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
TraesCS3B01G282300
chr3B
100.000
3033
0
0
1
3033
452718083
452715051
0.000000e+00
5602.0
1
TraesCS3B01G282300
chr4B
95.556
2925
70
19
157
3033
24744760
24747672
0.000000e+00
4626.0
2
TraesCS3B01G282300
chr4B
88.973
1859
127
34
667
2483
24758963
24760785
0.000000e+00
2226.0
3
TraesCS3B01G282300
chr4B
86.441
1475
143
29
661
2111
24741174
24742615
0.000000e+00
1563.0
4
TraesCS3B01G282300
chr4B
82.982
570
51
12
120
662
24758303
24758853
9.840000e-130
473.0
5
TraesCS3B01G282300
chr4B
91.613
155
12
1
318
471
24739550
24739704
2.370000e-51
213.0
6
TraesCS3B01G282300
chr4B
88.679
106
9
2
226
331
24688308
24688206
3.170000e-25
126.0
7
TraesCS3B01G282300
chr4A
85.893
2403
234
54
695
3033
586683187
586680826
0.000000e+00
2462.0
8
TraesCS3B01G282300
chr4A
84.861
1691
184
41
564
2212
456437726
456436066
0.000000e+00
1639.0
9
TraesCS3B01G282300
chr4A
85.411
1604
156
41
846
2407
586700187
586698620
0.000000e+00
1594.0
10
TraesCS3B01G282300
chr4A
87.263
581
41
14
2208
2773
456420488
456419926
1.530000e-177
632.0
11
TraesCS3B01G282300
chr4A
82.278
474
30
22
157
596
586683708
586683255
7.990000e-96
361.0
12
TraesCS3B01G282300
chr4A
78.475
446
34
28
157
567
456443768
456443350
5.060000e-58
235.0
13
TraesCS3B01G282300
chr4A
92.929
99
6
1
318
415
456451808
456451710
3.150000e-30
143.0
14
TraesCS3B01G282300
chr4A
80.882
136
18
6
179
310
456451975
456451844
1.920000e-17
100.0
15
TraesCS3B01G282300
chr4A
89.706
68
6
1
57
123
586686420
586686353
5.390000e-13
86.1
16
TraesCS3B01G282300
chr4A
83.721
86
12
2
39
123
456446003
456445919
2.510000e-11
80.5
17
TraesCS3B01G282300
chr4D
88.535
1823
133
31
714
2495
14914191
14915978
0.000000e+00
2139.0
18
TraesCS3B01G282300
chr4D
86.283
1633
160
29
883
2467
14862538
14864154
0.000000e+00
1716.0
19
TraesCS3B01G282300
chr4D
87.186
1475
146
25
659
2107
14908894
14910351
0.000000e+00
1637.0
20
TraesCS3B01G282300
chr4D
86.450
1535
150
30
659
2151
14460238
14458720
0.000000e+00
1629.0
21
TraesCS3B01G282300
chr4D
84.807
1685
182
37
846
2494
14851054
14852700
0.000000e+00
1626.0
22
TraesCS3B01G282300
chr4D
87.147
778
73
10
1849
2614
14433509
14432747
0.000000e+00
857.0
23
TraesCS3B01G282300
chr4D
87.814
558
44
13
2495
3033
14918974
14919526
1.530000e-177
632.0
24
TraesCS3B01G282300
chr4D
84.890
589
41
21
120
662
14908077
14908663
4.420000e-153
551.0
25
TraesCS3B01G282300
chr4D
81.038
559
42
21
140
662
14460953
14460423
1.320000e-103
387.0
26
TraesCS3B01G282300
chr4D
84.577
402
43
10
120
513
14867123
14867513
6.140000e-102
381.0
27
TraesCS3B01G282300
chr4D
78.634
571
66
28
512
1041
14895607
14896162
8.110000e-86
327.0
28
TraesCS3B01G282300
chr4D
84.120
233
23
5
661
884
14840237
14840010
2.370000e-51
213.0
29
TraesCS3B01G282300
chr4D
87.912
182
13
3
704
881
14850864
14851040
3.960000e-49
206.0
30
TraesCS3B01G282300
chr4D
88.889
135
12
2
155
286
14438716
14438582
2.420000e-36
163.0
31
TraesCS3B01G282300
chr4D
86.014
143
19
1
2511
2652
14854023
14854165
5.240000e-33
152.0
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
TraesCS3B01G282300
chr3B
452715051
452718083
3032
True
5602.000000
5602
100.000000
1
3033
1
chr3B.!!$R1
3032
1
TraesCS3B01G282300
chr4B
24739550
24747672
8122
False
2134.000000
4626
91.203333
157
3033
3
chr4B.!!$F1
2876
2
TraesCS3B01G282300
chr4B
24758303
24760785
2482
False
1349.500000
2226
85.977500
120
2483
2
chr4B.!!$F2
2363
3
TraesCS3B01G282300
chr4A
456436066
456437726
1660
True
1639.000000
1639
84.861000
564
2212
1
chr4A.!!$R2
1648
4
TraesCS3B01G282300
chr4A
586698620
586700187
1567
True
1594.000000
1594
85.411000
846
2407
1
chr4A.!!$R3
1561
5
TraesCS3B01G282300
chr4A
586680826
586686420
5594
True
969.700000
2462
85.959000
57
3033
3
chr4A.!!$R6
2976
6
TraesCS3B01G282300
chr4A
456419926
456420488
562
True
632.000000
632
87.263000
2208
2773
1
chr4A.!!$R1
565
7
TraesCS3B01G282300
chr4D
14908077
14919526
11449
False
1239.750000
2139
87.106250
120
3033
4
chr4D.!!$F4
2913
8
TraesCS3B01G282300
chr4D
14862538
14867513
4975
False
1048.500000
1716
85.430000
120
2467
2
chr4D.!!$F3
2347
9
TraesCS3B01G282300
chr4D
14458720
14460953
2233
True
1008.000000
1629
83.744000
140
2151
2
chr4D.!!$R4
2011
10
TraesCS3B01G282300
chr4D
14432747
14433509
762
True
857.000000
857
87.147000
1849
2614
1
chr4D.!!$R1
765
11
TraesCS3B01G282300
chr4D
14850864
14854165
3301
False
661.333333
1626
86.244333
704
2652
3
chr4D.!!$F2
1948
12
TraesCS3B01G282300
chr4D
14895607
14896162
555
False
327.000000
327
78.634000
512
1041
1
chr4D.!!$F1
529
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.