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
TraesCS4B01G091900
chr4B
100.000
4805
0
0
1
4805
95068156
95072960
0.000000e+00
8874.0
1
TraesCS4B01G091900
chr4B
89.232
3241
297
37
1060
4289
94791602
94788403
0.000000e+00
4004.0
2
TraesCS4B01G091900
chr4A
96.474
4197
120
12
1
4176
531681614
531677425
0.000000e+00
6905.0
3
TraesCS4B01G091900
chr4A
85.225
3181
408
44
1020
4170
531386675
531383527
0.000000e+00
3214.0
4
TraesCS4B01G091900
chr4A
84.828
2564
311
37
1548
4091
532215674
532218179
0.000000e+00
2508.0
5
TraesCS4B01G091900
chr4A
80.723
996
131
27
1024
1992
626302384
626301423
0.000000e+00
719.0
6
TraesCS4B01G091900
chr4A
79.621
898
157
17
2124
3000
626299911
626299019
5.280000e-174
621.0
7
TraesCS4B01G091900
chr4D
95.607
4052
113
24
794
4805
64537714
64541740
0.000000e+00
6436.0
8
TraesCS4B01G091900
chr4D
89.919
1478
130
3
1078
2554
64356168
64354709
0.000000e+00
1886.0
9
TraesCS4B01G091900
chr4D
84.773
1655
190
33
2550
4170
64349333
64347707
0.000000e+00
1604.0
10
TraesCS4B01G091900
chr4D
94.975
796
33
5
2
795
64536884
64537674
0.000000e+00
1242.0
11
TraesCS4B01G091900
chr2D
84.150
2940
419
23
1020
3952
580192054
580194953
0.000000e+00
2804.0
12
TraesCS4B01G091900
chr2D
78.032
437
72
11
351
775
580191431
580191855
2.220000e-63
254.0
13
TraesCS4B01G091900
chr2B
83.988
2929
420
25
1032
3952
699107712
699110599
0.000000e+00
2765.0
14
TraesCS4B01G091900
chr2B
76.839
639
125
14
1144
1782
1574292
1573677
5.960000e-89
339.0
15
TraesCS4B01G091900
chr2A
83.617
1764
248
20
2199
3952
718119194
718120926
0.000000e+00
1618.0
16
TraesCS4B01G091900
chr2A
83.010
671
98
10
1020
1686
718117765
718118423
1.150000e-165
593.0
17
TraesCS4B01G091900
chr2A
97.143
35
1
0
981
1015
722734228
722734194
5.190000e-05
60.2
18
TraesCS4B01G091900
chrUn
76.960
625
121
14
1158
1782
358384049
358384650
7.710000e-88
335.0
19
TraesCS4B01G091900
chr3D
80.313
447
78
7
1020
1461
438451673
438452114
3.590000e-86
329.0
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
TraesCS4B01G091900
chr4B
95068156
95072960
4804
False
8874.0
8874
100.0000
1
4805
1
chr4B.!!$F1
4804
1
TraesCS4B01G091900
chr4B
94788403
94791602
3199
True
4004.0
4004
89.2320
1060
4289
1
chr4B.!!$R1
3229
2
TraesCS4B01G091900
chr4A
531677425
531681614
4189
True
6905.0
6905
96.4740
1
4176
1
chr4A.!!$R2
4175
3
TraesCS4B01G091900
chr4A
531383527
531386675
3148
True
3214.0
3214
85.2250
1020
4170
1
chr4A.!!$R1
3150
4
TraesCS4B01G091900
chr4A
532215674
532218179
2505
False
2508.0
2508
84.8280
1548
4091
1
chr4A.!!$F1
2543
5
TraesCS4B01G091900
chr4A
626299019
626302384
3365
True
670.0
719
80.1720
1024
3000
2
chr4A.!!$R3
1976
6
TraesCS4B01G091900
chr4D
64536884
64541740
4856
False
3839.0
6436
95.2910
2
4805
2
chr4D.!!$F1
4803
7
TraesCS4B01G091900
chr4D
64354709
64356168
1459
True
1886.0
1886
89.9190
1078
2554
1
chr4D.!!$R2
1476
8
TraesCS4B01G091900
chr4D
64347707
64349333
1626
True
1604.0
1604
84.7730
2550
4170
1
chr4D.!!$R1
1620
9
TraesCS4B01G091900
chr2D
580191431
580194953
3522
False
1529.0
2804
81.0910
351
3952
2
chr2D.!!$F1
3601
10
TraesCS4B01G091900
chr2B
699107712
699110599
2887
False
2765.0
2765
83.9880
1032
3952
1
chr2B.!!$F1
2920
11
TraesCS4B01G091900
chr2B
1573677
1574292
615
True
339.0
339
76.8390
1144
1782
1
chr2B.!!$R1
638
12
TraesCS4B01G091900
chr2A
718117765
718120926
3161
False
1105.5
1618
83.3135
1020
3952
2
chr2A.!!$F1
2932
13
TraesCS4B01G091900
chrUn
358384049
358384650
601
False
335.0
335
76.9600
1158
1782
1
chrUn.!!$F1
624
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.