Multiple sequence alignment - TraesCS6B01G266400

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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 TraesCS6B01G266400 chr6B 100.000 2549 0 0 1 2549 478999397 479001945 0 4708
1 TraesCS6B01G266400 chr6B 95.886 1993 72 10 564 2549 478991317 478989328 0 3217
2 TraesCS6B01G266400 chr1B 95.613 1983 80 6 569 2549 520844119 520842142 0 3173
3 TraesCS6B01G266400 chr1B 95.363 1984 83 6 569 2549 561526130 561528107 0 3145
4 TraesCS6B01G266400 chr1B 95.279 1991 82 10 567 2549 581717563 581715577 0 3145
5 TraesCS6B01G266400 chr1B 95.320 1987 81 10 568 2549 671392209 671394188 0 3144
6 TraesCS6B01G266400 chr3B 95.372 1988 83 8 566 2549 46395683 46393701 0 3153
7 TraesCS6B01G266400 chr3B 95.224 1989 85 9 568 2549 19701236 19703221 0 3138
8 TraesCS6B01G266400 chr3B 97.711 568 13 0 1 568 660279002 660278435 0 977
9 TraesCS6B01G266400 chr3B 97.203 572 15 1 1 571 730916074 730916645 0 966
10 TraesCS6B01G266400 chr4A 95.363 1984 85 6 569 2549 705529252 705527273 0 3147
11 TraesCS6B01G266400 chr2B 95.219 1987 86 6 567 2549 692955895 692957876 0 3134
12 TraesCS6B01G266400 chr2B 97.203 572 15 1 1 571 339654030 339653459 0 966
13 TraesCS6B01G266400 chr2B 97.203 572 15 1 1 571 356248464 356247893 0 966
14 TraesCS6B01G266400 chr2B 97.203 572 15 1 1 571 740049342 740048771 0 966
15 TraesCS6B01G266400 chr7B 97.711 568 13 0 1 568 25301063 25300496 0 977
16 TraesCS6B01G266400 chr7B 97.552 572 13 1 1 571 236382668 236383239 0 977
17 TraesCS6B01G266400 chr7B 97.203 572 15 1 1 571 43158676 43158105 0 966
18 TraesCS6B01G266400 chr4B 97.203 572 15 1 1 571 272152790 272153361 0 966


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 TraesCS6B01G266400 chr6B 478999397 479001945 2548 False 4708 4708 100.000 1 2549 1 chr6B.!!$F1 2548
1 TraesCS6B01G266400 chr6B 478989328 478991317 1989 True 3217 3217 95.886 564 2549 1 chr6B.!!$R1 1985
2 TraesCS6B01G266400 chr1B 520842142 520844119 1977 True 3173 3173 95.613 569 2549 1 chr1B.!!$R1 1980
3 TraesCS6B01G266400 chr1B 561526130 561528107 1977 False 3145 3145 95.363 569 2549 1 chr1B.!!$F1 1980
4 TraesCS6B01G266400 chr1B 581715577 581717563 1986 True 3145 3145 95.279 567 2549 1 chr1B.!!$R2 1982
5 TraesCS6B01G266400 chr1B 671392209 671394188 1979 False 3144 3144 95.320 568 2549 1 chr1B.!!$F2 1981
6 TraesCS6B01G266400 chr3B 46393701 46395683 1982 True 3153 3153 95.372 566 2549 1 chr3B.!!$R1 1983
7 TraesCS6B01G266400 chr3B 19701236 19703221 1985 False 3138 3138 95.224 568 2549 1 chr3B.!!$F1 1981
8 TraesCS6B01G266400 chr3B 660278435 660279002 567 True 977 977 97.711 1 568 1 chr3B.!!$R2 567
9 TraesCS6B01G266400 chr3B 730916074 730916645 571 False 966 966 97.203 1 571 1 chr3B.!!$F2 570
10 TraesCS6B01G266400 chr4A 705527273 705529252 1979 True 3147 3147 95.363 569 2549 1 chr4A.!!$R1 1980
11 TraesCS6B01G266400 chr2B 692955895 692957876 1981 False 3134 3134 95.219 567 2549 1 chr2B.!!$F1 1982
12 TraesCS6B01G266400 chr2B 339653459 339654030 571 True 966 966 97.203 1 571 1 chr2B.!!$R1 570
13 TraesCS6B01G266400 chr2B 356247893 356248464 571 True 966 966 97.203 1 571 1 chr2B.!!$R2 570
14 TraesCS6B01G266400 chr2B 740048771 740049342 571 True 966 966 97.203 1 571 1 chr2B.!!$R3 570
15 TraesCS6B01G266400 chr7B 25300496 25301063 567 True 977 977 97.711 1 568 1 chr7B.!!$R1 567
16 TraesCS6B01G266400 chr7B 236382668 236383239 571 False 977 977 97.552 1 571 1 chr7B.!!$F1 570
17 TraesCS6B01G266400 chr7B 43158105 43158676 571 True 966 966 97.203 1 571 1 chr7B.!!$R2 570
18 TraesCS6B01G266400 chr4B 272152790 272153361 571 False 966 966 97.203 1 571 1 chr4B.!!$F1 570

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
902 905 1.153066 ATGGCGAGAGAGCGAGAGA 60.153 57.895 0.0 0.0 38.18 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2232 1.571955 TCTTGCCATCTGTCCTAGCA 58.428 50.0 0.0 0.0 0.0 3.49 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
105 106 2.437413 AGCAAGGATTCGGAAAGGAAC 58.563 47.619 0.00 0.00 0.00 3.62
106 107 2.159382 GCAAGGATTCGGAAAGGAACA 58.841 47.619 0.00 0.00 0.00 3.18
819 820 2.159282 CCGTTGAGTATAGAGCCGTTGT 60.159 50.000 0.00 0.00 0.00 3.32
877 880 4.724602 GCGACAGAGAGCACGGCA 62.725 66.667 0.00 0.00 0.00 5.69
902 905 1.153066 ATGGCGAGAGAGCGAGAGA 60.153 57.895 0.00 0.00 38.18 3.10
952 956 1.445942 CGCGGTGGTGGGAATCTAT 59.554 57.895 0.00 0.00 0.00 1.98
1220 1224 3.440173 GGATCTTTGAGCAATCGGTTGAA 59.560 43.478 13.85 0.00 37.53 2.69
1221 1225 4.082787 GGATCTTTGAGCAATCGGTTGAAA 60.083 41.667 13.85 3.04 37.53 2.69
1251 1255 2.749076 GTTCATGCAGGTGACATGCTTA 59.251 45.455 23.05 4.09 43.71 3.09
1258 1262 4.156556 TGCAGGTGACATGCTTATTTCTTC 59.843 41.667 23.05 0.00 44.17 2.87
1287 1291 1.065564 GCTCTGGCCAAGACTCTGATT 60.066 52.381 7.01 0.00 0.00 2.57
1630 1635 6.173339 TGGCCAAAGTTGTTTAAATGTTGAA 58.827 32.000 0.61 0.00 0.00 2.69
1737 1747 8.644216 TGAAATGCAGCTAATGAATTATTCCAT 58.356 29.630 2.22 0.00 35.98 3.41
1905 1916 7.818930 ACCTAGTGCCAAAATAAATGAACATTG 59.181 33.333 0.69 0.00 0.00 2.82
2049 2063 0.464452 GCGCTGGTAACCACTAGGAT 59.536 55.000 0.00 0.00 38.69 3.24
2214 2232 1.550130 TTAGGGCTGCGCTGGTAACT 61.550 55.000 27.01 3.65 37.61 2.24
2234 2252 1.908619 TGCTAGGACAGATGGCAAGAA 59.091 47.619 0.00 0.00 30.56 2.52
2440 2460 5.365619 CACTTGGTTTAGTGTTAGAGTGGT 58.634 41.667 0.00 0.00 40.48 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.093235 CCTCTCTCTTGGTGGTGATTCC 60.093 54.545 0.00 0.00 0.00 3.01
105 106 4.153117 GTGTAGCTCCTTGATGACTTGTTG 59.847 45.833 0.00 0.00 0.00 3.33
106 107 4.202357 TGTGTAGCTCCTTGATGACTTGTT 60.202 41.667 0.00 0.00 0.00 2.83
543 544 7.436673 CCTAAAAGTTCTCGATGATCTTCGAAT 59.563 37.037 27.36 14.94 46.54 3.34
877 880 1.954362 GCTCTCTCGCCATGGTCAGT 61.954 60.000 14.67 0.00 0.00 3.41
902 905 1.375523 GCTTCCCACCATCGTCGTT 60.376 57.895 0.00 0.00 0.00 3.85
1220 1224 1.541147 CCTGCATGAACACGGAACATT 59.459 47.619 0.00 0.00 0.00 2.71
1221 1225 1.167851 CCTGCATGAACACGGAACAT 58.832 50.000 0.00 0.00 0.00 2.71
1251 1255 1.482593 AGAGCATCGACCCGAAGAAAT 59.517 47.619 0.00 0.00 42.67 2.17
1258 1262 4.899239 GGCCAGAGCATCGACCCG 62.899 72.222 0.00 0.00 42.67 5.28
1287 1291 4.397103 CCATGCTCTTCTTGCAGTTCATTA 59.603 41.667 0.00 0.00 44.04 1.90
1327 1331 1.760086 CCACTGTGGTTTGGGGCAA 60.760 57.895 18.76 0.00 31.35 4.52
1905 1916 7.859325 TCTACTCAATGTAATGCCCTTAAAC 57.141 36.000 0.00 0.00 0.00 2.01
2049 2063 4.264253 CCATGTCAAACTCTTGCCATCTA 58.736 43.478 0.00 0.00 28.75 1.98
2214 2232 1.571955 TCTTGCCATCTGTCCTAGCA 58.428 50.000 0.00 0.00 0.00 3.49
2234 2252 4.946160 TTCTTCCCTACCCATGTCAAAT 57.054 40.909 0.00 0.00 0.00 2.32
2393 2413 4.141287 CACTCTAACCAAAACCACATGGA 58.859 43.478 4.53 0.00 39.12 3.41
2440 2460 8.866970 ATTCCGTTTAAATCCTAAACCAAGTA 57.133 30.769 0.00 0.00 34.81 2.24


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

AutoCloner maintained by Alex Coulton.