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
TraesCS2D01G417500
chr2D
100.000
2921
0
0
1
2921
531766219
531769139
0.000000e+00
5395.0
1
TraesCS2D01G417500
chr2D
87.884
1626
132
23
610
2206
448223705
448222116
0.000000e+00
1851.0
2
TraesCS2D01G417500
chr3B
93.022
2207
141
2
1
2206
27469981
27472175
0.000000e+00
3210.0
3
TraesCS2D01G417500
chr3B
87.755
1715
145
24
521
2206
525631730
525630052
0.000000e+00
1943.0
4
TraesCS2D01G417500
chr3B
86.639
1699
176
27
516
2206
528611409
528613064
0.000000e+00
1832.0
5
TraesCS2D01G417500
chr4A
92.544
2213
144
8
1
2206
627998439
628000637
0.000000e+00
3153.0
6
TraesCS2D01G417500
chr4A
89.815
324
22
7
2601
2921
736822544
736822229
3.510000e-109
405.0
7
TraesCS2D01G417500
chr4A
88.720
328
26
7
2596
2921
736425694
736426012
9.810000e-105
390.0
8
TraesCS2D01G417500
chr5A
92.020
2218
163
12
1
2206
40620897
40623112
0.000000e+00
3103.0
9
TraesCS2D01G417500
chr5A
94.462
1282
70
1
929
2209
23920845
23919564
0.000000e+00
1973.0
10
TraesCS2D01G417500
chr1B
89.864
2062
169
19
114
2173
10357505
10355482
0.000000e+00
2614.0
11
TraesCS2D01G417500
chr1B
90.373
322
30
1
2600
2921
661931914
661931594
3.480000e-114
422.0
12
TraesCS2D01G417500
chr1A
93.097
1666
101
6
1
1664
35281900
35283553
0.000000e+00
2427.0
13
TraesCS2D01G417500
chr7A
91.978
1658
98
7
550
2206
48841187
48842810
0.000000e+00
2292.0
14
TraesCS2D01G417500
chr7A
86.111
144
19
1
2445
2587
706715461
706715604
1.400000e-33
154.0
15
TraesCS2D01G417500
chr2B
88.482
1693
169
13
519
2198
123197557
123195878
0.000000e+00
2023.0
16
TraesCS2D01G417500
chr2B
88.482
1693
169
13
519
2198
123287776
123286097
0.000000e+00
2023.0
17
TraesCS2D01G417500
chr2B
94.782
1169
57
4
1040
2206
94862962
94864128
0.000000e+00
1818.0
18
TraesCS2D01G417500
chr2B
90.303
330
28
1
2592
2921
631607729
631608054
2.080000e-116
429.0
19
TraesCS2D01G417500
chr2B
93.689
206
13
0
1
206
94813044
94813249
2.830000e-80
309.0
20
TraesCS2D01G417500
chr2B
87.500
248
18
8
2205
2442
631607497
631607741
1.030000e-69
274.0
21
TraesCS2D01G417500
chr2B
90.541
74
7
0
143
216
142737319
142737392
6.660000e-17
99.0
22
TraesCS2D01G417500
chr6A
86.903
1718
160
34
521
2209
569975226
569973545
0.000000e+00
1866.0
23
TraesCS2D01G417500
chr6B
85.908
1696
187
28
519
2207
5728719
5727069
0.000000e+00
1760.0
24
TraesCS2D01G417500
chr6B
91.818
330
26
1
2592
2921
688752630
688752958
2.650000e-125
459.0
25
TraesCS2D01G417500
chr6B
89.634
328
31
3
2595
2921
27900369
27900044
5.820000e-112
414.0
26
TraesCS2D01G417500
chr6B
84.028
144
22
1
2445
2587
568880842
568880985
1.410000e-28
137.0
27
TraesCS2D01G417500
chr2A
89.819
717
56
6
2213
2921
676374429
676375136
0.000000e+00
904.0
28
TraesCS2D01G417500
chr1D
89.474
323
30
2
2599
2921
475867847
475867529
3.510000e-109
405.0
29
TraesCS2D01G417500
chr1D
84.270
89
13
1
328
415
253216690
253216602
5.190000e-13
86.1
30
TraesCS2D01G417500
chr7D
89.124
331
27
7
2592
2919
5779990
5780314
1.260000e-108
403.0
31
TraesCS2D01G417500
chr3A
84.337
249
31
7
1964
2210
466778287
466778045
1.350000e-58
237.0
32
TraesCS2D01G417500
chrUn
84.028
144
22
1
2445
2587
322258151
322258294
1.410000e-28
137.0
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
TraesCS2D01G417500
chr2D
531766219
531769139
2920
False
5395.0
5395
100.0000
1
2921
1
chr2D.!!$F1
2920
1
TraesCS2D01G417500
chr2D
448222116
448223705
1589
True
1851.0
1851
87.8840
610
2206
1
chr2D.!!$R1
1596
2
TraesCS2D01G417500
chr3B
27469981
27472175
2194
False
3210.0
3210
93.0220
1
2206
1
chr3B.!!$F1
2205
3
TraesCS2D01G417500
chr3B
525630052
525631730
1678
True
1943.0
1943
87.7550
521
2206
1
chr3B.!!$R1
1685
4
TraesCS2D01G417500
chr3B
528611409
528613064
1655
False
1832.0
1832
86.6390
516
2206
1
chr3B.!!$F2
1690
5
TraesCS2D01G417500
chr4A
627998439
628000637
2198
False
3153.0
3153
92.5440
1
2206
1
chr4A.!!$F1
2205
6
TraesCS2D01G417500
chr5A
40620897
40623112
2215
False
3103.0
3103
92.0200
1
2206
1
chr5A.!!$F1
2205
7
TraesCS2D01G417500
chr5A
23919564
23920845
1281
True
1973.0
1973
94.4620
929
2209
1
chr5A.!!$R1
1280
8
TraesCS2D01G417500
chr1B
10355482
10357505
2023
True
2614.0
2614
89.8640
114
2173
1
chr1B.!!$R1
2059
9
TraesCS2D01G417500
chr1A
35281900
35283553
1653
False
2427.0
2427
93.0970
1
1664
1
chr1A.!!$F1
1663
10
TraesCS2D01G417500
chr7A
48841187
48842810
1623
False
2292.0
2292
91.9780
550
2206
1
chr7A.!!$F1
1656
11
TraesCS2D01G417500
chr2B
123195878
123197557
1679
True
2023.0
2023
88.4820
519
2198
1
chr2B.!!$R1
1679
12
TraesCS2D01G417500
chr2B
123286097
123287776
1679
True
2023.0
2023
88.4820
519
2198
1
chr2B.!!$R2
1679
13
TraesCS2D01G417500
chr2B
94862962
94864128
1166
False
1818.0
1818
94.7820
1040
2206
1
chr2B.!!$F2
1166
14
TraesCS2D01G417500
chr2B
631607497
631608054
557
False
351.5
429
88.9015
2205
2921
2
chr2B.!!$F4
716
15
TraesCS2D01G417500
chr6A
569973545
569975226
1681
True
1866.0
1866
86.9030
521
2209
1
chr6A.!!$R1
1688
16
TraesCS2D01G417500
chr6B
5727069
5728719
1650
True
1760.0
1760
85.9080
519
2207
1
chr6B.!!$R1
1688
17
TraesCS2D01G417500
chr2A
676374429
676375136
707
False
904.0
904
89.8190
2213
2921
1
chr2A.!!$F1
708
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.