Multiple sequence alignment - TraesCS4A01G175900
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
TraesCS4A01G175900
chr4A
100.000
5224
0
0
1
5224
446952708
446947485
0.000000e+00
9648.0
1
TraesCS4A01G175900
chr4B
90.566
2862
106
50
389
3209
187431884
187434622
0.000000e+00
3639.0
2
TraesCS4A01G175900
chr4B
94.784
786
32
6
3719
4500
187435262
187436042
0.000000e+00
1216.0
3
TraesCS4A01G175900
chr4B
89.474
741
71
4
4491
5224
187436293
187437033
0.000000e+00
929.0
4
TraesCS4A01G175900
chr4B
88.312
539
40
9
3191
3712
187434638
187435170
4.440000e-175
625.0
5
TraesCS4A01G175900
chr4B
89.526
401
18
10
1
391
187431085
187431471
2.190000e-133
486.0
6
TraesCS4A01G175900
chr4B
90.741
54
3
1
3670
3723
187435186
187435237
2.610000e-08
71.3
7
TraesCS4A01G175900
chr4D
93.427
2495
92
30
1235
3701
122758065
122760515
0.000000e+00
3633.0
8
TraesCS4A01G175900
chr4D
93.110
1611
49
23
1
1583
122756134
122757710
0.000000e+00
2303.0
9
TraesCS4A01G175900
chr4D
94.764
783
35
3
3719
4500
122760592
122761369
0.000000e+00
1214.0
10
TraesCS4A01G175900
chr4D
77.211
294
58
7
4937
5224
49307258
49306968
4.190000e-36
163.0
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
TraesCS4A01G175900
chr4A
446947485
446952708
5223
True
9648.000000
9648
100.000000
1
5224
1
chr4A.!!$R1
5223
1
TraesCS4A01G175900
chr4B
187431085
187437033
5948
False
1161.050000
3639
90.567167
1
5224
6
chr4B.!!$F1
5223
2
TraesCS4A01G175900
chr4D
122756134
122761369
5235
False
2383.333333
3633
93.767000
1
4500
3
chr4D.!!$F1
4499
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
238
249
0.107897
CCATCCACCGTCCAAATCGA
60.108
55.000
0.00
0.0
0.00
3.59
F
420
846
0.528466
CATCGATACGCACACCAGCT
60.528
55.000
0.00
0.0
0.00
4.24
F
1743
2907
1.271054
GCCCAGATGGACGCAATCTAT
60.271
52.381
0.00
0.0
37.39
1.98
F
2596
3768
0.179018
AACGGCTGCCTTTCTTGACT
60.179
50.000
17.92
0.0
0.00
3.41
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1743
2907
0.179111
CGAGCTTCTTCATGGCGGTA
60.179
55.000
0.00
0.00
0.00
4.02
R
2007
3171
1.881602
GTAGACGGGCGTGAAGTCT
59.118
57.895
2.85
2.85
45.85
3.24
R
3570
4819
0.316204
CAAAGCAGGGCAAGTCCAAG
59.684
55.000
0.00
0.00
36.21
3.61
R
4318
5657
0.249238
CGGCAGTATGAGCAGTCCTC
60.249
60.000
0.00
0.00
39.69
3.71
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
71
72
2.815211
CCTGCCGACCACACGATG
60.815
66.667
0.00
0.00
35.09
3.84
156
163
0.165944
GAAGCGTCACAATCCAACCG
59.834
55.000
0.00
0.00
0.00
4.44
166
173
0.183971
AATCCAACCGGGTCAACACA
59.816
50.000
6.32
0.00
38.11
3.72
169
176
1.720694
CCAACCGGGTCAACACACAC
61.721
60.000
6.32
0.00
0.00
3.82
170
177
1.816259
AACCGGGTCAACACACACG
60.816
57.895
6.32
0.00
43.17
4.49
238
249
0.107897
CCATCCACCGTCCAAATCGA
60.108
55.000
0.00
0.00
0.00
3.59
262
273
7.952101
CGATGATTATCCAAGCAATACTTTACG
59.048
37.037
0.00
0.00
36.04
3.18
263
274
8.902540
ATGATTATCCAAGCAATACTTTACGA
57.097
30.769
0.00
0.00
36.04
3.43
264
275
8.365399
TGATTATCCAAGCAATACTTTACGAG
57.635
34.615
0.00
0.00
36.04
4.18
271
282
6.292168
CCAAGCAATACTTTACGAGTAATCGG
60.292
42.308
17.70
1.19
43.76
4.18
279
290
9.813446
ATACTTTACGAGTAATCGGAATTTTCT
57.187
29.630
17.70
0.00
43.76
2.52
285
296
6.183360
ACGAGTAATCGGAATTTTCTAGTCGA
60.183
38.462
17.70
6.67
33.95
4.20
294
305
2.807631
TTTCTAGTCGACGCGTGCCC
62.808
60.000
20.70
0.00
0.00
5.36
299
310
2.589442
TCGACGCGTGCCCTTTTT
60.589
55.556
20.70
0.00
0.00
1.94
302
313
3.263503
GACGCGTGCCCTTTTTCCC
62.264
63.158
20.70
0.00
0.00
3.97
303
314
3.291383
CGCGTGCCCTTTTTCCCA
61.291
61.111
0.00
0.00
0.00
4.37
304
315
2.338620
GCGTGCCCTTTTTCCCAC
59.661
61.111
0.00
0.00
0.00
4.61
305
316
2.642700
CGTGCCCTTTTTCCCACG
59.357
61.111
0.00
0.00
43.83
4.94
306
317
2.338620
GTGCCCTTTTTCCCACGC
59.661
61.111
0.00
0.00
0.00
5.34
386
397
3.558418
CCGTCGTTTCCTTTTTCTCTTCA
59.442
43.478
0.00
0.00
0.00
3.02
412
838
2.279186
CCGGCACATCGATACGCA
60.279
61.111
17.21
0.00
0.00
5.24
420
846
0.528466
CATCGATACGCACACCAGCT
60.528
55.000
0.00
0.00
0.00
4.24
431
857
5.364778
ACGCACACCAGCTGAATAATATTA
58.635
37.500
17.39
0.00
0.00
0.98
432
858
5.997746
ACGCACACCAGCTGAATAATATTAT
59.002
36.000
17.39
1.91
0.00
1.28
433
859
6.486657
ACGCACACCAGCTGAATAATATTATT
59.513
34.615
17.39
18.55
36.14
1.40
551
978
9.762381
TTCTTTAGAAAAGGCTTGGGATTATTA
57.238
29.630
0.00
0.00
0.00
0.98
556
983
8.608185
AGAAAAGGCTTGGGATTATTAATTCA
57.392
30.769
0.00
0.00
0.00
2.57
582
1013
1.737793
ACGCATGCTTTGGTTACTAGC
59.262
47.619
17.13
0.00
35.50
3.42
686
1121
4.976864
AGTAGTGTACCAACCCGAAAAAT
58.023
39.130
0.00
0.00
0.00
1.82
693
1131
9.856162
AGTGTACCAACCCGAAAAATATATTAT
57.144
29.630
0.00
0.00
0.00
1.28
826
1268
7.545265
AGCAAAGCGAGAAATAAAAATGCATTA
59.455
29.630
13.39
0.00
32.76
1.90
953
1411
1.836604
GGAAGCCCCAGTTGCCAAA
60.837
57.895
0.00
0.00
34.14
3.28
968
1426
3.237746
TGCCAAATCAGATTCAAACCCA
58.762
40.909
0.00
0.00
0.00
4.51
992
1450
2.923035
ACTCCACACTCCACCCCG
60.923
66.667
0.00
0.00
0.00
5.73
993
1451
3.706373
CTCCACACTCCACCCCGG
61.706
72.222
0.00
0.00
0.00
5.73
994
1452
4.242586
TCCACACTCCACCCCGGA
62.243
66.667
0.73
0.00
43.61
5.14
1188
1649
2.434359
CTCTTCGACGCCAACCCC
60.434
66.667
0.00
0.00
0.00
4.95
1557
2721
1.577328
CGGGCTACAACACCAAGCTG
61.577
60.000
0.00
0.00
36.48
4.24
1560
2724
1.681264
GGCTACAACACCAAGCTGTTT
59.319
47.619
0.00
0.00
36.48
2.83
1692
2856
4.603946
GGCATCTACGACCCGGCC
62.604
72.222
0.00
0.00
0.00
6.13
1695
2859
3.152400
ATCTACGACCCGGCCACC
61.152
66.667
2.24
0.00
0.00
4.61
1743
2907
1.271054
GCCCAGATGGACGCAATCTAT
60.271
52.381
0.00
0.00
37.39
1.98
2007
3171
0.555769
ACTTTGGCCTCTTCAACCCA
59.444
50.000
3.32
0.00
0.00
4.51
2173
3341
4.382040
GCTGGGGCCTAAAATCTTTTCTTC
60.382
45.833
0.84
0.00
0.00
2.87
2174
3342
5.010708
TGGGGCCTAAAATCTTTTCTTCT
57.989
39.130
0.84
0.00
0.00
2.85
2175
3343
5.402630
TGGGGCCTAAAATCTTTTCTTCTT
58.597
37.500
0.84
0.00
0.00
2.52
2178
3346
7.039293
TGGGGCCTAAAATCTTTTCTTCTTTAC
60.039
37.037
0.84
0.00
0.00
2.01
2252
3420
8.609176
GCCTGTCTTTACAATCGTGATTTTATA
58.391
33.333
0.00
0.00
34.49
0.98
2288
3456
5.600696
GGAGAATGTGGTTTCAATTGTGTT
58.399
37.500
5.13
0.00
0.00
3.32
2299
3467
9.743057
TGGTTTCAATTGTGTTAAATTCAGTAG
57.257
29.630
5.13
0.00
0.00
2.57
2356
3526
8.702819
GGATGAACCCAGTAAAAGTAGTATAGT
58.297
37.037
0.00
0.00
0.00
2.12
2407
3577
1.238439
GGCTGCAGCAACTCTGTTTA
58.762
50.000
37.63
0.00
44.66
2.01
2411
3581
1.603802
TGCAGCAACTCTGTTTACAGC
59.396
47.619
5.00
0.00
44.66
4.40
2564
3736
1.377994
GCTCCTATCCCCTGCATGG
59.622
63.158
0.13
0.13
0.00
3.66
2596
3768
0.179018
AACGGCTGCCTTTCTTGACT
60.179
50.000
17.92
0.00
0.00
3.41
2618
3790
2.176273
CCAGTATGACAGCAGGCGC
61.176
63.158
0.00
0.00
39.69
6.53
2648
3820
2.358737
GCCTTGGACACGTCTGGG
60.359
66.667
0.00
0.00
0.00
4.45
2825
4017
7.490000
ACGTAGTACTCCCTATCAAAATCTTG
58.510
38.462
0.00
0.00
41.94
3.02
2826
4018
7.123847
ACGTAGTACTCCCTATCAAAATCTTGT
59.876
37.037
0.00
0.00
41.94
3.16
2827
4019
8.627403
CGTAGTACTCCCTATCAAAATCTTGTA
58.373
37.037
0.00
0.00
33.94
2.41
2828
4020
9.968870
GTAGTACTCCCTATCAAAATCTTGTAG
57.031
37.037
0.00
0.00
33.94
2.74
2891
4086
9.566432
ACTAGGATCTGATATTTGAATTGGAAC
57.434
33.333
0.00
0.00
0.00
3.62
2894
4089
6.486657
GGATCTGATATTTGAATTGGAACGGA
59.513
38.462
0.00
0.00
0.00
4.69
2895
4090
7.175641
GGATCTGATATTTGAATTGGAACGGAT
59.824
37.037
0.00
0.00
0.00
4.18
2957
4152
7.306866
CGGTACTGTTTTGAGAAGAAGAAGAAG
60.307
40.741
0.00
0.00
0.00
2.85
2968
4163
9.177608
TGAGAAGAAGAAGAAGAAAAATCAACA
57.822
29.630
0.00
0.00
0.00
3.33
2982
4177
4.637483
AATCAACAGGTTGTCAACACTG
57.363
40.909
22.41
22.41
41.16
3.66
3209
4441
5.437289
TTGGACTTGCTATCTGTTGTTTG
57.563
39.130
0.00
0.00
0.00
2.93
3218
4450
4.201891
GCTATCTGTTGTTTGCTGAGATGG
60.202
45.833
0.00
0.00
0.00
3.51
3219
4451
3.213206
TCTGTTGTTTGCTGAGATGGT
57.787
42.857
0.00
0.00
0.00
3.55
3230
4462
2.357009
GCTGAGATGGTTGCCTATTGTG
59.643
50.000
0.00
0.00
0.00
3.33
3342
4580
2.364632
CTTTCCGTGGCATCCAATACA
58.635
47.619
0.00
0.00
34.18
2.29
3343
4581
2.036958
TTCCGTGGCATCCAATACAG
57.963
50.000
0.00
0.00
34.18
2.74
3344
4582
0.180171
TCCGTGGCATCCAATACAGG
59.820
55.000
0.00
0.00
34.18
4.00
3345
4583
0.180171
CCGTGGCATCCAATACAGGA
59.820
55.000
0.00
0.00
43.01
3.86
3347
4585
1.942657
CGTGGCATCCAATACAGGAAG
59.057
52.381
0.00
0.00
41.92
3.46
3409
4647
0.475906
GCATGTGGATTAGGCCCTCT
59.524
55.000
0.00
0.00
0.00
3.69
3467
4712
1.640428
TCGGATGCTTAGCGAAAGTG
58.360
50.000
0.00
0.00
37.53
3.16
3468
4713
1.203758
TCGGATGCTTAGCGAAAGTGA
59.796
47.619
0.00
0.00
37.53
3.41
3487
4732
1.566298
AACCATGTGGAGGAGAGGGC
61.566
60.000
5.96
0.00
38.94
5.19
3488
4733
2.750657
CCATGTGGAGGAGAGGGCC
61.751
68.421
0.00
0.00
37.39
5.80
3489
4734
1.692042
CATGTGGAGGAGAGGGCCT
60.692
63.158
5.25
5.25
42.17
5.19
3490
4735
1.692042
ATGTGGAGGAGAGGGCCTG
60.692
63.158
12.95
0.00
38.73
4.85
3492
4737
2.039624
TGGAGGAGAGGGCCTGAC
59.960
66.667
12.95
4.06
38.73
3.51
3494
4739
2.063378
GGAGGAGAGGGCCTGACTG
61.063
68.421
12.95
0.00
38.73
3.51
3495
4740
2.686835
AGGAGAGGGCCTGACTGC
60.687
66.667
12.95
8.46
36.76
4.40
3496
4741
3.005539
GGAGAGGGCCTGACTGCA
61.006
66.667
12.95
0.00
0.00
4.41
3497
4742
2.373707
GGAGAGGGCCTGACTGCAT
61.374
63.158
12.95
0.00
0.00
3.96
3500
4749
0.543749
AGAGGGCCTGACTGCATTAC
59.456
55.000
12.95
0.00
0.00
1.89
3503
4752
2.170607
GAGGGCCTGACTGCATTACTAA
59.829
50.000
12.95
0.00
0.00
2.24
3508
4757
5.450550
GGGCCTGACTGCATTACTAATTTTC
60.451
44.000
0.84
0.00
0.00
2.29
3515
4764
7.094248
TGACTGCATTACTAATTTTCAGCATGT
60.094
33.333
0.00
0.00
37.40
3.21
3527
4776
0.813184
CAGCATGTTGATTCGGCCTT
59.187
50.000
2.97
0.00
0.00
4.35
3529
4778
0.248215
GCATGTTGATTCGGCCTTCG
60.248
55.000
0.00
0.00
40.90
3.79
3530
4779
0.378257
CATGTTGATTCGGCCTTCGG
59.622
55.000
0.00
0.00
39.77
4.30
3531
4780
0.748005
ATGTTGATTCGGCCTTCGGG
60.748
55.000
0.00
0.00
39.77
5.14
3557
4806
5.468746
GGCTAGTGTGTGTCAACAATCTTAA
59.531
40.000
0.00
0.00
38.27
1.85
3559
4808
6.423905
GCTAGTGTGTGTCAACAATCTTAAGA
59.576
38.462
7.82
7.82
38.27
2.10
3570
4819
9.020813
GTCAACAATCTTAAGAAGAAAACCAAC
57.979
33.333
9.71
0.00
41.63
3.77
3574
4823
8.197439
ACAATCTTAAGAAGAAAACCAACTTGG
58.803
33.333
9.71
6.24
41.71
3.61
3578
4827
7.614192
TCTTAAGAAGAAAACCAACTTGGACTT
59.386
33.333
15.14
12.62
36.28
3.01
3644
4893
5.590530
TTTGTTGTCAAAGCACCACTAAT
57.409
34.783
0.00
0.00
38.44
1.73
3717
5022
5.128827
AGTTGAGAATCTAAAGTATGGCCGA
59.871
40.000
0.00
0.00
34.92
5.54
3765
5099
3.258372
TCCTGTGCTGTTACCTGACTTAG
59.742
47.826
0.00
0.00
0.00
2.18
3798
5133
2.548875
TGTTGTTTTGCATTGCAGTCC
58.451
42.857
11.76
4.23
40.61
3.85
3850
5185
2.808206
AATCCGAGCCCTAAGCCCG
61.808
63.158
0.00
0.00
45.47
6.13
4110
5445
0.462047
GCGACCCCAGTAAGTCCATG
60.462
60.000
0.00
0.00
0.00
3.66
4146
5481
0.538287
AGTTTCTGAACCTGGCTGCC
60.538
55.000
12.87
12.87
36.39
4.85
4167
5506
2.107953
GGCATCGGAGGAGCTGAC
59.892
66.667
0.00
0.00
33.94
3.51
4172
5511
1.459455
ATCGGAGGAGCTGACGATGG
61.459
60.000
9.69
0.00
43.55
3.51
4184
5523
0.889186
GACGATGGCACCCTTGTTGT
60.889
55.000
0.00
0.00
0.00
3.32
4185
5524
1.172180
ACGATGGCACCCTTGTTGTG
61.172
55.000
0.00
0.00
36.79
3.33
4186
5525
1.172180
CGATGGCACCCTTGTTGTGT
61.172
55.000
0.00
0.00
36.11
3.72
4436
5775
1.483424
CGCCTCTTAGCTTAGCGCAC
61.483
60.000
11.47
0.00
42.61
5.34
4467
5806
2.845752
TAGCGTGATGTTGGGCCGTC
62.846
60.000
0.00
0.00
0.00
4.79
4500
5839
8.317460
TGCATCGCATTAATTTATTTTTCGTTC
58.683
29.630
0.00
0.00
31.71
3.95
4501
5840
8.531530
GCATCGCATTAATTTATTTTTCGTTCT
58.468
29.630
0.00
0.00
0.00
3.01
4515
6114
6.598753
TTTTCGTTCTCTTCGACTCATTTT
57.401
33.333
0.00
0.00
37.05
1.82
4530
6129
5.559770
ACTCATTTTTGGCCCAAATTTAGG
58.440
37.500
10.24
0.00
33.19
2.69
4546
6145
1.895020
TAGGCCGAGTTTGCATCCGT
61.895
55.000
0.00
0.00
0.00
4.69
4580
6179
2.360980
CCCTCTCCCTGTCCTCGT
59.639
66.667
0.00
0.00
0.00
4.18
4582
6181
1.304952
CCTCTCCCTGTCCTCGTCT
59.695
63.158
0.00
0.00
0.00
4.18
4621
6220
2.031768
GCCATCGCCATCTCTCCC
59.968
66.667
0.00
0.00
0.00
4.30
4630
6229
1.590932
CCATCTCTCCCAATTCGCTG
58.409
55.000
0.00
0.00
0.00
5.18
4636
6235
3.012518
CTCTCCCAATTCGCTGTCAAAT
58.987
45.455
0.00
0.00
0.00
2.32
4638
6237
2.091541
TCCCAATTCGCTGTCAAATCC
58.908
47.619
0.00
0.00
0.00
3.01
4650
6249
2.124695
AAATCCTTCCGCGCTCCC
60.125
61.111
5.56
0.00
0.00
4.30
4724
6324
2.266055
GCCGTGGTCCTGAGGAAG
59.734
66.667
0.96
0.00
31.38
3.46
4725
6325
2.584391
GCCGTGGTCCTGAGGAAGT
61.584
63.158
0.96
0.00
31.38
3.01
4727
6327
1.185618
CCGTGGTCCTGAGGAAGTCA
61.186
60.000
0.96
0.00
31.38
3.41
4795
6398
1.299850
AAAAAGAAGCCGCCGTTGC
60.300
52.632
0.00
0.00
0.00
4.17
4865
6468
2.594592
GCCACGCAACAGGTCCTT
60.595
61.111
0.00
0.00
0.00
3.36
4907
6510
2.432628
CTTCTCGTCACCACCGCC
60.433
66.667
0.00
0.00
0.00
6.13
4908
6511
3.220999
CTTCTCGTCACCACCGCCA
62.221
63.158
0.00
0.00
0.00
5.69
4931
6534
1.378882
CCAACATGGGCTCATCGGTG
61.379
60.000
0.00
1.19
32.67
4.94
4950
6553
3.830192
CAAGCCCGCCCATGCTTC
61.830
66.667
0.00
0.00
45.59
3.86
4972
6575
1.421410
GAATCGTCGCGCCTGTCAAT
61.421
55.000
0.00
0.00
0.00
2.57
5003
6606
0.393077
CATACGGGTGCCTTCCTAGG
59.607
60.000
0.82
0.82
45.02
3.02
5012
6615
1.987855
CCTTCCTAGGCACGACCCA
60.988
63.158
2.96
0.00
40.58
4.51
5015
6618
0.970937
TTCCTAGGCACGACCCAGAG
60.971
60.000
2.96
0.00
40.58
3.35
5036
6639
2.159226
GGTGTCCTACTTCTCCATGTCG
60.159
54.545
0.00
0.00
0.00
4.35
5051
6654
4.043100
TCGCCTCGGGACCTCTCA
62.043
66.667
0.00
0.00
0.00
3.27
5052
6655
3.827898
CGCCTCGGGACCTCTCAC
61.828
72.222
0.00
0.00
0.00
3.51
5054
6657
2.037367
CCTCGGGACCTCTCACCA
59.963
66.667
0.00
0.00
0.00
4.17
5070
6673
2.043411
CACCAAAAATGCACGACTTCG
58.957
47.619
0.00
0.00
46.33
3.79
5120
6723
0.740868
ATCTCAACGCCACACCGATG
60.741
55.000
0.00
0.00
33.08
3.84
5136
6739
3.588511
TGGCCAGCCAATCCACCA
61.589
61.111
9.42
0.00
44.12
4.17
5142
6746
3.499737
GCCAATCCACCAGACGCG
61.500
66.667
3.53
3.53
0.00
6.01
5148
6752
3.691342
CCACCAGACGCGAAGGGA
61.691
66.667
15.93
0.00
46.37
4.20
5207
6811
2.548920
GCCTCCTTCCTATTCGATGGTG
60.549
54.545
0.00
0.00
0.00
4.17
5208
6812
2.548920
CCTCCTTCCTATTCGATGGTGC
60.549
54.545
0.00
0.00
0.00
5.01
5209
6813
1.416401
TCCTTCCTATTCGATGGTGCC
59.584
52.381
0.00
0.00
0.00
5.01
5210
6814
1.502231
CTTCCTATTCGATGGTGCCG
58.498
55.000
0.00
0.00
0.00
5.69
5211
6815
1.068588
CTTCCTATTCGATGGTGCCGA
59.931
52.381
0.00
0.00
0.00
5.54
5212
6816
0.387929
TCCTATTCGATGGTGCCGAC
59.612
55.000
0.00
0.00
35.61
4.79
5215
6819
0.821517
TATTCGATGGTGCCGACACT
59.178
50.000
0.81
0.00
46.57
3.55
5216
6820
0.740868
ATTCGATGGTGCCGACACTG
60.741
55.000
0.81
0.00
46.57
3.66
5217
6821
2.779951
TTCGATGGTGCCGACACTGG
62.780
60.000
0.81
0.00
46.57
4.00
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
40
41
2.328099
GCAGGGAGAAACGCACAGG
61.328
63.158
0.00
0.00
0.00
4.00
41
42
2.328099
GGCAGGGAGAAACGCACAG
61.328
63.158
0.00
0.00
0.00
3.66
42
43
2.281484
GGCAGGGAGAAACGCACA
60.281
61.111
0.00
0.00
0.00
4.57
43
44
3.423154
CGGCAGGGAGAAACGCAC
61.423
66.667
0.00
0.00
0.00
5.34
44
45
3.621805
TCGGCAGGGAGAAACGCA
61.622
61.111
0.00
0.00
0.00
5.24
45
46
3.119096
GTCGGCAGGGAGAAACGC
61.119
66.667
0.00
0.00
0.00
4.84
49
50
2.525629
TGTGGTCGGCAGGGAGAA
60.526
61.111
0.00
0.00
0.00
2.87
71
72
0.801067
GCACGTACACGGAGATGGAC
60.801
60.000
6.72
0.00
44.95
4.02
119
126
0.969149
TCTCAATCTCACCAGCGTGT
59.031
50.000
0.00
0.00
41.09
4.49
156
163
1.494824
GAGTACGTGTGTGTTGACCC
58.505
55.000
0.00
0.00
0.00
4.46
169
176
2.413142
GGTGGGGAGGACGAGTACG
61.413
68.421
0.00
0.00
45.75
3.67
170
177
2.413142
CGGTGGGGAGGACGAGTAC
61.413
68.421
0.00
0.00
0.00
2.73
238
249
8.902540
TCGTAAAGTATTGCTTGGATAATCAT
57.097
30.769
0.00
0.00
37.52
2.45
262
273
6.140422
CGTCGACTAGAAAATTCCGATTACTC
59.860
42.308
14.70
0.00
0.00
2.59
263
274
5.970023
CGTCGACTAGAAAATTCCGATTACT
59.030
40.000
14.70
0.00
0.00
2.24
264
275
5.331383
GCGTCGACTAGAAAATTCCGATTAC
60.331
44.000
14.70
0.00
0.00
1.89
271
282
2.532388
GCACGCGTCGACTAGAAAATTC
60.532
50.000
9.86
0.00
0.00
2.17
279
290
2.424705
AAAAGGGCACGCGTCGACTA
62.425
55.000
9.86
0.00
0.00
2.59
285
296
3.292159
GGGAAAAAGGGCACGCGT
61.292
61.111
5.58
5.58
0.00
6.01
294
305
1.524008
GAGGTGGGCGTGGGAAAAAG
61.524
60.000
0.00
0.00
0.00
2.27
302
313
3.423154
GAAAGCGAGGTGGGCGTG
61.423
66.667
0.00
0.00
35.00
5.34
303
314
3.178540
AAGAAAGCGAGGTGGGCGT
62.179
57.895
0.00
0.00
35.00
5.68
304
315
2.358737
AAGAAAGCGAGGTGGGCG
60.359
61.111
0.00
0.00
35.00
6.13
305
316
2.391389
CGAAGAAAGCGAGGTGGGC
61.391
63.158
0.00
0.00
0.00
5.36
306
317
1.292223
TCGAAGAAAGCGAGGTGGG
59.708
57.895
0.00
0.00
33.33
4.61
386
397
1.138859
TCGATGTGCCGGAGAATGAAT
59.861
47.619
5.05
0.00
0.00
2.57
431
857
3.149196
TGCTCGAAGCTTTCCTTTGAAT
58.851
40.909
0.00
0.00
42.12
2.57
432
858
2.549754
CTGCTCGAAGCTTTCCTTTGAA
59.450
45.455
0.00
0.00
42.12
2.69
433
859
2.146342
CTGCTCGAAGCTTTCCTTTGA
58.854
47.619
0.00
0.00
42.97
2.69
439
865
0.671781
TGCCTCTGCTCGAAGCTTTC
60.672
55.000
0.00
0.00
42.97
2.62
551
978
4.152759
CCAAAGCATGCGTTTGAATGAATT
59.847
37.500
28.78
8.76
37.10
2.17
555
982
2.406130
ACCAAAGCATGCGTTTGAATG
58.594
42.857
28.78
20.03
37.10
2.67
556
983
2.818130
ACCAAAGCATGCGTTTGAAT
57.182
40.000
28.78
19.54
37.10
2.57
582
1013
6.043411
GCAAGAAAGAGGGTATACTGTACTG
58.957
44.000
2.25
0.00
0.00
2.74
664
1099
4.420522
TTTTTCGGGTTGGTACACTACT
57.579
40.909
0.00
0.00
39.29
2.57
779
1221
2.564975
GCTGCCATGTGTCACTGC
59.435
61.111
4.27
5.28
0.00
4.40
826
1268
9.816787
TTACAGTATTCTTATTCCCTTGGTTTT
57.183
29.630
0.00
0.00
0.00
2.43
830
1272
7.040409
GCCATTACAGTATTCTTATTCCCTTGG
60.040
40.741
0.00
0.00
0.00
3.61
953
1411
4.396166
GTCGATTGTGGGTTTGAATCTGAT
59.604
41.667
0.00
0.00
0.00
2.90
968
1426
1.000955
GTGGAGTGTGGAGTCGATTGT
59.999
52.381
0.00
0.00
0.00
2.71
1012
1470
1.747145
CGAGCAGCATGAGGAGGAT
59.253
57.895
0.00
0.00
39.69
3.24
1188
1649
0.807667
CGAAGGCGGAGATGAAGGTG
60.808
60.000
0.00
0.00
0.00
4.00
1296
2460
4.161295
TTGGCGCGGATCCAGGAG
62.161
66.667
13.41
0.00
34.66
3.69
1557
2721
3.346631
CTGCAGCATGGCCGGAAAC
62.347
63.158
5.05
0.00
35.86
2.78
1560
2724
4.349503
AACTGCAGCATGGCCGGA
62.350
61.111
15.27
0.00
35.86
5.14
1692
2856
2.146342
CTGGTGTAGTTGAGCTTGGTG
58.854
52.381
0.00
0.00
0.00
4.17
1695
2859
1.882912
TGCTGGTGTAGTTGAGCTTG
58.117
50.000
0.00
0.00
32.41
4.01
1743
2907
0.179111
CGAGCTTCTTCATGGCGGTA
60.179
55.000
0.00
0.00
0.00
4.02
2007
3171
1.881602
GTAGACGGGCGTGAAGTCT
59.118
57.895
2.85
2.85
45.85
3.24
2181
3349
8.507249
GCAATCAACCAATCATTATACTCCTAC
58.493
37.037
0.00
0.00
0.00
3.18
2182
3350
8.217111
TGCAATCAACCAATCATTATACTCCTA
58.783
33.333
0.00
0.00
0.00
2.94
2184
3352
7.275888
TGCAATCAACCAATCATTATACTCC
57.724
36.000
0.00
0.00
0.00
3.85
2252
3420
4.142315
CCACATTCTCCGCAGAAATGAAAT
60.142
41.667
5.50
0.00
42.14
2.17
2256
3424
2.086869
ACCACATTCTCCGCAGAAATG
58.913
47.619
0.00
0.00
42.14
2.32
2350
3520
9.282247
CGGAATGTCCATTATTACGTACTATAC
57.718
37.037
0.00
0.00
37.15
1.47
2407
3577
2.101582
GTCGGATCATCTGTAAGGCTGT
59.898
50.000
0.00
0.00
0.00
4.40
2411
3581
4.655762
TCAAGTCGGATCATCTGTAAGG
57.344
45.455
0.00
0.00
0.00
2.69
2564
3736
2.644992
CCGTTTGGGCAAGCAGAC
59.355
61.111
0.00
0.00
0.00
3.51
2596
3768
1.139654
GCCTGCTGTCATACTGGATCA
59.860
52.381
0.00
0.00
0.00
2.92
2618
3790
0.729116
CCAAGGCTGCTATCAACACG
59.271
55.000
0.00
0.00
0.00
4.49
2648
3820
1.931705
TCCCACCCCACCCATAACC
60.932
63.158
0.00
0.00
0.00
2.85
2733
3925
2.083774
GGTACATTTACAGCAGCAGCA
58.916
47.619
3.17
0.00
45.49
4.41
2734
3926
2.083774
TGGTACATTTACAGCAGCAGC
58.916
47.619
0.00
0.00
42.56
5.25
2735
3927
3.338249
ACTGGTACATTTACAGCAGCAG
58.662
45.455
0.00
0.00
42.62
4.24
2736
3928
3.417069
ACTGGTACATTTACAGCAGCA
57.583
42.857
0.00
0.00
42.62
4.41
2737
3929
4.201822
GCTTACTGGTACATTTACAGCAGC
60.202
45.833
0.00
0.76
42.62
5.25
2738
3930
5.178797
AGCTTACTGGTACATTTACAGCAG
58.821
41.667
0.00
0.00
44.04
4.24
2739
3931
5.160607
AGCTTACTGGTACATTTACAGCA
57.839
39.130
0.00
0.00
38.20
4.41
2740
3932
5.673818
GCAAGCTTACTGGTACATTTACAGC
60.674
44.000
0.00
0.00
38.20
4.40
2741
3933
5.411361
TGCAAGCTTACTGGTACATTTACAG
59.589
40.000
0.00
0.00
38.20
2.74
2742
3934
5.180492
GTGCAAGCTTACTGGTACATTTACA
59.820
40.000
0.00
0.00
38.20
2.41
2743
3935
5.391629
GGTGCAAGCTTACTGGTACATTTAC
60.392
44.000
0.00
0.00
34.29
2.01
2744
3936
4.698304
GGTGCAAGCTTACTGGTACATTTA
59.302
41.667
0.00
0.00
34.29
1.40
2828
4020
9.021863
GCATGTACTCACTCTGTAAACTAATAC
57.978
37.037
0.00
0.00
0.00
1.89
2931
4126
5.983720
TCTTCTTCTTCTCAAAACAGTACCG
59.016
40.000
0.00
0.00
0.00
4.02
2957
4152
6.034898
CAGTGTTGACAACCTGTTGATTTTTC
59.965
38.462
16.41
4.18
42.93
2.29
2968
4163
1.210478
ACTCAGCAGTGTTGACAACCT
59.790
47.619
15.59
9.29
0.00
3.50
3026
4224
1.365699
CCCTTAACGTGTTGATCCGG
58.634
55.000
0.00
0.00
0.00
5.14
3029
4227
3.335579
AGAAGCCCTTAACGTGTTGATC
58.664
45.455
0.00
0.00
0.00
2.92
3132
4330
3.916989
AGACCACCAGAATCTTAAACCCT
59.083
43.478
0.00
0.00
0.00
4.34
3209
4441
2.357009
CACAATAGGCAACCATCTCAGC
59.643
50.000
0.00
0.00
37.17
4.26
3218
4450
8.601476
GTCATTTACTAGTACACAATAGGCAAC
58.399
37.037
0.91
0.00
0.00
4.17
3219
4451
8.315482
TGTCATTTACTAGTACACAATAGGCAA
58.685
33.333
0.91
0.00
0.00
4.52
3230
4462
5.857517
GCGCTATCCTGTCATTTACTAGTAC
59.142
44.000
0.91
0.00
0.00
2.73
3342
4580
1.284198
AGAACAGATGCATGCCTTCCT
59.716
47.619
16.68
3.80
0.00
3.36
3343
4581
1.404391
CAGAACAGATGCATGCCTTCC
59.596
52.381
16.68
1.28
0.00
3.46
3344
4582
1.202268
GCAGAACAGATGCATGCCTTC
60.202
52.381
16.68
12.33
43.31
3.46
3345
4583
0.815734
GCAGAACAGATGCATGCCTT
59.184
50.000
16.68
1.92
43.31
4.35
3347
4585
0.815734
AAGCAGAACAGATGCATGCC
59.184
50.000
16.68
0.00
46.31
4.40
3409
4647
2.440409
GCTGCTTCCTTCCTTTGATGA
58.560
47.619
0.00
0.00
0.00
2.92
3444
4688
3.125316
ACTTTCGCTAAGCATCCGAAAAG
59.875
43.478
12.74
6.44
46.24
2.27
3467
4712
0.543749
CCCTCTCCTCCACATGGTTC
59.456
60.000
0.00
0.00
36.34
3.62
3468
4713
1.566298
GCCCTCTCCTCCACATGGTT
61.566
60.000
0.00
0.00
36.34
3.67
3487
4732
6.127925
TGCTGAAAATTAGTAATGCAGTCAGG
60.128
38.462
17.98
7.89
32.48
3.86
3488
4733
6.845302
TGCTGAAAATTAGTAATGCAGTCAG
58.155
36.000
16.01
15.43
34.46
3.51
3489
4734
6.816134
TGCTGAAAATTAGTAATGCAGTCA
57.184
33.333
16.01
12.96
0.00
3.41
3490
4735
7.253422
ACATGCTGAAAATTAGTAATGCAGTC
58.747
34.615
16.01
11.46
32.65
3.51
3492
4737
7.756272
TCAACATGCTGAAAATTAGTAATGCAG
59.244
33.333
9.77
11.35
32.65
4.41
3494
4739
8.638685
ATCAACATGCTGAAAATTAGTAATGC
57.361
30.769
2.34
0.00
0.00
3.56
3496
4741
9.507280
CGAATCAACATGCTGAAAATTAGTAAT
57.493
29.630
2.34
0.00
0.00
1.89
3497
4742
7.967854
CCGAATCAACATGCTGAAAATTAGTAA
59.032
33.333
2.34
0.00
0.00
2.24
3500
4749
5.230726
GCCGAATCAACATGCTGAAAATTAG
59.769
40.000
2.34
0.00
0.00
1.73
3503
4752
3.514645
GCCGAATCAACATGCTGAAAAT
58.485
40.909
2.34
0.00
0.00
1.82
3508
4757
0.813184
AAGGCCGAATCAACATGCTG
59.187
50.000
0.00
0.00
0.00
4.41
3527
4776
4.063967
CACACACTAGCCGCCCGA
62.064
66.667
0.00
0.00
0.00
5.14
3529
4778
2.434359
GACACACACTAGCCGCCC
60.434
66.667
0.00
0.00
0.00
6.13
3530
4779
1.301401
TTGACACACACTAGCCGCC
60.301
57.895
0.00
0.00
0.00
6.13
3531
4780
0.878523
TGTTGACACACACTAGCCGC
60.879
55.000
0.00
0.00
0.00
6.53
3557
4806
4.142160
GCAAGTCCAAGTTGGTTTTCTTCT
60.142
41.667
21.35
7.17
39.03
2.85
3559
4808
3.118775
GGCAAGTCCAAGTTGGTTTTCTT
60.119
43.478
21.35
16.76
39.03
2.52
3570
4819
0.316204
CAAAGCAGGGCAAGTCCAAG
59.684
55.000
0.00
0.00
36.21
3.61
3574
4823
1.856265
CGTCCAAAGCAGGGCAAGTC
61.856
60.000
0.00
0.00
30.91
3.01
3578
4827
3.884774
ACCGTCCAAAGCAGGGCA
61.885
61.111
0.00
0.00
30.91
5.36
3644
4893
1.065926
CATACTGGAAGGCTGTGCAGA
60.066
52.381
19.27
0.00
39.16
4.26
3717
5022
5.078411
ACGAATCTAAGCATCAGAACTGT
57.922
39.130
0.00
0.00
0.00
3.55
3765
5099
0.596082
AACAACATAACGGCACCTGC
59.404
50.000
0.00
0.00
41.14
4.85
3798
5133
2.359975
GAAGGGGTTGGAGCCACG
60.360
66.667
0.00
0.00
37.54
4.94
3819
5154
2.186826
CGGATTGGGCGATGGGTTC
61.187
63.158
0.00
0.00
0.00
3.62
4053
5388
2.357517
CCCTTGAAGTCGCACGCT
60.358
61.111
0.00
0.00
0.00
5.07
4078
5413
2.885861
GTCGCTGGAGGTGACGAT
59.114
61.111
0.00
0.00
44.05
3.73
4110
5445
8.193250
TCAGAAACTTCACAAACTGTTAGTAC
57.807
34.615
0.00
0.00
0.00
2.73
4146
5481
2.202987
GCTCCTCCGATGCCACAG
60.203
66.667
0.00
0.00
0.00
3.66
4167
5506
1.172180
ACACAACAAGGGTGCCATCG
61.172
55.000
0.00
0.00
39.87
3.84
4172
5511
1.639280
CAACAACACAACAAGGGTGC
58.361
50.000
0.00
0.00
39.87
5.01
4184
5523
0.820074
CCCCGTAACCTGCAACAACA
60.820
55.000
0.00
0.00
0.00
3.33
4185
5524
1.520600
CCCCCGTAACCTGCAACAAC
61.521
60.000
0.00
0.00
0.00
3.32
4186
5525
1.228306
CCCCCGTAACCTGCAACAA
60.228
57.895
0.00
0.00
0.00
2.83
4318
5657
0.249238
CGGCAGTATGAGCAGTCCTC
60.249
60.000
0.00
0.00
39.69
3.71
4467
5806
5.398176
AAATTAATGCGATGCAATGCAAG
57.602
34.783
13.45
10.90
45.45
4.01
4500
5839
2.162408
GGGCCAAAAATGAGTCGAAGAG
59.838
50.000
4.39
0.00
36.95
2.85
4501
5840
2.159382
GGGCCAAAAATGAGTCGAAGA
58.841
47.619
4.39
0.00
0.00
2.87
4530
6129
2.480555
CACGGATGCAAACTCGGC
59.519
61.111
0.00
0.00
0.00
5.54
4571
6170
1.384989
ATACGGGCAGACGAGGACAG
61.385
60.000
0.00
0.00
37.61
3.51
4600
6199
2.969238
GAGATGGCGATGGCGTGG
60.969
66.667
0.00
0.00
41.24
4.94
4603
6202
2.356793
GGAGAGATGGCGATGGCG
60.357
66.667
0.00
0.00
41.24
5.69
4610
6209
0.179034
AGCGAATTGGGAGAGATGGC
60.179
55.000
0.00
0.00
0.00
4.40
4621
6220
3.728864
CGGAAGGATTTGACAGCGAATTG
60.729
47.826
0.00
0.00
0.00
2.32
4630
6229
1.706287
GGAGCGCGGAAGGATTTGAC
61.706
60.000
8.83
0.00
0.00
3.18
4650
6249
4.899239
GGGCATGTCGAGAGGGCG
62.899
72.222
14.36
0.00
0.00
6.13
4654
6253
2.105128
GGTCGGGCATGTCGAGAG
59.895
66.667
12.26
0.00
37.31
3.20
4656
6255
4.530857
GGGGTCGGGCATGTCGAG
62.531
72.222
12.26
0.00
37.31
4.04
4678
6278
3.943137
ATGACTGGGAAGGGGGCGA
62.943
63.158
0.00
0.00
0.00
5.54
4710
6310
2.368875
TCTTTGACTTCCTCAGGACCAC
59.631
50.000
0.00
0.00
0.00
4.16
4717
6317
2.172505
TGCACCTTCTTTGACTTCCTCA
59.827
45.455
0.00
0.00
0.00
3.86
4744
6344
3.838565
CTCTAGGCATCCCTCTACTTCA
58.161
50.000
0.00
0.00
41.75
3.02
4865
6468
1.267121
GCTCTTGGTACCCTGACAGA
58.733
55.000
10.07
2.33
0.00
3.41
4889
6492
3.112709
GCGGTGGTGACGAGAAGC
61.113
66.667
0.00
0.00
0.00
3.86
4918
6521
3.626996
CTTGCCACCGATGAGCCCA
62.627
63.158
0.00
0.00
0.00
5.36
4945
6548
2.508439
GCGACGATTCCGGAAGCA
60.508
61.111
30.16
4.82
40.78
3.91
4994
6597
1.961180
CTGGGTCGTGCCTAGGAAGG
61.961
65.000
14.75
8.32
46.76
3.46
5003
6606
2.048127
GACACCTCTGGGTCGTGC
60.048
66.667
0.00
0.00
45.41
5.34
5006
6609
0.323542
AGTAGGACACCTCTGGGTCG
60.324
60.000
0.00
0.00
45.41
4.79
5012
6615
3.245803
ACATGGAGAAGTAGGACACCTCT
60.246
47.826
0.00
0.00
34.61
3.69
5015
6618
2.159226
CGACATGGAGAAGTAGGACACC
60.159
54.545
0.00
0.00
0.00
4.16
5023
6626
1.513158
CGAGGCGACATGGAGAAGT
59.487
57.895
0.00
0.00
0.00
3.01
5027
6630
3.147595
TCCCGAGGCGACATGGAG
61.148
66.667
0.00
0.00
0.00
3.86
5036
6639
3.462678
GGTGAGAGGTCCCGAGGC
61.463
72.222
0.00
0.00
0.00
4.70
5051
6654
2.399396
CGAAGTCGTGCATTTTTGGT
57.601
45.000
0.00
0.00
34.11
3.67
5078
6681
4.269523
GCAGGCACCACTGGGACA
62.270
66.667
0.00
0.00
38.90
4.02
5084
6687
2.490270
GATCAAGGGCAGGCACCACT
62.490
60.000
0.00
0.00
0.00
4.00
5120
6723
2.757099
CTGGTGGATTGGCTGGCC
60.757
66.667
4.43
4.43
0.00
5.36
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.