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
TraesCS3B01G346100
chr3B
100.000
2411
0
0
1
2411
555553781
555551371
0.000000e+00
4453
1
TraesCS3B01G346100
chr3B
88.752
1218
82
22
1224
2411
685078796
685077604
0.000000e+00
1439
2
TraesCS3B01G346100
chr3D
94.240
2448
93
21
1
2411
16446569
16449005
0.000000e+00
3696
3
TraesCS3B01G346100
chr3D
88.734
1216
81
22
1221
2411
32171969
32173153
0.000000e+00
1435
4
TraesCS3B01G346100
chr5A
94.957
2340
65
18
1
2300
606397326
606395000
0.000000e+00
3618
5
TraesCS3B01G346100
chr5A
85.864
573
68
6
67
632
135038279
135037713
4.440000e-167
597
6
TraesCS3B01G346100
chr4A
97.462
1970
25
7
3
1965
729647899
729645948
0.000000e+00
3338
7
TraesCS3B01G346100
chr4A
97.927
579
11
1
1832
2409
729645949
729645371
0.000000e+00
1002
8
TraesCS3B01G346100
chr4A
97.222
72
2
0
1
72
729647826
729647755
3.260000e-24
122
9
TraesCS3B01G346100
chr4B
99.395
1818
9
2
596
2411
16784613
16786430
0.000000e+00
3295
10
TraesCS3B01G346100
chr4B
99.050
842
5
1
1
839
16783771
16784612
0.000000e+00
1507
11
TraesCS3B01G346100
chr7D
93.121
1730
60
11
706
2411
446553579
446551885
0.000000e+00
2481
12
TraesCS3B01G346100
chr2A
93.271
1397
56
12
1039
2411
46334480
46335862
0.000000e+00
2025
13
TraesCS3B01G346100
chr2A
95.829
1007
36
4
1
1001
46333474
46334480
0.000000e+00
1622
14
TraesCS3B01G346100
chr2A
88.811
715
59
10
1495
2202
363365172
363365872
0.000000e+00
857
15
TraesCS3B01G346100
chr2A
90.334
569
49
3
68
632
594379107
594378541
0.000000e+00
741
16
TraesCS3B01G346100
chr2A
87.267
322
34
6
631
947
648745695
648745376
6.340000e-96
361
17
TraesCS3B01G346100
chr6B
97.346
829
15
3
1142
1965
247037488
247036662
0.000000e+00
1402
18
TraesCS3B01G346100
chr6B
97.762
581
11
2
1832
2411
247036663
247036084
0.000000e+00
1000
19
TraesCS3B01G346100
chr6B
91.457
714
39
10
1495
2202
247042266
247041569
0.000000e+00
961
20
TraesCS3B01G346100
chr7A
96.406
473
14
3
1
471
321637382
321636911
0.000000e+00
776
21
TraesCS3B01G346100
chr7A
86.834
319
35
6
631
944
704664407
704664723
1.370000e-92
350
22
TraesCS3B01G346100
chr7A
97.222
72
2
0
1
72
321637307
321637236
3.260000e-24
122
23
TraesCS3B01G346100
chr3A
89.789
568
46
5
68
630
640035643
640035083
0.000000e+00
717
24
TraesCS3B01G346100
chr2B
85.442
577
70
7
67
635
31912766
31913336
2.670000e-164
588
25
TraesCS3B01G346100
chr1A
88.389
422
34
6
1224
1634
505878737
505878320
5.990000e-136
494
26
TraesCS3B01G346100
chr1D
86.404
456
41
8
942
1379
210228969
210228517
1.680000e-131
479
27
TraesCS3B01G346100
chr1D
87.770
139
16
1
941
1079
298144710
298144573
6.900000e-36
161
28
TraesCS3B01G346100
chr5B
86.031
451
42
7
944
1376
199657515
199657962
4.690000e-127
464
29
TraesCS3B01G346100
chr6D
85.000
460
41
11
942
1378
472510517
472510063
2.200000e-120
442
30
TraesCS3B01G346100
chrUn
100.000
128
0
0
1
128
476762808
476762935
1.110000e-58
237
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
TraesCS3B01G346100
chr3B
555551371
555553781
2410
True
4453.000000
4453
100.0000
1
2411
1
chr3B.!!$R1
2410
1
TraesCS3B01G346100
chr3B
685077604
685078796
1192
True
1439.000000
1439
88.7520
1224
2411
1
chr3B.!!$R2
1187
2
TraesCS3B01G346100
chr3D
16446569
16449005
2436
False
3696.000000
3696
94.2400
1
2411
1
chr3D.!!$F1
2410
3
TraesCS3B01G346100
chr3D
32171969
32173153
1184
False
1435.000000
1435
88.7340
1221
2411
1
chr3D.!!$F2
1190
4
TraesCS3B01G346100
chr5A
606395000
606397326
2326
True
3618.000000
3618
94.9570
1
2300
1
chr5A.!!$R2
2299
5
TraesCS3B01G346100
chr5A
135037713
135038279
566
True
597.000000
597
85.8640
67
632
1
chr5A.!!$R1
565
6
TraesCS3B01G346100
chr4A
729645371
729647899
2528
True
1487.333333
3338
97.5370
1
2409
3
chr4A.!!$R1
2408
7
TraesCS3B01G346100
chr4B
16783771
16786430
2659
False
2401.000000
3295
99.2225
1
2411
2
chr4B.!!$F1
2410
8
TraesCS3B01G346100
chr7D
446551885
446553579
1694
True
2481.000000
2481
93.1210
706
2411
1
chr7D.!!$R1
1705
9
TraesCS3B01G346100
chr2A
46333474
46335862
2388
False
1823.500000
2025
94.5500
1
2411
2
chr2A.!!$F2
2410
10
TraesCS3B01G346100
chr2A
363365172
363365872
700
False
857.000000
857
88.8110
1495
2202
1
chr2A.!!$F1
707
11
TraesCS3B01G346100
chr2A
594378541
594379107
566
True
741.000000
741
90.3340
68
632
1
chr2A.!!$R1
564
12
TraesCS3B01G346100
chr6B
247036084
247037488
1404
True
1201.000000
1402
97.5540
1142
2411
2
chr6B.!!$R2
1269
13
TraesCS3B01G346100
chr6B
247041569
247042266
697
True
961.000000
961
91.4570
1495
2202
1
chr6B.!!$R1
707
14
TraesCS3B01G346100
chr3A
640035083
640035643
560
True
717.000000
717
89.7890
68
630
1
chr3A.!!$R1
562
15
TraesCS3B01G346100
chr2B
31912766
31913336
570
False
588.000000
588
85.4420
67
635
1
chr2B.!!$F1
568
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.