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
TraesCS1A01G266400
chr1A
100.000
2584
0
0
1
2584
461966787
461964204
0.000000e+00
4772
1
TraesCS1A01G266400
chr1A
96.679
1054
32
3
2
1054
35564001
35562950
0.000000e+00
1749
2
TraesCS1A01G266400
chr2D
94.926
2089
70
14
2
2056
469107932
469105846
0.000000e+00
3238
3
TraesCS1A01G266400
chr2D
91.215
1696
110
22
2
1692
631749570
631747909
0.000000e+00
2270
4
TraesCS1A01G266400
chr2D
93.633
534
34
0
2051
2584
344390040
344390573
0.000000e+00
798
5
TraesCS1A01G266400
chr2D
92.833
293
20
1
1763
2054
617438833
617438541
8.550000e-115
424
6
TraesCS1A01G266400
chr7B
93.566
2067
108
18
2
2054
551484717
551482662
0.000000e+00
3057
7
TraesCS1A01G266400
chr3B
92.754
2084
97
24
2
2053
597426788
597428849
0.000000e+00
2963
8
TraesCS1A01G266400
chr3B
92.033
1343
92
12
359
1692
8505221
8506557
0.000000e+00
1873
9
TraesCS1A01G266400
chr4D
95.868
1694
64
6
2
1692
459191345
459193035
0.000000e+00
2736
10
TraesCS1A01G266400
chrUn
94.803
1674
48
15
416
2052
96553413
96555084
0.000000e+00
2573
11
TraesCS1A01G266400
chrUn
93.881
523
27
5
2
520
96553078
96553599
0.000000e+00
784
12
TraesCS1A01G266400
chr1B
91.774
1702
124
11
2
1692
127026367
127024671
0.000000e+00
2353
13
TraesCS1A01G266400
chr1B
92.884
801
41
11
1264
2052
470720338
470721134
0.000000e+00
1149
14
TraesCS1A01G266400
chr1B
91.185
329
21
5
1734
2055
127024686
127024359
8.490000e-120
440
15
TraesCS1A01G266400
chr7A
88.524
1612
119
34
495
2052
48781641
48783240
0.000000e+00
1892
16
TraesCS1A01G266400
chr7A
94.216
536
31
0
2049
2584
53984855
53984320
0.000000e+00
819
17
TraesCS1A01G266400
chr7A
93.657
536
34
0
2049
2584
290204221
290204756
0.000000e+00
802
18
TraesCS1A01G266400
chr2B
93.180
1085
70
4
610
1692
677292471
677293553
0.000000e+00
1591
19
TraesCS1A01G266400
chr7D
92.011
701
27
10
1381
2052
69948231
69948931
0.000000e+00
957
20
TraesCS1A01G266400
chr7D
93.820
534
33
0
2051
2584
185897798
185898331
0.000000e+00
804
21
TraesCS1A01G266400
chr3A
94.216
536
31
0
2049
2584
259353476
259354011
0.000000e+00
819
22
TraesCS1A01G266400
chr3A
93.843
536
33
0
2049
2584
132376254
132375719
0.000000e+00
808
23
TraesCS1A01G266400
chr5A
94.030
536
32
0
2049
2584
291197952
291197417
0.000000e+00
813
24
TraesCS1A01G266400
chr5A
89.813
589
51
8
2
586
570488398
570488981
0.000000e+00
747
25
TraesCS1A01G266400
chr3D
93.680
538
33
1
2048
2584
213025760
213025223
0.000000e+00
804
26
TraesCS1A01G266400
chr4A
93.470
536
35
0
2049
2584
161955456
161954921
0.000000e+00
797
27
TraesCS1A01G266400
chr6B
94.059
303
17
1
1759
2060
658405685
658405383
2.340000e-125
459
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
TraesCS1A01G266400
chr1A
461964204
461966787
2583
True
4772.0
4772
100.0000
1
2584
1
chr1A.!!$R2
2583
1
TraesCS1A01G266400
chr1A
35562950
35564001
1051
True
1749.0
1749
96.6790
2
1054
1
chr1A.!!$R1
1052
2
TraesCS1A01G266400
chr2D
469105846
469107932
2086
True
3238.0
3238
94.9260
2
2056
1
chr2D.!!$R1
2054
3
TraesCS1A01G266400
chr2D
631747909
631749570
1661
True
2270.0
2270
91.2150
2
1692
1
chr2D.!!$R3
1690
4
TraesCS1A01G266400
chr2D
344390040
344390573
533
False
798.0
798
93.6330
2051
2584
1
chr2D.!!$F1
533
5
TraesCS1A01G266400
chr7B
551482662
551484717
2055
True
3057.0
3057
93.5660
2
2054
1
chr7B.!!$R1
2052
6
TraesCS1A01G266400
chr3B
597426788
597428849
2061
False
2963.0
2963
92.7540
2
2053
1
chr3B.!!$F2
2051
7
TraesCS1A01G266400
chr3B
8505221
8506557
1336
False
1873.0
1873
92.0330
359
1692
1
chr3B.!!$F1
1333
8
TraesCS1A01G266400
chr4D
459191345
459193035
1690
False
2736.0
2736
95.8680
2
1692
1
chr4D.!!$F1
1690
9
TraesCS1A01G266400
chrUn
96553078
96555084
2006
False
1678.5
2573
94.3420
2
2052
2
chrUn.!!$F1
2050
10
TraesCS1A01G266400
chr1B
127024359
127026367
2008
True
1396.5
2353
91.4795
2
2055
2
chr1B.!!$R1
2053
11
TraesCS1A01G266400
chr1B
470720338
470721134
796
False
1149.0
1149
92.8840
1264
2052
1
chr1B.!!$F1
788
12
TraesCS1A01G266400
chr7A
48781641
48783240
1599
False
1892.0
1892
88.5240
495
2052
1
chr7A.!!$F1
1557
13
TraesCS1A01G266400
chr7A
53984320
53984855
535
True
819.0
819
94.2160
2049
2584
1
chr7A.!!$R1
535
14
TraesCS1A01G266400
chr7A
290204221
290204756
535
False
802.0
802
93.6570
2049
2584
1
chr7A.!!$F2
535
15
TraesCS1A01G266400
chr2B
677292471
677293553
1082
False
1591.0
1591
93.1800
610
1692
1
chr2B.!!$F1
1082
16
TraesCS1A01G266400
chr7D
69948231
69948931
700
False
957.0
957
92.0110
1381
2052
1
chr7D.!!$F1
671
17
TraesCS1A01G266400
chr7D
185897798
185898331
533
False
804.0
804
93.8200
2051
2584
1
chr7D.!!$F2
533
18
TraesCS1A01G266400
chr3A
259353476
259354011
535
False
819.0
819
94.2160
2049
2584
1
chr3A.!!$F1
535
19
TraesCS1A01G266400
chr3A
132375719
132376254
535
True
808.0
808
93.8430
2049
2584
1
chr3A.!!$R1
535
20
TraesCS1A01G266400
chr5A
291197417
291197952
535
True
813.0
813
94.0300
2049
2584
1
chr5A.!!$R1
535
21
TraesCS1A01G266400
chr5A
570488398
570488981
583
False
747.0
747
89.8130
2
586
1
chr5A.!!$F1
584
22
TraesCS1A01G266400
chr3D
213025223
213025760
537
True
804.0
804
93.6800
2048
2584
1
chr3D.!!$R1
536
23
TraesCS1A01G266400
chr4A
161954921
161955456
535
True
797.0
797
93.4700
2049
2584
1
chr4A.!!$R1
535
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.