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
TraesCS7D01G461800
chr7D
100.000
2505
0
0
1
2505
577777719
577780223
0.000000e+00
4626.0
1
TraesCS7D01G461800
chr7D
80.892
314
46
10
1726
2033
399646458
399646153
4.170000e-58
235.0
2
TraesCS7D01G461800
chr2D
89.090
1659
137
23
1
1627
86073645
86075291
0.000000e+00
2021.0
3
TraesCS7D01G461800
chr2D
94.485
272
13
2
2227
2496
86075313
86075584
3.850000e-113
418.0
4
TraesCS7D01G461800
chr5D
88.721
1658
146
21
1
1627
371866802
371865155
0.000000e+00
1988.0
5
TraesCS7D01G461800
chr5D
91.063
414
36
1
2090
2503
78506248
78505836
2.180000e-155
558.0
6
TraesCS7D01G461800
chr5D
93.238
281
17
2
2227
2505
371865133
371864853
1.790000e-111
412.0
7
TraesCS7D01G461800
chr5D
91.525
236
16
2
1793
2024
78506492
78506257
3.110000e-84
322.0
8
TraesCS7D01G461800
chr2A
88.587
1656
149
22
1
1627
5095709
5097353
0.000000e+00
1975.0
9
TraesCS7D01G461800
chr2A
94.118
272
16
0
2225
2496
5097419
5097690
4.990000e-112
414.0
10
TraesCS7D01G461800
chr5A
84.765
1746
187
33
339
2024
512074178
512072452
0.000000e+00
1677.0
11
TraesCS7D01G461800
chr5A
86.137
844
83
19
18
837
512074596
512073763
0.000000e+00
880.0
12
TraesCS7D01G461800
chr5A
90.466
451
43
0
2043
2493
512072469
512072019
1.660000e-166
595.0
13
TraesCS7D01G461800
chr5A
75.962
208
35
13
342
543
512073834
512073636
2.650000e-15
93.5
14
TraesCS7D01G461800
chr7A
88.528
1386
118
21
1
1357
635284566
635283193
0.000000e+00
1640.0
15
TraesCS7D01G461800
chr7A
93.238
281
19
0
2225
2505
635282465
635282185
4.990000e-112
414.0
16
TraesCS7D01G461800
chr7A
76.261
337
45
19
1726
2033
457601898
457601568
2.010000e-31
147.0
17
TraesCS7D01G461800
chr1B
87.569
1086
101
13
576
1639
563966627
563965554
0.000000e+00
1227.0
18
TraesCS7D01G461800
chr1B
88.085
940
81
12
576
1493
398967617
398968547
0.000000e+00
1086.0
19
TraesCS7D01G461800
chr1B
87.584
596
67
5
1710
2300
398992573
398993166
0.000000e+00
684.0
20
TraesCS7D01G461800
chr1B
87.563
595
63
8
1710
2300
563964739
563964152
0.000000e+00
678.0
21
TraesCS7D01G461800
chr1B
81.655
894
88
33
1
851
563967318
563966458
0.000000e+00
673.0
22
TraesCS7D01G461800
chr1B
86.111
216
29
1
2290
2505
563964012
563963798
5.390000e-57
231.0
23
TraesCS7D01G461800
chr7B
82.647
801
91
24
339
1098
589924324
589925117
0.000000e+00
665.0
24
TraesCS7D01G461800
chr7B
86.522
601
69
7
1710
2300
589933517
589934115
0.000000e+00
651.0
25
TraesCS7D01G461800
chr7B
87.701
561
54
8
1084
1639
589932152
589932702
7.560000e-180
640.0
26
TraesCS7D01G461800
chr4A
89.507
467
44
5
2039
2503
646534100
646534563
9.980000e-164
586.0
27
TraesCS7D01G461800
chr4A
94.253
87
5
0
1938
2024
646534035
646534121
1.560000e-27
134.0
28
TraesCS7D01G461800
chr3B
84.793
217
32
1
2288
2504
592858063
592858278
1.510000e-52
217.0
29
TraesCS7D01G461800
chr4B
83.230
161
21
6
1757
1916
665424357
665424202
2.600000e-30
143.0
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
TraesCS7D01G461800
chr7D
577777719
577780223
2504
False
4626.000
4626
100.0000
1
2505
1
chr7D.!!$F1
2504
1
TraesCS7D01G461800
chr2D
86073645
86075584
1939
False
1219.500
2021
91.7875
1
2496
2
chr2D.!!$F1
2495
2
TraesCS7D01G461800
chr5D
371864853
371866802
1949
True
1200.000
1988
90.9795
1
2505
2
chr5D.!!$R2
2504
3
TraesCS7D01G461800
chr5D
78505836
78506492
656
True
440.000
558
91.2940
1793
2503
2
chr5D.!!$R1
710
4
TraesCS7D01G461800
chr2A
5095709
5097690
1981
False
1194.500
1975
91.3525
1
2496
2
chr2A.!!$F1
2495
5
TraesCS7D01G461800
chr5A
512072019
512074596
2577
True
811.375
1677
84.3325
18
2493
4
chr5A.!!$R1
2475
6
TraesCS7D01G461800
chr7A
635282185
635284566
2381
True
1027.000
1640
90.8830
1
2505
2
chr7A.!!$R2
2504
7
TraesCS7D01G461800
chr1B
398967617
398968547
930
False
1086.000
1086
88.0850
576
1493
1
chr1B.!!$F1
917
8
TraesCS7D01G461800
chr1B
563963798
563967318
3520
True
702.250
1227
85.7245
1
2505
4
chr1B.!!$R1
2504
9
TraesCS7D01G461800
chr1B
398992573
398993166
593
False
684.000
684
87.5840
1710
2300
1
chr1B.!!$F2
590
10
TraesCS7D01G461800
chr7B
589924324
589925117
793
False
665.000
665
82.6470
339
1098
1
chr7B.!!$F1
759
11
TraesCS7D01G461800
chr7B
589932152
589934115
1963
False
645.500
651
87.1115
1084
2300
2
chr7B.!!$F2
1216
12
TraesCS7D01G461800
chr4A
646534035
646534563
528
False
360.000
586
91.8800
1938
2503
2
chr4A.!!$F1
565
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.