Multiple sequence alignment - TraesCS6D01G189900

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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 TraesCS6D01G189900 chr6D 100.000 2201 0 0 1 2201 262753646 262751446 0.000000e+00 4065.0
1 TraesCS6D01G189900 chr6A 97.500 2160 45 5 34 2189 356973423 356971269 0.000000e+00 3681.0
2 TraesCS6D01G189900 chr6B 92.638 1535 61 20 676 2199 347229212 347230705 0.000000e+00 2161.0
3 TraesCS6D01G189900 chr6B 90.270 555 29 10 34 581 347228651 347229187 0.000000e+00 702.0
4 TraesCS6D01G189900 chr3D 80.460 87 17 0 1414 1500 4972508 4972422 1.410000e-07 67.6


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 TraesCS6D01G189900 chr6D 262751446 262753646 2200 True 4065.0 4065 100.000 1 2201 1 chr6D.!!$R1 2200
1 TraesCS6D01G189900 chr6A 356971269 356973423 2154 True 3681.0 3681 97.500 34 2189 1 chr6A.!!$R1 2155
2 TraesCS6D01G189900 chr6B 347228651 347230705 2054 False 1431.5 2161 91.454 34 2199 2 chr6B.!!$F1 2165

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
664 672 0.960861 GTTCCTAACCAGCCTGCACC 60.961 60.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2166 0.251165 CCCCTTGTCCAACGGAATGT 60.251 55.0 0.0 0.0 31.38 2.71 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
21 22 4.803098 GGTATACACGAGGAGCCATATT 57.197 45.455 5.01 0.00 0.00 1.28
22 23 5.909621 GGTATACACGAGGAGCCATATTA 57.090 43.478 5.01 0.00 0.00 0.98
23 24 6.466885 GGTATACACGAGGAGCCATATTAT 57.533 41.667 5.01 0.00 0.00 1.28
24 25 6.875076 GGTATACACGAGGAGCCATATTATT 58.125 40.000 5.01 0.00 0.00 1.40
25 26 8.004087 GGTATACACGAGGAGCCATATTATTA 57.996 38.462 5.01 0.00 0.00 0.98
26 27 8.639761 GGTATACACGAGGAGCCATATTATTAT 58.360 37.037 5.01 0.00 0.00 1.28
27 28 9.464714 GTATACACGAGGAGCCATATTATTATG 57.535 37.037 0.00 0.00 35.87 1.90
28 29 5.178797 ACACGAGGAGCCATATTATTATGC 58.821 41.667 0.00 0.00 34.94 3.14
29 30 5.046304 ACACGAGGAGCCATATTATTATGCT 60.046 40.000 0.00 0.00 34.94 3.79
30 31 6.154534 ACACGAGGAGCCATATTATTATGCTA 59.845 38.462 0.00 0.00 34.94 3.49
31 32 7.041721 CACGAGGAGCCATATTATTATGCTAA 58.958 38.462 0.00 0.00 34.94 3.09
32 33 7.223582 CACGAGGAGCCATATTATTATGCTAAG 59.776 40.741 0.00 0.00 34.94 2.18
188 189 4.305989 TGTTGCACCTGACTTTGATTTC 57.694 40.909 0.00 0.00 0.00 2.17
189 190 3.698539 TGTTGCACCTGACTTTGATTTCA 59.301 39.130 0.00 0.00 0.00 2.69
320 322 5.050644 TCTGTTGTAATGCTTGCATTCAG 57.949 39.130 21.96 20.63 33.06 3.02
372 380 9.148104 CCCACTGTTACACTAAAAAGTATAGAC 57.852 37.037 0.00 0.00 0.00 2.59
601 609 9.042008 TGTTCTCTATATCGTTCCAATTTTAGC 57.958 33.333 0.00 0.00 0.00 3.09
602 610 9.262358 GTTCTCTATATCGTTCCAATTTTAGCT 57.738 33.333 0.00 0.00 0.00 3.32
664 672 0.960861 GTTCCTAACCAGCCTGCACC 60.961 60.000 0.00 0.00 0.00 5.01
778 786 1.419381 TGGCTTCACTGTGGTACTGA 58.581 50.000 8.11 0.00 0.00 3.41
791 799 8.999431 CACTGTGGTACTGAACATAAAAAGTAT 58.001 33.333 0.00 0.00 0.00 2.12
887 895 6.485171 ACTTACATTCCTGCTTCCATTTACT 58.515 36.000 0.00 0.00 0.00 2.24
1245 1264 0.679002 TTGCTTGCTCCTCATCAGCC 60.679 55.000 0.00 0.00 35.89 4.85
1659 1678 3.244700 CCAGAAGCCTCTCTTTTCCTTCA 60.245 47.826 0.00 0.00 35.54 3.02
1864 1883 4.498241 CTCTTCACGAAATCCATCTGTCA 58.502 43.478 0.00 0.00 0.00 3.58
1922 1941 0.620556 AATGCCTCGGGACTCATTGT 59.379 50.000 0.00 0.00 0.00 2.71
2004 2023 7.230747 TGGAGATGAGGAAAACAATAACAAGA 58.769 34.615 0.00 0.00 0.00 3.02
2145 2164 1.757118 ACTGATCCCACTATGTCACCG 59.243 52.381 0.00 0.00 0.00 4.94
2146 2165 2.031870 CTGATCCCACTATGTCACCGA 58.968 52.381 0.00 0.00 0.00 4.69
2147 2166 2.430694 CTGATCCCACTATGTCACCGAA 59.569 50.000 0.00 0.00 0.00 4.30
2199 2218 5.483685 TCCAGCAAGAACTGTTGTAGTAT 57.516 39.130 0.00 0.00 39.18 2.12
2200 2219 6.599356 TCCAGCAAGAACTGTTGTAGTATA 57.401 37.500 0.00 0.00 39.18 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.803098 AATATGGCTCCTCGTGTATACC 57.197 45.455 0.00 0.00 0.00 2.73
1 2 9.464714 CATAATAATATGGCTCCTCGTGTATAC 57.535 37.037 0.00 0.00 36.13 1.47
2 3 8.141909 GCATAATAATATGGCTCCTCGTGTATA 58.858 37.037 0.08 0.00 39.49 1.47
3 4 6.986817 GCATAATAATATGGCTCCTCGTGTAT 59.013 38.462 0.08 0.00 39.49 2.29
4 5 6.154534 AGCATAATAATATGGCTCCTCGTGTA 59.845 38.462 0.08 0.00 39.49 2.90
5 6 5.046304 AGCATAATAATATGGCTCCTCGTGT 60.046 40.000 0.08 0.00 39.49 4.49
6 7 5.423015 AGCATAATAATATGGCTCCTCGTG 58.577 41.667 0.08 0.00 39.49 4.35
7 8 5.683876 AGCATAATAATATGGCTCCTCGT 57.316 39.130 0.08 0.00 39.49 4.18
8 9 6.201806 GCTTAGCATAATAATATGGCTCCTCG 59.798 42.308 0.00 0.00 39.49 4.63
9 10 7.278875 AGCTTAGCATAATAATATGGCTCCTC 58.721 38.462 7.07 0.00 39.49 3.71
10 11 7.205515 AGCTTAGCATAATAATATGGCTCCT 57.794 36.000 7.07 0.00 39.49 3.69
11 12 8.964476 TTAGCTTAGCATAATAATATGGCTCC 57.036 34.615 7.07 0.00 39.49 4.70
188 189 3.545703 ACACTTTCCCTCTTGAACTGTG 58.454 45.455 0.00 0.00 36.17 3.66
189 190 3.933861 ACACTTTCCCTCTTGAACTGT 57.066 42.857 0.00 0.00 0.00 3.55
300 302 4.852134 ACTGAATGCAAGCATTACAACA 57.148 36.364 19.21 12.18 45.50 3.33
372 380 1.269726 ACTGGAAATTTGGCAACTGCG 60.270 47.619 0.00 0.00 43.26 5.18
380 388 7.209475 AGTGTTTTATGTCACTGGAAATTTGG 58.791 34.615 0.00 0.00 42.30 3.28
457 465 1.505353 CTTTACGAGCGACCGACCT 59.495 57.895 3.95 0.00 0.00 3.85
543 551 2.987149 CGTTCACGACTGAAATGCTAGT 59.013 45.455 0.00 0.00 43.02 2.57
587 595 4.438744 GGGACATCAGCTAAAATTGGAACG 60.439 45.833 0.00 0.00 0.00 3.95
664 672 0.588252 CAAGGAAACAGTGAGGTGCG 59.412 55.000 0.00 0.00 0.00 5.34
912 920 6.767524 TTGGACTACCGCAAATGATAAATT 57.232 33.333 0.00 0.00 39.42 1.82
920 928 6.420913 AGAGTATATTGGACTACCGCAAAT 57.579 37.500 0.00 0.00 39.42 2.32
1107 1126 1.743623 CTTCGTGGCCGTGGCATTA 60.744 57.895 13.76 0.00 44.11 1.90
1245 1264 1.268794 CGGAATGTGGAGCTAGAGACG 60.269 57.143 0.00 0.00 0.00 4.18
1659 1678 2.280797 TTGCTCGGTTTCTGCGCT 60.281 55.556 9.73 0.00 0.00 5.92
1864 1883 3.833070 ACGTACAAGGAGATTGAGAAGGT 59.167 43.478 0.00 0.00 41.83 3.50
1922 1941 1.635487 AGAAGCCAGCCCAGATACAAA 59.365 47.619 0.00 0.00 0.00 2.83
2004 2023 0.619832 TGCTCCTTGGAGGATCTGCT 60.620 55.000 17.33 0.00 44.81 4.24
2145 2164 1.539827 CCCTTGTCCAACGGAATGTTC 59.460 52.381 0.00 0.00 39.29 3.18
2146 2165 1.616159 CCCTTGTCCAACGGAATGTT 58.384 50.000 0.00 0.00 43.09 2.71
2147 2166 0.251165 CCCCTTGTCCAACGGAATGT 60.251 55.000 0.00 0.00 31.38 2.71


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

AutoCloner maintained by Alex Coulton.