Multiple sequence alignment - TraesCS5A01G499600

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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 TraesCS5A01G499600 chr5A 100.000 2303 0 0 1 2303 666200207 666197905 0 4253
1 TraesCS5A01G499600 chr6D 95.693 2322 77 10 1 2303 25731607 25733924 0 3712
2 TraesCS5A01G499600 chr3D 95.211 2318 76 11 2 2300 334442 336743 0 3633
3 TraesCS5A01G499600 chr3D 94.727 1024 35 7 1285 2303 610059709 610058700 0 1574
4 TraesCS5A01G499600 chr1D 95.134 2322 78 11 1 2303 316243661 316241356 0 3629
5 TraesCS5A01G499600 chr4D 95.041 2319 80 11 1 2300 491381798 491384100 0 3613
6 TraesCS5A01G499600 chr5D 94.807 2311 85 11 1 2303 552028737 552026454 0 3570
7 TraesCS5A01G499600 chr5D 95.496 1754 59 6 2 1751 555413844 555415581 0 2784
8 TraesCS5A01G499600 chr5D 95.485 753 28 1 1 753 27863376 27864122 0 1197
9 TraesCS5A01G499600 chr5D 97.547 530 12 1 1772 2300 555415558 555416087 0 905
10 TraesCS5A01G499600 chr2D 94.626 2326 85 16 2 2303 130078826 130076517 0 3567
11 TraesCS5A01G499600 chr4A 94.166 2314 107 9 1 2302 731637041 731634744 0 3500
12 TraesCS5A01G499600 chr4A 93.980 2309 94 10 2 2303 478227440 478229710 0 3452
13 TraesCS5A01G499600 chr4A 95.661 991 42 1 1 990 731191387 731190397 0 1591
14 TraesCS5A01G499600 chr7B 93.458 2308 120 12 1 2303 619624251 619626532 0 3397
15 TraesCS5A01G499600 chr7B 93.369 2081 108 12 1 2076 672859253 672857198 0 3051
16 TraesCS5A01G499600 chr7B 92.081 1629 106 15 1 1624 730310453 730312063 0 2272
17 TraesCS5A01G499600 chr7B 92.105 684 45 5 1618 2300 43572063 43572738 0 955
18 TraesCS5A01G499600 chr6B 92.129 2325 145 16 1 2302 630833637 630831328 0 3245
19 TraesCS5A01G499600 chr2B 94.487 907 48 2 1399 2303 191887813 191886907 0 1397
20 TraesCS5A01G499600 chr2A 94.538 769 38 4 1536 2302 695189713 695190479 0 1184


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 TraesCS5A01G499600 chr5A 666197905 666200207 2302 True 4253.0 4253 100.0000 1 2303 1 chr5A.!!$R1 2302
1 TraesCS5A01G499600 chr6D 25731607 25733924 2317 False 3712.0 3712 95.6930 1 2303 1 chr6D.!!$F1 2302
2 TraesCS5A01G499600 chr3D 334442 336743 2301 False 3633.0 3633 95.2110 2 2300 1 chr3D.!!$F1 2298
3 TraesCS5A01G499600 chr3D 610058700 610059709 1009 True 1574.0 1574 94.7270 1285 2303 1 chr3D.!!$R1 1018
4 TraesCS5A01G499600 chr1D 316241356 316243661 2305 True 3629.0 3629 95.1340 1 2303 1 chr1D.!!$R1 2302
5 TraesCS5A01G499600 chr4D 491381798 491384100 2302 False 3613.0 3613 95.0410 1 2300 1 chr4D.!!$F1 2299
6 TraesCS5A01G499600 chr5D 552026454 552028737 2283 True 3570.0 3570 94.8070 1 2303 1 chr5D.!!$R1 2302
7 TraesCS5A01G499600 chr5D 555413844 555416087 2243 False 1844.5 2784 96.5215 2 2300 2 chr5D.!!$F2 2298
8 TraesCS5A01G499600 chr5D 27863376 27864122 746 False 1197.0 1197 95.4850 1 753 1 chr5D.!!$F1 752
9 TraesCS5A01G499600 chr2D 130076517 130078826 2309 True 3567.0 3567 94.6260 2 2303 1 chr2D.!!$R1 2301
10 TraesCS5A01G499600 chr4A 731634744 731637041 2297 True 3500.0 3500 94.1660 1 2302 1 chr4A.!!$R2 2301
11 TraesCS5A01G499600 chr4A 478227440 478229710 2270 False 3452.0 3452 93.9800 2 2303 1 chr4A.!!$F1 2301
12 TraesCS5A01G499600 chr4A 731190397 731191387 990 True 1591.0 1591 95.6610 1 990 1 chr4A.!!$R1 989
13 TraesCS5A01G499600 chr7B 619624251 619626532 2281 False 3397.0 3397 93.4580 1 2303 1 chr7B.!!$F2 2302
14 TraesCS5A01G499600 chr7B 672857198 672859253 2055 True 3051.0 3051 93.3690 1 2076 1 chr7B.!!$R1 2075
15 TraesCS5A01G499600 chr7B 730310453 730312063 1610 False 2272.0 2272 92.0810 1 1624 1 chr7B.!!$F3 1623
16 TraesCS5A01G499600 chr7B 43572063 43572738 675 False 955.0 955 92.1050 1618 2300 1 chr7B.!!$F1 682
17 TraesCS5A01G499600 chr6B 630831328 630833637 2309 True 3245.0 3245 92.1290 1 2302 1 chr6B.!!$R1 2301
18 TraesCS5A01G499600 chr2B 191886907 191887813 906 True 1397.0 1397 94.4870 1399 2303 1 chr2B.!!$R1 904
19 TraesCS5A01G499600 chr2A 695189713 695190479 766 False 1184.0 1184 94.5380 1536 2302 1 chr2A.!!$F1 766

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
314 329 1.090728 TTGTTGTTGCAGCGAACTCA 58.909 45.0 13.7 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2009 1.966354 CTCCTCCCATCATCGTCATCA 59.034 52.381 0.0 0.0 0.0 3.07 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
204 212 2.534990 CTCTCCCTCTCCTGTCTGTTT 58.465 52.381 0.00 0.00 0.00 2.83
308 323 1.210870 ATGCTTTTGTTGTTGCAGCG 58.789 45.000 0.00 0.00 38.87 5.18
314 329 1.090728 TTGTTGTTGCAGCGAACTCA 58.909 45.000 13.70 0.00 0.00 3.41
339 354 6.250711 TGACACTGTGATAGACCCTAGTTTA 58.749 40.000 15.86 0.00 0.00 2.01
417 432 3.740764 GCAAGTTTGTGGCATTTGAAGGA 60.741 43.478 0.00 0.00 0.00 3.36
516 534 6.092122 TGAATTTCTGCTATGTAGTGGAAACG 59.908 38.462 0.00 0.00 33.03 3.60
524 542 3.102052 TGTAGTGGAAACGGAGTGTTC 57.898 47.619 0.00 0.00 45.00 3.18
537 555 3.695816 GGAGTGTTCAGTTGCTGTTTTC 58.304 45.455 0.00 0.00 32.61 2.29
780 806 3.035363 TGAACTGTGGTGTTCTGGAGTA 58.965 45.455 8.52 0.00 44.63 2.59
873 900 3.477210 CTTGGTAGAGCCCAGGATAAC 57.523 52.381 0.00 0.00 33.59 1.89
903 930 2.041620 TGGGATAGAGGCTGCAAAACTT 59.958 45.455 0.50 0.00 0.00 2.66
1062 1089 1.889545 AGAAGCAACTTGAGGAGCAC 58.110 50.000 0.00 0.00 0.00 4.40
1096 1123 6.600822 TGAGCTTCAAATGGAGAATCTTAAGG 59.399 38.462 1.85 0.00 33.73 2.69
1133 1160 2.027745 GGTGCATCCTTCAGAGTCAAGA 60.028 50.000 0.00 0.00 0.00 3.02
1161 1188 4.751767 AATCCAAAACACAAAGAAGGCA 57.248 36.364 0.00 0.00 0.00 4.75
1209 1236 6.999950 AGACCTCCTTAAAGAAGAGAAGAAC 58.000 40.000 0.00 0.00 34.25 3.01
1507 1541 5.651139 CCCAAATATTATCCTGATGCTGAGG 59.349 44.000 0.00 0.00 0.00 3.86
1576 1612 7.138081 TGCAGTTTATTTCTGTGTGTTGTATG 58.862 34.615 0.00 0.00 35.60 2.39
1715 1753 4.164822 AGCACATGTACACTGAAATTGC 57.835 40.909 0.00 4.45 0.00 3.56
1766 1804 4.077300 TCTCACTGAGATTGCAAACACT 57.923 40.909 1.71 3.36 33.35 3.55
1767 1805 4.454678 TCTCACTGAGATTGCAAACACTT 58.545 39.130 1.71 0.00 33.35 3.16
1800 1866 6.625362 TGACAGAACTGAATCTCACATAGAC 58.375 40.000 8.87 0.00 36.93 2.59
1943 2009 1.827969 CACCTCCTCTTCGTCTCCATT 59.172 52.381 0.00 0.00 0.00 3.16
2209 2276 1.306642 TTCTCCTCAGTCGTCGCCTC 61.307 60.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
204 212 4.106324 CCCTAACCCTAACCCTAGAACAA 58.894 47.826 0.00 0.0 0.00 2.83
308 323 5.105752 GGTCTATCACAGTGTCATGAGTTC 58.894 45.833 0.00 0.0 0.00 3.01
314 329 4.873010 ACTAGGGTCTATCACAGTGTCAT 58.127 43.478 0.00 0.0 0.00 3.06
339 354 2.040813 AGATTCAGTCACAAGCCCACAT 59.959 45.455 0.00 0.0 0.00 3.21
417 432 1.356124 ATCTCCTGCCAGTGTCAGTT 58.644 50.000 0.00 0.0 0.00 3.16
516 534 3.489229 GGAAAACAGCAACTGAACACTCC 60.489 47.826 0.78 0.0 35.18 3.85
524 542 5.234972 GGAAAATTCAGGAAAACAGCAACTG 59.765 40.000 0.00 0.0 37.52 3.16
700 726 6.169800 ACACCACAGTTAACAAGCAAATTTT 58.830 32.000 8.61 0.0 0.00 1.82
701 727 5.729510 ACACCACAGTTAACAAGCAAATTT 58.270 33.333 8.61 0.0 0.00 1.82
828 855 6.233434 GTTCTGCTCATGATACATATCCCAA 58.767 40.000 0.00 0.0 31.71 4.12
873 900 0.894141 CCTCTATCCCATGAGCCTCG 59.106 60.000 0.00 0.0 0.00 4.63
903 930 4.383552 GCCAGAGAATCAAGCTCCTTCTAA 60.384 45.833 5.62 0.0 37.82 2.10
1062 1089 3.611113 CCATTTGAAGCTCAATCTTTGCG 59.389 43.478 0.00 0.0 36.11 4.85
1096 1123 4.370364 TGCACCTTTGTTCTTTCTTGAC 57.630 40.909 0.00 0.0 0.00 3.18
1154 1181 3.110705 TCTAGCTCCTTCATTGCCTTCT 58.889 45.455 0.00 0.0 0.00 2.85
1161 1188 3.037549 CTCCACCTCTAGCTCCTTCATT 58.962 50.000 0.00 0.0 0.00 2.57
1209 1236 2.753452 AGCAATGACATTCTCCAGCTTG 59.247 45.455 0.00 0.0 0.00 4.01
1507 1541 7.656542 AGTTCTTAACTTAACTTAGCACCAGTC 59.343 37.037 0.00 0.0 39.04 3.51
1540 1574 7.335422 ACAGAAATAAACTGCATCAGACTTAGG 59.665 37.037 0.29 0.0 38.74 2.69
1576 1612 5.938438 AACAGATCTCAGCAAGAACTTTC 57.062 39.130 0.00 0.0 35.09 2.62
1702 1740 5.822519 AGTGTCTTTGAGCAATTTCAGTGTA 59.177 36.000 0.00 0.0 0.00 2.90
1715 1753 9.046296 AGTTATGTCAGTTTAAGTGTCTTTGAG 57.954 33.333 0.00 0.0 0.00 3.02
1766 1804 8.908786 AGATTCAGTTCTGTCAGTTTATCAAA 57.091 30.769 0.00 0.0 0.00 2.69
1767 1805 8.150296 TGAGATTCAGTTCTGTCAGTTTATCAA 58.850 33.333 0.00 0.0 0.00 2.57
1800 1866 5.547465 TCAGTTACAACAGTTATCACCAGG 58.453 41.667 0.00 0.0 0.00 4.45
1943 2009 1.966354 CTCCTCCCATCATCGTCATCA 59.034 52.381 0.00 0.0 0.00 3.07
2209 2276 2.419851 GCATCAGAAGAGGTGAGGAAGG 60.420 54.545 0.00 0.0 0.00 3.46


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

AutoCloner maintained by Alex Coulton.