Multiple sequence alignment - TraesCS1A01G130200

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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 TraesCS1A01G130200 chr1A 100.000 2432 0 0 1 2432 168448969 168446538 0.000000e+00 4492
1 TraesCS1A01G130200 chr1D 96.266 2464 60 10 1 2432 254499599 254502062 0.000000e+00 4012
2 TraesCS1A01G130200 chr1D 96.547 2201 45 8 263 2432 206075500 206073300 0.000000e+00 3615
3 TraesCS1A01G130200 chr5D 96.227 2465 60 9 1 2432 560874069 560876533 0.000000e+00 4006
4 TraesCS1A01G130200 chr5D 94.846 2464 73 14 1 2432 6199681 6197240 0.000000e+00 3797
5 TraesCS1A01G130200 chr5D 95.558 1711 48 5 750 2432 329192306 329194016 0.000000e+00 2713
6 TraesCS1A01G130200 chr5D 96.610 885 14 2 1564 2432 503209088 503209972 0.000000e+00 1454
7 TraesCS1A01G130200 chr5D 95.364 755 30 5 1 752 329163778 329164530 0.000000e+00 1195
8 TraesCS1A01G130200 chr3B 96.021 2463 66 9 1 2432 201516281 201518742 0.000000e+00 3976
9 TraesCS1A01G130200 chr3B 93.432 807 45 4 961 1759 524772238 524771432 0.000000e+00 1190
10 TraesCS1A01G130200 chr3B 91.603 131 4 2 1371 1494 29150436 29150566 8.940000e-40 174
11 TraesCS1A01G130200 chr4D 95.203 2460 87 11 1 2432 19918094 19920550 0.000000e+00 3860
12 TraesCS1A01G130200 chr7B 94.352 2461 89 17 1 2427 102632029 102629585 0.000000e+00 3729
13 TraesCS1A01G130200 chr7A 93.953 2464 110 17 1 2432 352192425 352189969 0.000000e+00 3688
14 TraesCS1A01G130200 chr6A 95.428 2034 58 8 430 2432 260130741 260128712 0.000000e+00 3208
15 TraesCS1A01G130200 chr5A 95.184 1495 49 3 961 2432 283490209 283488715 0.000000e+00 2340
16 TraesCS1A01G130200 chrUn 96.382 1216 21 3 1240 2432 93422015 93420800 0.000000e+00 1980
17 TraesCS1A01G130200 chrUn 96.824 1102 27 5 178 1272 439559440 439558340 0.000000e+00 1834
18 TraesCS1A01G130200 chrUn 92.812 320 8 1 2128 2432 93420604 93420285 1.330000e-122 449
19 TraesCS1A01G130200 chrUn 92.361 288 7 1 2160 2432 449522460 449522747 1.750000e-106 396
20 TraesCS1A01G130200 chr6B 94.257 505 14 1 1943 2432 540055031 540055535 0.000000e+00 758


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 TraesCS1A01G130200 chr1A 168446538 168448969 2431 True 4492.0 4492 100.000 1 2432 1 chr1A.!!$R1 2431
1 TraesCS1A01G130200 chr1D 254499599 254502062 2463 False 4012.0 4012 96.266 1 2432 1 chr1D.!!$F1 2431
2 TraesCS1A01G130200 chr1D 206073300 206075500 2200 True 3615.0 3615 96.547 263 2432 1 chr1D.!!$R1 2169
3 TraesCS1A01G130200 chr5D 560874069 560876533 2464 False 4006.0 4006 96.227 1 2432 1 chr5D.!!$F4 2431
4 TraesCS1A01G130200 chr5D 6197240 6199681 2441 True 3797.0 3797 94.846 1 2432 1 chr5D.!!$R1 2431
5 TraesCS1A01G130200 chr5D 329192306 329194016 1710 False 2713.0 2713 95.558 750 2432 1 chr5D.!!$F2 1682
6 TraesCS1A01G130200 chr5D 503209088 503209972 884 False 1454.0 1454 96.610 1564 2432 1 chr5D.!!$F3 868
7 TraesCS1A01G130200 chr5D 329163778 329164530 752 False 1195.0 1195 95.364 1 752 1 chr5D.!!$F1 751
8 TraesCS1A01G130200 chr3B 201516281 201518742 2461 False 3976.0 3976 96.021 1 2432 1 chr3B.!!$F2 2431
9 TraesCS1A01G130200 chr3B 524771432 524772238 806 True 1190.0 1190 93.432 961 1759 1 chr3B.!!$R1 798
10 TraesCS1A01G130200 chr4D 19918094 19920550 2456 False 3860.0 3860 95.203 1 2432 1 chr4D.!!$F1 2431
11 TraesCS1A01G130200 chr7B 102629585 102632029 2444 True 3729.0 3729 94.352 1 2427 1 chr7B.!!$R1 2426
12 TraesCS1A01G130200 chr7A 352189969 352192425 2456 True 3688.0 3688 93.953 1 2432 1 chr7A.!!$R1 2431
13 TraesCS1A01G130200 chr6A 260128712 260130741 2029 True 3208.0 3208 95.428 430 2432 1 chr6A.!!$R1 2002
14 TraesCS1A01G130200 chr5A 283488715 283490209 1494 True 2340.0 2340 95.184 961 2432 1 chr5A.!!$R1 1471
15 TraesCS1A01G130200 chrUn 439558340 439559440 1100 True 1834.0 1834 96.824 178 1272 1 chrUn.!!$R1 1094
16 TraesCS1A01G130200 chrUn 93420285 93422015 1730 True 1214.5 1980 94.597 1240 2432 2 chrUn.!!$R2 1192
17 TraesCS1A01G130200 chr6B 540055031 540055535 504 False 758.0 758 94.257 1943 2432 1 chr6B.!!$F1 489

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
223 227 2.364324 TCACTGTTAAGACCTCGCAACT 59.636 45.455 0.0 0.0 0.00 3.16 F
823 834 4.610605 TGATTGGTTTGAGGAACGTCTA 57.389 40.909 0.0 0.0 39.22 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 1213 2.925966 AGCCAATTTGATCCCAAGGA 57.074 45.000 0.0 0.0 35.55 3.36 R
2326 2880 4.715297 TGGGATAGGTGAACTCTTTAGGAC 59.285 45.833 0.0 0.0 0.00 3.85 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
52 54 6.540083 TCGGTATCTCTGGAATATGAGTGTA 58.460 40.000 0.00 0.00 0.00 2.90
109 111 8.986991 ACATAGAAAGGGCCTATTATCTCTATG 58.013 37.037 25.23 25.23 43.49 2.23
207 211 8.899427 AATGGAACTATGATTCATACTCACTG 57.101 34.615 2.14 0.00 0.00 3.66
223 227 2.364324 TCACTGTTAAGACCTCGCAACT 59.636 45.455 0.00 0.00 0.00 3.16
404 409 4.836125 TGCCTTTTGTTTAGCTTGAGAG 57.164 40.909 0.00 0.00 0.00 3.20
437 442 5.474825 GTGGCTCTAGTATGAATCTAAGGC 58.525 45.833 0.00 0.00 0.00 4.35
557 565 6.889722 CCTCTAATGACCAACATAAGGGAAAA 59.110 38.462 0.00 0.00 38.38 2.29
823 834 4.610605 TGATTGGTTTGAGGAACGTCTA 57.389 40.909 0.00 0.00 39.22 2.59
966 981 5.280654 TGACTTTTTACTACCGACCAACT 57.719 39.130 0.00 0.00 0.00 3.16
973 988 5.726980 TTACTACCGACCAACTGTTACAT 57.273 39.130 0.00 0.00 0.00 2.29
1197 1213 8.919145 TCATTTGGTGTAACTGGTTATTCTTTT 58.081 29.630 0.00 0.00 36.74 2.27
1360 1376 6.540083 AGTTTACATACCTTTGTACTGCCTT 58.460 36.000 0.00 0.00 31.98 4.35
1481 1504 3.202829 TCATATCGGGTAGGTTTTGGC 57.797 47.619 0.00 0.00 0.00 4.52
1931 1955 4.201657 TCTTTGCATCGATTGTGATCCAT 58.798 39.130 0.00 0.00 0.00 3.41
1940 1964 9.102757 GCATCGATTGTGATCCATAATACTATT 57.897 33.333 0.00 0.00 0.00 1.73
2037 2061 4.274147 TGTTTGGAGGTAAGAAACTTGCA 58.726 39.130 0.00 0.00 33.59 4.08
2102 2126 6.103997 ACAATCCACAAAGCAATTGATCATC 58.896 36.000 10.34 0.00 41.85 2.92
2326 2880 0.339510 ATGTTCCTTTGGGGGATGGG 59.660 55.000 0.00 0.00 35.07 4.00
2362 2916 7.938140 TCACCTATCCCAATAACAAAGAAAG 57.062 36.000 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 211 4.082895 TCAGTCTAGTTGCGAGGTCTTAAC 60.083 45.833 0.00 0.00 0.00 2.01
269 273 6.998074 GGGAAACAAAATTGGAAGGAAGAAAT 59.002 34.615 0.00 0.00 0.00 2.17
404 409 6.678878 TCATACTAGAGCCACGATGATTTAC 58.321 40.000 0.00 0.00 0.00 2.01
511 519 3.187432 GGCTTCTTGACTTTTCTCTTCCG 59.813 47.826 0.00 0.00 0.00 4.30
557 565 3.194005 TGGCACGTCTTTCTTTCTTCT 57.806 42.857 0.00 0.00 0.00 2.85
823 834 3.361281 TCTGCAATTGCCTGAATCTCT 57.639 42.857 26.94 0.00 41.18 3.10
966 981 4.258543 CCGAGGAAAAAGCCTATGTAACA 58.741 43.478 0.00 0.00 38.73 2.41
973 988 3.495434 TTGAACCGAGGAAAAAGCCTA 57.505 42.857 0.00 0.00 38.73 3.93
1122 1138 4.062293 CTGTGACCCAAGTTAATTCACGA 58.938 43.478 0.00 0.00 39.59 4.35
1197 1213 2.925966 AGCCAATTTGATCCCAAGGA 57.074 45.000 0.00 0.00 35.55 3.36
1518 1541 7.550551 TGAAGAGAAGTATCCAAATGACATGTC 59.449 37.037 19.27 19.27 0.00 3.06
1940 1964 6.269194 TCCTTAGATCCCTTCTTTTACTCCA 58.731 40.000 0.00 0.00 35.79 3.86
2102 2126 4.931002 CCAAGTGGGCTTACAAATTTGATG 59.069 41.667 24.64 13.70 32.87 3.07
2326 2880 4.715297 TGGGATAGGTGAACTCTTTAGGAC 59.285 45.833 0.00 0.00 0.00 3.85
2362 2916 9.547753 TCTTAATACAGGATCATTTAAGTCTGC 57.452 33.333 8.92 0.00 33.61 4.26


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

AutoCloner maintained by Alex Coulton.