Multiple sequence alignment - TraesCS4A01G155400

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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 TraesCS4A01G155400 chr4A 100.000 2213 0 0 1 2213 310761291 310763503 0 4087
1 TraesCS4A01G155400 chr4A 93.318 2215 121 11 1 2213 219340979 219338790 0 3245
2 TraesCS4A01G155400 chr3A 95.674 2219 85 9 1 2213 672879550 672877337 0 3555
3 TraesCS4A01G155400 chr3B 95.236 2225 91 7 1 2213 201561898 201559677 0 3507
4 TraesCS4A01G155400 chr1B 95.189 2224 91 9 1 2213 633729987 633727769 0 3500
5 TraesCS4A01G155400 chr2D 95.277 2223 77 11 1 2213 272802780 272800576 0 3498
6 TraesCS4A01G155400 chr2D 96.147 1817 59 6 1 1808 630268106 630269920 0 2957
7 TraesCS4A01G155400 chr2D 96.535 1616 45 4 600 2213 33933300 33934906 0 2663
8 TraesCS4A01G155400 chr2D 96.522 1150 33 1 1064 2213 630270241 630271383 0 1895
9 TraesCS4A01G155400 chr5D 95.081 2216 103 6 1 2213 432293834 432291622 0 3483
10 TraesCS4A01G155400 chr5B 95.081 2216 99 6 1 2213 432875609 432877817 0 3480
11 TraesCS4A01G155400 chr7A 92.561 2218 138 14 1 2213 352678563 352676368 0 3157


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 TraesCS4A01G155400 chr4A 310761291 310763503 2212 False 4087 4087 100.0000 1 2213 1 chr4A.!!$F1 2212
1 TraesCS4A01G155400 chr4A 219338790 219340979 2189 True 3245 3245 93.3180 1 2213 1 chr4A.!!$R1 2212
2 TraesCS4A01G155400 chr3A 672877337 672879550 2213 True 3555 3555 95.6740 1 2213 1 chr3A.!!$R1 2212
3 TraesCS4A01G155400 chr3B 201559677 201561898 2221 True 3507 3507 95.2360 1 2213 1 chr3B.!!$R1 2212
4 TraesCS4A01G155400 chr1B 633727769 633729987 2218 True 3500 3500 95.1890 1 2213 1 chr1B.!!$R1 2212
5 TraesCS4A01G155400 chr2D 272800576 272802780 2204 True 3498 3498 95.2770 1 2213 1 chr2D.!!$R1 2212
6 TraesCS4A01G155400 chr2D 33933300 33934906 1606 False 2663 2663 96.5350 600 2213 1 chr2D.!!$F1 1613
7 TraesCS4A01G155400 chr2D 630268106 630271383 3277 False 2426 2957 96.3345 1 2213 2 chr2D.!!$F2 2212
8 TraesCS4A01G155400 chr5D 432291622 432293834 2212 True 3483 3483 95.0810 1 2213 1 chr5D.!!$R1 2212
9 TraesCS4A01G155400 chr5B 432875609 432877817 2208 False 3480 3480 95.0810 1 2213 1 chr5B.!!$F1 2212
10 TraesCS4A01G155400 chr7A 352676368 352678563 2195 True 3157 3157 92.5610 1 2213 1 chr7A.!!$R1 2212

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
239 243 2.995765 TTAAATACCCCCTCCCTGGA 57.004 50.0 0.0 0.0 38.35 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1357 1903 2.159142 ACCTATGTACCTTGTAGCACGC 60.159 50.0 0.0 0.0 0.0 5.34 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
188 189 6.374333 TCACTTGTTAAGGAAATGGCTATCAC 59.626 38.462 0.00 0.00 0.00 3.06
192 193 5.941058 TGTTAAGGAAATGGCTATCACGAAA 59.059 36.000 0.00 0.00 0.00 3.46
239 243 2.995765 TTAAATACCCCCTCCCTGGA 57.004 50.000 0.00 0.00 38.35 3.86
259 263 9.467796 CCCTGGAGAAAGAAGAATAGTAAAAAT 57.532 33.333 0.00 0.00 0.00 1.82
512 525 7.614192 GGAATTCCTTTGGTCTAATTTAGGACA 59.386 37.037 17.73 1.14 34.49 4.02
582 599 4.207955 AGGAACAAAACAGTCCTTTCCTC 58.792 43.478 0.00 0.00 38.82 3.71
584 601 5.132144 AGGAACAAAACAGTCCTTTCCTCTA 59.868 40.000 0.00 0.00 38.82 2.43
640 657 7.229907 AGGTTTCATGTACGGTTTTGAAATAGT 59.770 33.333 12.70 3.20 39.48 2.12
656 673 4.657814 AATAGTGGTGGGAACTGTGATT 57.342 40.909 0.00 0.00 0.00 2.57
662 679 4.006989 TGGTGGGAACTGTGATTTTATCG 58.993 43.478 0.00 0.00 0.00 2.92
746 765 6.694445 TGGTTTTTGGATGGAATATTTGGT 57.306 33.333 0.00 0.00 0.00 3.67
819 838 8.934023 TGTGAAAGATTACCCTTTGATTTACT 57.066 30.769 0.00 0.00 36.58 2.24
826 845 8.548877 AGATTACCCTTTGATTTACTAGAAGCA 58.451 33.333 0.00 0.00 0.00 3.91
1357 1903 7.369607 TCATGAGTTATGGTCAACAAACAATG 58.630 34.615 0.00 0.00 37.39 2.82
1385 1931 6.438108 TGCTACAAGGTACATAGGTCAAAGTA 59.562 38.462 0.00 0.00 0.00 2.24
1468 2014 5.705609 AATCAATTACACCAGAGCGTTTT 57.294 34.783 0.00 0.00 0.00 2.43
1487 2033 4.627284 TTTCGAGGGTGAATCCACTTTA 57.373 40.909 0.00 0.00 42.77 1.85
1489 2035 3.934068 TCGAGGGTGAATCCACTTTAAC 58.066 45.455 0.00 0.00 42.77 2.01
1742 2828 8.865590 TTACAACCAAATTTCTTTAAGTCAGC 57.134 30.769 0.00 0.00 0.00 4.26
1753 2839 6.605471 TCTTTAAGTCAGCTACCAATCTCA 57.395 37.500 0.00 0.00 0.00 3.27
1754 2840 7.187824 TCTTTAAGTCAGCTACCAATCTCAT 57.812 36.000 0.00 0.00 0.00 2.90
1848 2934 9.611284 TTTGAATTCAAGAACGATTACTGATTG 57.389 29.630 19.64 0.00 37.15 2.67
2075 3162 7.390718 TCCTTGAATCCTTTAGTTTTAGTCAGC 59.609 37.037 0.00 0.00 0.00 4.26
2139 3226 7.645058 AATGGATTTACTTGGACCAATACAG 57.355 36.000 7.54 0.00 34.28 2.74
2179 3266 6.652205 TTGGGGGATTTGTTCTTCTACTAT 57.348 37.500 0.00 0.00 0.00 2.12
2185 3272 6.100714 GGGATTTGTTCTTCTACTATGGGGTA 59.899 42.308 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 9.869757 AAAATGGATAAAGGGTTAATTCTTTCG 57.130 29.630 8.60 0.00 35.22 3.46
458 471 7.880195 TCTGCTAGAATAAGAAAAAGCACTTCT 59.120 33.333 0.00 0.00 35.20 2.85
550 567 1.074889 GTTTTGTTCCTAGCCCCTGGA 59.925 52.381 0.00 0.00 0.00 3.86
582 599 5.895636 ACGGCTTCTCTATGATCAGATAG 57.104 43.478 0.09 0.00 0.00 2.08
584 601 5.948758 TCATACGGCTTCTCTATGATCAGAT 59.051 40.000 0.09 0.00 0.00 2.90
640 657 4.006989 CGATAAAATCACAGTTCCCACCA 58.993 43.478 0.00 0.00 0.00 4.17
662 679 9.731819 TTGAACTGTTAGATAATCATAGTCGAC 57.268 33.333 7.70 7.70 0.00 4.20
723 740 6.043706 ACACCAAATATTCCATCCAAAAACCA 59.956 34.615 0.00 0.00 0.00 3.67
746 765 3.844211 ACCAGAAAACCTATAGGCTGACA 59.156 43.478 19.25 0.00 39.32 3.58
783 802 6.351286 GGGTAATCTTTCACATTCTGCCAAAT 60.351 38.462 0.00 0.00 0.00 2.32
819 838 6.607600 TGCTACTAATTCTTCCTCTGCTTCTA 59.392 38.462 0.00 0.00 0.00 2.10
826 845 6.098552 GGTAACCTGCTACTAATTCTTCCTCT 59.901 42.308 0.00 0.00 0.00 3.69
1010 1031 7.095102 CCATTGTCATTTCCAAAATTCCAACTC 60.095 37.037 0.00 0.00 0.00 3.01
1325 1871 3.054434 TGACCATAACTCATGAACCCAGG 60.054 47.826 0.00 0.00 36.69 4.45
1357 1903 2.159142 ACCTATGTACCTTGTAGCACGC 60.159 50.000 0.00 0.00 0.00 5.34
1385 1931 7.446106 TTGTGTGGGATAAGGTAGTTATGAT 57.554 36.000 0.00 0.00 30.93 2.45
1468 2014 3.581332 AGTTAAAGTGGATTCACCCTCGA 59.419 43.478 0.00 0.00 44.64 4.04
1487 2033 9.979578 TTCACAAGCAATACATTTATCAAAGTT 57.020 25.926 0.00 0.00 0.00 2.66
1489 2035 9.630098 ACTTCACAAGCAATACATTTATCAAAG 57.370 29.630 0.00 0.00 0.00 2.77
1730 2816 6.605471 TGAGATTGGTAGCTGACTTAAAGA 57.395 37.500 0.00 0.00 0.00 2.52
1740 2826 5.608437 TCTCCCATTAATGAGATTGGTAGCT 59.392 40.000 17.23 0.00 32.84 3.32
1754 2840 9.083422 TGTTTGAATTGTGTAATCTCCCATTAA 57.917 29.630 0.00 0.00 0.00 1.40
1824 2910 7.119699 AGCAATCAGTAATCGTTCTTGAATTCA 59.880 33.333 3.38 3.38 0.00 2.57
2126 3213 5.779241 AAGAATCTCCTGTATTGGTCCAA 57.221 39.130 6.80 6.80 0.00 3.53
2139 3226 5.012893 CCCCCAAATAGCATAAGAATCTCC 58.987 45.833 0.00 0.00 0.00 3.71
2179 3266 8.394040 GGTAAGTAATACTACTCCTATACCCCA 58.606 40.741 0.00 0.00 37.39 4.96
2185 3272 7.732140 GGGGTTGGTAAGTAATACTACTCCTAT 59.268 40.741 2.69 0.00 37.39 2.57


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

AutoCloner maintained by Alex Coulton.