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
TraesCS5D01G095100
chr5D
100.000
5864
0
0
1
5864
104474742
104468879
0.000000e+00
10829.0
1
TraesCS5D01G095100
chr5D
92.182
2699
182
18
932
3612
104157600
104154913
0.000000e+00
3788.0
2
TraesCS5D01G095100
chr5D
87.746
457
43
8
4627
5081
104153818
104153373
6.730000e-144
521.0
3
TraesCS5D01G095100
chr5D
86.500
200
24
3
4623
4821
450611540
450611343
3.560000e-52
217.0
4
TraesCS5D01G095100
chr5D
80.476
210
27
9
5096
5299
104153334
104153133
1.320000e-31
148.0
5
TraesCS5D01G095100
chr5A
98.114
5248
77
12
627
5864
107392617
107387382
0.000000e+00
9123.0
6
TraesCS5D01G095100
chr5A
92.145
2699
185
19
932
3612
94083195
94085884
0.000000e+00
3784.0
7
TraesCS5D01G095100
chr5A
96.960
625
12
2
7
629
107393262
107392643
0.000000e+00
1042.0
8
TraesCS5D01G095100
chr5A
87.939
456
49
6
4628
5081
94087949
94088400
3.110000e-147
532.0
9
TraesCS5D01G095100
chr5A
80.476
210
27
9
5096
5299
94088439
94088640
1.320000e-31
148.0
10
TraesCS5D01G095100
chr5B
97.926
3519
60
6
1
3518
113877549
113874043
0.000000e+00
6082.0
11
TraesCS5D01G095100
chr5B
91.775
2699
193
23
932
3612
113559959
113557272
0.000000e+00
3727.0
12
TraesCS5D01G095100
chr5B
96.782
2144
49
10
3723
5864
113874043
113871918
0.000000e+00
3559.0
13
TraesCS5D01G095100
chr5B
88.377
456
47
6
4628
5081
113556194
113555743
1.440000e-150
544.0
14
TraesCS5D01G095100
chr5B
83.986
281
43
2
3032
3311
119392257
119391978
9.690000e-68
268.0
15
TraesCS5D01G095100
chr5B
78.098
347
56
12
2967
3312
320823491
320823818
9.960000e-48
202.0
16
TraesCS5D01G095100
chr4D
84.351
262
40
1
3058
3318
304184272
304184533
7.540000e-64
255.0
17
TraesCS5D01G095100
chr4D
87.000
200
21
5
4623
4821
465418402
465418207
2.750000e-53
220.0
18
TraesCS5D01G095100
chr4D
93.590
78
5
0
1624
1701
178522915
178522838
3.710000e-22
117.0
19
TraesCS5D01G095100
chr7D
87.500
200
22
3
4623
4821
65501908
65502105
1.640000e-55
228.0
20
TraesCS5D01G095100
chr3B
89.130
138
15
0
1564
1701
522886039
522886176
7.810000e-39
172.0
21
TraesCS5D01G095100
chr3B
94.382
89
5
0
2274
2362
522886170
522886258
2.850000e-28
137.0
22
TraesCS5D01G095100
chr1A
95.294
85
4
0
1617
1701
532211265
532211181
1.030000e-27
135.0
23
TraesCS5D01G095100
chr1A
93.590
78
4
1
1624
1701
233202843
233202919
1.340000e-21
115.0
24
TraesCS5D01G095100
chr1A
88.764
89
10
0
2274
2362
233202913
233203001
6.210000e-20
110.0
25
TraesCS5D01G095100
chr7B
84.259
108
5
5
2255
2362
279198500
279198405
1.740000e-15
95.3
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
TraesCS5D01G095100
chr5D
104468879
104474742
5863
True
10829.000000
10829
100.000000
1
5864
1
chr5D.!!$R1
5863
1
TraesCS5D01G095100
chr5D
104153133
104157600
4467
True
1485.666667
3788
86.801333
932
5299
3
chr5D.!!$R3
4367
2
TraesCS5D01G095100
chr5A
107387382
107393262
5880
True
5082.500000
9123
97.537000
7
5864
2
chr5A.!!$R1
5857
3
TraesCS5D01G095100
chr5A
94083195
94088640
5445
False
1488.000000
3784
86.853333
932
5299
3
chr5A.!!$F1
4367
4
TraesCS5D01G095100
chr5B
113871918
113877549
5631
True
4820.500000
6082
97.354000
1
5864
2
chr5B.!!$R3
5863
5
TraesCS5D01G095100
chr5B
113555743
113559959
4216
True
2135.500000
3727
90.076000
932
5081
2
chr5B.!!$R2
4149
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.