Multiple sequence alignment - TraesCS1B01G406100

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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 TraesCS1B01G406100 chr1B 100.000 2201 0 0 1 2201 633734146 633736346 0 4065
1 TraesCS1B01G406100 chr2A 98.001 2201 44 0 1 2201 726901129 726903329 0 3821
2 TraesCS1B01G406100 chr3B 97.683 2201 51 0 1 2201 201569461 201571661 0 3783
3 TraesCS1B01G406100 chr3D 97.592 2201 52 1 1 2201 589258202 589260401 0 3770
4 TraesCS1B01G406100 chr7B 97.547 2201 53 1 1 2201 662732239 662730040 0 3764
5 TraesCS1B01G406100 chr7B 97.501 2201 54 1 1 2201 663094100 663096299 0 3759
6 TraesCS1B01G406100 chr5D 97.547 2201 53 1 1 2201 503250596 503248397 0 3764
7 TraesCS1B01G406100 chr3A 97.456 2201 54 2 1 2201 695645709 695643511 0 3753
8 TraesCS1B01G406100 chr7A 97.410 2201 56 1 1 2201 258305488 258307687 0 3747


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 TraesCS1B01G406100 chr1B 633734146 633736346 2200 False 4065 4065 100.000 1 2201 1 chr1B.!!$F1 2200
1 TraesCS1B01G406100 chr2A 726901129 726903329 2200 False 3821 3821 98.001 1 2201 1 chr2A.!!$F1 2200
2 TraesCS1B01G406100 chr3B 201569461 201571661 2200 False 3783 3783 97.683 1 2201 1 chr3B.!!$F1 2200
3 TraesCS1B01G406100 chr3D 589258202 589260401 2199 False 3770 3770 97.592 1 2201 1 chr3D.!!$F1 2200
4 TraesCS1B01G406100 chr7B 662730040 662732239 2199 True 3764 3764 97.547 1 2201 1 chr7B.!!$R1 2200
5 TraesCS1B01G406100 chr7B 663094100 663096299 2199 False 3759 3759 97.501 1 2201 1 chr7B.!!$F1 2200
6 TraesCS1B01G406100 chr5D 503248397 503250596 2199 True 3764 3764 97.547 1 2201 1 chr5D.!!$R1 2200
7 TraesCS1B01G406100 chr3A 695643511 695645709 2198 True 3753 3753 97.456 1 2201 1 chr3A.!!$R1 2200
8 TraesCS1B01G406100 chr7A 258305488 258307687 2199 False 3747 3747 97.410 1 2201 1 chr7A.!!$F1 2200

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
298 299 3.729965 CTGAGCTACAGGCCCAGCG 62.73 68.421 14.09 0.0 39.77 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1802 0.252696 TGGACTACCTGCACCTGGAT 60.253 55.0 0.0 0.0 37.04 3.41 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 3.771479 CCTTAGGAGTAGGTAACCCGTTT 59.229 47.826 0.00 0.00 35.12 3.60
298 299 3.729965 CTGAGCTACAGGCCCAGCG 62.730 68.421 14.09 0.00 39.77 5.18
353 354 6.405176 CCCTTCATTTCAGGTTAAGAAGATGC 60.405 42.308 0.00 0.00 35.67 3.91
378 379 4.577834 AGCGCCTTTCTCTCTATAAGAC 57.422 45.455 2.29 0.00 0.00 3.01
460 461 5.803020 AGACGACCTTTGCATTTTAGATC 57.197 39.130 0.00 0.00 0.00 2.75
533 534 8.965819 TGTTAAGCTTTTTATCATTCTGGCATA 58.034 29.630 3.20 0.00 0.00 3.14
880 882 4.513692 CGTGTAGGAACAAGGTTCAAATCA 59.486 41.667 10.86 2.59 37.36 2.57
887 889 5.983118 GGAACAAGGTTCAAATCATTCGTTT 59.017 36.000 10.86 0.00 0.00 3.60
943 945 7.309194 GCACTTCCACTTGACACCTATTTAAAT 60.309 37.037 5.89 5.89 0.00 1.40
1222 1224 2.275318 GAAAGGTCCTCTCAATGCTCG 58.725 52.381 0.00 0.00 0.00 5.03
1336 1338 1.158705 ACCTACAGCTCCAGGTGGT 59.841 57.895 13.84 3.36 46.90 4.16
1357 1359 0.965866 AAGAGCCGACATCGAGGTGA 60.966 55.000 7.79 0.00 43.02 4.02
1434 1436 5.416947 AGTAACTTTTATCCGTTGAGCGAT 58.583 37.500 0.00 0.00 44.77 4.58
1477 1480 2.677037 CGGATCACTAAGGCCGACTTTT 60.677 50.000 0.00 0.00 46.29 2.27
1531 1534 0.185901 TCCCTTCTGCCTTTGCACTT 59.814 50.000 0.00 0.00 44.23 3.16
1577 1580 0.968405 GAAACCTTTGCATGCCTCCA 59.032 50.000 16.68 0.00 0.00 3.86
1599 1602 1.131928 ACCTTTTGGGAGGCCTACGT 61.132 55.000 9.48 0.00 46.08 3.57
1743 1746 1.002134 GCCTTCCACCTAAGCTGCA 60.002 57.895 1.02 0.00 0.00 4.41
1799 1802 7.180408 ACAGTAAAGCTTCATAGGGTCTTTCTA 59.820 37.037 0.00 0.00 0.00 2.10
1818 1821 0.252696 ATCCAGGTGCAGGTAGTCCA 60.253 55.000 0.00 0.00 35.89 4.02
1835 1838 2.417933 GTCCACATCTTCACAGACATGC 59.582 50.000 0.00 0.00 0.00 4.06
1886 1889 1.734163 CCCAGATCGTTACGCCTTTT 58.266 50.000 0.00 0.00 0.00 2.27
1920 1923 4.360951 ACTTACCCGACAAGGAATTTCA 57.639 40.909 0.00 0.00 45.00 2.69
2066 2069 1.610038 TCTTACGACTTTGCGGAGACA 59.390 47.619 0.00 0.00 35.12 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.979678 ACTCCTAAGGGTCAAAGCAAGA 59.020 45.455 0.00 0.00 0.00 3.02
41 42 8.840321 GCAATAGAAATAGAAACAAGGATAGCA 58.160 33.333 0.00 0.00 0.00 3.49
220 221 2.511452 CGAATCCCTCCTCGCCCAT 61.511 63.158 0.00 0.00 0.00 4.00
244 245 0.039798 GCTACGAACCACAGTGTCGA 60.040 55.000 17.84 3.94 0.00 4.20
533 534 0.253044 TCCTGCGGCAAAATAGCTCT 59.747 50.000 3.44 0.00 34.17 4.09
880 882 3.941483 CTGAGGCATCCTAACAAACGAAT 59.059 43.478 0.00 0.00 31.76 3.34
887 889 0.107508 GCAGCTGAGGCATCCTAACA 60.108 55.000 20.43 0.00 41.70 2.41
1109 1111 1.202698 GCCAAGTGCGGAGAGGATAAT 60.203 52.381 0.00 0.00 0.00 1.28
1222 1224 1.145377 ATATCCGGTGTGGGCGTTC 59.855 57.895 0.00 0.00 38.76 3.95
1336 1338 0.965866 ACCTCGATGTCGGCTCTTCA 60.966 55.000 2.25 0.00 40.29 3.02
1357 1359 0.395312 ACATCGACGGGAAGGTTTGT 59.605 50.000 0.00 0.00 0.00 2.83
1477 1480 2.282251 ACCCGTCGAGCAGAGACA 60.282 61.111 0.00 0.00 38.46 3.41
1577 1580 2.092592 CGTAGGCCTCCCAAAAGGTAAT 60.093 50.000 9.68 0.00 38.79 1.89
1599 1602 4.942944 TCAGGTAGACAGTTTCTATGGGA 58.057 43.478 0.00 0.00 39.13 4.37
1648 1651 4.279145 AGAGCTCGGATTCTAACCTTGTA 58.721 43.478 8.37 0.00 0.00 2.41
1743 1746 4.198087 GCTTTGGGCCTTTCCTGT 57.802 55.556 4.53 0.00 34.39 4.00
1799 1802 0.252696 TGGACTACCTGCACCTGGAT 60.253 55.000 0.00 0.00 37.04 3.41
1818 1821 4.767578 ATAGGCATGTCTGTGAAGATGT 57.232 40.909 10.89 0.00 0.00 3.06
1835 1838 2.035321 GAGAGAGGCTCGGTGAAATAGG 59.965 54.545 9.22 0.00 35.36 2.57
1886 1889 1.005867 GTAAGTTCCGACCCGCACA 60.006 57.895 0.00 0.00 0.00 4.57
1920 1923 6.483640 CGTAACTATAACGGTCCTAAGGTAGT 59.516 42.308 0.00 0.00 36.71 2.73
2066 2069 4.356289 GCGACTGTTTACCAAAAACACAT 58.644 39.130 0.00 0.00 35.45 3.21


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

AutoCloner maintained by Alex Coulton.