Multiple sequence alignment - TraesCS3A01G336800
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
TraesCS3A01G336800
chr3A
100.000
2882
0
0
1
2882
583747193
583750074
0.000000e+00
5323.0
1
TraesCS3A01G336800
chr3A
86.632
1339
95
35
932
2256
434799150
434800418
0.000000e+00
1404.0
2
TraesCS3A01G336800
chr3A
81.443
97
15
3
2535
2629
448326160
448326065
3.080000e-10
76.8
3
TraesCS3A01G336800
chr3B
88.294
1905
112
49
435
2256
580062075
580063951
0.000000e+00
2180.0
4
TraesCS3A01G336800
chr3B
92.381
630
42
4
2257
2882
580063986
580064613
0.000000e+00
893.0
5
TraesCS3A01G336800
chr3B
83.945
218
17
12
177
388
580061754
580061959
2.930000e-45
193.0
6
TraesCS3A01G336800
chr3B
100.000
38
0
0
17
54
580061560
580061597
1.430000e-08
71.3
7
TraesCS3A01G336800
chr3D
92.701
1370
64
11
906
2256
442511362
442512714
0.000000e+00
1943.0
8
TraesCS3A01G336800
chr3D
92.031
640
36
6
2257
2882
442512749
442513387
0.000000e+00
885.0
9
TraesCS3A01G336800
chr3D
88.473
347
23
7
420
759
442510824
442511160
1.240000e-108
403.0
10
TraesCS3A01G336800
chr3D
84.375
256
16
14
151
388
442510453
442510702
2.230000e-56
230.0
11
TraesCS3A01G336800
chr3D
81.529
157
11
10
1
149
442510259
442510405
2.350000e-21
113.0
12
TraesCS3A01G336800
chr2D
89.222
1234
87
18
932
2150
568757274
568758476
0.000000e+00
1500.0
13
TraesCS3A01G336800
chr5B
88.943
1239
87
20
932
2150
524221797
524220589
0.000000e+00
1483.0
14
TraesCS3A01G336800
chr1B
88.673
1236
93
19
932
2150
443488938
443487733
0.000000e+00
1463.0
15
TraesCS3A01G336800
chr1B
85.437
103
5
4
2706
2802
310311835
310311933
6.570000e-17
99.0
16
TraesCS3A01G336800
chr7A
88.483
1233
83
17
932
2150
48766855
48765668
0.000000e+00
1435.0
17
TraesCS3A01G336800
chr4D
87.916
1233
83
27
932
2150
30394034
30395214
0.000000e+00
1391.0
18
TraesCS3A01G336800
chr7D
89.454
1081
74
12
1083
2150
207789238
207788185
0.000000e+00
1328.0
19
TraesCS3A01G336800
chr1A
87.343
798
58
22
1474
2256
512465714
512466483
0.000000e+00
874.0
20
TraesCS3A01G336800
chr6A
90.476
462
28
8
1703
2150
535421583
535421124
1.910000e-166
595.0
21
TraesCS3A01G336800
chr6A
83.733
375
27
16
932
1300
535421936
535421590
9.960000e-85
324.0
22
TraesCS3A01G336800
chr7B
85.417
96
6
2
2711
2802
3130714
3130623
3.060000e-15
93.5
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
TraesCS3A01G336800
chr3A
583747193
583750074
2881
False
5323.000
5323
100.0000
1
2882
1
chr3A.!!$F2
2881
1
TraesCS3A01G336800
chr3A
434799150
434800418
1268
False
1404.000
1404
86.6320
932
2256
1
chr3A.!!$F1
1324
2
TraesCS3A01G336800
chr3B
580061560
580064613
3053
False
834.325
2180
91.1550
17
2882
4
chr3B.!!$F1
2865
3
TraesCS3A01G336800
chr3D
442510259
442513387
3128
False
714.800
1943
87.8218
1
2882
5
chr3D.!!$F1
2881
4
TraesCS3A01G336800
chr2D
568757274
568758476
1202
False
1500.000
1500
89.2220
932
2150
1
chr2D.!!$F1
1218
5
TraesCS3A01G336800
chr5B
524220589
524221797
1208
True
1483.000
1483
88.9430
932
2150
1
chr5B.!!$R1
1218
6
TraesCS3A01G336800
chr1B
443487733
443488938
1205
True
1463.000
1463
88.6730
932
2150
1
chr1B.!!$R1
1218
7
TraesCS3A01G336800
chr7A
48765668
48766855
1187
True
1435.000
1435
88.4830
932
2150
1
chr7A.!!$R1
1218
8
TraesCS3A01G336800
chr4D
30394034
30395214
1180
False
1391.000
1391
87.9160
932
2150
1
chr4D.!!$F1
1218
9
TraesCS3A01G336800
chr7D
207788185
207789238
1053
True
1328.000
1328
89.4540
1083
2150
1
chr7D.!!$R1
1067
10
TraesCS3A01G336800
chr1A
512465714
512466483
769
False
874.000
874
87.3430
1474
2256
1
chr1A.!!$F1
782
11
TraesCS3A01G336800
chr6A
535421124
535421936
812
True
459.500
595
87.1045
932
2150
2
chr6A.!!$R1
1218
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
414
608
0.034198
TCTGGTCGCCGTGAAAATCA
59.966
50.0
0.00
0.0
0.00
2.57
F
894
1238
0.320334
GGCCCGGTTTGTTTGGAATG
60.320
55.0
0.00
0.0
0.00
2.67
F
1117
1504
0.321671
CTTCCACTTCGAGAAGCCCA
59.678
55.0
12.32
0.0
41.99
5.36
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1301
1711
0.312416
GGAGAGGACGATGATGACGG
59.688
60.0
0.0
0.0
34.93
4.79
R
1866
2281
0.390472
GGCGTCAGTTCCTCCAGAAG
60.390
60.0
0.0
0.0
34.29
2.85
R
2142
2579
0.746204
TCCGTCAGCAGCAACACAAA
60.746
50.0
0.0
0.0
0.00
2.83
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
60
110
1.851304
TGGGCATGGACCAAGAATTC
58.149
50.000
0.00
0.00
38.06
2.17
61
111
0.740737
GGGCATGGACCAAGAATTCG
59.259
55.000
0.00
0.00
0.00
3.34
62
112
1.463674
GGCATGGACCAAGAATTCGT
58.536
50.000
0.00
0.00
0.00
3.85
63
113
1.401905
GGCATGGACCAAGAATTCGTC
59.598
52.381
0.00
1.74
0.00
4.20
64
114
2.083774
GCATGGACCAAGAATTCGTCA
58.916
47.619
0.00
0.00
0.00
4.35
65
115
2.684881
GCATGGACCAAGAATTCGTCAT
59.315
45.455
0.00
2.05
0.00
3.06
66
116
3.242870
GCATGGACCAAGAATTCGTCATC
60.243
47.826
0.00
4.27
0.00
2.92
67
117
2.616960
TGGACCAAGAATTCGTCATCG
58.383
47.619
12.24
0.00
38.55
3.84
68
118
2.028476
TGGACCAAGAATTCGTCATCGT
60.028
45.455
12.24
0.41
38.33
3.73
69
119
3.193903
TGGACCAAGAATTCGTCATCGTA
59.806
43.478
12.24
0.00
38.33
3.43
70
120
3.550678
GGACCAAGAATTCGTCATCGTAC
59.449
47.826
12.24
0.00
38.33
3.67
71
121
4.421948
GACCAAGAATTCGTCATCGTACT
58.578
43.478
0.00
0.00
38.33
2.73
72
122
4.421948
ACCAAGAATTCGTCATCGTACTC
58.578
43.478
0.00
0.00
38.33
2.59
73
123
4.158025
ACCAAGAATTCGTCATCGTACTCT
59.842
41.667
0.00
0.00
38.33
3.24
74
124
5.356190
ACCAAGAATTCGTCATCGTACTCTA
59.644
40.000
0.00
0.00
38.33
2.43
75
125
5.910166
CCAAGAATTCGTCATCGTACTCTAG
59.090
44.000
0.00
0.00
38.33
2.43
76
126
5.676532
AGAATTCGTCATCGTACTCTAGG
57.323
43.478
0.00
0.00
38.33
3.02
77
127
5.366460
AGAATTCGTCATCGTACTCTAGGA
58.634
41.667
0.00
0.00
38.33
2.94
78
128
5.467399
AGAATTCGTCATCGTACTCTAGGAG
59.533
44.000
0.00
0.00
38.33
3.69
79
129
2.481854
TCGTCATCGTACTCTAGGAGC
58.518
52.381
0.00
0.00
38.33
4.70
80
130
1.532007
CGTCATCGTACTCTAGGAGCC
59.468
57.143
0.00
0.00
32.04
4.70
81
131
2.807472
CGTCATCGTACTCTAGGAGCCT
60.807
54.545
0.00
0.00
32.04
4.58
82
132
2.809696
GTCATCGTACTCTAGGAGCCTC
59.190
54.545
0.00
0.00
32.04
4.70
83
133
2.156098
CATCGTACTCTAGGAGCCTCC
58.844
57.143
1.26
1.26
36.58
4.30
96
146
2.818132
CCTCCTGAGGCGTCCATC
59.182
66.667
3.56
0.00
42.44
3.51
97
147
2.801631
CCTCCTGAGGCGTCCATCC
61.802
68.421
3.56
0.00
42.44
3.51
98
148
2.038813
TCCTGAGGCGTCCATCCA
59.961
61.111
3.56
0.00
0.00
3.41
99
149
2.025767
CTCCTGAGGCGTCCATCCAG
62.026
65.000
3.56
0.00
0.00
3.86
100
150
2.202987
CTGAGGCGTCCATCCAGC
60.203
66.667
3.56
0.00
0.00
4.85
142
192
4.209703
GGATACTCCGTCGATCGATCTATC
59.790
50.000
22.50
18.18
42.86
2.08
145
195
2.074576
TCCGTCGATCGATCTATCCAC
58.925
52.381
22.50
5.14
42.86
4.02
146
196
2.077627
CCGTCGATCGATCTATCCACT
58.922
52.381
22.50
0.00
42.86
4.00
147
197
2.159639
CCGTCGATCGATCTATCCACTG
60.160
54.545
22.50
5.20
42.86
3.66
148
198
2.726373
CGTCGATCGATCTATCCACTGC
60.726
54.545
22.50
2.42
42.86
4.40
149
199
2.226674
GTCGATCGATCTATCCACTGCA
59.773
50.000
22.50
0.00
0.00
4.41
150
200
3.084786
TCGATCGATCTATCCACTGCAT
58.915
45.455
22.43
0.00
0.00
3.96
152
202
4.333926
TCGATCGATCTATCCACTGCATAG
59.666
45.833
22.43
2.68
0.00
2.23
153
203
3.857549
TCGATCTATCCACTGCATAGC
57.142
47.619
0.00
0.00
0.00
2.97
154
204
3.157087
TCGATCTATCCACTGCATAGCA
58.843
45.455
0.00
0.00
36.92
3.49
156
206
3.056962
CGATCTATCCACTGCATAGCACT
60.057
47.826
0.00
0.00
33.79
4.40
157
207
4.156739
CGATCTATCCACTGCATAGCACTA
59.843
45.833
0.00
0.00
33.79
2.74
158
208
5.649557
GATCTATCCACTGCATAGCACTAG
58.350
45.833
0.00
0.00
33.79
2.57
165
261
3.634448
CACTGCATAGCACTAGTAGGAGT
59.366
47.826
1.45
0.00
33.79
3.85
170
266
5.996513
TGCATAGCACTAGTAGGAGTACTAC
59.003
44.000
4.13
4.13
42.26
2.73
223
378
0.602638
CGTGTTGGACCAAGCTGCTA
60.603
55.000
7.31
0.00
0.00
3.49
226
381
1.168714
GTTGGACCAAGCTGCTAAGG
58.831
55.000
7.31
16.74
0.00
2.69
289
462
4.749310
CGCGCCTCTGCTGGTTCT
62.749
66.667
0.00
0.00
34.43
3.01
291
464
2.507992
CGCCTCTGCTGGTTCTCG
60.508
66.667
0.00
0.00
34.43
4.04
294
467
2.125350
CTCTGCTGGTTCTCGCCC
60.125
66.667
0.00
0.00
0.00
6.13
309
482
4.404098
CCCCTACCCGTGTGCACC
62.404
72.222
15.69
4.74
0.00
5.01
310
483
3.632080
CCCTACCCGTGTGCACCA
61.632
66.667
15.69
0.00
0.00
4.17
401
595
2.125350
CGCCTTCCTGCTCTGGTC
60.125
66.667
0.00
0.00
0.00
4.02
411
605
1.959226
GCTCTGGTCGCCGTGAAAA
60.959
57.895
0.00
0.00
0.00
2.29
413
607
0.721718
CTCTGGTCGCCGTGAAAATC
59.278
55.000
0.00
0.00
0.00
2.17
414
608
0.034198
TCTGGTCGCCGTGAAAATCA
59.966
50.000
0.00
0.00
0.00
2.57
415
609
1.086696
CTGGTCGCCGTGAAAATCAT
58.913
50.000
0.00
0.00
0.00
2.45
416
610
2.093921
TCTGGTCGCCGTGAAAATCATA
60.094
45.455
0.00
0.00
0.00
2.15
417
611
2.004017
TGGTCGCCGTGAAAATCATAC
58.996
47.619
0.00
0.00
0.00
2.39
418
612
2.277084
GGTCGCCGTGAAAATCATACT
58.723
47.619
0.00
0.00
0.00
2.12
419
613
2.284417
GGTCGCCGTGAAAATCATACTC
59.716
50.000
0.00
0.00
0.00
2.59
420
614
2.034842
GTCGCCGTGAAAATCATACTCG
60.035
50.000
0.00
0.00
0.00
4.18
421
615
1.257936
CGCCGTGAAAATCATACTCGG
59.742
52.381
0.00
0.00
41.50
4.63
422
616
1.597663
GCCGTGAAAATCATACTCGGG
59.402
52.381
0.00
0.00
39.81
5.14
424
618
2.550978
CGTGAAAATCATACTCGGGCT
58.449
47.619
0.00
0.00
0.00
5.19
466
737
2.944349
GTCCCCTCGAACTACTCTACTG
59.056
54.545
0.00
0.00
0.00
2.74
468
739
3.458857
TCCCCTCGAACTACTCTACTGAT
59.541
47.826
0.00
0.00
0.00
2.90
492
767
1.890979
GCCGATGGATCCAGCTGTG
60.891
63.158
26.56
15.90
0.00
3.66
551
826
3.446570
GCATCGCTTGCCTTGCCT
61.447
61.111
0.00
0.00
46.15
4.75
574
854
2.045926
GCGGTGCAGTCCAGGATT
60.046
61.111
0.00
0.00
0.00
3.01
597
877
1.783071
TTCACACCTTTGTTTCCCCC
58.217
50.000
0.00
0.00
31.66
5.40
622
902
5.400066
AATCAAAACCTTCCATAAACCCG
57.600
39.130
0.00
0.00
0.00
5.28
652
939
3.411351
CCACGCGGTTTCCAGTCG
61.411
66.667
12.47
0.00
0.00
4.18
656
943
2.087009
CGCGGTTTCCAGTCGAGTC
61.087
63.158
0.00
0.00
0.00
3.36
657
944
1.737008
GCGGTTTCCAGTCGAGTCC
60.737
63.158
0.00
0.00
0.00
3.85
658
945
1.663739
CGGTTTCCAGTCGAGTCCA
59.336
57.895
0.00
0.00
0.00
4.02
659
946
0.388649
CGGTTTCCAGTCGAGTCCAG
60.389
60.000
0.00
0.00
0.00
3.86
660
947
0.680061
GGTTTCCAGTCGAGTCCAGT
59.320
55.000
0.00
0.00
0.00
4.00
731
1018
2.159366
CCGCCCTCTGCTCTATATAACG
60.159
54.545
0.00
0.00
38.05
3.18
741
1028
0.892755
CTATATAACGCCCTCCGCCA
59.107
55.000
0.00
0.00
41.76
5.69
759
1046
4.517934
CCGACCCTCCCCGCTCTA
62.518
72.222
0.00
0.00
0.00
2.43
762
1049
1.909287
GACCCTCCCCGCTCTATCC
60.909
68.421
0.00
0.00
0.00
2.59
763
1050
2.374781
GACCCTCCCCGCTCTATCCT
62.375
65.000
0.00
0.00
0.00
3.24
764
1051
1.152226
CCCTCCCCGCTCTATCCTT
60.152
63.158
0.00
0.00
0.00
3.36
766
1053
1.188871
CCTCCCCGCTCTATCCTTCC
61.189
65.000
0.00
0.00
0.00
3.46
772
1107
0.682292
CGCTCTATCCTTCCCCTTCC
59.318
60.000
0.00
0.00
0.00
3.46
775
1110
2.427150
GCTCTATCCTTCCCCTTCCTCT
60.427
54.545
0.00
0.00
0.00
3.69
776
1111
3.238597
CTCTATCCTTCCCCTTCCTCTG
58.761
54.545
0.00
0.00
0.00
3.35
784
1119
1.676967
CCCTTCCTCTGCCACAAGC
60.677
63.158
0.00
0.00
44.14
4.01
809
1144
0.962855
GAGAGAAACCCCAAGCCAGC
60.963
60.000
0.00
0.00
0.00
4.85
890
1234
3.984749
CCGGCCCGGTTTGTTTGG
61.985
66.667
15.86
0.00
42.73
3.28
891
1235
2.907917
CGGCCCGGTTTGTTTGGA
60.908
61.111
0.00
0.00
0.00
3.53
893
1237
1.811645
CGGCCCGGTTTGTTTGGAAT
61.812
55.000
0.00
0.00
0.00
3.01
894
1238
0.320334
GGCCCGGTTTGTTTGGAATG
60.320
55.000
0.00
0.00
0.00
2.67
896
1240
1.614413
GCCCGGTTTGTTTGGAATGTA
59.386
47.619
0.00
0.00
0.00
2.29
897
1241
2.608506
GCCCGGTTTGTTTGGAATGTAC
60.609
50.000
0.00
0.00
0.00
2.90
912
1293
4.275936
GGAATGTACTACCAATGTGCATCC
59.724
45.833
0.00
0.00
39.22
3.51
917
1298
6.600388
TGTACTACCAATGTGCATCCATTAT
58.400
36.000
2.51
0.00
33.37
1.28
927
1308
4.576053
TGTGCATCCATTATAACTGACAGC
59.424
41.667
1.25
0.00
0.00
4.40
930
1311
4.084328
GCATCCATTATAACTGACAGCGTC
60.084
45.833
1.25
2.32
0.00
5.19
945
1326
2.547798
GTCGCACGGACGGTTTTC
59.452
61.111
0.00
0.00
35.61
2.29
947
1328
1.301087
TCGCACGGACGGTTTTCAT
60.301
52.632
0.00
0.00
0.00
2.57
948
1329
1.154488
CGCACGGACGGTTTTCATG
60.154
57.895
0.00
0.00
0.00
3.07
949
1330
1.209127
GCACGGACGGTTTTCATGG
59.791
57.895
0.00
0.00
0.00
3.66
1004
1385
2.356793
GGAGCGGCCGATGATGAG
60.357
66.667
33.48
0.00
0.00
2.90
1117
1504
0.321671
CTTCCACTTCGAGAAGCCCA
59.678
55.000
12.32
0.00
41.99
5.36
1248
1647
0.737715
GCCTCTTCCAGCACTACACG
60.738
60.000
0.00
0.00
0.00
4.49
1306
1716
3.449227
CCTGCCTCTACGCCGTCA
61.449
66.667
0.00
0.00
0.00
4.35
1309
1719
2.004808
CTGCCTCTACGCCGTCATCA
62.005
60.000
0.00
0.00
0.00
3.07
1310
1720
1.364171
GCCTCTACGCCGTCATCAT
59.636
57.895
0.00
0.00
0.00
2.45
1866
2281
2.027625
CGTCAAGGTGCCGTTCCTC
61.028
63.158
0.00
0.00
33.76
3.71
1911
2326
3.658757
TGCAAGACAAAAATGGCTACC
57.341
42.857
0.00
0.00
0.00
3.18
1928
2343
2.049985
CGGCCGATTAGGAGAGCG
60.050
66.667
24.07
0.00
45.00
5.03
1941
2356
1.294659
GAGAGCGGTTCTTGCAGGTG
61.295
60.000
0.00
0.00
35.87
4.00
2045
2478
2.561733
TTGTCCGTCGAGATCATGTC
57.438
50.000
0.00
0.00
0.00
3.06
2133
2570
4.141756
TGAAAGAAAATGGTGTTGGTGCAT
60.142
37.500
0.00
0.00
0.00
3.96
2295
2781
7.882179
ACTCCACTTTACAATTGGTCATTTAC
58.118
34.615
10.83
0.00
0.00
2.01
2349
2835
2.951642
ACACACAAGTCCCATGACAAAG
59.048
45.455
0.00
0.00
44.33
2.77
2375
2861
0.675633
ATTCAGCACCAAGGCAACAC
59.324
50.000
0.00
0.00
41.41
3.32
2392
2878
2.201732
ACACGCATGCTTATTAGTCCG
58.798
47.619
17.13
0.00
0.00
4.79
2450
2936
0.459063
CTCAGCTCGTGCATGCACTA
60.459
55.000
39.46
31.25
44.16
2.74
2496
2992
6.106003
TGAACAAATCAGCTCGTACATATGT
58.894
36.000
13.93
13.93
33.04
2.29
2518
3014
4.397481
TCAGACTTGCAGGTCAGATATG
57.603
45.455
28.25
17.88
38.57
1.78
2565
3061
3.370978
TCGTTCAGATCCATTTCGAAAGC
59.629
43.478
16.80
0.00
0.00
3.51
2566
3062
3.125146
CGTTCAGATCCATTTCGAAAGCA
59.875
43.478
16.80
2.82
0.00
3.91
2623
3120
2.300433
TCAGCACTTCAGCACAACAAT
58.700
42.857
0.00
0.00
36.85
2.71
2636
3133
7.085746
TCAGCACAACAATCTTTGACAATATG
58.914
34.615
0.00
0.00
0.00
1.78
2747
3244
0.806492
GCGGCTAAGTGTAGTGCCTC
60.806
60.000
0.00
0.00
42.90
4.70
2769
3266
3.423154
GTCTTGGCCGGCTGAACG
61.423
66.667
28.56
10.32
0.00
3.95
2863
3360
2.735663
CTCAAGACAGTTAGTGCAGCTG
59.264
50.000
10.11
10.11
41.05
4.24
2876
3373
2.427232
GCAGCTGCATGAACTTTGAA
57.573
45.000
33.36
0.00
41.59
2.69
2877
3374
2.056577
GCAGCTGCATGAACTTTGAAC
58.943
47.619
33.36
0.00
41.59
3.18
2878
3375
2.288030
GCAGCTGCATGAACTTTGAACT
60.288
45.455
33.36
0.00
41.59
3.01
2880
3377
4.557296
GCAGCTGCATGAACTTTGAACTAA
60.557
41.667
33.36
0.00
41.59
2.24
2881
3378
5.706916
CAGCTGCATGAACTTTGAACTAAT
58.293
37.500
0.00
0.00
0.00
1.73
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
54
104
5.366460
TCCTAGAGTACGATGACGAATTCT
58.634
41.667
3.52
0.00
42.66
2.40
55
105
5.670149
TCCTAGAGTACGATGACGAATTC
57.330
43.478
0.00
0.00
42.66
2.17
56
106
4.023878
GCTCCTAGAGTACGATGACGAATT
60.024
45.833
0.00
0.00
36.31
2.17
57
107
3.499157
GCTCCTAGAGTACGATGACGAAT
59.501
47.826
0.00
0.00
36.31
3.34
58
108
2.871022
GCTCCTAGAGTACGATGACGAA
59.129
50.000
0.00
0.00
36.31
3.85
59
109
2.481854
GCTCCTAGAGTACGATGACGA
58.518
52.381
0.00
0.00
36.31
4.20
60
110
1.532007
GGCTCCTAGAGTACGATGACG
59.468
57.143
0.00
0.00
37.49
4.35
61
111
2.809696
GAGGCTCCTAGAGTACGATGAC
59.190
54.545
2.15
0.00
31.39
3.06
62
112
2.224572
GGAGGCTCCTAGAGTACGATGA
60.225
54.545
26.44
0.00
32.53
2.92
63
113
2.156098
GGAGGCTCCTAGAGTACGATG
58.844
57.143
26.44
0.00
32.53
3.84
64
114
2.572209
GGAGGCTCCTAGAGTACGAT
57.428
55.000
26.44
0.00
32.53
3.73
80
130
2.025767
CTGGATGGACGCCTCAGGAG
62.026
65.000
0.00
0.00
0.00
3.69
81
131
2.038813
TGGATGGACGCCTCAGGA
59.961
61.111
0.00
0.00
0.00
3.86
82
132
2.503061
CTGGATGGACGCCTCAGG
59.497
66.667
0.00
0.00
0.00
3.86
83
133
2.202987
GCTGGATGGACGCCTCAG
60.203
66.667
0.00
0.00
0.00
3.35
84
134
2.685017
AGCTGGATGGACGCCTCA
60.685
61.111
0.00
0.00
0.00
3.86
85
135
2.107953
GAGCTGGATGGACGCCTC
59.892
66.667
0.00
0.00
0.00
4.70
86
136
3.474570
GGAGCTGGATGGACGCCT
61.475
66.667
0.00
0.00
0.00
5.52
87
137
3.746949
CTGGAGCTGGATGGACGCC
62.747
68.421
0.00
0.00
0.00
5.68
88
138
2.202987
CTGGAGCTGGATGGACGC
60.203
66.667
0.00
0.00
0.00
5.19
89
139
2.202987
GCTGGAGCTGGATGGACG
60.203
66.667
0.00
0.00
38.21
4.79
127
177
2.726373
GCAGTGGATAGATCGATCGACG
60.726
54.545
22.06
16.38
38.98
5.12
142
192
2.959030
TCCTACTAGTGCTATGCAGTGG
59.041
50.000
5.39
9.28
42.60
4.00
145
195
5.067273
AGTACTCCTACTAGTGCTATGCAG
58.933
45.833
5.39
0.00
40.17
4.41
146
196
5.050126
AGTACTCCTACTAGTGCTATGCA
57.950
43.478
5.39
0.00
40.17
3.96
147
197
6.484818
GTAGTACTCCTACTAGTGCTATGC
57.515
45.833
5.39
0.00
43.56
3.14
158
208
7.255555
GGAGCCAAAGAATAGTAGTACTCCTAC
60.256
44.444
5.96
0.00
45.47
3.18
165
261
7.113658
CTCTTGGAGCCAAAGAATAGTAGTA
57.886
40.000
3.24
0.00
35.33
1.82
223
378
1.449601
CGTATTGGTGCTCCGCCTT
60.450
57.895
0.00
0.00
34.70
4.35
226
381
2.461110
CCACGTATTGGTGCTCCGC
61.461
63.158
0.00
0.00
41.10
5.54
237
392
2.812178
GCAACGCGACCCACGTAT
60.812
61.111
15.93
0.00
44.30
3.06
276
442
2.125350
GGCGAGAACCAGCAGAGG
60.125
66.667
0.00
0.00
34.54
3.69
283
449
2.686106
GGGTAGGGGCGAGAACCA
60.686
66.667
0.00
0.00
33.46
3.67
286
452
3.072468
CACGGGTAGGGGCGAGAA
61.072
66.667
0.00
0.00
0.00
2.87
294
467
2.047274
CTGGTGCACACGGGTAGG
60.047
66.667
20.43
0.00
0.00
3.18
388
566
4.069232
CGGCGACCAGAGCAGGAA
62.069
66.667
0.00
0.00
36.08
3.36
401
595
1.257936
CCGAGTATGATTTTCACGGCG
59.742
52.381
4.80
4.80
28.15
6.46
411
605
0.674534
GAACCGAGCCCGAGTATGAT
59.325
55.000
0.00
0.00
38.22
2.45
413
607
0.527817
GTGAACCGAGCCCGAGTATG
60.528
60.000
0.00
0.00
38.22
2.39
414
608
1.673808
GGTGAACCGAGCCCGAGTAT
61.674
60.000
0.00
0.00
38.22
2.12
415
609
2.345760
GGTGAACCGAGCCCGAGTA
61.346
63.158
0.00
0.00
38.22
2.59
416
610
3.692406
GGTGAACCGAGCCCGAGT
61.692
66.667
0.00
0.00
38.22
4.18
417
611
3.019003
ATGGTGAACCGAGCCCGAG
62.019
63.158
0.00
0.00
39.43
4.63
418
612
3.000819
ATGGTGAACCGAGCCCGA
61.001
61.111
0.00
0.00
39.43
5.14
419
613
2.819595
CATGGTGAACCGAGCCCG
60.820
66.667
0.00
0.00
39.43
6.13
420
614
3.134127
GCATGGTGAACCGAGCCC
61.134
66.667
0.00
0.00
39.43
5.19
421
615
3.499737
CGCATGGTGAACCGAGCC
61.500
66.667
9.52
0.00
39.43
4.70
422
616
1.815421
ATCGCATGGTGAACCGAGC
60.815
57.895
0.00
6.03
39.43
5.03
424
618
2.106074
GCATCGCATGGTGAACCGA
61.106
57.895
0.00
0.00
39.43
4.69
492
767
2.541762
GGATCTCTGCTCGTTAATGCAC
59.458
50.000
0.00
0.00
35.20
4.57
574
854
3.386402
GGGGAAACAAAGGTGTGAAATCA
59.614
43.478
0.00
0.00
38.27
2.57
597
877
7.033185
CGGGTTTATGGAAGGTTTTGATTAAG
58.967
38.462
0.00
0.00
0.00
1.85
652
939
0.978667
GAAGGAGGGGGACTGGACTC
60.979
65.000
0.00
0.00
0.00
3.36
656
943
2.038975
TCGAAGGAGGGGGACTGG
59.961
66.667
0.00
0.00
0.00
4.00
657
944
1.608717
CTGTCGAAGGAGGGGGACTG
61.609
65.000
0.00
0.00
0.00
3.51
658
945
1.305381
CTGTCGAAGGAGGGGGACT
60.305
63.158
0.00
0.00
0.00
3.85
659
946
3.020237
GCTGTCGAAGGAGGGGGAC
62.020
68.421
0.00
0.00
0.00
4.46
660
947
2.683933
GCTGTCGAAGGAGGGGGA
60.684
66.667
0.00
0.00
0.00
4.81
712
999
2.417515
GGCGTTATATAGAGCAGAGGGC
60.418
54.545
11.82
0.00
45.30
5.19
713
1000
2.166664
GGGCGTTATATAGAGCAGAGGG
59.833
54.545
11.82
0.00
0.00
4.30
714
1001
3.093057
AGGGCGTTATATAGAGCAGAGG
58.907
50.000
11.82
0.00
0.00
3.69
715
1002
3.129638
GGAGGGCGTTATATAGAGCAGAG
59.870
52.174
11.82
0.00
0.00
3.35
716
1003
3.090037
GGAGGGCGTTATATAGAGCAGA
58.910
50.000
11.82
0.00
0.00
4.26
717
1004
2.159366
CGGAGGGCGTTATATAGAGCAG
60.159
54.545
11.82
0.00
0.00
4.24
718
1005
1.816835
CGGAGGGCGTTATATAGAGCA
59.183
52.381
11.82
0.00
0.00
4.26
759
1046
0.990818
GGCAGAGGAAGGGGAAGGAT
60.991
60.000
0.00
0.00
0.00
3.24
762
1049
1.301293
GTGGCAGAGGAAGGGGAAG
59.699
63.158
0.00
0.00
0.00
3.46
763
1050
1.065410
TTGTGGCAGAGGAAGGGGAA
61.065
55.000
0.00
0.00
0.00
3.97
764
1051
1.463214
TTGTGGCAGAGGAAGGGGA
60.463
57.895
0.00
0.00
0.00
4.81
766
1053
1.676967
GCTTGTGGCAGAGGAAGGG
60.677
63.158
0.00
0.00
41.35
3.95
776
1111
0.604780
TCTCTCTGCTTGCTTGTGGC
60.605
55.000
0.00
0.00
42.22
5.01
784
1119
2.157738
CTTGGGGTTTCTCTCTGCTTG
58.842
52.381
0.00
0.00
0.00
4.01
785
1120
1.546548
GCTTGGGGTTTCTCTCTGCTT
60.547
52.381
0.00
0.00
0.00
3.91
786
1121
0.037447
GCTTGGGGTTTCTCTCTGCT
59.963
55.000
0.00
0.00
0.00
4.24
787
1122
0.962855
GGCTTGGGGTTTCTCTCTGC
60.963
60.000
0.00
0.00
0.00
4.26
788
1123
0.401738
TGGCTTGGGGTTTCTCTCTG
59.598
55.000
0.00
0.00
0.00
3.35
789
1124
0.695347
CTGGCTTGGGGTTTCTCTCT
59.305
55.000
0.00
0.00
0.00
3.10
790
1125
0.962855
GCTGGCTTGGGGTTTCTCTC
60.963
60.000
0.00
0.00
0.00
3.20
791
1126
1.075659
GCTGGCTTGGGGTTTCTCT
59.924
57.895
0.00
0.00
0.00
3.10
809
1144
2.325082
CCGGCGTTGTTTCTCCCTG
61.325
63.158
6.01
0.00
0.00
4.45
836
1171
2.667318
CGCACCTTGTACGGCTGTG
61.667
63.158
8.92
0.00
0.00
3.66
879
1214
4.515944
TGGTAGTACATTCCAAACAAACCG
59.484
41.667
2.06
0.00
0.00
4.44
881
1225
7.381139
CACATTGGTAGTACATTCCAAACAAAC
59.619
37.037
16.26
0.00
43.11
2.93
890
1234
4.881273
TGGATGCACATTGGTAGTACATTC
59.119
41.667
2.06
0.00
0.00
2.67
891
1235
4.854173
TGGATGCACATTGGTAGTACATT
58.146
39.130
2.06
0.00
0.00
2.71
893
1237
3.990959
TGGATGCACATTGGTAGTACA
57.009
42.857
2.06
0.00
0.00
2.90
894
1238
8.504005
GTTATAATGGATGCACATTGGTAGTAC
58.496
37.037
11.69
0.00
40.97
2.73
896
1240
7.229306
CAGTTATAATGGATGCACATTGGTAGT
59.771
37.037
11.69
0.00
40.97
2.73
897
1241
7.445096
TCAGTTATAATGGATGCACATTGGTAG
59.555
37.037
11.69
0.11
40.97
3.18
912
1293
2.857748
TGCGACGCTGTCAGTTATAATG
59.142
45.455
22.08
0.00
32.09
1.90
917
1298
1.728074
CGTGCGACGCTGTCAGTTA
60.728
57.895
22.08
0.00
33.65
2.24
930
1311
1.154488
CATGAAAACCGTCCGTGCG
60.154
57.895
0.00
0.00
0.00
5.34
945
1326
2.286008
CGAATCAATCTGCGACACCATG
60.286
50.000
0.00
0.00
0.00
3.66
947
1328
1.358877
CGAATCAATCTGCGACACCA
58.641
50.000
0.00
0.00
0.00
4.17
948
1329
0.026803
GCGAATCAATCTGCGACACC
59.973
55.000
0.00
0.00
0.00
4.16
949
1330
0.721154
TGCGAATCAATCTGCGACAC
59.279
50.000
0.00
0.00
32.55
3.67
1128
1515
4.750695
TTCTGGGGATGCGGGGGA
62.751
66.667
0.00
0.00
0.00
4.81
1300
1710
0.318275
GAGAGGACGATGATGACGGC
60.318
60.000
0.00
0.00
38.12
5.68
1301
1711
0.312416
GGAGAGGACGATGATGACGG
59.688
60.000
0.00
0.00
34.93
4.79
1304
1714
1.815795
CGAGGGAGAGGACGATGATGA
60.816
57.143
0.00
0.00
0.00
2.92
1306
1716
1.175983
GCGAGGGAGAGGACGATGAT
61.176
60.000
0.00
0.00
0.00
2.45
1309
1719
2.519780
GGCGAGGGAGAGGACGAT
60.520
66.667
0.00
0.00
0.00
3.73
1344
1754
4.371417
AGGTAGACGGCCCCGACA
62.371
66.667
14.44
0.00
42.83
4.35
1502
1912
3.583276
TAGTGCACGCCGACCTTGG
62.583
63.158
12.01
0.00
0.00
3.61
1699
2109
4.651008
GTCGAACGGCACCGACCA
62.651
66.667
17.40
0.00
46.54
4.02
1866
2281
0.390472
GGCGTCAGTTCCTCCAGAAG
60.390
60.000
0.00
0.00
34.29
2.85
1911
2326
2.049985
CGCTCTCCTAATCGGCCG
60.050
66.667
22.12
22.12
0.00
6.13
1928
2343
3.365265
CCGCCACCTGCAAGAACC
61.365
66.667
0.00
0.00
41.33
3.62
1941
2356
2.485122
CACGAATCCTTTGCCGCC
59.515
61.111
0.00
0.00
0.00
6.13
1981
2401
7.967908
TCAAACCAACATACAAATTAATGGGT
58.032
30.769
0.00
0.00
0.00
4.51
2045
2478
2.504681
GCACAATTTCGCGGCAGG
60.505
61.111
6.13
0.00
0.00
4.85
2066
2499
2.415512
GCACCTCGTGAACATCTTAACC
59.584
50.000
0.00
0.00
35.23
2.85
2133
2570
2.159170
GCAGCAACACAAAAGGTACCAA
60.159
45.455
15.94
0.00
0.00
3.67
2142
2579
0.746204
TCCGTCAGCAGCAACACAAA
60.746
50.000
0.00
0.00
0.00
2.83
2236
2685
4.674475
TGCGAACGATATGTAGTTGCTAA
58.326
39.130
0.00
0.00
0.00
3.09
2276
2762
7.867445
AAAGCGTAAATGACCAATTGTAAAG
57.133
32.000
4.43
0.00
0.00
1.85
2283
2769
4.250116
TGCAAAAGCGTAAATGACCAAT
57.750
36.364
0.00
0.00
0.00
3.16
2285
2771
3.717400
TTGCAAAAGCGTAAATGACCA
57.283
38.095
0.00
0.00
0.00
4.02
2295
2781
3.670055
AGTTCGAATTGATTGCAAAAGCG
59.330
39.130
1.71
3.08
37.59
4.68
2312
2798
2.668457
GTGTGTGAGCCTTCATAGTTCG
59.332
50.000
0.00
0.00
35.39
3.95
2349
2835
2.863704
GCCTTGGTGCTGAATGTTCAAC
60.864
50.000
0.00
0.00
36.64
3.18
2375
2861
1.148310
CCCGGACTAATAAGCATGCG
58.852
55.000
13.01
0.00
0.00
4.73
2392
2878
5.048013
CACAGAATTTTGAGTTACTTCCCCC
60.048
44.000
2.48
0.00
0.00
5.40
2450
2936
4.750098
CAGTCGGTGTTAGTCTGAACATTT
59.250
41.667
0.00
0.00
41.21
2.32
2496
2992
4.223700
ACATATCTGACCTGCAAGTCTGAA
59.776
41.667
23.61
15.30
44.59
3.02
2623
3120
6.697455
GTCATCGAGCTACATATTGTCAAAGA
59.303
38.462
0.00
0.00
0.00
2.52
2731
3228
2.732597
CGTGAGAGGCACTACACTTAGC
60.733
54.545
10.71
0.00
45.49
3.09
2747
3244
4.379243
AGCCGGCCAAGACGTGAG
62.379
66.667
26.15
0.00
28.54
3.51
2769
3266
8.514594
TGACAATTTCTCTGATATGGTTTTCAC
58.485
33.333
0.00
0.00
0.00
3.18
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.