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
TraesCS2D01G406200
chr2D
100.000
3500
0
0
1
3500
521532439
521535938
0.000000e+00
6464
1
TraesCS2D01G406200
chr2A
91.949
1888
83
31
506
2388
666027037
666025214
0.000000e+00
2580
2
TraesCS2D01G406200
chr2A
96.843
887
23
3
2619
3500
777817420
777818306
0.000000e+00
1478
3
TraesCS2D01G406200
chr2A
83.908
435
41
16
1
428
666027455
666027043
4.240000e-104
388
4
TraesCS2D01G406200
chr2A
96.970
231
5
2
2389
2617
777817146
777817376
1.520000e-103
387
5
TraesCS2D01G406200
chr2B
91.025
1181
52
17
478
1640
614330617
614329473
0.000000e+00
1544
6
TraesCS2D01G406200
chr2B
90.855
1181
54
16
478
1640
614433989
614432845
0.000000e+00
1533
7
TraesCS2D01G406200
chr2B
96.272
751
28
0
1636
2386
614314512
614313762
0.000000e+00
1232
8
TraesCS2D01G406200
chr2B
95.739
751
32
0
1636
2386
614419583
614418833
0.000000e+00
1210
9
TraesCS2D01G406200
chr2B
89.252
214
11
5
1
206
614330996
614330787
1.250000e-64
257
10
TraesCS2D01G406200
chr2B
89.252
214
11
5
1
206
614434403
614434194
1.250000e-64
257
11
TraesCS2D01G406200
chrUn
90.885
1141
63
20
2386
3500
82683795
82682670
0.000000e+00
1493
12
TraesCS2D01G406200
chrUn
90.608
1086
61
20
2386
3445
390432673
390433743
0.000000e+00
1402
13
TraesCS2D01G406200
chrUn
90.608
1086
61
20
2386
3445
390434318
390435388
0.000000e+00
1402
14
TraesCS2D01G406200
chr7A
90.806
1142
63
21
2386
3500
95223372
95224498
0.000000e+00
1489
15
TraesCS2D01G406200
chr7A
90.674
1083
61
19
2443
3500
95230639
95231706
0.000000e+00
1404
16
TraesCS2D01G406200
chr7A
88.102
1059
124
2
1328
2385
198511298
198512355
0.000000e+00
1256
17
TraesCS2D01G406200
chr7B
86.496
1370
166
12
1016
2374
329516550
329515189
0.000000e+00
1487
18
TraesCS2D01G406200
chr7B
92.122
622
20
10
2390
2991
645246757
645246145
0.000000e+00
850
19
TraesCS2D01G406200
chr7B
95.192
520
17
4
2986
3500
645205081
645204565
0.000000e+00
815
20
TraesCS2D01G406200
chr7B
76.141
1052
213
26
1344
2385
557491304
557490281
5.180000e-143
518
21
TraesCS2D01G406200
chr7D
86.291
1386
164
13
1016
2383
186428460
186427083
0.000000e+00
1483
22
TraesCS2D01G406200
chr7D
76.660
964
185
28
1344
2296
523127854
523126920
6.750000e-137
497
23
TraesCS2D01G406200
chr7D
87.079
178
22
1
259
436
478362095
478362271
2.130000e-47
200
24
TraesCS2D01G406200
chr4A
93.576
934
34
17
2379
3289
35792358
35793288
0.000000e+00
1369
25
TraesCS2D01G406200
chr5D
92.889
900
36
20
2386
3276
417829911
417830791
0.000000e+00
1282
26
TraesCS2D01G406200
chr5D
94.650
243
9
2
3262
3500
417830806
417831048
1.190000e-99
374
27
TraesCS2D01G406200
chr6A
83.454
1384
190
30
1029
2385
496577643
496579014
0.000000e+00
1251
28
TraesCS2D01G406200
chr6B
82.893
1362
196
23
1029
2364
534235376
534236726
0.000000e+00
1190
29
TraesCS2D01G406200
chr6D
82.480
1387
204
25
1029
2388
346834309
346832935
0.000000e+00
1179
30
TraesCS2D01G406200
chr1A
92.602
784
38
8
2722
3500
568379031
568379799
0.000000e+00
1109
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
TraesCS2D01G406200
chr2D
521532439
521535938
3499
False
6464.0
6464
100.0000
1
3500
1
chr2D.!!$F1
3499
1
TraesCS2D01G406200
chr2A
666025214
666027455
2241
True
1484.0
2580
87.9285
1
2388
2
chr2A.!!$R1
2387
2
TraesCS2D01G406200
chr2A
777817146
777818306
1160
False
932.5
1478
96.9065
2389
3500
2
chr2A.!!$F1
1111
3
TraesCS2D01G406200
chr2B
614313762
614314512
750
True
1232.0
1232
96.2720
1636
2386
1
chr2B.!!$R1
750
4
TraesCS2D01G406200
chr2B
614418833
614419583
750
True
1210.0
1210
95.7390
1636
2386
1
chr2B.!!$R2
750
5
TraesCS2D01G406200
chr2B
614329473
614330996
1523
True
900.5
1544
90.1385
1
1640
2
chr2B.!!$R3
1639
6
TraesCS2D01G406200
chr2B
614432845
614434403
1558
True
895.0
1533
90.0535
1
1640
2
chr2B.!!$R4
1639
7
TraesCS2D01G406200
chrUn
82682670
82683795
1125
True
1493.0
1493
90.8850
2386
3500
1
chrUn.!!$R1
1114
8
TraesCS2D01G406200
chrUn
390432673
390435388
2715
False
1402.0
1402
90.6080
2386
3445
2
chrUn.!!$F1
1059
9
TraesCS2D01G406200
chr7A
95223372
95224498
1126
False
1489.0
1489
90.8060
2386
3500
1
chr7A.!!$F1
1114
10
TraesCS2D01G406200
chr7A
95230639
95231706
1067
False
1404.0
1404
90.6740
2443
3500
1
chr7A.!!$F2
1057
11
TraesCS2D01G406200
chr7A
198511298
198512355
1057
False
1256.0
1256
88.1020
1328
2385
1
chr7A.!!$F3
1057
12
TraesCS2D01G406200
chr7B
329515189
329516550
1361
True
1487.0
1487
86.4960
1016
2374
1
chr7B.!!$R1
1358
13
TraesCS2D01G406200
chr7B
645246145
645246757
612
True
850.0
850
92.1220
2390
2991
1
chr7B.!!$R4
601
14
TraesCS2D01G406200
chr7B
645204565
645205081
516
True
815.0
815
95.1920
2986
3500
1
chr7B.!!$R3
514
15
TraesCS2D01G406200
chr7B
557490281
557491304
1023
True
518.0
518
76.1410
1344
2385
1
chr7B.!!$R2
1041
16
TraesCS2D01G406200
chr7D
186427083
186428460
1377
True
1483.0
1483
86.2910
1016
2383
1
chr7D.!!$R1
1367
17
TraesCS2D01G406200
chr7D
523126920
523127854
934
True
497.0
497
76.6600
1344
2296
1
chr7D.!!$R2
952
18
TraesCS2D01G406200
chr4A
35792358
35793288
930
False
1369.0
1369
93.5760
2379
3289
1
chr4A.!!$F1
910
19
TraesCS2D01G406200
chr5D
417829911
417831048
1137
False
828.0
1282
93.7695
2386
3500
2
chr5D.!!$F1
1114
20
TraesCS2D01G406200
chr6A
496577643
496579014
1371
False
1251.0
1251
83.4540
1029
2385
1
chr6A.!!$F1
1356
21
TraesCS2D01G406200
chr6B
534235376
534236726
1350
False
1190.0
1190
82.8930
1029
2364
1
chr6B.!!$F1
1335
22
TraesCS2D01G406200
chr6D
346832935
346834309
1374
True
1179.0
1179
82.4800
1029
2388
1
chr6D.!!$R1
1359
23
TraesCS2D01G406200
chr1A
568379031
568379799
768
False
1109.0
1109
92.6020
2722
3500
1
chr1A.!!$F1
778
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.