Multiple sequence alignment - TraesCS6A01G077300

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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 TraesCS6A01G077300 chr6A 100.000 4802 0 0 1 4802 47633571 47638372 0 8868
1 TraesCS6A01G077300 chr6A 98.855 4804 51 4 1 4802 73516470 73521271 0 8564
2 TraesCS6A01G077300 chr7A 98.774 4242 51 1 562 4802 28245253 28249494 0 7544
3 TraesCS6A01G077300 chr2B 98.728 4244 48 5 562 4802 615343764 615339524 0 7533
4 TraesCS6A01G077300 chr2B 98.633 4243 53 5 562 4802 616522473 616518234 0 7509
5 TraesCS6A01G077300 chr2B 95.038 665 29 4 1 661 615346855 615346191 0 1042
6 TraesCS6A01G077300 chr2B 94.595 666 30 6 1 661 615344421 615343757 0 1026
7 TraesCS6A01G077300 chr2B 94.428 664 32 5 1 661 616523127 616522466 0 1016
8 TraesCS6A01G077300 chr7B 98.680 4242 54 2 562 4802 75051561 75047321 0 7522
9 TraesCS6A01G077300 chr7B 98.680 4242 53 3 562 4802 628742368 628746607 0 7520
10 TraesCS6A01G077300 chr7B 94.880 664 29 5 2 661 628741713 628742375 0 1033
11 TraesCS6A01G077300 chr7B 94.428 664 32 4 1 661 75052215 75051554 0 1016
12 TraesCS6A01G077300 chr6B 98.680 4242 54 2 562 4802 482837663 482833423 0 7522
13 TraesCS6A01G077300 chr6B 98.467 4241 63 2 562 4802 482818030 482813792 0 7470
14 TraesCS6A01G077300 chr3A 98.562 4243 52 6 562 4802 742304185 742308420 0 7489
15 TraesCS6A01G077300 chrUn 95.038 665 29 4 1 661 373125399 373124735 0 1042
16 TraesCS6A01G077300 chrUn 94.595 666 30 5 1 661 289561549 289560885 0 1026
17 TraesCS6A01G077300 chr2A 95.038 665 28 4 1 661 70021147 70020484 0 1040


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 TraesCS6A01G077300 chr6A 47633571 47638372 4801 False 8868.000000 8868 100.000000 1 4802 1 chr6A.!!$F1 4801
1 TraesCS6A01G077300 chr6A 73516470 73521271 4801 False 8564.000000 8564 98.855000 1 4802 1 chr6A.!!$F2 4801
2 TraesCS6A01G077300 chr7A 28245253 28249494 4241 False 7544.000000 7544 98.774000 562 4802 1 chr7A.!!$F1 4240
3 TraesCS6A01G077300 chr2B 616518234 616523127 4893 True 4262.500000 7509 96.530500 1 4802 2 chr2B.!!$R2 4801
4 TraesCS6A01G077300 chr2B 615339524 615346855 7331 True 3200.333333 7533 96.120333 1 4802 3 chr2B.!!$R1 4801
5 TraesCS6A01G077300 chr7B 628741713 628746607 4894 False 4276.500000 7520 96.780000 2 4802 2 chr7B.!!$F1 4800
6 TraesCS6A01G077300 chr7B 75047321 75052215 4894 True 4269.000000 7522 96.554000 1 4802 2 chr7B.!!$R1 4801
7 TraesCS6A01G077300 chr6B 482833423 482837663 4240 True 7522.000000 7522 98.680000 562 4802 1 chr6B.!!$R2 4240
8 TraesCS6A01G077300 chr6B 482813792 482818030 4238 True 7470.000000 7470 98.467000 562 4802 1 chr6B.!!$R1 4240
9 TraesCS6A01G077300 chr3A 742304185 742308420 4235 False 7489.000000 7489 98.562000 562 4802 1 chr3A.!!$F1 4240
10 TraesCS6A01G077300 chrUn 373124735 373125399 664 True 1042.000000 1042 95.038000 1 661 1 chrUn.!!$R2 660
11 TraesCS6A01G077300 chrUn 289560885 289561549 664 True 1026.000000 1026 94.595000 1 661 1 chrUn.!!$R1 660
12 TraesCS6A01G077300 chr2A 70020484 70021147 663 True 1040.000000 1040 95.038000 1 661 1 chr2A.!!$R1 660

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
97 98 1.185315 CCCTCACGGCCAAAATGAAT 58.815 50.000 2.24 0.0 0.00 2.57 F
176 177 4.522789 TCTGCCTGGAAAATGGTAGAAAAC 59.477 41.667 0.00 0.0 41.01 2.43 F
1247 3781 4.676986 GCACCAGTGTCTCATGAATACGTA 60.677 45.833 0.00 0.0 0.00 3.57 F
1839 4374 1.183549 TACTGGAACGAGGGAAGAGC 58.816 55.000 0.00 0.0 0.00 4.09 F
2090 4625 3.954904 CCTGGAAGAGGACGAAGAGAATA 59.045 47.826 0.00 0.0 46.33 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 4092 0.898320 CCGTCCAGTTCCTCATCAGT 59.102 55.000 0.00 0.00 0.00 3.41 R
1833 4368 1.226717 CCGAGGTACTGCGCTCTTC 60.227 63.158 9.73 1.93 41.55 2.87 R
2375 4910 0.396811 ACTCCTTGAGAACCAACCGG 59.603 55.000 0.00 0.00 34.01 5.28 R
3609 6144 3.403968 TGCGTACCTGTGAAAATAAGCA 58.596 40.909 0.00 0.00 31.07 3.91 R
4288 6829 4.746466 ACCTGCTTATATACTCAGCTCCT 58.254 43.478 6.49 0.00 34.42 3.69 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
97 98 1.185315 CCCTCACGGCCAAAATGAAT 58.815 50.000 2.24 0.0 0.00 2.57
176 177 4.522789 TCTGCCTGGAAAATGGTAGAAAAC 59.477 41.667 0.00 0.0 41.01 2.43
1247 3781 4.676986 GCACCAGTGTCTCATGAATACGTA 60.677 45.833 0.00 0.0 0.00 3.57
1833 4368 2.947652 TCTAACGATACTGGAACGAGGG 59.052 50.000 0.00 0.0 0.00 4.30
1839 4374 1.183549 TACTGGAACGAGGGAAGAGC 58.816 55.000 0.00 0.0 0.00 4.09
2090 4625 3.954904 CCTGGAAGAGGACGAAGAGAATA 59.045 47.826 0.00 0.0 46.33 1.75
2261 4796 5.337578 AAACACACCTTTTTACTGCACAT 57.662 34.783 0.00 0.0 0.00 3.21
2910 5445 7.447374 TTGGTCGACAAAGTTAATGATGATT 57.553 32.000 18.91 0.0 35.79 2.57
3495 6030 6.647895 GGGTGAGTTTTTACTTCGACAGAATA 59.352 38.462 0.00 0.0 35.56 1.75
4288 6829 2.143122 GAGGAGTTCAATGCAACGACA 58.857 47.619 0.00 0.0 0.00 4.35
4636 7177 3.927142 GTCGTTGTATTGAACTCCTCTGG 59.073 47.826 0.00 0.0 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 4.493547 GATTTCATTCATTTTGGCCGTGA 58.506 39.130 0.00 0.00 0.00 4.35
97 98 0.509499 GCGTTCGTTGTCGGATTTCA 59.491 50.000 0.00 0.00 37.69 2.69
176 177 1.469126 CCGTTTCGAGTCCGTATGCG 61.469 60.000 0.00 0.00 37.05 4.73
207 208 4.435436 CTAGCAGGGCACGCACGA 62.435 66.667 5.62 0.00 0.00 4.35
431 435 0.788391 GCGTCGTTTGTTAGTGGGAG 59.212 55.000 0.00 0.00 0.00 4.30
1247 3781 5.873164 CACTAAGGCATAGTACTTTTTCGGT 59.127 40.000 0.00 0.00 43.12 4.69
1557 4092 0.898320 CCGTCCAGTTCCTCATCAGT 59.102 55.000 0.00 0.00 0.00 3.41
1833 4368 1.226717 CCGAGGTACTGCGCTCTTC 60.227 63.158 9.73 1.93 41.55 2.87
1839 4374 2.615262 GAAGCCTCCGAGGTACTGCG 62.615 65.000 16.09 0.00 41.55 5.18
2090 4625 4.345257 AGACTCATTAATGCCTCCGTACAT 59.655 41.667 10.76 0.00 0.00 2.29
2261 4796 5.422331 CCTTGAAACTATCCCAGTACTCAGA 59.578 44.000 0.00 0.00 36.04 3.27
2375 4910 0.396811 ACTCCTTGAGAACCAACCGG 59.603 55.000 0.00 0.00 34.01 5.28
2910 5445 6.833041 TCCTCCAAGTAGTTAACATGAAACA 58.167 36.000 8.61 0.00 0.00 2.83
2924 5459 4.227300 AGCAACCAATGTATCCTCCAAGTA 59.773 41.667 0.00 0.00 0.00 2.24
2975 5510 5.985530 CGACTCTGCTTCATAATCATTACCA 59.014 40.000 0.00 0.00 0.00 3.25
3049 5584 8.344098 CCGTGTTAACAATCAAACTTACCTTTA 58.656 33.333 10.51 0.00 0.00 1.85
3609 6144 3.403968 TGCGTACCTGTGAAAATAAGCA 58.596 40.909 0.00 0.00 31.07 3.91
4288 6829 4.746466 ACCTGCTTATATACTCAGCTCCT 58.254 43.478 6.49 0.00 34.42 3.69
4636 7177 1.800286 GCACATCGACGGGGTAGTAAC 60.800 57.143 0.00 0.00 0.00 2.50


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

AutoCloner maintained by Alex Coulton.