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
TraesCS3D01G499900
chr3D
100.000
2576
0
0
1
2576
589494288
589491713
0.000000e+00
4758.0
1
TraesCS3D01G499900
chr3D
87.585
1031
71
26
674
1649
589506462
589505434
0.000000e+00
1142.0
2
TraesCS3D01G499900
chr3D
93.077
650
33
5
1930
2576
62951077
62950437
0.000000e+00
941.0
3
TraesCS3D01G499900
chr3D
89.189
740
59
12
939
1660
589426748
589426012
0.000000e+00
904.0
4
TraesCS3D01G499900
chr3D
91.896
654
37
6
939
1576
589432975
589432322
0.000000e+00
900.0
5
TraesCS3D01G499900
chr3D
88.328
574
58
8
1109
1677
589417750
589417181
0.000000e+00
680.0
6
TraesCS3D01G499900
chr3D
87.195
492
41
10
68
547
589564148
589563667
8.110000e-150
540.0
7
TraesCS3D01G499900
chr3D
85.801
493
43
12
68
543
589437786
589437304
4.950000e-137
497.0
8
TraesCS3D01G499900
chr3D
81.963
438
40
16
693
1108
589418199
589417779
4.110000e-88
335.0
9
TraesCS3D01G499900
chr3D
91.667
240
18
2
1671
1909
62951394
62951156
5.310000e-87
331.0
10
TraesCS3D01G499900
chr3D
81.088
386
36
19
740
1091
589573293
589572911
9.080000e-70
274.0
11
TraesCS3D01G499900
chr3D
97.727
44
1
0
555
598
589437270
589437227
2.750000e-10
76.8
12
TraesCS3D01G499900
chr3A
86.678
1719
134
51
1
1668
719355191
719353517
0.000000e+00
1818.0
13
TraesCS3D01G499900
chr3A
89.298
570
48
11
1109
1667
719337323
719336756
0.000000e+00
702.0
14
TraesCS3D01G499900
chr3A
88.393
560
53
7
1109
1664
719350076
719349525
0.000000e+00
664.0
15
TraesCS3D01G499900
chr3A
84.911
338
39
9
693
1018
719361254
719360917
5.310000e-87
331.0
16
TraesCS3D01G499900
chr3B
83.804
1593
132
49
151
1651
787989222
787990780
0.000000e+00
1397.0
17
TraesCS3D01G499900
chr3B
87.759
1013
81
21
674
1660
787472102
787473097
0.000000e+00
1144.0
18
TraesCS3D01G499900
chr3B
90.295
237
17
1
320
556
788059140
788058910
3.220000e-79
305.0
19
TraesCS3D01G499900
chr3B
79.419
413
48
17
715
1091
788074041
788073630
9.150000e-65
257.0
20
TraesCS3D01G499900
chr3B
97.727
44
1
0
555
598
788058886
788058843
2.750000e-10
76.8
21
TraesCS3D01G499900
chr4B
89.140
930
70
23
1671
2576
667579174
667578252
0.000000e+00
1129.0
22
TraesCS3D01G499900
chr4B
92.769
650
36
5
1930
2576
439746848
439746207
0.000000e+00
929.0
23
TraesCS3D01G499900
chr4B
90.833
240
20
2
1671
1909
439747165
439746927
1.150000e-83
320.0
24
TraesCS3D01G499900
chr2A
96.291
647
24
0
1930
2576
718219830
718219184
0.000000e+00
1062.0
25
TraesCS3D01G499900
chr2B
95.922
564
22
1
2014
2576
8436267
8436830
0.000000e+00
913.0
26
TraesCS3D01G499900
chr2B
92.623
244
13
5
1671
1911
8435868
8436109
1.900000e-91
346.0
27
TraesCS3D01G499900
chr2B
84.848
66
10
0
3
68
27499843
27499908
1.650000e-07
67.6
28
TraesCS3D01G499900
chr4A
95.271
571
26
1
2007
2576
714168039
714168609
0.000000e+00
904.0
29
TraesCS3D01G499900
chr4A
92.593
243
15
3
1671
1911
714167660
714167901
1.900000e-91
346.0
30
TraesCS3D01G499900
chr4A
91.358
243
17
4
1671
1911
657373557
657373797
1.910000e-86
329.0
31
TraesCS3D01G499900
chr4A
90.947
243
18
4
1671
1911
657313913
657314153
8.890000e-85
324.0
32
TraesCS3D01G499900
chr7B
91.667
648
51
2
1930
2576
660233955
660233310
0.000000e+00
894.0
33
TraesCS3D01G499900
chr7B
94.046
571
33
1
2007
2576
2557157
2556587
0.000000e+00
865.0
34
TraesCS3D01G499900
chr7B
92.562
242
16
2
1671
1911
2557535
2557295
1.900000e-91
346.0
35
TraesCS3D01G499900
chr5D
93.807
549
34
0
2028
2576
236451215
236451763
0.000000e+00
826.0
36
TraesCS3D01G499900
chr5B
91.250
240
19
2
1671
1909
669454390
669454628
2.470000e-85
326.0
37
TraesCS3D01G499900
chr7D
94.030
67
4
0
1
67
65505391
65505325
4.530000e-18
102.0
38
TraesCS3D01G499900
chr1A
88.158
76
6
3
472
545
20963173
20963099
1.270000e-13
87.9
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
TraesCS3D01G499900
chr3D
589491713
589494288
2575
True
4758.0
4758
100.0000
1
2576
1
chr3D.!!$R3
2575
1
TraesCS3D01G499900
chr3D
589505434
589506462
1028
True
1142.0
1142
87.5850
674
1649
1
chr3D.!!$R4
975
2
TraesCS3D01G499900
chr3D
589426012
589426748
736
True
904.0
904
89.1890
939
1660
1
chr3D.!!$R1
721
3
TraesCS3D01G499900
chr3D
589432322
589432975
653
True
900.0
900
91.8960
939
1576
1
chr3D.!!$R2
637
4
TraesCS3D01G499900
chr3D
62950437
62951394
957
True
636.0
941
92.3720
1671
2576
2
chr3D.!!$R7
905
5
TraesCS3D01G499900
chr3D
589417181
589418199
1018
True
507.5
680
85.1455
693
1677
2
chr3D.!!$R8
984
6
TraesCS3D01G499900
chr3D
589437227
589437786
559
True
286.9
497
91.7640
68
598
2
chr3D.!!$R9
530
7
TraesCS3D01G499900
chr3A
719349525
719355191
5666
True
1241.0
1818
87.5355
1
1668
2
chr3A.!!$R3
1667
8
TraesCS3D01G499900
chr3A
719336756
719337323
567
True
702.0
702
89.2980
1109
1667
1
chr3A.!!$R1
558
9
TraesCS3D01G499900
chr3B
787989222
787990780
1558
False
1397.0
1397
83.8040
151
1651
1
chr3B.!!$F2
1500
10
TraesCS3D01G499900
chr3B
787472102
787473097
995
False
1144.0
1144
87.7590
674
1660
1
chr3B.!!$F1
986
11
TraesCS3D01G499900
chr4B
667578252
667579174
922
True
1129.0
1129
89.1400
1671
2576
1
chr4B.!!$R1
905
12
TraesCS3D01G499900
chr4B
439746207
439747165
958
True
624.5
929
91.8010
1671
2576
2
chr4B.!!$R2
905
13
TraesCS3D01G499900
chr2A
718219184
718219830
646
True
1062.0
1062
96.2910
1930
2576
1
chr2A.!!$R1
646
14
TraesCS3D01G499900
chr2B
8435868
8436830
962
False
629.5
913
94.2725
1671
2576
2
chr2B.!!$F2
905
15
TraesCS3D01G499900
chr4A
714167660
714168609
949
False
625.0
904
93.9320
1671
2576
2
chr4A.!!$F3
905
16
TraesCS3D01G499900
chr7B
660233310
660233955
645
True
894.0
894
91.6670
1930
2576
1
chr7B.!!$R1
646
17
TraesCS3D01G499900
chr7B
2556587
2557535
948
True
605.5
865
93.3040
1671
2576
2
chr7B.!!$R2
905
18
TraesCS3D01G499900
chr5D
236451215
236451763
548
False
826.0
826
93.8070
2028
2576
1
chr5D.!!$F1
548
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.