Multiple sequence alignment - TraesCS7D01G318000

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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 TraesCS7D01G318000 chr7D 100.000 2834 0 0 1 2834 405878995 405881828 0.000000e+00 5234.0
1 TraesCS7D01G318000 chr7D 90.909 77 4 3 2731 2807 586784245 586784172 1.800000e-17 100.0
2 TraesCS7D01G318000 chr7D 88.312 77 4 2 2731 2807 44398466 44398537 1.400000e-13 87.9
3 TraesCS7D01G318000 chr7D 88.312 77 4 2 2731 2807 44564110 44564181 1.400000e-13 87.9
4 TraesCS7D01G318000 chr7D 87.654 81 3 4 2731 2805 471054606 471054685 1.400000e-13 87.9
5 TraesCS7D01G318000 chr7B 96.888 2667 65 9 184 2834 413972324 413974988 0.000000e+00 4449.0
6 TraesCS7D01G318000 chr7B 96.970 99 3 0 1 99 413933176 413933274 1.750000e-37 167.0
7 TraesCS7D01G318000 chr7B 87.654 81 3 3 2731 2805 494742438 494742517 1.400000e-13 87.9
8 TraesCS7D01G318000 chr7A 95.458 2774 79 23 59 2791 463204065 463206832 0.000000e+00 4381.0
9 TraesCS7D01G318000 chr5D 91.892 74 5 1 2731 2804 549851430 549851358 4.990000e-18 102.0
10 TraesCS7D01G318000 chr4B 89.041 73 4 3 2731 2803 22815857 22815789 1.400000e-13 87.9


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 TraesCS7D01G318000 chr7D 405878995 405881828 2833 False 5234 5234 100.000 1 2834 1 chr7D.!!$F3 2833
1 TraesCS7D01G318000 chr7B 413972324 413974988 2664 False 4449 4449 96.888 184 2834 1 chr7B.!!$F2 2650
2 TraesCS7D01G318000 chr7A 463204065 463206832 2767 False 4381 4381 95.458 59 2791 1 chr7A.!!$F1 2732

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
906 954 0.251165 CCGTCCTTGTGGGTTGGATT 60.251 55.0 0.0 0.0 34.12 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1982 3.596046 AGTTCAAATCCCCTCCATTACCA 59.404 43.478 0.0 0.0 0.0 3.25 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 4.759516 ACACCGCGAGTTAAATTTTCAT 57.240 36.364 8.23 0.00 0.00 2.57
22 23 5.866335 ACACCGCGAGTTAAATTTTCATA 57.134 34.783 8.23 0.00 0.00 2.15
23 24 6.431198 ACACCGCGAGTTAAATTTTCATAT 57.569 33.333 8.23 0.00 0.00 1.78
24 25 6.848451 ACACCGCGAGTTAAATTTTCATATT 58.152 32.000 8.23 0.00 0.00 1.28
25 26 6.745450 ACACCGCGAGTTAAATTTTCATATTG 59.255 34.615 8.23 0.00 0.00 1.90
26 27 6.745450 CACCGCGAGTTAAATTTTCATATTGT 59.255 34.615 8.23 0.00 0.00 2.71
27 28 7.906010 CACCGCGAGTTAAATTTTCATATTGTA 59.094 33.333 8.23 0.00 0.00 2.41
28 29 8.617809 ACCGCGAGTTAAATTTTCATATTGTAT 58.382 29.630 8.23 0.00 0.00 2.29
99 100 8.085296 TCAAGTTTGCTAAGTTTGACTTTTCAA 58.915 29.630 0.00 2.01 39.51 2.69
166 179 8.796475 CCGGATCCAAATTGTATTGATCTAAAT 58.204 33.333 13.41 0.00 31.84 1.40
192 205 5.924475 AGTCAACCTAAATCACAAACTCG 57.076 39.130 0.00 0.00 0.00 4.18
294 328 6.605496 TTCTTTTAATGCATTTTCGTACGC 57.395 33.333 18.75 0.00 0.00 4.42
360 394 7.996098 TTGGACGATTTCCTAGAAAAAGAAT 57.004 32.000 0.00 0.00 46.10 2.40
471 517 1.467190 TCAAATCCCCACCCCACCT 60.467 57.895 0.00 0.00 0.00 4.00
696 742 4.695455 TCCGTGATCAAGAAATGGTCTTTC 59.305 41.667 10.47 0.00 44.64 2.62
697 743 4.697352 CCGTGATCAAGAAATGGTCTTTCT 59.303 41.667 10.47 0.00 44.64 2.52
698 744 5.163814 CCGTGATCAAGAAATGGTCTTTCTC 60.164 44.000 10.47 0.00 44.64 2.87
699 745 5.445142 CGTGATCAAGAAATGGTCTTTCTCG 60.445 44.000 2.01 0.00 44.64 4.04
700 746 4.393062 TGATCAAGAAATGGTCTTTCTCGC 59.607 41.667 0.00 0.00 44.64 5.03
743 790 0.327095 TAGTAATGGGGGCAGAGGCA 60.327 55.000 0.00 0.00 43.71 4.75
839 887 4.372999 GCCCCCTGCCAAGAAGCT 62.373 66.667 0.00 0.00 0.00 3.74
863 911 4.816984 GGTCGCCGGAGAGGAGGA 62.817 72.222 8.65 0.00 45.00 3.71
891 939 3.792053 ATCGCTGCCGGATTCCGTC 62.792 63.158 22.83 11.95 46.80 4.79
900 948 1.683441 GGATTCCGTCCTTGTGGGT 59.317 57.895 0.00 0.00 44.16 4.51
906 954 0.251165 CCGTCCTTGTGGGTTGGATT 60.251 55.000 0.00 0.00 34.12 3.01
931 980 3.327404 GAGGGCCCCGGTTCTTGA 61.327 66.667 21.43 0.00 0.00 3.02
942 991 2.000447 CGGTTCTTGAGGTTCGGAATC 59.000 52.381 0.00 0.00 0.00 2.52
1461 1513 4.690719 CCCCGTGCCGCACTTGTA 62.691 66.667 20.87 0.00 31.34 2.41
1602 1654 2.829384 GCCTATGGGGGATGGCGAA 61.829 63.158 0.00 0.00 35.79 4.70
1725 1777 2.050351 CAGTCGTCGCGGTCACTT 60.050 61.111 6.13 0.00 0.00 3.16
1957 2009 1.209747 GGAGGGGATTTGAACTACGCT 59.790 52.381 0.00 0.00 0.00 5.07
2092 2144 4.117685 ACGTTTGTGGTCTTTCTGTAGTC 58.882 43.478 0.00 0.00 0.00 2.59
2286 2340 6.093633 GGTAAGTAGCTATTTTCACACCTTGG 59.906 42.308 6.82 0.00 0.00 3.61
2362 2416 2.255406 CCATGGATTTGTTGTCCCCAA 58.745 47.619 5.56 0.00 34.76 4.12
2513 2567 4.541973 ATTGTCTTGGCTTGGGATTTTC 57.458 40.909 0.00 0.00 0.00 2.29
2734 2788 7.668525 TTCTCCTTTTTCTTCGGAAATACTC 57.331 36.000 0.00 0.00 42.61 2.59
2745 2799 6.383147 TCTTCGGAAATACTCCCTCTGTAAAT 59.617 38.462 0.00 0.00 41.87 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.759516 ATGAAAATTTAACTCGCGGTGT 57.240 36.364 6.13 2.54 0.00 4.16
1 2 6.745450 ACAATATGAAAATTTAACTCGCGGTG 59.255 34.615 6.13 1.77 0.00 4.94
2 3 6.848451 ACAATATGAAAATTTAACTCGCGGT 58.152 32.000 6.13 0.00 0.00 5.68
71 72 8.634475 AAAAGTCAAACTTAGCAAACTTGATC 57.366 30.769 0.00 0.00 37.47 2.92
137 150 7.689299 AGATCAATACAATTTGGATCCGGATA 58.311 34.615 19.15 1.03 0.00 2.59
141 154 9.616634 CATTTAGATCAATACAATTTGGATCCG 57.383 33.333 7.39 0.00 0.00 4.18
166 179 7.330946 CGAGTTTGTGATTTAGGTTGACTATCA 59.669 37.037 0.00 0.00 0.00 2.15
294 328 5.991606 TGTAGCTTTCGGATCATTATTGAGG 59.008 40.000 0.00 0.00 34.73 3.86
360 394 2.350192 CAGTGTGTGTGTGCGTTTCTTA 59.650 45.455 0.00 0.00 0.00 2.10
700 746 1.224075 AGAATCGCGCATCAAGGATG 58.776 50.000 8.75 1.90 42.37 3.51
869 917 1.643832 GAATCCGGCAGCGATTCAC 59.356 57.895 14.78 0.00 43.35 3.18
891 939 1.165270 GACGAATCCAACCCACAAGG 58.835 55.000 0.00 0.00 43.78 3.61
900 948 1.956629 GCCCTCTCCGACGAATCCAA 61.957 60.000 0.00 0.00 0.00 3.53
931 980 3.006728 TGCCCCGATTCCGAACCT 61.007 61.111 0.00 0.00 38.22 3.50
942 991 3.697747 TACGGACAACCTGCCCCG 61.698 66.667 0.00 0.00 40.91 5.73
983 1035 1.074727 TCATCAAAAGCCCCCGAAGAA 59.925 47.619 0.00 0.00 0.00 2.52
984 1036 0.695924 TCATCAAAAGCCCCCGAAGA 59.304 50.000 0.00 0.00 0.00 2.87
1326 1378 2.926250 AGGAACTGCAAGGCACCA 59.074 55.556 0.00 0.00 39.30 4.17
1396 1448 4.681978 GACAGCCGGAACCAGCGT 62.682 66.667 5.05 0.00 0.00 5.07
1602 1654 0.038599 TTGTGCCATGGTGCTCATCT 59.961 50.000 14.67 0.00 35.00 2.90
1930 1982 3.596046 AGTTCAAATCCCCTCCATTACCA 59.404 43.478 0.00 0.00 0.00 3.25
1957 2009 7.738847 TCATCTGATCCTGAACATATTGCTAA 58.261 34.615 0.00 0.00 0.00 3.09
2803 2857 7.820386 TCGTGCTTCAATAAATTTACAGGTAGA 59.180 33.333 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.