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
TraesCS3B01G093700
chr3B
100.000
6611
0
0
1
6611
62666578
62673188
0.000000e+00
12209.0
1
TraesCS3B01G093700
chr5B
96.649
3193
76
8
1790
4953
6666923
6670113
0.000000e+00
5275.0
2
TraesCS3B01G093700
chr5B
94.136
1620
71
16
3474
5076
24390866
24392478
0.000000e+00
2444.0
3
TraesCS3B01G093700
chr5B
91.204
1387
93
15
2421
3781
30941682
30940299
0.000000e+00
1858.0
4
TraesCS3B01G093700
chr5B
91.276
1089
73
11
2421
3488
31017526
31016439
0.000000e+00
1465.0
5
TraesCS3B01G093700
chr5B
96.245
799
18
6
5072
5862
24392549
24393343
0.000000e+00
1299.0
6
TraesCS3B01G093700
chr5B
90.385
988
74
12
3807
4784
24627819
24626843
0.000000e+00
1279.0
7
TraesCS3B01G093700
chr5B
90.375
987
74
12
3807
4784
6834931
6833957
0.000000e+00
1277.0
8
TraesCS3B01G093700
chr5B
86.534
854
39
31
923
1764
6666138
6666927
0.000000e+00
870.0
9
TraesCS3B01G093700
chr5B
93.345
556
17
10
6073
6611
24393335
24393887
0.000000e+00
804.0
10
TraesCS3B01G093700
chr5B
82.580
907
116
20
1508
2376
13911513
13910611
0.000000e+00
761.0
11
TraesCS3B01G093700
chr5B
95.065
385
7
1
5072
5456
6671048
6671420
4.410000e-166
595.0
12
TraesCS3B01G093700
chr5B
94.118
323
18
1
915
1237
31017894
31017573
2.140000e-134
490.0
13
TraesCS3B01G093700
chr5B
93.519
324
18
3
915
1237
30942050
30941729
4.640000e-131
479.0
14
TraesCS3B01G093700
chr5B
87.087
333
28
8
5331
5650
30921877
30921547
4.870000e-96
363.0
15
TraesCS3B01G093700
chr5B
82.254
417
60
11
2431
2841
24676734
24676326
1.360000e-91
348.0
16
TraesCS3B01G093700
chr5B
85.799
338
28
10
5331
5650
6833768
6833433
2.280000e-89
340.0
17
TraesCS3B01G093700
chr5B
85.757
337
28
13
5332
5650
24626653
24626319
8.210000e-89
339.0
18
TraesCS3B01G093700
chr5B
93.665
221
13
1
5862
6081
267548109
267547889
4.940000e-86
329.0
19
TraesCS3B01G093700
chr5B
99.010
101
1
0
4951
5051
6670220
6670320
1.460000e-41
182.0
20
TraesCS3B01G093700
chr5B
84.831
178
20
4
6074
6246
30819996
30819821
8.810000e-39
172.0
21
TraesCS3B01G093700
chr5B
83.500
200
15
10
5301
5485
6852969
6852773
3.170000e-38
171.0
22
TraesCS3B01G093700
chr5D
97.903
2671
47
5
2414
5076
5102526
5099857
0.000000e+00
4614.0
23
TraesCS3B01G093700
chr5D
90.903
1495
60
20
915
2387
5103962
5102522
0.000000e+00
1938.0
24
TraesCS3B01G093700
chr5D
84.229
1395
166
37
2400
3774
3930435
3929075
0.000000e+00
1308.0
25
TraesCS3B01G093700
chr5D
85.506
890
109
11
1498
2369
420928307
420927420
0.000000e+00
911.0
26
TraesCS3B01G093700
chr5D
96.324
544
15
1
6073
6611
5099035
5098492
0.000000e+00
889.0
27
TraesCS3B01G093700
chr5D
98.305
472
5
2
5392
5862
5099496
5099027
0.000000e+00
824.0
28
TraesCS3B01G093700
chr5D
98.551
276
4
0
5072
5347
5099786
5099511
7.710000e-134
488.0
29
TraesCS3B01G093700
chr5D
83.438
320
36
9
5304
5606
3927513
3927194
1.400000e-71
281.0
30
TraesCS3B01G093700
chr5D
84.979
233
31
3
5071
5300
235200176
235200407
3.990000e-57
233.0
31
TraesCS3B01G093700
chr5D
92.617
149
8
1
6278
6423
4797617
4797469
1.870000e-50
211.0
32
TraesCS3B01G093700
chr5D
88.276
145
14
2
5667
5810
3927086
3926944
3.170000e-38
171.0
33
TraesCS3B01G093700
chr5A
94.104
2595
100
29
2241
4793
3725343
3727926
0.000000e+00
3895.0
34
TraesCS3B01G093700
chr5A
93.719
2595
109
31
2241
4793
3770510
3773092
0.000000e+00
3840.0
35
TraesCS3B01G093700
chr5A
94.060
2357
89
29
2472
4793
3758145
3760485
0.000000e+00
3530.0
36
TraesCS3B01G093700
chr5A
93.994
1665
63
21
3164
4793
3798938
3800600
0.000000e+00
2486.0
37
TraesCS3B01G093700
chr5A
93.783
933
41
9
2241
3166
3783635
3784557
0.000000e+00
1386.0
38
TraesCS3B01G093700
chr5A
94.229
901
35
9
2241
3134
3712805
3713695
0.000000e+00
1360.0
39
TraesCS3B01G093700
chr5A
84.435
1407
152
38
2400
3773
4608371
4609743
0.000000e+00
1323.0
40
TraesCS3B01G093700
chr5A
93.976
830
44
5
3969
4793
3714076
3714904
0.000000e+00
1251.0
41
TraesCS3B01G093700
chr5A
84.797
592
46
19
915
1482
3756463
3757034
7.490000e-154
555.0
42
TraesCS3B01G093700
chr5A
84.915
590
44
21
915
1479
3769471
3770040
7.490000e-154
555.0
43
TraesCS3B01G093700
chr5A
84.628
592
47
18
915
1482
3711767
3712338
3.480000e-152
549.0
44
TraesCS3B01G093700
chr5A
84.459
592
48
18
915
1482
3724305
3724876
1.620000e-150
544.0
45
TraesCS3B01G093700
chr5A
95.808
334
14
0
2472
2805
3749696
3750029
2.100000e-149
540.0
46
TraesCS3B01G093700
chr5A
92.655
354
24
2
5301
5652
3800798
3801151
5.910000e-140
508.0
47
TraesCS3B01G093700
chr5A
89.516
372
29
4
915
1276
3782707
3783078
4.670000e-126
462.0
48
TraesCS3B01G093700
chr5A
80.561
535
68
23
5307
5810
4611382
4611911
4.840000e-101
379.0
49
TraesCS3B01G093700
chr5A
83.541
401
27
16
6245
6611
3801544
3801939
8.210000e-89
339.0
50
TraesCS3B01G093700
chr5A
81.205
415
43
14
6074
6460
4056199
4056606
1.080000e-77
302.0
51
TraesCS3B01G093700
chr5A
92.647
204
14
1
5301
5503
3773290
3773493
6.480000e-75
292.0
52
TraesCS3B01G093700
chr5A
92.157
204
14
2
5301
5503
3728125
3728327
3.020000e-73
287.0
53
TraesCS3B01G093700
chr5A
92.157
204
14
2
5301
5503
3760683
3760885
3.020000e-73
287.0
54
TraesCS3B01G093700
chr5A
91.176
204
16
2
5301
5503
3715102
3715304
6.530000e-70
276.0
55
TraesCS3B01G093700
chr5A
91.257
183
9
3
2241
2416
3757501
3757683
6.620000e-60
243.0
56
TraesCS3B01G093700
chr5A
89.024
164
18
0
4790
4953
3727965
3728128
3.130000e-48
204.0
57
TraesCS3B01G093700
chr5A
89.024
164
18
0
4790
4953
3760523
3760686
3.130000e-48
204.0
58
TraesCS3B01G093700
chr5A
88.415
164
19
0
4790
4953
3714942
3715105
1.450000e-46
198.0
59
TraesCS3B01G093700
chr5A
88.415
164
19
0
4790
4953
3800638
3800801
1.450000e-46
198.0
60
TraesCS3B01G093700
chr5A
87.805
164
20
0
4790
4953
3773130
3773293
6.770000e-45
193.0
61
TraesCS3B01G093700
chr5A
91.892
74
6
0
1409
1482
3783095
3783168
3.260000e-18
104.0
62
TraesCS3B01G093700
chr6B
91.253
926
56
12
1
905
223256133
223257054
0.000000e+00
1238.0
63
TraesCS3B01G093700
chr7B
91.295
919
47
5
1
899
40894812
40893907
0.000000e+00
1223.0
64
TraesCS3B01G093700
chr7B
90.584
924
58
12
1
899
501938206
501937287
0.000000e+00
1197.0
65
TraesCS3B01G093700
chr7B
95.755
212
7
2
5862
6072
645395994
645396204
2.280000e-89
340.0
66
TraesCS3B01G093700
chr7B
95.349
215
5
2
5863
6072
733770551
733770765
2.950000e-88
337.0
67
TraesCS3B01G093700
chr2A
90.337
921
61
10
1
900
346060983
346061896
0.000000e+00
1182.0
68
TraesCS3B01G093700
chr2A
78.799
849
143
24
1516
2332
533883868
533884711
2.710000e-148
536.0
69
TraesCS3B01G093700
chr1B
90.316
919
51
19
2
898
614175919
614176821
0.000000e+00
1170.0
70
TraesCS3B01G093700
chr1B
90.471
850
55
9
70
895
623541475
623542322
0.000000e+00
1098.0
71
TraesCS3B01G093700
chr1B
88.726
683
49
15
243
900
428543089
428542410
0.000000e+00
809.0
72
TraesCS3B01G093700
chr1B
95.794
214
8
1
5863
6075
643043036
643042823
1.760000e-90
344.0
73
TraesCS3B01G093700
chr1B
92.609
230
13
4
5853
6081
593563481
593563255
1.780000e-85
327.0
74
TraesCS3B01G093700
chr1A
90.000
920
64
10
1
899
146943412
146942500
0.000000e+00
1164.0
75
TraesCS3B01G093700
chr1A
89.848
857
59
11
66
899
540889558
540888707
0.000000e+00
1075.0
76
TraesCS3B01G093700
chr1A
94.293
368
18
3
1
367
540889794
540889429
1.610000e-155
560.0
77
TraesCS3B01G093700
chr1A
79.156
758
126
23
1499
2239
20365441
20366183
4.600000e-136
496.0
78
TraesCS3B01G093700
chr1A
96.209
211
8
0
5862
6072
566517310
566517100
4.910000e-91
346.0
79
TraesCS3B01G093700
chr6A
89.902
921
64
11
1
900
534982259
534983171
0.000000e+00
1158.0
80
TraesCS3B01G093700
chr6A
89.805
922
65
11
1
901
499621678
499620765
0.000000e+00
1155.0
81
TraesCS3B01G093700
chr3A
89.378
772
53
10
1
751
125482567
125481804
0.000000e+00
944.0
82
TraesCS3B01G093700
chr2B
79.697
857
131
25
1516
2332
468555022
468555875
4.440000e-161
579.0
83
TraesCS3B01G093700
chr2B
78.207
647
129
10
1729
2367
238629030
238629672
2.870000e-108
403.0
84
TraesCS3B01G093700
chr2B
96.804
219
5
2
5858
6075
27547924
27548141
1.350000e-96
364.0
85
TraesCS3B01G093700
chr2B
84.451
328
51
0
2042
2369
198170584
198170911
2.300000e-84
324.0
86
TraesCS3B01G093700
chr2B
74.732
839
153
35
1501
2307
735856082
735855271
2.970000e-83
320.0
87
TraesCS3B01G093700
chr2D
79.138
858
134
27
1516
2332
395560526
395561379
9.690000e-153
551.0
88
TraesCS3B01G093700
chr2D
86.747
83
10
1
4965
5046
137853072
137853154
2.540000e-14
91.6
89
TraesCS3B01G093700
chr7D
80.134
745
120
20
1642
2369
239011589
239010856
1.260000e-146
531.0
90
TraesCS3B01G093700
chr1D
80.053
752
113
30
1507
2239
18377729
18378462
2.110000e-144
523.0
91
TraesCS3B01G093700
chr7A
95.283
212
9
1
5862
6072
608323754
608323543
1.060000e-87
335.0
92
TraesCS3B01G093700
chrUn
92.982
228
11
3
5854
6078
234337042
234336817
1.780000e-85
327.0
93
TraesCS3B01G093700
chr4A
82.558
258
32
5
5359
5603
18650712
18650969
1.440000e-51
215.0
94
TraesCS3B01G093700
chr4A
82.171
258
33
5
5359
5603
18684525
18684782
6.720000e-50
209.0
95
TraesCS3B01G093700
chr4A
89.051
137
12
2
5675
5810
18666078
18666212
4.100000e-37
167.0
96
TraesCS3B01G093700
chr4A
87.591
137
14
2
5675
5810
18691036
18691170
8.880000e-34
156.0
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
TraesCS3B01G093700
chr3B
62666578
62673188
6610
False
12209.000000
12209
100.000000
1
6611
1
chr3B.!!$F1
6610
1
TraesCS3B01G093700
chr5B
6666138
6671420
5282
False
1730.500000
5275
94.314500
923
5456
4
chr5B.!!$F1
4533
2
TraesCS3B01G093700
chr5B
24390866
24393887
3021
False
1515.666667
2444
94.575333
3474
6611
3
chr5B.!!$F2
3137
3
TraesCS3B01G093700
chr5B
30940299
30942050
1751
True
1168.500000
1858
92.361500
915
3781
2
chr5B.!!$R9
2866
4
TraesCS3B01G093700
chr5B
31016439
31017894
1455
True
977.500000
1465
92.697000
915
3488
2
chr5B.!!$R10
2573
5
TraesCS3B01G093700
chr5B
24626319
24627819
1500
True
809.000000
1279
88.071000
3807
5650
2
chr5B.!!$R8
1843
6
TraesCS3B01G093700
chr5B
6833433
6834931
1498
True
808.500000
1277
88.087000
3807
5650
2
chr5B.!!$R7
1843
7
TraesCS3B01G093700
chr5B
13910611
13911513
902
True
761.000000
761
82.580000
1508
2376
1
chr5B.!!$R2
868
8
TraesCS3B01G093700
chr5D
5098492
5103962
5470
True
1750.600000
4614
96.397200
915
6611
5
chr5D.!!$R4
5696
9
TraesCS3B01G093700
chr5D
420927420
420928307
887
True
911.000000
911
85.506000
1498
2369
1
chr5D.!!$R2
871
10
TraesCS3B01G093700
chr5D
3926944
3930435
3491
True
586.666667
1308
85.314333
2400
5810
3
chr5D.!!$R3
3410
11
TraesCS3B01G093700
chr5A
3724305
3728327
4022
False
1232.500000
3895
89.936000
915
5503
4
chr5A.!!$F4
4588
12
TraesCS3B01G093700
chr5A
3769471
3773493
4022
False
1220.000000
3840
89.771500
915
5503
4
chr5A.!!$F6
4588
13
TraesCS3B01G093700
chr5A
3756463
3760885
4422
False
963.800000
3530
90.259000
915
5503
5
chr5A.!!$F5
4588
14
TraesCS3B01G093700
chr5A
3798938
3801939
3001
False
882.750000
2486
89.651250
3164
6611
4
chr5A.!!$F8
3447
15
TraesCS3B01G093700
chr5A
4608371
4611911
3540
False
851.000000
1323
82.498000
2400
5810
2
chr5A.!!$F9
3410
16
TraesCS3B01G093700
chr5A
3711767
3715304
3537
False
726.800000
1360
90.484800
915
5503
5
chr5A.!!$F3
4588
17
TraesCS3B01G093700
chr5A
3782707
3784557
1850
False
650.666667
1386
91.730333
915
3166
3
chr5A.!!$F7
2251
18
TraesCS3B01G093700
chr6B
223256133
223257054
921
False
1238.000000
1238
91.253000
1
905
1
chr6B.!!$F1
904
19
TraesCS3B01G093700
chr7B
40893907
40894812
905
True
1223.000000
1223
91.295000
1
899
1
chr7B.!!$R1
898
20
TraesCS3B01G093700
chr7B
501937287
501938206
919
True
1197.000000
1197
90.584000
1
899
1
chr7B.!!$R2
898
21
TraesCS3B01G093700
chr2A
346060983
346061896
913
False
1182.000000
1182
90.337000
1
900
1
chr2A.!!$F1
899
22
TraesCS3B01G093700
chr2A
533883868
533884711
843
False
536.000000
536
78.799000
1516
2332
1
chr2A.!!$F2
816
23
TraesCS3B01G093700
chr1B
614175919
614176821
902
False
1170.000000
1170
90.316000
2
898
1
chr1B.!!$F1
896
24
TraesCS3B01G093700
chr1B
623541475
623542322
847
False
1098.000000
1098
90.471000
70
895
1
chr1B.!!$F2
825
25
TraesCS3B01G093700
chr1B
428542410
428543089
679
True
809.000000
809
88.726000
243
900
1
chr1B.!!$R1
657
26
TraesCS3B01G093700
chr1A
146942500
146943412
912
True
1164.000000
1164
90.000000
1
899
1
chr1A.!!$R1
898
27
TraesCS3B01G093700
chr1A
540888707
540889794
1087
True
817.500000
1075
92.070500
1
899
2
chr1A.!!$R3
898
28
TraesCS3B01G093700
chr1A
20365441
20366183
742
False
496.000000
496
79.156000
1499
2239
1
chr1A.!!$F1
740
29
TraesCS3B01G093700
chr6A
534982259
534983171
912
False
1158.000000
1158
89.902000
1
900
1
chr6A.!!$F1
899
30
TraesCS3B01G093700
chr6A
499620765
499621678
913
True
1155.000000
1155
89.805000
1
901
1
chr6A.!!$R1
900
31
TraesCS3B01G093700
chr3A
125481804
125482567
763
True
944.000000
944
89.378000
1
751
1
chr3A.!!$R1
750
32
TraesCS3B01G093700
chr2B
468555022
468555875
853
False
579.000000
579
79.697000
1516
2332
1
chr2B.!!$F4
816
33
TraesCS3B01G093700
chr2B
238629030
238629672
642
False
403.000000
403
78.207000
1729
2367
1
chr2B.!!$F3
638
34
TraesCS3B01G093700
chr2B
735855271
735856082
811
True
320.000000
320
74.732000
1501
2307
1
chr2B.!!$R1
806
35
TraesCS3B01G093700
chr2D
395560526
395561379
853
False
551.000000
551
79.138000
1516
2332
1
chr2D.!!$F2
816
36
TraesCS3B01G093700
chr7D
239010856
239011589
733
True
531.000000
531
80.134000
1642
2369
1
chr7D.!!$R1
727
37
TraesCS3B01G093700
chr1D
18377729
18378462
733
False
523.000000
523
80.053000
1507
2239
1
chr1D.!!$F1
732
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.