Multiple sequence alignment - TraesCS2A01G439400
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
TraesCS2A01G439400
chr2A
100.000
3900
0
0
1
3900
690737159
690741058
0.000000e+00
7203.0
1
TraesCS2A01G439400
chr2A
87.097
465
60
0
2233
2697
689710082
689709618
9.600000e-146
527.0
2
TraesCS2A01G439400
chr2A
96.552
58
2
0
3773
3830
690740873
690740930
3.210000e-16
97.1
3
TraesCS2A01G439400
chr2A
96.552
58
2
0
3715
3772
690740931
690740988
3.210000e-16
97.1
4
TraesCS2A01G439400
chr2D
89.480
3137
167
70
246
3269
547249462
547252548
0.000000e+00
3814.0
5
TraesCS2A01G439400
chr2D
93.515
1064
56
7
2212
3269
555133696
555134752
0.000000e+00
1570.0
6
TraesCS2A01G439400
chr2D
86.486
481
64
1
2218
2697
546872603
546873083
9.600000e-146
527.0
7
TraesCS2A01G439400
chr2D
86.214
486
67
0
2212
2697
546932410
546932895
9.600000e-146
527.0
8
TraesCS2A01G439400
chr2D
88.125
160
16
3
2108
2265
29675311
29675153
1.850000e-43
187.0
9
TraesCS2A01G439400
chr2D
93.750
64
4
0
3837
3900
555135238
555135301
3.210000e-16
97.1
10
TraesCS2A01G439400
chr2B
89.451
2114
125
50
1616
3670
653746614
653748688
0.000000e+00
2579.0
11
TraesCS2A01G439400
chr2B
90.762
1050
69
20
590
1619
653745551
653746592
0.000000e+00
1376.0
12
TraesCS2A01G439400
chr2B
87.868
544
39
17
2
532
653745001
653745530
7.160000e-172
614.0
13
TraesCS2A01G439400
chr2B
87.421
477
60
0
2221
2697
653611135
653611611
2.050000e-152
549.0
14
TraesCS2A01G439400
chr2B
86.008
486
68
0
2212
2697
653619729
653620214
4.470000e-144
521.0
15
TraesCS2A01G439400
chr6B
88.762
703
68
7
918
1616
464408069
464408764
0.000000e+00
850.0
16
TraesCS2A01G439400
chr6B
85.366
82
9
3
1232
1313
532151725
532151647
8.980000e-12
82.4
17
TraesCS2A01G439400
chr7B
88.666
697
46
6
925
1616
616911545
616912213
0.000000e+00
819.0
18
TraesCS2A01G439400
chr3B
87.483
719
56
7
902
1616
280583873
280584561
0.000000e+00
798.0
19
TraesCS2A01G439400
chr3B
85.971
278
28
7
1937
2213
369097385
369097118
1.770000e-73
287.0
20
TraesCS2A01G439400
chr3B
89.375
160
14
3
2108
2265
717559892
717559734
8.550000e-47
198.0
21
TraesCS2A01G439400
chr3B
89.381
113
6
1
1118
1230
369101085
369100979
1.890000e-28
137.0
22
TraesCS2A01G439400
chr4B
87.246
690
55
10
928
1612
548863916
548863255
0.000000e+00
756.0
23
TraesCS2A01G439400
chr3D
84.861
502
76
0
2204
2705
33298448
33297947
1.250000e-139
507.0
24
TraesCS2A01G439400
chr3D
88.125
160
16
3
2108
2265
440213374
440213216
1.850000e-43
187.0
25
TraesCS2A01G439400
chr5A
85.612
278
30
6
1937
2213
262335446
262335714
2.290000e-72
283.0
26
TraesCS2A01G439400
chr1D
89.375
160
14
3
2108
2265
359549101
359548943
8.550000e-47
198.0
27
TraesCS2A01G439400
chr5D
88.750
160
15
3
2108
2265
12362691
12362849
3.980000e-45
193.0
28
TraesCS2A01G439400
chr6D
85.185
81
9
3
1232
1312
348029477
348029554
3.230000e-11
80.5
29
TraesCS2A01G439400
chr6A
85.185
81
9
3
1232
1312
495465163
495465086
3.230000e-11
80.5
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
TraesCS2A01G439400
chr2A
690737159
690741058
3899
False
2465.733333
7203
97.701333
1
3900
3
chr2A.!!$F1
3899
1
TraesCS2A01G439400
chr2D
547249462
547252548
3086
False
3814.000000
3814
89.480000
246
3269
1
chr2D.!!$F3
3023
2
TraesCS2A01G439400
chr2D
555133696
555135301
1605
False
833.550000
1570
93.632500
2212
3900
2
chr2D.!!$F4
1688
3
TraesCS2A01G439400
chr2B
653745001
653748688
3687
False
1523.000000
2579
89.360333
2
3670
3
chr2B.!!$F3
3668
4
TraesCS2A01G439400
chr6B
464408069
464408764
695
False
850.000000
850
88.762000
918
1616
1
chr6B.!!$F1
698
5
TraesCS2A01G439400
chr7B
616911545
616912213
668
False
819.000000
819
88.666000
925
1616
1
chr7B.!!$F1
691
6
TraesCS2A01G439400
chr3B
280583873
280584561
688
False
798.000000
798
87.483000
902
1616
1
chr3B.!!$F1
714
7
TraesCS2A01G439400
chr3B
369097118
369101085
3967
True
212.000000
287
87.676000
1118
2213
2
chr3B.!!$R2
1095
8
TraesCS2A01G439400
chr4B
548863255
548863916
661
True
756.000000
756
87.246000
928
1612
1
chr4B.!!$R1
684
9
TraesCS2A01G439400
chr3D
33297947
33298448
501
True
507.000000
507
84.861000
2204
2705
1
chr3D.!!$R1
501
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
568
584
0.101040
CGTAATTCGTGTCCCGCCTA
59.899
55.000
0.0
0.0
36.19
3.93
F
635
651
0.742281
CCTCTCGTTGGATGCCAGTG
60.742
60.000
0.0
0.0
33.81
3.66
F
955
984
1.416049
CGTCAGCATCAAACGACGG
59.584
57.895
0.0
0.0
45.60
4.79
F
1497
2285
1.681327
ATGGGAGACGTACACCGCT
60.681
57.895
0.0
0.0
41.42
5.52
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1727
3769
0.178068
ATGCTACATCCGTCACCCAC
59.822
55.0
0.00
0.0
0.00
4.61
R
1858
3902
0.459585
CATCCCCACGAACGAACGAT
60.460
55.0
11.97
0.0
37.03
3.73
R
2753
5817
0.107312
ACAGATGAGCATGGACTGGC
60.107
55.0
0.00
0.0
33.57
4.85
R
3430
6537
0.393267
CGGGGTTTAAAGGATGCGGA
60.393
55.0
0.00
0.0
0.00
5.54
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
101
107
1.134580
CATCTGCCGGAACACATCTCT
60.135
52.381
5.05
0.00
0.00
3.10
122
128
5.901552
TCTCATTTCGCTTTGTTTCCTTTT
58.098
33.333
0.00
0.00
0.00
2.27
144
150
1.202290
GCCAGATATTTGCCAACCGTG
60.202
52.381
0.00
0.00
0.00
4.94
146
152
2.951642
CCAGATATTTGCCAACCGTGAT
59.048
45.455
0.00
0.00
0.00
3.06
154
160
6.767524
ATTTGCCAACCGTGATAAAGATAA
57.232
33.333
0.00
0.00
0.00
1.75
156
162
5.554822
TGCCAACCGTGATAAAGATAAAC
57.445
39.130
0.00
0.00
0.00
2.01
157
163
4.093703
TGCCAACCGTGATAAAGATAAACG
59.906
41.667
0.00
0.00
0.00
3.60
190
196
1.109323
GCCAAGTGTGAAAGGGTGCT
61.109
55.000
0.00
0.00
0.00
4.40
205
211
5.717119
AGGGTGCTAAACAGAATATTCCT
57.283
39.130
11.92
0.00
0.00
3.36
208
214
5.760743
GGGTGCTAAACAGAATATTCCTCTC
59.239
44.000
11.92
0.00
0.00
3.20
215
221
6.642707
AACAGAATATTCCTCTCCTACGAG
57.357
41.667
11.92
0.00
37.48
4.18
243
255
3.334583
TCAGAACCTGATTGTACAGCC
57.665
47.619
0.00
0.00
35.39
4.85
259
271
1.599240
GCCAGGCTTCGATGATCCC
60.599
63.158
3.29
0.00
0.00
3.85
320
332
3.829886
AAATCGTCGTTCATTGTGCAT
57.170
38.095
0.00
0.00
0.00
3.96
367
380
4.021102
ACCACTAACCAAACTCCATGAG
57.979
45.455
0.00
0.00
35.52
2.90
379
392
4.308526
CATGAGTGGAGGCACACC
57.691
61.111
8.46
0.00
42.28
4.16
492
508
4.740741
AATGCCCGCAAAATAAACAAAC
57.259
36.364
0.00
0.00
0.00
2.93
495
511
4.192317
TGCCCGCAAAATAAACAAACTTT
58.808
34.783
0.00
0.00
0.00
2.66
542
558
1.933853
CGAGTGCTTACATGGCTAACC
59.066
52.381
0.00
0.00
0.00
2.85
568
584
0.101040
CGTAATTCGTGTCCCGCCTA
59.899
55.000
0.00
0.00
36.19
3.93
569
585
1.849097
GTAATTCGTGTCCCGCCTAG
58.151
55.000
0.00
0.00
36.19
3.02
581
597
2.125147
GCCTAGGCATCACACGCA
60.125
61.111
29.33
0.00
41.49
5.24
582
598
2.464459
GCCTAGGCATCACACGCAC
61.464
63.158
29.33
0.00
41.49
5.34
583
599
2.167219
CCTAGGCATCACACGCACG
61.167
63.158
0.00
0.00
0.00
5.34
584
600
2.802667
CTAGGCATCACACGCACGC
61.803
63.158
0.00
0.00
0.00
5.34
602
618
3.423154
CAGTCCGGTCGCAAAGCC
61.423
66.667
0.00
0.00
0.00
4.35
619
635
3.470567
CGCGAACACGTGAGCCTC
61.471
66.667
25.01
11.57
39.45
4.70
635
651
0.742281
CCTCTCGTTGGATGCCAGTG
60.742
60.000
0.00
0.00
33.81
3.66
648
664
2.357517
CAGTGGTCACAGGCCGTC
60.358
66.667
0.00
0.00
0.00
4.79
735
752
3.006967
TCGACTTGGAGGAGAAGAAAAGG
59.993
47.826
0.00
0.00
0.00
3.11
738
755
1.747444
TGGAGGAGAAGAAAAGGCCT
58.253
50.000
0.00
0.00
0.00
5.19
747
764
3.139211
AGAAGAAAAGGCCTCCTCAGTTT
59.861
43.478
5.23
0.44
30.89
2.66
841
859
2.419198
CATCGCTCCTCCTTCCCG
59.581
66.667
0.00
0.00
0.00
5.14
856
874
4.222145
TCCTTCCCGATATAAAATCCCTCG
59.778
45.833
0.00
0.00
0.00
4.63
860
878
2.027561
CCGATATAAAATCCCTCGGCCA
60.028
50.000
2.24
0.00
41.95
5.36
881
899
1.534729
AAGACCCTTCCATTCGCAAC
58.465
50.000
0.00
0.00
0.00
4.17
916
938
4.966787
CACCCCAACCACCCACCG
62.967
72.222
0.00
0.00
0.00
4.94
955
984
1.416049
CGTCAGCATCAAACGACGG
59.584
57.895
0.00
0.00
45.60
4.79
1178
1239
4.883354
GGATGAGGCGGCCAAGGG
62.883
72.222
23.09
0.00
0.00
3.95
1392
1475
2.353607
CCAGATCGGAGCGCGTAC
60.354
66.667
8.43
1.52
36.56
3.67
1426
1509
4.267690
GGCGCTGTTATTTTATTTCCTTGC
59.732
41.667
7.64
0.00
0.00
4.01
1497
2285
1.681327
ATGGGAGACGTACACCGCT
60.681
57.895
0.00
0.00
41.42
5.52
1692
3733
2.486636
TTCGCCGAAGACAGCACGAT
62.487
55.000
0.00
0.00
0.00
3.73
1727
3769
2.244436
CTTTGCGTGTCATGGCCTCG
62.244
60.000
3.32
7.47
0.00
4.63
1774
3817
4.209452
TGTCACGCTTTTGATTCTGTTC
57.791
40.909
0.00
0.00
0.00
3.18
1833
3876
2.791501
TTAGAACGCGGACCCAAGCC
62.792
60.000
12.47
0.00
0.00
4.35
1839
3882
2.511600
CGGACCCAAGCCGTCATC
60.512
66.667
0.00
0.00
43.66
2.92
1841
3884
2.124695
GACCCAAGCCGTCATCCC
60.125
66.667
0.00
0.00
0.00
3.85
1988
5049
4.757149
AGACTGTCAGCAAACATTAGGAAC
59.243
41.667
10.88
0.00
0.00
3.62
1991
5052
3.820467
TGTCAGCAAACATTAGGAACTGG
59.180
43.478
0.00
0.00
41.52
4.00
2009
5070
4.881920
ACTGGAAACACAAATAACATGGC
58.118
39.130
0.00
0.00
35.60
4.40
2031
5093
4.045104
CGACCTTGACATGCTACTACATC
58.955
47.826
0.00
0.00
0.00
3.06
2035
5097
3.710326
TGACATGCTACTACATCGGAC
57.290
47.619
0.00
0.00
0.00
4.79
2044
5106
9.203421
CATGCTACTACATCGGACATTTTATTA
57.797
33.333
0.00
0.00
0.00
0.98
2068
5130
4.774124
TGATTAAAGCACCAGAGAGGATG
58.226
43.478
0.00
0.00
41.22
3.51
2132
5194
7.116662
TCTGTTTATCATGATTTTTGCACAAGC
59.883
33.333
14.65
2.22
42.57
4.01
2151
5213
5.129980
ACAAGCTGTATCATCTTGATCTCCA
59.870
40.000
16.53
0.00
39.15
3.86
2169
5231
7.604164
TGATCTCCACTCTGTATTTTGAAGTTC
59.396
37.037
0.00
0.00
0.00
3.01
2251
5313
2.743928
CTGGAGACTGTTGCCGCC
60.744
66.667
0.00
0.00
0.00
6.13
2485
5547
1.741401
CATCTCGCCCAAGTTCGCA
60.741
57.895
0.00
0.00
0.00
5.10
2737
5799
3.128242
CCACAAGATCAGCAAGTCAATCC
59.872
47.826
0.00
0.00
0.00
3.01
2753
5817
0.929244
ATCCTGACCCCATTTCCTGG
59.071
55.000
0.00
0.00
45.51
4.45
2805
5871
4.005650
TGGTTCTGAACTTCTGATGATGC
58.994
43.478
19.05
0.12
0.00
3.91
2820
5888
2.730382
TGATGCATGCTGATTTGGTCT
58.270
42.857
20.33
0.00
0.00
3.85
2928
5996
3.114809
CGTGTTCTGCTGAATTTTGCAA
58.885
40.909
9.40
0.00
38.81
4.08
2937
6008
3.846335
GCTGAATTTTGCAACGCTACTAC
59.154
43.478
0.00
0.00
0.00
2.73
2938
6009
4.378459
GCTGAATTTTGCAACGCTACTACT
60.378
41.667
0.00
0.00
0.00
2.57
2939
6010
5.029650
TGAATTTTGCAACGCTACTACTG
57.970
39.130
0.00
0.00
0.00
2.74
3041
6116
5.600908
TTGTTGCTCGTTTGGTAACTATC
57.399
39.130
0.00
0.00
32.13
2.08
3189
6264
9.628500
ATTGATCTACCTCGCTATGTACATATA
57.372
33.333
15.81
4.09
0.00
0.86
3222
6298
8.877864
TGAATATTCTTCCTTTTCCTTGCTAA
57.122
30.769
16.24
0.00
0.00
3.09
3228
6304
6.068010
TCTTCCTTTTCCTTGCTAATGTTGA
58.932
36.000
0.00
0.00
0.00
3.18
3250
6326
8.457261
GTTGAATTTTCTGATCTGCAGTAGATT
58.543
33.333
14.67
7.77
46.12
2.40
3306
6396
1.594331
GCTTCTGACGGTTGGACTTT
58.406
50.000
0.00
0.00
0.00
2.66
3308
6398
2.357952
GCTTCTGACGGTTGGACTTTTT
59.642
45.455
0.00
0.00
0.00
1.94
3334
6424
2.573009
TGACAGAATTCTGAGCATCCCA
59.427
45.455
36.15
19.36
46.59
4.37
3355
6450
3.702048
CTTCCCGGGGCGAACTGA
61.702
66.667
23.50
0.00
0.00
3.41
3356
6451
3.006728
TTCCCGGGGCGAACTGAT
61.007
61.111
23.50
0.00
0.00
2.90
3357
6452
2.925162
CTTCCCGGGGCGAACTGATC
62.925
65.000
23.50
0.00
0.00
2.92
3362
6457
0.878416
CGGGGCGAACTGATCAAAAA
59.122
50.000
0.00
0.00
0.00
1.94
3365
6460
1.886542
GGGCGAACTGATCAAAAACCT
59.113
47.619
0.00
0.00
0.00
3.50
3369
6469
4.499019
GGCGAACTGATCAAAAACCTTTCA
60.499
41.667
0.00
0.00
0.00
2.69
3382
6482
3.652057
ACCTTTCACCCGATCATTGAT
57.348
42.857
0.00
0.00
0.00
2.57
3384
6484
3.054434
ACCTTTCACCCGATCATTGATCA
60.054
43.478
22.95
0.00
38.84
2.92
3391
6491
3.129109
CCCGATCATTGATCAGTCACAG
58.871
50.000
22.95
7.69
38.84
3.66
3399
6506
5.349543
TCATTGATCAGTCACAGAATCAACG
59.650
40.000
0.00
0.00
33.11
4.10
3400
6507
2.995939
TGATCAGTCACAGAATCAACGC
59.004
45.455
0.00
0.00
0.00
4.84
3421
6528
3.769300
GCAACCCTTCAAACCATCCTATT
59.231
43.478
0.00
0.00
0.00
1.73
3422
6529
4.142160
GCAACCCTTCAAACCATCCTATTC
60.142
45.833
0.00
0.00
0.00
1.75
3423
6530
3.886123
ACCCTTCAAACCATCCTATTCG
58.114
45.455
0.00
0.00
0.00
3.34
3424
6531
3.214328
CCCTTCAAACCATCCTATTCGG
58.786
50.000
0.00
0.00
0.00
4.30
3426
6533
2.341846
TCAAACCATCCTATTCGGGC
57.658
50.000
0.00
0.00
0.00
6.13
3427
6534
1.843851
TCAAACCATCCTATTCGGGCT
59.156
47.619
0.00
0.00
0.00
5.19
3428
6535
1.949525
CAAACCATCCTATTCGGGCTG
59.050
52.381
0.00
0.00
0.00
4.85
3430
6537
1.213296
ACCATCCTATTCGGGCTGTT
58.787
50.000
0.00
0.00
0.00
3.16
3431
6538
1.141053
ACCATCCTATTCGGGCTGTTC
59.859
52.381
0.00
0.00
0.00
3.18
3439
6546
4.473520
CGGGCTGTTCCGCATCCT
62.474
66.667
0.00
0.00
43.71
3.24
3466
6575
2.768253
CCGCATATCTATGAGGGCAA
57.232
50.000
11.02
0.00
46.05
4.52
3467
6576
3.272574
CCGCATATCTATGAGGGCAAT
57.727
47.619
11.02
0.00
46.05
3.56
3485
6594
4.320275
GGCAATTATTAGAAGGCCTAACGC
60.320
45.833
5.16
1.90
39.93
4.84
3498
6607
1.470805
CCTAACGCGTCCATCATGTCA
60.471
52.381
14.44
0.00
0.00
3.58
3501
6610
0.458543
ACGCGTCCATCATGTCAGAC
60.459
55.000
5.58
0.00
0.00
3.51
3524
6633
3.416880
ATAACCTGGCCCACCCCG
61.417
66.667
0.00
0.00
33.59
5.73
3535
6644
4.609018
CACCCCGAGCCATAGCCG
62.609
72.222
0.00
0.00
41.25
5.52
3555
6664
0.322008
CTTGCCACTCCACTTCCTCC
60.322
60.000
0.00
0.00
0.00
4.30
3670
6789
4.140900
TCCCAGGAGGAAACAAATTTACCA
60.141
41.667
0.00
0.00
43.78
3.25
3671
6790
4.591072
CCCAGGAGGAAACAAATTTACCAA
59.409
41.667
0.00
0.00
38.24
3.67
3672
6791
5.071115
CCCAGGAGGAAACAAATTTACCAAA
59.929
40.000
0.00
0.00
38.24
3.28
3673
6792
6.239858
CCCAGGAGGAAACAAATTTACCAAAT
60.240
38.462
0.00
0.00
38.24
2.32
3674
6793
7.223584
CCAGGAGGAAACAAATTTACCAAATT
58.776
34.615
0.00
0.00
38.90
1.82
3675
6794
7.719193
CCAGGAGGAAACAAATTTACCAAATTT
59.281
33.333
4.23
4.23
43.41
1.82
3676
6795
9.771534
CAGGAGGAAACAAATTTACCAAATTTA
57.228
29.630
8.78
0.00
46.34
1.40
3677
6796
9.772973
AGGAGGAAACAAATTTACCAAATTTAC
57.227
29.630
8.78
3.32
46.34
2.01
3681
6800
7.095144
GGAAACAAATTTACCAAATTTACCCCG
60.095
37.037
8.78
1.31
46.34
5.73
3684
6803
2.197283
TTACCAAATTTACCCCGCGT
57.803
45.000
4.92
0.00
0.00
6.01
3686
6805
0.883153
ACCAAATTTACCCCGCGTTC
59.117
50.000
4.92
0.00
0.00
3.95
3706
6825
2.173356
TCCGCCATTCAATCCTTCTGAT
59.827
45.455
0.00
0.00
34.22
2.90
3727
6846
2.500910
TGGGAATCCATTGTTTCCATGC
59.499
45.455
0.09
2.59
40.65
4.06
3728
6847
2.500910
GGGAATCCATTGTTTCCATGCA
59.499
45.455
0.09
0.00
40.65
3.96
3729
6848
3.055240
GGGAATCCATTGTTTCCATGCAA
60.055
43.478
0.09
0.00
40.65
4.08
3730
6849
4.186159
GGAATCCATTGTTTCCATGCAAG
58.814
43.478
0.00
0.00
39.29
4.01
3731
6850
4.322953
GGAATCCATTGTTTCCATGCAAGT
60.323
41.667
0.00
0.00
39.29
3.16
3732
6851
3.663995
TCCATTGTTTCCATGCAAGTG
57.336
42.857
0.00
0.00
0.00
3.16
3733
6852
2.299582
TCCATTGTTTCCATGCAAGTGG
59.700
45.455
0.00
0.00
40.76
4.00
3734
6853
2.613474
CCATTGTTTCCATGCAAGTGGG
60.613
50.000
6.50
0.00
39.80
4.61
3735
6854
0.392336
TTGTTTCCATGCAAGTGGGC
59.608
50.000
6.50
0.00
39.80
5.36
3736
6855
1.080569
GTTTCCATGCAAGTGGGCG
60.081
57.895
6.50
0.00
39.80
6.13
3737
6856
2.929903
TTTCCATGCAAGTGGGCGC
61.930
57.895
6.50
0.00
39.80
6.53
3738
6857
3.866379
TTCCATGCAAGTGGGCGCT
62.866
57.895
7.64
0.00
39.80
5.92
3739
6858
4.124351
CCATGCAAGTGGGCGCTG
62.124
66.667
7.64
0.00
35.55
5.18
3740
6859
4.124351
CATGCAAGTGGGCGCTGG
62.124
66.667
7.64
0.00
36.28
4.85
3781
6900
1.034292
GGAGGCTCCACATTGCTTCC
61.034
60.000
28.55
0.00
45.59
3.46
3782
6901
0.322816
GAGGCTCCACATTGCTTCCA
60.323
55.000
2.15
0.00
30.50
3.53
3794
6913
2.879907
CTTCCATGCAAGTGGGCG
59.120
61.111
6.50
0.00
39.80
6.13
3796
6915
3.866379
TTCCATGCAAGTGGGCGCT
62.866
57.895
7.64
0.00
39.80
5.92
3797
6916
4.124351
CCATGCAAGTGGGCGCTG
62.124
66.667
7.64
0.00
35.55
5.18
3798
6917
4.124351
CATGCAAGTGGGCGCTGG
62.124
66.667
7.64
0.00
36.28
4.85
3835
6954
2.665603
GCGGAGGCTCCAGAACTT
59.334
61.111
31.69
0.00
35.91
2.66
3850
6980
0.884704
AACTTGTGGCAGTACAGGCG
60.885
55.000
7.32
0.00
36.77
5.52
3891
7021
1.583495
GCTGGTCGCAAAACCCCTAC
61.583
60.000
0.00
0.00
38.65
3.18
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
6.992715
GGCAACCGCTATTAATAGATCCATAT
59.007
38.462
23.84
2.59
38.60
1.78
3
4
4.575885
GGCAACCGCTATTAATAGATCCA
58.424
43.478
23.84
0.00
38.60
3.41
57
59
5.814040
GCCCATCCATCCATCCCAATATTTA
60.814
44.000
0.00
0.00
0.00
1.40
65
67
0.324091
GATGCCCATCCATCCATCCC
60.324
60.000
0.00
0.00
36.46
3.85
93
99
4.675190
ACAAAGCGAAATGAGAGATGTG
57.325
40.909
0.00
0.00
0.00
3.21
101
107
4.737765
CGAAAAGGAAACAAAGCGAAATGA
59.262
37.500
0.00
0.00
0.00
2.57
122
128
1.388547
GGTTGGCAAATATCTGGCGA
58.611
50.000
0.00
0.00
44.56
5.54
144
150
3.308866
ACGTGCAGCCGTTTATCTTTATC
59.691
43.478
3.38
0.00
37.96
1.75
146
152
2.690786
ACGTGCAGCCGTTTATCTTTA
58.309
42.857
3.38
0.00
37.96
1.85
174
180
3.626930
TGTTTAGCACCCTTTCACACTT
58.373
40.909
0.00
0.00
0.00
3.16
190
196
7.997223
TCTCGTAGGAGAGGAATATTCTGTTTA
59.003
37.037
14.95
0.00
44.28
2.01
208
214
4.701171
AGGTTCTGAAGTAGTTCTCGTAGG
59.299
45.833
11.52
0.00
33.38
3.18
215
221
7.152645
TGTACAATCAGGTTCTGAAGTAGTTC
58.847
38.462
3.15
3.15
44.04
3.01
243
255
2.216898
GAAAGGGATCATCGAAGCCTG
58.783
52.381
0.00
0.00
0.00
4.85
317
329
8.768957
ATATAATATGTGAGACAGTGTCATGC
57.231
34.615
24.73
13.73
34.60
4.06
367
380
2.665185
GTGACGGTGTGCCTCCAC
60.665
66.667
0.00
0.00
42.40
4.02
379
392
5.675970
AGTGAACGTATTCAATTTGTGACG
58.324
37.500
14.40
14.40
46.40
4.35
474
490
4.804608
AAAGTTTGTTTATTTTGCGGGC
57.195
36.364
0.00
0.00
0.00
6.13
511
527
6.293190
CCATGTAAGCACTCGTTTTAACTTCA
60.293
38.462
0.00
0.00
0.00
3.02
583
599
3.423154
CTTTGCGACCGGACTGGC
61.423
66.667
9.46
6.11
43.94
4.85
584
600
3.423154
GCTTTGCGACCGGACTGG
61.423
66.667
9.46
0.00
46.41
4.00
585
601
3.423154
GGCTTTGCGACCGGACTG
61.423
66.667
9.46
0.00
0.00
3.51
602
618
3.470567
GAGGCTCACGTGTTCGCG
61.471
66.667
16.51
0.00
41.18
5.87
605
621
0.318784
AACGAGAGGCTCACGTGTTC
60.319
55.000
34.19
13.95
42.48
3.18
619
635
1.003355
ACCACTGGCATCCAACGAG
60.003
57.895
0.00
0.00
30.80
4.18
635
651
3.311110
TGGAGACGGCCTGTGACC
61.311
66.667
0.00
6.96
0.00
4.02
675
692
1.135774
GGTCGTTGCGATTTTCTTCCC
60.136
52.381
0.00
0.00
38.42
3.97
735
752
0.915364
ATCCCAGAAACTGAGGAGGC
59.085
55.000
0.00
0.00
35.48
4.70
738
755
1.584724
GGGATCCCAGAAACTGAGGA
58.415
55.000
26.95
0.00
36.08
3.71
747
764
4.172232
CCTCCCGGGGATCCCAGA
62.172
72.222
32.07
22.42
45.83
3.86
829
847
5.338463
GGGATTTTATATCGGGAAGGAGGAG
60.338
48.000
0.00
0.00
0.00
3.69
841
859
5.768164
TCTTTTGGCCGAGGGATTTTATATC
59.232
40.000
0.00
0.00
0.00
1.63
856
874
1.550524
GAATGGAAGGGTCTTTTGGCC
59.449
52.381
0.00
0.00
45.31
5.36
860
878
2.286365
TGCGAATGGAAGGGTCTTTT
57.714
45.000
0.00
0.00
0.00
2.27
905
927
4.514585
TTGCTGCGGTGGGTGGTT
62.515
61.111
0.00
0.00
0.00
3.67
916
938
2.356673
GCTTGCCCTTGTTGCTGC
60.357
61.111
0.00
0.00
0.00
5.25
987
1021
4.598894
CTCATCTGGGCGCCGAGG
62.599
72.222
34.26
22.15
0.00
4.63
1441
1524
5.358922
ACAAAACCAACCAATCAATCACAG
58.641
37.500
0.00
0.00
0.00
3.66
1497
2285
1.062148
GTCAGATCGATCGACGTGTCA
59.938
52.381
22.06
3.03
43.13
3.58
1706
3748
1.210155
GGCCATGACACGCAAAGAC
59.790
57.895
0.00
0.00
0.00
3.01
1727
3769
0.178068
ATGCTACATCCGTCACCCAC
59.822
55.000
0.00
0.00
0.00
4.61
1739
3781
0.613260
GTGACAGGGACCATGCTACA
59.387
55.000
5.94
1.65
0.00
2.74
1852
3896
2.159393
CCCACGAACGAACGATTAGGTA
60.159
50.000
11.97
0.00
37.03
3.08
1853
3897
1.403249
CCCACGAACGAACGATTAGGT
60.403
52.381
11.97
0.00
37.03
3.08
1855
3899
1.135315
TCCCCACGAACGAACGATTAG
60.135
52.381
11.97
0.00
37.03
1.73
1856
3900
0.887247
TCCCCACGAACGAACGATTA
59.113
50.000
11.97
0.00
37.03
1.75
1858
3902
0.459585
CATCCCCACGAACGAACGAT
60.460
55.000
11.97
0.00
37.03
3.73
1859
3903
1.080366
CATCCCCACGAACGAACGA
60.080
57.895
11.97
0.00
37.03
3.85
1860
3904
2.098233
CCATCCCCACGAACGAACG
61.098
63.158
0.14
0.00
39.31
3.95
1861
3905
1.743995
CCCATCCCCACGAACGAAC
60.744
63.158
0.14
0.00
0.00
3.95
1862
3906
2.218454
ACCCATCCCCACGAACGAA
61.218
57.895
0.14
0.00
0.00
3.85
1946
5007
8.101654
ACAGTCTATAATCTGTCGATACTTCC
57.898
38.462
0.00
0.00
40.28
3.46
1988
5049
3.919804
CGCCATGTTATTTGTGTTTCCAG
59.080
43.478
0.00
0.00
0.00
3.86
1991
5052
3.917985
GGTCGCCATGTTATTTGTGTTTC
59.082
43.478
0.00
0.00
0.00
2.78
2009
5070
3.503827
TGTAGTAGCATGTCAAGGTCG
57.496
47.619
0.00
0.00
0.00
4.79
2044
5106
5.441718
TCCTCTCTGGTGCTTTAATCAAT
57.558
39.130
0.00
0.00
37.07
2.57
2068
5130
3.663025
AGTACATGGCAAAACAAATGGC
58.337
40.909
0.00
0.00
43.15
4.40
2132
5194
6.040729
ACAGAGTGGAGATCAAGATGATACAG
59.959
42.308
0.00
0.00
37.20
2.74
2151
5213
8.853077
TCATGATGAACTTCAAAATACAGAGT
57.147
30.769
0.00
0.00
0.00
3.24
2169
5231
3.139850
GGGTCAGCTTCAGATCATGATG
58.860
50.000
14.30
0.68
37.89
3.07
2452
5514
2.099263
CGAGATGAGGTAGCCGAAGAAA
59.901
50.000
0.00
0.00
0.00
2.52
2753
5817
0.107312
ACAGATGAGCATGGACTGGC
60.107
55.000
0.00
0.00
33.57
4.85
2805
5871
2.743664
TCGACAAGACCAAATCAGCATG
59.256
45.455
0.00
0.00
37.54
4.06
2820
5888
1.840630
CTGCACGGCACAATCGACAA
61.841
55.000
0.00
0.00
33.79
3.18
2928
5996
2.941720
GTGGTAGTAGCAGTAGTAGCGT
59.058
50.000
1.37
0.00
35.94
5.07
2937
6008
2.472695
TTGCTTGGTGGTAGTAGCAG
57.527
50.000
1.37
0.00
43.71
4.24
2938
6009
2.940994
TTTGCTTGGTGGTAGTAGCA
57.059
45.000
0.00
0.00
41.51
3.49
2939
6010
3.343617
TCATTTGCTTGGTGGTAGTAGC
58.656
45.455
0.00
0.00
0.00
3.58
3041
6116
5.287274
CACACTGCTTATTTCTCAGTACTCG
59.713
44.000
0.00
0.00
38.85
4.18
3189
6264
9.201989
GGAAAAGGAAGAATATTCAAATAGGGT
57.798
33.333
17.56
0.00
0.00
4.34
3222
6298
6.585695
ACTGCAGATCAGAAAATTCAACAT
57.414
33.333
23.35
0.00
45.72
2.71
3228
6304
8.270744
ACCTAATCTACTGCAGATCAGAAAATT
58.729
33.333
23.35
12.47
43.56
1.82
3250
6326
1.134340
ACGTCAAGCCACAAACACCTA
60.134
47.619
0.00
0.00
0.00
3.08
3309
6399
5.047802
GGGATGCTCAGAATTCTGTCAAAAA
60.048
40.000
29.80
12.62
44.12
1.94
3310
6400
4.460382
GGGATGCTCAGAATTCTGTCAAAA
59.540
41.667
29.80
13.27
44.12
2.44
3311
6401
4.012374
GGGATGCTCAGAATTCTGTCAAA
58.988
43.478
29.80
16.98
44.12
2.69
3312
6402
3.009363
TGGGATGCTCAGAATTCTGTCAA
59.991
43.478
29.80
18.49
44.12
3.18
3313
6403
2.573009
TGGGATGCTCAGAATTCTGTCA
59.427
45.455
29.80
26.71
44.12
3.58
3314
6404
2.941720
GTGGGATGCTCAGAATTCTGTC
59.058
50.000
29.80
22.99
44.12
3.51
3315
6405
2.679059
CGTGGGATGCTCAGAATTCTGT
60.679
50.000
29.80
14.62
44.12
3.41
3316
6406
1.938577
CGTGGGATGCTCAGAATTCTG
59.061
52.381
26.56
26.56
45.08
3.02
3317
6407
1.745141
GCGTGGGATGCTCAGAATTCT
60.745
52.381
0.88
0.88
0.00
2.40
3318
6408
0.659957
GCGTGGGATGCTCAGAATTC
59.340
55.000
0.00
0.00
0.00
2.17
3319
6409
0.749454
GGCGTGGGATGCTCAGAATT
60.749
55.000
0.00
0.00
0.00
2.17
3320
6410
1.153086
GGCGTGGGATGCTCAGAAT
60.153
57.895
0.00
0.00
0.00
2.40
3321
6411
1.841302
AAGGCGTGGGATGCTCAGAA
61.841
55.000
0.00
0.00
0.00
3.02
3322
6412
2.244117
GAAGGCGTGGGATGCTCAGA
62.244
60.000
0.00
0.00
0.00
3.27
3323
6413
1.817099
GAAGGCGTGGGATGCTCAG
60.817
63.158
0.00
0.00
0.00
3.35
3324
6414
2.268920
GAAGGCGTGGGATGCTCA
59.731
61.111
0.00
0.00
0.00
4.26
3353
6448
3.556999
TCGGGTGAAAGGTTTTTGATCA
58.443
40.909
0.00
0.00
0.00
2.92
3355
6450
4.148838
TGATCGGGTGAAAGGTTTTTGAT
58.851
39.130
0.00
0.00
0.00
2.57
3356
6451
3.556999
TGATCGGGTGAAAGGTTTTTGA
58.443
40.909
0.00
0.00
0.00
2.69
3357
6452
4.519540
ATGATCGGGTGAAAGGTTTTTG
57.480
40.909
0.00
0.00
0.00
2.44
3362
6457
3.054434
TGATCAATGATCGGGTGAAAGGT
60.054
43.478
17.31
0.00
41.51
3.50
3365
6460
4.191544
GACTGATCAATGATCGGGTGAAA
58.808
43.478
29.26
6.95
46.40
2.69
3369
6469
2.501316
TGTGACTGATCAATGATCGGGT
59.499
45.455
29.26
22.98
46.40
5.28
3382
6482
2.524569
TGCGTTGATTCTGTGACTGA
57.475
45.000
0.00
0.00
0.00
3.41
3384
6484
1.873591
GGTTGCGTTGATTCTGTGACT
59.126
47.619
0.00
0.00
0.00
3.41
3391
6491
3.049912
GTTTGAAGGGTTGCGTTGATTC
58.950
45.455
0.00
0.00
0.00
2.52
3399
6506
1.632589
AGGATGGTTTGAAGGGTTGC
58.367
50.000
0.00
0.00
0.00
4.17
3400
6507
4.096382
CGAATAGGATGGTTTGAAGGGTTG
59.904
45.833
0.00
0.00
0.00
3.77
3426
6533
2.163613
GGGTTTAAAGGATGCGGAACAG
59.836
50.000
0.00
0.00
0.00
3.16
3427
6534
2.164338
GGGTTTAAAGGATGCGGAACA
58.836
47.619
0.00
0.00
0.00
3.18
3428
6535
1.475280
GGGGTTTAAAGGATGCGGAAC
59.525
52.381
0.00
0.00
0.00
3.62
3430
6537
0.393267
CGGGGTTTAAAGGATGCGGA
60.393
55.000
0.00
0.00
0.00
5.54
3431
6538
2.000215
GCGGGGTTTAAAGGATGCGG
62.000
60.000
0.00
0.00
0.00
5.69
3433
6540
1.111277
ATGCGGGGTTTAAAGGATGC
58.889
50.000
0.00
0.00
0.00
3.91
3434
6541
4.398319
AGATATGCGGGGTTTAAAGGATG
58.602
43.478
0.00
0.00
0.00
3.51
3435
6542
4.724279
AGATATGCGGGGTTTAAAGGAT
57.276
40.909
0.00
0.00
0.00
3.24
3436
6543
5.308497
TCATAGATATGCGGGGTTTAAAGGA
59.692
40.000
0.00
0.00
33.76
3.36
3437
6544
5.556915
TCATAGATATGCGGGGTTTAAAGG
58.443
41.667
0.00
0.00
33.76
3.11
3438
6545
5.643777
CCTCATAGATATGCGGGGTTTAAAG
59.356
44.000
1.58
0.00
35.46
1.85
3439
6546
5.556915
CCTCATAGATATGCGGGGTTTAAA
58.443
41.667
1.58
0.00
35.46
1.52
3466
6575
4.304939
GACGCGTTAGGCCTTCTAATAAT
58.695
43.478
15.53
0.00
39.82
1.28
3467
6576
3.491447
GGACGCGTTAGGCCTTCTAATAA
60.491
47.826
15.53
0.00
39.82
1.40
3485
6594
0.536724
TGGGTCTGACATGATGGACG
59.463
55.000
10.38
0.00
0.00
4.79
3498
6607
1.609783
GCCAGGTTATGCTGGGTCT
59.390
57.895
0.00
0.00
40.87
3.85
3501
6610
2.123726
GGGCCAGGTTATGCTGGG
60.124
66.667
4.39
0.00
40.87
4.45
3524
6633
3.282920
GGCAAGCGGCTATGGCTC
61.283
66.667
22.08
10.59
40.53
4.70
3526
6635
3.892581
GTGGCAAGCGGCTATGGC
61.893
66.667
22.37
22.37
44.01
4.40
3529
6638
2.190578
GGAGTGGCAAGCGGCTAT
59.809
61.111
1.35
0.00
44.01
2.97
3535
6644
0.957888
GAGGAAGTGGAGTGGCAAGC
60.958
60.000
0.00
0.00
0.00
4.01
3568
6677
4.323333
CCGGAGATGAGCTATGATTGGATT
60.323
45.833
0.00
0.00
0.00
3.01
3684
6803
2.026356
TCAGAAGGATTGAATGGCGGAA
60.026
45.455
0.00
0.00
0.00
4.30
3686
6805
2.042686
TCAGAAGGATTGAATGGCGG
57.957
50.000
0.00
0.00
0.00
6.13
3718
6837
1.080569
CGCCCACTTGCATGGAAAC
60.081
57.895
7.97
0.00
43.02
2.78
3719
6838
2.929903
GCGCCCACTTGCATGGAAA
61.930
57.895
7.97
0.00
43.02
3.13
3720
6839
3.372730
GCGCCCACTTGCATGGAA
61.373
61.111
7.97
0.00
43.02
3.53
3721
6840
4.349503
AGCGCCCACTTGCATGGA
62.350
61.111
7.97
0.00
43.02
3.41
3722
6841
4.124351
CAGCGCCCACTTGCATGG
62.124
66.667
2.29
1.66
39.71
3.66
3723
6842
4.124351
CCAGCGCCCACTTGCATG
62.124
66.667
2.29
0.00
0.00
4.06
3741
6860
3.741476
GTTGGCCGCCTTGAGCTG
61.741
66.667
11.61
0.00
40.39
4.24
3754
6873
3.636231
TGGAGCCTCCACGGTTGG
61.636
66.667
10.05
0.00
42.67
3.77
3761
6880
0.322816
GAAGCAATGTGGAGCCTCCA
60.323
55.000
10.05
10.05
45.98
3.86
3762
6881
1.034292
GGAAGCAATGTGGAGCCTCC
61.034
60.000
2.98
2.98
34.52
4.30
3763
6882
0.322816
TGGAAGCAATGTGGAGCCTC
60.323
55.000
0.00
0.00
0.00
4.70
3764
6883
0.333993
ATGGAAGCAATGTGGAGCCT
59.666
50.000
0.00
0.00
0.00
4.58
3765
6884
0.458669
CATGGAAGCAATGTGGAGCC
59.541
55.000
0.00
0.00
0.00
4.70
3766
6885
0.179119
GCATGGAAGCAATGTGGAGC
60.179
55.000
0.00
0.00
0.00
4.70
3767
6886
1.179152
TGCATGGAAGCAATGTGGAG
58.821
50.000
0.00
0.00
42.46
3.86
3768
6887
3.360296
TGCATGGAAGCAATGTGGA
57.640
47.368
0.00
0.00
42.46
4.02
3775
6894
2.277591
GCCCACTTGCATGGAAGCA
61.278
57.895
25.09
0.00
43.02
3.91
3781
6900
4.124351
CCAGCGCCCACTTGCATG
62.124
66.667
2.29
0.00
0.00
4.06
3799
6918
3.741476
GTTGGCCGCCTTGAGCTG
61.741
66.667
11.61
0.00
40.39
4.24
3835
6954
3.589654
GAGCGCCTGTACTGCCACA
62.590
63.158
2.29
0.00
0.00
4.17
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.