Multiple sequence alignment - TraesCS4B01G146900

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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 TraesCS4B01G146900 chr4B 100.000 2324 0 0 1 2324 209242458 209244781 0 4292
1 TraesCS4B01G146900 chr3B 97.245 2323 62 2 3 2324 483333115 483335436 0 3934
2 TraesCS4B01G146900 chr3B 96.859 2324 70 3 3 2324 575839839 575837517 0 3884
3 TraesCS4B01G146900 chr2A 97.073 2323 67 1 3 2324 750453688 750451366 0 3912
4 TraesCS4B01G146900 chr6A 96.816 2324 70 4 3 2324 155857202 155859523 0 3879
5 TraesCS4B01G146900 chr6A 96.685 2323 74 3 3 2324 375860856 375858536 0 3860
6 TraesCS4B01G146900 chr4A 96.040 2323 90 2 3 2324 350172143 350174464 0 3779
7 TraesCS4B01G146900 chr3A 96.098 1999 64 10 337 2324 230228524 230226529 0 3247
8 TraesCS4B01G146900 chr7A 98.433 1404 22 0 3 1406 60084839 60086242 0 2471
9 TraesCS4B01G146900 chr7B 98.294 1407 24 0 3 1409 742948835 742947429 0 2466
10 TraesCS4B01G146900 chrUn 98.635 1026 13 1 1300 2324 261512824 261511799 0 1816
11 TraesCS4B01G146900 chr5B 98.635 1026 13 1 1300 2324 439641088 439642113 0 1816
12 TraesCS4B01G146900 chr6B 92.946 723 49 2 1153 1874 401858415 401859136 0 1051


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 TraesCS4B01G146900 chr4B 209242458 209244781 2323 False 4292 4292 100.000 1 2324 1 chr4B.!!$F1 2323
1 TraesCS4B01G146900 chr3B 483333115 483335436 2321 False 3934 3934 97.245 3 2324 1 chr3B.!!$F1 2321
2 TraesCS4B01G146900 chr3B 575837517 575839839 2322 True 3884 3884 96.859 3 2324 1 chr3B.!!$R1 2321
3 TraesCS4B01G146900 chr2A 750451366 750453688 2322 True 3912 3912 97.073 3 2324 1 chr2A.!!$R1 2321
4 TraesCS4B01G146900 chr6A 155857202 155859523 2321 False 3879 3879 96.816 3 2324 1 chr6A.!!$F1 2321
5 TraesCS4B01G146900 chr6A 375858536 375860856 2320 True 3860 3860 96.685 3 2324 1 chr6A.!!$R1 2321
6 TraesCS4B01G146900 chr4A 350172143 350174464 2321 False 3779 3779 96.040 3 2324 1 chr4A.!!$F1 2321
7 TraesCS4B01G146900 chr3A 230226529 230228524 1995 True 3247 3247 96.098 337 2324 1 chr3A.!!$R1 1987
8 TraesCS4B01G146900 chr7A 60084839 60086242 1403 False 2471 2471 98.433 3 1406 1 chr7A.!!$F1 1403
9 TraesCS4B01G146900 chr7B 742947429 742948835 1406 True 2466 2466 98.294 3 1409 1 chr7B.!!$R1 1406
10 TraesCS4B01G146900 chrUn 261511799 261512824 1025 True 1816 1816 98.635 1300 2324 1 chrUn.!!$R1 1024
11 TraesCS4B01G146900 chr5B 439641088 439642113 1025 False 1816 1816 98.635 1300 2324 1 chr5B.!!$F1 1024
12 TraesCS4B01G146900 chr6B 401858415 401859136 721 False 1051 1051 92.946 1153 1874 1 chr6B.!!$F1 721

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
354 355 0.035630 AGTCAGACCTTGATGCTGCC 60.036 55.000 0.0 0.0 38.29 4.85 F
1073 1076 1.597663 ACAGCGAAGGAAAAACGTGAG 59.402 47.619 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1164 0.098728 GGACATTTCCAATGCCGACG 59.901 55.000 0.0 0.0 42.3 5.12 R
2066 2072 3.492656 GCAATGGTTGATAGAGCGAGGTA 60.493 47.826 0.0 0.0 0.0 3.08 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
50 51 4.530710 TCTTAGAAAGAGCCGCTAAACA 57.469 40.909 0.00 0.00 32.71 2.83
65 66 3.616560 GCTAAACAATCGGACCAGACAGA 60.617 47.826 0.00 0.00 0.00 3.41
335 336 1.922135 GCCGCCTTCGCTCAATTTGA 61.922 55.000 0.00 0.00 0.00 2.69
354 355 0.035630 AGTCAGACCTTGATGCTGCC 60.036 55.000 0.00 0.00 38.29 4.85
381 382 2.802816 GGCATTACTGAATAGAGGTGCG 59.197 50.000 0.00 0.00 32.68 5.34
580 581 7.994334 TCTTAGAAAAAGGTGGCTTAACTAACA 59.006 33.333 0.00 0.00 0.00 2.41
1073 1076 1.597663 ACAGCGAAGGAAAAACGTGAG 59.402 47.619 0.00 0.00 0.00 3.51
1759 1765 5.363580 AGAAAGTTTTGGAAAATGGAGCTGA 59.636 36.000 0.00 0.00 0.00 4.26
1932 1938 1.713647 TCCCCCTAATGGCTTTTCACA 59.286 47.619 0.00 0.00 0.00 3.58
2066 2072 4.035112 TCGGTCTACCCAATCAAGGTTAT 58.965 43.478 0.00 0.00 38.89 1.89
2244 2258 6.893020 AGATGGTATATAAACATCTCCCCC 57.107 41.667 18.59 0.31 45.99 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.014230 CGGGAATGTAAATAGAAAACATCCCAT 59.986 37.037 15.84 0.0 38.98 4.00
1 2 6.320164 CGGGAATGTAAATAGAAAACATCCCA 59.680 38.462 15.84 0.0 38.98 4.37
50 51 0.904649 TGCATCTGTCTGGTCCGATT 59.095 50.000 0.00 0.0 0.00 3.34
84 85 4.320935 GCTTGTGTTTCAATCACGGGTAAT 60.321 41.667 0.00 0.0 38.48 1.89
335 336 0.035630 GGCAGCATCAAGGTCTGACT 60.036 55.000 7.85 0.0 36.69 3.41
354 355 5.163364 ACCTCTATTCAGTAATGCCTGAGTG 60.163 44.000 0.00 0.0 42.16 3.51
369 370 2.100916 TGTAAGCCTCGCACCTCTATTC 59.899 50.000 0.00 0.0 0.00 1.75
381 382 0.324943 TGGGCACTTCTGTAAGCCTC 59.675 55.000 0.00 0.0 46.23 4.70
469 470 2.306341 AGTGGCATTCGATCACAGAG 57.694 50.000 0.00 0.0 34.17 3.35
580 581 5.082425 AGCATCTGGTTCCATCTTTCTTTT 58.918 37.500 0.00 0.0 0.00 2.27
1123 1126 2.184020 ATTGTAGCAGCTCCGGCACA 62.184 55.000 0.00 0.0 41.70 4.57
1161 1164 0.098728 GGACATTTCCAATGCCGACG 59.901 55.000 0.00 0.0 42.30 5.12
1167 1170 5.972107 AAGAACTGAGGACATTTCCAATG 57.028 39.130 0.00 0.0 45.72 2.82
1176 1179 5.707298 GGAATGAATCAAAGAACTGAGGACA 59.293 40.000 0.00 0.0 0.00 4.02
1759 1765 3.118149 AGGGACCAAAGTAGTGAAAACGT 60.118 43.478 0.00 0.0 0.00 3.99
2066 2072 3.492656 GCAATGGTTGATAGAGCGAGGTA 60.493 47.826 0.00 0.0 0.00 3.08
2244 2258 5.777732 AGATACTATAGCACCTTCCCTTCAG 59.222 44.000 0.00 0.0 0.00 3.02


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

AutoCloner maintained by Alex Coulton.