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
TraesCS3D01G081200
chr3D
100.000
3783
0
0
1
3783
40772894
40776676
0.000000e+00
6986
1
TraesCS3D01G081200
chr3D
98.284
874
15
0
2910
3783
448464897
448464024
0.000000e+00
1531
2
TraesCS3D01G081200
chr3D
93.220
177
9
3
1333
1509
40774151
40774324
1.350000e-64
257
3
TraesCS3D01G081200
chr3D
98.889
90
0
1
1
90
339967755
339967843
3.910000e-35
159
4
TraesCS3D01G081200
chr3D
93.878
98
5
1
1
98
395497525
395497429
3.050000e-31
147
5
TraesCS3D01G081200
chrUn
94.584
2585
98
25
79
2628
19785994
19783417
0.000000e+00
3960
6
TraesCS3D01G081200
chrUn
97.356
1437
20
2
1493
2911
19742818
19741382
0.000000e+00
2427
7
TraesCS3D01G081200
chrUn
96.440
1264
28
6
183
1431
19744437
19743176
0.000000e+00
2069
8
TraesCS3D01G081200
chrUn
93.277
595
14
4
2342
2911
19783667
19783074
0.000000e+00
854
9
TraesCS3D01G081200
chrUn
91.489
235
15
5
1333
1566
19784805
19784575
6.100000e-83
318
10
TraesCS3D01G081200
chrUn
93.782
193
9
3
1333
1525
19743349
19743160
1.720000e-73
287
11
TraesCS3D01G081200
chrUn
89.302
215
22
1
79
293
92963957
92963744
6.230000e-68
268
12
TraesCS3D01G081200
chr6A
92.922
1653
80
18
1271
2911
57424053
57425680
0.000000e+00
2370
13
TraesCS3D01G081200
chr6A
94.900
902
34
7
666
1563
57423374
57424267
0.000000e+00
1400
14
TraesCS3D01G081200
chr6A
94.350
177
7
3
1333
1509
57423962
57424135
6.230000e-68
268
15
TraesCS3D01G081200
chr6A
93.333
90
6
0
1271
1360
57424131
57424220
2.370000e-27
134
16
TraesCS3D01G081200
chr6B
89.020
1612
139
21
1320
2911
93017442
93019035
0.000000e+00
1962
17
TraesCS3D01G081200
chr6B
86.328
1280
96
23
676
1903
93101497
93102749
0.000000e+00
1321
18
TraesCS3D01G081200
chr6B
90.379
1029
65
11
1907
2911
93103526
93104544
0.000000e+00
1321
19
TraesCS3D01G081200
chr6B
85.846
325
17
11
676
984
93017132
93017443
6.100000e-83
318
20
TraesCS3D01G081200
chr6B
89.558
249
25
1
1307
1555
93102075
93102322
7.890000e-82
315
21
TraesCS3D01G081200
chr6B
92.500
80
6
0
1271
1350
93017471
93017550
8.590000e-22
115
22
TraesCS3D01G081200
chr6B
92.500
80
6
0
1271
1350
93102195
93102274
8.590000e-22
115
23
TraesCS3D01G081200
chr2D
98.398
874
13
1
2910
3783
627933279
627934151
0.000000e+00
1535
24
TraesCS3D01G081200
chr2D
85.949
548
39
12
79
598
615473927
615473390
5.520000e-153
551
25
TraesCS3D01G081200
chr2D
85.792
549
42
12
79
598
36236331
36236872
1.990000e-152
549
26
TraesCS3D01G081200
chr2D
85.793
542
42
15
79
593
558910265
558909732
3.320000e-150
542
27
TraesCS3D01G081200
chr2D
84.000
525
59
18
79
598
373764804
373765308
7.350000e-132
481
28
TraesCS3D01G081200
chr2D
94.949
99
4
1
1
99
68834855
68834952
1.820000e-33
154
29
TraesCS3D01G081200
chr2D
94.949
99
4
1
1
99
68892820
68892723
1.820000e-33
154
30
TraesCS3D01G081200
chr2D
93.137
102
4
3
1
101
441839795
441839696
3.050000e-31
147
31
TraesCS3D01G081200
chr1D
97.826
874
19
0
2910
3783
110003677
110002804
0.000000e+00
1509
32
TraesCS3D01G081200
chr1D
95.876
97
2
2
1
97
85486139
85486233
5.060000e-34
156
33
TraesCS3D01G081200
chr7D
97.254
874
24
0
2910
3783
183311079
183311952
0.000000e+00
1482
34
TraesCS3D01G081200
chr7D
84.954
545
43
17
79
598
631440058
631440588
2.010000e-142
516
35
TraesCS3D01G081200
chr5D
96.918
876
24
3
2910
3783
280763969
280764843
0.000000e+00
1465
36
TraesCS3D01G081200
chr5D
95.995
874
30
2
2910
3783
502865076
502864208
0.000000e+00
1415
37
TraesCS3D01G081200
chr5D
95.886
875
33
2
2910
3783
537374568
537373696
0.000000e+00
1413
38
TraesCS3D01G081200
chr5D
84.190
525
56
20
79
598
546675812
546676314
5.680000e-133
484
39
TraesCS3D01G081200
chr5D
83.704
540
36
20
79
593
396445216
396444704
2.660000e-126
462
40
TraesCS3D01G081200
chr4D
96.689
876
26
3
2910
3783
37501200
37502074
0.000000e+00
1454
41
TraesCS3D01G081200
chr4D
85.455
550
43
14
79
598
464169348
464169890
4.300000e-149
538
42
TraesCS3D01G081200
chr4D
83.206
524
62
18
79
598
296724810
296725311
1.240000e-124
457
43
TraesCS3D01G081200
chr4D
97.802
91
0
1
1
89
404904254
404904164
5.060000e-34
156
44
TraesCS3D01G081200
chr4D
95.745
94
0
4
1
94
381854823
381854912
8.470000e-32
148
45
TraesCS3D01G081200
chr6D
95.771
875
33
3
2910
3783
439677131
439676260
0.000000e+00
1408
46
TraesCS3D01G081200
chr6D
98.795
83
0
1
1
83
322994348
322994429
3.050000e-31
147
47
TraesCS3D01G081200
chr1A
91.776
535
25
5
79
598
482331266
482330736
0.000000e+00
726
48
TraesCS3D01G081200
chr5B
85.595
479
28
19
153
598
572740659
572740189
7.400000e-127
464
49
TraesCS3D01G081200
chr4B
85.132
491
32
19
153
608
650784589
650784105
7.400000e-127
464
50
TraesCS3D01G081200
chr4B
83.880
366
30
11
79
420
480830025
480829665
4.710000e-84
322
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
TraesCS3D01G081200
chr3D
40772894
40776676
3782
False
3621.500000
6986
96.610000
1
3783
2
chr3D.!!$F2
3782
1
TraesCS3D01G081200
chr3D
448464024
448464897
873
True
1531.000000
1531
98.284000
2910
3783
1
chr3D.!!$R2
873
2
TraesCS3D01G081200
chrUn
19783074
19785994
2920
True
1710.666667
3960
93.116667
79
2911
3
chrUn.!!$R3
2832
3
TraesCS3D01G081200
chrUn
19741382
19744437
3055
True
1594.333333
2427
95.859333
183
2911
3
chrUn.!!$R2
2728
4
TraesCS3D01G081200
chr6A
57423374
57425680
2306
False
1043.000000
2370
93.876250
666
2911
4
chr6A.!!$F1
2245
5
TraesCS3D01G081200
chr6B
93017132
93019035
1903
False
798.333333
1962
89.122000
676
2911
3
chr6B.!!$F1
2235
6
TraesCS3D01G081200
chr6B
93101497
93104544
3047
False
768.000000
1321
89.691250
676
2911
4
chr6B.!!$F2
2235
7
TraesCS3D01G081200
chr2D
627933279
627934151
872
False
1535.000000
1535
98.398000
2910
3783
1
chr2D.!!$F4
873
8
TraesCS3D01G081200
chr2D
615473390
615473927
537
True
551.000000
551
85.949000
79
598
1
chr2D.!!$R4
519
9
TraesCS3D01G081200
chr2D
36236331
36236872
541
False
549.000000
549
85.792000
79
598
1
chr2D.!!$F1
519
10
TraesCS3D01G081200
chr2D
558909732
558910265
533
True
542.000000
542
85.793000
79
593
1
chr2D.!!$R3
514
11
TraesCS3D01G081200
chr2D
373764804
373765308
504
False
481.000000
481
84.000000
79
598
1
chr2D.!!$F3
519
12
TraesCS3D01G081200
chr1D
110002804
110003677
873
True
1509.000000
1509
97.826000
2910
3783
1
chr1D.!!$R1
873
13
TraesCS3D01G081200
chr7D
183311079
183311952
873
False
1482.000000
1482
97.254000
2910
3783
1
chr7D.!!$F1
873
14
TraesCS3D01G081200
chr7D
631440058
631440588
530
False
516.000000
516
84.954000
79
598
1
chr7D.!!$F2
519
15
TraesCS3D01G081200
chr5D
280763969
280764843
874
False
1465.000000
1465
96.918000
2910
3783
1
chr5D.!!$F1
873
16
TraesCS3D01G081200
chr5D
502864208
502865076
868
True
1415.000000
1415
95.995000
2910
3783
1
chr5D.!!$R2
873
17
TraesCS3D01G081200
chr5D
537373696
537374568
872
True
1413.000000
1413
95.886000
2910
3783
1
chr5D.!!$R3
873
18
TraesCS3D01G081200
chr5D
546675812
546676314
502
False
484.000000
484
84.190000
79
598
1
chr5D.!!$F2
519
19
TraesCS3D01G081200
chr5D
396444704
396445216
512
True
462.000000
462
83.704000
79
593
1
chr5D.!!$R1
514
20
TraesCS3D01G081200
chr4D
37501200
37502074
874
False
1454.000000
1454
96.689000
2910
3783
1
chr4D.!!$F1
873
21
TraesCS3D01G081200
chr4D
464169348
464169890
542
False
538.000000
538
85.455000
79
598
1
chr4D.!!$F4
519
22
TraesCS3D01G081200
chr4D
296724810
296725311
501
False
457.000000
457
83.206000
79
598
1
chr4D.!!$F2
519
23
TraesCS3D01G081200
chr6D
439676260
439677131
871
True
1408.000000
1408
95.771000
2910
3783
1
chr6D.!!$R1
873
24
TraesCS3D01G081200
chr1A
482330736
482331266
530
True
726.000000
726
91.776000
79
598
1
chr1A.!!$R1
519
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.