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
TraesCS7B01G332000
chr7B
100.000
3655
0
0
1
3655
587266106
587269760
0.000000e+00
6750.0
1
TraesCS7B01G332000
chr7B
98.636
3667
35
5
1
3655
587100889
587104552
0.000000e+00
6481.0
2
TraesCS7B01G332000
chr7B
93.442
2211
91
16
1
2160
587478792
587480999
0.000000e+00
3230.0
3
TraesCS7B01G332000
chr7B
92.833
2065
84
26
1
2019
587518051
587520097
0.000000e+00
2935.0
4
TraesCS7B01G332000
chr7B
95.616
1095
37
3
2209
3302
587520088
587521172
0.000000e+00
1746.0
5
TraesCS7B01G332000
chr7B
94.558
1121
24
7
870
1953
587440662
587441782
0.000000e+00
1698.0
6
TraesCS7B01G332000
chr7B
97.622
883
17
3
1
880
587438246
587439127
0.000000e+00
1511.0
7
TraesCS7B01G332000
chr7B
96.189
866
32
1
2790
3655
587442620
587443484
0.000000e+00
1415.0
8
TraesCS7B01G332000
chr7B
95.843
866
32
4
2790
3655
587481947
587482808
0.000000e+00
1397.0
9
TraesCS7B01G332000
chr7B
92.943
836
32
7
1511
2334
587620573
587621393
0.000000e+00
1192.0
10
TraesCS7B01G332000
chr7B
93.226
620
17
12
2178
2792
587441940
587442539
0.000000e+00
889.0
11
TraesCS7B01G332000
chr7B
93.160
614
19
5
928
1518
587615264
587615877
0.000000e+00
880.0
12
TraesCS7B01G332000
chr7B
91.276
619
32
6
228
846
587614631
587615227
0.000000e+00
824.0
13
TraesCS7B01G332000
chr7B
98.365
367
6
0
3289
3655
587522619
587522985
0.000000e+00
645.0
14
TraesCS7B01G332000
chr7B
96.721
305
6
3
2178
2479
587480986
587481289
4.210000e-139
505.0
15
TraesCS7B01G332000
chr7B
96.861
223
7
0
1
223
587600125
587600347
1.240000e-99
374.0
16
TraesCS7B01G332000
chr7B
88.379
327
12
11
2472
2792
587481560
587481866
1.600000e-98
370.0
17
TraesCS7B01G332000
chr7B
94.667
150
3
1
1988
2132
587441782
587441931
1.020000e-55
228.0
18
TraesCS7B01G332000
chr7B
83.398
259
27
6
2799
3043
587653122
587653378
3.670000e-55
226.0
19
TraesCS7B01G332000
chr7B
83.616
177
27
2
534
709
639285740
639285565
8.120000e-37
165.0
20
TraesCS7B01G332000
chr7B
85.714
154
12
2
2395
2539
587635764
587635916
1.760000e-33
154.0
21
TraesCS7B01G332000
chr7B
95.556
90
4
0
2317
2406
587635354
587635443
1.060000e-30
145.0
22
TraesCS7B01G332000
chr7B
77.193
228
18
5
3060
3255
587654479
587654704
6.460000e-18
102.0
23
TraesCS7B01G332000
chr7B
87.097
62
4
3
2347
2406
587635687
587635746
2.360000e-07
67.6
24
TraesCS7B01G332000
chr6B
96.814
2982
52
15
711
3655
694681056
694684031
0.000000e+00
4940.0
25
TraesCS7B01G332000
chr6B
84.692
503
60
12
3
493
617126804
617127301
1.530000e-133
486.0
26
TraesCS7B01G332000
chr7D
89.919
1359
65
30
706
2031
543731495
543732814
0.000000e+00
1685.0
27
TraesCS7B01G332000
chr7D
86.288
299
19
5
2896
3194
543733522
543733798
4.590000e-79
305.0
28
TraesCS7B01G332000
chr7D
85.121
289
26
9
2127
2406
543732833
543733113
2.780000e-71
279.0
29
TraesCS7B01G332000
chr7D
85.827
254
21
8
2395
2639
543733131
543733378
4.680000e-64
255.0
30
TraesCS7B01G332000
chr7D
92.857
126
7
1
2775
2900
543733374
543733497
8.060000e-42
182.0
31
TraesCS7B01G332000
chr7A
89.487
1170
84
21
706
1841
625642256
625643420
0.000000e+00
1443.0
32
TraesCS7B01G332000
chr7A
88.786
1186
76
25
706
1841
625675038
625676216
0.000000e+00
1400.0
33
TraesCS7B01G332000
chr1D
85.601
882
63
23
706
1531
110905255
110906128
0.000000e+00
867.0
34
TraesCS7B01G332000
chr3B
83.357
715
94
19
3
706
762402190
762402890
3.980000e-179
638.0
35
TraesCS7B01G332000
chr3B
94.118
323
19
0
3333
3655
187547164
187546842
3.280000e-135
492.0
36
TraesCS7B01G332000
chr5D
82.627
708
108
9
3
702
72198332
72197632
2.410000e-171
612.0
37
TraesCS7B01G332000
chr5D
85.000
180
24
3
533
709
559603428
559603607
2.900000e-41
180.0
38
TraesCS7B01G332000
chr4A
81.466
723
109
17
3
706
732795043
732795759
1.470000e-158
569.0
39
TraesCS7B01G332000
chr6D
95.666
323
12
1
3333
3655
388547382
388547702
5.410000e-143
518.0
40
TraesCS7B01G332000
chr2D
95.356
323
15
0
3333
3655
102820227
102819905
7.000000e-142
514.0
41
TraesCS7B01G332000
chr2D
85.465
172
24
1
530
700
501552961
501552790
1.040000e-40
178.0
42
TraesCS7B01G332000
chr5B
94.704
321
16
1
3333
3653
467381311
467380992
7.050000e-137
497.0
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
TraesCS7B01G332000
chr7B
587266106
587269760
3654
False
6750.000000
6750
100.000000
1
3655
1
chr7B.!!$F2
3654
1
TraesCS7B01G332000
chr7B
587100889
587104552
3663
False
6481.000000
6481
98.636000
1
3655
1
chr7B.!!$F1
3654
2
TraesCS7B01G332000
chr7B
587518051
587522985
4934
False
1775.333333
2935
95.604667
1
3655
3
chr7B.!!$F7
3654
3
TraesCS7B01G332000
chr7B
587478792
587482808
4016
False
1375.500000
3230
93.596250
1
3655
4
chr7B.!!$F6
3654
4
TraesCS7B01G332000
chr7B
587620573
587621393
820
False
1192.000000
1192
92.943000
1511
2334
1
chr7B.!!$F4
823
5
TraesCS7B01G332000
chr7B
587438246
587443484
5238
False
1148.200000
1698
95.252400
1
3655
5
chr7B.!!$F5
3654
6
TraesCS7B01G332000
chr7B
587614631
587615877
1246
False
852.000000
880
92.218000
228
1518
2
chr7B.!!$F8
1290
7
TraesCS7B01G332000
chr6B
694681056
694684031
2975
False
4940.000000
4940
96.814000
711
3655
1
chr6B.!!$F2
2944
8
TraesCS7B01G332000
chr7D
543731495
543733798
2303
False
541.200000
1685
88.002400
706
3194
5
chr7D.!!$F1
2488
9
TraesCS7B01G332000
chr7A
625642256
625643420
1164
False
1443.000000
1443
89.487000
706
1841
1
chr7A.!!$F1
1135
10
TraesCS7B01G332000
chr7A
625675038
625676216
1178
False
1400.000000
1400
88.786000
706
1841
1
chr7A.!!$F2
1135
11
TraesCS7B01G332000
chr1D
110905255
110906128
873
False
867.000000
867
85.601000
706
1531
1
chr1D.!!$F1
825
12
TraesCS7B01G332000
chr3B
762402190
762402890
700
False
638.000000
638
83.357000
3
706
1
chr3B.!!$F1
703
13
TraesCS7B01G332000
chr5D
72197632
72198332
700
True
612.000000
612
82.627000
3
702
1
chr5D.!!$R1
699
14
TraesCS7B01G332000
chr4A
732795043
732795759
716
False
569.000000
569
81.466000
3
706
1
chr4A.!!$F1
703
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.