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
TraesCS7D01G070200
chr7D
100.000
2503
0
0
1
2503
41258589
41261091
0.000000e+00
4623.0
1
TraesCS7D01G070200
chr7D
96.823
1511
32
6
1
1507
41366844
41365346
0.000000e+00
2510.0
2
TraesCS7D01G070200
chr7D
89.526
802
60
7
480
1270
41274844
41275632
0.000000e+00
994.0
3
TraesCS7D01G070200
chr7D
89.228
622
52
11
887
1504
41325313
41325923
0.000000e+00
763.0
4
TraesCS7D01G070200
chr7D
87.473
455
48
6
2052
2499
41348818
41348366
1.330000e-142
516.0
5
TraesCS7D01G070200
chr7D
84.532
459
47
11
2045
2499
41401705
41402143
1.380000e-117
433.0
6
TraesCS7D01G070200
chr7D
85.934
391
36
9
455
838
41306750
41307128
1.390000e-107
399.0
7
TraesCS7D01G070200
chr7D
85.156
384
49
7
2
382
41274231
41274609
1.090000e-103
387.0
8
TraesCS7D01G070200
chr7D
84.416
385
56
4
2
382
41302604
41302988
2.350000e-100
375.0
9
TraesCS7D01G070200
chr7D
80.967
331
35
9
605
916
41273000
41273321
1.160000e-58
237.0
10
TraesCS7D01G070200
chr7D
87.200
125
11
2
462
581
41274712
41274836
1.210000e-28
137.0
11
TraesCS7D01G070200
chr7D
74.877
406
48
20
453
836
41344168
41343795
4.340000e-28
135.0
12
TraesCS7D01G070200
chr7A
87.282
1321
91
29
475
1757
40694881
40696162
0.000000e+00
1437.0
13
TraesCS7D01G070200
chr7A
92.683
451
29
3
2052
2499
40698008
40698457
0.000000e+00
647.0
14
TraesCS7D01G070200
chr7A
79.583
480
67
14
2
478
40693271
40693722
5.200000e-82
315.0
15
TraesCS7D01G070200
chr4A
91.071
784
53
7
1007
1781
648654189
648654964
0.000000e+00
1044.0
16
TraesCS7D01G070200
chr4A
85.221
1042
67
41
287
1303
648132815
648133794
0.000000e+00
990.0
17
TraesCS7D01G070200
chr4A
84.646
762
62
25
585
1303
648260572
648261321
0.000000e+00
708.0
18
TraesCS7D01G070200
chr4A
95.204
417
17
2
2016
2429
648142501
648142917
0.000000e+00
656.0
19
TraesCS7D01G070200
chr4A
88.278
418
40
4
1366
1781
648133883
648134293
2.240000e-135
492.0
20
TraesCS7D01G070200
chr4A
87.441
422
40
8
1366
1781
648261410
648261824
8.100000e-130
473.0
21
TraesCS7D01G070200
chr4A
88.824
340
38
0
962
1301
648337292
648337631
3.850000e-113
418.0
22
TraesCS7D01G070200
chr4A
89.354
263
22
2
2241
2503
648658424
648658680
2.400000e-85
326.0
23
TraesCS7D01G070200
chr4A
96.795
156
4
1
2052
2206
648658270
648658425
2.470000e-65
259.0
24
TraesCS7D01G070200
chr4A
86.592
179
19
2
1459
1637
648134564
648134737
2.540000e-45
193.0
25
TraesCS7D01G070200
chr4A
92.241
116
7
1
1897
2012
648263496
648263609
1.990000e-36
163.0
26
TraesCS7D01G070200
chr4A
90.179
112
10
1
450
560
648328159
648328270
7.220000e-31
145.0
27
TraesCS7D01G070200
chr4A
94.737
76
2
2
2387
2460
648142918
648142993
1.570000e-22
117.0
28
TraesCS7D01G070200
chr4A
87.879
99
12
0
450
548
648312213
648312311
1.570000e-22
117.0
29
TraesCS7D01G070200
chr4A
82.540
126
18
4
1381
1504
648671985
648672108
9.470000e-20
108.0
30
TraesCS7D01G070200
chr4A
84.545
110
13
2
590
699
648335570
648335675
3.400000e-19
106.0
31
TraesCS7D01G070200
chr4A
81.343
134
22
2
1371
1504
648582733
648582863
3.400000e-19
106.0
32
TraesCS7D01G070200
chr4A
95.349
43
2
0
1862
1904
648262390
648262432
4.470000e-08
69.4
33
TraesCS7D01G070200
chrUn
85.370
540
45
16
765
1283
48835683
48836209
1.700000e-146
529.0
34
TraesCS7D01G070200
chrUn
84.922
451
44
14
2052
2499
48812690
48813119
3.820000e-118
435.0
35
TraesCS7D01G070200
chrUn
82.418
91
14
2
1396
1485
48826707
48826796
7.420000e-11
78.7
36
TraesCS7D01G070200
chr5A
75.633
316
61
14
73
376
473037330
473037641
2.600000e-30
143.0
37
TraesCS7D01G070200
chr3B
100.000
29
0
0
2017
2045
675283770
675283742
1.000000e-03
54.7
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
TraesCS7D01G070200
chr7D
41258589
41261091
2502
False
4623.000000
4623
100.000000
1
2503
1
chr7D.!!$F1
2502
1
TraesCS7D01G070200
chr7D
41365346
41366844
1498
True
2510.000000
2510
96.823000
1
1507
1
chr7D.!!$R3
1506
2
TraesCS7D01G070200
chr7D
41325313
41325923
610
False
763.000000
763
89.228000
887
1504
1
chr7D.!!$F2
617
3
TraesCS7D01G070200
chr7D
41273000
41275632
2632
False
438.750000
994
85.712250
2
1270
4
chr7D.!!$F4
1268
4
TraesCS7D01G070200
chr7D
41302604
41307128
4524
False
387.000000
399
85.175000
2
838
2
chr7D.!!$F5
836
5
TraesCS7D01G070200
chr7A
40693271
40698457
5186
False
799.666667
1437
86.516000
2
2499
3
chr7A.!!$F1
2497
6
TraesCS7D01G070200
chr4A
648132815
648134737
1922
False
558.333333
990
86.697000
287
1781
3
chr4A.!!$F5
1494
7
TraesCS7D01G070200
chr4A
648654189
648658680
4491
False
543.000000
1044
92.406667
1007
2503
3
chr4A.!!$F9
1496
8
TraesCS7D01G070200
chr4A
648260572
648263609
3037
False
353.350000
708
89.919250
585
2012
4
chr4A.!!$F7
1427
9
TraesCS7D01G070200
chr4A
648335570
648337631
2061
False
262.000000
418
86.684500
590
1301
2
chr4A.!!$F8
711
10
TraesCS7D01G070200
chrUn
48835683
48836209
526
False
529.000000
529
85.370000
765
1283
1
chrUn.!!$F3
518
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.