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
TraesCS3B01G552500
chr3B
100.000
2375
0
0
1
2375
787153342
787155716
0.000000e+00
4386
1
TraesCS3B01G552500
chr3B
89.834
2410
121
53
3
2353
228481181
228478837
0.000000e+00
2979
2
TraesCS3B01G552500
chr3B
92.116
1243
62
14
3
1209
142227112
142228354
0.000000e+00
1720
3
TraesCS3B01G552500
chr3B
87.915
753
43
9
1
738
557721172
557721891
0.000000e+00
843
4
TraesCS3B01G552500
chr3B
87.733
750
44
11
3
737
751890851
751890135
0.000000e+00
832
5
TraesCS3B01G552500
chr7B
90.959
2389
140
21
3
2353
719311841
719309491
0.000000e+00
3145
6
TraesCS3B01G552500
chr7B
91.398
1674
83
24
705
2354
611048023
611046387
0.000000e+00
2237
7
TraesCS3B01G552500
chr7B
92.426
1426
71
8
1
1404
122469482
122470892
0.000000e+00
2001
8
TraesCS3B01G552500
chr7B
91.734
1355
60
21
3
1319
452428141
452429481
0.000000e+00
1834
9
TraesCS3B01G552500
chr7B
89.894
1415
65
21
3
1395
692776112
692777470
0.000000e+00
1749
10
TraesCS3B01G552500
chr7B
94.295
894
28
8
705
1575
610755081
610754188
0.000000e+00
1347
11
TraesCS3B01G552500
chr7B
86.111
72
6
3
1449
1520
655319740
655319673
9.100000e-10
75
12
TraesCS3B01G552500
chr6B
90.642
2383
138
38
3
2351
208208899
208211230
0.000000e+00
3086
13
TraesCS3B01G552500
chr6B
92.933
1415
66
11
3
1384
674459819
674461232
0.000000e+00
2028
14
TraesCS3B01G552500
chr6B
92.666
1418
68
17
1
1384
152499875
152501290
0.000000e+00
2010
15
TraesCS3B01G552500
chr6B
92.308
1404
78
14
3
1384
663072534
663073929
0.000000e+00
1967
16
TraesCS3B01G552500
chr4B
89.888
2413
118
34
3
2358
647871594
647869251
0.000000e+00
2988
17
TraesCS3B01G552500
chr4B
89.780
1634
94
37
747
2351
613137502
613139091
0.000000e+00
2025
18
TraesCS3B01G552500
chr4B
92.244
1444
76
11
3
1424
15088514
15087085
0.000000e+00
2013
19
TraesCS3B01G552500
chr4B
91.789
1425
79
11
3
1404
6840361
6841770
0.000000e+00
1949
20
TraesCS3B01G552500
chr4B
91.496
635
32
11
771
1383
366559669
366559035
0.000000e+00
854
21
TraesCS3B01G552500
chr5B
93.329
1424
71
9
3
1404
345189442
345188021
0.000000e+00
2082
22
TraesCS3B01G552500
chr5B
92.281
1438
76
15
1
1404
638199732
638198296
0.000000e+00
2008
23
TraesCS3B01G552500
chr2B
93.101
1435
66
9
3
1404
739863648
739862214
0.000000e+00
2071
24
TraesCS3B01G552500
chr2B
92.867
1444
74
9
3
1424
103758505
103757069
0.000000e+00
2069
25
TraesCS3B01G552500
chr2B
92.519
802
53
5
1555
2351
750617896
750618695
0.000000e+00
1142
26
TraesCS3B01G552500
chr6A
92.757
1422
59
21
3
1387
11912216
11910802
0.000000e+00
2015
27
TraesCS3B01G552500
chr6A
90.157
1402
95
15
958
2351
436399600
436400966
0.000000e+00
1784
28
TraesCS3B01G552500
chr6A
90.148
1147
62
33
1210
2351
136675188
136676288
0.000000e+00
1445
29
TraesCS3B01G552500
chr3A
92.546
1422
69
12
3
1387
153244976
153243555
0.000000e+00
2004
30
TraesCS3B01G552500
chr3A
92.689
848
38
12
3
826
233466931
233466084
0.000000e+00
1201
31
TraesCS3B01G552500
chr1B
92.313
1418
72
17
3
1383
600337947
600336530
0.000000e+00
1980
32
TraesCS3B01G552500
chr1B
86.077
1616
139
39
771
2351
63662501
63664065
0.000000e+00
1659
33
TraesCS3B01G552500
chr1B
85.588
1249
89
44
771
1970
447998914
448000120
0.000000e+00
1225
34
TraesCS3B01G552500
chr1B
91.943
633
30
12
771
1383
6182272
6182903
0.000000e+00
867
35
TraesCS3B01G552500
chr1B
83.879
825
62
40
771
1564
627365095
627364311
0.000000e+00
721
36
TraesCS3B01G552500
chrUn
89.129
1619
114
41
771
2351
236932330
236933924
0.000000e+00
1958
37
TraesCS3B01G552500
chrUn
92.283
635
27
11
771
1383
34511865
34512499
0.000000e+00
881
38
TraesCS3B01G552500
chrUn
92.283
635
27
11
771
1383
301822107
301821473
0.000000e+00
881
39
TraesCS3B01G552500
chrUn
92.283
635
27
11
771
1383
315136932
315136298
0.000000e+00
881
40
TraesCS3B01G552500
chrUn
92.283
635
27
11
771
1383
322611231
322611865
0.000000e+00
881
41
TraesCS3B01G552500
chrUn
92.283
635
27
11
771
1383
338929953
338930587
0.000000e+00
881
42
TraesCS3B01G552500
chrUn
91.943
633
29
13
771
1383
294406491
294405861
0.000000e+00
867
43
TraesCS3B01G552500
chrUn
91.737
472
18
12
771
1222
291783865
291784335
9.260000e-179
636
44
TraesCS3B01G552500
chrUn
91.525
472
19
12
771
1222
281296110
281295640
4.310000e-177
630
45
TraesCS3B01G552500
chr4A
91.295
1436
69
24
3
1387
404403602
404402172
0.000000e+00
1908
46
TraesCS3B01G552500
chr4A
90.650
1401
79
33
958
2351
525153233
525151878
0.000000e+00
1814
47
TraesCS3B01G552500
chr4A
92.341
927
52
14
1429
2351
29672779
29671868
0.000000e+00
1301
48
TraesCS3B01G552500
chr4A
86.111
72
6
3
1449
1520
677749154
677749087
9.100000e-10
75
49
TraesCS3B01G552500
chr5A
90.371
1402
92
16
958
2351
345652582
345651216
0.000000e+00
1801
50
TraesCS3B01G552500
chr7A
90.235
1403
93
14
958
2351
578423386
578422019
0.000000e+00
1792
51
TraesCS3B01G552500
chr7A
89.808
1403
101
15
958
2351
639852151
639850782
0.000000e+00
1760
52
TraesCS3B01G552500
chr7A
87.362
815
64
16
958
1771
734443662
734444438
0.000000e+00
898
53
TraesCS3B01G552500
chr2A
90.178
1405
92
18
958
2353
599671328
599669961
0.000000e+00
1788
54
TraesCS3B01G552500
chr2A
90.007
1411
96
17
958
2357
55068692
55067316
0.000000e+00
1783
55
TraesCS3B01G552500
chr2A
90.071
1400
87
31
958
2351
340609033
340607680
0.000000e+00
1768
56
TraesCS3B01G552500
chr2A
89.530
1213
63
26
1149
2351
538620864
538619706
0.000000e+00
1478
57
TraesCS3B01G552500
chr2A
91.262
927
54
18
1429
2351
605787710
605788613
0.000000e+00
1238
58
TraesCS3B01G552500
chr2A
91.573
534
30
1
3
521
538629455
538628922
0.000000e+00
723
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
TraesCS3B01G552500
chr3B
787153342
787155716
2374
False
4386
4386
100.000
1
2375
1
chr3B.!!$F3
2374
1
TraesCS3B01G552500
chr3B
228478837
228481181
2344
True
2979
2979
89.834
3
2353
1
chr3B.!!$R1
2350
2
TraesCS3B01G552500
chr3B
142227112
142228354
1242
False
1720
1720
92.116
3
1209
1
chr3B.!!$F1
1206
3
TraesCS3B01G552500
chr3B
557721172
557721891
719
False
843
843
87.915
1
738
1
chr3B.!!$F2
737
4
TraesCS3B01G552500
chr3B
751890135
751890851
716
True
832
832
87.733
3
737
1
chr3B.!!$R2
734
5
TraesCS3B01G552500
chr7B
719309491
719311841
2350
True
3145
3145
90.959
3
2353
1
chr7B.!!$R4
2350
6
TraesCS3B01G552500
chr7B
611046387
611048023
1636
True
2237
2237
91.398
705
2354
1
chr7B.!!$R2
1649
7
TraesCS3B01G552500
chr7B
122469482
122470892
1410
False
2001
2001
92.426
1
1404
1
chr7B.!!$F1
1403
8
TraesCS3B01G552500
chr7B
452428141
452429481
1340
False
1834
1834
91.734
3
1319
1
chr7B.!!$F2
1316
9
TraesCS3B01G552500
chr7B
692776112
692777470
1358
False
1749
1749
89.894
3
1395
1
chr7B.!!$F3
1392
10
TraesCS3B01G552500
chr7B
610754188
610755081
893
True
1347
1347
94.295
705
1575
1
chr7B.!!$R1
870
11
TraesCS3B01G552500
chr6B
208208899
208211230
2331
False
3086
3086
90.642
3
2351
1
chr6B.!!$F2
2348
12
TraesCS3B01G552500
chr6B
674459819
674461232
1413
False
2028
2028
92.933
3
1384
1
chr6B.!!$F4
1381
13
TraesCS3B01G552500
chr6B
152499875
152501290
1415
False
2010
2010
92.666
1
1384
1
chr6B.!!$F1
1383
14
TraesCS3B01G552500
chr6B
663072534
663073929
1395
False
1967
1967
92.308
3
1384
1
chr6B.!!$F3
1381
15
TraesCS3B01G552500
chr4B
647869251
647871594
2343
True
2988
2988
89.888
3
2358
1
chr4B.!!$R3
2355
16
TraesCS3B01G552500
chr4B
613137502
613139091
1589
False
2025
2025
89.780
747
2351
1
chr4B.!!$F2
1604
17
TraesCS3B01G552500
chr4B
15087085
15088514
1429
True
2013
2013
92.244
3
1424
1
chr4B.!!$R1
1421
18
TraesCS3B01G552500
chr4B
6840361
6841770
1409
False
1949
1949
91.789
3
1404
1
chr4B.!!$F1
1401
19
TraesCS3B01G552500
chr4B
366559035
366559669
634
True
854
854
91.496
771
1383
1
chr4B.!!$R2
612
20
TraesCS3B01G552500
chr5B
345188021
345189442
1421
True
2082
2082
93.329
3
1404
1
chr5B.!!$R1
1401
21
TraesCS3B01G552500
chr5B
638198296
638199732
1436
True
2008
2008
92.281
1
1404
1
chr5B.!!$R2
1403
22
TraesCS3B01G552500
chr2B
739862214
739863648
1434
True
2071
2071
93.101
3
1404
1
chr2B.!!$R2
1401
23
TraesCS3B01G552500
chr2B
103757069
103758505
1436
True
2069
2069
92.867
3
1424
1
chr2B.!!$R1
1421
24
TraesCS3B01G552500
chr2B
750617896
750618695
799
False
1142
1142
92.519
1555
2351
1
chr2B.!!$F1
796
25
TraesCS3B01G552500
chr6A
11910802
11912216
1414
True
2015
2015
92.757
3
1387
1
chr6A.!!$R1
1384
26
TraesCS3B01G552500
chr6A
436399600
436400966
1366
False
1784
1784
90.157
958
2351
1
chr6A.!!$F2
1393
27
TraesCS3B01G552500
chr6A
136675188
136676288
1100
False
1445
1445
90.148
1210
2351
1
chr6A.!!$F1
1141
28
TraesCS3B01G552500
chr3A
153243555
153244976
1421
True
2004
2004
92.546
3
1387
1
chr3A.!!$R1
1384
29
TraesCS3B01G552500
chr3A
233466084
233466931
847
True
1201
1201
92.689
3
826
1
chr3A.!!$R2
823
30
TraesCS3B01G552500
chr1B
600336530
600337947
1417
True
1980
1980
92.313
3
1383
1
chr1B.!!$R1
1380
31
TraesCS3B01G552500
chr1B
63662501
63664065
1564
False
1659
1659
86.077
771
2351
1
chr1B.!!$F2
1580
32
TraesCS3B01G552500
chr1B
447998914
448000120
1206
False
1225
1225
85.588
771
1970
1
chr1B.!!$F3
1199
33
TraesCS3B01G552500
chr1B
6182272
6182903
631
False
867
867
91.943
771
1383
1
chr1B.!!$F1
612
34
TraesCS3B01G552500
chr1B
627364311
627365095
784
True
721
721
83.879
771
1564
1
chr1B.!!$R2
793
35
TraesCS3B01G552500
chrUn
236932330
236933924
1594
False
1958
1958
89.129
771
2351
1
chrUn.!!$F2
1580
36
TraesCS3B01G552500
chrUn
34511865
34512499
634
False
881
881
92.283
771
1383
1
chrUn.!!$F1
612
37
TraesCS3B01G552500
chrUn
301821473
301822107
634
True
881
881
92.283
771
1383
1
chrUn.!!$R3
612
38
TraesCS3B01G552500
chrUn
315136298
315136932
634
True
881
881
92.283
771
1383
1
chrUn.!!$R4
612
39
TraesCS3B01G552500
chrUn
322611231
322611865
634
False
881
881
92.283
771
1383
1
chrUn.!!$F4
612
40
TraesCS3B01G552500
chrUn
338929953
338930587
634
False
881
881
92.283
771
1383
1
chrUn.!!$F5
612
41
TraesCS3B01G552500
chrUn
294405861
294406491
630
True
867
867
91.943
771
1383
1
chrUn.!!$R2
612
42
TraesCS3B01G552500
chr4A
404402172
404403602
1430
True
1908
1908
91.295
3
1387
1
chr4A.!!$R2
1384
43
TraesCS3B01G552500
chr4A
525151878
525153233
1355
True
1814
1814
90.650
958
2351
1
chr4A.!!$R3
1393
44
TraesCS3B01G552500
chr4A
29671868
29672779
911
True
1301
1301
92.341
1429
2351
1
chr4A.!!$R1
922
45
TraesCS3B01G552500
chr5A
345651216
345652582
1366
True
1801
1801
90.371
958
2351
1
chr5A.!!$R1
1393
46
TraesCS3B01G552500
chr7A
578422019
578423386
1367
True
1792
1792
90.235
958
2351
1
chr7A.!!$R1
1393
47
TraesCS3B01G552500
chr7A
639850782
639852151
1369
True
1760
1760
89.808
958
2351
1
chr7A.!!$R2
1393
48
TraesCS3B01G552500
chr7A
734443662
734444438
776
False
898
898
87.362
958
1771
1
chr7A.!!$F1
813
49
TraesCS3B01G552500
chr2A
599669961
599671328
1367
True
1788
1788
90.178
958
2353
1
chr2A.!!$R5
1395
50
TraesCS3B01G552500
chr2A
55067316
55068692
1376
True
1783
1783
90.007
958
2357
1
chr2A.!!$R1
1399
51
TraesCS3B01G552500
chr2A
340607680
340609033
1353
True
1768
1768
90.071
958
2351
1
chr2A.!!$R2
1393
52
TraesCS3B01G552500
chr2A
538619706
538620864
1158
True
1478
1478
89.530
1149
2351
1
chr2A.!!$R3
1202
53
TraesCS3B01G552500
chr2A
605787710
605788613
903
False
1238
1238
91.262
1429
2351
1
chr2A.!!$F1
922
54
TraesCS3B01G552500
chr2A
538628922
538629455
533
True
723
723
91.573
3
521
1
chr2A.!!$R4
518
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.