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
TraesCS3B01G228100
chr3B
100.000
6724
0
0
1
6724
328466448
328473171
0.000000e+00
12417.0
1
TraesCS3B01G228100
chr3B
95.890
6083
237
13
647
6724
632785826
632791900
0.000000e+00
9836.0
2
TraesCS3B01G228100
chr3B
95.231
4299
177
17
622
4914
322354750
322359026
0.000000e+00
6778.0
3
TraesCS3B01G228100
chr3B
93.515
956
38
5
3081
4034
347920102
347919169
0.000000e+00
1400.0
4
TraesCS3B01G228100
chr3B
95.462
617
27
1
5426
6042
85699885
85700500
0.000000e+00
983.0
5
TraesCS3B01G228100
chr3B
93.161
658
33
5
6067
6724
628846900
628847545
0.000000e+00
955.0
6
TraesCS3B01G228100
chr3B
88.034
702
35
14
2369
3035
456613157
456612470
0.000000e+00
785.0
7
TraesCS3B01G228100
chr3B
95.489
266
9
2
331
594
322354103
322354367
8.060000e-114
422.0
8
TraesCS3B01G228100
chr3B
89.172
314
34
0
2060
2373
119782103
119781790
6.320000e-105
392.0
9
TraesCS3B01G228100
chr3B
97.222
216
5
1
5426
5641
327810018
327810232
1.380000e-96
364.0
10
TraesCS3B01G228100
chr2B
96.956
4303
104
15
643
4939
320341077
320345358
0.000000e+00
7195.0
11
TraesCS3B01G228100
chr2B
96.722
1739
35
2
4987
6724
320345363
320347080
0.000000e+00
2876.0
12
TraesCS3B01G228100
chr2B
89.493
1066
92
10
1311
2373
520206603
520207651
0.000000e+00
1330.0
13
TraesCS3B01G228100
chr2B
96.622
296
9
1
334
628
320340463
320340758
2.180000e-134
490.0
14
TraesCS3B01G228100
chr2B
95.263
190
6
2
336
522
134306033
134305844
1.420000e-76
298.0
15
TraesCS3B01G228100
chr2B
94.444
126
7
0
4644
4769
49128606
49128731
1.910000e-45
195.0
16
TraesCS3B01G228100
chr2B
83.920
199
30
2
147
344
367272142
367271945
8.900000e-44
189.0
17
TraesCS3B01G228100
chr2B
92.424
66
2
2
3497
3559
546204114
546204049
2.580000e-14
91.6
18
TraesCS3B01G228100
chr6B
96.742
3960
123
6
2767
6724
462293657
462297612
0.000000e+00
6593.0
19
TraesCS3B01G228100
chr6B
93.996
2132
101
23
645
2771
462282808
462284917
0.000000e+00
3203.0
20
TraesCS3B01G228100
chr6B
87.281
456
37
7
6067
6521
123579693
123580128
1.010000e-137
501.0
21
TraesCS3B01G228100
chr6B
93.820
178
9
2
622
798
462282809
462282985
4.000000e-67
267.0
22
TraesCS3B01G228100
chr4D
96.955
3054
81
6
2368
5417
249168074
249165029
0.000000e+00
5114.0
23
TraesCS3B01G228100
chr4D
95.212
1629
69
6
700
2324
249193623
249192000
0.000000e+00
2567.0
24
TraesCS3B01G228100
chr4D
94.325
652
28
4
4767
5417
266761251
266760608
0.000000e+00
990.0
25
TraesCS3B01G228100
chr4D
98.246
171
3
0
6554
6724
192252468
192252298
3.940000e-77
300.0
26
TraesCS3B01G228100
chr4D
87.845
181
20
2
147
325
274232135
274232315
1.900000e-50
211.0
27
TraesCS3B01G228100
chr4D
78.857
175
23
10
336
506
249194325
249194161
9.220000e-19
106.0
28
TraesCS3B01G228100
chr4D
93.750
64
4
0
5979
6042
249136493
249136556
5.550000e-16
97.1
29
TraesCS3B01G228100
chr2A
93.132
1558
77
13
3081
4631
645828503
645826969
0.000000e+00
2257.0
30
TraesCS3B01G228100
chr2A
90.366
1038
60
11
3212
4243
356885362
356884359
0.000000e+00
1327.0
31
TraesCS3B01G228100
chr2A
92.355
654
28
9
4765
5417
380539259
380539891
0.000000e+00
911.0
32
TraesCS3B01G228100
chr2A
93.075
491
28
3
5493
5982
279780089
279780574
0.000000e+00
713.0
33
TraesCS3B01G228100
chr2A
91.479
399
23
5
4240
4631
356875661
356875267
7.670000e-149
538.0
34
TraesCS3B01G228100
chr2D
94.341
1343
50
3
1752
3073
298537645
298538982
0.000000e+00
2036.0
35
TraesCS3B01G228100
chr5A
93.173
1245
66
7
999
2242
122832925
122834151
0.000000e+00
1810.0
36
TraesCS3B01G228100
chr5A
82.633
357
40
17
2369
2705
80929827
80930181
5.100000e-76
296.0
37
TraesCS3B01G228100
chr5A
90.184
163
14
2
447
609
274964720
274964880
1.900000e-50
211.0
38
TraesCS3B01G228100
chr4B
89.839
1427
120
21
542
1964
442238465
442237060
0.000000e+00
1808.0
39
TraesCS3B01G228100
chr4B
92.665
968
60
10
999
1964
167719133
167718175
0.000000e+00
1384.0
40
TraesCS3B01G228100
chr4B
92.189
973
65
10
994
1964
427399140
427398177
0.000000e+00
1365.0
41
TraesCS3B01G228100
chr4B
95.392
651
27
3
6074
6724
287898086
287897439
0.000000e+00
1033.0
42
TraesCS3B01G228100
chr4B
93.182
396
20
1
5426
5814
465832701
465833096
5.850000e-160
575.0
43
TraesCS3B01G228100
chr4B
82.624
282
37
7
469
750
442238583
442238314
8.710000e-59
239.0
44
TraesCS3B01G228100
chr4B
95.238
126
6
0
4644
4769
241686415
241686540
4.110000e-47
200.0
45
TraesCS3B01G228100
chr4B
93.750
112
5
2
331
440
413716770
413716881
4.170000e-37
167.0
46
TraesCS3B01G228100
chr4B
91.011
89
4
3
331
416
335193517
335193604
4.260000e-22
117.0
47
TraesCS3B01G228100
chr4B
92.593
81
3
2
331
410
536485532
536485454
5.510000e-21
113.0
48
TraesCS3B01G228100
chr4B
89.888
89
4
5
331
416
279963404
279963490
7.130000e-20
110.0
49
TraesCS3B01G228100
chr4B
93.750
64
4
0
5979
6042
240639650
240639587
5.550000e-16
97.1
50
TraesCS3B01G228100
chr6A
89.363
1194
74
14
3134
4314
587377950
587376797
0.000000e+00
1452.0
51
TraesCS3B01G228100
chr6A
92.627
651
27
8
4767
5417
121236176
121236805
0.000000e+00
917.0
52
TraesCS3B01G228100
chr6A
88.462
728
40
15
2369
3066
11893417
11894130
0.000000e+00
839.0
53
TraesCS3B01G228100
chr6A
96.491
171
6
0
6554
6724
409741156
409741326
3.970000e-72
283.0
54
TraesCS3B01G228100
chr6A
94.444
126
7
0
4644
4769
356107068
356106943
1.910000e-45
195.0
55
TraesCS3B01G228100
chr3D
90.939
905
47
16
3081
3953
288639393
288640294
0.000000e+00
1184.0
56
TraesCS3B01G228100
chr1B
95.903
659
25
2
6067
6724
327716091
327716748
0.000000e+00
1066.0
57
TraesCS3B01G228100
chr1B
89.451
474
36
6
4764
5237
303012908
303013367
2.700000e-163
586.0
58
TraesCS3B01G228100
chr1B
88.462
312
20
6
1
300
82073931
82073624
4.960000e-96
363.0
59
TraesCS3B01G228100
chr1B
84.615
195
28
2
5790
5982
220393084
220393278
6.880000e-45
193.0
60
TraesCS3B01G228100
chr5B
90.213
797
36
23
3081
3872
636464085
636463326
0.000000e+00
1002.0
61
TraesCS3B01G228100
chr5B
91.858
565
32
7
5426
5982
430299647
430300205
0.000000e+00
776.0
62
TraesCS3B01G228100
chr5B
91.002
489
35
5
4148
4631
88875677
88875193
0.000000e+00
651.0
63
TraesCS3B01G228100
chr5B
90.506
474
31
5
4764
5237
235763199
235762740
1.240000e-171
614.0
64
TraesCS3B01G228100
chr7B
89.727
769
50
4
4649
5417
90425863
90426602
0.000000e+00
955.0
65
TraesCS3B01G228100
chr7B
94.064
219
6
2
5199
5417
666894866
666894655
6.500000e-85
326.0
66
TraesCS3B01G228100
chr7B
94.937
79
0
3
336
411
428791699
428791622
3.290000e-23
121.0
67
TraesCS3B01G228100
chr3A
92.249
658
31
9
6067
6724
301064864
301064227
0.000000e+00
915.0
68
TraesCS3B01G228100
chr3A
94.501
491
25
2
5493
5982
596167131
596166642
0.000000e+00
756.0
69
TraesCS3B01G228100
chr3A
91.282
390
33
1
6067
6456
39916341
39916729
1.280000e-146
531.0
70
TraesCS3B01G228100
chr6D
89.280
625
52
11
653
1276
366992772
366992162
0.000000e+00
769.0
71
TraesCS3B01G228100
chr6D
92.164
536
26
5
2532
3066
10401067
10401587
0.000000e+00
743.0
72
TraesCS3B01G228100
chr6D
84.536
291
27
11
3134
3410
301256414
301256700
8.590000e-69
272.0
73
TraesCS3B01G228100
chr6D
83.137
255
25
13
331
580
366993358
366993117
4.080000e-52
217.0
74
TraesCS3B01G228100
chr6D
93.651
63
4
0
5979
6041
428045707
428045645
2.000000e-15
95.3
75
TraesCS3B01G228100
chr5D
90.287
453
26
6
4965
5417
53010110
53009676
1.630000e-160
577.0
76
TraesCS3B01G228100
chr5D
91.667
84
3
2
331
411
18549360
18549442
5.510000e-21
113.0
77
TraesCS3B01G228100
chr7D
89.812
373
19
8
2537
2890
176344491
176344863
1.710000e-125
460.0
78
TraesCS3B01G228100
chr7D
81.529
314
40
12
39
343
468269266
468268962
6.740000e-60
243.0
79
TraesCS3B01G228100
chr7D
88.235
170
20
0
173
342
468268960
468268791
3.180000e-48
204.0
80
TraesCS3B01G228100
chr7D
98.438
64
1
0
5979
6042
289566011
289566074
5.510000e-21
113.0
81
TraesCS3B01G228100
chr7D
98.438
64
1
0
5979
6042
291384186
291384123
5.510000e-21
113.0
82
TraesCS3B01G228100
chr4A
89.008
373
22
8
2537
2890
242661014
242660642
1.720000e-120
444.0
83
TraesCS3B01G228100
chr7A
86.378
323
30
11
3957
4277
327389207
327389517
2.320000e-89
340.0
84
TraesCS3B01G228100
chr1D
80.952
147
22
4
4407
4549
6326894
6326750
1.980000e-20
111.0
85
TraesCS3B01G228100
chrUn
80.000
145
29
0
185
329
468947957
468947813
2.560000e-19
108.0
86
TraesCS3B01G228100
chrUn
81.818
110
8
8
6494
6591
77287320
77287211
1.550000e-11
82.4
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
TraesCS3B01G228100
chr3B
328466448
328473171
6723
False
12417.000000
12417
100.000000
1
6724
1
chr3B.!!$F3
6723
1
TraesCS3B01G228100
chr3B
632785826
632791900
6074
False
9836.000000
9836
95.890000
647
6724
1
chr3B.!!$F5
6077
2
TraesCS3B01G228100
chr3B
322354103
322359026
4923
False
3600.000000
6778
95.360000
331
4914
2
chr3B.!!$F6
4583
3
TraesCS3B01G228100
chr3B
347919169
347920102
933
True
1400.000000
1400
93.515000
3081
4034
1
chr3B.!!$R2
953
4
TraesCS3B01G228100
chr3B
85699885
85700500
615
False
983.000000
983
95.462000
5426
6042
1
chr3B.!!$F1
616
5
TraesCS3B01G228100
chr3B
628846900
628847545
645
False
955.000000
955
93.161000
6067
6724
1
chr3B.!!$F4
657
6
TraesCS3B01G228100
chr3B
456612470
456613157
687
True
785.000000
785
88.034000
2369
3035
1
chr3B.!!$R3
666
7
TraesCS3B01G228100
chr2B
320340463
320347080
6617
False
3520.333333
7195
96.766667
334
6724
3
chr2B.!!$F3
6390
8
TraesCS3B01G228100
chr2B
520206603
520207651
1048
False
1330.000000
1330
89.493000
1311
2373
1
chr2B.!!$F2
1062
9
TraesCS3B01G228100
chr6B
462293657
462297612
3955
False
6593.000000
6593
96.742000
2767
6724
1
chr6B.!!$F2
3957
10
TraesCS3B01G228100
chr6B
462282808
462284917
2109
False
1735.000000
3203
93.908000
622
2771
2
chr6B.!!$F3
2149
11
TraesCS3B01G228100
chr4D
249165029
249168074
3045
True
5114.000000
5114
96.955000
2368
5417
1
chr4D.!!$R2
3049
12
TraesCS3B01G228100
chr4D
249192000
249194325
2325
True
1336.500000
2567
87.034500
336
2324
2
chr4D.!!$R4
1988
13
TraesCS3B01G228100
chr4D
266760608
266761251
643
True
990.000000
990
94.325000
4767
5417
1
chr4D.!!$R3
650
14
TraesCS3B01G228100
chr2A
645826969
645828503
1534
True
2257.000000
2257
93.132000
3081
4631
1
chr2A.!!$R3
1550
15
TraesCS3B01G228100
chr2A
356884359
356885362
1003
True
1327.000000
1327
90.366000
3212
4243
1
chr2A.!!$R2
1031
16
TraesCS3B01G228100
chr2A
380539259
380539891
632
False
911.000000
911
92.355000
4765
5417
1
chr2A.!!$F2
652
17
TraesCS3B01G228100
chr2D
298537645
298538982
1337
False
2036.000000
2036
94.341000
1752
3073
1
chr2D.!!$F1
1321
18
TraesCS3B01G228100
chr5A
122832925
122834151
1226
False
1810.000000
1810
93.173000
999
2242
1
chr5A.!!$F2
1243
19
TraesCS3B01G228100
chr4B
167718175
167719133
958
True
1384.000000
1384
92.665000
999
1964
1
chr4B.!!$R1
965
20
TraesCS3B01G228100
chr4B
427398177
427399140
963
True
1365.000000
1365
92.189000
994
1964
1
chr4B.!!$R4
970
21
TraesCS3B01G228100
chr4B
287897439
287898086
647
True
1033.000000
1033
95.392000
6074
6724
1
chr4B.!!$R3
650
22
TraesCS3B01G228100
chr4B
442237060
442238583
1523
True
1023.500000
1808
86.231500
469
1964
2
chr4B.!!$R6
1495
23
TraesCS3B01G228100
chr6A
587376797
587377950
1153
True
1452.000000
1452
89.363000
3134
4314
1
chr6A.!!$R2
1180
24
TraesCS3B01G228100
chr6A
121236176
121236805
629
False
917.000000
917
92.627000
4767
5417
1
chr6A.!!$F2
650
25
TraesCS3B01G228100
chr6A
11893417
11894130
713
False
839.000000
839
88.462000
2369
3066
1
chr6A.!!$F1
697
26
TraesCS3B01G228100
chr3D
288639393
288640294
901
False
1184.000000
1184
90.939000
3081
3953
1
chr3D.!!$F1
872
27
TraesCS3B01G228100
chr1B
327716091
327716748
657
False
1066.000000
1066
95.903000
6067
6724
1
chr1B.!!$F3
657
28
TraesCS3B01G228100
chr5B
636463326
636464085
759
True
1002.000000
1002
90.213000
3081
3872
1
chr5B.!!$R3
791
29
TraesCS3B01G228100
chr5B
430299647
430300205
558
False
776.000000
776
91.858000
5426
5982
1
chr5B.!!$F1
556
30
TraesCS3B01G228100
chr7B
90425863
90426602
739
False
955.000000
955
89.727000
4649
5417
1
chr7B.!!$F1
768
31
TraesCS3B01G228100
chr3A
301064227
301064864
637
True
915.000000
915
92.249000
6067
6724
1
chr3A.!!$R1
657
32
TraesCS3B01G228100
chr6D
10401067
10401587
520
False
743.000000
743
92.164000
2532
3066
1
chr6D.!!$F1
534
33
TraesCS3B01G228100
chr6D
366992162
366993358
1196
True
493.000000
769
86.208500
331
1276
2
chr6D.!!$R2
945
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.