Multiple sequence alignment - TraesCS6D01G200900

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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 TraesCS6D01G200900 chr6D 100.000 2861 0 0 1 2861 283220230 283223090 0 5284
1 TraesCS6D01G200900 chr6D 98.149 2864 44 5 1 2861 124530621 124533478 0 4987
2 TraesCS6D01G200900 chr7D 98.255 2865 42 5 1 2861 381960662 381957802 0 5007
3 TraesCS6D01G200900 chr7D 98.254 2864 43 4 1 2861 382063177 382066036 0 5005
4 TraesCS6D01G200900 chr7D 97.976 2865 49 5 1 2861 626684737 626681878 0 4961
5 TraesCS6D01G200900 chrUn 98.186 2866 43 5 1 2861 189405582 189408443 0 4996
6 TraesCS6D01G200900 chr7B 98.081 2866 46 5 1 2861 644461942 644464803 0 4979
7 TraesCS6D01G200900 chr1D 98.080 2864 47 5 1 2861 141318635 141315777 0 4977
8 TraesCS6D01G200900 chr1B 97.839 2869 50 6 1 2861 668810664 668807800 0 4944
9 TraesCS6D01G200900 chr1B 97.732 2866 55 6 1 2861 638706166 638703306 0 4924


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 TraesCS6D01G200900 chr6D 283220230 283223090 2860 False 5284 5284 100.000 1 2861 1 chr6D.!!$F2 2860
1 TraesCS6D01G200900 chr6D 124530621 124533478 2857 False 4987 4987 98.149 1 2861 1 chr6D.!!$F1 2860
2 TraesCS6D01G200900 chr7D 381957802 381960662 2860 True 5007 5007 98.255 1 2861 1 chr7D.!!$R1 2860
3 TraesCS6D01G200900 chr7D 382063177 382066036 2859 False 5005 5005 98.254 1 2861 1 chr7D.!!$F1 2860
4 TraesCS6D01G200900 chr7D 626681878 626684737 2859 True 4961 4961 97.976 1 2861 1 chr7D.!!$R2 2860
5 TraesCS6D01G200900 chrUn 189405582 189408443 2861 False 4996 4996 98.186 1 2861 1 chrUn.!!$F1 2860
6 TraesCS6D01G200900 chr7B 644461942 644464803 2861 False 4979 4979 98.081 1 2861 1 chr7B.!!$F1 2860
7 TraesCS6D01G200900 chr1D 141315777 141318635 2858 True 4977 4977 98.080 1 2861 1 chr1D.!!$R1 2860
8 TraesCS6D01G200900 chr1B 668807800 668810664 2864 True 4944 4944 97.839 1 2861 1 chr1B.!!$R2 2860
9 TraesCS6D01G200900 chr1B 638703306 638706166 2860 True 4924 4924 97.732 1 2861 1 chr1B.!!$R1 2860

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
899 905 1.135315 CCGAACCGCTTGCAGAATG 59.865 57.895 0.0 0.0 40.87 2.67 F
1088 1094 0.103755 CTGCTTCGCTCTGCTGGATA 59.896 55.000 0.0 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1827 1.076339 CATAATGGGGCGGGGTTGT 60.076 57.895 0.0 0.0 0.00 3.32 R
2773 2789 2.488952 TGCATTTTAGAGTGTCGTGCA 58.511 42.857 0.0 0.0 38.62 4.57 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 4.440663 CCGCTGAGACTGAGACATATCAAA 60.441 45.833 0.00 0.00 0.00 2.69
42 43 4.502282 CGCTGAGACTGAGACATATCAAAC 59.498 45.833 0.00 0.00 0.00 2.93
43 44 5.414360 GCTGAGACTGAGACATATCAAACA 58.586 41.667 0.00 0.00 0.00 2.83
44 45 5.519566 GCTGAGACTGAGACATATCAAACAG 59.480 44.000 0.00 0.00 0.00 3.16
104 105 3.326588 TGGTTACCGGATGATGGGAATAG 59.673 47.826 9.46 0.00 30.36 1.73
197 198 4.607235 GTCTTTTCGTTGCATTCACTTACG 59.393 41.667 0.00 0.00 0.00 3.18
464 467 5.563842 CCATAATGTCTCAAAACGAAGAGC 58.436 41.667 0.00 0.00 0.00 4.09
469 472 4.245660 TGTCTCAAAACGAAGAGCCTATG 58.754 43.478 0.00 0.00 0.00 2.23
628 634 4.851010 GCAAAGTAAGCGTCCTTTTAACA 58.149 39.130 0.00 0.00 32.47 2.41
791 797 2.384899 TCGTCTATCGATGAACAGCG 57.615 50.000 8.54 6.11 44.01 5.18
833 839 6.215845 GCATTGCTTTGTTTTTCTCTCCTTA 58.784 36.000 0.16 0.00 0.00 2.69
842 848 7.554959 TGTTTTTCTCTCCTTACCTATCAGT 57.445 36.000 0.00 0.00 0.00 3.41
899 905 1.135315 CCGAACCGCTTGCAGAATG 59.865 57.895 0.00 0.00 40.87 2.67
1088 1094 0.103755 CTGCTTCGCTCTGCTGGATA 59.896 55.000 0.00 0.00 0.00 2.59
1282 1288 2.459904 CGAAGCGTGTCGTTCGTG 59.540 61.111 13.75 0.00 40.52 4.35
1380 1386 5.104374 CAGGAACCAATTCGAATTTGGATG 58.896 41.667 29.79 21.59 35.48 3.51
1390 1396 5.703978 TCGAATTTGGATGTTGACATGTT 57.296 34.783 0.00 0.00 36.57 2.71
1477 1483 0.613260 CTGGTGGTTTCGGGATCTCA 59.387 55.000 0.00 0.00 0.00 3.27
1480 1486 2.841266 TGGTGGTTTCGGGATCTCATAA 59.159 45.455 0.00 0.00 0.00 1.90
1553 1559 7.928873 TCAGTAATTCTACCCCTTCTTCATTT 58.071 34.615 0.00 0.00 0.00 2.32
1652 1658 2.296471 CTCCCGTTCATAGTTCCGCTAT 59.704 50.000 0.00 0.00 40.86 2.97
1751 1757 3.785859 GCAGGAGGCATCGGTCCA 61.786 66.667 0.00 0.00 43.97 4.02
1846 1852 2.159382 CCCGCCCCATTATGTTATGTC 58.841 52.381 0.00 0.00 0.00 3.06
2197 2207 2.328099 CGAGCCACCAGGTTTGAGC 61.328 63.158 0.00 0.00 37.19 4.26
2399 2409 4.881850 ACAAAGATTCAGACAAAACCGAGT 59.118 37.500 0.00 0.00 0.00 4.18
2433 2443 3.059188 TGAAGAAGATTTGGCGAACGAAC 60.059 43.478 0.00 0.00 0.00 3.95
2493 2507 2.143925 GGTTATTCAGTAGCCATCGCC 58.856 52.381 0.00 0.00 34.08 5.54
2495 2509 1.037493 TATTCAGTAGCCATCGCCGT 58.963 50.000 0.00 0.00 34.57 5.68
2810 2826 2.120274 ATGTTGGGTTGGGCCAGG 59.880 61.111 6.23 0.00 39.65 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 6.757947 TGCTCATTTCCAAATTTATGCTTAGC 59.242 34.615 0.00 0.00 0.00 3.09
170 171 1.533731 GAATGCAACGAAAAGACCCGA 59.466 47.619 0.00 0.00 0.00 5.14
197 198 1.268539 CGCTGGTGGTTGTTTCTTGTC 60.269 52.381 0.00 0.00 0.00 3.18
545 551 2.281208 TGTACAACTGGGGCGCAC 60.281 61.111 10.83 4.83 0.00 5.34
628 634 0.904649 GCATTAAAAAGGGCTGGCCT 59.095 50.000 18.27 18.27 36.10 5.19
747 753 4.240888 CTCTCTCTTTTTCATCTCGTGCA 58.759 43.478 0.00 0.00 0.00 4.57
791 797 1.092345 GCCAAGAGCTCCGTCAATCC 61.092 60.000 10.93 0.00 38.99 3.01
833 839 2.959707 GGATCGGAACTCACTGATAGGT 59.040 50.000 0.00 0.00 36.21 3.08
842 848 3.064207 CGAACAAAAGGATCGGAACTCA 58.936 45.455 0.00 0.00 38.05 3.41
899 905 4.593956 AGGATCTTGTGGAACTGGATTTC 58.406 43.478 0.00 0.00 38.04 2.17
1088 1094 3.056749 GCTTCTTATATGGGATCCGACGT 60.057 47.826 5.45 0.00 0.00 4.34
1185 1191 2.816958 CGCCGAAGCAGCATGAGT 60.817 61.111 0.00 0.00 39.69 3.41
1282 1288 5.552178 AGTAGTGGTGTCTTTCTTTCCATC 58.448 41.667 0.00 0.00 0.00 3.51
1380 1386 6.767080 GGTTAAAAACAACCAACATGTCAAC 58.233 36.000 0.00 0.00 46.14 3.18
1480 1486 4.165779 CGAGGCATAAAAGACGCATTTTT 58.834 39.130 3.81 1.36 34.35 1.94
1553 1559 2.859165 ATTCAGAAGCGAGGTCCAAA 57.141 45.000 0.00 0.00 0.00 3.28
1652 1658 6.446781 AAAATCTTCCTCGTGTATCGTCTA 57.553 37.500 0.00 0.00 40.80 2.59
1821 1827 1.076339 CATAATGGGGCGGGGTTGT 60.076 57.895 0.00 0.00 0.00 3.32
2197 2207 4.796606 ACATTCTTGGATCCCACCTTATG 58.203 43.478 9.90 8.02 30.78 1.90
2399 2409 7.094205 GCCAAATCTTCTTCAGTTCTATCCAAA 60.094 37.037 0.00 0.00 0.00 3.28
2463 2477 6.122964 GGCTACTGAATAACCTCCTTTGAAT 58.877 40.000 0.00 0.00 0.00 2.57
2464 2478 5.013704 TGGCTACTGAATAACCTCCTTTGAA 59.986 40.000 0.00 0.00 0.00 2.69
2493 2507 8.795786 TGAATGGAAGAAAAGTAATGAAAACG 57.204 30.769 0.00 0.00 0.00 3.60
2773 2789 2.488952 TGCATTTTAGAGTGTCGTGCA 58.511 42.857 0.00 0.00 38.62 4.57
2810 2826 4.095334 GTCTCCCTAGTCGAAGTCTTCTTC 59.905 50.000 10.81 3.85 44.55 2.87


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

AutoCloner maintained by Alex Coulton.