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
TraesCS3B01G429800
chr3B
100.000
2524
0
0
1
2524
669396467
669393944
0.000000e+00
4662
1
TraesCS3B01G429800
chr3B
89.077
1712
143
23
203
1876
246274084
246275789
0.000000e+00
2085
2
TraesCS3B01G429800
chr3B
93.237
207
11
1
5
208
377246255
377246049
4.080000e-78
302
3
TraesCS3B01G429800
chr4B
89.050
2338
209
23
3
2306
136097234
136099558
0.000000e+00
2856
4
TraesCS3B01G429800
chr5D
91.231
2121
150
23
203
2306
361378700
361380801
0.000000e+00
2854
5
TraesCS3B01G429800
chr5D
91.135
1692
125
13
625
2306
125554850
125553174
0.000000e+00
2270
6
TraesCS3B01G429800
chr5D
91.846
650
48
4
1658
2306
530656191
530655546
0.000000e+00
902
7
TraesCS3B01G429800
chr5D
92.823
209
12
1
2
207
125555680
125555472
1.470000e-77
300
8
TraesCS3B01G429800
chr1D
88.865
2371
167
45
203
2524
409935795
409933473
0.000000e+00
2826
9
TraesCS3B01G429800
chr1D
88.691
1910
156
36
2
1876
80778646
80776762
0.000000e+00
2276
10
TraesCS3B01G429800
chr1D
88.649
1762
150
29
2
1736
361507804
361509542
0.000000e+00
2100
11
TraesCS3B01G429800
chr1D
94.224
277
14
1
2248
2524
386743761
386744035
3.000000e-114
422
12
TraesCS3B01G429800
chr1D
94.182
275
14
1
2250
2524
250772194
250772466
3.880000e-113
418
13
TraesCS3B01G429800
chr7D
90.306
2125
150
27
203
2306
29347535
29349624
0.000000e+00
2732
14
TraesCS3B01G429800
chr7D
89.718
1702
141
20
203
1877
461787417
461789111
0.000000e+00
2143
15
TraesCS3B01G429800
chr7D
88.464
1725
128
28
203
1876
165224611
165222907
0.000000e+00
2017
16
TraesCS3B01G429800
chr7D
88.033
1713
152
24
203
1876
584364550
584362852
0.000000e+00
1978
17
TraesCS3B01G429800
chr7D
92.090
885
65
4
1424
2306
281452728
281451847
0.000000e+00
1242
18
TraesCS3B01G429800
chr3D
90.991
1998
140
21
539
2524
327716858
327718827
0.000000e+00
2656
19
TraesCS3B01G429800
chr2A
89.563
2127
176
26
203
2306
363692249
363690146
0.000000e+00
2656
20
TraesCS3B01G429800
chr2A
88.867
1545
147
16
203
1728
514289420
514290958
0.000000e+00
1877
21
TraesCS3B01G429800
chr2A
91.413
920
61
9
1612
2524
435085932
435085024
0.000000e+00
1245
22
TraesCS3B01G429800
chr2D
89.480
1635
137
22
203
1809
511279496
511281123
0.000000e+00
2034
23
TraesCS3B01G429800
chr2D
91.881
973
66
6
1341
2306
504125770
504124804
0.000000e+00
1347
24
TraesCS3B01G429800
chr6D
91.913
1385
89
16
932
2306
56950693
56949322
0.000000e+00
1916
25
TraesCS3B01G429800
chr6D
90.100
697
52
11
1612
2306
139950662
139951343
0.000000e+00
889
26
TraesCS3B01G429800
chr6D
89.894
564
31
8
1984
2524
126948518
126947958
0.000000e+00
702
27
TraesCS3B01G429800
chr6D
89.753
566
33
8
1984
2524
465238166
465238731
0.000000e+00
701
28
TraesCS3B01G429800
chr6D
96.029
277
9
1
2248
2524
56949338
56949064
1.380000e-122
449
29
TraesCS3B01G429800
chr6D
94.464
289
15
1
2236
2524
214765860
214765573
6.410000e-121
444
30
TraesCS3B01G429800
chr6D
93.502
277
16
1
2248
2524
9801589
9801315
6.500000e-111
411
31
TraesCS3B01G429800
chr6D
92.419
277
18
1
2248
2524
344611318
344611045
2.350000e-105
392
32
TraesCS3B01G429800
chr6D
92.419
277
15
2
2248
2524
11449114
11448844
8.470000e-105
390
33
TraesCS3B01G429800
chr6D
91.336
277
18
3
2248
2524
143365452
143365722
8.530000e-100
374
34
TraesCS3B01G429800
chr2B
90.634
1388
107
16
932
2306
604524682
604523305
0.000000e+00
1821
35
TraesCS3B01G429800
chr2B
90.113
971
75
10
2
954
604525590
604524623
0.000000e+00
1242
36
TraesCS3B01G429800
chr2B
89.397
962
80
11
2
947
504508720
504507765
0.000000e+00
1192
37
TraesCS3B01G429800
chr4D
90.360
1390
117
9
929
2306
394549107
394550491
0.000000e+00
1808
38
TraesCS3B01G429800
chr4D
93.966
348
18
2
2177
2524
450006198
450006542
8.000000e-145
523
39
TraesCS3B01G429800
chr6B
90.248
646
38
14
2
630
120041463
120042100
0.000000e+00
821
40
TraesCS3B01G429800
chr7B
93.301
209
11
1
2
207
117602481
117602273
3.150000e-79
305
41
TraesCS3B01G429800
chr3A
93.269
208
11
2
2
207
51344593
51344799
1.130000e-78
303
42
TraesCS3B01G429800
chr4A
92.308
208
14
1
2
207
33374968
33374761
6.830000e-76
294
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
TraesCS3B01G429800
chr3B
669393944
669396467
2523
True
4662.0
4662
100.0000
1
2524
1
chr3B.!!$R2
2523
1
TraesCS3B01G429800
chr3B
246274084
246275789
1705
False
2085.0
2085
89.0770
203
1876
1
chr3B.!!$F1
1673
2
TraesCS3B01G429800
chr4B
136097234
136099558
2324
False
2856.0
2856
89.0500
3
2306
1
chr4B.!!$F1
2303
3
TraesCS3B01G429800
chr5D
361378700
361380801
2101
False
2854.0
2854
91.2310
203
2306
1
chr5D.!!$F1
2103
4
TraesCS3B01G429800
chr5D
125553174
125555680
2506
True
1285.0
2270
91.9790
2
2306
2
chr5D.!!$R2
2304
5
TraesCS3B01G429800
chr5D
530655546
530656191
645
True
902.0
902
91.8460
1658
2306
1
chr5D.!!$R1
648
6
TraesCS3B01G429800
chr1D
409933473
409935795
2322
True
2826.0
2826
88.8650
203
2524
1
chr1D.!!$R2
2321
7
TraesCS3B01G429800
chr1D
80776762
80778646
1884
True
2276.0
2276
88.6910
2
1876
1
chr1D.!!$R1
1874
8
TraesCS3B01G429800
chr1D
361507804
361509542
1738
False
2100.0
2100
88.6490
2
1736
1
chr1D.!!$F2
1734
9
TraesCS3B01G429800
chr7D
29347535
29349624
2089
False
2732.0
2732
90.3060
203
2306
1
chr7D.!!$F1
2103
10
TraesCS3B01G429800
chr7D
461787417
461789111
1694
False
2143.0
2143
89.7180
203
1877
1
chr7D.!!$F2
1674
11
TraesCS3B01G429800
chr7D
165222907
165224611
1704
True
2017.0
2017
88.4640
203
1876
1
chr7D.!!$R1
1673
12
TraesCS3B01G429800
chr7D
584362852
584364550
1698
True
1978.0
1978
88.0330
203
1876
1
chr7D.!!$R3
1673
13
TraesCS3B01G429800
chr7D
281451847
281452728
881
True
1242.0
1242
92.0900
1424
2306
1
chr7D.!!$R2
882
14
TraesCS3B01G429800
chr3D
327716858
327718827
1969
False
2656.0
2656
90.9910
539
2524
1
chr3D.!!$F1
1985
15
TraesCS3B01G429800
chr2A
363690146
363692249
2103
True
2656.0
2656
89.5630
203
2306
1
chr2A.!!$R1
2103
16
TraesCS3B01G429800
chr2A
514289420
514290958
1538
False
1877.0
1877
88.8670
203
1728
1
chr2A.!!$F1
1525
17
TraesCS3B01G429800
chr2A
435085024
435085932
908
True
1245.0
1245
91.4130
1612
2524
1
chr2A.!!$R2
912
18
TraesCS3B01G429800
chr2D
511279496
511281123
1627
False
2034.0
2034
89.4800
203
1809
1
chr2D.!!$F1
1606
19
TraesCS3B01G429800
chr2D
504124804
504125770
966
True
1347.0
1347
91.8810
1341
2306
1
chr2D.!!$R1
965
20
TraesCS3B01G429800
chr6D
56949064
56950693
1629
True
1182.5
1916
93.9710
932
2524
2
chr6D.!!$R6
1592
21
TraesCS3B01G429800
chr6D
139950662
139951343
681
False
889.0
889
90.1000
1612
2306
1
chr6D.!!$F1
694
22
TraesCS3B01G429800
chr6D
126947958
126948518
560
True
702.0
702
89.8940
1984
2524
1
chr6D.!!$R3
540
23
TraesCS3B01G429800
chr6D
465238166
465238731
565
False
701.0
701
89.7530
1984
2524
1
chr6D.!!$F3
540
24
TraesCS3B01G429800
chr2B
604523305
604525590
2285
True
1531.5
1821
90.3735
2
2306
2
chr2B.!!$R2
2304
25
TraesCS3B01G429800
chr2B
504507765
504508720
955
True
1192.0
1192
89.3970
2
947
1
chr2B.!!$R1
945
26
TraesCS3B01G429800
chr4D
394549107
394550491
1384
False
1808.0
1808
90.3600
929
2306
1
chr4D.!!$F1
1377
27
TraesCS3B01G429800
chr6B
120041463
120042100
637
False
821.0
821
90.2480
2
630
1
chr6B.!!$F1
628
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.