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
TraesCS7D01G334500
chr7D
100.000
2565
0
0
1
2565
426546747
426549311
0.000000e+00
4737.0
1
TraesCS7D01G334500
chr7D
96.109
1208
28
5
1360
2565
38024321
38023131
0.000000e+00
1953.0
2
TraesCS7D01G334500
chr7D
96.410
780
21
5
593
1368
426632101
426632877
0.000000e+00
1279.0
3
TraesCS7D01G334500
chr7D
94.268
785
19
4
610
1368
426495977
426496761
0.000000e+00
1177.0
4
TraesCS7D01G334500
chr7D
98.316
594
9
1
1
593
153661797
153662390
0.000000e+00
1040.0
5
TraesCS7D01G334500
chr7D
79.022
634
84
36
721
1338
426643794
426644394
3.090000e-104
388.0
6
TraesCS7D01G334500
chr7D
87.135
342
31
7
1035
1363
426450361
426450702
2.410000e-100
375.0
7
TraesCS7D01G334500
chr7D
89.384
292
26
4
1077
1364
426517875
426518165
1.880000e-96
363.0
8
TraesCS7D01G334500
chr7D
85.484
62
3
4
721
781
426453995
426454051
2.760000e-05
60.2
9
TraesCS7D01G334500
chr2D
96.437
1207
26
3
1361
2565
643059169
643060360
0.000000e+00
1975.0
10
TraesCS7D01G334500
chr2D
98.316
594
9
1
1
593
422562699
422563292
0.000000e+00
1040.0
11
TraesCS7D01G334500
chr2D
98.475
590
8
1
1
589
78071245
78071834
0.000000e+00
1038.0
12
TraesCS7D01G334500
chr5D
96.262
1204
28
5
1365
2565
447258515
447257326
0.000000e+00
1958.0
13
TraesCS7D01G334500
chr5D
94.886
1232
26
4
1355
2565
175961924
175960709
0.000000e+00
1892.0
14
TraesCS7D01G334500
chr5D
97.997
599
10
2
1
598
151927642
151928239
0.000000e+00
1038.0
15
TraesCS7D01G334500
chr5B
96.262
1204
26
7
1365
2565
689115428
689114241
0.000000e+00
1956.0
16
TraesCS7D01G334500
chr7B
96.096
1204
29
4
1365
2565
133522048
133523236
0.000000e+00
1947.0
17
TraesCS7D01G334500
chr7B
95.918
784
24
2
593
1368
443701765
443702548
0.000000e+00
1264.0
18
TraesCS7D01G334500
chr7B
89.899
297
22
7
1077
1368
443696498
443696791
2.410000e-100
375.0
19
TraesCS7D01G334500
chr7B
86.957
69
5
4
721
786
443730464
443730531
9.840000e-10
75.0
20
TraesCS7D01G334500
chr3D
96.144
1193
28
5
1376
2565
144291112
144289935
0.000000e+00
1932.0
21
TraesCS7D01G334500
chr3D
95.690
1137
25
7
1437
2565
438456522
438457642
0.000000e+00
1807.0
22
TraesCS7D01G334500
chr3D
96.415
809
15
1
1362
2170
229473350
229474144
0.000000e+00
1321.0
23
TraesCS7D01G334500
chr3D
98.651
593
7
1
1
592
364981045
364981637
0.000000e+00
1050.0
24
TraesCS7D01G334500
chr6D
95.631
1213
33
6
1358
2565
19898723
19897526
0.000000e+00
1929.0
25
TraesCS7D01G334500
chr6D
98.319
595
8
2
1
594
436857382
436857975
0.000000e+00
1042.0
26
TraesCS7D01G334500
chr6D
98.316
594
9
1
1
593
162223882
162223289
0.000000e+00
1040.0
27
TraesCS7D01G334500
chr3A
95.768
1205
32
7
1365
2565
572457233
572458422
0.000000e+00
1925.0
28
TraesCS7D01G334500
chr6A
95.195
1207
35
9
1365
2565
534788574
534787385
0.000000e+00
1886.0
29
TraesCS7D01G334500
chr3B
95.460
771
19
3
1365
2134
695580992
695581747
0.000000e+00
1216.0
30
TraesCS7D01G334500
chr1D
98.644
590
7
1
1
589
442082189
442082778
0.000000e+00
1044.0
31
TraesCS7D01G334500
chr1D
98.148
594
10
1
1
593
201297032
201296439
0.000000e+00
1035.0
32
TraesCS7D01G334500
chr7A
88.520
331
32
3
1035
1362
507022926
507022599
1.850000e-106
396.0
33
TraesCS7D01G334500
chr7A
85.976
328
37
5
1045
1364
507014425
507014099
2.440000e-90
342.0
34
TraesCS7D01G334500
chr7A
85.714
91
9
4
721
811
507018913
507018827
2.720000e-15
93.5
35
TraesCS7D01G334500
chr7A
80.508
118
18
4
721
834
506873927
506873811
4.550000e-13
86.1
36
TraesCS7D01G334500
chr2B
89.130
322
28
5
1053
1368
753834742
753835062
6.650000e-106
394.0
37
TraesCS7D01G334500
chr2A
89.370
254
13
2
1367
1620
732235798
732236037
8.910000e-80
307.0
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
TraesCS7D01G334500
chr7D
426546747
426549311
2564
False
4737.00
4737
100.0000
1
2565
1
chr7D.!!$F4
2564
1
TraesCS7D01G334500
chr7D
38023131
38024321
1190
True
1953.00
1953
96.1090
1360
2565
1
chr7D.!!$R1
1205
2
TraesCS7D01G334500
chr7D
426632101
426632877
776
False
1279.00
1279
96.4100
593
1368
1
chr7D.!!$F5
775
3
TraesCS7D01G334500
chr7D
426495977
426496761
784
False
1177.00
1177
94.2680
610
1368
1
chr7D.!!$F2
758
4
TraesCS7D01G334500
chr7D
153661797
153662390
593
False
1040.00
1040
98.3160
1
593
1
chr7D.!!$F1
592
5
TraesCS7D01G334500
chr7D
426643794
426644394
600
False
388.00
388
79.0220
721
1338
1
chr7D.!!$F6
617
6
TraesCS7D01G334500
chr7D
426450361
426454051
3690
False
217.60
375
86.3095
721
1363
2
chr7D.!!$F7
642
7
TraesCS7D01G334500
chr2D
643059169
643060360
1191
False
1975.00
1975
96.4370
1361
2565
1
chr2D.!!$F3
1204
8
TraesCS7D01G334500
chr2D
422562699
422563292
593
False
1040.00
1040
98.3160
1
593
1
chr2D.!!$F2
592
9
TraesCS7D01G334500
chr2D
78071245
78071834
589
False
1038.00
1038
98.4750
1
589
1
chr2D.!!$F1
588
10
TraesCS7D01G334500
chr5D
447257326
447258515
1189
True
1958.00
1958
96.2620
1365
2565
1
chr5D.!!$R2
1200
11
TraesCS7D01G334500
chr5D
175960709
175961924
1215
True
1892.00
1892
94.8860
1355
2565
1
chr5D.!!$R1
1210
12
TraesCS7D01G334500
chr5D
151927642
151928239
597
False
1038.00
1038
97.9970
1
598
1
chr5D.!!$F1
597
13
TraesCS7D01G334500
chr5B
689114241
689115428
1187
True
1956.00
1956
96.2620
1365
2565
1
chr5B.!!$R1
1200
14
TraesCS7D01G334500
chr7B
133522048
133523236
1188
False
1947.00
1947
96.0960
1365
2565
1
chr7B.!!$F1
1200
15
TraesCS7D01G334500
chr7B
443701765
443702548
783
False
1264.00
1264
95.9180
593
1368
1
chr7B.!!$F3
775
16
TraesCS7D01G334500
chr3D
144289935
144291112
1177
True
1932.00
1932
96.1440
1376
2565
1
chr3D.!!$R1
1189
17
TraesCS7D01G334500
chr3D
438456522
438457642
1120
False
1807.00
1807
95.6900
1437
2565
1
chr3D.!!$F3
1128
18
TraesCS7D01G334500
chr3D
229473350
229474144
794
False
1321.00
1321
96.4150
1362
2170
1
chr3D.!!$F1
808
19
TraesCS7D01G334500
chr3D
364981045
364981637
592
False
1050.00
1050
98.6510
1
592
1
chr3D.!!$F2
591
20
TraesCS7D01G334500
chr6D
19897526
19898723
1197
True
1929.00
1929
95.6310
1358
2565
1
chr6D.!!$R1
1207
21
TraesCS7D01G334500
chr6D
436857382
436857975
593
False
1042.00
1042
98.3190
1
594
1
chr6D.!!$F1
593
22
TraesCS7D01G334500
chr6D
162223289
162223882
593
True
1040.00
1040
98.3160
1
593
1
chr6D.!!$R2
592
23
TraesCS7D01G334500
chr3A
572457233
572458422
1189
False
1925.00
1925
95.7680
1365
2565
1
chr3A.!!$F1
1200
24
TraesCS7D01G334500
chr6A
534787385
534788574
1189
True
1886.00
1886
95.1950
1365
2565
1
chr6A.!!$R1
1200
25
TraesCS7D01G334500
chr3B
695580992
695581747
755
False
1216.00
1216
95.4600
1365
2134
1
chr3B.!!$F1
769
26
TraesCS7D01G334500
chr1D
442082189
442082778
589
False
1044.00
1044
98.6440
1
589
1
chr1D.!!$F1
588
27
TraesCS7D01G334500
chr1D
201296439
201297032
593
True
1035.00
1035
98.1480
1
593
1
chr1D.!!$R1
592
28
TraesCS7D01G334500
chr7A
507018827
507022926
4099
True
244.75
396
87.1170
721
1362
2
chr7A.!!$R3
641
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.