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
TraesCS4D01G153600
chr4D
100.000
2578
0
0
1
2578
195032608
195030031
0.000000e+00
4761.0
1
TraesCS4D01G153600
chr4D
88.399
1724
172
16
139
1835
52079016
52080738
0.000000e+00
2050.0
2
TraesCS4D01G153600
chr1D
89.542
1989
159
28
1
1955
165150102
165152075
0.000000e+00
2475.0
3
TraesCS4D01G153600
chr1D
87.654
81
6
3
2501
2578
165152059
165152138
9.820000e-15
91.6
4
TraesCS4D01G153600
chr7A
89.397
1858
162
13
1
1835
133735937
133737782
0.000000e+00
2307.0
5
TraesCS4D01G153600
chr7A
96.745
553
16
2
1949
2500
319592009
319591458
0.000000e+00
920.0
6
TraesCS4D01G153600
chr3D
88.811
1859
183
14
1
1835
373976007
373977864
0.000000e+00
2257.0
7
TraesCS4D01G153600
chr3D
87.627
1867
196
21
1
1835
262962002
262960139
0.000000e+00
2135.0
8
TraesCS4D01G153600
chr3D
91.332
946
76
4
1
942
543638873
543637930
0.000000e+00
1288.0
9
TraesCS4D01G153600
chr3D
96.869
543
16
1
1959
2500
365531887
365531345
0.000000e+00
907.0
10
TraesCS4D01G153600
chr2D
87.830
1972
173
31
7
1955
422741514
422739587
0.000000e+00
2250.0
11
TraesCS4D01G153600
chr2D
85.112
1874
233
31
1
1833
6325365
6323497
0.000000e+00
1873.0
12
TraesCS4D01G153600
chr7B
87.924
1946
185
28
2
1909
686793060
686791127
0.000000e+00
2246.0
13
TraesCS4D01G153600
chr7B
88.020
1369
120
24
618
1955
337174734
337176089
0.000000e+00
1580.0
14
TraesCS4D01G153600
chr7B
88.889
81
5
3
2501
2578
337176073
337176152
2.110000e-16
97.1
15
TraesCS4D01G153600
chr5A
88.530
1857
169
26
2
1835
148245147
148243312
0.000000e+00
2209.0
16
TraesCS4D01G153600
chr5A
96.703
546
16
2
1957
2500
47457305
47456760
0.000000e+00
907.0
17
TraesCS4D01G153600
chr5A
95.139
576
24
4
1929
2500
8513450
8512875
0.000000e+00
905.0
18
TraesCS4D01G153600
chr6D
88.049
1866
186
21
2
1835
370681389
370679529
0.000000e+00
2176.0
19
TraesCS4D01G153600
chr2A
87.507
1873
190
23
4
1835
298392990
298391121
0.000000e+00
2122.0
20
TraesCS4D01G153600
chr2A
96.886
546
16
1
1956
2500
90419683
90420228
0.000000e+00
913.0
21
TraesCS4D01G153600
chr2B
86.205
1979
205
32
3
1955
293939400
293941336
0.000000e+00
2080.0
22
TraesCS4D01G153600
chr2B
89.058
1380
128
15
240
1607
350425113
350423745
0.000000e+00
1690.0
23
TraesCS4D01G153600
chr2B
81.543
1387
197
35
458
1817
260986122
260984768
0.000000e+00
1088.0
24
TraesCS4D01G153600
chr3B
96.886
546
16
1
1956
2500
398842376
398842921
0.000000e+00
913.0
25
TraesCS4D01G153600
chr3B
87.928
613
50
9
1233
1835
146636602
146637200
0.000000e+00
701.0
26
TraesCS4D01G153600
chr6A
96.703
546
17
1
1956
2500
410901504
410902049
0.000000e+00
907.0
27
TraesCS4D01G153600
chr4B
96.703
546
17
1
1956
2500
199715570
199715025
0.000000e+00
907.0
28
TraesCS4D01G153600
chr3A
96.703
546
17
1
1956
2500
369399092
369399637
0.000000e+00
907.0
29
TraesCS4D01G153600
chr5B
97.778
45
1
0
2532
2576
457866278
457866234
7.650000e-11
78.7
30
TraesCS4D01G153600
chr5B
97.778
45
1
0
2532
2576
457946611
457946567
7.650000e-11
78.7
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
TraesCS4D01G153600
chr4D
195030031
195032608
2577
True
4761.00
4761
100.0000
1
2578
1
chr4D.!!$R1
2577
1
TraesCS4D01G153600
chr4D
52079016
52080738
1722
False
2050.00
2050
88.3990
139
1835
1
chr4D.!!$F1
1696
2
TraesCS4D01G153600
chr1D
165150102
165152138
2036
False
1283.30
2475
88.5980
1
2578
2
chr1D.!!$F1
2577
3
TraesCS4D01G153600
chr7A
133735937
133737782
1845
False
2307.00
2307
89.3970
1
1835
1
chr7A.!!$F1
1834
4
TraesCS4D01G153600
chr7A
319591458
319592009
551
True
920.00
920
96.7450
1949
2500
1
chr7A.!!$R1
551
5
TraesCS4D01G153600
chr3D
373976007
373977864
1857
False
2257.00
2257
88.8110
1
1835
1
chr3D.!!$F1
1834
6
TraesCS4D01G153600
chr3D
262960139
262962002
1863
True
2135.00
2135
87.6270
1
1835
1
chr3D.!!$R1
1834
7
TraesCS4D01G153600
chr3D
543637930
543638873
943
True
1288.00
1288
91.3320
1
942
1
chr3D.!!$R3
941
8
TraesCS4D01G153600
chr3D
365531345
365531887
542
True
907.00
907
96.8690
1959
2500
1
chr3D.!!$R2
541
9
TraesCS4D01G153600
chr2D
422739587
422741514
1927
True
2250.00
2250
87.8300
7
1955
1
chr2D.!!$R2
1948
10
TraesCS4D01G153600
chr2D
6323497
6325365
1868
True
1873.00
1873
85.1120
1
1833
1
chr2D.!!$R1
1832
11
TraesCS4D01G153600
chr7B
686791127
686793060
1933
True
2246.00
2246
87.9240
2
1909
1
chr7B.!!$R1
1907
12
TraesCS4D01G153600
chr7B
337174734
337176152
1418
False
838.55
1580
88.4545
618
2578
2
chr7B.!!$F1
1960
13
TraesCS4D01G153600
chr5A
148243312
148245147
1835
True
2209.00
2209
88.5300
2
1835
1
chr5A.!!$R3
1833
14
TraesCS4D01G153600
chr5A
47456760
47457305
545
True
907.00
907
96.7030
1957
2500
1
chr5A.!!$R2
543
15
TraesCS4D01G153600
chr5A
8512875
8513450
575
True
905.00
905
95.1390
1929
2500
1
chr5A.!!$R1
571
16
TraesCS4D01G153600
chr6D
370679529
370681389
1860
True
2176.00
2176
88.0490
2
1835
1
chr6D.!!$R1
1833
17
TraesCS4D01G153600
chr2A
298391121
298392990
1869
True
2122.00
2122
87.5070
4
1835
1
chr2A.!!$R1
1831
18
TraesCS4D01G153600
chr2A
90419683
90420228
545
False
913.00
913
96.8860
1956
2500
1
chr2A.!!$F1
544
19
TraesCS4D01G153600
chr2B
293939400
293941336
1936
False
2080.00
2080
86.2050
3
1955
1
chr2B.!!$F1
1952
20
TraesCS4D01G153600
chr2B
350423745
350425113
1368
True
1690.00
1690
89.0580
240
1607
1
chr2B.!!$R2
1367
21
TraesCS4D01G153600
chr2B
260984768
260986122
1354
True
1088.00
1088
81.5430
458
1817
1
chr2B.!!$R1
1359
22
TraesCS4D01G153600
chr3B
398842376
398842921
545
False
913.00
913
96.8860
1956
2500
1
chr3B.!!$F2
544
23
TraesCS4D01G153600
chr3B
146636602
146637200
598
False
701.00
701
87.9280
1233
1835
1
chr3B.!!$F1
602
24
TraesCS4D01G153600
chr6A
410901504
410902049
545
False
907.00
907
96.7030
1956
2500
1
chr6A.!!$F1
544
25
TraesCS4D01G153600
chr4B
199715025
199715570
545
True
907.00
907
96.7030
1956
2500
1
chr4B.!!$R1
544
26
TraesCS4D01G153600
chr3A
369399092
369399637
545
False
907.00
907
96.7030
1956
2500
1
chr3A.!!$F1
544
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.