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
TraesCS4A01G199600
chr4A
100.000
5195
0
0
890
6084
487862038
487867232
0.000000e+00
9594
1
TraesCS4A01G199600
chr4A
100.000
508
0
0
1
508
487861149
487861656
0.000000e+00
939
2
TraesCS4A01G199600
chr4A
81.511
741
118
12
3532
4261
486641621
486642353
5.250000e-165
592
3
TraesCS4A01G199600
chr4A
80.918
697
91
30
910
1596
486639789
486640453
4.210000e-141
512
4
TraesCS4A01G199600
chr4A
76.822
535
83
24
2515
3024
486640461
486640979
4.680000e-66
263
5
TraesCS4A01G199600
chr4A
84.766
256
36
2
3239
3492
486641241
486641495
2.810000e-63
254
6
TraesCS4A01G199600
chr4B
95.994
2696
57
15
890
3565
132338528
132335864
0.000000e+00
4333
7
TraesCS4A01G199600
chr4B
95.779
2085
72
11
3563
5639
132335771
132333695
0.000000e+00
3349
8
TraesCS4A01G199600
chr4B
95.813
406
9
2
104
508
132339043
132338645
0.000000e+00
649
9
TraesCS4A01G199600
chr4B
81.157
743
119
13
3532
4264
132854647
132853916
1.470000e-160
577
10
TraesCS4A01G199600
chr4B
79.953
424
51
17
2621
3024
132855682
132855273
1.290000e-71
281
11
TraesCS4A01G199600
chr4B
81.418
409
14
17
5709
6084
132333695
132333316
1.670000e-70
278
12
TraesCS4A01G199600
chr4B
84.109
258
37
4
3237
3492
132855018
132854763
4.710000e-61
246
13
TraesCS4A01G199600
chr4B
98.095
105
1
1
1
105
132339269
132339166
1.350000e-41
182
14
TraesCS4A01G199600
chr4D
94.741
2434
87
16
2513
4933
93846603
93844198
0.000000e+00
3747
15
TraesCS4A01G199600
chr4D
96.050
1595
47
10
891
2476
93848189
93846602
0.000000e+00
2582
16
TraesCS4A01G199600
chr4D
89.897
1168
58
26
4939
6077
93844093
93842957
0.000000e+00
1448
17
TraesCS4A01G199600
chr4D
81.316
760
121
12
3518
4265
94260321
94259571
1.130000e-166
597
18
TraesCS4A01G199600
chr4D
81.530
693
94
26
910
1596
94262240
94261576
1.930000e-149
540
19
TraesCS4A01G199600
chr4D
95.331
257
8
2
1
257
93848956
93848704
7.340000e-109
405
20
TraesCS4A01G199600
chr4D
90.830
229
7
6
283
508
93848711
93848494
1.660000e-75
294
21
TraesCS4A01G199600
chr4D
82.663
323
32
11
2714
3024
94261240
94260930
1.300000e-66
265
22
TraesCS4A01G199600
chr4D
84.766
256
38
1
3237
3492
94260676
94260422
7.830000e-64
255
23
TraesCS4A01G199600
chr2B
79.790
1049
146
45
3197
4231
511275970
511276966
0.000000e+00
702
24
TraesCS4A01G199600
chr2B
81.781
494
68
16
910
1387
511273381
511273868
1.590000e-105
394
25
TraesCS4A01G199600
chr2A
79.042
1107
160
48
3151
4231
553487490
553486430
0.000000e+00
693
26
TraesCS4A01G199600
chr2A
80.000
660
110
20
909
1558
553489981
553489334
9.230000e-128
468
27
TraesCS4A01G199600
chr2D
82.186
668
100
15
3576
4231
433506432
433507092
1.920000e-154
556
28
TraesCS4A01G199600
chr2D
79.909
662
108
22
909
1558
433503414
433504062
4.300000e-126
462
29
TraesCS4A01G199600
chr2D
82.609
299
45
5
3151
3445
433505893
433506188
2.180000e-64
257
30
TraesCS4A01G199600
chrUn
84.184
392
53
8
996
1383
477061841
477062227
7.450000e-99
372
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
TraesCS4A01G199600
chr4A
487861149
487867232
6083
False
5266.50
9594
100.000000
1
6084
2
chr4A.!!$F2
6083
1
TraesCS4A01G199600
chr4A
486639789
486642353
2564
False
405.25
592
81.004250
910
4261
4
chr4A.!!$F1
3351
2
TraesCS4A01G199600
chr4B
132333316
132339269
5953
True
1758.20
4333
93.419800
1
6084
5
chr4B.!!$R1
6083
3
TraesCS4A01G199600
chr4B
132853916
132855682
1766
True
368.00
577
81.739667
2621
4264
3
chr4B.!!$R2
1643
4
TraesCS4A01G199600
chr4D
93842957
93848956
5999
True
1695.20
3747
93.369800
1
6077
5
chr4D.!!$R1
6076
5
TraesCS4A01G199600
chr4D
94259571
94262240
2669
True
414.25
597
82.568750
910
4265
4
chr4D.!!$R2
3355
6
TraesCS4A01G199600
chr2B
511273381
511276966
3585
False
548.00
702
80.785500
910
4231
2
chr2B.!!$F1
3321
7
TraesCS4A01G199600
chr2A
553486430
553489981
3551
True
580.50
693
79.521000
909
4231
2
chr2A.!!$R1
3322
8
TraesCS4A01G199600
chr2D
433503414
433507092
3678
False
425.00
556
81.568000
909
4231
3
chr2D.!!$F1
3322
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.