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
TraesCS3B01G507400
chr3B
100.000
3364
0
0
1
3364
751016149
751012786
0.000000e+00
6213.0
1
TraesCS3B01G507400
chr3B
79.277
415
81
5
1892
2304
750901067
750900656
5.490000e-73
285.0
2
TraesCS3B01G507400
chr3B
80.418
383
44
14
902
1253
751842880
751843262
2.570000e-66
263.0
3
TraesCS3B01G507400
chr3B
89.894
188
17
2
1165
1351
751511284
751511098
1.210000e-59
241.0
4
TraesCS3B01G507400
chr3B
88.060
67
7
1
3239
3304
555153074
555153140
1.000000e-10
78.7
5
TraesCS3B01G507400
chr3D
95.308
2387
86
9
247
2616
563597083
563594706
0.000000e+00
3764.0
6
TraesCS3B01G507400
chr3D
95.706
815
30
3
2552
3364
563594705
563593894
0.000000e+00
1306.0
7
TraesCS3B01G507400
chr3D
81.643
1193
155
45
1778
2927
563446569
563445398
0.000000e+00
931.0
8
TraesCS3B01G507400
chr3D
87.832
452
44
10
913
1362
563447438
563446996
1.380000e-143
520.0
9
TraesCS3B01G507400
chr3D
89.865
296
30
0
1310
1605
563447000
563446705
6.810000e-102
381.0
10
TraesCS3B01G507400
chr3D
82.075
424
51
17
2929
3348
563445319
563444917
4.160000e-89
339.0
11
TraesCS3B01G507400
chr3D
80.128
468
65
15
2384
2845
563434511
563434066
1.160000e-84
324.0
12
TraesCS3B01G507400
chr3D
89.593
221
23
0
1133
1353
563435829
563435609
7.110000e-72
281.0
13
TraesCS3B01G507400
chr3D
91.626
203
16
1
1
203
563597286
563597085
2.560000e-71
279.0
14
TraesCS3B01G507400
chr3D
77.801
482
76
20
1081
1533
577028942
577029421
5.530000e-68
268.0
15
TraesCS3B01G507400
chr3D
87.050
139
17
1
2372
2509
563433856
563433718
4.490000e-34
156.0
16
TraesCS3B01G507400
chr3D
87.619
105
11
2
2372
2475
563432832
563432729
1.640000e-23
121.0
17
TraesCS3B01G507400
chr3A
92.660
2357
123
19
1
2338
698169896
698167571
0.000000e+00
3349.0
18
TraesCS3B01G507400
chr3A
94.600
1037
45
8
2334
3364
698167492
698166461
0.000000e+00
1594.0
19
TraesCS3B01G507400
chr3A
88.470
451
43
4
913
1362
698146645
698146203
1.370000e-148
536.0
20
TraesCS3B01G507400
chr3A
89.189
296
32
0
1310
1605
698146207
698145912
1.470000e-98
370.0
21
TraesCS3B01G507400
chr3A
92.019
213
17
0
1133
1345
698032330
698032118
1.960000e-77
300.0
22
TraesCS3B01G507400
chr3A
79.032
372
47
17
2374
2727
698030264
698029906
3.380000e-55
226.0
23
TraesCS3B01G507400
chr3A
83.803
142
18
3
2373
2509
698029859
698029718
2.720000e-26
130.0
24
TraesCS3B01G507400
chr3A
88.060
67
7
1
3239
3304
691599565
691599631
1.000000e-10
78.7
25
TraesCS3B01G507400
chr6B
81.648
267
37
8
1095
1351
704550539
704550275
9.460000e-51
211.0
26
TraesCS3B01G507400
chr6B
88.060
67
7
1
3239
3304
21122264
21122330
1.000000e-10
78.7
27
TraesCS3B01G507400
chr6A
72.938
388
79
14
1161
1532
115504994
115504617
9.870000e-21
111.0
28
TraesCS3B01G507400
chr7B
88.060
67
7
1
3239
3304
728283949
728284015
1.000000e-10
78.7
29
TraesCS3B01G507400
chr5B
88.060
67
7
1
3239
3304
37112946
37113012
1.000000e-10
78.7
30
TraesCS3B01G507400
chr2B
94.231
52
2
1
3254
3304
784304972
784304921
1.000000e-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
TraesCS3B01G507400
chr3B
751012786
751016149
3363
True
6213.000000
6213
100.000000
1
3364
1
chr3B.!!$R2
3363
1
TraesCS3B01G507400
chr3D
563593894
563597286
3392
True
1783.000000
3764
94.213333
1
3364
3
chr3D.!!$R3
3363
2
TraesCS3B01G507400
chr3D
563444917
563447438
2521
True
542.750000
931
85.353750
913
3348
4
chr3D.!!$R2
2435
3
TraesCS3B01G507400
chr3D
563432729
563435829
3100
True
220.500000
324
86.097500
1133
2845
4
chr3D.!!$R1
1712
4
TraesCS3B01G507400
chr3A
698166461
698169896
3435
True
2471.500000
3349
93.630000
1
3364
2
chr3A.!!$R3
3363
5
TraesCS3B01G507400
chr3A
698145912
698146645
733
True
453.000000
536
88.829500
913
1605
2
chr3A.!!$R2
692
6
TraesCS3B01G507400
chr3A
698029718
698032330
2612
True
218.666667
300
84.951333
1133
2727
3
chr3A.!!$R1
1594
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.