Multiple sequence alignment - TraesCS3D01G240700

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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 TraesCS3D01G240700 chr3D 100.000 2564 0 0 1 2564 333285118 333282555 0.000000e+00 4735
1 TraesCS3D01G240700 chr3B 92.747 2082 88 26 1 2038 432335768 432333706 0.000000e+00 2950
2 TraesCS3D01G240700 chr3B 95.989 374 10 3 2022 2390 432333401 432333028 1.010000e-168 603
3 TraesCS3D01G240700 chr3B 95.506 178 7 1 2388 2564 432332947 432332770 1.500000e-72 283
4 TraesCS3D01G240700 chr3A 89.019 2049 81 51 79 2046 450953271 450951286 0.000000e+00 2405
5 TraesCS3D01G240700 chr3A 92.132 394 25 4 2071 2458 450951289 450950896 3.730000e-153 551


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 TraesCS3D01G240700 chr3D 333282555 333285118 2563 True 4735.000000 4735 100.000000 1 2564 1 chr3D.!!$R1 2563
1 TraesCS3D01G240700 chr3B 432332770 432335768 2998 True 1278.666667 2950 94.747333 1 2564 3 chr3B.!!$R1 2563
2 TraesCS3D01G240700 chr3A 450950896 450953271 2375 True 1478.000000 2405 90.575500 79 2458 2 chr3A.!!$R1 2379

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
411 431 0.537188 CAGTAGCCAGACCGGATTGT 59.463 55.0 9.46 0.0 36.56 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2698 0.46546 TCTGAACATAATGCCGGGGC 60.465 55.0 2.18 1.86 42.35 5.8 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
46 47 4.884164 GTCCAATAATGAAACAGAGGAGGG 59.116 45.833 0.00 0.00 0.00 4.30
58 59 4.979335 ACAGAGGAGGGAGAAAAGAAAAG 58.021 43.478 0.00 0.00 0.00 2.27
63 64 5.958321 AGGAGGGAGAAAAGAAAAGAACAT 58.042 37.500 0.00 0.00 0.00 2.71
65 66 7.526918 AGGAGGGAGAAAAGAAAAGAACATAA 58.473 34.615 0.00 0.00 0.00 1.90
77 78 6.535508 AGAAAAGAACATAATCGTGGTCTAGC 59.464 38.462 0.00 0.00 45.11 3.42
99 100 2.789339 GGAAACAAAGCGTGAAAGAAGC 59.211 45.455 0.00 0.00 0.00 3.86
411 431 0.537188 CAGTAGCCAGACCGGATTGT 59.463 55.000 9.46 0.00 36.56 2.71
499 519 4.704833 CACGCCACCACAGGGAGG 62.705 72.222 0.00 0.00 46.81 4.30
505 525 3.208592 ACCACAGGGAGGGAGGGA 61.209 66.667 0.00 0.00 38.05 4.20
592 631 8.978472 AGGAGATTTATTAGCGCCATAGTATAA 58.022 33.333 2.29 0.00 0.00 0.98
612 651 1.611977 AGCACGCATATCTTACCGCTA 59.388 47.619 0.00 0.00 0.00 4.26
622 661 3.650070 TCTTACCGCTATGAGCATCTG 57.350 47.619 0.00 0.00 42.58 2.90
638 678 2.982744 CTGCGTGAGACTGAGCCGA 61.983 63.158 0.00 0.00 0.00 5.54
654 694 5.597806 TGAGCCGACGTATCATCTTAAATT 58.402 37.500 0.00 0.00 0.00 1.82
657 697 6.715464 AGCCGACGTATCATCTTAAATTTTG 58.285 36.000 0.00 0.00 0.00 2.44
662 702 7.463648 CGACGTATCATCTTAAATTTTGACGGT 60.464 37.037 0.00 0.00 0.00 4.83
663 703 8.706492 ACGTATCATCTTAAATTTTGACGGTA 57.294 30.769 0.00 0.00 0.00 4.02
664 704 9.321562 ACGTATCATCTTAAATTTTGACGGTAT 57.678 29.630 0.00 0.00 0.00 2.73
670 710 6.616947 TCTTAAATTTTGACGGTATTGCCTG 58.383 36.000 0.00 0.00 34.25 4.85
673 713 0.963355 TTTGACGGTATTGCCTGGCC 60.963 55.000 17.53 0.00 34.25 5.36
675 715 1.152963 GACGGTATTGCCTGGCCAT 60.153 57.895 17.53 13.68 34.25 4.40
676 716 1.152963 ACGGTATTGCCTGGCCATC 60.153 57.895 17.53 1.22 34.25 3.51
677 717 1.149174 CGGTATTGCCTGGCCATCT 59.851 57.895 17.53 0.28 34.25 2.90
678 718 1.168407 CGGTATTGCCTGGCCATCTG 61.168 60.000 17.53 6.45 34.25 2.90
679 719 0.825010 GGTATTGCCTGGCCATCTGG 60.825 60.000 17.53 5.27 37.51 3.86
735 776 1.202177 GCATTTACTGGCATGTGTCCG 60.202 52.381 0.00 0.00 0.00 4.79
789 830 1.131126 CTACATTGCCAGTTTGCTCGG 59.869 52.381 0.00 0.00 0.00 4.63
967 1018 2.045926 GGCATGAGGCGTTGACCT 60.046 61.111 0.00 0.00 46.16 3.85
1260 1326 2.964174 CGGCATGGAAAGCTGCAA 59.036 55.556 1.02 0.00 40.18 4.08
1577 1643 1.971167 TGTGAGATGGCCAAACCGC 60.971 57.895 10.96 8.92 43.94 5.68
1629 1699 1.608717 GGTCTGTCCCTGTCGCTGAT 61.609 60.000 0.00 0.00 0.00 2.90
1829 1899 2.734591 GTGTCCTGGTCGACTGCA 59.265 61.111 16.46 4.86 33.70 4.41
1830 1900 1.664965 GTGTCCTGGTCGACTGCAC 60.665 63.158 16.46 12.79 33.70 4.57
1831 1901 2.131067 TGTCCTGGTCGACTGCACA 61.131 57.895 16.46 8.53 33.70 4.57
1832 1902 1.069090 GTCCTGGTCGACTGCACAA 59.931 57.895 16.46 0.00 0.00 3.33
1833 1903 0.320771 GTCCTGGTCGACTGCACAAT 60.321 55.000 16.46 0.00 0.00 2.71
1834 1904 0.320683 TCCTGGTCGACTGCACAATG 60.321 55.000 16.46 0.00 0.00 2.82
1860 1941 2.159114 GCCTCCAACTAGAAGAGCTCAG 60.159 54.545 17.77 6.88 0.00 3.35
2065 2491 4.262463 CGTACTACTATGTGGGATTGCCAT 60.262 45.833 0.00 0.00 35.15 4.40
2126 2552 5.754890 GGCAACATTTGACAAAATCAGTTCT 59.245 36.000 4.41 0.00 38.99 3.01
2420 2936 3.695816 GAGAACACACAAAAGACTTGCC 58.304 45.455 0.00 0.00 0.00 4.52
2445 2962 8.033626 CCTATTACTCGAATGAAGGGGTATAAC 58.966 40.741 0.00 0.00 0.00 1.89
2472 2989 2.952978 ACTGGTTTTACAAACATCCGCA 59.047 40.909 2.00 0.00 0.00 5.69
2498 3015 3.074412 ACGCCAACTTAGGTGAATTCAG 58.926 45.455 8.80 0.00 41.75 3.02
2501 3018 4.023193 CGCCAACTTAGGTGAATTCAGTTT 60.023 41.667 8.80 0.00 41.75 2.66
2530 3047 4.381932 CCCCAATGGAAAACATTCAGTAGC 60.382 45.833 0.00 0.00 46.67 3.58
2532 3049 3.764885 ATGGAAAACATTCAGTAGCGC 57.235 42.857 0.00 0.00 35.97 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.880047 TTCATTATTGGACGACGAGGT 57.120 42.857 0.00 0.00 0.00 3.85
46 47 8.290325 ACCACGATTATGTTCTTTTCTTTTCTC 58.710 33.333 0.00 0.00 0.00 2.87
58 59 3.050619 CCGCTAGACCACGATTATGTTC 58.949 50.000 0.00 0.00 0.00 3.18
63 64 2.492881 TGTTTCCGCTAGACCACGATTA 59.507 45.455 0.00 0.00 0.00 1.75
65 66 0.892755 TGTTTCCGCTAGACCACGAT 59.107 50.000 0.00 0.00 0.00 3.73
77 78 2.748461 TCTTTCACGCTTTGTTTCCG 57.252 45.000 0.00 0.00 0.00 4.30
99 100 2.814097 CGGGTCCAAATAATGCCCTAGG 60.814 54.545 0.06 0.06 37.24 3.02
187 194 0.712380 ATTCAAAGGCATGGGGTCCT 59.288 50.000 0.00 0.00 0.00 3.85
411 431 2.671619 GCGTGCAGTGGGGCTTTA 60.672 61.111 0.00 0.00 34.04 1.85
434 454 1.355916 GACGTAGGAGTAGCTGCGG 59.644 63.158 0.00 0.00 33.20 5.69
505 525 6.266103 TGCTGAGTTTCAAAATGAGGAGAATT 59.734 34.615 0.00 0.00 0.00 2.17
545 566 1.376543 AACTCCATGATCAAGCAGCG 58.623 50.000 0.00 0.00 0.00 5.18
592 631 0.389391 AGCGGTAAGATATGCGTGCT 59.611 50.000 0.00 0.00 0.00 4.40
612 651 0.822811 AGTCTCACGCAGATGCTCAT 59.177 50.000 2.95 0.00 39.32 2.90
622 661 2.505118 GTCGGCTCAGTCTCACGC 60.505 66.667 0.00 0.00 0.00 5.34
638 678 7.605410 ACCGTCAAAATTTAAGATGATACGT 57.395 32.000 12.10 0.00 0.00 3.57
654 694 0.963355 GGCCAGGCAATACCGTCAAA 60.963 55.000 15.19 0.00 46.52 2.69
657 697 1.152963 ATGGCCAGGCAATACCGTC 60.153 57.895 15.19 0.00 46.52 4.79
735 776 4.095036 GCTGTAAATTAAGCCTCTGGACAC 59.905 45.833 0.00 0.00 33.12 3.67
789 830 1.580845 AAGGCGATTGAGCACAGTGC 61.581 55.000 18.55 18.55 45.46 4.40
856 900 5.352643 ACGAAAGTAATACTTGTGGCAAC 57.647 39.130 6.41 0.00 46.88 4.17
1251 1317 1.534595 CGCTTCTTGTGTTGCAGCTTT 60.535 47.619 1.17 0.00 0.00 3.51
1260 1326 4.000557 CGCACGCGCTTCTTGTGT 62.001 61.111 5.73 0.00 36.04 3.72
1829 1899 0.773644 AGTTGGAGGCTCACCATTGT 59.226 50.000 17.69 0.00 39.06 2.71
1830 1900 2.237143 TCTAGTTGGAGGCTCACCATTG 59.763 50.000 17.69 2.30 39.06 2.82
1831 1901 2.551270 TCTAGTTGGAGGCTCACCATT 58.449 47.619 17.69 1.34 39.06 3.16
1832 1902 2.254152 TCTAGTTGGAGGCTCACCAT 57.746 50.000 17.69 1.79 39.06 3.55
1833 1903 1.902508 CTTCTAGTTGGAGGCTCACCA 59.097 52.381 17.69 3.46 39.06 4.17
1834 1904 2.167487 CTCTTCTAGTTGGAGGCTCACC 59.833 54.545 17.69 0.23 0.00 4.02
1838 1919 2.107366 GAGCTCTTCTAGTTGGAGGCT 58.893 52.381 6.43 0.00 0.00 4.58
1842 1923 2.232452 GCACTGAGCTCTTCTAGTTGGA 59.768 50.000 16.19 0.00 41.15 3.53
1845 1926 2.630098 TGTGCACTGAGCTCTTCTAGTT 59.370 45.455 19.41 0.00 45.94 2.24
1860 1941 2.562912 CGGCTCACCATTGTGCAC 59.437 61.111 10.75 10.75 42.88 4.57
1886 1968 1.174783 TGAACACTCTAGGAGCCGAC 58.825 55.000 0.00 0.00 32.04 4.79
2014 2117 6.149633 CAGAACTGTTAATTTTTCCCGGAAG 58.850 40.000 0.73 0.00 0.00 3.46
2065 2491 1.284657 TTTCACGGTGAAACGCGTAA 58.715 45.000 27.49 8.41 41.02 3.18
2126 2552 7.936584 ACTGATTTTATTTCGAACCTTCAACA 58.063 30.769 0.00 0.00 0.00 3.33
2269 2698 0.465460 TCTGAACATAATGCCGGGGC 60.465 55.000 2.18 1.86 42.35 5.80
2420 2936 7.754027 CGTTATACCCCTTCATTCGAGTAATAG 59.246 40.741 0.00 0.00 0.00 1.73
2445 2962 4.022464 TGTTTGTAAAACCAGTCTTGCG 57.978 40.909 0.71 0.00 0.00 4.85
2472 2989 4.546829 TTCACCTAAGTTGGCGTATTCT 57.453 40.909 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.