Multiple sequence alignment - TraesCS5B01G058700

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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 TraesCS5B01G058700 chr5B 100.000 2414 0 0 1 2414 64374159 64371746 0.000000e+00 4458.0
1 TraesCS5B01G058700 chr5B 90.774 2352 177 19 1 2327 109361434 109363770 0.000000e+00 3105.0
2 TraesCS5B01G058700 chr3B 90.551 2360 174 21 1 2333 617154784 617157121 0.000000e+00 3077.0
3 TraesCS5B01G058700 chr3B 91.787 2143 133 26 1 2137 36555563 36557668 0.000000e+00 2942.0
4 TraesCS5B01G058700 chr3B 89.614 2359 181 25 1 2336 140104627 140106944 0.000000e+00 2940.0
5 TraesCS5B01G058700 chr3B 89.862 1667 114 16 680 2329 660237961 660236333 0.000000e+00 2091.0
6 TraesCS5B01G058700 chr3B 84.816 652 49 12 1646 2266 456368954 456369586 5.710000e-171 610.0
7 TraesCS5B01G058700 chr2B 90.573 2355 161 21 1 2332 527469717 527467401 0.000000e+00 3062.0
8 TraesCS5B01G058700 chr2B 91.601 2143 156 14 1 2137 80331778 80333902 0.000000e+00 2939.0
9 TraesCS5B01G058700 chr2B 91.925 1647 113 11 1 1645 80280023 80281651 0.000000e+00 2287.0
10 TraesCS5B01G058700 chr1B 91.240 2146 134 26 2 2139 285358349 285356250 0.000000e+00 2872.0
11 TraesCS5B01G058700 chr7B 90.812 2144 175 12 1 2137 365345316 365347444 0.000000e+00 2848.0
12 TraesCS5B01G058700 chr6D 88.739 2371 159 57 1 2328 357454091 357451786 0.000000e+00 2800.0
13 TraesCS5B01G058700 chr1A 88.769 1861 141 23 518 2333 252021470 252023307 0.000000e+00 2217.0
14 TraesCS5B01G058700 chr7A 90.771 1647 100 15 702 2327 481817962 481816347 0.000000e+00 2152.0
15 TraesCS5B01G058700 chr6A 90.048 1678 114 20 680 2340 297840372 297842013 0.000000e+00 2124.0
16 TraesCS5B01G058700 chr4B 86.582 790 71 14 1555 2329 438496232 438495463 0.000000e+00 839.0
17 TraesCS5B01G058700 chr4D 93.370 362 21 2 1973 2333 509563815 509563456 1.270000e-147 532.0
18 TraesCS5B01G058700 chr4A 93.023 43 3 0 2370 2412 327395728 327395686 2.000000e-06 63.9


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 TraesCS5B01G058700 chr5B 64371746 64374159 2413 True 4458 4458 100.000 1 2414 1 chr5B.!!$R1 2413
1 TraesCS5B01G058700 chr5B 109361434 109363770 2336 False 3105 3105 90.774 1 2327 1 chr5B.!!$F1 2326
2 TraesCS5B01G058700 chr3B 617154784 617157121 2337 False 3077 3077 90.551 1 2333 1 chr3B.!!$F4 2332
3 TraesCS5B01G058700 chr3B 36555563 36557668 2105 False 2942 2942 91.787 1 2137 1 chr3B.!!$F1 2136
4 TraesCS5B01G058700 chr3B 140104627 140106944 2317 False 2940 2940 89.614 1 2336 1 chr3B.!!$F2 2335
5 TraesCS5B01G058700 chr3B 660236333 660237961 1628 True 2091 2091 89.862 680 2329 1 chr3B.!!$R1 1649
6 TraesCS5B01G058700 chr3B 456368954 456369586 632 False 610 610 84.816 1646 2266 1 chr3B.!!$F3 620
7 TraesCS5B01G058700 chr2B 527467401 527469717 2316 True 3062 3062 90.573 1 2332 1 chr2B.!!$R1 2331
8 TraesCS5B01G058700 chr2B 80331778 80333902 2124 False 2939 2939 91.601 1 2137 1 chr2B.!!$F2 2136
9 TraesCS5B01G058700 chr2B 80280023 80281651 1628 False 2287 2287 91.925 1 1645 1 chr2B.!!$F1 1644
10 TraesCS5B01G058700 chr1B 285356250 285358349 2099 True 2872 2872 91.240 2 2139 1 chr1B.!!$R1 2137
11 TraesCS5B01G058700 chr7B 365345316 365347444 2128 False 2848 2848 90.812 1 2137 1 chr7B.!!$F1 2136
12 TraesCS5B01G058700 chr6D 357451786 357454091 2305 True 2800 2800 88.739 1 2328 1 chr6D.!!$R1 2327
13 TraesCS5B01G058700 chr1A 252021470 252023307 1837 False 2217 2217 88.769 518 2333 1 chr1A.!!$F1 1815
14 TraesCS5B01G058700 chr7A 481816347 481817962 1615 True 2152 2152 90.771 702 2327 1 chr7A.!!$R1 1625
15 TraesCS5B01G058700 chr6A 297840372 297842013 1641 False 2124 2124 90.048 680 2340 1 chr6A.!!$F1 1660
16 TraesCS5B01G058700 chr4B 438495463 438496232 769 True 839 839 86.582 1555 2329 1 chr4B.!!$R1 774

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
445 454 0.179009 CATCGTTGGATCATGGGGCT 60.179 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2282 0.172578 GTCCCTTGCATTAAACGCCC 59.827 55.0 0.0 0.0 0.0 6.13 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
97 101 1.460504 TTGACCTCGATCGTGCTAGT 58.539 50.000 15.94 6.15 0.00 2.57
103 109 1.948145 CTCGATCGTGCTAGTTAGGGT 59.052 52.381 15.94 0.00 0.00 4.34
104 110 2.358267 CTCGATCGTGCTAGTTAGGGTT 59.642 50.000 15.94 0.00 0.00 4.11
445 454 0.179009 CATCGTTGGATCATGGGGCT 60.179 55.000 0.00 0.00 0.00 5.19
475 484 1.559682 AGGCGATCCTATTGGTTGTGT 59.440 47.619 0.00 0.00 42.06 3.72
498 507 1.599047 CTTCTCGCCCACCACTGAT 59.401 57.895 0.00 0.00 0.00 2.90
536 548 2.903135 TGTTATTGGGCCCAAAAGGAAG 59.097 45.455 40.00 0.00 39.55 3.46
565 577 2.033448 TTGGGCCGTCGAATTGCT 59.967 55.556 0.00 0.00 0.00 3.91
567 579 1.861542 TTGGGCCGTCGAATTGCTTG 61.862 55.000 0.00 0.00 0.00 4.01
615 631 2.666190 TGAACGTGCTGGCTCTGC 60.666 61.111 0.00 0.00 0.00 4.26
798 829 7.538303 TTCTTCTTCTTTTTCAAACCATTGC 57.462 32.000 0.00 0.00 36.45 3.56
950 993 1.505098 TCCCATCCTCTCTGCCATCTA 59.495 52.381 0.00 0.00 0.00 1.98
1248 1291 0.482446 TCCTTGCCCACTTCACCAAT 59.518 50.000 0.00 0.00 0.00 3.16
1275 1318 1.453379 CGCCTTCTACCTCCTCGGA 60.453 63.158 0.00 0.00 36.31 4.55
1316 1360 1.391485 CGAGTTCATCGCTTTCACCAG 59.609 52.381 0.00 0.00 45.98 4.00
1386 1430 1.045407 TGCACACTCTTTCGTACCCT 58.955 50.000 0.00 0.00 0.00 4.34
1912 2013 1.893919 GAAGAGAGGAACCAGCGGCT 61.894 60.000 0.00 0.00 0.00 5.52
2002 2106 3.402095 ATCAGCGCATGCAGGCTCT 62.402 57.895 22.31 16.70 46.23 4.09
2026 2198 4.819761 GCATGCAGGCTCGGTCGA 62.820 66.667 17.57 0.00 0.00 4.20
2207 2411 1.594293 CAAAGCACTGACCCGACGT 60.594 57.895 0.00 0.00 0.00 4.34
2239 2443 3.583228 TCTGACCTGTTCTGAGGGTTTA 58.417 45.455 0.00 0.00 37.45 2.01
2269 2474 2.893489 GAGTGGGGAAAAGTGAGCAAAT 59.107 45.455 0.00 0.00 0.00 2.32
2291 2496 3.452990 TGTTAAGAGCGTGGGGATGAATA 59.547 43.478 0.00 0.00 0.00 1.75
2378 2583 8.996651 TCTTCTAACTTTTGGGAGAAAATTCT 57.003 30.769 0.00 0.00 41.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.402011 CGCACAATGTTGTCTTATGTGACATA 60.402 38.462 0.23 0.23 45.03 2.29
281 289 1.416772 GGAGCTAGGGTTAGGCGAATT 59.583 52.381 0.00 0.00 0.00 2.17
282 290 1.049402 GGAGCTAGGGTTAGGCGAAT 58.951 55.000 0.00 0.00 0.00 3.34
316 324 1.681486 TTGGCGCGAGGGTATGATCA 61.681 55.000 12.10 0.00 0.00 2.92
591 607 0.920664 GCCAGCACGTTCACAAAAAC 59.079 50.000 0.00 0.00 0.00 2.43
753 784 0.811281 AAGAAGCTAATTGCACGCCC 59.189 50.000 0.00 0.00 45.94 6.13
754 785 2.636768 AAAGAAGCTAATTGCACGCC 57.363 45.000 0.00 0.00 45.94 5.68
798 829 2.292267 GGAGTGTACATGCATGGGAAG 58.708 52.381 29.41 5.50 0.00 3.46
950 993 3.917072 GTCGAAGAGCAAGAAGGGT 57.083 52.632 0.00 0.00 36.95 4.34
1062 1105 3.089784 CGCTCAACGTACATGCCC 58.910 61.111 0.00 0.00 36.87 5.36
1248 1291 2.357009 GAGGTAGAAGGCGTCGAATGTA 59.643 50.000 0.00 0.00 0.00 2.29
1275 1318 2.419739 GCCACACCAAAACACCCGT 61.420 57.895 0.00 0.00 0.00 5.28
1316 1360 0.238289 CTCCGTGAACATGTTGTGGC 59.762 55.000 17.58 1.54 0.00 5.01
1386 1430 2.755064 TCCGGGGCGTTGTCGATA 60.755 61.111 0.00 0.00 39.71 2.92
1425 1469 3.522731 CTCCACCTCGCTCCTCCG 61.523 72.222 0.00 0.00 0.00 4.63
1597 1672 6.269077 TCACATAGTTGAAACTAGGAAGACCA 59.731 38.462 18.73 0.00 43.81 4.02
1599 1674 7.221067 CGATCACATAGTTGAAACTAGGAAGAC 59.779 40.741 18.73 10.60 43.81 3.01
1815 1916 0.599466 CGATCCACTCGCATCTGCAT 60.599 55.000 2.72 0.00 41.14 3.96
2110 2282 0.172578 GTCCCTTGCATTAAACGCCC 59.827 55.000 0.00 0.00 0.00 6.13
2137 2341 1.287815 CGGTGTAGCTGTTCGACCA 59.712 57.895 0.00 0.00 0.00 4.02
2179 2383 2.032290 GTCAGTGCTTTGACCGTTAACC 60.032 50.000 9.23 0.00 41.24 2.85
2210 2414 1.282930 GAACAGGTCAGAACGGACGC 61.283 60.000 0.00 0.00 38.70 5.19
2239 2443 3.829311 TTCCCCACTCCCTTGCCCT 62.829 63.158 0.00 0.00 0.00 5.19
2269 2474 1.271856 TCATCCCCACGCTCTTAACA 58.728 50.000 0.00 0.00 0.00 2.41
2291 2496 3.108376 CCCTGGTTCCTTAGCTCTACTT 58.892 50.000 0.00 0.00 0.00 2.24
2352 2557 9.421399 AGAATTTTCTCCCAAAAGTTAGAAGAA 57.579 29.630 0.00 0.00 29.94 2.52
2353 2558 8.996651 AGAATTTTCTCCCAAAAGTTAGAAGA 57.003 30.769 0.00 0.00 29.94 2.87


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

AutoCloner maintained by Alex Coulton.