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
TraesCS7B01G066900
chr7B
100.000
3325
0
0
1
3325
72336597
72339921
0.000000e+00
6141.0
1
TraesCS7B01G066900
chr7B
100.000
900
0
0
3426
4325
72340022
72340921
0.000000e+00
1663.0
2
TraesCS7B01G066900
chr7B
94.007
901
51
3
3426
4325
721405919
721406817
0.000000e+00
1362.0
3
TraesCS7B01G066900
chr2A
95.679
2615
74
9
714
3325
628678660
628681238
0.000000e+00
4167.0
4
TraesCS7B01G066900
chr2A
96.741
1350
42
1
714
2061
445752152
445750803
0.000000e+00
2248.0
5
TraesCS7B01G066900
chr2A
97.634
1268
29
1
2059
3325
445750755
445749488
0.000000e+00
2174.0
6
TraesCS7B01G066900
chr2A
92.970
697
34
3
1
683
148498659
148499354
0.000000e+00
1002.0
7
TraesCS7B01G066900
chr7A
96.370
1350
43
3
714
2061
89127824
89129169
0.000000e+00
2217.0
8
TraesCS7B01G066900
chr7A
97.731
1234
27
1
2059
3291
89129217
89130450
0.000000e+00
2122.0
9
TraesCS7B01G066900
chr7A
96.743
1228
39
1
2059
3285
38245861
38247088
0.000000e+00
2045.0
10
TraesCS7B01G066900
chr7A
90.455
660
41
11
1
646
662585746
662586397
0.000000e+00
850.0
11
TraesCS7B01G066900
chr7A
95.886
316
10
1
3013
3325
21451426
21451741
3.860000e-140
508.0
12
TraesCS7B01G066900
chr7A
100.000
31
0
0
682
712
733083889
733083859
1.680000e-04
58.4
13
TraesCS7B01G066900
chr3A
96.148
1350
50
2
714
2061
19596746
19598095
0.000000e+00
2204.0
14
TraesCS7B01G066900
chr3A
97.319
1268
33
1
2059
3325
19598143
19599410
0.000000e+00
2152.0
15
TraesCS7B01G066900
chr5A
95.926
1350
53
1
714
2061
561198567
561197218
0.000000e+00
2187.0
16
TraesCS7B01G066900
chr5A
96.688
1268
40
2
2059
3325
561197170
561195904
0.000000e+00
2108.0
17
TraesCS7B01G066900
chr6A
97.792
1268
26
2
2059
3325
105156464
105155198
0.000000e+00
2185.0
18
TraesCS7B01G066900
chr6A
89.697
660
32
6
1
646
98251782
98252419
0.000000e+00
809.0
19
TraesCS7B01G066900
chr6A
100.000
32
0
0
682
713
26825363
26825332
4.670000e-05
60.2
20
TraesCS7B01G066900
chr1A
95.643
1354
50
3
714
2061
381287035
381285685
0.000000e+00
2165.0
21
TraesCS7B01G066900
chr1A
97.506
1203
27
2
2059
3260
381285637
381284437
0.000000e+00
2052.0
22
TraesCS7B01G066900
chr7D
94.918
1338
62
5
714
2049
623788988
623787655
0.000000e+00
2089.0
23
TraesCS7B01G066900
chr7D
93.960
1341
79
1
711
2049
53443702
53445042
0.000000e+00
2026.0
24
TraesCS7B01G066900
chr3D
94.772
1339
68
1
713
2049
184626318
184627656
0.000000e+00
2084.0
25
TraesCS7B01G066900
chr3D
94.619
1338
70
1
714
2049
578222310
578223647
0.000000e+00
2071.0
26
TraesCS7B01G066900
chr3D
94.340
901
48
3
3426
4325
602770139
602769241
0.000000e+00
1378.0
27
TraesCS7B01G066900
chr4A
96.670
961
30
2
2059
3017
618193573
618194533
0.000000e+00
1596.0
28
TraesCS7B01G066900
chr6D
94.586
905
40
5
3426
4325
451214982
451214082
0.000000e+00
1391.0
29
TraesCS7B01G066900
chr3B
94.365
905
44
4
3426
4325
767002014
767002916
0.000000e+00
1382.0
30
TraesCS7B01G066900
chr3B
93.929
906
47
5
3426
4325
9676721
9677624
0.000000e+00
1362.0
31
TraesCS7B01G066900
chr3B
90.455
660
29
12
1
646
807487899
807487260
0.000000e+00
839.0
32
TraesCS7B01G066900
chr3B
100.000
29
0
0
684
712
741626595
741626567
2.000000e-03
54.7
33
TraesCS7B01G066900
chr1B
94.340
901
47
4
3426
4325
307311754
307310857
0.000000e+00
1378.0
34
TraesCS7B01G066900
chrUn
94.144
905
46
4
3426
4325
28571390
28570488
0.000000e+00
1371.0
35
TraesCS7B01G066900
chrUn
95.604
728
17
4
1
713
278751920
278751193
0.000000e+00
1153.0
36
TraesCS7B01G066900
chrUn
94.911
727
15
3
1
713
238594473
238593755
0.000000e+00
1118.0
37
TraesCS7B01G066900
chrUn
94.911
727
15
3
1
713
280920220
280919502
0.000000e+00
1118.0
38
TraesCS7B01G066900
chrUn
95.845
698
14
2
1
683
214072494
214071797
0.000000e+00
1114.0
39
TraesCS7B01G066900
chr2D
94.144
905
46
4
3426
4325
549286756
549285854
0.000000e+00
1371.0
40
TraesCS7B01G066900
chr2D
87.671
657
56
12
1
634
150130154
150130808
0.000000e+00
741.0
41
TraesCS7B01G066900
chr2D
100.000
30
0
0
684
713
8662229
8662200
6.040000e-04
56.5
42
TraesCS7B01G066900
chr2D
100.000
30
0
0
684
713
359665476
359665505
6.040000e-04
56.5
43
TraesCS7B01G066900
chr2B
94.216
899
45
4
3432
4325
47209660
47208764
0.000000e+00
1365.0
44
TraesCS7B01G066900
chr5D
100.000
30
0
0
684
713
547445168
547445197
6.040000e-04
56.5
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
TraesCS7B01G066900
chr7B
72336597
72340921
4324
False
3902.0
6141
100.0000
1
4325
2
chr7B.!!$F2
4324
1
TraesCS7B01G066900
chr7B
721405919
721406817
898
False
1362.0
1362
94.0070
3426
4325
1
chr7B.!!$F1
899
2
TraesCS7B01G066900
chr2A
628678660
628681238
2578
False
4167.0
4167
95.6790
714
3325
1
chr2A.!!$F2
2611
3
TraesCS7B01G066900
chr2A
445749488
445752152
2664
True
2211.0
2248
97.1875
714
3325
2
chr2A.!!$R1
2611
4
TraesCS7B01G066900
chr2A
148498659
148499354
695
False
1002.0
1002
92.9700
1
683
1
chr2A.!!$F1
682
5
TraesCS7B01G066900
chr7A
89127824
89130450
2626
False
2169.5
2217
97.0505
714
3291
2
chr7A.!!$F4
2577
6
TraesCS7B01G066900
chr7A
38245861
38247088
1227
False
2045.0
2045
96.7430
2059
3285
1
chr7A.!!$F2
1226
7
TraesCS7B01G066900
chr7A
662585746
662586397
651
False
850.0
850
90.4550
1
646
1
chr7A.!!$F3
645
8
TraesCS7B01G066900
chr3A
19596746
19599410
2664
False
2178.0
2204
96.7335
714
3325
2
chr3A.!!$F1
2611
9
TraesCS7B01G066900
chr5A
561195904
561198567
2663
True
2147.5
2187
96.3070
714
3325
2
chr5A.!!$R1
2611
10
TraesCS7B01G066900
chr6A
105155198
105156464
1266
True
2185.0
2185
97.7920
2059
3325
1
chr6A.!!$R2
1266
11
TraesCS7B01G066900
chr6A
98251782
98252419
637
False
809.0
809
89.6970
1
646
1
chr6A.!!$F1
645
12
TraesCS7B01G066900
chr1A
381284437
381287035
2598
True
2108.5
2165
96.5745
714
3260
2
chr1A.!!$R1
2546
13
TraesCS7B01G066900
chr7D
623787655
623788988
1333
True
2089.0
2089
94.9180
714
2049
1
chr7D.!!$R1
1335
14
TraesCS7B01G066900
chr7D
53443702
53445042
1340
False
2026.0
2026
93.9600
711
2049
1
chr7D.!!$F1
1338
15
TraesCS7B01G066900
chr3D
184626318
184627656
1338
False
2084.0
2084
94.7720
713
2049
1
chr3D.!!$F1
1336
16
TraesCS7B01G066900
chr3D
578222310
578223647
1337
False
2071.0
2071
94.6190
714
2049
1
chr3D.!!$F2
1335
17
TraesCS7B01G066900
chr3D
602769241
602770139
898
True
1378.0
1378
94.3400
3426
4325
1
chr3D.!!$R1
899
18
TraesCS7B01G066900
chr4A
618193573
618194533
960
False
1596.0
1596
96.6700
2059
3017
1
chr4A.!!$F1
958
19
TraesCS7B01G066900
chr6D
451214082
451214982
900
True
1391.0
1391
94.5860
3426
4325
1
chr6D.!!$R1
899
20
TraesCS7B01G066900
chr3B
767002014
767002916
902
False
1382.0
1382
94.3650
3426
4325
1
chr3B.!!$F2
899
21
TraesCS7B01G066900
chr3B
9676721
9677624
903
False
1362.0
1362
93.9290
3426
4325
1
chr3B.!!$F1
899
22
TraesCS7B01G066900
chr3B
807487260
807487899
639
True
839.0
839
90.4550
1
646
1
chr3B.!!$R2
645
23
TraesCS7B01G066900
chr1B
307310857
307311754
897
True
1378.0
1378
94.3400
3426
4325
1
chr1B.!!$R1
899
24
TraesCS7B01G066900
chrUn
28570488
28571390
902
True
1371.0
1371
94.1440
3426
4325
1
chrUn.!!$R1
899
25
TraesCS7B01G066900
chrUn
278751193
278751920
727
True
1153.0
1153
95.6040
1
713
1
chrUn.!!$R4
712
26
TraesCS7B01G066900
chrUn
238593755
238594473
718
True
1118.0
1118
94.9110
1
713
1
chrUn.!!$R3
712
27
TraesCS7B01G066900
chrUn
280919502
280920220
718
True
1118.0
1118
94.9110
1
713
1
chrUn.!!$R5
712
28
TraesCS7B01G066900
chrUn
214071797
214072494
697
True
1114.0
1114
95.8450
1
683
1
chrUn.!!$R2
682
29
TraesCS7B01G066900
chr2D
549285854
549286756
902
True
1371.0
1371
94.1440
3426
4325
1
chr2D.!!$R2
899
30
TraesCS7B01G066900
chr2D
150130154
150130808
654
False
741.0
741
87.6710
1
634
1
chr2D.!!$F1
633
31
TraesCS7B01G066900
chr2B
47208764
47209660
896
True
1365.0
1365
94.2160
3432
4325
1
chr2B.!!$R1
893
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.