Multiple sequence alignment - TraesCS3A01G243900

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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 TraesCS3A01G243900 chr3A 100.000 2705 0 0 1 2705 457085766 457083062 0.000000e+00 4996
1 TraesCS3A01G243900 chr3A 84.577 201 22 7 284 484 550416958 550417149 9.890000e-45 191
2 TraesCS3A01G243900 chr3D 94.911 1788 37 19 584 2350 346643147 346644901 0.000000e+00 2748
3 TraesCS3A01G243900 chr3D 93.606 563 16 7 52 597 346642570 346643129 0.000000e+00 822
4 TraesCS3A01G243900 chr3D 95.077 325 12 2 2381 2705 346644899 346645219 2.400000e-140 508
5 TraesCS3A01G243900 chr3B 96.471 935 30 3 813 1744 446172525 446173459 0.000000e+00 1541
6 TraesCS3A01G243900 chr3B 85.884 843 57 24 1870 2705 446173531 446174318 0.000000e+00 841
7 TraesCS3A01G243900 chr3B 80.000 295 40 16 286 573 157245935 157245653 1.640000e-47 200
8 TraesCS3A01G243900 chr3B 78.059 237 40 9 321 551 734164130 734164360 3.630000e-29 139
9 TraesCS3A01G243900 chr6D 83.206 262 42 1 284 543 30131298 30131037 3.480000e-59 239
10 TraesCS3A01G243900 chr1A 77.206 272 54 8 284 551 492270531 492270264 4.660000e-33 152
11 TraesCS3A01G243900 chr1D 75.277 271 55 12 284 546 392951001 392951267 4.730000e-23 119
12 TraesCS3A01G243900 chr2A 75.269 279 50 17 284 551 564615786 564615516 6.120000e-22 115
13 TraesCS3A01G243900 chr1B 77.143 210 40 8 346 549 529701298 529701091 6.120000e-22 115


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 TraesCS3A01G243900 chr3A 457083062 457085766 2704 True 4996.000000 4996 100.000000 1 2705 1 chr3A.!!$R1 2704
1 TraesCS3A01G243900 chr3D 346642570 346645219 2649 False 1359.333333 2748 94.531333 52 2705 3 chr3D.!!$F1 2653
2 TraesCS3A01G243900 chr3B 446172525 446174318 1793 False 1191.000000 1541 91.177500 813 2705 2 chr3B.!!$F2 1892

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
996 1049 0.39113 CCTGAACCCGATCGAGCAAA 60.391 55.0 18.66 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2565 2668 1.856265 GCAAACTGGAAGGAGTGGCG 61.856 60.0 0.0 0.0 39.3 5.69 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
24 25 7.656707 GTGCACTTGTAAAAATTCATCCAAT 57.343 32.000 10.32 0.00 0.00 3.16
25 26 8.755696 GTGCACTTGTAAAAATTCATCCAATA 57.244 30.769 10.32 0.00 0.00 1.90
26 27 9.202273 GTGCACTTGTAAAAATTCATCCAATAA 57.798 29.630 10.32 0.00 0.00 1.40
27 28 9.941325 TGCACTTGTAAAAATTCATCCAATAAT 57.059 25.926 0.00 0.00 0.00 1.28
390 392 5.300792 TCCAAAAGTGGTATTTTCGAAAGCT 59.699 36.000 10.98 5.56 46.11 3.74
409 411 4.374399 AGCTTTTTGGAGTGCTGATTTTG 58.626 39.130 0.00 0.00 34.19 2.44
410 412 3.495753 GCTTTTTGGAGTGCTGATTTTGG 59.504 43.478 0.00 0.00 0.00 3.28
473 475 3.648339 TTTGCAGGCACTCAAAAGATC 57.352 42.857 0.00 0.00 34.60 2.75
480 482 4.276678 CAGGCACTCAAAAGATCTGTCAAA 59.723 41.667 0.00 0.00 34.60 2.69
491 500 8.598075 CAAAAGATCTGTCAAAGTTGGAAAAAG 58.402 33.333 0.00 0.00 0.00 2.27
492 501 7.645058 AAGATCTGTCAAAGTTGGAAAAAGA 57.355 32.000 0.00 0.00 0.00 2.52
657 706 1.693062 TCCACCCTTTTAGCACGTGTA 59.307 47.619 18.38 5.61 0.00 2.90
996 1049 0.391130 CCTGAACCCGATCGAGCAAA 60.391 55.000 18.66 0.00 0.00 3.68
1005 1058 1.737236 CGATCGAGCAAACCAATGGAA 59.263 47.619 10.26 0.00 0.00 3.53
1440 1502 3.884091 CGCCAGGTCTACTCATAGTTAGT 59.116 47.826 0.00 0.00 0.00 2.24
1754 1816 5.768164 GGTCCTCTCTTTTATGGTTGAAACA 59.232 40.000 0.00 0.00 0.00 2.83
1775 1837 4.119136 CAATTCCTGGTGTTGGTTTGAAC 58.881 43.478 0.00 0.00 0.00 3.18
1861 1929 8.195436 TGCTACATAGGAAGTGAGTTGTAATAC 58.805 37.037 0.00 0.00 0.00 1.89
1862 1930 8.414778 GCTACATAGGAAGTGAGTTGTAATACT 58.585 37.037 0.00 0.00 0.00 2.12
1879 1977 8.004087 TGTAATACTAATAGGTATCGGCCATC 57.996 38.462 2.24 0.00 31.98 3.51
1966 2064 2.157738 GCCTGTGCAGTTTGAGATCTT 58.842 47.619 0.00 0.00 37.47 2.40
1979 2077 7.377928 CAGTTTGAGATCTTGTACAAAGCAAAG 59.622 37.037 10.03 0.00 33.86 2.77
2122 2221 1.126113 CATTAGACCAACGACACGTGC 59.874 52.381 17.22 7.72 39.99 5.34
2232 2333 0.596082 GAGTCGAGAGCTCCTATGGC 59.404 60.000 10.93 0.00 0.00 4.40
2243 2344 7.084268 AGAGCTCCTATGGCAGTATAATTTT 57.916 36.000 10.93 0.00 0.00 1.82
2269 2370 8.356533 TGTCTAATTATTCGTCCGATTTAACC 57.643 34.615 0.00 0.00 0.00 2.85
2270 2371 8.199449 TGTCTAATTATTCGTCCGATTTAACCT 58.801 33.333 0.00 0.00 0.00 3.50
2271 2372 8.697960 GTCTAATTATTCGTCCGATTTAACCTC 58.302 37.037 0.00 0.00 0.00 3.85
2272 2373 8.415553 TCTAATTATTCGTCCGATTTAACCTCA 58.584 33.333 0.00 0.00 0.00 3.86
2273 2374 7.852971 AATTATTCGTCCGATTTAACCTCAA 57.147 32.000 0.00 0.00 0.00 3.02
2274 2375 7.852971 ATTATTCGTCCGATTTAACCTCAAA 57.147 32.000 0.00 0.00 0.00 2.69
2275 2376 7.852971 TTATTCGTCCGATTTAACCTCAAAT 57.147 32.000 0.00 0.00 0.00 2.32
2276 2377 6.753107 ATTCGTCCGATTTAACCTCAAATT 57.247 33.333 0.00 0.00 0.00 1.82
2353 2454 4.274459 AGAAACTGACAGCTTCATGTTGAC 59.726 41.667 18.36 0.00 32.17 3.18
2379 2480 2.367567 GCCTGGGCATCATTCATGATTT 59.632 45.455 6.75 0.00 44.70 2.17
2389 2490 9.531942 GGCATCATTCATGATTTTGTGTATTTA 57.468 29.630 0.00 0.00 44.70 1.40
2503 2606 5.744666 TTAAGTTTGTCTTGGTTCTTCCG 57.255 39.130 0.00 0.00 39.52 4.30
2505 2608 1.947456 GTTTGTCTTGGTTCTTCCGCT 59.053 47.619 0.00 0.00 39.52 5.52
2522 2625 3.054655 TCCGCTGAATTTTAACCTAGCCT 60.055 43.478 0.00 0.00 0.00 4.58
2565 2668 4.243007 ACTAATGGCAAGCACACTTTTC 57.757 40.909 0.00 0.00 32.29 2.29
2694 2797 9.899661 TTTGACCTTATGTTTAGCATATACACT 57.100 29.630 0.00 0.00 39.56 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.656707 ATTGGATGAATTTTTACAAGTGCAC 57.343 32.000 9.40 9.40 0.00 4.57
1 2 9.941325 ATTATTGGATGAATTTTTACAAGTGCA 57.059 25.926 0.00 0.00 0.00 4.57
146 147 2.979813 GCACCTGCAAAAACTCATTACG 59.020 45.455 0.00 0.00 41.59 3.18
233 234 1.345422 TGCACCCCATATTCTCCCTCT 60.345 52.381 0.00 0.00 0.00 3.69
390 392 4.751767 ACCAAAATCAGCACTCCAAAAA 57.248 36.364 0.00 0.00 0.00 1.94
421 423 4.468713 TGAAATGACATTTGTGGGAGTCA 58.531 39.130 18.00 4.66 44.16 3.41
473 475 7.483307 TCTGATTCTTTTTCCAACTTTGACAG 58.517 34.615 0.00 0.00 0.00 3.51
528 537 6.402118 GCAAGCTCGTGATGAACAGTAAAATA 60.402 38.462 0.00 0.00 0.00 1.40
657 706 7.119262 CGTACAGAAAGGTATTTTGAATGGAGT 59.881 37.037 0.00 0.00 0.00 3.85
699 748 5.790593 TGTTGGAGAAGTAAGGTGATGTAC 58.209 41.667 0.00 0.00 0.00 2.90
806 855 1.407618 GAAGGCCAACACTCGGTTTTT 59.592 47.619 5.01 0.00 37.72 1.94
807 856 1.029681 GAAGGCCAACACTCGGTTTT 58.970 50.000 5.01 0.00 37.72 2.43
808 857 0.822121 GGAAGGCCAACACTCGGTTT 60.822 55.000 5.01 0.00 37.72 3.27
809 858 1.228154 GGAAGGCCAACACTCGGTT 60.228 57.895 5.01 0.00 41.47 4.44
810 859 1.705997 AAGGAAGGCCAACACTCGGT 61.706 55.000 5.01 0.00 36.29 4.69
996 1049 0.318120 CGGCTTGCTTTTCCATTGGT 59.682 50.000 1.86 0.00 0.00 3.67
1440 1502 2.831685 ACACGGCACATGAAGACTTA 57.168 45.000 0.00 0.00 0.00 2.24
1754 1816 3.181480 CGTTCAAACCAACACCAGGAATT 60.181 43.478 0.00 0.00 0.00 2.17
1775 1837 1.933181 TCATAAGATTTCACGGCAGCG 59.067 47.619 0.00 0.00 0.00 5.18
1811 1873 6.659745 TGAAGCTTTGACAGTAACCTAGTA 57.340 37.500 0.00 0.00 0.00 1.82
1966 2064 6.430925 AGCATTGAGTATCTTTGCTTTGTACA 59.569 34.615 0.00 0.00 46.62 2.90
1979 2077 6.846283 CGTTTTAATCGGAAGCATTGAGTATC 59.154 38.462 0.00 0.00 0.00 2.24
2122 2221 9.658475 TCACTTCGTGTTTTTGTCATATAAAAG 57.342 29.630 0.00 0.00 34.79 2.27
2243 2344 8.819974 GGTTAAATCGGACGAATAATTAGACAA 58.180 33.333 0.00 0.00 0.00 3.18
2256 2357 5.121768 AGTCAATTTGAGGTTAAATCGGACG 59.878 40.000 0.00 0.00 38.24 4.79
2261 2362 9.841880 GAGGTTAAGTCAATTTGAGGTTAAATC 57.158 33.333 12.33 10.65 30.33 2.17
2262 2363 9.362151 TGAGGTTAAGTCAATTTGAGGTTAAAT 57.638 29.630 12.33 7.25 31.87 1.40
2263 2364 8.754991 TGAGGTTAAGTCAATTTGAGGTTAAA 57.245 30.769 12.33 0.00 0.00 1.52
2264 2365 8.754991 TTGAGGTTAAGTCAATTTGAGGTTAA 57.245 30.769 0.00 4.85 0.00 2.01
2265 2366 8.754991 TTTGAGGTTAAGTCAATTTGAGGTTA 57.245 30.769 0.00 0.00 33.95 2.85
2266 2367 7.654022 TTTGAGGTTAAGTCAATTTGAGGTT 57.346 32.000 0.00 0.00 33.95 3.50
2267 2368 7.839680 ATTTGAGGTTAAGTCAATTTGAGGT 57.160 32.000 0.00 0.00 33.95 3.85
2268 2369 8.359642 TCAATTTGAGGTTAAGTCAATTTGAGG 58.640 33.333 20.86 8.03 43.04 3.86
2269 2370 9.748708 TTCAATTTGAGGTTAAGTCAATTTGAG 57.251 29.630 22.13 9.53 45.57 3.02
2273 2374 9.480053 CACATTCAATTTGAGGTTAAGTCAATT 57.520 29.630 0.00 0.00 33.95 2.32
2274 2375 7.599998 GCACATTCAATTTGAGGTTAAGTCAAT 59.400 33.333 0.00 0.00 33.95 2.57
2275 2376 6.922957 GCACATTCAATTTGAGGTTAAGTCAA 59.077 34.615 0.00 0.00 31.98 3.18
2276 2377 6.446318 GCACATTCAATTTGAGGTTAAGTCA 58.554 36.000 0.00 0.00 0.00 3.41
2353 2454 2.589720 TGAATGATGCCCAGGCTATTG 58.410 47.619 10.58 0.00 42.51 1.90
2389 2490 7.391148 AGGAACGACATAAATTTTGTAGCAT 57.609 32.000 0.00 0.00 0.00 3.79
2443 2546 9.619316 CAAATATGAAAATACGAAGTTGGAACA 57.381 29.630 0.00 0.00 37.78 3.18
2447 2550 8.980143 AACCAAATATGAAAATACGAAGTTGG 57.020 30.769 0.00 0.00 37.78 3.77
2503 2606 4.944317 AGTGAGGCTAGGTTAAAATTCAGC 59.056 41.667 0.00 0.00 0.00 4.26
2505 2608 6.539173 TGAAGTGAGGCTAGGTTAAAATTCA 58.461 36.000 0.00 0.00 0.00 2.57
2522 2625 7.639113 AGTAACCTGTCAAAAATTGAAGTGA 57.361 32.000 0.00 0.00 42.15 3.41
2565 2668 1.856265 GCAAACTGGAAGGAGTGGCG 61.856 60.000 0.00 0.00 39.30 5.69


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

AutoCloner maintained by Alex Coulton.