Multiple sequence alignment - TraesCS6A01G192000

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 TraesCS6A01G192000 chr6A 100.000 2498 0 0 1 2498 260115639 260118136 0.000000e+00 4614
1 TraesCS6A01G192000 chrUn 97.960 2500 44 5 1 2498 93408990 93411484 0.000000e+00 4327
2 TraesCS6A01G192000 chrUn 98.061 2321 42 3 1 2319 216517961 216520280 0.000000e+00 4034
3 TraesCS6A01G192000 chr5D 97.959 2499 46 3 1 2498 503218859 503216365 0.000000e+00 4327
4 TraesCS6A01G192000 chr2D 97.840 2500 48 4 1 2498 272793252 272795747 0.000000e+00 4313
5 TraesCS6A01G192000 chr3B 97.760 2500 49 5 1 2498 201527665 201525171 0.000000e+00 4300
6 TraesCS6A01G192000 chr3A 97.242 2502 60 6 1 2498 672909366 672911862 0.000000e+00 4229
7 TraesCS6A01G192000 chr3A 95.455 66 3 0 2349 2414 198495309 198495244 3.400000e-19 106
8 TraesCS6A01G192000 chr5A 96.601 2501 77 5 1 2498 619267012 619264517 0.000000e+00 4141
9 TraesCS6A01G192000 chr6D 98.363 2321 35 3 1 2319 168255567 168253248 0.000000e+00 4072
10 TraesCS6A01G192000 chr3D 98.135 2091 34 4 1 2090 589278903 589280989 0.000000e+00 3640
11 TraesCS6A01G192000 chr2A 96.822 409 10 1 2090 2498 726910483 726910888 0.000000e+00 680


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 TraesCS6A01G192000 chr6A 260115639 260118136 2497 False 4614 4614 100.000 1 2498 1 chr6A.!!$F1 2497
1 TraesCS6A01G192000 chrUn 93408990 93411484 2494 False 4327 4327 97.960 1 2498 1 chrUn.!!$F1 2497
2 TraesCS6A01G192000 chrUn 216517961 216520280 2319 False 4034 4034 98.061 1 2319 1 chrUn.!!$F2 2318
3 TraesCS6A01G192000 chr5D 503216365 503218859 2494 True 4327 4327 97.959 1 2498 1 chr5D.!!$R1 2497
4 TraesCS6A01G192000 chr2D 272793252 272795747 2495 False 4313 4313 97.840 1 2498 1 chr2D.!!$F1 2497
5 TraesCS6A01G192000 chr3B 201525171 201527665 2494 True 4300 4300 97.760 1 2498 1 chr3B.!!$R1 2497
6 TraesCS6A01G192000 chr3A 672909366 672911862 2496 False 4229 4229 97.242 1 2498 1 chr3A.!!$F1 2497
7 TraesCS6A01G192000 chr5A 619264517 619267012 2495 True 4141 4141 96.601 1 2498 1 chr5A.!!$R1 2497
8 TraesCS6A01G192000 chr6D 168253248 168255567 2319 True 4072 4072 98.363 1 2319 1 chr6D.!!$R1 2318
9 TraesCS6A01G192000 chr3D 589278903 589280989 2086 False 3640 3640 98.135 1 2090 1 chr3D.!!$F1 2089

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
664 665 2.519013 CCCCTTGTTTCAAAGAGAGGG 58.481 52.381 5.69 5.69 42.79 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1566 1.378514 ATGCGCGGGTTCAATTCCT 60.379 52.632 8.83 0.0 0.0 3.36 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
99 100 7.461182 AGTGAAATCCAATCCACGAAATAAA 57.539 32.000 0.00 0.00 34.93 1.40
113 114 6.183360 CCACGAAATAAATTGATCCATGGACA 60.183 38.462 18.99 14.43 0.00 4.02
194 195 2.561419 GAGGTCATAAGCGCCTATACCA 59.439 50.000 18.62 0.00 31.89 3.25
257 258 7.025963 GGTAGAATCGTAACCATAGAATACGG 58.974 42.308 4.94 0.00 41.89 4.02
627 628 6.397272 AGAAGACAAAATTGTTTGAAGCACA 58.603 32.000 6.21 0.00 45.99 4.57
664 665 2.519013 CCCCTTGTTTCAAAGAGAGGG 58.481 52.381 5.69 5.69 42.79 4.30
728 729 5.880054 TGAAAGCTAAGCAGTGGTAATTC 57.120 39.130 0.00 0.00 0.00 2.17
977 978 9.866655 ATATAAGATCCATCTGTCTAGAGATCC 57.133 37.037 11.72 0.00 36.22 3.36
1068 1069 9.705290 GAGAGAAAAGAAGAATCTACTTCAACT 57.295 33.333 0.00 0.00 45.83 3.16
1168 1169 2.475187 GCTGTAGCGAAACTCATTGCAG 60.475 50.000 0.00 0.00 0.00 4.41
1212 1213 3.151542 AGATTACCATCTGGGGAGGTT 57.848 47.619 0.54 0.00 38.44 3.50
1308 1309 2.180276 AGAGCCGGATCTAAGTGTTGT 58.820 47.619 23.29 0.00 0.00 3.32
1429 1430 2.210644 CAACCCCTTGGGGTTATCCTA 58.789 52.381 34.97 0.00 42.24 2.94
1637 1640 1.909302 CTACATCCGCCCCTTATCCAT 59.091 52.381 0.00 0.00 0.00 3.41
2215 2224 1.475682 AGTTCCAACCGATCGTCTACC 59.524 52.381 15.09 0.00 0.00 3.18
2297 2306 4.681942 CAAAGAGTTCTTGACGAGATTCGT 59.318 41.667 3.49 3.49 45.46 3.85
2328 2337 9.079833 GTTACTACGAGCAAACTGTTATGATAA 57.920 33.333 0.00 0.00 0.00 1.75
2386 2395 5.766174 TCTTAAAGTTGGTTTATTCGGCAGT 59.234 36.000 0.00 0.00 30.46 4.40
2414 2423 8.579863 GCAAATGCTACTCATTATAGGGATTTT 58.420 33.333 0.00 0.00 44.23 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.072330 TGGATTTCACTTGCCTGTCTACA 59.928 43.478 0.00 0.00 0.00 2.74
99 100 3.454719 TGGTGTTGTCCATGGATCAAT 57.545 42.857 19.62 0.00 31.96 2.57
167 168 1.447643 CGCTTATGACCTCCCCCTG 59.552 63.158 0.00 0.00 0.00 4.45
627 628 2.665185 GCGCTTCCGGTTCTGTGT 60.665 61.111 0.00 0.00 34.32 3.72
664 665 6.459670 AATTAAATGTGAATAACCCGTCCC 57.540 37.500 0.00 0.00 0.00 4.46
977 978 7.433719 GCATACGGCTTTCTAGATGTATATGAG 59.566 40.741 0.00 0.00 40.25 2.90
1085 1086 5.009911 GTGATTTCTATGTTATGCATGGCCA 59.990 40.000 8.56 8.56 38.47 5.36
1168 1169 1.209747 AGTGGCCGATTTACCCTCTTC 59.790 52.381 0.00 0.00 0.00 2.87
1308 1309 3.036452 ACTATGGGGCGTTTACCTAGA 57.964 47.619 0.00 0.00 0.00 2.43
1429 1430 2.897969 TCCTAGTTCTTCTTCCAAGCGT 59.102 45.455 0.00 0.00 0.00 5.07
1563 1566 1.378514 ATGCGCGGGTTCAATTCCT 60.379 52.632 8.83 0.00 0.00 3.36
1601 1604 2.265367 TGTAGCCAAGTGGATCAAGGA 58.735 47.619 0.18 0.00 37.39 3.36
2215 2224 6.201044 TGCTTTGAAAACTCTCTCGAACTTAG 59.799 38.462 0.00 0.00 0.00 2.18
2248 2257 6.945435 TGCTTTGAAAACAGACATAGGGATAA 59.055 34.615 0.00 0.00 0.00 1.75
2313 2322 9.726232 CATGAGGTTCATTATCATAACAGTTTG 57.274 33.333 0.00 0.00 34.28 2.93
2328 2337 2.301296 CTCGATAGGGCATGAGGTTCAT 59.699 50.000 0.00 0.00 37.65 2.57
2386 2395 5.011635 TCCCTATAATGAGTAGCATTTGCGA 59.988 40.000 0.00 0.00 44.68 5.10
2439 2448 1.819903 ACTCCTACTGACTTCGGCTTC 59.180 52.381 0.00 0.00 0.00 3.86
2474 2483 2.628178 TCGAGCTTGAGGTCTGAAGAAA 59.372 45.455 0.00 0.00 40.17 2.52
2475 2484 2.230025 CTCGAGCTTGAGGTCTGAAGAA 59.770 50.000 21.73 0.00 40.17 2.52
2476 2485 1.815613 CTCGAGCTTGAGGTCTGAAGA 59.184 52.381 21.73 0.00 40.17 2.87
2477 2486 2.276472 CTCGAGCTTGAGGTCTGAAG 57.724 55.000 21.73 0.00 40.17 3.02


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

AutoCloner maintained by Alex Coulton.