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
TraesCS1D01G297100
chr1D
100.000
3157
0
0
1
3157
395453241
395450085
0.000000e+00
5830.0
1
TraesCS1D01G297100
chr1D
92.648
1537
56
24
787
2271
395055386
395053855
0.000000e+00
2159.0
2
TraesCS1D01G297100
chr1D
87.671
730
72
10
1
716
395056121
395055396
0.000000e+00
833.0
3
TraesCS1D01G297100
chr1D
77.253
1376
234
48
939
2269
395410497
395409156
0.000000e+00
734.0
4
TraesCS1D01G297100
chr1D
96.783
373
3
1
1535
1907
395382263
395381900
5.790000e-172
614.0
5
TraesCS1D01G297100
chr1D
85.821
536
26
14
2285
2801
395053463
395052959
1.000000e-144
523.0
6
TraesCS1D01G297100
chr1D
93.391
348
17
5
605
950
395382676
395382333
7.810000e-141
510.0
7
TraesCS1D01G297100
chr1D
89.487
390
35
5
2771
3157
395351409
395351023
3.660000e-134
488.0
8
TraesCS1D01G297100
chr1D
89.628
376
27
7
2790
3157
395052446
395052075
4.770000e-128
468.0
9
TraesCS1D01G297100
chr1D
89.119
386
23
10
1905
2271
395379714
395379329
2.220000e-126
462.0
10
TraesCS1D01G297100
chr1D
73.951
1359
243
71
941
2242
394950242
394948938
2.230000e-121
446.0
11
TraesCS1D01G297100
chr1D
94.521
73
4
0
2696
2768
395351510
395351438
2.570000e-21
113.0
12
TraesCS1D01G297100
chr1D
98.039
51
0
1
939
988
395382318
395382268
1.560000e-13
87.9
13
TraesCS1D01G297100
chr1D
100.000
46
0
0
2285
2330
395378954
395378909
5.610000e-13
86.1
14
TraesCS1D01G297100
chr1D
85.714
63
9
0
347
409
479116745
479116683
2.030000e-07
67.6
15
TraesCS1D01G297100
chr1B
93.824
1522
47
16
787
2271
526272372
526270861
0.000000e+00
2246.0
16
TraesCS1D01G297100
chr1B
88.250
800
75
9
1
786
526273126
526272332
0.000000e+00
939.0
17
TraesCS1D01G297100
chr1B
76.923
1378
238
43
943
2275
526291290
526289948
0.000000e+00
710.0
18
TraesCS1D01G297100
chr1B
88.916
415
30
10
2285
2686
526270468
526270057
6.080000e-137
497.0
19
TraesCS1D01G297100
chr1B
90.038
261
20
4
2901
3157
526269273
526269015
1.810000e-87
333.0
20
TraesCS1D01G297100
chr1B
91.034
145
11
1
2771
2913
526269450
526269306
8.930000e-46
195.0
21
TraesCS1D01G297100
chr1B
94.186
86
4
1
2696
2780
526269552
526269467
2.560000e-26
130.0
22
TraesCS1D01G297100
chr1B
79.208
202
28
11
586
782
526291621
526291429
9.190000e-26
128.0
23
TraesCS1D01G297100
chr1A
93.525
1529
52
13
787
2271
489325673
489324148
0.000000e+00
2231.0
24
TraesCS1D01G297100
chr1A
92.894
774
31
14
1518
2271
489382861
489382092
0.000000e+00
1103.0
25
TraesCS1D01G297100
chr1A
91.099
764
39
17
787
1521
489383726
489382963
0.000000e+00
1007.0
26
TraesCS1D01G297100
chr1A
88.848
807
63
10
1
786
489326433
489325633
0.000000e+00
966.0
27
TraesCS1D01G297100
chr1A
85.970
727
87
6
4
716
489384461
489383736
0.000000e+00
763.0
28
TraesCS1D01G297100
chr1A
77.575
1369
233
43
939
2265
489393637
489392301
0.000000e+00
760.0
29
TraesCS1D01G297100
chr1A
80.334
1017
162
27
939
1937
489361069
489360073
0.000000e+00
736.0
30
TraesCS1D01G297100
chr1A
90.361
415
29
6
2285
2693
489323755
489323346
4.630000e-148
534.0
31
TraesCS1D01G297100
chr1A
91.105
371
27
6
2285
2652
489381663
489381296
6.080000e-137
497.0
32
TraesCS1D01G297100
chr1A
85.366
492
38
16
2696
3157
489322643
489322156
2.200000e-131
479.0
33
TraesCS1D01G297100
chr1A
82.365
482
30
15
2696
3149
489380438
489379984
4.970000e-98
368.0
34
TraesCS1D01G297100
chr1A
78.431
204
24
12
586
782
489361393
489361203
7.160000e-22
115.0
35
TraesCS1D01G297100
chr1A
78.109
201
31
11
586
782
489393975
489393784
7.160000e-22
115.0
36
TraesCS1D01G297100
chr3D
79.703
808
109
27
1508
2271
57021778
57022574
1.670000e-147
532.0
37
TraesCS1D01G297100
chr2B
74.207
473
92
14
59
527
26450813
26450367
1.510000e-38
171.0
38
TraesCS1D01G297100
chr6D
92.105
76
6
0
334
409
467078166
467078241
1.200000e-19
108.0
39
TraesCS1D01G297100
chr7D
77.401
177
33
3
1766
1940
42737685
42737514
7.210000e-17
99.0
40
TraesCS1D01G297100
chr7A
77.528
178
31
5
1766
1940
42311016
42310845
7.210000e-17
99.0
41
TraesCS1D01G297100
chr4A
77.473
182
30
7
1762
1940
650074829
650074656
7.210000e-17
99.0
42
TraesCS1D01G297100
chr2D
79.333
150
19
6
258
407
156817457
156817320
9.320000e-16
95.3
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
TraesCS1D01G297100
chr1D
395450085
395453241
3156
True
5830.000000
5830
100.000000
1
3157
1
chr1D.!!$R3
3156
1
TraesCS1D01G297100
chr1D
395052075
395056121
4046
True
995.750000
2159
88.942000
1
3157
4
chr1D.!!$R5
3156
2
TraesCS1D01G297100
chr1D
395409156
395410497
1341
True
734.000000
734
77.253000
939
2269
1
chr1D.!!$R2
1330
3
TraesCS1D01G297100
chr1D
394948938
394950242
1304
True
446.000000
446
73.951000
941
2242
1
chr1D.!!$R1
1301
4
TraesCS1D01G297100
chr1D
395378909
395382676
3767
True
352.000000
614
95.466400
605
2330
5
chr1D.!!$R7
1725
5
TraesCS1D01G297100
chr1B
526269015
526273126
4111
True
723.333333
2246
91.041333
1
3157
6
chr1B.!!$R1
3156
6
TraesCS1D01G297100
chr1B
526289948
526291621
1673
True
419.000000
710
78.065500
586
2275
2
chr1B.!!$R2
1689
7
TraesCS1D01G297100
chr1A
489322156
489326433
4277
True
1052.500000
2231
89.525000
1
3157
4
chr1A.!!$R1
3156
8
TraesCS1D01G297100
chr1A
489379984
489384461
4477
True
747.600000
1103
88.686600
4
3149
5
chr1A.!!$R3
3145
9
TraesCS1D01G297100
chr1A
489392301
489393975
1674
True
437.500000
760
77.842000
586
2265
2
chr1A.!!$R4
1679
10
TraesCS1D01G297100
chr1A
489360073
489361393
1320
True
425.500000
736
79.382500
586
1937
2
chr1A.!!$R2
1351
11
TraesCS1D01G297100
chr3D
57021778
57022574
796
False
532.000000
532
79.703000
1508
2271
1
chr3D.!!$F1
763
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.