Multiple sequence alignment - TraesCS5A01G250000

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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 TraesCS5A01G250000 chr5A 100.000 2288 0 0 1 2288 464635927 464633640 0.000000e+00 4226.0
1 TraesCS5A01G250000 chr5B 94.926 2306 93 17 1 2288 429821769 429819470 0.000000e+00 3589.0
2 TraesCS5A01G250000 chr5B 94.716 1514 50 15 790 2288 429727948 429726450 0.000000e+00 2326.0
3 TraesCS5A01G250000 chr5B 85.129 928 86 23 1401 2288 429883154 429882239 0.000000e+00 902.0
4 TraesCS5A01G250000 chr5B 97.041 507 15 0 864 1370 429883657 429883151 0.000000e+00 854.0
5 TraesCS5A01G250000 chr5B 86.494 348 36 8 480 822 429884367 429884026 2.780000e-99 372.0
6 TraesCS5A01G250000 chr5D 94.567 1638 71 15 1 1624 363977384 363975751 0.000000e+00 2516.0
7 TraesCS5A01G250000 chr5D 94.675 1108 28 12 535 1624 363340809 363339715 0.000000e+00 1690.0
8 TraesCS5A01G250000 chr5D 94.786 1074 32 12 564 1627 363178524 363177465 0.000000e+00 1652.0
9 TraesCS5A01G250000 chr5D 97.811 594 12 1 1696 2288 363339711 363339118 0.000000e+00 1024.0
10 TraesCS5A01G250000 chr5D 97.306 594 15 1 1696 2288 363975747 363975154 0.000000e+00 1007.0
11 TraesCS5A01G250000 chr5D 96.512 602 21 0 1687 2288 363177366 363176765 0.000000e+00 996.0
12 TraesCS5A01G250000 chr5D 86.000 150 21 0 8 157 228960801 228960950 6.540000e-36 161.0
13 TraesCS5A01G250000 chr5D 100.000 31 0 0 1628 1658 363177395 363177365 8.830000e-05 58.4
14 TraesCS5A01G250000 chr6B 82.700 474 80 2 881 1353 179464594 179464122 9.770000e-114 420.0
15 TraesCS5A01G250000 chr3A 92.308 52 2 1 222 271 94194157 94194106 3.150000e-09 73.1


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 TraesCS5A01G250000 chr5A 464633640 464635927 2287 True 4226.000000 4226 100.000000 1 2288 1 chr5A.!!$R1 2287
1 TraesCS5A01G250000 chr5B 429819470 429821769 2299 True 3589.000000 3589 94.926000 1 2288 1 chr5B.!!$R2 2287
2 TraesCS5A01G250000 chr5B 429726450 429727948 1498 True 2326.000000 2326 94.716000 790 2288 1 chr5B.!!$R1 1498
3 TraesCS5A01G250000 chr5B 429882239 429884367 2128 True 709.333333 902 89.554667 480 2288 3 chr5B.!!$R3 1808
4 TraesCS5A01G250000 chr5D 363975154 363977384 2230 True 1761.500000 2516 95.936500 1 2288 2 chr5D.!!$R3 2287
5 TraesCS5A01G250000 chr5D 363339118 363340809 1691 True 1357.000000 1690 96.243000 535 2288 2 chr5D.!!$R2 1753
6 TraesCS5A01G250000 chr5D 363176765 363178524 1759 True 902.133333 1652 97.099333 564 2288 3 chr5D.!!$R1 1724

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
34 36 0.466543 TAAGTGCCACACGTCAGGTT 59.533 50.0 0.0 0.0 39.64 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1827 1.017387 GGTAAGCCTAGTGCATGCAC 58.983 55.0 37.87 37.87 46.5 4.57 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
34 36 0.466543 TAAGTGCCACACGTCAGGTT 59.533 50.000 0.00 0.00 39.64 3.50
46 48 1.269102 CGTCAGGTTCGTGACACTCTT 60.269 52.381 20.27 0.00 46.19 2.85
89 92 2.542020 TTTCAGTCACGCAAGGATGA 57.458 45.000 0.00 0.00 46.39 2.92
90 93 2.542020 TTCAGTCACGCAAGGATGAA 57.458 45.000 0.00 0.00 46.39 2.57
121 124 2.747989 TGACACACGGCAAGTTTTTGTA 59.252 40.909 0.00 0.00 36.65 2.41
122 125 3.378742 TGACACACGGCAAGTTTTTGTAT 59.621 39.130 0.00 0.00 36.65 2.29
178 185 8.616076 GCTTGCTAACTGAAGTGATGTTATAAT 58.384 33.333 0.00 0.00 0.00 1.28
297 304 8.506168 TGAACTTTGTTATCTTTCTGTTGAGT 57.494 30.769 0.00 0.00 0.00 3.41
315 323 8.893563 TGTTGAGTAATTAATGGAAAGGGATT 57.106 30.769 0.00 0.00 0.00 3.01
1224 1593 2.441164 ATCTCCCGCAGCGTCTCT 60.441 61.111 15.05 0.00 0.00 3.10
1380 1752 5.511729 GCAAAGGATGCGTTGATTAACTAAC 59.488 40.000 16.52 0.00 46.87 2.34
1455 1827 4.058124 TCCGAATTGAAATAGCTCATCCG 58.942 43.478 0.00 0.00 0.00 4.18
1583 1969 1.968017 TACCACGGAAGCTCGTCGT 60.968 57.895 3.88 3.88 41.86 4.34
1737 2219 0.673644 GCCAGCCCGCATACGATATT 60.674 55.000 0.00 0.00 43.93 1.28
1953 2436 2.357034 GAAAGCACGACGCCCTGA 60.357 61.111 0.00 0.00 44.04 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 11 4.180817 CTGACGTGTGGCACTTATCATTA 58.819 43.478 19.83 0.00 31.34 1.90
46 48 4.370049 TGTCATCGAAAAACGTTAGGACA 58.630 39.130 10.48 10.48 43.13 4.02
52 54 6.262601 ACTGAAATTGTCATCGAAAAACGTT 58.737 32.000 0.00 0.00 35.07 3.99
89 92 2.223711 GCCGTGTGTCACTGGAATTTTT 60.224 45.455 16.21 0.00 32.71 1.94
90 93 1.336755 GCCGTGTGTCACTGGAATTTT 59.663 47.619 16.21 0.00 32.71 1.82
140 147 4.678287 CAGTTAGCAAGCATGACAACTTTG 59.322 41.667 0.00 0.00 0.00 2.77
355 367 1.877443 GCGCTCCCTTCAGTAACAAAA 59.123 47.619 0.00 0.00 0.00 2.44
363 375 3.496130 CAGTAATTATGCGCTCCCTTCAG 59.504 47.826 9.73 0.00 0.00 3.02
364 376 3.466836 CAGTAATTATGCGCTCCCTTCA 58.533 45.455 9.73 0.00 0.00 3.02
366 378 2.222027 GCAGTAATTATGCGCTCCCTT 58.778 47.619 9.73 0.00 33.31 3.95
452 464 5.070313 ACCCACAACAGAATTGCACTAAAAT 59.930 36.000 0.00 0.00 0.00 1.82
1310 1679 2.643272 ACGTGCTGATGACGACGT 59.357 55.556 0.00 0.00 39.21 4.34
1380 1752 5.890110 ACGAACGCACTCTATCAATTATG 57.110 39.130 0.00 0.00 0.00 1.90
1455 1827 1.017387 GGTAAGCCTAGTGCATGCAC 58.983 55.000 37.87 37.87 46.50 4.57
1737 2219 8.944029 GCTCGTGAATAATACTACTCCTATACA 58.056 37.037 0.00 0.00 0.00 2.29
1953 2436 2.048597 TCGTTGCGCCGAGTTGAT 60.049 55.556 4.18 0.00 32.18 2.57


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

AutoCloner maintained by Alex Coulton.