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
TraesCS3B01G444400
chr3B
100.000
3134
0
0
1
3134
684514993
684511860
0.000000e+00
5788
1
TraesCS3B01G444400
chr3B
86.288
1568
118
37
1391
2922
684638623
684637117
0.000000e+00
1615
2
TraesCS3B01G444400
chr3B
85.554
1336
127
26
958
2255
685393499
685394806
0.000000e+00
1338
3
TraesCS3B01G444400
chr3B
84.506
981
88
27
2182
3134
685394806
685395750
0.000000e+00
911
4
TraesCS3B01G444400
chr3B
74.586
1208
225
49
989
2134
773747038
773748225
3.680000e-124
455
5
TraesCS3B01G444400
chr3B
73.469
1176
247
46
991
2135
685630646
685631787
1.760000e-102
383
6
TraesCS3B01G444400
chr3B
73.469
1176
247
46
991
2135
685659141
685660282
1.760000e-102
383
7
TraesCS3B01G444400
chr3A
91.820
2225
126
17
960
3134
655570668
655568450
0.000000e+00
3049
8
TraesCS3B01G444400
chr3D
92.299
1688
94
14
1109
2768
520097641
520095962
0.000000e+00
2364
9
TraesCS3B01G444400
chr3D
85.628
1329
132
24
958
2255
520426552
520427852
0.000000e+00
1341
10
TraesCS3B01G444400
chr3D
87.331
963
81
22
1
957
296430136
296431063
0.000000e+00
1064
11
TraesCS3B01G444400
chr3D
87.110
962
84
21
1
956
568577851
568576924
0.000000e+00
1053
12
TraesCS3B01G444400
chr3D
86.993
961
75
17
1
947
511068076
511069000
0.000000e+00
1037
13
TraesCS3B01G444400
chr3D
86.509
971
80
17
1
956
571451591
571450657
0.000000e+00
1020
14
TraesCS3B01G444400
chr3D
85.844
989
86
27
2182
3134
520427924
520428894
0.000000e+00
1002
15
TraesCS3B01G444400
chr3D
76.058
1725
276
86
1038
2672
579582755
579581078
0.000000e+00
771
16
TraesCS3B01G444400
chr3D
74.557
1128
237
37
1022
2135
520595042
520596133
6.170000e-122
448
17
TraesCS3B01G444400
chr3D
87.532
393
26
5
2763
3134
520082573
520082183
1.730000e-117
433
18
TraesCS3B01G444400
chr3D
77.219
755
148
18
1395
2134
58089426
58088681
1.340000e-113
420
19
TraesCS3B01G444400
chr3D
73.854
1178
216
60
991
2116
565641909
565643046
4.900000e-103
385
20
TraesCS3B01G444400
chr3D
81.773
406
66
8
1013
1416
520080501
520080102
1.800000e-87
333
21
TraesCS3B01G444400
chr3D
73.770
793
170
20
1351
2128
568017769
568018538
8.560000e-71
278
22
TraesCS3B01G444400
chr3D
73.494
747
167
21
1396
2128
566743056
566743785
1.440000e-63
254
23
TraesCS3B01G444400
chr3D
74.172
604
125
22
1547
2127
568111385
568111980
4.070000e-54
222
24
TraesCS3B01G444400
chr3D
76.562
320
64
8
1809
2121
569466472
569466157
6.950000e-37
165
25
TraesCS3B01G444400
chr1B
97.934
968
18
2
1
967
622622121
622621155
0.000000e+00
1676
26
TraesCS3B01G444400
chr2B
97.604
960
16
6
1
957
364960441
364961396
0.000000e+00
1639
27
TraesCS3B01G444400
chr7D
95.436
964
40
4
1
961
85599832
85598870
0.000000e+00
1533
28
TraesCS3B01G444400
chr4B
95.142
988
16
4
1
956
95668506
95669493
0.000000e+00
1530
29
TraesCS3B01G444400
chr4B
90.979
388
29
6
574
957
610788405
610788020
4.630000e-143
518
30
TraesCS3B01G444400
chr1A
94.573
866
33
10
94
956
13251695
13250841
0.000000e+00
1327
31
TraesCS3B01G444400
chr1A
94.651
860
29
10
94
950
9308650
9307805
0.000000e+00
1317
32
TraesCS3B01G444400
chr1D
87.111
931
80
21
1
925
321329266
321330162
0.000000e+00
1018
33
TraesCS3B01G444400
chr2A
75.773
776
160
15
1351
2106
45080376
45081143
1.780000e-97
366
34
TraesCS3B01G444400
chrUn
75.418
598
128
13
1544
2127
40962868
40963460
3.980000e-69
272
35
TraesCS3B01G444400
chrUn
75.418
598
128
13
1544
2127
326502005
326502597
3.980000e-69
272
36
TraesCS3B01G444400
chrUn
73.101
803
181
29
1351
2134
340248930
340248144
1.440000e-63
254
37
TraesCS3B01G444400
chr5A
90.361
83
8
0
2509
2591
16491618
16491700
3.300000e-20
110
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
TraesCS3B01G444400
chr3B
684511860
684514993
3133
True
5788.0
5788
100.0000
1
3134
1
chr3B.!!$R1
3133
1
TraesCS3B01G444400
chr3B
684637117
684638623
1506
True
1615.0
1615
86.2880
1391
2922
1
chr3B.!!$R2
1531
2
TraesCS3B01G444400
chr3B
685393499
685395750
2251
False
1124.5
1338
85.0300
958
3134
2
chr3B.!!$F4
2176
3
TraesCS3B01G444400
chr3B
773747038
773748225
1187
False
455.0
455
74.5860
989
2134
1
chr3B.!!$F3
1145
4
TraesCS3B01G444400
chr3B
685630646
685631787
1141
False
383.0
383
73.4690
991
2135
1
chr3B.!!$F1
1144
5
TraesCS3B01G444400
chr3B
685659141
685660282
1141
False
383.0
383
73.4690
991
2135
1
chr3B.!!$F2
1144
6
TraesCS3B01G444400
chr3A
655568450
655570668
2218
True
3049.0
3049
91.8200
960
3134
1
chr3A.!!$R1
2174
7
TraesCS3B01G444400
chr3D
520095962
520097641
1679
True
2364.0
2364
92.2990
1109
2768
1
chr3D.!!$R2
1659
8
TraesCS3B01G444400
chr3D
520426552
520428894
2342
False
1171.5
1341
85.7360
958
3134
2
chr3D.!!$F8
2176
9
TraesCS3B01G444400
chr3D
296430136
296431063
927
False
1064.0
1064
87.3310
1
957
1
chr3D.!!$F1
956
10
TraesCS3B01G444400
chr3D
568576924
568577851
927
True
1053.0
1053
87.1100
1
956
1
chr3D.!!$R3
955
11
TraesCS3B01G444400
chr3D
511068076
511069000
924
False
1037.0
1037
86.9930
1
947
1
chr3D.!!$F2
946
12
TraesCS3B01G444400
chr3D
571450657
571451591
934
True
1020.0
1020
86.5090
1
956
1
chr3D.!!$R5
955
13
TraesCS3B01G444400
chr3D
579581078
579582755
1677
True
771.0
771
76.0580
1038
2672
1
chr3D.!!$R6
1634
14
TraesCS3B01G444400
chr3D
520595042
520596133
1091
False
448.0
448
74.5570
1022
2135
1
chr3D.!!$F3
1113
15
TraesCS3B01G444400
chr3D
58088681
58089426
745
True
420.0
420
77.2190
1395
2134
1
chr3D.!!$R1
739
16
TraesCS3B01G444400
chr3D
565641909
565643046
1137
False
385.0
385
73.8540
991
2116
1
chr3D.!!$F4
1125
17
TraesCS3B01G444400
chr3D
520080102
520082573
2471
True
383.0
433
84.6525
1013
3134
2
chr3D.!!$R7
2121
18
TraesCS3B01G444400
chr3D
568017769
568018538
769
False
278.0
278
73.7700
1351
2128
1
chr3D.!!$F6
777
19
TraesCS3B01G444400
chr3D
566743056
566743785
729
False
254.0
254
73.4940
1396
2128
1
chr3D.!!$F5
732
20
TraesCS3B01G444400
chr3D
568111385
568111980
595
False
222.0
222
74.1720
1547
2127
1
chr3D.!!$F7
580
21
TraesCS3B01G444400
chr1B
622621155
622622121
966
True
1676.0
1676
97.9340
1
967
1
chr1B.!!$R1
966
22
TraesCS3B01G444400
chr2B
364960441
364961396
955
False
1639.0
1639
97.6040
1
957
1
chr2B.!!$F1
956
23
TraesCS3B01G444400
chr7D
85598870
85599832
962
True
1533.0
1533
95.4360
1
961
1
chr7D.!!$R1
960
24
TraesCS3B01G444400
chr4B
95668506
95669493
987
False
1530.0
1530
95.1420
1
956
1
chr4B.!!$F1
955
25
TraesCS3B01G444400
chr1A
13250841
13251695
854
True
1327.0
1327
94.5730
94
956
1
chr1A.!!$R2
862
26
TraesCS3B01G444400
chr1A
9307805
9308650
845
True
1317.0
1317
94.6510
94
950
1
chr1A.!!$R1
856
27
TraesCS3B01G444400
chr1D
321329266
321330162
896
False
1018.0
1018
87.1110
1
925
1
chr1D.!!$F1
924
28
TraesCS3B01G444400
chr2A
45080376
45081143
767
False
366.0
366
75.7730
1351
2106
1
chr2A.!!$F1
755
29
TraesCS3B01G444400
chrUn
40962868
40963460
592
False
272.0
272
75.4180
1544
2127
1
chrUn.!!$F1
583
30
TraesCS3B01G444400
chrUn
326502005
326502597
592
False
272.0
272
75.4180
1544
2127
1
chrUn.!!$F2
583
31
TraesCS3B01G444400
chrUn
340248144
340248930
786
True
254.0
254
73.1010
1351
2134
1
chrUn.!!$R1
783
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.