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
TraesCS5D01G110300
chr5D
100.000
2342
0
0
1
2342
125175933
125173592
0.000000e+00
4325.0
1
TraesCS5D01G110300
chr5D
89.256
121
10
1
1593
1713
125174263
125174146
5.210000e-32
148.0
2
TraesCS5D01G110300
chr5D
89.256
121
10
1
1671
1788
125174341
125174221
5.210000e-32
148.0
3
TraesCS5D01G110300
chr7D
90.656
1434
62
25
183
1552
45500860
45502285
0.000000e+00
1840.0
4
TraesCS5D01G110300
chr7D
87.079
743
53
20
1608
2341
45502599
45503307
0.000000e+00
800.0
5
TraesCS5D01G110300
chr7D
97.872
47
1
0
1549
1595
45502351
45502397
5.360000e-12
82.4
6
TraesCS5D01G110300
chr3D
86.396
1676
75
64
1
1595
423666788
423668391
0.000000e+00
1690.0
7
TraesCS5D01G110300
chr3D
86.445
723
54
17
2
693
423665850
423666559
0.000000e+00
752.0
8
TraesCS5D01G110300
chr3D
90.000
140
12
1
1954
2093
423669909
423670046
1.850000e-41
180.0
9
TraesCS5D01G110300
chr3D
89.000
100
5
4
1822
1916
423669809
423669907
4.090000e-23
119.0
10
TraesCS5D01G110300
chr4A
89.010
1101
56
34
500
1552
657488579
657489662
0.000000e+00
1303.0
11
TraesCS5D01G110300
chr4A
85.617
737
63
23
1608
2333
657489972
657490676
0.000000e+00
734.0
12
TraesCS5D01G110300
chr4A
86.364
418
48
5
3
419
657487953
657488362
4.590000e-122
448.0
13
TraesCS5D01G110300
chr4A
90.476
105
6
2
1609
1713
657490040
657490140
4.060000e-28
135.0
14
TraesCS5D01G110300
chr4A
90.698
43
1
1
1593
1635
657490101
657490140
1.000000e-03
54.7
15
TraesCS5D01G110300
chr7A
88.778
1105
51
29
489
1528
47554568
47555664
0.000000e+00
1286.0
16
TraesCS5D01G110300
chr7A
85.077
717
62
24
1
693
47553088
47553783
0.000000e+00
689.0
17
TraesCS5D01G110300
chr7A
85.757
667
71
16
1687
2341
47556962
47557616
0.000000e+00
684.0
18
TraesCS5D01G110300
chr7A
88.957
489
38
8
1
487
47554013
47554487
7.210000e-165
590.0
19
TraesCS5D01G110300
chr7A
87.139
381
28
7
1687
2051
47556011
47556386
1.670000e-111
412.0
20
TraesCS5D01G110300
chr7A
91.509
106
4
3
1495
1596
47555663
47555767
8.730000e-30
141.0
21
TraesCS5D01G110300
chr7A
89.524
105
7
3
1609
1712
47556011
47556112
1.890000e-26
130.0
22
TraesCS5D01G110300
chr7A
93.103
58
1
1
447
504
47554500
47554554
5.360000e-12
82.4
23
TraesCS5D01G110300
chr7A
93.878
49
2
1
1549
1596
47556497
47556545
3.230000e-09
73.1
24
TraesCS5D01G110300
chr2D
86.248
829
54
14
1
811
34683343
34684129
0.000000e+00
845.0
25
TraesCS5D01G110300
chr2D
86.050
724
51
23
1
693
34682410
34683114
0.000000e+00
732.0
26
TraesCS5D01G110300
chr2D
86.072
639
42
17
3
607
34681226
34681851
0.000000e+00
643.0
27
TraesCS5D01G110300
chr6A
83.478
460
38
20
1
458
525607544
525607967
6.070000e-106
394.0
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
TraesCS5D01G110300
chr5D
125173592
125175933
2341
True
1540.333333
4325
92.837333
1
2342
3
chr5D.!!$R1
2341
1
TraesCS5D01G110300
chr7D
45500860
45503307
2447
False
907.466667
1840
91.869000
183
2341
3
chr7D.!!$F1
2158
2
TraesCS5D01G110300
chr3D
423665850
423670046
4196
False
685.250000
1690
87.960250
1
2093
4
chr3D.!!$F1
2092
3
TraesCS5D01G110300
chr4A
657487953
657490676
2723
False
534.940000
1303
88.433000
3
2333
5
chr4A.!!$F1
2330
4
TraesCS5D01G110300
chr7A
47553088
47557616
4528
False
454.166667
1286
89.302444
1
2341
9
chr7A.!!$F1
2340
5
TraesCS5D01G110300
chr2D
34681226
34684129
2903
False
740.000000
845
86.123333
1
811
3
chr2D.!!$F1
810
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.