Multiple sequence alignment - TraesCS3B01G544900

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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 TraesCS3B01G544900 chr3B 100.000 2617 0 0 1 2617 782175083 782172467 0.000000e+00 4833
1 TraesCS3B01G544900 chr3B 98.871 2569 25 2 53 2617 782216127 782213559 0.000000e+00 4580
2 TraesCS3B01G544900 chr3B 98.715 2569 28 3 53 2617 782257535 782254968 0.000000e+00 4556
3 TraesCS3B01G544900 chr3B 98.715 2569 26 5 53 2617 782299347 782296782 0.000000e+00 4554
4 TraesCS3B01G544900 chr7B 97.742 2170 34 8 53 2213 505223857 505221694 0.000000e+00 3722
5 TraesCS3B01G544900 chr7B 87.409 413 15 22 2209 2617 505221664 505221285 8.600000e-120 440
6 TraesCS3B01G544900 chr5A 97.648 2168 37 8 55 2213 457097469 457099631 0.000000e+00 3709
7 TraesCS3B01G544900 chr5A 87.167 413 16 22 2209 2617 457099661 457100040 4.000000e-118 435
8 TraesCS3B01G544900 chr5D 97.635 1776 29 7 53 1820 468181572 468179802 0.000000e+00 3035
9 TraesCS3B01G544900 chr5D 97.902 143 3 0 2431 2573 468179801 468179659 5.590000e-62 248
10 TraesCS3B01G544900 chr4B 97.635 1776 29 7 53 1820 42253639 42255409 0.000000e+00 3035
11 TraesCS3B01G544900 chr4B 97.902 143 3 0 2431 2573 42255410 42255552 5.590000e-62 248
12 TraesCS3B01G544900 chr3A 97.624 1768 30 6 53 1812 690942544 690944307 0.000000e+00 3022
13 TraesCS3B01G544900 chr7D 97.624 1768 29 7 53 1812 64828281 64826519 0.000000e+00 3020
14 TraesCS3B01G544900 chr2A 91.909 309 25 0 2209 2517 21632184 21632492 1.440000e-117 433
15 TraesCS3B01G544900 chr4D 97.902 143 3 0 2431 2573 505348908 505348766 5.590000e-62 248


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 TraesCS3B01G544900 chr3B 782172467 782175083 2616 True 4833.0 4833 100.0000 1 2617 1 chr3B.!!$R1 2616
1 TraesCS3B01G544900 chr3B 782213559 782216127 2568 True 4580.0 4580 98.8710 53 2617 1 chr3B.!!$R2 2564
2 TraesCS3B01G544900 chr3B 782254968 782257535 2567 True 4556.0 4556 98.7150 53 2617 1 chr3B.!!$R3 2564
3 TraesCS3B01G544900 chr3B 782296782 782299347 2565 True 4554.0 4554 98.7150 53 2617 1 chr3B.!!$R4 2564
4 TraesCS3B01G544900 chr7B 505221285 505223857 2572 True 2081.0 3722 92.5755 53 2617 2 chr7B.!!$R1 2564
5 TraesCS3B01G544900 chr5A 457097469 457100040 2571 False 2072.0 3709 92.4075 55 2617 2 chr5A.!!$F1 2562
6 TraesCS3B01G544900 chr5D 468179659 468181572 1913 True 1641.5 3035 97.7685 53 2573 2 chr5D.!!$R1 2520
7 TraesCS3B01G544900 chr4B 42253639 42255552 1913 False 1641.5 3035 97.7685 53 2573 2 chr4B.!!$F1 2520
8 TraesCS3B01G544900 chr3A 690942544 690944307 1763 False 3022.0 3022 97.6240 53 1812 1 chr3A.!!$F1 1759
9 TraesCS3B01G544900 chr7D 64826519 64828281 1762 True 3020.0 3020 97.6240 53 1812 1 chr7D.!!$R1 1759

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
20 21 0.673644 GCTCGCCCAAGCACTTTCTA 60.674 55.0 0.0 0.0 42.05 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1697 1.048601 GGGAGGGATATGACTTGCGA 58.951 55.0 0.0 0.0 0.0 5.1 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
17 18 2.113986 AGCTCGCCCAAGCACTTT 59.886 55.556 3.55 0.00 45.00 2.66
18 19 1.968540 AGCTCGCCCAAGCACTTTC 60.969 57.895 3.55 0.00 45.00 2.62
19 20 1.968540 GCTCGCCCAAGCACTTTCT 60.969 57.895 0.00 0.00 42.05 2.52
20 21 0.673644 GCTCGCCCAAGCACTTTCTA 60.674 55.000 0.00 0.00 42.05 2.10
21 22 1.363744 CTCGCCCAAGCACTTTCTAG 58.636 55.000 0.00 0.00 39.83 2.43
22 23 0.973632 TCGCCCAAGCACTTTCTAGA 59.026 50.000 0.00 0.00 39.83 2.43
23 24 1.066858 TCGCCCAAGCACTTTCTAGAG 60.067 52.381 0.00 0.00 39.83 2.43
24 25 1.066858 CGCCCAAGCACTTTCTAGAGA 60.067 52.381 0.00 0.00 39.83 3.10
25 26 2.612972 CGCCCAAGCACTTTCTAGAGAA 60.613 50.000 0.00 0.00 39.83 2.87
26 27 3.006247 GCCCAAGCACTTTCTAGAGAAG 58.994 50.000 11.03 11.03 39.53 2.85
27 28 3.604582 CCCAAGCACTTTCTAGAGAAGG 58.395 50.000 14.91 0.18 37.19 3.46
28 29 3.006247 CCAAGCACTTTCTAGAGAAGGC 58.994 50.000 14.91 14.21 34.89 4.35
29 30 3.307339 CCAAGCACTTTCTAGAGAAGGCT 60.307 47.826 14.91 15.49 38.48 4.58
30 31 3.885724 AGCACTTTCTAGAGAAGGCTC 57.114 47.619 14.91 0.00 41.62 4.70
31 32 2.165437 AGCACTTTCTAGAGAAGGCTCG 59.835 50.000 14.91 5.91 45.98 5.03
32 33 2.737039 GCACTTTCTAGAGAAGGCTCGG 60.737 54.545 14.91 0.00 45.98 4.63
33 34 1.478916 ACTTTCTAGAGAAGGCTCGGC 59.521 52.381 14.91 0.00 45.98 5.54
34 35 1.754226 CTTTCTAGAGAAGGCTCGGCT 59.246 52.381 0.00 0.00 45.98 5.52
35 36 1.394618 TTCTAGAGAAGGCTCGGCTC 58.605 55.000 0.00 0.00 45.98 4.70
36 37 0.816018 TCTAGAGAAGGCTCGGCTCG 60.816 60.000 0.00 0.00 45.98 5.03
37 38 1.791103 CTAGAGAAGGCTCGGCTCGG 61.791 65.000 0.00 0.00 45.98 4.63
38 39 4.882396 GAGAAGGCTCGGCTCGGC 62.882 72.222 0.00 0.00 0.00 5.54
40 41 4.882396 GAAGGCTCGGCTCGGCTC 62.882 72.222 0.00 0.00 36.12 4.70
49 50 4.742201 GCTCGGCTCGGTGCTTGA 62.742 66.667 1.77 0.50 42.39 3.02
50 51 2.048222 CTCGGCTCGGTGCTTGAA 60.048 61.111 1.77 0.00 42.39 2.69
51 52 1.667830 CTCGGCTCGGTGCTTGAAA 60.668 57.895 1.77 0.00 42.39 2.69
318 322 4.742201 GTGCGAGCTTCTCCGGCA 62.742 66.667 0.00 0.00 0.00 5.69
1054 1063 1.081892 CATGTTGAGGCGGAGAACTG 58.918 55.000 0.00 0.00 0.00 3.16
1499 1508 3.254166 CACACAAAAATCACTAGCAGCCT 59.746 43.478 0.00 0.00 0.00 4.58
1614 1623 7.881232 TGAACTTCCCTTTTTCATATTCGTAGT 59.119 33.333 0.00 0.00 0.00 2.73
1688 1697 3.181412 ACATGGTGGACAAATTTAGGGGT 60.181 43.478 0.00 0.00 0.00 4.95
1974 1984 1.903404 GCAAGGCCGGGGATATTGG 60.903 63.158 2.18 0.00 0.00 3.16
2338 2383 7.430793 CAGATAGAGAGAATGTAAGTGACAACG 59.569 40.741 0.00 0.00 42.78 4.10
2556 2601 2.622942 TGTTGCTGAAGATGGGTGTTTC 59.377 45.455 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.968540 GAAAGTGCTTGGGCGAGCT 60.969 57.895 11.89 0.00 43.11 4.09
1 2 0.673644 TAGAAAGTGCTTGGGCGAGC 60.674 55.000 4.72 4.72 43.00 5.03
2 3 1.066858 TCTAGAAAGTGCTTGGGCGAG 60.067 52.381 0.00 0.00 42.25 5.03
3 4 0.973632 TCTAGAAAGTGCTTGGGCGA 59.026 50.000 0.00 0.00 42.25 5.54
4 5 1.066858 TCTCTAGAAAGTGCTTGGGCG 60.067 52.381 0.00 0.00 42.25 6.13
5 6 2.770164 TCTCTAGAAAGTGCTTGGGC 57.230 50.000 0.00 0.00 39.26 5.36
6 7 3.604582 CCTTCTCTAGAAAGTGCTTGGG 58.395 50.000 0.00 0.00 33.07 4.12
7 8 3.006247 GCCTTCTCTAGAAAGTGCTTGG 58.994 50.000 0.00 0.00 33.07 3.61
8 9 3.932089 GAGCCTTCTCTAGAAAGTGCTTG 59.068 47.826 19.15 7.28 35.21 4.01
9 10 3.367910 CGAGCCTTCTCTAGAAAGTGCTT 60.368 47.826 19.15 11.16 35.21 3.91
10 11 2.165437 CGAGCCTTCTCTAGAAAGTGCT 59.835 50.000 18.71 18.71 36.68 4.40
11 12 2.535331 CGAGCCTTCTCTAGAAAGTGC 58.465 52.381 0.00 6.88 37.19 4.40
12 13 2.737039 GCCGAGCCTTCTCTAGAAAGTG 60.737 54.545 0.00 0.00 37.19 3.16
13 14 1.478916 GCCGAGCCTTCTCTAGAAAGT 59.521 52.381 0.00 0.00 37.19 2.66
14 15 1.754226 AGCCGAGCCTTCTCTAGAAAG 59.246 52.381 0.00 1.18 37.19 2.62
15 16 1.751924 GAGCCGAGCCTTCTCTAGAAA 59.248 52.381 0.00 0.00 37.19 2.52
16 17 1.394618 GAGCCGAGCCTTCTCTAGAA 58.605 55.000 0.00 0.00 37.19 2.10
17 18 0.816018 CGAGCCGAGCCTTCTCTAGA 60.816 60.000 0.00 0.00 37.19 2.43
18 19 1.652012 CGAGCCGAGCCTTCTCTAG 59.348 63.158 0.00 0.00 37.19 2.43
19 20 1.824329 CCGAGCCGAGCCTTCTCTA 60.824 63.158 0.00 0.00 37.19 2.43
20 21 3.144193 CCGAGCCGAGCCTTCTCT 61.144 66.667 0.00 0.00 37.19 3.10
21 22 4.882396 GCCGAGCCGAGCCTTCTC 62.882 72.222 0.00 0.00 35.99 2.87
23 24 4.882396 GAGCCGAGCCGAGCCTTC 62.882 72.222 0.00 0.00 0.00 3.46
37 38 0.598065 ATGGTTTTCAAGCACCGAGC 59.402 50.000 0.00 0.00 42.32 5.03
38 39 3.369546 AAATGGTTTTCAAGCACCGAG 57.630 42.857 0.00 0.00 42.32 4.63
39 40 3.810310 AAAATGGTTTTCAAGCACCGA 57.190 38.095 0.00 0.00 42.32 4.69
40 41 3.002144 CCAAAAATGGTTTTCAAGCACCG 59.998 43.478 0.00 0.00 42.32 4.94
41 42 3.243035 GCCAAAAATGGTTTTCAAGCACC 60.243 43.478 0.00 0.00 42.32 5.01
42 43 3.627123 AGCCAAAAATGGTTTTCAAGCAC 59.373 39.130 0.00 0.00 42.32 4.40
43 44 3.876320 GAGCCAAAAATGGTTTTCAAGCA 59.124 39.130 0.00 0.00 43.83 3.91
44 45 3.059665 CGAGCCAAAAATGGTTTTCAAGC 60.060 43.478 0.00 0.00 34.64 4.01
45 46 3.059665 GCGAGCCAAAAATGGTTTTCAAG 60.060 43.478 0.00 0.00 34.64 3.02
46 47 2.869192 GCGAGCCAAAAATGGTTTTCAA 59.131 40.909 0.00 0.00 34.64 2.69
47 48 2.478831 GCGAGCCAAAAATGGTTTTCA 58.521 42.857 0.00 0.00 34.64 2.69
48 49 1.798223 GGCGAGCCAAAAATGGTTTTC 59.202 47.619 9.58 0.00 34.64 2.29
49 50 1.139853 TGGCGAGCCAAAAATGGTTTT 59.860 42.857 15.24 0.00 44.12 2.43
50 51 0.755686 TGGCGAGCCAAAAATGGTTT 59.244 45.000 15.24 0.00 44.12 3.27
51 52 2.435418 TGGCGAGCCAAAAATGGTT 58.565 47.368 15.24 0.00 44.12 3.67
711 719 8.424918 CAGACCATACTACTTTCAGAACCATAT 58.575 37.037 0.00 0.00 0.00 1.78
948 957 5.109210 TGAATGAGCTAACTTGGTACATCG 58.891 41.667 0.00 0.00 39.30 3.84
1054 1063 6.128526 GCCAAGAGTAGAACAATAACACAGAC 60.129 42.308 0.00 0.00 0.00 3.51
1499 1508 5.244402 TCAAAGTACGGGTAGAATCTGTTCA 59.756 40.000 0.00 0.00 36.79 3.18
1554 1563 5.593679 GGCTAGGCCGATCTTGTATAATA 57.406 43.478 4.61 0.00 39.62 0.98
1614 1623 2.101640 TCTAGTGCCCCTATGCATCA 57.898 50.000 0.19 0.00 44.30 3.07
1688 1697 1.048601 GGGAGGGATATGACTTGCGA 58.951 55.000 0.00 0.00 0.00 5.10
1974 1984 2.607892 GCACACCACGACAAGGAGC 61.608 63.158 0.00 0.00 0.00 4.70
2513 2558 9.382244 CAACACTTGAAGCTTACATACTAAAAC 57.618 33.333 0.00 0.00 0.00 2.43
2556 2601 3.753294 AATAAGTCCGGACCAGCATAG 57.247 47.619 30.82 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.