Multiple sequence alignment - TraesCS3A01G443700

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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 TraesCS3A01G443700 chr3A 100.000 3060 0 0 1 3060 685118818 685121877 0 5651
1 TraesCS3A01G443700 chr3B 94.156 3097 129 17 1 3060 725706336 725709417 0 4669
2 TraesCS3A01G443700 chr3D 92.046 2590 111 38 544 3060 548246698 548249265 0 3554
3 TraesCS3A01G443700 chr3D 94.096 542 31 1 1 542 548246109 548246649 0 822


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 TraesCS3A01G443700 chr3A 685118818 685121877 3059 False 5651 5651 100.000 1 3060 1 chr3A.!!$F1 3059
1 TraesCS3A01G443700 chr3B 725706336 725709417 3081 False 4669 4669 94.156 1 3060 1 chr3B.!!$F1 3059
2 TraesCS3A01G443700 chr3D 548246109 548249265 3156 False 2188 3554 93.071 1 3060 2 chr3D.!!$F1 3059

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
489 490 0.522180 GAAGTTGAGGAGAGACGCGA 59.478 55.0 15.93 0.0 0.0 5.87 F
1301 1391 0.309922 CTTGCTGCTGTGTTGTCTGG 59.690 55.0 0.00 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1785 0.178767 CCATTCCGAGGATGACTGCA 59.821 55.0 0.0 0.0 0.0 4.41 R
2785 2888 2.368221 AGCAGATAGGAGAATGACCAGC 59.632 50.0 0.0 0.0 0.0 4.85 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
41 42 6.482308 TGAGTTCTTACAGCCTTTTCTTGTAC 59.518 38.462 0.00 0.00 0.00 2.90
44 45 5.925509 TCTTACAGCCTTTTCTTGTACTGT 58.074 37.500 0.00 0.00 41.06 3.55
52 53 6.206829 AGCCTTTTCTTGTACTGTTTCATACC 59.793 38.462 0.00 0.00 0.00 2.73
60 61 3.855689 ACTGTTTCATACCTGCATTGC 57.144 42.857 0.46 0.46 0.00 3.56
272 273 6.491714 AATGAGATCATTGGTGCTACTACT 57.508 37.500 7.26 0.00 44.22 2.57
293 294 2.305635 TGAGGAGCTGGTTATGAAAGCA 59.694 45.455 0.00 0.00 40.68 3.91
313 314 4.686554 AGCAAGACAAAGCTAGTAAACTCG 59.313 41.667 0.00 0.00 39.78 4.18
329 330 6.993902 AGTAAACTCGATTTGAACCAGGTAAA 59.006 34.615 0.00 0.00 0.00 2.01
347 348 7.255139 CCAGGTAAACTTCTTGTAAACTCTTGG 60.255 40.741 0.00 0.00 0.00 3.61
404 405 2.747989 CAAGAAGTGCTGACATGCTGAT 59.252 45.455 0.00 0.00 0.00 2.90
408 409 3.623906 AGTGCTGACATGCTGATACTT 57.376 42.857 0.00 0.00 0.00 2.24
417 418 7.364522 TGACATGCTGATACTTAGTTTGTTC 57.635 36.000 0.00 0.00 0.00 3.18
489 490 0.522180 GAAGTTGAGGAGAGACGCGA 59.478 55.000 15.93 0.00 0.00 5.87
580 628 9.722184 GGTGTAAGAATTAAATATCCCCTACTC 57.278 37.037 0.00 0.00 28.70 2.59
610 660 4.647564 ATGGAGATGTTCAAGGAAGTGT 57.352 40.909 0.00 0.00 0.00 3.55
718 774 3.895656 GGGTATTTTCCTTCCCCTTATGC 59.104 47.826 0.00 0.00 34.32 3.14
721 777 4.513406 ATTTTCCTTCCCCTTATGCGTA 57.487 40.909 0.00 0.00 0.00 4.42
947 1018 2.419297 GGAGGTACATGTGCAGGAGAAG 60.419 54.545 16.11 0.00 0.00 2.85
1003 1076 2.682563 GCGTTTGGGGGTGAGATAATGA 60.683 50.000 0.00 0.00 0.00 2.57
1004 1077 3.206150 CGTTTGGGGGTGAGATAATGAG 58.794 50.000 0.00 0.00 0.00 2.90
1005 1078 2.952310 GTTTGGGGGTGAGATAATGAGC 59.048 50.000 0.00 0.00 0.00 4.26
1006 1079 1.891933 TGGGGGTGAGATAATGAGCA 58.108 50.000 0.00 0.00 0.00 4.26
1007 1080 1.770658 TGGGGGTGAGATAATGAGCAG 59.229 52.381 0.00 0.00 0.00 4.24
1008 1081 1.544314 GGGGGTGAGATAATGAGCAGC 60.544 57.143 0.00 0.00 0.00 5.25
1301 1391 0.309922 CTTGCTGCTGTGTTGTCTGG 59.690 55.000 0.00 0.00 0.00 3.86
1365 1455 7.187824 AGACTTTGTGTATGGAGTGTATGAT 57.812 36.000 0.00 0.00 0.00 2.45
1396 1486 3.136443 CACCTATGATGAAGGCCAAGGTA 59.864 47.826 5.01 0.00 37.67 3.08
1403 1495 5.624159 TGATGAAGGCCAAGGTATTATCTG 58.376 41.667 5.01 0.00 0.00 2.90
1406 1498 4.972568 TGAAGGCCAAGGTATTATCTGGTA 59.027 41.667 5.01 0.00 0.00 3.25
1411 1503 8.232098 AGGCCAAGGTATTATCTGGTATATTT 57.768 34.615 5.01 0.00 0.00 1.40
1446 1538 5.327091 GCATAAACTATATGCATTCGCTGG 58.673 41.667 3.54 0.00 46.89 4.85
1447 1539 3.904136 AAACTATATGCATTCGCTGGC 57.096 42.857 3.54 0.00 39.64 4.85
1449 1541 2.420642 ACTATATGCATTCGCTGGCTG 58.579 47.619 3.54 0.00 39.64 4.85
1453 1549 0.454600 ATGCATTCGCTGGCTGAAAG 59.545 50.000 0.00 2.63 39.64 2.62
1454 1550 0.890542 TGCATTCGCTGGCTGAAAGT 60.891 50.000 0.00 0.00 39.64 2.66
1471 1567 6.348786 GCTGAAAGTTTGTGCTGATTCTGATA 60.349 38.462 0.00 0.00 35.30 2.15
1481 1577 5.049612 GTGCTGATTCTGATATGATGTGGTG 60.050 44.000 0.00 0.00 0.00 4.17
1510 1606 6.723052 ACCAATCATCCAACTGAAGAAAAGAT 59.277 34.615 0.00 0.00 0.00 2.40
1529 1625 0.846427 TGGGCTTCTGGGAGGATGTT 60.846 55.000 0.00 0.00 0.00 2.71
1559 1655 1.130054 ACCAAGAAGCTGAGCCTCCA 61.130 55.000 0.00 0.00 0.00 3.86
1565 1661 3.005539 GCTGAGCCTCCACAGGGA 61.006 66.667 0.00 0.00 40.75 4.20
1648 1744 7.914346 CCTTGAATCTTTCTCATTAGCATCAAC 59.086 37.037 0.00 0.00 0.00 3.18
1726 1822 0.814010 GGCTTTCGATGTGCCGGTAT 60.814 55.000 1.90 0.00 37.11 2.73
1797 1897 0.033504 GTCTTGGGCTCACTGAACGA 59.966 55.000 0.00 0.00 0.00 3.85
1808 1908 2.031069 TCACTGAACGAAGGAAGACTCG 60.031 50.000 0.00 0.00 0.00 4.18
1831 1931 1.004277 GTCTATTTGTGCCACCAGGGA 59.996 52.381 0.00 0.00 40.01 4.20
2029 2129 1.882989 GCGAGCTCTGGGACTTCACT 61.883 60.000 12.85 0.00 0.00 3.41
2047 2147 3.643320 TCACTGTCAACAGAGATGACCTT 59.357 43.478 16.71 0.00 46.59 3.50
2236 2336 4.613944 TGCAGAGCAAATTGTCAGAAAAG 58.386 39.130 0.00 0.00 34.76 2.27
2239 2339 5.218139 CAGAGCAAATTGTCAGAAAAGACC 58.782 41.667 0.00 0.00 37.73 3.85
2242 2342 6.716628 AGAGCAAATTGTCAGAAAAGACCATA 59.283 34.615 0.00 0.00 37.73 2.74
2247 2347 8.783093 CAAATTGTCAGAAAAGACCATACTACA 58.217 33.333 0.00 0.00 37.73 2.74
2269 2372 9.421806 CTACAAATGGCAAATGTCTAAAATTGA 57.578 29.630 11.22 0.00 0.00 2.57
2378 2481 6.674760 GCAAGTTGAAACCCTATGTCGAATAC 60.675 42.308 7.16 0.00 0.00 1.89
2379 2482 6.045072 AGTTGAAACCCTATGTCGAATACA 57.955 37.500 0.00 0.00 43.86 2.29
2392 2495 9.831054 CTATGTCGAATACAACGAAGAAAATAC 57.169 33.333 0.00 0.00 42.70 1.89
2724 2827 2.956964 CGGACGATCCTCGCTTGC 60.957 66.667 0.00 0.00 45.12 4.01
2771 2874 2.733227 CGCAACAATTCCTTCATGCCTC 60.733 50.000 0.00 0.00 0.00 4.70
2785 2888 2.125269 CCTCGTGGGGTAAAGCCG 60.125 66.667 0.00 0.00 38.44 5.52
2870 2999 7.357429 TGCATATCAGAGATGGATAGTATGG 57.643 40.000 7.15 0.00 31.27 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.492881 TGGCAATGCAGGTATGAAACAG 59.507 45.455 7.79 0.00 0.00 3.16
44 45 2.754552 GACTGGCAATGCAGGTATGAAA 59.245 45.455 7.79 0.00 0.00 2.69
52 53 4.499188 CCTTTCATATGACTGGCAATGCAG 60.499 45.833 7.79 5.36 0.00 4.41
60 61 7.921786 TTGTAAGAACCTTTCATATGACTGG 57.078 36.000 17.18 17.18 0.00 4.00
140 141 6.043938 AGGGATAACAATACGATGGGTAATGT 59.956 38.462 0.00 0.00 45.02 2.71
201 202 9.620259 AACAATTCTTCCTATAGAATCCTGAAC 57.380 33.333 0.00 0.00 42.53 3.18
272 273 2.305635 TGCTTTCATAACCAGCTCCTCA 59.694 45.455 0.00 0.00 34.42 3.86
293 294 7.656137 TCAAATCGAGTTTACTAGCTTTGTCTT 59.344 33.333 14.50 0.00 36.64 3.01
313 314 7.039313 ACAAGAAGTTTACCTGGTTCAAATC 57.961 36.000 3.84 0.00 0.00 2.17
329 330 4.137543 CTGGCCAAGAGTTTACAAGAAGT 58.862 43.478 7.01 0.00 0.00 3.01
363 364 8.561738 TTCTTGGAGTAATCCAGAAACATTAC 57.438 34.615 12.37 0.00 41.35 1.89
417 418 3.436243 TGTACTTGCCCCCTTAAAATGG 58.564 45.455 0.00 0.00 0.00 3.16
489 490 5.407407 AGAATCTACGACCAAATCACAGT 57.593 39.130 0.00 0.00 0.00 3.55
573 621 5.531122 TCTCCATATTTGTTCGAGTAGGG 57.469 43.478 0.00 0.00 0.00 3.53
580 628 6.316140 TCCTTGAACATCTCCATATTTGTTCG 59.684 38.462 9.33 0.00 46.87 3.95
589 637 4.647564 ACACTTCCTTGAACATCTCCAT 57.352 40.909 0.00 0.00 0.00 3.41
635 686 8.374743 CCAATCCAGGGAATTTCTTTTCTTTAA 58.625 33.333 0.00 0.00 0.00 1.52
656 707 4.219288 AGAACAGATCCAGCAAAACCAATC 59.781 41.667 0.00 0.00 0.00 2.67
718 774 4.671766 GCTCACAGGGCTTTATGTTTTACG 60.672 45.833 0.00 0.00 0.00 3.18
721 777 3.230134 TGCTCACAGGGCTTTATGTTTT 58.770 40.909 0.00 0.00 0.00 2.43
786 842 2.783135 ACTGTTACATGGCTGGACAAG 58.217 47.619 0.00 0.00 0.00 3.16
947 1018 2.328099 CCACACCCTCTTCGCTTGC 61.328 63.158 0.00 0.00 0.00 4.01
977 1050 3.977244 CACCCCCAAACGCTGTGC 61.977 66.667 0.00 0.00 0.00 4.57
1264 1352 3.741075 GCAAGAACAAGAAAACCAAGGGG 60.741 47.826 0.00 0.00 41.29 4.79
1265 1353 3.132824 AGCAAGAACAAGAAAACCAAGGG 59.867 43.478 0.00 0.00 0.00 3.95
1301 1391 1.284785 TCCAGTGTCATCCCAATTCCC 59.715 52.381 0.00 0.00 0.00 3.97
1365 1455 0.255604 CATCATAGGTGTGGTGGCCA 59.744 55.000 0.00 0.00 0.00 5.36
1424 1516 5.122869 AGCCAGCGAATGCATATAGTTTATG 59.877 40.000 0.00 0.00 46.23 1.90
1440 1532 0.662619 CACAAACTTTCAGCCAGCGA 59.337 50.000 0.00 0.00 0.00 4.93
1443 1535 1.677576 TCAGCACAAACTTTCAGCCAG 59.322 47.619 0.00 0.00 0.00 4.85
1445 1537 3.005155 AGAATCAGCACAAACTTTCAGCC 59.995 43.478 0.00 0.00 0.00 4.85
1446 1538 3.979495 CAGAATCAGCACAAACTTTCAGC 59.021 43.478 0.00 0.00 0.00 4.26
1447 1539 5.428496 TCAGAATCAGCACAAACTTTCAG 57.572 39.130 0.00 0.00 0.00 3.02
1449 1541 7.755591 TCATATCAGAATCAGCACAAACTTTC 58.244 34.615 0.00 0.00 0.00 2.62
1453 1549 6.910972 CACATCATATCAGAATCAGCACAAAC 59.089 38.462 0.00 0.00 0.00 2.93
1454 1550 6.038936 CCACATCATATCAGAATCAGCACAAA 59.961 38.462 0.00 0.00 0.00 2.83
1481 1577 4.766891 TCTTCAGTTGGATGATTGGTTTCC 59.233 41.667 0.00 0.00 0.00 3.13
1510 1606 0.846427 AACATCCTCCCAGAAGCCCA 60.846 55.000 0.00 0.00 0.00 5.36
1529 1625 2.972713 AGCTTCTTGGTACCACTCAGAA 59.027 45.455 21.07 21.07 0.00 3.02
1559 1655 2.572104 GAGTGTACCTTGGAATCCCTGT 59.428 50.000 0.00 0.00 0.00 4.00
1565 1661 4.323792 CCATGAGTGAGTGTACCTTGGAAT 60.324 45.833 0.00 0.00 0.00 3.01
1614 1710 8.868522 AATGAGAAAGATTCAAGGACATGTAA 57.131 30.769 0.00 0.00 0.00 2.41
1648 1744 1.136147 GTGCTGCAAGAGATTGCCG 59.864 57.895 2.77 5.38 46.82 5.69
1689 1785 0.178767 CCATTCCGAGGATGACTGCA 59.821 55.000 0.00 0.00 0.00 4.41
1726 1822 6.443849 AGAGGTTAATGGAACTACTCAATCCA 59.556 38.462 0.00 0.00 46.60 3.41
1831 1931 2.916934 TGCCCCAATGTAAAGGTACTCT 59.083 45.455 0.00 0.00 38.49 3.24
2029 2129 4.777366 TGGATAAGGTCATCTCTGTTGACA 59.223 41.667 6.20 0.00 44.22 3.58
2047 2147 3.461458 TGAATGGCACCTATGGTTGGATA 59.539 43.478 0.00 0.00 31.02 2.59
2236 2336 6.095440 AGACATTTGCCATTTGTAGTATGGTC 59.905 38.462 0.00 0.00 43.65 4.02
2239 2339 9.853555 TTTTAGACATTTGCCATTTGTAGTATG 57.146 29.630 0.00 0.00 0.00 2.39
2242 2342 9.206870 CAATTTTAGACATTTGCCATTTGTAGT 57.793 29.630 0.00 0.00 0.00 2.73
2247 2347 9.211485 CTCTTCAATTTTAGACATTTGCCATTT 57.789 29.630 0.00 0.00 0.00 2.32
2269 2372 9.125026 CCAAACTGGCAACTTTATATATCTCTT 57.875 33.333 0.00 0.00 37.61 2.85
2353 2456 3.071479 TCGACATAGGGTTTCAACTTGC 58.929 45.455 0.00 0.00 0.00 4.01
2378 2481 3.190535 CCCCTGGTGTATTTTCTTCGTTG 59.809 47.826 0.00 0.00 0.00 4.10
2379 2482 3.181437 ACCCCTGGTGTATTTTCTTCGTT 60.181 43.478 0.00 0.00 32.98 3.85
2540 2643 4.593956 AGCATTTCAAAGGCTAAGCTAGT 58.406 39.130 7.70 0.00 35.82 2.57
2771 2874 3.124921 CAGCGGCTTTACCCCACG 61.125 66.667 0.00 0.00 33.26 4.94
2785 2888 2.368221 AGCAGATAGGAGAATGACCAGC 59.632 50.000 0.00 0.00 0.00 4.85
2897 3026 7.033791 CCTGATGATTGTTCAATTCCTCTTTG 58.966 38.462 0.00 0.00 34.96 2.77


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

AutoCloner maintained by Alex Coulton.