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
TraesCS4B01G375400
chr4B
100.000
5292
0
0
1
5292
659501961
659496670
0.000000e+00
9773.0
1
TraesCS4B01G375400
chr4B
96.301
4542
98
17
594
5126
659485821
659481341
0.000000e+00
7393.0
2
TraesCS4B01G375400
chr4B
99.692
2273
1
1
170
2442
659514556
659512290
0.000000e+00
4154.0
3
TraesCS4B01G375400
chr4B
94.693
358
11
3
257
609
659486614
659486260
2.790000e-152
549.0
4
TraesCS4B01G375400
chr4B
100.000
168
0
0
1
168
659514824
659514657
1.430000e-80
311.0
5
TraesCS4B01G375400
chr4B
100.000
35
0
0
5123
5157
659481411
659481377
1.230000e-06
65.8
6
TraesCS4B01G375400
chr4B
100.000
35
0
0
5056
5090
659496839
659496805
1.230000e-06
65.8
7
TraesCS4B01G375400
chr4B
100.000
35
0
0
5123
5157
659496906
659496872
1.230000e-06
65.8
8
TraesCS4B01G375400
chrUn
97.409
3397
51
7
1501
4887
264518339
264521708
0.000000e+00
5751.0
9
TraesCS4B01G375400
chr5A
84.918
3355
388
65
1135
4420
704368590
704371895
0.000000e+00
3284.0
10
TraesCS4B01G375400
chr5A
86.098
1971
209
38
2499
4432
694577706
694579648
0.000000e+00
2061.0
11
TraesCS4B01G375400
chr5A
85.895
1971
213
39
2499
4432
694556175
694558117
0.000000e+00
2039.0
12
TraesCS4B01G375400
chr5A
85.791
1872
202
37
2598
4432
694535868
694537712
0.000000e+00
1925.0
13
TraesCS4B01G375400
chr5A
85.985
1320
157
16
1078
2395
694551705
694552998
0.000000e+00
1387.0
14
TraesCS4B01G375400
chr5A
85.909
1320
158
16
1078
2395
694531274
694532567
0.000000e+00
1382.0
15
TraesCS4B01G375400
chr5A
85.909
1320
158
16
1078
2395
694572076
694573369
0.000000e+00
1382.0
16
TraesCS4B01G375400
chr5A
79.130
1931
340
46
1083
2970
708848126
708850036
0.000000e+00
1275.0
17
TraesCS4B01G375400
chr5A
85.993
1078
125
16
2609
3674
704452042
704453105
0.000000e+00
1131.0
18
TraesCS4B01G375400
chr5A
91.940
335
22
2
324
658
400793466
400793795
1.040000e-126
464.0
19
TraesCS4B01G375400
chr5A
78.571
252
45
3
3979
4221
708850924
708851175
1.970000e-34
158.0
20
TraesCS4B01G375400
chr5A
84.868
152
22
1
4572
4722
694558579
694558730
9.180000e-33
152.0
21
TraesCS4B01G375400
chr5A
84.211
152
23
1
4572
4722
694538173
694538324
4.270000e-31
147.0
22
TraesCS4B01G375400
chr5A
82.895
152
25
1
4572
4722
694580110
694580261
9.240000e-28
135.0
23
TraesCS4B01G375400
chr5A
92.000
50
3
1
142
191
374902790
374902838
9.510000e-08
69.4
24
TraesCS4B01G375400
chr5A
94.595
37
1
1
203
239
692059699
692059734
7.400000e-04
56.5
25
TraesCS4B01G375400
chr4D
84.496
3425
401
59
1067
4420
508339587
508342952
0.000000e+00
3264.0
26
TraesCS4B01G375400
chr4D
88.010
1251
130
11
2502
3746
504520348
504521584
0.000000e+00
1461.0
27
TraesCS4B01G375400
chr4D
84.171
1333
180
19
1067
2395
504518216
504519521
0.000000e+00
1264.0
28
TraesCS4B01G375400
chr4D
89.323
384
36
5
3981
4360
504521788
504522170
1.330000e-130
477.0
29
TraesCS4B01G375400
chr2B
92.492
333
20
2
324
656
619961261
619961588
6.200000e-129
472.0
30
TraesCS4B01G375400
chr2B
80.114
352
47
18
327
666
523078658
523078318
1.900000e-59
241.0
31
TraesCS4B01G375400
chr7B
91.369
336
22
5
324
656
734292054
734291723
2.250000e-123
453.0
32
TraesCS4B01G375400
chr7B
91.975
324
18
5
324
646
657081699
657081383
1.050000e-121
448.0
33
TraesCS4B01G375400
chr7B
91.304
46
4
0
137
182
31131710
31131755
4.420000e-06
63.9
34
TraesCS4B01G375400
chr7B
100.000
28
0
0
4435
4462
732277002
732277029
1.000000e-02
52.8
35
TraesCS4B01G375400
chr3D
92.284
324
16
6
324
647
21380694
21381008
8.080000e-123
451.0
36
TraesCS4B01G375400
chr1B
92.025
326
19
4
324
647
683036900
683037220
8.080000e-123
451.0
37
TraesCS4B01G375400
chr1B
98.551
138
2
0
5154
5291
26386863
26386726
1.470000e-60
244.0
38
TraesCS4B01G375400
chr1B
98.551
138
2
0
5154
5291
40630048
40629911
1.470000e-60
244.0
39
TraesCS4B01G375400
chr1B
98.551
138
2
0
5154
5291
50054170
50054307
1.470000e-60
244.0
40
TraesCS4B01G375400
chr1B
98.551
138
2
0
5154
5291
629611526
629611663
1.470000e-60
244.0
41
TraesCS4B01G375400
chr1B
89.796
49
5
0
135
183
503833133
503833181
4.420000e-06
63.9
42
TraesCS4B01G375400
chr6B
91.071
336
21
6
324
657
420771181
420770853
3.760000e-121
446.0
43
TraesCS4B01G375400
chr6B
98.551
138
2
0
5154
5291
4238783
4238920
1.470000e-60
244.0
44
TraesCS4B01G375400
chr6B
98.551
138
2
0
5154
5291
52965286
52965423
1.470000e-60
244.0
45
TraesCS4B01G375400
chr6B
98.551
138
2
0
5154
5291
642390956
642391093
1.470000e-60
244.0
46
TraesCS4B01G375400
chr6B
98.551
138
2
0
5154
5291
646156611
646156748
1.470000e-60
244.0
47
TraesCS4B01G375400
chr6B
98.551
138
2
0
5154
5291
671898041
671898178
1.470000e-60
244.0
48
TraesCS4B01G375400
chr7D
97.778
45
1
0
4435
4479
3181144
3181100
1.580000e-10
78.7
49
TraesCS4B01G375400
chr3B
95.556
45
2
0
4435
4479
793358238
793358282
7.350000e-09
73.1
50
TraesCS4B01G375400
chr4A
93.478
46
3
0
135
180
15772400
15772445
9.510000e-08
69.4
51
TraesCS4B01G375400
chr5D
93.333
45
3
0
4435
4479
25450891
25450935
3.420000e-07
67.6
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
TraesCS4B01G375400
chr4B
659496670
659501961
5291
True
9773.000000
9773
100.000000
1
5292
1
chr4B.!!$R4
5291
1
TraesCS4B01G375400
chr4B
659481341
659485821
4480
True
7393.000000
7393
96.301000
594
5126
1
chr4B.!!$R1
4532
2
TraesCS4B01G375400
chr4B
659512290
659514824
2534
True
2232.500000
4154
99.846000
1
2442
2
chr4B.!!$R6
2441
3
TraesCS4B01G375400
chrUn
264518339
264521708
3369
False
5751.000000
5751
97.409000
1501
4887
1
chrUn.!!$F1
3386
4
TraesCS4B01G375400
chr5A
704368590
704371895
3305
False
3284.000000
3284
84.918000
1135
4420
1
chr5A.!!$F5
3285
5
TraesCS4B01G375400
chr5A
694572076
694573369
1293
False
1382.000000
1382
85.909000
1078
2395
1
chr5A.!!$F4
1317
6
TraesCS4B01G375400
chr5A
694551705
694558730
7025
False
1192.666667
2039
85.582667
1078
4722
3
chr5A.!!$F8
3644
7
TraesCS4B01G375400
chr5A
694531274
694538324
7050
False
1151.333333
1925
85.303667
1078
4722
3
chr5A.!!$F7
3644
8
TraesCS4B01G375400
chr5A
704452042
704453105
1063
False
1131.000000
1131
85.993000
2609
3674
1
chr5A.!!$F6
1065
9
TraesCS4B01G375400
chr5A
694577706
694580261
2555
False
1098.000000
2061
84.496500
2499
4722
2
chr5A.!!$F9
2223
10
TraesCS4B01G375400
chr5A
708848126
708851175
3049
False
716.500000
1275
78.850500
1083
4221
2
chr5A.!!$F10
3138
11
TraesCS4B01G375400
chr4D
508339587
508342952
3365
False
3264.000000
3264
84.496000
1067
4420
1
chr4D.!!$F1
3353
12
TraesCS4B01G375400
chr4D
504518216
504522170
3954
False
1067.333333
1461
87.168000
1067
4360
3
chr4D.!!$F2
3293
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.