Multiple sequence alignment - TraesCS5D01G297100
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
TraesCS5D01G297100
chr5D
100.000
3309
0
0
1
3309
393996441
393993133
0.000000e+00
6111.0
1
TraesCS5D01G297100
chr5A
86.949
2766
169
83
105
2758
496012750
496010065
0.000000e+00
2931.0
2
TraesCS5D01G297100
chr5A
94.444
72
4
0
1
72
496012813
496012742
9.710000e-21
111.0
3
TraesCS5D01G297100
chr5B
91.976
1857
85
29
489
2316
473873237
473871416
0.000000e+00
2545.0
4
TraesCS5D01G297100
chr5B
91.368
950
59
13
2363
3309
473871334
473870405
0.000000e+00
1279.0
5
TraesCS5D01G297100
chr5B
75.949
237
18
21
96
313
473873487
473873271
5.880000e-13
86.1
6
TraesCS5D01G297100
chr7A
78.912
588
95
17
1352
1932
254897402
254897967
4.030000e-99
372.0
7
TraesCS5D01G297100
chr7B
78.547
592
93
22
1352
1932
218548777
218548209
3.140000e-95
359.0
8
TraesCS5D01G297100
chr7D
82.292
384
64
4
1352
1733
242784689
242784308
2.460000e-86
329.0
9
TraesCS5D01G297100
chr6D
86.517
89
8
4
1383
1469
455251636
455251722
9.780000e-16
95.3
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
TraesCS5D01G297100
chr5D
393993133
393996441
3308
True
6111.000000
6111
100.0000
1
3309
1
chr5D.!!$R1
3308
1
TraesCS5D01G297100
chr5A
496010065
496012813
2748
True
1521.000000
2931
90.6965
1
2758
2
chr5A.!!$R1
2757
2
TraesCS5D01G297100
chr5B
473870405
473873487
3082
True
1303.366667
2545
86.4310
96
3309
3
chr5B.!!$R1
3213
3
TraesCS5D01G297100
chr7A
254897402
254897967
565
False
372.000000
372
78.9120
1352
1932
1
chr7A.!!$F1
580
4
TraesCS5D01G297100
chr7B
218548209
218548777
568
True
359.000000
359
78.5470
1352
1932
1
chr7B.!!$R1
580
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
75
76
0.031817
TACCTGCCTACCTGTACCCC
60.032
60.0
0.00
0.0
0.00
4.95
F
79
80
0.117541
TGCCTACCTGTACCCCTCAA
59.882
55.0
0.00
0.0
0.00
3.02
F
359
383
0.456221
GGACGACTCATGGACGATGT
59.544
55.0
11.45
0.0
33.29
3.06
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2021
2189
0.109153
TTCGGGAGCTGCATGCATAT
59.891
50.000
22.97
12.96
45.94
1.78
R
2022
2190
0.815213
GTTCGGGAGCTGCATGCATA
60.815
55.000
22.97
0.00
45.94
3.14
R
2316
2484
1.519234
TGCGTGCATCGGTCATCTC
60.519
57.895
10.02
0.00
40.26
2.75
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
45
46
3.372206
CACTCGCTGCAAGTTTTAGCTAT
59.628
43.478
0.00
0.00
35.36
2.97
53
54
8.271157
GCTGCAAGTTTTAGCTATCAGCTTCA
62.271
42.308
5.92
0.00
43.27
3.02
66
67
3.371087
GCTTCAGCTACCTGCCTAC
57.629
57.895
0.00
0.00
44.23
3.18
67
68
0.179070
GCTTCAGCTACCTGCCTACC
60.179
60.000
0.00
0.00
44.23
3.18
68
69
1.490574
CTTCAGCTACCTGCCTACCT
58.509
55.000
0.00
0.00
44.23
3.08
69
70
1.137872
CTTCAGCTACCTGCCTACCTG
59.862
57.143
0.00
0.00
44.23
4.00
70
71
0.041238
TCAGCTACCTGCCTACCTGT
59.959
55.000
0.00
0.00
44.23
4.00
71
72
1.286849
TCAGCTACCTGCCTACCTGTA
59.713
52.381
0.00
0.00
44.23
2.74
72
73
1.409427
CAGCTACCTGCCTACCTGTAC
59.591
57.143
0.00
0.00
44.23
2.90
73
74
0.751452
GCTACCTGCCTACCTGTACC
59.249
60.000
0.00
0.00
35.15
3.34
74
75
1.411041
CTACCTGCCTACCTGTACCC
58.589
60.000
0.00
0.00
0.00
3.69
75
76
0.031817
TACCTGCCTACCTGTACCCC
60.032
60.000
0.00
0.00
0.00
4.95
76
77
1.003051
CCTGCCTACCTGTACCCCT
59.997
63.158
0.00
0.00
0.00
4.79
77
78
1.049289
CCTGCCTACCTGTACCCCTC
61.049
65.000
0.00
0.00
0.00
4.30
78
79
0.325296
CTGCCTACCTGTACCCCTCA
60.325
60.000
0.00
0.00
0.00
3.86
79
80
0.117541
TGCCTACCTGTACCCCTCAA
59.882
55.000
0.00
0.00
0.00
3.02
80
81
1.282382
GCCTACCTGTACCCCTCAAA
58.718
55.000
0.00
0.00
0.00
2.69
81
82
1.631898
GCCTACCTGTACCCCTCAAAA
59.368
52.381
0.00
0.00
0.00
2.44
82
83
2.040679
GCCTACCTGTACCCCTCAAAAA
59.959
50.000
0.00
0.00
0.00
1.94
164
171
6.507900
CGGGATAAACGATAGCATCATATCT
58.492
40.000
0.00
0.00
42.67
1.98
165
172
6.980978
CGGGATAAACGATAGCATCATATCTT
59.019
38.462
0.00
0.00
42.67
2.40
166
173
7.043125
CGGGATAAACGATAGCATCATATCTTG
60.043
40.741
0.00
0.00
42.67
3.02
167
174
7.766278
GGGATAAACGATAGCATCATATCTTGT
59.234
37.037
0.00
0.00
42.67
3.16
201
208
0.841289
TGGATCAGAGCATGCATCCA
59.159
50.000
25.76
25.76
40.40
3.41
253
273
1.677576
ACCATGGCATTGTTATCGCAG
59.322
47.619
13.04
0.00
0.00
5.18
258
278
1.004927
GGCATTGTTATCGCAGACGTC
60.005
52.381
7.70
7.70
42.51
4.34
265
285
4.413969
TGTTATCGCAGACGTCGATTTTA
58.586
39.130
14.70
1.90
43.27
1.52
268
288
2.937591
TCGCAGACGTCGATTTTAACT
58.062
42.857
10.46
0.00
41.18
2.24
322
345
4.985538
ACATATATACTAGAGCCGTGCC
57.014
45.455
0.00
0.00
0.00
5.01
326
349
6.605995
ACATATATACTAGAGCCGTGCCATAA
59.394
38.462
0.00
0.00
0.00
1.90
327
350
3.662247
ATACTAGAGCCGTGCCATAAC
57.338
47.619
0.00
0.00
0.00
1.89
341
365
4.024893
GTGCCATAACACGACAAGATATGG
60.025
45.833
5.89
5.89
36.85
2.74
351
375
3.977579
CGACAAGATATGGACGACTCATG
59.022
47.826
0.00
0.00
35.86
3.07
359
383
0.456221
GGACGACTCATGGACGATGT
59.544
55.000
11.45
0.00
33.29
3.06
371
395
6.734137
TCATGGACGATGTTTAAAATATGGC
58.266
36.000
0.00
0.00
33.29
4.40
373
397
4.035792
TGGACGATGTTTAAAATATGGCCG
59.964
41.667
0.00
0.00
0.00
6.13
414
438
4.830765
CGGGCCGCTGGATTTCGA
62.831
66.667
15.42
0.00
0.00
3.71
448
472
1.101635
CAGGCACCAGGATCATGCAG
61.102
60.000
0.73
0.00
41.27
4.41
465
489
3.927552
GCAGGAAGCAGTTTCGTATAC
57.072
47.619
0.00
0.00
44.79
1.47
505
546
2.284190
GGTTAGTAGCCTCGACGTACT
58.716
52.381
0.00
0.00
0.00
2.73
541
587
6.250527
GTGGAATTAATGTACATGCACGTTTC
59.749
38.462
9.63
7.26
0.00
2.78
668
722
3.942748
GGTAATGTCCAAACGGAATGCTA
59.057
43.478
0.00
0.00
33.16
3.49
820
874
7.901752
GGAATTCCACTACGTACTCGTCGTC
62.902
52.000
20.04
0.00
42.46
4.20
833
887
1.403323
TCGTCGTCGTAGAGCTAGAGA
59.597
52.381
1.33
0.00
36.95
3.10
837
893
2.629137
TCGTCGTAGAGCTAGAGAGGAT
59.371
50.000
0.00
0.00
36.95
3.24
843
899
2.081043
AGAGCTAGAGAGGATGGGGAT
58.919
52.381
0.00
0.00
0.00
3.85
850
906
2.451294
AGGATGGGGATGGGCTCC
60.451
66.667
0.00
0.00
44.11
4.70
871
927
3.699538
CCCCTGCTGCTATATATACACGA
59.300
47.826
0.00
0.00
0.00
4.35
883
939
8.464404
GCTATATATACACGACTTGTTCCCATA
58.536
37.037
0.00
0.00
39.91
2.74
886
942
2.253610
ACACGACTTGTTCCCATAGGA
58.746
47.619
0.00
0.00
41.88
2.94
922
1004
1.203313
ACTGCCTTCCTTCCCTAGTCA
60.203
52.381
0.00
0.00
0.00
3.41
947
1029
3.433740
GGGAAGGAGAAGAACACACAGTT
60.434
47.826
0.00
0.00
44.93
3.16
983
1070
2.649331
TCTGCTTAGTTACCGTGCTC
57.351
50.000
0.00
0.00
0.00
4.26
1108
1202
3.119637
TGCTCAACTGTTGATGCATCATG
60.120
43.478
29.13
22.60
38.20
3.07
1181
1276
3.945285
ACACAAAGTGTCATTTCTCCGTT
59.055
39.130
0.00
0.00
43.92
4.44
1184
1279
3.771577
AAGTGTCATTTCTCCGTTCCT
57.228
42.857
0.00
0.00
0.00
3.36
1185
1280
3.045601
AGTGTCATTTCTCCGTTCCTG
57.954
47.619
0.00
0.00
0.00
3.86
1230
1325
1.738099
CTTCCTGGTGTTCCTCGCG
60.738
63.158
0.00
0.00
34.23
5.87
1273
1368
3.188460
TCGAGCACCTTAATCTTTTGCAC
59.812
43.478
0.00
0.00
35.57
4.57
1276
1371
2.351738
GCACCTTAATCTTTTGCACGCT
60.352
45.455
0.00
0.00
33.24
5.07
1304
1399
3.569277
TGTTGTGATCACCATGAGTTTGG
59.431
43.478
22.85
0.00
42.82
3.28
1501
1645
0.537143
TGCTCACCATCAACGCCTTT
60.537
50.000
0.00
0.00
0.00
3.11
1753
1897
6.482898
AGTACTACTACTACTGCTGCTCTA
57.517
41.667
0.00
0.00
30.81
2.43
1793
1940
7.068348
GGACCATGAGATCTACAGTAACTAACA
59.932
40.741
0.00
0.00
0.00
2.41
1797
1944
6.188407
TGAGATCTACAGTAACTAACAGGCT
58.812
40.000
0.00
0.00
0.00
4.58
1913
2062
0.460311
CCGTCGCCTGGTTCTTCTAT
59.540
55.000
0.00
0.00
0.00
1.98
1956
2109
1.324718
CGTCACCGTACGTCTTCTTG
58.675
55.000
15.21
0.00
38.07
3.02
1972
2132
5.855395
GTCTTCTTGCACAATCAGTTTCATC
59.145
40.000
0.00
0.00
0.00
2.92
1973
2133
4.408993
TCTTGCACAATCAGTTTCATCG
57.591
40.909
0.00
0.00
0.00
3.84
1975
2143
3.811722
TGCACAATCAGTTTCATCGTC
57.188
42.857
0.00
0.00
0.00
4.20
1977
2145
3.187022
TGCACAATCAGTTTCATCGTCAG
59.813
43.478
0.00
0.00
0.00
3.51
1982
2150
6.476706
CACAATCAGTTTCATCGTCAGCTATA
59.523
38.462
0.00
0.00
0.00
1.31
1983
2151
7.170489
CACAATCAGTTTCATCGTCAGCTATAT
59.830
37.037
0.00
0.00
0.00
0.86
1992
2160
4.655762
TCGTCAGCTATATATCCATGGC
57.344
45.455
6.96
0.00
32.92
4.40
1996
2164
5.625426
CGTCAGCTATATATCCATGGCACTT
60.625
44.000
6.96
0.00
35.04
3.16
2002
2170
6.696148
GCTATATATCCATGGCACTTACGTAC
59.304
42.308
6.96
0.00
32.99
3.67
2007
2175
2.671396
CCATGGCACTTACGTACTTGAC
59.329
50.000
0.00
0.00
0.00
3.18
2008
2176
3.585862
CATGGCACTTACGTACTTGACT
58.414
45.455
9.35
0.00
0.00
3.41
2009
2177
3.293311
TGGCACTTACGTACTTGACTC
57.707
47.619
9.35
0.00
0.00
3.36
2012
2180
3.243336
GCACTTACGTACTTGACTCCTG
58.757
50.000
0.00
0.00
0.00
3.86
2013
2181
3.305199
GCACTTACGTACTTGACTCCTGT
60.305
47.826
0.00
0.00
0.00
4.00
2014
2182
4.227538
CACTTACGTACTTGACTCCTGTG
58.772
47.826
0.00
0.00
0.00
3.66
2015
2183
3.887716
ACTTACGTACTTGACTCCTGTGT
59.112
43.478
0.00
0.00
0.00
3.72
2016
2184
5.049198
CACTTACGTACTTGACTCCTGTGTA
60.049
44.000
0.00
0.00
0.00
2.90
2017
2185
5.532406
ACTTACGTACTTGACTCCTGTGTAA
59.468
40.000
0.00
0.00
0.00
2.41
2018
2186
4.924305
ACGTACTTGACTCCTGTGTAAA
57.076
40.909
0.00
0.00
0.00
2.01
2019
2187
5.266733
ACGTACTTGACTCCTGTGTAAAA
57.733
39.130
0.00
0.00
0.00
1.52
2020
2188
5.045872
ACGTACTTGACTCCTGTGTAAAAC
58.954
41.667
0.00
0.00
0.00
2.43
2021
2189
5.045215
CGTACTTGACTCCTGTGTAAAACA
58.955
41.667
0.00
0.00
37.22
2.83
2022
2190
5.694910
CGTACTTGACTCCTGTGTAAAACAT
59.305
40.000
0.00
0.00
38.39
2.71
2023
2191
6.864685
CGTACTTGACTCCTGTGTAAAACATA
59.135
38.462
0.00
0.00
38.39
2.29
2024
2192
7.544566
CGTACTTGACTCCTGTGTAAAACATAT
59.455
37.037
0.00
0.00
38.39
1.78
2025
2193
7.672983
ACTTGACTCCTGTGTAAAACATATG
57.327
36.000
0.00
0.00
38.39
1.78
2026
2194
6.149474
ACTTGACTCCTGTGTAAAACATATGC
59.851
38.462
1.58
0.00
38.39
3.14
2059
2227
1.599797
CGTGGGCGGGTTCTTCTTT
60.600
57.895
0.00
0.00
0.00
2.52
2316
2484
1.863454
CAAGGCTTTCTGATCCGATCG
59.137
52.381
8.51
8.51
0.00
3.69
2319
2487
1.338337
GGCTTTCTGATCCGATCGAGA
59.662
52.381
18.66
12.67
0.00
4.04
2320
2488
2.029470
GGCTTTCTGATCCGATCGAGAT
60.029
50.000
18.66
16.99
0.00
2.75
2321
2489
2.985809
GCTTTCTGATCCGATCGAGATG
59.014
50.000
18.66
8.37
0.00
2.90
2322
2490
3.304996
GCTTTCTGATCCGATCGAGATGA
60.305
47.826
18.66
10.74
0.00
2.92
2324
2492
2.155279
TCTGATCCGATCGAGATGACC
58.845
52.381
18.66
6.73
0.00
4.02
2350
2518
3.813143
CACGGGCGCATGCATTCA
61.813
61.111
19.57
0.00
45.35
2.57
2351
2519
3.511595
ACGGGCGCATGCATTCAG
61.512
61.111
19.57
9.26
45.35
3.02
2353
2521
2.829914
GGGCGCATGCATTCAGGA
60.830
61.111
19.57
0.00
45.35
3.86
2354
2522
2.719979
GGCGCATGCATTCAGGAG
59.280
61.111
19.57
0.00
45.35
3.69
2355
2523
1.820906
GGCGCATGCATTCAGGAGA
60.821
57.895
19.57
0.00
45.35
3.71
2356
2524
1.170919
GGCGCATGCATTCAGGAGAT
61.171
55.000
19.57
0.00
45.35
2.75
2357
2525
0.040336
GCGCATGCATTCAGGAGATG
60.040
55.000
19.57
0.00
42.15
2.90
2358
2526
1.589803
CGCATGCATTCAGGAGATGA
58.410
50.000
19.57
0.00
35.62
2.92
2371
2574
6.106648
TCAGGAGATGAATCAATCGCTAAT
57.893
37.500
0.00
0.00
34.02
1.73
2448
2658
4.681025
TCGTTCGTTTGTAATGGTCTGTAC
59.319
41.667
0.00
0.00
0.00
2.90
2459
2669
5.584253
AATGGTCTGTACTAGTAGCACAG
57.416
43.478
20.46
20.46
40.21
3.66
2516
2726
2.478033
CCGGCCGGGCAAGTAATTC
61.478
63.158
37.42
0.00
0.00
2.17
2525
2735
4.196193
CGGGCAAGTAATTCATCTACCAA
58.804
43.478
0.00
0.00
0.00
3.67
2616
2828
3.487574
GCGAACTGATACTGCACTATGTC
59.512
47.826
0.00
0.00
0.00
3.06
2628
2840
2.096496
GCACTATGTCTGTTGCATGTCC
59.904
50.000
0.00
0.00
0.00
4.02
2692
2914
1.460504
CACAATGCATGAGAGGTGCT
58.539
50.000
0.00
0.00
42.92
4.40
2707
2929
3.368822
GCTTGTGGCATGGAAGCA
58.631
55.556
18.47
0.00
41.48
3.91
2727
2949
2.360475
GAGTGGGAGTTGGCTGGC
60.360
66.667
0.00
0.00
0.00
4.85
2742
2964
0.537188
CTGGCTGGTCGGAGTACAAT
59.463
55.000
0.00
0.00
0.00
2.71
2781
3004
3.766068
ATCAGAGATGCCCACATACAG
57.234
47.619
0.00
0.00
36.35
2.74
2798
3021
5.045942
ACATACAGACACATACATTCACCCA
60.046
40.000
0.00
0.00
0.00
4.51
2799
3022
4.574674
ACAGACACATACATTCACCCAT
57.425
40.909
0.00
0.00
0.00
4.00
2800
3023
5.692115
ACAGACACATACATTCACCCATA
57.308
39.130
0.00
0.00
0.00
2.74
2801
3024
6.252599
ACAGACACATACATTCACCCATAT
57.747
37.500
0.00
0.00
0.00
1.78
2802
3025
7.373617
ACAGACACATACATTCACCCATATA
57.626
36.000
0.00
0.00
0.00
0.86
2803
3026
7.801104
ACAGACACATACATTCACCCATATAA
58.199
34.615
0.00
0.00
0.00
0.98
2804
3027
8.271458
ACAGACACATACATTCACCCATATAAA
58.729
33.333
0.00
0.00
0.00
1.40
2805
3028
9.288576
CAGACACATACATTCACCCATATAAAT
57.711
33.333
0.00
0.00
0.00
1.40
2813
3036
8.995027
ACATTCACCCATATAAATACACACAT
57.005
30.769
0.00
0.00
0.00
3.21
2819
3042
8.556194
CACCCATATAAATACACACATACACAC
58.444
37.037
0.00
0.00
0.00
3.82
2820
3043
8.268605
ACCCATATAAATACACACATACACACA
58.731
33.333
0.00
0.00
0.00
3.72
2836
3059
3.969976
ACACACACTATCCCTATGAGCAT
59.030
43.478
0.00
0.00
0.00
3.79
2840
3063
5.011533
ACACACTATCCCTATGAGCATCTTC
59.988
44.000
0.00
0.00
34.92
2.87
2846
3069
4.155709
TCCCTATGAGCATCTTCGAGATT
58.844
43.478
0.00
0.00
31.32
2.40
2847
3070
4.021632
TCCCTATGAGCATCTTCGAGATTG
60.022
45.833
0.00
0.00
31.32
2.67
2848
3071
3.679025
CCTATGAGCATCTTCGAGATTGC
59.321
47.826
7.28
7.28
31.32
3.56
2862
3085
3.585862
GAGATTGCCTTGTAGTCGACAA
58.414
45.455
19.50
2.93
46.03
3.18
2880
3103
4.336101
GACAAAAACATGTTCGTCGACAA
58.664
39.130
17.16
6.36
32.57
3.18
2884
3107
3.854286
AACATGTTCGTCGACAAAGTC
57.146
42.857
17.16
1.59
32.47
3.01
2899
3122
0.946221
AAGTCGAAGCTGCTTGGTCG
60.946
55.000
21.25
17.25
0.00
4.79
2901
3124
1.069090
TCGAAGCTGCTTGGTCGTT
59.931
52.632
21.25
0.00
0.00
3.85
2912
3136
1.084935
TTGGTCGTTGACGTGTGTGG
61.085
55.000
0.00
0.00
40.80
4.17
2919
3143
2.542597
GTTGACGTGTGTGGTTGACTA
58.457
47.619
0.00
0.00
0.00
2.59
2948
3172
4.778415
CCGACACAGGCCTCGACG
62.778
72.222
13.28
13.78
31.24
5.12
2986
3210
2.159558
GCACTTCAGTAGTCGTCGATGA
60.160
50.000
2.39
2.39
33.85
2.92
3008
3232
0.319641
GAGTCGAAGTCGCCCTTTGT
60.320
55.000
0.00
0.00
39.60
2.83
3014
3238
1.705997
AAGTCGCCCTTTGTGGAGGT
61.706
55.000
0.00
0.00
38.35
3.85
3015
3239
1.966451
GTCGCCCTTTGTGGAGGTG
60.966
63.158
0.00
0.00
38.35
4.00
3149
3373
7.237173
GTCAATTAATTGGACAACTCTCTTCG
58.763
38.462
24.40
0.00
38.30
3.79
3156
3380
3.134081
TGGACAACTCTCTTCGACCTTTT
59.866
43.478
0.00
0.00
0.00
2.27
3193
3417
2.432444
CTAAGGGACCGCATTTCAACA
58.568
47.619
0.00
0.00
0.00
3.33
3194
3418
1.698506
AAGGGACCGCATTTCAACAA
58.301
45.000
0.00
0.00
0.00
2.83
3195
3419
1.698506
AGGGACCGCATTTCAACAAA
58.301
45.000
0.00
0.00
0.00
2.83
3196
3420
2.035632
AGGGACCGCATTTCAACAAAA
58.964
42.857
0.00
0.00
0.00
2.44
3234
3458
3.023832
CCACCAAACAAGACTTGAACCT
58.976
45.455
21.95
0.00
0.00
3.50
3235
3459
3.181487
CCACCAAACAAGACTTGAACCTG
60.181
47.826
21.95
11.59
0.00
4.00
3257
3482
2.165030
GTGGGCTGATTCCATCACAAAG
59.835
50.000
0.00
0.00
36.58
2.77
3278
3503
8.734386
ACAAAGAAATCTAACCATCTAAGCAAG
58.266
33.333
0.00
0.00
0.00
4.01
3280
3505
5.825151
AGAAATCTAACCATCTAAGCAAGGC
59.175
40.000
0.00
0.00
0.00
4.35
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
53
54
1.688627
GGTACAGGTAGGCAGGTAGCT
60.689
57.143
0.00
0.00
44.79
3.32
60
61
0.117541
TTGAGGGGTACAGGTAGGCA
59.882
55.000
0.00
0.00
0.00
4.75
86
87
5.068591
CAGGTAGTAGGCAGGTTTTGTTTTT
59.931
40.000
0.00
0.00
0.00
1.94
87
88
4.583073
CAGGTAGTAGGCAGGTTTTGTTTT
59.417
41.667
0.00
0.00
0.00
2.43
88
89
4.142038
CAGGTAGTAGGCAGGTTTTGTTT
58.858
43.478
0.00
0.00
0.00
2.83
89
90
3.137728
ACAGGTAGTAGGCAGGTTTTGTT
59.862
43.478
0.00
0.00
0.00
2.83
90
91
2.709397
ACAGGTAGTAGGCAGGTTTTGT
59.291
45.455
0.00
0.00
0.00
2.83
91
92
3.418684
ACAGGTAGTAGGCAGGTTTTG
57.581
47.619
0.00
0.00
0.00
2.44
92
93
4.820894
CTACAGGTAGTAGGCAGGTTTT
57.179
45.455
0.00
0.00
45.28
2.43
164
171
1.358877
CATCGATCGCCAACAGACAA
58.641
50.000
11.09
0.00
0.00
3.18
165
172
0.460109
CCATCGATCGCCAACAGACA
60.460
55.000
11.09
0.00
0.00
3.41
166
173
0.179111
TCCATCGATCGCCAACAGAC
60.179
55.000
11.09
0.00
0.00
3.51
167
174
0.752658
ATCCATCGATCGCCAACAGA
59.247
50.000
11.09
1.49
0.00
3.41
192
199
2.027325
CATCACCGGTGGATGCATG
58.973
57.895
33.40
23.95
36.12
4.06
201
208
2.045926
GAGCCTTGCATCACCGGT
60.046
61.111
0.00
0.00
0.00
5.28
249
269
2.779969
GCAGTTAAAATCGACGTCTGCG
60.780
50.000
14.70
0.70
44.93
5.18
253
273
6.089150
ACTTTAGAGCAGTTAAAATCGACGTC
59.911
38.462
5.18
5.18
0.00
4.34
265
285
8.507249
CAGCACTTAAATTACTTTAGAGCAGTT
58.493
33.333
0.00
0.00
0.00
3.16
268
288
7.979444
ACAGCACTTAAATTACTTTAGAGCA
57.021
32.000
0.00
0.00
0.00
4.26
282
305
3.992643
TGTACGCCTTTACAGCACTTAA
58.007
40.909
0.00
0.00
0.00
1.85
322
345
5.173312
GTCGTCCATATCTTGTCGTGTTATG
59.827
44.000
0.00
0.00
0.00
1.90
326
349
2.753452
AGTCGTCCATATCTTGTCGTGT
59.247
45.455
0.00
0.00
0.00
4.49
327
350
3.181500
TGAGTCGTCCATATCTTGTCGTG
60.181
47.826
0.00
0.00
0.00
4.35
335
359
2.552743
TCGTCCATGAGTCGTCCATATC
59.447
50.000
0.00
0.00
0.00
1.63
341
365
2.279582
AACATCGTCCATGAGTCGTC
57.720
50.000
0.00
0.00
36.21
4.20
351
375
4.533222
CGGCCATATTTTAAACATCGTCC
58.467
43.478
2.24
0.00
0.00
4.79
359
383
4.641094
ACGAATGTCCGGCCATATTTTAAA
59.359
37.500
0.00
0.00
0.00
1.52
371
395
1.526887
GATGTATGCACGAATGTCCGG
59.473
52.381
0.00
0.00
0.00
5.14
373
397
1.526887
CCGATGTATGCACGAATGTCC
59.473
52.381
0.00
0.00
0.00
4.02
414
438
1.019673
GCCTGATGAATGCACGACAT
58.980
50.000
0.00
0.00
42.30
3.06
448
472
4.666237
AGTACGTATACGAAACTGCTTCC
58.334
43.478
30.77
5.72
43.02
3.46
465
489
5.025986
ACCAAAGCATAAAACGAAGTACG
57.974
39.130
0.00
0.00
45.00
3.67
569
615
0.179108
GCACGTAGCCTCTACAAGGG
60.179
60.000
0.00
0.00
46.32
3.95
645
699
2.490115
GCATTCCGTTTGGACATTACCA
59.510
45.455
0.00
0.00
46.45
3.25
668
722
3.313526
GCCAAGATGAAGAATACGTGCAT
59.686
43.478
0.00
0.00
0.00
3.96
820
874
2.432444
CCCATCCTCTCTAGCTCTACG
58.568
57.143
0.00
0.00
0.00
3.51
821
875
2.377193
TCCCCATCCTCTCTAGCTCTAC
59.623
54.545
0.00
0.00
0.00
2.59
822
876
2.719676
TCCCCATCCTCTCTAGCTCTA
58.280
52.381
0.00
0.00
0.00
2.43
833
887
2.451294
GGAGCCCATCCCCATCCT
60.451
66.667
0.00
0.00
43.01
3.24
850
906
4.399618
AGTCGTGTATATATAGCAGCAGGG
59.600
45.833
0.00
0.00
0.00
4.45
851
907
5.568685
AGTCGTGTATATATAGCAGCAGG
57.431
43.478
0.00
0.00
0.00
4.85
854
910
6.308282
GGAACAAGTCGTGTATATATAGCAGC
59.692
42.308
0.00
0.00
40.60
5.25
922
1004
3.138283
TGTGTGTTCTTCTCCTTCCCAAT
59.862
43.478
0.00
0.00
0.00
3.16
947
1029
7.892771
ACTAAGCAGATCAGATGGATGTATCTA
59.107
37.037
0.00
0.00
35.70
1.98
1108
1202
3.859443
TGGTTTGGAAATACATGCATGC
58.141
40.909
26.53
11.82
0.00
4.06
1259
1354
4.154918
AGGAGAAGCGTGCAAAAGATTAAG
59.845
41.667
0.00
0.00
0.00
1.85
1273
1368
1.728971
GTGATCACAACAGGAGAAGCG
59.271
52.381
21.07
0.00
0.00
4.68
1276
1371
3.678289
CATGGTGATCACAACAGGAGAA
58.322
45.455
26.47
1.72
46.61
2.87
1753
1897
3.584406
TCATGGTCCTGATCACTCAAACT
59.416
43.478
0.00
0.00
0.00
2.66
1793
1940
0.466189
CATTATTCACCGGCCAGCCT
60.466
55.000
0.00
0.00
0.00
4.58
1797
1944
1.031235
CATGCATTATTCACCGGCCA
58.969
50.000
0.00
0.00
0.00
5.36
1913
2062
1.059584
TGTCCTTGGTGAAGAGGCCA
61.060
55.000
5.01
0.00
32.93
5.36
1956
2109
3.740590
CTGACGATGAAACTGATTGTGC
58.259
45.455
0.00
0.00
0.00
4.57
1972
2132
4.115516
GTGCCATGGATATATAGCTGACG
58.884
47.826
18.40
0.00
0.00
4.35
1973
2133
5.350504
AGTGCCATGGATATATAGCTGAC
57.649
43.478
18.40
0.00
0.00
3.51
1975
2143
5.750547
CGTAAGTGCCATGGATATATAGCTG
59.249
44.000
18.40
0.00
0.00
4.24
1996
2164
6.183360
TGTTTTACACAGGAGTCAAGTACGTA
60.183
38.462
0.00
0.00
0.00
3.57
2002
2170
6.149308
TGCATATGTTTTACACAGGAGTCAAG
59.851
38.462
4.29
0.00
39.40
3.02
2007
2175
5.163632
TGCATGCATATGTTTTACACAGGAG
60.164
40.000
18.46
0.00
39.40
3.69
2008
2176
4.704057
TGCATGCATATGTTTTACACAGGA
59.296
37.500
18.46
0.00
39.40
3.86
2009
2177
4.996344
TGCATGCATATGTTTTACACAGG
58.004
39.130
18.46
0.00
39.40
4.00
2012
2180
4.675510
AGCTGCATGCATATGTTTTACAC
58.324
39.130
22.97
0.00
45.94
2.90
2013
2181
4.202040
GGAGCTGCATGCATATGTTTTACA
60.202
41.667
22.97
0.00
45.94
2.41
2014
2182
4.293415
GGAGCTGCATGCATATGTTTTAC
58.707
43.478
22.97
5.44
45.94
2.01
2015
2183
3.318839
GGGAGCTGCATGCATATGTTTTA
59.681
43.478
22.97
0.00
45.94
1.52
2016
2184
2.101917
GGGAGCTGCATGCATATGTTTT
59.898
45.455
22.97
1.63
45.94
2.43
2017
2185
1.684983
GGGAGCTGCATGCATATGTTT
59.315
47.619
22.97
3.13
45.94
2.83
2018
2186
1.325355
GGGAGCTGCATGCATATGTT
58.675
50.000
22.97
7.76
45.94
2.71
2019
2187
0.887836
CGGGAGCTGCATGCATATGT
60.888
55.000
22.97
5.86
45.94
2.29
2020
2188
0.604511
TCGGGAGCTGCATGCATATG
60.605
55.000
22.97
11.19
45.94
1.78
2021
2189
0.109153
TTCGGGAGCTGCATGCATAT
59.891
50.000
22.97
12.96
45.94
1.78
2022
2190
0.815213
GTTCGGGAGCTGCATGCATA
60.815
55.000
22.97
0.00
45.94
3.14
2023
2191
2.117156
GTTCGGGAGCTGCATGCAT
61.117
57.895
22.97
7.28
45.94
3.96
2024
2192
2.747460
GTTCGGGAGCTGCATGCA
60.747
61.111
21.29
21.29
45.94
3.96
2025
2193
3.869272
CGTTCGGGAGCTGCATGC
61.869
66.667
11.82
11.82
43.29
4.06
2026
2194
2.434884
ACGTTCGGGAGCTGCATG
60.435
61.111
7.79
0.00
0.00
4.06
2050
2218
2.351777
GGCCACCCCAAAGAAGAAC
58.648
57.895
0.00
0.00
0.00
3.01
2316
2484
1.519234
TGCGTGCATCGGTCATCTC
60.519
57.895
10.02
0.00
40.26
2.75
2319
2487
3.188100
CGTGCGTGCATCGGTCAT
61.188
61.111
0.00
0.00
40.26
3.06
2348
2516
5.535753
TTAGCGATTGATTCATCTCCTGA
57.464
39.130
0.00
0.00
0.00
3.86
2350
2518
6.106648
TCATTAGCGATTGATTCATCTCCT
57.893
37.500
0.00
0.00
0.00
3.69
2351
2519
6.981762
ATCATTAGCGATTGATTCATCTCC
57.018
37.500
0.00
0.00
0.00
3.71
2371
2574
2.433491
CGGTCGGTTCGCCAATCA
60.433
61.111
0.00
0.00
37.00
2.57
2459
2669
0.296642
GACGACAACACACACACGAC
59.703
55.000
0.00
0.00
0.00
4.34
2468
2678
0.106149
AGACCCTTGGACGACAACAC
59.894
55.000
0.00
0.00
34.76
3.32
2469
2679
0.105964
CAGACCCTTGGACGACAACA
59.894
55.000
0.00
0.00
34.76
3.33
2514
2724
2.627945
GCACGTGGATTGGTAGATGAA
58.372
47.619
18.88
0.00
0.00
2.57
2516
2726
1.299541
GGCACGTGGATTGGTAGATG
58.700
55.000
18.88
0.00
0.00
2.90
2616
2828
0.813184
GGGACATGGACATGCAACAG
59.187
55.000
11.96
0.00
42.39
3.16
2628
2840
2.223021
CGTGCGAATAAACAGGGACATG
60.223
50.000
0.00
0.00
0.00
3.21
2692
2914
0.178967
TCCTTGCTTCCATGCCACAA
60.179
50.000
0.00
0.00
0.00
3.33
2707
2929
1.763770
CAGCCAACTCCCACTCCTT
59.236
57.895
0.00
0.00
0.00
3.36
2755
2978
2.092968
TGTGGGCATCTCTGATTGTACC
60.093
50.000
0.00
0.00
0.00
3.34
2764
2987
2.169352
GTGTCTGTATGTGGGCATCTCT
59.831
50.000
0.00
0.00
36.58
3.10
2800
3023
9.542462
GGATAGTGTGTGTATGTGTGTATTTAT
57.458
33.333
0.00
0.00
0.00
1.40
2801
3024
7.982919
GGGATAGTGTGTGTATGTGTGTATTTA
59.017
37.037
0.00
0.00
0.00
1.40
2802
3025
6.821665
GGGATAGTGTGTGTATGTGTGTATTT
59.178
38.462
0.00
0.00
0.00
1.40
2803
3026
6.156256
AGGGATAGTGTGTGTATGTGTGTATT
59.844
38.462
0.00
0.00
0.00
1.89
2804
3027
5.661312
AGGGATAGTGTGTGTATGTGTGTAT
59.339
40.000
0.00
0.00
0.00
2.29
2805
3028
5.020795
AGGGATAGTGTGTGTATGTGTGTA
58.979
41.667
0.00
0.00
0.00
2.90
2813
3036
4.542697
TGCTCATAGGGATAGTGTGTGTA
58.457
43.478
0.00
0.00
0.00
2.90
2814
3037
3.374764
TGCTCATAGGGATAGTGTGTGT
58.625
45.455
0.00
0.00
0.00
3.72
2819
3042
4.460731
TCGAAGATGCTCATAGGGATAGTG
59.539
45.833
0.00
0.00
0.00
2.74
2820
3043
4.667573
TCGAAGATGCTCATAGGGATAGT
58.332
43.478
0.00
0.00
0.00
2.12
2836
3059
3.427638
CGACTACAAGGCAATCTCGAAGA
60.428
47.826
0.00
0.00
0.00
2.87
2840
3063
2.186076
GTCGACTACAAGGCAATCTCG
58.814
52.381
8.70
0.00
0.00
4.04
2862
3085
4.584394
GACTTTGTCGACGAACATGTTTT
58.416
39.130
14.37
2.72
0.00
2.43
2880
3103
0.946221
CGACCAAGCAGCTTCGACTT
60.946
55.000
4.07
0.00
33.20
3.01
2884
3107
1.205064
CAACGACCAAGCAGCTTCG
59.795
57.895
12.50
12.50
37.50
3.79
2899
3122
1.365699
AGTCAACCACACACGTCAAC
58.634
50.000
0.00
0.00
0.00
3.18
2901
3124
3.462483
AATAGTCAACCACACACGTCA
57.538
42.857
0.00
0.00
0.00
4.35
2912
3136
2.475200
GCCGATGCCAAATAGTCAAC
57.525
50.000
0.00
0.00
0.00
3.18
2936
3160
2.660258
AAACAAGCGTCGAGGCCTGT
62.660
55.000
24.51
24.51
39.17
4.00
2948
3172
1.661509
GCCTTCACCGCAAACAAGC
60.662
57.895
0.00
0.00
0.00
4.01
2972
3196
2.873472
GACTCCATCATCGACGACTACT
59.127
50.000
0.00
0.00
0.00
2.57
2975
3199
0.658368
CGACTCCATCATCGACGACT
59.342
55.000
0.00
0.00
40.86
4.18
3008
3232
1.221566
CATCGCCATCACACCTCCA
59.778
57.895
0.00
0.00
0.00
3.86
3014
3238
1.447663
CGGTGTCATCGCCATCACA
60.448
57.895
0.00
0.00
43.79
3.58
3015
3239
2.173669
CCGGTGTCATCGCCATCAC
61.174
63.158
0.00
0.00
43.79
3.06
3079
3303
3.035503
CGCCCGCAAAAACAAGGC
61.036
61.111
0.00
0.00
40.33
4.35
3122
3346
6.464222
AGAGAGTTGTCCAATTAATTGACGA
58.536
36.000
26.32
18.46
40.14
4.20
3126
3350
7.237173
GTCGAAGAGAGTTGTCCAATTAATTG
58.763
38.462
19.40
19.40
36.95
2.32
3133
3357
2.317040
AGGTCGAAGAGAGTTGTCCAA
58.683
47.619
0.00
0.00
36.95
3.53
3156
3380
4.387437
CCCTTAGGGCCTGATCCATTAAAA
60.387
45.833
18.53
0.00
35.35
1.52
3170
3394
1.076995
AAATGCGGTCCCTTAGGGC
60.077
57.895
13.54
7.82
43.94
5.19
3172
3396
1.743394
GTTGAAATGCGGTCCCTTAGG
59.257
52.381
0.00
0.00
0.00
2.69
3257
3482
5.825151
AGCCTTGCTTAGATGGTTAGATTTC
59.175
40.000
0.00
0.00
33.89
2.17
3278
3503
2.416972
CCTTGTACTCGTGGACTAAGCC
60.417
54.545
0.93
0.00
0.00
4.35
3280
3505
2.731341
CGCCTTGTACTCGTGGACTAAG
60.731
54.545
0.93
3.77
0.00
2.18
3284
3509
0.172803
ATCGCCTTGTACTCGTGGAC
59.827
55.000
0.00
0.00
0.00
4.02
3285
3510
0.172578
CATCGCCTTGTACTCGTGGA
59.827
55.000
0.00
0.00
0.00
4.02
3286
3511
1.421410
GCATCGCCTTGTACTCGTGG
61.421
60.000
0.00
0.00
0.00
4.94
3287
3512
0.458543
AGCATCGCCTTGTACTCGTG
60.459
55.000
0.00
0.00
0.00
4.35
3288
3513
0.246635
AAGCATCGCCTTGTACTCGT
59.753
50.000
0.00
0.00
0.00
4.18
3289
3514
2.203800
TAAGCATCGCCTTGTACTCG
57.796
50.000
0.00
0.00
0.00
4.18
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.