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
TraesCS1B01G280300
chr1B
100.000
2516
0
0
1
2516
488473761
488476276
0.000000e+00
4647.0
1
TraesCS1B01G280300
chr1B
78.057
597
110
18
1860
2447
678204987
678205571
8.560000e-95
357.0
2
TraesCS1B01G280300
chr1D
93.088
1823
82
32
1
1795
365082060
365083866
0.000000e+00
2628.0
3
TraesCS1B01G280300
chr1A
94.796
1595
74
3
66
1660
463958524
463960109
0.000000e+00
2477.0
4
TraesCS1B01G280300
chr1A
97.436
39
1
0
1
39
463948962
463949000
1.620000e-07
67.6
5
TraesCS1B01G280300
chr2D
81.791
670
109
11
1830
2491
304335030
304335694
1.320000e-152
549.0
6
TraesCS1B01G280300
chr3A
82.371
641
100
7
1859
2492
749182172
749182806
1.700000e-151
545.0
7
TraesCS1B01G280300
chr3A
79.857
700
123
17
155
845
632041222
632040532
1.740000e-136
496.0
8
TraesCS1B01G280300
chr3A
85.366
328
37
9
1118
1441
632040292
632039972
1.870000e-86
329.0
9
TraesCS1B01G280300
chr3A
77.226
584
105
23
176
742
632295260
632294688
1.450000e-82
316.0
10
TraesCS1B01G280300
chr2A
82.154
650
100
14
1850
2491
382344316
382344957
6.120000e-151
544.0
11
TraesCS1B01G280300
chr2A
81.447
636
111
6
1860
2492
617430062
617429431
4.800000e-142
514.0
12
TraesCS1B01G280300
chr4D
84.007
569
75
9
1929
2493
51456893
51456337
1.320000e-147
532.0
13
TraesCS1B01G280300
chr3B
80.258
699
122
15
155
845
651427238
651426548
1.730000e-141
512.0
14
TraesCS1B01G280300
chr3B
79.450
691
120
18
166
845
489351530
489350851
1.050000e-128
470.0
15
TraesCS1B01G280300
chr3B
85.366
328
37
9
1118
1441
651426299
651425979
1.870000e-86
329.0
16
TraesCS1B01G280300
chr3B
84.756
328
39
9
1118
1441
489350602
489350282
4.040000e-83
318.0
17
TraesCS1B01G280300
chr4B
79.913
687
122
15
167
845
46934226
46933548
8.090000e-135
490.0
18
TraesCS1B01G280300
chr4B
83.841
328
42
9
1118
1441
46933299
46932979
4.070000e-78
302.0
19
TraesCS1B01G280300
chr4B
89.655
58
6
0
156
213
672128282
672128339
9.650000e-10
75.0
20
TraesCS1B01G280300
chr3D
79.881
671
121
12
155
818
488950102
488950765
1.750000e-131
479.0
21
TraesCS1B01G280300
chr3D
78.700
554
96
18
149
691
488893876
488894418
1.430000e-92
350.0
22
TraesCS1B01G280300
chr3D
85.075
335
37
11
1112
1441
488951035
488951361
1.870000e-86
329.0
23
TraesCS1B01G280300
chr2B
79.506
688
125
14
166
845
254626190
254626869
2.260000e-130
475.0
24
TraesCS1B01G280300
chr2B
79.153
614
114
10
1860
2468
164627435
164626831
1.800000e-111
412.0
25
TraesCS1B01G280300
chr2B
85.030
334
39
9
1112
1441
254627112
254627438
1.870000e-86
329.0
26
TraesCS1B01G280300
chr5D
80.404
643
109
15
1859
2491
56806657
56807292
8.150000e-130
473.0
27
TraesCS1B01G280300
chr5D
77.686
605
114
18
1858
2453
260681293
260680701
1.430000e-92
350.0
28
TraesCS1B01G280300
chr5A
79.647
624
119
8
1860
2480
547713899
547713281
2.300000e-120
442.0
29
TraesCS1B01G280300
chr7D
78.223
698
138
12
144
834
89310951
89311641
3.840000e-118
435.0
30
TraesCS1B01G280300
chr7D
85.666
293
38
3
1118
1408
89311908
89312198
3.140000e-79
305.0
31
TraesCS1B01G280300
chr7B
77.983
704
138
14
147
845
40275610
40276301
2.310000e-115
425.0
32
TraesCS1B01G280300
chr6D
77.707
628
119
14
1858
2471
334239106
334238486
5.110000e-97
364.0
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
TraesCS1B01G280300
chr1B
488473761
488476276
2515
False
4647.0
4647
100.0000
1
2516
1
chr1B.!!$F1
2515
1
TraesCS1B01G280300
chr1B
678204987
678205571
584
False
357.0
357
78.0570
1860
2447
1
chr1B.!!$F2
587
2
TraesCS1B01G280300
chr1D
365082060
365083866
1806
False
2628.0
2628
93.0880
1
1795
1
chr1D.!!$F1
1794
3
TraesCS1B01G280300
chr1A
463958524
463960109
1585
False
2477.0
2477
94.7960
66
1660
1
chr1A.!!$F2
1594
4
TraesCS1B01G280300
chr2D
304335030
304335694
664
False
549.0
549
81.7910
1830
2491
1
chr2D.!!$F1
661
5
TraesCS1B01G280300
chr3A
749182172
749182806
634
False
545.0
545
82.3710
1859
2492
1
chr3A.!!$F1
633
6
TraesCS1B01G280300
chr3A
632039972
632041222
1250
True
412.5
496
82.6115
155
1441
2
chr3A.!!$R2
1286
7
TraesCS1B01G280300
chr3A
632294688
632295260
572
True
316.0
316
77.2260
176
742
1
chr3A.!!$R1
566
8
TraesCS1B01G280300
chr2A
382344316
382344957
641
False
544.0
544
82.1540
1850
2491
1
chr2A.!!$F1
641
9
TraesCS1B01G280300
chr2A
617429431
617430062
631
True
514.0
514
81.4470
1860
2492
1
chr2A.!!$R1
632
10
TraesCS1B01G280300
chr4D
51456337
51456893
556
True
532.0
532
84.0070
1929
2493
1
chr4D.!!$R1
564
11
TraesCS1B01G280300
chr3B
651425979
651427238
1259
True
420.5
512
82.8120
155
1441
2
chr3B.!!$R2
1286
12
TraesCS1B01G280300
chr3B
489350282
489351530
1248
True
394.0
470
82.1030
166
1441
2
chr3B.!!$R1
1275
13
TraesCS1B01G280300
chr4B
46932979
46934226
1247
True
396.0
490
81.8770
167
1441
2
chr4B.!!$R1
1274
14
TraesCS1B01G280300
chr3D
488950102
488951361
1259
False
404.0
479
82.4780
155
1441
2
chr3D.!!$F2
1286
15
TraesCS1B01G280300
chr3D
488893876
488894418
542
False
350.0
350
78.7000
149
691
1
chr3D.!!$F1
542
16
TraesCS1B01G280300
chr2B
164626831
164627435
604
True
412.0
412
79.1530
1860
2468
1
chr2B.!!$R1
608
17
TraesCS1B01G280300
chr2B
254626190
254627438
1248
False
402.0
475
82.2680
166
1441
2
chr2B.!!$F1
1275
18
TraesCS1B01G280300
chr5D
56806657
56807292
635
False
473.0
473
80.4040
1859
2491
1
chr5D.!!$F1
632
19
TraesCS1B01G280300
chr5D
260680701
260681293
592
True
350.0
350
77.6860
1858
2453
1
chr5D.!!$R1
595
20
TraesCS1B01G280300
chr5A
547713281
547713899
618
True
442.0
442
79.6470
1860
2480
1
chr5A.!!$R1
620
21
TraesCS1B01G280300
chr7D
89310951
89312198
1247
False
370.0
435
81.9445
144
1408
2
chr7D.!!$F1
1264
22
TraesCS1B01G280300
chr7B
40275610
40276301
691
False
425.0
425
77.9830
147
845
1
chr7B.!!$F1
698
23
TraesCS1B01G280300
chr6D
334238486
334239106
620
True
364.0
364
77.7070
1858
2471
1
chr6D.!!$R1
613
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.