Multiple sequence alignment - TraesCS7B01G065200

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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 TraesCS7B01G065200 chr7B 100.000 4973 0 0 1 4973 70528228 70523256 0.000000e+00 9184.0
1 TraesCS7B01G065200 chr7D 89.548 2411 169 34 1866 4225 111066046 111063668 0.000000e+00 2979.0
2 TraesCS7B01G065200 chr7D 90.931 838 49 13 805 1629 111067088 111066265 0.000000e+00 1101.0
3 TraesCS7B01G065200 chr7D 81.714 700 110 8 84 779 111067851 111067166 7.220000e-158 568.0
4 TraesCS7B01G065200 chr7D 86.145 332 30 8 4575 4898 111063316 111062993 1.330000e-90 344.0
5 TraesCS7B01G065200 chr7A 90.823 1373 79 32 3019 4363 116128918 116127565 0.000000e+00 1794.0
6 TraesCS7B01G065200 chr7A 90.827 665 34 10 810 1467 116130720 116130076 0.000000e+00 865.0
7 TraesCS7B01G065200 chr7A 90.036 281 21 4 785 1059 116146302 116146023 1.700000e-94 357.0
8 TraesCS7B01G065200 chr7A 81.324 423 36 15 4561 4973 116127347 116126958 2.250000e-78 303.0
9 TraesCS7B01G065200 chr7A 91.667 72 6 0 342 413 116146588 116146517 3.170000e-17 100.0
10 TraesCS7B01G065200 chr6D 95.833 48 2 0 1642 1689 378290424 378290377 1.480000e-10 78.7
11 TraesCS7B01G065200 chr6B 95.833 48 2 0 1642 1689 221293184 221293137 1.480000e-10 78.7
12 TraesCS7B01G065200 chr6B 95.833 48 2 0 1642 1689 572555543 572555496 1.480000e-10 78.7
13 TraesCS7B01G065200 chr4D 94.118 51 3 0 1642 1692 329882975 329883025 1.480000e-10 78.7
14 TraesCS7B01G065200 chr3D 92.727 55 3 1 1642 1696 591338402 591338455 1.480000e-10 78.7
15 TraesCS7B01G065200 chr3B 95.833 48 2 0 1642 1689 57556456 57556409 1.480000e-10 78.7
16 TraesCS7B01G065200 chr3B 89.655 58 5 1 1642 1698 590683152 590683209 6.910000e-09 73.1
17 TraesCS7B01G065200 chr1A 90.909 55 5 0 1642 1696 102806141 102806195 1.920000e-09 75.0
18 TraesCS7B01G065200 chr5B 90.741 54 5 0 1642 1695 173565314 173565261 6.910000e-09 73.1


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 TraesCS7B01G065200 chr7B 70523256 70528228 4972 True 9184.000000 9184 100.0000 1 4973 1 chr7B.!!$R1 4972
1 TraesCS7B01G065200 chr7D 111062993 111067851 4858 True 1248.000000 2979 87.0845 84 4898 4 chr7D.!!$R1 4814
2 TraesCS7B01G065200 chr7A 116126958 116130720 3762 True 987.333333 1794 87.6580 810 4973 3 chr7A.!!$R1 4163
3 TraesCS7B01G065200 chr7A 116146023 116146588 565 True 228.500000 357 90.8515 342 1059 2 chr7A.!!$R2 717


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
477 483 0.038526 TCGTGGGAGCTCGAGAAAAC 60.039 55.0 18.75 5.41 0.00 2.43 F
569 575 0.311165 TCGCCTATGAAGAGTAGCGC 59.689 55.0 0.00 0.00 0.00 5.92 F
722 729 0.322816 TGCTTCAATGGTGAGGGCTC 60.323 55.0 0.00 0.00 36.16 4.70 F
1806 1955 0.831307 ACGGATTTGGGGCTCTAGTC 59.169 55.0 0.00 0.00 0.00 2.59 F
2934 3165 0.033405 CGGTCCCTCCTACTTCCTCA 60.033 60.0 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1304 1399 0.104671 CCTGCAACCAACCAACCAAG 59.895 55.0 0.0 0.0 0.00 3.61 R
1483 1578 0.388659 TGGATGCACAAACTGTTGCC 59.611 50.0 0.0 0.0 38.39 4.52 R
1823 1972 0.823356 ACACGCCCTTGCAACTTGAT 60.823 50.0 0.0 0.0 37.32 2.57 R
3293 4035 0.037975 GGTCATGGCAAGGTGCTTTG 60.038 55.0 0.0 0.0 44.28 2.77 R
4438 5284 0.182299 TTGGACACATGACACTGGCA 59.818 50.0 0.0 0.0 0.00 4.92 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.