Multiple sequence alignment - TraesCS5B01G490300

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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 TraesCS5B01G490300 chr5B 100.000 2489 0 0 1 2489 659550497 659548009 0.000000e+00 4597.0
1 TraesCS5B01G490300 chr5B 90.710 775 53 8 774 1534 659523444 659522675 0.000000e+00 1014.0
2 TraesCS5B01G490300 chr5B 90.444 743 60 3 828 1563 659506330 659505592 0.000000e+00 968.0
3 TraesCS5B01G490300 chr5B 80.299 670 53 37 139 763 659532474 659531839 1.370000e-117 433.0
4 TraesCS5B01G490300 chr5B 82.150 493 62 20 37 521 659507361 659506887 1.390000e-107 399.0
5 TraesCS5B01G490300 chr5B 92.607 257 8 4 556 807 659506884 659506634 2.350000e-95 359.0
6 TraesCS5B01G490300 chr5B 82.045 401 49 13 1138 1534 659471590 659471209 1.110000e-83 320.0
7 TraesCS5B01G490300 chr5B 79.481 424 63 17 1000 1417 659704430 659704835 1.890000e-71 279.0
8 TraesCS5B01G490300 chr5B 85.876 177 17 5 2270 2442 659521849 659521677 5.470000e-42 182.0
9 TraesCS5B01G490300 chr5B 91.379 58 3 2 2005 2062 659521992 659521937 7.380000e-11 78.7
10 TraesCS5B01G490300 chr5A 91.130 1567 88 23 111 1657 651541587 651540052 0.000000e+00 2076.0
11 TraesCS5B01G490300 chr5A 85.675 1445 102 44 267 1674 651529109 651527733 0.000000e+00 1424.0
12 TraesCS5B01G490300 chr5A 84.821 112 8 6 2218 2328 651539462 651539359 1.220000e-18 104.0
13 TraesCS5B01G490300 chr5D 90.594 1297 72 17 289 1568 525127273 525126010 0.000000e+00 1674.0
14 TraesCS5B01G490300 chr5D 85.846 1519 109 55 38 1534 525178431 525176997 0.000000e+00 1517.0
15 TraesCS5B01G490300 chr5D 82.090 402 47 15 1138 1534 525086305 525085924 1.110000e-83 320.0
16 TraesCS5B01G490300 chr5D 86.139 101 8 3 2227 2327 525123449 525123355 1.220000e-18 104.0
17 TraesCS5B01G490300 chr5D 82.540 126 15 6 1800 1921 525176848 525176726 1.220000e-18 104.0
18 TraesCS5B01G490300 chr5D 95.833 48 2 0 2442 2489 525176437 525176390 7.380000e-11 78.7


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 TraesCS5B01G490300 chr5B 659548009 659550497 2488 True 4597.000000 4597 100.000000 1 2489 1 chr5B.!!$R3 2488
1 TraesCS5B01G490300 chr5B 659505592 659507361 1769 True 575.333333 968 88.400333 37 1563 3 chr5B.!!$R4 1526
2 TraesCS5B01G490300 chr5B 659531839 659532474 635 True 433.000000 433 80.299000 139 763 1 chr5B.!!$R2 624
3 TraesCS5B01G490300 chr5B 659521677 659523444 1767 True 424.900000 1014 89.321667 774 2442 3 chr5B.!!$R5 1668
4 TraesCS5B01G490300 chr5A 651527733 651529109 1376 True 1424.000000 1424 85.675000 267 1674 1 chr5A.!!$R1 1407
5 TraesCS5B01G490300 chr5A 651539359 651541587 2228 True 1090.000000 2076 87.975500 111 2328 2 chr5A.!!$R2 2217
6 TraesCS5B01G490300 chr5D 525123355 525127273 3918 True 889.000000 1674 88.366500 289 2327 2 chr5D.!!$R2 2038
7 TraesCS5B01G490300 chr5D 525176390 525178431 2041 True 566.566667 1517 88.073000 38 2489 3 chr5D.!!$R3 2451


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
68 69 0.250513 GAACGTGATCTCAAGGCCCT 59.749 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 3488 1.13379 CACCCCTACACTAGTGCGTAC 59.866 57.143 22.9 0.0 0.0 3.67 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.