Multiple sequence alignment - TraesCS2A01G387600

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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 TraesCS2A01G387600 chr2A 100.000 2450 0 0 1 2450 633254260 633251811 0 4525
1 TraesCS2A01G387600 chr6A 94.670 2458 120 6 3 2450 605867152 605864696 0 3803
2 TraesCS2A01G387600 chr6A 93.279 2455 160 4 1 2450 419676935 419674481 0 3615
3 TraesCS2A01G387600 chr6A 92.474 2458 173 7 1 2450 419648196 419645743 0 3504
4 TraesCS2A01G387600 chr6A 93.175 2315 150 6 144 2450 419605349 419603035 0 3393
5 TraesCS2A01G387600 chr6A 92.569 2328 157 11 135 2450 419637921 419635598 0 3326
6 TraesCS2A01G387600 chr6A 92.837 1787 117 7 135 1915 419587643 419585862 0 2580
7 TraesCS2A01G387600 chr4B 93.238 2455 152 6 1 2450 644317522 644319967 0 3602
8 TraesCS2A01G387600 chr3D 88.045 2476 264 16 1 2448 520362666 520365137 0 2904
9 TraesCS2A01G387600 chr2D 87.990 2473 266 20 2 2448 75661042 75663509 0 2892
10 TraesCS2A01G387600 chr1A 95.857 1738 67 5 718 2450 539728273 539726536 0 2806
11 TraesCS2A01G387600 chr1A 94.009 651 39 0 1 651 539729043 539728393 0 987


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 TraesCS2A01G387600 chr2A 633251811 633254260 2449 True 4525.0 4525 100.000 1 2450 1 chr2A.!!$R1 2449
1 TraesCS2A01G387600 chr6A 605864696 605867152 2456 True 3803.0 3803 94.670 3 2450 1 chr6A.!!$R6 2447
2 TraesCS2A01G387600 chr6A 419674481 419676935 2454 True 3615.0 3615 93.279 1 2450 1 chr6A.!!$R5 2449
3 TraesCS2A01G387600 chr6A 419645743 419648196 2453 True 3504.0 3504 92.474 1 2450 1 chr6A.!!$R4 2449
4 TraesCS2A01G387600 chr6A 419603035 419605349 2314 True 3393.0 3393 93.175 144 2450 1 chr6A.!!$R2 2306
5 TraesCS2A01G387600 chr6A 419635598 419637921 2323 True 3326.0 3326 92.569 135 2450 1 chr6A.!!$R3 2315
6 TraesCS2A01G387600 chr6A 419585862 419587643 1781 True 2580.0 2580 92.837 135 1915 1 chr6A.!!$R1 1780
7 TraesCS2A01G387600 chr4B 644317522 644319967 2445 False 3602.0 3602 93.238 1 2450 1 chr4B.!!$F1 2449
8 TraesCS2A01G387600 chr3D 520362666 520365137 2471 False 2904.0 2904 88.045 1 2448 1 chr3D.!!$F1 2447
9 TraesCS2A01G387600 chr2D 75661042 75663509 2467 False 2892.0 2892 87.990 2 2448 1 chr2D.!!$F1 2446
10 TraesCS2A01G387600 chr1A 539726536 539729043 2507 True 1896.5 2806 94.933 1 2450 2 chr1A.!!$R1 2449

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
530 531 0.183971 TGGAAGGACGCCTTTTTGGA 59.816 50.0 11.62 0.0 44.82 3.53 F
885 962 0.749454 GCCCCATGCTTCGACTCAAT 60.749 55.0 0.00 0.0 36.87 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1436 0.390998 TTGCGATCGCCTTGATGTCA 60.391 50.0 35.12 12.26 37.47 3.58 R
2078 2165 0.987081 AGCATCCATGGCTCTGAGGT 60.987 55.0 6.96 0.00 36.81 3.85 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
79 80 1.525077 GGCCACACCAAGACGTTCA 60.525 57.895 0.00 0.00 38.86 3.18
264 265 0.261696 TGGATCGGATGGAGGACTGA 59.738 55.000 0.00 0.00 0.00 3.41
502 503 2.521708 GCAACCAAGGTGGGCTGT 60.522 61.111 8.43 0.00 43.37 4.40
530 531 0.183971 TGGAAGGACGCCTTTTTGGA 59.816 50.000 11.62 0.00 44.82 3.53
635 655 1.076485 ATGATGACCAGGGCAAGCC 60.076 57.895 0.00 1.52 0.00 4.35
665 685 3.646715 CCCCGTCCTCAAGGCCAA 61.647 66.667 5.01 0.00 34.44 4.52
752 825 1.981495 CAGTTCTTCTCCTTCCCAGGT 59.019 52.381 0.00 0.00 41.69 4.00
782 855 1.212934 TCTCCCCTCCACCTCGTACT 61.213 60.000 0.00 0.00 0.00 2.73
885 962 0.749454 GCCCCATGCTTCGACTCAAT 60.749 55.000 0.00 0.00 36.87 2.57
1200 1279 1.587054 CTCCTTCTCACCGAAGCGT 59.413 57.895 0.00 0.00 46.29 5.07
1560 1643 2.093235 GCAGGATCAGTTTCTAGCCACT 60.093 50.000 0.00 0.00 0.00 4.00
1632 1716 6.363065 TGTAATGTGTGTTGTAACCCCTTTA 58.637 36.000 0.00 0.00 0.00 1.85
1847 1933 1.624813 ACGACGTTGGGGGAAATCTTA 59.375 47.619 7.90 0.00 0.00 2.10
2059 2146 6.488006 AGAAAGCAAATTTTCTGTCTGAGCTA 59.512 34.615 9.44 0.00 43.75 3.32
2278 2365 3.244422 ACCCAACTCTTTGTAGCATCGAA 60.244 43.478 0.00 0.00 0.00 3.71
2416 2504 1.272092 CCAGGGCAAGGTTCAGATTCA 60.272 52.381 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 1.845205 AAGTCCAGAGCCAGCAGGT 60.845 57.895 0.00 0.00 37.19 4.00
128 129 1.675801 CTCTTGAGCACCCAGAGCA 59.324 57.895 0.00 0.00 0.00 4.26
295 296 4.804420 AGGGATCCCGCTCTGGCA 62.804 66.667 25.48 0.00 41.95 4.92
353 354 3.170362 CCCAGGAACCAGGCTCAA 58.830 61.111 0.00 0.00 0.00 3.02
479 480 1.603455 CCACCTTGGTTGCCATCGT 60.603 57.895 0.00 0.00 31.53 3.73
502 503 2.347490 GTCCTTCCAAGAGCGCCA 59.653 61.111 2.29 0.00 0.00 5.69
530 531 1.447317 CTTGGCGTGGCAAGAGTTGT 61.447 55.000 26.58 0.00 0.00 3.32
782 855 0.678950 TCTCCAGTTGCATGACGTCA 59.321 50.000 22.48 22.48 0.00 4.35
1353 1436 0.390998 TTGCGATCGCCTTGATGTCA 60.391 50.000 35.12 12.26 37.47 3.58
1632 1716 7.262772 TCACTTCGTCGACTATCCATTAAAAT 58.737 34.615 14.70 0.00 0.00 1.82
1701 1785 1.482593 CGTTAAGGCCTCTCACTCCAT 59.517 52.381 5.23 0.00 0.00 3.41
1708 1794 1.810030 CGGTGCGTTAAGGCCTCTC 60.810 63.158 16.94 0.00 0.00 3.20
1895 1982 2.639347 TCTGCTTGTCCCAGAAGATTGA 59.361 45.455 0.00 0.00 36.46 2.57
2078 2165 0.987081 AGCATCCATGGCTCTGAGGT 60.987 55.000 6.96 0.00 36.81 3.85
2416 2504 6.210584 TGAGGAAAGACTGTCCAAAAGTTTTT 59.789 34.615 14.43 0.00 37.65 1.94


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

AutoCloner maintained by Alex Coulton.