Multiple sequence alignment - TraesCS6D01G060600

Loading Multiple Alignment...

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 TraesCS6D01G060600 chr6D 100.000 2364 0 0 1 2364 28310706 28308343 0.000000e+00 4366.0
1 TraesCS6D01G060600 chr6D 93.358 1611 60 18 688 2273 420225684 420224096 0.000000e+00 2338.0
2 TraesCS6D01G060600 chr6D 95.468 331 13 2 1 331 420228697 420228369 5.790000e-146 527.0
3 TraesCS6D01G060600 chr6D 88.312 385 34 7 630 1006 13921681 13922062 3.580000e-123 451.0
4 TraesCS6D01G060600 chr6D 90.123 162 10 3 1286 1442 13922058 13922218 3.080000e-49 206.0
5 TraesCS6D01G060600 chr7D 93.147 2364 113 23 1 2337 44717284 44714943 0.000000e+00 3422.0
6 TraesCS6D01G060600 chr6A 93.384 2358 58 19 1 2334 29577340 29579623 0.000000e+00 3400.0
7 TraesCS6D01G060600 chr6A 100.000 31 0 0 2334 2364 29579644 29579674 9.130000e-05 58.4
8 TraesCS6D01G060600 chr5D 92.002 2388 97 24 1 2337 441569756 441567412 0.000000e+00 3265.0
9 TraesCS6D01G060600 chr5D 91.420 1387 59 23 961 2332 490431474 490430133 0.000000e+00 1847.0
10 TraesCS6D01G060600 chr5D 94.333 900 37 7 1 889 490437530 490436634 0.000000e+00 1367.0
11 TraesCS6D01G060600 chr5D 100.000 29 0 0 2334 2362 490430110 490430082 1.000000e-03 54.7
12 TraesCS6D01G060600 chr7A 93.340 2132 96 22 1 2109 47295339 47293231 0.000000e+00 3109.0
13 TraesCS6D01G060600 chr7A 89.416 274 13 3 2064 2337 47293235 47292978 4.870000e-87 331.0
14 TraesCS6D01G060600 chr5A 93.750 2032 81 15 335 2337 611977603 611975589 0.000000e+00 3007.0
15 TraesCS6D01G060600 chr5A 95.455 330 14 1 1 330 611978630 611978302 2.080000e-145 525.0
16 TraesCS6D01G060600 chr5A 100.000 29 0 0 2334 2362 611975571 611975543 1.000000e-03 54.7
17 TraesCS6D01G060600 chr5B 93.671 1975 79 17 390 2337 604858078 604856123 0.000000e+00 2913.0
18 TraesCS6D01G060600 chr5B 94.878 410 21 0 1 410 604871957 604872366 1.980000e-180 641.0
19 TraesCS6D01G060600 chr5B 100.000 29 0 0 2334 2362 604856105 604856077 1.000000e-03 54.7
20 TraesCS6D01G060600 chr4A 80.129 775 119 28 917 1682 542044242 542043494 1.600000e-151 545.0
21 TraesCS6D01G060600 chr4A 94.562 331 17 1 1 331 581493293 581492964 5.830000e-141 510.0
22 TraesCS6D01G060600 chr3A 90.842 273 20 3 2044 2315 128520855 128520587 6.210000e-96 361.0
23 TraesCS6D01G060600 chr2B 82.373 295 38 6 323 606 138115682 138115391 6.530000e-61 244.0
24 TraesCS6D01G060600 chr1D 82.166 314 22 8 1741 2050 310148264 310148547 3.040000e-59 239.0
25 TraesCS6D01G060600 chr1A 93.210 162 8 3 2044 2203 389877130 389877290 3.930000e-58 235.0
26 TraesCS6D01G060600 chr1A 92.500 120 6 1 2196 2315 389877448 389877564 4.040000e-38 169.0
27 TraesCS6D01G060600 chr4D 86.667 210 20 4 917 1125 55035065 55035267 2.360000e-55 226.0
28 TraesCS6D01G060600 chr2A 86.471 170 20 1 433 599 46323254 46323085 1.440000e-42 183.0


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 TraesCS6D01G060600 chr6D 28308343 28310706 2363 True 4366.000000 4366 100.000000 1 2364 1 chr6D.!!$R1 2363
1 TraesCS6D01G060600 chr6D 420224096 420228697 4601 True 1432.500000 2338 94.413000 1 2273 2 chr6D.!!$R2 2272
2 TraesCS6D01G060600 chr6D 13921681 13922218 537 False 328.500000 451 89.217500 630 1442 2 chr6D.!!$F1 812
3 TraesCS6D01G060600 chr7D 44714943 44717284 2341 True 3422.000000 3422 93.147000 1 2337 1 chr7D.!!$R1 2336
4 TraesCS6D01G060600 chr6A 29577340 29579674 2334 False 1729.200000 3400 96.692000 1 2364 2 chr6A.!!$F1 2363
5 TraesCS6D01G060600 chr5D 441567412 441569756 2344 True 3265.000000 3265 92.002000 1 2337 1 chr5D.!!$R1 2336
6 TraesCS6D01G060600 chr5D 490436634 490437530 896 True 1367.000000 1367 94.333000 1 889 1 chr5D.!!$R2 888
7 TraesCS6D01G060600 chr5D 490430082 490431474 1392 True 950.850000 1847 95.710000 961 2362 2 chr5D.!!$R3 1401
8 TraesCS6D01G060600 chr7A 47292978 47295339 2361 True 1720.000000 3109 91.378000 1 2337 2 chr7A.!!$R1 2336
9 TraesCS6D01G060600 chr5A 611975543 611978630 3087 True 1195.566667 3007 96.401667 1 2362 3 chr5A.!!$R1 2361
10 TraesCS6D01G060600 chr5B 604856077 604858078 2001 True 1483.850000 2913 96.835500 390 2362 2 chr5B.!!$R1 1972
11 TraesCS6D01G060600 chr4A 542043494 542044242 748 True 545.000000 545 80.129000 917 1682 1 chr4A.!!$R1 765

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
940 3356 1.007387 GGGTGCGCTGGTTTTCAAG 60.007 57.895 9.73 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 4733 2.874701 ACTTCATGTGATTCGCCATAGC 59.125 45.455 0.0 0.0 0.0 2.97 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
399 1102 3.845781 TCTTGTGTTCTGCCTTTCTCT 57.154 42.857 0.00 0.00 0.00 3.10
532 1643 9.606631 ACTTATTTCAGAGATGATTGGAGTAAC 57.393 33.333 0.00 0.00 0.00 2.50
535 1646 4.023980 TCAGAGATGATTGGAGTAACCGT 58.976 43.478 0.00 0.00 42.61 4.83
536 1647 4.466370 TCAGAGATGATTGGAGTAACCGTT 59.534 41.667 0.00 0.00 42.61 4.44
537 1648 5.046591 TCAGAGATGATTGGAGTAACCGTTT 60.047 40.000 0.00 0.00 42.61 3.60
539 1650 6.255887 CAGAGATGATTGGAGTAACCGTTTAC 59.744 42.308 0.00 0.00 42.61 2.01
541 1652 3.587923 TGATTGGAGTAACCGTTTACCG 58.412 45.455 0.00 0.00 38.79 4.02
568 1679 4.687948 CAGTAGCCACCATCTAATCGAATG 59.312 45.833 0.00 0.00 0.00 2.67
696 3072 3.004315 ACGGCAATACTGGTGAACAAAAG 59.996 43.478 0.00 0.00 0.00 2.27
938 3354 2.124109 TGGGTGCGCTGGTTTTCA 60.124 55.556 9.73 0.00 0.00 2.69
940 3356 1.007387 GGGTGCGCTGGTTTTCAAG 60.007 57.895 9.73 0.00 0.00 3.02
1026 3445 1.254026 TACAGTGCTACACGCCTCTT 58.746 50.000 0.00 0.00 39.64 2.85
1050 3469 2.201210 CCCCAACTGGCCCAAGTT 59.799 61.111 0.00 0.32 41.08 2.66
1053 3472 0.758685 CCCAACTGGCCCAAGTTTCA 60.759 55.000 5.74 0.00 38.34 2.69
1175 3595 0.873721 TGTTGATGTGTGGATGCACG 59.126 50.000 13.03 0.00 41.94 5.34
1319 3740 1.811941 GCCAGCCCTTCTCTAAATCGG 60.812 57.143 0.00 0.00 0.00 4.18
1480 3915 7.069578 AGGAGTAGCAGATTTTACGGATCTTTA 59.930 37.037 0.00 0.00 31.66 1.85
1522 3958 9.638239 TGCTTCATCAAATGGAAATTTAAGTAC 57.362 29.630 0.00 0.00 0.00 2.73
1901 4349 8.390921 TCCCAGTATTCTCCTAAATCTTTTTGT 58.609 33.333 0.00 0.00 0.00 2.83
1915 4363 7.992180 AATCTTTTTGTTGTCTTGATGTGAC 57.008 32.000 0.00 0.00 35.21 3.67
2011 4459 9.725019 CTAATTATCTGCAATCCACAGGTTATA 57.275 33.333 0.00 0.00 35.78 0.98
2072 4535 9.388506 CCTTCTCTGTTATGATATTGTTGTCTT 57.611 33.333 0.00 0.00 0.00 3.01
2180 4684 2.706339 ATTCTGTGGATGCTCCTCAC 57.294 50.000 4.21 0.00 35.34 3.51
2229 4733 8.905660 ATCAATTCTCTGGATGTTCTTCATAG 57.094 34.615 0.00 0.00 36.83 2.23
2262 4766 8.229811 CGAATCACATGAAGTTCAAATGTTAGA 58.770 33.333 10.14 5.97 32.27 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 15 6.755141 CCATGAATAATGCCAGAAGAACAAAG 59.245 38.462 0.00 0.00 34.67 2.77
106 108 0.107312 AGTAGCCAGGCAAGCTCATG 60.107 55.000 15.80 0.00 41.83 3.07
222 227 0.779997 AGCAACCCCAATGGACTCTT 59.220 50.000 0.00 0.00 38.00 2.85
223 228 0.329596 GAGCAACCCCAATGGACTCT 59.670 55.000 0.00 0.00 38.00 3.24
535 1646 1.002315 GGTGGCTACTGAACCGGTAAA 59.998 52.381 8.00 0.00 0.00 2.01
536 1647 0.609662 GGTGGCTACTGAACCGGTAA 59.390 55.000 8.00 0.00 0.00 2.85
537 1648 0.542467 TGGTGGCTACTGAACCGGTA 60.542 55.000 8.00 0.00 36.73 4.02
539 1650 0.462047 GATGGTGGCTACTGAACCGG 60.462 60.000 0.00 0.00 36.73 5.28
541 1652 3.906720 TTAGATGGTGGCTACTGAACC 57.093 47.619 0.00 0.00 34.38 3.62
542 1653 4.051922 CGATTAGATGGTGGCTACTGAAC 58.948 47.826 0.00 0.00 0.00 3.18
543 1654 3.958147 TCGATTAGATGGTGGCTACTGAA 59.042 43.478 0.00 0.00 0.00 3.02
545 1656 4.322080 TTCGATTAGATGGTGGCTACTG 57.678 45.455 0.00 0.00 0.00 2.74
546 1657 4.588951 TCATTCGATTAGATGGTGGCTACT 59.411 41.667 0.00 0.00 0.00 2.57
547 1658 4.686554 GTCATTCGATTAGATGGTGGCTAC 59.313 45.833 0.00 0.00 0.00 3.58
548 1659 4.343814 TGTCATTCGATTAGATGGTGGCTA 59.656 41.667 0.00 0.00 0.00 3.93
907 3321 1.269726 GCACCCACACATTCCAAAGTG 60.270 52.381 0.00 0.00 41.40 3.16
1050 3469 5.470777 CGTGTTAATGGAAGGGTTAACTGAA 59.529 40.000 5.42 0.00 40.01 3.02
1053 3472 5.231702 TCGTGTTAATGGAAGGGTTAACT 57.768 39.130 5.42 0.00 40.01 2.24
1175 3595 8.468399 AGTATTAGAATAACTAATCGCTAGCCC 58.532 37.037 9.66 0.00 45.35 5.19
1240 3660 0.391793 GCACTGACTCTGTAAGGCCC 60.392 60.000 0.00 0.00 28.35 5.80
1367 3796 6.808008 AATGAAATATGGCCAGAGATAACG 57.192 37.500 13.05 0.00 0.00 3.18
1522 3958 1.134521 TCCATTTGACGAATCTCCCGG 60.135 52.381 0.00 0.00 0.00 5.73
1818 4258 7.008628 CGGAACAAAGTACTAAACCGTATAGTG 59.991 40.741 14.34 0.00 35.34 2.74
1901 4349 4.622260 TGATCAGGTCACATCAAGACAA 57.378 40.909 0.00 0.00 37.74 3.18
1915 4363 4.822350 AGTTCATGCATTCTGATGATCAGG 59.178 41.667 21.27 7.61 44.39 3.86
2180 4684 4.481930 TTGCCAAACTTCATAACGAGTG 57.518 40.909 0.00 0.00 0.00 3.51
2229 4733 2.874701 ACTTCATGTGATTCGCCATAGC 59.125 45.455 0.00 0.00 0.00 2.97
2262 4766 6.183360 GCCGAACACACAACTTATTAGCTATT 60.183 38.462 0.00 0.00 0.00 1.73


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.