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
TraesCS2B01G478800
chr2B
100.000
2466
0
0
1
2466
676078325
676080790
0.000000e+00
4554.0
1
TraesCS2B01G478800
chr2B
88.100
1042
112
7
548
1586
161990733
161991765
0.000000e+00
1227.0
2
TraesCS2B01G478800
chr1D
85.867
1217
131
17
551
1736
490936347
490935141
0.000000e+00
1256.0
3
TraesCS2B01G478800
chr1D
83.830
940
137
14
551
1480
445585136
445586070
0.000000e+00
880.0
4
TraesCS2B01G478800
chr3D
85.750
1207
132
16
551
1736
111923304
111924491
0.000000e+00
1240.0
5
TraesCS2B01G478800
chr3D
93.593
718
41
3
1741
2458
335234830
335234118
0.000000e+00
1066.0
6
TraesCS2B01G478800
chr3D
81.290
1101
157
35
557
1646
549352374
549351312
0.000000e+00
846.0
7
TraesCS2B01G478800
chr5B
85.287
1203
150
11
553
1735
588387288
588388483
0.000000e+00
1216.0
8
TraesCS2B01G478800
chr2D
84.901
1159
151
16
551
1685
505537327
505538485
0.000000e+00
1149.0
9
TraesCS2B01G478800
chr2D
92.181
729
51
5
1741
2466
43051164
43051889
0.000000e+00
1026.0
10
TraesCS2B01G478800
chr7D
84.327
1174
134
31
548
1686
28535143
28536301
0.000000e+00
1103.0
11
TraesCS2B01G478800
chr7D
93.260
727
42
4
1741
2466
402385937
402385217
0.000000e+00
1064.0
12
TraesCS2B01G478800
chr7D
93.409
531
33
1
1
531
484026239
484026767
0.000000e+00
785.0
13
TraesCS2B01G478800
chr7D
92.655
531
37
2
1
531
483995937
483996465
0.000000e+00
763.0
14
TraesCS2B01G478800
chr7D
92.467
531
40
0
1
531
484060996
484061526
0.000000e+00
760.0
15
TraesCS2B01G478800
chr7D
92.090
531
42
0
1
531
483935113
483935643
0.000000e+00
749.0
16
TraesCS2B01G478800
chr7D
92.090
531
42
0
1
531
484019230
484019760
0.000000e+00
749.0
17
TraesCS2B01G478800
chr7D
92.090
531
42
0
1
531
484021023
484021553
0.000000e+00
749.0
18
TraesCS2B01G478800
chr7D
92.090
531
42
0
1
531
484022816
484023346
0.000000e+00
749.0
19
TraesCS2B01G478800
chr7D
91.902
531
43
0
1
531
484017437
484017967
0.000000e+00
743.0
20
TraesCS2B01G478800
chr7D
91.902
531
42
1
1
531
484016014
484016543
0.000000e+00
741.0
21
TraesCS2B01G478800
chr7D
94.595
37
2
0
1700
1736
141299478
141299514
9.530000e-05
58.4
22
TraesCS2B01G478800
chr7B
87.766
940
113
2
553
1490
43210784
43209845
0.000000e+00
1098.0
23
TraesCS2B01G478800
chr7B
83.652
942
136
16
551
1480
410481177
410482112
0.000000e+00
870.0
24
TraesCS2B01G478800
chr6D
93.269
728
42
6
1741
2466
120615931
120616653
0.000000e+00
1066.0
25
TraesCS2B01G478800
chr6D
93.132
728
42
5
1740
2466
139398019
139398739
0.000000e+00
1061.0
26
TraesCS2B01G478800
chr6D
92.926
721
41
6
1741
2458
394773293
394772580
0.000000e+00
1040.0
27
TraesCS2B01G478800
chr6D
92.455
729
45
5
1740
2466
291073570
291074290
0.000000e+00
1033.0
28
TraesCS2B01G478800
chr5D
93.398
727
36
3
1741
2466
230995567
230996282
0.000000e+00
1066.0
29
TraesCS2B01G478800
chr5D
87.075
294
26
3
241
531
493291397
493291113
3.060000e-84
322.0
30
TraesCS2B01G478800
chr5D
74.561
228
24
21
1533
1736
63414335
63414118
4.400000e-08
69.4
31
TraesCS2B01G478800
chr4B
93.014
730
45
4
1739
2466
475960436
475959711
0.000000e+00
1061.0
32
TraesCS2B01G478800
chr5A
85.328
1036
135
12
551
1582
645695147
645694125
0.000000e+00
1055.0
33
TraesCS2B01G478800
chr5A
79.891
736
130
15
800
1529
644113351
644112628
7.810000e-145
523.0
34
TraesCS2B01G478800
chr3A
83.015
1101
161
20
551
1646
1372437
1371358
0.000000e+00
974.0
35
TraesCS2B01G478800
chr4D
81.728
1215
169
32
548
1736
497181638
497182825
0.000000e+00
965.0
36
TraesCS2B01G478800
chr7A
93.797
532
31
2
1
531
551534408
551534938
0.000000e+00
798.0
37
TraesCS2B01G478800
chr7A
93.233
532
35
1
1
531
551506944
551507475
0.000000e+00
782.0
38
TraesCS2B01G478800
chr7A
92.467
531
40
0
1
531
551499421
551499951
0.000000e+00
760.0
39
TraesCS2B01G478800
chr1A
87.759
531
49
8
1
528
215640222
215640739
7.540000e-170
606.0
40
TraesCS2B01G478800
chr1A
87.382
531
51
8
1
528
215649328
215649845
1.630000e-166
595.0
41
TraesCS2B01G478800
chr6A
87.266
534
52
8
1
531
268140285
268139765
1.630000e-166
595.0
42
TraesCS2B01G478800
chr6A
87.079
534
53
8
1
531
268141881
268141361
7.600000e-165
590.0
43
TraesCS2B01G478800
chr6A
80.583
103
7
6
1645
1736
511036223
511036123
1.580000e-07
67.6
44
TraesCS2B01G478800
chr2A
83.700
546
85
4
938
1480
26765212
26764668
1.690000e-141
512.0
45
TraesCS2B01G478800
chr1B
78.740
762
102
37
1000
1736
526619479
526618753
2.890000e-124
455.0
46
TraesCS2B01G478800
chr3B
82.407
108
9
6
1572
1673
1482954
1482851
4.370000e-13
86.1
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
TraesCS2B01G478800
chr2B
676078325
676080790
2465
False
4554.000000
4554
100.000000
1
2466
1
chr2B.!!$F2
2465
1
TraesCS2B01G478800
chr2B
161990733
161991765
1032
False
1227.000000
1227
88.100000
548
1586
1
chr2B.!!$F1
1038
2
TraesCS2B01G478800
chr1D
490935141
490936347
1206
True
1256.000000
1256
85.867000
551
1736
1
chr1D.!!$R1
1185
3
TraesCS2B01G478800
chr1D
445585136
445586070
934
False
880.000000
880
83.830000
551
1480
1
chr1D.!!$F1
929
4
TraesCS2B01G478800
chr3D
111923304
111924491
1187
False
1240.000000
1240
85.750000
551
1736
1
chr3D.!!$F1
1185
5
TraesCS2B01G478800
chr3D
335234118
335234830
712
True
1066.000000
1066
93.593000
1741
2458
1
chr3D.!!$R1
717
6
TraesCS2B01G478800
chr3D
549351312
549352374
1062
True
846.000000
846
81.290000
557
1646
1
chr3D.!!$R2
1089
7
TraesCS2B01G478800
chr5B
588387288
588388483
1195
False
1216.000000
1216
85.287000
553
1735
1
chr5B.!!$F1
1182
8
TraesCS2B01G478800
chr2D
505537327
505538485
1158
False
1149.000000
1149
84.901000
551
1685
1
chr2D.!!$F2
1134
9
TraesCS2B01G478800
chr2D
43051164
43051889
725
False
1026.000000
1026
92.181000
1741
2466
1
chr2D.!!$F1
725
10
TraesCS2B01G478800
chr7D
28535143
28536301
1158
False
1103.000000
1103
84.327000
548
1686
1
chr7D.!!$F1
1138
11
TraesCS2B01G478800
chr7D
402385217
402385937
720
True
1064.000000
1064
93.260000
1741
2466
1
chr7D.!!$R1
725
12
TraesCS2B01G478800
chr7D
483995937
483996465
528
False
763.000000
763
92.655000
1
531
1
chr7D.!!$F4
530
13
TraesCS2B01G478800
chr7D
484060996
484061526
530
False
760.000000
760
92.467000
1
531
1
chr7D.!!$F5
530
14
TraesCS2B01G478800
chr7D
484016014
484026767
10753
False
752.666667
785
92.247167
1
531
6
chr7D.!!$F6
530
15
TraesCS2B01G478800
chr7D
483935113
483935643
530
False
749.000000
749
92.090000
1
531
1
chr7D.!!$F3
530
16
TraesCS2B01G478800
chr7B
43209845
43210784
939
True
1098.000000
1098
87.766000
553
1490
1
chr7B.!!$R1
937
17
TraesCS2B01G478800
chr7B
410481177
410482112
935
False
870.000000
870
83.652000
551
1480
1
chr7B.!!$F1
929
18
TraesCS2B01G478800
chr6D
120615931
120616653
722
False
1066.000000
1066
93.269000
1741
2466
1
chr6D.!!$F1
725
19
TraesCS2B01G478800
chr6D
139398019
139398739
720
False
1061.000000
1061
93.132000
1740
2466
1
chr6D.!!$F2
726
20
TraesCS2B01G478800
chr6D
394772580
394773293
713
True
1040.000000
1040
92.926000
1741
2458
1
chr6D.!!$R1
717
21
TraesCS2B01G478800
chr6D
291073570
291074290
720
False
1033.000000
1033
92.455000
1740
2466
1
chr6D.!!$F3
726
22
TraesCS2B01G478800
chr5D
230995567
230996282
715
False
1066.000000
1066
93.398000
1741
2466
1
chr5D.!!$F1
725
23
TraesCS2B01G478800
chr4B
475959711
475960436
725
True
1061.000000
1061
93.014000
1739
2466
1
chr4B.!!$R1
727
24
TraesCS2B01G478800
chr5A
645694125
645695147
1022
True
1055.000000
1055
85.328000
551
1582
1
chr5A.!!$R2
1031
25
TraesCS2B01G478800
chr5A
644112628
644113351
723
True
523.000000
523
79.891000
800
1529
1
chr5A.!!$R1
729
26
TraesCS2B01G478800
chr3A
1371358
1372437
1079
True
974.000000
974
83.015000
551
1646
1
chr3A.!!$R1
1095
27
TraesCS2B01G478800
chr4D
497181638
497182825
1187
False
965.000000
965
81.728000
548
1736
1
chr4D.!!$F1
1188
28
TraesCS2B01G478800
chr7A
551534408
551534938
530
False
798.000000
798
93.797000
1
531
1
chr7A.!!$F3
530
29
TraesCS2B01G478800
chr7A
551506944
551507475
531
False
782.000000
782
93.233000
1
531
1
chr7A.!!$F2
530
30
TraesCS2B01G478800
chr7A
551499421
551499951
530
False
760.000000
760
92.467000
1
531
1
chr7A.!!$F1
530
31
TraesCS2B01G478800
chr1A
215640222
215640739
517
False
606.000000
606
87.759000
1
528
1
chr1A.!!$F1
527
32
TraesCS2B01G478800
chr1A
215649328
215649845
517
False
595.000000
595
87.382000
1
528
1
chr1A.!!$F2
527
33
TraesCS2B01G478800
chr6A
268139765
268141881
2116
True
592.500000
595
87.172500
1
531
2
chr6A.!!$R2
530
34
TraesCS2B01G478800
chr2A
26764668
26765212
544
True
512.000000
512
83.700000
938
1480
1
chr2A.!!$R1
542
35
TraesCS2B01G478800
chr1B
526618753
526619479
726
True
455.000000
455
78.740000
1000
1736
1
chr1B.!!$R1
736
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.