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
TraesCS6A01G103700
chr6A
100.000
3740
0
0
1
3740
72972536
72976275
0.000000e+00
6907
1
TraesCS6A01G103700
chr6A
87.202
461
51
4
1842
2302
3633001
3633453
5.540000e-143
518
2
TraesCS6A01G103700
chr3A
95.732
3140
69
24
623
3737
11236995
11233896
0.000000e+00
4996
3
TraesCS6A01G103700
chr3A
91.775
1459
77
14
2309
3738
217961361
217959917
0.000000e+00
1989
4
TraesCS6A01G103700
chr3A
87.441
1481
98
47
582
2014
217962911
217961471
0.000000e+00
1624
5
TraesCS6A01G103700
chr3A
93.511
863
40
5
2887
3738
721022058
721022915
0.000000e+00
1269
6
TraesCS6A01G103700
chr3A
92.563
874
38
7
2887
3738
720985128
720985996
0.000000e+00
1229
7
TraesCS6A01G103700
chr3A
91.320
553
25
8
582
1134
726714176
726714705
0.000000e+00
734
8
TraesCS6A01G103700
chr3A
86.551
461
54
4
1842
2302
12634779
12635231
5.580000e-138
501
9
TraesCS6A01G103700
chr3A
85.326
368
25
13
582
946
720983220
720983561
1.650000e-93
353
10
TraesCS6A01G103700
chr3A
83.427
356
26
16
230
582
706782504
706782829
2.180000e-77
300
11
TraesCS6A01G103700
chr7B
92.823
1449
72
12
2309
3738
714303096
714304531
0.000000e+00
2071
12
TraesCS6A01G103700
chr7B
88.730
488
41
10
1858
2339
709586361
709586840
5.380000e-163
584
13
TraesCS6A01G103700
chr7B
86.355
557
30
13
852
1380
706979913
706979375
1.950000e-157
566
14
TraesCS6A01G103700
chr7B
87.202
461
51
4
1842
2302
133702677
133703129
5.540000e-143
518
15
TraesCS6A01G103700
chr7B
86.985
461
52
4
1842
2302
616409241
616408789
2.580000e-141
512
16
TraesCS6A01G103700
chr7A
92.749
1448
71
14
2309
3737
718438198
718436766
0.000000e+00
2061
17
TraesCS6A01G103700
chr7A
92.192
1460
71
14
2309
3738
48001587
48003033
0.000000e+00
2025
18
TraesCS6A01G103700
chr7A
91.712
1460
77
14
2309
3738
91012061
91010616
0.000000e+00
1986
19
TraesCS6A01G103700
chr7A
90.847
1464
91
19
2309
3738
20774183
20775637
0.000000e+00
1921
20
TraesCS6A01G103700
chr7A
90.512
1465
93
22
2309
3738
24428627
24430080
0.000000e+00
1893
21
TraesCS6A01G103700
chr7A
88.184
1481
86
34
582
2014
718439747
718438308
0.000000e+00
1683
22
TraesCS6A01G103700
chr7A
88.116
1481
87
34
582
2014
91013610
91012171
0.000000e+00
1677
23
TraesCS6A01G103700
chr7A
93.326
869
47
6
1155
2014
692046341
692047207
0.000000e+00
1273
24
TraesCS6A01G103700
chr7A
88.119
808
58
15
582
1380
663799324
663800102
0.000000e+00
926
25
TraesCS6A01G103700
chr7A
84.170
777
81
28
621
1380
24427146
24427897
0.000000e+00
715
26
TraesCS6A01G103700
chr7A
82.861
776
84
27
621
1380
20772710
20773452
0.000000e+00
651
27
TraesCS6A01G103700
chr7A
85.598
368
24
13
582
946
692045806
692046147
3.550000e-95
359
28
TraesCS6A01G103700
chr7A
82.749
371
26
7
579
947
48000598
48000932
2.820000e-76
296
29
TraesCS6A01G103700
chr5A
92.192
1460
70
14
2309
3738
565689256
565687811
0.000000e+00
2025
30
TraesCS6A01G103700
chr5A
88.327
1482
84
34
582
2014
565690807
565689366
0.000000e+00
1696
31
TraesCS6A01G103700
chr5A
86.768
461
53
4
1842
2302
513706671
513706219
1.200000e-139
507
32
TraesCS6A01G103700
chr5A
91.304
230
14
5
1
228
580280675
580280900
3.630000e-80
309
33
TraesCS6A01G103700
chr5A
88.189
127
14
1
253
379
580281012
580281137
2.330000e-32
150
34
TraesCS6A01G103700
chr3B
87.922
1482
90
33
582
2014
115499064
115500505
0.000000e+00
1663
35
TraesCS6A01G103700
chr3B
84.908
815
82
27
582
1380
735123307
735124096
0.000000e+00
785
36
TraesCS6A01G103700
chr4B
93.433
868
47
6
1155
2014
660883082
660882217
0.000000e+00
1279
37
TraesCS6A01G103700
chr4B
93.511
863
40
4
2887
3738
660881709
660880852
0.000000e+00
1269
38
TraesCS6A01G103700
chr4B
85.246
366
25
13
583
946
660883614
660883276
2.140000e-92
350
39
TraesCS6A01G103700
chrUn
93.203
868
49
6
1155
2014
271466976
271467841
0.000000e+00
1267
40
TraesCS6A01G103700
chrUn
84.417
815
86
28
582
1380
81450187
81449398
0.000000e+00
763
41
TraesCS6A01G103700
chrUn
85.598
368
24
13
582
946
48296286
48295945
3.550000e-95
359
42
TraesCS6A01G103700
chrUn
85.326
368
25
12
582
946
271466441
271466782
1.650000e-93
353
43
TraesCS6A01G103700
chr2A
93.163
863
43
5
2887
3738
41759009
41759866
0.000000e+00
1253
44
TraesCS6A01G103700
chr2A
86.985
461
52
4
1842
2302
750958942
750959394
2.580000e-141
512
45
TraesCS6A01G103700
chr2A
85.870
368
23
13
582
946
41757102
41757443
7.630000e-97
364
46
TraesCS6A01G103700
chr2A
82.595
316
32
5
3445
3738
750961531
750961845
1.330000e-64
257
47
TraesCS6A01G103700
chr4A
93.003
586
36
3
1
582
528610727
528610143
0.000000e+00
850
48
TraesCS6A01G103700
chr4A
92.491
586
40
2
1
582
528651191
528650606
0.000000e+00
835
49
TraesCS6A01G103700
chr4A
87.202
461
51
4
1842
2302
741025659
741026111
5.540000e-143
518
50
TraesCS6A01G103700
chr4A
83.416
404
28
11
569
969
17745629
17745262
4.630000e-89
339
51
TraesCS6A01G103700
chr6B
88.594
640
42
13
3129
3738
714428941
714429579
0.000000e+00
749
52
TraesCS6A01G103700
chr5B
95.946
444
18
0
139
582
63248776
63248333
0.000000e+00
721
53
TraesCS6A01G103700
chr5B
86.985
461
52
4
1842
2302
484823033
484823485
2.580000e-141
512
54
TraesCS6A01G103700
chr5B
92.667
150
10
1
1
149
63249302
63249153
8.140000e-52
215
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
TraesCS6A01G103700
chr6A
72972536
72976275
3739
False
6907.0
6907
100.0000
1
3740
1
chr6A.!!$F2
3739
1
TraesCS6A01G103700
chr3A
11233896
11236995
3099
True
4996.0
4996
95.7320
623
3737
1
chr3A.!!$R1
3114
2
TraesCS6A01G103700
chr3A
217959917
217962911
2994
True
1806.5
1989
89.6080
582
3738
2
chr3A.!!$R2
3156
3
TraesCS6A01G103700
chr3A
721022058
721022915
857
False
1269.0
1269
93.5110
2887
3738
1
chr3A.!!$F3
851
4
TraesCS6A01G103700
chr3A
720983220
720985996
2776
False
791.0
1229
88.9445
582
3738
2
chr3A.!!$F5
3156
5
TraesCS6A01G103700
chr3A
726714176
726714705
529
False
734.0
734
91.3200
582
1134
1
chr3A.!!$F4
552
6
TraesCS6A01G103700
chr7B
714303096
714304531
1435
False
2071.0
2071
92.8230
2309
3738
1
chr7B.!!$F3
1429
7
TraesCS6A01G103700
chr7B
706979375
706979913
538
True
566.0
566
86.3550
852
1380
1
chr7B.!!$R2
528
8
TraesCS6A01G103700
chr7A
718436766
718439747
2981
True
1872.0
2061
90.4665
582
3737
2
chr7A.!!$R2
3155
9
TraesCS6A01G103700
chr7A
91010616
91013610
2994
True
1831.5
1986
89.9140
582
3738
2
chr7A.!!$R1
3156
10
TraesCS6A01G103700
chr7A
24427146
24430080
2934
False
1304.0
1893
87.3410
621
3738
2
chr7A.!!$F3
3117
11
TraesCS6A01G103700
chr7A
20772710
20775637
2927
False
1286.0
1921
86.8540
621
3738
2
chr7A.!!$F2
3117
12
TraesCS6A01G103700
chr7A
48000598
48003033
2435
False
1160.5
2025
87.4705
579
3738
2
chr7A.!!$F4
3159
13
TraesCS6A01G103700
chr7A
663799324
663800102
778
False
926.0
926
88.1190
582
1380
1
chr7A.!!$F1
798
14
TraesCS6A01G103700
chr7A
692045806
692047207
1401
False
816.0
1273
89.4620
582
2014
2
chr7A.!!$F5
1432
15
TraesCS6A01G103700
chr5A
565687811
565690807
2996
True
1860.5
2025
90.2595
582
3738
2
chr5A.!!$R2
3156
16
TraesCS6A01G103700
chr3B
115499064
115500505
1441
False
1663.0
1663
87.9220
582
2014
1
chr3B.!!$F1
1432
17
TraesCS6A01G103700
chr3B
735123307
735124096
789
False
785.0
785
84.9080
582
1380
1
chr3B.!!$F2
798
18
TraesCS6A01G103700
chr4B
660880852
660883614
2762
True
966.0
1279
90.7300
583
3738
3
chr4B.!!$R1
3155
19
TraesCS6A01G103700
chrUn
271466441
271467841
1400
False
810.0
1267
89.2645
582
2014
2
chrUn.!!$F1
1432
20
TraesCS6A01G103700
chrUn
81449398
81450187
789
True
763.0
763
84.4170
582
1380
1
chrUn.!!$R2
798
21
TraesCS6A01G103700
chr2A
41757102
41759866
2764
False
808.5
1253
89.5165
582
3738
2
chr2A.!!$F1
3156
22
TraesCS6A01G103700
chr2A
750958942
750961845
2903
False
384.5
512
84.7900
1842
3738
2
chr2A.!!$F2
1896
23
TraesCS6A01G103700
chr4A
528610143
528610727
584
True
850.0
850
93.0030
1
582
1
chr4A.!!$R2
581
24
TraesCS6A01G103700
chr4A
528650606
528651191
585
True
835.0
835
92.4910
1
582
1
chr4A.!!$R3
581
25
TraesCS6A01G103700
chr6B
714428941
714429579
638
False
749.0
749
88.5940
3129
3738
1
chr6B.!!$F1
609
26
TraesCS6A01G103700
chr5B
63248333
63249302
969
True
468.0
721
94.3065
1
582
2
chr5B.!!$R1
581
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.