Multiple sequence alignment - TraesCS1B01G334300

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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 TraesCS1B01G334300 chr1B 100.000 2549 0 0 1 2549 561525562 561528110 0 4708
1 TraesCS1B01G334300 chr1B 95.716 1984 80 5 569 2549 671392210 671394191 0 3188
2 TraesCS1B01G334300 chr1B 95.436 1994 79 9 565 2549 581717564 581715574 0 3168
3 TraesCS1B01G334300 chr1B 95.391 1996 80 9 560 2549 585423176 585425165 0 3166
4 TraesCS1B01G334300 chr7B 95.639 1995 75 9 563 2549 720989196 720987206 0 3192
5 TraesCS1B01G334300 chr7B 98.768 568 7 0 1 568 539316122 539316689 0 1011
6 TraesCS1B01G334300 chr7B 98.592 568 8 0 1 568 48689728 48690295 0 1005
7 TraesCS1B01G334300 chr4A 95.491 1996 82 7 559 2549 705529262 705527270 0 3181
8 TraesCS1B01G334300 chr2B 95.537 1994 76 11 563 2549 692955892 692957879 0 3177
9 TraesCS1B01G334300 chr2B 95.525 1989 81 6 565 2549 458657420 458659404 0 3173
10 TraesCS1B01G334300 chr4B 95.257 2003 81 11 555 2549 372353130 372351134 0 3160
11 TraesCS1B01G334300 chr4B 95.295 1998 83 6 555 2549 17791865 17789876 0 3158
12 TraesCS1B01G334300 chr4B 98.768 568 7 0 1 568 61430845 61431412 0 1011
13 TraesCS1B01G334300 chr6B 98.768 568 7 0 1 568 135529503 135530070 0 1011
14 TraesCS1B01G334300 chr6B 98.592 568 8 0 1 568 502036579 502036012 0 1005
15 TraesCS1B01G334300 chr5B 98.592 568 8 0 1 568 141927866 141927299 0 1005
16 TraesCS1B01G334300 chr5B 98.592 568 8 0 1 568 357940665 357941232 0 1005
17 TraesCS1B01G334300 chr5B 98.415 568 9 0 1 568 205731368 205730801 0 1000
18 TraesCS1B01G334300 chr3B 98.592 568 8 0 1 568 541369795 541370362 0 1005


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 TraesCS1B01G334300 chr1B 561525562 561528110 2548 False 4708 4708 100.000 1 2549 1 chr1B.!!$F1 2548
1 TraesCS1B01G334300 chr1B 671392210 671394191 1981 False 3188 3188 95.716 569 2549 1 chr1B.!!$F3 1980
2 TraesCS1B01G334300 chr1B 581715574 581717564 1990 True 3168 3168 95.436 565 2549 1 chr1B.!!$R1 1984
3 TraesCS1B01G334300 chr1B 585423176 585425165 1989 False 3166 3166 95.391 560 2549 1 chr1B.!!$F2 1989
4 TraesCS1B01G334300 chr7B 720987206 720989196 1990 True 3192 3192 95.639 563 2549 1 chr7B.!!$R1 1986
5 TraesCS1B01G334300 chr7B 539316122 539316689 567 False 1011 1011 98.768 1 568 1 chr7B.!!$F2 567
6 TraesCS1B01G334300 chr7B 48689728 48690295 567 False 1005 1005 98.592 1 568 1 chr7B.!!$F1 567
7 TraesCS1B01G334300 chr4A 705527270 705529262 1992 True 3181 3181 95.491 559 2549 1 chr4A.!!$R1 1990
8 TraesCS1B01G334300 chr2B 692955892 692957879 1987 False 3177 3177 95.537 563 2549 1 chr2B.!!$F2 1986
9 TraesCS1B01G334300 chr2B 458657420 458659404 1984 False 3173 3173 95.525 565 2549 1 chr2B.!!$F1 1984
10 TraesCS1B01G334300 chr4B 372351134 372353130 1996 True 3160 3160 95.257 555 2549 1 chr4B.!!$R2 1994
11 TraesCS1B01G334300 chr4B 17789876 17791865 1989 True 3158 3158 95.295 555 2549 1 chr4B.!!$R1 1994
12 TraesCS1B01G334300 chr4B 61430845 61431412 567 False 1011 1011 98.768 1 568 1 chr4B.!!$F1 567
13 TraesCS1B01G334300 chr6B 135529503 135530070 567 False 1011 1011 98.768 1 568 1 chr6B.!!$F1 567
14 TraesCS1B01G334300 chr6B 502036012 502036579 567 True 1005 1005 98.592 1 568 1 chr6B.!!$R1 567
15 TraesCS1B01G334300 chr5B 141927299 141927866 567 True 1005 1005 98.592 1 568 1 chr5B.!!$R1 567
16 TraesCS1B01G334300 chr5B 357940665 357941232 567 False 1005 1005 98.592 1 568 1 chr5B.!!$F1 567
17 TraesCS1B01G334300 chr5B 205730801 205731368 567 True 1000 1000 98.415 1 568 1 chr5B.!!$R2 567
18 TraesCS1B01G334300 chr3B 541369795 541370362 567 False 1005 1005 98.592 1 568 1 chr3B.!!$F1 567

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
935 938 1.903877 GAAGCTAGCTGTGGAGGGCA 61.904 60.0 20.16 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2162 0.889638 TTCGAGTCCTCAGTCGCACT 60.89 55.0 0.0 0.0 44.02 4.4 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
64 65 9.227777 GTATTGGTGTTTCTAACTATTTGGTCT 57.772 33.333 0.00 0.00 0.00 3.85
432 433 9.988350 GTGTGTTTGGACTTCATTTATATACAG 57.012 33.333 0.00 0.00 0.00 2.74
736 737 2.198304 CTTACAGGTGGGACCAGGCC 62.198 65.000 0.00 0.00 41.95 5.19
935 938 1.903877 GAAGCTAGCTGTGGAGGGCA 61.904 60.000 20.16 0.00 0.00 5.36
954 957 4.858680 GGCGGTGGGAAGCTAGCC 62.859 72.222 12.13 0.00 37.61 3.93
1070 1073 1.086634 GTGGAGATGCCTGTCTTCGC 61.087 60.000 0.00 0.00 37.63 4.70
1076 1079 1.548357 ATGCCTGTCTTCGCCTGTCT 61.548 55.000 0.00 0.00 0.00 3.41
1170 1173 3.448660 GCAGCAAGAATGGGGTAAGAATT 59.551 43.478 0.00 0.00 0.00 2.17
1171 1174 4.644685 GCAGCAAGAATGGGGTAAGAATTA 59.355 41.667 0.00 0.00 0.00 1.40
1308 1311 3.911661 AATGAACTGCAAGAAGAGCAC 57.088 42.857 0.00 0.00 37.02 4.40
1475 1478 6.068461 TCAAGCACTACCAATACCCATTTA 57.932 37.500 0.00 0.00 0.00 1.40
2158 2172 4.990543 CACAGAAAATTAGTGCGACTGA 57.009 40.909 0.00 0.00 0.00 3.41
2176 2190 1.258676 GAGGACTCGAACCCAAGACT 58.741 55.000 5.66 0.00 0.00 3.24
2178 2192 0.680061 GGACTCGAACCCAAGACTGT 59.320 55.000 0.00 0.00 0.00 3.55
2236 2251 3.620966 GCTAGGACAGATGGCAAGAGTTT 60.621 47.826 0.00 0.00 0.00 2.66
2237 2252 2.787994 AGGACAGATGGCAAGAGTTTG 58.212 47.619 0.00 0.00 37.36 2.93
2238 2253 1.815003 GGACAGATGGCAAGAGTTTGG 59.185 52.381 0.00 0.00 34.79 3.28
2313 2328 4.749245 AATGTGAGACCGTGAATGTTTC 57.251 40.909 0.00 0.00 0.00 2.78
2331 2346 3.857854 CACGCGCATGAGAGTGGC 61.858 66.667 22.22 2.93 38.09 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.259609 ACGGTACCCAAACTCATCGA 58.740 50.000 6.25 0.00 0.00 3.59
432 433 4.991687 GCACTTGGCTAGATATGGTCTTAC 59.008 45.833 2.20 0.00 38.42 2.34
855 858 2.083522 GTGCTCTCTGTCGACGTGC 61.084 63.158 11.62 9.73 0.00 5.34
860 863 4.103103 CGCCGTGCTCTCTGTCGA 62.103 66.667 0.00 0.00 0.00 4.20
935 938 3.771160 CTAGCTTCCCACCGCCGT 61.771 66.667 0.00 0.00 0.00 5.68
1046 1049 2.267006 CAGGCATCTCCACACGCT 59.733 61.111 0.00 0.00 37.29 5.07
1170 1173 2.094286 CGAAAATGGTGCAATTGCCCTA 60.094 45.455 26.94 14.93 41.18 3.53
1171 1174 1.338011 CGAAAATGGTGCAATTGCCCT 60.338 47.619 26.94 11.63 41.18 5.19
1796 1805 5.948588 TCACGGTGTATTTGAATTGGATTG 58.051 37.500 8.17 0.00 0.00 2.67
2141 2155 4.246458 AGTCCTCAGTCGCACTAATTTTC 58.754 43.478 0.00 0.00 0.00 2.29
2148 2162 0.889638 TTCGAGTCCTCAGTCGCACT 60.890 55.000 0.00 0.00 44.02 4.40
2154 2168 0.969894 CTTGGGTTCGAGTCCTCAGT 59.030 55.000 8.28 0.00 0.00 3.41
2158 2172 0.969894 CAGTCTTGGGTTCGAGTCCT 59.030 55.000 8.28 0.00 0.00 3.85
2176 2190 1.633774 AAACACCACAAACCCACACA 58.366 45.000 0.00 0.00 0.00 3.72
2178 2192 2.379972 CCTAAACACCACAAACCCACA 58.620 47.619 0.00 0.00 0.00 4.17
2236 2251 1.377690 TTTCTTCCCTACCCATGCCA 58.622 50.000 0.00 0.00 0.00 4.92
2237 2252 2.310538 CATTTCTTCCCTACCCATGCC 58.689 52.381 0.00 0.00 0.00 4.40
2238 2253 3.018423 ACATTTCTTCCCTACCCATGC 57.982 47.619 0.00 0.00 0.00 4.06
2313 2328 3.190849 CCACTCTCATGCGCGTGG 61.191 66.667 28.29 20.89 40.71 4.94
2317 2332 1.427020 GAAAGCCACTCTCATGCGC 59.573 57.895 0.00 0.00 0.00 6.09
2331 2346 6.667007 ATTTCAGTGCAAAACAAAGGAAAG 57.333 33.333 0.00 0.00 31.46 2.62
2496 2519 4.510571 GTGAGAAGCCCTCCGTTTTATTA 58.489 43.478 1.79 0.00 41.25 0.98
2521 2544 6.696411 ACTTGTGGTTGTCATTCAAAAGAAA 58.304 32.000 10.89 0.00 37.81 2.52


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

AutoCloner maintained by Alex Coulton.