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
TraesCS5A01G329800
chr5A
100.000
2913
0
0
1
2913
539077772
539074860
0.000000e+00
5380
1
TraesCS5A01G329800
chr5A
92.398
1618
88
12
304
1903
139476653
139475053
0.000000e+00
2274
2
TraesCS5A01G329800
chr5A
93.271
431
25
4
2007
2434
139472297
139471868
1.470000e-177
632
3
TraesCS5A01G329800
chr2A
98.028
2434
45
3
1
2434
605005105
605002675
0.000000e+00
4226
4
TraesCS5A01G329800
chr2A
97.593
457
9
2
2429
2884
605002600
605002145
0.000000e+00
782
5
TraesCS5A01G329800
chr2A
92.098
367
25
4
2526
2890
364416100
364416464
5.570000e-142
514
6
TraesCS5A01G329800
chr6D
97.336
2140
43
6
304
2434
433251086
433253220
0.000000e+00
3624
7
TraesCS5A01G329800
chr6D
97.152
2142
46
7
304
2434
32038880
32036743
0.000000e+00
3603
8
TraesCS5A01G329800
chr6D
97.064
1158
24
3
304
1452
420713556
420714712
0.000000e+00
1941
9
TraesCS5A01G329800
chr6D
96.663
869
25
4
1511
2376
420714702
420715569
0.000000e+00
1441
10
TraesCS5A01G329800
chr6D
95.614
456
19
1
2429
2884
433253295
433253749
0.000000e+00
730
11
TraesCS5A01G329800
chr6D
95.561
428
18
1
2429
2856
32036668
32036242
0.000000e+00
684
12
TraesCS5A01G329800
chr2B
96.684
2141
52
9
304
2434
616459530
616461661
0.000000e+00
3542
13
TraesCS5A01G329800
chr2B
93.407
455
29
1
2429
2883
616461736
616462189
0.000000e+00
673
14
TraesCS5A01G329800
chr2B
96.333
300
10
1
1
300
616458179
616458477
2.610000e-135
492
15
TraesCS5A01G329800
chr2D
92.645
1618
83
13
304
1903
644817950
644819549
0.000000e+00
2296
16
TraesCS5A01G329800
chr2D
93.287
432
24
5
2007
2434
644822341
644822771
1.470000e-177
632
17
TraesCS5A01G329800
chr2D
93.151
365
23
2
2521
2883
644823076
644823440
4.270000e-148
534
18
TraesCS5A01G329800
chr2D
93.266
297
18
2
4
298
60006708
60007004
1.240000e-118
436
19
TraesCS5A01G329800
chr4D
92.460
1618
86
13
304
1903
403009182
403010781
0.000000e+00
2279
20
TraesCS5A01G329800
chr7D
92.331
1617
88
13
304
1903
29571537
29569940
0.000000e+00
2266
21
TraesCS5A01G329800
chr7D
93.533
433
22
5
2007
2434
29567148
29566717
8.800000e-180
640
22
TraesCS5A01G329800
chr7D
92.877
365
25
1
2521
2884
29566412
29566048
1.990000e-146
529
23
TraesCS5A01G329800
chr1D
91.899
1617
95
13
304
1903
187808656
187810253
0.000000e+00
2228
24
TraesCS5A01G329800
chr1D
93.056
432
25
5
2007
2434
187813044
187813474
6.850000e-176
627
25
TraesCS5A01G329800
chr1D
92.857
364
25
1
2521
2883
187813779
187814142
7.150000e-146
527
26
TraesCS5A01G329800
chr6A
92.580
1186
65
8
304
1473
615073658
615072480
0.000000e+00
1681
27
TraesCS5A01G329800
chr1A
84.527
1312
160
28
724
2024
50508945
50510224
0.000000e+00
1258
28
TraesCS5A01G329800
chr5B
92.500
360
26
1
2526
2884
691750779
691750420
5.570000e-142
514
29
TraesCS5A01G329800
chr5B
94.352
301
15
2
1
300
545167413
545167712
7.360000e-126
460
30
TraesCS5A01G329800
chr1B
84.502
271
30
8
24
291
121208790
121209051
1.040000e-64
257
31
TraesCS5A01G329800
chr4B
84.133
271
31
8
24
291
483740151
483740412
4.820000e-63
252
32
TraesCS5A01G329800
chr7B
83.142
261
37
5
24
282
559151409
559151154
6.280000e-57
231
33
TraesCS5A01G329800
chr7A
95.146
103
5
0
1
103
322623251
322623149
2.320000e-36
163
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
TraesCS5A01G329800
chr5A
539074860
539077772
2912
True
5380.000000
5380
100.000000
1
2913
1
chr5A.!!$R1
2912
1
TraesCS5A01G329800
chr5A
139471868
139476653
4785
True
1453.000000
2274
92.834500
304
2434
2
chr5A.!!$R2
2130
2
TraesCS5A01G329800
chr2A
605002145
605005105
2960
True
2504.000000
4226
97.810500
1
2884
2
chr2A.!!$R1
2883
3
TraesCS5A01G329800
chr6D
433251086
433253749
2663
False
2177.000000
3624
96.475000
304
2884
2
chr6D.!!$F2
2580
4
TraesCS5A01G329800
chr6D
32036242
32038880
2638
True
2143.500000
3603
96.356500
304
2856
2
chr6D.!!$R1
2552
5
TraesCS5A01G329800
chr6D
420713556
420715569
2013
False
1691.000000
1941
96.863500
304
2376
2
chr6D.!!$F1
2072
6
TraesCS5A01G329800
chr2B
616458179
616462189
4010
False
1569.000000
3542
95.474667
1
2883
3
chr2B.!!$F1
2882
7
TraesCS5A01G329800
chr2D
644817950
644823440
5490
False
1154.000000
2296
93.027667
304
2883
3
chr2D.!!$F2
2579
8
TraesCS5A01G329800
chr4D
403009182
403010781
1599
False
2279.000000
2279
92.460000
304
1903
1
chr4D.!!$F1
1599
9
TraesCS5A01G329800
chr7D
29566048
29571537
5489
True
1145.000000
2266
92.913667
304
2884
3
chr7D.!!$R1
2580
10
TraesCS5A01G329800
chr1D
187808656
187814142
5486
False
1127.333333
2228
92.604000
304
2883
3
chr1D.!!$F1
2579
11
TraesCS5A01G329800
chr6A
615072480
615073658
1178
True
1681.000000
1681
92.580000
304
1473
1
chr6A.!!$R1
1169
12
TraesCS5A01G329800
chr1A
50508945
50510224
1279
False
1258.000000
1258
84.527000
724
2024
1
chr1A.!!$F1
1300
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.