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
TraesCS3B01G423100
chr3B
100.000
2339
0
0
1
2339
660332195
660334533
0.000000e+00
4320
1
TraesCS3B01G423100
chr3D
95.441
2347
84
9
1
2339
499597675
499600006
0.000000e+00
3720
2
TraesCS3B01G423100
chr3D
94.216
1141
53
6
1
1135
225357596
225358729
0.000000e+00
1729
3
TraesCS3B01G423100
chr3D
84.971
1364
188
13
3
1359
300565481
300566834
0.000000e+00
1367
4
TraesCS3B01G423100
chr3D
87.054
224
18
4
1472
1684
499594000
499593777
2.320000e-60
243
5
TraesCS3B01G423100
chr5D
93.933
1368
74
6
2
1362
117351130
117352495
0.000000e+00
2058
6
TraesCS3B01G423100
chr6D
93.050
1367
85
7
3
1362
158872462
158871099
0.000000e+00
1989
7
TraesCS3B01G423100
chr6D
85.777
1364
186
7
3
1362
48683473
48682114
0.000000e+00
1437
8
TraesCS3B01G423100
chr2B
91.387
1370
104
11
3
1362
361567414
361568779
0.000000e+00
1864
9
TraesCS3B01G423100
chr2B
83.871
124
19
1
1561
1684
182845744
182845866
1.470000e-22
117
10
TraesCS3B01G423100
chr1D
86.404
1368
171
12
3
1362
216023919
216022559
0.000000e+00
1482
11
TraesCS3B01G423100
chr2D
85.359
1366
185
15
3
1362
574398710
574397354
0.000000e+00
1400
12
TraesCS3B01G423100
chr6B
91.768
656
42
3
1685
2339
295781466
295782110
0.000000e+00
902
13
TraesCS3B01G423100
chr7B
91.077
650
48
1
1690
2339
679174035
679173396
0.000000e+00
870
14
TraesCS3B01G423100
chr5B
90.382
655
52
2
1685
2339
139195378
139194735
0.000000e+00
850
15
TraesCS3B01G423100
chr5B
84.545
110
15
2
1577
1685
549123676
549123568
8.840000e-20
108
16
TraesCS3B01G423100
chr5B
80.420
143
23
5
1543
1684
549165412
549165550
1.140000e-18
104
17
TraesCS3B01G423100
chr3A
86.350
652
74
7
1688
2339
375744129
375743493
0.000000e+00
697
18
TraesCS3B01G423100
chr3A
83.019
159
26
1
1822
1979
511997834
511997676
2.420000e-30
143
19
TraesCS3B01G423100
chr7D
86.239
109
15
0
1577
1685
638400294
638400402
4.080000e-23
119
20
TraesCS3B01G423100
chr7D
82.069
145
18
8
1543
1684
459895472
459895611
1.470000e-22
117
21
TraesCS3B01G423100
chr6A
78.431
204
27
10
1496
1686
92886745
92886546
1.470000e-22
117
22
TraesCS3B01G423100
chr7A
83.065
124
20
1
1561
1684
617979749
617979627
6.830000e-21
111
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
TraesCS3B01G423100
chr3B
660332195
660334533
2338
False
4320
4320
100.000
1
2339
1
chr3B.!!$F1
2338
1
TraesCS3B01G423100
chr3D
499597675
499600006
2331
False
3720
3720
95.441
1
2339
1
chr3D.!!$F3
2338
2
TraesCS3B01G423100
chr3D
225357596
225358729
1133
False
1729
1729
94.216
1
1135
1
chr3D.!!$F1
1134
3
TraesCS3B01G423100
chr3D
300565481
300566834
1353
False
1367
1367
84.971
3
1359
1
chr3D.!!$F2
1356
4
TraesCS3B01G423100
chr5D
117351130
117352495
1365
False
2058
2058
93.933
2
1362
1
chr5D.!!$F1
1360
5
TraesCS3B01G423100
chr6D
158871099
158872462
1363
True
1989
1989
93.050
3
1362
1
chr6D.!!$R2
1359
6
TraesCS3B01G423100
chr6D
48682114
48683473
1359
True
1437
1437
85.777
3
1362
1
chr6D.!!$R1
1359
7
TraesCS3B01G423100
chr2B
361567414
361568779
1365
False
1864
1864
91.387
3
1362
1
chr2B.!!$F2
1359
8
TraesCS3B01G423100
chr1D
216022559
216023919
1360
True
1482
1482
86.404
3
1362
1
chr1D.!!$R1
1359
9
TraesCS3B01G423100
chr2D
574397354
574398710
1356
True
1400
1400
85.359
3
1362
1
chr2D.!!$R1
1359
10
TraesCS3B01G423100
chr6B
295781466
295782110
644
False
902
902
91.768
1685
2339
1
chr6B.!!$F1
654
11
TraesCS3B01G423100
chr7B
679173396
679174035
639
True
870
870
91.077
1690
2339
1
chr7B.!!$R1
649
12
TraesCS3B01G423100
chr5B
139194735
139195378
643
True
850
850
90.382
1685
2339
1
chr5B.!!$R1
654
13
TraesCS3B01G423100
chr3A
375743493
375744129
636
True
697
697
86.350
1688
2339
1
chr3A.!!$R1
651
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.