Multiple sequence alignment - TraesCS1A01G166800

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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 TraesCS1A01G166800 chr1A 100.000 2507 0 0 1 2507 299542000 299544506 0.000000e+00 4630.0
1 TraesCS1A01G166800 chr1A 96.496 1741 46 6 275 2002 97423109 97421371 0.000000e+00 2863.0
2 TraesCS1A01G166800 chr1A 95.059 506 25 0 2002 2507 236141164 236140659 0.000000e+00 797.0
3 TraesCS1A01G166800 chr1A 96.875 192 6 0 1810 2001 299539683 299539492 3.110000e-84 322.0
4 TraesCS1A01G166800 chr2A 96.476 2015 37 8 1 2001 102021922 102019928 0.000000e+00 3297.0
5 TraesCS1A01G166800 chr2A 95.455 506 20 3 2002 2506 76205933 76205430 0.000000e+00 804.0
6 TraesCS1A01G166800 chr2A 96.875 192 5 1 1810 2001 102024226 102024416 1.120000e-83 320.0
7 TraesCS1A01G166800 chr1D 96.686 1931 50 5 93 2009 50969151 50971081 0.000000e+00 3199.0
8 TraesCS1A01G166800 chr1D 96.392 194 7 0 1810 2003 51000187 50999994 1.120000e-83 320.0
9 TraesCS1A01G166800 chr1D 95.876 194 7 1 1810 2003 50967068 50966876 1.870000e-81 313.0
10 TraesCS1A01G166800 chr7A 92.713 892 48 8 1098 1986 533036606 533037483 0.000000e+00 1271.0
11 TraesCS1A01G166800 chr4A 95.644 505 22 0 2002 2506 589984147 589983643 0.000000e+00 811.0
12 TraesCS1A01G166800 chr4A 95.059 506 25 0 2002 2507 446748505 446748000 0.000000e+00 797.0
13 TraesCS1A01G166800 chr6A 95.437 504 21 2 2002 2505 490964794 490965295 0.000000e+00 802.0
14 TraesCS1A01G166800 chr5A 95.257 506 24 0 2002 2507 629640431 629639926 0.000000e+00 802.0
15 TraesCS1A01G166800 chr5A 95.257 506 23 1 2002 2507 313744346 313743842 0.000000e+00 800.0
16 TraesCS1A01G166800 chr3A 95.059 506 25 0 2002 2507 487078045 487078550 0.000000e+00 797.0
17 TraesCS1A01G166800 chr3A 95.059 506 25 0 2002 2507 581140274 581139769 0.000000e+00 797.0
18 TraesCS1A01G166800 chr3B 94.248 452 20 5 1558 2005 448752602 448753051 0.000000e+00 686.0
19 TraesCS1A01G166800 chr4D 88.187 491 34 8 1518 2003 76028347 76028818 4.680000e-157 564.0
20 TraesCS1A01G166800 chr6D 78.070 114 24 1 73 186 452314465 452314353 1.240000e-08 71.3
21 TraesCS1A01G166800 chr5B 93.617 47 3 0 148 194 260237153 260237107 1.240000e-08 71.3
22 TraesCS1A01G166800 chr2B 93.617 47 3 0 136 182 697521724 697521770 1.240000e-08 71.3
23 TraesCS1A01G166800 chr2B 76.336 131 31 0 62 192 801009330 801009200 1.240000e-08 71.3
24 TraesCS1A01G166800 chr7D 91.489 47 4 0 136 182 552506640 552506686 5.790000e-07 65.8


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 TraesCS1A01G166800 chr1A 299542000 299544506 2506 False 4630 4630 100.000 1 2507 1 chr1A.!!$F1 2506
1 TraesCS1A01G166800 chr1A 97421371 97423109 1738 True 2863 2863 96.496 275 2002 1 chr1A.!!$R1 1727
2 TraesCS1A01G166800 chr1A 236140659 236141164 505 True 797 797 95.059 2002 2507 1 chr1A.!!$R2 505
3 TraesCS1A01G166800 chr2A 102019928 102021922 1994 True 3297 3297 96.476 1 2001 1 chr2A.!!$R2 2000
4 TraesCS1A01G166800 chr2A 76205430 76205933 503 True 804 804 95.455 2002 2506 1 chr2A.!!$R1 504
5 TraesCS1A01G166800 chr1D 50969151 50971081 1930 False 3199 3199 96.686 93 2009 1 chr1D.!!$F1 1916
6 TraesCS1A01G166800 chr7A 533036606 533037483 877 False 1271 1271 92.713 1098 1986 1 chr7A.!!$F1 888
7 TraesCS1A01G166800 chr4A 589983643 589984147 504 True 811 811 95.644 2002 2506 1 chr4A.!!$R2 504
8 TraesCS1A01G166800 chr4A 446748000 446748505 505 True 797 797 95.059 2002 2507 1 chr4A.!!$R1 505
9 TraesCS1A01G166800 chr6A 490964794 490965295 501 False 802 802 95.437 2002 2505 1 chr6A.!!$F1 503
10 TraesCS1A01G166800 chr5A 629639926 629640431 505 True 802 802 95.257 2002 2507 1 chr5A.!!$R2 505
11 TraesCS1A01G166800 chr5A 313743842 313744346 504 True 800 800 95.257 2002 2507 1 chr5A.!!$R1 505
12 TraesCS1A01G166800 chr3A 487078045 487078550 505 False 797 797 95.059 2002 2507 1 chr3A.!!$F1 505
13 TraesCS1A01G166800 chr3A 581139769 581140274 505 True 797 797 95.059 2002 2507 1 chr3A.!!$R1 505

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
334 335 0.250901 GACCCACAACACTGGAGCAT 60.251 55.0 0.0 0.0 32.3 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1837 0.962489 CAGGTCAACTCGTCCAGTCT 59.038 55.0 0.0 0.0 32.3 3.24 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
71 72 2.814805 AAGTTGGAGATGGTGATGGG 57.185 50.000 0.00 0.00 0.00 4.00
85 86 5.594777 TGGTGATGGGTGGGTTATAATTTT 58.405 37.500 0.00 0.00 0.00 1.82
112 113 7.493320 TGATCAGCAAAAAGGAATATTGAATGC 59.507 33.333 0.00 0.00 0.00 3.56
334 335 0.250901 GACCCACAACACTGGAGCAT 60.251 55.000 0.00 0.00 32.30 3.79
368 369 5.048713 CAGGTTAGGAAGTTGTTGTGATTCC 60.049 44.000 0.00 0.00 41.29 3.01
430 431 6.293004 AGTTGAGGCTAGATTATATCCTGC 57.707 41.667 0.00 0.00 0.00 4.85
486 499 8.950210 GGATACAAGAAATGAGAAGTGAAATGA 58.050 33.333 0.00 0.00 0.00 2.57
512 525 0.531532 GGACTGGCATCATCTGTCCG 60.532 60.000 5.70 0.00 41.20 4.79
567 580 8.405418 AGATTATTCTGCTTATTGTCATGCAT 57.595 30.769 0.00 0.00 34.79 3.96
635 648 4.002982 GGTACACTGTCAGATTGCATGAA 58.997 43.478 6.91 0.00 0.00 2.57
849 863 1.209261 CAAAACCAAAAGCACCTGGGT 59.791 47.619 0.00 0.00 37.00 4.51
977 991 1.755959 TGCAAGCAAAGTGGACACAAT 59.244 42.857 5.14 0.00 0.00 2.71
1049 1063 1.137282 GCTTCTGCTCCTAGTGGTACC 59.863 57.143 4.43 4.43 36.03 3.34
1145 1159 3.126343 GCTCGTTCACCATATTTTTCCGT 59.874 43.478 0.00 0.00 0.00 4.69
1545 1559 1.628340 TGAGGTTTGGGTGTCGATCAT 59.372 47.619 0.00 0.00 0.00 2.45
1821 1837 1.893801 TCATTGTTGACATGGCATGCA 59.106 42.857 26.70 21.15 0.00 3.96
1880 1896 1.471829 CCAAAACCAGGGTCAAGGCC 61.472 60.000 0.00 0.00 0.00 5.19
1884 1900 1.142688 AACCAGGGTCAAGGCCAGAT 61.143 55.000 5.01 0.00 0.00 2.90
2115 2131 9.448438 AAAATTCTAAAATAAATTGCTGGACCC 57.552 29.630 0.00 0.00 0.00 4.46
2135 2151 9.328975 TGGACCCGAGGAATTTATCTATTAATA 57.671 33.333 0.00 0.00 0.00 0.98
2185 2202 5.413499 CACTCTCCAAATAAAAATGGCAGG 58.587 41.667 0.00 0.00 36.62 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 8.770438 TTTGCTGATCAAAAATTATAACCCAC 57.230 30.769 0.00 0.00 41.36 4.61
85 86 9.373603 CATTCAATATTCCTTTTTGCTGATCAA 57.626 29.630 0.00 0.00 0.00 2.57
112 113 1.302832 GGAGCCCAGTGGTGAACAG 60.303 63.158 8.74 0.00 0.00 3.16
334 335 1.440618 TCCTAACCTGAACCAAGCCA 58.559 50.000 0.00 0.00 0.00 4.75
368 369 3.961477 TCAGAAATGTTGTTGTCCACG 57.039 42.857 0.00 0.00 0.00 4.94
430 431 9.729023 TCATAATTTGTTGCCTAATTGTTATCG 57.271 29.630 0.00 0.00 30.42 2.92
486 499 3.508793 CAGATGATGCCAGTCCAACTTTT 59.491 43.478 0.00 0.00 0.00 2.27
512 525 7.948278 TTTCTGTAGCTTCTTCAGTACTTTC 57.052 36.000 0.00 0.00 32.11 2.62
635 648 6.650120 CCAATACCTACAACTACATGTCCTT 58.350 40.000 0.00 0.00 34.75 3.36
849 863 6.508030 TTTCCTACCAGGCATATTGATGTA 57.492 37.500 0.00 0.00 34.61 2.29
977 991 8.233190 CCATTTCTTTGTTTGCAAGTTGTTTTA 58.767 29.630 4.48 0.00 35.82 1.52
1049 1063 2.363807 CGTAGCAGAAAGTGGAGCG 58.636 57.895 0.00 0.00 0.00 5.03
1821 1837 0.962489 CAGGTCAACTCGTCCAGTCT 59.038 55.000 0.00 0.00 32.30 3.24
2056 2072 8.304596 TCCATAAGTATACGTTTGATCCAGATC 58.695 37.037 10.03 0.47 38.29 2.75
2185 2202 2.924290 ACTTTAGCGCTCACGAGAATTC 59.076 45.455 16.34 0.00 43.93 2.17
2348 2365 6.953101 ACCCAACTTTATTTTTGTTCCTTGT 58.047 32.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.