Multiple sequence alignment - TraesCS7D01G285800

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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 TraesCS7D01G285800 chr7D 100.000 3699 0 0 1 3699 307046182 307049880 0.000000e+00 6831
1 TraesCS7D01G285800 chr2B 98.327 3706 50 7 1 3699 449213198 449209498 0.000000e+00 6490
2 TraesCS7D01G285800 chr2B 97.679 3705 66 7 1 3699 234535020 234531330 0.000000e+00 6348
3 TraesCS7D01G285800 chr6D 97.841 3705 71 5 1 3699 458922226 458918525 0.000000e+00 6390
4 TraesCS7D01G285800 chr3B 97.733 3706 68 8 1 3699 6004632 6000936 0.000000e+00 6364
5 TraesCS7D01G285800 chr3B 97.463 3705 80 6 1 3699 92290609 92286913 0.000000e+00 6309
6 TraesCS7D01G285800 chr3B 96.748 369 9 1 141 506 237095511 237095879 2.440000e-171 612
7 TraesCS7D01G285800 chr7A 97.681 3708 74 6 1 3699 563515962 563512258 0.000000e+00 6360
8 TraesCS7D01G285800 chr1B 97.625 3705 73 7 1 3699 619189196 619185501 0.000000e+00 6340
9 TraesCS7D01G285800 chr4B 97.468 3712 73 8 1 3699 495582120 495578417 0.000000e+00 6314
10 TraesCS7D01G285800 chr3D 96.877 3714 98 8 1 3699 48690277 48693987 0.000000e+00 6200
11 TraesCS7D01G285800 chr2A 96.371 248 6 1 1 245 335841737 335841490 4.450000e-109 405


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 TraesCS7D01G285800 chr7D 307046182 307049880 3698 False 6831 6831 100.000 1 3699 1 chr7D.!!$F1 3698
1 TraesCS7D01G285800 chr2B 449209498 449213198 3700 True 6490 6490 98.327 1 3699 1 chr2B.!!$R2 3698
2 TraesCS7D01G285800 chr2B 234531330 234535020 3690 True 6348 6348 97.679 1 3699 1 chr2B.!!$R1 3698
3 TraesCS7D01G285800 chr6D 458918525 458922226 3701 True 6390 6390 97.841 1 3699 1 chr6D.!!$R1 3698
4 TraesCS7D01G285800 chr3B 6000936 6004632 3696 True 6364 6364 97.733 1 3699 1 chr3B.!!$R1 3698
5 TraesCS7D01G285800 chr3B 92286913 92290609 3696 True 6309 6309 97.463 1 3699 1 chr3B.!!$R2 3698
6 TraesCS7D01G285800 chr7A 563512258 563515962 3704 True 6360 6360 97.681 1 3699 1 chr7A.!!$R1 3698
7 TraesCS7D01G285800 chr1B 619185501 619189196 3695 True 6340 6340 97.625 1 3699 1 chr1B.!!$R1 3698
8 TraesCS7D01G285800 chr4B 495578417 495582120 3703 True 6314 6314 97.468 1 3699 1 chr4B.!!$R1 3698
9 TraesCS7D01G285800 chr3D 48690277 48693987 3710 False 6200 6200 96.877 1 3699 1 chr3D.!!$F1 3698

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
46 47 1.602377 CGGGTCGAAATATGGCTTTCC 59.398 52.381 0.0 0.0 32.60 3.13 F
448 463 5.473504 ACTTTTCGTAGATTGGATGCAGTTT 59.526 36.000 0.0 0.0 35.04 2.66 F
1081 1105 2.293118 TGGTTCATCTGGGGAGAGATCA 60.293 50.000 0.0 0.0 29.72 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1002 1018 0.039035 TGCCCCACCCATGAGTAAAC 59.961 55.000 0.0 0.0 0.0 2.01 R
1319 1343 1.457831 GGTCGGAGTGGGGATAGCT 60.458 63.158 0.0 0.0 0.0 3.32 R
2886 2916 0.758734 CCATAGGCTCGAATGACCCA 59.241 55.000 0.0 0.0 0.0 4.51 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 1.602377 CGGGTCGAAATATGGCTTTCC 59.398 52.381 0.00 0.00 32.60 3.13
195 196 8.580720 AGAATCTATGTATGTAGACACATGGAC 58.419 37.037 0.00 0.00 45.17 4.02
250 254 6.775142 AGGAGAATCAGACGATATCTTTCTCA 59.225 38.462 15.30 3.78 45.46 3.27
283 287 9.725019 ACAAAAAGGAAAAGAAAGAGAAAACAT 57.275 25.926 0.00 0.00 0.00 2.71
448 463 5.473504 ACTTTTCGTAGATTGGATGCAGTTT 59.526 36.000 0.00 0.00 35.04 2.66
610 625 5.982356 TCTTCTGATGATCGATTCAACCTT 58.018 37.500 0.00 0.00 38.03 3.50
1002 1018 6.587990 CGGTCTAATGAGGCTACTATGAAATG 59.412 42.308 0.00 0.00 0.00 2.32
1081 1105 2.293118 TGGTTCATCTGGGGAGAGATCA 60.293 50.000 0.00 0.00 29.72 2.92
1117 1141 7.915293 ATTGTGAACGGTCTTATCAATACAA 57.085 32.000 0.33 1.24 0.00 2.41
1319 1343 6.053632 TCCATAGACATGCAGAAGAGAAAA 57.946 37.500 0.00 0.00 0.00 2.29
1343 1367 1.221840 CCCCACTCCGACCAAGATG 59.778 63.158 0.00 0.00 0.00 2.90
1432 1456 9.334947 TCAGGAACAATGAATCTCTTTATGATC 57.665 33.333 0.00 0.00 0.00 2.92
2008 2036 0.605860 CTGCTTCAGCTTCAGCCACT 60.606 55.000 10.75 0.00 43.38 4.00
2109 2137 4.608170 TTTTGGGGAATCTCCTTGCTAT 57.392 40.909 0.00 0.00 36.57 2.97
2309 2339 7.220300 GTCTACGTACCAGAACTGATAACATTG 59.780 40.741 3.19 0.00 0.00 2.82
2377 2407 6.349777 CCTCTTTAGCCCTATGTCTCTTATCG 60.350 46.154 0.00 0.00 0.00 2.92
2886 2916 6.767902 ACCGTGCACATTCTTATTATGAGAAT 59.232 34.615 18.64 6.43 42.89 2.40
3652 3685 3.380320 CCCTTTTCCTTCTCAAACAACGT 59.620 43.478 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 196 0.949397 TTCCGATCGAGATGTACGGG 59.051 55.000 18.66 0.00 43.14 5.28
283 287 7.141758 AGAGGGCTTAGTTGATCATGATTTA 57.858 36.000 10.14 0.00 0.00 1.40
420 435 4.770795 CATCCAATCTACGAAAAGTCCCT 58.229 43.478 0.00 0.00 0.00 4.20
432 447 8.843262 CATGAATTAGAAACTGCATCCAATCTA 58.157 33.333 0.00 0.00 0.00 1.98
448 463 6.829849 TGTACATGCCAGATCATGAATTAGA 58.170 36.000 0.00 0.00 44.94 2.10
610 625 7.944554 AGAACCAAGGTCTATCTTTTTGATCAA 59.055 33.333 3.38 3.38 36.65 2.57
733 748 8.694975 TTGAAAGATTTCGTTGAAATTGTTCA 57.305 26.923 18.02 18.02 41.56 3.18
1002 1018 0.039035 TGCCCCACCCATGAGTAAAC 59.961 55.000 0.00 0.00 0.00 2.01
1081 1105 4.097892 ACCGTTCACAATTTCTTGAAGCTT 59.902 37.500 0.00 0.00 36.20 3.74
1117 1141 7.898636 TGAAATTCCTGGGGAGTTATACATTTT 59.101 33.333 0.00 0.00 30.35 1.82
1319 1343 1.457831 GGTCGGAGTGGGGATAGCT 60.458 63.158 0.00 0.00 0.00 3.32
1376 1400 7.870445 TGCTTCACCTTAATTGTTATTTGAACC 59.130 33.333 0.00 0.00 0.00 3.62
1432 1456 4.383649 CGAACTTGCAAAATGGATCTGTTG 59.616 41.667 0.00 0.00 0.00 3.33
1787 1815 4.620184 GCGTATGTATAAGACCGAATCCAC 59.380 45.833 0.00 0.00 0.00 4.02
2109 2137 5.493133 ACGTTTCATGCTTGTTTGAGTAA 57.507 34.783 0.00 0.00 0.00 2.24
2294 2324 7.994911 TGCATAATCTCCAATGTTATCAGTTCT 59.005 33.333 0.00 0.00 0.00 3.01
2309 2339 6.631016 TCGTGTATAATCCTGCATAATCTCC 58.369 40.000 0.00 0.00 0.00 3.71
2352 2382 6.349777 CGATAAGAGACATAGGGCTAAAGAGG 60.350 46.154 0.00 0.00 0.00 3.69
2516 2546 7.591006 TTCGTCCAGTCATTAATAACTTGAC 57.409 36.000 11.39 11.39 40.00 3.18
2886 2916 0.758734 CCATAGGCTCGAATGACCCA 59.241 55.000 0.00 0.00 0.00 4.51
3160 3190 8.202137 TCTCCTTTCGTTCTCTTCTTTCTTTTA 58.798 33.333 0.00 0.00 0.00 1.52
3652 3685 8.713708 TTTGGTATAAGGAAGGAAATCAAACA 57.286 30.769 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.