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
TraesCS7A01G390600
chr7A
100.000
3113
0
0
1
3113
566787490
566790602
0.000000e+00
5749
1
TraesCS7A01G390600
chr7A
88.281
1425
147
14
735
2144
603331689
603330270
0.000000e+00
1688
2
TraesCS7A01G390600
chr7A
78.545
536
43
39
2491
2993
566909830
566910326
1.410000e-73
287
3
TraesCS7A01G390600
chr7A
82.517
286
24
14
2187
2462
566988828
566989097
8.680000e-56
228
4
TraesCS7A01G390600
chr7A
81.496
254
19
12
2499
2737
566989086
566989326
1.910000e-42
183
5
TraesCS7A01G390600
chr7A
100.000
96
0
0
3010
3105
566989673
566989768
8.870000e-41
178
6
TraesCS7A01G390600
chr7A
96.970
99
0
1
3010
3105
566910398
566910496
2.480000e-36
163
7
TraesCS7A01G390600
chr7A
89.831
118
9
2
2237
2352
566909654
566909770
6.960000e-32
148
8
TraesCS7A01G390600
chr7B
91.193
2725
143
36
398
3074
73173848
73176523
0.000000e+00
3613
9
TraesCS7A01G390600
chr7B
93.735
2123
117
8
302
2416
528871190
528873304
0.000000e+00
3169
10
TraesCS7A01G390600
chr7B
87.850
1465
153
10
701
2144
557491665
557490205
0.000000e+00
1696
11
TraesCS7A01G390600
chr7B
87.026
1449
168
11
705
2140
557257487
557256046
0.000000e+00
1616
12
TraesCS7A01G390600
chr7B
85.915
1427
184
14
675
2094
557460718
557459302
0.000000e+00
1506
13
TraesCS7A01G390600
chr7B
85.000
560
34
21
2474
3010
528873308
528873840
9.890000e-145
523
14
TraesCS7A01G390600
chr7B
87.560
418
24
6
2
399
73173278
73173687
2.830000e-125
459
15
TraesCS7A01G390600
chr7B
88.235
221
17
6
7
220
528870940
528871158
3.980000e-64
255
16
TraesCS7A01G390600
chr7B
75.000
712
50
53
2493
3103
664399451
664398767
8.750000e-51
211
17
TraesCS7A01G390600
chr7D
93.428
2176
119
8
302
2471
500773301
500775458
0.000000e+00
3205
18
TraesCS7A01G390600
chr7D
93.451
1649
99
5
398
2043
113581187
113582829
0.000000e+00
2438
19
TraesCS7A01G390600
chr7D
88.746
1404
138
17
756
2144
523057027
523055629
0.000000e+00
1700
20
TraesCS7A01G390600
chr7D
87.509
1401
163
10
701
2094
523128208
523126813
0.000000e+00
1607
21
TraesCS7A01G390600
chr7D
90.459
566
27
8
2472
3010
500775617
500776182
0.000000e+00
721
22
TraesCS7A01G390600
chr7D
85.948
427
23
10
2
399
113580513
113580931
3.710000e-114
422
23
TraesCS7A01G390600
chr7D
92.784
291
12
2
2809
3096
113582861
113583145
2.230000e-111
412
24
TraesCS7A01G390600
chr7D
88.841
233
17
6
7
232
500773047
500773277
8.500000e-71
278
25
TraesCS7A01G390600
chr7D
93.458
107
4
1
3010
3113
500776216
500776322
4.160000e-34
156
26
TraesCS7A01G390600
chr3D
88.477
972
71
14
485
1434
603682150
603683102
0.000000e+00
1136
27
TraesCS7A01G390600
chr3D
86.344
227
22
4
2187
2405
598726927
598726702
4.010000e-59
239
28
TraesCS7A01G390600
chr3D
80.233
258
19
14
2499
2737
598726670
598726426
6.910000e-37
165
29
TraesCS7A01G390600
chrUn
84.645
521
31
20
2491
2988
86611602
86612096
1.010000e-129
473
30
TraesCS7A01G390600
chrUn
93.333
90
3
1
3010
3096
86612154
86612243
2.520000e-26
130
31
TraesCS7A01G390600
chrUn
89.216
102
6
2
2187
2288
86611297
86611393
4.220000e-24
122
32
TraesCS7A01G390600
chr3A
77.823
487
53
35
2539
2994
732405069
732404607
1.850000e-62
250
33
TraesCS7A01G390600
chr3B
86.784
227
21
4
2187
2405
806016605
806016380
8.620000e-61
244
34
TraesCS7A01G390600
chr3B
77.640
483
44
40
2539
2994
810195314
810194869
5.190000e-58
235
35
TraesCS7A01G390600
chr3B
88.119
202
17
5
2187
2384
805979808
805979610
1.870000e-57
233
36
TraesCS7A01G390600
chr3B
87.222
180
18
3
2248
2422
805812637
805812458
1.890000e-47
200
37
TraesCS7A01G390600
chr3B
80.952
252
21
12
2499
2736
805977934
805977696
1.150000e-39
174
38
TraesCS7A01G390600
chr3B
80.237
253
23
12
2499
2737
805812446
805812207
6.910000e-37
165
39
TraesCS7A01G390600
chr3B
82.069
145
6
2
2313
2457
810195482
810195358
4.250000e-19
106
40
TraesCS7A01G390600
chr5A
92.000
100
5
1
3017
3113
605245730
605245631
1.510000e-28
137
41
TraesCS7A01G390600
chr5B
90.909
99
6
1
3018
3113
595010251
595010153
2.520000e-26
130
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
TraesCS7A01G390600
chr7A
566787490
566790602
3112
False
5749.000000
5749
100.000000
1
3113
1
chr7A.!!$F1
3112
1
TraesCS7A01G390600
chr7A
603330270
603331689
1419
True
1688.000000
1688
88.281000
735
2144
1
chr7A.!!$R1
1409
2
TraesCS7A01G390600
chr7B
73173278
73176523
3245
False
2036.000000
3613
89.376500
2
3074
2
chr7B.!!$F1
3072
3
TraesCS7A01G390600
chr7B
557490205
557491665
1460
True
1696.000000
1696
87.850000
701
2144
1
chr7B.!!$R3
1443
4
TraesCS7A01G390600
chr7B
557256046
557257487
1441
True
1616.000000
1616
87.026000
705
2140
1
chr7B.!!$R1
1435
5
TraesCS7A01G390600
chr7B
557459302
557460718
1416
True
1506.000000
1506
85.915000
675
2094
1
chr7B.!!$R2
1419
6
TraesCS7A01G390600
chr7B
528870940
528873840
2900
False
1315.666667
3169
88.990000
7
3010
3
chr7B.!!$F2
3003
7
TraesCS7A01G390600
chr7B
664398767
664399451
684
True
211.000000
211
75.000000
2493
3103
1
chr7B.!!$R4
610
8
TraesCS7A01G390600
chr7D
523055629
523057027
1398
True
1700.000000
1700
88.746000
756
2144
1
chr7D.!!$R1
1388
9
TraesCS7A01G390600
chr7D
523126813
523128208
1395
True
1607.000000
1607
87.509000
701
2094
1
chr7D.!!$R2
1393
10
TraesCS7A01G390600
chr7D
113580513
113583145
2632
False
1090.666667
2438
90.727667
2
3096
3
chr7D.!!$F1
3094
11
TraesCS7A01G390600
chr7D
500773047
500776322
3275
False
1090.000000
3205
91.546500
7
3113
4
chr7D.!!$F2
3106
12
TraesCS7A01G390600
chr3D
603682150
603683102
952
False
1136.000000
1136
88.477000
485
1434
1
chr3D.!!$F1
949
13
TraesCS7A01G390600
chr3D
598726426
598726927
501
True
202.000000
239
83.288500
2187
2737
2
chr3D.!!$R1
550
14
TraesCS7A01G390600
chrUn
86611297
86612243
946
False
241.666667
473
89.064667
2187
3096
3
chrUn.!!$F1
909
15
TraesCS7A01G390600
chr3B
805977696
805979808
2112
True
203.500000
233
84.535500
2187
2736
2
chr3B.!!$R3
549
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.