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
TraesCS3B01G348400
chr3B
100.000
2786
0
0
1
2786
557704315
557707100
0.000000e+00
5145
1
TraesCS3B01G348400
chr3B
94.711
2817
97
15
1
2786
751900620
751897825
0.000000e+00
4329
2
TraesCS3B01G348400
chr3B
94.646
2092
78
11
724
2783
766268394
766270483
0.000000e+00
3212
3
TraesCS3B01G348400
chr3B
87.909
397
14
6
1
364
517884030
517883635
1.180000e-118
436
4
TraesCS3B01G348400
chr4A
95.029
2756
106
13
61
2786
660540612
660543366
0.000000e+00
4301
5
TraesCS3B01G348400
chr4A
96.279
215
8
0
1
215
691941346
691941560
1.230000e-93
353
6
TraesCS3B01G348400
chr5B
94.705
2493
97
17
324
2786
492520713
492518226
0.000000e+00
3840
7
TraesCS3B01G348400
chr1B
94.494
2488
125
10
309
2786
627378457
627375972
0.000000e+00
3825
8
TraesCS3B01G348400
chr1B
93.436
2605
110
24
236
2786
600347580
600344983
0.000000e+00
3807
9
TraesCS3B01G348400
chr1B
96.537
1155
33
7
1637
2786
6174572
6175724
0.000000e+00
1905
10
TraesCS3B01G348400
chr1B
94.419
215
12
0
1
215
600347847
600347633
5.750000e-87
331
11
TraesCS3B01G348400
chr1B
94.419
215
8
1
1
215
337579824
337579614
7.440000e-86
327
12
TraesCS3B01G348400
chr2B
95.392
2257
80
10
1
2235
700669614
700671868
0.000000e+00
3570
13
TraesCS3B01G348400
chr2B
90.505
495
18
8
1
495
796942831
796943296
6.550000e-176
627
14
TraesCS3B01G348400
chr2B
89.516
496
22
9
1
495
750608093
750608559
3.970000e-168
601
15
TraesCS3B01G348400
chrUn
95.902
2123
55
11
1
2113
236924716
236926816
0.000000e+00
3410
16
TraesCS3B01G348400
chrUn
93.744
2094
83
11
724
2786
290561338
290559262
0.000000e+00
3097
17
TraesCS3B01G348400
chrUn
95.350
1527
42
8
1
1520
35192606
35191102
0.000000e+00
2399
18
TraesCS3B01G348400
chrUn
89.495
495
23
3
1
495
290561792
290561327
1.430000e-167
599
19
TraesCS3B01G348400
chrUn
96.135
207
8
0
1
207
264980718
264980924
3.440000e-89
339
20
TraesCS3B01G348400
chrUn
96.875
192
5
1
304
495
264980973
264981163
1.250000e-83
320
21
TraesCS3B01G348400
chr4B
94.556
2094
67
10
725
2786
668352629
668350551
0.000000e+00
3192
22
TraesCS3B01G348400
chr4B
94.286
1785
84
5
1
1768
263067658
263065875
0.000000e+00
2715
23
TraesCS3B01G348400
chr4B
89.600
500
18
5
1
495
668353089
668352619
3.070000e-169
604
24
TraesCS3B01G348400
chr4B
93.953
215
9
1
1
215
613127412
613127622
3.460000e-84
322
25
TraesCS3B01G348400
chr7B
94.012
1386
51
9
1432
2786
749266896
749268280
0.000000e+00
2071
26
TraesCS3B01G348400
chr6B
89.113
496
12
4
1
495
630184798
630184344
1.860000e-161
579
27
TraesCS3B01G348400
chr3D
97.000
200
6
0
263
462
330477837
330477638
1.240000e-88
337
28
TraesCS3B01G348400
chr3D
91.176
204
10
3
1
200
57605980
57606179
1.270000e-68
270
29
TraesCS3B01G348400
chr4D
96.000
200
8
0
263
462
222630779
222630580
2.680000e-85
326
30
TraesCS3B01G348400
chr4D
92.019
213
9
4
1
209
125862128
125861920
2.710000e-75
292
31
TraesCS3B01G348400
chr4D
92.157
204
8
3
1
200
125871860
125872059
5.880000e-72
281
32
TraesCS3B01G348400
chr4D
90.686
204
11
3
1
200
261240324
261240125
5.920000e-67
265
33
TraesCS3B01G348400
chr4D
88.263
213
11
6
1
209
125937716
125937514
2.770000e-60
243
34
TraesCS3B01G348400
chr6D
95.000
200
10
0
263
462
46527962
46527763
5.790000e-82
315
35
TraesCS3B01G348400
chr6D
86.224
196
13
4
1
192
297180008
297179823
1.690000e-47
200
36
TraesCS3B01G348400
chr1D
89.732
224
10
8
1
215
428056569
428056350
9.830000e-70
274
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
TraesCS3B01G348400
chr3B
557704315
557707100
2785
False
5145
5145
100.0000
1
2786
1
chr3B.!!$F1
2785
1
TraesCS3B01G348400
chr3B
751897825
751900620
2795
True
4329
4329
94.7110
1
2786
1
chr3B.!!$R2
2785
2
TraesCS3B01G348400
chr3B
766268394
766270483
2089
False
3212
3212
94.6460
724
2783
1
chr3B.!!$F2
2059
3
TraesCS3B01G348400
chr4A
660540612
660543366
2754
False
4301
4301
95.0290
61
2786
1
chr4A.!!$F1
2725
4
TraesCS3B01G348400
chr5B
492518226
492520713
2487
True
3840
3840
94.7050
324
2786
1
chr5B.!!$R1
2462
5
TraesCS3B01G348400
chr1B
627375972
627378457
2485
True
3825
3825
94.4940
309
2786
1
chr1B.!!$R2
2477
6
TraesCS3B01G348400
chr1B
600344983
600347847
2864
True
2069
3807
93.9275
1
2786
2
chr1B.!!$R3
2785
7
TraesCS3B01G348400
chr1B
6174572
6175724
1152
False
1905
1905
96.5370
1637
2786
1
chr1B.!!$F1
1149
8
TraesCS3B01G348400
chr2B
700669614
700671868
2254
False
3570
3570
95.3920
1
2235
1
chr2B.!!$F1
2234
9
TraesCS3B01G348400
chrUn
236924716
236926816
2100
False
3410
3410
95.9020
1
2113
1
chrUn.!!$F1
2112
10
TraesCS3B01G348400
chrUn
35191102
35192606
1504
True
2399
2399
95.3500
1
1520
1
chrUn.!!$R1
1519
11
TraesCS3B01G348400
chrUn
290559262
290561792
2530
True
1848
3097
91.6195
1
2786
2
chrUn.!!$R2
2785
12
TraesCS3B01G348400
chr4B
263065875
263067658
1783
True
2715
2715
94.2860
1
1768
1
chr4B.!!$R1
1767
13
TraesCS3B01G348400
chr4B
668350551
668353089
2538
True
1898
3192
92.0780
1
2786
2
chr4B.!!$R2
2785
14
TraesCS3B01G348400
chr7B
749266896
749268280
1384
False
2071
2071
94.0120
1432
2786
1
chr7B.!!$F1
1354
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.