Multiple sequence alignment - TraesCS7B01G314900
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
TraesCS7B01G314900
chr7B
100.000
3815
0
0
1
3815
562410442
562406628
0.000000e+00
7046.0
1
TraesCS7B01G314900
chr7D
92.190
1959
114
20
968
2920
525774602
525772677
0.000000e+00
2734.0
2
TraesCS7B01G314900
chr7D
91.910
445
22
7
479
918
525775334
525774899
9.060000e-171
610.0
3
TraesCS7B01G314900
chr7D
85.179
641
38
27
3211
3815
525772316
525771697
4.220000e-169
604.0
4
TraesCS7B01G314900
chr7D
88.750
320
36
0
1033
1352
525989239
525988920
3.570000e-105
392.0
5
TraesCS7B01G314900
chr7D
87.500
64
3
1
3017
3075
525772610
525772547
6.840000e-08
69.4
6
TraesCS7B01G314900
chr7A
92.723
1594
77
19
1048
2611
606331062
606329478
0.000000e+00
2265.0
7
TraesCS7B01G314900
chr7A
90.846
1016
54
17
37
1024
606332506
606331502
0.000000e+00
1325.0
8
TraesCS7B01G314900
chr7A
83.121
1333
89
57
2543
3815
606329513
606328257
0.000000e+00
1090.0
9
TraesCS7B01G314900
chr6D
84.834
1022
140
15
1088
2101
60168277
60167263
0.000000e+00
1014.0
10
TraesCS7B01G314900
chr6B
84.375
1024
141
17
1088
2101
134000320
133999306
0.000000e+00
987.0
11
TraesCS7B01G314900
chr6A
83.965
1029
145
16
1088
2101
76638901
76637878
0.000000e+00
968.0
12
TraesCS7B01G314900
chr1D
78.933
731
142
11
1107
1834
119010762
119010041
1.590000e-133
486.0
13
TraesCS7B01G314900
chr1B
78.729
724
140
13
1115
1834
181218229
181217516
4.460000e-129
472.0
14
TraesCS7B01G314900
chr3D
79.815
649
120
11
1103
1747
75355796
75356437
2.680000e-126
462.0
15
TraesCS7B01G314900
chr1A
78.279
732
145
13
1107
1834
131521550
131520829
3.470000e-125
459.0
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
TraesCS7B01G314900
chr7B
562406628
562410442
3814
True
7046.00
7046
100.000000
1
3815
1
chr7B.!!$R1
3814
1
TraesCS7B01G314900
chr7D
525771697
525775334
3637
True
1004.35
2734
89.194750
479
3815
4
chr7D.!!$R2
3336
2
TraesCS7B01G314900
chr7A
606328257
606332506
4249
True
1560.00
2265
88.896667
37
3815
3
chr7A.!!$R1
3778
3
TraesCS7B01G314900
chr6D
60167263
60168277
1014
True
1014.00
1014
84.834000
1088
2101
1
chr6D.!!$R1
1013
4
TraesCS7B01G314900
chr6B
133999306
134000320
1014
True
987.00
987
84.375000
1088
2101
1
chr6B.!!$R1
1013
5
TraesCS7B01G314900
chr6A
76637878
76638901
1023
True
968.00
968
83.965000
1088
2101
1
chr6A.!!$R1
1013
6
TraesCS7B01G314900
chr1D
119010041
119010762
721
True
486.00
486
78.933000
1107
1834
1
chr1D.!!$R1
727
7
TraesCS7B01G314900
chr1B
181217516
181218229
713
True
472.00
472
78.729000
1115
1834
1
chr1B.!!$R1
719
8
TraesCS7B01G314900
chr3D
75355796
75356437
641
False
462.00
462
79.815000
1103
1747
1
chr3D.!!$F1
644
9
TraesCS7B01G314900
chr1A
131520829
131521550
721
True
459.00
459
78.279000
1107
1834
1
chr1A.!!$R1
727
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
870
890
0.120377
TAACCCTCCATGTGACCCCT
59.880
55.000
0.00
0.0
0.00
4.79
F
1540
2245
1.005394
TTCAACGAGTTCGAGGGCC
60.005
57.895
8.72
0.0
43.02
5.80
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2089
2794
0.390340
GCTGATTCCTGACACTGCGA
60.390
55.0
0.0
0.0
0.0
5.10
R
3138
3940
0.178885
AACTAGTACCCCAGTGCCCA
60.179
55.0
0.0
0.0
0.0
5.36
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
18
19
1.059681
GACGACAGAGACTCGAGCG
59.940
63.158
13.61
8.60
35.08
5.03
19
20
1.352882
GACGACAGAGACTCGAGCGA
61.353
60.000
13.61
0.00
35.08
4.93
20
21
1.346879
CGACAGAGACTCGAGCGAG
59.653
63.158
13.61
17.46
46.91
5.03
21
22
1.079317
CGACAGAGACTCGAGCGAGA
61.079
60.000
24.81
0.00
44.53
4.04
22
23
0.650512
GACAGAGACTCGAGCGAGAG
59.349
60.000
24.81
9.44
44.53
3.20
23
24
0.248012
ACAGAGACTCGAGCGAGAGA
59.752
55.000
24.81
0.00
44.53
3.10
24
25
0.930310
CAGAGACTCGAGCGAGAGAG
59.070
60.000
24.81
8.47
44.53
3.20
25
26
0.179084
AGAGACTCGAGCGAGAGAGG
60.179
60.000
24.81
0.86
44.53
3.69
26
27
1.153249
AGACTCGAGCGAGAGAGGG
60.153
63.158
24.81
0.14
44.53
4.30
27
28
1.153329
GACTCGAGCGAGAGAGGGA
60.153
63.158
24.81
0.00
44.53
4.20
28
29
0.745128
GACTCGAGCGAGAGAGGGAA
60.745
60.000
24.81
0.00
44.53
3.97
29
30
0.322636
ACTCGAGCGAGAGAGGGAAA
60.323
55.000
24.81
0.00
44.53
3.13
30
31
0.811915
CTCGAGCGAGAGAGGGAAAA
59.188
55.000
14.28
0.00
44.53
2.29
31
32
0.526662
TCGAGCGAGAGAGGGAAAAC
59.473
55.000
0.00
0.00
0.00
2.43
32
33
0.528470
CGAGCGAGAGAGGGAAAACT
59.472
55.000
0.00
0.00
0.00
2.66
33
34
1.067495
CGAGCGAGAGAGGGAAAACTT
60.067
52.381
0.00
0.00
0.00
2.66
34
35
2.610727
CGAGCGAGAGAGGGAAAACTTT
60.611
50.000
0.00
0.00
0.00
2.66
35
36
3.367087
CGAGCGAGAGAGGGAAAACTTTA
60.367
47.826
0.00
0.00
0.00
1.85
36
37
4.678309
CGAGCGAGAGAGGGAAAACTTTAT
60.678
45.833
0.00
0.00
0.00
1.40
37
38
5.167303
AGCGAGAGAGGGAAAACTTTATT
57.833
39.130
0.00
0.00
0.00
1.40
38
39
5.561679
AGCGAGAGAGGGAAAACTTTATTT
58.438
37.500
0.00
0.00
0.00
1.40
39
40
6.004574
AGCGAGAGAGGGAAAACTTTATTTT
58.995
36.000
0.00
0.00
0.00
1.82
40
41
6.490381
AGCGAGAGAGGGAAAACTTTATTTTT
59.510
34.615
0.00
0.00
0.00
1.94
41
42
6.802348
GCGAGAGAGGGAAAACTTTATTTTTC
59.198
38.462
0.00
0.58
42.45
2.29
42
43
7.308649
GCGAGAGAGGGAAAACTTTATTTTTCT
60.309
37.037
7.94
0.00
42.68
2.52
43
44
8.017946
CGAGAGAGGGAAAACTTTATTTTTCTG
58.982
37.037
7.94
0.00
42.68
3.02
44
45
8.996651
AGAGAGGGAAAACTTTATTTTTCTGA
57.003
30.769
7.94
0.00
42.68
3.27
64
65
7.351414
TCTGAATATGTTTGAAGAAGTCGTG
57.649
36.000
0.00
0.00
0.00
4.35
69
70
3.057019
TGTTTGAAGAAGTCGTGGATCG
58.943
45.455
0.00
0.00
41.41
3.69
90
91
2.273588
TTAATAGGGGCCCGGTGTGC
62.274
60.000
18.95
0.00
0.00
4.57
151
152
3.119495
GGTGCACACTACAAAATCCCATC
60.119
47.826
20.43
0.00
0.00
3.51
154
155
3.627577
GCACACTACAAAATCCCATCGAT
59.372
43.478
0.00
0.00
0.00
3.59
198
199
9.378551
TGTATTTTAGTCATCGATTAAAGTGCT
57.621
29.630
0.00
0.00
28.53
4.40
201
202
6.662414
TTAGTCATCGATTAAAGTGCTTGG
57.338
37.500
0.00
0.00
0.00
3.61
202
203
3.941483
AGTCATCGATTAAAGTGCTTGGG
59.059
43.478
0.00
0.00
0.00
4.12
211
212
6.349777
CGATTAAAGTGCTTGGGTTGGATTAA
60.350
38.462
0.00
0.00
0.00
1.40
217
218
3.768757
TGCTTGGGTTGGATTAAATCTGG
59.231
43.478
0.00
0.00
0.00
3.86
231
232
1.496060
ATCTGGCCGTAACCATCTCA
58.504
50.000
0.00
0.00
39.54
3.27
237
238
1.859080
GCCGTAACCATCTCAATCGAC
59.141
52.381
0.00
0.00
0.00
4.20
254
255
3.521560
TCGACCAACAATATGTGAGCTC
58.478
45.455
6.82
6.82
0.00
4.09
267
268
2.231235
TGTGAGCTCGTACACACATGAT
59.769
45.455
9.64
0.00
41.19
2.45
274
275
4.202020
GCTCGTACACACATGATAAGAGGA
60.202
45.833
0.00
0.00
0.00
3.71
275
276
5.500645
TCGTACACACATGATAAGAGGAG
57.499
43.478
0.00
0.00
0.00
3.69
281
282
4.406972
CACACATGATAAGAGGAGGGAAGA
59.593
45.833
0.00
0.00
0.00
2.87
307
308
4.499696
CCCGAGAAGTTCAAACAAATTGCT
60.500
41.667
5.50
0.00
38.98
3.91
366
367
8.024865
TCAACAATTAAGAACATGATCTGCTTG
58.975
33.333
6.22
12.00
0.00
4.01
370
371
9.282247
CAATTAAGAACATGATCTGCTTGTTAC
57.718
33.333
6.22
0.00
42.77
2.50
374
375
7.175347
AGAACATGATCTGCTTGTTACTAGA
57.825
36.000
4.45
0.00
42.77
2.43
378
379
8.067751
ACATGATCTGCTTGTTACTAGAACTA
57.932
34.615
0.00
0.00
31.44
2.24
381
382
7.763356
TGATCTGCTTGTTACTAGAACTAGAC
58.237
38.462
14.64
5.14
36.97
2.59
462
463
2.093658
TGGACGGGACTAATCTTTGAGC
60.094
50.000
0.00
0.00
0.00
4.26
496
500
5.049405
TGCGATTTTTCTCTCCTTGAAAGTC
60.049
40.000
0.00
0.00
35.27
3.01
502
506
7.568199
TTTTCTCTCCTTGAAAGTCGATTTT
57.432
32.000
5.50
5.50
35.27
1.82
531
535
2.802816
CAATTGGAGGCATAGCTCGTAC
59.197
50.000
0.00
0.00
0.00
3.67
532
536
1.776662
TTGGAGGCATAGCTCGTACT
58.223
50.000
0.00
0.00
0.00
2.73
535
539
2.158652
TGGAGGCATAGCTCGTACTACT
60.159
50.000
0.00
0.00
0.00
2.57
536
540
3.072038
TGGAGGCATAGCTCGTACTACTA
59.928
47.826
0.00
0.00
0.00
1.82
537
541
3.436359
GGAGGCATAGCTCGTACTACTAC
59.564
52.174
0.00
0.00
0.00
2.73
539
543
2.805099
GGCATAGCTCGTACTACTACGT
59.195
50.000
0.00
0.00
45.14
3.57
540
544
3.363772
GGCATAGCTCGTACTACTACGTG
60.364
52.174
0.00
1.85
45.14
4.49
541
545
3.363772
GCATAGCTCGTACTACTACGTGG
60.364
52.174
0.00
0.00
45.14
4.94
542
546
1.012841
AGCTCGTACTACTACGTGGC
58.987
55.000
0.00
11.26
45.14
5.01
543
547
0.315706
GCTCGTACTACTACGTGGCG
60.316
60.000
0.00
0.00
45.14
5.69
587
591
2.821969
CCTGGGGATGTCAAGTCTTTTG
59.178
50.000
0.00
0.00
0.00
2.44
653
662
2.038557
ACTCAACTAATGAAGCCACGGT
59.961
45.455
0.00
0.00
37.67
4.83
701
711
4.744137
TGCACGGATCAAACATTCAAAAAG
59.256
37.500
0.00
0.00
0.00
2.27
714
725
4.759516
TTCAAAAAGATTAGCACGGACC
57.240
40.909
0.00
0.00
0.00
4.46
760
774
2.601194
TTTGACTCTGCGGCCACACA
62.601
55.000
2.24
0.00
0.00
3.72
870
890
0.120377
TAACCCTCCATGTGACCCCT
59.880
55.000
0.00
0.00
0.00
4.79
1540
2245
1.005394
TTCAACGAGTTCGAGGGCC
60.005
57.895
8.72
0.00
43.02
5.80
1789
2494
1.225704
GGGATGCTCAGGAAGGTGG
59.774
63.158
0.00
0.00
0.00
4.61
2089
2794
2.356313
CGTTCGACTGCAGCAGGT
60.356
61.111
26.38
11.96
35.51
4.00
2102
2807
3.051210
CAGGTCGCAGTGTCAGGA
58.949
61.111
0.00
0.00
0.00
3.86
2104
2809
0.036952
CAGGTCGCAGTGTCAGGAAT
60.037
55.000
0.00
0.00
0.00
3.01
2107
2812
1.354040
GTCGCAGTGTCAGGAATCAG
58.646
55.000
0.00
0.00
0.00
2.90
2110
2815
1.085091
GCAGTGTCAGGAATCAGCAG
58.915
55.000
0.00
0.00
0.00
4.24
2111
2816
1.735386
CAGTGTCAGGAATCAGCAGG
58.265
55.000
0.00
0.00
0.00
4.85
2136
2841
2.825836
CCAGGCAAGGGATCGCAC
60.826
66.667
12.83
0.87
0.00
5.34
2137
2842
3.197790
CAGGCAAGGGATCGCACG
61.198
66.667
12.83
3.39
0.00
5.34
2138
2843
4.473520
AGGCAAGGGATCGCACGG
62.474
66.667
12.83
1.99
0.00
4.94
2139
2844
4.467084
GGCAAGGGATCGCACGGA
62.467
66.667
12.83
0.00
0.00
4.69
2191
2896
3.833645
CGAGGGGCCATCGTCGAA
61.834
66.667
30.65
0.00
44.61
3.71
2192
2897
2.107141
GAGGGGCCATCGTCGAAG
59.893
66.667
4.39
0.00
0.00
3.79
2194
2899
3.782443
GGGGCCATCGTCGAAGGT
61.782
66.667
17.19
0.00
0.00
3.50
2195
2900
2.202892
GGGCCATCGTCGAAGGTC
60.203
66.667
17.19
15.01
0.00
3.85
2196
2901
2.582498
GGCCATCGTCGAAGGTCG
60.582
66.667
17.19
0.00
42.10
4.79
2197
2902
3.255379
GCCATCGTCGAAGGTCGC
61.255
66.667
17.19
0.29
40.21
5.19
2200
2905
4.849329
ATCGTCGAAGGTCGCCGC
62.849
66.667
0.00
0.00
41.26
6.53
2371
3097
4.394712
CCTCCTCCGCACCACCAC
62.395
72.222
0.00
0.00
0.00
4.16
2557
3283
3.650950
CACCACCCCCTCCACCAG
61.651
72.222
0.00
0.00
0.00
4.00
2595
3354
3.036429
ATCCTCTCCACCAAGCGGC
62.036
63.158
0.00
0.00
34.57
6.53
2770
3529
2.270205
CTCCAATGCCGCTGGTCT
59.730
61.111
0.00
0.00
35.30
3.85
2778
3537
4.143333
CCGCTGGTCTACGGGGTG
62.143
72.222
0.00
0.00
45.74
4.61
2781
3540
2.882876
CTGGTCTACGGGGTGTCG
59.117
66.667
0.00
0.00
0.00
4.35
2929
3692
4.767255
CCAGCCAGCCAGTCCGTC
62.767
72.222
0.00
0.00
0.00
4.79
2930
3693
4.767255
CAGCCAGCCAGTCCGTCC
62.767
72.222
0.00
0.00
0.00
4.79
2933
3696
4.436998
CCAGCCAGTCCGTCCGTC
62.437
72.222
0.00
0.00
0.00
4.79
2934
3697
4.436998
CAGCCAGTCCGTCCGTCC
62.437
72.222
0.00
0.00
0.00
4.79
2937
3700
3.677648
CCAGTCCGTCCGTCCGTT
61.678
66.667
0.00
0.00
0.00
4.44
2938
3701
2.126580
CAGTCCGTCCGTCCGTTC
60.127
66.667
0.00
0.00
0.00
3.95
2939
3702
3.730761
AGTCCGTCCGTCCGTTCG
61.731
66.667
0.00
0.00
0.00
3.95
2940
3703
4.030452
GTCCGTCCGTCCGTTCGT
62.030
66.667
0.00
0.00
0.00
3.85
2941
3704
3.726517
TCCGTCCGTCCGTTCGTC
61.727
66.667
0.00
0.00
0.00
4.20
2942
3705
4.766088
CCGTCCGTCCGTTCGTCC
62.766
72.222
0.00
0.00
0.00
4.79
2944
3707
4.030452
GTCCGTCCGTTCGTCCGT
62.030
66.667
0.00
0.00
0.00
4.69
2945
3708
3.726517
TCCGTCCGTTCGTCCGTC
61.727
66.667
0.00
0.00
0.00
4.79
2946
3709
4.766088
CCGTCCGTTCGTCCGTCC
62.766
72.222
0.00
0.00
0.00
4.79
2948
3711
4.030452
GTCCGTTCGTCCGTCCGT
62.030
66.667
0.00
0.00
0.00
4.69
2949
3712
3.726517
TCCGTTCGTCCGTCCGTC
61.727
66.667
0.00
0.00
0.00
4.79
2950
3713
4.766088
CCGTTCGTCCGTCCGTCC
62.766
72.222
0.00
0.00
0.00
4.79
2952
3715
4.030452
GTTCGTCCGTCCGTCCGT
62.030
66.667
0.00
0.00
0.00
4.69
2953
3716
4.029186
TTCGTCCGTCCGTCCGTG
62.029
66.667
0.00
0.00
0.00
4.94
2960
3723
4.773117
GTCCGTCCGTGGCTCGTC
62.773
72.222
8.25
0.35
37.94
4.20
2979
3754
2.092323
TCCGTCACCAGTACATCTCTG
58.908
52.381
0.00
0.00
0.00
3.35
2987
3762
3.027412
CCAGTACATCTCTGCCTGTAGT
58.973
50.000
0.00
0.00
32.94
2.73
2993
3768
4.573900
ACATCTCTGCCTGTAGTTTCTTG
58.426
43.478
0.00
0.00
0.00
3.02
2994
3769
3.045601
TCTCTGCCTGTAGTTTCTTGC
57.954
47.619
0.00
0.00
0.00
4.01
2995
3770
2.634940
TCTCTGCCTGTAGTTTCTTGCT
59.365
45.455
0.00
0.00
0.00
3.91
2997
3772
2.634940
TCTGCCTGTAGTTTCTTGCTCT
59.365
45.455
0.00
0.00
0.00
4.09
2999
3774
2.289694
TGCCTGTAGTTTCTTGCTCTCC
60.290
50.000
0.00
0.00
0.00
3.71
3000
3775
2.027653
GCCTGTAGTTTCTTGCTCTCCT
60.028
50.000
0.00
0.00
0.00
3.69
3006
3781
2.831526
AGTTTCTTGCTCTCCTCCTCTC
59.168
50.000
0.00
0.00
0.00
3.20
3011
3786
0.707024
TGCTCTCCTCCTCTCCTTGA
59.293
55.000
0.00
0.00
0.00
3.02
3022
3797
5.705905
CCTCCTCTCCTTGAACGTTATTTTT
59.294
40.000
0.00
0.00
0.00
1.94
3086
3884
7.367285
CGAATTAAATTCCAAACAAGTCTCCA
58.633
34.615
0.00
0.00
35.89
3.86
3103
3901
2.985896
TCCACGGTGGATTCTTTCATC
58.014
47.619
25.53
0.00
42.67
2.92
3104
3902
2.304470
TCCACGGTGGATTCTTTCATCA
59.696
45.455
25.53
0.00
42.67
3.07
3105
3903
3.054434
TCCACGGTGGATTCTTTCATCAT
60.054
43.478
25.53
0.00
42.67
2.45
3108
3906
5.335127
CACGGTGGATTCTTTCATCATTTC
58.665
41.667
0.00
0.00
0.00
2.17
3115
3917
9.264719
GTGGATTCTTTCATCATTTCTGTTTTT
57.735
29.630
0.00
0.00
0.00
1.94
3136
3938
1.171549
TGCTCGATTGCTGTTTGCCA
61.172
50.000
0.00
0.00
42.00
4.92
3138
3940
0.877071
CTCGATTGCTGTTTGCCACT
59.123
50.000
0.00
0.00
42.00
4.00
3141
3943
0.037975
GATTGCTGTTTGCCACTGGG
60.038
55.000
0.00
0.00
42.00
4.45
3153
3955
2.207189
ACTGGGCACTGGGGTACT
59.793
61.111
0.00
0.00
0.00
2.73
3154
3956
0.907704
CACTGGGCACTGGGGTACTA
60.908
60.000
0.00
0.00
0.00
1.82
3158
3960
0.989602
GGGCACTGGGGTACTAGTTT
59.010
55.000
0.00
0.00
0.00
2.66
3166
3968
2.916934
TGGGGTACTAGTTTCCATGCTT
59.083
45.455
0.00
0.00
0.00
3.91
3227
4124
2.260154
TGGTTGTGGCATGCACGAG
61.260
57.895
21.36
0.00
0.00
4.18
3231
4128
3.857854
GTGGCATGCACGAGCGAG
61.858
66.667
21.36
0.00
46.23
5.03
3261
4162
0.247419
CATGCATGCGAGAACACGTC
60.247
55.000
14.93
0.00
35.59
4.34
3287
4188
1.709760
CACACGAGTTATGCTGGCG
59.290
57.895
0.00
0.00
0.00
5.69
3366
4275
3.897239
TGCCTAATGAATGGAACGGATT
58.103
40.909
0.00
0.00
0.00
3.01
3427
4336
3.317993
GTGGCGCCATTTATTTACTCCAT
59.682
43.478
35.23
0.00
0.00
3.41
3429
4338
3.308530
GCGCCATTTATTTACTCCATGC
58.691
45.455
0.00
0.00
0.00
4.06
3450
4359
1.388065
ATGGACTTCGAGCCTCTCCG
61.388
60.000
0.00
0.00
0.00
4.63
3451
4360
2.776913
GGACTTCGAGCCTCTCCGG
61.777
68.421
0.00
0.00
0.00
5.14
3452
4361
2.035940
ACTTCGAGCCTCTCCGGT
59.964
61.111
0.00
0.00
34.25
5.28
3458
4367
3.966930
GAGCCTCTCCGGTGGGTCT
62.967
68.421
24.57
10.68
45.00
3.85
3459
4368
3.462678
GCCTCTCCGGTGGGTCTC
61.463
72.222
0.00
0.00
34.25
3.36
3461
4370
2.037367
CTCTCCGGTGGGTCTCCA
59.963
66.667
0.00
0.00
41.58
3.86
3469
4378
2.447572
TGGGTCTCCACAGGTGCA
60.448
61.111
0.00
0.00
38.32
4.57
3525
4434
4.345859
ACCAGAACGTTATGACTTGGAA
57.654
40.909
23.78
0.00
0.00
3.53
3528
4437
4.627467
CCAGAACGTTATGACTTGGAAGAG
59.373
45.833
23.78
0.00
0.00
2.85
3532
4441
4.566987
ACGTTATGACTTGGAAGAGGTTC
58.433
43.478
0.00
0.00
0.00
3.62
3533
4442
4.283722
ACGTTATGACTTGGAAGAGGTTCT
59.716
41.667
0.00
0.00
32.72
3.01
3570
4498
2.955614
TCTTTCGAGGTCCGTGATTTC
58.044
47.619
0.00
0.00
39.75
2.17
3592
4528
2.362503
ACGTGGGAGCGGATGAGA
60.363
61.111
0.00
0.00
35.98
3.27
3595
4531
3.157252
TGGGAGCGGATGAGAGGC
61.157
66.667
0.00
0.00
0.00
4.70
3596
4532
3.934962
GGGAGCGGATGAGAGGCC
61.935
72.222
0.00
0.00
0.00
5.19
3614
4550
1.312815
CCCTAGTAATTGCTGCCTGC
58.687
55.000
6.28
0.00
43.25
4.85
3615
4551
1.312815
CCTAGTAATTGCTGCCTGCC
58.687
55.000
6.28
0.00
42.00
4.85
3616
4552
1.408683
CCTAGTAATTGCTGCCTGCCA
60.409
52.381
6.28
0.00
42.00
4.92
3617
4553
1.945394
CTAGTAATTGCTGCCTGCCAG
59.055
52.381
6.28
0.00
44.67
4.85
3660
4615
0.534877
TCTGCAACCACAACTGCGAT
60.535
50.000
0.00
0.00
41.63
4.58
3732
4698
4.662961
GCCGTTTGCCACCCAAGC
62.663
66.667
0.00
0.00
34.34
4.01
3733
4699
3.222855
CCGTTTGCCACCCAAGCA
61.223
61.111
0.00
0.00
38.81
3.91
3734
4700
2.027460
CGTTTGCCACCCAAGCAC
59.973
61.111
0.00
0.00
40.69
4.40
3787
4755
0.037790
GAGATCCTATGAGCGTGCCC
60.038
60.000
0.00
0.00
30.37
5.36
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
1.059681
CGCTCGAGTCTCTGTCGTC
59.940
63.158
15.13
0.00
38.60
4.20
1
2
1.355796
CTCGCTCGAGTCTCTGTCGT
61.356
60.000
15.13
0.00
38.60
4.34
2
3
1.079317
TCTCGCTCGAGTCTCTGTCG
61.079
60.000
15.13
7.15
42.49
4.35
3
4
0.650512
CTCTCGCTCGAGTCTCTGTC
59.349
60.000
15.13
0.00
42.49
3.51
4
5
0.248012
TCTCTCGCTCGAGTCTCTGT
59.752
55.000
15.13
0.00
42.49
3.41
5
6
0.930310
CTCTCTCGCTCGAGTCTCTG
59.070
60.000
15.13
2.59
42.49
3.35
6
7
0.179084
CCTCTCTCGCTCGAGTCTCT
60.179
60.000
15.13
0.00
42.49
3.10
7
8
1.157870
CCCTCTCTCGCTCGAGTCTC
61.158
65.000
15.13
0.00
42.49
3.36
9
10
0.745128
TTCCCTCTCTCGCTCGAGTC
60.745
60.000
15.13
5.54
42.49
3.36
10
11
0.322636
TTTCCCTCTCTCGCTCGAGT
60.323
55.000
15.13
0.00
42.49
4.18
11
12
0.811915
TTTTCCCTCTCTCGCTCGAG
59.188
55.000
8.45
8.45
43.21
4.04
12
13
0.526662
GTTTTCCCTCTCTCGCTCGA
59.473
55.000
0.00
0.00
0.00
4.04
13
14
0.528470
AGTTTTCCCTCTCTCGCTCG
59.472
55.000
0.00
0.00
0.00
5.03
14
15
2.753055
AAGTTTTCCCTCTCTCGCTC
57.247
50.000
0.00
0.00
0.00
5.03
15
16
4.828072
ATAAAGTTTTCCCTCTCTCGCT
57.172
40.909
0.00
0.00
0.00
4.93
16
17
5.881777
AAATAAAGTTTTCCCTCTCTCGC
57.118
39.130
0.00
0.00
0.00
5.03
17
18
8.017946
CAGAAAAATAAAGTTTTCCCTCTCTCG
58.982
37.037
10.93
0.00
44.93
4.04
18
19
9.067986
TCAGAAAAATAAAGTTTTCCCTCTCTC
57.932
33.333
10.93
0.00
44.93
3.20
19
20
8.996651
TCAGAAAAATAAAGTTTTCCCTCTCT
57.003
30.769
10.93
0.00
44.93
3.10
36
37
9.663904
CGACTTCTTCAAACATATTCAGAAAAA
57.336
29.630
0.00
0.00
0.00
1.94
37
38
8.836413
ACGACTTCTTCAAACATATTCAGAAAA
58.164
29.630
0.00
0.00
0.00
2.29
38
39
8.282592
CACGACTTCTTCAAACATATTCAGAAA
58.717
33.333
0.00
0.00
0.00
2.52
39
40
7.095229
CCACGACTTCTTCAAACATATTCAGAA
60.095
37.037
0.00
0.00
0.00
3.02
40
41
6.368791
CCACGACTTCTTCAAACATATTCAGA
59.631
38.462
0.00
0.00
0.00
3.27
41
42
6.368791
TCCACGACTTCTTCAAACATATTCAG
59.631
38.462
0.00
0.00
0.00
3.02
42
43
6.227522
TCCACGACTTCTTCAAACATATTCA
58.772
36.000
0.00
0.00
0.00
2.57
43
44
6.721571
TCCACGACTTCTTCAAACATATTC
57.278
37.500
0.00
0.00
0.00
1.75
44
45
6.036083
CGATCCACGACTTCTTCAAACATATT
59.964
38.462
0.00
0.00
45.77
1.28
64
65
1.134491
CGGGCCCCTATTAATCGATCC
60.134
57.143
18.66
0.00
0.00
3.36
69
70
0.769247
ACACCGGGCCCCTATTAATC
59.231
55.000
18.66
0.00
0.00
1.75
71
72
1.916738
CACACCGGGCCCCTATTAA
59.083
57.895
18.66
0.00
0.00
1.40
90
91
1.691196
TTGAGGGTTTCAAGGCACAG
58.309
50.000
0.00
0.00
40.82
3.66
145
146
1.679680
GAACGGTAGTGATCGATGGGA
59.320
52.381
0.54
0.00
31.88
4.37
151
152
3.551890
CAGATTTGGAACGGTAGTGATCG
59.448
47.826
0.00
0.00
34.43
3.69
154
155
5.670792
ATACAGATTTGGAACGGTAGTGA
57.329
39.130
0.00
0.00
0.00
3.41
191
192
5.543790
AGATTTAATCCAACCCAAGCACTTT
59.456
36.000
0.78
0.00
0.00
2.66
198
199
3.103742
GGCCAGATTTAATCCAACCCAA
58.896
45.455
0.00
0.00
0.00
4.12
199
200
2.745968
GGCCAGATTTAATCCAACCCA
58.254
47.619
0.00
0.00
0.00
4.51
200
201
1.681264
CGGCCAGATTTAATCCAACCC
59.319
52.381
2.24
0.00
0.00
4.11
201
202
2.375146
ACGGCCAGATTTAATCCAACC
58.625
47.619
2.24
0.07
0.00
3.77
202
203
4.201980
GGTTACGGCCAGATTTAATCCAAC
60.202
45.833
2.24
0.00
0.00
3.77
211
212
1.837439
TGAGATGGTTACGGCCAGATT
59.163
47.619
2.24
0.00
42.47
2.40
217
218
1.859080
GTCGATTGAGATGGTTACGGC
59.141
52.381
0.00
0.00
0.00
5.68
231
232
4.517285
AGCTCACATATTGTTGGTCGATT
58.483
39.130
0.00
0.00
0.00
3.34
237
238
4.032900
GTGTACGAGCTCACATATTGTTGG
59.967
45.833
15.40
0.00
35.04
3.77
254
255
4.499865
CCCTCCTCTTATCATGTGTGTACG
60.500
50.000
0.00
0.00
0.00
3.67
261
262
3.970640
GGTCTTCCCTCCTCTTATCATGT
59.029
47.826
0.00
0.00
0.00
3.21
281
282
0.841289
TGTTTGAACTTCTCGGGGGT
59.159
50.000
0.00
0.00
0.00
4.95
344
345
9.282247
GTAACAAGCAGATCATGTTCTTAATTG
57.718
33.333
3.44
10.76
37.69
2.32
345
346
9.236006
AGTAACAAGCAGATCATGTTCTTAATT
57.764
29.630
3.44
0.00
37.69
1.40
347
348
9.371136
CTAGTAACAAGCAGATCATGTTCTTAA
57.629
33.333
3.44
0.00
37.69
1.85
350
351
7.175347
TCTAGTAACAAGCAGATCATGTTCT
57.825
36.000
0.16
0.16
37.69
3.01
432
433
2.249309
AGTCCCGTCCATTAGACCTT
57.751
50.000
0.00
0.00
43.08
3.50
496
500
4.277257
TCCAATTGCTCATCGAAAATCG
57.723
40.909
0.00
0.00
42.10
3.34
502
506
0.252761
TGCCTCCAATTGCTCATCGA
59.747
50.000
0.00
0.00
0.00
3.59
531
535
1.722636
GAGGGGACGCCACGTAGTAG
61.723
65.000
11.67
0.00
41.61
2.57
532
536
1.750399
GAGGGGACGCCACGTAGTA
60.750
63.158
11.67
0.00
41.61
1.82
541
545
1.158484
GCGATTTAAGGAGGGGACGC
61.158
60.000
0.00
0.00
38.23
5.19
542
546
0.464452
AGCGATTTAAGGAGGGGACG
59.536
55.000
0.00
0.00
0.00
4.79
543
547
1.954927
CAGCGATTTAAGGAGGGGAC
58.045
55.000
0.00
0.00
0.00
4.46
587
591
1.425428
GTGCGAACCATGTAGCTGC
59.575
57.895
0.00
0.00
0.00
5.25
653
662
5.351948
TCGAATCAGTGGTAAATGGATGA
57.648
39.130
0.00
0.00
0.00
2.92
701
711
3.006940
TGATGTTTGGTCCGTGCTAATC
58.993
45.455
0.00
0.00
0.00
1.75
714
725
0.717896
CGTGTGCGTCGTGATGTTTG
60.718
55.000
0.00
0.00
0.00
2.93
743
757
3.545574
TGTGTGGCCGCAGAGTCA
61.546
61.111
21.93
11.57
0.00
3.41
1789
2494
2.778679
GCTGACATCGAACACGGC
59.221
61.111
0.00
0.00
0.00
5.68
1920
2625
0.540830
AGTTCCTCAGACTCGGCAGT
60.541
55.000
0.00
0.00
34.57
4.40
2064
2769
4.379243
CAGTCGAACGGGCTGGCT
62.379
66.667
0.00
0.00
0.00
4.75
2089
2794
0.390340
GCTGATTCCTGACACTGCGA
60.390
55.000
0.00
0.00
0.00
5.10
2094
2799
1.028868
GCCCTGCTGATTCCTGACAC
61.029
60.000
0.00
0.00
0.00
3.67
2102
2807
4.453892
GGCCTGGCCCTGCTGATT
62.454
66.667
27.77
0.00
44.06
2.57
2119
2824
2.825836
GTGCGATCCCTTGCCTGG
60.826
66.667
0.00
0.00
0.00
4.45
2120
2825
3.197790
CGTGCGATCCCTTGCCTG
61.198
66.667
0.00
0.00
0.00
4.85
2121
2826
4.473520
CCGTGCGATCCCTTGCCT
62.474
66.667
0.00
0.00
0.00
4.75
2122
2827
4.467084
TCCGTGCGATCCCTTGCC
62.467
66.667
0.00
0.00
0.00
4.52
2125
2830
4.162690
GCCTCCGTGCGATCCCTT
62.163
66.667
0.00
0.00
0.00
3.95
2179
2884
2.582498
CGACCTTCGACGATGGCC
60.582
66.667
25.16
16.13
43.74
5.36
2202
2907
2.033602
GTAAACCAGCCTGGCGGT
59.966
61.111
23.39
23.39
42.67
5.68
2313
3039
4.988716
TCGCTGTGGGTCGGAGGT
62.989
66.667
0.00
0.00
0.00
3.85
2316
3042
3.062466
CTCTCGCTGTGGGTCGGA
61.062
66.667
0.00
0.00
0.00
4.55
2424
3150
2.668550
GGTTGGTGACTGGACGGC
60.669
66.667
0.00
0.00
0.00
5.68
2754
3513
1.220749
GTAGACCAGCGGCATTGGA
59.779
57.895
14.49
0.00
39.08
3.53
2765
3524
0.960364
GTACGACACCCCGTAGACCA
60.960
60.000
0.00
0.00
44.40
4.02
2770
3529
2.749839
CCCGTACGACACCCCGTA
60.750
66.667
18.76
0.00
43.20
4.02
2775
3534
4.783734
GGCGACCCGTACGACACC
62.784
72.222
18.76
6.92
38.75
4.16
2920
3683
3.621892
GAACGGACGGACGGACTGG
62.622
68.421
6.00
0.00
38.39
4.00
2922
3685
3.730761
CGAACGGACGGACGGACT
61.731
66.667
6.00
0.00
38.39
3.85
2927
3690
3.935665
GACGGACGAACGGACGGAC
62.936
68.421
14.41
6.96
38.39
4.79
2928
3691
3.726517
GACGGACGAACGGACGGA
61.727
66.667
14.41
0.00
38.39
4.69
2929
3692
4.766088
GGACGGACGAACGGACGG
62.766
72.222
14.41
8.07
38.39
4.79
2931
3694
3.935665
GACGGACGGACGAACGGAC
62.936
68.421
8.01
6.96
38.39
4.79
2932
3695
3.726517
GACGGACGGACGAACGGA
61.727
66.667
8.01
0.00
38.39
4.69
2933
3696
4.766088
GGACGGACGGACGAACGG
62.766
72.222
8.01
8.07
38.39
4.44
2935
3698
4.030452
ACGGACGGACGGACGAAC
62.030
66.667
15.02
2.13
38.39
3.95
2936
3699
4.029186
CACGGACGGACGGACGAA
62.029
66.667
15.02
0.00
38.39
3.85
2951
3714
3.916392
CTGGTGACGGACGAGCCAC
62.916
68.421
0.00
3.72
39.98
5.01
2952
3715
3.680786
CTGGTGACGGACGAGCCA
61.681
66.667
0.00
2.93
39.98
4.75
2953
3716
2.338015
TACTGGTGACGGACGAGCC
61.338
63.158
0.00
0.00
41.09
4.70
2954
3717
1.154073
GTACTGGTGACGGACGAGC
60.154
63.158
0.00
0.00
41.09
5.03
2955
3718
0.809385
ATGTACTGGTGACGGACGAG
59.191
55.000
0.00
0.00
41.09
4.18
2956
3719
0.806868
GATGTACTGGTGACGGACGA
59.193
55.000
0.00
0.00
41.09
4.20
2957
3720
0.809385
AGATGTACTGGTGACGGACG
59.191
55.000
0.00
0.00
41.09
4.79
2958
3721
2.093106
AGAGATGTACTGGTGACGGAC
58.907
52.381
0.00
0.00
41.09
4.79
2959
3722
2.092323
CAGAGATGTACTGGTGACGGA
58.908
52.381
0.00
0.00
41.09
4.69
2960
3723
1.469940
GCAGAGATGTACTGGTGACGG
60.470
57.143
0.00
0.00
44.60
4.79
2979
3754
2.027653
AGGAGAGCAAGAAACTACAGGC
60.028
50.000
0.00
0.00
0.00
4.85
2987
3762
2.183679
GGAGAGGAGGAGAGCAAGAAA
58.816
52.381
0.00
0.00
0.00
2.52
2993
3768
1.480545
GTTCAAGGAGAGGAGGAGAGC
59.519
57.143
0.00
0.00
0.00
4.09
2994
3769
1.748493
CGTTCAAGGAGAGGAGGAGAG
59.252
57.143
0.00
0.00
0.00
3.20
2995
3770
1.075698
ACGTTCAAGGAGAGGAGGAGA
59.924
52.381
0.00
0.00
0.00
3.71
2997
3772
2.011122
AACGTTCAAGGAGAGGAGGA
57.989
50.000
0.00
0.00
0.00
3.71
2999
3774
6.803154
AAAAATAACGTTCAAGGAGAGGAG
57.197
37.500
2.82
0.00
0.00
3.69
3022
3797
5.913137
AACAAATGGACAACAGAGAACAA
57.087
34.783
0.00
0.00
0.00
2.83
3076
3874
4.288234
TCCACCGTGGAGACTTGT
57.712
55.556
16.73
0.00
42.67
3.16
3086
3884
5.124457
CAGAAATGATGAAAGAATCCACCGT
59.876
40.000
0.00
0.00
0.00
4.83
3115
3917
1.769733
GCAAACAGCAATCGAGCAAA
58.230
45.000
0.00
0.00
44.79
3.68
3136
3938
0.617820
CTAGTACCCCAGTGCCCAGT
60.618
60.000
0.00
0.00
0.00
4.00
3138
3940
0.178885
AACTAGTACCCCAGTGCCCA
60.179
55.000
0.00
0.00
0.00
5.36
3141
3943
1.626825
TGGAAACTAGTACCCCAGTGC
59.373
52.381
13.99
0.00
0.00
4.40
3142
3944
3.873910
CATGGAAACTAGTACCCCAGTG
58.126
50.000
13.99
9.62
0.00
3.66
3143
3945
2.238898
GCATGGAAACTAGTACCCCAGT
59.761
50.000
13.99
0.00
0.00
4.00
3144
3946
2.505819
AGCATGGAAACTAGTACCCCAG
59.494
50.000
13.99
7.05
0.00
4.45
3145
3947
2.557869
AGCATGGAAACTAGTACCCCA
58.442
47.619
13.99
12.83
0.00
4.96
3147
3949
4.216411
TCAAGCATGGAAACTAGTACCC
57.784
45.455
13.99
10.46
0.00
3.69
3148
3950
5.741388
CATCAAGCATGGAAACTAGTACC
57.259
43.478
10.86
10.86
0.00
3.34
3166
3968
3.172229
TGCGTCGTTATTCATCCATCA
57.828
42.857
0.00
0.00
0.00
3.07
3197
3999
2.380285
ACAACCACCGGTCCAAGGT
61.380
57.895
2.59
6.25
43.97
3.50
3227
4124
1.947013
CATGCATGTGATCCCTCGC
59.053
57.895
18.91
0.00
0.00
5.03
3231
4128
3.886044
CATGCATGCATGTGATCCC
57.114
52.632
40.30
10.36
46.20
3.85
3287
4188
9.307121
ACACTATGTATAGTATCGTATCGTACC
57.693
37.037
4.35
0.00
41.44
3.34
3300
4201
9.083422
ACTGCTTATCATCACACTATGTATAGT
57.917
33.333
0.00
0.00
44.03
2.12
3301
4202
9.351570
CACTGCTTATCATCACACTATGTATAG
57.648
37.037
0.00
0.00
36.46
1.31
3302
4203
9.077885
TCACTGCTTATCATCACACTATGTATA
57.922
33.333
0.00
0.00
0.00
1.47
3366
4275
9.613428
CCCTAATTGACTAGTCATTCAACATTA
57.387
33.333
25.68
20.99
39.64
1.90
3427
4336
0.391661
GAGGCTCGAAGTCCATTGCA
60.392
55.000
0.00
0.00
0.00
4.08
3429
4338
1.472376
GGAGAGGCTCGAAGTCCATTG
60.472
57.143
13.93
0.00
0.00
2.82
3452
4361
2.447572
TGCACCTGTGGAGACCCA
60.448
61.111
0.00
0.00
40.95
4.51
3458
4367
2.421314
CACGTCTGCACCTGTGGA
59.579
61.111
0.00
0.00
0.00
4.02
3459
4368
3.349006
GCACGTCTGCACCTGTGG
61.349
66.667
8.91
0.00
43.62
4.17
3467
4376
0.318699
TCACTGTACTGCACGTCTGC
60.319
55.000
0.00
0.00
44.52
4.26
3468
4377
2.134201
TTCACTGTACTGCACGTCTG
57.866
50.000
0.00
0.00
0.00
3.51
3469
4378
2.558795
AGATTCACTGTACTGCACGTCT
59.441
45.455
0.00
0.00
0.00
4.18
3570
4498
1.079127
ATCCGCTCCCACGTGAAAG
60.079
57.895
19.30
14.56
0.00
2.62
3592
4528
0.183731
GGCAGCAATTACTAGGGCCT
59.816
55.000
12.58
12.58
37.00
5.19
3595
4531
1.312815
GCAGGCAGCAATTACTAGGG
58.687
55.000
0.00
0.00
44.79
3.53
3660
4615
2.983030
AGGCCGACGCAATTGCAA
60.983
55.556
28.77
0.00
42.21
4.08
3730
4696
5.978814
AGTAATTAACTCCGATCAAGTGCT
58.021
37.500
0.00
0.00
30.33
4.40
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.