Multiple sequence alignment - TraesCS4A01G079400

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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 TraesCS4A01G079400 chr4A 100.000 2402 0 0 1 2402 80856377 80858778 0.000000e+00 4436.0
1 TraesCS4A01G079400 chr4D 96.099 2435 60 11 1 2402 409168446 409170878 0.000000e+00 3938.0
2 TraesCS4A01G079400 chr4B 95.258 2425 74 11 4 2399 506911282 506908870 0.000000e+00 3803.0
3 TraesCS4A01G079400 chr5D 86.614 127 17 0 908 1034 344884937 344885063 8.950000e-30 141.0
4 TraesCS4A01G079400 chr5D 85.393 89 9 3 948 1034 436971925 436971839 3.290000e-14 89.8
5 TraesCS4A01G079400 chr5A 89.908 109 11 0 926 1034 447305171 447305063 8.950000e-30 141.0
6 TraesCS4A01G079400 chr7D 91.753 97 8 0 938 1034 117792210 117792114 4.170000e-28 135.0
7 TraesCS4A01G079400 chr7B 90.722 97 9 0 938 1034 79051522 79051426 1.940000e-26 130.0
8 TraesCS4A01G079400 chr7A 90.722 97 9 0 938 1034 122207745 122207649 1.940000e-26 130.0
9 TraesCS4A01G079400 chr5B 85.393 89 9 3 948 1034 531187599 531187513 3.290000e-14 89.8


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 TraesCS4A01G079400 chr4A 80856377 80858778 2401 False 4436 4436 100.000 1 2402 1 chr4A.!!$F1 2401
1 TraesCS4A01G079400 chr4D 409168446 409170878 2432 False 3938 3938 96.099 1 2402 1 chr4D.!!$F1 2401
2 TraesCS4A01G079400 chr4B 506908870 506911282 2412 True 3803 3803 95.258 4 2399 1 chr4B.!!$R1 2395

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
745 769 0.322546 GCAGAGGGTTCCCGTTGATT 60.323 55.0 15.25 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 1765 0.397187 CCATCTAGCAGCAGCAGGAT 59.603 55.0 3.17 3.49 45.49 3.24 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
251 267 7.970061 GTCTTGCTGCATGAAAGTTATAAATCA 59.030 33.333 18.30 0.00 33.01 2.57
322 338 4.802563 GCAAATAGCAGGATCAAAGCTTTC 59.197 41.667 9.23 0.00 44.79 2.62
338 354 7.779326 TCAAAGCTTTCATGGATGGACATATTA 59.221 33.333 9.23 0.00 0.00 0.98
424 448 5.607939 AAAAGGGTAGTTTCAACCAAAGG 57.392 39.130 0.00 0.00 38.87 3.11
745 769 0.322546 GCAGAGGGTTCCCGTTGATT 60.323 55.000 15.25 0.00 0.00 2.57
795 819 1.419387 GAACTGCTGGCCATAGGAGAT 59.581 52.381 18.67 8.13 38.28 2.75
826 850 1.141019 CGTGGTCCATGACGGGTAG 59.859 63.158 4.96 0.00 32.65 3.18
1147 1171 4.097135 GCTTCTTTAATTCTTCCCTCAGGC 59.903 45.833 0.00 0.00 0.00 4.85
1356 1380 1.823250 GCAACCAGAACCAGGTGGATT 60.823 52.381 2.10 0.00 39.86 3.01
1408 1432 3.397482 AGCAGCTCTTTGTGAAGTACAG 58.603 45.455 0.00 0.00 41.10 2.74
1409 1433 2.096019 GCAGCTCTTTGTGAAGTACAGC 60.096 50.000 0.00 0.00 41.10 4.40
1483 1512 2.368011 GGAGGAAGAGGAACCCCGG 61.368 68.421 0.00 0.00 37.58 5.73
1554 1583 3.052186 AGAGCCAAGGAGAGAGAAGGTAT 60.052 47.826 0.00 0.00 0.00 2.73
1586 1615 0.402121 GGGCAAGAAGAAGGTCTGGT 59.598 55.000 0.00 0.00 0.00 4.00
1736 1765 2.887846 TTAGGAGGAGGTGGGGGCA 61.888 63.158 0.00 0.00 0.00 5.36
1949 1994 2.035961 TCACTGAGTCTGAGGAAAACCG 59.964 50.000 3.76 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 8.262715 TCAGATACACATTTTTATTTCTCGCA 57.737 30.769 0.00 0.00 0.00 5.10
314 330 7.781693 AGTAATATGTCCATCCATGAAAGCTTT 59.218 33.333 12.53 12.53 0.00 3.51
322 338 5.541845 ACGTGAGTAATATGTCCATCCATG 58.458 41.667 0.00 0.00 46.88 3.66
424 448 6.317857 CGAGAACTGATTTCCCAATCTTTTC 58.682 40.000 0.00 0.00 39.81 2.29
817 841 0.108992 GTGCGACATTCTACCCGTCA 60.109 55.000 0.00 0.00 0.00 4.35
1147 1171 3.630148 GACGTCCCGCATGCATCG 61.630 66.667 19.57 17.06 0.00 3.84
1330 1354 0.540365 CTGGTTCTGGTTGCATGGGT 60.540 55.000 0.00 0.00 0.00 4.51
1356 1380 4.104383 AGGAAATTCTGTGCCTTTCTCA 57.896 40.909 0.00 0.00 0.00 3.27
1408 1432 1.085091 CTGAGCCTGAGACATTGTGC 58.915 55.000 0.00 0.00 0.00 4.57
1409 1433 1.085091 GCTGAGCCTGAGACATTGTG 58.915 55.000 0.00 0.00 0.00 3.33
1554 1583 6.636454 TCTTCTTGCCCTTTCTATTCCTAA 57.364 37.500 0.00 0.00 0.00 2.69
1586 1615 2.416747 CTCCTTTGAGCGACATGAACA 58.583 47.619 0.00 0.00 0.00 3.18
1652 1681 1.146263 GGTACCCCATTCGCCTCAG 59.854 63.158 0.00 0.00 0.00 3.35
1736 1765 0.397187 CCATCTAGCAGCAGCAGGAT 59.603 55.000 3.17 3.49 45.49 3.24
1949 1994 2.026262 AGAGTGAGGGAGTGAGAGAGAC 60.026 54.545 0.00 0.00 0.00 3.36
2298 2353 3.051081 AGAAACTAAGACAGCAGCAGG 57.949 47.619 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.