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
TraesCS7D01G473600
chr7D
100.000
2294
0
0
901
3194
586509023
586506730
0.000000e+00
4237
1
TraesCS7D01G473600
chr7D
85.839
1716
153
24
963
2638
586688696
586690361
0.000000e+00
1740
2
TraesCS7D01G473600
chr7D
100.000
666
0
0
1
666
586509923
586509258
0.000000e+00
1230
3
TraesCS7D01G473600
chr7D
77.991
2140
313
86
1002
3062
586700213
586702273
0.000000e+00
1197
4
TraesCS7D01G473600
chr7D
81.453
771
88
30
1997
2739
586500928
586500185
5.940000e-162
580
5
TraesCS7D01G473600
chr7A
90.859
2188
135
31
901
3063
677723818
677721671
0.000000e+00
2872
6
TraesCS7D01G473600
chr7A
88.915
2138
171
26
906
2997
677821288
677823405
0.000000e+00
2575
7
TraesCS7D01G473600
chr7A
78.627
1151
205
24
966
2103
677838965
677840087
0.000000e+00
725
8
TraesCS7D01G473600
chr7A
75.882
1530
285
47
1003
2483
678146203
678144709
0.000000e+00
704
9
TraesCS7D01G473600
chr7A
88.912
487
32
11
185
666
677724297
677723828
5.940000e-162
580
10
TraesCS7D01G473600
chr7A
97.015
67
2
0
3125
3191
677823400
677823466
2.600000e-21
113
11
TraesCS7D01G473600
chr7B
93.795
1402
67
6
901
2287
656552251
656550855
0.000000e+00
2089
12
TraesCS7D01G473600
chr7B
86.778
1732
156
25
963
2638
656928762
656930476
0.000000e+00
1862
13
TraesCS7D01G473600
chr7B
78.629
2101
343
51
1002
3062
657084641
657086675
0.000000e+00
1295
14
TraesCS7D01G473600
chr7B
87.135
925
65
28
2121
3014
657077063
657077964
0.000000e+00
1000
15
TraesCS7D01G473600
chr7B
93.202
559
36
2
2637
3194
656550291
656549734
0.000000e+00
821
16
TraesCS7D01G473600
chr7B
76.749
1587
289
49
929
2491
656529660
656528130
0.000000e+00
813
17
TraesCS7D01G473600
chr7B
89.583
624
34
12
49
666
657076432
657077030
0.000000e+00
763
18
TraesCS7D01G473600
chr7B
76.272
1572
273
56
963
2483
657663318
657661796
0.000000e+00
745
19
TraesCS7D01G473600
chr7B
86.371
587
46
17
2440
3014
656550851
656550287
7.570000e-171
610
20
TraesCS7D01G473600
chr7B
89.407
472
48
2
2425
2896
731586078
731585609
7.630000e-166
593
21
TraesCS7D01G473600
chr7B
83.213
554
89
4
966
1517
657338812
657339363
3.680000e-139
505
22
TraesCS7D01G473600
chr7B
91.758
364
26
4
2637
2997
657077960
657078322
1.320000e-138
503
23
TraesCS7D01G473600
chr7B
75.487
1130
208
39
1002
2113
657420548
657421626
3.700000e-134
488
24
TraesCS7D01G473600
chr7B
92.075
265
14
2
2926
3189
657080877
657081135
1.810000e-97
366
25
TraesCS7D01G473600
chr7B
85.763
295
36
4
966
1254
657317983
657318277
1.110000e-79
307
26
TraesCS7D01G473600
chr7B
89.868
227
15
6
444
666
656552483
656552261
5.210000e-73
285
27
TraesCS7D01G473600
chr7B
73.783
534
85
34
1996
2485
657314568
657315090
3.300000e-35
159
28
TraesCS7D01G473600
chr7B
98.507
67
1
0
3125
3191
657078317
657078383
5.600000e-23
119
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
TraesCS7D01G473600
chr7D
586506730
586509923
3193
True
2733.500000
4237
100.0000
1
3194
2
chr7D.!!$R2
3193
1
TraesCS7D01G473600
chr7D
586688696
586690361
1665
False
1740.000000
1740
85.8390
963
2638
1
chr7D.!!$F1
1675
2
TraesCS7D01G473600
chr7D
586700213
586702273
2060
False
1197.000000
1197
77.9910
1002
3062
1
chr7D.!!$F2
2060
3
TraesCS7D01G473600
chr7D
586500185
586500928
743
True
580.000000
580
81.4530
1997
2739
1
chr7D.!!$R1
742
4
TraesCS7D01G473600
chr7A
677721671
677724297
2626
True
1726.000000
2872
89.8855
185
3063
2
chr7A.!!$R2
2878
5
TraesCS7D01G473600
chr7A
677821288
677823466
2178
False
1344.000000
2575
92.9650
906
3191
2
chr7A.!!$F2
2285
6
TraesCS7D01G473600
chr7A
677838965
677840087
1122
False
725.000000
725
78.6270
966
2103
1
chr7A.!!$F1
1137
7
TraesCS7D01G473600
chr7A
678144709
678146203
1494
True
704.000000
704
75.8820
1003
2483
1
chr7A.!!$R1
1480
8
TraesCS7D01G473600
chr7B
656928762
656930476
1714
False
1862.000000
1862
86.7780
963
2638
1
chr7B.!!$F1
1675
9
TraesCS7D01G473600
chr7B
656549734
656552483
2749
True
951.250000
2089
90.8090
444
3194
4
chr7B.!!$R4
2750
10
TraesCS7D01G473600
chr7B
656528130
656529660
1530
True
813.000000
813
76.7490
929
2491
1
chr7B.!!$R1
1562
11
TraesCS7D01G473600
chr7B
657661796
657663318
1522
True
745.000000
745
76.2720
963
2483
1
chr7B.!!$R2
1520
12
TraesCS7D01G473600
chr7B
657076432
657086675
10243
False
674.333333
1295
89.6145
49
3191
6
chr7B.!!$F4
3142
13
TraesCS7D01G473600
chr7B
657338812
657339363
551
False
505.000000
505
83.2130
966
1517
1
chr7B.!!$F2
551
14
TraesCS7D01G473600
chr7B
657420548
657421626
1078
False
488.000000
488
75.4870
1002
2113
1
chr7B.!!$F3
1111
15
TraesCS7D01G473600
chr7B
657314568
657318277
3709
False
233.000000
307
79.7730
966
2485
2
chr7B.!!$F5
1519
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.