Multiple sequence alignment - TraesCS3B01G475800
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
TraesCS3B01G475800
chr3B
100.000
6020
0
0
1
6020
724736622
724742641
0.000000e+00
11117.0
1
TraesCS3B01G475800
chr3B
80.659
2761
350
107
1126
3786
732619327
732616651
0.000000e+00
1971.0
2
TraesCS3B01G475800
chr3B
83.429
525
74
10
3789
4312
732616606
732616094
5.460000e-130
475.0
3
TraesCS3B01G475800
chr3B
84.958
472
55
11
4564
5035
732615723
732615268
1.180000e-126
464.0
4
TraesCS3B01G475800
chr3B
79.412
306
48
11
4765
5064
175096909
175096613
1.020000e-47
202.0
5
TraesCS3B01G475800
chr3B
95.833
48
2
0
5732
5779
21324405
21324452
1.800000e-10
78.7
6
TraesCS3B01G475800
chr3A
94.306
4830
218
32
943
5742
684040775
684045577
0.000000e+00
7343.0
7
TraesCS3B01G475800
chr3A
81.170
2735
362
91
1126
3786
688693498
688690843
0.000000e+00
2056.0
8
TraesCS3B01G475800
chr3A
89.141
792
43
16
2
773
684039468
684040236
0.000000e+00
946.0
9
TraesCS3B01G475800
chr3A
91.294
402
29
4
951
1351
122540187
122540583
1.480000e-150
544.0
10
TraesCS3B01G475800
chr3A
91.111
405
26
6
951
1351
433768343
433767945
1.910000e-149
540.0
11
TraesCS3B01G475800
chr3A
82.659
519
77
10
3789
4306
688690798
688690292
1.190000e-121
448.0
12
TraesCS3B01G475800
chr3A
83.898
472
60
11
4564
5035
688689930
688689475
2.580000e-118
436.0
13
TraesCS3B01G475800
chr3A
91.093
247
9
3
5774
6020
684045572
684045805
7.530000e-84
322.0
14
TraesCS3B01G475800
chr3D
93.150
4394
169
51
1
4346
547297250
547301559
0.000000e+00
6325.0
15
TraesCS3B01G475800
chr3D
81.084
2749
342
100
1126
3786
552003086
552000428
0.000000e+00
2032.0
16
TraesCS3B01G475800
chr3D
93.900
1295
59
13
4453
5742
547301664
547302943
0.000000e+00
1936.0
17
TraesCS3B01G475800
chr3D
82.798
529
78
10
3789
4316
552000383
551999867
1.530000e-125
460.0
18
TraesCS3B01G475800
chr3D
84.110
472
59
10
4564
5035
551999456
551999001
5.540000e-120
442.0
19
TraesCS3B01G475800
chr3D
90.000
250
9
5
5774
6020
547302938
547303174
5.860000e-80
309.0
20
TraesCS3B01G475800
chr7D
91.119
563
44
6
4652
5210
12707764
12707204
0.000000e+00
758.0
21
TraesCS3B01G475800
chr7D
94.527
402
16
4
951
1351
85519670
85520066
3.080000e-172
616.0
22
TraesCS3B01G475800
chr6D
93.532
402
20
4
951
1351
32521951
32521555
1.440000e-165
593.0
23
TraesCS3B01G475800
chr6D
92.786
402
17
7
951
1351
65145476
65145866
6.770000e-159
571.0
24
TraesCS3B01G475800
chrUn
92.040
402
25
6
951
1351
31512450
31512055
5.270000e-155
558.0
25
TraesCS3B01G475800
chr2B
91.791
402
28
3
951
1351
765132716
765132319
6.820000e-154
555.0
26
TraesCS3B01G475800
chr1A
84.170
259
35
3
4546
4804
22935698
22935950
4.660000e-61
246.0
27
TraesCS3B01G475800
chr1A
80.142
282
41
11
4765
5040
244562253
244561981
4.760000e-46
196.0
28
TraesCS3B01G475800
chr2A
83.012
259
38
3
4546
4804
536571028
536570776
4.690000e-56
230.0
29
TraesCS3B01G475800
chr2A
97.727
44
1
0
5736
5779
373090476
373090519
6.470000e-10
76.8
30
TraesCS3B01G475800
chr4B
80.496
282
40
11
4765
5040
489161469
489161741
1.020000e-47
202.0
31
TraesCS3B01G475800
chr4B
77.778
288
42
17
2107
2385
17357155
17357429
2.250000e-34
158.0
32
TraesCS3B01G475800
chr4B
92.308
52
3
1
5728
5779
35768673
35768623
8.370000e-09
73.1
33
TraesCS3B01G475800
chr7B
79.085
306
49
11
4765
5064
665368557
665368261
4.760000e-46
196.0
34
TraesCS3B01G475800
chr5D
85.366
123
5
6
1359
1481
562973358
562973249
1.370000e-21
115.0
35
TraesCS3B01G475800
chr5B
97.778
45
1
0
5735
5779
461566625
461566669
1.800000e-10
78.7
36
TraesCS3B01G475800
chr5B
85.075
67
6
4
5715
5779
445557692
445557756
1.400000e-06
65.8
37
TraesCS3B01G475800
chr6B
97.727
44
1
0
5736
5779
3717459
3717416
6.470000e-10
76.8
38
TraesCS3B01G475800
chr6A
97.727
44
1
0
5736
5779
595647203
595647160
6.470000e-10
76.8
39
TraesCS3B01G475800
chr6A
92.308
52
3
1
5729
5779
35575711
35575762
8.370000e-09
73.1
40
TraesCS3B01G475800
chr1B
95.745
47
2
0
5733
5779
503660289
503660243
6.470000e-10
76.8
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
TraesCS3B01G475800
chr3B
724736622
724742641
6019
False
11117.000000
11117
100.000000
1
6020
1
chr3B.!!$F2
6019
1
TraesCS3B01G475800
chr3B
732615268
732619327
4059
True
970.000000
1971
83.015333
1126
5035
3
chr3B.!!$R2
3909
2
TraesCS3B01G475800
chr3A
684039468
684045805
6337
False
2870.333333
7343
91.513333
2
6020
3
chr3A.!!$F2
6018
3
TraesCS3B01G475800
chr3A
688689475
688693498
4023
True
980.000000
2056
82.575667
1126
5035
3
chr3A.!!$R2
3909
4
TraesCS3B01G475800
chr3D
547297250
547303174
5924
False
2856.666667
6325
92.350000
1
6020
3
chr3D.!!$F1
6019
5
TraesCS3B01G475800
chr3D
551999001
552003086
4085
True
978.000000
2032
82.664000
1126
5035
3
chr3D.!!$R1
3909
6
TraesCS3B01G475800
chr7D
12707204
12707764
560
True
758.000000
758
91.119000
4652
5210
1
chr7D.!!$R1
558
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
338
351
0.106217
GGAGAGGAGAGGAGGTGAGG
60.106
65.000
0.00
0.00
0.00
3.86
F
821
858
0.119358
GCCTACCCCATATCCCCTCT
59.881
60.000
0.00
0.00
0.00
3.69
F
1348
1793
0.110056
CGCGCTGAATTTGCTTGTCT
60.110
50.000
5.56
0.00
0.00
3.41
F
2548
3053
0.249826
GAGGGCTATGAGACAGCTGC
60.250
60.000
15.27
6.85
39.09
5.25
F
3176
3706
1.134560
GAGCCGTCAACTATTCCTCGT
59.865
52.381
0.00
0.00
0.00
4.18
F
4397
5214
0.108424
GCCTCTGTGCGTGAATCTCT
60.108
55.000
0.00
0.00
0.00
3.10
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1347
1792
0.580104
AACGAAAAACACCGCGAGAG
59.420
50.0
8.23
0.00
0.00
3.20
R
2706
3227
0.108186
AGAATGAGCCGATGCGAACA
60.108
50.0
0.00
0.00
44.33
3.18
R
3140
3670
0.179045
GCTCATCCCAACGCACCTAT
60.179
55.0
0.00
0.00
0.00
2.57
R
3683
4238
0.034670
AGGTCTGCATGAAGAAGCCC
60.035
55.0
4.49
2.56
0.00
5.19
R
4958
5815
0.248377
GTTTGCGCCATCAGCATCTC
60.248
55.0
4.18
0.00
44.74
2.75
R
5835
6719
0.308068
ATCGATACAGACAGCGACGG
59.692
55.0
0.00
0.00
35.44
4.79
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
81
82
0.109532
TCCTGACAAATCAACGCCCA
59.890
50.000
0.00
0.00
33.30
5.36
129
130
8.930846
TTAGAACACAAGTACTAGGAGTAGTT
57.069
34.615
0.00
1.63
43.17
2.24
176
177
6.477688
CCTTCTCGATTTACTTGCGGTTAATA
59.522
38.462
0.00
0.00
28.85
0.98
199
201
1.745232
TTAAATGGATCGCAACGCCT
58.255
45.000
0.00
0.00
0.00
5.52
201
203
0.676466
AAATGGATCGCAACGCCTGA
60.676
50.000
0.00
0.00
0.00
3.86
210
212
1.666553
CAACGCCTGACGGTAGCAA
60.667
57.895
0.00
0.00
42.45
3.91
211
213
1.374252
AACGCCTGACGGTAGCAAG
60.374
57.895
0.00
0.00
42.60
4.01
234
236
3.185594
TGAAACTGGCGACAATTTACTCG
59.814
43.478
0.00
0.00
40.35
4.18
323
331
9.799106
AAAATAAATGTTTTCAGAGAGAGGAGA
57.201
29.630
0.00
0.00
0.00
3.71
331
344
2.126882
CAGAGAGAGGAGAGGAGAGGA
58.873
57.143
0.00
0.00
0.00
3.71
332
345
2.105477
CAGAGAGAGGAGAGGAGAGGAG
59.895
59.091
0.00
0.00
0.00
3.69
333
346
1.421646
GAGAGAGGAGAGGAGAGGAGG
59.578
61.905
0.00
0.00
0.00
4.30
334
347
1.222567
GAGAGGAGAGGAGAGGAGGT
58.777
60.000
0.00
0.00
0.00
3.85
335
348
0.926293
AGAGGAGAGGAGAGGAGGTG
59.074
60.000
0.00
0.00
0.00
4.00
336
349
0.923358
GAGGAGAGGAGAGGAGGTGA
59.077
60.000
0.00
0.00
0.00
4.02
337
350
0.926293
AGGAGAGGAGAGGAGGTGAG
59.074
60.000
0.00
0.00
0.00
3.51
338
351
0.106217
GGAGAGGAGAGGAGGTGAGG
60.106
65.000
0.00
0.00
0.00
3.86
745
782
0.179113
CTCTCTCTCCTCCGCTTTGC
60.179
60.000
0.00
0.00
0.00
3.68
821
858
0.119358
GCCTACCCCATATCCCCTCT
59.881
60.000
0.00
0.00
0.00
3.69
826
872
1.158705
CCCATATCCCCTCTCCCGT
59.841
63.158
0.00
0.00
0.00
5.28
855
901
3.897505
CACAAAACATTTCCTTCCCCTCT
59.102
43.478
0.00
0.00
0.00
3.69
884
930
2.439701
TGCCGCTCCGCTACTACT
60.440
61.111
0.00
0.00
0.00
2.57
885
931
1.153107
TGCCGCTCCGCTACTACTA
60.153
57.895
0.00
0.00
0.00
1.82
886
932
1.282265
GCCGCTCCGCTACTACTAC
59.718
63.158
0.00
0.00
0.00
2.73
887
933
1.165284
GCCGCTCCGCTACTACTACT
61.165
60.000
0.00
0.00
0.00
2.57
888
934
0.867086
CCGCTCCGCTACTACTACTC
59.133
60.000
0.00
0.00
0.00
2.59
889
935
0.867086
CGCTCCGCTACTACTACTCC
59.133
60.000
0.00
0.00
0.00
3.85
890
936
1.540797
CGCTCCGCTACTACTACTCCT
60.541
57.143
0.00
0.00
0.00
3.69
891
937
2.145536
GCTCCGCTACTACTACTCCTC
58.854
57.143
0.00
0.00
0.00
3.71
892
938
2.224354
GCTCCGCTACTACTACTCCTCT
60.224
54.545
0.00
0.00
0.00
3.69
893
939
3.656559
CTCCGCTACTACTACTCCTCTC
58.343
54.545
0.00
0.00
0.00
3.20
894
940
3.307506
TCCGCTACTACTACTCCTCTCT
58.692
50.000
0.00
0.00
0.00
3.10
895
941
3.321682
TCCGCTACTACTACTCCTCTCTC
59.678
52.174
0.00
0.00
0.00
3.20
896
942
3.555586
CCGCTACTACTACTCCTCTCTCC
60.556
56.522
0.00
0.00
0.00
3.71
930
976
2.378634
CCTCCATCTCCCACCCCAC
61.379
68.421
0.00
0.00
0.00
4.61
933
979
2.286425
CATCTCCCACCCCACCCT
60.286
66.667
0.00
0.00
0.00
4.34
934
980
2.042930
ATCTCCCACCCCACCCTC
59.957
66.667
0.00
0.00
0.00
4.30
935
981
4.715130
TCTCCCACCCCACCCTCG
62.715
72.222
0.00
0.00
0.00
4.63
1124
1542
0.535553
TTTACCGGCGCTGGTTTTCT
60.536
50.000
43.53
22.78
43.56
2.52
1347
1792
1.668253
GCGCGCTGAATTTGCTTGTC
61.668
55.000
26.67
0.00
0.00
3.18
1348
1793
0.110056
CGCGCTGAATTTGCTTGTCT
60.110
50.000
5.56
0.00
0.00
3.41
1350
1795
1.198637
GCGCTGAATTTGCTTGTCTCT
59.801
47.619
0.00
0.00
0.00
3.10
1352
1797
2.473540
CGCTGAATTTGCTTGTCTCTCG
60.474
50.000
3.52
0.00
0.00
4.04
1353
1798
2.727298
GCTGAATTTGCTTGTCTCTCGC
60.727
50.000
0.00
0.00
0.00
5.03
1356
1801
0.320771
ATTTGCTTGTCTCTCGCGGT
60.321
50.000
6.13
0.00
0.00
5.68
1529
1979
2.124487
CAATTCCGCCCCGCCTTA
60.124
61.111
0.00
0.00
0.00
2.69
1592
2042
1.618343
TCGGTCAGCTGATTTGTCTGA
59.382
47.619
21.47
13.89
34.78
3.27
1601
2056
4.461781
AGCTGATTTGTCTGAGGGATTTTG
59.538
41.667
0.00
0.00
0.00
2.44
1602
2057
4.741342
CTGATTTGTCTGAGGGATTTTGC
58.259
43.478
0.00
0.00
0.00
3.68
1944
2416
3.841255
TGGTATGTGTCCATTCTACACCA
59.159
43.478
4.09
0.00
45.33
4.17
2236
2723
1.079405
ACGCCCCAACACATCTACG
60.079
57.895
0.00
0.00
0.00
3.51
2441
2930
2.033801
CAGGTCTGTTGCTGTTTCCTTG
59.966
50.000
0.00
0.00
0.00
3.61
2442
2931
2.092429
AGGTCTGTTGCTGTTTCCTTGA
60.092
45.455
0.00
0.00
0.00
3.02
2457
2947
4.508551
TCCTTGATCACCAGCATAACAT
57.491
40.909
0.00
0.00
0.00
2.71
2483
2988
2.863132
ACCCGGTGCTAAATGTGTTA
57.137
45.000
0.00
0.00
0.00
2.41
2530
3035
1.414919
AGCTTCGTGTTGGTGTTAGGA
59.585
47.619
0.00
0.00
0.00
2.94
2548
3053
0.249826
GAGGGCTATGAGACAGCTGC
60.250
60.000
15.27
6.85
39.09
5.25
2676
3190
7.328737
ACAAACCTAGGTATGAACATGTCTAC
58.671
38.462
16.67
1.79
0.00
2.59
2689
3203
4.621991
ACATGTCTACGGCAATCATACTC
58.378
43.478
0.00
0.00
0.00
2.59
2864
3385
2.496899
TCAGGATGAGGTTTGAAGGC
57.503
50.000
0.00
0.00
42.56
4.35
2919
3445
6.999272
TGTTGTATTTGCTTTCCCTACAAGTA
59.001
34.615
0.00
0.00
34.11
2.24
2934
3460
6.205853
CCCTACAAGTATAGTTTTGTGTGCAA
59.794
38.462
0.00
0.00
37.98
4.08
2952
3478
2.438434
GATCCCCCAACAGCACCG
60.438
66.667
0.00
0.00
0.00
4.94
2981
3508
8.868522
AGATCATTTCTAATCTGTTGTTTCCA
57.131
30.769
0.00
0.00
31.09
3.53
3111
3641
7.339721
TGTTATTTTGTACAACTTGAAGGGTGA
59.660
33.333
8.07
0.00
0.00
4.02
3129
3659
4.019174
GGTGACATGTTCATGGAGGATTT
58.981
43.478
15.71
0.00
36.32
2.17
3140
3670
5.879763
TCATGGAGGATTTCTTCTGAAACA
58.120
37.500
0.00
0.00
43.90
2.83
3173
3703
2.103263
GGATGAGCCGTCAACTATTCCT
59.897
50.000
0.00
0.00
35.88
3.36
3176
3706
1.134560
GAGCCGTCAACTATTCCTCGT
59.865
52.381
0.00
0.00
0.00
4.18
3302
3832
6.313411
CAGTTTCTCCTGAATCATCTGTTCTC
59.687
42.308
0.00
0.00
34.23
2.87
3683
4238
4.381292
GCTCAATCTTTTGGTGATTCCCAG
60.381
45.833
0.00
0.00
35.49
4.45
4041
4644
5.941647
GGGTTTAAAGTTGATACTACCAGCA
59.058
40.000
0.00
0.00
32.96
4.41
4065
4668
3.054065
CCCTTCTAACCATTTGAGCTCCT
60.054
47.826
12.15
0.00
0.00
3.69
4115
4718
2.114056
CAAATTCAAGCATCCGCATCG
58.886
47.619
0.00
0.00
42.27
3.84
4125
4728
2.536928
GCATCCGCATCGTTAACTCAAC
60.537
50.000
3.71
0.00
38.36
3.18
4134
4737
3.920446
TCGTTAACTCAACTGCAGCATA
58.080
40.909
15.27
0.00
34.77
3.14
4193
4796
3.173151
TGCTGGGACTACTGAGAATGAA
58.827
45.455
0.00
0.00
0.00
2.57
4283
4886
3.568007
GGAGTTGCACAAAGGTATTGTCA
59.432
43.478
0.00
0.00
0.00
3.58
4382
5013
6.088824
CACTTTGTCATAAATCTGTTGCCTC
58.911
40.000
0.00
0.00
0.00
4.70
4394
5211
0.166814
GTTGCCTCTGTGCGTGAATC
59.833
55.000
0.00
0.00
0.00
2.52
4396
5213
0.390340
TGCCTCTGTGCGTGAATCTC
60.390
55.000
0.00
0.00
0.00
2.75
4397
5214
0.108424
GCCTCTGTGCGTGAATCTCT
60.108
55.000
0.00
0.00
0.00
3.10
4400
5217
2.414481
CCTCTGTGCGTGAATCTCTTTG
59.586
50.000
0.00
0.00
0.00
2.77
4401
5218
3.062763
CTCTGTGCGTGAATCTCTTTGT
58.937
45.455
0.00
0.00
0.00
2.83
4403
5220
4.627058
TCTGTGCGTGAATCTCTTTGTTA
58.373
39.130
0.00
0.00
0.00
2.41
4412
5231
8.653338
GCGTGAATCTCTTTGTTACTTATGTTA
58.347
33.333
0.00
0.00
0.00
2.41
4538
5393
4.231718
TCTTGCGTTATTTGTTTGGTCC
57.768
40.909
0.00
0.00
0.00
4.46
4582
5437
1.270252
CCCATGGTTTTGCAGGTTCAC
60.270
52.381
11.73
0.00
0.00
3.18
4672
5527
7.358655
AGCTGAGCTAGACAGGATGTTTGAG
62.359
48.000
4.49
0.00
44.93
3.02
4788
5643
5.655090
GGGAGTAAGCCCTCTATCTATCTTC
59.345
48.000
0.00
0.00
45.12
2.87
4806
5663
2.073117
TCGTGCTTGCTTTGATACGA
57.927
45.000
0.00
0.00
38.10
3.43
4887
5744
3.426695
GCAACATAGTGCGCAAGATCTTT
60.427
43.478
14.00
0.00
43.02
2.52
4947
5804
1.710244
TCATCTGCCCCAAGAAAGGAA
59.290
47.619
0.00
0.00
0.00
3.36
4958
5815
3.823304
CCAAGAAAGGAAGAAGGTTCTGG
59.177
47.826
0.00
0.00
37.65
3.86
4959
5816
4.446311
CCAAGAAAGGAAGAAGGTTCTGGA
60.446
45.833
0.00
0.00
37.65
3.86
5020
5877
6.201044
CACGTCAAGCCATTTAGATAACTAGG
59.799
42.308
0.00
0.00
0.00
3.02
5061
5918
5.187621
TCCCGAATCCTTTCTATTGGTTT
57.812
39.130
0.00
0.00
0.00
3.27
5077
5934
3.734463
TGGTTTAAGCTGATGTCGTTCA
58.266
40.909
0.00
0.00
0.00
3.18
5158
6016
7.342799
AGCATGGTCACAGGATATTATTGTTTT
59.657
33.333
0.00
0.00
0.00
2.43
5267
6130
0.034059
GGCATGAGGTGAGGTATCGG
59.966
60.000
0.00
0.00
0.00
4.18
5343
6206
6.826668
TGAAGTAACTCCTGATGTCTTTTGA
58.173
36.000
0.00
0.00
0.00
2.69
5397
6260
0.467804
CAACCCAACCCAACCCTTTG
59.532
55.000
0.00
0.00
0.00
2.77
5437
6302
6.901300
TGCTAGGTAATGTAGAGAGAGAGAA
58.099
40.000
0.00
0.00
0.00
2.87
5438
6303
6.995686
TGCTAGGTAATGTAGAGAGAGAGAAG
59.004
42.308
0.00
0.00
0.00
2.85
5439
6304
7.147461
TGCTAGGTAATGTAGAGAGAGAGAAGA
60.147
40.741
0.00
0.00
0.00
2.87
5524
6396
4.278419
AGGGCCAAGATTTATTATTGTCGC
59.722
41.667
6.18
0.00
0.00
5.19
5573
6446
1.765904
CTTAGCCCTCCCTCCTCTTTC
59.234
57.143
0.00
0.00
0.00
2.62
5633
6512
4.453339
GCTAGCTAGCGTTAGTAAGTACG
58.547
47.826
28.89
0.00
39.82
3.67
5634
6513
4.025313
GCTAGCTAGCGTTAGTAAGTACGT
60.025
45.833
28.89
0.00
39.82
3.57
5635
6514
5.175856
GCTAGCTAGCGTTAGTAAGTACGTA
59.824
44.000
28.89
0.00
39.82
3.57
5736
6620
8.818141
ATATGTACGTCTGATCCTGTTTAATG
57.182
34.615
0.00
0.00
0.00
1.90
5737
6621
6.032956
TGTACGTCTGATCCTGTTTAATGT
57.967
37.500
0.00
0.00
0.00
2.71
5738
6622
7.160547
TGTACGTCTGATCCTGTTTAATGTA
57.839
36.000
0.00
0.00
0.00
2.29
5739
6623
7.031372
TGTACGTCTGATCCTGTTTAATGTAC
58.969
38.462
0.00
0.00
0.00
2.90
5740
6624
6.282199
ACGTCTGATCCTGTTTAATGTACT
57.718
37.500
0.00
0.00
0.00
2.73
5741
6625
7.400599
ACGTCTGATCCTGTTTAATGTACTA
57.599
36.000
0.00
0.00
0.00
1.82
5742
6626
7.256286
ACGTCTGATCCTGTTTAATGTACTAC
58.744
38.462
0.00
0.00
0.00
2.73
5743
6627
6.696148
CGTCTGATCCTGTTTAATGTACTACC
59.304
42.308
0.00
0.00
0.00
3.18
5744
6628
7.416438
CGTCTGATCCTGTTTAATGTACTACCT
60.416
40.741
0.00
0.00
0.00
3.08
5745
6629
7.921745
GTCTGATCCTGTTTAATGTACTACCTC
59.078
40.741
0.00
0.00
0.00
3.85
5746
6630
7.069578
TCTGATCCTGTTTAATGTACTACCTCC
59.930
40.741
0.00
0.00
0.00
4.30
5747
6631
5.587388
TCCTGTTTAATGTACTACCTCCG
57.413
43.478
0.00
0.00
0.00
4.63
5748
6632
5.018809
TCCTGTTTAATGTACTACCTCCGT
58.981
41.667
0.00
0.00
0.00
4.69
5749
6633
5.126061
TCCTGTTTAATGTACTACCTCCGTC
59.874
44.000
0.00
0.00
0.00
4.79
5750
6634
5.126707
CCTGTTTAATGTACTACCTCCGTCT
59.873
44.000
0.00
0.00
0.00
4.18
5751
6635
6.319658
CCTGTTTAATGTACTACCTCCGTCTA
59.680
42.308
0.00
0.00
0.00
2.59
5752
6636
7.325660
TGTTTAATGTACTACCTCCGTCTAG
57.674
40.000
0.00
0.00
0.00
2.43
5753
6637
6.319658
TGTTTAATGTACTACCTCCGTCTAGG
59.680
42.308
0.00
0.00
42.82
3.02
5763
6647
4.571372
CCTCCGTCTAGGTGAATAAGTC
57.429
50.000
0.00
0.00
41.99
3.01
5764
6648
3.952323
CCTCCGTCTAGGTGAATAAGTCA
59.048
47.826
0.00
0.00
41.99
3.41
5765
6649
4.585162
CCTCCGTCTAGGTGAATAAGTCAT
59.415
45.833
0.00
0.00
38.90
3.06
5766
6650
5.069251
CCTCCGTCTAGGTGAATAAGTCATT
59.931
44.000
0.00
0.00
38.90
2.57
5767
6651
6.145338
TCCGTCTAGGTGAATAAGTCATTC
57.855
41.667
0.00
0.00
40.27
2.67
5768
6652
5.655090
TCCGTCTAGGTGAATAAGTCATTCA
59.345
40.000
0.00
0.00
43.86
2.57
5849
6733
3.755628
GGCCCGTCGCTGTCTGTA
61.756
66.667
0.00
0.00
37.74
2.74
5897
6781
4.974468
CACCGTATGTGCAATCGC
57.026
55.556
0.00
0.00
38.34
4.58
5909
6793
0.179105
GCAATCGCAATGCAATCCCA
60.179
50.000
5.91
0.00
43.29
4.37
5969
6856
4.898320
TGATTTATCAGTCGGATGGATGG
58.102
43.478
0.00
0.00
36.72
3.51
5974
6861
3.510459
ATCAGTCGGATGGATGGATACA
58.490
45.455
0.00
0.00
43.71
2.29
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
113
114
9.069082
CAGCATATACAACTACTCCTAGTACTT
57.931
37.037
0.00
0.00
32.46
2.24
134
135
9.950496
ATCGAGAAGGATATAAATTAACAGCAT
57.050
29.630
0.00
0.00
0.00
3.79
176
177
4.518970
AGGCGTTGCGATCCATTTAATTAT
59.481
37.500
0.00
0.00
0.00
1.28
184
185
1.815421
GTCAGGCGTTGCGATCCAT
60.815
57.895
0.00
0.00
0.00
3.41
199
201
2.479837
CAGTTTCACTTGCTACCGTCA
58.520
47.619
0.00
0.00
0.00
4.35
201
203
1.878953
CCAGTTTCACTTGCTACCGT
58.121
50.000
0.00
0.00
0.00
4.83
204
206
1.194772
GTCGCCAGTTTCACTTGCTAC
59.805
52.381
0.00
0.00
35.00
3.58
210
212
4.134563
AGTAAATTGTCGCCAGTTTCACT
58.865
39.130
0.00
0.00
33.23
3.41
211
213
4.464112
GAGTAAATTGTCGCCAGTTTCAC
58.536
43.478
0.00
0.00
33.23
3.18
223
225
4.857588
CGTAGAGTGAAGCGAGTAAATTGT
59.142
41.667
0.00
0.00
0.00
2.71
224
226
5.093457
TCGTAGAGTGAAGCGAGTAAATTG
58.907
41.667
0.00
0.00
0.00
2.32
234
236
2.342910
TCGGTTTCGTAGAGTGAAGC
57.657
50.000
0.00
0.00
38.43
3.86
239
241
1.665161
CGTGCTTCGGTTTCGTAGAGT
60.665
52.381
0.00
0.00
36.14
3.24
294
302
9.415544
CCTCTCTCTGAAAACATTTATTTTTGG
57.584
33.333
0.00
0.00
31.90
3.28
306
314
4.340617
TCTCCTCTCCTCTCTCTGAAAAC
58.659
47.826
0.00
0.00
0.00
2.43
311
319
2.105477
CTCCTCTCCTCTCCTCTCTCTG
59.895
59.091
0.00
0.00
0.00
3.35
323
331
2.366570
GCCCTCACCTCCTCTCCT
59.633
66.667
0.00
0.00
0.00
3.69
655
676
4.379243
AAGCCGAGCCGACTGTGG
62.379
66.667
0.00
0.00
0.00
4.17
721
752
0.107410
GCGGAGGAGAGAGAGAGACA
60.107
60.000
0.00
0.00
0.00
3.41
745
782
2.101209
GAAACACACTCACCCACGCG
62.101
60.000
3.53
3.53
0.00
6.01
821
858
1.770927
TTTTGTGGGGAGGACGGGA
60.771
57.895
0.00
0.00
0.00
5.14
826
872
2.178984
AGGAAATGTTTTGTGGGGAGGA
59.821
45.455
0.00
0.00
0.00
3.71
855
901
0.818296
GAGCGGCAGTAGAAAGAGGA
59.182
55.000
1.45
0.00
0.00
3.71
884
930
1.502690
AGCGAGAGGAGAGAGGAGTA
58.497
55.000
0.00
0.00
0.00
2.59
885
931
0.623723
AAGCGAGAGGAGAGAGGAGT
59.376
55.000
0.00
0.00
0.00
3.85
886
932
1.308998
GAAGCGAGAGGAGAGAGGAG
58.691
60.000
0.00
0.00
0.00
3.69
887
933
0.106918
GGAAGCGAGAGGAGAGAGGA
60.107
60.000
0.00
0.00
0.00
3.71
888
934
1.106944
GGGAAGCGAGAGGAGAGAGG
61.107
65.000
0.00
0.00
0.00
3.69
889
935
1.106944
GGGGAAGCGAGAGGAGAGAG
61.107
65.000
0.00
0.00
0.00
3.20
890
936
1.076632
GGGGAAGCGAGAGGAGAGA
60.077
63.158
0.00
0.00
0.00
3.10
891
937
0.686112
AAGGGGAAGCGAGAGGAGAG
60.686
60.000
0.00
0.00
0.00
3.20
892
938
0.252284
AAAGGGGAAGCGAGAGGAGA
60.252
55.000
0.00
0.00
0.00
3.71
893
939
0.176910
GAAAGGGGAAGCGAGAGGAG
59.823
60.000
0.00
0.00
0.00
3.69
894
940
1.265454
GGAAAGGGGAAGCGAGAGGA
61.265
60.000
0.00
0.00
0.00
3.71
895
941
1.222113
GGAAAGGGGAAGCGAGAGG
59.778
63.158
0.00
0.00
0.00
3.69
896
942
0.176910
GAGGAAAGGGGAAGCGAGAG
59.823
60.000
0.00
0.00
0.00
3.20
1077
1483
3.159298
CCAACGAGGTGGAGGATTG
57.841
57.895
0.00
0.00
41.65
2.67
1347
1792
0.580104
AACGAAAAACACCGCGAGAG
59.420
50.000
8.23
0.00
0.00
3.20
1348
1793
1.008329
AAACGAAAAACACCGCGAGA
58.992
45.000
8.23
0.00
0.00
4.04
1350
1795
1.531470
GGAAAACGAAAAACACCGCGA
60.531
47.619
8.23
0.00
0.00
5.87
1352
1797
1.849829
CTGGAAAACGAAAAACACCGC
59.150
47.619
0.00
0.00
0.00
5.68
1353
1798
2.159352
ACCTGGAAAACGAAAAACACCG
60.159
45.455
0.00
0.00
0.00
4.94
1356
1801
3.090037
TCCACCTGGAAAACGAAAAACA
58.910
40.909
0.00
0.00
42.18
2.83
1529
1979
6.766467
ACGAACAAGTAGAAGACAATTTTCCT
59.234
34.615
0.00
0.00
0.00
3.36
1592
2042
2.362889
CCGCCTGGCAAAATCCCT
60.363
61.111
20.29
0.00
0.00
4.20
1659
2115
3.482722
TTCACGGTAGAGCTTACTTCG
57.517
47.619
0.00
0.00
0.00
3.79
1944
2416
0.767375
AAGCCCCATACGCATGATCT
59.233
50.000
0.00
0.00
33.67
2.75
2236
2723
9.661187
CTCACAATTTATAGACAGATTTGATGC
57.339
33.333
0.00
0.00
0.00
3.91
2399
2888
0.746659
GGAAAATGAAGGCATCCCCG
59.253
55.000
0.00
0.00
39.21
5.73
2441
2930
7.196331
GGTTAAGAAATGTTATGCTGGTGATC
58.804
38.462
0.00
0.00
0.00
2.92
2442
2931
6.096846
GGGTTAAGAAATGTTATGCTGGTGAT
59.903
38.462
0.00
0.00
0.00
3.06
2457
2947
4.216687
CACATTTAGCACCGGGTTAAGAAA
59.783
41.667
6.32
0.00
0.00
2.52
2530
3035
1.694133
GGCAGCTGTCTCATAGCCCT
61.694
60.000
16.64
0.00
42.07
5.19
2548
3053
0.535102
ACTGAAGAAGGCACGTTGGG
60.535
55.000
0.00
0.00
0.00
4.12
2676
3190
9.809096
ATTACATATAGAAGAGTATGATTGCCG
57.191
33.333
0.00
0.00
33.56
5.69
2703
3224
1.382522
ATGAGCCGATGCGAACAAAT
58.617
45.000
0.00
0.00
44.33
2.32
2704
3225
1.130373
GAATGAGCCGATGCGAACAAA
59.870
47.619
0.00
0.00
44.33
2.83
2705
3226
0.726827
GAATGAGCCGATGCGAACAA
59.273
50.000
0.00
0.00
44.33
2.83
2706
3227
0.108186
AGAATGAGCCGATGCGAACA
60.108
50.000
0.00
0.00
44.33
3.18
2864
3385
1.447489
CTGCTCTGGTGCCTCTTCG
60.447
63.158
0.00
0.00
0.00
3.79
2889
3410
8.861086
TGTAGGGAAAGCAAATACAACAAATAA
58.139
29.630
0.00
0.00
0.00
1.40
2890
3411
8.410673
TGTAGGGAAAGCAAATACAACAAATA
57.589
30.769
0.00
0.00
0.00
1.40
2891
3412
7.296628
TGTAGGGAAAGCAAATACAACAAAT
57.703
32.000
0.00
0.00
0.00
2.32
2892
3413
6.716934
TGTAGGGAAAGCAAATACAACAAA
57.283
33.333
0.00
0.00
0.00
2.83
2893
3414
6.322712
ACTTGTAGGGAAAGCAAATACAACAA
59.677
34.615
0.00
0.00
33.89
2.83
2919
3445
3.763897
GGGGATCTTGCACACAAAACTAT
59.236
43.478
0.00
0.00
34.74
2.12
2934
3460
2.971598
CGGTGCTGTTGGGGGATCT
61.972
63.158
0.00
0.00
0.00
2.75
2981
3508
7.253905
AGTACCAGTAAACCTACATGACAAT
57.746
36.000
0.00
0.00
0.00
2.71
3107
3637
2.787473
TCCTCCATGAACATGTCACC
57.213
50.000
12.74
0.00
39.72
4.02
3111
3641
5.651139
CAGAAGAAATCCTCCATGAACATGT
59.349
40.000
12.74
0.00
37.11
3.21
3129
3659
3.678056
ACGCACCTATGTTTCAGAAGA
57.322
42.857
0.00
0.00
0.00
2.87
3140
3670
0.179045
GCTCATCCCAACGCACCTAT
60.179
55.000
0.00
0.00
0.00
2.57
3173
3703
3.042682
AGGAGAGACTCTATCTGGACGA
58.957
50.000
4.57
0.00
38.00
4.20
3176
3706
3.788708
TCCAAGGAGAGACTCTATCTGGA
59.211
47.826
18.49
18.49
38.00
3.86
3364
3895
5.988310
TTCAAGAGCATCACATTTGGAAT
57.012
34.783
0.00
0.00
37.82
3.01
3377
3908
1.000060
GGCAGCAACATTTCAAGAGCA
60.000
47.619
0.00
0.00
0.00
4.26
3683
4238
0.034670
AGGTCTGCATGAAGAAGCCC
60.035
55.000
4.49
2.56
0.00
5.19
3987
4590
1.268079
GAAACCACTGCCTTCTCTTGC
59.732
52.381
0.00
0.00
0.00
4.01
4041
4644
2.649816
AGCTCAAATGGTTAGAAGGGGT
59.350
45.455
0.00
0.00
0.00
4.95
4065
4668
0.322366
TCGTGGATTGCAGCCATTGA
60.322
50.000
12.77
11.09
37.81
2.57
4099
4702
2.017138
TAACGATGCGGATGCTTGAA
57.983
45.000
0.00
0.00
43.34
2.69
4115
4718
4.213270
TGTGTATGCTGCAGTTGAGTTAAC
59.787
41.667
16.64
0.00
39.65
2.01
4134
4737
3.002791
CAGGAATACAATCAGCGTGTGT
58.997
45.455
0.00
0.00
0.00
3.72
4193
4796
2.631545
AGGAGCTTGCTGAATGCTTTTT
59.368
40.909
0.00
0.00
43.37
1.94
4283
4886
5.664294
TGGCATGAACATAAAGAAAGCAT
57.336
34.783
0.00
0.00
0.00
3.79
4382
5013
3.885484
AACAAAGAGATTCACGCACAG
57.115
42.857
0.00
0.00
0.00
3.66
4412
5231
9.211410
AGTATCCTGCTATATCTTGCTCATAAT
57.789
33.333
0.00
0.00
0.00
1.28
4427
5246
5.902681
GTGTGAACACATAGTATCCTGCTA
58.097
41.667
10.78
0.00
45.75
3.49
4475
5314
5.067413
CAGGATAGTGCAATTGAATTCAGCT
59.933
40.000
10.34
3.76
0.00
4.24
4538
5393
6.700520
GGGAGTATCATAAAAGTTAGTGGTCG
59.299
42.308
0.00
0.00
36.25
4.79
4551
5406
4.892934
GCAAAACCATGGGGAGTATCATAA
59.107
41.667
18.09
0.00
36.25
1.90
4672
5527
5.239306
TGAAGACATCAGTTCACCATCAAAC
59.761
40.000
0.00
0.00
33.04
2.93
4788
5643
2.495939
GTTCGTATCAAAGCAAGCACG
58.504
47.619
0.00
0.00
0.00
5.34
4806
5663
1.263217
GAAGCGGATTTGTGTGACGTT
59.737
47.619
0.00
0.00
0.00
3.99
4887
5744
3.373877
GGACCTCCTCCTTGGTGTAGATA
60.374
52.174
0.00
0.00
36.59
1.98
4947
5804
2.544721
TCAGCATCTCCAGAACCTTCT
58.455
47.619
0.00
0.00
38.25
2.85
4958
5815
0.248377
GTTTGCGCCATCAGCATCTC
60.248
55.000
4.18
0.00
44.74
2.75
4959
5816
1.805254
GTTTGCGCCATCAGCATCT
59.195
52.632
4.18
0.00
44.74
2.90
5020
5877
2.280628
GAGGCACACATACCTAGTTGC
58.719
52.381
0.00
0.00
36.05
4.17
5061
5918
2.736721
GCACTTGAACGACATCAGCTTA
59.263
45.455
0.00
0.00
0.00
3.09
5077
5934
6.006449
AGGTCAAGTAGAATTTGATGCACTT
58.994
36.000
0.00
0.00
36.96
3.16
5158
6016
5.352293
GGTGATGCGAATCATATCATAGCAA
59.648
40.000
9.89
0.00
36.69
3.91
5267
6130
1.376037
CAGGACAAAGCTCCCCGTC
60.376
63.158
0.00
0.00
0.00
4.79
5407
6270
8.998277
TCTCTCTACATTACCTAGCAAGTAAT
57.002
34.615
1.47
1.47
40.26
1.89
5632
6511
7.781548
AAATAATACAGGGTACTTGCTTACG
57.218
36.000
0.00
0.00
0.00
3.18
5634
6513
9.617523
GGTTAAATAATACAGGGTACTTGCTTA
57.382
33.333
0.00
0.00
0.00
3.09
5635
6514
7.281549
CGGTTAAATAATACAGGGTACTTGCTT
59.718
37.037
0.00
0.00
0.00
3.91
5742
6626
3.952323
TGACTTATTCACCTAGACGGAGG
59.048
47.826
0.00
0.00
42.89
4.30
5743
6627
5.776173
ATGACTTATTCACCTAGACGGAG
57.224
43.478
0.00
0.00
36.92
4.63
5744
6628
6.145338
GAATGACTTATTCACCTAGACGGA
57.855
41.667
0.00
0.00
43.79
4.69
5759
6643
9.745880
CCATTAATAGTACTACGTGAATGACTT
57.254
33.333
19.60
6.45
0.00
3.01
5760
6644
7.866393
GCCATTAATAGTACTACGTGAATGACT
59.134
37.037
19.60
0.00
0.00
3.41
5761
6645
7.866393
AGCCATTAATAGTACTACGTGAATGAC
59.134
37.037
19.60
13.21
0.00
3.06
5762
6646
7.948357
AGCCATTAATAGTACTACGTGAATGA
58.052
34.615
19.60
0.00
0.00
2.57
5763
6647
9.856488
ATAGCCATTAATAGTACTACGTGAATG
57.144
33.333
4.31
11.52
0.00
2.67
5766
6650
9.948964
TCTATAGCCATTAATAGTACTACGTGA
57.051
33.333
4.31
0.00
0.00
4.35
5768
6652
9.956640
ACTCTATAGCCATTAATAGTACTACGT
57.043
33.333
4.31
0.00
0.00
3.57
5772
6656
9.809395
TCACACTCTATAGCCATTAATAGTACT
57.191
33.333
0.00
0.00
0.00
2.73
5835
6719
0.308068
ATCGATACAGACAGCGACGG
59.692
55.000
0.00
0.00
35.44
4.79
5849
6733
2.917751
ATGCGTCCCGGGATCGAT
60.918
61.111
34.74
24.93
39.00
3.59
5895
6779
1.514657
CGTGTGGGATTGCATTGCG
60.515
57.895
3.84
0.00
0.00
4.85
5896
6780
1.806758
GCGTGTGGGATTGCATTGC
60.807
57.895
0.46
0.46
0.00
3.56
5897
6781
0.733566
GTGCGTGTGGGATTGCATTG
60.734
55.000
0.00
0.00
39.85
2.82
5898
6782
1.586028
GTGCGTGTGGGATTGCATT
59.414
52.632
0.00
0.00
39.85
3.56
5899
6783
2.689785
CGTGCGTGTGGGATTGCAT
61.690
57.895
0.00
0.00
39.85
3.96
5900
6784
3.353029
CGTGCGTGTGGGATTGCA
61.353
61.111
0.00
0.00
34.44
4.08
5909
6793
1.831389
GATCAGTTGTGCGTGCGTGT
61.831
55.000
0.00
0.00
0.00
4.49
5969
6856
2.743938
CACTGCTCCGTGGTATGTATC
58.256
52.381
0.00
0.00
0.00
2.24
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.