Multiple sequence alignment - TraesCS6A01G261900

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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 TraesCS6A01G261900 chr6A 100.000 4415 0 0 1 4415 485109130 485104716 0.000000e+00 8154
1 TraesCS6A01G261900 chr6A 74.783 460 83 23 442 876 404633047 404633498 4.540000e-40 176
2 TraesCS6A01G261900 chr6D 96.087 3552 85 24 898 4410 344368143 344364607 0.000000e+00 5740
3 TraesCS6A01G261900 chr6D 85.011 934 63 18 1 904 344370368 344369482 0.000000e+00 878
4 TraesCS6A01G261900 chr6D 91.781 73 6 0 4343 4415 37932505 37932577 7.810000e-18 102
5 TraesCS6A01G261900 chr6B 97.953 2833 51 2 936 3767 520240816 520237990 0.000000e+00 4903
6 TraesCS6A01G261900 chr6B 91.785 353 21 6 3960 4309 520230779 520230432 6.640000e-133 484
7 TraesCS6A01G261900 chr6B 75.219 456 80 23 445 876 51740750 51740304 7.540000e-43 185
8 TraesCS6A01G261900 chr6B 82.888 187 27 5 442 626 260118379 260118562 3.530000e-36 163
9 TraesCS6A01G261900 chr6B 93.333 75 5 0 4341 4415 520230303 520230229 1.300000e-20 111
10 TraesCS6A01G261900 chr2D 76.872 454 74 22 442 874 71203078 71203521 1.240000e-55 228
11 TraesCS6A01G261900 chr2D 83.069 189 27 5 442 628 579325914 579326099 2.730000e-37 167
12 TraesCS6A01G261900 chr4B 81.293 294 35 9 66 344 406750108 406750396 2.070000e-53 220
13 TraesCS6A01G261900 chr4B 82.796 186 28 4 445 628 615385314 615385131 3.530000e-36 163
14 TraesCS6A01G261900 chr4B 91.781 73 6 0 4343 4415 602210499 602210427 7.810000e-18 102
15 TraesCS6A01G261900 chr7A 75.870 460 77 24 442 876 191820456 191820906 2.080000e-48 204
16 TraesCS6A01G261900 chr1A 75.355 422 83 18 471 876 440670087 440670503 2.710000e-42 183
17 TraesCS6A01G261900 chr4D 82.979 188 27 5 442 627 488687425 488687609 9.820000e-37 165
18 TraesCS6A01G261900 chr3D 82.199 191 29 5 445 633 420484412 420484225 4.570000e-35 159
19 TraesCS6A01G261900 chr3D 91.781 73 6 0 4343 4415 526190426 526190354 7.810000e-18 102
20 TraesCS6A01G261900 chr3D 91.781 73 6 0 4343 4415 613354961 613354889 7.810000e-18 102
21 TraesCS6A01G261900 chr5B 74.017 458 87 21 445 876 338718188 338717737 1.640000e-34 158
22 TraesCS6A01G261900 chr4A 93.151 73 5 0 4343 4415 607312015 607312087 1.680000e-19 108
23 TraesCS6A01G261900 chr7D 91.781 73 6 0 4343 4415 7568358 7568286 7.810000e-18 102
24 TraesCS6A01G261900 chr5D 91.781 73 6 0 4343 4415 454727413 454727485 7.810000e-18 102
25 TraesCS6A01G261900 chr1D 91.781 73 6 0 4343 4415 431764122 431764050 7.810000e-18 102


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 TraesCS6A01G261900 chr6A 485104716 485109130 4414 True 8154.0 8154 100.000 1 4415 1 chr6A.!!$R1 4414
1 TraesCS6A01G261900 chr6D 344364607 344370368 5761 True 3309.0 5740 90.549 1 4410 2 chr6D.!!$R1 4409
2 TraesCS6A01G261900 chr6B 520237990 520240816 2826 True 4903.0 4903 97.953 936 3767 1 chr6B.!!$R2 2831
3 TraesCS6A01G261900 chr6B 520230229 520230779 550 True 297.5 484 92.559 3960 4415 2 chr6B.!!$R3 455


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
316 317 0.116342 TCTAGCCAGACAAGACCCCA 59.884 55.0 0.0 0.0 0.00 4.96 F
705 721 0.179062 GAGGCCGAACAGCAGATGAT 60.179 55.0 0.0 0.0 0.00 2.45 F
706 722 0.463295 AGGCCGAACAGCAGATGATG 60.463 55.0 0.0 0.0 37.48 3.07 F
2505 3881 0.251341 GTGTGGCTCTTGGGGATGTT 60.251 55.0 0.0 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 3142 1.203187 TCAGCTGTAGTTCCCTGGACT 60.203 52.381 14.67 0.0 0.00 3.85 R
2505 3881 1.131638 GGATCTCCATGCCACCTACA 58.868 55.000 0.00 0.0 35.64 2.74 R
2628 4004 3.745975 CACGGTTTGAGAGTGATAAGCAA 59.254 43.478 0.00 0.0 38.06 3.91 R
4097 5488 0.036388 TTCAATCCGACTGCCTCCAC 60.036 55.000 0.00 0.0 0.00 4.02 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.