Multiple sequence alignment - TraesCS1B01G170800

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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 TraesCS1B01G170800 chr1B 100.000 2640 0 0 1 2640 302772357 302769718 0 4876
1 TraesCS1B01G170800 chr7B 98.750 2640 31 1 1 2640 102652613 102655250 0 4691
2 TraesCS1B01G170800 chr7B 98.859 2454 27 1 1 2454 133432652 133430200 0 4375
3 TraesCS1B01G170800 chr7B 92.429 700 41 6 1953 2640 235456169 235455470 0 989
4 TraesCS1B01G170800 chr5B 98.674 2640 35 0 1 2640 351469615 351466976 0 4682
5 TraesCS1B01G170800 chr5B 97.992 2640 50 2 1 2640 471294932 471292296 0 4578
6 TraesCS1B01G170800 chr5B 98.248 2455 41 2 1 2454 433002512 433000059 0 4294
7 TraesCS1B01G170800 chr4B 98.561 2640 35 2 1 2640 649623168 649625804 0 4662
8 TraesCS1B01G170800 chr4B 98.372 2641 33 3 1 2640 655790979 655793610 0 4630
9 TraesCS1B01G170800 chr7A 98.297 2642 39 5 1 2640 16005012 16007649 0 4625
10 TraesCS1B01G170800 chr4A 98.878 2406 26 1 1 2406 735292696 735295100 0 4292
11 TraesCS1B01G170800 chr2B 91.501 706 47 7 1947 2640 717653971 717654675 0 959
12 TraesCS1B01G170800 chr6B 87.779 761 43 18 1913 2640 661053590 661054333 0 845


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 TraesCS1B01G170800 chr1B 302769718 302772357 2639 True 4876 4876 100.000 1 2640 1 chr1B.!!$R1 2639
1 TraesCS1B01G170800 chr7B 102652613 102655250 2637 False 4691 4691 98.750 1 2640 1 chr7B.!!$F1 2639
2 TraesCS1B01G170800 chr7B 133430200 133432652 2452 True 4375 4375 98.859 1 2454 1 chr7B.!!$R1 2453
3 TraesCS1B01G170800 chr7B 235455470 235456169 699 True 989 989 92.429 1953 2640 1 chr7B.!!$R2 687
4 TraesCS1B01G170800 chr5B 351466976 351469615 2639 True 4682 4682 98.674 1 2640 1 chr5B.!!$R1 2639
5 TraesCS1B01G170800 chr5B 471292296 471294932 2636 True 4578 4578 97.992 1 2640 1 chr5B.!!$R3 2639
6 TraesCS1B01G170800 chr5B 433000059 433002512 2453 True 4294 4294 98.248 1 2454 1 chr5B.!!$R2 2453
7 TraesCS1B01G170800 chr4B 649623168 649625804 2636 False 4662 4662 98.561 1 2640 1 chr4B.!!$F1 2639
8 TraesCS1B01G170800 chr4B 655790979 655793610 2631 False 4630 4630 98.372 1 2640 1 chr4B.!!$F2 2639
9 TraesCS1B01G170800 chr7A 16005012 16007649 2637 False 4625 4625 98.297 1 2640 1 chr7A.!!$F1 2639
10 TraesCS1B01G170800 chr4A 735292696 735295100 2404 False 4292 4292 98.878 1 2406 1 chr4A.!!$F1 2405
11 TraesCS1B01G170800 chr2B 717653971 717654675 704 False 959 959 91.501 1947 2640 1 chr2B.!!$F1 693
12 TraesCS1B01G170800 chr6B 661053590 661054333 743 False 845 845 87.779 1913 2640 1 chr6B.!!$F1 727

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
766 772 0.038159 GGTCGAGCTAGCACAAGTGT 60.038 55.0 18.83 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 1942 0.979709 CTGGATCTGGGAGGCAGACA 60.98 60.0 0.0 0.0 0.0 3.41 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
718 724 2.231478 GTGCTAGAGGTGCTAGTGTTCA 59.769 50.000 0.00 0.0 46.81 3.18
766 772 0.038159 GGTCGAGCTAGCACAAGTGT 60.038 55.000 18.83 0.0 0.00 3.55
1053 1059 1.813859 CGCGGACCAAGAGGACATA 59.186 57.895 0.00 0.0 38.69 2.29
1059 1065 2.235402 GGACCAAGAGGACATACCGAAA 59.765 50.000 0.00 0.0 44.74 3.46
1220 1226 3.054508 TGTCCCAACTATGCACATGATCA 60.055 43.478 0.00 0.0 0.00 2.92
1823 1829 8.851541 ATGCTTTGTTCATATTTTTGGTTGAT 57.148 26.923 0.00 0.0 0.00 2.57
1891 1897 6.816140 TGCTAAGCAAAAACTTAAACAAGCTT 59.184 30.769 0.00 0.0 42.87 3.74
1905 1911 3.663025 ACAAGCTTTGTGCAAAAACACT 58.337 36.364 0.00 0.0 43.48 3.55
1936 1942 4.722700 GACGCCAGGGTGCATGGT 62.723 66.667 6.68 0.0 40.17 3.55
2128 2134 2.348998 GCAGGTGACCAGACAGGG 59.651 66.667 3.63 0.0 43.89 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
718 724 1.577736 AGCACTTGTGCTCCCTCTAT 58.422 50.000 20.95 0.0 42.12 1.98
766 772 0.541063 TGCTCGACCACCACCTCTAA 60.541 55.000 0.00 0.0 0.00 2.10
1059 1065 2.113139 CTGGCCTCCAACCACGTT 59.887 61.111 3.32 0.0 30.80 3.99
1220 1226 0.036765 TGCGTTAGTTGGCCTTCGAT 60.037 50.000 3.32 0.0 0.00 3.59
1402 1408 1.017177 TCCGTAACCAATCTGCACGC 61.017 55.000 0.00 0.0 0.00 5.34
1566 1572 2.202878 GTGCATCGCGAGCCCTTA 60.203 61.111 16.66 0.0 0.00 2.69
1882 1888 4.514816 AGTGTTTTTGCACAAAGCTTGTTT 59.485 33.333 0.00 0.0 43.23 2.83
1891 1897 1.410882 GGGCCTAGTGTTTTTGCACAA 59.589 47.619 0.84 0.0 41.52 3.33
1905 1911 3.000819 CGTCTGGGTGTGGGCCTA 61.001 66.667 4.53 0.0 0.00 3.93
1936 1942 0.979709 CTGGATCTGGGAGGCAGACA 60.980 60.000 0.00 0.0 0.00 3.41
2128 2134 1.016130 CCATCAGACACACCAGACGC 61.016 60.000 0.00 0.0 0.00 5.19
2476 2523 3.131933 ACCGATTTGTGAGAGATCTGAGG 59.868 47.826 0.00 0.0 0.00 3.86
2477 2524 4.358851 GACCGATTTGTGAGAGATCTGAG 58.641 47.826 0.00 0.0 0.00 3.35
2598 2645 3.118149 ACCACGAGGAAAACAAACTAGGT 60.118 43.478 5.68 0.0 38.69 3.08


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

AutoCloner maintained by Alex Coulton.