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
TraesCS4A01G386400
chr4A
100.000
2909
0
0
1
2909
663985138
663988046
0.000000e+00
5373.0
1
TraesCS4A01G386400
chr4A
80.488
861
89
34
999
1849
664153150
664153941
1.160000e-163
586.0
2
TraesCS4A01G386400
chr4A
92.638
163
11
1
1
162
598291504
598291342
1.740000e-57
233.0
3
TraesCS4A01G386400
chr7A
90.766
888
66
8
471
1351
52278373
52279251
0.000000e+00
1171.0
4
TraesCS4A01G386400
chr7A
91.274
848
33
11
1429
2257
52279264
52280089
0.000000e+00
1118.0
5
TraesCS4A01G386400
chr7A
85.200
750
75
10
999
1742
52386913
52387632
0.000000e+00
737.0
6
TraesCS4A01G386400
chr7A
81.871
513
61
16
1
482
52277820
52278331
1.260000e-108
403.0
7
TraesCS4A01G386400
chr7A
80.591
541
74
23
1778
2306
52387720
52388241
3.520000e-104
388.0
8
TraesCS4A01G386400
chr7A
77.333
750
100
34
839
1566
50389280
50388579
2.120000e-101
379.0
9
TraesCS4A01G386400
chr7A
91.429
175
14
1
1569
1742
50388520
50388346
3.750000e-59
239.0
10
TraesCS4A01G386400
chr7D
89.509
896
65
13
471
1351
49380636
49381517
0.000000e+00
1107.0
11
TraesCS4A01G386400
chr7D
93.223
546
20
8
1805
2342
49381981
49382517
0.000000e+00
787.0
12
TraesCS4A01G386400
chr7D
83.988
687
70
17
1569
2235
47763350
47762684
8.850000e-175
623.0
13
TraesCS4A01G386400
chr7D
84.828
580
76
7
2341
2909
631182615
631183193
9.040000e-160
573.0
14
TraesCS4A01G386400
chr7D
88.089
403
26
5
1433
1819
49635923
49636319
2.640000e-125
459.0
15
TraesCS4A01G386400
chr7D
86.423
383
29
6
1431
1806
49381533
49381899
5.840000e-107
398.0
16
TraesCS4A01G386400
chr7D
89.444
180
16
3
1
177
269892743
269892564
1.050000e-54
224.0
17
TraesCS4A01G386400
chr7D
87.000
200
21
3
1845
2041
49636515
49636712
1.360000e-53
220.0
18
TraesCS4A01G386400
chr2B
94.271
576
24
6
2341
2907
571513438
571512863
0.000000e+00
872.0
19
TraesCS4A01G386400
chr2B
92.683
164
11
1
1
163
177780398
177780235
4.850000e-58
235.0
20
TraesCS4A01G386400
chr1D
88.256
579
50
11
2341
2909
462360164
462360734
0.000000e+00
676.0
21
TraesCS4A01G386400
chr6A
84.629
579
78
8
2341
2909
13045631
13045054
1.510000e-157
566.0
22
TraesCS4A01G386400
chr2A
84.602
578
78
7
2342
2909
133503917
133503341
5.440000e-157
564.0
23
TraesCS4A01G386400
chr2A
84.859
568
77
6
2339
2897
750110739
750111306
5.440000e-157
564.0
24
TraesCS4A01G386400
chr4B
84.256
578
78
12
2343
2909
660293451
660292876
4.240000e-153
551.0
25
TraesCS4A01G386400
chr4B
89.444
180
16
3
1
177
389088733
389088554
1.050000e-54
224.0
26
TraesCS4A01G386400
chr1A
85.038
528
76
3
2342
2868
482276900
482276375
4.270000e-148
534.0
27
TraesCS4A01G386400
chr6B
83.419
585
82
11
2338
2909
101464243
101464825
1.990000e-146
529.0
28
TraesCS4A01G386400
chr5D
90.000
180
15
3
1
177
175606240
175606061
2.250000e-56
230.0
29
TraesCS4A01G386400
chr5D
91.463
164
13
1
1
163
355110111
355110274
1.050000e-54
224.0
30
TraesCS4A01G386400
chr5D
89.381
113
12
0
1000
1112
329796631
329796519
3.020000e-30
143.0
31
TraesCS4A01G386400
chr3D
92.073
164
12
1
1
163
417979603
417979766
2.250000e-56
230.0
32
TraesCS4A01G386400
chr3D
89.444
180
16
3
1
177
433974750
433974571
1.050000e-54
224.0
33
TraesCS4A01G386400
chr2D
89.444
180
16
3
1
177
466989990
466989811
1.050000e-54
224.0
34
TraesCS4A01G386400
chr5A
86.614
127
15
2
1000
1126
426903901
426904025
3.910000e-29
139.0
35
TraesCS4A01G386400
chr5B
91.398
93
8
0
1000
1092
382909954
382909862
8.460000e-26
128.0
36
TraesCS4A01G386400
chr5B
100.000
33
0
0
1672
1704
382909497
382909465
8.700000e-06
62.1
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
TraesCS4A01G386400
chr4A
663985138
663988046
2908
False
5373.000000
5373
100.000000
1
2909
1
chr4A.!!$F1
2908
1
TraesCS4A01G386400
chr4A
664153150
664153941
791
False
586.000000
586
80.488000
999
1849
1
chr4A.!!$F2
850
2
TraesCS4A01G386400
chr7A
52277820
52280089
2269
False
897.333333
1171
87.970333
1
2257
3
chr7A.!!$F1
2256
3
TraesCS4A01G386400
chr7A
52386913
52388241
1328
False
562.500000
737
82.895500
999
2306
2
chr7A.!!$F2
1307
4
TraesCS4A01G386400
chr7A
50388346
50389280
934
True
309.000000
379
84.381000
839
1742
2
chr7A.!!$R1
903
5
TraesCS4A01G386400
chr7D
49380636
49382517
1881
False
764.000000
1107
89.718333
471
2342
3
chr7D.!!$F2
1871
6
TraesCS4A01G386400
chr7D
47762684
47763350
666
True
623.000000
623
83.988000
1569
2235
1
chr7D.!!$R1
666
7
TraesCS4A01G386400
chr7D
631182615
631183193
578
False
573.000000
573
84.828000
2341
2909
1
chr7D.!!$F1
568
8
TraesCS4A01G386400
chr7D
49635923
49636712
789
False
339.500000
459
87.544500
1433
2041
2
chr7D.!!$F3
608
9
TraesCS4A01G386400
chr2B
571512863
571513438
575
True
872.000000
872
94.271000
2341
2907
1
chr2B.!!$R2
566
10
TraesCS4A01G386400
chr1D
462360164
462360734
570
False
676.000000
676
88.256000
2341
2909
1
chr1D.!!$F1
568
11
TraesCS4A01G386400
chr6A
13045054
13045631
577
True
566.000000
566
84.629000
2341
2909
1
chr6A.!!$R1
568
12
TraesCS4A01G386400
chr2A
133503341
133503917
576
True
564.000000
564
84.602000
2342
2909
1
chr2A.!!$R1
567
13
TraesCS4A01G386400
chr2A
750110739
750111306
567
False
564.000000
564
84.859000
2339
2897
1
chr2A.!!$F1
558
14
TraesCS4A01G386400
chr4B
660292876
660293451
575
True
551.000000
551
84.256000
2343
2909
1
chr4B.!!$R2
566
15
TraesCS4A01G386400
chr1A
482276375
482276900
525
True
534.000000
534
85.038000
2342
2868
1
chr1A.!!$R1
526
16
TraesCS4A01G386400
chr6B
101464243
101464825
582
False
529.000000
529
83.419000
2338
2909
1
chr6B.!!$F1
571
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.