Multiple sequence alignment - TraesCS4D01G215900

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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 TraesCS4D01G215900 chr4D 100.000 3645 0 0 1 3645 369863702 369860058 0.000000e+00 6732.0
1 TraesCS4D01G215900 chr4D 98.996 2988 28 2 658 3645 369873537 369876522 0.000000e+00 5350.0
2 TraesCS4D01G215900 chr4D 97.528 890 11 4 1 888 249077988 249077108 0.000000e+00 1511.0
3 TraesCS4D01G215900 chr4D 77.431 288 53 10 2362 2643 97383997 97384278 1.050000e-35 161.0
4 TraesCS4D01G215900 chr4D 77.778 270 50 10 2370 2636 97379113 97379375 1.350000e-34 158.0
5 TraesCS4D01G215900 chr4D 85.185 81 12 0 1856 1936 349410899 349410819 2.330000e-12 84.2
6 TraesCS4D01G215900 chr4A 96.273 2522 89 3 955 3472 94823295 94825815 0.000000e+00 4132.0
7 TraesCS4D01G215900 chr4A 93.714 175 10 1 3472 3645 704519432 704519258 1.000000e-65 261.0
8 TraesCS4D01G215900 chr4B 95.695 2509 98 6 955 3457 455012727 455010223 0.000000e+00 4026.0
9 TraesCS4D01G215900 chr4B 76.817 289 55 10 2361 2643 139106968 139107250 6.300000e-33 152.0
10 TraesCS4D01G215900 chr4B 76.879 173 40 0 1772 1944 432257692 432257520 8.330000e-17 99.0
11 TraesCS4D01G215900 chr3D 98.649 888 8 2 1 888 121309014 121308131 0.000000e+00 1570.0
12 TraesCS4D01G215900 chr7D 98.086 888 8 1 1 888 178479699 178478821 0.000000e+00 1537.0
13 TraesCS4D01G215900 chr7D 95.923 883 11 8 1 882 175881344 175882202 0.000000e+00 1408.0
14 TraesCS4D01G215900 chr7D 93.916 904 41 12 1 893 21973480 21972580 0.000000e+00 1352.0
15 TraesCS4D01G215900 chr7D 93.729 893 44 10 1 882 116418132 116417241 0.000000e+00 1328.0
16 TraesCS4D01G215900 chr7D 92.737 179 11 2 3468 3645 576643959 576644136 1.300000e-64 257.0
17 TraesCS4D01G215900 chr5D 96.749 892 21 7 1 888 135673706 135674593 0.000000e+00 1480.0
18 TraesCS4D01G215900 chr5D 91.351 185 15 1 3462 3645 324409398 324409582 6.040000e-63 252.0
19 TraesCS4D01G215900 chr1D 96.637 892 23 4 1 890 296919945 296920831 0.000000e+00 1474.0
20 TraesCS4D01G215900 chr6D 96.437 898 21 6 1 888 286469791 286470687 0.000000e+00 1471.0
21 TraesCS4D01G215900 chr6D 92.778 180 11 2 3467 3645 464697145 464696967 3.610000e-65 259.0
22 TraesCS4D01G215900 chr6D 92.350 183 11 3 3465 3645 446133046 446133227 1.300000e-64 257.0
23 TraesCS4D01G215900 chr2D 95.349 172 7 1 3475 3645 276935676 276935847 4.640000e-69 272.0
24 TraesCS4D01G215900 chr2D 93.923 181 8 3 3467 3645 425743736 425743915 1.670000e-68 270.0
25 TraesCS4D01G215900 chr2D 94.186 172 9 1 3474 3644 285350084 285349913 1.000000e-65 261.0


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 TraesCS4D01G215900 chr4D 369860058 369863702 3644 True 6732 6732 100.000 1 3645 1 chr4D.!!$R3 3644
1 TraesCS4D01G215900 chr4D 369873537 369876522 2985 False 5350 5350 98.996 658 3645 1 chr4D.!!$F3 2987
2 TraesCS4D01G215900 chr4D 249077108 249077988 880 True 1511 1511 97.528 1 888 1 chr4D.!!$R1 887
3 TraesCS4D01G215900 chr4A 94823295 94825815 2520 False 4132 4132 96.273 955 3472 1 chr4A.!!$F1 2517
4 TraesCS4D01G215900 chr4B 455010223 455012727 2504 True 4026 4026 95.695 955 3457 1 chr4B.!!$R2 2502
5 TraesCS4D01G215900 chr3D 121308131 121309014 883 True 1570 1570 98.649 1 888 1 chr3D.!!$R1 887
6 TraesCS4D01G215900 chr7D 178478821 178479699 878 True 1537 1537 98.086 1 888 1 chr7D.!!$R3 887
7 TraesCS4D01G215900 chr7D 175881344 175882202 858 False 1408 1408 95.923 1 882 1 chr7D.!!$F1 881
8 TraesCS4D01G215900 chr7D 21972580 21973480 900 True 1352 1352 93.916 1 893 1 chr7D.!!$R1 892
9 TraesCS4D01G215900 chr7D 116417241 116418132 891 True 1328 1328 93.729 1 882 1 chr7D.!!$R2 881
10 TraesCS4D01G215900 chr5D 135673706 135674593 887 False 1480 1480 96.749 1 888 1 chr5D.!!$F1 887
11 TraesCS4D01G215900 chr1D 296919945 296920831 886 False 1474 1474 96.637 1 890 1 chr1D.!!$F1 889
12 TraesCS4D01G215900 chr6D 286469791 286470687 896 False 1471 1471 96.437 1 888 1 chr6D.!!$F1 887

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
122 123 1.878975 TGCGTGCGAACGAAGAACA 60.879 52.632 22.89 4.31 34.64 3.18 F
902 938 5.354842 AATTTAGCCACTAGTAGGTCACC 57.645 43.478 1.45 0.00 0.00 4.02 F
1327 1363 3.574396 CCTCCTTATCTACGGCAATGAGA 59.426 47.826 0.00 0.00 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1232 1268 1.089481 GCCAAGATCGCCGTTGATCA 61.089 55.000 14.33 0.0 45.81 2.92 R
1816 1852 2.304221 TCCAGCCGTATAGTAGCCAT 57.696 50.000 0.00 0.0 0.00 4.40 R
3551 3595 2.030007 ACCACAAACATGCCAAGATTCG 60.030 45.455 0.00 0.0 0.00 3.34 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
122 123 1.878975 TGCGTGCGAACGAAGAACA 60.879 52.632 22.89 4.31 34.64 3.18
902 938 5.354842 AATTTAGCCACTAGTAGGTCACC 57.645 43.478 1.45 0.00 0.00 4.02
1327 1363 3.574396 CCTCCTTATCTACGGCAATGAGA 59.426 47.826 0.00 0.00 0.00 3.27
1816 1852 1.070786 GGTGAGGCTTTGGACACGA 59.929 57.895 0.00 0.00 34.59 4.35
2188 2225 4.539870 ACTTTGCAACAATTCACGATGAG 58.460 39.130 0.00 0.00 0.00 2.90
3270 3314 2.425578 TGTCGCGTATGTCAGTTTCA 57.574 45.000 5.77 0.00 0.00 2.69
3551 3595 0.939106 GCGTTCATTTGTGGGTGCAC 60.939 55.000 8.80 8.80 0.00 4.57
3595 3639 2.269241 GTAGGACTGGGCTGGTGC 59.731 66.667 0.00 0.00 38.76 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 2.283351 CGTTCGTGGTTCTTCGTTCTTT 59.717 45.455 0.00 0.0 0.00 2.52
1232 1268 1.089481 GCCAAGATCGCCGTTGATCA 61.089 55.000 14.33 0.0 45.81 2.92
1327 1363 1.918800 CCACGAAGAACCCCCTCCT 60.919 63.158 0.00 0.0 0.00 3.69
1816 1852 2.304221 TCCAGCCGTATAGTAGCCAT 57.696 50.000 0.00 0.0 0.00 4.40
3551 3595 2.030007 ACCACAAACATGCCAAGATTCG 60.030 45.455 0.00 0.0 0.00 3.34


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

AutoCloner maintained by Alex Coulton.