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
TraesCS3B01G535200
chr3B
100.000
2249
0
0
1
2249
775177108
775174860
0.000000e+00
4154
1
TraesCS3B01G535200
chr3B
94.545
825
43
1
1422
2246
581153502
581154324
0.000000e+00
1273
2
TraesCS3B01G535200
chr3B
94.203
828
46
1
1422
2249
661094790
661095615
0.000000e+00
1262
3
TraesCS3B01G535200
chr3B
93.939
825
48
1
1422
2246
581189599
581190421
0.000000e+00
1245
4
TraesCS3B01G535200
chr3B
93.932
824
45
2
1423
2246
305512770
305513588
0.000000e+00
1240
5
TraesCS3B01G535200
chr3B
89.744
780
52
6
659
1421
769385940
769385172
0.000000e+00
972
6
TraesCS3B01G535200
chr3B
91.169
385
24
2
1
385
769386345
769385971
4.280000e-142
514
7
TraesCS3B01G535200
chr3D
88.011
1126
99
21
324
1418
134639833
134640953
0.000000e+00
1299
8
TraesCS3B01G535200
chr3D
93.576
825
48
2
1422
2246
297584784
297585603
0.000000e+00
1225
9
TraesCS3B01G535200
chr3D
87.291
779
62
9
1
779
49966188
49965447
0.000000e+00
856
10
TraesCS3B01G535200
chr3D
87.500
560
49
9
874
1425
49965418
49964872
5.270000e-176
627
11
TraesCS3B01G535200
chr4D
87.566
1142
102
14
324
1425
398867132
398868273
0.000000e+00
1286
12
TraesCS3B01G535200
chr4D
93.357
828
49
3
1422
2249
32622589
32621768
0.000000e+00
1219
13
TraesCS3B01G535200
chr7B
94.565
828
43
1
1422
2249
638990107
638990932
0.000000e+00
1279
14
TraesCS3B01G535200
chr5A
89.220
1039
91
4
324
1341
697889419
697890457
0.000000e+00
1279
15
TraesCS3B01G535200
chr5A
87.011
1124
114
16
324
1422
651581534
651580418
0.000000e+00
1238
16
TraesCS3B01G535200
chr1B
87.014
1132
110
20
324
1423
414556747
414557873
0.000000e+00
1242
17
TraesCS3B01G535200
chr1B
87.948
1004
98
7
324
1308
494554996
494553997
0.000000e+00
1162
18
TraesCS3B01G535200
chr2D
93.818
825
46
2
1422
2246
448013970
448014789
0.000000e+00
1236
19
TraesCS3B01G535200
chr2D
87.163
779
60
9
1
779
103241373
103240635
0.000000e+00
848
20
TraesCS3B01G535200
chr2D
87.410
556
48
9
874
1421
103240606
103240065
8.820000e-174
619
21
TraesCS3B01G535200
chr6B
93.357
828
53
1
1422
2249
539146256
539145431
0.000000e+00
1223
22
TraesCS3B01G535200
chr6B
86.544
1137
111
24
324
1423
132658482
132657351
0.000000e+00
1214
23
TraesCS3B01G535200
chr6B
89.803
559
46
7
1
557
203463113
203462564
0.000000e+00
706
24
TraesCS3B01G535200
chr6B
83.714
657
73
16
799
1421
508174474
508173818
6.920000e-165
590
25
TraesCS3B01G535200
chr4A
88.048
1004
97
7
324
1308
718008537
718007538
0.000000e+00
1168
26
TraesCS3B01G535200
chr4A
90.877
559
41
3
1
557
709875894
709875344
0.000000e+00
741
27
TraesCS3B01G535200
chr5B
85.394
1116
91
30
324
1418
607482454
607483518
0.000000e+00
1092
28
TraesCS3B01G535200
chr5B
84.143
782
76
6
1
779
178915485
178914749
0.000000e+00
713
29
TraesCS3B01G535200
chr1A
85.897
780
68
11
1
779
571865583
571864845
0.000000e+00
793
30
TraesCS3B01G535200
chr1A
86.964
560
52
11
874
1425
571864816
571864270
5.310000e-171
610
31
TraesCS3B01G535200
chr1A
84.783
552
49
13
898
1418
517326750
517327297
2.560000e-144
521
32
TraesCS3B01G535200
chr1A
83.932
529
69
5
900
1418
97261565
97262087
2.010000e-135
492
33
TraesCS3B01G535200
chr1A
83.932
529
69
5
900
1418
353279788
353280310
2.010000e-135
492
34
TraesCS3B01G535200
chr2B
91.449
421
27
4
1007
1422
227897557
227897141
9.010000e-159
569
35
TraesCS3B01G535200
chr2B
90.823
316
22
2
36
351
227898103
227897795
1.240000e-112
416
36
TraesCS3B01G535200
chr7A
84.392
551
52
12
898
1418
712074120
712074666
5.540000e-141
510
37
TraesCS3B01G535200
chr7A
84.079
559
53
14
898
1424
706403194
706402640
7.170000e-140
507
38
TraesCS3B01G535200
chr2A
83.114
533
74
5
900
1422
702409727
702410253
2.610000e-129
472
39
TraesCS3B01G535200
chr5D
86.875
320
37
5
6
325
292765467
292765153
9.880000e-94
353
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
TraesCS3B01G535200
chr3B
775174860
775177108
2248
True
4154.0
4154
100.0000
1
2249
1
chr3B.!!$R1
2248
1
TraesCS3B01G535200
chr3B
581153502
581154324
822
False
1273.0
1273
94.5450
1422
2246
1
chr3B.!!$F2
824
2
TraesCS3B01G535200
chr3B
661094790
661095615
825
False
1262.0
1262
94.2030
1422
2249
1
chr3B.!!$F4
827
3
TraesCS3B01G535200
chr3B
581189599
581190421
822
False
1245.0
1245
93.9390
1422
2246
1
chr3B.!!$F3
824
4
TraesCS3B01G535200
chr3B
305512770
305513588
818
False
1240.0
1240
93.9320
1423
2246
1
chr3B.!!$F1
823
5
TraesCS3B01G535200
chr3B
769385172
769386345
1173
True
743.0
972
90.4565
1
1421
2
chr3B.!!$R2
1420
6
TraesCS3B01G535200
chr3D
134639833
134640953
1120
False
1299.0
1299
88.0110
324
1418
1
chr3D.!!$F1
1094
7
TraesCS3B01G535200
chr3D
297584784
297585603
819
False
1225.0
1225
93.5760
1422
2246
1
chr3D.!!$F2
824
8
TraesCS3B01G535200
chr3D
49964872
49966188
1316
True
741.5
856
87.3955
1
1425
2
chr3D.!!$R1
1424
9
TraesCS3B01G535200
chr4D
398867132
398868273
1141
False
1286.0
1286
87.5660
324
1425
1
chr4D.!!$F1
1101
10
TraesCS3B01G535200
chr4D
32621768
32622589
821
True
1219.0
1219
93.3570
1422
2249
1
chr4D.!!$R1
827
11
TraesCS3B01G535200
chr7B
638990107
638990932
825
False
1279.0
1279
94.5650
1422
2249
1
chr7B.!!$F1
827
12
TraesCS3B01G535200
chr5A
697889419
697890457
1038
False
1279.0
1279
89.2200
324
1341
1
chr5A.!!$F1
1017
13
TraesCS3B01G535200
chr5A
651580418
651581534
1116
True
1238.0
1238
87.0110
324
1422
1
chr5A.!!$R1
1098
14
TraesCS3B01G535200
chr1B
414556747
414557873
1126
False
1242.0
1242
87.0140
324
1423
1
chr1B.!!$F1
1099
15
TraesCS3B01G535200
chr1B
494553997
494554996
999
True
1162.0
1162
87.9480
324
1308
1
chr1B.!!$R1
984
16
TraesCS3B01G535200
chr2D
448013970
448014789
819
False
1236.0
1236
93.8180
1422
2246
1
chr2D.!!$F1
824
17
TraesCS3B01G535200
chr2D
103240065
103241373
1308
True
733.5
848
87.2865
1
1421
2
chr2D.!!$R1
1420
18
TraesCS3B01G535200
chr6B
539145431
539146256
825
True
1223.0
1223
93.3570
1422
2249
1
chr6B.!!$R4
827
19
TraesCS3B01G535200
chr6B
132657351
132658482
1131
True
1214.0
1214
86.5440
324
1423
1
chr6B.!!$R1
1099
20
TraesCS3B01G535200
chr6B
203462564
203463113
549
True
706.0
706
89.8030
1
557
1
chr6B.!!$R2
556
21
TraesCS3B01G535200
chr6B
508173818
508174474
656
True
590.0
590
83.7140
799
1421
1
chr6B.!!$R3
622
22
TraesCS3B01G535200
chr4A
718007538
718008537
999
True
1168.0
1168
88.0480
324
1308
1
chr4A.!!$R2
984
23
TraesCS3B01G535200
chr4A
709875344
709875894
550
True
741.0
741
90.8770
1
557
1
chr4A.!!$R1
556
24
TraesCS3B01G535200
chr5B
607482454
607483518
1064
False
1092.0
1092
85.3940
324
1418
1
chr5B.!!$F1
1094
25
TraesCS3B01G535200
chr5B
178914749
178915485
736
True
713.0
713
84.1430
1
779
1
chr5B.!!$R1
778
26
TraesCS3B01G535200
chr1A
571864270
571865583
1313
True
701.5
793
86.4305
1
1425
2
chr1A.!!$R1
1424
27
TraesCS3B01G535200
chr1A
517326750
517327297
547
False
521.0
521
84.7830
898
1418
1
chr1A.!!$F3
520
28
TraesCS3B01G535200
chr1A
97261565
97262087
522
False
492.0
492
83.9320
900
1418
1
chr1A.!!$F1
518
29
TraesCS3B01G535200
chr1A
353279788
353280310
522
False
492.0
492
83.9320
900
1418
1
chr1A.!!$F2
518
30
TraesCS3B01G535200
chr2B
227897141
227898103
962
True
492.5
569
91.1360
36
1422
2
chr2B.!!$R1
1386
31
TraesCS3B01G535200
chr7A
712074120
712074666
546
False
510.0
510
84.3920
898
1418
1
chr7A.!!$F1
520
32
TraesCS3B01G535200
chr7A
706402640
706403194
554
True
507.0
507
84.0790
898
1424
1
chr7A.!!$R1
526
33
TraesCS3B01G535200
chr2A
702409727
702410253
526
False
472.0
472
83.1140
900
1422
1
chr2A.!!$F1
522
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.