Multiple sequence alignment - TraesCS5A01G099400

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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 TraesCS5A01G099400 chr5A 100.000 3445 0 0 1 3445 142248024 142244580 0 6362
1 TraesCS5A01G099400 chr5A 97.275 3449 85 9 1 3445 141905801 141909244 0 5840
2 TraesCS5A01G099400 chr5A 97.585 1905 44 2 1542 3445 541982194 541984097 0 3262
3 TraesCS5A01G099400 chr5A 97.537 1908 41 5 1542 3445 465659413 465661318 0 3258
4 TraesCS5A01G099400 chr5A 97.431 1907 45 2 1542 3445 34938067 34936162 0 3247
5 TraesCS5A01G099400 chr5A 96.682 1567 49 3 1 1564 34939664 34938098 0 2603
6 TraesCS5A01G099400 chr5A 96.613 1565 50 3 1 1563 465657818 465659381 0 2593
7 TraesCS5A01G099400 chr2A 97.954 1906 36 2 1542 3445 685099020 685097116 0 3301
8 TraesCS5A01G099400 chr2A 97.589 1908 41 5 1542 3445 284805209 284807115 0 3264
9 TraesCS5A01G099400 chr2A 97.269 1904 48 2 1542 3445 572964622 572962723 0 3225
10 TraesCS5A01G099400 chr2A 96.871 1566 47 2 1 1564 685100616 685099051 0 2619
11 TraesCS5A01G099400 chr2A 96.871 1566 46 3 1 1564 716650470 716648906 0 2617
12 TraesCS5A01G099400 chr2A 96.869 1565 46 3 1 1564 284803616 284805178 0 2615
13 TraesCS5A01G099400 chr6A 97.690 1905 38 3 1542 3445 158978168 158976269 0 3269
14 TraesCS5A01G099400 chr6A 97.510 1566 37 2 1 1564 158979764 158978199 0 2675
15 TraesCS5A01G099400 chr1A 97.482 1906 43 4 1542 3445 70940469 70938567 0 3249
16 TraesCS5A01G099400 chr1A 97.063 1566 43 3 1 1564 70942064 70940500 0 2634
17 TraesCS5A01G099400 chr3A 96.618 1567 48 5 1 1564 662006703 662005139 0 2595


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 TraesCS5A01G099400 chr5A 142244580 142248024 3444 True 6362.0 6362 100.0000 1 3445 1 chr5A.!!$R1 3444
1 TraesCS5A01G099400 chr5A 141905801 141909244 3443 False 5840.0 5840 97.2750 1 3445 1 chr5A.!!$F1 3444
2 TraesCS5A01G099400 chr5A 541982194 541984097 1903 False 3262.0 3262 97.5850 1542 3445 1 chr5A.!!$F2 1903
3 TraesCS5A01G099400 chr5A 465657818 465661318 3500 False 2925.5 3258 97.0750 1 3445 2 chr5A.!!$F3 3444
4 TraesCS5A01G099400 chr5A 34936162 34939664 3502 True 2925.0 3247 97.0565 1 3445 2 chr5A.!!$R2 3444
5 TraesCS5A01G099400 chr2A 572962723 572964622 1899 True 3225.0 3225 97.2690 1542 3445 1 chr2A.!!$R1 1903
6 TraesCS5A01G099400 chr2A 685097116 685100616 3500 True 2960.0 3301 97.4125 1 3445 2 chr2A.!!$R3 3444
7 TraesCS5A01G099400 chr2A 284803616 284807115 3499 False 2939.5 3264 97.2290 1 3445 2 chr2A.!!$F1 3444
8 TraesCS5A01G099400 chr2A 716648906 716650470 1564 True 2617.0 2617 96.8710 1 1564 1 chr2A.!!$R2 1563
9 TraesCS5A01G099400 chr6A 158976269 158979764 3495 True 2972.0 3269 97.6000 1 3445 2 chr6A.!!$R1 3444
10 TraesCS5A01G099400 chr1A 70938567 70942064 3497 True 2941.5 3249 97.2725 1 3445 2 chr1A.!!$R1 3444
11 TraesCS5A01G099400 chr3A 662005139 662006703 1564 True 2595.0 2595 96.6180 1 1564 1 chr3A.!!$R1 1563

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
356 360 4.008933 AGGCCACTCGCACCACTC 62.009 66.667 5.01 0.0 40.31 3.51 F
1106 1114 0.246635 AAGCGCGAGTACACCAGAAT 59.753 50.000 12.10 0.0 0.00 2.40 F
1150 1158 1.098129 CGAGGAGACGCTGGAGATCA 61.098 60.000 0.00 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2103 0.693049 ACAATTTCTCCTCCCGCAGT 59.307 50.0 0.00 0.0 0.00 4.40 R
2100 2164 0.843309 TCCAAACCAGACTCCTGCAA 59.157 50.0 0.00 0.0 39.07 4.08 R
3038 3107 1.411394 ATGAACGTACCGTGTGTTCG 58.589 50.0 11.04 0.0 43.74 3.95 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
356 360 4.008933 AGGCCACTCGCACCACTC 62.009 66.667 5.01 0.00 40.31 3.51
642 646 5.068987 ACATCACCTAAACAGTGCAAAATGT 59.931 36.000 0.00 0.00 35.14 2.71
1106 1114 0.246635 AAGCGCGAGTACACCAGAAT 59.753 50.000 12.10 0.00 0.00 2.40
1150 1158 1.098129 CGAGGAGACGCTGGAGATCA 61.098 60.000 0.00 0.00 0.00 2.92
1167 1175 1.376424 CATCTGCACCAGCGAACCT 60.376 57.895 0.00 0.00 46.23 3.50
1712 1774 5.245531 TCAAGCACTGGTATAGGTCTTTTG 58.754 41.667 0.00 0.00 0.00 2.44
2039 2103 1.610624 CCCAAGCGCCTCAAAGACTTA 60.611 52.381 2.29 0.00 0.00 2.24
2100 2164 1.296715 GGAGGTGACAAGCGGATGT 59.703 57.895 0.00 0.00 35.90 3.06
2463 2527 5.220340 GCATGAAAGTCTGCATTTGTTATGC 60.220 40.000 0.00 2.90 44.76 3.14
2492 2556 3.513912 AGCTACCTTATGCTGTGTGTGTA 59.486 43.478 0.00 0.00 38.21 2.90
2529 2593 7.542890 TGTTTCAGATTTGTAGTTTGCTTTCA 58.457 30.769 0.00 0.00 0.00 2.69
2584 2648 2.159310 TCAGGGTTTGAACAAGTTTGCG 60.159 45.455 0.00 0.00 31.34 4.85
2702 2766 0.961019 GAAACTTGATGGCTGCCACA 59.039 50.000 25.99 20.22 35.80 4.17
2807 2874 3.187700 CAAATAGTAGCCTTCGACGCTT 58.812 45.455 11.19 0.00 37.79 4.68
2985 3054 3.132111 TCAGGAAAAGCAAAGAAACACCC 59.868 43.478 0.00 0.00 0.00 4.61
3092 3161 2.358322 AAAGGAACGGGAAGCTTCAA 57.642 45.000 27.02 0.00 0.00 2.69
3117 3186 4.024387 TCGCATTCCTTAAAACAGTGACAC 60.024 41.667 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 309 7.360101 CCTGCTGTTTTAGTACTGATGTTGTAC 60.360 40.741 5.39 0.00 40.19 2.90
356 360 5.121142 GCATGGGTTTGAAATTTGATGTCAG 59.879 40.000 0.00 0.00 0.00 3.51
642 646 3.614870 CGTCTCTGTGGTTGTGATGATGA 60.615 47.826 0.00 0.00 0.00 2.92
792 797 1.264020 GTCAGCATTTGCACTTCGTCA 59.736 47.619 5.20 0.00 45.16 4.35
808 813 1.608336 TAGTGGTCGTGGGGGTCAG 60.608 63.158 0.00 0.00 0.00 3.51
981 989 3.145551 GCCTTCCTCCGGCGACTA 61.146 66.667 9.30 0.00 37.87 2.59
1031 1039 1.618343 TCTTGTCTGACATCTCGGCAA 59.382 47.619 11.86 0.00 0.00 4.52
1132 1140 1.269448 GATGATCTCCAGCGTCTCCTC 59.731 57.143 0.00 0.00 0.00 3.71
1150 1158 1.376424 CAGGTTCGCTGGTGCAGAT 60.376 57.895 0.00 0.00 39.64 2.90
1167 1175 1.215382 CATCTCGTCGGCCTTGTCA 59.785 57.895 0.00 0.00 0.00 3.58
2039 2103 0.693049 ACAATTTCTCCTCCCGCAGT 59.307 50.000 0.00 0.00 0.00 4.40
2100 2164 0.843309 TCCAAACCAGACTCCTGCAA 59.157 50.000 0.00 0.00 39.07 4.08
2463 2527 3.550437 AGCATAAGGTAGCTGGTTCAG 57.450 47.619 0.00 0.00 40.13 3.02
2529 2593 6.263168 GCATAAGGTAGCTGGTTCAACATAAT 59.737 38.462 0.00 0.00 0.00 1.28
2584 2648 7.435488 AGCAAACGATGTACTTGATAGACATAC 59.565 37.037 0.00 0.00 33.99 2.39
2702 2766 4.623932 TTTTCTCCATGACTAGTGCTGT 57.376 40.909 0.00 0.00 0.00 4.40
2807 2874 6.579666 ACCGTTCATGTCTAAGTTGTACTA 57.420 37.500 0.00 0.00 0.00 1.82
2851 2920 5.963586 GTGTTCGTCTGAAACTAAAAACTGG 59.036 40.000 0.00 0.00 35.46 4.00
2985 3054 6.967135 TGCTAGTGACTAGGAAATATGTACG 58.033 40.000 20.24 0.00 34.88 3.67
3038 3107 1.411394 ATGAACGTACCGTGTGTTCG 58.589 50.000 11.04 0.00 43.74 3.95
3092 3161 5.240623 TGTCACTGTTTTAAGGAATGCGAAT 59.759 36.000 0.00 0.00 0.00 3.34
3117 3186 8.039603 TGTATTGCCACTGTTAATTCTTAGTG 57.960 34.615 8.24 8.24 40.06 2.74
3343 3414 8.045176 AGATTCCAATTGTGCTAGTACTTTTC 57.955 34.615 12.42 1.82 0.00 2.29


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

AutoCloner maintained by Alex Coulton.