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
TraesCS7B01G112600
chr7B
100.000
2549
0
0
1
2549
129570001
129567453
0.000000e+00
4708.0
1
TraesCS7B01G112600
chr7B
94.548
1981
96
9
569
2549
81247811
81249779
0.000000e+00
3049.0
2
TraesCS7B01G112600
chr2B
95.661
1982
75
7
569
2549
62450928
62452899
0.000000e+00
3173.0
3
TraesCS7B01G112600
chr2B
94.675
1953
90
7
569
2519
565228142
565226202
0.000000e+00
3018.0
4
TraesCS7B01G112600
chr2B
85.311
531
61
13
44
568
418933652
418934171
1.340000e-147
532.0
5
TraesCS7B01G112600
chr1B
95.516
1985
82
6
566
2549
639164488
639162510
0.000000e+00
3166.0
6
TraesCS7B01G112600
chr1B
89.205
528
53
4
44
568
327827535
327828061
0.000000e+00
656.0
7
TraesCS7B01G112600
chr1B
86.142
534
61
9
44
568
689374642
689374113
4.760000e-157
564.0
8
TraesCS7B01G112600
chr4B
95.411
1983
85
4
567
2549
648881435
648879459
0.000000e+00
3153.0
9
TraesCS7B01G112600
chr4B
95.626
1966
77
7
566
2528
657233509
657231550
0.000000e+00
3145.0
10
TraesCS7B01G112600
chr4B
95.264
1985
74
9
567
2549
89561741
89563707
0.000000e+00
3127.0
11
TraesCS7B01G112600
chr4B
95.182
1951
82
6
569
2512
80653674
80651729
0.000000e+00
3072.0
12
TraesCS7B01G112600
chr2D
94.475
1991
89
15
566
2549
64508695
64510671
0.000000e+00
3048.0
13
TraesCS7B01G112600
chr6B
94.355
1984
97
10
567
2549
44370163
44368194
0.000000e+00
3029.0
14
TraesCS7B01G112600
chr3B
91.579
570
43
4
4
568
504705188
504705757
0.000000e+00
782.0
15
TraesCS7B01G112600
chr1A
91.009
545
38
9
32
568
423643035
423643576
0.000000e+00
725.0
16
TraesCS7B01G112600
chr1D
90.702
527
46
3
44
568
208065199
208064674
0.000000e+00
699.0
17
TraesCS7B01G112600
chr1D
89.943
527
49
4
44
568
228082107
228082631
0.000000e+00
676.0
18
TraesCS7B01G112600
chr1D
88.994
527
52
6
44
568
228281284
228281806
0.000000e+00
647.0
19
TraesCS7B01G112600
chr1D
94.872
39
2
0
4
42
208065263
208065225
7.610000e-06
62.1
20
TraesCS7B01G112600
chr1D
92.857
42
3
0
1
42
228281217
228281258
7.610000e-06
62.1
21
TraesCS7B01G112600
chr4A
88.750
560
52
8
12
563
122741117
122740561
0.000000e+00
675.0
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
TraesCS7B01G112600
chr7B
129567453
129570001
2548
True
4708.00
4708
100.0000
1
2549
1
chr7B.!!$R1
2548
1
TraesCS7B01G112600
chr7B
81247811
81249779
1968
False
3049.00
3049
94.5480
569
2549
1
chr7B.!!$F1
1980
2
TraesCS7B01G112600
chr2B
62450928
62452899
1971
False
3173.00
3173
95.6610
569
2549
1
chr2B.!!$F1
1980
3
TraesCS7B01G112600
chr2B
565226202
565228142
1940
True
3018.00
3018
94.6750
569
2519
1
chr2B.!!$R1
1950
4
TraesCS7B01G112600
chr2B
418933652
418934171
519
False
532.00
532
85.3110
44
568
1
chr2B.!!$F2
524
5
TraesCS7B01G112600
chr1B
639162510
639164488
1978
True
3166.00
3166
95.5160
566
2549
1
chr1B.!!$R1
1983
6
TraesCS7B01G112600
chr1B
327827535
327828061
526
False
656.00
656
89.2050
44
568
1
chr1B.!!$F1
524
7
TraesCS7B01G112600
chr1B
689374113
689374642
529
True
564.00
564
86.1420
44
568
1
chr1B.!!$R2
524
8
TraesCS7B01G112600
chr4B
648879459
648881435
1976
True
3153.00
3153
95.4110
567
2549
1
chr4B.!!$R2
1982
9
TraesCS7B01G112600
chr4B
657231550
657233509
1959
True
3145.00
3145
95.6260
566
2528
1
chr4B.!!$R3
1962
10
TraesCS7B01G112600
chr4B
89561741
89563707
1966
False
3127.00
3127
95.2640
567
2549
1
chr4B.!!$F1
1982
11
TraesCS7B01G112600
chr4B
80651729
80653674
1945
True
3072.00
3072
95.1820
569
2512
1
chr4B.!!$R1
1943
12
TraesCS7B01G112600
chr2D
64508695
64510671
1976
False
3048.00
3048
94.4750
566
2549
1
chr2D.!!$F1
1983
13
TraesCS7B01G112600
chr6B
44368194
44370163
1969
True
3029.00
3029
94.3550
567
2549
1
chr6B.!!$R1
1982
14
TraesCS7B01G112600
chr3B
504705188
504705757
569
False
782.00
782
91.5790
4
568
1
chr3B.!!$F1
564
15
TraesCS7B01G112600
chr1A
423643035
423643576
541
False
725.00
725
91.0090
32
568
1
chr1A.!!$F1
536
16
TraesCS7B01G112600
chr1D
228082107
228082631
524
False
676.00
676
89.9430
44
568
1
chr1D.!!$F1
524
17
TraesCS7B01G112600
chr1D
208064674
208065263
589
True
380.55
699
92.7870
4
568
2
chr1D.!!$R1
564
18
TraesCS7B01G112600
chr1D
228281217
228281806
589
False
354.55
647
90.9255
1
568
2
chr1D.!!$F2
567
19
TraesCS7B01G112600
chr4A
122740561
122741117
556
True
675.00
675
88.7500
12
563
1
chr4A.!!$R1
551
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.