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
TraesCS4A01G471900
chr4A
100.000
2405
0
0
1
2405
732353894
732356298
0.000000e+00
4442.0
1
TraesCS4A01G471900
chr4A
90.586
2082
172
14
331
2405
731851993
731849929
0.000000e+00
2737.0
2
TraesCS4A01G471900
chr4A
86.848
1437
175
7
977
2405
731616801
731615371
0.000000e+00
1594.0
3
TraesCS4A01G471900
chr4A
83.291
1562
241
13
857
2405
731861877
731860323
0.000000e+00
1421.0
4
TraesCS4A01G471900
chr4A
83.226
1240
187
12
704
1935
732408716
732409942
0.000000e+00
1118.0
5
TraesCS4A01G471900
chr4A
84.503
755
78
12
3
750
731665151
731664429
0.000000e+00
710.0
6
TraesCS4A01G471900
chr4A
88.255
298
31
4
411
705
732395490
732395786
1.060000e-93
353.0
7
TraesCS4A01G471900
chr4A
77.722
395
68
13
130
514
731606540
731606156
8.650000e-55
224.0
8
TraesCS4A01G471900
chr4A
79.016
305
41
12
3
285
731852289
731851986
1.140000e-43
187.0
9
TraesCS4A01G471900
chr4A
81.773
203
22
8
516
708
732058217
732058414
3.200000e-34
156.0
10
TraesCS4A01G471900
chr4A
87.786
131
16
0
764
894
731664445
731664315
1.150000e-33
154.0
11
TraesCS4A01G471900
chr7A
93.885
2077
107
11
336
2405
56204321
56206384
0.000000e+00
3114.0
12
TraesCS4A01G471900
chr7A
82.935
1506
227
21
917
2404
80861975
80863468
0.000000e+00
1330.0
13
TraesCS4A01G471900
chr7A
79.605
304
37
13
3
285
56204023
56204322
6.780000e-46
195.0
14
TraesCS4A01G471900
chr7A
82.432
222
25
9
4
212
8587868
8588088
5.280000e-42
182.0
15
TraesCS4A01G471900
chr7D
82.931
1904
242
44
522
2405
8256417
8254577
0.000000e+00
1639.0
16
TraesCS4A01G471900
chr7D
82.147
1910
249
48
522
2405
7923965
7925808
0.000000e+00
1554.0
17
TraesCS4A01G471900
chr7D
84.570
1510
215
11
904
2405
8030614
8032113
0.000000e+00
1482.0
18
TraesCS4A01G471900
chr7D
83.422
1502
230
11
915
2405
8052779
8054272
0.000000e+00
1376.0
19
TraesCS4A01G471900
chr7D
82.768
1503
242
9
911
2405
7820321
7821814
0.000000e+00
1325.0
20
TraesCS4A01G471900
chr7D
82.594
1511
227
25
917
2404
76743550
76745047
0.000000e+00
1301.0
21
TraesCS4A01G471900
chr7D
83.974
755
81
13
3
750
8222507
8223228
0.000000e+00
688.0
22
TraesCS4A01G471900
chr7D
89.333
75
8
0
516
590
8233163
8233237
7.080000e-16
95.3
23
TraesCS4A01G471900
chr3B
86.209
1501
188
10
915
2405
741463153
741464644
0.000000e+00
1607.0
24
TraesCS4A01G471900
chr3B
91.304
69
6
0
177
245
741456834
741456902
7.080000e-16
95.3
25
TraesCS4A01G471900
chr7B
82.577
1498
239
16
917
2398
23596695
23598186
0.000000e+00
1301.0
26
TraesCS4A01G471900
chr7B
83.333
1296
200
11
1113
2398
23958186
23959475
0.000000e+00
1182.0
27
TraesCS4A01G471900
chr5B
80.697
373
49
19
71
428
37467602
37467966
3.940000e-68
268.0
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
TraesCS4A01G471900
chr4A
732353894
732356298
2404
False
4442.0
4442
100.0000
1
2405
1
chr4A.!!$F2
2404
1
TraesCS4A01G471900
chr4A
731615371
731616801
1430
True
1594.0
1594
86.8480
977
2405
1
chr4A.!!$R2
1428
2
TraesCS4A01G471900
chr4A
731849929
731852289
2360
True
1462.0
2737
84.8010
3
2405
2
chr4A.!!$R5
2402
3
TraesCS4A01G471900
chr4A
731860323
731861877
1554
True
1421.0
1421
83.2910
857
2405
1
chr4A.!!$R3
1548
4
TraesCS4A01G471900
chr4A
732408716
732409942
1226
False
1118.0
1118
83.2260
704
1935
1
chr4A.!!$F4
1231
5
TraesCS4A01G471900
chr4A
731664315
731665151
836
True
432.0
710
86.1445
3
894
2
chr4A.!!$R4
891
6
TraesCS4A01G471900
chr7A
56204023
56206384
2361
False
1654.5
3114
86.7450
3
2405
2
chr7A.!!$F3
2402
7
TraesCS4A01G471900
chr7A
80861975
80863468
1493
False
1330.0
1330
82.9350
917
2404
1
chr7A.!!$F2
1487
8
TraesCS4A01G471900
chr7D
8254577
8256417
1840
True
1639.0
1639
82.9310
522
2405
1
chr7D.!!$R1
1883
9
TraesCS4A01G471900
chr7D
7923965
7925808
1843
False
1554.0
1554
82.1470
522
2405
1
chr7D.!!$F2
1883
10
TraesCS4A01G471900
chr7D
8030614
8032113
1499
False
1482.0
1482
84.5700
904
2405
1
chr7D.!!$F3
1501
11
TraesCS4A01G471900
chr7D
8052779
8054272
1493
False
1376.0
1376
83.4220
915
2405
1
chr7D.!!$F4
1490
12
TraesCS4A01G471900
chr7D
7820321
7821814
1493
False
1325.0
1325
82.7680
911
2405
1
chr7D.!!$F1
1494
13
TraesCS4A01G471900
chr7D
76743550
76745047
1497
False
1301.0
1301
82.5940
917
2404
1
chr7D.!!$F7
1487
14
TraesCS4A01G471900
chr7D
8222507
8223228
721
False
688.0
688
83.9740
3
750
1
chr7D.!!$F5
747
15
TraesCS4A01G471900
chr3B
741463153
741464644
1491
False
1607.0
1607
86.2090
915
2405
1
chr3B.!!$F2
1490
16
TraesCS4A01G471900
chr7B
23596695
23598186
1491
False
1301.0
1301
82.5770
917
2398
1
chr7B.!!$F1
1481
17
TraesCS4A01G471900
chr7B
23958186
23959475
1289
False
1182.0
1182
83.3330
1113
2398
1
chr7B.!!$F2
1285
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.