Multiple sequence alignment - TraesCS5A01G124400

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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 TraesCS5A01G124400 chr5A 100.000 2514 0 0 1 2514 272196020 272198533 0 4643
1 TraesCS5A01G124400 chr3D 94.988 2534 98 16 1 2513 360444228 360441703 0 3949
2 TraesCS5A01G124400 chr3D 94.907 2533 95 15 1 2513 543133975 543131457 0 3932
3 TraesCS5A01G124400 chr3D 94.758 2537 105 13 1 2513 551735223 551732691 0 3923
4 TraesCS5A01G124400 chr3D 94.567 2540 102 19 1 2513 384995243 384997773 0 3893
5 TraesCS5A01G124400 chr3D 92.616 948 39 8 1 930 434077741 434078675 0 1334
6 TraesCS5A01G124400 chr2D 94.907 2533 100 15 1 2513 46525239 46527762 0 3936
7 TraesCS5A01G124400 chr2D 93.016 945 38 7 1 930 304671611 304672542 0 1354
8 TraesCS5A01G124400 chr7D 94.868 2533 103 16 1 2513 510254720 510257245 0 3932
9 TraesCS5A01G124400 chr7D 93.031 947 35 10 1 930 207213986 207213054 0 1354
10 TraesCS5A01G124400 chr7D 93.661 631 22 6 1 615 591992522 591991894 0 928
11 TraesCS5A01G124400 chr6B 94.793 2535 107 12 1 2513 151617793 151620324 0 3927
12 TraesCS5A01G124400 chr5D 94.799 2538 99 21 1 2513 306886184 306883655 0 3925
13 TraesCS5A01G124400 chr7B 94.512 2533 115 10 1 2513 432966832 432969360 0 3886
14 TraesCS5A01G124400 chr6D 94.353 2072 81 15 1 2054 451600149 451598096 0 3145
15 TraesCS5A01G124400 chr6D 94.316 2076 79 15 1 2054 397854472 397852414 0 3144
16 TraesCS5A01G124400 chr1D 93.822 2072 86 17 1 2054 374127036 374129083 0 3079
17 TraesCS5A01G124400 chr1D 91.719 954 38 13 1 934 466981907 466980975 0 1286
18 TraesCS5A01G124400 chr4D 91.209 728 34 12 1 711 90542456 90541742 0 963


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 TraesCS5A01G124400 chr5A 272196020 272198533 2513 False 4643 4643 100.000 1 2514 1 chr5A.!!$F1 2513
1 TraesCS5A01G124400 chr3D 360441703 360444228 2525 True 3949 3949 94.988 1 2513 1 chr3D.!!$R1 2512
2 TraesCS5A01G124400 chr3D 543131457 543133975 2518 True 3932 3932 94.907 1 2513 1 chr3D.!!$R2 2512
3 TraesCS5A01G124400 chr3D 551732691 551735223 2532 True 3923 3923 94.758 1 2513 1 chr3D.!!$R3 2512
4 TraesCS5A01G124400 chr3D 384995243 384997773 2530 False 3893 3893 94.567 1 2513 1 chr3D.!!$F1 2512
5 TraesCS5A01G124400 chr3D 434077741 434078675 934 False 1334 1334 92.616 1 930 1 chr3D.!!$F2 929
6 TraesCS5A01G124400 chr2D 46525239 46527762 2523 False 3936 3936 94.907 1 2513 1 chr2D.!!$F1 2512
7 TraesCS5A01G124400 chr2D 304671611 304672542 931 False 1354 1354 93.016 1 930 1 chr2D.!!$F2 929
8 TraesCS5A01G124400 chr7D 510254720 510257245 2525 False 3932 3932 94.868 1 2513 1 chr7D.!!$F1 2512
9 TraesCS5A01G124400 chr7D 207213054 207213986 932 True 1354 1354 93.031 1 930 1 chr7D.!!$R1 929
10 TraesCS5A01G124400 chr7D 591991894 591992522 628 True 928 928 93.661 1 615 1 chr7D.!!$R2 614
11 TraesCS5A01G124400 chr6B 151617793 151620324 2531 False 3927 3927 94.793 1 2513 1 chr6B.!!$F1 2512
12 TraesCS5A01G124400 chr5D 306883655 306886184 2529 True 3925 3925 94.799 1 2513 1 chr5D.!!$R1 2512
13 TraesCS5A01G124400 chr7B 432966832 432969360 2528 False 3886 3886 94.512 1 2513 1 chr7B.!!$F1 2512
14 TraesCS5A01G124400 chr6D 451598096 451600149 2053 True 3145 3145 94.353 1 2054 1 chr6D.!!$R2 2053
15 TraesCS5A01G124400 chr6D 397852414 397854472 2058 True 3144 3144 94.316 1 2054 1 chr6D.!!$R1 2053
16 TraesCS5A01G124400 chr1D 374127036 374129083 2047 False 3079 3079 93.822 1 2054 1 chr1D.!!$F1 2053
17 TraesCS5A01G124400 chr1D 466980975 466981907 932 True 1286 1286 91.719 1 934 1 chr1D.!!$R1 933
18 TraesCS5A01G124400 chr4D 90541742 90542456 714 True 963 963 91.209 1 711 1 chr4D.!!$R1 710


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
210 236 1.251251 AGCTCATTTGTGTGAAGCCC 58.749 50.0 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
1865 1925 1.202348 GTGGGCCTATTGCAACTTGAC 59.798 52.381 0.0 0.0 43.89 3.18 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
210 236 1.251251 AGCTCATTTGTGTGAAGCCC 58.749 50.000 0.00 0.00 0.00 5.19
355 391 6.483307 TGAACTTGATTTCGACAGATCACTTT 59.517 34.615 0.00 2.74 32.36 2.66
356 392 6.473397 ACTTGATTTCGACAGATCACTTTC 57.527 37.500 0.00 0.00 32.36 2.62
443 491 6.309737 GTCTCATAAACGGACGAACTATGTTT 59.690 38.462 0.00 0.00 36.74 2.83
570 624 1.432251 CCTAGCGTCGAACGTCCAT 59.568 57.895 0.00 0.00 44.73 3.41
605 659 1.894756 GCGCCAAACACCACCTGTA 60.895 57.895 0.00 0.00 30.51 2.74
656 711 1.678728 CGAGGCTGGTTTTGCATCCTA 60.679 52.381 0.00 0.00 37.88 2.94
661 716 3.195396 GGCTGGTTTTGCATCCTAATTGA 59.805 43.478 0.00 0.00 0.00 2.57
695 750 2.601763 CCTTCTCGGGTTTTTACGATCG 59.398 50.000 14.88 14.88 38.56 3.69
875 932 3.131933 GCAGATCTTGAGCAGTTCCTCTA 59.868 47.826 0.00 0.00 33.02 2.43
1397 1455 2.875087 TGTCGAACTGAAGACGGAAA 57.125 45.000 0.00 0.00 40.05 3.13
1734 1792 2.373335 ACCCTAGCTCGTCAGATGAT 57.627 50.000 0.00 0.00 0.00 2.45
1812 1870 1.587946 GCACTTGCCAAACTTTTGTCG 59.412 47.619 1.21 0.00 36.45 4.35
1828 1886 2.883574 TGTCGTCGAGTTTGTCAGTTT 58.116 42.857 0.00 0.00 0.00 2.66
1865 1925 0.955919 GTTCACGGGCCCAAAGAGAG 60.956 60.000 24.92 5.71 0.00 3.20
1871 1931 0.402121 GGGCCCAAAGAGAGTCAAGT 59.598 55.000 19.95 0.00 0.00 3.16
2016 2081 6.294176 CCCAATCGCTTCTATTTCATTAAGGG 60.294 42.308 0.00 0.00 34.30 3.95
2135 2204 5.616488 TTGGCGGTGAAGTAATTTTAGAC 57.384 39.130 0.00 0.00 0.00 2.59
2377 2446 1.494721 ACAGAGCTCCCAAACCAAAGA 59.505 47.619 10.93 0.00 0.00 2.52
2464 2533 7.014422 TGGTTAATTTTTCCCACGTCAATTAGT 59.986 33.333 0.00 0.00 0.00 2.24
2477 2546 5.855395 ACGTCAATTAGTCGTGTCTAAACTC 59.145 40.000 0.00 0.00 40.37 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 70 9.877178 GAGTGAATAAGAAGGATCTGAACTTAA 57.123 33.333 0.00 0.00 35.59 1.85
143 154 5.965486 AGAGAGGGTTTAGGGTTTGAAAAT 58.035 37.500 0.00 0.00 0.00 1.82
210 236 7.432869 TGGTGTAGGTCATTTTCATGAAAAAG 58.567 34.615 31.39 27.38 41.30 2.27
482 536 4.901250 AGGGTTTGACCAGATTTCAAATGT 59.099 37.500 1.17 0.00 43.16 2.71
570 624 1.721664 CGCTTGGTAGGATCCGACGA 61.722 60.000 17.58 11.97 0.00 4.20
605 659 2.629498 ATGCCTGCCCCCACATCTT 61.629 57.895 0.00 0.00 0.00 2.40
639 694 3.195396 TCAATTAGGATGCAAAACCAGCC 59.805 43.478 9.88 0.00 41.51 4.85
656 711 5.564550 AGAAGGACAATGCAGTAGTCAATT 58.435 37.500 15.16 10.23 34.04 2.32
661 716 2.093973 CCGAGAAGGACAATGCAGTAGT 60.094 50.000 0.00 0.00 45.00 2.73
695 750 5.128663 ACAATTTCATATGTAAAGTGGGGCC 59.871 40.000 21.13 0.00 36.50 5.80
730 785 2.079158 CACTGACATGTGGTGGTCATC 58.921 52.381 1.15 0.00 42.62 2.92
861 916 5.491982 GGAAAGAAATAGAGGAACTGCTCA 58.508 41.667 0.86 0.00 41.55 4.26
875 932 4.576330 ACGAGAAGATGGGGAAAGAAAT 57.424 40.909 0.00 0.00 0.00 2.17
1044 1101 6.607004 TTCTTCTCCTCCTTCGAAGTTAAT 57.393 37.500 23.03 0.00 36.44 1.40
1047 1104 4.323104 CCATTCTTCTCCTCCTTCGAAGTT 60.323 45.833 23.03 0.00 36.44 2.66
1099 1156 3.085223 CCCCTCTGGCTTGCTCTT 58.915 61.111 0.00 0.00 0.00 2.85
1397 1455 8.455903 TTGAAGTTCTTGTTCATCTTCTTCAT 57.544 30.769 4.17 0.00 39.34 2.57
1495 1553 1.482593 CTCTAACGAGAGGTGGCCATT 59.517 52.381 9.72 0.00 44.92 3.16
1734 1792 3.509967 TGCTGCTCAAGTACTGCTTACTA 59.490 43.478 0.00 0.00 40.44 1.82
1812 1870 3.675467 AGCAAAACTGACAAACTCGAC 57.325 42.857 0.00 0.00 0.00 4.20
1865 1925 1.202348 GTGGGCCTATTGCAACTTGAC 59.798 52.381 0.00 0.00 43.89 3.18
1871 1931 1.203112 TCCTTTGTGGGCCTATTGCAA 60.203 47.619 4.53 0.00 43.89 4.08
2157 2226 9.326413 GTATTGGTTCGCTAGGCATAATAATAT 57.674 33.333 0.00 0.00 0.00 1.28
2323 2392 8.170730 AGGTATTCCAAGAATACTTTGGTTTCT 58.829 33.333 20.90 9.00 34.44 2.52
2464 2533 1.608055 TGTCCCGAGTTTAGACACGA 58.392 50.000 4.82 0.00 41.50 4.35



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

AutoCloner maintained by Alex Coulton.