Multiple sequence alignment - TraesCS5D01G278700

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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 TraesCS5D01G278700 chr5D 100.000 5459 0 0 1 5459 381020733 381026191 0.000000e+00 10081.0
1 TraesCS5D01G278700 chr5D 80.612 392 37 19 593 958 380854097 380854475 3.240000e-67 267.0
2 TraesCS5D01G278700 chr5D 84.000 150 6 9 1 149 380852387 380852519 1.600000e-25 128.0
3 TraesCS5D01G278700 chr5B 89.368 3800 222 101 7 3722 457119790 457123491 0.000000e+00 4612.0
4 TraesCS5D01G278700 chr5B 89.399 1764 127 31 3708 5426 457123511 457125259 0.000000e+00 2167.0
5 TraesCS5D01G278700 chr5B 80.913 241 22 11 1 230 457018066 457018293 9.400000e-38 169.0
6 TraesCS5D01G278700 chr5B 86.014 143 8 5 427 562 457018659 457018796 5.700000e-30 143.0
7 TraesCS5D01G278700 chr5B 94.595 37 2 0 5423 5459 57017476 57017512 2.120000e-04 58.4
8 TraesCS5D01G278700 chr5A 94.655 2058 83 13 3383 5426 481891691 481893735 0.000000e+00 3166.0
9 TraesCS5D01G278700 chr5A 93.626 1459 77 15 1930 3380 481890080 481891530 0.000000e+00 2165.0
10 TraesCS5D01G278700 chr5A 81.980 1010 100 49 634 1621 481888858 481889807 0.000000e+00 782.0
11 TraesCS5D01G278700 chr5A 79.082 937 84 68 1 879 481888231 481889113 4.810000e-150 542.0
12 TraesCS5D01G278700 chr5A 93.333 195 13 0 1744 1938 481889859 481890053 6.920000e-74 289.0
13 TraesCS5D01G278700 chr1A 93.750 64 4 0 2925 2988 333536581 333536644 4.500000e-16 97.1
14 TraesCS5D01G278700 chr1D 100.000 37 0 0 5423 5459 207658418 207658382 9.810000e-08 69.4
15 TraesCS5D01G278700 chr6A 97.436 39 1 0 5421 5459 100668018 100668056 3.530000e-07 67.6
16 TraesCS5D01G278700 chr6A 97.297 37 1 0 5423 5459 119604382 119604346 4.570000e-06 63.9
17 TraesCS5D01G278700 chr7D 94.595 37 2 0 5423 5459 309508850 309508814 2.120000e-04 58.4


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 TraesCS5D01G278700 chr5D 381020733 381026191 5458 False 10081.0 10081 100.0000 1 5459 1 chr5D.!!$F1 5458
1 TraesCS5D01G278700 chr5B 457119790 457125259 5469 False 3389.5 4612 89.3835 7 5426 2 chr5B.!!$F3 5419
2 TraesCS5D01G278700 chr5A 481888231 481893735 5504 False 1388.8 3166 88.5352 1 5426 5 chr5A.!!$F1 5425


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
92 94 0.036732 GGAGCATCACCAGTTCACCA 59.963 55.0 0.0 0.0 36.25 4.17 F
1092 1200 0.034767 CCTCCTGCAATCTCCAGCAA 60.035 55.0 0.0 0.0 40.73 3.91 F
1806 1938 0.029300 CCTTGTGTGCCGTTTCAGTG 59.971 55.0 0.0 0.0 0.00 3.66 F
2153 2321 0.793104 CGCCGAATCGCAAGGTTTTC 60.793 55.0 0.0 0.0 43.78 2.29 F
4112 4495 0.114954 ATTGCCCACACCATTGTCCT 59.885 50.0 0.0 0.0 31.66 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1824 0.108851 CCATGCCAAAACCCGCTAAC 60.109 55.0 0.00 0.0 0.00 2.34 R
2104 2271 0.171903 AATGTGCGAGGATTTGCAGC 59.828 50.0 0.00 0.0 44.28 5.25 R
2618 2792 1.032794 CGCATCTGTCTAGCACCCTA 58.967 55.0 0.00 0.0 0.00 3.53 R
4130 4513 0.523072 CTGCCACAGGGTGAATTTCG 59.477 55.0 0.00 0.0 35.23 3.46 R
5366 5793 0.097325 CGAGTCGTCTCTTTCCCGAG 59.903 60.0 3.82 0.0 38.45 4.63 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)



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AutoCloner maintained by Alex Coulton.