Multiple sequence alignment - TraesCS5B01G444400

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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 TraesCS5B01G444400 chr5B 100.000 2356 0 0 1 2356 617032708 617035063 0 4351
1 TraesCS5B01G444400 chr2B 97.502 2362 52 5 1 2356 449213739 449211379 0 4028
2 TraesCS5B01G444400 chr2B 96.860 2357 68 4 4 2356 474915890 474913536 0 3938
3 TraesCS5B01G444400 chr5D 97.375 2362 54 6 1 2356 503225671 503223312 0 4012
4 TraesCS5B01G444400 chr5D 96.827 2364 65 6 1 2356 503235987 503233626 0 3941
5 TraesCS5B01G444400 chr3A 97.163 2362 59 6 1 2356 66010170 66012529 0 3984
6 TraesCS5B01G444400 chr1B 97.079 2362 57 7 1 2356 619189737 619187382 0 3969
7 TraesCS5B01G444400 chr6A 97.038 2363 59 6 1 2356 84403953 84401595 0 3965
8 TraesCS5B01G444400 chr1A 96.952 2362 65 5 1 2356 278526787 278529147 0 3956
9 TraesCS5B01G444400 chr3B 96.825 2362 63 6 1 2356 6005172 6002817 0 3936


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 TraesCS5B01G444400 chr5B 617032708 617035063 2355 False 4351 4351 100.000 1 2356 1 chr5B.!!$F1 2355
1 TraesCS5B01G444400 chr2B 449211379 449213739 2360 True 4028 4028 97.502 1 2356 1 chr2B.!!$R1 2355
2 TraesCS5B01G444400 chr2B 474913536 474915890 2354 True 3938 3938 96.860 4 2356 1 chr2B.!!$R2 2352
3 TraesCS5B01G444400 chr5D 503223312 503225671 2359 True 4012 4012 97.375 1 2356 1 chr5D.!!$R1 2355
4 TraesCS5B01G444400 chr5D 503233626 503235987 2361 True 3941 3941 96.827 1 2356 1 chr5D.!!$R2 2355
5 TraesCS5B01G444400 chr3A 66010170 66012529 2359 False 3984 3984 97.163 1 2356 1 chr3A.!!$F1 2355
6 TraesCS5B01G444400 chr1B 619187382 619189737 2355 True 3969 3969 97.079 1 2356 1 chr1B.!!$R1 2355
7 TraesCS5B01G444400 chr6A 84401595 84403953 2358 True 3965 3965 97.038 1 2356 1 chr6A.!!$R1 2355
8 TraesCS5B01G444400 chr1A 278526787 278529147 2360 False 3956 3956 96.952 1 2356 1 chr1A.!!$F1 2355
9 TraesCS5B01G444400 chr3B 6002817 6005172 2355 True 3936 3936 96.825 1 2356 1 chr3B.!!$R1 2355

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
752 756 1.31569 GGACCCGTACATCTCGATCA 58.684 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 1739 0.904394 TTGATGAAAAGGGGCTGGGC 60.904 55.0 0.0 0.0 0.0 5.36 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
104 105 7.578852 TCGTATTCGATGAAAGTCGTATGTAT 58.421 34.615 0.00 0.00 41.35 2.29
238 241 2.407090 CTCTTTCACGCTCATGTCACA 58.593 47.619 0.00 0.00 0.00 3.58
331 334 5.509501 TGGTTAACCGTATTCTGAAAGACGT 60.510 40.000 19.65 0.00 46.01 4.34
385 389 4.613622 CGAGCCGTGAAAAAGATTCAACAT 60.614 41.667 0.00 0.00 0.00 2.71
429 433 5.752892 TTGGTTTTACGTCAAGCAATACA 57.247 34.783 16.82 0.93 36.85 2.29
444 448 7.071196 TCAAGCAATACATAGAGTAACTCCCAT 59.929 37.037 0.00 0.00 36.05 4.00
495 499 6.661304 AAAAGGATTGATGCAGAAAGTTCT 57.339 33.333 0.00 0.00 38.25 3.01
736 740 8.580720 AGAATCTATGTATGTAGACACATGGAC 58.419 37.037 0.00 0.00 45.17 4.02
752 756 1.315690 GGACCCGTACATCTCGATCA 58.684 55.000 0.00 0.00 0.00 2.92
853 857 4.033009 TCATGATCAACTAAGCCCTCTCA 58.967 43.478 0.00 0.00 0.00 3.27
953 957 9.463443 GATTCCGTAAATATCCCATTTCAAAAG 57.537 33.333 0.00 0.00 0.00 2.27
964 968 6.578023 TCCCATTTCAAAAGTCGAAACAATT 58.422 32.000 0.00 0.00 35.31 2.32
973 977 4.830826 AGTCGAAACAATTGGGACTTTC 57.169 40.909 10.83 9.41 0.00 2.62
1008 1012 9.988815 GGATGTAGTTACTAATTCATGATCTGT 57.011 33.333 0.00 0.00 0.00 3.41
1291 1295 7.602517 AATTTCCAAACGAACAATTTCAACA 57.397 28.000 0.00 0.00 0.00 3.33
1416 1423 6.012157 TCGTATTAATAGCTACTCTAGGGGGT 60.012 42.308 0.00 0.00 0.00 4.95
1438 1445 6.071840 GGGTATGTTTTTATGTGGTGCTAACA 60.072 38.462 0.00 0.00 0.00 2.41
1556 1563 8.669243 GGCTACTATGAAATATTTACTCATGGC 58.331 37.037 10.20 6.31 32.87 4.40
1698 1709 6.460123 CCAGGAATTTCAGTTGCGCTTATATT 60.460 38.462 9.73 0.00 0.00 1.28
1728 1739 4.825085 TGTAGGACTTGGGTTTAAGCTTTG 59.175 41.667 3.20 0.00 0.00 2.77
1900 1911 8.512138 CGACCAAGATAGAACTTTTACCAAAAT 58.488 33.333 0.00 0.00 0.00 1.82
2224 2239 1.207329 GACTTGCTCCTACGGAACCAT 59.793 52.381 0.00 0.00 0.00 3.55
2234 2249 0.953960 ACGGAACCATGGTCGAAAGC 60.954 55.000 27.30 10.18 0.00 3.51
2336 2351 7.139896 TCGATTTCGAAAAAGAATGGATTCA 57.860 32.000 15.66 0.00 46.30 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 1.561542 GAAAGATCTCCCTCCAAGCCA 59.438 52.381 0.00 0.00 0.00 4.75
172 175 7.923414 TTCTAAGGGCTAAAATCACTTCTTC 57.077 36.000 0.00 0.00 0.00 2.87
175 178 8.793592 TCTTTTTCTAAGGGCTAAAATCACTTC 58.206 33.333 0.00 0.00 0.00 3.01
495 499 9.973661 TTCCTTGTTTAGATCCTATTTCAATCA 57.026 29.630 0.00 0.00 0.00 2.57
651 655 2.103771 GCCTCTGCCATTCTATGAGTCA 59.896 50.000 0.00 0.00 0.00 3.41
736 740 3.710326 TTTCTGATCGAGATGTACGGG 57.290 47.619 0.00 0.00 0.00 5.28
825 829 7.071698 AGAGGGCTTAGTTGATCATGATTTCTA 59.928 37.037 10.14 9.86 0.00 2.10
853 857 4.862641 TCTTATTCTTAGGCAAGCCCTT 57.137 40.909 7.62 0.00 43.06 3.95
953 957 3.608474 CGGAAAGTCCCAATTGTTTCGAC 60.608 47.826 4.43 4.65 31.13 4.20
964 968 0.618458 CCAATCTCCGGAAAGTCCCA 59.382 55.000 5.23 0.00 31.13 4.37
973 977 4.939052 AGTAACTACATCCAATCTCCGG 57.061 45.455 0.00 0.00 0.00 5.14
1400 1407 5.414133 AAACATACCCCCTAGAGTAGCTA 57.586 43.478 0.00 0.00 0.00 3.32
1416 1423 9.988815 AAATTGTTAGCACCACATAAAAACATA 57.011 25.926 0.00 0.00 0.00 2.29
1556 1563 3.204526 CAGAATAGAAGAGCTTGCCCAG 58.795 50.000 0.00 0.00 0.00 4.45
1698 1709 2.902608 ACCCAAGTCCTACAGTGATGA 58.097 47.619 0.00 0.00 0.00 2.92
1728 1739 0.904394 TTGATGAAAAGGGGCTGGGC 60.904 55.000 0.00 0.00 0.00 5.36
2224 2239 4.097135 TGACTTTTTCAATGCTTTCGACCA 59.903 37.500 0.00 0.00 0.00 4.02
2234 2249 7.043192 GGTTGTGAATGACTGACTTTTTCAATG 60.043 37.037 0.00 0.00 32.21 2.82


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

AutoCloner maintained by Alex Coulton.