Multiple sequence alignment - TraesCS4A01G054100

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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 TraesCS4A01G054100 chr4A 100.000 2513 0 0 1 2513 45631396 45633908 0 4641
1 TraesCS4A01G054100 chr4A 96.743 614 14 2 1900 2513 9468754 9469361 0 1018
2 TraesCS4A01G054100 chr4A 96.580 614 13 3 1900 2513 246821249 246820644 0 1011
3 TraesCS4A01G054100 chr2A 96.823 2518 69 11 1 2513 677262024 677264535 0 4196
4 TraesCS4A01G054100 chr6A 96.457 2512 77 10 8 2513 484784646 484782141 0 4135
5 TraesCS4A01G054100 chr6A 95.749 2517 92 8 1 2513 176534599 176532094 0 4041
6 TraesCS4A01G054100 chr6A 96.417 614 15 3 1900 2513 357524783 357524177 0 1005
7 TraesCS4A01G054100 chr6D 96.172 2534 69 9 1 2511 451600147 451597619 0 4117
8 TraesCS4A01G054100 chr6D 96.340 2514 60 12 1 2490 459129172 459131677 0 4104
9 TraesCS4A01G054100 chr6D 95.671 2541 65 14 1 2513 397854470 397851947 0 4041
10 TraesCS4A01G054100 chr5A 96.261 2514 70 11 8 2513 13143396 13140899 0 4100
11 TraesCS4A01G054100 chr1A 96.253 2509 71 9 8 2513 519376696 519374208 0 4091
12 TraesCS4A01G054100 chr1A 96.743 614 13 3 1900 2513 517445084 517444478 0 1016
13 TraesCS4A01G054100 chr5D 96.047 2378 62 12 1 2353 58009615 58007245 0 3842


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 TraesCS4A01G054100 chr4A 45631396 45633908 2512 False 4641 4641 100.000 1 2513 1 chr4A.!!$F2 2512
1 TraesCS4A01G054100 chr4A 9468754 9469361 607 False 1018 1018 96.743 1900 2513 1 chr4A.!!$F1 613
2 TraesCS4A01G054100 chr4A 246820644 246821249 605 True 1011 1011 96.580 1900 2513 1 chr4A.!!$R1 613
3 TraesCS4A01G054100 chr2A 677262024 677264535 2511 False 4196 4196 96.823 1 2513 1 chr2A.!!$F1 2512
4 TraesCS4A01G054100 chr6A 484782141 484784646 2505 True 4135 4135 96.457 8 2513 1 chr6A.!!$R3 2505
5 TraesCS4A01G054100 chr6A 176532094 176534599 2505 True 4041 4041 95.749 1 2513 1 chr6A.!!$R1 2512
6 TraesCS4A01G054100 chr6A 357524177 357524783 606 True 1005 1005 96.417 1900 2513 1 chr6A.!!$R2 613
7 TraesCS4A01G054100 chr6D 451597619 451600147 2528 True 4117 4117 96.172 1 2511 1 chr6D.!!$R2 2510
8 TraesCS4A01G054100 chr6D 459129172 459131677 2505 False 4104 4104 96.340 1 2490 1 chr6D.!!$F1 2489
9 TraesCS4A01G054100 chr6D 397851947 397854470 2523 True 4041 4041 95.671 1 2513 1 chr6D.!!$R1 2512
10 TraesCS4A01G054100 chr5A 13140899 13143396 2497 True 4100 4100 96.261 8 2513 1 chr5A.!!$R1 2505
11 TraesCS4A01G054100 chr1A 519374208 519376696 2488 True 4091 4091 96.253 8 2513 1 chr1A.!!$R2 2505
12 TraesCS4A01G054100 chr1A 517444478 517445084 606 True 1016 1016 96.743 1900 2513 1 chr1A.!!$R1 613
13 TraesCS4A01G054100 chr5D 58007245 58009615 2370 True 3842 3842 96.047 1 2353 1 chr5D.!!$R1 2352

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
569 580 1.751351 GAAATGCTCCAAACCCTAGCC 59.249 52.381 0.0 0.0 35.33 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1658 2.047061 ACTGGTAGTTGTCTTCTGCCA 58.953 47.619 3.15 3.15 43.31 4.92 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
569 580 1.751351 GAAATGCTCCAAACCCTAGCC 59.249 52.381 0.00 0.00 35.33 3.93
614 625 4.514585 AGCGCCAAACACCACCCA 62.515 61.111 2.29 0.00 0.00 4.51
695 706 3.999001 GTCCTTCTCGGGTTTTTACGATT 59.001 43.478 0.00 0.00 38.56 3.34
828 839 2.950990 AGCTTCCCCTTCTCCTCTTA 57.049 50.000 0.00 0.00 0.00 2.10
1052 1064 1.308998 CCACTGAAGCGGTTGACTTT 58.691 50.000 3.70 0.00 0.00 2.66
1089 1101 1.652563 GAACTTTGGGCGCGAGTTT 59.347 52.632 12.10 5.17 34.02 2.66
1287 1301 0.899717 GGTTGGGCTTGCTGGATTCA 60.900 55.000 0.00 0.00 0.00 2.57
1331 1345 0.700564 AATCTGCCCCATGACAGTGT 59.299 50.000 0.00 0.00 35.37 3.55
1644 1658 7.586747 TGTTAAGTTTCGACACTTTCAGTTTT 58.413 30.769 21.08 0.00 38.07 2.43
1666 1680 3.118038 TGGCAGAAGACAACTACCAGTTT 60.118 43.478 0.00 0.00 36.03 2.66
1753 1767 4.021104 TGACAGTAAGCAGTACTTGAGCAT 60.021 41.667 6.47 0.00 41.37 3.79
1808 1822 2.946329 TCTCGCACTTGCCAAACTTTTA 59.054 40.909 0.00 0.00 37.91 1.52
1829 1843 2.228059 TCCTCGAGTTCGTCAGTTCTT 58.772 47.619 12.31 0.00 40.80 2.52
2006 2028 6.257994 TGATTGCCCAATCTCTTCTATCTT 57.742 37.500 18.63 0.00 45.55 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
335 343 9.825972 TCTATCGAAATCAAGTTCAAATGTTTC 57.174 29.630 0.00 0.00 0.00 2.78
584 595 2.280186 GCGCTTGGTAGGATCCGG 60.280 66.667 5.98 0.00 0.00 5.14
614 625 1.652187 ATGCCTGCCCCACATCTGAT 61.652 55.000 0.00 0.00 0.00 2.90
695 706 6.212388 ACAATTTCATATGTAAAGTGGGGCAA 59.788 34.615 21.13 0.00 36.50 4.52
828 839 2.306805 TGCCTTTGTCTGTCAGATGGAT 59.693 45.455 5.68 0.00 0.00 3.41
1052 1064 3.205519 TCCCATTCTTCTCCTCCTTCA 57.794 47.619 0.00 0.00 0.00 3.02
1287 1301 0.684153 CACGGATTGCATTCCCCCTT 60.684 55.000 19.46 1.87 31.61 3.95
1644 1658 2.047061 ACTGGTAGTTGTCTTCTGCCA 58.953 47.619 3.15 3.15 43.31 4.92
1699 1713 3.388024 GCTAGGGTATGATCCAACACTCA 59.612 47.826 2.76 0.00 30.36 3.41
1753 1767 7.194112 TGAACTTGATGTATATCCCTTGTGA 57.806 36.000 0.00 0.00 32.09 3.58
1808 1822 2.438411 AGAACTGACGAACTCGAGGAT 58.562 47.619 18.41 4.87 43.02 3.24


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

AutoCloner maintained by Alex Coulton.