Multiple sequence alignment - TraesCS1A01G098300

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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 TraesCS1A01G098300 chr1A 100.000 3354 0 0 1 3354 94765608 94762255 0 6194
1 TraesCS1A01G098300 chr5D 98.422 3359 47 2 1 3354 562925169 562928526 0 5904
2 TraesCS1A01G098300 chr2D 98.273 3359 53 1 1 3354 200934930 200938288 0 5877
3 TraesCS1A01G098300 chr2D 97.529 3359 76 3 1 3354 604416901 604420257 0 5736
4 TraesCS1A01G098300 chr7A 98.123 3357 58 1 3 3354 211308104 211311460 0 5845
5 TraesCS1A01G098300 chr7A 97.915 3357 65 1 3 3354 563544629 563547985 0 5806
6 TraesCS1A01G098300 chr7A 98.613 2524 35 0 831 3354 60348516 60345993 0 4468
7 TraesCS1A01G098300 chr7A 98.069 1554 24 2 1 1549 211265015 211263463 0 2699
8 TraesCS1A01G098300 chr1D 97.976 3359 61 2 1 3354 185786582 185783226 0 5819
9 TraesCS1A01G098300 chr6D 98.477 3284 45 1 76 3354 458889921 458893204 0 5782
10 TraesCS1A01G098300 chr4A 97.380 3359 77 5 1 3354 275495387 275498739 0 5705


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 TraesCS1A01G098300 chr1A 94762255 94765608 3353 True 6194 6194 100.000 1 3354 1 chr1A.!!$R1 3353
1 TraesCS1A01G098300 chr5D 562925169 562928526 3357 False 5904 5904 98.422 1 3354 1 chr5D.!!$F1 3353
2 TraesCS1A01G098300 chr2D 200934930 200938288 3358 False 5877 5877 98.273 1 3354 1 chr2D.!!$F1 3353
3 TraesCS1A01G098300 chr2D 604416901 604420257 3356 False 5736 5736 97.529 1 3354 1 chr2D.!!$F2 3353
4 TraesCS1A01G098300 chr7A 211308104 211311460 3356 False 5845 5845 98.123 3 3354 1 chr7A.!!$F1 3351
5 TraesCS1A01G098300 chr7A 563544629 563547985 3356 False 5806 5806 97.915 3 3354 1 chr7A.!!$F2 3351
6 TraesCS1A01G098300 chr7A 60345993 60348516 2523 True 4468 4468 98.613 831 3354 1 chr7A.!!$R1 2523
7 TraesCS1A01G098300 chr7A 211263463 211265015 1552 True 2699 2699 98.069 1 1549 1 chr7A.!!$R2 1548
8 TraesCS1A01G098300 chr1D 185783226 185786582 3356 True 5819 5819 97.976 1 3354 1 chr1D.!!$R1 3353
9 TraesCS1A01G098300 chr6D 458889921 458893204 3283 False 5782 5782 98.477 76 3354 1 chr6D.!!$F1 3278
10 TraesCS1A01G098300 chr4A 275495387 275498739 3352 False 5705 5705 97.380 1 3354 1 chr4A.!!$F1 3353

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
136 137 1.736126 CGCATGGCTATCCTGCTAATG 59.264 52.381 0.0 0.0 35.63 1.90 F
856 862 3.645687 AGAAGTGTTCTCTTTCTCCAGCT 59.354 43.478 0.0 0.0 34.07 4.24 F
1453 1459 9.342308 GATCTTATAATTCATGGACCAAAGTCA 57.658 33.333 0.0 0.0 45.48 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1491 0.821711 CCCCTTGCCGACTTTGAACA 60.822 55.000 0.0 0.0 0.0 3.18 R
1674 1680 2.827921 GTGTGCCCCTTCATTCAATCTT 59.172 45.455 0.0 0.0 0.0 2.40 R
3299 3305 1.484653 TGGCATAGCTGTATTGGACGT 59.515 47.619 0.0 0.0 0.0 4.34 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
119 120 2.672961 AACTAGCTGCTGAATACGCA 57.327 45.000 13.43 0.0 35.80 5.24
120 121 2.898729 ACTAGCTGCTGAATACGCAT 57.101 45.000 13.43 0.0 36.70 4.73
136 137 1.736126 CGCATGGCTATCCTGCTAATG 59.264 52.381 0.00 0.0 35.63 1.90
649 650 6.078664 AGAGAGAGACCACTTTAAGAAAGGA 58.921 40.000 0.00 0.0 42.82 3.36
856 862 3.645687 AGAAGTGTTCTCTTTCTCCAGCT 59.354 43.478 0.00 0.0 34.07 4.24
1453 1459 9.342308 GATCTTATAATTCATGGACCAAAGTCA 57.658 33.333 0.00 0.0 45.48 3.41
1674 1680 6.442564 AGGTATGTGGGTAGACATTGAGTTAA 59.557 38.462 0.00 0.0 37.70 2.01
2023 2029 9.838975 CAGTCTTTATTGTTGTGTGCATATTAA 57.161 29.630 0.00 0.0 0.00 1.40
2467 2473 4.441079 GGTTAGCTGTTCACGGATTAGCTA 60.441 45.833 0.00 0.0 42.45 3.32
2644 2650 5.486063 TCCACCTACAACTAATAAAGCTCCA 59.514 40.000 0.00 0.0 0.00 3.86
3058 3064 2.687370 GCCTTCGATGCAACCAAATTT 58.313 42.857 0.00 0.0 0.00 1.82
3072 3078 8.851145 TGCAACCAAATTTACTATTGACTTACA 58.149 29.630 0.00 0.0 0.00 2.41
3299 3305 2.747177 AGGGACTCATTCACCGTATCA 58.253 47.619 0.00 0.0 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 3.069079 CAGCATTAGCAGGATAGCCAT 57.931 47.619 0.00 0.00 45.49 4.40
120 121 2.556144 CAGCATTAGCAGGATAGCCA 57.444 50.000 0.00 0.00 45.49 4.75
136 137 0.961019 TCATGTCTTTGGTTGCCAGC 59.039 50.000 0.00 0.00 33.81 4.85
616 617 6.432403 AAGTGGTCTCTCTCTTCTTTTCAT 57.568 37.500 0.00 0.00 0.00 2.57
649 650 3.953612 TGAGCAACTTCTTTTGTGGACAT 59.046 39.130 0.00 0.00 0.00 3.06
856 862 4.038763 TCTTCCTGCGAGACTGTTCTTTTA 59.961 41.667 0.00 0.00 29.47 1.52
1485 1491 0.821711 CCCCTTGCCGACTTTGAACA 60.822 55.000 0.00 0.00 0.00 3.18
1674 1680 2.827921 GTGTGCCCCTTCATTCAATCTT 59.172 45.455 0.00 0.00 0.00 2.40
2023 2029 9.717942 GTCCTATTCAAAGCTATAATCAGTGAT 57.282 33.333 0.00 0.00 0.00 3.06
2090 2096 3.507233 TCGCTTCTTTCCATTGCTTCAAT 59.493 39.130 0.00 0.00 34.04 2.57
2467 2473 7.795047 TCTCATATGTGTTGTCATTCCAGTAT 58.205 34.615 1.90 0.00 0.00 2.12
2644 2650 3.320129 TGTTGTAGTAGTCCCCAAAGGT 58.680 45.455 0.00 0.00 36.75 3.50
3072 3078 5.927281 AGGAATGAAGCATGCATAAACTT 57.073 34.783 21.98 3.54 27.94 2.66
3299 3305 1.484653 TGGCATAGCTGTATTGGACGT 59.515 47.619 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.