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
TraesCS7D01G107700
chr7D
100.000
4720
0
0
1
4720
64730406
64735125
0.000000e+00
8717.0
1
TraesCS7D01G107700
chr7D
88.000
75
3
2
4070
4138
64704241
64704167
3.030000e-12
84.2
2
TraesCS7D01G107700
chr7B
96.676
2226
54
7
1853
4068
6370600
6372815
0.000000e+00
3683.0
3
TraesCS7D01G107700
chr7B
94.428
1651
57
13
1
1629
6368905
6370542
0.000000e+00
2507.0
4
TraesCS7D01G107700
chr7B
97.549
204
5
0
4517
4720
6373285
6373488
2.700000e-92
350.0
5
TraesCS7D01G107700
chr7B
96.154
130
5
0
4358
4487
6372815
6372944
3.700000e-51
213.0
6
TraesCS7D01G107700
chr7B
82.524
103
12
6
4350
4451
6234149
6234052
8.420000e-13
86.1
7
TraesCS7D01G107700
chr7B
97.872
47
1
0
1748
1794
6370547
6370593
1.090000e-11
82.4
8
TraesCS7D01G107700
chr7B
86.667
75
3
3
4070
4138
6234678
6234605
5.060000e-10
76.8
9
TraesCS7D01G107700
chr7A
97.368
1786
33
4
2032
3804
68887670
68889454
0.000000e+00
3025.0
10
TraesCS7D01G107700
chr7A
90.634
1452
54
19
1
1444
68884284
68885661
0.000000e+00
1853.0
11
TraesCS7D01G107700
chr7A
96.528
288
10
0
1746
2033
68887289
68887576
1.190000e-130
477.0
12
TraesCS7D01G107700
chr7A
96.679
271
9
0
3852
4122
68889451
68889721
7.200000e-123
451.0
13
TraesCS7D01G107700
chr7A
93.066
274
4
5
4155
4414
68890435
68890707
2.060000e-103
387.0
14
TraesCS7D01G107700
chr7A
97.487
199
5
0
4522
4720
68900194
68900392
1.630000e-89
340.0
15
TraesCS7D01G107700
chr7A
98.160
163
3
0
1470
1632
68887128
68887290
7.730000e-73
285.0
16
TraesCS7D01G107700
chr7A
86.624
157
16
5
1631
1785
626943973
626944126
8.120000e-38
169.0
17
TraesCS7D01G107700
chr7A
87.209
86
5
1
4442
4521
68890700
68890785
5.030000e-15
93.5
18
TraesCS7D01G107700
chr7A
88.000
75
3
3
4070
4138
68880657
68880583
3.030000e-12
84.2
19
TraesCS7D01G107700
chr7A
100.000
30
0
0
4350
4379
68880127
68880098
6.600000e-04
56.5
20
TraesCS7D01G107700
chr4B
90.882
1985
123
23
1833
3768
673191027
673189052
0.000000e+00
2610.0
21
TraesCS7D01G107700
chr4B
79.829
937
80
51
279
1126
673193104
673192188
2.450000e-162
582.0
22
TraesCS7D01G107700
chr4B
95.283
106
2
1
1746
1848
673191328
673191223
1.050000e-36
165.0
23
TraesCS7D01G107700
chr2D
92.984
1354
74
9
2008
3351
614871715
614873057
0.000000e+00
1954.0
24
TraesCS7D01G107700
chr2D
85.526
608
59
9
1
602
614867553
614868137
4.040000e-170
608.0
25
TraesCS7D01G107700
chr2D
84.950
598
29
23
594
1160
614868570
614869137
2.480000e-152
549.0
26
TraesCS7D01G107700
chr2D
93.030
330
23
0
3423
3752
614875292
614875621
2.550000e-132
483.0
27
TraesCS7D01G107700
chr2D
90.217
276
19
2
1746
2013
614871262
614871537
2.090000e-93
353.0
28
TraesCS7D01G107700
chr2D
93.431
137
5
4
1620
1752
381869753
381869617
2.880000e-47
200.0
29
TraesCS7D01G107700
chr2D
87.826
115
7
3
1517
1629
614871151
614871260
1.380000e-25
128.0
30
TraesCS7D01G107700
chr2D
79.259
135
17
7
4281
4407
614848398
614848267
3.030000e-12
84.2
31
TraesCS7D01G107700
chr4A
86.141
1306
121
26
2422
3695
628330554
628329277
0.000000e+00
1354.0
32
TraesCS7D01G107700
chr4A
97.521
121
3
0
1628
1748
702148912
702148792
1.720000e-49
207.0
33
TraesCS7D01G107700
chr4A
95.349
129
4
2
1623
1750
658949239
658949112
2.230000e-48
204.0
34
TraesCS7D01G107700
chr4A
92.105
76
3
1
1520
1592
628332921
628332846
2.320000e-18
104.0
35
TraesCS7D01G107700
chr5B
88.298
940
81
12
2422
3352
682700496
682699577
0.000000e+00
1099.0
36
TraesCS7D01G107700
chr5B
86.792
318
35
2
3378
3695
682699412
682699102
9.720000e-92
348.0
37
TraesCS7D01G107700
chr5B
83.764
271
24
14
863
1123
535284562
535284822
6.100000e-59
239.0
38
TraesCS7D01G107700
chr5B
87.629
97
8
1
1389
1485
682703153
682703061
4.990000e-20
110.0
39
TraesCS7D01G107700
chr5D
87.979
940
84
12
2422
3352
540288857
540287938
0.000000e+00
1083.0
40
TraesCS7D01G107700
chr5D
87.975
316
31
2
3380
3695
540287712
540287404
2.680000e-97
366.0
41
TraesCS7D01G107700
chr5D
99.145
117
1
0
1631
1747
74721881
74721997
1.330000e-50
211.0
42
TraesCS7D01G107700
chr5D
85.124
121
12
2
998
1118
540290145
540290031
8.300000e-23
119.0
43
TraesCS7D01G107700
chr5A
90.505
653
41
10
2483
3123
707643607
707644250
0.000000e+00
843.0
44
TraesCS7D01G107700
chr5A
82.286
175
11
3
3397
3566
707644633
707644792
2.960000e-27
134.0
45
TraesCS7D01G107700
chr5A
90.385
52
5
0
2142
2193
622432175
622432226
8.480000e-08
69.4
46
TraesCS7D01G107700
chr5A
88.462
52
6
0
2142
2193
622425313
622425364
3.940000e-06
63.9
47
TraesCS7D01G107700
chrUn
88.366
404
36
4
2463
2855
99838357
99838760
4.270000e-130
475.0
48
TraesCS7D01G107700
chr2B
94.479
163
9
0
3423
3585
749287792
749287954
7.840000e-63
252.0
49
TraesCS7D01G107700
chr2B
97.521
121
3
0
1630
1750
52463335
52463215
1.720000e-49
207.0
50
TraesCS7D01G107700
chr2B
93.600
125
8
0
3585
3709
749300741
749300865
2.240000e-43
187.0
51
TraesCS7D01G107700
chr2B
97.222
108
3
0
2878
2985
749306151
749306258
2.900000e-42
183.0
52
TraesCS7D01G107700
chr2B
79.259
135
17
7
4281
4407
749233896
749233765
3.030000e-12
84.2
53
TraesCS7D01G107700
chr3B
83.150
273
27
14
863
1126
830562882
830562620
1.020000e-56
231.0
54
TraesCS7D01G107700
chr3B
97.521
121
2
1
1627
1747
637086448
637086329
6.190000e-49
206.0
55
TraesCS7D01G107700
chr3B
91.667
144
11
1
1622
1764
556520657
556520800
1.040000e-46
198.0
56
TraesCS7D01G107700
chr3B
87.903
124
14
1
1647
1770
4488202
4488324
1.370000e-30
145.0
57
TraesCS7D01G107700
chr3B
91.228
57
5
0
482
538
778413136
778413192
1.410000e-10
78.7
58
TraesCS7D01G107700
chr6B
95.312
128
6
0
1626
1753
563489226
563489353
2.230000e-48
204.0
59
TraesCS7D01G107700
chr1B
95.349
129
3
2
1631
1759
67115767
67115892
8.010000e-48
202.0
60
TraesCS7D01G107700
chr1B
85.000
160
10
9
863
1014
77961846
77961693
2.940000e-32
150.0
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
TraesCS7D01G107700
chr7D
64730406
64735125
4719
False
8717.000000
8717
100.000000
1
4720
1
chr7D.!!$F1
4719
1
TraesCS7D01G107700
chr7B
6368905
6373488
4583
False
1367.080000
3683
96.535800
1
4720
5
chr7B.!!$F1
4719
2
TraesCS7D01G107700
chr7A
68884284
68890785
6501
False
938.785714
3025
94.234857
1
4521
7
chr7A.!!$F3
4520
3
TraesCS7D01G107700
chr4B
673189052
673193104
4052
True
1119.000000
2610
88.664667
279
3768
3
chr4B.!!$R1
3489
4
TraesCS7D01G107700
chr2D
614867553
614875621
8068
False
679.166667
1954
89.088833
1
3752
6
chr2D.!!$F1
3751
5
TraesCS7D01G107700
chr4A
628329277
628332921
3644
True
729.000000
1354
89.123000
1520
3695
2
chr4A.!!$R3
2175
6
TraesCS7D01G107700
chr5B
682699102
682703153
4051
True
519.000000
1099
87.573000
1389
3695
3
chr5B.!!$R1
2306
7
TraesCS7D01G107700
chr5D
540287404
540290145
2741
True
522.666667
1083
87.026000
998
3695
3
chr5D.!!$R1
2697
8
TraesCS7D01G107700
chr5A
707643607
707644792
1185
False
488.500000
843
86.395500
2483
3566
2
chr5A.!!$F3
1083
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.