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
TraesCS2A01G160000
chr2A
100.000
3935
0
0
1
3935
109594511
109598445
0.000000e+00
7267
1
TraesCS2A01G160000
chr2A
97.526
485
12
0
1
485
744299855
744300339
0.000000e+00
830
2
TraesCS2A01G160000
chr2D
95.666
3138
109
8
809
3935
111233099
111236220
0.000000e+00
5016
3
TraesCS2A01G160000
chr2D
91.133
203
8
3
607
808
185368820
185369013
2.330000e-67
267
4
TraesCS2A01G160000
chr2D
86.854
213
9
3
607
809
166313466
166313263
1.840000e-53
220
5
TraesCS2A01G160000
chr2D
85.909
220
10
5
607
814
185367954
185367744
8.560000e-52
215
6
TraesCS2A01G160000
chr2B
93.264
2806
144
13
889
3676
161018581
161021359
0.000000e+00
4093
7
TraesCS2A01G160000
chr2B
82.374
834
96
17
1
808
95754438
95753630
0.000000e+00
678
8
TraesCS2A01G160000
chr2B
91.304
207
10
2
3730
3935
161021470
161021669
3.870000e-70
276
9
TraesCS2A01G160000
chr3A
98.632
585
8
0
1
585
680735591
680735007
0.000000e+00
1037
10
TraesCS2A01G160000
chr3A
82.467
827
110
16
1
808
606367949
606367139
0.000000e+00
691
11
TraesCS2A01G160000
chr3A
90.196
306
9
4
515
808
680734704
680734408
2.870000e-101
379
12
TraesCS2A01G160000
chr7B
87.651
826
68
12
1
812
673581215
673580410
0.000000e+00
929
13
TraesCS2A01G160000
chr7B
85.628
494
66
3
1
490
3141180
3140688
7.540000e-142
514
14
TraesCS2A01G160000
chr7A
98.140
484
9
0
1
484
692902394
692902877
0.000000e+00
845
15
TraesCS2A01G160000
chr7A
98.129
481
9
0
4
484
646955320
646954840
0.000000e+00
839
16
TraesCS2A01G160000
chr7A
100.000
320
0
0
266
585
646954693
646954374
3.390000e-165
592
17
TraesCS2A01G160000
chr7A
100.000
320
0
0
266
585
692902888
692903207
3.390000e-165
592
18
TraesCS2A01G160000
chr7A
80.000
660
57
30
169
801
243668495
243667884
6.080000e-113
418
19
TraesCS2A01G160000
chr7A
89.302
215
4
3
604
808
692903439
692903644
6.530000e-63
252
20
TraesCS2A01G160000
chr7A
86.420
162
17
4
387
546
243668423
243668265
5.230000e-39
172
21
TraesCS2A01G160000
chr1B
91.781
584
44
3
1
580
391963403
391962820
0.000000e+00
809
22
TraesCS2A01G160000
chr5A
82.676
837
92
22
1
809
596051613
596052424
0.000000e+00
693
23
TraesCS2A01G160000
chr5A
86.449
214
8
5
607
808
83626350
83626146
8.560000e-52
215
24
TraesCS2A01G160000
chr5A
85.311
177
5
5
607
771
83627104
83627271
3.150000e-36
163
25
TraesCS2A01G160000
chr5B
89.855
207
7
6
607
809
488560463
488560659
1.810000e-63
254
26
TraesCS2A01G160000
chr5B
86.916
214
7
5
607
808
586868110
586868314
1.840000e-53
220
27
TraesCS2A01G160000
chr4D
86.697
218
9
4
602
809
475746783
475746990
1.420000e-54
224
28
TraesCS2A01G160000
chr4D
86.636
217
9
4
605
810
417468179
417468386
5.120000e-54
222
29
TraesCS2A01G160000
chr3D
86.473
207
22
5
607
809
231894370
231894166
5.120000e-54
222
30
TraesCS2A01G160000
chr4A
86.036
222
10
4
598
808
59317443
59317232
6.620000e-53
219
31
TraesCS2A01G160000
chr4A
83.562
219
10
10
607
808
672270738
672270529
8.690000e-42
182
32
TraesCS2A01G160000
chr4A
81.818
220
13
11
607
808
672177079
672176869
4.070000e-35
159
33
TraesCS2A01G160000
chr6D
86.512
215
8
4
607
809
216837348
216837553
2.380000e-52
217
34
TraesCS2A01G160000
chr6B
86.449
214
9
4
607
809
166592066
166591862
2.380000e-52
217
35
TraesCS2A01G160000
chr5D
85.463
227
11
4
597
810
296180025
296180242
2.380000e-52
217
36
TraesCS2A01G160000
chr4B
85.514
214
11
4
607
809
605789082
605789286
5.150000e-49
206
37
TraesCS2A01G160000
chr1D
92.086
139
11
0
408
546
256547728
256547866
3.100000e-46
196
38
TraesCS2A01G160000
chrUn
82.243
214
17
9
607
809
263126282
263126079
8.750000e-37
165
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
TraesCS2A01G160000
chr2A
109594511
109598445
3934
False
7267.0
7267
100.0000
1
3935
1
chr2A.!!$F1
3934
1
TraesCS2A01G160000
chr2D
111233099
111236220
3121
False
5016.0
5016
95.6660
809
3935
1
chr2D.!!$F1
3126
2
TraesCS2A01G160000
chr2B
161018581
161021669
3088
False
2184.5
4093
92.2840
889
3935
2
chr2B.!!$F1
3046
3
TraesCS2A01G160000
chr2B
95753630
95754438
808
True
678.0
678
82.3740
1
808
1
chr2B.!!$R1
807
4
TraesCS2A01G160000
chr3A
680734408
680735591
1183
True
708.0
1037
94.4140
1
808
2
chr3A.!!$R2
807
5
TraesCS2A01G160000
chr3A
606367139
606367949
810
True
691.0
691
82.4670
1
808
1
chr3A.!!$R1
807
6
TraesCS2A01G160000
chr7B
673580410
673581215
805
True
929.0
929
87.6510
1
812
1
chr7B.!!$R2
811
7
TraesCS2A01G160000
chr7A
646954374
646955320
946
True
715.5
839
99.0645
4
585
2
chr7A.!!$R2
581
8
TraesCS2A01G160000
chr7A
692902394
692903644
1250
False
563.0
845
95.8140
1
808
3
chr7A.!!$F1
807
9
TraesCS2A01G160000
chr7A
243667884
243668495
611
True
295.0
418
83.2100
169
801
2
chr7A.!!$R1
632
10
TraesCS2A01G160000
chr1B
391962820
391963403
583
True
809.0
809
91.7810
1
580
1
chr1B.!!$R1
579
11
TraesCS2A01G160000
chr5A
596051613
596052424
811
False
693.0
693
82.6760
1
809
1
chr5A.!!$F2
808
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.