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
TraesCS6D01G335600
chr6D
100.000
2654
0
0
664
3317
436832065
436834718
0.000000e+00
4902
1
TraesCS6D01G335600
chr6D
100.000
351
0
0
1
351
436831402
436831752
0.000000e+00
649
2
TraesCS6D01G335600
chr6A
91.826
2716
95
64
664
3317
585108239
585110889
0.000000e+00
3668
3
TraesCS6D01G335600
chr6A
87.535
361
9
12
8
351
585107869
585108210
5.190000e-103
385
4
TraesCS6D01G335600
chr6B
90.774
2699
98
51
670
3317
660564723
660562125
0.000000e+00
3465
5
TraesCS6D01G335600
chr6B
89.503
362
13
8
1
351
660565359
660565012
5.080000e-118
435
6
TraesCS6D01G335600
chr7D
87.209
1290
162
2
1012
2301
101783170
101781884
0.000000e+00
1465
7
TraesCS6D01G335600
chr7A
87.142
1291
161
4
1012
2301
105641655
105640369
0.000000e+00
1459
8
TraesCS6D01G335600
chr7B
86.522
1291
171
2
1012
2302
59100888
59099601
0.000000e+00
1417
9
TraesCS6D01G335600
chr7B
78.085
1013
200
20
1289
2287
204686952
204685948
3.630000e-174
621
10
TraesCS6D01G335600
chr5B
81.180
983
143
31
1289
2253
466333657
466332699
0.000000e+00
752
11
TraesCS6D01G335600
chr5D
80.957
982
147
29
1289
2253
387728912
387727954
0.000000e+00
741
12
TraesCS6D01G335600
chr5A
80.635
976
149
32
1295
2253
490816292
490815340
0.000000e+00
719
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
TraesCS6D01G335600
chr6D
436831402
436834718
3316
False
2775.5
4902
100.0000
1
3317
2
chr6D.!!$F1
3316
1
TraesCS6D01G335600
chr6A
585107869
585110889
3020
False
2026.5
3668
89.6805
8
3317
2
chr6A.!!$F1
3309
2
TraesCS6D01G335600
chr6B
660562125
660565359
3234
True
1950.0
3465
90.1385
1
3317
2
chr6B.!!$R1
3316
3
TraesCS6D01G335600
chr7D
101781884
101783170
1286
True
1465.0
1465
87.2090
1012
2301
1
chr7D.!!$R1
1289
4
TraesCS6D01G335600
chr7A
105640369
105641655
1286
True
1459.0
1459
87.1420
1012
2301
1
chr7A.!!$R1
1289
5
TraesCS6D01G335600
chr7B
59099601
59100888
1287
True
1417.0
1417
86.5220
1012
2302
1
chr7B.!!$R1
1290
6
TraesCS6D01G335600
chr7B
204685948
204686952
1004
True
621.0
621
78.0850
1289
2287
1
chr7B.!!$R2
998
7
TraesCS6D01G335600
chr5B
466332699
466333657
958
True
752.0
752
81.1800
1289
2253
1
chr5B.!!$R1
964
8
TraesCS6D01G335600
chr5D
387727954
387728912
958
True
741.0
741
80.9570
1289
2253
1
chr5D.!!$R1
964
9
TraesCS6D01G335600
chr5A
490815340
490816292
952
True
719.0
719
80.6350
1295
2253
1
chr5A.!!$R1
958
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.
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.