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
TraesCS6A01G205900
chr6A
100.000
2429
0
0
1
2429
360193722
360196150
0.000000e+00
4486.0
1
TraesCS6A01G205900
chr6A
84.529
446
50
7
848
1277
87298831
87298389
8.030000e-115
424.0
2
TraesCS6A01G205900
chr6A
91.729
266
20
2
124
387
376699787
376699522
3.820000e-98
368.0
3
TraesCS6A01G205900
chr6A
96.774
124
4
0
1
124
571155212
571155335
8.800000e-50
207.0
4
TraesCS6A01G205900
chr6A
96.748
123
4
0
2
124
184527370
184527248
3.170000e-49
206.0
5
TraesCS6A01G205900
chr2D
95.088
1140
55
1
1291
2429
407454075
407455214
0.000000e+00
1794.0
6
TraesCS6A01G205900
chr2D
92.720
989
58
7
308
1296
622710987
622711961
0.000000e+00
1415.0
7
TraesCS6A01G205900
chr2D
93.556
419
18
2
886
1296
407453494
407453911
1.230000e-172
616.0
8
TraesCS6A01G205900
chr2D
94.536
366
18
1
335
698
407438635
407439000
4.530000e-157
564.0
9
TraesCS6A01G205900
chr2D
93.382
136
9
0
1291
1426
622712125
622712260
4.100000e-48
202.0
10
TraesCS6A01G205900
chr2D
93.600
125
8
0
765
889
407439742
407439866
1.150000e-43
187.0
11
TraesCS6A01G205900
chr2D
100.000
37
0
0
780
816
106627779
106627743
4.330000e-08
69.4
12
TraesCS6A01G205900
chr4D
95.154
1135
52
2
1296
2429
328701246
328700114
0.000000e+00
1788.0
13
TraesCS6A01G205900
chr4D
94.490
363
20
0
886
1248
328704140
328703778
5.860000e-156
560.0
14
TraesCS6A01G205900
chr4D
90.647
417
31
6
335
747
46140184
46139772
4.570000e-152
547.0
15
TraesCS6A01G205900
chr4D
88.010
417
43
5
335
747
45005730
45005317
1.010000e-133
486.0
16
TraesCS6A01G205900
chr4D
95.133
226
9
2
124
347
328719738
328719513
2.970000e-94
355.0
17
TraesCS6A01G205900
chr4D
96.800
125
4
0
765
889
328718072
328717948
2.450000e-50
209.0
18
TraesCS6A01G205900
chr4D
96.748
123
4
0
2
124
287521436
287521558
3.170000e-49
206.0
19
TraesCS6A01G205900
chr4D
100.000
37
0
0
780
816
46139697
46139661
4.330000e-08
69.4
20
TraesCS6A01G205900
chr3A
94.401
1143
54
4
1291
2425
697840851
697841991
0.000000e+00
1748.0
21
TraesCS6A01G205900
chr3A
93.865
1141
68
2
1291
2429
152000319
151999179
0.000000e+00
1718.0
22
TraesCS6A01G205900
chr3A
92.586
580
32
5
124
692
697838996
697839575
0.000000e+00
822.0
23
TraesCS6A01G205900
chr3A
95.923
466
19
0
1962
2427
11774632
11774167
0.000000e+00
756.0
24
TraesCS6A01G205900
chr3A
95.335
343
16
0
954
1296
152000825
152000483
1.640000e-151
545.0
25
TraesCS6A01G205900
chr3A
95.045
222
9
2
124
343
744948533
744948754
4.970000e-92
348.0
26
TraesCS6A01G205900
chr3A
95.676
185
8
0
765
949
697840446
697840630
5.080000e-77
298.0
27
TraesCS6A01G205900
chr3A
96.748
123
3
1
2
124
198448608
198448729
1.140000e-48
204.0
28
TraesCS6A01G205900
chr4A
93.070
1140
78
1
1291
2429
407815448
407816587
0.000000e+00
1666.0
29
TraesCS6A01G205900
chr4A
91.615
966
74
4
335
1296
407814322
407815284
0.000000e+00
1328.0
30
TraesCS6A01G205900
chr4A
90.637
267
20
4
125
386
690206309
690206575
1.380000e-92
350.0
31
TraesCS6A01G205900
chr4A
92.366
131
8
1
1291
1421
657666177
657666049
4.120000e-43
185.0
32
TraesCS6A01G205900
chr1A
94.275
1083
59
3
1349
2429
16474745
16473664
0.000000e+00
1653.0
33
TraesCS6A01G205900
chr1A
94.872
39
2
0
778
816
570975032
570974994
7.250000e-06
62.1
34
TraesCS6A01G205900
chr7B
92.514
1082
79
2
1349
2429
346799476
346800556
0.000000e+00
1548.0
35
TraesCS6A01G205900
chr7B
95.513
468
21
0
1962
2429
62055738
62056205
0.000000e+00
749.0
36
TraesCS6A01G205900
chr7B
95.111
225
9
2
125
347
26705566
26705790
1.070000e-93
353.0
37
TraesCS6A01G205900
chr2B
89.978
928
68
2
350
1277
795407810
795408712
0.000000e+00
1175.0
38
TraesCS6A01G205900
chr2B
92.432
555
38
4
1421
1972
795317409
795316856
0.000000e+00
789.0
39
TraesCS6A01G205900
chr2B
90.000
450
32
11
125
568
311737556
311737998
9.740000e-159
569.0
40
TraesCS6A01G205900
chr2B
94.690
226
10
2
124
347
710351198
710351423
1.380000e-92
350.0
41
TraesCS6A01G205900
chr2A
89.282
933
74
3
346
1277
762023366
762024273
0.000000e+00
1146.0
42
TraesCS6A01G205900
chr2A
92.793
555
36
4
1421
1972
762079974
762080527
0.000000e+00
800.0
43
TraesCS6A01G205900
chr6B
90.440
795
73
3
335
1127
310606688
310605895
0.000000e+00
1044.0
44
TraesCS6A01G205900
chr6B
92.405
553
41
1
1421
1972
310605584
310605032
0.000000e+00
787.0
45
TraesCS6A01G205900
chr7D
91.065
526
34
2
780
1296
475101232
475100711
0.000000e+00
699.0
46
TraesCS6A01G205900
chr6D
87.580
467
38
7
848
1296
69198059
69197595
7.690000e-145
523.0
47
TraesCS6A01G205900
chr6D
95.968
124
5
0
1
124
445382404
445382527
4.100000e-48
202.0
48
TraesCS6A01G205900
chr3B
95.111
225
9
2
125
347
40890526
40890750
1.070000e-93
353.0
49
TraesCS6A01G205900
chr5A
97.561
123
3
0
2
124
527991693
527991815
6.800000e-51
211.0
50
TraesCS6A01G205900
chr5A
96.748
123
4
0
2
124
484465917
484465795
3.170000e-49
206.0
51
TraesCS6A01G205900
chr5A
96.748
123
4
0
2
124
499649324
499649446
3.170000e-49
206.0
52
TraesCS6A01G205900
chr7A
96.748
123
4
0
2
124
222559639
222559761
3.170000e-49
206.0
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
TraesCS6A01G205900
chr6A
360193722
360196150
2428
False
4486.0
4486
100.0000
1
2429
1
chr6A.!!$F1
2428
1
TraesCS6A01G205900
chr2D
407453494
407455214
1720
False
1205.0
1794
94.3220
886
2429
2
chr2D.!!$F2
1543
2
TraesCS6A01G205900
chr2D
622710987
622712260
1273
False
808.5
1415
93.0510
308
1426
2
chr2D.!!$F3
1118
3
TraesCS6A01G205900
chr2D
407438635
407439866
1231
False
375.5
564
94.0680
335
889
2
chr2D.!!$F1
554
4
TraesCS6A01G205900
chr4D
328700114
328704140
4026
True
1174.0
1788
94.8220
886
2429
2
chr4D.!!$R3
1543
5
TraesCS6A01G205900
chr4D
46139661
46140184
523
True
308.2
547
95.3235
335
816
2
chr4D.!!$R2
481
6
TraesCS6A01G205900
chr4D
328717948
328719738
1790
True
282.0
355
95.9665
124
889
2
chr4D.!!$R4
765
7
TraesCS6A01G205900
chr3A
151999179
152000825
1646
True
1131.5
1718
94.6000
954
2429
2
chr3A.!!$R2
1475
8
TraesCS6A01G205900
chr3A
697838996
697841991
2995
False
956.0
1748
94.2210
124
2425
3
chr3A.!!$F3
2301
9
TraesCS6A01G205900
chr4A
407814322
407816587
2265
False
1497.0
1666
92.3425
335
2429
2
chr4A.!!$F2
2094
10
TraesCS6A01G205900
chr1A
16473664
16474745
1081
True
1653.0
1653
94.2750
1349
2429
1
chr1A.!!$R1
1080
11
TraesCS6A01G205900
chr7B
346799476
346800556
1080
False
1548.0
1548
92.5140
1349
2429
1
chr7B.!!$F3
1080
12
TraesCS6A01G205900
chr2B
795407810
795408712
902
False
1175.0
1175
89.9780
350
1277
1
chr2B.!!$F3
927
13
TraesCS6A01G205900
chr2B
795316856
795317409
553
True
789.0
789
92.4320
1421
1972
1
chr2B.!!$R1
551
14
TraesCS6A01G205900
chr2A
762023366
762024273
907
False
1146.0
1146
89.2820
346
1277
1
chr2A.!!$F1
931
15
TraesCS6A01G205900
chr2A
762079974
762080527
553
False
800.0
800
92.7930
1421
1972
1
chr2A.!!$F2
551
16
TraesCS6A01G205900
chr6B
310605032
310606688
1656
True
915.5
1044
91.4225
335
1972
2
chr6B.!!$R1
1637
17
TraesCS6A01G205900
chr7D
475100711
475101232
521
True
699.0
699
91.0650
780
1296
1
chr7D.!!$R1
516
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.