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
TraesCS1B01G223800
chr1B
100.000
2432
0
0
1
2432
401993366
401990935
0.000000e+00
4492.0
1
TraesCS1B01G223800
chr1B
94.339
1837
80
6
600
2431
401763967
401762150
0.000000e+00
2795.0
2
TraesCS1B01G223800
chr1B
91.607
977
55
16
644
1609
402039921
402038961
0.000000e+00
1325.0
3
TraesCS1B01G223800
chr1B
98.507
268
3
1
336
602
401764299
401764032
2.830000e-129
472.0
4
TraesCS1B01G223800
chr1B
97.500
240
6
0
101
340
401765701
401765462
6.260000e-111
411.0
5
TraesCS1B01G223800
chr1B
89.167
240
26
0
1664
1903
2770258
2770497
1.410000e-77
300.0
6
TraesCS1B01G223800
chr1B
94.828
116
6
0
474
589
402040038
402039923
5.340000e-42
182.0
7
TraesCS1B01G223800
chr1B
92.857
112
8
0
1
112
401766225
401766114
1.930000e-36
163.0
8
TraesCS1B01G223800
chr1D
92.395
1052
57
13
602
1637
298604698
298603654
0.000000e+00
1478.0
9
TraesCS1B01G223800
chr1D
85.921
554
50
19
1901
2432
298598676
298598129
1.260000e-157
566.0
10
TraesCS1B01G223800
chr1D
94.488
127
7
0
474
600
298604892
298604766
1.910000e-46
196.0
11
TraesCS1B01G223800
chr1D
92.373
118
7
1
1550
1665
298598792
298598675
1.500000e-37
167.0
12
TraesCS1B01G223800
chr1D
96.774
31
1
0
600
630
298599862
298599832
4.000000e-03
52.8
13
TraesCS1B01G223800
chr1A
91.392
1092
58
16
600
1665
372287997
372286916
0.000000e+00
1463.0
14
TraesCS1B01G223800
chr1A
90.169
1007
72
16
602
1591
372316468
372315472
0.000000e+00
1286.0
15
TraesCS1B01G223800
chr1A
92.193
602
23
2
1
602
372288639
372288062
0.000000e+00
830.0
16
TraesCS1B01G223800
chr1A
88.608
237
23
4
366
600
372316770
372316536
3.960000e-73
285.0
17
TraesCS1B01G223800
chr1A
89.773
176
16
2
2259
2432
372285910
372285735
8.750000e-55
224.0
18
TraesCS1B01G223800
chr4B
82.604
983
116
29
677
1628
602873972
602873014
0.000000e+00
817.0
19
TraesCS1B01G223800
chr4B
83.333
924
113
25
627
1529
603037675
603038578
0.000000e+00
815.0
20
TraesCS1B01G223800
chr4B
89.669
242
22
3
1664
1904
139755999
139756238
3.040000e-79
305.0
21
TraesCS1B01G223800
chr4D
83.808
877
106
22
773
1628
477543741
477542880
0.000000e+00
800.0
22
TraesCS1B01G223800
chr4D
83.620
873
91
27
627
1473
477558660
477559506
0.000000e+00
773.0
23
TraesCS1B01G223800
chr5B
90.717
237
22
0
1666
1902
64626076
64626312
1.400000e-82
316.0
24
TraesCS1B01G223800
chr3D
89.540
239
25
0
1664
1902
209677726
209677488
1.090000e-78
303.0
25
TraesCS1B01G223800
chr3D
89.344
244
23
2
1663
1905
593241647
593241406
1.090000e-78
303.0
26
TraesCS1B01G223800
chr7A
89.121
239
26
0
1664
1902
383095996
383096234
5.080000e-77
298.0
27
TraesCS1B01G223800
chr2A
88.142
253
27
3
1650
1902
468294297
468294048
5.080000e-77
298.0
28
TraesCS1B01G223800
chr2B
86.923
260
31
2
1664
1923
557173662
557173918
3.060000e-74
289.0
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
TraesCS1B01G223800
chr1B
401990935
401993366
2431
True
4492.00
4492
100.000000
1
2432
1
chr1B.!!$R1
2431
1
TraesCS1B01G223800
chr1B
401762150
401766225
4075
True
960.25
2795
95.800750
1
2431
4
chr1B.!!$R2
2430
2
TraesCS1B01G223800
chr1B
402038961
402040038
1077
True
753.50
1325
93.217500
474
1609
2
chr1B.!!$R3
1135
3
TraesCS1B01G223800
chr1D
298598129
298604892
6763
True
491.96
1478
92.390200
474
2432
5
chr1D.!!$R1
1958
4
TraesCS1B01G223800
chr1A
372285735
372288639
2904
True
839.00
1463
91.119333
1
2432
3
chr1A.!!$R1
2431
5
TraesCS1B01G223800
chr1A
372315472
372316770
1298
True
785.50
1286
89.388500
366
1591
2
chr1A.!!$R2
1225
6
TraesCS1B01G223800
chr4B
602873014
602873972
958
True
817.00
817
82.604000
677
1628
1
chr4B.!!$R1
951
7
TraesCS1B01G223800
chr4B
603037675
603038578
903
False
815.00
815
83.333000
627
1529
1
chr4B.!!$F2
902
8
TraesCS1B01G223800
chr4D
477542880
477543741
861
True
800.00
800
83.808000
773
1628
1
chr4D.!!$R1
855
9
TraesCS1B01G223800
chr4D
477558660
477559506
846
False
773.00
773
83.620000
627
1473
1
chr4D.!!$F1
846
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.