Multiple sequence alignment - TraesCS3B01G456300
Loading Multiple Alignment...
BLAST Results
BLAST Results - Input Sequence
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
TraesCS3B01G456300
chr3B
100.000
4925
0
0
1
4925
697898360
697903284
0.000000e+00
9095.0
1
TraesCS3B01G456300
chr3B
81.384
795
148
0
3116
3910
71119782
71120576
0.000000e+00
649.0
2
TraesCS3B01G456300
chr3B
81.132
795
150
0
3116
3910
71143521
71144315
5.380000e-179
638.0
3
TraesCS3B01G456300
chr3B
88.821
492
37
9
746
1221
697856205
697856694
5.490000e-164
588.0
4
TraesCS3B01G456300
chr3B
86.082
194
17
3
128
321
697855975
697856158
3.010000e-47
200.0
5
TraesCS3B01G456300
chr3B
90.625
96
6
3
1208
1303
697858065
697858157
1.860000e-24
124.0
6
TraesCS3B01G456300
chr3B
92.982
57
3
1
2829
2884
748777138
748777082
1.140000e-11
82.4
7
TraesCS3B01G456300
chr3A
94.893
2565
56
10
1
2519
662393770
662396305
0.000000e+00
3941.0
8
TraesCS3B01G456300
chr3A
96.589
1964
40
6
2524
4464
662396406
662398365
0.000000e+00
3230.0
9
TraesCS3B01G456300
chr3A
81.807
797
141
4
3116
3910
57199536
57200330
0.000000e+00
665.0
10
TraesCS3B01G456300
chr3A
86.916
214
22
3
4444
4656
662401451
662401659
8.240000e-58
235.0
11
TraesCS3B01G456300
chr3A
92.500
160
5
3
4645
4803
662406894
662407047
6.420000e-54
222.0
12
TraesCS3B01G456300
chr3A
97.980
99
2
0
2566
2664
662396298
662396396
6.550000e-39
172.0
13
TraesCS3B01G456300
chr3A
93.506
77
5
0
4836
4912
662407047
662407123
1.120000e-21
115.0
14
TraesCS3B01G456300
chr3D
95.978
2337
63
13
2342
4656
527666970
527669297
0.000000e+00
3766.0
15
TraesCS3B01G456300
chr3D
98.351
1395
23
0
899
2293
527665576
527666970
0.000000e+00
2449.0
16
TraesCS3B01G456300
chr3D
80.300
868
163
5
3045
3910
45410039
45410900
0.000000e+00
649.0
17
TraesCS3B01G456300
chr3D
92.424
198
12
2
128
325
527588074
527588268
3.750000e-71
279.0
18
TraesCS3B01G456300
chr3D
92.262
168
7
4
4638
4803
527670200
527670363
2.960000e-57
233.0
19
TraesCS3B01G456300
chr3D
86.364
154
6
1
746
884
527588319
527588472
2.370000e-33
154.0
20
TraesCS3B01G456300
chr3D
93.506
77
5
0
4836
4912
527670363
527670439
1.120000e-21
115.0
21
TraesCS3B01G456300
chr3D
97.619
42
0
1
2611
2652
149236000
149236040
2.460000e-08
71.3
22
TraesCS3B01G456300
chr6B
91.546
414
31
1
330
743
579922819
579923228
7.150000e-158
568.0
23
TraesCS3B01G456300
chr6B
91.437
327
24
1
420
746
579888850
579889172
3.500000e-121
446.0
24
TraesCS3B01G456300
chr6B
90.566
53
3
2
2602
2652
79946898
79946950
8.850000e-08
69.4
25
TraesCS3B01G456300
chr6B
90.566
53
3
2
2602
2652
80000974
80001026
8.850000e-08
69.4
26
TraesCS3B01G456300
chr1D
92.331
326
21
2
421
746
491975060
491975381
1.250000e-125
460.0
27
TraesCS3B01G456300
chr1D
93.750
48
2
1
2606
2652
10536557
10536604
2.460000e-08
71.3
28
TraesCS3B01G456300
chr1D
92.000
50
3
1
2603
2652
461081984
461082032
8.850000e-08
69.4
29
TraesCS3B01G456300
chr4B
89.266
354
32
4
391
744
27863236
27863583
5.850000e-119
438.0
30
TraesCS3B01G456300
chr4B
86.478
318
36
3
432
746
27838112
27838425
4.720000e-90
342.0
31
TraesCS3B01G456300
chr4B
90.000
60
6
0
2812
2871
462218877
462218936
1.470000e-10
78.7
32
TraesCS3B01G456300
chr2B
94.828
116
5
1
11
126
638012827
638012713
3.920000e-41
180.0
33
TraesCS3B01G456300
chr7D
90.476
126
12
0
1
126
184210272
184210397
3.050000e-37
167.0
34
TraesCS3B01G456300
chr7D
87.903
124
14
1
1
124
436874626
436874504
1.430000e-30
145.0
35
TraesCS3B01G456300
chr7D
95.455
44
1
1
2609
2652
40006504
40006546
8.850000e-08
69.4
36
TraesCS3B01G456300
chr4D
89.516
124
13
0
1
124
421316830
421316707
1.840000e-34
158.0
37
TraesCS3B01G456300
chr4D
87.903
124
15
0
1
124
320191944
320191821
3.970000e-31
147.0
38
TraesCS3B01G456300
chr1B
93.396
106
7
0
1
106
61648922
61648817
1.840000e-34
158.0
39
TraesCS3B01G456300
chr1B
93.333
60
2
2
2828
2886
621061911
621061969
2.440000e-13
87.9
40
TraesCS3B01G456300
chr6D
91.509
106
9
0
1
106
324755205
324755310
3.970000e-31
147.0
41
TraesCS3B01G456300
chr6D
100.000
28
0
0
2806
2833
405119640
405119613
9.000000e-03
52.8
42
TraesCS3B01G456300
chr2A
91.509
106
9
0
1
106
667953124
667953229
3.970000e-31
147.0
43
TraesCS3B01G456300
chr2A
86.957
69
6
3
2818
2885
742692562
742692628
1.900000e-09
75.0
44
TraesCS3B01G456300
chr7B
95.604
91
1
1
603
693
115194516
115194429
5.140000e-30
143.0
45
TraesCS3B01G456300
chr5D
90.909
66
1
1
2814
2879
354697320
354697380
3.160000e-12
84.2
46
TraesCS3B01G456300
chr5B
90.909
66
1
1
2814
2879
419395704
419395764
3.160000e-12
84.2
47
TraesCS3B01G456300
chr5A
90.909
66
1
1
2814
2879
456599630
456599690
3.160000e-12
84.2
BLAST Results - HSPs grouped
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
TraesCS3B01G456300
chr3B
697898360
697903284
4924
False
9095.00
9095
100.000000
1
4925
1
chr3B.!!$F3
4924
1
TraesCS3B01G456300
chr3B
71119782
71120576
794
False
649.00
649
81.384000
3116
3910
1
chr3B.!!$F1
794
2
TraesCS3B01G456300
chr3B
71143521
71144315
794
False
638.00
638
81.132000
3116
3910
1
chr3B.!!$F2
794
3
TraesCS3B01G456300
chr3B
697855975
697858157
2182
False
304.00
588
88.509333
128
1303
3
chr3B.!!$F4
1175
4
TraesCS3B01G456300
chr3A
662393770
662401659
7889
False
1894.50
3941
94.094500
1
4656
4
chr3A.!!$F2
4655
5
TraesCS3B01G456300
chr3A
57199536
57200330
794
False
665.00
665
81.807000
3116
3910
1
chr3A.!!$F1
794
6
TraesCS3B01G456300
chr3D
527665576
527670439
4863
False
1640.75
3766
95.024250
899
4912
4
chr3D.!!$F4
4013
7
TraesCS3B01G456300
chr3D
45410039
45410900
861
False
649.00
649
80.300000
3045
3910
1
chr3D.!!$F1
865
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
390
391
0.107703
TTCCATCTACAGCGCCTTGG
60.108
55.000
2.29
2.46
0.00
3.61
F
557
558
0.531090
GTGCGTGTGTGGGTTGAGTA
60.531
55.000
0.00
0.00
0.00
2.59
F
1647
3076
0.179084
TTCGATTCATCTGGGGCGTC
60.179
55.000
0.00
0.00
0.00
5.19
F
3228
4774
1.946768
TCTGCTTGGTTAGTGCACAAC
59.053
47.619
21.04
19.29
32.91
3.32
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1303
2732
0.034896
GACCCCTCGCTTGAGTTGAA
59.965
55.000
0.0
0.0
38.10
2.69
R
2090
3522
2.095853
GCCATTGTCCACACATAAGTCG
59.904
50.000
0.0
0.0
30.55
4.18
R
3389
4935
1.376942
CAGAGCTGCCCTCCAACAG
60.377
63.158
0.0
0.0
41.74
3.16
R
4804
10402
0.036732
GGTGACCTGATGTTGCTGGA
59.963
55.000
0.0
0.0
0.00
3.86
R
All possible primers
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
88
89
6.017109
CACATAAGTGCCTAAAACAGTCACTT
60.017
38.462
10.22
10.22
46.09
3.16
109
110
0.918258
TATCTGCTCCCACCATTGCA
59.082
50.000
0.00
0.00
0.00
4.08
110
111
0.260816
ATCTGCTCCCACCATTGCAT
59.739
50.000
0.00
0.00
34.79
3.96
126
127
3.226682
TGCATGCAGGCCAAGATATTA
57.773
42.857
22.16
0.00
0.00
0.98
202
203
3.569701
AGATGAATGTGCCGTTCAAACTT
59.430
39.130
12.06
0.00
41.73
2.66
254
255
1.022735
GCGAACTCGGATCTACCTGA
58.977
55.000
0.69
0.00
40.23
3.86
316
317
0.409876
GCCTTCCTTTCCCCTTCCTT
59.590
55.000
0.00
0.00
0.00
3.36
350
351
2.713967
TGGCAACATGGGAGGATCT
58.286
52.632
0.00
0.00
46.17
2.75
360
361
1.663173
GGAGGATCTAGTGGCGCTC
59.337
63.158
7.64
0.45
33.73
5.03
382
383
3.744942
CCATCGCTGATTTCCATCTACAG
59.255
47.826
0.00
0.00
0.00
2.74
390
391
0.107703
TTCCATCTACAGCGCCTTGG
60.108
55.000
2.29
2.46
0.00
3.61
395
396
2.925706
TACAGCGCCTTGGGGACA
60.926
61.111
2.29
0.00
39.83
4.02
422
423
1.379642
GCTCAAGAAGGGGCGAATGG
61.380
60.000
0.00
0.00
0.00
3.16
456
457
1.673665
GGCTCCACCTGCAGACAAG
60.674
63.158
17.39
8.08
34.51
3.16
465
466
1.584380
CTGCAGACAAGCAAGAGGGC
61.584
60.000
8.42
0.00
45.13
5.19
557
558
0.531090
GTGCGTGTGTGGGTTGAGTA
60.531
55.000
0.00
0.00
0.00
2.59
561
562
1.821216
GTGTGTGGGTTGAGTATGGG
58.179
55.000
0.00
0.00
0.00
4.00
570
571
3.264897
GAGTATGGGCTGCGTGCG
61.265
66.667
0.00
0.00
44.05
5.34
650
652
3.816524
CGAACCGAGAGCGAGGCT
61.817
66.667
0.00
0.00
43.88
4.58
652
654
2.676822
AACCGAGAGCGAGGCTGA
60.677
61.111
0.00
0.00
39.88
4.26
653
655
2.010582
GAACCGAGAGCGAGGCTGAT
62.011
60.000
0.00
0.00
39.88
2.90
654
656
2.010582
AACCGAGAGCGAGGCTGATC
62.011
60.000
0.00
0.00
39.88
2.92
655
657
2.334653
CGAGAGCGAGGCTGATCC
59.665
66.667
0.00
0.00
39.88
3.36
664
666
3.238987
AGGCTGATCCTCCTCCTTC
57.761
57.895
0.00
0.00
43.20
3.46
665
667
0.641601
AGGCTGATCCTCCTCCTTCT
59.358
55.000
0.00
0.00
43.20
2.85
666
668
1.862911
AGGCTGATCCTCCTCCTTCTA
59.137
52.381
0.00
0.00
43.20
2.10
667
669
2.454381
AGGCTGATCCTCCTCCTTCTAT
59.546
50.000
0.00
0.00
43.20
1.98
668
670
2.831526
GGCTGATCCTCCTCCTTCTATC
59.168
54.545
0.00
0.00
0.00
2.08
669
671
2.831526
GCTGATCCTCCTCCTTCTATCC
59.168
54.545
0.00
0.00
0.00
2.59
670
672
3.502119
GCTGATCCTCCTCCTTCTATCCT
60.502
52.174
0.00
0.00
0.00
3.24
671
673
4.344104
CTGATCCTCCTCCTTCTATCCTC
58.656
52.174
0.00
0.00
0.00
3.71
672
674
3.729524
TGATCCTCCTCCTTCTATCCTCA
59.270
47.826
0.00
0.00
0.00
3.86
673
675
3.603965
TCCTCCTCCTTCTATCCTCAC
57.396
52.381
0.00
0.00
0.00
3.51
674
676
2.178106
TCCTCCTCCTTCTATCCTCACC
59.822
54.545
0.00
0.00
0.00
4.02
675
677
2.091055
CCTCCTCCTTCTATCCTCACCA
60.091
54.545
0.00
0.00
0.00
4.17
742
744
7.122048
TCCAGAAGAGAGAATTGAGTAGATCA
58.878
38.462
0.00
0.00
35.62
2.92
743
745
7.285172
TCCAGAAGAGAGAATTGAGTAGATCAG
59.715
40.741
0.00
0.00
39.68
2.90
744
746
7.428020
CAGAAGAGAGAATTGAGTAGATCAGG
58.572
42.308
0.00
0.00
39.68
3.86
977
1022
2.489722
GCCCTTGGAGAAATCACTTGAC
59.510
50.000
0.00
0.00
0.00
3.18
1229
2658
3.378339
GCAAGAATGATATTGCCACTGC
58.622
45.455
4.45
0.00
45.71
4.40
1303
2732
0.527565
CAGCGCCCAAAATGCTACTT
59.472
50.000
2.29
0.00
37.15
2.24
1342
2771
5.394773
GGGTCTCTGAATACAAGAGAGGTTC
60.395
48.000
3.44
0.00
39.09
3.62
1537
2966
0.464036
TTCCCGCTGCACTATACTGG
59.536
55.000
0.00
0.00
0.00
4.00
1647
3076
0.179084
TTCGATTCATCTGGGGCGTC
60.179
55.000
0.00
0.00
0.00
5.19
1935
3364
5.500234
TCACTGCAATTTGCCTAAGTAGAT
58.500
37.500
18.27
0.00
44.23
1.98
2090
3522
5.240121
TGGTCCGAGTTAAGGTGTTATTTC
58.760
41.667
0.00
0.00
0.00
2.17
2239
3671
8.573035
GTTCCTGTAAACTGGTGAAAATTATCA
58.427
33.333
6.00
0.00
36.48
2.15
2491
3938
6.716628
TGGGATGAAATTGTAATATCAGCTCC
59.283
38.462
0.00
0.00
27.76
4.70
2664
4210
3.369471
GGCCTCTGCAACTTCACTATACA
60.369
47.826
0.00
0.00
40.13
2.29
2834
4380
6.854091
AAGTACTCCCTCTGTAAACTAAGG
57.146
41.667
0.00
0.00
0.00
2.69
3027
4573
4.574013
GCTGGAATGTTCAGATCAACCTAG
59.426
45.833
0.00
0.00
34.36
3.02
3189
4735
3.058224
GGATCTTCAGGTCAACCAAAACG
60.058
47.826
1.33
0.00
38.89
3.60
3196
4742
4.513692
TCAGGTCAACCAAAACGACTATTG
59.486
41.667
1.33
0.00
38.89
1.90
3228
4774
1.946768
TCTGCTTGGTTAGTGCACAAC
59.053
47.619
21.04
19.29
32.91
3.32
3296
4842
3.646534
TCCTGGATGTAGCAGATGAGAA
58.353
45.455
0.00
0.00
0.00
2.87
3774
5320
2.044492
TCCTGGTCCATACAGAAGTCCT
59.956
50.000
0.00
0.00
38.20
3.85
3898
5444
2.673368
CTGTTTGAGACCATACGAAGCC
59.327
50.000
0.00
0.00
0.00
4.35
4019
5568
8.087136
CAGTGTATATCAGAGTGCTTATGATGT
58.913
37.037
8.53
5.45
35.39
3.06
4020
5569
8.646004
AGTGTATATCAGAGTGCTTATGATGTT
58.354
33.333
8.53
1.36
35.39
2.71
4021
5570
8.706936
GTGTATATCAGAGTGCTTATGATGTTG
58.293
37.037
8.53
0.00
35.39
3.33
4097
5646
4.596643
AGTTGAGATAGGGAATGGGAGATG
59.403
45.833
0.00
0.00
0.00
2.90
4114
5663
5.488341
GGAGATGTCTTTTAGCACCTAACA
58.512
41.667
0.00
0.00
0.00
2.41
4148
5708
1.002069
AGAGGGATGGAAATGCACCA
58.998
50.000
0.00
0.00
41.83
4.17
4415
5984
2.036604
GGTCTAGCTTAGGCATGTCTCC
59.963
54.545
1.25
0.00
41.70
3.71
4465
9141
3.986277
AGAAACGGTCTATCAAACACGT
58.014
40.909
0.00
0.00
33.56
4.49
4466
9142
3.739300
AGAAACGGTCTATCAAACACGTG
59.261
43.478
15.48
15.48
33.56
4.49
4501
9177
8.055279
CTTCCTTGAGAAGCATTTTATTACCA
57.945
34.615
0.00
0.00
45.38
3.25
4504
9180
7.121168
TCCTTGAGAAGCATTTTATTACCACTG
59.879
37.037
0.00
0.00
0.00
3.66
4525
9201
3.630312
TGTCAGCTTTGGTTTGGTTACTC
59.370
43.478
0.00
0.00
0.00
2.59
4529
9205
4.020543
AGCTTTGGTTTGGTTACTCAACA
58.979
39.130
0.00
0.00
36.29
3.33
4585
9261
1.734465
GCTAGCAGCAAGGTTGTGTAG
59.266
52.381
10.63
0.00
41.89
2.74
4586
9262
1.734465
CTAGCAGCAAGGTTGTGTAGC
59.266
52.381
0.00
0.00
0.00
3.58
4587
9263
0.109342
AGCAGCAAGGTTGTGTAGCT
59.891
50.000
0.00
0.00
35.72
3.32
4588
9264
1.347707
AGCAGCAAGGTTGTGTAGCTA
59.652
47.619
0.00
0.00
33.29
3.32
4589
9265
1.734465
GCAGCAAGGTTGTGTAGCTAG
59.266
52.381
0.00
0.00
33.29
3.42
4590
9266
2.350522
CAGCAAGGTTGTGTAGCTAGG
58.649
52.381
0.00
0.00
33.29
3.02
4620
9296
8.361889
GGCCTTTGTTAAACAAACCTTTATAGA
58.638
33.333
0.00
0.00
42.55
1.98
4621
9297
9.752961
GCCTTTGTTAAACAAACCTTTATAGAA
57.247
29.630
0.00
0.00
42.55
2.10
4631
9307
8.950007
ACAAACCTTTATAGAATTGAAGGGAA
57.050
30.769
6.02
0.00
42.30
3.97
4633
9309
8.802267
CAAACCTTTATAGAATTGAAGGGAACA
58.198
33.333
6.02
0.00
42.30
3.18
4643
9319
8.893563
AGAATTGAAGGGAACATATAAAACCA
57.106
30.769
0.00
0.00
0.00
3.67
4650
9326
5.650703
AGGGAACATATAAAACCAAAGGTCG
59.349
40.000
0.00
0.00
33.12
4.79
4698
10296
1.929038
GCCTTTCTTTTTCGCGGGAAC
60.929
52.381
15.20
0.00
0.00
3.62
4714
10312
2.418334
GGGAACGATGGAAGTGACCTAC
60.418
54.545
0.00
0.00
0.00
3.18
4716
10314
2.233305
ACGATGGAAGTGACCTACCT
57.767
50.000
0.00
0.00
0.00
3.08
4717
10315
3.377253
ACGATGGAAGTGACCTACCTA
57.623
47.619
0.00
0.00
0.00
3.08
4718
10316
3.705051
ACGATGGAAGTGACCTACCTAA
58.295
45.455
0.00
0.00
0.00
2.69
4719
10317
3.446516
ACGATGGAAGTGACCTACCTAAC
59.553
47.826
0.00
0.00
0.00
2.34
4720
10318
3.181478
CGATGGAAGTGACCTACCTAACC
60.181
52.174
0.00
0.00
0.00
2.85
4721
10319
3.555117
TGGAAGTGACCTACCTAACCT
57.445
47.619
0.00
0.00
0.00
3.50
4722
10320
3.865571
TGGAAGTGACCTACCTAACCTT
58.134
45.455
0.00
0.00
0.00
3.50
4723
10321
5.014534
TGGAAGTGACCTACCTAACCTTA
57.985
43.478
0.00
0.00
0.00
2.69
4724
10322
5.405279
TGGAAGTGACCTACCTAACCTTAA
58.595
41.667
0.00
0.00
0.00
1.85
4725
10323
5.482878
TGGAAGTGACCTACCTAACCTTAAG
59.517
44.000
0.00
0.00
0.00
1.85
4726
10324
5.718607
GGAAGTGACCTACCTAACCTTAAGA
59.281
44.000
3.36
0.00
0.00
2.10
4756
10354
2.421424
CAGATGCCTTCCTGCTGTAAAC
59.579
50.000
0.00
0.00
0.00
2.01
4777
10375
3.113322
CGGATATTCTTTCTGCGTTCGA
58.887
45.455
0.00
0.00
0.00
3.71
4799
10397
2.727123
TTCTTCTGGTGCCTTGTCAA
57.273
45.000
0.00
0.00
0.00
3.18
4802
10400
4.365514
TCTTCTGGTGCCTTGTCAATTA
57.634
40.909
0.00
0.00
0.00
1.40
4803
10401
4.072131
TCTTCTGGTGCCTTGTCAATTAC
58.928
43.478
0.00
0.00
0.00
1.89
4804
10402
3.788227
TCTGGTGCCTTGTCAATTACT
57.212
42.857
0.00
0.00
0.00
2.24
4805
10403
3.674997
TCTGGTGCCTTGTCAATTACTC
58.325
45.455
0.00
0.00
0.00
2.59
4806
10404
2.749621
CTGGTGCCTTGTCAATTACTCC
59.250
50.000
0.00
0.00
0.00
3.85
4807
10405
2.107378
TGGTGCCTTGTCAATTACTCCA
59.893
45.455
0.00
0.00
0.00
3.86
4808
10406
2.749621
GGTGCCTTGTCAATTACTCCAG
59.250
50.000
0.00
0.00
0.00
3.86
4809
10407
2.162408
GTGCCTTGTCAATTACTCCAGC
59.838
50.000
0.00
0.00
0.00
4.85
4810
10408
2.224744
TGCCTTGTCAATTACTCCAGCA
60.225
45.455
0.00
0.00
0.00
4.41
4811
10409
2.819608
GCCTTGTCAATTACTCCAGCAA
59.180
45.455
0.00
0.00
0.00
3.91
4812
10410
3.366374
GCCTTGTCAATTACTCCAGCAAC
60.366
47.826
0.00
0.00
0.00
4.17
4813
10411
3.820467
CCTTGTCAATTACTCCAGCAACA
59.180
43.478
0.00
0.00
0.00
3.33
4814
10412
4.460382
CCTTGTCAATTACTCCAGCAACAT
59.540
41.667
0.00
0.00
0.00
2.71
4815
10413
5.392380
CCTTGTCAATTACTCCAGCAACATC
60.392
44.000
0.00
0.00
0.00
3.06
4816
10414
4.650734
TGTCAATTACTCCAGCAACATCA
58.349
39.130
0.00
0.00
0.00
3.07
4817
10415
4.696877
TGTCAATTACTCCAGCAACATCAG
59.303
41.667
0.00
0.00
0.00
2.90
4818
10416
4.095483
GTCAATTACTCCAGCAACATCAGG
59.905
45.833
0.00
0.00
0.00
3.86
4819
10417
4.012374
CAATTACTCCAGCAACATCAGGT
58.988
43.478
0.00
0.00
0.00
4.00
4820
10418
3.334583
TTACTCCAGCAACATCAGGTC
57.665
47.619
0.00
0.00
0.00
3.85
4821
10419
1.059098
ACTCCAGCAACATCAGGTCA
58.941
50.000
0.00
0.00
0.00
4.02
4822
10420
1.271054
ACTCCAGCAACATCAGGTCAC
60.271
52.381
0.00
0.00
0.00
3.67
4823
10421
0.036732
TCCAGCAACATCAGGTCACC
59.963
55.000
0.00
0.00
0.00
4.02
4824
10422
0.962356
CCAGCAACATCAGGTCACCC
60.962
60.000
0.00
0.00
0.00
4.61
4825
10423
0.037303
CAGCAACATCAGGTCACCCT
59.963
55.000
0.00
0.00
44.02
4.34
4826
10424
0.326264
AGCAACATCAGGTCACCCTC
59.674
55.000
0.00
0.00
39.89
4.30
4827
10425
0.678048
GCAACATCAGGTCACCCTCC
60.678
60.000
0.00
0.00
39.89
4.30
4828
10426
0.692476
CAACATCAGGTCACCCTCCA
59.308
55.000
0.00
0.00
39.89
3.86
4829
10427
0.987294
AACATCAGGTCACCCTCCAG
59.013
55.000
0.00
0.00
39.89
3.86
4830
10428
0.178891
ACATCAGGTCACCCTCCAGT
60.179
55.000
0.00
0.00
39.89
4.00
4831
10429
1.078823
ACATCAGGTCACCCTCCAGTA
59.921
52.381
0.00
0.00
39.89
2.74
4832
10430
2.187958
CATCAGGTCACCCTCCAGTAA
58.812
52.381
0.00
0.00
39.89
2.24
4833
10431
1.640917
TCAGGTCACCCTCCAGTAAC
58.359
55.000
0.00
0.00
39.89
2.50
4834
10432
1.132977
TCAGGTCACCCTCCAGTAACA
60.133
52.381
0.00
0.00
39.89
2.41
4869
10467
3.558931
TGATGTGGTCAGTTGTTCTGT
57.441
42.857
0.00
0.00
43.97
3.41
4871
10469
5.227569
TGATGTGGTCAGTTGTTCTGTAT
57.772
39.130
0.00
0.00
43.97
2.29
4872
10470
5.620206
TGATGTGGTCAGTTGTTCTGTATT
58.380
37.500
0.00
0.00
43.97
1.89
4876
10474
4.452455
GTGGTCAGTTGTTCTGTATTCCAG
59.548
45.833
0.00
0.00
43.97
3.86
4887
10485
7.500992
TGTTCTGTATTCCAGTTGATATCTCC
58.499
38.462
3.98
0.00
42.19
3.71
4912
10510
0.471617
CATCAGGTCACCCTCCCATC
59.528
60.000
0.00
0.00
39.89
3.51
4913
10511
0.695803
ATCAGGTCACCCTCCCATCC
60.696
60.000
0.00
0.00
39.89
3.51
4914
10512
2.042930
AGGTCACCCTCCCATCCC
59.957
66.667
0.00
0.00
35.62
3.85
4915
10513
2.286121
GGTCACCCTCCCATCCCA
60.286
66.667
0.00
0.00
0.00
4.37
4916
10514
1.697754
GGTCACCCTCCCATCCCAT
60.698
63.158
0.00
0.00
0.00
4.00
4917
10515
1.289244
GGTCACCCTCCCATCCCATT
61.289
60.000
0.00
0.00
0.00
3.16
4918
10516
0.631212
GTCACCCTCCCATCCCATTT
59.369
55.000
0.00
0.00
0.00
2.32
4919
10517
1.850345
GTCACCCTCCCATCCCATTTA
59.150
52.381
0.00
0.00
0.00
1.40
4920
10518
1.850345
TCACCCTCCCATCCCATTTAC
59.150
52.381
0.00
0.00
0.00
2.01
4921
10519
1.568597
CACCCTCCCATCCCATTTACA
59.431
52.381
0.00
0.00
0.00
2.41
4922
10520
1.852965
ACCCTCCCATCCCATTTACAG
59.147
52.381
0.00
0.00
0.00
2.74
4923
10521
1.479389
CCCTCCCATCCCATTTACAGC
60.479
57.143
0.00
0.00
0.00
4.40
4924
10522
1.479389
CCTCCCATCCCATTTACAGCC
60.479
57.143
0.00
0.00
0.00
4.85
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
88
89
1.141657
GCAATGGTGGGAGCAGATAGA
59.858
52.381
0.00
0.00
0.00
1.98
109
110
6.736110
ACATTTTAATATCTTGGCCTGCAT
57.264
33.333
3.32
0.00
0.00
3.96
110
111
6.833416
AGTACATTTTAATATCTTGGCCTGCA
59.167
34.615
3.32
0.00
0.00
4.41
152
153
9.226345
GATGTTTTTGTTTTCACTCTACTCTTG
57.774
33.333
0.00
0.00
0.00
3.02
202
203
3.827722
CCAGAGGGTTAAACCAACTCAA
58.172
45.455
13.24
0.00
40.41
3.02
316
317
4.586421
TGTTGCCAATGTTGTAGATGGAAA
59.414
37.500
0.00
0.00
34.82
3.13
360
361
3.732212
TGTAGATGGAAATCAGCGATGG
58.268
45.455
0.00
0.00
36.78
3.51
367
368
1.486310
AGGCGCTGTAGATGGAAATCA
59.514
47.619
7.64
0.00
0.00
2.57
397
398
3.130160
CCCTTCTTGAGCAGCGGC
61.130
66.667
0.00
0.00
41.61
6.53
422
423
3.357079
CCCACCTGACAAGCGTGC
61.357
66.667
0.00
0.00
0.00
5.34
456
457
3.123620
CAGCTCACGCCCTCTTGC
61.124
66.667
0.00
0.00
36.60
4.01
474
475
2.910737
ATCAGTGGTGGTGGCAGGG
61.911
63.158
0.00
0.00
0.00
4.45
481
482
2.532715
AGGCCCATCAGTGGTGGT
60.533
61.111
21.14
0.00
44.48
4.16
561
562
0.731514
TAACTAGTCACGCACGCAGC
60.732
55.000
0.00
0.00
40.87
5.25
570
571
1.547372
TCGCACCCCTTAACTAGTCAC
59.453
52.381
0.00
0.00
0.00
3.67
575
576
1.822990
CAGTCTCGCACCCCTTAACTA
59.177
52.381
0.00
0.00
0.00
2.24
650
652
3.729524
TGAGGATAGAAGGAGGAGGATCA
59.270
47.826
0.00
0.00
36.25
2.92
652
654
3.181412
GGTGAGGATAGAAGGAGGAGGAT
60.181
52.174
0.00
0.00
0.00
3.24
653
655
2.178106
GGTGAGGATAGAAGGAGGAGGA
59.822
54.545
0.00
0.00
0.00
3.71
654
656
2.091055
TGGTGAGGATAGAAGGAGGAGG
60.091
54.545
0.00
0.00
0.00
4.30
655
657
3.320610
TGGTGAGGATAGAAGGAGGAG
57.679
52.381
0.00
0.00
0.00
3.69
656
658
3.375699
GTTGGTGAGGATAGAAGGAGGA
58.624
50.000
0.00
0.00
0.00
3.71
657
659
2.436173
GGTTGGTGAGGATAGAAGGAGG
59.564
54.545
0.00
0.00
0.00
4.30
658
660
2.436173
GGGTTGGTGAGGATAGAAGGAG
59.564
54.545
0.00
0.00
0.00
3.69
659
661
2.478292
GGGTTGGTGAGGATAGAAGGA
58.522
52.381
0.00
0.00
0.00
3.36
660
662
1.490910
GGGGTTGGTGAGGATAGAAGG
59.509
57.143
0.00
0.00
0.00
3.46
661
663
1.490910
GGGGGTTGGTGAGGATAGAAG
59.509
57.143
0.00
0.00
0.00
2.85
662
664
1.082194
AGGGGGTTGGTGAGGATAGAA
59.918
52.381
0.00
0.00
0.00
2.10
663
665
0.722676
AGGGGGTTGGTGAGGATAGA
59.277
55.000
0.00
0.00
0.00
1.98
664
666
1.132500
GAGGGGGTTGGTGAGGATAG
58.868
60.000
0.00
0.00
0.00
2.08
665
667
0.722676
AGAGGGGGTTGGTGAGGATA
59.277
55.000
0.00
0.00
0.00
2.59
666
668
0.916358
CAGAGGGGGTTGGTGAGGAT
60.916
60.000
0.00
0.00
0.00
3.24
667
669
1.538876
CAGAGGGGGTTGGTGAGGA
60.539
63.158
0.00
0.00
0.00
3.71
668
670
3.081554
CAGAGGGGGTTGGTGAGG
58.918
66.667
0.00
0.00
0.00
3.86
669
671
1.783250
AAGCAGAGGGGGTTGGTGAG
61.783
60.000
0.00
0.00
0.00
3.51
670
672
1.774217
AAGCAGAGGGGGTTGGTGA
60.774
57.895
0.00
0.00
0.00
4.02
671
673
1.303643
GAAGCAGAGGGGGTTGGTG
60.304
63.158
0.00
0.00
0.00
4.17
672
674
2.539081
GGAAGCAGAGGGGGTTGGT
61.539
63.158
0.00
0.00
0.00
3.67
673
675
1.793820
AAGGAAGCAGAGGGGGTTGG
61.794
60.000
0.00
0.00
0.00
3.77
674
676
0.113190
AAAGGAAGCAGAGGGGGTTG
59.887
55.000
0.00
0.00
0.00
3.77
675
677
1.354705
GTAAAGGAAGCAGAGGGGGTT
59.645
52.381
0.00
0.00
0.00
4.11
977
1022
2.885644
CATCCGAGACCCGCAACG
60.886
66.667
0.00
0.00
36.84
4.10
1303
2732
0.034896
GACCCCTCGCTTGAGTTGAA
59.965
55.000
0.00
0.00
38.10
2.69
1342
2771
1.480545
TGGATCCGGTACTGTGTCATG
59.519
52.381
7.39
0.00
0.00
3.07
1537
2966
7.072030
CAGCTACGCCTTTATCATGAATAAAC
58.928
38.462
0.00
0.00
35.38
2.01
1647
3076
2.286772
GGGCAAGAGTTGTTTGTGTACG
60.287
50.000
0.00
0.00
0.00
3.67
1918
3347
6.058183
AGCTACCATCTACTTAGGCAAATTG
58.942
40.000
0.00
0.00
0.00
2.32
1935
3364
6.043822
TGGATAGTATAATTGGCAAGCTACCA
59.956
38.462
5.96
4.29
34.65
3.25
2090
3522
2.095853
GCCATTGTCCACACATAAGTCG
59.904
50.000
0.00
0.00
30.55
4.18
2239
3671
9.877178
AACTGACAATAAATCTTCTACGAGATT
57.123
29.630
0.00
0.00
45.75
2.40
2664
4210
5.957842
TCAACCGCTAAAATCAACAATCT
57.042
34.783
0.00
0.00
0.00
2.40
2810
4356
6.786461
ACCTTAGTTTACAGAGGGAGTACTTT
59.214
38.462
0.00
0.00
33.51
2.66
3027
4573
6.456501
ACAAGTACAGGATCACTAAGTTGAC
58.543
40.000
0.00
0.00
32.78
3.18
3189
4735
2.101582
AGACCAGATGCGGACAATAGTC
59.898
50.000
0.00
0.00
44.21
2.59
3228
4774
1.915141
ACCCCACAGCTTCAATTGAG
58.085
50.000
8.41
4.57
0.00
3.02
3296
4842
5.824904
AGAAGCGATAAATTGCATGAACT
57.175
34.783
0.00
0.00
39.70
3.01
3389
4935
1.376942
CAGAGCTGCCCTCCAACAG
60.377
63.158
0.00
0.00
41.74
3.16
3774
5320
3.924114
TGAGTCTTCTTGTTTGGGTCA
57.076
42.857
0.00
0.00
0.00
4.02
3898
5444
1.134848
GCTGCTGTCTCCCTCTAGTTG
60.135
57.143
0.00
0.00
0.00
3.16
4019
5568
3.833650
TCTTCCTATCCGTGGTACAACAA
59.166
43.478
0.35
0.00
44.16
2.83
4020
5569
3.433343
TCTTCCTATCCGTGGTACAACA
58.567
45.455
0.35
0.00
44.16
3.33
4021
5570
4.081807
AGTTCTTCCTATCCGTGGTACAAC
60.082
45.833
0.00
0.00
44.16
3.32
4097
5646
5.106277
GGATTGGTGTTAGGTGCTAAAAGAC
60.106
44.000
0.00
0.00
0.00
3.01
4114
5663
0.040204
CCTCTTGCCAAGGGATTGGT
59.960
55.000
5.72
0.00
43.90
3.67
4148
5708
3.829026
TGCAGCGAATATCTCCAGATACT
59.171
43.478
0.00
0.00
39.57
2.12
4329
5898
1.887854
CACATCACAATGGTGGCAAGA
59.112
47.619
0.00
0.00
45.32
3.02
4415
5984
4.202233
ACAGTGCAGGATCATCATAGACTG
60.202
45.833
7.88
7.88
35.50
3.51
4465
9141
1.902508
CTCAAGGAAGTAGGACCAGCA
59.097
52.381
0.00
0.00
0.00
4.41
4466
9142
2.180276
TCTCAAGGAAGTAGGACCAGC
58.820
52.381
0.00
0.00
0.00
4.85
4500
9176
1.750778
ACCAAACCAAAGCTGACAGTG
59.249
47.619
3.99
0.00
0.00
3.66
4501
9177
2.143876
ACCAAACCAAAGCTGACAGT
57.856
45.000
3.99
0.00
0.00
3.55
4504
9180
3.630312
TGAGTAACCAAACCAAAGCTGAC
59.370
43.478
0.00
0.00
0.00
3.51
4525
9201
1.019673
ACTGCACAGCTTCAGTGTTG
58.980
50.000
11.07
4.57
41.53
3.33
4529
9205
1.446907
GCATACTGCACAGCTTCAGT
58.553
50.000
14.94
14.94
44.26
3.41
4577
9253
1.202545
GGCCTAGCCTAGCTACACAAC
60.203
57.143
0.00
0.00
46.69
3.32
4579
9255
2.822215
GGCCTAGCCTAGCTACACA
58.178
57.895
0.00
0.00
46.69
3.72
4589
9265
4.594123
TTTGTTTAACAAAGGCCTAGCC
57.406
40.909
17.93
0.00
42.55
3.93
4606
9282
8.803235
GTTCCCTTCAATTCTATAAAGGTTTGT
58.197
33.333
0.00
0.00
37.22
2.83
4607
9283
8.802267
TGTTCCCTTCAATTCTATAAAGGTTTG
58.198
33.333
0.00
0.00
37.22
2.93
4608
9284
8.950007
TGTTCCCTTCAATTCTATAAAGGTTT
57.050
30.769
0.00
0.00
37.22
3.27
4620
9296
9.942850
CTTTGGTTTTATATGTTCCCTTCAATT
57.057
29.630
0.00
0.00
0.00
2.32
4621
9297
8.539544
CCTTTGGTTTTATATGTTCCCTTCAAT
58.460
33.333
0.00
0.00
0.00
2.57
4628
9304
6.746745
TCGACCTTTGGTTTTATATGTTCC
57.253
37.500
0.00
0.00
35.25
3.62
4631
9307
8.026607
CACAATTCGACCTTTGGTTTTATATGT
58.973
33.333
6.82
0.00
35.25
2.29
4633
9309
8.117813
ACACAATTCGACCTTTGGTTTTATAT
57.882
30.769
6.82
0.00
35.25
0.86
4643
9319
3.945285
ACACTTGACACAATTCGACCTTT
59.055
39.130
0.00
0.00
0.00
3.11
4650
9326
4.756642
TCCATCAGACACTTGACACAATTC
59.243
41.667
0.00
0.00
0.00
2.17
4698
10296
3.181478
GGTTAGGTAGGTCACTTCCATCG
60.181
52.174
0.00
0.00
36.68
3.84
4714
10312
6.472887
TCTGGTGTCAAATCTTAAGGTTAGG
58.527
40.000
0.30
0.00
0.00
2.69
4716
10314
6.374333
GCATCTGGTGTCAAATCTTAAGGTTA
59.626
38.462
0.30
0.00
0.00
2.85
4717
10315
5.183904
GCATCTGGTGTCAAATCTTAAGGTT
59.816
40.000
1.85
0.00
0.00
3.50
4718
10316
4.702131
GCATCTGGTGTCAAATCTTAAGGT
59.298
41.667
1.85
0.00
0.00
3.50
4719
10317
4.096984
GGCATCTGGTGTCAAATCTTAAGG
59.903
45.833
1.85
0.00
30.99
2.69
4720
10318
4.946157
AGGCATCTGGTGTCAAATCTTAAG
59.054
41.667
0.00
0.00
33.88
1.85
4721
10319
4.922206
AGGCATCTGGTGTCAAATCTTAA
58.078
39.130
0.00
0.00
33.88
1.85
4722
10320
4.574674
AGGCATCTGGTGTCAAATCTTA
57.425
40.909
0.00
0.00
33.88
2.10
4723
10321
3.446442
AGGCATCTGGTGTCAAATCTT
57.554
42.857
0.00
0.00
33.88
2.40
4724
10322
3.350833
GAAGGCATCTGGTGTCAAATCT
58.649
45.455
0.00
0.00
33.88
2.40
4725
10323
2.424956
GGAAGGCATCTGGTGTCAAATC
59.575
50.000
0.00
0.00
33.88
2.17
4726
10324
2.042162
AGGAAGGCATCTGGTGTCAAAT
59.958
45.455
0.00
0.00
33.88
2.32
4756
10354
3.113322
TCGAACGCAGAAAGAATATCCG
58.887
45.455
0.00
0.00
0.00
4.18
4777
10375
3.565307
TGACAAGGCACCAGAAGAATTT
58.435
40.909
0.00
0.00
0.00
1.82
4799
10397
3.264193
TGACCTGATGTTGCTGGAGTAAT
59.736
43.478
0.00
0.00
0.00
1.89
4802
10400
1.059098
TGACCTGATGTTGCTGGAGT
58.941
50.000
0.00
0.00
0.00
3.85
4803
10401
1.446907
GTGACCTGATGTTGCTGGAG
58.553
55.000
0.00
0.00
0.00
3.86
4804
10402
0.036732
GGTGACCTGATGTTGCTGGA
59.963
55.000
0.00
0.00
0.00
3.86
4805
10403
2.559785
GGTGACCTGATGTTGCTGG
58.440
57.895
0.00
0.00
0.00
4.85
4818
10416
3.202829
TGTTTGTTACTGGAGGGTGAC
57.797
47.619
0.00
0.00
0.00
3.67
4819
10417
3.935818
TTGTTTGTTACTGGAGGGTGA
57.064
42.857
0.00
0.00
0.00
4.02
4820
10418
4.795962
GCAATTGTTTGTTACTGGAGGGTG
60.796
45.833
7.40
0.00
35.17
4.61
4821
10419
3.320826
GCAATTGTTTGTTACTGGAGGGT
59.679
43.478
7.40
0.00
35.17
4.34
4822
10420
3.320541
TGCAATTGTTTGTTACTGGAGGG
59.679
43.478
7.40
0.00
35.17
4.30
4823
10421
4.582701
TGCAATTGTTTGTTACTGGAGG
57.417
40.909
7.40
0.00
35.17
4.30
4824
10422
5.809562
TGTTTGCAATTGTTTGTTACTGGAG
59.190
36.000
7.40
0.00
35.17
3.86
4825
10423
5.724328
TGTTTGCAATTGTTTGTTACTGGA
58.276
33.333
7.40
0.00
35.17
3.86
4826
10424
6.257411
TCATGTTTGCAATTGTTTGTTACTGG
59.743
34.615
7.40
0.00
35.17
4.00
4827
10425
7.231705
TCATGTTTGCAATTGTTTGTTACTG
57.768
32.000
7.40
0.00
35.17
2.74
4828
10426
7.495279
ACATCATGTTTGCAATTGTTTGTTACT
59.505
29.630
7.40
0.00
35.17
2.24
4829
10427
7.583401
CACATCATGTTTGCAATTGTTTGTTAC
59.417
33.333
7.40
0.00
35.17
2.50
4830
10428
7.254692
CCACATCATGTTTGCAATTGTTTGTTA
60.255
33.333
7.40
0.00
35.17
2.41
4831
10429
6.458478
CCACATCATGTTTGCAATTGTTTGTT
60.458
34.615
7.40
0.00
35.17
2.83
4832
10430
5.007823
CCACATCATGTTTGCAATTGTTTGT
59.992
36.000
7.40
5.31
35.17
2.83
4833
10431
5.007823
ACCACATCATGTTTGCAATTGTTTG
59.992
36.000
7.40
4.76
35.85
2.93
4834
10432
5.124645
ACCACATCATGTTTGCAATTGTTT
58.875
33.333
7.40
0.00
0.00
2.83
4869
10467
6.126796
TGTTGCTGGAGATATCAACTGGAATA
60.127
38.462
5.32
4.71
39.44
1.75
4871
10469
4.019411
TGTTGCTGGAGATATCAACTGGAA
60.019
41.667
5.32
6.04
39.44
3.53
4872
10470
3.519107
TGTTGCTGGAGATATCAACTGGA
59.481
43.478
5.32
0.00
39.44
3.86
4876
10474
4.514441
CCTGATGTTGCTGGAGATATCAAC
59.486
45.833
5.32
0.81
39.23
3.18
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.