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
TraesCS4D01G288100
chr4D
100.000
4670
0
0
1
4670
459318861
459323530
0.000000e+00
8624
1
TraesCS4D01G288100
chr4D
81.297
2144
341
39
1028
3156
478311014
478313112
0.000000e+00
1683
2
TraesCS4D01G288100
chr4D
81.075
2140
347
35
1031
3156
478320071
478322166
0.000000e+00
1655
3
TraesCS4D01G288100
chr4D
84.255
1664
213
23
1507
3162
478280152
478281774
0.000000e+00
1576
4
TraesCS4D01G288100
chr4D
83.975
1298
174
18
1734
3028
478431271
478432537
0.000000e+00
1214
5
TraesCS4D01G288100
chr4D
85.490
1144
138
17
2019
3156
478291726
478292847
0.000000e+00
1168
6
TraesCS4D01G288100
chr4D
79.753
889
121
34
3153
4022
478281805
478282653
1.450000e-164
590
7
TraesCS4D01G288100
chr4D
80.294
817
120
25
3194
3989
478313185
478313981
3.130000e-161
579
8
TraesCS4D01G288100
chr4D
79.618
314
42
12
3392
3701
478314021
478314316
6.130000e-49
206
9
TraesCS4D01G288100
chr4A
94.949
3999
169
19
678
4670
9451914
9447943
0.000000e+00
6235
10
TraesCS4D01G288100
chr4A
94.863
292
13
2
1
290
9452810
9452519
5.510000e-124
455
11
TraesCS4D01G288100
chr4A
88.142
253
11
4
454
687
9452349
9452097
2.750000e-72
283
12
TraesCS4D01G288100
chr4A
94.413
179
8
1
308
486
9452528
9452352
1.660000e-69
274
13
TraesCS4D01G288100
chr4B
90.857
4222
307
47
505
4670
574063142
574067340
0.000000e+00
5585
14
TraesCS4D01G288100
chr4B
82.317
1640
247
29
1523
3156
605005211
605006813
0.000000e+00
1382
15
TraesCS4D01G288100
chr4B
85.251
1356
161
18
1813
3162
604905240
604906562
0.000000e+00
1360
16
TraesCS4D01G288100
chr4B
85.435
1023
117
19
2034
3048
604943707
604944705
0.000000e+00
1035
17
TraesCS4D01G288100
chr4B
84.805
691
101
2
1977
2667
604957872
604958558
0.000000e+00
691
18
TraesCS4D01G288100
chr4B
80.024
841
121
23
3200
4022
604906632
604907443
3.130000e-161
579
19
TraesCS4D01G288100
chr4B
83.974
468
69
4
2692
3156
604969163
604969627
1.190000e-120
444
20
TraesCS4D01G288100
chr4B
94.313
211
9
3
314
522
574060782
574060991
2.100000e-83
320
21
TraesCS4D01G288100
chr4B
90.400
125
9
2
1
122
574060542
574060666
1.340000e-35
161
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
TraesCS4D01G288100
chr4D
459318861
459323530
4669
False
8624.000000
8624
100.000000
1
4670
1
chr4D.!!$F1
4669
1
TraesCS4D01G288100
chr4D
478320071
478322166
2095
False
1655.000000
1655
81.075000
1031
3156
1
chr4D.!!$F3
2125
2
TraesCS4D01G288100
chr4D
478431271
478432537
1266
False
1214.000000
1214
83.975000
1734
3028
1
chr4D.!!$F4
1294
3
TraesCS4D01G288100
chr4D
478291726
478292847
1121
False
1168.000000
1168
85.490000
2019
3156
1
chr4D.!!$F2
1137
4
TraesCS4D01G288100
chr4D
478280152
478282653
2501
False
1083.000000
1576
82.004000
1507
4022
2
chr4D.!!$F5
2515
5
TraesCS4D01G288100
chr4D
478311014
478314316
3302
False
822.666667
1683
80.403000
1028
3989
3
chr4D.!!$F6
2961
6
TraesCS4D01G288100
chr4A
9447943
9452810
4867
True
1811.750000
6235
93.091750
1
4670
4
chr4A.!!$R1
4669
7
TraesCS4D01G288100
chr4B
574060542
574067340
6798
False
2022.000000
5585
91.856667
1
4670
3
chr4B.!!$F5
4669
8
TraesCS4D01G288100
chr4B
605005211
605006813
1602
False
1382.000000
1382
82.317000
1523
3156
1
chr4B.!!$F4
1633
9
TraesCS4D01G288100
chr4B
604943707
604944705
998
False
1035.000000
1035
85.435000
2034
3048
1
chr4B.!!$F1
1014
10
TraesCS4D01G288100
chr4B
604905240
604907443
2203
False
969.500000
1360
82.637500
1813
4022
2
chr4B.!!$F6
2209
11
TraesCS4D01G288100
chr4B
604957872
604958558
686
False
691.000000
691
84.805000
1977
2667
1
chr4B.!!$F2
690
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.