Multiple sequence alignment - TraesCS6D01G269500

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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 TraesCS6D01G269500 chr6D 100.000 3702 0 0 1 3702 379571213 379574914 0.000000e+00 6837
1 TraesCS6D01G269500 chr6B 96.106 2748 97 7 961 3702 567399458 567396715 0.000000e+00 4473
2 TraesCS6D01G269500 chr6B 93.177 894 55 5 1 892 567400353 567399464 0.000000e+00 1308
3 TraesCS6D01G269500 chr6A 97.712 2185 47 3 1 2183 521454783 521452600 0.000000e+00 3755
4 TraesCS6D01G269500 chr6A 96.952 1542 40 4 2167 3702 521452243 521450703 0.000000e+00 2580
5 TraesCS6D01G269500 chr7A 78.535 396 60 14 2312 2702 174205059 174205434 1.720000e-58 237
6 TraesCS6D01G269500 chr7D 78.283 396 61 14 2312 2702 171313850 171314225 8.000000e-57 231
7 TraesCS6D01G269500 chr7B 77.330 397 63 17 2312 2702 137795620 137795995 3.750000e-50 209
8 TraesCS6D01G269500 chr7B 78.022 182 34 6 77 255 137793006 137793184 3.910000e-20 110


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 TraesCS6D01G269500 chr6D 379571213 379574914 3701 False 6837.0 6837 100.0000 1 3702 1 chr6D.!!$F1 3701
1 TraesCS6D01G269500 chr6B 567396715 567400353 3638 True 2890.5 4473 94.6415 1 3702 2 chr6B.!!$R1 3701
2 TraesCS6D01G269500 chr6A 521450703 521454783 4080 True 3167.5 3755 97.3320 1 3702 2 chr6A.!!$R1 3701

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
742 744 1.092921 TCCACGTGCAACCACAAGAC 61.093 55.000 10.91 0.0 42.17 3.01 F
2158 2166 1.699634 ACTTAGGCAGCTTGTTCCTCA 59.300 47.619 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2192 2200 3.551046 CCGGTAGATGAGTTTGAGATCCG 60.551 52.174 0.0 0.0 35.02 4.18 R
3389 3774 1.071239 CAACATAGCGCGACAGCATAC 60.071 52.381 12.1 0.0 45.49 2.39 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
177 178 1.135083 CGTGTATCTTCCGCTTCCTGT 60.135 52.381 0.00 0.00 0.00 4.00
604 606 7.052873 ACTCCTGTTCAATTAGATGATTCCAG 58.947 38.462 0.00 0.00 0.00 3.86
742 744 1.092921 TCCACGTGCAACCACAAGAC 61.093 55.000 10.91 0.00 42.17 3.01
828 831 4.481280 ACCCTCCTATTAGTACTCCTCACA 59.519 45.833 0.00 0.00 0.00 3.58
849 852 3.316029 CAGAAATTCCAACACTGACTGCA 59.684 43.478 0.00 0.00 0.00 4.41
892 895 5.363580 AGTTCAAGAAAAGGATCAAAAGCCA 59.636 36.000 0.00 0.00 31.46 4.75
956 959 2.424246 GGACACACTAGAGACTAGCCAC 59.576 54.545 0.00 0.00 0.00 5.01
1823 1829 5.411977 TGTTTTGAGTTCGTACCACTTCAAA 59.588 36.000 4.08 4.08 0.00 2.69
1837 1843 3.565482 CACTTCAAAGCAGCTCAGGTTAA 59.435 43.478 0.00 0.00 0.00 2.01
1961 1967 6.795590 TCCTTCCTCTTTTCTCTCTTCTCTA 58.204 40.000 0.00 0.00 0.00 2.43
2158 2166 1.699634 ACTTAGGCAGCTTGTTCCTCA 59.300 47.619 0.00 0.00 0.00 3.86
2192 2200 8.139521 ACTTTGAACTGCTGTTAGTTACTTAC 57.860 34.615 9.14 0.00 40.78 2.34
2214 2594 3.551046 CGGATCTCAAACTCATCTACCGG 60.551 52.174 0.00 0.00 34.27 5.28
2233 2613 3.694734 CGGCATATAAGTGCAGGTTTTG 58.305 45.455 1.00 0.00 46.81 2.44
2297 2677 3.378427 GTGTTCAAAACCAGCACTTCTCT 59.622 43.478 0.00 0.00 0.00 3.10
2635 3015 8.433249 AAAGATCAGATATAGAGCATGAGGAA 57.567 34.615 0.00 0.00 0.00 3.36
2702 3082 8.827677 GTTATAATACTGTTCCATGGTTCTGAC 58.172 37.037 12.58 5.00 0.00 3.51
2843 3223 7.270779 TCTGAGACCATATGAAGACAAATCAG 58.729 38.462 3.65 6.35 0.00 2.90
2889 3269 7.800380 GTGAAGTGTGACATAAGAGAAAACATG 59.200 37.037 0.00 0.00 0.00 3.21
2926 3306 6.019075 CCAGTATTTCACGCGATTATCAAGAA 60.019 38.462 15.93 0.59 0.00 2.52
2957 3337 7.562135 ACAAAGGTTGAGACTTCTACTGTTAA 58.438 34.615 0.00 0.00 31.01 2.01
2995 3375 6.054941 TGTCAAGATGAACAACTCTGCTTTA 58.945 36.000 0.00 0.00 0.00 1.85
3025 3408 6.704937 GGGTAAACATGGAGCATAGTAGTTAC 59.295 42.308 0.00 0.00 0.00 2.50
3104 3487 7.653311 GGACATTAAATAAGAAACATCATGGCC 59.347 37.037 0.00 0.00 30.19 5.36
3389 3774 8.084073 TCTTTGAGAAAGGCACATAAATTTCAG 58.916 33.333 0.00 0.00 39.01 3.02
3530 3918 9.778741 TCATACTTTCCATGAAGTATTGTATCC 57.221 33.333 14.19 0.00 45.77 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.819564 TCGCTGCAGTTATTCATAGGT 57.180 42.857 16.64 0.00 0.00 3.08
15 16 5.973651 TTCTTCGCTGCAGTTATTCATAG 57.026 39.130 16.64 2.46 0.00 2.23
177 178 4.104738 ACCTTTTGGAACCTCATCAAGAGA 59.895 41.667 0.00 0.00 44.52 3.10
553 554 5.930837 AACATTTGAGAAACCCAGTTTGA 57.069 34.783 0.00 0.00 35.77 2.69
604 606 6.549912 AAGGGTAACAACTTTCACGTAATC 57.450 37.500 0.00 0.00 39.74 1.75
638 640 6.516739 TTATTCGTTGGAATTTGGCACATA 57.483 33.333 0.00 0.00 42.71 2.29
639 641 3.959535 ATTCGTTGGAATTTGGCACAT 57.040 38.095 0.00 0.00 39.90 3.21
763 766 1.064017 ACAGGTGGTGTCATTTGTGGT 60.064 47.619 0.00 0.00 31.90 4.16
828 831 3.554934 TGCAGTCAGTGTTGGAATTTCT 58.445 40.909 0.00 0.00 0.00 2.52
849 852 1.482593 CTTACTTGGGAGTGAGCGGAT 59.517 52.381 0.00 0.00 36.60 4.18
892 895 1.827969 CTCATGTTCCTCTTCTCCCGT 59.172 52.381 0.00 0.00 0.00 5.28
930 933 5.595133 GGCTAGTCTCTAGTGTGTCCTATTT 59.405 44.000 5.82 0.00 0.00 1.40
1823 1829 3.659183 AATGGATTAACCTGAGCTGCT 57.341 42.857 0.00 0.00 39.86 4.24
2113 2121 9.232473 GTTCTCTGGGAGTTATTTCTACATTTT 57.768 33.333 0.00 0.00 0.00 1.82
2158 2166 4.252073 CAGCAGTTCAAAGTCTAGATGCT 58.748 43.478 7.27 7.27 43.14 3.79
2192 2200 3.551046 CCGGTAGATGAGTTTGAGATCCG 60.551 52.174 0.00 0.00 35.02 4.18
2214 2594 6.436843 ACTACAAAACCTGCACTTATATGC 57.563 37.500 0.00 0.00 46.32 3.14
2257 2637 5.538053 TGAACACCCTGCAATAAGATGAAAA 59.462 36.000 0.00 0.00 0.00 2.29
2384 2764 4.141846 GCTGTTTGAGATATCTGGTCTGGA 60.142 45.833 10.74 0.00 0.00 3.86
2753 3133 6.602803 ACAATGCACTGAACCATATGATTACA 59.397 34.615 0.26 0.00 0.00 2.41
2843 3223 2.614983 ACATTTACGTTGGACCACACAC 59.385 45.455 0.00 0.00 0.00 3.82
2889 3269 6.304683 GCGTGAAATACTGGAATTGTTGTTAC 59.695 38.462 0.00 0.00 0.00 2.50
2957 3337 9.793252 GTTCATCTTGACATGTAAAAATGCTAT 57.207 29.630 4.53 0.00 0.00 2.97
2995 3375 1.427368 TGCTCCATGTTTACCCAAGGT 59.573 47.619 0.00 0.00 40.16 3.50
3143 3528 6.313519 AGTAATTATTCTCCCAGAAGTGCA 57.686 37.500 0.00 0.00 37.69 4.57
3389 3774 1.071239 CAACATAGCGCGACAGCATAC 60.071 52.381 12.10 0.00 45.49 2.39
3418 3803 5.480642 TTGGCCAACATACAATGTCAATT 57.519 34.783 16.05 0.00 44.07 2.32
3425 3812 8.076910 TCTAATCAAATTGGCCAACATACAAT 57.923 30.769 23.27 7.19 36.46 2.71
3436 3823 5.237048 TGCAAGGTTTCTAATCAAATTGGC 58.763 37.500 0.00 0.00 0.00 4.52
3530 3918 6.100004 AGGTCAAACTGAATAGTATCACACG 58.900 40.000 0.00 0.00 35.69 4.49


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

AutoCloner maintained by Alex Coulton.