Multiple sequence alignment - TraesCS6B01G261600

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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 TraesCS6B01G261600 chr6B 100.000 2369 0 0 1 2369 471276405 471278773 0.000000e+00 4375
1 TraesCS6B01G261600 chr6B 92.623 1708 117 6 665 2369 359364818 359363117 0.000000e+00 2447
2 TraesCS6B01G261600 chr6B 94.981 1315 54 8 986 2291 504814641 504815952 0.000000e+00 2052
3 TraesCS6B01G261600 chr3B 94.202 2294 124 5 5 2291 261627550 261629841 0.000000e+00 3491
4 TraesCS6B01G261600 chr3B 91.195 2385 176 15 10 2369 286885355 286882980 0.000000e+00 3210
5 TraesCS6B01G261600 chr7B 93.712 2147 124 8 10 2149 233949267 233951409 0.000000e+00 3206
6 TraesCS6B01G261600 chr5B 90.647 2288 183 16 5 2268 274671455 274673735 0.000000e+00 3011
7 TraesCS6B01G261600 chr5B 95.185 1246 52 7 1128 2369 575859607 575860848 0.000000e+00 1962
8 TraesCS6B01G261600 chr5B 83.893 149 15 7 2229 2369 4634660 4634513 1.480000e-27 134
9 TraesCS6B01G261600 chr2A 87.587 2304 236 27 8 2297 82414426 82412159 0.000000e+00 2625
10 TraesCS6B01G261600 chr2B 91.966 1755 128 9 619 2369 286175369 286173624 0.000000e+00 2447
11 TraesCS6B01G261600 chr2B 92.804 1487 101 4 5 1486 295832492 295833977 0.000000e+00 2148
12 TraesCS6B01G261600 chr4B 95.946 1480 60 0 8 1487 154113294 154111815 0.000000e+00 2401
13 TraesCS6B01G261600 chr4B 94.421 1416 74 5 880 2291 256903986 256905400 0.000000e+00 2172
14 TraesCS6B01G261600 chr4B 92.975 1210 76 8 1 1207 534533196 534534399 0.000000e+00 1755


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 TraesCS6B01G261600 chr6B 471276405 471278773 2368 False 4375 4375 100.000 1 2369 1 chr6B.!!$F1 2368
1 TraesCS6B01G261600 chr6B 359363117 359364818 1701 True 2447 2447 92.623 665 2369 1 chr6B.!!$R1 1704
2 TraesCS6B01G261600 chr6B 504814641 504815952 1311 False 2052 2052 94.981 986 2291 1 chr6B.!!$F2 1305
3 TraesCS6B01G261600 chr3B 261627550 261629841 2291 False 3491 3491 94.202 5 2291 1 chr3B.!!$F1 2286
4 TraesCS6B01G261600 chr3B 286882980 286885355 2375 True 3210 3210 91.195 10 2369 1 chr3B.!!$R1 2359
5 TraesCS6B01G261600 chr7B 233949267 233951409 2142 False 3206 3206 93.712 10 2149 1 chr7B.!!$F1 2139
6 TraesCS6B01G261600 chr5B 274671455 274673735 2280 False 3011 3011 90.647 5 2268 1 chr5B.!!$F1 2263
7 TraesCS6B01G261600 chr5B 575859607 575860848 1241 False 1962 1962 95.185 1128 2369 1 chr5B.!!$F2 1241
8 TraesCS6B01G261600 chr2A 82412159 82414426 2267 True 2625 2625 87.587 8 2297 1 chr2A.!!$R1 2289
9 TraesCS6B01G261600 chr2B 286173624 286175369 1745 True 2447 2447 91.966 619 2369 1 chr2B.!!$R1 1750
10 TraesCS6B01G261600 chr2B 295832492 295833977 1485 False 2148 2148 92.804 5 1486 1 chr2B.!!$F1 1481
11 TraesCS6B01G261600 chr4B 154111815 154113294 1479 True 2401 2401 95.946 8 1487 1 chr4B.!!$R1 1479
12 TraesCS6B01G261600 chr4B 256903986 256905400 1414 False 2172 2172 94.421 880 2291 1 chr4B.!!$F1 1411
13 TraesCS6B01G261600 chr4B 534533196 534534399 1203 False 1755 1755 92.975 1 1207 1 chr4B.!!$F2 1206

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
498 520 3.958018 ACCAACACCTTCAACACAAGTA 58.042 40.909 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 1969 0.539986 GCTACCGATCCAGGGAACAA 59.46 55.0 0.0 0.0 35.02 2.83 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
70 71 5.854010 TCAGTTAGATGATTTAGCTCGGT 57.146 39.130 0.00 0.00 0.00 4.69
498 520 3.958018 ACCAACACCTTCAACACAAGTA 58.042 40.909 0.00 0.00 0.00 2.24
820 845 9.820725 CTCAGATTGAAGAAGATGAACTAGAAT 57.179 33.333 0.00 0.00 0.00 2.40
876 901 4.151335 CCAAGTGATCAAGTTGAAGACTCG 59.849 45.833 10.14 4.34 41.10 4.18
1027 1052 3.985925 GCCTTGTGATTTCTTTGCTTCTG 59.014 43.478 0.00 0.00 0.00 3.02
1527 1556 5.048434 GCAAAGGAGAAGAGTTGCAGTTTAT 60.048 40.000 2.53 0.00 44.53 1.40
1530 1559 6.613153 AGGAGAAGAGTTGCAGTTTATAGT 57.387 37.500 0.00 0.00 0.00 2.12
1562 1591 5.811100 GCGAGTGCTACTTCCTATAAAAACT 59.189 40.000 0.00 0.00 38.39 2.66
1659 1690 7.377131 GTCGCTTGAGCAATTTCTTAAATATCC 59.623 37.037 3.65 0.00 42.21 2.59
1735 1766 5.359576 TGAGTGTTGAATGCCTTGTAAACTT 59.640 36.000 0.00 0.00 0.00 2.66
1746 1777 5.700832 TGCCTTGTAAACTTGTGATCTACAG 59.299 40.000 0.00 0.00 41.10 2.74
1842 1875 9.077885 ACTTAATCATTTTCTGCTTTTACCTCA 57.922 29.630 0.00 0.00 0.00 3.86
1849 1882 7.817418 TTTTCTGCTTTTACCTCAATACACT 57.183 32.000 0.00 0.00 0.00 3.55
1935 1969 4.443978 ACCACTATGGATTAGCATGCTT 57.556 40.909 28.02 8.95 40.96 3.91
1997 2032 8.641498 AGAAGTGATGATTCCTATTTTTGTGT 57.359 30.769 0.00 0.00 0.00 3.72
2094 2130 1.750778 GGATCGGTGGCATGTGAAATT 59.249 47.619 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 6.726490 ATCCTCAAAAACTATACCTCGCTA 57.274 37.500 0.00 0.00 0.00 4.26
311 312 1.137872 ACGATGAGATCTCAGGGTTGC 59.862 52.381 28.26 13.04 43.61 4.17
475 476 4.337145 ACTTGTGTTGAAGGTGTTGGTTA 58.663 39.130 0.00 0.00 0.00 2.85
804 829 8.816894 TGTTCCTTGTATTCTAGTTCATCTTCT 58.183 33.333 0.00 0.00 0.00 2.85
805 830 9.436957 TTGTTCCTTGTATTCTAGTTCATCTTC 57.563 33.333 0.00 0.00 0.00 2.87
806 831 9.442047 CTTGTTCCTTGTATTCTAGTTCATCTT 57.558 33.333 0.00 0.00 0.00 2.40
820 845 5.877012 GCTCTTGATCATCTTGTTCCTTGTA 59.123 40.000 0.00 0.00 0.00 2.41
876 901 4.883006 ACTTCTTCGGGAGTAGTAGATGAC 59.117 45.833 0.00 0.00 34.62 3.06
1208 1233 3.886123 AGCACATGTTTAGGATGGTACC 58.114 45.455 4.43 4.43 0.00 3.34
1527 1556 1.209383 GCACTCGCTCGACACACTA 59.791 57.895 0.00 0.00 34.30 2.74
1562 1591 1.608025 GGTCATGAAACAGCTCACCGA 60.608 52.381 0.00 0.00 0.00 4.69
1659 1690 4.392138 GTCGAAGGTAAAATTCAGTGGGAG 59.608 45.833 0.00 0.00 0.00 4.30
1735 1766 4.212143 AGCAAGCATTCTGTAGATCACA 57.788 40.909 0.00 0.00 35.30 3.58
1746 1777 5.636543 ACTAATTTCAGCAAAGCAAGCATTC 59.363 36.000 0.00 0.00 0.00 2.67
1849 1882 7.785033 TCAGCATCTGACACTTAATGATCTAA 58.215 34.615 0.00 0.00 35.39 2.10
1935 1969 0.539986 GCTACCGATCCAGGGAACAA 59.460 55.000 0.00 0.00 35.02 2.83
2094 2130 1.068948 TTACTGCCCAAGCTAACCCA 58.931 50.000 0.00 0.00 40.80 4.51
2144 2182 3.638860 TCCCGAGAACATGGTATACACT 58.361 45.455 5.01 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.