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
TraesCS5B01G367300
chr5B
100.000
3443
0
0
1
3443
545925282
545921840
0.000000e+00
6359.0
1
TraesCS5B01G367300
chr5B
98.007
1104
21
1
11
1113
546132765
546131662
0.000000e+00
1916.0
2
TraesCS5B01G367300
chr5B
92.925
947
54
5
1111
2050
546124331
546123391
0.000000e+00
1365.0
3
TraesCS5B01G367300
chr5B
96.135
621
22
2
2167
2787
111157313
111157931
0.000000e+00
1013.0
4
TraesCS5B01G367300
chr5B
94.958
238
12
0
2788
3025
545903584
545903347
1.170000e-99
374.0
5
TraesCS5B01G367300
chr5B
94.958
238
11
1
2788
3025
545883871
545883635
4.200000e-99
372.0
6
TraesCS5B01G367300
chr5B
95.853
217
9
0
3227
3443
540442501
540442285
5.470000e-93
351.0
7
TraesCS5B01G367300
chr5B
91.538
260
15
4
3189
3443
540466097
540465840
5.470000e-93
351.0
8
TraesCS5B01G367300
chr5B
92.920
226
8
3
3015
3239
545902961
545902743
4.290000e-84
322.0
9
TraesCS5B01G367300
chr5B
94.488
127
5
1
2037
2163
546123375
546123251
9.750000e-46
195.0
10
TraesCS5B01G367300
chr5D
91.206
1376
86
17
795
2163
447433145
447431798
0.000000e+00
1838.0
11
TraesCS5B01G367300
chr5D
74.785
1047
191
50
1078
2073
447510051
447509027
1.490000e-108
403.0
12
TraesCS5B01G367300
chr6B
96.940
621
17
2
2171
2790
21917324
21916705
0.000000e+00
1040.0
13
TraesCS5B01G367300
chr6B
95.484
620
26
2
2171
2790
660041950
660042567
0.000000e+00
989.0
14
TraesCS5B01G367300
chr6B
92.883
562
34
4
2885
3443
159084777
159084219
0.000000e+00
811.0
15
TraesCS5B01G367300
chr6B
85.986
421
28
13
2788
3186
159068650
159068239
4.110000e-114
422.0
16
TraesCS5B01G367300
chr6B
77.273
308
59
9
13
314
701606280
701605978
1.640000e-38
171.0
17
TraesCS5B01G367300
chr6B
87.234
94
9
3
11
102
1939574
1939482
1.690000e-18
104.0
18
TraesCS5B01G367300
chr6B
94.737
38
1
1
1602
1638
460207114
460207151
1.330000e-04
58.4
19
TraesCS5B01G367300
chr3B
96.429
616
22
0
2171
2786
171789106
171788491
0.000000e+00
1016.0
20
TraesCS5B01G367300
chr3B
96.104
616
24
0
2171
2786
792196504
792195889
0.000000e+00
1005.0
21
TraesCS5B01G367300
chr3B
74.649
927
156
37
1166
2051
783623252
783622364
1.530000e-88
337.0
22
TraesCS5B01G367300
chr7D
95.161
620
30
0
2170
2789
574165993
574165374
0.000000e+00
979.0
23
TraesCS5B01G367300
chr2B
95.300
617
26
3
2171
2786
770668939
770668325
0.000000e+00
976.0
24
TraesCS5B01G367300
chr2B
90.079
252
23
2
3192
3443
25427411
25427162
3.310000e-85
326.0
25
TraesCS5B01G367300
chr7A
95.130
616
30
0
2171
2786
726103803
726104418
0.000000e+00
972.0
26
TraesCS5B01G367300
chr7A
86.207
464
46
8
2788
3237
733822589
733823048
1.440000e-133
486.0
27
TraesCS5B01G367300
chr7A
86.207
464
46
8
2788
3237
733853763
733854222
1.440000e-133
486.0
28
TraesCS5B01G367300
chr7A
85.529
463
47
8
2788
3237
733841261
733841716
1.870000e-127
466.0
29
TraesCS5B01G367300
chr5A
94.984
618
31
0
2170
2787
110511614
110510997
0.000000e+00
970.0
30
TraesCS5B01G367300
chr5A
86.111
108
12
1
1597
1701
225778945
225778838
2.810000e-21
113.0
31
TraesCS5B01G367300
chrUn
87.310
394
44
5
2788
3179
377054542
377054931
2.440000e-121
446.0
32
TraesCS5B01G367300
chr3D
76.064
940
147
42
1166
2051
587050608
587049693
5.310000e-113
418.0
33
TraesCS5B01G367300
chr3D
91.810
232
18
1
3212
3443
611724529
611724299
4.290000e-84
322.0
34
TraesCS5B01G367300
chr3D
91.810
232
18
1
3212
3443
611738425
611738195
4.290000e-84
322.0
35
TraesCS5B01G367300
chr3D
90.948
232
20
1
3212
3443
611728887
611728657
9.280000e-81
311.0
36
TraesCS5B01G367300
chr3D
84.247
146
20
3
11
155
92873500
92873357
4.630000e-29
139.0
37
TraesCS5B01G367300
chr7B
88.650
326
34
3
2788
3112
749378275
749377952
8.960000e-106
394.0
38
TraesCS5B01G367300
chr7B
82.174
460
52
20
2788
3244
749374031
749373599
5.430000e-98
368.0
39
TraesCS5B01G367300
chr4B
94.495
218
12
0
3226
3443
340992643
340992860
1.530000e-88
337.0
40
TraesCS5B01G367300
chr4B
75.929
673
107
35
1081
1735
3776916
3777551
9.340000e-76
294.0
41
TraesCS5B01G367300
chr2D
90.244
246
22
2
3198
3443
603996204
603995961
1.540000e-83
320.0
42
TraesCS5B01G367300
chr6D
79.032
248
40
9
12
253
67519267
67519508
3.560000e-35
159.0
43
TraesCS5B01G367300
chr6D
94.737
38
1
1
1602
1638
296826057
296826020
1.330000e-04
58.4
44
TraesCS5B01G367300
chr6A
94.737
38
1
1
1602
1638
423535041
423535004
1.330000e-04
58.4
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
TraesCS5B01G367300
chr5B
545921840
545925282
3442
True
6359
6359
100.0000
1
3443
1
chr5B.!!$R4
3442
1
TraesCS5B01G367300
chr5B
546131662
546132765
1103
True
1916
1916
98.0070
11
1113
1
chr5B.!!$R5
1102
2
TraesCS5B01G367300
chr5B
111157313
111157931
618
False
1013
1013
96.1350
2167
2787
1
chr5B.!!$F1
620
3
TraesCS5B01G367300
chr5B
546123251
546124331
1080
True
780
1365
93.7065
1111
2163
2
chr5B.!!$R7
1052
4
TraesCS5B01G367300
chr5B
545902743
545903584
841
True
348
374
93.9390
2788
3239
2
chr5B.!!$R6
451
5
TraesCS5B01G367300
chr5D
447431798
447433145
1347
True
1838
1838
91.2060
795
2163
1
chr5D.!!$R1
1368
6
TraesCS5B01G367300
chr5D
447509027
447510051
1024
True
403
403
74.7850
1078
2073
1
chr5D.!!$R2
995
7
TraesCS5B01G367300
chr6B
21916705
21917324
619
True
1040
1040
96.9400
2171
2790
1
chr6B.!!$R2
619
8
TraesCS5B01G367300
chr6B
660041950
660042567
617
False
989
989
95.4840
2171
2790
1
chr6B.!!$F2
619
9
TraesCS5B01G367300
chr6B
159084219
159084777
558
True
811
811
92.8830
2885
3443
1
chr6B.!!$R4
558
10
TraesCS5B01G367300
chr3B
171788491
171789106
615
True
1016
1016
96.4290
2171
2786
1
chr3B.!!$R1
615
11
TraesCS5B01G367300
chr3B
792195889
792196504
615
True
1005
1005
96.1040
2171
2786
1
chr3B.!!$R3
615
12
TraesCS5B01G367300
chr3B
783622364
783623252
888
True
337
337
74.6490
1166
2051
1
chr3B.!!$R2
885
13
TraesCS5B01G367300
chr7D
574165374
574165993
619
True
979
979
95.1610
2170
2789
1
chr7D.!!$R1
619
14
TraesCS5B01G367300
chr2B
770668325
770668939
614
True
976
976
95.3000
2171
2786
1
chr2B.!!$R2
615
15
TraesCS5B01G367300
chr7A
726103803
726104418
615
False
972
972
95.1300
2171
2786
1
chr7A.!!$F1
615
16
TraesCS5B01G367300
chr5A
110510997
110511614
617
True
970
970
94.9840
2170
2787
1
chr5A.!!$R1
617
17
TraesCS5B01G367300
chr3D
587049693
587050608
915
True
418
418
76.0640
1166
2051
1
chr3D.!!$R2
885
18
TraesCS5B01G367300
chr7B
749373599
749378275
4676
True
381
394
85.4120
2788
3244
2
chr7B.!!$R1
456
19
TraesCS5B01G367300
chr4B
3776916
3777551
635
False
294
294
75.9290
1081
1735
1
chr4B.!!$F1
654
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.