Multiple sequence alignment - TraesCS5A01G436700

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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 TraesCS5A01G436700 chr5A 100.000 2497 0 0 1 2497 619267012 619264516 0 4612
1 TraesCS5A01G436700 chrUn 97.759 2499 51 5 1 2497 93408990 93411485 0 4300
2 TraesCS5A01G436700 chrUn 97.674 2322 50 4 1 2320 216517961 216520280 0 3986
3 TraesCS5A01G436700 chr5D 97.598 2498 57 3 1 2497 503218859 503216364 0 4277
4 TraesCS5A01G436700 chr2D 97.559 2499 57 4 1 2497 272793252 272795748 0 4274
5 TraesCS5A01G436700 chr3B 97.399 2499 60 5 1 2497 201527665 201525170 0 4250
6 TraesCS5A01G436700 chr3A 96.999 2499 72 3 1 2497 672909366 672911863 0 4196
7 TraesCS5A01G436700 chr6A 96.603 2502 77 5 1 2497 260115639 260118137 0 4143
8 TraesCS5A01G436700 chr6D 97.804 2322 47 4 1 2320 168255567 168253248 0 4002
9 TraesCS5A01G436700 chr6D 97.524 2100 47 4 399 2497 168251781 168249686 0 3585
10 TraesCS5A01G436700 chr2B 97.506 401 10 0 55 455 771170104 771170504 0 686


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 TraesCS5A01G436700 chr5A 619264516 619267012 2496 True 4612.0 4612 100.000 1 2497 1 chr5A.!!$R1 2496
1 TraesCS5A01G436700 chrUn 93408990 93411485 2495 False 4300.0 4300 97.759 1 2497 1 chrUn.!!$F1 2496
2 TraesCS5A01G436700 chrUn 216517961 216520280 2319 False 3986.0 3986 97.674 1 2320 1 chrUn.!!$F2 2319
3 TraesCS5A01G436700 chr5D 503216364 503218859 2495 True 4277.0 4277 97.598 1 2497 1 chr5D.!!$R1 2496
4 TraesCS5A01G436700 chr2D 272793252 272795748 2496 False 4274.0 4274 97.559 1 2497 1 chr2D.!!$F1 2496
5 TraesCS5A01G436700 chr3B 201525170 201527665 2495 True 4250.0 4250 97.399 1 2497 1 chr3B.!!$R1 2496
6 TraesCS5A01G436700 chr3A 672909366 672911863 2497 False 4196.0 4196 96.999 1 2497 1 chr3A.!!$F1 2496
7 TraesCS5A01G436700 chr6A 260115639 260118137 2498 False 4143.0 4143 96.603 1 2497 1 chr6A.!!$F1 2496
8 TraesCS5A01G436700 chr6D 168249686 168255567 5881 True 3793.5 4002 97.664 1 2497 2 chr6D.!!$R1 2496

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
186 187 0.759436 GAGGGGGAGGTCATAAGCGA 60.759 60.0 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 1960 0.923358 TCCCCCAATTTGCGACCTAT 59.077 50.0 0.0 0.0 0.0 2.57 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
41 42 7.271868 GGCGAAACATTTATACAAAACACCTAC 59.728 37.037 0.00 0.00 0.00 3.18
53 54 2.203728 ACCTACCCCGAGCACACA 60.204 61.111 0.00 0.00 0.00 3.72
143 144 6.459848 CGTTGTGGTAAAGGTTGTAATTCCAA 60.460 38.462 0.00 0.00 0.00 3.53
186 187 0.759436 GAGGGGGAGGTCATAAGCGA 60.759 60.000 0.00 0.00 0.00 4.93
200 201 6.142958 GGTCATAAGCGACTATACCGTAAAAC 59.857 42.308 0.00 0.00 36.12 2.43
208 209 7.332678 AGCGACTATACCGTAAAACAGATTTTT 59.667 33.333 0.00 0.00 38.91 1.94
501 502 7.345653 TCACTGATCCAATTTGACTACCTCTAT 59.654 37.037 0.00 0.00 0.00 1.98
518 519 4.901849 CCTCTATGGGATAGACCTCAACAA 59.098 45.833 0.00 0.00 36.98 2.83
805 806 9.448294 GAAGTATCGACGTAATTTCATAGAGTT 57.552 33.333 0.00 0.00 0.00 3.01
826 827 8.797438 AGAGTTATTCGATCTGAATGCTACATA 58.203 33.333 17.47 0.36 46.72 2.29
1119 1120 5.147330 ACATAGAAATCACACGTGGAAGA 57.853 39.130 21.57 14.78 0.00 2.87
1241 1242 5.264395 AGTATCCCAAAACTGCTTAGCAAT 58.736 37.500 8.68 0.00 38.41 3.56
1246 1247 4.458989 CCCAAAACTGCTTAGCAATAGTCA 59.541 41.667 8.68 0.00 38.41 3.41
1726 1730 5.934043 CGAGATATTGGACATAGAATGCCAA 59.066 40.000 14.05 14.05 44.45 4.52
1739 1743 9.034800 ACATAGAATGCCAATCTTTAAAAAGGA 57.965 29.630 2.77 0.00 36.67 3.36
1801 1806 6.690098 CGAATCCTTTTGTAGCTCATCATTTG 59.310 38.462 0.00 0.00 0.00 2.32
1854 1859 9.674068 GAAGGAGGAGAAAGAAACAATAGTAAT 57.326 33.333 0.00 0.00 0.00 1.89
1863 1868 6.134535 AGAAACAATAGTAATGTGGTCCCA 57.865 37.500 0.00 0.00 0.00 4.37
1914 1919 4.996758 TGGCCATACAATCGTGATTCATAG 59.003 41.667 0.00 0.00 0.00 2.23
1979 1984 1.548269 GTCGCAAATTGGGGGAATTCA 59.452 47.619 10.15 0.00 32.76 2.57
2116 5509 2.435437 TGTAGGCGGGGAATAACCTTAC 59.565 50.000 0.00 0.00 38.98 2.34
2188 5581 3.876309 AAAGTGGGCTAAGGAAACTCA 57.124 42.857 0.00 0.00 42.68 3.41
2262 5655 4.393680 GCACAAAAACGTATCCCTATGTCA 59.606 41.667 0.00 0.00 0.00 3.58
2331 5724 8.743085 ACTACGAGGAAACTGTTATGATACTA 57.257 34.615 0.00 0.00 44.43 1.82
2335 5728 8.308931 ACGAGGAAACTGTTATGATACTAAACA 58.691 33.333 0.00 0.00 44.43 2.83
2348 5741 7.315066 TGATACTAAACATCATGCCCTATCA 57.685 36.000 0.00 0.00 0.00 2.15
2371 5764 7.000472 TCAAGCATCTTATCCCATCTTAAAGG 59.000 38.462 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.669569 CCTTGTGTGTGCTCGGGG 60.670 66.667 0.00 0.00 0.00 5.73
53 54 1.282157 GCCTGTCTATGGTTCCCTTGT 59.718 52.381 0.00 0.00 0.00 3.16
64 65 4.574674 TGGATTTCACTTGCCTGTCTAT 57.425 40.909 0.00 0.00 0.00 1.98
143 144 2.024414 GCCTTGCGGTAATGATTCCTT 58.976 47.619 0.00 0.00 0.00 3.36
186 187 8.437742 CGTCAAAAATCTGTTTTACGGTATAGT 58.562 33.333 0.00 0.00 36.42 2.12
208 209 6.316140 CCAGATATGTCTTTTTGATTCCGTCA 59.684 38.462 0.00 0.00 30.42 4.35
472 473 6.070021 AGGTAGTCAAATTGGATCAGTGATCA 60.070 38.462 29.56 14.32 40.50 2.92
518 519 6.588719 TGCTGCCATTACTCAATAGTTTTT 57.411 33.333 0.00 0.00 37.15 1.94
746 747 4.807783 GGGTAACGTAGGAGACATCCCTG 61.808 56.522 0.00 0.00 42.56 4.45
805 806 9.981114 TTCTTTATGTAGCATTCAGATCGAATA 57.019 29.630 10.91 0.00 42.70 1.75
826 827 5.759059 TCCATCATCTGGCTTATGTTCTTT 58.241 37.500 0.00 0.00 45.52 2.52
1119 1120 1.141858 GCTCTAGCTAATTGCCCACCT 59.858 52.381 0.00 0.00 44.23 4.00
1150 1151 5.392380 CCTCTTTTGCAATGAGTTTCGCTAT 60.392 40.000 21.02 0.00 32.43 2.97
1241 1242 5.512404 CCAACATTACCCACTTGTCTGACTA 60.512 44.000 9.51 0.09 0.00 2.59
1246 1247 2.225017 CCCCAACATTACCCACTTGTCT 60.225 50.000 0.00 0.00 0.00 3.41
1280 1281 1.807814 AGATCCGGCTCTACCCAAAT 58.192 50.000 5.89 0.00 33.26 2.32
1801 1806 5.705609 TGACCTTTTCTATCTTTGCCAAC 57.294 39.130 0.00 0.00 0.00 3.77
1854 1859 1.626356 GCTAGATGCCTGGGACCACA 61.626 60.000 0.00 0.00 35.15 4.17
1863 1868 2.370189 GTGGGTAGAATGCTAGATGCCT 59.630 50.000 0.00 0.00 42.00 4.75
1914 1919 9.841295 TGTAAATAGGTATATGTTCCTTTCCAC 57.159 33.333 0.00 0.00 35.51 4.02
1955 1960 0.923358 TCCCCCAATTTGCGACCTAT 59.077 50.000 0.00 0.00 0.00 2.57
2095 5488 1.587066 AAGGTTATTCCCCGCCTACA 58.413 50.000 0.00 0.00 36.75 2.74
2262 5655 6.272822 AGAACTCTTTGTGCTTTGAAAACT 57.727 33.333 0.00 0.00 27.44 2.66
2331 5724 3.634504 TGCTTGATAGGGCATGATGTTT 58.365 40.909 0.00 0.00 33.23 2.83
2348 5741 6.774656 CACCTTTAAGATGGGATAAGATGCTT 59.225 38.462 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.