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
TraesCS3A01G196500
chr3A
100.000
2636
0
0
1
2636
298372023
298369388
0.000000e+00
4868.0
1
TraesCS3A01G196500
chr3A
92.035
2373
181
5
1
2369
298397054
298394686
0.000000e+00
3328.0
2
TraesCS3A01G196500
chr3A
89.626
2458
202
22
182
2636
298404558
298402151
0.000000e+00
3077.0
3
TraesCS3A01G196500
chr3A
92.382
722
54
1
1916
2636
270755666
270754945
0.000000e+00
1027.0
4
TraesCS3A01G196500
chr3A
91.907
729
57
2
1909
2636
270760488
270759761
0.000000e+00
1018.0
5
TraesCS3A01G196500
chr3A
91.482
587
45
3
2050
2636
304543924
304544505
0.000000e+00
802.0
6
TraesCS3A01G196500
chr3A
89.965
578
52
5
2050
2627
304551627
304552198
0.000000e+00
741.0
7
TraesCS3A01G196500
chr3A
84.322
708
81
23
1
688
242389586
242390283
0.000000e+00
665.0
8
TraesCS3A01G196500
chr3A
77.834
785
130
34
1
760
350531681
350532446
1.860000e-121
446.0
9
TraesCS3A01G196500
chr3A
81.378
537
70
22
1
518
144369873
144370398
6.790000e-111
411.0
10
TraesCS3A01G196500
chr3A
87.654
243
26
4
989
1229
288745865
288746105
2.000000e-71
279.0
11
TraesCS3A01G196500
chr3A
87.719
171
17
4
1141
1309
220774610
220774442
2.070000e-46
196.0
12
TraesCS3A01G196500
chr3A
93.846
65
3
1
908
972
396591813
396591876
2.160000e-16
97.1
13
TraesCS3A01G196500
chr4A
81.207
1309
171
54
1365
2636
426445971
426444701
0.000000e+00
985.0
14
TraesCS3A01G196500
chr4A
79.792
1346
178
65
1328
2630
426437556
426436262
0.000000e+00
893.0
15
TraesCS3A01G196500
chr4A
82.097
782
113
22
2
765
272732621
272733393
0.000000e+00
643.0
16
TraesCS3A01G196500
chr4A
91.497
294
21
4
835
1126
70896463
70896172
4.090000e-108
401.0
17
TraesCS3A01G196500
chr4A
88.115
244
24
5
987
1227
263897636
263897395
4.290000e-73
285.0
18
TraesCS3A01G196500
chr4A
90.141
213
20
1
1361
1573
277542956
277543167
2.580000e-70
276.0
19
TraesCS3A01G196500
chr4A
88.372
172
20
0
1138
1309
214278677
214278848
9.560000e-50
207.0
20
TraesCS3A01G196500
chr4A
85.965
171
24
0
1139
1309
214229405
214229575
1.610000e-42
183.0
21
TraesCS3A01G196500
chr4A
86.842
76
6
4
894
967
270685694
270685621
6.050000e-12
82.4
22
TraesCS3A01G196500
chr1A
83.317
1019
127
32
1628
2636
357479991
357480976
0.000000e+00
900.0
23
TraesCS3A01G196500
chr1A
82.694
1017
126
34
1628
2636
357494590
357495564
0.000000e+00
857.0
24
TraesCS3A01G196500
chr1A
81.970
1015
134
37
1636
2636
281398312
281397333
0.000000e+00
815.0
25
TraesCS3A01G196500
chr1A
81.961
1020
124
45
1636
2636
281412504
281411526
0.000000e+00
809.0
26
TraesCS3A01G196500
chr1A
90.136
294
25
4
835
1126
100884320
100884029
1.910000e-101
379.0
27
TraesCS3A01G196500
chr1A
87.234
235
23
6
961
1191
135528764
135528533
7.240000e-66
261.0
28
TraesCS3A01G196500
chr2A
87.680
763
75
11
1
751
239452580
239451825
0.000000e+00
870.0
29
TraesCS3A01G196500
chr2A
84.981
779
91
22
1
765
416727532
416728298
0.000000e+00
767.0
30
TraesCS3A01G196500
chr2A
88.676
574
54
9
182
751
239470869
239470303
0.000000e+00
689.0
31
TraesCS3A01G196500
chr2A
82.157
779
110
23
1
761
124337165
124336398
2.210000e-180
641.0
32
TraesCS3A01G196500
chr2A
85.586
333
38
4
1303
1633
637095058
637095382
9.040000e-90
340.0
33
TraesCS3A01G196500
chr5A
82.041
1019
144
30
1628
2636
212978848
212979837
0.000000e+00
832.0
34
TraesCS3A01G196500
chr5A
87.285
582
52
19
2053
2625
97788265
97788833
0.000000e+00
645.0
35
TraesCS3A01G196500
chr5A
88.822
331
36
1
1303
1633
283760188
283759859
3.160000e-109
405.0
36
TraesCS3A01G196500
chr5A
88.218
331
39
0
1303
1633
283792662
283792332
1.900000e-106
396.0
37
TraesCS3A01G196500
chr5A
84.290
331
51
1
1303
1633
541322808
541323137
3.270000e-84
322.0
38
TraesCS3A01G196500
chr5A
91.509
106
7
2
831
934
136737905
136738010
7.600000e-31
145.0
39
TraesCS3A01G196500
chr5A
92.473
93
6
1
835
926
136734116
136734208
5.920000e-27
132.0
40
TraesCS3A01G196500
chr7A
89.542
612
62
2
835
1444
152816281
152815670
0.000000e+00
774.0
41
TraesCS3A01G196500
chr7A
88.926
605
62
4
835
1437
152823879
152823278
0.000000e+00
741.0
42
TraesCS3A01G196500
chr7A
79.883
681
90
39
1969
2631
355762729
355763380
3.090000e-124
455.0
43
TraesCS3A01G196500
chr7A
78.414
681
101
35
1969
2631
355307169
355306517
4.090000e-108
401.0
44
TraesCS3A01G196500
chr7A
88.535
314
35
1
1320
1633
316589684
316589996
1.910000e-101
379.0
45
TraesCS3A01G196500
chr7A
90.411
73
4
3
835
906
616028908
616028978
2.790000e-15
93.5
46
TraesCS3A01G196500
chr6A
88.727
550
52
8
2079
2625
429938181
429937639
0.000000e+00
664.0
47
TraesCS3A01G196500
chr6A
87.609
573
58
9
2056
2625
429933436
429932874
0.000000e+00
652.0
48
TraesCS3A01G196500
chr6A
86.047
86
9
2
1384
1469
175911339
175911257
3.610000e-14
89.8
49
TraesCS3A01G196500
chr4D
82.181
752
108
22
1
738
251278042
251278781
8.010000e-175
623.0
50
TraesCS3A01G196500
chr7D
78.084
689
102
35
1958
2636
153368533
153369182
8.850000e-105
390.0
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
TraesCS3A01G196500
chr3A
298369388
298372023
2635
True
4868
4868
100.000
1
2636
1
chr3A.!!$R4
2635
1
TraesCS3A01G196500
chr3A
298394686
298397054
2368
True
3328
3328
92.035
1
2369
1
chr3A.!!$R5
2368
2
TraesCS3A01G196500
chr3A
298402151
298404558
2407
True
3077
3077
89.626
182
2636
1
chr3A.!!$R6
2454
3
TraesCS3A01G196500
chr3A
270754945
270755666
721
True
1027
1027
92.382
1916
2636
1
chr3A.!!$R2
720
4
TraesCS3A01G196500
chr3A
270759761
270760488
727
True
1018
1018
91.907
1909
2636
1
chr3A.!!$R3
727
5
TraesCS3A01G196500
chr3A
304543924
304544505
581
False
802
802
91.482
2050
2636
1
chr3A.!!$F4
586
6
TraesCS3A01G196500
chr3A
304551627
304552198
571
False
741
741
89.965
2050
2627
1
chr3A.!!$F5
577
7
TraesCS3A01G196500
chr3A
242389586
242390283
697
False
665
665
84.322
1
688
1
chr3A.!!$F2
687
8
TraesCS3A01G196500
chr3A
350531681
350532446
765
False
446
446
77.834
1
760
1
chr3A.!!$F6
759
9
TraesCS3A01G196500
chr3A
144369873
144370398
525
False
411
411
81.378
1
518
1
chr3A.!!$F1
517
10
TraesCS3A01G196500
chr4A
426444701
426445971
1270
True
985
985
81.207
1365
2636
1
chr4A.!!$R5
1271
11
TraesCS3A01G196500
chr4A
426436262
426437556
1294
True
893
893
79.792
1328
2630
1
chr4A.!!$R4
1302
12
TraesCS3A01G196500
chr4A
272732621
272733393
772
False
643
643
82.097
2
765
1
chr4A.!!$F3
763
13
TraesCS3A01G196500
chr1A
357479991
357480976
985
False
900
900
83.317
1628
2636
1
chr1A.!!$F1
1008
14
TraesCS3A01G196500
chr1A
357494590
357495564
974
False
857
857
82.694
1628
2636
1
chr1A.!!$F2
1008
15
TraesCS3A01G196500
chr1A
281397333
281398312
979
True
815
815
81.970
1636
2636
1
chr1A.!!$R3
1000
16
TraesCS3A01G196500
chr1A
281411526
281412504
978
True
809
809
81.961
1636
2636
1
chr1A.!!$R4
1000
17
TraesCS3A01G196500
chr2A
239451825
239452580
755
True
870
870
87.680
1
751
1
chr2A.!!$R2
750
18
TraesCS3A01G196500
chr2A
416727532
416728298
766
False
767
767
84.981
1
765
1
chr2A.!!$F1
764
19
TraesCS3A01G196500
chr2A
239470303
239470869
566
True
689
689
88.676
182
751
1
chr2A.!!$R3
569
20
TraesCS3A01G196500
chr2A
124336398
124337165
767
True
641
641
82.157
1
761
1
chr2A.!!$R1
760
21
TraesCS3A01G196500
chr5A
212978848
212979837
989
False
832
832
82.041
1628
2636
1
chr5A.!!$F2
1008
22
TraesCS3A01G196500
chr5A
97788265
97788833
568
False
645
645
87.285
2053
2625
1
chr5A.!!$F1
572
23
TraesCS3A01G196500
chr7A
152815670
152816281
611
True
774
774
89.542
835
1444
1
chr7A.!!$R1
609
24
TraesCS3A01G196500
chr7A
152823278
152823879
601
True
741
741
88.926
835
1437
1
chr7A.!!$R2
602
25
TraesCS3A01G196500
chr7A
355762729
355763380
651
False
455
455
79.883
1969
2631
1
chr7A.!!$F2
662
26
TraesCS3A01G196500
chr7A
355306517
355307169
652
True
401
401
78.414
1969
2631
1
chr7A.!!$R3
662
27
TraesCS3A01G196500
chr6A
429937639
429938181
542
True
664
664
88.727
2079
2625
1
chr6A.!!$R3
546
28
TraesCS3A01G196500
chr6A
429932874
429933436
562
True
652
652
87.609
2056
2625
1
chr6A.!!$R2
569
29
TraesCS3A01G196500
chr4D
251278042
251278781
739
False
623
623
82.181
1
738
1
chr4D.!!$F1
737
30
TraesCS3A01G196500
chr7D
153368533
153369182
649
False
390
390
78.084
1958
2636
1
chr7D.!!$F1
678
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.