Multiple sequence alignment - TraesCS3A01G502700

Loading Multiple Alignment...

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 TraesCS3A01G502700 chr3A 100.000 2646 0 0 1 2646 725803458 725800813 0 4887
1 TraesCS3A01G502700 chrUn 98.411 2643 42 0 1 2643 186201715 186204357 0 4649
2 TraesCS3A01G502700 chr1A 98.299 2646 42 2 1 2646 498684525 498687167 0 4634
3 TraesCS3A01G502700 chr7B 98.262 2646 46 0 1 2646 742996151 742993506 0 4632
4 TraesCS3A01G502700 chr7B 98.224 2646 46 1 1 2646 716872076 716874720 0 4625
5 TraesCS3A01G502700 chr5A 98.186 2646 48 0 1 2646 492862433 492859788 0 4621
6 TraesCS3A01G502700 chr4A 97.922 2647 53 2 1 2646 67603672 67601027 0 4582
7 TraesCS3A01G502700 chr2B 97.732 2646 60 0 1 2646 391167714 391165069 0 4554
8 TraesCS3A01G502700 chr4B 97.695 2646 59 2 1 2646 209306366 209303723 0 4547


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 TraesCS3A01G502700 chr3A 725800813 725803458 2645 True 4887 4887 100.000 1 2646 1 chr3A.!!$R1 2645
1 TraesCS3A01G502700 chrUn 186201715 186204357 2642 False 4649 4649 98.411 1 2643 1 chrUn.!!$F1 2642
2 TraesCS3A01G502700 chr1A 498684525 498687167 2642 False 4634 4634 98.299 1 2646 1 chr1A.!!$F1 2645
3 TraesCS3A01G502700 chr7B 742993506 742996151 2645 True 4632 4632 98.262 1 2646 1 chr7B.!!$R1 2645
4 TraesCS3A01G502700 chr7B 716872076 716874720 2644 False 4625 4625 98.224 1 2646 1 chr7B.!!$F1 2645
5 TraesCS3A01G502700 chr5A 492859788 492862433 2645 True 4621 4621 98.186 1 2646 1 chr5A.!!$R1 2645
6 TraesCS3A01G502700 chr4A 67601027 67603672 2645 True 4582 4582 97.922 1 2646 1 chr4A.!!$R1 2645
7 TraesCS3A01G502700 chr2B 391165069 391167714 2645 True 4554 4554 97.732 1 2646 1 chr2B.!!$R1 2645
8 TraesCS3A01G502700 chr4B 209303723 209306366 2643 True 4547 4547 97.695 1 2646 1 chr4B.!!$R1 2645

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
332 334 0.107831 ACCTGACACCGCTTTGCTAA 59.892 50.0 0.0 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2114 0.322816 ATGGGCACGCTGAACAATCT 60.323 50.0 0.0 0.0 0.0 2.4 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
65 66 4.018960 AGGCACTACATGAACAAGAAGGAT 60.019 41.667 0.00 0.00 36.02 3.24
131 132 4.118093 TGTCTCAGTCAAAGTTCGACAA 57.882 40.909 0.00 0.00 35.77 3.18
206 208 3.197766 AGTGCCATCATTAGAAAGTCCGA 59.802 43.478 0.00 0.00 0.00 4.55
332 334 0.107831 ACCTGACACCGCTTTGCTAA 59.892 50.000 0.00 0.00 0.00 3.09
520 523 1.227263 GGATAGAGCGCCGCAAGAA 60.227 57.895 13.36 0.00 43.02 2.52
573 576 2.820787 AGAATTCTGGTCTCTCGAACGT 59.179 45.455 7.30 0.00 0.00 3.99
642 645 5.755849 TGGAGGAAAGGAGATTATTGGAAC 58.244 41.667 0.00 0.00 0.00 3.62
685 688 4.332428 AAGAACTACTGGCTGTAAACGT 57.668 40.909 5.72 0.00 0.00 3.99
723 726 6.013119 TCCTCCTAAAACCCTTTTCGATAGTT 60.013 38.462 0.00 0.00 34.19 2.24
1192 1195 7.538334 TCATTAATGCTTTCAAACTCGATTGTG 59.462 33.333 10.76 0.00 0.00 3.33
1203 1206 3.782046 ACTCGATTGTGAACTATTCCCG 58.218 45.455 0.00 0.00 0.00 5.14
1297 1300 0.099968 CATTCCAGCCAATGACAGCG 59.900 55.000 0.00 0.00 36.03 5.18
1540 1543 2.705658 TCTACTATCCAACTGCCATGGG 59.294 50.000 15.13 0.00 38.54 4.00
1579 1582 1.202976 AGGCTCACATTCTGGCACTTT 60.203 47.619 0.00 0.00 0.00 2.66
2111 2114 1.530419 GTGTTGTGGGTGGCCATCA 60.530 57.895 20.00 13.03 0.00 3.07
2405 2408 1.046472 TCACCTCACTGGACCAACGT 61.046 55.000 0.00 0.00 39.71 3.99
2506 2509 5.445939 CGTACTATGCGCAATGAAAGTTTCT 60.446 40.000 17.11 0.00 0.00 2.52
2592 2595 4.201657 CCATACTGGCATGAAACTGATCA 58.798 43.478 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 8.295288 GCAGCCGACTTATAATTCTAGTTACTA 58.705 37.037 1.85 0.00 0.00 1.82
131 132 0.687427 ACAGCAACTGTTTTGCCCCT 60.687 50.000 5.38 0.00 42.59 4.79
206 208 4.892934 TGAACTGGCTGAAACTAAAATGGT 59.107 37.500 0.00 0.00 0.00 3.55
332 334 6.293680 GCAACTTCTCTTCCTCTTTCGAAAAT 60.294 38.462 12.41 0.00 0.00 1.82
520 523 4.897670 CCTTCCCTTCAATATGCCATCTTT 59.102 41.667 0.00 0.00 0.00 2.52
573 576 2.228103 CGGCTCGTATTAGTATGCCAGA 59.772 50.000 0.00 0.00 40.27 3.86
642 645 0.745468 GGGCGTAACTCCCTCTAGTG 59.255 60.000 0.00 0.00 40.66 2.74
685 688 0.543883 AGGAGGAGCAGAGCAAGTCA 60.544 55.000 0.00 0.00 0.00 3.41
959 962 2.856760 AGGTCATCCTCTTCAGCCTA 57.143 50.000 0.00 0.00 40.58 3.93
1192 1195 6.073167 GCTTATCTTTTAGGCGGGAATAGTTC 60.073 42.308 0.00 0.00 0.00 3.01
1203 1206 8.943909 TGAAGTAGTAAGCTTATCTTTTAGGC 57.056 34.615 9.88 4.31 36.25 3.93
1289 1292 3.321497 GAAAAGAGTGAGTCGCTGTCAT 58.679 45.455 11.81 0.00 0.00 3.06
1297 1300 3.060205 GTGCAGTTCGAAAAGAGTGAGTC 60.060 47.826 0.00 0.00 0.00 3.36
1540 1543 0.685097 TAGGGTGAACAGTGGTGCTC 59.315 55.000 0.00 0.00 0.00 4.26
1579 1582 2.101750 TCCTTTGAGTACACAGCGAACA 59.898 45.455 0.00 0.00 0.00 3.18
1670 1673 1.127343 GATAGGAGAAGGCCAGCTGT 58.873 55.000 13.81 0.00 0.00 4.40
2111 2114 0.322816 ATGGGCACGCTGAACAATCT 60.323 50.000 0.00 0.00 0.00 2.40
2313 2316 6.393897 TCTGATGGGAAATAGGACTAGGATT 58.606 40.000 0.00 0.00 0.00 3.01
2405 2408 0.034896 GACCAGCTTCCGACCAGAAA 59.965 55.000 0.00 0.00 0.00 2.52
2592 2595 4.161565 GGGTGTTTTTGAGGTCCTTTTTCT 59.838 41.667 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.