Multiple sequence alignment - TraesCS7D01G111500

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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 TraesCS7D01G111500 chr7D 100.000 3565 0 0 1 3565 67548836 67552400 0 6584
1 TraesCS7D01G111500 chr2D 97.478 3569 80 5 2 3565 54820743 54824306 0 6083
2 TraesCS7D01G111500 chr2D 95.279 3580 122 8 2 3565 442840158 442836610 0 5631
3 TraesCS7D01G111500 chr5D 97.317 3578 78 5 4 3565 543760796 543757221 0 6059
4 TraesCS7D01G111500 chr1D 96.933 3587 83 7 4 3565 429378589 429375005 0 5989
5 TraesCS7D01G111500 chr6D 94.972 3580 96 26 1 3565 429638834 429635324 0 5537
6 TraesCS7D01G111500 chr4A 94.800 3577 138 9 4 3565 619884452 619880909 0 5531
7 TraesCS7D01G111500 chr4A 93.310 1136 56 3 2 1135 712593050 712591933 0 1659
8 TraesCS7D01G111500 chr6B 94.466 3578 144 11 2 3565 91484808 91481271 0 5461
9 TraesCS7D01G111500 chr7A 94.176 2507 116 12 2 2490 99546005 99548499 0 3794
10 TraesCS7D01G111500 chr1A 93.166 2107 65 37 1478 3565 80807447 80805401 0 3020
11 TraesCS7D01G111500 chr5B 95.200 1896 51 5 1686 3565 592167410 592165539 0 2961
12 TraesCS7D01G111500 chr5B 94.177 1082 56 3 584 1664 592168478 592167403 0 1642
13 TraesCS7D01G111500 chr5A 94.865 1558 37 18 1478 3019 565598152 565596622 0 2394
14 TraesCS7D01G111500 chr7B 95.592 1452 54 7 2119 3565 748482638 748484084 0 2318
15 TraesCS7D01G111500 chr3A 85.488 882 62 23 1099 1950 716262815 716263660 0 859


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 TraesCS7D01G111500 chr7D 67548836 67552400 3564 False 6584.0 6584 100.0000 1 3565 1 chr7D.!!$F1 3564
1 TraesCS7D01G111500 chr2D 54820743 54824306 3563 False 6083.0 6083 97.4780 2 3565 1 chr2D.!!$F1 3563
2 TraesCS7D01G111500 chr2D 442836610 442840158 3548 True 5631.0 5631 95.2790 2 3565 1 chr2D.!!$R1 3563
3 TraesCS7D01G111500 chr5D 543757221 543760796 3575 True 6059.0 6059 97.3170 4 3565 1 chr5D.!!$R1 3561
4 TraesCS7D01G111500 chr1D 429375005 429378589 3584 True 5989.0 5989 96.9330 4 3565 1 chr1D.!!$R1 3561
5 TraesCS7D01G111500 chr6D 429635324 429638834 3510 True 5537.0 5537 94.9720 1 3565 1 chr6D.!!$R1 3564
6 TraesCS7D01G111500 chr4A 619880909 619884452 3543 True 5531.0 5531 94.8000 4 3565 1 chr4A.!!$R1 3561
7 TraesCS7D01G111500 chr4A 712591933 712593050 1117 True 1659.0 1659 93.3100 2 1135 1 chr4A.!!$R2 1133
8 TraesCS7D01G111500 chr6B 91481271 91484808 3537 True 5461.0 5461 94.4660 2 3565 1 chr6B.!!$R1 3563
9 TraesCS7D01G111500 chr7A 99546005 99548499 2494 False 3794.0 3794 94.1760 2 2490 1 chr7A.!!$F1 2488
10 TraesCS7D01G111500 chr1A 80805401 80807447 2046 True 3020.0 3020 93.1660 1478 3565 1 chr1A.!!$R1 2087
11 TraesCS7D01G111500 chr5B 592165539 592168478 2939 True 2301.5 2961 94.6885 584 3565 2 chr5B.!!$R1 2981
12 TraesCS7D01G111500 chr5A 565596622 565598152 1530 True 2394.0 2394 94.8650 1478 3019 1 chr5A.!!$R1 1541
13 TraesCS7D01G111500 chr7B 748482638 748484084 1446 False 2318.0 2318 95.5920 2119 3565 1 chr7B.!!$F1 1446
14 TraesCS7D01G111500 chr3A 716262815 716263660 845 False 859.0 859 85.4880 1099 1950 1 chr3A.!!$F1 851

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
465 467 1.606889 ACACTCTCCGTCAGTCCCC 60.607 63.158 0.0 0.0 0.0 4.81 F
937 954 2.032681 GCTGCCCGAACAAGACCT 59.967 61.111 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2090 1.219393 CGACCAAAGAGGGCTCCTC 59.781 63.158 12.03 12.03 46.64 3.71 R
2828 2914 7.026562 GGTCGATCATGAGATAGTGTTCATAG 58.973 42.308 0.09 0.00 33.72 2.23 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
73 75 7.063426 CGTTCATAGCTAGTTGTTGAATCTTGA 59.937 37.037 9.34 0.00 0.00 3.02
182 184 4.331968 ACTGCAGATTAAATTTGACCCGA 58.668 39.130 23.35 0.00 0.00 5.14
416 418 1.841302 AATCAGGAAGCAGCCCACGA 61.841 55.000 0.00 0.00 0.00 4.35
456 458 3.343788 GAGCCGTCCACACTCTCCG 62.344 68.421 0.00 0.00 0.00 4.63
465 467 1.606889 ACACTCTCCGTCAGTCCCC 60.607 63.158 0.00 0.00 0.00 4.81
831 848 3.319198 GAAGACCCCTGTCCGGCA 61.319 66.667 0.00 0.00 42.81 5.69
937 954 2.032681 GCTGCCCGAACAAGACCT 59.967 61.111 0.00 0.00 0.00 3.85
1013 1030 2.178273 CGACATGAGCACCGACGA 59.822 61.111 0.00 0.00 0.00 4.20
1258 1280 2.139323 ATGTCCTAGCTCGGTACACA 57.861 50.000 3.89 2.01 0.00 3.72
2009 2086 9.965824 TCTTTATTTCTTTGTTCTGTTTGGATC 57.034 29.630 0.00 0.00 0.00 3.36
2013 2090 4.065088 TCTTTGTTCTGTTTGGATCGAGG 58.935 43.478 0.00 0.00 0.00 4.63
2156 2234 1.338107 GTGGCCCTTAAACCAAGCTT 58.662 50.000 0.00 0.00 37.79 3.74
2522 2608 7.756272 ACATGTACGTTTAGTTATTCGACATGA 59.244 33.333 20.46 0.00 40.10 3.07
2828 2914 5.302823 ACAATGGCCTATTTCTTCCTAATGC 59.697 40.000 3.32 0.00 0.00 3.56
3347 3438 5.257262 TGCCCATGTGTACTTGCTTTATAA 58.743 37.500 0.00 0.00 0.00 0.98
3357 3448 5.582689 ACTTGCTTTATAAATGTGCTCCC 57.417 39.130 0.00 0.00 0.00 4.30
3446 3537 2.837591 TGTTTGCTCCTATGTGGCTCTA 59.162 45.455 0.00 0.00 35.26 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
236 238 2.951642 ACCAATTTGTATGCATCTCCGG 59.048 45.455 0.19 0.00 0.00 5.14
416 418 4.090090 CAGATCGACTATAGGGGGTGATT 58.910 47.826 4.43 0.00 0.00 2.57
465 467 2.329690 CGAGAGACGCTGGATCGG 59.670 66.667 0.00 0.00 34.51 4.18
551 553 1.938596 AGAGAGAGAGGGGGAGGCA 60.939 63.158 0.00 0.00 0.00 4.75
586 593 2.042843 GGAAGGGAGGAGAGGCGA 60.043 66.667 0.00 0.00 0.00 5.54
796 803 2.721167 CGATTCCCGCCTGAGGTCA 61.721 63.158 0.00 0.00 0.00 4.02
928 945 2.116125 GCCCAGGCAGGTCTTGTT 59.884 61.111 3.12 0.00 41.49 2.83
2013 2090 1.219393 CGACCAAAGAGGGCTCCTC 59.781 63.158 12.03 12.03 46.64 3.71
2522 2608 9.176460 ACCAAATCAAACAGAAAAATGTTGAAT 57.824 25.926 0.00 0.00 42.49 2.57
2828 2914 7.026562 GGTCGATCATGAGATAGTGTTCATAG 58.973 42.308 0.09 0.00 33.72 2.23
3347 3438 0.745845 GAGCATCACGGGAGCACATT 60.746 55.000 10.94 0.00 33.17 2.71
3357 3448 1.575244 CATACCACCAGAGCATCACG 58.425 55.000 0.00 0.00 37.82 4.35
3446 3537 3.019564 GAGCCACATAGGAGCAAACAAT 58.980 45.455 0.00 0.00 41.22 2.71


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

AutoCloner maintained by Alex Coulton.