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
TraesCS5D01G015400
chr5D
100.000
3084
0
0
1
3084
8936059
8939142
0.000000e+00
5696.0
1
TraesCS5D01G015400
chr5B
85.578
1366
110
25
805
2136
9009200
9010512
0.000000e+00
1351.0
2
TraesCS5D01G015400
chr5B
86.272
896
89
17
1
893
9006363
9007227
0.000000e+00
942.0
3
TraesCS5D01G015400
chr5B
87.119
295
35
3
149
442
438504625
438504333
6.370000e-87
331.0
4
TraesCS5D01G015400
chr5B
80.451
399
51
15
149
535
117890845
117890462
2.340000e-71
279.0
5
TraesCS5D01G015400
chr5B
83.333
114
15
3
458
569
21596349
21596238
5.440000e-18
102.0
6
TraesCS5D01G015400
chr5B
93.617
47
1
2
1236
1280
681001209
681001163
5.520000e-08
69.4
7
TraesCS5D01G015400
chr5A
89.531
1003
55
24
524
1514
6982033
6982997
0.000000e+00
1225.0
8
TraesCS5D01G015400
chr5A
91.224
490
31
4
1
487
6981551
6982031
0.000000e+00
656.0
9
TraesCS5D01G015400
chr5A
85.085
590
58
10
1570
2136
6983221
6983803
2.670000e-160
575.0
10
TraesCS5D01G015400
chr5A
83.649
422
57
6
149
570
302298319
302298728
1.340000e-103
387.0
11
TraesCS5D01G015400
chr3D
90.011
941
90
4
2141
3080
301964372
301963435
0.000000e+00
1214.0
12
TraesCS5D01G015400
chr2B
89.446
957
95
5
2129
3084
41824601
41823650
0.000000e+00
1203.0
13
TraesCS5D01G015400
chr2B
89.496
952
88
8
2138
3081
137001783
137000836
0.000000e+00
1194.0
14
TraesCS5D01G015400
chrUn
91.228
855
71
4
2141
2994
92181117
92180266
0.000000e+00
1160.0
15
TraesCS5D01G015400
chr2D
88.655
952
104
4
2132
3081
328367467
328368416
0.000000e+00
1157.0
16
TraesCS5D01G015400
chr3B
88.025
952
109
4
2135
3084
425753033
425752085
0.000000e+00
1122.0
17
TraesCS5D01G015400
chr6A
87.844
946
111
4
2141
3084
433064986
433064043
0.000000e+00
1107.0
18
TraesCS5D01G015400
chr1B
87.831
945
105
7
2141
3081
100553834
100554772
0.000000e+00
1099.0
19
TraesCS5D01G015400
chr1B
87.606
944
108
9
2141
3081
297528421
297529358
0.000000e+00
1086.0
20
TraesCS5D01G015400
chr1B
81.435
237
34
8
49
284
142528765
142528538
5.250000e-43
185.0
21
TraesCS5D01G015400
chr7A
86.014
429
45
11
146
567
69317757
69318177
2.180000e-121
446.0
22
TraesCS5D01G015400
chr7A
83.252
412
57
10
161
568
39779145
39778742
4.860000e-98
368.0
23
TraesCS5D01G015400
chr7A
82.809
413
59
10
161
568
39795421
39795016
2.920000e-95
359.0
24
TraesCS5D01G015400
chr7A
88.679
159
18
0
13
171
69317653
69317811
8.730000e-46
195.0
25
TraesCS5D01G015400
chr7A
88.889
45
5
0
1236
1280
975640
975684
4.300000e-04
56.5
26
TraesCS5D01G015400
chr2A
82.210
371
58
6
49
415
608053465
608053099
2.310000e-81
313.0
27
TraesCS5D01G015400
chr4B
93.878
49
2
1
1233
1280
500865850
500865802
4.270000e-09
73.1
28
TraesCS5D01G015400
chr6D
92.000
50
3
1
1232
1280
179834774
179834823
5.520000e-08
69.4
29
TraesCS5D01G015400
chr6D
91.837
49
4
0
1232
1280
423215387
423215435
5.520000e-08
69.4
30
TraesCS5D01G015400
chr3A
93.478
46
3
0
1235
1280
664692846
664692891
5.520000e-08
69.4
31
TraesCS5D01G015400
chr3A
93.333
45
3
0
1236
1280
162081988
162081944
1.980000e-07
67.6
32
TraesCS5D01G015400
chr7D
91.304
46
3
1
1235
1280
222771486
222771442
9.230000e-06
62.1
33
TraesCS5D01G015400
chr4A
91.111
45
3
1
1231
1275
632853105
632853062
3.320000e-05
60.2
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
TraesCS5D01G015400
chr5D
8936059
8939142
3083
False
5696.000000
5696
100.000000
1
3084
1
chr5D.!!$F1
3083
1
TraesCS5D01G015400
chr5B
9006363
9010512
4149
False
1146.500000
1351
85.925000
1
2136
2
chr5B.!!$F1
2135
2
TraesCS5D01G015400
chr5A
6981551
6983803
2252
False
818.666667
1225
88.613333
1
2136
3
chr5A.!!$F2
2135
3
TraesCS5D01G015400
chr3D
301963435
301964372
937
True
1214.000000
1214
90.011000
2141
3080
1
chr3D.!!$R1
939
4
TraesCS5D01G015400
chr2B
41823650
41824601
951
True
1203.000000
1203
89.446000
2129
3084
1
chr2B.!!$R1
955
5
TraesCS5D01G015400
chr2B
137000836
137001783
947
True
1194.000000
1194
89.496000
2138
3081
1
chr2B.!!$R2
943
6
TraesCS5D01G015400
chrUn
92180266
92181117
851
True
1160.000000
1160
91.228000
2141
2994
1
chrUn.!!$R1
853
7
TraesCS5D01G015400
chr2D
328367467
328368416
949
False
1157.000000
1157
88.655000
2132
3081
1
chr2D.!!$F1
949
8
TraesCS5D01G015400
chr3B
425752085
425753033
948
True
1122.000000
1122
88.025000
2135
3084
1
chr3B.!!$R1
949
9
TraesCS5D01G015400
chr6A
433064043
433064986
943
True
1107.000000
1107
87.844000
2141
3084
1
chr6A.!!$R1
943
10
TraesCS5D01G015400
chr1B
100553834
100554772
938
False
1099.000000
1099
87.831000
2141
3081
1
chr1B.!!$F1
940
11
TraesCS5D01G015400
chr1B
297528421
297529358
937
False
1086.000000
1086
87.606000
2141
3081
1
chr1B.!!$F2
940
12
TraesCS5D01G015400
chr7A
69317653
69318177
524
False
320.500000
446
87.346500
13
567
2
chr7A.!!$F2
554
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.