Multiple sequence alignment - TraesCS3B01G175900

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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 TraesCS3B01G175900 chr3B 100.000 1760 0 0 1 1760 177969937 177968178 0 3251
1 TraesCS3B01G175900 chr3B 100.000 740 0 0 2005 2744 177967933 177967194 0 1367
2 TraesCS3B01G175900 chr3D 94.400 1768 70 16 1 1760 123910355 123908609 0 2689
3 TraesCS3B01G175900 chr3D 91.509 742 59 4 2006 2744 347627613 347626873 0 1018
4 TraesCS3B01G175900 chr3A 92.390 1774 87 27 1 1760 131460104 131458365 0 2484
5 TraesCS3B01G175900 chr5D 91.105 742 63 3 2006 2744 502076856 502076115 0 1002
6 TraesCS3B01G175900 chr5D 90.310 743 68 4 2006 2744 456097291 456098033 0 970
7 TraesCS3B01G175900 chr1D 91.105 742 63 3 2006 2744 249346401 249345660 0 1002
8 TraesCS3B01G175900 chr1D 90.579 743 65 5 2006 2744 274259274 274258533 0 979
9 TraesCS3B01G175900 chr7D 90.836 742 64 4 2006 2744 469201120 469200380 0 990
10 TraesCS3B01G175900 chr7D 90.431 742 68 3 2006 2744 156786070 156785329 0 974
11 TraesCS3B01G175900 chr2D 90.984 732 58 7 2017 2744 220355944 220355217 0 979
12 TraesCS3B01G175900 chr2D 90.431 742 60 7 2006 2744 405814087 405814820 0 966


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 TraesCS3B01G175900 chr3B 177967194 177969937 2743 True 2309 3251 100.000 1 2744 2 chr3B.!!$R1 2743
1 TraesCS3B01G175900 chr3D 123908609 123910355 1746 True 2689 2689 94.400 1 1760 1 chr3D.!!$R1 1759
2 TraesCS3B01G175900 chr3D 347626873 347627613 740 True 1018 1018 91.509 2006 2744 1 chr3D.!!$R2 738
3 TraesCS3B01G175900 chr3A 131458365 131460104 1739 True 2484 2484 92.390 1 1760 1 chr3A.!!$R1 1759
4 TraesCS3B01G175900 chr5D 502076115 502076856 741 True 1002 1002 91.105 2006 2744 1 chr5D.!!$R1 738
5 TraesCS3B01G175900 chr5D 456097291 456098033 742 False 970 970 90.310 2006 2744 1 chr5D.!!$F1 738
6 TraesCS3B01G175900 chr1D 249345660 249346401 741 True 1002 1002 91.105 2006 2744 1 chr1D.!!$R1 738
7 TraesCS3B01G175900 chr1D 274258533 274259274 741 True 979 979 90.579 2006 2744 1 chr1D.!!$R2 738
8 TraesCS3B01G175900 chr7D 469200380 469201120 740 True 990 990 90.836 2006 2744 1 chr7D.!!$R2 738
9 TraesCS3B01G175900 chr7D 156785329 156786070 741 True 974 974 90.431 2006 2744 1 chr7D.!!$R1 738
10 TraesCS3B01G175900 chr2D 220355217 220355944 727 True 979 979 90.984 2017 2744 1 chr2D.!!$R1 727
11 TraesCS3B01G175900 chr2D 405814087 405814820 733 False 966 966 90.431 2006 2744 1 chr2D.!!$F1 738

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
618 626 0.401738 TGGCAGCCTGCTCTTAGTTT 59.598 50.0 17.55 0.0 44.28 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2430 2462 0.536006 AAGTGTCAGGAGGCTTGCAC 60.536 55.0 0.0 0.0 0.0 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
216 219 3.054434 TGGTACTGTAGCATGGAAGCAAT 60.054 43.478 15.14 0.00 36.85 3.56
237 240 6.524734 CAATAGTGGCACCTCATACTTATCA 58.475 40.000 15.27 0.00 0.00 2.15
276 279 3.383761 GGGGTACACCAAATACGTATCG 58.616 50.000 10.04 3.30 42.91 2.92
338 342 1.342474 ACAGTCGACATCTGGGATCCT 60.342 52.381 19.50 0.00 37.25 3.24
387 391 8.677300 GGTAATTATCACTTTCAATGCAAGAGA 58.323 33.333 0.00 0.00 0.00 3.10
458 464 3.837213 AAATCCACTTGCGATTGTGAG 57.163 42.857 0.00 0.00 36.38 3.51
473 479 3.475566 TGTGAGCACAAGAGCTTTAGT 57.524 42.857 0.00 0.00 46.75 2.24
508 514 7.490657 TCTGCCACTTTATCTTAAAGAGGTA 57.509 36.000 18.46 15.05 39.29 3.08
523 529 9.454859 CTTAAAGAGGTAATCCACTGAGATTTT 57.545 33.333 0.00 0.00 37.62 1.82
529 535 6.881602 AGGTAATCCACTGAGATTTTTGAGAC 59.118 38.462 0.00 0.00 37.62 3.36
537 544 6.580041 CACTGAGATTTTTGAGACCAAATTCG 59.420 38.462 0.00 0.00 41.43 3.34
618 626 0.401738 TGGCAGCCTGCTCTTAGTTT 59.598 50.000 17.55 0.00 44.28 2.66
620 628 2.284190 GGCAGCCTGCTCTTAGTTTAG 58.716 52.381 17.55 0.00 44.28 1.85
658 666 8.491045 AGGATTTTTGTAGAAATTTGGAGGAA 57.509 30.769 0.00 0.00 29.75 3.36
676 684 8.575649 TGGAGGAACAAAATATTAAGAACCTC 57.424 34.615 16.05 16.05 39.26 3.85
890 898 6.327279 ACTTGGGTAAAATTTTCTCTTCCG 57.673 37.500 6.72 0.00 0.00 4.30
895 903 5.163683 GGGTAAAATTTTCTCTTCCGCTACC 60.164 44.000 6.72 5.26 0.00 3.18
902 910 3.361281 TCTCTTCCGCTACCTGTCTTA 57.639 47.619 0.00 0.00 0.00 2.10
903 911 3.899726 TCTCTTCCGCTACCTGTCTTAT 58.100 45.455 0.00 0.00 0.00 1.73
1021 1039 3.826729 CCTATAAAATTGCCCCCTAGCAC 59.173 47.826 0.00 0.00 43.97 4.40
1059 1077 5.133941 TCCATCTGCTACTAACCTCACTAG 58.866 45.833 0.00 0.00 0.00 2.57
1357 1375 1.270893 GGCACCGAGAAGGAGAAAACT 60.271 52.381 0.00 0.00 45.00 2.66
1369 1387 1.166531 AGAAAACTGACGCACCTGCC 61.167 55.000 0.00 0.00 37.91 4.85
1406 1424 2.825836 CGGATGCACCCAAGGAGC 60.826 66.667 0.00 0.00 39.68 4.70
1452 1470 0.458716 GAGGAAGAGAAAGCGTCCGG 60.459 60.000 0.00 0.00 40.72 5.14
1519 1537 0.827368 GGAAGAAGAGTGGCGAGGAT 59.173 55.000 0.00 0.00 0.00 3.24
1650 1668 3.369756 CGCTGCGTTCCTTCTGTATTTTA 59.630 43.478 14.93 0.00 0.00 1.52
1686 1706 6.739550 GTCGTGGTTGTGCTTAATTATGTTAC 59.260 38.462 0.84 2.02 0.00 2.50
1697 1717 9.573166 TGCTTAATTATGTTACCTGCTGATATT 57.427 29.630 0.00 0.00 0.00 1.28
1726 1753 9.651718 GTTCTGTAAAGTTTCTTAAGTCATGTG 57.348 33.333 1.63 0.00 0.00 3.21
2111 2141 0.458543 CACATCGAGCTAGGCGTTGT 60.459 55.000 4.65 4.65 40.92 3.32
2149 2179 0.951558 GCTCCACCAAATCGTGTTGT 59.048 50.000 0.00 0.00 31.47 3.32
2162 2192 2.729360 TCGTGTTGTAGTTCTTGATGCG 59.271 45.455 0.00 0.00 0.00 4.73
2166 2196 3.259064 GTTGTAGTTCTTGATGCGCCTA 58.741 45.455 4.18 0.00 0.00 3.93
2186 2216 3.551635 ATGGGTCTCGGATCTCCTAAT 57.448 47.619 0.00 0.00 0.00 1.73
2224 2254 1.476845 TTCAGGTTGCCGGTAGCTGA 61.477 55.000 26.29 26.29 45.42 4.26
2259 2290 3.279434 CAAAGGACCCTGCCTGTAATAC 58.721 50.000 0.00 0.00 38.58 1.89
2323 2355 2.223845 TCATGTTGTGCAAGATGACACG 59.776 45.455 17.21 0.00 43.38 4.49
2334 2366 4.377370 TGACACGGCAAGTCATGG 57.623 55.556 5.05 0.00 40.80 3.66
2350 2382 2.761767 TCATGGCTTCCCACATTTGATG 59.238 45.455 0.00 0.00 45.77 3.07
2360 2392 3.564511 CCACATTTGATGTTTCGACCAC 58.435 45.455 0.00 0.00 42.70 4.16
2401 2433 4.012374 ACAACAGCAAATCGAGATTGGAT 58.988 39.130 13.66 0.00 0.00 3.41
2407 2439 3.374988 GCAAATCGAGATTGGATCACACA 59.625 43.478 13.66 0.00 0.00 3.72
2416 2448 2.307496 TGGATCACACAAAATGCCCT 57.693 45.000 0.00 0.00 0.00 5.19
2422 2454 1.466167 CACACAAAATGCCCTCTCGAG 59.534 52.381 5.93 5.93 0.00 4.04
2430 2462 1.103987 TGCCCTCTCGAGATCCTTCG 61.104 60.000 17.03 2.61 41.79 3.79
2557 2589 6.774656 GCTAGGTAGTATCCCTTGTTGTAGTA 59.225 42.308 0.00 0.00 33.35 1.82
2627 2660 1.825090 TGGCAAAGACATTCGAGCAT 58.175 45.000 0.00 0.00 0.00 3.79
2644 2677 4.270808 CGAGCATTGCAGTATGTTGATGTA 59.729 41.667 11.91 0.00 39.31 2.29
2699 2735 3.490348 CCAAATTCAGAGGTCCTGTGTT 58.510 45.455 15.34 1.23 43.38 3.32
2710 2746 1.829533 CCTGTGTTGCCACTGCCTT 60.830 57.895 0.00 0.00 42.34 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
216 219 5.454966 TCTGATAAGTATGAGGTGCCACTA 58.545 41.667 0.00 0.00 0.00 2.74
273 276 0.108992 TAACGGCTGAAACGAGCGAT 60.109 50.000 0.00 0.00 40.13 4.58
276 279 1.289109 TGCTAACGGCTGAAACGAGC 61.289 55.000 0.00 0.71 42.39 5.03
387 391 1.394266 ATACGGCGGGGATACGTGTT 61.394 55.000 13.24 0.00 41.40 3.32
458 464 4.216257 TGGAATCAACTAAAGCTCTTGTGC 59.784 41.667 0.00 0.00 0.00 4.57
473 479 7.520798 AGATAAAGTGGCAGATATGGAATCAA 58.479 34.615 0.00 0.00 0.00 2.57
508 514 5.634118 TGGTCTCAAAAATCTCAGTGGATT 58.366 37.500 0.00 0.00 37.51 3.01
523 529 3.872182 TCACGAAACGAATTTGGTCTCAA 59.128 39.130 0.00 0.00 34.84 3.02
529 535 2.307049 GCAGTCACGAAACGAATTTGG 58.693 47.619 0.00 0.00 0.00 3.28
537 544 0.935196 AAGAACCGCAGTCACGAAAC 59.065 50.000 0.00 0.00 34.06 2.78
577 585 4.220821 CAGTGTTACTGTGTATCTGTCCCT 59.779 45.833 0.90 0.00 41.19 4.20
582 590 3.925379 TGCCAGTGTTACTGTGTATCTG 58.075 45.455 8.04 0.00 44.50 2.90
592 600 1.301677 GAGCAGGCTGCCAGTGTTAC 61.302 60.000 34.33 12.62 46.52 2.50
679 687 8.994429 TTCTACAAATCAAACAAACAACACAT 57.006 26.923 0.00 0.00 0.00 3.21
709 717 7.112452 ACTGCTTGAAAATTCCTAACAAACT 57.888 32.000 0.00 0.00 0.00 2.66
715 723 9.344772 TGTAAAGTACTGCTTGAAAATTCCTAA 57.655 29.630 0.00 0.00 37.52 2.69
765 773 5.502153 TTCTAAGAGCTTCGAGTGGATAC 57.498 43.478 0.00 0.00 0.00 2.24
871 879 5.163683 GGTAGCGGAAGAGAAAATTTTACCC 60.164 44.000 2.75 0.72 0.00 3.69
874 882 6.235664 ACAGGTAGCGGAAGAGAAAATTTTA 58.764 36.000 2.75 0.00 0.00 1.52
890 898 8.580720 TCTTCAGATGATAATAAGACAGGTAGC 58.419 37.037 0.00 0.00 0.00 3.58
934 950 6.073927 GCTACTTGTGTGGTTGAGTTTAGTAC 60.074 42.308 0.00 0.00 0.00 2.73
935 951 5.987347 GCTACTTGTGTGGTTGAGTTTAGTA 59.013 40.000 0.00 0.00 0.00 1.82
936 952 4.814771 GCTACTTGTGTGGTTGAGTTTAGT 59.185 41.667 0.00 0.00 0.00 2.24
937 953 5.057149 AGCTACTTGTGTGGTTGAGTTTAG 58.943 41.667 0.00 0.00 0.00 1.85
938 954 5.031066 AGCTACTTGTGTGGTTGAGTTTA 57.969 39.130 0.00 0.00 0.00 2.01
939 955 3.886123 AGCTACTTGTGTGGTTGAGTTT 58.114 40.909 0.00 0.00 0.00 2.66
940 956 3.560636 AGCTACTTGTGTGGTTGAGTT 57.439 42.857 0.00 0.00 0.00 3.01
941 957 3.560636 AAGCTACTTGTGTGGTTGAGT 57.439 42.857 0.00 0.00 0.00 3.41
1021 1039 4.996122 GCAGATGGAGTGAAAGAGGATATG 59.004 45.833 0.00 0.00 0.00 1.78
1059 1077 6.479990 AGCAAAAATCTTTTGTGGCTTAAGAC 59.520 34.615 6.67 3.27 32.54 3.01
1309 1327 2.302157 GCTGTACTGTTTCAGGTACCCT 59.698 50.000 8.74 0.00 35.51 4.34
1519 1537 3.452786 CCGCCGCTCTCCTTCTCA 61.453 66.667 0.00 0.00 0.00 3.27
1609 1627 1.264020 CGCACAAACTTAGCAAGAGCA 59.736 47.619 3.37 0.00 45.49 4.26
1650 1668 3.737266 CACAACCACGACGTTACAGTAAT 59.263 43.478 0.00 0.00 0.00 1.89
1663 1683 6.025280 GGTAACATAATTAAGCACAACCACG 58.975 40.000 0.00 0.00 0.00 4.94
1686 1706 3.185246 ACAGAACCGAATATCAGCAGG 57.815 47.619 0.00 0.00 0.00 4.85
1697 1717 7.267128 TGACTTAAGAAACTTTACAGAACCGA 58.733 34.615 10.09 0.00 0.00 4.69
1698 1718 7.473027 TGACTTAAGAAACTTTACAGAACCG 57.527 36.000 10.09 0.00 0.00 4.44
1726 1753 8.837788 TGGATTATTGATCATCATACAGACAC 57.162 34.615 0.00 0.00 36.43 3.67
2004 2032 8.812147 TTATACGATTTCTGCGATGAAGTATT 57.188 30.769 0.00 0.00 0.00 1.89
2008 2036 7.787084 TGATTTATACGATTTCTGCGATGAAG 58.213 34.615 0.00 0.00 0.00 3.02
2077 2107 4.363138 TCGATGTGTGATGAACTATGAGC 58.637 43.478 0.00 0.00 0.00 4.26
2149 2179 2.224281 CCCATAGGCGCATCAAGAACTA 60.224 50.000 10.83 0.00 0.00 2.24
2162 2192 0.892063 GAGATCCGAGACCCATAGGC 59.108 60.000 0.00 0.00 36.11 3.93
2166 2196 3.169099 CATTAGGAGATCCGAGACCCAT 58.831 50.000 0.00 0.00 42.08 4.00
2186 2216 3.282021 GAACTGCCTTCCTCAATATGCA 58.718 45.455 0.00 0.00 0.00 3.96
2224 2254 2.827921 GTCCTTTGCCCAAGTTGATCAT 59.172 45.455 3.87 0.00 0.00 2.45
2334 2366 3.057596 TCGAAACATCAAATGTGGGAAGC 60.058 43.478 0.00 0.00 44.07 3.86
2350 2382 0.596600 TGCTCTGACGTGGTCGAAAC 60.597 55.000 0.00 0.00 40.62 2.78
2360 2392 0.965866 TCCAGTACCCTGCTCTGACG 60.966 60.000 0.00 0.00 37.38 4.35
2401 2433 1.071542 TCGAGAGGGCATTTTGTGTGA 59.928 47.619 0.00 0.00 0.00 3.58
2407 2439 2.122768 AGGATCTCGAGAGGGCATTTT 58.877 47.619 21.52 0.32 0.00 1.82
2416 2448 1.133216 CTTGCACGAAGGATCTCGAGA 59.867 52.381 19.19 19.19 41.44 4.04
2422 2454 1.092345 GGAGGCTTGCACGAAGGATC 61.092 60.000 0.00 0.00 31.56 3.36
2430 2462 0.536006 AAGTGTCAGGAGGCTTGCAC 60.536 55.000 0.00 0.00 0.00 4.57
2557 2589 2.859273 CTTCGAGGTCAATGGGCGCT 62.859 60.000 7.64 0.00 0.00 5.92
2627 2660 7.174772 ACTCACAATTACATCAACATACTGCAA 59.825 33.333 0.00 0.00 0.00 4.08
2644 2677 3.245229 TGGTATGCCAGGAACTCACAATT 60.245 43.478 0.00 0.00 40.46 2.32
2699 2735 1.060729 TGGTACTTAAGGCAGTGGCA 58.939 50.000 20.04 0.00 43.71 4.92
2710 2746 2.289444 GGAGCTTGCAGTGTGGTACTTA 60.289 50.000 0.00 0.00 37.60 2.24


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

AutoCloner maintained by Alex Coulton.