Multiple sequence alignment - TraesCS3B01G246500
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
TraesCS3B01G246500
chr3B
100.000
5203
0
0
1
5203
392293123
392298325
0.000000e+00
9609.0
1
TraesCS3B01G246500
chr3D
94.314
3957
131
34
878
4786
297491458
297495368
0.000000e+00
5975.0
2
TraesCS3B01G246500
chr3D
87.077
828
70
22
1
794
16121057
16121881
0.000000e+00
902.0
3
TraesCS3B01G246500
chr3D
86.506
830
71
24
1
793
468665341
468666166
0.000000e+00
874.0
4
TraesCS3B01G246500
chr3D
85.612
834
72
21
1
793
182085531
182084705
0.000000e+00
832.0
5
TraesCS3B01G246500
chr3D
96.471
425
10
1
4784
5203
297495413
297495837
0.000000e+00
697.0
6
TraesCS3B01G246500
chr3D
95.522
67
2
1
815
881
297491369
297491434
7.130000e-19
106.0
7
TraesCS3B01G246500
chr3A
93.745
2302
77
23
2946
5203
391474844
391472566
0.000000e+00
3391.0
8
TraesCS3B01G246500
chr3A
90.775
1496
61
34
893
2350
391476928
391475472
0.000000e+00
1927.0
9
TraesCS3B01G246500
chr3A
97.482
556
12
1
2350
2905
391475392
391474839
0.000000e+00
948.0
10
TraesCS3B01G246500
chr6D
87.273
825
71
21
1
793
100211631
100212453
0.000000e+00
911.0
11
TraesCS3B01G246500
chr5D
87.742
775
68
18
39
793
489756054
489755287
0.000000e+00
880.0
12
TraesCS3B01G246500
chr5D
87.047
772
71
17
39
793
525156318
525155559
0.000000e+00
845.0
13
TraesCS3B01G246500
chr5D
85.841
791
72
24
39
793
474543330
474542544
0.000000e+00
804.0
14
TraesCS3B01G246500
chr7D
86.445
841
62
32
1
793
154002285
154001449
0.000000e+00
874.0
15
TraesCS3B01G246500
chr7D
86.565
789
65
15
39
793
508795841
508795060
0.000000e+00
832.0
16
TraesCS3B01G246500
chr7D
85.612
834
72
21
1
793
574240750
574241576
0.000000e+00
832.0
17
TraesCS3B01G246500
chr2B
86.038
838
74
23
1
797
54453034
54453869
0.000000e+00
859.0
18
TraesCS3B01G246500
chr4A
85.663
837
66
32
1
793
693356029
693356855
0.000000e+00
832.0
19
TraesCS3B01G246500
chr4A
87.145
669
77
4
126
793
65493963
65494623
0.000000e+00
750.0
20
TraesCS3B01G246500
chr1D
85.714
791
73
24
39
793
481960845
481961631
0.000000e+00
798.0
21
TraesCS3B01G246500
chr1D
94.118
34
2
0
2997
3030
318118771
318118738
9.000000e-03
52.8
22
TraesCS3B01G246500
chr6B
84.184
784
84
27
40
793
609120130
609119357
0.000000e+00
725.0
23
TraesCS3B01G246500
chr6B
91.892
37
3
0
2961
2997
52988159
52988123
9.000000e-03
52.8
24
TraesCS3B01G246500
chr6A
78.873
284
40
11
4067
4334
52719441
52719720
1.930000e-39
174.0
25
TraesCS3B01G246500
chr5A
76.451
293
39
14
4067
4334
452925341
452925628
1.180000e-26
132.0
26
TraesCS3B01G246500
chr1B
100.000
28
0
0
2961
2988
129884873
129884846
9.000000e-03
52.8
27
TraesCS3B01G246500
chr1B
100.000
28
0
0
2961
2988
557130316
557130343
9.000000e-03
52.8
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
TraesCS3B01G246500
chr3B
392293123
392298325
5202
False
9609.000000
9609
100.000000
1
5203
1
chr3B.!!$F1
5202
1
TraesCS3B01G246500
chr3D
297491369
297495837
4468
False
2259.333333
5975
95.435667
815
5203
3
chr3D.!!$F3
4388
2
TraesCS3B01G246500
chr3D
16121057
16121881
824
False
902.000000
902
87.077000
1
794
1
chr3D.!!$F1
793
3
TraesCS3B01G246500
chr3D
468665341
468666166
825
False
874.000000
874
86.506000
1
793
1
chr3D.!!$F2
792
4
TraesCS3B01G246500
chr3D
182084705
182085531
826
True
832.000000
832
85.612000
1
793
1
chr3D.!!$R1
792
5
TraesCS3B01G246500
chr3A
391472566
391476928
4362
True
2088.666667
3391
94.000667
893
5203
3
chr3A.!!$R1
4310
6
TraesCS3B01G246500
chr6D
100211631
100212453
822
False
911.000000
911
87.273000
1
793
1
chr6D.!!$F1
792
7
TraesCS3B01G246500
chr5D
489755287
489756054
767
True
880.000000
880
87.742000
39
793
1
chr5D.!!$R2
754
8
TraesCS3B01G246500
chr5D
525155559
525156318
759
True
845.000000
845
87.047000
39
793
1
chr5D.!!$R3
754
9
TraesCS3B01G246500
chr5D
474542544
474543330
786
True
804.000000
804
85.841000
39
793
1
chr5D.!!$R1
754
10
TraesCS3B01G246500
chr7D
154001449
154002285
836
True
874.000000
874
86.445000
1
793
1
chr7D.!!$R1
792
11
TraesCS3B01G246500
chr7D
508795060
508795841
781
True
832.000000
832
86.565000
39
793
1
chr7D.!!$R2
754
12
TraesCS3B01G246500
chr7D
574240750
574241576
826
False
832.000000
832
85.612000
1
793
1
chr7D.!!$F1
792
13
TraesCS3B01G246500
chr2B
54453034
54453869
835
False
859.000000
859
86.038000
1
797
1
chr2B.!!$F1
796
14
TraesCS3B01G246500
chr4A
693356029
693356855
826
False
832.000000
832
85.663000
1
793
1
chr4A.!!$F2
792
15
TraesCS3B01G246500
chr4A
65493963
65494623
660
False
750.000000
750
87.145000
126
793
1
chr4A.!!$F1
667
16
TraesCS3B01G246500
chr1D
481960845
481961631
786
False
798.000000
798
85.714000
39
793
1
chr1D.!!$F1
754
17
TraesCS3B01G246500
chr6B
609119357
609120130
773
True
725.000000
725
84.184000
40
793
1
chr6B.!!$R2
753
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
523
596
0.099791
GAGTAGCGTGGAGAGTGAGC
59.900
60.0
0.00
0.00
0.00
4.26
F
661
750
0.325933
TGGACCTGCCATGTCAGAAG
59.674
55.0
5.06
0.00
43.33
2.85
F
1805
1946
0.323178
AAGGGCAACAGCATCTCAGG
60.323
55.0
0.00
0.00
39.74
3.86
F
2020
2176
0.687354
GGGTCCAAGACTTGAGCTCA
59.313
55.0
13.74
13.74
32.47
4.26
F
3482
3718
1.774110
TGGCTTGCAAAAGTTCCTGA
58.226
45.0
0.00
0.00
0.00
3.86
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1716
1857
0.739813
GTAGCTTCCCGTCACGCAAT
60.740
55.0
0.00
0.00
0.00
3.56
R
2046
2202
0.847373
TAGGCGGCCATTATTTCCCA
59.153
50.0
23.09
0.00
0.00
4.37
R
3069
3305
1.453155
GTGTTGCCGATTCCTGTGAT
58.547
50.0
0.00
0.00
0.00
3.06
R
3815
4060
0.036483
TGCTTTCTCTATGTGCGCCA
60.036
50.0
4.18
2.31
0.00
5.69
R
4943
5266
1.362224
CCTTCTGGGACTTTGGAGGA
58.638
55.0
0.00
0.00
37.23
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
31
32
1.511850
TGTGCAGACAGTCCAAATCG
58.488
50.000
0.00
0.00
0.00
3.34
55
56
8.286800
TCGTGTTTCATTAACTGAATTTACTGG
58.713
33.333
2.52
0.00
43.30
4.00
107
126
5.887754
ACACAAACCCTAGTTGGATAACAT
58.112
37.500
0.00
0.00
39.30
2.71
120
139
7.121382
AGTTGGATAACATTGACATGAGGAAT
58.879
34.615
0.00
0.00
39.30
3.01
130
149
4.441792
TGACATGAGGAATAACACATCCG
58.558
43.478
0.00
0.00
40.78
4.18
145
164
0.105607
ATCCGTAGAACCTCCTCCCC
60.106
60.000
0.00
0.00
0.00
4.81
252
279
4.125703
CAGAAGGATGCATCTTAGTGGTC
58.874
47.826
25.28
12.29
0.00
4.02
346
375
4.937201
AATTGAAGAACACTTGAACCCC
57.063
40.909
0.00
0.00
0.00
4.95
357
387
1.146152
CTTGAACCCCAACCCTAACCA
59.854
52.381
0.00
0.00
0.00
3.67
416
446
1.142748
CCATGTCGACCAGCTCCTC
59.857
63.158
14.12
0.00
0.00
3.71
417
447
1.142748
CATGTCGACCAGCTCCTCC
59.857
63.158
14.12
0.00
0.00
4.30
418
448
1.000993
ATGTCGACCAGCTCCTCCT
59.999
57.895
14.12
0.00
0.00
3.69
510
574
0.686112
AGGGGACAGAGCAGAGTAGC
60.686
60.000
0.00
0.00
0.00
3.58
519
592
0.322997
AGCAGAGTAGCGTGGAGAGT
60.323
55.000
0.00
0.00
40.15
3.24
523
596
0.099791
GAGTAGCGTGGAGAGTGAGC
59.900
60.000
0.00
0.00
0.00
4.26
527
600
2.983930
GCGTGGAGAGTGAGCGAGT
61.984
63.158
0.00
0.00
0.00
4.18
551
630
2.574955
GGAGTGGAGTGTGAGCGGT
61.575
63.158
0.00
0.00
0.00
5.68
577
663
2.108250
AGTGGTGGGCTCTGTTTTGTAT
59.892
45.455
0.00
0.00
0.00
2.29
607
693
2.042404
TAACGGCCGTCAACCCAGTT
62.042
55.000
34.29
15.38
0.00
3.16
609
695
2.203294
GGCCGTCAACCCAGTTGT
60.203
61.111
7.30
0.00
43.23
3.32
661
750
0.325933
TGGACCTGCCATGTCAGAAG
59.674
55.000
5.06
0.00
43.33
2.85
707
796
9.757227
ACGGTCATTTGATTTTATTGAGAAAAA
57.243
25.926
0.00
0.00
32.29
1.94
783
872
4.430137
GATGCTTGAGCTTCAAATGTGA
57.570
40.909
12.42
0.00
42.61
3.58
819
908
5.880054
TTTTGCAATTCAGTCTAGTAGGC
57.120
39.130
0.00
0.00
0.00
3.93
820
909
4.551702
TTGCAATTCAGTCTAGTAGGCA
57.448
40.909
4.25
0.00
0.00
4.75
821
910
3.861840
TGCAATTCAGTCTAGTAGGCAC
58.138
45.455
4.25
0.00
0.00
5.01
822
911
2.860735
GCAATTCAGTCTAGTAGGCACG
59.139
50.000
4.25
0.00
0.00
5.34
823
912
3.676324
GCAATTCAGTCTAGTAGGCACGT
60.676
47.826
4.25
0.00
0.00
4.49
850
939
4.827087
AGATGCAGCGAGCCCACG
62.827
66.667
0.00
0.00
44.83
4.94
919
1035
3.123620
GAGTTGCTGCCGCTGGAG
61.124
66.667
0.70
0.00
36.97
3.86
949
1074
2.290705
GCCAGGGTGTAATGTAACCACT
60.291
50.000
0.00
0.00
38.27
4.00
968
1093
1.477295
CTCCGTCCTTCCACTTACTCC
59.523
57.143
0.00
0.00
0.00
3.85
1079
1204
4.131581
CTCGTCGTCGTCGTCGCT
62.132
66.667
15.28
0.00
44.86
4.93
1124
1249
1.559149
GCCGCTGAAAACCGTACGAA
61.559
55.000
18.76
0.00
0.00
3.85
1126
1251
0.854062
CGCTGAAAACCGTACGAACA
59.146
50.000
18.76
8.06
0.00
3.18
1149
1274
2.175931
TCCCCTTGCTTTGGTTTCTACA
59.824
45.455
0.00
0.00
0.00
2.74
1150
1275
2.296190
CCCCTTGCTTTGGTTTCTACAC
59.704
50.000
0.00
0.00
0.00
2.90
1151
1276
2.955660
CCCTTGCTTTGGTTTCTACACA
59.044
45.455
0.00
0.00
0.00
3.72
1152
1277
3.573967
CCCTTGCTTTGGTTTCTACACAT
59.426
43.478
0.00
0.00
0.00
3.21
1153
1278
4.764823
CCCTTGCTTTGGTTTCTACACATA
59.235
41.667
0.00
0.00
0.00
2.29
1154
1279
5.335661
CCCTTGCTTTGGTTTCTACACATAC
60.336
44.000
0.00
0.00
0.00
2.39
1155
1280
5.240623
CCTTGCTTTGGTTTCTACACATACA
59.759
40.000
0.00
0.00
0.00
2.29
1159
1284
6.937465
TGCTTTGGTTTCTACACATACATACA
59.063
34.615
0.00
0.00
0.00
2.29
1181
1306
0.825010
CTGCAGTTTCCTTGCCCACT
60.825
55.000
5.25
0.00
40.81
4.00
1223
1348
1.004440
GCGCCTCCTGACTTGACTT
60.004
57.895
0.00
0.00
0.00
3.01
1236
1361
2.034558
ACTTGACTTGATGGGTTTTGCG
59.965
45.455
0.00
0.00
0.00
4.85
1258
1383
0.534877
TGCTTGCAGCCCATATACCG
60.535
55.000
5.82
0.00
41.51
4.02
1259
1384
1.237285
GCTTGCAGCCCATATACCGG
61.237
60.000
0.00
0.00
34.48
5.28
1408
1533
7.066284
GGATACAAGTGCAAACAAGATATCAGT
59.934
37.037
5.32
0.02
0.00
3.41
1440
1565
4.564821
CGAGAGGGACAAGGTAAATCCAAA
60.565
45.833
0.00
0.00
39.02
3.28
1443
1568
4.270008
AGGGACAAGGTAAATCCAAATCG
58.730
43.478
0.00
0.00
39.02
3.34
1454
1593
0.889994
TCCAAATCGCATTGCTGCTT
59.110
45.000
7.12
0.00
46.65
3.91
1475
1614
3.887741
TCATTGTGAACACGCTTTCATG
58.112
40.909
2.87
0.00
37.80
3.07
1485
1626
3.058914
ACACGCTTTCATGCTTGTACTTC
60.059
43.478
0.00
0.00
42.32
3.01
1500
1641
5.339008
TGTACTTCGTGGCAGAGAATAAT
57.661
39.130
5.89
0.00
0.00
1.28
1504
1645
3.610040
TCGTGGCAGAGAATAATGTGT
57.390
42.857
0.00
0.00
0.00
3.72
1505
1646
3.261580
TCGTGGCAGAGAATAATGTGTG
58.738
45.455
0.00
0.00
0.00
3.82
1511
1652
4.572389
GGCAGAGAATAATGTGTGTCGATT
59.428
41.667
0.00
0.00
0.00
3.34
1512
1653
5.496387
GCAGAGAATAATGTGTGTCGATTG
58.504
41.667
0.00
0.00
0.00
2.67
1513
1654
5.063944
GCAGAGAATAATGTGTGTCGATTGT
59.936
40.000
0.00
0.00
0.00
2.71
1514
1655
6.472680
CAGAGAATAATGTGTGTCGATTGTG
58.527
40.000
0.00
0.00
0.00
3.33
1519
1660
2.017138
TGTGTGTCGATTGTGTGTGT
57.983
45.000
0.00
0.00
0.00
3.72
1644
1785
2.249743
AGGGAGGTCTGAGGAGATCATT
59.750
50.000
0.00
0.00
37.28
2.57
1716
1857
2.494059
CGTGGCCTTTTCTCTTTCTCA
58.506
47.619
3.32
0.00
0.00
3.27
1734
1875
0.739462
CATTGCGTGACGGGAAGCTA
60.739
55.000
7.25
0.00
0.00
3.32
1805
1946
0.323178
AAGGGCAACAGCATCTCAGG
60.323
55.000
0.00
0.00
39.74
3.86
1848
1989
2.198827
TTGTTGATCAATGCGAGGGT
57.801
45.000
12.12
0.00
0.00
4.34
1863
2004
4.049869
GCGAGGGTACTCTTTATGTAAGC
58.950
47.826
0.00
0.00
41.71
3.09
1879
2020
3.332485
TGTAAGCCCTTATTTCACTGGGT
59.668
43.478
0.00
0.00
41.59
4.51
1881
2022
3.646736
AGCCCTTATTTCACTGGGTAC
57.353
47.619
0.00
0.00
41.59
3.34
1955
2111
5.858381
TGACTGAGCAGATATCAAATACCC
58.142
41.667
5.32
0.00
0.00
3.69
1972
2128
0.842635
CCCAAGGCCAGCTCTATTCT
59.157
55.000
5.01
0.00
0.00
2.40
1989
2145
8.253810
GCTCTATTCTATGTACATTCATAGCCA
58.746
37.037
14.77
2.80
43.84
4.75
2020
2176
0.687354
GGGTCCAAGACTTGAGCTCA
59.313
55.000
13.74
13.74
32.47
4.26
2046
2202
2.682856
ACAAAGTCGTGACAATTGCACT
59.317
40.909
22.12
9.10
35.30
4.40
2080
2236
2.550208
CCGCCTATACATTGTCCTTCCC
60.550
54.545
0.00
0.00
0.00
3.97
2161
2317
5.548406
AGTGTTGGTCCACTTAGTAATGAC
58.452
41.667
0.00
0.00
42.99
3.06
2339
2495
7.652300
TCGTATACCAACATCTATTTGCATC
57.348
36.000
0.00
0.00
0.00
3.91
2438
2674
6.749139
TCGTTAGATGGGATCTTGTATTCAG
58.251
40.000
0.00
0.00
40.76
3.02
2505
2741
5.352569
CACCTAACTCAGTGATCCATTCAAC
59.647
44.000
0.00
0.00
35.70
3.18
2698
2934
4.364415
TCCTGGTTTGTTTCGTTCTTTG
57.636
40.909
0.00
0.00
0.00
2.77
2699
2935
3.129638
TCCTGGTTTGTTTCGTTCTTTGG
59.870
43.478
0.00
0.00
0.00
3.28
2971
3207
7.519347
AATTGGTAAAGTTATACTCCCTCCA
57.481
36.000
0.00
0.00
0.00
3.86
2994
3230
3.181497
CCCCAAAATAAGTGTCGCTGATG
60.181
47.826
0.00
0.00
0.00
3.07
3069
3305
6.259550
GCTTTGAGCTCCTGAAATTTCTTA
57.740
37.500
18.64
4.03
38.45
2.10
3124
3360
5.107453
ACACGAGAAGTATGCTTTCTTTTCG
60.107
40.000
21.46
21.46
46.30
3.46
3482
3718
1.774110
TGGCTTGCAAAAGTTCCTGA
58.226
45.000
0.00
0.00
0.00
3.86
3815
4060
4.649692
AGCACAAGAGTCACTCATTTCAT
58.350
39.130
7.77
0.00
32.06
2.57
3953
4198
4.522022
AGCTTTGAAGAAATGGAACTGGAG
59.478
41.667
0.00
0.00
0.00
3.86
3955
4200
5.335504
GCTTTGAAGAAATGGAACTGGAGAG
60.336
44.000
0.00
0.00
0.00
3.20
4034
4279
5.827797
TCAAGACAAATTGCCAGTAGAAGTT
59.172
36.000
0.00
0.00
0.00
2.66
4043
4288
3.054875
TGCCAGTAGAAGTTGCATCATCT
60.055
43.478
7.59
7.59
0.00
2.90
4049
4294
7.496920
CCAGTAGAAGTTGCATCATCTTATCAA
59.503
37.037
7.75
0.00
0.00
2.57
4061
4306
9.687210
GCATCATCTTATCAAGCATTTATGAAA
57.313
29.630
0.00
0.00
0.00
2.69
4102
4347
2.185004
AGCAGTAGCAAATCACCGTT
57.815
45.000
0.00
0.00
45.49
4.44
4139
4384
1.890979
GATGGAGACCATGCGGCAG
60.891
63.158
9.25
0.00
45.26
4.85
4212
4457
7.936847
TGTCCTCAACAAACTGATATGTAACTT
59.063
33.333
0.00
0.00
34.03
2.66
4254
4499
2.703416
AGCTTGCTTGATTGTCGATGA
58.297
42.857
0.00
0.00
0.00
2.92
4388
4633
7.974243
TTCATTTTGATTCAGATTGCATACG
57.026
32.000
0.00
0.00
0.00
3.06
4392
4637
6.741992
TTTGATTCAGATTGCATACGAACT
57.258
33.333
0.00
0.00
0.00
3.01
4393
4638
6.741992
TTGATTCAGATTGCATACGAACTT
57.258
33.333
0.00
0.00
0.00
2.66
4394
4639
6.741992
TGATTCAGATTGCATACGAACTTT
57.258
33.333
0.00
0.00
0.00
2.66
4396
4641
8.437360
TGATTCAGATTGCATACGAACTTTAT
57.563
30.769
0.00
0.00
0.00
1.40
4401
4646
7.017645
CAGATTGCATACGAACTTTATATGCC
58.982
38.462
11.74
0.00
46.99
4.40
4402
4647
6.936900
AGATTGCATACGAACTTTATATGCCT
59.063
34.615
11.74
1.34
46.99
4.75
4403
4648
6.935741
TTGCATACGAACTTTATATGCCTT
57.064
33.333
11.74
0.00
46.99
4.35
4404
4649
6.299023
TGCATACGAACTTTATATGCCTTG
57.701
37.500
11.74
0.00
46.99
3.61
4406
4651
6.540551
TGCATACGAACTTTATATGCCTTGAA
59.459
34.615
11.74
0.00
46.99
2.69
4407
4652
6.851330
GCATACGAACTTTATATGCCTTGAAC
59.149
38.462
4.47
0.00
43.50
3.18
4408
4653
7.466725
GCATACGAACTTTATATGCCTTGAACA
60.467
37.037
4.47
0.00
43.50
3.18
4409
4654
6.811253
ACGAACTTTATATGCCTTGAACAA
57.189
33.333
0.00
0.00
0.00
2.83
4410
4655
7.209471
ACGAACTTTATATGCCTTGAACAAA
57.791
32.000
0.00
0.00
0.00
2.83
4433
4692
6.566197
ACTTGTCATTTTGTTTTGCCAAAA
57.434
29.167
0.00
0.00
45.43
2.44
4446
4705
6.541641
TGTTTTGCCAAAATAGAGCAACATTT
59.458
30.769
5.81
0.00
45.57
2.32
4450
4709
6.620678
TGCCAAAATAGAGCAACATTTAGAC
58.379
36.000
0.00
0.00
32.56
2.59
4478
4737
1.532868
GTGTAACAGCTGCTCCAGTTG
59.467
52.381
15.27
7.40
45.77
3.16
4519
4778
4.850680
TCCCCTGACCAAATATTGTACAC
58.149
43.478
0.00
0.00
0.00
2.90
4617
4880
8.625786
TCAATCAACAGAATACATGGATATGG
57.374
34.615
7.72
0.00
38.66
2.74
4676
4941
9.030452
AGTAAGATATGAACATGTCTATCCTCC
57.970
37.037
12.87
0.00
38.15
4.30
4747
5018
0.603065
AATCCCGGCTGAAACAAAGC
59.397
50.000
0.00
0.00
40.06
3.51
4811
5129
8.743085
ATTTATATGCTGCCCATATAGAACTG
57.257
34.615
11.64
0.00
45.42
3.16
4812
5130
2.936919
TGCTGCCCATATAGAACTGG
57.063
50.000
0.00
0.00
0.00
4.00
4943
5266
2.158549
AGCAAGAACTGAAGGGCTTTCT
60.159
45.455
10.86
0.00
36.71
2.52
5006
5329
2.280592
GACGTGAACCGGTGGCTT
60.281
61.111
8.52
0.00
42.24
4.35
5153
5476
1.676384
GTCCCTCTGCTTGAGCTGT
59.324
57.895
4.44
0.00
41.35
4.40
5190
5513
3.018423
TCATCTTCTCCATCTCGGACA
57.982
47.619
0.00
0.00
39.64
4.02
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
13
14
1.195448
CACGATTTGGACTGTCTGCAC
59.805
52.381
7.85
0.00
0.00
4.57
107
126
4.875536
CGGATGTGTTATTCCTCATGTCAA
59.124
41.667
0.00
0.00
0.00
3.18
120
139
3.698040
GAGGAGGTTCTACGGATGTGTTA
59.302
47.826
0.00
0.00
0.00
2.41
130
149
0.614134
ACACGGGGAGGAGGTTCTAC
60.614
60.000
0.00
0.00
0.00
2.59
145
164
2.293122
TGCATTTGAAGGAAAGGACACG
59.707
45.455
0.00
0.00
0.00
4.49
357
387
4.500499
AAGAGATCTGCTTTGCACCTAT
57.500
40.909
0.00
0.00
33.79
2.57
403
433
2.043852
GGAGGAGGAGCTGGTCGA
60.044
66.667
0.00
0.00
0.00
4.20
416
446
2.441901
AGGAGAGCAGCGAGGAGG
60.442
66.667
0.00
0.00
0.00
4.30
417
447
1.447317
GAGAGGAGAGCAGCGAGGAG
61.447
65.000
0.00
0.00
0.00
3.69
418
448
1.453015
GAGAGGAGAGCAGCGAGGA
60.453
63.158
0.00
0.00
0.00
3.71
487
551
0.689623
CTCTGCTCTGTCCCCTGTTT
59.310
55.000
0.00
0.00
0.00
2.83
510
574
1.154131
CACTCGCTCACTCTCCACG
60.154
63.158
0.00
0.00
0.00
4.94
519
592
1.228583
ACTCCACTCCACTCGCTCA
60.229
57.895
0.00
0.00
0.00
4.26
523
596
0.896019
ACTCCACTCCACTCCACTCG
60.896
60.000
0.00
0.00
0.00
4.18
527
600
0.105709
TCACACTCCACTCCACTCCA
60.106
55.000
0.00
0.00
0.00
3.86
645
734
0.036952
CGACTTCTGACATGGCAGGT
60.037
55.000
28.28
18.90
36.55
4.00
661
750
0.308376
TTTGCCGCAACTAAACCGAC
59.692
50.000
4.98
0.00
0.00
4.79
707
796
9.054922
CAAGAATCCACCATTTTTGTTGTAAAT
57.945
29.630
0.00
0.00
33.66
1.40
720
809
0.394352
GCGTCCCAAGAATCCACCAT
60.394
55.000
0.00
0.00
0.00
3.55
730
819
0.652592
CATTTCTAGCGCGTCCCAAG
59.347
55.000
8.43
0.00
0.00
3.61
797
886
5.181245
GTGCCTACTAGACTGAATTGCAAAA
59.819
40.000
1.71
0.00
0.00
2.44
798
887
4.695455
GTGCCTACTAGACTGAATTGCAAA
59.305
41.667
1.71
0.00
0.00
3.68
799
888
4.253685
GTGCCTACTAGACTGAATTGCAA
58.746
43.478
0.00
0.00
0.00
4.08
800
889
3.676049
CGTGCCTACTAGACTGAATTGCA
60.676
47.826
0.00
0.00
0.00
4.08
801
890
2.860735
CGTGCCTACTAGACTGAATTGC
59.139
50.000
0.00
0.00
0.00
3.56
802
891
4.111375
ACGTGCCTACTAGACTGAATTG
57.889
45.455
0.00
0.00
0.00
2.32
803
892
4.803098
AACGTGCCTACTAGACTGAATT
57.197
40.909
0.00
0.00
0.00
2.17
804
893
4.703575
TGTAACGTGCCTACTAGACTGAAT
59.296
41.667
0.00
0.00
0.00
2.57
805
894
4.074259
TGTAACGTGCCTACTAGACTGAA
58.926
43.478
0.00
0.00
0.00
3.02
806
895
3.438087
GTGTAACGTGCCTACTAGACTGA
59.562
47.826
0.00
0.00
0.00
3.41
807
896
3.756069
GTGTAACGTGCCTACTAGACTG
58.244
50.000
0.00
0.00
0.00
3.51
845
934
1.011968
TTTCTCGCAATCGTCGTGGG
61.012
55.000
0.00
0.00
36.96
4.61
850
939
2.537730
GCAGGAATTTCTCGCAATCGTC
60.538
50.000
3.99
0.00
36.96
4.20
949
1074
1.203087
TGGAGTAAGTGGAAGGACGGA
60.203
52.381
0.00
0.00
0.00
4.69
968
1093
4.261363
GGTTGCAGAGAGGAAGAGTTTTTG
60.261
45.833
0.00
0.00
0.00
2.44
1079
1204
2.189191
ATTGAGCCTCTGAAGCGCCA
62.189
55.000
2.29
0.00
34.64
5.69
1124
1249
2.101640
AACCAAAGCAAGGGGATTGT
57.898
45.000
0.00
0.00
41.29
2.71
1126
1251
2.976440
AGAAACCAAAGCAAGGGGATT
58.024
42.857
0.00
0.00
0.00
3.01
1149
1274
5.046304
AGGAAACTGCAGACTGTATGTATGT
60.046
40.000
23.35
0.00
39.83
2.29
1150
1275
5.423015
AGGAAACTGCAGACTGTATGTATG
58.577
41.667
23.35
0.00
41.13
2.39
1151
1276
5.683876
AGGAAACTGCAGACTGTATGTAT
57.316
39.130
23.35
0.00
41.13
2.29
1152
1277
5.237815
CAAGGAAACTGCAGACTGTATGTA
58.762
41.667
23.35
0.00
42.68
2.29
1153
1278
4.067896
CAAGGAAACTGCAGACTGTATGT
58.932
43.478
23.35
0.00
42.68
2.29
1154
1279
3.120060
GCAAGGAAACTGCAGACTGTATG
60.120
47.826
23.35
13.07
42.68
2.39
1155
1280
3.077359
GCAAGGAAACTGCAGACTGTAT
58.923
45.455
23.35
0.00
42.68
2.29
1159
1284
0.538287
GGGCAAGGAAACTGCAGACT
60.538
55.000
23.35
9.85
42.68
3.24
1198
1323
4.680237
TCAGGAGGCGCAACCGTG
62.680
66.667
10.83
9.40
46.52
4.94
1199
1324
4.681978
GTCAGGAGGCGCAACCGT
62.682
66.667
10.83
0.00
46.52
4.83
1223
1348
1.112315
AGCAACCGCAAAACCCATCA
61.112
50.000
0.00
0.00
42.27
3.07
1390
1515
5.772521
ACCAAACTGATATCTTGTTTGCAC
58.227
37.500
28.90
0.00
45.12
4.57
1393
1518
5.634859
GGCAACCAAACTGATATCTTGTTTG
59.365
40.000
28.15
28.15
45.68
2.93
1408
1533
1.072505
GTCCCTCTCGGCAACCAAA
59.927
57.895
0.00
0.00
0.00
3.28
1440
1565
1.475280
ACAATGAAGCAGCAATGCGAT
59.525
42.857
0.00
0.00
40.27
4.58
1443
1568
2.357327
TCACAATGAAGCAGCAATGC
57.643
45.000
0.00
0.00
0.00
3.56
1454
1593
3.852939
GCATGAAAGCGTGTTCACAATGA
60.853
43.478
0.00
0.00
40.22
2.57
1475
1614
1.071605
CTCTGCCACGAAGTACAAGC
58.928
55.000
0.00
0.00
41.61
4.01
1485
1626
3.002791
ACACACATTATTCTCTGCCACG
58.997
45.455
0.00
0.00
0.00
4.94
1500
1641
2.017138
ACACACACAATCGACACACA
57.983
45.000
0.00
0.00
0.00
3.72
1504
1645
7.329588
AGTATATCTACACACACAATCGACA
57.670
36.000
0.00
0.00
0.00
4.35
1505
1646
7.167635
CCAAGTATATCTACACACACAATCGAC
59.832
40.741
0.00
0.00
0.00
4.20
1511
1652
5.625886
GCCACCAAGTATATCTACACACACA
60.626
44.000
0.00
0.00
0.00
3.72
1512
1653
4.809426
GCCACCAAGTATATCTACACACAC
59.191
45.833
0.00
0.00
0.00
3.82
1513
1654
4.468153
TGCCACCAAGTATATCTACACACA
59.532
41.667
0.00
0.00
0.00
3.72
1514
1655
5.018539
TGCCACCAAGTATATCTACACAC
57.981
43.478
0.00
0.00
0.00
3.82
1519
1660
8.721133
TTATCTTCTGCCACCAAGTATATCTA
57.279
34.615
0.00
0.00
0.00
1.98
1644
1785
3.047807
GCTGCTGGTGGATAGGCCA
62.048
63.158
5.01
0.00
46.96
5.36
1716
1857
0.739813
GTAGCTTCCCGTCACGCAAT
60.740
55.000
0.00
0.00
0.00
3.56
1805
1946
5.762825
TGGAGATGAATTGAAATAGCAGC
57.237
39.130
0.00
0.00
0.00
5.25
1848
1989
9.609346
GTGAAATAAGGGCTTACATAAAGAGTA
57.391
33.333
0.00
0.00
37.38
2.59
1863
2004
4.569719
ACAGTACCCAGTGAAATAAGGG
57.430
45.455
0.00
0.00
46.96
3.95
1955
2111
4.348863
ACATAGAATAGAGCTGGCCTTG
57.651
45.455
3.32
0.00
0.00
3.61
1989
2145
5.721225
AGTCTTGGACCCATCTATACTGAT
58.279
41.667
0.00
0.00
32.18
2.90
2046
2202
0.847373
TAGGCGGCCATTATTTCCCA
59.153
50.000
23.09
0.00
0.00
4.37
2080
2236
2.816087
CCCCATCACAGTTGACTTTCTG
59.184
50.000
0.00
0.00
33.38
3.02
2161
2317
1.614903
TCCACAGCTGGCAAGATTTTG
59.385
47.619
19.93
3.32
37.49
2.44
2297
2453
7.114529
GGTATACGAATACGAATGTTGAAGAGG
59.885
40.741
0.00
0.00
39.16
3.69
2478
2714
3.506398
TGGATCACTGAGTTAGGTGTCA
58.494
45.455
0.00
0.00
35.26
3.58
2479
2715
4.744795
ATGGATCACTGAGTTAGGTGTC
57.255
45.455
0.00
0.00
35.26
3.67
2480
2716
4.532126
TGAATGGATCACTGAGTTAGGTGT
59.468
41.667
0.00
0.00
35.26
4.16
2698
2934
5.416952
AGGAACAAGAATGACACATTCATCC
59.583
40.000
21.15
19.85
44.86
3.51
2699
2935
6.404074
GGAGGAACAAGAATGACACATTCATC
60.404
42.308
21.15
14.45
44.86
2.92
2971
3207
2.159382
CAGCGACACTTATTTTGGGGT
58.841
47.619
0.00
0.00
0.00
4.95
2994
3230
7.523415
TCCCTCCATCCCAAAATAAGTATTAC
58.477
38.462
0.00
0.00
30.46
1.89
3069
3305
1.453155
GTGTTGCCGATTCCTGTGAT
58.547
50.000
0.00
0.00
0.00
3.06
3124
3360
7.446625
AGGATGGAAAATCAACTAGATACATGC
59.553
37.037
0.00
0.00
35.39
4.06
3219
3455
7.657761
TGAACAAACTTTGGTTTTGCTTTTCTA
59.342
29.630
6.47
0.00
42.96
2.10
3451
3687
3.540314
TGCAAGCCATTGTTTTGAAGT
57.460
38.095
0.00
0.00
38.76
3.01
3482
3718
8.434392
TGTTTCTAGTACACATACCCTCTTTTT
58.566
33.333
0.00
0.00
30.88
1.94
3815
4060
0.036483
TGCTTTCTCTATGTGCGCCA
60.036
50.000
4.18
2.31
0.00
5.69
3953
4198
3.883830
TCTGCTGACTTGGATCTTCTC
57.116
47.619
0.00
0.00
0.00
2.87
3955
4200
4.183101
CTCTTCTGCTGACTTGGATCTTC
58.817
47.826
0.00
0.00
0.00
2.87
4034
4279
8.398878
TCATAAATGCTTGATAAGATGATGCA
57.601
30.769
0.00
0.00
31.87
3.96
4043
4288
7.598278
ACAACGGTTTCATAAATGCTTGATAA
58.402
30.769
0.00
0.00
0.00
1.75
4049
4294
6.321717
CACATACAACGGTTTCATAAATGCT
58.678
36.000
0.00
0.00
0.00
3.79
4061
4306
1.346395
TCTCCTTGCACATACAACGGT
59.654
47.619
0.00
0.00
0.00
4.83
4139
4384
1.815003
CTCTTGGTTGGTGCAAGATCC
59.185
52.381
0.00
0.00
34.87
3.36
4216
4461
8.743085
AGCAAGCTAAATCTTCATCTAATTCA
57.257
30.769
0.00
0.00
0.00
2.57
4275
4520
9.874205
AAATGAACCACAATAAATAACATCCTG
57.126
29.630
0.00
0.00
0.00
3.86
4388
4633
8.915654
CAAGTTTGTTCAAGGCATATAAAGTTC
58.084
33.333
0.00
0.00
0.00
3.01
4392
4637
7.946207
TGACAAGTTTGTTCAAGGCATATAAA
58.054
30.769
0.00
0.00
42.43
1.40
4393
4638
7.517614
TGACAAGTTTGTTCAAGGCATATAA
57.482
32.000
0.00
0.00
42.43
0.98
4394
4639
7.701539
ATGACAAGTTTGTTCAAGGCATATA
57.298
32.000
0.00
0.00
42.43
0.86
4396
4641
6.403866
AATGACAAGTTTGTTCAAGGCATA
57.596
33.333
0.00
0.00
42.43
3.14
4398
4643
4.734398
AATGACAAGTTTGTTCAAGGCA
57.266
36.364
0.00
0.00
42.43
4.75
4407
4652
5.936054
TGGCAAAACAAAATGACAAGTTTG
58.064
33.333
11.49
11.49
44.80
2.93
4408
4653
6.566197
TTGGCAAAACAAAATGACAAGTTT
57.434
29.167
0.00
0.00
39.57
2.66
4409
4654
6.566197
TTTGGCAAAACAAAATGACAAGTT
57.434
29.167
10.83
0.00
44.80
2.66
4410
4655
6.566197
TTTTGGCAAAACAAAATGACAAGT
57.434
29.167
20.81
0.00
44.80
3.16
4433
4692
7.697691
CATTTTCCGTCTAAATGTTGCTCTAT
58.302
34.615
0.00
0.00
37.90
1.98
4435
4694
5.942872
CATTTTCCGTCTAAATGTTGCTCT
58.057
37.500
0.00
0.00
37.90
4.09
4446
4705
4.688879
CAGCTGTTACACATTTTCCGTCTA
59.311
41.667
5.25
0.00
0.00
2.59
4450
4709
2.226437
AGCAGCTGTTACACATTTTCCG
59.774
45.455
16.64
0.00
0.00
4.30
4478
4737
6.015940
CAGGGGAGAGAACATTTATATTTGGC
60.016
42.308
0.00
0.00
0.00
4.52
4593
4856
8.400184
ACCATATCCATGTATTCTGTTGATTG
57.600
34.615
0.00
0.00
0.00
2.67
4609
4872
6.905736
TGCTAATTGGAGTTTACCATATCCA
58.094
36.000
0.00
0.00
40.04
3.41
4617
4880
6.538742
TGTCAGCTATGCTAATTGGAGTTTAC
59.461
38.462
0.00
0.00
36.40
2.01
4676
4941
1.857217
CTCAGGAGACGAATGAATGCG
59.143
52.381
0.00
0.00
0.00
4.73
4747
5018
1.819632
GGCCTCACCCTGCATTACG
60.820
63.158
0.00
0.00
0.00
3.18
4943
5266
1.362224
CCTTCTGGGACTTTGGAGGA
58.638
55.000
0.00
0.00
37.23
3.71
4984
5307
1.661480
CACCGGTTCACGTCACCTA
59.339
57.895
2.97
0.00
42.24
3.08
5153
5476
7.967908
AGAAGATGAAGAAGGAACACTTTCTA
58.032
34.615
0.00
0.00
40.21
2.10
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.