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
TraesCS1B01G286400
chr1B
100.000
2549
0
0
1
2549
498442987
498440439
0
4708
1
TraesCS1B01G286400
chr1B
94.542
568
31
0
1
568
415019381
415018814
0
878
2
TraesCS1B01G286400
chr5B
96.429
1988
63
4
567
2548
446193256
446191271
0
3271
3
TraesCS1B01G286400
chr5B
95.926
1988
72
5
569
2549
269389473
269391458
0
3214
4
TraesCS1B01G286400
chr5B
94.190
568
33
0
1
568
48894651
48895218
0
867
5
TraesCS1B01G286400
chr5B
93.673
569
33
3
1
568
493412759
493412193
0
848
6
TraesCS1B01G286400
chr5B
93.486
568
37
0
1
568
502679548
502678981
0
845
7
TraesCS1B01G286400
chr2B
96.121
1985
73
3
568
2549
36241849
36243832
0
3236
8
TraesCS1B01G286400
chr2B
96.028
1989
73
3
567
2549
596962067
596964055
0
3230
9
TraesCS1B01G286400
chr2B
95.980
1990
70
6
569
2549
602077185
602075197
0
3223
10
TraesCS1B01G286400
chr2B
95.917
1984
74
6
569
2549
544319641
544317662
0
3208
11
TraesCS1B01G286400
chr2B
95.867
1984
75
6
569
2549
543889470
543887491
0
3203
12
TraesCS1B01G286400
chr3B
95.980
1990
70
8
568
2549
722334705
722336692
0
3223
13
TraesCS1B01G286400
chr3B
94.014
568
34
0
1
568
158348440
158349007
0
861
14
TraesCS1B01G286400
chr7B
95.968
1984
75
4
569
2549
718488474
718486493
0
3216
15
TraesCS1B01G286400
chr7B
94.014
568
32
2
1
568
655016152
655015587
0
859
16
TraesCS1B01G286400
chr7B
93.310
568
38
0
1
568
529571643
529571076
0
839
17
TraesCS1B01G286400
chr4B
94.366
568
32
0
1
568
77778927
77779494
0
872
18
TraesCS1B01G286400
chr6B
94.190
568
32
1
1
568
632148647
632148081
0
865
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
TraesCS1B01G286400
chr1B
498440439
498442987
2548
True
4708
4708
100.000
1
2549
1
chr1B.!!$R2
2548
1
TraesCS1B01G286400
chr1B
415018814
415019381
567
True
878
878
94.542
1
568
1
chr1B.!!$R1
567
2
TraesCS1B01G286400
chr5B
446191271
446193256
1985
True
3271
3271
96.429
567
2548
1
chr5B.!!$R1
1981
3
TraesCS1B01G286400
chr5B
269389473
269391458
1985
False
3214
3214
95.926
569
2549
1
chr5B.!!$F2
1980
4
TraesCS1B01G286400
chr5B
48894651
48895218
567
False
867
867
94.190
1
568
1
chr5B.!!$F1
567
5
TraesCS1B01G286400
chr5B
493412193
493412759
566
True
848
848
93.673
1
568
1
chr5B.!!$R2
567
6
TraesCS1B01G286400
chr5B
502678981
502679548
567
True
845
845
93.486
1
568
1
chr5B.!!$R3
567
7
TraesCS1B01G286400
chr2B
36241849
36243832
1983
False
3236
3236
96.121
568
2549
1
chr2B.!!$F1
1981
8
TraesCS1B01G286400
chr2B
596962067
596964055
1988
False
3230
3230
96.028
567
2549
1
chr2B.!!$F2
1982
9
TraesCS1B01G286400
chr2B
602075197
602077185
1988
True
3223
3223
95.980
569
2549
1
chr2B.!!$R3
1980
10
TraesCS1B01G286400
chr2B
544317662
544319641
1979
True
3208
3208
95.917
569
2549
1
chr2B.!!$R2
1980
11
TraesCS1B01G286400
chr2B
543887491
543889470
1979
True
3203
3203
95.867
569
2549
1
chr2B.!!$R1
1980
12
TraesCS1B01G286400
chr3B
722334705
722336692
1987
False
3223
3223
95.980
568
2549
1
chr3B.!!$F2
1981
13
TraesCS1B01G286400
chr3B
158348440
158349007
567
False
861
861
94.014
1
568
1
chr3B.!!$F1
567
14
TraesCS1B01G286400
chr7B
718486493
718488474
1981
True
3216
3216
95.968
569
2549
1
chr7B.!!$R3
1980
15
TraesCS1B01G286400
chr7B
655015587
655016152
565
True
859
859
94.014
1
568
1
chr7B.!!$R2
567
16
TraesCS1B01G286400
chr7B
529571076
529571643
567
True
839
839
93.310
1
568
1
chr7B.!!$R1
567
17
TraesCS1B01G286400
chr4B
77778927
77779494
567
False
872
872
94.366
1
568
1
chr4B.!!$F1
567
18
TraesCS1B01G286400
chr6B
632148081
632148647
566
True
865
865
94.190
1
568
1
chr6B.!!$R1
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.
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.