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
TraesCS5B01G503000
chr5B
100.000
5376
0
0
1
5376
669730121
669735496
0.000000e+00
9928
1
TraesCS5B01G503000
chr5B
97.388
536
11
1
4841
5376
507221906
507221374
0.000000e+00
909
2
TraesCS5B01G503000
chr7D
91.786
2435
145
26
1
2398
52490672
52493088
0.000000e+00
3338
3
TraesCS5B01G503000
chr7D
89.564
1284
121
8
3559
4837
15224985
15226260
0.000000e+00
1616
4
TraesCS5B01G503000
chr7D
93.253
415
26
2
2374
2787
75333119
75333532
1.280000e-170
610
5
TraesCS5B01G503000
chr2D
90.025
2406
178
28
3
2371
16922285
16919905
0.000000e+00
3057
6
TraesCS5B01G503000
chr2D
89.583
1296
115
13
3556
4842
21212299
21213583
0.000000e+00
1628
7
TraesCS5B01G503000
chr2D
93.073
794
45
6
2783
3576
16919411
16918628
0.000000e+00
1153
8
TraesCS5B01G503000
chr2D
91.787
414
29
4
2374
2785
221292355
221292765
6.040000e-159
571
9
TraesCS5B01G503000
chr1A
92.260
2080
140
14
2771
4841
38344449
38342382
0.000000e+00
2929
10
TraesCS5B01G503000
chr1A
88.896
1558
131
24
3
1557
38347227
38345709
0.000000e+00
1881
11
TraesCS5B01G503000
chr1A
94.409
787
36
4
1591
2371
38345705
38344921
0.000000e+00
1203
12
TraesCS5B01G503000
chr1A
90.820
817
51
12
1343
2144
576696661
576695854
0.000000e+00
1072
13
TraesCS5B01G503000
chr1A
92.233
412
25
3
2374
2785
38344874
38344470
1.300000e-160
577
14
TraesCS5B01G503000
chr2B
90.892
2086
154
23
2756
4838
51798280
51796228
0.000000e+00
2767
15
TraesCS5B01G503000
chr2B
88.457
1646
158
14
1
1628
51802604
51800973
0.000000e+00
1958
16
TraesCS5B01G503000
chr2B
87.123
1491
160
21
30
1505
723976940
723978413
0.000000e+00
1661
17
TraesCS5B01G503000
chr2B
94.286
840
39
3
1537
2367
723978411
723979250
0.000000e+00
1277
18
TraesCS5B01G503000
chr6A
90.931
2062
171
8
2783
4842
193177359
193175312
0.000000e+00
2758
19
TraesCS5B01G503000
chr6A
89.774
1281
118
9
3559
4832
441294615
441293341
0.000000e+00
1628
20
TraesCS5B01G503000
chr4A
90.552
2064
162
16
2785
4843
605879882
605881917
0.000000e+00
2700
21
TraesCS5B01G503000
chr4A
91.304
1288
101
4
3556
4841
294601268
294602546
0.000000e+00
1748
22
TraesCS5B01G503000
chr4A
91.587
416
29
2
2374
2785
605879433
605879846
2.170000e-158
569
23
TraesCS5B01G503000
chr4A
91.155
407
33
1
1363
1769
605878654
605879057
2.830000e-152
549
24
TraesCS5B01G503000
chr3A
88.760
1557
134
23
3
1556
732955209
732953691
0.000000e+00
1868
25
TraesCS5B01G503000
chr3A
92.572
1104
73
6
2771
3872
732952428
732951332
0.000000e+00
1576
26
TraesCS5B01G503000
chr3A
94.917
787
34
2
1591
2371
732953686
732952900
0.000000e+00
1227
27
TraesCS5B01G503000
chr3A
94.395
785
40
1
1591
2371
101775648
101776432
0.000000e+00
1203
28
TraesCS5B01G503000
chr3A
92.095
797
53
4
2780
3576
101776921
101777707
0.000000e+00
1114
29
TraesCS5B01G503000
chr3A
91.940
794
55
3
2783
3576
297823372
297822588
0.000000e+00
1103
30
TraesCS5B01G503000
chr3A
85.826
642
69
11
933
1557
297837477
297836841
0.000000e+00
662
31
TraesCS5B01G503000
chr3A
92.029
414
29
3
2374
2785
101776479
101776890
3.610000e-161
579
32
TraesCS5B01G503000
chr2A
88.469
1561
136
22
3
1557
671215379
671216901
0.000000e+00
1845
33
TraesCS5B01G503000
chr2A
92.121
863
61
5
2771
3631
671218164
671219021
0.000000e+00
1210
34
TraesCS5B01G503000
chr2A
94.289
788
38
2
1591
2371
671216905
671217692
0.000000e+00
1199
35
TraesCS5B01G503000
chr2A
91.587
416
28
6
2374
2785
547852437
547852849
7.810000e-158
568
36
TraesCS5B01G503000
chr7B
90.994
1288
109
5
3557
4842
710130406
710129124
0.000000e+00
1729
37
TraesCS5B01G503000
chr7B
90.980
1286
110
4
3557
4840
710107700
710106419
0.000000e+00
1727
38
TraesCS5B01G503000
chr7B
90.388
1290
114
10
3557
4842
710047751
710046468
0.000000e+00
1687
39
TraesCS5B01G503000
chr7B
88.830
1128
78
19
1043
2145
747463023
747464127
0.000000e+00
1341
40
TraesCS5B01G503000
chr7B
87.988
1024
93
13
15
1034
710113765
710112768
0.000000e+00
1182
41
TraesCS5B01G503000
chr7B
96.828
536
14
1
4841
5376
610202281
610201749
0.000000e+00
893
42
TraesCS5B01G503000
chr7B
93.431
411
27
0
2374
2784
21654798
21655208
1.280000e-170
610
43
TraesCS5B01G503000
chr7B
84.317
644
62
16
1043
1665
710111283
710110658
1.290000e-165
593
44
TraesCS5B01G503000
chr7B
84.031
645
62
17
1043
1665
710133988
710133363
2.790000e-162
582
45
TraesCS5B01G503000
chr7B
83.851
644
65
16
1043
1665
710122382
710121757
1.300000e-160
577
46
TraesCS5B01G503000
chr7B
83.066
561
60
15
1043
1586
710080841
710080299
1.350000e-130
477
47
TraesCS5B01G503000
chr7A
85.152
1549
154
31
3
1529
128297778
128299272
0.000000e+00
1517
48
TraesCS5B01G503000
chr7A
90.568
827
55
12
1332
2144
650510714
650509897
0.000000e+00
1074
49
TraesCS5B01G503000
chr7A
97.201
536
12
1
4841
5376
656988340
656987808
0.000000e+00
904
50
TraesCS5B01G503000
chr7A
96.455
536
18
1
4841
5376
288921063
288921597
0.000000e+00
883
51
TraesCS5B01G503000
chr7A
91.325
415
33
2
2374
2787
79626304
79626716
1.010000e-156
564
52
TraesCS5B01G503000
chr5D
94.656
786
38
1
1591
2372
4661353
4662138
0.000000e+00
1216
53
TraesCS5B01G503000
chr5D
92.472
797
49
5
2780
3576
4662626
4663411
0.000000e+00
1129
54
TraesCS5B01G503000
chr5D
92.271
414
28
3
2374
2785
4662184
4662595
7.760000e-163
584
55
TraesCS5B01G503000
chr6D
89.499
838
79
4
2
837
435847286
435846456
0.000000e+00
1051
56
TraesCS5B01G503000
chr6B
89.286
840
80
5
3
840
133745968
133745137
0.000000e+00
1044
57
TraesCS5B01G503000
chr3B
88.862
835
86
4
1
830
824976227
824975395
0.000000e+00
1020
58
TraesCS5B01G503000
chrUn
88.987
790
84
3
1
789
158032035
158031248
0.000000e+00
974
59
TraesCS5B01G503000
chr5A
97.015
536
12
2
4841
5376
474838446
474837915
0.000000e+00
898
60
TraesCS5B01G503000
chr5A
96.828
536
14
1
4841
5376
331012510
331013042
0.000000e+00
893
61
TraesCS5B01G503000
chr1B
97.015
536
13
1
4841
5376
659232532
659232000
0.000000e+00
898
62
TraesCS5B01G503000
chr4B
96.828
536
11
1
4841
5376
223029904
223030433
0.000000e+00
891
63
TraesCS5B01G503000
chr4B
95.896
536
19
1
4841
5376
655278602
655279134
0.000000e+00
865
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
TraesCS5B01G503000
chr5B
669730121
669735496
5375
False
9928.000000
9928
100.000000
1
5376
1
chr5B.!!$F1
5375
1
TraesCS5B01G503000
chr5B
507221374
507221906
532
True
909.000000
909
97.388000
4841
5376
1
chr5B.!!$R1
535
2
TraesCS5B01G503000
chr7D
52490672
52493088
2416
False
3338.000000
3338
91.786000
1
2398
1
chr7D.!!$F2
2397
3
TraesCS5B01G503000
chr7D
15224985
15226260
1275
False
1616.000000
1616
89.564000
3559
4837
1
chr7D.!!$F1
1278
4
TraesCS5B01G503000
chr2D
16918628
16922285
3657
True
2105.000000
3057
91.549000
3
3576
2
chr2D.!!$R1
3573
5
TraesCS5B01G503000
chr2D
21212299
21213583
1284
False
1628.000000
1628
89.583000
3556
4842
1
chr2D.!!$F1
1286
6
TraesCS5B01G503000
chr1A
38342382
38347227
4845
True
1647.500000
2929
91.949500
3
4841
4
chr1A.!!$R2
4838
7
TraesCS5B01G503000
chr1A
576695854
576696661
807
True
1072.000000
1072
90.820000
1343
2144
1
chr1A.!!$R1
801
8
TraesCS5B01G503000
chr2B
51796228
51802604
6376
True
2362.500000
2767
89.674500
1
4838
2
chr2B.!!$R1
4837
9
TraesCS5B01G503000
chr2B
723976940
723979250
2310
False
1469.000000
1661
90.704500
30
2367
2
chr2B.!!$F1
2337
10
TraesCS5B01G503000
chr6A
193175312
193177359
2047
True
2758.000000
2758
90.931000
2783
4842
1
chr6A.!!$R1
2059
11
TraesCS5B01G503000
chr6A
441293341
441294615
1274
True
1628.000000
1628
89.774000
3559
4832
1
chr6A.!!$R2
1273
12
TraesCS5B01G503000
chr4A
294601268
294602546
1278
False
1748.000000
1748
91.304000
3556
4841
1
chr4A.!!$F1
1285
13
TraesCS5B01G503000
chr4A
605878654
605881917
3263
False
1272.666667
2700
91.098000
1363
4843
3
chr4A.!!$F2
3480
14
TraesCS5B01G503000
chr3A
732951332
732955209
3877
True
1557.000000
1868
92.083000
3
3872
3
chr3A.!!$R3
3869
15
TraesCS5B01G503000
chr3A
297822588
297823372
784
True
1103.000000
1103
91.940000
2783
3576
1
chr3A.!!$R1
793
16
TraesCS5B01G503000
chr3A
101775648
101777707
2059
False
965.333333
1203
92.839667
1591
3576
3
chr3A.!!$F1
1985
17
TraesCS5B01G503000
chr3A
297836841
297837477
636
True
662.000000
662
85.826000
933
1557
1
chr3A.!!$R2
624
18
TraesCS5B01G503000
chr2A
671215379
671219021
3642
False
1418.000000
1845
91.626333
3
3631
3
chr2A.!!$F2
3628
19
TraesCS5B01G503000
chr7B
710046468
710047751
1283
True
1687.000000
1687
90.388000
3557
4842
1
chr7B.!!$R2
1285
20
TraesCS5B01G503000
chr7B
747463023
747464127
1104
False
1341.000000
1341
88.830000
1043
2145
1
chr7B.!!$F2
1102
21
TraesCS5B01G503000
chr7B
710106419
710113765
7346
True
1167.333333
1727
87.761667
15
4840
3
chr7B.!!$R5
4825
22
TraesCS5B01G503000
chr7B
710129124
710133988
4864
True
1155.500000
1729
87.512500
1043
4842
2
chr7B.!!$R6
3799
23
TraesCS5B01G503000
chr7B
610201749
610202281
532
True
893.000000
893
96.828000
4841
5376
1
chr7B.!!$R1
535
24
TraesCS5B01G503000
chr7B
710121757
710122382
625
True
577.000000
577
83.851000
1043
1665
1
chr7B.!!$R4
622
25
TraesCS5B01G503000
chr7B
710080299
710080841
542
True
477.000000
477
83.066000
1043
1586
1
chr7B.!!$R3
543
26
TraesCS5B01G503000
chr7A
128297778
128299272
1494
False
1517.000000
1517
85.152000
3
1529
1
chr7A.!!$F2
1526
27
TraesCS5B01G503000
chr7A
650509897
650510714
817
True
1074.000000
1074
90.568000
1332
2144
1
chr7A.!!$R1
812
28
TraesCS5B01G503000
chr7A
656987808
656988340
532
True
904.000000
904
97.201000
4841
5376
1
chr7A.!!$R2
535
29
TraesCS5B01G503000
chr7A
288921063
288921597
534
False
883.000000
883
96.455000
4841
5376
1
chr7A.!!$F3
535
30
TraesCS5B01G503000
chr5D
4661353
4663411
2058
False
976.333333
1216
93.133000
1591
3576
3
chr5D.!!$F1
1985
31
TraesCS5B01G503000
chr6D
435846456
435847286
830
True
1051.000000
1051
89.499000
2
837
1
chr6D.!!$R1
835
32
TraesCS5B01G503000
chr6B
133745137
133745968
831
True
1044.000000
1044
89.286000
3
840
1
chr6B.!!$R1
837
33
TraesCS5B01G503000
chr3B
824975395
824976227
832
True
1020.000000
1020
88.862000
1
830
1
chr3B.!!$R1
829
34
TraesCS5B01G503000
chrUn
158031248
158032035
787
True
974.000000
974
88.987000
1
789
1
chrUn.!!$R1
788
35
TraesCS5B01G503000
chr5A
474837915
474838446
531
True
898.000000
898
97.015000
4841
5376
1
chr5A.!!$R1
535
36
TraesCS5B01G503000
chr5A
331012510
331013042
532
False
893.000000
893
96.828000
4841
5376
1
chr5A.!!$F1
535
37
TraesCS5B01G503000
chr1B
659232000
659232532
532
True
898.000000
898
97.015000
4841
5376
1
chr1B.!!$R1
535
38
TraesCS5B01G503000
chr4B
223029904
223030433
529
False
891.000000
891
96.828000
4841
5376
1
chr4B.!!$F1
535
39
TraesCS5B01G503000
chr4B
655278602
655279134
532
False
865.000000
865
95.896000
4841
5376
1
chr4B.!!$F2
535
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.