0 0.00 2.69
1674 5344 7.921786 TGTTCTTTCAAAGTCTTCTTCTTGA 57.078 32.000 0.00 0.0 32.90 3.02
2019 5689 7.890127 AGGTTTGGATCTTTCAATCTTATGTCA 59.110 33.333 0.00 0.0 0.00 3.58
2188 5858 8.016054 GGGATCCCTATCTTTATCTCTATCCAT 58.984 40.741 24.69 0.0 32.56 3.41
2412 6083 1.139853 GCCATGTTTCCCGAGAGAGAT 59.860 52.381 0.00 0.0 0.00 2.75
2434 6105 7.702348 CCGTGTGAAAAGAAAGAAGAGAAATTT 59.298 33.333 0.00 0.0 0.00 1.82
2508 6179 3.587061 TGGAGAATGCACTCTTCCCTTTA 59.413 43.478 0.00 0.0 37.13 1.85
2663 6338 3.129109 CGCCAGTCACTCGTACTATAGA 58.871 50.000 6.78 0.0 0.00 1.98
2666 6341 0.381089 GCGCCAGTCACTCGTACTAT 59.619 55.000 0.00 0.0 0.00 2.12
2766 6445 0.890996 CTTGTTTCCCCTTGCGCTCT 60.891 55.000 9.73 0.0 0.00 4.09
2847 6526 5.071250 GGTTCTTTTTCCCCTGGTTTGTATT 59.929 40.000 0.00 0.0 0.00 1.89


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

AutoCloner maintained by Alex Coulton.