Multiple sequence alignment - TraesCS1A01G044300

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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 TraesCS1A01G044300 chr1A 100.000 2468 0 0 1 2468 25270891 25268424 0 4558
1 TraesCS1A01G044300 chr1A 96.386 2490 65 5 1 2468 77263481 77265967 0 4076
2 TraesCS1A01G044300 chr3A 96.372 2481 65 4 1 2468 693613513 693611045 0 4060
3 TraesCS1A01G044300 chr6A 95.743 2490 82 10 1 2468 587986709 587984222 0 3989
4 TraesCS1A01G044300 chr1D 95.564 2502 72 11 1 2467 316243853 316241356 0 3969
5 TraesCS1A01G044300 chr4D 95.525 2503 75 12 1 2468 491381604 491384104 0 3967
6 TraesCS1A01G044300 chr5A 95.513 2496 84 3 1 2468 540625056 540622561 0 3964
7 TraesCS1A01G044300 chr7D 95.506 2492 85 9 1 2468 531067612 531065124 0 3956
8 TraesCS1A01G044300 chr2D 95.366 2503 77 13 1 2468 617340860 617343358 0 3943
9 TraesCS1A01G044300 chr5D 95.458 2488 84 16 1 2468 552028931 552026453 0 3941
10 TraesCS1A01G044300 chr5D 94.886 2503 85 14 1 2468 78602819 78600325 0 3873
11 TraesCS1A01G044300 chr5D 95.659 1935 53 11 1 1909 555413652 555415581 0 3079
12 TraesCS1A01G044300 chr4A 93.969 2487 107 19 1 2468 478227249 478229711 0 3722
13 TraesCS1A01G044300 chr6B 91.086 2513 168 34 1 2466 630833831 630831328 0 3349
14 TraesCS1A01G044300 chr7B 90.876 2499 170 30 1 2468 619624062 619626533 0 3299
15 TraesCS1A01G044300 chr7A 96.635 1813 49 3 668 2468 70256082 70254270 0 3000
16 TraesCS1A01G044300 chr3D 95.365 1467 57 6 1 1458 610062606 610061142 0 2322
17 TraesCS1A01G044300 chr3D 95.695 1022 30 10 1450 2468 610059709 610058699 0 1631


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 TraesCS1A01G044300 chr1A 25268424 25270891 2467 True 4558.0 4558 100.000 1 2468 1 chr1A.!!$R1 2467
1 TraesCS1A01G044300 chr1A 77263481 77265967 2486 False 4076.0 4076 96.386 1 2468 1 chr1A.!!$F1 2467
2 TraesCS1A01G044300 chr3A 693611045 693613513 2468 True 4060.0 4060 96.372 1 2468 1 chr3A.!!$R1 2467
3 TraesCS1A01G044300 chr6A 587984222 587986709 2487 True 3989.0 3989 95.743 1 2468 1 chr6A.!!$R1 2467
4 TraesCS1A01G044300 chr1D 316241356 316243853 2497 True 3969.0 3969 95.564 1 2467 1 chr1D.!!$R1 2466
5 TraesCS1A01G044300 chr4D 491381604 491384104 2500 False 3967.0 3967 95.525 1 2468 1 chr4D.!!$F1 2467
6 TraesCS1A01G044300 chr5A 540622561 540625056 2495 True 3964.0 3964 95.513 1 2468 1 chr5A.!!$R1 2467
7 TraesCS1A01G044300 chr7D 531065124 531067612 2488 True 3956.0 3956 95.506 1 2468 1 chr7D.!!$R1 2467
8 TraesCS1A01G044300 chr2D 617340860 617343358 2498 False 3943.0 3943 95.366 1 2468 1 chr2D.!!$F1 2467
9 TraesCS1A01G044300 chr5D 552026453 552028931 2478 True 3941.0 3941 95.458 1 2468 1 chr5D.!!$R2 2467
10 TraesCS1A01G044300 chr5D 78600325 78602819 2494 True 3873.0 3873 94.886 1 2468 1 chr5D.!!$R1 2467
11 TraesCS1A01G044300 chr5D 555413652 555415581 1929 False 3079.0 3079 95.659 1 1909 1 chr5D.!!$F1 1908
12 TraesCS1A01G044300 chr4A 478227249 478229711 2462 False 3722.0 3722 93.969 1 2468 1 chr4A.!!$F1 2467
13 TraesCS1A01G044300 chr6B 630831328 630833831 2503 True 3349.0 3349 91.086 1 2466 1 chr6B.!!$R1 2465
14 TraesCS1A01G044300 chr7B 619624062 619626533 2471 False 3299.0 3299 90.876 1 2468 1 chr7B.!!$F1 2467
15 TraesCS1A01G044300 chr7A 70254270 70256082 1812 True 3000.0 3000 96.635 668 2468 1 chr7A.!!$R1 1800
16 TraesCS1A01G044300 chr3D 610058699 610062606 3907 True 1976.5 2322 95.530 1 2468 2 chr3D.!!$R1 2467

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
973 1034 0.625849 CCCCTGGCCTGTAATTCTGT 59.374 55.0 3.32 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 3822 0.036732 ATCGACATGTTGCTGTGGGT 59.963 50.0 8.34 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
43 44 3.945285 ACCATTTTAACCGCGATTCTGAT 59.055 39.130 8.23 0.00 0.00 2.90
299 305 1.741770 GGCCGAACAGCAACGAGAT 60.742 57.895 0.00 0.00 0.00 2.75
327 333 3.628032 ACGACGATGATGAGTACATGAGT 59.372 43.478 0.00 0.00 36.82 3.41
373 379 6.809196 GGAGTACTTTGTAAGTCATCTCAGTG 59.191 42.308 0.00 0.00 41.77 3.66
551 584 2.306805 TGGGCTTGTGACTGAATCTGAT 59.693 45.455 0.00 0.00 0.00 2.90
616 649 2.418368 TTTGAAGGCACTGACACTGT 57.582 45.000 0.00 0.00 40.86 3.55
619 652 1.209261 TGAAGGCACTGACACTGTCAA 59.791 47.619 12.92 0.00 42.26 3.18
681 714 6.323739 AGTTGGTGTGGATTTGATTAGTTTGT 59.676 34.615 0.00 0.00 0.00 2.83
798 835 7.284489 ACTTGTAATAAAGAGCACTGGAAACAA 59.716 33.333 0.00 0.00 42.06 2.83
801 838 7.934665 TGTAATAAAGAGCACTGGAAACAAGTA 59.065 33.333 0.00 0.00 42.06 2.24
810 856 6.595716 AGCACTGGAAACAAGTATGAATACTC 59.404 38.462 3.51 0.00 42.47 2.59
929 990 5.875224 TGATTTTCAGGATGGTGTGAACTA 58.125 37.500 0.00 0.00 36.16 2.24
973 1034 0.625849 CCCCTGGCCTGTAATTCTGT 59.374 55.000 3.32 0.00 0.00 3.41
974 1035 1.683011 CCCCTGGCCTGTAATTCTGTG 60.683 57.143 3.32 0.00 0.00 3.66
1092 1153 1.200092 AGGAGCTTGCTTCTCTGGCT 61.200 55.000 0.00 0.00 35.86 4.75
1169 1230 4.891168 TGGAATCAAATCTCATGACATGGG 59.109 41.667 15.37 12.46 0.00 4.00
1406 1467 3.920231 TGTCATTGCTGAGCTCCTTAT 57.080 42.857 12.15 0.00 30.18 1.73
1904 3431 7.770897 AGACACTTAAACTGACAGAACTGAATT 59.229 33.333 10.08 0.00 0.00 2.17
1948 3476 6.371825 CCCTGATAAACTGACAGAACTAAACC 59.628 42.308 10.08 0.00 34.07 3.27
1977 3505 6.805016 AACTGAATCTCACATAGATCTGGT 57.195 37.500 5.18 0.25 44.56 4.00
2157 3694 2.596851 CCAGCAGTGCTAGTGGGGT 61.597 63.158 19.26 0.00 36.40 4.95
2207 3744 3.685550 GCCCATAGTAGTTGGAGTTGCAT 60.686 47.826 0.00 0.00 36.26 3.96
2362 3899 2.178890 CATGCGCTGCTTCTCCTCC 61.179 63.158 9.73 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.634004 TCACATCAGAATCGCGGTTAAAAT 59.366 37.500 3.66 0.00 0.00 1.82
43 44 4.927782 GCACGTGGGCCACTCACA 62.928 66.667 32.28 0.00 35.03 3.58
278 284 3.276091 CGTTGCTGTTCGGCCACA 61.276 61.111 2.24 0.00 0.00 4.17
327 333 0.035739 TCTGCATGCTGCTGAACTCA 59.964 50.000 20.33 0.00 46.01 3.41
373 379 2.445525 AGACAGGAGAGGGAGAGGATAC 59.554 54.545 0.00 0.00 0.00 2.24
616 649 5.883685 AGCACATCCTATGAATCTCTTGA 57.116 39.130 0.00 0.00 0.00 3.02
619 652 6.073981 TCAGTAGCACATCCTATGAATCTCT 58.926 40.000 0.00 0.00 0.00 3.10
681 714 7.847096 TCTGTTTCCACTACATAGCAGAAATA 58.153 34.615 7.04 4.80 33.24 1.40
779 816 7.168219 TCATACTTGTTTCCAGTGCTCTTTAT 58.832 34.615 0.00 0.00 0.00 1.40
929 990 1.909302 CTACCCACTCCAGAACACCAT 59.091 52.381 0.00 0.00 0.00 3.55
996 1057 6.931790 AGGTTCTGCTCATGATACATATCT 57.068 37.500 0.00 0.00 33.88 1.98
1092 1153 3.324846 CCACCAGCTGGCTATACTGATTA 59.675 47.826 33.06 0.00 39.32 1.75
1169 1230 0.668401 GATTGCCTGGCTTGTGCAAC 60.668 55.000 21.03 0.00 46.60 4.17
1406 1467 0.827089 CTTGCACCCATGACCAACCA 60.827 55.000 0.00 0.00 0.00 3.67
1579 3099 6.496565 ACCAAAATGATCTGAACCCATTACAA 59.503 34.615 0.00 0.00 31.07 2.41
1904 3431 2.622942 GGGTGTTTGCAATCTCAGTGAA 59.377 45.455 0.00 0.00 0.00 3.18
1948 3476 8.296000 AGATCTATGTGAGATTCAGTTATGTCG 58.704 37.037 0.00 0.00 45.48 4.35
1977 3505 9.778741 AACAGTAAGTTTCAGATTCAGTTATCA 57.221 29.630 0.00 0.00 37.03 2.15
2157 3694 0.749049 CGAGGACCTGCAGATCATCA 59.251 55.000 22.02 0.00 0.00 3.07
2207 3744 2.634940 GCTATATCCCTCCAGCACAAGA 59.365 50.000 0.00 0.00 34.13 3.02
2240 3777 3.316573 CTGGGCAGAGGGAACGGTC 62.317 68.421 0.00 0.00 0.00 4.79
2285 3822 0.036732 ATCGACATGTTGCTGTGGGT 59.963 50.000 8.34 0.00 0.00 4.51
2362 3899 1.514443 GAGGAAGAAGGCGACGACG 60.514 63.158 2.12 2.12 42.93 5.12


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

AutoCloner maintained by Alex Coulton.