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
TraesCS4A01G175500
chr4A
100.000
3430
0
0
986
4415
446608843
446612272
0.000000e+00
6335.0
1
TraesCS4A01G175500
chr4A
100.000
803
0
0
1
803
446607858
446608660
0.000000e+00
1483.0
2
TraesCS4A01G175500
chr4A
96.000
250
6
4
154
403
450333071
450332826
1.910000e-108
403.0
3
TraesCS4A01G175500
chr1B
95.372
3133
100
16
990
4109
173131783
173128683
0.000000e+00
4940.0
4
TraesCS4A01G175500
chr1B
98.406
251
3
1
155
404
664059142
664059392
1.460000e-119
440.0
5
TraesCS4A01G175500
chr1B
97.189
249
4
3
156
404
304518614
304518369
6.830000e-113
418.0
6
TraesCS4A01G175500
chr1B
94.928
138
5
2
4279
4415
173126268
173126132
9.620000e-52
215.0
7
TraesCS4A01G175500
chr1B
92.553
94
3
3
4018
4109
597450204
597450113
9.960000e-27
132.0
8
TraesCS4A01G175500
chr1B
96.552
58
2
0
4134
4191
173127603
173127546
3.630000e-16
97.1
9
TraesCS4A01G175500
chr1B
96.552
58
2
0
4134
4191
173128487
173128430
3.630000e-16
97.1
10
TraesCS4A01G175500
chr4D
94.957
3113
137
10
991
4090
123146653
123143548
0.000000e+00
4861.0
11
TraesCS4A01G175500
chr4D
92.580
283
17
4
4134
4415
123143380
123143101
1.910000e-108
403.0
12
TraesCS4A01G175500
chr4D
95.946
74
3
0
4019
4092
505968141
505968214
2.160000e-23
121.0
13
TraesCS4A01G175500
chr4D
95.588
68
3
0
4021
4088
505921838
505921905
4.670000e-20
110.0
14
TraesCS4A01G175500
chr4B
94.609
3135
151
7
990
4112
187732817
187729689
0.000000e+00
4837.0
15
TraesCS4A01G175500
chr4B
96.838
253
6
2
154
404
249050049
249050301
5.280000e-114
422.0
16
TraesCS4A01G175500
chr4B
91.697
277
16
3
4139
4415
187729547
187729278
1.160000e-100
377.0
17
TraesCS4A01G175500
chr4B
90.583
223
14
3
4193
4415
187729178
187728963
5.590000e-74
289.0
18
TraesCS4A01G175500
chr1A
96.935
2545
61
8
1392
3922
121135464
121132923
0.000000e+00
4252.0
19
TraesCS4A01G175500
chr1A
96.560
407
14
0
990
1396
121136032
121135626
0.000000e+00
675.0
20
TraesCS4A01G175500
chr1A
88.384
198
16
4
3914
4111
121132521
121132331
9.550000e-57
231.0
21
TraesCS4A01G175500
chr1A
94.161
137
8
0
4279
4415
121131897
121131761
4.470000e-50
209.0
22
TraesCS4A01G175500
chr1A
89.726
146
12
3
656
800
439929213
439929356
2.710000e-42
183.0
23
TraesCS4A01G175500
chr1A
91.398
93
6
2
4018
4109
537973601
537973692
4.640000e-25
126.0
24
TraesCS4A01G175500
chr7D
93.393
1665
85
10
1615
3266
590451994
590450342
0.000000e+00
2442.0
25
TraesCS4A01G175500
chr7D
90.141
639
48
5
987
1613
590518600
590517965
0.000000e+00
817.0
26
TraesCS4A01G175500
chr7D
87.156
327
26
4
3261
3571
590447425
590447099
1.510000e-94
357.0
27
TraesCS4A01G175500
chr7D
89.262
149
11
5
656
803
517561176
517561320
9.750000e-42
182.0
28
TraesCS4A01G175500
chr7D
77.593
241
41
9
3858
4092
590446937
590446704
2.770000e-27
134.0
29
TraesCS4A01G175500
chr3B
98.367
245
2
2
160
404
820904401
820904159
3.160000e-116
429.0
30
TraesCS4A01G175500
chr3B
97.959
245
2
1
160
404
820904036
820903795
5.280000e-114
422.0
31
TraesCS4A01G175500
chr3B
97.951
244
2
1
161
404
820904217
820903977
1.900000e-113
420.0
32
TraesCS4A01G175500
chr3B
97.942
243
2
1
162
404
265849532
265849771
6.830000e-113
418.0
33
TraesCS4A01G175500
chr3B
85.455
110
8
4
426
528
29949708
29949600
1.680000e-19
108.0
34
TraesCS4A01G175500
chr2B
97.541
244
3
1
161
404
69371620
69371860
8.830000e-112
414.0
35
TraesCS4A01G175500
chr2B
86.957
92
9
2
456
545
714256873
714256963
2.810000e-17
100.0
36
TraesCS4A01G175500
chr2B
86.957
92
9
2
456
545
714311870
714311960
2.810000e-17
100.0
37
TraesCS4A01G175500
chr2A
94.862
253
12
1
550
802
1819443
1819694
1.150000e-105
394.0
38
TraesCS4A01G175500
chr2A
88.571
105
10
2
561
664
578037791
578037894
4.640000e-25
126.0
39
TraesCS4A01G175500
chr2A
87.619
105
11
2
561
664
577441918
577442021
2.160000e-23
121.0
40
TraesCS4A01G175500
chr2A
88.043
92
8
2
456
545
577443004
577443094
6.040000e-19
106.0
41
TraesCS4A01G175500
chr2A
88.043
92
8
2
456
545
578035841
578035931
6.040000e-19
106.0
42
TraesCS4A01G175500
chr7B
91.852
270
12
7
543
803
623819234
623818966
6.980000e-98
368.0
43
TraesCS4A01G175500
chr7B
90.957
188
7
7
598
784
707011215
707011037
1.230000e-60
244.0
44
TraesCS4A01G175500
chr7B
94.776
134
4
1
24
154
623819647
623819514
5.790000e-49
206.0
45
TraesCS4A01G175500
chr7B
93.284
134
6
1
24
154
707011942
707011809
1.250000e-45
195.0
46
TraesCS4A01G175500
chr7B
89.922
129
12
1
418
545
707011638
707011510
9.820000e-37
165.0
47
TraesCS4A01G175500
chr7B
92.063
63
3
2
540
601
707011373
707011312
2.190000e-13
87.9
48
TraesCS4A01G175500
chrUn
92.095
253
19
1
1562
1813
261868755
261869007
5.430000e-94
355.0
49
TraesCS4A01G175500
chrUn
90.769
130
10
2
659
787
19790449
19790321
5.870000e-39
172.0
50
TraesCS4A01G175500
chrUn
84.496
129
10
5
426
545
19793105
19792978
7.760000e-23
119.0
51
TraesCS4A01G175500
chr2D
92.095
253
19
1
1562
1813
453710421
453710169
5.430000e-94
355.0
52
TraesCS4A01G175500
chr5D
91.406
256
21
1
1559
1813
119459884
119460139
2.530000e-92
350.0
53
TraesCS4A01G175500
chr5D
91.034
145
8
5
659
803
185254091
185253952
1.620000e-44
191.0
54
TraesCS4A01G175500
chr5D
89.865
148
11
4
656
803
528401088
528401231
2.100000e-43
187.0
55
TraesCS4A01G175500
chr5D
94.048
84
3
2
4010
4092
305712686
305712768
4.640000e-25
126.0
56
TraesCS4A01G175500
chr5D
96.000
75
3
0
4018
4092
539481167
539481241
6.000000e-24
122.0
57
TraesCS4A01G175500
chr5D
90.110
91
7
2
456
545
185256701
185256612
2.790000e-22
117.0
58
TraesCS4A01G175500
chr6D
90.734
259
20
3
1559
1813
285487738
285487996
4.230000e-90
342.0
59
TraesCS4A01G175500
chr5B
89.189
148
11
5
656
803
704108449
704108591
3.510000e-41
180.0
60
TraesCS4A01G175500
chr3A
92.079
101
4
3
4014
4111
703902586
703902685
5.950000e-29
139.0
61
TraesCS4A01G175500
chr3A
92.473
93
5
2
4004
4095
718376636
718376727
9.960000e-27
132.0
62
TraesCS4A01G175500
chr3A
93.333
90
5
1
4004
4093
719333510
719333598
9.960000e-27
132.0
63
TraesCS4A01G175500
chr3A
90.816
98
7
2
3995
4092
719044454
719044359
3.580000e-26
130.0
64
TraesCS4A01G175500
chr3A
89.423
104
8
3
4008
4111
718372550
718372650
1.290000e-25
128.0
65
TraesCS4A01G175500
chr3A
87.500
112
8
4
4003
4112
655646780
655646673
1.670000e-24
124.0
66
TraesCS4A01G175500
chr6B
86.290
124
13
4
561
682
578003265
578003386
9.960000e-27
132.0
67
TraesCS4A01G175500
chr3D
92.473
93
6
1
4003
4095
589373609
589373518
9.960000e-27
132.0
68
TraesCS4A01G175500
chr3D
91.398
93
6
2
4004
4095
588345396
588345487
4.640000e-25
126.0
69
TraesCS4A01G175500
chr3D
90.526
95
8
1
4019
4113
497869618
497869525
1.670000e-24
124.0
70
TraesCS4A01G175500
chr3D
92.135
89
6
1
4004
4092
588335053
588335140
1.670000e-24
124.0
71
TraesCS4A01G175500
chr3D
92.135
89
6
1
4020
4108
589411004
589411091
1.670000e-24
124.0
72
TraesCS4A01G175500
chr3D
89.320
103
6
3
4015
4112
612302310
612302412
1.670000e-24
124.0
73
TraesCS4A01G175500
chr3D
91.398
93
3
4
4019
4111
570803527
570803440
6.000000e-24
122.0
74
TraesCS4A01G175500
chr7A
85.484
124
14
4
561
682
54671083
54670962
4.640000e-25
126.0
75
TraesCS4A01G175500
chr7A
89.130
92
7
2
456
545
54673033
54672943
1.300000e-20
111.0
76
TraesCS4A01G175500
chr1D
90.625
96
8
1
4018
4112
439868664
439868569
4.640000e-25
126.0
77
TraesCS4A01G175500
chr1D
91.304
92
6
2
4018
4109
315607882
315607971
1.670000e-24
124.0
78
TraesCS4A01G175500
chr1D
96.000
75
3
0
4018
4092
47880388
47880462
6.000000e-24
122.0
79
TraesCS4A01G175500
chr1D
96.000
75
3
0
4018
4092
432396620
432396546
6.000000e-24
122.0
80
TraesCS4A01G175500
chr1D
94.667
75
4
0
4018
4092
433679605
433679679
2.790000e-22
117.0
81
TraesCS4A01G175500
chr1D
89.247
93
8
2
4019
4111
381067956
381067866
1.000000e-21
115.0
82
TraesCS4A01G175500
chr1D
97.015
67
2
0
4018
4084
315609616
315609682
3.610000e-21
113.0
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
TraesCS4A01G175500
chr4A
446607858
446612272
4414
False
3909.000000
6335
100.000000
1
4415
2
chr4A.!!$F1
4414
1
TraesCS4A01G175500
chr1B
173126132
173131783
5651
True
1337.300000
4940
95.851000
990
4415
4
chr1B.!!$R3
3425
2
TraesCS4A01G175500
chr4D
123143101
123146653
3552
True
2632.000000
4861
93.768500
991
4415
2
chr4D.!!$R1
3424
3
TraesCS4A01G175500
chr4B
187728963
187732817
3854
True
1834.333333
4837
92.296333
990
4415
3
chr4B.!!$R1
3425
4
TraesCS4A01G175500
chr1A
121131761
121136032
4271
True
1341.750000
4252
94.010000
990
4415
4
chr1A.!!$R1
3425
5
TraesCS4A01G175500
chr7D
590446704
590451994
5290
True
977.666667
2442
86.047333
1615
4092
3
chr7D.!!$R2
2477
6
TraesCS4A01G175500
chr7D
590517965
590518600
635
True
817.000000
817
90.141000
987
1613
1
chr7D.!!$R1
626
7
TraesCS4A01G175500
chr3B
820903795
820904401
606
True
423.666667
429
98.092333
160
404
3
chr3B.!!$R2
244
8
TraesCS4A01G175500
chr7B
623818966
623819647
681
True
287.000000
368
93.314000
24
803
2
chr7B.!!$R1
779
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.