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
TraesCS6B01G365400
chr6B
100.000
1969
0
0
1
1969
637145542
637143574
0.000000e+00
3637
1
TraesCS6B01G365400
chr6B
100.000
301
0
0
2270
2570
637143273
637142973
8.030000e-155
556
2
TraesCS6B01G365400
chr4D
92.208
1078
82
2
893
1969
639020
637944
0.000000e+00
1524
3
TraesCS6B01G365400
chr4D
90.676
858
78
2
1
857
658335
657479
0.000000e+00
1140
4
TraesCS6B01G365400
chr2B
91.261
1110
95
2
861
1969
784891054
784889946
0.000000e+00
1511
5
TraesCS6B01G365400
chr2B
89.431
1107
105
10
858
1960
773662255
773661157
0.000000e+00
1386
6
TraesCS6B01G365400
chr2B
90.316
1012
90
7
960
1969
693431517
693432522
0.000000e+00
1319
7
TraesCS6B01G365400
chr2B
90.105
859
81
3
2
857
784891992
784891135
0.000000e+00
1112
8
TraesCS6B01G365400
chr2B
87.485
839
97
7
22
857
773663166
773662333
0.000000e+00
961
9
TraesCS6B01G365400
chr2B
87.869
305
32
4
2270
2570
693432523
693432826
1.130000e-93
353
10
TraesCS6B01G365400
chr5B
89.630
1109
110
5
858
1963
660222097
660223203
0.000000e+00
1406
11
TraesCS6B01G365400
chr5B
86.176
1114
146
7
858
1969
577863004
577861897
0.000000e+00
1197
12
TraesCS6B01G365400
chr5B
86.033
852
115
4
2
851
660221164
660222013
0.000000e+00
911
13
TraesCS6B01G365400
chr5B
83.019
848
131
11
17
857
577863923
577863082
0.000000e+00
756
14
TraesCS6B01G365400
chr5B
87.417
302
36
2
2270
2570
660223210
660223510
1.890000e-91
346
15
TraesCS6B01G365400
chr3B
87.376
1109
134
6
858
1963
699289766
699290871
0.000000e+00
1267
16
TraesCS6B01G365400
chr5D
93.124
858
57
2
1
857
444076465
444075609
0.000000e+00
1256
17
TraesCS6B01G365400
chr5D
92.384
302
22
1
2270
2570
444074208
444073907
1.830000e-116
429
18
TraesCS6B01G365400
chr1D
87.047
1104
141
2
858
1960
72612948
72614050
0.000000e+00
1245
19
TraesCS6B01G365400
chr2D
86.355
1114
136
5
858
1969
36077686
36076587
0.000000e+00
1201
20
TraesCS6B01G365400
chr2D
82.827
856
139
8
6
857
619579325
619580176
0.000000e+00
760
21
TraesCS6B01G365400
chr2D
82.506
846
139
9
15
857
36078603
36077764
0.000000e+00
734
22
TraesCS6B01G365400
chr7D
84.928
836
114
9
24
857
501785051
501784226
0.000000e+00
835
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
TraesCS6B01G365400
chr6B
637142973
637145542
2569
True
2096.500000
3637
100.000000
1
2570
2
chr6B.!!$R1
2569
1
TraesCS6B01G365400
chr4D
637944
639020
1076
True
1524.000000
1524
92.208000
893
1969
1
chr4D.!!$R1
1076
2
TraesCS6B01G365400
chr4D
657479
658335
856
True
1140.000000
1140
90.676000
1
857
1
chr4D.!!$R2
856
3
TraesCS6B01G365400
chr2B
784889946
784891992
2046
True
1311.500000
1511
90.683000
2
1969
2
chr2B.!!$R2
1967
4
TraesCS6B01G365400
chr2B
773661157
773663166
2009
True
1173.500000
1386
88.458000
22
1960
2
chr2B.!!$R1
1938
5
TraesCS6B01G365400
chr2B
693431517
693432826
1309
False
836.000000
1319
89.092500
960
2570
2
chr2B.!!$F1
1610
6
TraesCS6B01G365400
chr5B
577861897
577863923
2026
True
976.500000
1197
84.597500
17
1969
2
chr5B.!!$R1
1952
7
TraesCS6B01G365400
chr5B
660221164
660223510
2346
False
887.666667
1406
87.693333
2
2570
3
chr5B.!!$F1
2568
8
TraesCS6B01G365400
chr3B
699289766
699290871
1105
False
1267.000000
1267
87.376000
858
1963
1
chr3B.!!$F1
1105
9
TraesCS6B01G365400
chr5D
444073907
444076465
2558
True
842.500000
1256
92.754000
1
2570
2
chr5D.!!$R1
2569
10
TraesCS6B01G365400
chr1D
72612948
72614050
1102
False
1245.000000
1245
87.047000
858
1960
1
chr1D.!!$F1
1102
11
TraesCS6B01G365400
chr2D
36076587
36078603
2016
True
967.500000
1201
84.430500
15
1969
2
chr2D.!!$R1
1954
12
TraesCS6B01G365400
chr2D
619579325
619580176
851
False
760.000000
760
82.827000
6
857
1
chr2D.!!$F1
851
13
TraesCS6B01G365400
chr7D
501784226
501785051
825
True
835.000000
835
84.928000
24
857
1
chr7D.!!$R1
833
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.