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
TraesCS2B01G553900
chr2B
100.000
2324
0
0
1
2324
749148995
749146672
0.000000e+00
4292.0
1
TraesCS2B01G553900
chr2B
95.786
617
21
5
1
614
554729815
554729201
0.000000e+00
990.0
2
TraesCS2B01G553900
chr2B
94.712
624
18
5
1
610
672037412
672038034
0.000000e+00
955.0
3
TraesCS2B01G553900
chr2B
81.757
740
61
33
985
1689
749139123
749138423
3.380000e-153
551.0
4
TraesCS2B01G553900
chr2B
84.543
427
44
9
1918
2323
749178359
749177934
1.000000e-108
403.0
5
TraesCS2B01G553900
chr2B
90.421
261
14
4
634
891
749139453
749139201
1.330000e-87
333.0
6
TraesCS2B01G553900
chr2B
81.218
394
39
21
985
1368
749181510
749181142
3.780000e-73
285.0
7
TraesCS2B01G553900
chr2B
95.833
144
3
3
767
908
749183302
749183160
1.800000e-56
230.0
8
TraesCS2B01G553900
chr2A
94.494
1471
66
11
804
2265
745097279
745095815
0.000000e+00
2254.0
9
TraesCS2B01G553900
chr2A
87.302
630
68
9
1704
2324
745110371
745109745
0.000000e+00
710.0
10
TraesCS2B01G553900
chr2A
83.376
782
79
31
611
1368
745112550
745111796
0.000000e+00
676.0
11
TraesCS2B01G553900
chr2A
79.443
754
67
37
985
1689
745092836
745092122
9.790000e-124
453.0
12
TraesCS2B01G553900
chr2A
89.247
279
19
8
1414
1689
745091346
745091076
2.860000e-89
339.0
13
TraesCS2B01G553900
chr2A
89.231
260
17
6
635
891
745093202
745092951
4.820000e-82
315.0
14
TraesCS2B01G553900
chr2A
98.958
96
1
0
1316
1411
745091479
745091384
3.070000e-39
172.0
15
TraesCS2B01G553900
chr2A
95.238
42
2
0
909
950
745112307
745112266
1.490000e-07
67.6
16
TraesCS2B01G553900
chr2D
91.935
1054
48
13
649
1689
614812197
614811168
0.000000e+00
1441.0
17
TraesCS2B01G553900
chr2D
82.368
777
48
30
967
1689
614804914
614804173
5.530000e-166
593.0
18
TraesCS2B01G553900
chr2D
80.204
783
85
38
612
1368
614819918
614819180
7.360000e-145
523.0
19
TraesCS2B01G553900
chr2D
90.291
206
11
3
687
891
614805147
614804950
6.370000e-66
261.0
20
TraesCS2B01G553900
chr2D
77.174
368
53
20
992
1347
614735175
614734827
3.940000e-43
185.0
21
TraesCS2B01G553900
chr2D
95.238
42
2
0
909
950
614819685
614819644
1.490000e-07
67.6
22
TraesCS2B01G553900
chr2D
97.059
34
1
0
875
908
614811941
614811908
8.970000e-05
58.4
23
TraesCS2B01G553900
chr2D
100.000
31
0
0
611
641
614812222
614812192
8.970000e-05
58.4
24
TraesCS2B01G553900
chr1B
94.888
626
17
5
1
612
450049968
450050592
0.000000e+00
965.0
25
TraesCS2B01G553900
chr7B
94.745
628
16
7
1
613
625711778
625711153
0.000000e+00
961.0
26
TraesCS2B01G553900
chr7B
93.120
625
26
10
1
610
709349761
709349139
0.000000e+00
900.0
27
TraesCS2B01G553900
chr4B
94.880
625
15
7
1
610
604543828
604543206
0.000000e+00
961.0
28
TraesCS2B01G553900
chr3B
94.551
624
20
4
1
610
98010967
98010344
0.000000e+00
952.0
29
TraesCS2B01G553900
chr3B
87.107
318
22
13
1
304
228652261
228651949
2.210000e-90
342.0
30
TraesCS2B01G553900
chr1D
89.776
626
39
19
1
610
355478548
355479164
0.000000e+00
778.0
31
TraesCS2B01G553900
chr1D
93.238
281
13
5
1
280
299879709
299879434
2.150000e-110
409.0
32
TraesCS2B01G553900
chr1D
87.582
306
17
14
1
292
438310206
438310504
3.700000e-88
335.0
33
TraesCS2B01G553900
chr5D
85.984
635
56
20
1
609
385123103
385122476
0.000000e+00
649.0
34
TraesCS2B01G553900
chr5D
90.253
277
15
10
1
269
65991967
65991695
3.670000e-93
351.0
35
TraesCS2B01G553900
chr5B
85.023
641
52
34
1
610
554681865
554681238
1.530000e-171
612.0
36
TraesCS2B01G553900
chr5B
85.451
488
37
16
1
474
692639749
692639282
5.810000e-131
477.0
37
TraesCS2B01G553900
chr7D
88.611
360
16
13
1
340
173594364
173594010
4.620000e-112
414.0
38
TraesCS2B01G553900
chr1A
100.000
30
0
0
1704
1733
364224321
364224350
3.230000e-04
56.5
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
TraesCS2B01G553900
chr2B
749146672
749148995
2323
True
4292.000000
4292
100.000000
1
2324
1
chr2B.!!$R2
2323
1
TraesCS2B01G553900
chr2B
554729201
554729815
614
True
990.000000
990
95.786000
1
614
1
chr2B.!!$R1
613
2
TraesCS2B01G553900
chr2B
672037412
672038034
622
False
955.000000
955
94.712000
1
610
1
chr2B.!!$F1
609
3
TraesCS2B01G553900
chr2B
749138423
749139453
1030
True
442.000000
551
86.089000
634
1689
2
chr2B.!!$R3
1055
4
TraesCS2B01G553900
chr2B
749177934
749183302
5368
True
306.000000
403
87.198000
767
2323
3
chr2B.!!$R4
1556
5
TraesCS2B01G553900
chr2A
745091076
745097279
6203
True
706.600000
2254
90.274600
635
2265
5
chr2A.!!$R1
1630
6
TraesCS2B01G553900
chr2A
745109745
745112550
2805
True
484.533333
710
88.638667
611
2324
3
chr2A.!!$R2
1713
7
TraesCS2B01G553900
chr2D
614811168
614812222
1054
True
519.266667
1441
96.331333
611
1689
3
chr2D.!!$R3
1078
8
TraesCS2B01G553900
chr2D
614804173
614805147
974
True
427.000000
593
86.329500
687
1689
2
chr2D.!!$R2
1002
9
TraesCS2B01G553900
chr2D
614819180
614819918
738
True
295.300000
523
87.721000
612
1368
2
chr2D.!!$R4
756
10
TraesCS2B01G553900
chr1B
450049968
450050592
624
False
965.000000
965
94.888000
1
612
1
chr1B.!!$F1
611
11
TraesCS2B01G553900
chr7B
625711153
625711778
625
True
961.000000
961
94.745000
1
613
1
chr7B.!!$R1
612
12
TraesCS2B01G553900
chr7B
709349139
709349761
622
True
900.000000
900
93.120000
1
610
1
chr7B.!!$R2
609
13
TraesCS2B01G553900
chr4B
604543206
604543828
622
True
961.000000
961
94.880000
1
610
1
chr4B.!!$R1
609
14
TraesCS2B01G553900
chr3B
98010344
98010967
623
True
952.000000
952
94.551000
1
610
1
chr3B.!!$R1
609
15
TraesCS2B01G553900
chr1D
355478548
355479164
616
False
778.000000
778
89.776000
1
610
1
chr1D.!!$F1
609
16
TraesCS2B01G553900
chr5D
385122476
385123103
627
True
649.000000
649
85.984000
1
609
1
chr5D.!!$R2
608
17
TraesCS2B01G553900
chr5B
554681238
554681865
627
True
612.000000
612
85.023000
1
610
1
chr5B.!!$R1
609
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.