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
TraesCS4A01G143400
chr4A
100.000
2686
0
0
1
2686
236226264
236228949
0.000000e+00
4961
1
TraesCS4A01G143400
chr4A
90.631
523
44
4
434
952
561094309
561094830
0.000000e+00
689
2
TraesCS4A01G143400
chr7D
95.801
2715
80
16
1
2686
636968414
636965705
0.000000e+00
4351
3
TraesCS4A01G143400
chr6A
93.128
2692
151
17
1
2686
443932324
443929661
0.000000e+00
3916
4
TraesCS4A01G143400
chr3A
94.518
1277
59
5
357
1624
608075713
608076987
0.000000e+00
1960
5
TraesCS4A01G143400
chr3A
93.388
242
15
1
1804
2045
608076983
608077223
9.140000e-95
357
6
TraesCS4A01G143400
chr3A
90.650
246
22
1
1
246
608075476
608075720
2.580000e-85
326
7
TraesCS4A01G143400
chr3A
94.118
102
6
0
2186
2287
608077224
608077325
3.580000e-34
156
8
TraesCS4A01G143400
chr1B
89.944
895
64
11
61
953
206375673
206376543
0.000000e+00
1131
9
TraesCS4A01G143400
chr1B
97.059
68
2
0
1618
1685
206376546
206376613
6.080000e-22
115
10
TraesCS4A01G143400
chr5B
86.520
957
70
10
1
956
166718401
166717503
0.000000e+00
998
11
TraesCS4A01G143400
chr5B
86.373
954
71
10
1
953
166719048
166719943
0.000000e+00
987
12
TraesCS4A01G143400
chr5B
85.893
957
75
16
1
956
161651469
161650572
0.000000e+00
965
13
TraesCS4A01G143400
chr5B
98.529
68
1
0
1618
1685
161650572
161650505
1.310000e-23
121
14
TraesCS4A01G143400
chr5B
98.529
68
1
0
1618
1685
166717503
166717436
1.310000e-23
121
15
TraesCS4A01G143400
chr5B
97.059
68
2
0
1618
1685
166719946
166720013
6.080000e-22
115
16
TraesCS4A01G143400
chr2D
87.372
681
47
14
956
1618
614849940
614850599
0.000000e+00
745
17
TraesCS4A01G143400
chr2D
90.996
522
44
3
434
953
68349984
68350504
0.000000e+00
701
18
TraesCS4A01G143400
chr2D
94.118
68
4
0
1618
1685
68350507
68350574
1.320000e-18
104
19
TraesCS4A01G143400
chr7A
91.358
405
25
5
1220
1619
68882301
68882700
1.820000e-151
545
20
TraesCS4A01G143400
chr7A
89.919
248
21
2
955
1198
68881813
68882060
1.550000e-82
316
21
TraesCS4A01G143400
chr7B
90.819
403
24
6
1225
1619
6236255
6236652
6.590000e-146
527
22
TraesCS4A01G143400
chr7B
89.516
248
22
2
955
1198
6235759
6236006
7.220000e-81
311
23
TraesCS4A01G143400
chr4D
90.604
149
14
0
1
149
285714676
285714528
5.870000e-47
198
24
TraesCS4A01G143400
chr2A
85.955
178
19
6
1964
2138
763967030
763966856
4.570000e-43
185
25
TraesCS4A01G143400
chr2B
88.073
109
11
2
1689
1797
797210153
797210259
7.810000e-26
128
26
TraesCS4A01G143400
chr2B
89.796
98
9
1
1700
1797
797256546
797256642
1.010000e-24
124
27
TraesCS4A01G143400
chr2B
95.455
66
3
0
1618
1683
619205987
619205922
3.660000e-19
106
28
TraesCS4A01G143400
chr6D
97.015
67
2
0
1618
1684
211547822
211547756
2.190000e-21
113
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
TraesCS4A01G143400
chr4A
236226264
236228949
2685
False
4961.00
4961
100.0000
1
2686
1
chr4A.!!$F1
2685
1
TraesCS4A01G143400
chr4A
561094309
561094830
521
False
689.00
689
90.6310
434
952
1
chr4A.!!$F2
518
2
TraesCS4A01G143400
chr7D
636965705
636968414
2709
True
4351.00
4351
95.8010
1
2686
1
chr7D.!!$R1
2685
3
TraesCS4A01G143400
chr6A
443929661
443932324
2663
True
3916.00
3916
93.1280
1
2686
1
chr6A.!!$R1
2685
4
TraesCS4A01G143400
chr3A
608075476
608077325
1849
False
699.75
1960
93.1685
1
2287
4
chr3A.!!$F1
2286
5
TraesCS4A01G143400
chr1B
206375673
206376613
940
False
623.00
1131
93.5015
61
1685
2
chr1B.!!$F1
1624
6
TraesCS4A01G143400
chr5B
166717436
166718401
965
True
559.50
998
92.5245
1
1685
2
chr5B.!!$R2
1684
7
TraesCS4A01G143400
chr5B
166719048
166720013
965
False
551.00
987
91.7160
1
1685
2
chr5B.!!$F1
1684
8
TraesCS4A01G143400
chr5B
161650505
161651469
964
True
543.00
965
92.2110
1
1685
2
chr5B.!!$R1
1684
9
TraesCS4A01G143400
chr2D
614849940
614850599
659
False
745.00
745
87.3720
956
1618
1
chr2D.!!$F1
662
10
TraesCS4A01G143400
chr2D
68349984
68350574
590
False
402.50
701
92.5570
434
1685
2
chr2D.!!$F2
1251
11
TraesCS4A01G143400
chr7A
68881813
68882700
887
False
430.50
545
90.6385
955
1619
2
chr7A.!!$F1
664
12
TraesCS4A01G143400
chr7B
6235759
6236652
893
False
419.00
527
90.1675
955
1619
2
chr7B.!!$F1
664
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.