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
TraesCS3B01G343500
chr3B
100.000
3441
0
0
1
3441
552474702
552478142
0.000000e+00
6355.0
1
TraesCS3B01G343500
chr3B
92.840
810
32
7
1
784
409279270
409278461
0.000000e+00
1151.0
2
TraesCS3B01G343500
chr4D
95.672
1340
31
7
794
2115
183382749
183384079
0.000000e+00
2128.0
3
TraesCS3B01G343500
chr4D
97.134
314
7
2
2241
2552
183384086
183384399
2.350000e-146
529.0
4
TraesCS3B01G343500
chr4A
95.063
1357
41
16
783
2115
310239423
310240777
0.000000e+00
2111.0
5
TraesCS3B01G343500
chr4A
95.238
441
20
1
2113
2552
310240807
310241247
0.000000e+00
697.0
6
TraesCS3B01G343500
chr4A
95.604
91
4
0
2606
2696
741977194
741977284
2.770000e-31
147.0
7
TraesCS3B01G343500
chr3D
97.268
1208
20
7
921
2115
424002688
424001481
0.000000e+00
2036.0
8
TraesCS3B01G343500
chr3D
96.825
441
12
1
2116
2554
424001448
424001008
0.000000e+00
736.0
9
TraesCS3B01G343500
chr3D
97.260
219
6
0
2395
2613
424001001
424000783
4.190000e-99
372.0
10
TraesCS3B01G343500
chr3D
94.643
56
2
1
2693
2748
424000786
424000732
6.120000e-13
86.1
11
TraesCS3B01G343500
chr4B
96.360
1099
27
5
1018
2115
200657993
200656907
0.000000e+00
1796.0
12
TraesCS3B01G343500
chr4B
94.558
441
23
1
2113
2552
200656877
200656437
0.000000e+00
680.0
13
TraesCS3B01G343500
chr3A
95.326
813
14
10
963
1753
565042049
565042859
0.000000e+00
1269.0
14
TraesCS3B01G343500
chr3A
93.061
807
31
5
1
782
712722886
712723692
0.000000e+00
1157.0
15
TraesCS3B01G343500
chr3A
92.857
812
32
6
1
786
597968675
597969486
0.000000e+00
1155.0
16
TraesCS3B01G343500
chr3A
92.831
809
33
4
1
784
12178276
12177468
0.000000e+00
1149.0
17
TraesCS3B01G343500
chr3A
92.089
809
36
11
1
783
688890620
688891426
0.000000e+00
1114.0
18
TraesCS3B01G343500
chr3A
90.111
809
31
13
1
783
696640103
696639318
0.000000e+00
1005.0
19
TraesCS3B01G343500
chr3A
94.379
427
21
3
1753
2177
565042819
565043244
0.000000e+00
652.0
20
TraesCS3B01G343500
chr3A
96.144
389
15
0
2225
2613
565043247
565043635
1.350000e-178
636.0
21
TraesCS3B01G343500
chr7B
97.701
696
13
2
2748
3441
68096713
68097407
0.000000e+00
1194.0
22
TraesCS3B01G343500
chr7B
93.795
693
23
11
2749
3441
528878817
528879489
0.000000e+00
1024.0
23
TraesCS3B01G343500
chr5B
93.612
814
25
6
1
787
550170430
550171243
0.000000e+00
1190.0
24
TraesCS3B01G343500
chr5B
97.258
693
18
1
2749
3441
420716498
420717189
0.000000e+00
1173.0
25
TraesCS3B01G343500
chr5B
93.651
693
24
11
2749
3441
406871282
406870610
0.000000e+00
1018.0
26
TraesCS3B01G343500
chr5B
93.372
694
25
13
2749
3441
179226334
179227007
0.000000e+00
1007.0
27
TraesCS3B01G343500
chr6B
93.086
810
31
5
1
785
213304871
213305680
0.000000e+00
1162.0
28
TraesCS3B01G343500
chr6B
93.237
695
25
13
2749
3441
408661274
408661948
0.000000e+00
1003.0
29
TraesCS3B01G343500
chr6B
93.218
693
26
12
2749
3441
704851369
704850698
0.000000e+00
1000.0
30
TraesCS3B01G343500
chr1B
92.963
810
30
7
1
784
569979204
569980012
0.000000e+00
1155.0
31
TraesCS3B01G343500
chr1B
92.698
808
33
6
1
783
27083418
27084224
0.000000e+00
1142.0
32
TraesCS3B01G343500
chr1B
89.815
108
7
3
2591
2697
77543003
77543107
5.990000e-28
135.0
33
TraesCS3B01G343500
chr5A
92.822
808
33
5
1
783
143593738
143594545
0.000000e+00
1147.0
34
TraesCS3B01G343500
chr5A
90.566
106
7
3
2591
2694
450225342
450225446
1.670000e-28
137.0
35
TraesCS3B01G343500
chr2A
93.362
693
25
12
2749
3441
719453111
719453782
0.000000e+00
1005.0
36
TraesCS3B01G343500
chr7A
92.929
693
28
12
2749
3441
171417966
171418637
0.000000e+00
989.0
37
TraesCS3B01G343500
chr7A
91.114
709
35
11
105
786
202741132
202741839
0.000000e+00
935.0
38
TraesCS3B01G343500
chr7A
95.247
547
26
0
1
547
108783896
108784442
0.000000e+00
867.0
39
TraesCS3B01G343500
chrUn
94.845
97
5
0
2606
2702
17148595
17148691
5.950000e-33
152.0
40
TraesCS3B01G343500
chr2D
95.604
91
4
0
2610
2700
35026578
35026488
2.770000e-31
147.0
41
TraesCS3B01G343500
chr1A
93.000
100
4
3
2598
2694
572633046
572633145
3.580000e-30
143.0
42
TraesCS3B01G343500
chr6A
91.346
104
7
2
2597
2699
101438265
101438367
1.290000e-29
141.0
43
TraesCS3B01G343500
chr2B
91.429
105
5
4
2592
2694
736103138
736103240
1.290000e-29
141.0
44
TraesCS3B01G343500
chr7D
89.286
112
10
2
2591
2702
252265177
252265286
4.630000e-29
139.0
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
TraesCS3B01G343500
chr3B
552474702
552478142
3440
False
6355.000000
6355
100.0000
1
3441
1
chr3B.!!$F1
3440
1
TraesCS3B01G343500
chr3B
409278461
409279270
809
True
1151.000000
1151
92.8400
1
784
1
chr3B.!!$R1
783
2
TraesCS3B01G343500
chr4D
183382749
183384399
1650
False
1328.500000
2128
96.4030
794
2552
2
chr4D.!!$F1
1758
3
TraesCS3B01G343500
chr4A
310239423
310241247
1824
False
1404.000000
2111
95.1505
783
2552
2
chr4A.!!$F2
1769
4
TraesCS3B01G343500
chr3D
424000732
424002688
1956
True
807.525000
2036
96.4990
921
2748
4
chr3D.!!$R1
1827
5
TraesCS3B01G343500
chr4B
200656437
200657993
1556
True
1238.000000
1796
95.4590
1018
2552
2
chr4B.!!$R1
1534
6
TraesCS3B01G343500
chr3A
712722886
712723692
806
False
1157.000000
1157
93.0610
1
782
1
chr3A.!!$F3
781
7
TraesCS3B01G343500
chr3A
597968675
597969486
811
False
1155.000000
1155
92.8570
1
786
1
chr3A.!!$F1
785
8
TraesCS3B01G343500
chr3A
12177468
12178276
808
True
1149.000000
1149
92.8310
1
784
1
chr3A.!!$R1
783
9
TraesCS3B01G343500
chr3A
688890620
688891426
806
False
1114.000000
1114
92.0890
1
783
1
chr3A.!!$F2
782
10
TraesCS3B01G343500
chr3A
696639318
696640103
785
True
1005.000000
1005
90.1110
1
783
1
chr3A.!!$R2
782
11
TraesCS3B01G343500
chr3A
565042049
565043635
1586
False
852.333333
1269
95.2830
963
2613
3
chr3A.!!$F4
1650
12
TraesCS3B01G343500
chr7B
68096713
68097407
694
False
1194.000000
1194
97.7010
2748
3441
1
chr7B.!!$F1
693
13
TraesCS3B01G343500
chr7B
528878817
528879489
672
False
1024.000000
1024
93.7950
2749
3441
1
chr7B.!!$F2
692
14
TraesCS3B01G343500
chr5B
550170430
550171243
813
False
1190.000000
1190
93.6120
1
787
1
chr5B.!!$F3
786
15
TraesCS3B01G343500
chr5B
420716498
420717189
691
False
1173.000000
1173
97.2580
2749
3441
1
chr5B.!!$F2
692
16
TraesCS3B01G343500
chr5B
406870610
406871282
672
True
1018.000000
1018
93.6510
2749
3441
1
chr5B.!!$R1
692
17
TraesCS3B01G343500
chr5B
179226334
179227007
673
False
1007.000000
1007
93.3720
2749
3441
1
chr5B.!!$F1
692
18
TraesCS3B01G343500
chr6B
213304871
213305680
809
False
1162.000000
1162
93.0860
1
785
1
chr6B.!!$F1
784
19
TraesCS3B01G343500
chr6B
408661274
408661948
674
False
1003.000000
1003
93.2370
2749
3441
1
chr6B.!!$F2
692
20
TraesCS3B01G343500
chr6B
704850698
704851369
671
True
1000.000000
1000
93.2180
2749
3441
1
chr6B.!!$R1
692
21
TraesCS3B01G343500
chr1B
569979204
569980012
808
False
1155.000000
1155
92.9630
1
784
1
chr1B.!!$F3
783
22
TraesCS3B01G343500
chr1B
27083418
27084224
806
False
1142.000000
1142
92.6980
1
783
1
chr1B.!!$F1
782
23
TraesCS3B01G343500
chr5A
143593738
143594545
807
False
1147.000000
1147
92.8220
1
783
1
chr5A.!!$F1
782
24
TraesCS3B01G343500
chr2A
719453111
719453782
671
False
1005.000000
1005
93.3620
2749
3441
1
chr2A.!!$F1
692
25
TraesCS3B01G343500
chr7A
171417966
171418637
671
False
989.000000
989
92.9290
2749
3441
1
chr7A.!!$F2
692
26
TraesCS3B01G343500
chr7A
202741132
202741839
707
False
935.000000
935
91.1140
105
786
1
chr7A.!!$F3
681
27
TraesCS3B01G343500
chr7A
108783896
108784442
546
False
867.000000
867
95.2470
1
547
1
chr7A.!!$F1
546
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.