Multiple sequence alignment - TraesCS6B01G357400

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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 TraesCS6B01G357400 chr6B 100.000 2825 0 0 1 2825 625648936 625651760 0 5217
1 TraesCS6B01G357400 chr1B 97.002 2835 75 5 1 2825 683734148 683731314 0 4756
2 TraesCS6B01G357400 chrUn 96.933 2837 75 6 1 2825 223706940 223704104 0 4747
3 TraesCS6B01G357400 chrUn 96.616 2837 84 6 1 2825 40085853 40088689 0 4697
4 TraesCS6B01G357400 chr7B 96.862 2836 78 6 1 2825 698140154 698142989 0 4734
5 TraesCS6B01G357400 chr2A 96.893 2832 75 6 1 2820 605912883 605910053 0 4730
6 TraesCS6B01G357400 chr2A 96.471 2834 91 5 1 2825 563256636 563259469 0 4671
7 TraesCS6B01G357400 chr5B 96.542 2834 88 6 1 2825 713082224 713079392 0 4682
8 TraesCS6B01G357400 chr5B 96.366 2834 90 9 1 2825 713126493 713129322 0 4650
9 TraesCS6B01G357400 chr3B 96.439 2836 90 6 1 2825 92142918 92145753 0 4667


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 TraesCS6B01G357400 chr6B 625648936 625651760 2824 False 5217 5217 100.000 1 2825 1 chr6B.!!$F1 2824
1 TraesCS6B01G357400 chr1B 683731314 683734148 2834 True 4756 4756 97.002 1 2825 1 chr1B.!!$R1 2824
2 TraesCS6B01G357400 chrUn 223704104 223706940 2836 True 4747 4747 96.933 1 2825 1 chrUn.!!$R1 2824
3 TraesCS6B01G357400 chrUn 40085853 40088689 2836 False 4697 4697 96.616 1 2825 1 chrUn.!!$F1 2824
4 TraesCS6B01G357400 chr7B 698140154 698142989 2835 False 4734 4734 96.862 1 2825 1 chr7B.!!$F1 2824
5 TraesCS6B01G357400 chr2A 605910053 605912883 2830 True 4730 4730 96.893 1 2820 1 chr2A.!!$R1 2819
6 TraesCS6B01G357400 chr2A 563256636 563259469 2833 False 4671 4671 96.471 1 2825 1 chr2A.!!$F1 2824
7 TraesCS6B01G357400 chr5B 713079392 713082224 2832 True 4682 4682 96.542 1 2825 1 chr5B.!!$R1 2824
8 TraesCS6B01G357400 chr5B 713126493 713129322 2829 False 4650 4650 96.366 1 2825 1 chr5B.!!$F1 2824
9 TraesCS6B01G357400 chr3B 92142918 92145753 2835 False 4667 4667 96.439 1 2825 1 chr3B.!!$F1 2824

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
917 925 1.563924 TGGTCGGCAACATAGGTACT 58.436 50.0 0.0 0.0 46.37 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2649 2668 0.252742 ACCGGGGAAGTTGAGGAGAT 60.253 55.0 6.32 0.0 0.0 2.75 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
56 57 5.426689 TCACAAGAGGCTCATACAGAAAT 57.573 39.130 18.26 0.00 0.00 2.17
63 64 6.656902 AGAGGCTCATACAGAAATCAATCAA 58.343 36.000 18.26 0.00 0.00 2.57
178 179 2.689983 CAATACTCCTTTCCATGGCCAC 59.310 50.000 8.16 0.00 0.00 5.01
332 333 8.462811 TGATATGTATTCGAATCTTAGGAGCTC 58.537 37.037 15.25 4.71 0.00 4.09
356 357 9.363763 CTCGTAATCACTGATATGCTCATATTT 57.636 33.333 4.10 0.00 34.36 1.40
357 358 9.710900 TCGTAATCACTGATATGCTCATATTTT 57.289 29.630 4.10 0.00 34.36 1.82
425 430 9.693739 TCTAGAAAGATCAGACAGAAGTAAGAT 57.306 33.333 0.00 0.00 0.00 2.40
431 436 7.059788 AGATCAGACAGAAGTAAGATGAGCTA 58.940 38.462 0.00 0.00 30.83 3.32
598 603 5.714333 TCACTAAAAGAGTCTCATGAGCTCT 59.286 40.000 28.97 28.97 40.81 4.09
846 854 6.806388 GTCGAAAACCATAGGGAAAGTAAA 57.194 37.500 0.00 0.00 38.05 2.01
917 925 1.563924 TGGTCGGCAACATAGGTACT 58.436 50.000 0.00 0.00 46.37 2.73
973 981 2.665165 AGCGTCTCATCTTCTCTGGAT 58.335 47.619 0.00 0.00 0.00 3.41
988 996 6.166984 TCTCTGGATAAGCTCAAATCGAAT 57.833 37.500 0.00 0.00 0.00 3.34
1258 1268 3.368531 GCCGCCCTATTCTATTACCAGAG 60.369 52.174 0.00 0.00 0.00 3.35
1263 1273 6.424207 CGCCCTATTCTATTACCAGAGAAAAC 59.576 42.308 0.00 0.00 35.40 2.43
1310 1320 3.564644 TGCTTTATTTCGTTTCGTTCCCA 59.435 39.130 0.00 0.00 0.00 4.37
1367 1377 8.841300 GGGACTTGTCATATTTAGAATCTTTCC 58.159 37.037 3.08 0.00 0.00 3.13
1395 1405 7.064609 CGGTCTGCTCTATTTACAATTCTTTCA 59.935 37.037 0.00 0.00 0.00 2.69
1423 1433 3.943381 TCTTCTCTTTACCACGCGATAGA 59.057 43.478 15.93 4.84 39.76 1.98
1830 1847 4.124351 CGGGCGGCGTGAACTCTA 62.124 66.667 9.37 0.00 0.00 2.43
1838 1855 3.624900 CGGCGTGAACTCTAATTCGATA 58.375 45.455 0.00 0.00 0.00 2.92
1841 1858 4.277258 GCGTGAACTCTAATTCGATACGA 58.723 43.478 0.00 0.00 30.96 3.43
1854 1871 6.591750 ATTCGATACGAGTATTCAATCCCT 57.408 37.500 0.00 0.00 37.14 4.20
1865 1882 2.381752 TCAATCCCTCCGCTGAGATA 57.618 50.000 6.73 0.00 41.42 1.98
1905 1922 6.120507 ACCTTGATAGGAAGATGGCTTATC 57.879 41.667 0.00 0.00 45.05 1.75
2063 2080 1.335145 TAAGCATCCCTAGCGGTACC 58.665 55.000 0.16 0.16 37.01 3.34
2071 2088 0.464452 CCTAGCGGTACCCAAAGAGG 59.536 60.000 6.25 2.53 37.03 3.69
2138 2155 2.645192 CCCGCATTCAACCAACCCC 61.645 63.158 0.00 0.00 0.00 4.95
2316 2333 1.756408 TAAAAGCGGACGTGGGGACA 61.756 55.000 0.00 0.00 38.70 4.02
2331 2348 3.249189 ACACGGGTCAGGGCACAT 61.249 61.111 0.00 0.00 0.00 3.21
2577 2596 2.282106 GGGGGTGGGGCAATAAGG 59.718 66.667 0.00 0.00 0.00 2.69
2587 2606 2.567169 GGGGCAATAAGGTTGCTTCTTT 59.433 45.455 11.92 0.00 44.36 2.52
2638 2657 4.680237 CCGACCGGCAGCAGTTGA 62.680 66.667 0.00 0.00 0.00 3.18
2649 2668 1.833630 CAGCAGTTGAGTCTCCCCATA 59.166 52.381 0.00 0.00 0.00 2.74
2683 2702 3.145551 GGTCTTCGGCCCGAGCTA 61.146 66.667 5.73 0.00 37.14 3.32
2707 2726 1.070786 GGCAGAAACTCGTCCCACA 59.929 57.895 0.00 0.00 0.00 4.17
2767 2786 4.377897 GTGCGGCTTAGGTCAACTAATAT 58.622 43.478 0.00 0.00 40.71 1.28
2771 2790 5.177696 GCGGCTTAGGTCAACTAATATGAAG 59.822 44.000 0.00 0.00 40.71 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 3.686227 ATTGGGCTATGGGTTGATTGA 57.314 42.857 0.00 0.0 0.00 2.57
63 64 2.567615 GTCTCGATATTGGGCTATGGGT 59.432 50.000 0.00 0.0 0.00 4.51
178 179 1.586564 GATCTTCGCGGGTCGTGAG 60.587 63.158 6.13 0.0 46.71 3.51
357 358 8.977505 GCTTCTTTGATTACAGCAACAATAAAA 58.022 29.630 0.00 0.0 0.00 1.52
804 812 8.859517 TTTCGACCGTTTTCAATAAAATCTTT 57.140 26.923 0.00 0.0 36.96 2.52
808 816 7.397512 GGTTTTCGACCGTTTTCAATAAAAT 57.602 32.000 0.00 0.0 39.00 1.82
823 831 6.806388 TTTACTTTCCCTATGGTTTTCGAC 57.194 37.500 0.00 0.0 0.00 4.20
863 871 3.415087 GACCAGGAGCAGGGGCAT 61.415 66.667 0.00 0.0 44.61 4.40
917 925 1.136197 CGCAACGCATACCGAAAAAGA 60.136 47.619 0.00 0.0 41.02 2.52
973 981 5.928839 GCTCTATCCATTCGATTTGAGCTTA 59.071 40.000 14.59 0.0 44.41 3.09
988 996 2.435805 GTTGGACCATCTGCTCTATCCA 59.564 50.000 0.00 0.0 34.44 3.41
1059 1067 3.569701 CCATTTCAATAATACGGGCTGCT 59.430 43.478 0.00 0.0 0.00 4.24
1070 1080 7.608153 TCTCTACTGACGAACCATTTCAATAA 58.392 34.615 0.00 0.0 0.00 1.40
1258 1268 2.933260 GGATGAGCTTCTCTCCGTTTTC 59.067 50.000 0.00 0.0 41.18 2.29
1263 1273 1.299773 GCGGATGAGCTTCTCTCCG 60.300 63.158 20.20 20.2 45.14 4.63
1395 1405 4.201930 CGCGTGGTAAAGAGAAGAGAGTAT 60.202 45.833 0.00 0.0 0.00 2.12
1423 1433 2.882777 CGCTCACGCTTCGCTGAT 60.883 61.111 0.00 0.0 0.00 2.90
1610 1627 0.324943 AGCTTCAAGCCCGCTTTCTA 59.675 50.000 5.53 0.0 43.77 2.10
1767 1784 1.815421 GGCCACAGGTCGCACATAG 60.815 63.158 0.00 0.0 0.00 2.23
1830 1847 6.994221 AGGGATTGAATACTCGTATCGAATT 58.006 36.000 0.00 0.0 34.74 2.17
1838 1855 1.068741 GCGGAGGGATTGAATACTCGT 59.931 52.381 4.07 0.0 0.00 4.18
1841 1858 2.366916 CTCAGCGGAGGGATTGAATACT 59.633 50.000 5.89 0.0 37.51 2.12
1865 1882 4.654262 TCAAGGTTAAGGAGTCAACTGAGT 59.346 41.667 0.00 0.0 0.00 3.41
1905 1922 2.495669 ACCCTTATGCACGAATTTTGGG 59.504 45.455 0.00 0.0 38.13 4.12
1967 1984 2.281484 GGGTGTTTCCGAGCAGCA 60.281 61.111 0.00 0.0 36.37 4.41
2034 2051 1.173913 GGGATGCTTAACGCCACTTT 58.826 50.000 0.00 0.0 38.05 2.66
2063 2080 0.613260 TCATCACGACCCCTCTTTGG 59.387 55.000 0.00 0.0 0.00 3.28
2127 2144 2.112190 GGTCAAAAAGGGGTTGGTTGA 58.888 47.619 0.00 0.0 0.00 3.18
2138 2155 0.958822 CCCGTTCCCTGGTCAAAAAG 59.041 55.000 0.00 0.0 0.00 2.27
2165 2182 4.082523 GCCTGCCAGCGGTAGTGA 62.083 66.667 10.62 0.0 33.52 3.41
2316 2333 4.082523 CGATGTGCCCTGACCCGT 62.083 66.667 0.00 0.0 0.00 5.28
2323 2340 3.362706 TCTCTTAGTTACGATGTGCCCT 58.637 45.455 0.00 0.0 0.00 5.19
2331 2348 4.021229 TGGAATGGCTCTCTTAGTTACGA 58.979 43.478 0.00 0.0 0.00 3.43
2529 2547 2.158726 ACCGACCCAGCAAGAAAAGTAA 60.159 45.455 0.00 0.0 0.00 2.24
2587 2606 1.702022 GGGGCGGGGATAAGCTTGTA 61.702 60.000 9.86 0.0 0.00 2.41
2638 2657 3.208692 AGTTGAGGAGATATGGGGAGACT 59.791 47.826 0.00 0.0 0.00 3.24
2649 2668 0.252742 ACCGGGGAAGTTGAGGAGAT 60.253 55.000 6.32 0.0 0.00 2.75
2683 2702 2.103263 GGGACGAGTTTCTGCCTCATAT 59.897 50.000 0.00 0.0 0.00 1.78
2767 2786 7.151976 TCGTTGAGTGAATTGTATCTTCTTCA 58.848 34.615 0.00 0.0 0.00 3.02
2771 2790 6.684555 GCAATCGTTGAGTGAATTGTATCTTC 59.315 38.462 0.00 0.0 28.30 2.87
2780 2799 2.489329 CAAGGGCAATCGTTGAGTGAAT 59.511 45.455 0.00 0.0 42.11 2.57


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

AutoCloner maintained by Alex Coulton.