Multiple sequence alignment - TraesCS5A01G419200

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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 TraesCS5A01G419200 chr5A 100.000 2305 0 0 1 2305 606694011 606691707 0.000000e+00 4257
1 TraesCS5A01G419200 chr5A 95.839 2283 79 5 2 2281 288263580 288265849 0.000000e+00 3675
2 TraesCS5A01G419200 chr5A 98.230 113 2 0 2193 2305 288265791 288265903 5.020000e-47 198
3 TraesCS5A01G419200 chr7A 96.963 2305 62 3 2 2305 192630953 192628656 0.000000e+00 3862
4 TraesCS5A01G419200 chr7A 93.608 2331 109 26 3 2305 130562455 130560137 0.000000e+00 3443
5 TraesCS5A01G419200 chr7A 96.779 2018 65 0 2 2019 38742701 38740684 0.000000e+00 3367
6 TraesCS5A01G419200 chr7A 96.588 1905 56 4 2 1902 643632506 643630607 0.000000e+00 3149
7 TraesCS5A01G419200 chr7A 95.245 1977 82 6 3 1972 699317483 699319454 0.000000e+00 3120
8 TraesCS5A01G419200 chr7A 92.197 1038 43 12 1295 2305 16875058 16876084 0.000000e+00 1434
9 TraesCS5A01G419200 chr7A 94.866 409 20 1 1897 2305 38740763 38740356 2.500000e-179 638
10 TraesCS5A01G419200 chr7A 87.255 204 17 8 2104 2305 699319596 699319792 8.290000e-55 224
11 TraesCS5A01G419200 chr3A 96.311 2277 78 5 2 2273 635317547 635315272 0.000000e+00 3735
12 TraesCS5A01G419200 chr3A 88.690 168 13 6 2138 2305 635315340 635315179 1.400000e-47 200
13 TraesCS5A01G419200 chr6A 93.259 2329 103 26 3 2305 516292698 516294998 0.000000e+00 3382
14 TraesCS5A01G419200 chr2A 92.529 2329 110 18 3 2305 677893982 677896272 0.000000e+00 3278
15 TraesCS5A01G419200 chr2A 83.242 364 44 8 1943 2305 372746364 372746017 3.700000e-83 318
16 TraesCS5A01G419200 chr1B 92.471 2311 144 23 3 2305 629313342 629311054 0.000000e+00 3277
17 TraesCS5A01G419200 chr1A 95.747 1975 71 8 3 1970 559594938 559592970 0.000000e+00 3169
18 TraesCS5A01G419200 chr4A 94.510 255 12 2 1897 2150 637832342 637832595 2.150000e-105 392
19 TraesCS5A01G419200 chr4A 96.450 169 6 0 2137 2305 637833733 637833901 1.740000e-71 279


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 TraesCS5A01G419200 chr5A 606691707 606694011 2304 True 4257.0 4257 100.0000 1 2305 1 chr5A.!!$R1 2304
1 TraesCS5A01G419200 chr5A 288263580 288265903 2323 False 1936.5 3675 97.0345 2 2305 2 chr5A.!!$F1 2303
2 TraesCS5A01G419200 chr7A 192628656 192630953 2297 True 3862.0 3862 96.9630 2 2305 1 chr7A.!!$R2 2303
3 TraesCS5A01G419200 chr7A 130560137 130562455 2318 True 3443.0 3443 93.6080 3 2305 1 chr7A.!!$R1 2302
4 TraesCS5A01G419200 chr7A 643630607 643632506 1899 True 3149.0 3149 96.5880 2 1902 1 chr7A.!!$R3 1900
5 TraesCS5A01G419200 chr7A 38740356 38742701 2345 True 2002.5 3367 95.8225 2 2305 2 chr7A.!!$R4 2303
6 TraesCS5A01G419200 chr7A 699317483 699319792 2309 False 1672.0 3120 91.2500 3 2305 2 chr7A.!!$F2 2302
7 TraesCS5A01G419200 chr7A 16875058 16876084 1026 False 1434.0 1434 92.1970 1295 2305 1 chr7A.!!$F1 1010
8 TraesCS5A01G419200 chr3A 635315179 635317547 2368 True 1967.5 3735 92.5005 2 2305 2 chr3A.!!$R1 2303
9 TraesCS5A01G419200 chr6A 516292698 516294998 2300 False 3382.0 3382 93.2590 3 2305 1 chr6A.!!$F1 2302
10 TraesCS5A01G419200 chr2A 677893982 677896272 2290 False 3278.0 3278 92.5290 3 2305 1 chr2A.!!$F1 2302
11 TraesCS5A01G419200 chr1B 629311054 629313342 2288 True 3277.0 3277 92.4710 3 2305 1 chr1B.!!$R1 2302
12 TraesCS5A01G419200 chr1A 559592970 559594938 1968 True 3169.0 3169 95.7470 3 1970 1 chr1A.!!$R1 1967
13 TraesCS5A01G419200 chr4A 637832342 637833901 1559 False 335.5 392 95.4800 1897 2305 2 chr4A.!!$F1 408

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
333 334 1.681264 TGCTTCTTCACAGTCGAGTGA 59.319 47.619 26.62 15.01 46.12 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2135 2.127708 GGTCCCCTGACTTCATACCAT 58.872 52.381 0.0 0.0 41.47 3.55 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
84 85 2.434336 TGACAGTGTACACAGGAAGCTT 59.566 45.455 27.06 0.00 0.00 3.74
333 334 1.681264 TGCTTCTTCACAGTCGAGTGA 59.319 47.619 26.62 15.01 46.12 3.41
394 395 4.860022 ACAAGGTATTCCAATTGAGGAGG 58.140 43.478 7.12 0.00 39.25 4.30
575 576 2.675844 CCGTGCGTGGATAGAAATTTGA 59.324 45.455 0.00 0.00 0.00 2.69
621 622 6.541641 GCAATCAGAGAATAGACCTCACAATT 59.458 38.462 0.00 0.00 33.25 2.32
622 623 7.466996 GCAATCAGAGAATAGACCTCACAATTG 60.467 40.741 3.24 3.24 33.79 2.32
695 696 2.619074 GCTAAAGCCTGGTTGGACTCAT 60.619 50.000 0.00 0.00 38.35 2.90
888 893 9.677567 TGTCTTCTTTCAAATACATAAGTTTGC 57.322 29.630 0.00 0.00 35.76 3.68
1092 1098 5.107375 GCATATTTTGTGTTGTTGCAGAAGG 60.107 40.000 0.00 0.00 0.00 3.46
1655 1705 1.665679 CTAGGTGGCGTTTGTATGCAG 59.334 52.381 0.00 0.00 38.06 4.41
1775 1825 6.918626 TGAAAAATCTGTGAACTTGTTGTCA 58.081 32.000 0.00 0.00 0.00 3.58
1812 1888 2.980568 TGTCGTGGTGAAAGTTCTGTT 58.019 42.857 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.701951 TCATCATCATGCAGCCTGTCTA 59.298 45.455 0.00 0.00 0.00 2.59
1 2 1.489230 TCATCATCATGCAGCCTGTCT 59.511 47.619 0.00 0.00 0.00 3.41
5 6 1.423921 TGGATCATCATCATGCAGCCT 59.576 47.619 0.00 0.00 0.00 4.58
84 85 0.447406 GCACTTGTATCGCACATGCA 59.553 50.000 4.49 0.00 41.07 3.96
333 334 3.407698 TGCCACACGATCTACAAAATGT 58.592 40.909 0.00 0.00 0.00 2.71
336 337 3.496884 GTCTTGCCACACGATCTACAAAA 59.503 43.478 0.00 0.00 0.00 2.44
345 346 1.336440 CCAAATTGTCTTGCCACACGA 59.664 47.619 0.00 0.00 0.00 4.35
394 395 3.950395 AGAGATAGCATTTCCTTGTTGCC 59.050 43.478 0.00 0.00 37.07 4.52
590 591 7.725844 TGAGGTCTATTCTCTGATTGCACTATA 59.274 37.037 0.00 0.00 32.78 1.31
591 592 6.552725 TGAGGTCTATTCTCTGATTGCACTAT 59.447 38.462 0.00 0.00 32.78 2.12
621 622 6.098838 ACTTGATACTTCTGATATGCTGACCA 59.901 38.462 0.00 0.00 0.00 4.02
622 623 6.423302 CACTTGATACTTCTGATATGCTGACC 59.577 42.308 0.00 0.00 0.00 4.02
695 696 1.185618 CCAACTCCGACCACTCCTCA 61.186 60.000 0.00 0.00 0.00 3.86
888 893 2.997986 GCCCTGCAATTCATGAACAAAG 59.002 45.455 11.07 6.32 0.00 2.77
1092 1098 5.447818 CCATCTTATGAAACCGCTTCTTGAC 60.448 44.000 0.00 0.00 34.86 3.18
1302 1350 8.482852 TCAACATCATACTCATGATCCTCTTA 57.517 34.615 0.00 0.00 46.88 2.10
1655 1705 4.722361 TTTTACCACAACACCAAGTTCC 57.278 40.909 0.00 0.00 38.74 3.62
1775 1825 5.863397 CCACGACAAATTCTTGCATACAAAT 59.137 36.000 0.00 0.00 35.84 2.32
1856 1932 7.543947 TTCACACAAGAAGATAGCACATATG 57.456 36.000 0.00 0.00 0.00 1.78
1970 2133 3.910627 GGTCCCCTGACTTCATACCATAT 59.089 47.826 0.00 0.00 41.47 1.78
1972 2135 2.127708 GGTCCCCTGACTTCATACCAT 58.872 52.381 0.00 0.00 41.47 3.55
2119 2366 5.178623 TGTCATTCGATACAACAGGTGTTTC 59.821 40.000 0.00 0.00 41.98 2.78


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

AutoCloner maintained by Alex Coulton.