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
TraesCS7D01G380100
chr7D
100.000
5089
0
0
1
5089
492223607
492218519
0.000000e+00
9398.0
1
TraesCS7D01G380100
chr7D
79.915
234
42
5
237
467
607124464
607124233
3.150000e-37
167.0
2
TraesCS7D01G380100
chr7B
94.410
4562
155
31
577
5089
521619002
521614492
0.000000e+00
6920.0
3
TraesCS7D01G380100
chr7B
89.189
555
51
7
1
550
521667475
521666925
0.000000e+00
684.0
4
TraesCS7D01G380100
chr7B
93.182
44
2
1
140
183
7040453
7040495
4.250000e-06
63.9
5
TraesCS7D01G380100
chr7A
94.827
3847
122
24
535
4356
558758127
558754333
0.000000e+00
5930.0
6
TraesCS7D01G380100
chr7A
92.553
658
33
7
4446
5089
558754318
558753663
0.000000e+00
929.0
7
TraesCS7D01G380100
chr7A
86.174
311
40
3
186
495
558758945
558758637
2.940000e-87
333.0
8
TraesCS7D01G380100
chr7A
91.509
106
8
1
1
105
558759584
558759479
1.480000e-30
145.0
9
TraesCS7D01G380100
chr7A
91.935
62
5
0
4362
4423
87692491
87692430
2.520000e-13
87.9
10
TraesCS7D01G380100
chr4D
82.792
523
81
8
2433
2949
70119277
70119796
4.640000e-125
459.0
11
TraesCS7D01G380100
chr4D
82.990
194
31
2
3606
3798
70120253
70120445
1.880000e-39
174.0
12
TraesCS7D01G380100
chr4D
84.173
139
21
1
242
379
39236161
39236299
3.200000e-27
134.0
13
TraesCS7D01G380100
chr4D
78.010
191
39
3
266
454
341921538
341921727
3.220000e-22
117.0
14
TraesCS7D01G380100
chr4A
82.792
523
81
8
2433
2949
522294309
522294828
4.640000e-125
459.0
15
TraesCS7D01G380100
chr4A
82.990
194
31
2
3606
3798
522295285
522295477
1.880000e-39
174.0
16
TraesCS7D01G380100
chr4A
81.739
115
9
4
4317
4429
37060208
37060104
9.080000e-13
86.1
17
TraesCS7D01G380100
chr4B
84.058
483
68
8
2473
2949
103773177
103773656
1.670000e-124
457.0
18
TraesCS7D01G380100
chr4B
83.511
188
29
2
3606
3792
103774113
103774299
1.880000e-39
174.0
19
TraesCS7D01G380100
chr1D
96.491
228
8
0
1257
1484
42038588
42038815
1.340000e-100
377.0
20
TraesCS7D01G380100
chr1D
94.690
113
4
2
1096
1207
42038495
42038606
1.880000e-39
174.0
21
TraesCS7D01G380100
chr1D
96.739
92
3
0
1597
1688
42038810
42038901
2.450000e-33
154.0
22
TraesCS7D01G380100
chr1D
76.652
227
48
4
242
466
447549387
447549164
2.490000e-23
121.0
23
TraesCS7D01G380100
chr2D
95.175
228
11
0
1257
1484
28963979
28964206
1.350000e-95
361.0
24
TraesCS7D01G380100
chr2D
94.690
113
4
2
1096
1207
28963886
28963997
1.880000e-39
174.0
25
TraesCS7D01G380100
chr2D
94.565
92
5
0
1597
1688
28964201
28964292
5.310000e-30
143.0
26
TraesCS7D01G380100
chr2D
85.047
107
7
1
4318
4424
2476585
2476682
3.240000e-17
100.0
27
TraesCS7D01G380100
chr2D
91.176
68
4
2
4362
4427
290739008
290738941
1.950000e-14
91.6
28
TraesCS7D01G380100
chr5D
79.206
529
100
6
2433
2953
197152404
197151878
4.840000e-95
359.0
29
TraesCS7D01G380100
chr5A
79.800
500
93
5
2433
2925
227923754
227924252
1.740000e-94
357.0
30
TraesCS7D01G380100
chr3A
94.298
228
13
0
1257
1484
13265216
13264989
2.920000e-92
350.0
31
TraesCS7D01G380100
chr3A
80.335
239
42
4
237
472
60660788
60660552
5.240000e-40
176.0
32
TraesCS7D01G380100
chr3A
93.805
113
5
2
1096
1207
13265309
13265198
8.760000e-38
169.0
33
TraesCS7D01G380100
chr3A
88.000
100
6
3
1598
1691
13264993
13264894
4.160000e-21
113.0
34
TraesCS7D01G380100
chr3A
77.465
142
29
3
316
455
223202247
223202107
1.170000e-11
82.4
35
TraesCS7D01G380100
chr3A
95.833
48
2
0
1724
1771
13264840
13264887
1.520000e-10
78.7
36
TraesCS7D01G380100
chr5B
79.125
503
91
9
2433
2925
213250429
213250927
8.160000e-88
335.0
37
TraesCS7D01G380100
chr5B
77.778
216
46
2
241
455
536039842
536040056
1.150000e-26
132.0
38
TraesCS7D01G380100
chr2A
85.075
134
20
0
322
455
621852031
621851898
2.470000e-28
137.0
39
TraesCS7D01G380100
chr2A
92.308
65
3
2
4362
4424
315038017
315038081
1.950000e-14
91.6
40
TraesCS7D01G380100
chr2A
90.769
65
4
2
4362
4424
724414395
724414331
9.080000e-13
86.1
41
TraesCS7D01G380100
chrUn
85.047
107
7
1
4318
4424
15904017
15903920
3.240000e-17
100.0
42
TraesCS7D01G380100
chrUn
93.750
48
2
1
142
189
48220079
48220033
2.540000e-08
71.3
43
TraesCS7D01G380100
chrUn
93.750
48
2
1
142
189
378206971
378207017
2.540000e-08
71.3
44
TraesCS7D01G380100
chrUn
93.750
48
2
1
142
189
431966294
431966340
2.540000e-08
71.3
45
TraesCS7D01G380100
chr1A
83.636
110
6
8
4314
4423
460934573
460934476
5.430000e-15
93.5
46
TraesCS7D01G380100
chr2B
94.118
51
3
0
237
287
711709199
711709249
1.520000e-10
78.7
47
TraesCS7D01G380100
chr2B
94.118
51
3
0
237
287
711715271
711715321
1.520000e-10
78.7
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
TraesCS7D01G380100
chr7D
492218519
492223607
5088
True
9398.00
9398
100.00000
1
5089
1
chr7D.!!$R1
5088
1
TraesCS7D01G380100
chr7B
521614492
521619002
4510
True
6920.00
6920
94.41000
577
5089
1
chr7B.!!$R1
4512
2
TraesCS7D01G380100
chr7B
521666925
521667475
550
True
684.00
684
89.18900
1
550
1
chr7B.!!$R2
549
3
TraesCS7D01G380100
chr7A
558753663
558759584
5921
True
1834.25
5930
91.26575
1
5089
4
chr7A.!!$R2
5088
4
TraesCS7D01G380100
chr4D
70119277
70120445
1168
False
316.50
459
82.89100
2433
3798
2
chr4D.!!$F3
1365
5
TraesCS7D01G380100
chr4A
522294309
522295477
1168
False
316.50
459
82.89100
2433
3798
2
chr4A.!!$F1
1365
6
TraesCS7D01G380100
chr4B
103773177
103774299
1122
False
315.50
457
83.78450
2473
3792
2
chr4B.!!$F1
1319
7
TraesCS7D01G380100
chr5D
197151878
197152404
526
True
359.00
359
79.20600
2433
2953
1
chr5D.!!$R1
520
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.