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
TraesCS1B01G165400
chr1B
100.000
3602
0
0
1
3602
288755758
288759359
0.000000e+00
6652
1
TraesCS1B01G165400
chr1B
74.757
618
116
34
1979
2579
411154702
411154108
1.290000e-59
241
2
TraesCS1B01G165400
chr1A
95.647
1792
69
6
888
2674
254350306
254352093
0.000000e+00
2868
3
TraesCS1B01G165400
chr1A
88.358
670
65
13
240
900
254349619
254350284
0.000000e+00
793
4
TraesCS1B01G165400
chr1A
83.642
648
89
10
1927
2559
253728763
253728118
8.610000e-166
593
5
TraesCS1B01G165400
chr1A
75.815
583
105
31
2012
2579
381097054
381096493
2.760000e-66
263
6
TraesCS1B01G165400
chr1A
83.851
161
18
2
96
248
254347559
254347719
2.900000e-31
147
7
TraesCS1B01G165400
chr1A
86.408
103
13
1
1238
1340
253729562
253729461
1.060000e-20
111
8
TraesCS1B01G165400
chr1D
96.309
894
27
5
732
1619
200868379
200869272
0.000000e+00
1463
9
TraesCS1B01G165400
chr1D
90.897
736
66
1
2868
3602
360846667
360845932
0.000000e+00
987
10
TraesCS1B01G165400
chr1D
94.389
606
24
5
2273
2872
200869277
200869878
0.000000e+00
922
11
TraesCS1B01G165400
chr1D
88.581
613
66
4
78
687
200867769
200868380
0.000000e+00
741
12
TraesCS1B01G165400
chr1D
84.853
680
98
5
50
727
434233041
434233717
0.000000e+00
680
13
TraesCS1B01G165400
chr1D
75.243
618
113
35
1979
2579
303516910
303516316
1.280000e-64
257
14
TraesCS1B01G165400
chr7D
94.701
736
38
1
2868
3602
52521764
52522499
0.000000e+00
1142
15
TraesCS1B01G165400
chr7D
93.207
736
47
3
2868
3602
204025004
204025737
0.000000e+00
1079
16
TraesCS1B01G165400
chr3D
94.701
736
38
1
2868
3602
436233705
436234440
0.000000e+00
1142
17
TraesCS1B01G165400
chr5D
94.286
735
40
2
2868
3601
169005939
169005206
0.000000e+00
1123
18
TraesCS1B01G165400
chr5D
93.207
736
49
1
2868
3602
551874029
551874764
0.000000e+00
1081
19
TraesCS1B01G165400
chr5D
90.897
736
66
1
2868
3602
370636476
370635741
0.000000e+00
987
20
TraesCS1B01G165400
chr6A
91.973
735
58
1
2869
3602
435325551
435324817
0.000000e+00
1029
21
TraesCS1B01G165400
chr6D
91.033
736
65
1
2868
3602
65708944
65708209
0.000000e+00
992
22
TraesCS1B01G165400
chr5A
78.261
667
122
17
1927
2577
676966726
676966067
1.200000e-109
407
23
TraesCS1B01G165400
chr5A
79.798
297
44
11
1051
1340
676968273
676967986
6.100000e-48
202
24
TraesCS1B01G165400
chr4B
79.085
612
104
14
1982
2577
637737810
637737207
2.010000e-107
399
25
TraesCS1B01G165400
chr4B
79.592
294
50
8
1051
1340
637739317
637739030
6.100000e-48
202
26
TraesCS1B01G165400
chr4D
77.728
669
122
20
1927
2577
497166938
497166279
5.640000e-103
385
27
TraesCS1B01G165400
chr4D
79.125
297
46
11
1051
1340
497168484
497168197
1.320000e-44
191
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
TraesCS1B01G165400
chr1B
288755758
288759359
3601
False
6652.000000
6652
100.000000
1
3602
1
chr1B.!!$F1
3601
1
TraesCS1B01G165400
chr1B
411154108
411154702
594
True
241.000000
241
74.757000
1979
2579
1
chr1B.!!$R1
600
2
TraesCS1B01G165400
chr1A
254347559
254352093
4534
False
1269.333333
2868
89.285333
96
2674
3
chr1A.!!$F1
2578
3
TraesCS1B01G165400
chr1A
253728118
253729562
1444
True
352.000000
593
85.025000
1238
2559
2
chr1A.!!$R2
1321
4
TraesCS1B01G165400
chr1A
381096493
381097054
561
True
263.000000
263
75.815000
2012
2579
1
chr1A.!!$R1
567
5
TraesCS1B01G165400
chr1D
200867769
200869878
2109
False
1042.000000
1463
93.093000
78
2872
3
chr1D.!!$F2
2794
6
TraesCS1B01G165400
chr1D
360845932
360846667
735
True
987.000000
987
90.897000
2868
3602
1
chr1D.!!$R2
734
7
TraesCS1B01G165400
chr1D
434233041
434233717
676
False
680.000000
680
84.853000
50
727
1
chr1D.!!$F1
677
8
TraesCS1B01G165400
chr1D
303516316
303516910
594
True
257.000000
257
75.243000
1979
2579
1
chr1D.!!$R1
600
9
TraesCS1B01G165400
chr7D
52521764
52522499
735
False
1142.000000
1142
94.701000
2868
3602
1
chr7D.!!$F1
734
10
TraesCS1B01G165400
chr7D
204025004
204025737
733
False
1079.000000
1079
93.207000
2868
3602
1
chr7D.!!$F2
734
11
TraesCS1B01G165400
chr3D
436233705
436234440
735
False
1142.000000
1142
94.701000
2868
3602
1
chr3D.!!$F1
734
12
TraesCS1B01G165400
chr5D
169005206
169005939
733
True
1123.000000
1123
94.286000
2868
3601
1
chr5D.!!$R1
733
13
TraesCS1B01G165400
chr5D
551874029
551874764
735
False
1081.000000
1081
93.207000
2868
3602
1
chr5D.!!$F1
734
14
TraesCS1B01G165400
chr5D
370635741
370636476
735
True
987.000000
987
90.897000
2868
3602
1
chr5D.!!$R2
734
15
TraesCS1B01G165400
chr6A
435324817
435325551
734
True
1029.000000
1029
91.973000
2869
3602
1
chr6A.!!$R1
733
16
TraesCS1B01G165400
chr6D
65708209
65708944
735
True
992.000000
992
91.033000
2868
3602
1
chr6D.!!$R1
734
17
TraesCS1B01G165400
chr5A
676966067
676968273
2206
True
304.500000
407
79.029500
1051
2577
2
chr5A.!!$R1
1526
18
TraesCS1B01G165400
chr4B
637737207
637739317
2110
True
300.500000
399
79.338500
1051
2577
2
chr4B.!!$R1
1526
19
TraesCS1B01G165400
chr4D
497166279
497168484
2205
True
288.000000
385
78.426500
1051
2577
2
chr4D.!!$R1
1526
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.