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
TraesCS7B01G325900
chr7B
100.000
3224
0
0
1
3224
578715034
578718257
0.000000e+00
5954.0
1
TraesCS7B01G325900
chr7B
87.328
2249
203
40
1
2192
579484679
579486902
0.000000e+00
2499.0
2
TraesCS7B01G325900
chr7B
87.305
2245
206
40
3
2192
579435256
579437476
0.000000e+00
2494.0
3
TraesCS7B01G325900
chr7B
90.467
535
49
1
570
1104
578732362
578732894
0.000000e+00
704.0
4
TraesCS7B01G325900
chr7B
89.873
553
38
4
2204
2754
579486884
579487420
0.000000e+00
695.0
5
TraesCS7B01G325900
chr7B
87.382
531
55
10
2650
3175
579490486
579491009
1.660000e-167
599.0
6
TraesCS7B01G325900
chr7B
88.279
401
33
7
2204
2602
579490104
579490492
4.870000e-128
468.0
7
TraesCS7B01G325900
chr7B
84.804
408
45
8
2411
2817
578732900
578733291
8.380000e-106
394.0
8
TraesCS7B01G325900
chr7B
82.558
344
35
11
1865
2190
579489784
579490120
2.450000e-71
279.0
9
TraesCS7B01G325900
chr7B
87.448
239
23
6
2987
3224
579441942
579442174
5.300000e-68
268.0
10
TraesCS7B01G325900
chr7B
78.009
432
35
24
2850
3224
579487454
579487882
1.950000e-52
217.0
11
TraesCS7B01G325900
chr7A
96.611
1564
47
4
1
1562
617201565
617200006
0.000000e+00
2590.0
12
TraesCS7B01G325900
chr7A
92.500
600
34
4
2209
2806
617199293
617198703
0.000000e+00
848.0
13
TraesCS7B01G325900
chr7A
90.808
631
25
10
1560
2168
617199913
617199294
0.000000e+00
813.0
14
TraesCS7B01G325900
chr7A
83.810
210
22
9
3018
3224
617198474
617198274
4.250000e-44
189.0
15
TraesCS7B01G325900
chr7A
92.157
102
7
1
2854
2955
617198698
617198598
3.350000e-30
143.0
16
TraesCS7B01G325900
chr7A
91.000
100
7
2
2940
3038
617198583
617198485
2.020000e-27
134.0
17
TraesCS7B01G325900
chr7D
79.602
603
72
25
557
1154
560910067
560910623
5.050000e-103
385.0
18
TraesCS7B01G325900
chr7D
79.276
608
80
24
552
1154
560995515
560996081
1.810000e-102
383.0
19
TraesCS7B01G325900
chr7D
76.860
242
32
10
44
261
560909775
560910016
7.310000e-22
115.0
20
TraesCS7B01G325900
chr7D
87.500
80
8
2
3
81
560993471
560993549
1.230000e-14
91.6
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
TraesCS7B01G325900
chr7B
578715034
578718257
3223
False
5954.000000
5954
100.000000
1
3224
1
chr7B.!!$F1
3223
1
TraesCS7B01G325900
chr7B
579435256
579437476
2220
False
2494.000000
2494
87.305000
3
2192
1
chr7B.!!$F2
2189
2
TraesCS7B01G325900
chr7B
579484679
579491009
6330
False
792.833333
2499
85.571500
1
3224
6
chr7B.!!$F5
3223
3
TraesCS7B01G325900
chr7B
578732362
578733291
929
False
549.000000
704
87.635500
570
2817
2
chr7B.!!$F4
2247
4
TraesCS7B01G325900
chr7A
617198274
617201565
3291
True
786.166667
2590
91.147667
1
3224
6
chr7A.!!$R1
3223
5
TraesCS7B01G325900
chr7D
560909775
560910623
848
False
250.000000
385
78.231000
44
1154
2
chr7D.!!$F1
1110
6
TraesCS7B01G325900
chr7D
560993471
560996081
2610
False
237.300000
383
83.388000
3
1154
2
chr7D.!!$F2
1151
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.