Multiple sequence alignment - TraesCS6B01G216300

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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 TraesCS6B01G216300 chr6B 100.000 2246 0 0 1 2246 297457326 297459571 0 4148
1 TraesCS6B01G216300 chr6D 97.736 2253 42 7 1 2246 124501727 124503977 0 3869
2 TraesCS6B01G216300 chr4D 97.513 2252 45 7 1 2246 123319682 123321928 0 3838
3 TraesCS6B01G216300 chrUn 97.469 2252 46 8 1 2246 206782857 206785103 0 3832
4 TraesCS6B01G216300 chr7A 97.244 2250 53 7 1 2246 60263512 60265756 0 3803
5 TraesCS6B01G216300 chr1B 97.198 2248 52 7 1 2246 672569890 672567652 0 3792
6 TraesCS6B01G216300 chr5A 96.980 2252 59 8 1 2246 238848357 238846109 0 3773
7 TraesCS6B01G216300 chr2B 96.980 2252 56 8 1 2246 391092653 391090408 0 3771
8 TraesCS6B01G216300 chr3B 96.936 2252 60 6 1 2246 483384912 483387160 0 3768
9 TraesCS6B01G216300 chr3B 96.757 2251 67 5 1 2246 669796320 669794071 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 TraesCS6B01G216300 chr6B 297457326 297459571 2245 False 4148 4148 100.000 1 2246 1 chr6B.!!$F1 2245
1 TraesCS6B01G216300 chr6D 124501727 124503977 2250 False 3869 3869 97.736 1 2246 1 chr6D.!!$F1 2245
2 TraesCS6B01G216300 chr4D 123319682 123321928 2246 False 3838 3838 97.513 1 2246 1 chr4D.!!$F1 2245
3 TraesCS6B01G216300 chrUn 206782857 206785103 2246 False 3832 3832 97.469 1 2246 1 chrUn.!!$F1 2245
4 TraesCS6B01G216300 chr7A 60263512 60265756 2244 False 3803 3803 97.244 1 2246 1 chr7A.!!$F1 2245
5 TraesCS6B01G216300 chr1B 672567652 672569890 2238 True 3792 3792 97.198 1 2246 1 chr1B.!!$R1 2245
6 TraesCS6B01G216300 chr5A 238846109 238848357 2248 True 3773 3773 96.980 1 2246 1 chr5A.!!$R1 2245
7 TraesCS6B01G216300 chr2B 391090408 391092653 2245 True 3771 3771 96.980 1 2246 1 chr2B.!!$R1 2245
8 TraesCS6B01G216300 chr3B 483384912 483387160 2248 False 3768 3768 96.936 1 2246 1 chr3B.!!$F1 2245
9 TraesCS6B01G216300 chr3B 669794071 669796320 2249 True 3747 3747 96.757 1 2246 1 chr3B.!!$R1 2245

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
130 134 0.679505 AGGTAAGAGCACGCACAAGA 59.32 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1959 1973 1.008079 AAGTGACGGAACCGACGAC 60.008 57.895 20.14 13.24 42.83 4.34 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
130 134 0.679505 AGGTAAGAGCACGCACAAGA 59.320 50.000 0.00 0.00 0.00 3.02
252 256 8.311395 AGAATTGACCTCTGAATACAGTGATA 57.689 34.615 0.00 0.00 43.81 2.15
254 258 5.854010 TGACCTCTGAATACAGTGATACC 57.146 43.478 0.00 0.00 43.81 2.73
433 445 1.411612 CTTTTAGATCTACGGGCCGGT 59.588 52.381 31.78 20.77 0.00 5.28
486 498 2.528127 TTCGACTTGGCCCCTGGA 60.528 61.111 0.00 0.00 0.00 3.86
633 645 3.071023 TGAACATTGTCTTCCTCGGTTCT 59.929 43.478 0.00 0.00 35.45 3.01
644 656 1.134965 CCTCGGTTCTAGCTTCACTGG 60.135 57.143 0.00 0.00 0.00 4.00
654 666 3.170991 AGCTTCACTGGTGTAGGTAGA 57.829 47.619 9.61 0.00 37.03 2.59
693 706 3.391296 CCCCTCTTGCCTATTAGTAAGCA 59.609 47.826 0.00 0.00 0.00 3.91
709 722 1.078143 GCAGGCCTTCGATTCCACT 60.078 57.895 0.00 0.00 0.00 4.00
719 732 2.542550 TCGATTCCACTGGGGTCTTAA 58.457 47.619 0.00 0.00 38.11 1.85
734 747 4.387664 GGGTCTTAAGGTCTCATAGAGGGA 60.388 50.000 1.85 0.00 0.00 4.20
867 880 4.658901 ACCCAACCTTATGAGTATTCGGAT 59.341 41.667 0.00 0.00 0.00 4.18
1068 1081 2.161855 TCAGGTGTCAAATGTGATGCC 58.838 47.619 0.00 0.00 35.80 4.40
1203 1216 7.195839 AGAAGCAGTGACTTTGAAAGATTAC 57.804 36.000 12.53 7.30 0.00 1.89
1326 1339 2.783064 CTTCGCTCGCTCGCTCAAC 61.783 63.158 0.00 0.00 0.00 3.18
1562 1575 0.466124 GGAGCGATAGGAAGCCAAGT 59.534 55.000 0.00 0.00 0.00 3.16
1597 1610 0.099436 CGAGCAGCCCTTATTGCAAC 59.901 55.000 0.00 0.00 42.67 4.17
1724 1738 7.615365 AGTGGGATGCATTTTCTTACTTGATTA 59.385 33.333 0.00 0.00 0.00 1.75
1793 1807 0.403655 TGATGTACCAGCCAAGCCAA 59.596 50.000 0.00 0.00 0.00 4.52
1796 1810 1.060729 TGTACCAGCCAAGCCAACTA 58.939 50.000 0.00 0.00 0.00 2.24
1959 1973 1.613925 TCGCCCCTTATCTCTTCATCG 59.386 52.381 0.00 0.00 0.00 3.84
2029 2043 4.043037 ACTCGCTTACTCCTATTTTCCG 57.957 45.455 0.00 0.00 0.00 4.30
2034 2048 6.211515 TCGCTTACTCCTATTTTCCGTATTC 58.788 40.000 0.00 0.00 0.00 1.75
2234 2251 4.377021 TCTGTTGTACAGCTACTTTGGTG 58.623 43.478 11.22 0.00 45.54 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 134 1.057851 TGGTCCCCTTCGGTCAAGTT 61.058 55.000 0.00 0.00 0.00 2.66
252 256 5.249780 ACGGAGTCTATCTAGATCATGGT 57.750 43.478 8.95 0.00 29.74 3.55
406 418 4.561734 GCCCGTAGATCTAAAAGGATCCAG 60.562 50.000 15.82 2.06 42.02 3.86
433 445 2.107366 TCCCTATGCTCATGTGAACGA 58.893 47.619 0.00 0.00 0.00 3.85
633 645 4.270834 CTCTACCTACACCAGTGAAGCTA 58.729 47.826 4.48 0.00 0.00 3.32
644 656 1.035932 TCGCCCAGCTCTACCTACAC 61.036 60.000 0.00 0.00 0.00 2.90
654 666 3.394836 GACCCTTCTCGCCCAGCT 61.395 66.667 0.00 0.00 0.00 4.24
693 706 1.604378 CCAGTGGAATCGAAGGCCT 59.396 57.895 1.68 0.00 0.00 5.19
709 722 4.547671 CTCTATGAGACCTTAAGACCCCA 58.452 47.826 3.36 0.00 0.00 4.96
719 732 2.795556 TCTCCTCCCTCTATGAGACCT 58.204 52.381 0.00 0.00 31.26 3.85
734 747 8.953223 TTCTTCTTTAGTTAGGTAGTTCTCCT 57.047 34.615 0.00 0.00 38.91 3.69
887 900 5.907197 ATAACTGTCAAAAGTGAGTGACG 57.093 39.130 0.00 0.00 45.83 4.35
1068 1081 2.955614 AGATTTGAACGACCAGGTACG 58.044 47.619 0.00 0.49 0.00 3.67
1562 1575 1.508632 CTCGCCTTTCCTTTTGACGA 58.491 50.000 0.00 0.00 0.00 4.20
1597 1610 5.175090 GGCTATAAGTAGGCTTTTTGCTG 57.825 43.478 0.00 0.00 46.81 4.41
1959 1973 1.008079 AAGTGACGGAACCGACGAC 60.008 57.895 20.14 13.24 42.83 4.34


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

AutoCloner maintained by Alex Coulton.