Multiple sequence alignment - TraesCS3B01G469900

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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 TraesCS3B01G469900 chr3B 100.000 2414 0 0 1 2414 717179717 717182130 0 4458
1 TraesCS3B01G469900 chr3B 98.564 905 13 0 816 1720 201526089 201526993 0 1600
2 TraesCS3B01G469900 chr5D 98.674 905 12 0 816 1720 503217283 503218187 0 1605
3 TraesCS3B01G469900 chrUn 98.564 905 13 0 816 1720 216519537 216518633 0 1600
4 TraesCS3B01G469900 chrUn 98.564 905 13 0 816 1720 216520829 216521733 0 1600
5 TraesCS3B01G469900 chrUn 98.343 905 14 1 816 1720 93410565 93409662 0 1587
6 TraesCS3B01G469900 chrUn 98.126 907 15 1 816 1720 216522927 216522021 0 1580
7 TraesCS3B01G469900 chrUn 95.683 695 29 1 1721 2414 5643428 5642734 0 1116
8 TraesCS3B01G469900 chr6D 98.564 905 13 0 816 1720 168252699 168251795 0 1600
9 TraesCS3B01G469900 chr6D 98.564 905 13 0 816 1720 168253991 168254895 0 1600
10 TraesCS3B01G469900 chr3D 98.453 905 14 0 816 1720 589280477 589279573 0 1594
11 TraesCS3B01G469900 chr7B 96.187 813 28 2 1 811 376375504 376376315 0 1327
12 TraesCS3B01G469900 chr7B 96.069 814 29 2 1 812 151801229 151802041 0 1323
13 TraesCS3B01G469900 chr7B 95.732 820 27 4 1 812 503351419 503352238 0 1314
14 TraesCS3B01G469900 chr2B 95.946 814 31 1 1 812 608641005 608640192 0 1319
15 TraesCS3B01G469900 chr2B 95.504 823 27 5 1 813 539607296 539608118 0 1306
16 TraesCS3B01G469900 chr2B 95.702 698 24 4 1721 2414 444655712 444656407 0 1118
17 TraesCS3B01G469900 chr2B 95.683 695 28 2 1721 2414 210883793 210883100 0 1116
18 TraesCS3B01G469900 chr4A 95.936 812 33 0 1 812 724466064 724465253 0 1317
19 TraesCS3B01G469900 chr1B 95.818 813 32 1 1 811 289624047 289624859 0 1312
20 TraesCS3B01G469900 chr1B 95.588 816 33 2 1 813 278245734 278246549 0 1304
21 TraesCS3B01G469900 chr5B 95.695 813 33 1 2 812 362007967 362007155 0 1306
22 TraesCS3B01G469900 chr5B 96.403 695 23 2 1721 2414 497428588 497427895 0 1144
23 TraesCS3B01G469900 chr6B 96.006 701 19 4 1721 2414 436852521 436853219 0 1131
24 TraesCS3B01G469900 chr6B 95.690 696 25 5 1721 2414 333922612 333923304 0 1114
25 TraesCS3B01G469900 chr6B 95.683 695 26 4 1723 2414 436868965 436869658 0 1114
26 TraesCS3B01G469900 chr6B 95.552 697 27 4 1721 2414 98928683 98927988 0 1112
27 TraesCS3B01G469900 chr4B 95.552 697 27 3 1721 2414 404814885 404814190 0 1112


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 TraesCS3B01G469900 chr3B 717179717 717182130 2413 False 4458 4458 100.000 1 2414 1 chr3B.!!$F2 2413
1 TraesCS3B01G469900 chr3B 201526089 201526993 904 False 1600 1600 98.564 816 1720 1 chr3B.!!$F1 904
2 TraesCS3B01G469900 chr5D 503217283 503218187 904 False 1605 1605 98.674 816 1720 1 chr5D.!!$F1 904
3 TraesCS3B01G469900 chrUn 216520829 216521733 904 False 1600 1600 98.564 816 1720 1 chrUn.!!$F1 904
4 TraesCS3B01G469900 chrUn 216518633 216522927 4294 True 1590 1600 98.345 816 1720 2 chrUn.!!$R3 904
5 TraesCS3B01G469900 chrUn 93409662 93410565 903 True 1587 1587 98.343 816 1720 1 chrUn.!!$R2 904
6 TraesCS3B01G469900 chrUn 5642734 5643428 694 True 1116 1116 95.683 1721 2414 1 chrUn.!!$R1 693
7 TraesCS3B01G469900 chr6D 168251795 168252699 904 True 1600 1600 98.564 816 1720 1 chr6D.!!$R1 904
8 TraesCS3B01G469900 chr6D 168253991 168254895 904 False 1600 1600 98.564 816 1720 1 chr6D.!!$F1 904
9 TraesCS3B01G469900 chr3D 589279573 589280477 904 True 1594 1594 98.453 816 1720 1 chr3D.!!$R1 904
10 TraesCS3B01G469900 chr7B 376375504 376376315 811 False 1327 1327 96.187 1 811 1 chr7B.!!$F2 810
11 TraesCS3B01G469900 chr7B 151801229 151802041 812 False 1323 1323 96.069 1 812 1 chr7B.!!$F1 811
12 TraesCS3B01G469900 chr7B 503351419 503352238 819 False 1314 1314 95.732 1 812 1 chr7B.!!$F3 811
13 TraesCS3B01G469900 chr2B 608640192 608641005 813 True 1319 1319 95.946 1 812 1 chr2B.!!$R2 811
14 TraesCS3B01G469900 chr2B 539607296 539608118 822 False 1306 1306 95.504 1 813 1 chr2B.!!$F2 812
15 TraesCS3B01G469900 chr2B 444655712 444656407 695 False 1118 1118 95.702 1721 2414 1 chr2B.!!$F1 693
16 TraesCS3B01G469900 chr2B 210883100 210883793 693 True 1116 1116 95.683 1721 2414 1 chr2B.!!$R1 693
17 TraesCS3B01G469900 chr4A 724465253 724466064 811 True 1317 1317 95.936 1 812 1 chr4A.!!$R1 811
18 TraesCS3B01G469900 chr1B 289624047 289624859 812 False 1312 1312 95.818 1 811 1 chr1B.!!$F2 810
19 TraesCS3B01G469900 chr1B 278245734 278246549 815 False 1304 1304 95.588 1 813 1 chr1B.!!$F1 812
20 TraesCS3B01G469900 chr5B 362007155 362007967 812 True 1306 1306 95.695 2 812 1 chr5B.!!$R1 810
21 TraesCS3B01G469900 chr5B 497427895 497428588 693 True 1144 1144 96.403 1721 2414 1 chr5B.!!$R2 693
22 TraesCS3B01G469900 chr6B 436852521 436853219 698 False 1131 1131 96.006 1721 2414 1 chr6B.!!$F2 693
23 TraesCS3B01G469900 chr6B 333922612 333923304 692 False 1114 1114 95.690 1721 2414 1 chr6B.!!$F1 693
24 TraesCS3B01G469900 chr6B 436868965 436869658 693 False 1114 1114 95.683 1723 2414 1 chr6B.!!$F3 691
25 TraesCS3B01G469900 chr6B 98927988 98928683 695 True 1112 1112 95.552 1721 2414 1 chr6B.!!$R1 693
26 TraesCS3B01G469900 chr4B 404814190 404814885 695 True 1112 1112 95.552 1721 2414 1 chr4B.!!$R1 693

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
814 827 2.225382 TCACCGAGAAGTATCCCACA 57.775 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 5755 0.181587 TCCACGGAGGCACTTTTTCA 59.818 50.0 0.0 0.0 41.55 2.69 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
151 152 6.951256 TCAAGTTCTTCATAGTGATCAACG 57.049 37.500 0.00 0.00 0.00 4.10
185 186 4.159321 CCAAGTGACTCAGAGAATAGAGCA 59.841 45.833 3.79 0.00 35.28 4.26
298 301 7.877097 CCAAATTTATTGATTTGACACAAGGGA 59.123 33.333 10.89 0.00 45.47 4.20
649 662 8.677148 AAATAGTCATACGTGCTTATGGAAAT 57.323 30.769 0.00 0.00 31.33 2.17
683 696 2.426431 TCTTTTGTCCTACCCTCCCA 57.574 50.000 0.00 0.00 0.00 4.37
707 720 3.103091 GCGGGGTCCTAGCGGAAAT 62.103 63.158 0.00 0.00 42.08 2.17
813 826 2.693591 TCATCACCGAGAAGTATCCCAC 59.306 50.000 0.00 0.00 0.00 4.61
814 827 2.225382 TCACCGAGAAGTATCCCACA 57.775 50.000 0.00 0.00 0.00 4.17
1020 4423 3.827752 GGAGCTTCCCCTTCACCT 58.172 61.111 0.00 0.00 0.00 4.00
1092 4495 2.551032 GCGTTTACCTAGCCAACACTTT 59.449 45.455 0.00 0.00 0.00 2.66
1159 4562 2.364324 ACTTGTCCGACTGTTGCTAAGA 59.636 45.455 0.00 0.00 0.00 2.10
1272 4675 1.141858 GCTCTAGCTAATTGCCCACCT 59.858 52.381 0.00 0.00 44.23 4.00
1273 4676 2.843701 CTCTAGCTAATTGCCCACCTG 58.156 52.381 0.00 0.00 44.23 4.00
1333 4736 1.208776 AGGGCATACCGGTTGAAGTAC 59.791 52.381 15.04 0.00 46.96 2.73
1562 4965 4.439057 GTTCCGTCATCTGGCTTATGTTA 58.561 43.478 0.00 0.00 0.00 2.41
1572 4975 8.432013 TCATCTGGCTTATGTTATTCATGTAGT 58.568 33.333 0.00 0.00 37.91 2.73
1764 5167 7.375834 TGTCGGATCATAACACATAATAGGTC 58.624 38.462 0.00 0.00 0.00 3.85
2116 5519 0.327867 TCCAGATCAGCCCTCCCAAT 60.328 55.000 0.00 0.00 0.00 3.16
2221 5624 1.056660 TGGAGTTGGAGTTGAGGTCC 58.943 55.000 0.00 0.00 34.31 4.46
2312 5726 4.043100 GTGGGCCCCCTGGTGTAC 62.043 72.222 22.27 3.64 36.94 2.90
2341 5755 9.586435 CTTTCGCCCAGAAATTCTTATTAATTT 57.414 29.630 0.00 0.00 46.60 1.82
2342 5756 8.925161 TTCGCCCAGAAATTCTTATTAATTTG 57.075 30.769 0.00 0.00 38.77 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
206 207 8.934023 TTGTGGGTTATCAAGACTAATTTCTT 57.066 30.769 0.00 0.00 36.18 2.52
287 290 1.214175 TCTTTGGCTTCCCTTGTGTCA 59.786 47.619 0.00 0.00 0.00 3.58
324 327 6.099341 GTGGTTGAATTGAAAACTCAACTGT 58.901 36.000 12.39 0.00 45.33 3.55
335 338 3.304911 TCCAGGTGTGGTTGAATTGAA 57.695 42.857 0.00 0.00 45.28 2.69
649 662 5.518848 ACAAAAGATGTCATGCAAGTTCA 57.481 34.783 0.00 0.00 37.96 3.18
683 696 3.164269 CTAGGACCCCGCTGCCAT 61.164 66.667 0.00 0.00 0.00 4.40
707 720 6.858792 AAAGGAGGCCTTAATATCCCTTAA 57.141 37.500 17.50 0.00 43.92 1.85
1010 4413 2.287194 ATGGGGGAGGTGAAGGGG 60.287 66.667 0.00 0.00 0.00 4.79
1092 4495 0.539986 GTTTGGGTAGAGCCGGATCA 59.460 55.000 23.83 5.01 38.44 2.92
1159 4562 5.005740 GGTCCGTTTAGTATCCCAAAACTT 58.994 41.667 0.00 0.00 32.25 2.66
1272 4675 4.637276 ACATAGAAATCACACGTGGAACA 58.363 39.130 21.57 0.07 35.74 3.18
1273 4676 5.607119 AACATAGAAATCACACGTGGAAC 57.393 39.130 21.57 9.90 0.00 3.62
1321 4724 5.941948 AAAGAAGAATGTACTTCAACCGG 57.058 39.130 0.00 0.00 45.83 5.28
1562 4965 9.416794 GTCATTCGATCTGAATACTACATGAAT 57.583 33.333 0.00 0.00 45.59 2.57
1764 5167 7.890515 TGATCCTATCTTGCAAGTCTATAGTG 58.109 38.462 25.19 16.66 0.00 2.74
2025 5428 2.620115 CCATCCTCCATCACCAATTTCG 59.380 50.000 0.00 0.00 0.00 3.46
2116 5519 1.048601 CCGCCAAGCCCTAATCTCTA 58.951 55.000 0.00 0.00 0.00 2.43
2312 5726 4.773323 AAGAATTTCTGGGCGAAAGAAG 57.227 40.909 0.00 0.00 44.29 2.85
2341 5755 0.181587 TCCACGGAGGCACTTTTTCA 59.818 50.000 0.00 0.00 41.55 2.69
2342 5756 1.534729 ATCCACGGAGGCACTTTTTC 58.465 50.000 0.00 0.00 41.55 2.29


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

AutoCloner maintained by Alex Coulton.