Multiple sequence alignment - TraesCS3A01G456800

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 TraesCS3A01G456800 chr3A 100.000 2815 0 0 1 2815 694367026 694364212 0 5199
1 TraesCS3A01G456800 chr5B 98.652 2819 34 3 1 2815 533066664 533069482 0 4992
2 TraesCS3A01G456800 chrUn 98.652 2818 34 4 1 2815 86455117 86457933 0 4990
3 TraesCS3A01G456800 chrUn 98.617 2819 35 3 1 2815 222680160 222677342 0 4987
4 TraesCS3A01G456800 chrUn 98.546 2819 36 4 1 2815 86449117 86451934 0 4974
5 TraesCS3A01G456800 chr1A 98.546 2820 36 3 1 2815 238117485 238120304 0 4975
6 TraesCS3A01G456800 chr1A 98.439 2819 39 4 1 2815 238121408 238124225 0 4957
7 TraesCS3A01G456800 chr6B 98.510 2818 38 4 1 2815 596628844 596631660 0 4968
8 TraesCS3A01G456800 chr3B 98.085 2820 49 3 1 2815 92326382 92329201 0 4903
9 TraesCS3A01G456800 chr2A 96.345 2818 89 12 1 2815 444294984 444292178 0 4621


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 TraesCS3A01G456800 chr3A 694364212 694367026 2814 True 5199 5199 100.0000 1 2815 1 chr3A.!!$R1 2814
1 TraesCS3A01G456800 chr5B 533066664 533069482 2818 False 4992 4992 98.6520 1 2815 1 chr5B.!!$F1 2814
2 TraesCS3A01G456800 chrUn 222677342 222680160 2818 True 4987 4987 98.6170 1 2815 1 chrUn.!!$R1 2814
3 TraesCS3A01G456800 chrUn 86449117 86457933 8816 False 4982 4990 98.5990 1 2815 2 chrUn.!!$F1 2814
4 TraesCS3A01G456800 chr1A 238117485 238124225 6740 False 4966 4975 98.4925 1 2815 2 chr1A.!!$F1 2814
5 TraesCS3A01G456800 chr6B 596628844 596631660 2816 False 4968 4968 98.5100 1 2815 1 chr6B.!!$F1 2814
6 TraesCS3A01G456800 chr3B 92326382 92329201 2819 False 4903 4903 98.0850 1 2815 1 chr3B.!!$F1 2814
7 TraesCS3A01G456800 chr2A 444292178 444294984 2806 True 4621 4621 96.3450 1 2815 1 chr2A.!!$R1 2814


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
909 911 2.238646 TCGGGGTCTTGAGCAATGTTAT 59.761 45.455 2.24 0.0 0.00 1.89 F
1618 1622 0.317160 ACCTTCACGAGCAATCGTCA 59.683 50.000 0.00 0.0 45.26 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 7757 0.616111 ACTCGTCCAGCCCTCTTCAT 60.616 55.000 0.0 0.0 0.00 2.57 R
2608 12537 8.004801 TCTCAATCCTTGACTCCAGTATGTATA 58.995 37.037 0.0 0.0 35.46 1.47 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
463 464 6.093495 TGAACGAGGCATATTAAAGTGAAAGG 59.907 38.462 0.00 0.00 0.00 3.11
540 541 5.620879 GCACTGGACTTTGGAATTGATTCTC 60.621 44.000 3.94 0.00 37.00 2.87
589 590 2.301296 CTGCTCAGGACGATCCCATTAT 59.699 50.000 0.00 0.00 37.19 1.28
909 911 2.238646 TCGGGGTCTTGAGCAATGTTAT 59.761 45.455 2.24 0.00 0.00 1.89
1080 1082 8.678593 AAACTTTTCTAGGAGAAGTTCGAATT 57.321 30.769 13.78 0.00 43.10 2.17
1100 1102 3.507103 TCGTTCCGTTCGGATATTGAA 57.493 42.857 14.70 0.00 33.87 2.69
1114 1116 4.142469 GGATATTGAACGGTCTTGGTTTGG 60.142 45.833 0.33 0.00 0.00 3.28
1123 1125 2.158827 GGTCTTGGTTTGGCATGGTTTT 60.159 45.455 0.00 0.00 0.00 2.43
1333 1337 3.099141 CCAGTTGCTATGGGGAACAAAT 58.901 45.455 7.40 0.00 46.57 2.32
1463 1467 3.387374 TGGGTGCAACATCAACAAATTCT 59.613 39.130 3.06 0.00 39.98 2.40
1618 1622 0.317160 ACCTTCACGAGCAATCGTCA 59.683 50.000 0.00 0.00 45.26 4.35
1753 7757 4.582240 TGTGGCATTGATTGTACAAGTTCA 59.418 37.500 14.65 10.84 33.22 3.18
2041 8045 1.403323 GCTCTTGTTGCCCTTCTATGC 59.597 52.381 0.00 0.00 0.00 3.14
2320 8328 6.149142 GCAGAATGGAAGGAATGCTATTCTAG 59.851 42.308 0.00 0.00 34.24 2.43
2652 12581 0.173708 GACCACTAGTGAGAAGGCCG 59.826 60.000 24.68 7.17 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 3.510388 TTCATCTCGCGAAGAATCAGT 57.490 42.857 11.33 0.00 37.61 3.41
463 464 1.891616 GGGACTCGACCTGGAACTC 59.108 63.158 0.00 0.00 0.00 3.01
540 541 4.087892 CTGAGCAGGTGGGGGTCG 62.088 72.222 0.00 0.00 35.60 4.79
589 590 0.999712 GTCCCCCTCCAGAAAATCCA 59.000 55.000 0.00 0.00 0.00 3.41
783 785 2.588877 CTAATCCCCCAGCACGCG 60.589 66.667 3.53 3.53 0.00 6.01
855 857 0.966920 GAAGTGGGACCGTCTCTTCA 59.033 55.000 17.82 4.57 35.85 3.02
1100 1102 1.178534 CCATGCCAAACCAAGACCGT 61.179 55.000 0.00 0.00 0.00 4.83
1114 1116 1.602191 CAGTAACGCGAAAACCATGC 58.398 50.000 15.93 0.00 0.00 4.06
1333 1337 6.899089 TGGAGGATTCTATTGTATTTCTGCA 58.101 36.000 0.00 0.00 0.00 4.41
1463 1467 8.134202 TCTTAGGTTGTAACTTGATCATGAGA 57.866 34.615 15.03 1.31 0.00 3.27
1505 1509 9.620660 GGAATGAACAAAATACGAACAGTTAAT 57.379 29.630 0.00 0.00 0.00 1.40
1636 1640 1.683943 AAGAGCAGCTGTGAAAAGCA 58.316 45.000 16.64 0.00 46.08 3.91
1727 7731 5.288804 ACTTGTACAATCAATGCCACAAAC 58.711 37.500 9.13 0.00 37.04 2.93
1753 7757 0.616111 ACTCGTCCAGCCCTCTTCAT 60.616 55.000 0.00 0.00 0.00 2.57
2320 8328 1.202348 CATTCTTTTCCTGGTTCCCGC 59.798 52.381 0.00 0.00 0.00 6.13
2606 12535 9.159254 TCAATCCTTGACTCCAGTATGTATATT 57.841 33.333 0.00 0.00 34.08 1.28
2608 12537 8.004801 TCTCAATCCTTGACTCCAGTATGTATA 58.995 37.037 0.00 0.00 35.46 1.47



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

AutoCloner maintained by Alex Coulton.