Multiple sequence alignment - TraesCS6B01G216400

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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 TraesCS6B01G216400 chr6B 100.000 2573 0 0 1 2573 297468432 297471004 0 4752
1 TraesCS6B01G216400 chr5A 97.608 2592 43 4 1 2573 19253511 19250920 0 4425
2 TraesCS6B01G216400 chr7B 97.492 2592 46 4 1 2573 716883443 716880852 0 4409
3 TraesCS6B01G216400 chr7B 97.452 2590 49 4 1 2573 742984782 742987371 0 4401
4 TraesCS6B01G216400 chr7B 97.414 2591 49 4 1 2573 716843202 716840612 0 4397
5 TraesCS6B01G216400 chr6D 97.486 2586 48 10 1 2573 124512872 124515453 0 4399
6 TraesCS6B01G216400 chr7D 97.332 2586 52 11 1 2573 203495347 203497928 0 4377
7 TraesCS6B01G216400 chr7A 97.299 2592 46 8 1 2573 120845814 120843228 0 4377
8 TraesCS6B01G216400 chr2B 96.988 2590 61 4 1 2573 112836374 112838963 0 4335
9 TraesCS6B01G216400 chr2B 97.157 2075 42 4 1 2059 391081513 391079440 0 3489
10 TraesCS6B01G216400 chr1A 96.740 2423 44 12 168 2573 498695700 498693296 0 4004
11 TraesCS6B01G216400 chrUn 97.488 2229 37 4 364 2573 332213293 332211065 0 3788
12 TraesCS6B01G216400 chr1B 96.877 2081 45 5 1 2065 672558794 672556718 0 3465
13 TraesCS6B01G216400 chr6A 97.137 1991 40 4 600 2573 84400236 84398246 0 3345


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 TraesCS6B01G216400 chr6B 297468432 297471004 2572 False 4752 4752 100.000 1 2573 1 chr6B.!!$F1 2572
1 TraesCS6B01G216400 chr5A 19250920 19253511 2591 True 4425 4425 97.608 1 2573 1 chr5A.!!$R1 2572
2 TraesCS6B01G216400 chr7B 716880852 716883443 2591 True 4409 4409 97.492 1 2573 1 chr7B.!!$R2 2572
3 TraesCS6B01G216400 chr7B 742984782 742987371 2589 False 4401 4401 97.452 1 2573 1 chr7B.!!$F1 2572
4 TraesCS6B01G216400 chr7B 716840612 716843202 2590 True 4397 4397 97.414 1 2573 1 chr7B.!!$R1 2572
5 TraesCS6B01G216400 chr6D 124512872 124515453 2581 False 4399 4399 97.486 1 2573 1 chr6D.!!$F1 2572
6 TraesCS6B01G216400 chr7D 203495347 203497928 2581 False 4377 4377 97.332 1 2573 1 chr7D.!!$F1 2572
7 TraesCS6B01G216400 chr7A 120843228 120845814 2586 True 4377 4377 97.299 1 2573 1 chr7A.!!$R1 2572
8 TraesCS6B01G216400 chr2B 112836374 112838963 2589 False 4335 4335 96.988 1 2573 1 chr2B.!!$F1 2572
9 TraesCS6B01G216400 chr2B 391079440 391081513 2073 True 3489 3489 97.157 1 2059 1 chr2B.!!$R1 2058
10 TraesCS6B01G216400 chr1A 498693296 498695700 2404 True 4004 4004 96.740 168 2573 1 chr1A.!!$R1 2405
11 TraesCS6B01G216400 chrUn 332211065 332213293 2228 True 3788 3788 97.488 364 2573 1 chrUn.!!$R1 2209
12 TraesCS6B01G216400 chr1B 672556718 672558794 2076 True 3465 3465 96.877 1 2065 1 chr1B.!!$R1 2064
13 TraesCS6B01G216400 chr6A 84398246 84400236 1990 True 3345 3345 97.137 600 2573 1 chr6A.!!$R1 1973

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
763 766 1.226859 CCGAGCGATGGTTTAGCGA 60.227 57.895 0.0 0.0 41.6 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 1921 0.958822 TACTGACACTGAGCGAGCAA 59.041 50.0 0.0 0.0 0.0 3.91 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
49 50 9.924010 AACTGATTCTACCTTACTAGTGAGTAT 57.076 33.333 13.16 4.29 37.99 2.12
62 63 3.679389 AGTGAGTATTGCTTCCACCTTG 58.321 45.455 0.00 0.00 0.00 3.61
152 153 3.634397 AATCTAGCTGCCTTAACTGCA 57.366 42.857 0.00 0.00 37.00 4.41
161 162 4.226427 TGCCTTAACTGCAGATGATTCT 57.774 40.909 23.35 0.00 34.05 2.40
226 227 4.238514 GCCTCAAGCGTATAGATACCAAG 58.761 47.826 0.00 0.00 0.00 3.61
622 624 7.816640 TCAGAACAATAAAATAGAACCTGCAC 58.183 34.615 0.00 0.00 0.00 4.57
763 766 1.226859 CCGAGCGATGGTTTAGCGA 60.227 57.895 0.00 0.00 41.60 4.93
1044 1061 8.344939 TCCAATATAGTTGGGAGATTTTACCT 57.655 34.615 6.95 0.00 39.96 3.08
1170 1187 8.122472 CCTATACAAGGGTTCAAGTTTCAATT 57.878 34.615 0.00 0.00 42.32 2.32
1187 1204 3.631686 TCAATTGATATTTGCGGAGTGGG 59.368 43.478 3.38 0.00 0.00 4.61
1353 1370 3.131400 GGGAGCGAGAAGTATGGGATATC 59.869 52.174 0.00 0.00 0.00 1.63
1402 1419 4.445052 CGGATTTACGCCGTATATCAACAA 59.555 41.667 22.91 4.30 43.66 2.83
1443 1460 6.148811 GTCATCCATTACGAAAAGACTTTCCA 59.851 38.462 0.00 0.00 38.17 3.53
1768 1791 7.554835 TGGAAGAAGTAAAGAAAAAGTACTGCA 59.445 33.333 0.00 0.00 0.00 4.41
1897 1921 3.627577 CGGAAACTATTGCCTATGCTTGT 59.372 43.478 0.00 0.00 38.71 3.16
1989 2013 1.852942 GACTGTTGCACTTCACTCGA 58.147 50.000 0.00 0.00 0.00 4.04
2059 2083 3.075005 TCGCCTCCTTTCCTCCGG 61.075 66.667 0.00 0.00 0.00 5.14
2075 2099 0.811616 CCGGCGAAAGATGCTTAGCT 60.812 55.000 9.30 0.00 0.00 3.32
2097 2121 3.069318 GCGACGAAGGAGGGGAGT 61.069 66.667 0.00 0.00 0.00 3.85
2209 2233 8.711170 ACTAAATGACCTTATTTATTCTCCCGA 58.289 33.333 0.00 0.00 33.43 5.14
2238 2262 8.029522 CGCTAGCAAATCTAATAGTTCCATCTA 58.970 37.037 16.45 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 0.476338 TAGTGGCAAGGTGGAAGCAA 59.524 50.000 0.00 0.00 36.26 3.91
152 153 9.160496 GTATTCAACACTCTTCAAGAATCATCT 57.840 33.333 0.00 0.00 37.57 2.90
161 162 4.518970 GGCTTGGTATTCAACACTCTTCAA 59.481 41.667 0.00 0.00 0.00 2.69
226 227 6.459923 AGTAGCTTACCTATGCTTAAGATGC 58.540 40.000 6.67 0.00 40.35 3.91
763 766 5.394115 GGATGCTTGGTTACAATTCCGAATT 60.394 40.000 0.17 0.17 35.73 2.17
1074 1091 8.742125 TGGTATAAGATCTATTCCCATGTTCT 57.258 34.615 0.00 0.00 0.00 3.01
1105 1122 4.262420 GCACAACAATGGAAATGGGTAGTT 60.262 41.667 0.00 0.00 0.00 2.24
1167 1184 3.631250 ACCCACTCCGCAAATATCAATT 58.369 40.909 0.00 0.00 0.00 2.32
1170 1187 1.557371 TGACCCACTCCGCAAATATCA 59.443 47.619 0.00 0.00 0.00 2.15
1353 1370 5.005740 TGATTGATGGAAGAAACACCAGAG 58.994 41.667 0.00 0.00 39.62 3.35
1402 1419 4.080015 TGGATGACCCTCGAAACCATAATT 60.080 41.667 0.00 0.00 35.38 1.40
1443 1460 4.098044 CGTACTTCCACATATCCACTCAGT 59.902 45.833 0.00 0.00 0.00 3.41
1768 1791 4.079970 TGCCCTTTCGTATAGATCGAGAT 58.920 43.478 0.00 0.00 38.52 2.75
1897 1921 0.958822 TACTGACACTGAGCGAGCAA 59.041 50.000 0.00 0.00 0.00 3.91
1989 2013 2.417933 GAGCAAGTGAATGAACGAGCAT 59.582 45.455 0.00 0.00 0.00 3.79
2059 2083 4.707210 CTTCTAGCTAAGCATCTTTCGC 57.293 45.455 0.00 0.00 0.00 4.70
2075 2099 1.035932 CCCCTCCTTCGTCGCTTCTA 61.036 60.000 0.00 0.00 0.00 2.10
2097 2121 1.227102 CATCATCGGCCTTCCCCAA 59.773 57.895 0.00 0.00 0.00 4.12
2209 2233 6.821665 TGGAACTATTAGATTTGCTAGCGTTT 59.178 34.615 10.77 0.00 0.00 3.60
2323 2347 2.102109 TTTTGACCGCTCGGCCACTA 62.102 55.000 8.41 0.00 39.32 2.74
2353 2377 8.617290 ACGTAGAAAACCTTCAACAGATTTAT 57.383 30.769 0.00 0.00 33.64 1.40


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

AutoCloner maintained by Alex Coulton.