Multiple sequence alignment - TraesCS6A01G113800

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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 TraesCS6A01G113800 chr6A 100.000 4530 0 0 1 4530 83651583 83647054 0.000000e+00 8366.0
1 TraesCS6A01G113800 chr6A 91.071 56 3 2 4230 4283 83363924 83363869 1.750000e-09 75.0
2 TraesCS6A01G113800 chr6D 91.051 1151 83 10 2790 3937 65090783 65091916 0.000000e+00 1537.0
3 TraesCS6A01G113800 chr6D 89.640 1168 92 18 1637 2783 65089020 65090179 0.000000e+00 1459.0
4 TraesCS6A01G113800 chr6D 94.173 532 23 5 3999 4529 65092118 65092642 0.000000e+00 804.0
5 TraesCS6A01G113800 chr6D 86.916 749 35 23 872 1605 65088200 65088900 0.000000e+00 782.0
6 TraesCS6A01G113800 chr6D 87.755 147 18 0 1 147 305165340 305165194 6.020000e-39 172.0
7 TraesCS6A01G113800 chr6D 95.833 72 3 0 3904 3975 65091918 65091989 2.860000e-22 117.0
8 TraesCS6A01G113800 chr6B 89.732 1081 84 9 2790 3865 140092109 140093167 0.000000e+00 1356.0
9 TraesCS6A01G113800 chr6B 88.133 809 47 21 811 1605 140089490 140090263 0.000000e+00 917.0
10 TraesCS6A01G113800 chr6B 81.443 679 69 23 1636 2289 140090387 140091033 1.880000e-138 503.0
11 TraesCS6A01G113800 chr6B 93.907 279 16 1 4011 4289 140093344 140093621 1.950000e-113 420.0
12 TraesCS6A01G113800 chr6B 86.765 204 24 3 363 566 140070300 140070500 1.640000e-54 224.0
13 TraesCS6A01G113800 chr6B 93.043 115 6 2 4416 4529 140093622 140093735 2.800000e-37 167.0
14 TraesCS6A01G113800 chr6B 100.000 30 0 0 3906 3935 140093191 140093220 6.330000e-04 56.5
15 TraesCS6A01G113800 chr1B 90.278 144 13 1 1 144 340158260 340158402 2.150000e-43 187.0
16 TraesCS6A01G113800 chr1B 89.116 147 15 1 1 147 338620683 338620538 1.000000e-41 182.0
17 TraesCS6A01G113800 chr1B 88.889 144 15 1 1 144 340321297 340321439 4.660000e-40 176.0
18 TraesCS6A01G113800 chr2D 89.655 145 14 1 3 147 368477217 368477074 2.780000e-42 183.0
19 TraesCS6A01G113800 chr2A 89.116 147 16 0 1 147 498559419 498559273 2.780000e-42 183.0
20 TraesCS6A01G113800 chr4D 89.437 142 15 0 3 144 478523915 478524056 3.600000e-41 180.0
21 TraesCS6A01G113800 chr2B 89.928 139 14 0 3 141 437232260 437232122 3.600000e-41 180.0
22 TraesCS6A01G113800 chr3D 88.000 150 14 3 1 147 63255114 63255262 1.680000e-39 174.0


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 TraesCS6A01G113800 chr6A 83647054 83651583 4529 True 8366.000000 8366 100.0000 1 4530 1 chr6A.!!$R2 4529
1 TraesCS6A01G113800 chr6D 65088200 65092642 4442 False 939.800000 1537 91.5226 872 4529 5 chr6D.!!$F1 3657
2 TraesCS6A01G113800 chr6B 140089490 140093735 4245 False 569.916667 1356 91.0430 811 4529 6 chr6B.!!$F2 3718


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
279 280 0.031721 AGTTTCGTGTCTCCGTCACC 59.968 55.0 0.0 0.0 32.86 4.02 F
515 516 0.036671 GGTGGATCTCGTCGGGTTTT 60.037 55.0 0.0 0.0 0.00 2.43 F
674 675 0.175989 GGTAAGAGAGGAAGCGGTGG 59.824 60.0 0.0 0.0 0.00 4.61 F
708 709 0.443869 CTACATGGCGAGTGCAACAC 59.556 55.0 0.0 0.0 45.35 3.32 F
967 971 0.615331 TACAGCAGAGAAGCCTTGGG 59.385 55.0 0.0 0.0 34.23 4.12 F
2162 2312 0.187117 TGTGCATTTCCCCAAGGACA 59.813 50.0 0.0 0.0 43.90 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1722 0.036294 GCCCGCCTAACTTCTCTTGT 60.036 55.000 0.00 0.0 0.00 3.16 R
1639 1726 0.104487 GGTAGCCCGCCTAACTTCTC 59.896 60.000 0.00 0.0 30.73 2.87 R
1986 2136 1.267121 TCCAGAAACTAGAAGGCGCT 58.733 50.000 7.64 0.0 0.00 5.92 R
2029 2179 1.282157 GGAACCCTGAACTAGCCACAT 59.718 52.381 0.00 0.0 0.00 3.21 R
2814 3633 0.034574 TGGGTTGTATGCGCTTGGAT 60.035 50.000 9.73 0.0 0.00 3.41 R
3597 4422 0.469144 TTTCTCCCCACACAAAGGGC 60.469 55.000 0.00 0.0 45.39 5.19 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.