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
TraesCS3B01G271000
chr3B
100.000
3215
0
0
1
3215
436573547
436576761
0.000000e+00
5938.0
1
TraesCS3B01G271000
chr3B
89.951
1025
96
6
1195
2217
436728045
436727026
0.000000e+00
1315.0
2
TraesCS3B01G271000
chr3D
94.537
1922
79
15
783
2683
338320748
338322664
0.000000e+00
2944.0
3
TraesCS3B01G271000
chr3D
89.602
1029
100
5
1191
2217
338349825
338348802
0.000000e+00
1301.0
4
TraesCS3B01G271000
chr3A
96.005
1502
46
8
783
2273
456451780
456453278
0.000000e+00
2429.0
5
TraesCS3B01G271000
chr3A
89.932
1033
91
10
1189
2217
456700649
456699626
0.000000e+00
1319.0
6
TraesCS3B01G271000
chr3A
81.864
794
114
15
1
785
127842121
127841349
2.700000e-180
641.0
7
TraesCS3B01G271000
chr3A
90.909
418
27
4
2268
2683
456460686
456461094
4.690000e-153
551.0
8
TraesCS3B01G271000
chr3A
88.550
131
10
3
659
786
550651931
550652059
1.540000e-33
154.0
9
TraesCS3B01G271000
chr7D
92.484
785
33
4
1
785
631023132
631022374
0.000000e+00
1099.0
10
TraesCS3B01G271000
chr7D
86.643
554
62
11
2672
3215
568652058
568652609
1.280000e-168
603.0
11
TraesCS3B01G271000
chr2B
91.837
784
44
5
1
784
734840196
734839433
0.000000e+00
1075.0
12
TraesCS3B01G271000
chr7B
91.699
783
41
5
2
784
34232641
34233399
0.000000e+00
1064.0
13
TraesCS3B01G271000
chr7B
83.504
782
98
19
11
786
610636535
610637291
0.000000e+00
701.0
14
TraesCS3B01G271000
chr7B
87.013
539
58
10
2685
3215
76915192
76914658
5.940000e-167
597.0
15
TraesCS3B01G271000
chr2D
91.497
788
46
5
1
786
644242678
644243446
0.000000e+00
1064.0
16
TraesCS3B01G271000
chr2D
87.890
545
55
10
2680
3215
590329765
590329223
5.850000e-177
630.0
17
TraesCS3B01G271000
chr2D
87.636
550
53
12
2679
3215
194196022
194195475
2.720000e-175
625.0
18
TraesCS3B01G271000
chr2D
88.550
131
14
1
1311
1440
536380670
536380800
1.190000e-34
158.0
19
TraesCS3B01G271000
chr6D
91.731
774
42
5
14
787
101207337
101208088
0.000000e+00
1055.0
20
TraesCS3B01G271000
chr6D
87.477
551
53
13
2680
3215
306353794
306353245
3.520000e-174
621.0
21
TraesCS3B01G271000
chr6D
87.850
535
54
11
2688
3215
411996669
411996139
4.560000e-173
617.0
22
TraesCS3B01G271000
chr4B
91.360
787
42
8
1
786
81986338
81985577
0.000000e+00
1053.0
23
TraesCS3B01G271000
chr5B
90.978
787
49
6
1
786
375801118
375801883
0.000000e+00
1040.0
24
TraesCS3B01G271000
chr5B
87.684
544
47
13
2682
3215
532355068
532355601
1.640000e-172
616.0
25
TraesCS3B01G271000
chr5B
86.740
543
63
9
2680
3215
497201767
497202307
2.140000e-166
595.0
26
TraesCS3B01G271000
chr7A
90.736
788
53
6
1
787
287486705
287485937
0.000000e+00
1033.0
27
TraesCS3B01G271000
chr1A
89.427
785
64
5
1
785
579800596
579799831
0.000000e+00
972.0
28
TraesCS3B01G271000
chr1B
89.983
579
36
6
211
786
464140373
464139814
0.000000e+00
728.0
29
TraesCS3B01G271000
chr1B
82.964
722
92
19
70
785
356875778
356875082
9.790000e-175
623.0
30
TraesCS3B01G271000
chr6B
90.563
551
31
10
237
786
27846584
27847114
0.000000e+00
710.0
31
TraesCS3B01G271000
chr6B
89.552
67
7
0
1632
1698
347591969
347591903
5.710000e-13
86.1
32
TraesCS3B01G271000
chr2A
81.932
797
109
17
1
786
20473021
20472249
2.700000e-180
641.0
33
TraesCS3B01G271000
chr2A
87.477
543
59
8
2681
3215
624948239
624948780
4.560000e-173
617.0
34
TraesCS3B01G271000
chr6A
80.447
358
46
13
432
785
17028722
17028385
5.320000e-63
252.0
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
TraesCS3B01G271000
chr3B
436573547
436576761
3214
False
5938
5938
100.000
1
3215
1
chr3B.!!$F1
3214
1
TraesCS3B01G271000
chr3B
436727026
436728045
1019
True
1315
1315
89.951
1195
2217
1
chr3B.!!$R1
1022
2
TraesCS3B01G271000
chr3D
338320748
338322664
1916
False
2944
2944
94.537
783
2683
1
chr3D.!!$F1
1900
3
TraesCS3B01G271000
chr3D
338348802
338349825
1023
True
1301
1301
89.602
1191
2217
1
chr3D.!!$R1
1026
4
TraesCS3B01G271000
chr3A
456451780
456453278
1498
False
2429
2429
96.005
783
2273
1
chr3A.!!$F1
1490
5
TraesCS3B01G271000
chr3A
456699626
456700649
1023
True
1319
1319
89.932
1189
2217
1
chr3A.!!$R2
1028
6
TraesCS3B01G271000
chr3A
127841349
127842121
772
True
641
641
81.864
1
785
1
chr3A.!!$R1
784
7
TraesCS3B01G271000
chr7D
631022374
631023132
758
True
1099
1099
92.484
1
785
1
chr7D.!!$R1
784
8
TraesCS3B01G271000
chr7D
568652058
568652609
551
False
603
603
86.643
2672
3215
1
chr7D.!!$F1
543
9
TraesCS3B01G271000
chr2B
734839433
734840196
763
True
1075
1075
91.837
1
784
1
chr2B.!!$R1
783
10
TraesCS3B01G271000
chr7B
34232641
34233399
758
False
1064
1064
91.699
2
784
1
chr7B.!!$F1
782
11
TraesCS3B01G271000
chr7B
610636535
610637291
756
False
701
701
83.504
11
786
1
chr7B.!!$F2
775
12
TraesCS3B01G271000
chr7B
76914658
76915192
534
True
597
597
87.013
2685
3215
1
chr7B.!!$R1
530
13
TraesCS3B01G271000
chr2D
644242678
644243446
768
False
1064
1064
91.497
1
786
1
chr2D.!!$F2
785
14
TraesCS3B01G271000
chr2D
590329223
590329765
542
True
630
630
87.890
2680
3215
1
chr2D.!!$R2
535
15
TraesCS3B01G271000
chr2D
194195475
194196022
547
True
625
625
87.636
2679
3215
1
chr2D.!!$R1
536
16
TraesCS3B01G271000
chr6D
101207337
101208088
751
False
1055
1055
91.731
14
787
1
chr6D.!!$F1
773
17
TraesCS3B01G271000
chr6D
306353245
306353794
549
True
621
621
87.477
2680
3215
1
chr6D.!!$R1
535
18
TraesCS3B01G271000
chr6D
411996139
411996669
530
True
617
617
87.850
2688
3215
1
chr6D.!!$R2
527
19
TraesCS3B01G271000
chr4B
81985577
81986338
761
True
1053
1053
91.360
1
786
1
chr4B.!!$R1
785
20
TraesCS3B01G271000
chr5B
375801118
375801883
765
False
1040
1040
90.978
1
786
1
chr5B.!!$F1
785
21
TraesCS3B01G271000
chr5B
532355068
532355601
533
False
616
616
87.684
2682
3215
1
chr5B.!!$F3
533
22
TraesCS3B01G271000
chr5B
497201767
497202307
540
False
595
595
86.740
2680
3215
1
chr5B.!!$F2
535
23
TraesCS3B01G271000
chr7A
287485937
287486705
768
True
1033
1033
90.736
1
787
1
chr7A.!!$R1
786
24
TraesCS3B01G271000
chr1A
579799831
579800596
765
True
972
972
89.427
1
785
1
chr1A.!!$R1
784
25
TraesCS3B01G271000
chr1B
464139814
464140373
559
True
728
728
89.983
211
786
1
chr1B.!!$R2
575
26
TraesCS3B01G271000
chr1B
356875082
356875778
696
True
623
623
82.964
70
785
1
chr1B.!!$R1
715
27
TraesCS3B01G271000
chr6B
27846584
27847114
530
False
710
710
90.563
237
786
1
chr6B.!!$F1
549
28
TraesCS3B01G271000
chr2A
20472249
20473021
772
True
641
641
81.932
1
786
1
chr2A.!!$R1
785
29
TraesCS3B01G271000
chr2A
624948239
624948780
541
False
617
617
87.477
2681
3215
1
chr2A.!!$F1
534
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.