Multiple sequence alignment - TraesCS3B01G184600
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
TraesCS3B01G184600
chr3B
100.000
3227
0
0
1
3227
200478069
200481295
0.000000e+00
5960
1
TraesCS3B01G184600
chr3B
79.070
215
33
10
1348
1553
200479338
200479549
1.560000e-28
137
2
TraesCS3B01G184600
chr3B
79.070
215
33
10
1270
1481
200479416
200479621
1.560000e-28
137
3
TraesCS3B01G184600
chr3B
82.353
119
15
2
1440
1552
200479355
200479473
7.370000e-17
99
4
TraesCS3B01G184600
chr3B
82.353
119
15
2
1287
1405
200479508
200479620
7.370000e-17
99
5
TraesCS3B01G184600
chr3D
92.082
3170
120
61
121
3227
137008736
137005635
0.000000e+00
4342
6
TraesCS3B01G184600
chr3D
81.364
220
32
7
1341
1556
137007602
137007388
1.540000e-38
171
7
TraesCS3B01G184600
chr3D
87.719
114
12
2
1440
1552
137007579
137007467
7.260000e-27
132
8
TraesCS3B01G184600
chr3D
84.874
119
12
2
1287
1405
137007432
137007320
7.320000e-22
115
9
TraesCS3B01G184600
chr3A
92.035
2988
113
55
84
3014
155056601
155059520
0.000000e+00
4084
10
TraesCS3B01G184600
chr3A
84.874
119
12
2
1287
1405
155057925
155058037
7.320000e-22
115
11
TraesCS3B01G184600
chr5A
95.789
95
3
1
88
182
644821028
644821121
5.580000e-33
152
12
TraesCS3B01G184600
chr5A
89.381
113
7
4
69
179
650138213
650138104
1.560000e-28
137
13
TraesCS3B01G184600
chr5D
97.701
87
2
0
82
168
446400810
446400724
2.010000e-32
150
14
TraesCS3B01G184600
chr5D
95.604
91
2
2
88
177
521846310
521846221
9.330000e-31
145
15
TraesCS3B01G184600
chr5D
93.069
101
4
3
88
186
522112144
522112045
9.330000e-31
145
16
TraesCS3B01G184600
chr5B
94.565
92
5
0
84
175
544329729
544329638
3.360000e-30
143
17
TraesCS3B01G184600
chr5B
92.929
99
5
2
82
178
650023824
650023922
3.360000e-30
143
18
TraesCS3B01G184600
chr5B
94.565
92
5
0
88
179
658381120
658381029
3.360000e-30
143
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
TraesCS3B01G184600
chr3B
200478069
200481295
3226
False
1286.4
5960
84.56920
1
3227
5
chr3B.!!$F1
3226
1
TraesCS3B01G184600
chr3D
137005635
137008736
3101
True
1190.0
4342
86.50975
121
3227
4
chr3D.!!$R1
3106
2
TraesCS3B01G184600
chr3A
155056601
155059520
2919
False
2099.5
4084
88.45450
84
3014
2
chr3A.!!$F1
2930
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
794
835
0.110486
GAAAAGCACCTCCACCTCCA
59.890
55.0
0.0
0.0
0.0
3.86
F
829
870
0.171231
CGCAGCAGCTCACTACACTA
59.829
55.0
0.0
0.0
39.1
2.74
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2082
2140
1.152881
GTCCACCTCCATCATGGCC
60.153
63.158
0.0
0.0
37.47
5.36
R
2245
2311
1.345415
TCTTACAGTTCAACCCCCGAC
59.655
52.381
0.0
0.0
0.00
4.79
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
19
20
4.056125
CGTGCGCACTCCTCCAGA
62.056
66.667
35.27
0.00
0.00
3.86
31
32
3.233355
CTCCAGAGGAAACCGTTGG
57.767
57.895
0.00
0.00
34.66
3.77
32
33
0.955919
CTCCAGAGGAAACCGTTGGC
60.956
60.000
0.00
0.00
33.83
4.52
33
34
1.971695
CCAGAGGAAACCGTTGGCC
60.972
63.158
0.00
0.00
0.00
5.36
34
35
2.032071
AGAGGAAACCGTTGGCCG
59.968
61.111
0.00
0.00
0.00
6.13
35
36
2.031465
GAGGAAACCGTTGGCCGA
59.969
61.111
0.00
0.00
39.56
5.54
36
37
2.281276
AGGAAACCGTTGGCCGAC
60.281
61.111
13.74
13.74
39.56
4.79
37
38
2.592287
GGAAACCGTTGGCCGACA
60.592
61.111
23.21
0.00
39.56
4.35
38
39
1.969589
GGAAACCGTTGGCCGACAT
60.970
57.895
23.21
7.51
39.56
3.06
39
40
1.209127
GAAACCGTTGGCCGACATG
59.791
57.895
23.21
15.12
39.56
3.21
40
41
1.228003
AAACCGTTGGCCGACATGA
60.228
52.632
23.21
0.00
39.56
3.07
41
42
1.234615
AAACCGTTGGCCGACATGAG
61.235
55.000
23.21
10.47
39.56
2.90
42
43
2.819595
CCGTTGGCCGACATGAGG
60.820
66.667
23.21
11.86
39.56
3.86
43
44
2.047274
CGTTGGCCGACATGAGGT
60.047
61.111
23.21
0.00
39.56
3.85
44
45
1.671054
CGTTGGCCGACATGAGGTT
60.671
57.895
23.21
0.00
39.56
3.50
45
46
1.875963
GTTGGCCGACATGAGGTTG
59.124
57.895
18.96
0.00
0.00
3.77
51
52
1.586422
CCGACATGAGGTTGGCTATG
58.414
55.000
0.00
0.00
44.11
2.23
52
53
1.138859
CCGACATGAGGTTGGCTATGA
59.861
52.381
0.00
0.00
44.11
2.15
53
54
2.477825
CGACATGAGGTTGGCTATGAG
58.522
52.381
0.00
0.00
0.00
2.90
54
55
2.159043
CGACATGAGGTTGGCTATGAGT
60.159
50.000
0.00
0.00
0.00
3.41
55
56
3.679917
CGACATGAGGTTGGCTATGAGTT
60.680
47.826
0.00
0.00
0.00
3.01
56
57
3.873952
GACATGAGGTTGGCTATGAGTTC
59.126
47.826
0.00
0.00
0.00
3.01
57
58
3.521126
ACATGAGGTTGGCTATGAGTTCT
59.479
43.478
0.00
0.00
0.00
3.01
58
59
4.716784
ACATGAGGTTGGCTATGAGTTCTA
59.283
41.667
0.00
0.00
0.00
2.10
59
60
5.367937
ACATGAGGTTGGCTATGAGTTCTAT
59.632
40.000
0.00
0.00
0.00
1.98
60
61
6.554982
ACATGAGGTTGGCTATGAGTTCTATA
59.445
38.462
0.00
0.00
0.00
1.31
61
62
6.656632
TGAGGTTGGCTATGAGTTCTATAG
57.343
41.667
0.00
0.00
0.00
1.31
62
63
5.540337
TGAGGTTGGCTATGAGTTCTATAGG
59.460
44.000
0.00
0.00
0.00
2.57
64
65
4.563786
GGTTGGCTATGAGTTCTATAGGCC
60.564
50.000
13.68
0.00
47.00
5.19
65
66
3.173965
TGGCTATGAGTTCTATAGGCCC
58.826
50.000
0.00
0.72
47.00
5.80
66
67
3.181406
TGGCTATGAGTTCTATAGGCCCT
60.181
47.826
0.00
0.00
47.00
5.19
67
68
3.196685
GGCTATGAGTTCTATAGGCCCTG
59.803
52.174
0.00
0.00
43.82
4.45
68
69
3.196685
GCTATGAGTTCTATAGGCCCTGG
59.803
52.174
0.00
0.00
0.00
4.45
69
70
2.868964
TGAGTTCTATAGGCCCTGGT
57.131
50.000
0.00
0.00
0.00
4.00
70
71
3.130734
TGAGTTCTATAGGCCCTGGTT
57.869
47.619
0.00
0.00
0.00
3.67
71
72
2.771943
TGAGTTCTATAGGCCCTGGTTG
59.228
50.000
0.00
0.00
0.00
3.77
72
73
3.039011
GAGTTCTATAGGCCCTGGTTGA
58.961
50.000
0.00
0.00
0.00
3.18
73
74
3.454812
GAGTTCTATAGGCCCTGGTTGAA
59.545
47.826
0.00
0.00
0.00
2.69
74
75
3.850173
AGTTCTATAGGCCCTGGTTGAAA
59.150
43.478
0.00
0.00
0.00
2.69
75
76
3.926058
TCTATAGGCCCTGGTTGAAAC
57.074
47.619
0.00
0.00
0.00
2.78
76
77
3.460825
TCTATAGGCCCTGGTTGAAACT
58.539
45.455
0.00
0.00
0.00
2.66
77
78
3.850173
TCTATAGGCCCTGGTTGAAACTT
59.150
43.478
0.00
0.00
0.00
2.66
78
79
3.542969
ATAGGCCCTGGTTGAAACTTT
57.457
42.857
0.00
0.00
0.00
2.66
79
80
1.413118
AGGCCCTGGTTGAAACTTTG
58.587
50.000
0.00
0.00
0.00
2.77
80
81
1.119684
GGCCCTGGTTGAAACTTTGT
58.880
50.000
0.00
0.00
0.00
2.83
81
82
2.091555
AGGCCCTGGTTGAAACTTTGTA
60.092
45.455
0.00
0.00
0.00
2.41
82
83
2.035449
GGCCCTGGTTGAAACTTTGTAC
59.965
50.000
0.00
0.00
0.00
2.90
89
90
4.097286
TGGTTGAAACTTTGTACAAGCTCC
59.903
41.667
8.56
5.35
40.07
4.70
93
94
1.779569
ACTTTGTACAAGCTCCGTCG
58.220
50.000
8.56
0.00
0.00
5.12
149
150
1.152096
AGACCCGGGTTCAAGTCCT
60.152
57.895
30.89
15.82
0.00
3.85
242
253
0.758734
GGATGATCATCACCCCGTCA
59.241
55.000
31.49
0.00
39.54
4.35
363
380
4.745620
GCTAAGATCTTGTAGCTTTACCCG
59.254
45.833
18.47
0.00
39.73
5.28
442
460
5.175856
CCGAGAGCAACTAGAAAATAATCGG
59.824
44.000
0.00
3.77
38.85
4.18
443
461
5.977725
CGAGAGCAACTAGAAAATAATCGGA
59.022
40.000
0.00
0.00
0.00
4.55
470
488
4.288626
TCAAATTAACCTACTCCTGCTGGT
59.711
41.667
9.73
0.00
34.23
4.00
505
530
3.004106
CAGCAGCAGCCAATAGATAAACC
59.996
47.826
0.00
0.00
43.56
3.27
508
533
4.147321
CAGCAGCCAATAGATAAACCCAT
58.853
43.478
0.00
0.00
0.00
4.00
509
534
4.217118
CAGCAGCCAATAGATAAACCCATC
59.783
45.833
0.00
0.00
0.00
3.51
519
544
3.654806
AGATAAACCCATCCTCATCCCTG
59.345
47.826
0.00
0.00
0.00
4.45
566
592
2.461110
CCGTACTGTCCATTGGCGC
61.461
63.158
0.00
0.00
0.00
6.53
790
831
0.250338
AGTCGAAAAGCACCTCCACC
60.250
55.000
0.00
0.00
0.00
4.61
794
835
0.110486
GAAAAGCACCTCCACCTCCA
59.890
55.000
0.00
0.00
0.00
3.86
795
836
0.178990
AAAAGCACCTCCACCTCCAC
60.179
55.000
0.00
0.00
0.00
4.02
796
837
1.062488
AAAGCACCTCCACCTCCACT
61.062
55.000
0.00
0.00
0.00
4.00
797
838
1.484444
AAGCACCTCCACCTCCACTC
61.484
60.000
0.00
0.00
0.00
3.51
798
839
2.960688
GCACCTCCACCTCCACTCC
61.961
68.421
0.00
0.00
0.00
3.85
800
841
2.122729
CCTCCACCTCCACTCCCA
59.877
66.667
0.00
0.00
0.00
4.37
801
842
2.294078
CCTCCACCTCCACTCCCAC
61.294
68.421
0.00
0.00
0.00
4.61
802
843
1.229336
CTCCACCTCCACTCCCACT
60.229
63.158
0.00
0.00
0.00
4.00
803
844
0.838122
CTCCACCTCCACTCCCACTT
60.838
60.000
0.00
0.00
0.00
3.16
827
868
3.468007
CGCAGCAGCTCACTACAC
58.532
61.111
0.00
0.00
39.10
2.90
828
869
1.080230
CGCAGCAGCTCACTACACT
60.080
57.895
0.00
0.00
39.10
3.55
829
870
0.171231
CGCAGCAGCTCACTACACTA
59.829
55.000
0.00
0.00
39.10
2.74
830
871
1.634702
GCAGCAGCTCACTACACTAC
58.365
55.000
0.00
0.00
37.91
2.73
831
872
1.737363
GCAGCAGCTCACTACACTACC
60.737
57.143
0.00
0.00
37.91
3.18
832
873
1.134965
CAGCAGCTCACTACACTACCC
60.135
57.143
0.00
0.00
0.00
3.69
833
874
0.175989
GCAGCTCACTACACTACCCC
59.824
60.000
0.00
0.00
0.00
4.95
834
875
0.824759
CAGCTCACTACACTACCCCC
59.175
60.000
0.00
0.00
0.00
5.40
835
876
0.412244
AGCTCACTACACTACCCCCA
59.588
55.000
0.00
0.00
0.00
4.96
836
877
1.203262
AGCTCACTACACTACCCCCAA
60.203
52.381
0.00
0.00
0.00
4.12
837
878
1.207329
GCTCACTACACTACCCCCAAG
59.793
57.143
0.00
0.00
0.00
3.61
838
879
2.537143
CTCACTACACTACCCCCAAGT
58.463
52.381
0.00
0.00
0.00
3.16
839
880
3.705051
CTCACTACACTACCCCCAAGTA
58.295
50.000
0.00
0.00
0.00
2.24
840
881
3.434309
TCACTACACTACCCCCAAGTAC
58.566
50.000
0.00
0.00
0.00
2.73
841
882
2.498885
CACTACACTACCCCCAAGTACC
59.501
54.545
0.00
0.00
0.00
3.34
842
883
2.113807
CTACACTACCCCCAAGTACCC
58.886
57.143
0.00
0.00
0.00
3.69
843
884
0.194080
ACACTACCCCCAAGTACCCA
59.806
55.000
0.00
0.00
0.00
4.51
844
885
0.909623
CACTACCCCCAAGTACCCAG
59.090
60.000
0.00
0.00
0.00
4.45
896
943
2.854401
CGCACATGCCACCCAACAA
61.854
57.895
0.00
0.00
37.91
2.83
1337
1392
3.865830
GCCGGAGCAGCTTTACGC
61.866
66.667
5.05
0.00
39.53
4.42
1338
1393
2.434185
CCGGAGCAGCTTTACGCA
60.434
61.111
0.00
0.00
42.61
5.24
1339
1394
2.456119
CCGGAGCAGCTTTACGCAG
61.456
63.158
0.00
0.00
42.61
5.18
2220
2278
3.570212
AGGGTGCTTGGCTTCCGT
61.570
61.111
0.00
0.00
0.00
4.69
2227
2285
1.871772
CTTGGCTTCCGTTGCTGAG
59.128
57.895
0.00
0.00
0.00
3.35
2240
2300
2.670934
CTGAGCCGCAGCCAAGTT
60.671
61.111
0.00
0.00
41.25
2.66
2241
2301
2.669569
TGAGCCGCAGCCAAGTTC
60.670
61.111
0.00
0.00
41.25
3.01
2247
2313
3.056328
GCAGCCAAGTTCGGGGTC
61.056
66.667
0.00
0.00
32.88
4.46
2255
2321
4.710167
GTTCGGGGTCGGGGGTTG
62.710
72.222
0.00
0.00
36.95
3.77
2271
2337
5.474189
CGGGGGTTGAACTGTAAGAAATTAA
59.526
40.000
0.00
0.00
37.43
1.40
2273
2339
7.544622
GGGGGTTGAACTGTAAGAAATTAATC
58.455
38.462
0.00
0.00
37.43
1.75
2291
2357
7.961326
ATTAATCAAGGCAGGATTTTACAGT
57.039
32.000
8.61
0.00
36.45
3.55
2330
2412
2.871182
AGAATCGTGCGCTAGAATCA
57.129
45.000
9.73
0.00
0.00
2.57
2335
2417
0.578683
CGTGCGCTAGAATCATGTGG
59.421
55.000
9.73
0.00
0.00
4.17
2340
2422
3.561310
TGCGCTAGAATCATGTGGATTTC
59.439
43.478
9.73
0.00
46.17
2.17
2406
2489
6.690194
ATGAATTTGACATAGCCTGTTCTC
57.310
37.500
0.00
0.00
38.54
2.87
2424
2507
4.350368
TCTCCAGTAGCATGTTGAACAA
57.650
40.909
0.62
0.00
0.00
2.83
2433
2516
6.803320
AGTAGCATGTTGAACAAATTTCATCG
59.197
34.615
0.62
0.00
0.00
3.84
2437
2525
7.385752
AGCATGTTGAACAAATTTCATCGAAAT
59.614
29.630
0.62
0.00
43.07
2.17
2444
2532
8.924691
TGAACAAATTTCATCGAAATCATTTCC
58.075
29.630
4.47
0.00
40.77
3.13
2445
2533
8.830201
AACAAATTTCATCGAAATCATTTCCA
57.170
26.923
4.47
0.00
40.77
3.53
2446
2534
9.439500
AACAAATTTCATCGAAATCATTTCCAT
57.561
25.926
4.47
0.00
40.77
3.41
2447
2535
9.439500
ACAAATTTCATCGAAATCATTTCCATT
57.561
25.926
4.47
0.00
40.77
3.16
2451
2539
8.613613
TTTCATCGAAATCATTTCCATTTACG
57.386
30.769
4.47
0.00
36.30
3.18
2452
2540
6.724263
TCATCGAAATCATTTCCATTTACGG
58.276
36.000
4.47
0.00
36.30
4.02
2460
2548
5.885881
TCATTTCCATTTACGGTATGTTGC
58.114
37.500
0.00
0.00
0.00
4.17
2464
2552
3.013921
CCATTTACGGTATGTTGCCACT
58.986
45.455
0.00
0.00
0.00
4.00
2482
2570
5.046663
TGCCACTACAGATCTTACATGTTGA
60.047
40.000
2.30
3.47
0.00
3.18
2849
2937
1.141053
ACAGGGGCATACTTCCGAATC
59.859
52.381
0.00
0.00
0.00
2.52
2909
2997
8.914011
AGATTAATAAGAAAAAGTATGGTGGCC
58.086
33.333
0.00
0.00
0.00
5.36
2926
3014
2.497675
TGGCCAGTGTTGACTAGAGATC
59.502
50.000
0.00
0.00
0.00
2.75
3043
3131
1.985473
TGAGCAGTTTGTGGCAGATT
58.015
45.000
0.00
0.00
0.00
2.40
3055
3143
0.035820
GGCAGATTACAACGGGACCA
60.036
55.000
0.00
0.00
0.00
4.02
3057
3145
2.156098
GCAGATTACAACGGGACCAAA
58.844
47.619
0.00
0.00
0.00
3.28
3058
3146
2.161609
GCAGATTACAACGGGACCAAAG
59.838
50.000
0.00
0.00
0.00
2.77
3060
3148
3.818773
CAGATTACAACGGGACCAAAGTT
59.181
43.478
0.00
0.00
0.00
2.66
3061
3149
4.998672
CAGATTACAACGGGACCAAAGTTA
59.001
41.667
0.00
0.00
0.00
2.24
3062
3150
4.999311
AGATTACAACGGGACCAAAGTTAC
59.001
41.667
0.00
0.00
0.00
2.50
3066
3154
4.018490
ACAACGGGACCAAAGTTACTTTT
58.982
39.130
7.71
0.00
30.60
2.27
3067
3155
4.463539
ACAACGGGACCAAAGTTACTTTTT
59.536
37.500
7.71
0.00
30.60
1.94
3091
3179
9.979270
TTTTACTGCACATTGTTTATTTGTTTG
57.021
25.926
0.00
0.00
0.00
2.93
3092
3180
6.601741
ACTGCACATTGTTTATTTGTTTGG
57.398
33.333
0.00
0.00
0.00
3.28
3096
3184
6.478344
TGCACATTGTTTATTTGTTTGGAGTC
59.522
34.615
0.00
0.00
0.00
3.36
3106
3194
6.824305
ATTTGTTTGGAGTCAGGATTACAG
57.176
37.500
0.00
0.00
0.00
2.74
3107
3195
5.560722
TTGTTTGGAGTCAGGATTACAGA
57.439
39.130
0.00
0.00
0.00
3.41
3108
3196
4.894784
TGTTTGGAGTCAGGATTACAGAC
58.105
43.478
0.00
0.00
0.00
3.51
3109
3197
4.346709
TGTTTGGAGTCAGGATTACAGACA
59.653
41.667
0.00
0.00
34.80
3.41
3110
3198
5.163248
TGTTTGGAGTCAGGATTACAGACAA
60.163
40.000
0.00
0.00
34.80
3.18
3111
3199
4.537135
TGGAGTCAGGATTACAGACAAC
57.463
45.455
0.00
0.00
34.80
3.32
3112
3200
3.901222
TGGAGTCAGGATTACAGACAACA
59.099
43.478
0.00
0.00
34.80
3.33
3113
3201
4.346709
TGGAGTCAGGATTACAGACAACAA
59.653
41.667
0.00
0.00
34.80
2.83
3114
3202
5.163248
TGGAGTCAGGATTACAGACAACAAA
60.163
40.000
0.00
0.00
34.80
2.83
3115
3203
5.763204
GGAGTCAGGATTACAGACAACAAAA
59.237
40.000
0.00
0.00
34.80
2.44
3116
3204
6.431234
GGAGTCAGGATTACAGACAACAAAAT
59.569
38.462
0.00
0.00
34.80
1.82
3117
3205
7.040409
GGAGTCAGGATTACAGACAACAAAATT
60.040
37.037
0.00
0.00
34.80
1.82
3118
3206
8.237811
AGTCAGGATTACAGACAACAAAATTT
57.762
30.769
0.00
0.00
34.80
1.82
3119
3207
8.137437
AGTCAGGATTACAGACAACAAAATTTG
58.863
33.333
3.89
3.89
34.80
2.32
3155
3243
6.183359
CCAATCAAACTAAAATCGAAAGCACG
60.183
38.462
0.00
0.00
0.00
5.34
3163
3251
1.726853
ATCGAAAGCACGAGGGAAAG
58.273
50.000
0.00
0.00
45.22
2.62
3164
3252
0.391597
TCGAAAGCACGAGGGAAAGT
59.608
50.000
0.00
0.00
37.37
2.66
3165
3253
1.202604
TCGAAAGCACGAGGGAAAGTT
60.203
47.619
0.00
0.00
37.37
2.66
3166
3254
1.602377
CGAAAGCACGAGGGAAAGTTT
59.398
47.619
0.00
0.00
35.09
2.66
3167
3255
2.602217
CGAAAGCACGAGGGAAAGTTTG
60.602
50.000
0.00
0.00
35.09
2.93
3168
3256
2.052782
AAGCACGAGGGAAAGTTTGT
57.947
45.000
0.00
0.00
0.00
2.83
3169
3257
1.308998
AGCACGAGGGAAAGTTTGTG
58.691
50.000
0.00
0.00
32.88
3.33
3170
3258
0.310854
GCACGAGGGAAAGTTTGTGG
59.689
55.000
0.00
0.00
30.85
4.17
3172
3260
2.294074
CACGAGGGAAAGTTTGTGGAA
58.706
47.619
0.00
0.00
0.00
3.53
3173
3261
2.290641
CACGAGGGAAAGTTTGTGGAAG
59.709
50.000
0.00
0.00
0.00
3.46
3174
3262
2.092592
ACGAGGGAAAGTTTGTGGAAGT
60.093
45.455
0.00
0.00
0.00
3.01
3175
3263
3.135167
ACGAGGGAAAGTTTGTGGAAGTA
59.865
43.478
0.00
0.00
0.00
2.24
3176
3264
4.202430
ACGAGGGAAAGTTTGTGGAAGTAT
60.202
41.667
0.00
0.00
0.00
2.12
3177
3265
4.154195
CGAGGGAAAGTTTGTGGAAGTATG
59.846
45.833
0.00
0.00
0.00
2.39
3178
3266
3.826729
AGGGAAAGTTTGTGGAAGTATGC
59.173
43.478
0.00
0.00
0.00
3.14
3208
3296
2.691927
CTGCTCAACTGTCATGTGCTA
58.308
47.619
7.71
0.00
37.96
3.49
3216
3304
6.643388
TCAACTGTCATGTGCTATTCTACAT
58.357
36.000
0.00
0.00
37.99
2.29
3221
3309
8.883731
ACTGTCATGTGCTATTCTACATAAAAC
58.116
33.333
0.00
0.00
35.86
2.43
3222
3310
9.102757
CTGTCATGTGCTATTCTACATAAAACT
57.897
33.333
0.00
0.00
35.86
2.66
3223
3311
8.882736
TGTCATGTGCTATTCTACATAAAACTG
58.117
33.333
0.00
0.00
35.86
3.16
3224
3312
8.883731
GTCATGTGCTATTCTACATAAAACTGT
58.116
33.333
0.00
0.00
35.86
3.55
3225
3313
8.882736
TCATGTGCTATTCTACATAAAACTGTG
58.117
33.333
0.00
0.00
35.86
3.66
3226
3314
8.882736
CATGTGCTATTCTACATAAAACTGTGA
58.117
33.333
0.00
0.00
35.86
3.58
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
2
3
3.978723
CTCTGGAGGAGTGCGCACG
62.979
68.421
32.94
17.96
37.30
5.34
3
4
2.125753
CTCTGGAGGAGTGCGCAC
60.126
66.667
32.79
32.79
37.30
5.34
13
14
0.955919
GCCAACGGTTTCCTCTGGAG
60.956
60.000
0.00
0.00
31.21
3.86
14
15
1.072505
GCCAACGGTTTCCTCTGGA
59.927
57.895
0.00
0.00
0.00
3.86
15
16
1.971695
GGCCAACGGTTTCCTCTGG
60.972
63.158
0.00
0.00
0.00
3.86
16
17
2.325082
CGGCCAACGGTTTCCTCTG
61.325
63.158
2.24
0.00
39.42
3.35
17
18
2.032071
CGGCCAACGGTTTCCTCT
59.968
61.111
2.24
0.00
39.42
3.69
18
19
2.031465
TCGGCCAACGGTTTCCTC
59.969
61.111
2.24
0.00
44.45
3.71
19
20
2.281276
GTCGGCCAACGGTTTCCT
60.281
61.111
2.24
0.00
44.45
3.36
20
21
1.969589
ATGTCGGCCAACGGTTTCC
60.970
57.895
2.24
0.00
44.45
3.13
21
22
1.209127
CATGTCGGCCAACGGTTTC
59.791
57.895
2.24
0.00
44.45
2.78
22
23
1.228003
TCATGTCGGCCAACGGTTT
60.228
52.632
2.24
0.00
44.45
3.27
23
24
1.671054
CTCATGTCGGCCAACGGTT
60.671
57.895
2.24
0.00
44.45
4.44
24
25
2.047274
CTCATGTCGGCCAACGGT
60.047
61.111
2.24
0.00
44.45
4.83
25
26
2.819595
CCTCATGTCGGCCAACGG
60.820
66.667
2.24
0.00
44.45
4.44
26
27
1.671054
AACCTCATGTCGGCCAACG
60.671
57.895
2.24
0.00
46.11
4.10
27
28
1.586154
CCAACCTCATGTCGGCCAAC
61.586
60.000
2.24
0.00
0.00
3.77
28
29
1.303236
CCAACCTCATGTCGGCCAA
60.303
57.895
2.24
0.00
0.00
4.52
29
30
2.350895
CCAACCTCATGTCGGCCA
59.649
61.111
2.24
0.00
0.00
5.36
30
31
2.252072
TAGCCAACCTCATGTCGGCC
62.252
60.000
0.00
0.00
44.06
6.13
31
32
0.179045
ATAGCCAACCTCATGTCGGC
60.179
55.000
0.00
0.00
43.31
5.54
32
33
1.138859
TCATAGCCAACCTCATGTCGG
59.861
52.381
0.00
0.00
0.00
4.79
33
34
2.159043
ACTCATAGCCAACCTCATGTCG
60.159
50.000
0.00
0.00
0.00
4.35
34
35
3.550437
ACTCATAGCCAACCTCATGTC
57.450
47.619
0.00
0.00
0.00
3.06
35
36
3.521126
AGAACTCATAGCCAACCTCATGT
59.479
43.478
0.00
0.00
0.00
3.21
36
37
4.148128
AGAACTCATAGCCAACCTCATG
57.852
45.455
0.00
0.00
0.00
3.07
37
38
6.212388
CCTATAGAACTCATAGCCAACCTCAT
59.788
42.308
0.00
0.00
0.00
2.90
38
39
5.540337
CCTATAGAACTCATAGCCAACCTCA
59.460
44.000
0.00
0.00
0.00
3.86
39
40
5.567823
GCCTATAGAACTCATAGCCAACCTC
60.568
48.000
0.00
0.00
0.00
3.85
40
41
4.284746
GCCTATAGAACTCATAGCCAACCT
59.715
45.833
0.00
0.00
0.00
3.50
41
42
4.563786
GGCCTATAGAACTCATAGCCAACC
60.564
50.000
0.00
0.00
0.00
3.77
42
43
4.563786
GGGCCTATAGAACTCATAGCCAAC
60.564
50.000
0.84
0.00
30.28
3.77
43
44
3.583086
GGGCCTATAGAACTCATAGCCAA
59.417
47.826
0.84
0.00
30.28
4.52
44
45
3.173965
GGGCCTATAGAACTCATAGCCA
58.826
50.000
0.84
0.00
30.28
4.75
45
46
3.196685
CAGGGCCTATAGAACTCATAGCC
59.803
52.174
5.28
2.59
0.00
3.93
46
47
3.196685
CCAGGGCCTATAGAACTCATAGC
59.803
52.174
5.28
0.00
0.00
2.97
47
48
4.421131
ACCAGGGCCTATAGAACTCATAG
58.579
47.826
5.28
0.00
0.00
2.23
48
49
4.487282
ACCAGGGCCTATAGAACTCATA
57.513
45.455
5.28
0.00
0.00
2.15
49
50
3.352611
ACCAGGGCCTATAGAACTCAT
57.647
47.619
5.28
0.00
0.00
2.90
50
51
2.771943
CAACCAGGGCCTATAGAACTCA
59.228
50.000
5.28
0.00
0.00
3.41
51
52
3.039011
TCAACCAGGGCCTATAGAACTC
58.961
50.000
5.28
0.00
0.00
3.01
52
53
3.130734
TCAACCAGGGCCTATAGAACT
57.869
47.619
5.28
0.00
0.00
3.01
53
54
3.926058
TTCAACCAGGGCCTATAGAAC
57.074
47.619
5.28
0.00
0.00
3.01
54
55
3.850173
AGTTTCAACCAGGGCCTATAGAA
59.150
43.478
5.28
5.74
0.00
2.10
55
56
3.460825
AGTTTCAACCAGGGCCTATAGA
58.539
45.455
5.28
0.00
0.00
1.98
56
57
3.933861
AGTTTCAACCAGGGCCTATAG
57.066
47.619
5.28
0.00
0.00
1.31
57
58
4.202631
ACAAAGTTTCAACCAGGGCCTATA
60.203
41.667
5.28
0.00
0.00
1.31
58
59
3.165071
CAAAGTTTCAACCAGGGCCTAT
58.835
45.455
5.28
0.00
0.00
2.57
59
60
2.091555
ACAAAGTTTCAACCAGGGCCTA
60.092
45.455
5.28
0.00
0.00
3.93
60
61
1.342975
ACAAAGTTTCAACCAGGGCCT
60.343
47.619
0.00
0.00
0.00
5.19
61
62
1.119684
ACAAAGTTTCAACCAGGGCC
58.880
50.000
0.00
0.00
0.00
5.80
62
63
2.691011
TGTACAAAGTTTCAACCAGGGC
59.309
45.455
0.00
0.00
0.00
5.19
63
64
4.736464
GCTTGTACAAAGTTTCAACCAGGG
60.736
45.833
10.03
0.00
0.00
4.45
64
65
4.097892
AGCTTGTACAAAGTTTCAACCAGG
59.902
41.667
10.03
0.00
0.00
4.45
65
66
5.248870
AGCTTGTACAAAGTTTCAACCAG
57.751
39.130
10.03
0.00
0.00
4.00
66
67
4.097286
GGAGCTTGTACAAAGTTTCAACCA
59.903
41.667
10.03
0.00
0.00
3.67
67
68
4.607955
GGAGCTTGTACAAAGTTTCAACC
58.392
43.478
10.03
1.94
0.00
3.77
68
69
4.201881
ACGGAGCTTGTACAAAGTTTCAAC
60.202
41.667
10.03
0.00
0.00
3.18
69
70
3.942748
ACGGAGCTTGTACAAAGTTTCAA
59.057
39.130
10.03
0.00
0.00
2.69
70
71
3.537580
ACGGAGCTTGTACAAAGTTTCA
58.462
40.909
10.03
0.00
0.00
2.69
71
72
3.362693
CGACGGAGCTTGTACAAAGTTTC
60.363
47.826
10.03
5.01
0.00
2.78
72
73
2.542595
CGACGGAGCTTGTACAAAGTTT
59.457
45.455
10.03
0.00
0.00
2.66
73
74
2.132762
CGACGGAGCTTGTACAAAGTT
58.867
47.619
10.03
2.21
0.00
2.66
74
75
1.068127
ACGACGGAGCTTGTACAAAGT
59.932
47.619
10.03
5.09
0.00
2.66
75
76
1.779569
ACGACGGAGCTTGTACAAAG
58.220
50.000
10.03
5.34
0.00
2.77
76
77
2.294233
ACTACGACGGAGCTTGTACAAA
59.706
45.455
7.09
0.00
0.00
2.83
77
78
1.881973
ACTACGACGGAGCTTGTACAA
59.118
47.619
7.09
8.28
0.00
2.41
78
79
1.466167
GACTACGACGGAGCTTGTACA
59.534
52.381
7.09
0.00
0.00
2.90
79
80
1.736681
AGACTACGACGGAGCTTGTAC
59.263
52.381
7.09
0.00
0.00
2.90
80
81
2.105006
AGACTACGACGGAGCTTGTA
57.895
50.000
7.09
0.00
0.00
2.41
81
82
2.008329
CTAGACTACGACGGAGCTTGT
58.992
52.381
7.09
0.00
0.00
3.16
82
83
1.331138
CCTAGACTACGACGGAGCTTG
59.669
57.143
7.09
6.50
0.00
4.01
89
90
2.611292
CCTAACCACCTAGACTACGACG
59.389
54.545
0.00
0.00
0.00
5.12
93
94
5.700373
CGAGTATCCTAACCACCTAGACTAC
59.300
48.000
0.00
0.00
0.00
2.73
171
172
3.751175
TGCCTGTTAATCGAGGAACAAAG
59.249
43.478
13.94
10.29
35.24
2.77
175
176
2.673368
CTGTGCCTGTTAATCGAGGAAC
59.327
50.000
5.49
5.49
38.31
3.62
176
177
2.354704
CCTGTGCCTGTTAATCGAGGAA
60.355
50.000
0.00
0.00
0.00
3.36
258
269
1.548132
CGGCGTTTTGGCTTGCTTTC
61.548
55.000
0.00
0.00
42.02
2.62
302
317
2.956987
CTGGTTCCGCTTTGGCTG
59.043
61.111
0.00
0.00
37.80
4.85
386
403
9.683069
GAGATACACTTTGTTGTTTCATTCATT
57.317
29.630
0.00
0.00
31.82
2.57
442
460
7.011857
CAGCAGGAGTAGGTTAATTTGATCTTC
59.988
40.741
0.00
0.00
0.00
2.87
443
461
6.825721
CAGCAGGAGTAGGTTAATTTGATCTT
59.174
38.462
0.00
0.00
0.00
2.40
470
488
3.300934
CTGCTGCGCTGGTAGGTGA
62.301
63.158
16.47
0.00
0.00
4.02
479
497
3.982316
TATTGGCTGCTGCTGCGCT
62.982
57.895
22.39
13.04
43.34
5.92
493
518
6.012157
AGGGATGAGGATGGGTTTATCTATTG
60.012
42.308
0.00
0.00
0.00
1.90
494
519
6.012157
CAGGGATGAGGATGGGTTTATCTATT
60.012
42.308
0.00
0.00
0.00
1.73
505
530
0.179026
CAGCACAGGGATGAGGATGG
60.179
60.000
0.00
0.00
33.82
3.51
508
533
1.614525
AGCAGCACAGGGATGAGGA
60.615
57.895
0.00
0.00
33.82
3.71
509
534
1.451567
CAGCAGCACAGGGATGAGG
60.452
63.158
0.00
0.00
33.82
3.86
790
831
0.108615
CGCAGTAAGTGGGAGTGGAG
60.109
60.000
0.00
0.00
41.74
3.86
794
835
2.261671
CGCGCAGTAAGTGGGAGT
59.738
61.111
8.75
0.00
42.75
3.85
795
836
3.188786
GCGCGCAGTAAGTGGGAG
61.189
66.667
29.10
0.00
42.75
4.30
796
837
3.932580
CTGCGCGCAGTAAGTGGGA
62.933
63.158
44.44
16.25
42.75
4.37
797
838
3.490759
CTGCGCGCAGTAAGTGGG
61.491
66.667
44.44
23.83
42.97
4.61
816
857
0.412244
TGGGGGTAGTGTAGTGAGCT
59.588
55.000
0.00
0.00
0.00
4.09
817
858
1.207329
CTTGGGGGTAGTGTAGTGAGC
59.793
57.143
0.00
0.00
0.00
4.26
818
859
2.537143
ACTTGGGGGTAGTGTAGTGAG
58.463
52.381
0.00
0.00
0.00
3.51
819
860
2.708037
ACTTGGGGGTAGTGTAGTGA
57.292
50.000
0.00
0.00
0.00
3.41
820
861
2.498885
GGTACTTGGGGGTAGTGTAGTG
59.501
54.545
0.00
0.00
0.00
2.74
822
863
2.113807
GGGTACTTGGGGGTAGTGTAG
58.886
57.143
0.00
0.00
0.00
2.74
823
864
1.436355
TGGGTACTTGGGGGTAGTGTA
59.564
52.381
0.00
0.00
0.00
2.90
824
865
0.194080
TGGGTACTTGGGGGTAGTGT
59.806
55.000
0.00
0.00
0.00
3.55
825
866
0.909623
CTGGGTACTTGGGGGTAGTG
59.090
60.000
0.00
0.00
0.00
2.74
826
867
0.912968
GCTGGGTACTTGGGGGTAGT
60.913
60.000
0.00
0.00
0.00
2.73
827
868
1.632965
GGCTGGGTACTTGGGGGTAG
61.633
65.000
0.00
0.00
0.00
3.18
828
869
1.617233
GGCTGGGTACTTGGGGGTA
60.617
63.158
0.00
0.00
0.00
3.69
829
870
2.939353
GGCTGGGTACTTGGGGGT
60.939
66.667
0.00
0.00
0.00
4.95
830
871
3.739613
GGGCTGGGTACTTGGGGG
61.740
72.222
0.00
0.00
0.00
5.40
831
872
2.938798
TGGGCTGGGTACTTGGGG
60.939
66.667
0.00
0.00
0.00
4.96
832
873
2.198304
GACTGGGCTGGGTACTTGGG
62.198
65.000
0.00
0.00
0.00
4.12
833
874
1.299976
GACTGGGCTGGGTACTTGG
59.700
63.158
0.00
0.00
0.00
3.61
834
875
1.299976
GGACTGGGCTGGGTACTTG
59.700
63.158
0.00
0.00
0.00
3.16
835
876
1.923909
GGGACTGGGCTGGGTACTT
60.924
63.158
0.00
0.00
0.00
2.24
836
877
2.285442
GGGACTGGGCTGGGTACT
60.285
66.667
0.00
0.00
0.00
2.73
837
878
3.408853
GGGGACTGGGCTGGGTAC
61.409
72.222
0.00
0.00
0.00
3.34
838
879
3.948360
TGGGGACTGGGCTGGGTA
61.948
66.667
0.00
0.00
0.00
3.69
896
943
4.497300
GGCACAATAATGCTGAACAATGT
58.503
39.130
0.00
0.00
45.38
2.71
1851
1909
2.125350
GAGGCCACCTGCTCGAAG
60.125
66.667
5.01
0.00
40.92
3.79
2040
2098
4.760047
GTCATGTCCAGCGGCGGT
62.760
66.667
5.44
5.44
0.00
5.68
2082
2140
1.152881
GTCCACCTCCATCATGGCC
60.153
63.158
0.00
0.00
37.47
5.36
2237
2297
4.968311
AACCCCCGACCCCGAACT
62.968
66.667
0.00
0.00
38.22
3.01
2238
2298
4.710167
CAACCCCCGACCCCGAAC
62.710
72.222
0.00
0.00
38.22
3.95
2239
2299
4.958158
TCAACCCCCGACCCCGAA
62.958
66.667
0.00
0.00
38.22
4.30
2240
2300
4.958158
TTCAACCCCCGACCCCGA
62.958
66.667
0.00
0.00
38.22
5.14
2241
2301
4.710167
GTTCAACCCCCGACCCCG
62.710
72.222
0.00
0.00
0.00
5.73
2245
2311
1.345415
TCTTACAGTTCAACCCCCGAC
59.655
52.381
0.00
0.00
0.00
4.79
2247
2313
2.554370
TTCTTACAGTTCAACCCCCG
57.446
50.000
0.00
0.00
0.00
5.73
2255
2321
7.970614
CCTGCCTTGATTAATTTCTTACAGTTC
59.029
37.037
0.00
0.00
0.00
3.01
2271
2337
6.719370
TGTTTACTGTAAAATCCTGCCTTGAT
59.281
34.615
14.10
0.00
0.00
2.57
2273
2339
6.325919
TGTTTACTGTAAAATCCTGCCTTG
57.674
37.500
14.10
0.00
0.00
3.61
2291
2357
8.020819
CGATTCTAGTTGAAATTGCCTTGTTTA
58.979
33.333
0.00
0.00
38.29
2.01
2330
2412
2.577606
TTGACACGGGAAATCCACAT
57.422
45.000
0.00
0.00
37.91
3.21
2335
2417
5.174943
GTGAAATGTTTTGACACGGGAAATC
59.825
40.000
0.00
0.00
0.00
2.17
2340
2422
2.738135
GGTGAAATGTTTTGACACGGG
58.262
47.619
0.00
0.00
33.08
5.28
2388
2471
3.942829
CTGGAGAACAGGCTATGTCAAA
58.057
45.455
0.00
0.00
43.00
2.69
2406
2489
6.215121
TGAAATTTGTTCAACATGCTACTGG
58.785
36.000
0.00
0.00
0.00
4.00
2433
2516
9.019764
CAACATACCGTAAATGGAAATGATTTC
57.980
33.333
9.36
9.36
38.94
2.17
2437
2525
5.163602
GGCAACATACCGTAAATGGAAATGA
60.164
40.000
12.30
0.00
33.25
2.57
2460
2548
5.521735
GCTCAACATGTAAGATCTGTAGTGG
59.478
44.000
11.36
0.00
0.00
4.00
2464
2552
6.071391
TGTGAGCTCAACATGTAAGATCTGTA
60.071
38.462
20.19
9.34
0.00
2.74
2482
2570
5.859205
AATTGGTCTTCTTTTTGTGAGCT
57.141
34.783
0.00
0.00
0.00
4.09
2608
2696
4.620982
ACAGTAAACCCGTTGTGTAGTAC
58.379
43.478
0.00
0.00
0.00
2.73
2849
2937
2.168313
ACTTGTGGTTTTTCAGGCCTTG
59.832
45.455
0.00
0.00
0.00
3.61
2909
2997
3.099905
TGGGGATCTCTAGTCAACACTG
58.900
50.000
0.00
0.00
33.62
3.66
2926
3014
3.055963
TGCATTAACAAAGCAGAATGGGG
60.056
43.478
0.00
0.00
35.86
4.96
3043
3131
4.420522
AAGTAACTTTGGTCCCGTTGTA
57.579
40.909
0.00
0.00
0.00
2.41
3066
3154
8.607459
CCAAACAAATAAACAATGTGCAGTAAA
58.393
29.630
0.00
0.00
0.00
2.01
3067
3155
7.981789
TCCAAACAAATAAACAATGTGCAGTAA
59.018
29.630
0.00
0.00
0.00
2.24
3070
3158
6.479660
ACTCCAAACAAATAAACAATGTGCAG
59.520
34.615
0.00
0.00
0.00
4.41
3079
3167
8.573035
TGTAATCCTGACTCCAAACAAATAAAC
58.427
33.333
0.00
0.00
0.00
2.01
3091
3179
4.537135
TGTTGTCTGTAATCCTGACTCC
57.463
45.455
0.00
0.00
41.29
3.85
3092
3180
6.861065
TTTTGTTGTCTGTAATCCTGACTC
57.139
37.500
0.00
0.00
41.29
3.36
3121
3209
7.361713
CGATTTTAGTTTGATTGGCTACTTCCA
60.362
37.037
0.00
0.00
0.00
3.53
3137
3225
3.435671
CCCTCGTGCTTTCGATTTTAGTT
59.564
43.478
0.00
0.00
39.12
2.24
3155
3243
4.082733
GCATACTTCCACAAACTTTCCCTC
60.083
45.833
0.00
0.00
0.00
4.30
3163
3251
1.165270
AGCGGCATACTTCCACAAAC
58.835
50.000
1.45
0.00
0.00
2.93
3164
3252
1.539388
CAAGCGGCATACTTCCACAAA
59.461
47.619
1.45
0.00
0.00
2.83
3165
3253
1.164411
CAAGCGGCATACTTCCACAA
58.836
50.000
1.45
0.00
0.00
3.33
3166
3254
1.305219
GCAAGCGGCATACTTCCACA
61.305
55.000
1.45
0.00
43.97
4.17
3167
3255
1.429423
GCAAGCGGCATACTTCCAC
59.571
57.895
1.45
0.00
43.97
4.02
3168
3256
3.903783
GCAAGCGGCATACTTCCA
58.096
55.556
1.45
0.00
43.97
3.53
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.