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
TraesCS7B01G468000
chr7B
100.000
2375
0
0
1
2375
725310265
725312639
0.000000e+00
4386.0
1
TraesCS7B01G468000
chr2A
88.478
2352
168
51
1
2272
610789222
610791550
0.000000e+00
2747.0
2
TraesCS7B01G468000
chr4B
90.775
2027
126
16
283
2272
644611593
644613595
0.000000e+00
2651.0
3
TraesCS7B01G468000
chr4B
88.127
1575
94
31
1
1505
200942496
200944047
0.000000e+00
1786.0
4
TraesCS7B01G468000
chr4B
89.566
738
62
11
1547
2272
200944144
200944878
0.000000e+00
922.0
5
TraesCS7B01G468000
chr4B
87.520
633
49
14
1
606
39579694
39579065
0.000000e+00
704.0
6
TraesCS7B01G468000
chr4B
94.231
104
6
0
2272
2375
180495246
180495349
2.440000e-35
159.0
7
TraesCS7B01G468000
chr4A
87.479
2356
163
56
1
2273
129030504
129032810
0.000000e+00
2595.0
8
TraesCS7B01G468000
chr4A
89.414
888
57
14
1
864
433607543
433606669
0.000000e+00
1085.0
9
TraesCS7B01G468000
chr1B
89.720
1965
129
35
1
1916
681899096
681901036
0.000000e+00
2442.0
10
TraesCS7B01G468000
chr1B
90.116
1548
92
19
1
1505
516781493
516783022
0.000000e+00
1954.0
11
TraesCS7B01G468000
chr1B
90.959
730
57
6
1552
2274
516783156
516783883
0.000000e+00
974.0
12
TraesCS7B01G468000
chr1B
93.269
104
7
0
2272
2375
485315984
485315881
1.140000e-33
154.0
13
TraesCS7B01G468000
chr5B
91.924
1523
87
8
3
1505
639292984
639294490
0.000000e+00
2098.0
14
TraesCS7B01G468000
chr5B
90.921
749
54
7
1532
2272
639294608
639295350
0.000000e+00
994.0
15
TraesCS7B01G468000
chr5B
88.697
752
73
9
1532
2274
189834664
189835412
0.000000e+00
907.0
16
TraesCS7B01G468000
chr5B
93.333
45
3
0
1524
1568
639294550
639294594
1.520000e-07
67.6
17
TraesCS7B01G468000
chr2B
92.041
1470
92
4
1
1448
149803123
149804589
0.000000e+00
2043.0
18
TraesCS7B01G468000
chr2B
87.298
1606
110
44
1
1566
738345042
738343491
0.000000e+00
1749.0
19
TraesCS7B01G468000
chr2B
87.946
1543
101
21
1
1513
539886129
539887616
0.000000e+00
1740.0
20
TraesCS7B01G468000
chr2B
93.657
804
43
5
1476
2272
149804677
149805479
0.000000e+00
1195.0
21
TraesCS7B01G468000
chr2B
95.192
104
5
0
2272
2375
189210103
189210000
5.250000e-37
165.0
22
TraesCS7B01G468000
chr2B
95.161
62
3
0
1444
1505
149804611
149804672
5.400000e-17
99.0
23
TraesCS7B01G468000
chr7D
90.318
1539
88
19
1
1493
501764115
501765638
0.000000e+00
1960.0
24
TraesCS7B01G468000
chr7D
90.694
634
47
10
1647
2272
501767460
501768089
0.000000e+00
833.0
25
TraesCS7B01G468000
chr3B
89.334
1547
108
25
1
1505
318303753
318305284
0.000000e+00
1890.0
26
TraesCS7B01G468000
chr3B
92.036
879
50
14
628
1505
320671909
320671050
0.000000e+00
1218.0
27
TraesCS7B01G468000
chr3B
91.786
560
25
9
1
539
757822459
757823018
0.000000e+00
760.0
28
TraesCS7B01G468000
chr3B
86.705
173
5
12
751
923
766276405
766276559
2.430000e-40
176.0
29
TraesCS7B01G468000
chr3B
95.192
104
5
0
2272
2375
358759336
358759439
5.250000e-37
165.0
30
TraesCS7B01G468000
chr6D
88.599
1456
113
33
862
2273
446363510
446362064
0.000000e+00
1720.0
31
TraesCS7B01G468000
chr6D
88.140
1484
99
31
862
2272
297170603
297169124
0.000000e+00
1694.0
32
TraesCS7B01G468000
chr6D
89.205
704
48
10
1
682
46520644
46519947
0.000000e+00
854.0
33
TraesCS7B01G468000
chr3D
89.233
1421
79
23
1
1399
229427746
229426378
0.000000e+00
1709.0
34
TraesCS7B01G468000
chr3D
91.212
899
41
11
1
864
420358346
420359241
0.000000e+00
1188.0
35
TraesCS7B01G468000
chr3D
89.205
704
48
10
1
682
330465000
330464303
0.000000e+00
854.0
36
TraesCS7B01G468000
chr3D
88.651
608
33
7
291
864
571735992
571735387
0.000000e+00
708.0
37
TraesCS7B01G468000
chr1D
87.746
1420
110
25
862
2272
417113883
417115247
0.000000e+00
1600.0
38
TraesCS7B01G468000
chr4D
85.655
1450
136
30
862
2272
239784730
239783314
0.000000e+00
1459.0
39
TraesCS7B01G468000
chr4D
95.192
104
5
0
2272
2375
212284027
212283924
5.250000e-37
165.0
40
TraesCS7B01G468000
chr2D
91.648
898
35
10
1
864
397130442
397131333
0.000000e+00
1206.0
41
TraesCS7B01G468000
chr2D
93.269
104
7
0
2272
2375
331970624
331970521
1.140000e-33
154.0
42
TraesCS7B01G468000
chr5D
90.203
888
50
16
1
864
384512138
384511264
0.000000e+00
1123.0
43
TraesCS7B01G468000
chr7A
89.878
899
50
14
1
864
220999337
221000229
0.000000e+00
1118.0
44
TraesCS7B01G468000
chr7A
85.240
874
78
27
1416
2272
583704234
583705073
0.000000e+00
852.0
45
TraesCS7B01G468000
chrUn
87.816
632
48
10
1
606
291783105
291783733
0.000000e+00
713.0
46
TraesCS7B01G468000
chrUn
87.658
632
49
10
1
606
281296870
281296242
0.000000e+00
708.0
47
TraesCS7B01G468000
chrUn
87.658
632
49
10
1
606
281303790
281303162
0.000000e+00
708.0
48
TraesCS7B01G468000
chrUn
87.658
632
49
10
1
606
291788042
291787414
0.000000e+00
708.0
49
TraesCS7B01G468000
chr6B
95.192
104
5
0
2272
2375
393514016
393513913
5.250000e-37
165.0
50
TraesCS7B01G468000
chr6B
95.192
104
5
0
2272
2375
452932623
452932520
5.250000e-37
165.0
51
TraesCS7B01G468000
chr6B
93.269
104
7
0
2272
2375
452819663
452819560
1.140000e-33
154.0
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
TraesCS7B01G468000
chr7B
725310265
725312639
2374
False
4386.000000
4386
100.000000
1
2375
1
chr7B.!!$F1
2374
1
TraesCS7B01G468000
chr2A
610789222
610791550
2328
False
2747.000000
2747
88.478000
1
2272
1
chr2A.!!$F1
2271
2
TraesCS7B01G468000
chr4B
644611593
644613595
2002
False
2651.000000
2651
90.775000
283
2272
1
chr4B.!!$F2
1989
3
TraesCS7B01G468000
chr4B
200942496
200944878
2382
False
1354.000000
1786
88.846500
1
2272
2
chr4B.!!$F3
2271
4
TraesCS7B01G468000
chr4B
39579065
39579694
629
True
704.000000
704
87.520000
1
606
1
chr4B.!!$R1
605
5
TraesCS7B01G468000
chr4A
129030504
129032810
2306
False
2595.000000
2595
87.479000
1
2273
1
chr4A.!!$F1
2272
6
TraesCS7B01G468000
chr4A
433606669
433607543
874
True
1085.000000
1085
89.414000
1
864
1
chr4A.!!$R1
863
7
TraesCS7B01G468000
chr1B
681899096
681901036
1940
False
2442.000000
2442
89.720000
1
1916
1
chr1B.!!$F1
1915
8
TraesCS7B01G468000
chr1B
516781493
516783883
2390
False
1464.000000
1954
90.537500
1
2274
2
chr1B.!!$F2
2273
9
TraesCS7B01G468000
chr5B
639292984
639295350
2366
False
1053.200000
2098
92.059333
3
2272
3
chr5B.!!$F2
2269
10
TraesCS7B01G468000
chr5B
189834664
189835412
748
False
907.000000
907
88.697000
1532
2274
1
chr5B.!!$F1
742
11
TraesCS7B01G468000
chr2B
738343491
738345042
1551
True
1749.000000
1749
87.298000
1
1566
1
chr2B.!!$R2
1565
12
TraesCS7B01G468000
chr2B
539886129
539887616
1487
False
1740.000000
1740
87.946000
1
1513
1
chr2B.!!$F1
1512
13
TraesCS7B01G468000
chr2B
149803123
149805479
2356
False
1112.333333
2043
93.619667
1
2272
3
chr2B.!!$F2
2271
14
TraesCS7B01G468000
chr7D
501764115
501768089
3974
False
1396.500000
1960
90.506000
1
2272
2
chr7D.!!$F1
2271
15
TraesCS7B01G468000
chr3B
318303753
318305284
1531
False
1890.000000
1890
89.334000
1
1505
1
chr3B.!!$F1
1504
16
TraesCS7B01G468000
chr3B
320671050
320671909
859
True
1218.000000
1218
92.036000
628
1505
1
chr3B.!!$R1
877
17
TraesCS7B01G468000
chr3B
757822459
757823018
559
False
760.000000
760
91.786000
1
539
1
chr3B.!!$F3
538
18
TraesCS7B01G468000
chr6D
446362064
446363510
1446
True
1720.000000
1720
88.599000
862
2273
1
chr6D.!!$R3
1411
19
TraesCS7B01G468000
chr6D
297169124
297170603
1479
True
1694.000000
1694
88.140000
862
2272
1
chr6D.!!$R2
1410
20
TraesCS7B01G468000
chr6D
46519947
46520644
697
True
854.000000
854
89.205000
1
682
1
chr6D.!!$R1
681
21
TraesCS7B01G468000
chr3D
229426378
229427746
1368
True
1709.000000
1709
89.233000
1
1399
1
chr3D.!!$R1
1398
22
TraesCS7B01G468000
chr3D
420358346
420359241
895
False
1188.000000
1188
91.212000
1
864
1
chr3D.!!$F1
863
23
TraesCS7B01G468000
chr3D
330464303
330465000
697
True
854.000000
854
89.205000
1
682
1
chr3D.!!$R2
681
24
TraesCS7B01G468000
chr3D
571735387
571735992
605
True
708.000000
708
88.651000
291
864
1
chr3D.!!$R3
573
25
TraesCS7B01G468000
chr1D
417113883
417115247
1364
False
1600.000000
1600
87.746000
862
2272
1
chr1D.!!$F1
1410
26
TraesCS7B01G468000
chr4D
239783314
239784730
1416
True
1459.000000
1459
85.655000
862
2272
1
chr4D.!!$R2
1410
27
TraesCS7B01G468000
chr2D
397130442
397131333
891
False
1206.000000
1206
91.648000
1
864
1
chr2D.!!$F1
863
28
TraesCS7B01G468000
chr5D
384511264
384512138
874
True
1123.000000
1123
90.203000
1
864
1
chr5D.!!$R1
863
29
TraesCS7B01G468000
chr7A
220999337
221000229
892
False
1118.000000
1118
89.878000
1
864
1
chr7A.!!$F1
863
30
TraesCS7B01G468000
chr7A
583704234
583705073
839
False
852.000000
852
85.240000
1416
2272
1
chr7A.!!$F2
856
31
TraesCS7B01G468000
chrUn
291783105
291783733
628
False
713.000000
713
87.816000
1
606
1
chrUn.!!$F1
605
32
TraesCS7B01G468000
chrUn
281296242
281296870
628
True
708.000000
708
87.658000
1
606
1
chrUn.!!$R1
605
33
TraesCS7B01G468000
chrUn
281303162
281303790
628
True
708.000000
708
87.658000
1
606
1
chrUn.!!$R2
605
34
TraesCS7B01G468000
chrUn
291787414
291788042
628
True
708.000000
708
87.658000
1
606
1
chrUn.!!$R3
605
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.