Multiple sequence alignment - TraesCS3B01G365000
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
TraesCS3B01G365000
chr3B
100.000
5355
0
0
1
5355
576444732
576450086
0.000000e+00
9889.0
1
TraesCS3B01G365000
chr3D
92.297
4375
205
55
492
4784
439673122
439677446
0.000000e+00
6091.0
2
TraesCS3B01G365000
chr3D
95.969
1662
44
7
2113
3771
141540720
141539079
0.000000e+00
2676.0
3
TraesCS3B01G365000
chr3D
95.665
1661
50
10
2113
3771
141546904
141545264
0.000000e+00
2649.0
4
TraesCS3B01G365000
chr3D
96.170
1462
51
4
2312
3771
141563697
141562239
0.000000e+00
2385.0
5
TraesCS3B01G365000
chr3D
95.244
778
36
1
2557
3333
567166932
567166155
0.000000e+00
1230.0
6
TraesCS3B01G365000
chr3D
89.331
478
38
4
4882
5355
439677445
439677913
5.970000e-164
588.0
7
TraesCS3B01G365000
chr3D
91.049
324
16
6
146
457
439672684
439673006
4.960000e-115
425.0
8
TraesCS3B01G365000
chr3D
93.952
248
4
1
1974
2221
567167165
567166929
1.100000e-96
364.0
9
TraesCS3B01G365000
chr3D
96.970
132
4
0
15
146
439672524
439672655
6.980000e-54
222.0
10
TraesCS3B01G365000
chr3A
91.338
2563
145
36
2831
5355
579375210
579377733
0.000000e+00
3432.0
11
TraesCS3B01G365000
chr3A
91.971
2242
93
30
658
2846
579372989
579375196
0.000000e+00
3062.0
12
TraesCS3B01G365000
chr3A
89.014
355
12
8
165
493
579372244
579372597
1.070000e-111
414.0
13
TraesCS3B01G365000
chr3A
90.588
170
11
3
492
660
579372679
579372844
2.510000e-53
220.0
14
TraesCS3B01G365000
chr3A
92.366
131
7
1
16
146
579372061
579372188
3.290000e-42
183.0
15
TraesCS3B01G365000
chr7D
95.422
1660
70
5
2554
4211
141532783
141534438
0.000000e+00
2639.0
16
TraesCS3B01G365000
chr7D
95.432
1007
38
5
3208
4211
141540658
141541659
0.000000e+00
1598.0
17
TraesCS3B01G365000
chr7D
97.630
211
4
1
1974
2184
596365396
596365605
1.420000e-95
361.0
18
TraesCS3B01G365000
chr7D
97.156
211
5
1
1974
2184
141532553
141532762
6.600000e-94
355.0
19
TraesCS3B01G365000
chr5D
96.340
1530
51
4
2554
4081
28019631
28021157
0.000000e+00
2510.0
20
TraesCS3B01G365000
chr5D
97.156
211
5
1
1974
2184
28019401
28019610
6.600000e-94
355.0
21
TraesCS3B01G365000
chr5D
91.558
154
13
0
4058
4211
28021172
28021325
4.200000e-51
213.0
22
TraesCS3B01G365000
chr1D
93.870
1664
57
17
2113
3771
46647748
46646125
0.000000e+00
2466.0
23
TraesCS3B01G365000
chr1D
95.826
1150
43
4
2625
3771
335749814
335748667
0.000000e+00
1853.0
24
TraesCS3B01G365000
chr1D
97.630
211
4
1
1974
2184
288349054
288349263
1.420000e-95
361.0
25
TraesCS3B01G365000
chr1D
98.876
89
1
0
1974
2062
26569548
26569460
5.550000e-35
159.0
26
TraesCS3B01G365000
chr4D
93.735
431
26
1
3781
4211
108899053
108899482
0.000000e+00
645.0
27
TraesCS3B01G365000
chr6D
96.209
211
7
1
1974
2184
56369200
56369409
1.430000e-90
344.0
28
TraesCS3B01G365000
chr6D
94.286
35
1
1
1011
1045
473422593
473422560
1.000000e-02
52.8
29
TraesCS3B01G365000
chr2B
92.308
39
1
2
1011
1048
39428321
39428284
3.000000e-03
54.7
30
TraesCS3B01G365000
chr2A
86.792
53
1
4
994
1042
314683046
314683096
3.000000e-03
54.7
31
TraesCS3B01G365000
chrUn
96.875
32
0
1
1011
1042
304156377
304156407
1.000000e-02
52.8
32
TraesCS3B01G365000
chr4B
96.875
32
0
1
1011
1042
237021404
237021434
1.000000e-02
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
TraesCS3B01G365000
chr3B
576444732
576450086
5354
False
9889.0
9889
100.00000
1
5355
1
chr3B.!!$F1
5354
1
TraesCS3B01G365000
chr3D
141539079
141540720
1641
True
2676.0
2676
95.96900
2113
3771
1
chr3D.!!$R1
1658
2
TraesCS3B01G365000
chr3D
141545264
141546904
1640
True
2649.0
2649
95.66500
2113
3771
1
chr3D.!!$R2
1658
3
TraesCS3B01G365000
chr3D
141562239
141563697
1458
True
2385.0
2385
96.17000
2312
3771
1
chr3D.!!$R3
1459
4
TraesCS3B01G365000
chr3D
439672524
439677913
5389
False
1831.5
6091
92.41175
15
5355
4
chr3D.!!$F1
5340
5
TraesCS3B01G365000
chr3D
567166155
567167165
1010
True
797.0
1230
94.59800
1974
3333
2
chr3D.!!$R4
1359
6
TraesCS3B01G365000
chr3A
579372061
579377733
5672
False
1462.2
3432
91.05540
16
5355
5
chr3A.!!$F1
5339
7
TraesCS3B01G365000
chr7D
141540658
141541659
1001
False
1598.0
1598
95.43200
3208
4211
1
chr7D.!!$F1
1003
8
TraesCS3B01G365000
chr7D
141532553
141534438
1885
False
1497.0
2639
96.28900
1974
4211
2
chr7D.!!$F3
2237
9
TraesCS3B01G365000
chr5D
28019401
28021325
1924
False
1026.0
2510
95.01800
1974
4211
3
chr5D.!!$F1
2237
10
TraesCS3B01G365000
chr1D
46646125
46647748
1623
True
2466.0
2466
93.87000
2113
3771
1
chr1D.!!$R2
1658
11
TraesCS3B01G365000
chr1D
335748667
335749814
1147
True
1853.0
1853
95.82600
2625
3771
1
chr1D.!!$R3
1146
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
372
428
0.392193
CTGCGGATGCCAAGAAGAGT
60.392
55.0
0.00
0.00
41.78
3.24
F
450
509
0.468226
TTTGTCTGGCACCTTCTCGT
59.532
50.0
0.00
0.00
0.00
4.18
F
1053
1360
0.539518
GCCTCCTCTTCACCCTTCTC
59.460
60.0
0.00
0.00
0.00
2.87
F
2299
2663
0.695347
ACCTCCTCCTTCAAGGCTTG
59.305
55.0
21.17
21.17
36.29
4.01
F
3778
4200
0.616111
AGGAGACCGGCAAGATCACT
60.616
55.0
0.00
0.00
0.00
3.41
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1359
1677
0.326264
AATCTCCCAAACGCAGAGCT
59.674
50.0
0.00
0.0
0.00
4.09
R
1664
2019
0.606673
GGACAGCAAAGGGAGGACAC
60.607
60.0
0.00
0.0
0.00
3.67
R
2976
3393
0.179097
GTTCCCCGATGACTCTCTGC
60.179
60.0
0.00
0.0
0.00
4.26
R
3992
4414
0.036875
CGAAGCTCCTCTTGGGGTTT
59.963
55.0
0.00
0.0
40.10
3.27
R
4772
5274
0.178970
GCCTGGGCTTCATGGATCAT
60.179
55.0
4.12
0.0
38.26
2.45
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
138
139
5.244402
TGAAGATAGTCGTAACCACCTTTGA
59.756
40.000
0.00
0.00
0.00
2.69
274
321
0.629058
GGCCTAAGGTGGGGATCAAA
59.371
55.000
0.00
0.00
0.00
2.69
348
404
6.515531
GCATGTTTGGAATCTTCTTGACAGAA
60.516
38.462
0.00
0.00
36.62
3.02
372
428
0.392193
CTGCGGATGCCAAGAAGAGT
60.392
55.000
0.00
0.00
41.78
3.24
380
436
4.036144
GGATGCCAAGAAGAGTTGCTATTC
59.964
45.833
0.00
0.00
32.58
1.75
446
505
2.087646
GGATCTTTGTCTGGCACCTTC
58.912
52.381
0.00
0.00
0.00
3.46
450
509
0.468226
TTTGTCTGGCACCTTCTCGT
59.532
50.000
0.00
0.00
0.00
4.18
457
516
1.291132
GGCACCTTCTCGTATCAAGC
58.709
55.000
0.00
0.00
0.00
4.01
518
674
1.232119
TATGCAGAAGCGCCATGATG
58.768
50.000
2.29
0.00
46.23
3.07
522
678
2.117156
AGAAGCGCCATGATGCCAC
61.117
57.895
2.29
0.00
0.00
5.01
549
705
4.823989
ACTTGCTGGCCTGTATATGATTTC
59.176
41.667
11.69
0.00
0.00
2.17
598
754
1.460504
CATCTCCTGTGCTGCATGTT
58.539
50.000
5.27
0.00
0.00
2.71
599
755
1.132453
CATCTCCTGTGCTGCATGTTG
59.868
52.381
5.27
0.00
0.00
3.33
734
1038
1.137675
TCCACAGAATCATCGGCTCTG
59.862
52.381
0.00
0.00
41.93
3.35
760
1064
0.596082
CACACCGTGAAAATGACCCC
59.404
55.000
5.28
0.00
35.23
4.95
885
1189
3.064958
TCTGTTAGACAAGATACGCTCCG
59.935
47.826
0.00
0.00
0.00
4.63
929
1233
5.285134
CGTGAAACAAACCAACAAACTAGTG
59.715
40.000
0.00
0.00
35.74
2.74
938
1242
4.134563
CCAACAAACTAGTGCCACTACTT
58.865
43.478
0.00
0.00
32.19
2.24
989
1296
0.846693
AGCAGGAGTTGGAAAGTGGT
59.153
50.000
0.00
0.00
0.00
4.16
994
1301
1.515521
GAGTTGGAAAGTGGTGGCCG
61.516
60.000
0.00
0.00
0.00
6.13
997
1304
2.671963
GGAAAGTGGTGGCCGGAC
60.672
66.667
5.05
0.56
0.00
4.79
1045
1352
3.077556
GCCTCCGCCTCCTCTTCA
61.078
66.667
0.00
0.00
0.00
3.02
1046
1353
2.896443
CCTCCGCCTCCTCTTCAC
59.104
66.667
0.00
0.00
0.00
3.18
1047
1354
2.726351
CCTCCGCCTCCTCTTCACC
61.726
68.421
0.00
0.00
0.00
4.02
1048
1355
2.683933
TCCGCCTCCTCTTCACCC
60.684
66.667
0.00
0.00
0.00
4.61
1049
1356
2.685380
CCGCCTCCTCTTCACCCT
60.685
66.667
0.00
0.00
0.00
4.34
1050
1357
2.294078
CCGCCTCCTCTTCACCCTT
61.294
63.158
0.00
0.00
0.00
3.95
1051
1358
1.219393
CGCCTCCTCTTCACCCTTC
59.781
63.158
0.00
0.00
0.00
3.46
1052
1359
1.261238
CGCCTCCTCTTCACCCTTCT
61.261
60.000
0.00
0.00
0.00
2.85
1053
1360
0.539518
GCCTCCTCTTCACCCTTCTC
59.460
60.000
0.00
0.00
0.00
2.87
1054
1361
0.820871
CCTCCTCTTCACCCTTCTCG
59.179
60.000
0.00
0.00
0.00
4.04
1055
1362
1.551452
CTCCTCTTCACCCTTCTCGT
58.449
55.000
0.00
0.00
0.00
4.18
1056
1363
1.896465
CTCCTCTTCACCCTTCTCGTT
59.104
52.381
0.00
0.00
0.00
3.85
1089
1396
4.760047
GCGTCTCACCCGGCACAT
62.760
66.667
0.00
0.00
0.00
3.21
1175
1484
1.587933
TACGCGGTTGGATTTTGGGC
61.588
55.000
12.47
0.00
0.00
5.36
1359
1677
1.475280
CGAACATCCCGGTGAGTTCTA
59.525
52.381
20.66
0.00
38.50
2.10
1535
1860
1.068264
CGAACTGACACTGCTAGCTCA
60.068
52.381
17.23
10.15
0.00
4.26
1537
1862
1.626686
ACTGACACTGCTAGCTCACT
58.373
50.000
17.23
0.00
0.00
3.41
1577
1904
4.680171
CTTGAAAAGTACCGATGGGAAC
57.320
45.455
0.00
0.00
39.70
3.62
1595
1922
1.136828
ACCTGCAGGGACAGTAAACA
58.863
50.000
35.42
0.00
40.27
2.83
1604
1931
5.122396
GCAGGGACAGTAAACAGTAGATTTG
59.878
44.000
0.00
0.00
0.00
2.32
1630
1957
7.862873
GGACTGTTGACCTTATTTTTCTTTCTG
59.137
37.037
0.00
0.00
0.00
3.02
1661
2016
6.527023
GCATGAAGTGAAATGTTCTGATGAAG
59.473
38.462
0.00
0.00
32.15
3.02
1664
2019
5.852738
AGTGAAATGTTCTGATGAAGTCG
57.147
39.130
0.00
0.00
32.15
4.18
1674
2029
1.187087
GATGAAGTCGTGTCCTCCCT
58.813
55.000
0.00
0.00
0.00
4.20
1698
2054
2.352715
GCTGTCCAACCTTGCCAATTAC
60.353
50.000
0.00
0.00
0.00
1.89
1700
2056
3.153919
TGTCCAACCTTGCCAATTACTC
58.846
45.455
0.00
0.00
0.00
2.59
1735
2096
6.384015
TCTCATATCACTTGTAGGTTGGTGAT
59.616
38.462
11.28
11.28
46.67
3.06
1794
2155
1.134907
CATGCCAGGTGATTTCTTGCC
60.135
52.381
0.00
0.00
0.00
4.52
1808
2172
8.844244
GTGATTTCTTGCCATAGTTCTGAATAT
58.156
33.333
0.00
0.00
0.00
1.28
1809
2173
9.060347
TGATTTCTTGCCATAGTTCTGAATATC
57.940
33.333
0.00
0.00
0.00
1.63
1810
2174
8.985315
ATTTCTTGCCATAGTTCTGAATATCA
57.015
30.769
0.00
0.00
0.00
2.15
1823
2187
8.566260
AGTTCTGAATATCAATAATTCAGCTGC
58.434
33.333
9.47
11.06
46.43
5.25
1828
2192
9.565090
TGAATATCAATAATTCAGCTGCTACTT
57.435
29.630
9.47
2.12
31.50
2.24
1879
2243
5.835280
GGGAAATATCACAGGTGGAATTGAT
59.165
40.000
0.00
0.00
33.31
2.57
1969
2333
4.269523
GCACTGGCTGGTGGGACA
62.270
66.667
11.67
0.00
37.65
4.02
2071
2435
4.853007
AGGCTGCTATGGATTATGGATTC
58.147
43.478
0.00
0.00
0.00
2.52
2189
2553
9.476202
TCTTGGATTATTCTGTTACATATCGTG
57.524
33.333
0.00
0.00
0.00
4.35
2299
2663
0.695347
ACCTCCTCCTTCAAGGCTTG
59.305
55.000
21.17
21.17
36.29
4.01
2467
2831
3.314080
TGTCTTGACGGGTTCATGTTTTC
59.686
43.478
0.00
0.00
32.84
2.29
2632
3003
2.592459
GCAAAATTCGTCAATACACCGC
59.408
45.455
0.00
0.00
0.00
5.68
2701
3072
5.745227
CCAAGGCTAAAAGAGAAGGTATGA
58.255
41.667
0.00
0.00
0.00
2.15
2708
3079
5.441718
AAAAGAGAAGGTATGATGCCTGA
57.558
39.130
1.91
0.00
36.30
3.86
2744
3122
5.534207
ACAAGTTCCTCATCAATGCAAAA
57.466
34.783
0.00
0.00
0.00
2.44
2745
3123
5.535333
ACAAGTTCCTCATCAATGCAAAAG
58.465
37.500
0.00
0.00
0.00
2.27
2792
3171
5.880054
TTACTTTCAGAACATTGGCTAGC
57.120
39.130
6.04
6.04
0.00
3.42
2887
3303
2.651334
CCCATGGGATTGATCATACCCT
59.349
50.000
28.27
15.99
42.49
4.34
2891
3307
5.711976
CCATGGGATTGATCATACCCTAAAC
59.288
44.000
27.02
10.28
42.49
2.01
2976
3393
2.622942
TGTAAGCTCAAACTTTGCAGGG
59.377
45.455
0.00
0.00
0.00
4.45
3114
3531
4.737855
TTATGTAGCTGTGGTTCCTCTC
57.262
45.455
0.00
0.00
0.00
3.20
3116
3533
1.618837
TGTAGCTGTGGTTCCTCTCAC
59.381
52.381
0.00
0.00
34.71
3.51
3179
3596
3.573967
CGGGAAGCAGGGCATAATAAATT
59.426
43.478
0.00
0.00
0.00
1.82
3264
3681
8.290325
CACCTTAATTTCCTAAAGTGTGAAGTC
58.710
37.037
0.00
0.00
0.00
3.01
3274
3691
0.663568
GTGTGAAGTCGTGGAGTCCG
60.664
60.000
4.30
0.00
0.00
4.79
3492
3913
1.532868
CCACTCAGAAAGCTTTCGGTG
59.467
52.381
31.84
31.84
41.92
4.94
3560
3981
2.430694
GGGCTTGAACAAAGGAAACTGT
59.569
45.455
0.00
0.00
42.68
3.55
3561
3982
3.634910
GGGCTTGAACAAAGGAAACTGTA
59.365
43.478
0.00
0.00
42.68
2.74
3571
3992
5.204833
CAAAGGAAACTGTATGTTGTGTCG
58.795
41.667
0.00
0.00
42.68
4.35
3624
4045
6.215431
TCTCTTTTCATTACTTGATCCCAGGA
59.785
38.462
0.00
0.00
33.34
3.86
3715
4137
4.322499
CGTGATGGGTACTAAGTTGGTTCT
60.322
45.833
0.00
0.00
0.00
3.01
3721
4143
5.249852
TGGGTACTAAGTTGGTTCTATTGCT
59.750
40.000
0.00
0.00
0.00
3.91
3778
4200
0.616111
AGGAGACCGGCAAGATCACT
60.616
55.000
0.00
0.00
0.00
3.41
3833
4255
9.330063
CAGAATGGTAGTGCAGAAATTCTATAA
57.670
33.333
0.00
0.00
33.71
0.98
4081
4503
2.039418
GGGCAGAAAAGGAAAGGTTGT
58.961
47.619
0.00
0.00
0.00
3.32
4083
4505
2.035961
GGCAGAAAAGGAAAGGTTGTCC
59.964
50.000
0.00
0.00
35.17
4.02
4089
4511
0.767060
AGGAAAGGTTGTCCCCTCGT
60.767
55.000
0.00
0.00
35.59
4.18
4090
4512
0.109913
GGAAAGGTTGTCCCCTCGTT
59.890
55.000
0.00
0.00
32.13
3.85
4116
4576
6.128391
GCTCACAACTGTTAATCCGACATAAA
60.128
38.462
0.00
0.00
0.00
1.40
4149
4609
4.641396
CAACCTGTGGATGTTTCTGTCTA
58.359
43.478
0.00
0.00
0.00
2.59
4328
4788
0.543410
TTCCCTCCGAGCACCTGTAA
60.543
55.000
0.00
0.00
0.00
2.41
4330
4790
0.970937
CCCTCCGAGCACCTGTAAGA
60.971
60.000
0.00
0.00
34.07
2.10
4358
4826
1.154073
GCTGCTGCTGCTTAACTGC
60.154
57.895
22.10
7.59
43.16
4.40
4359
4827
1.134075
CTGCTGCTGCTTAACTGCG
59.866
57.895
17.00
0.00
45.63
5.18
4393
4861
1.222936
CTCATGGCACCCCTGACTC
59.777
63.158
0.00
0.00
0.00
3.36
4396
4864
1.135094
CATGGCACCCCTGACTCTAT
58.865
55.000
0.00
0.00
0.00
1.98
4505
4974
4.495422
CCTCGTTTATATCCAGATTCGGG
58.505
47.826
0.00
0.00
0.00
5.14
4511
4980
7.830697
TCGTTTATATCCAGATTCGGGTATAGA
59.169
37.037
2.66
0.00
36.25
1.98
4595
5075
5.012871
TCTGATTGGGGAAATTGCAAATTCA
59.987
36.000
24.67
8.23
0.00
2.57
4642
5122
5.596361
TGTCAAATAAGCTTTGGGAGTTTCA
59.404
36.000
3.20
0.00
30.83
2.69
4659
5139
5.670485
AGTTTCACCATATCACGCTGATAA
58.330
37.500
10.39
0.00
42.05
1.75
4725
5219
5.179452
CCACTAAAAAGGGAATGAGGAGA
57.821
43.478
0.00
0.00
0.00
3.71
4749
5246
9.788960
AGAATCACACTTCTTTTTAAACAGTTC
57.211
29.630
1.48
0.00
31.38
3.01
4756
5253
8.798153
CACTTCTTTTTAAACAGTTCATCACAC
58.202
33.333
1.48
0.00
0.00
3.82
4820
5322
0.106819
CTGAAGGGCTTCCTGATGGG
60.107
60.000
0.00
0.00
40.74
4.00
4821
5323
0.846427
TGAAGGGCTTCCTGATGGGT
60.846
55.000
0.00
0.00
40.74
4.51
4822
5324
1.213296
GAAGGGCTTCCTGATGGGTA
58.787
55.000
0.00
0.00
40.74
3.69
4823
5325
0.919710
AAGGGCTTCCTGATGGGTAC
59.080
55.000
0.00
0.00
40.74
3.34
4889
5420
5.594317
ACATGATCCATTAAGTAACTTGGCC
59.406
40.000
0.00
0.00
0.00
5.36
4894
5425
5.014202
TCCATTAAGTAACTTGGCCTTTCC
58.986
41.667
3.32
0.00
0.00
3.13
4936
5467
7.328005
CGATGTCGAGATGTTTATGAATCTGAT
59.672
37.037
0.00
0.00
43.02
2.90
4962
5493
2.432146
TGTCACCTCATCAGGCTGTATC
59.568
50.000
15.27
0.00
45.05
2.24
4974
5505
6.229936
TCAGGCTGTATCGTTTATTTAGGT
57.770
37.500
15.27
0.00
0.00
3.08
5164
5695
7.891498
TTCATCACATGATTCTGATCCAAAT
57.109
32.000
0.00
0.00
39.39
2.32
5180
5711
5.054390
TCCAAATTTCTCGCCAATACAAC
57.946
39.130
0.00
0.00
0.00
3.32
5206
5737
7.496346
ACATTGTGAAGAATCTAGGGAGTAA
57.504
36.000
0.00
0.00
0.00
2.24
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
12
13
9.512588
CCAAATAGGCTTCAATTCTGATATACT
57.487
33.333
0.00
0.00
0.00
2.12
13
14
9.289782
ACCAAATAGGCTTCAATTCTGATATAC
57.710
33.333
0.00
0.00
43.14
1.47
138
139
0.328258
CCCCTTCGTTGGTGGAGAAT
59.672
55.000
0.00
0.00
0.00
2.40
178
221
2.344950
CTCAGCTCATGGAGTGTGTTC
58.655
52.381
0.00
0.00
31.39
3.18
274
321
0.251341
GGAGTGACCCCAAAGCACAT
60.251
55.000
0.00
0.00
35.08
3.21
348
404
1.377725
CTTGGCATCCGCAGAACCT
60.378
57.895
0.00
0.00
41.24
3.50
357
413
1.831580
AGCAACTCTTCTTGGCATCC
58.168
50.000
0.00
0.00
0.00
3.51
392
448
5.694995
AGTACTATACCTTGGCGTAACCTA
58.305
41.667
0.00
0.00
40.22
3.08
433
492
1.476891
GATACGAGAAGGTGCCAGACA
59.523
52.381
0.00
0.00
0.00
3.41
446
505
1.671328
TCTCAGTCGGCTTGATACGAG
59.329
52.381
0.00
0.00
40.09
4.18
450
509
4.220821
AGAACTTTCTCAGTCGGCTTGATA
59.779
41.667
0.00
0.00
32.94
2.15
457
516
3.182572
CGTTGAAGAACTTTCTCAGTCGG
59.817
47.826
0.00
0.00
36.28
4.79
522
678
2.717639
ATACAGGCCAGCAAGTAAGG
57.282
50.000
5.01
0.00
0.00
2.69
598
754
3.957586
CCAGTGGGCAGACAGGCA
61.958
66.667
0.00
0.00
46.44
4.75
760
1064
1.268896
GCACCAATGGCAGATTCATCG
60.269
52.381
0.00
0.00
0.00
3.84
885
1189
1.948144
GCCTTCTCCCTCTTTGACAGC
60.948
57.143
0.00
0.00
0.00
4.40
929
1233
1.080995
CGCAGCAGAGAAGTAGTGGC
61.081
60.000
0.00
0.00
0.00
5.01
938
1242
1.079888
TCGCAAATCGCAGCAGAGA
60.080
52.632
0.00
0.00
42.60
3.10
1029
1336
2.726351
GGTGAAGAGGAGGCGGAGG
61.726
68.421
0.00
0.00
0.00
4.30
1033
1340
1.219393
GAAGGGTGAAGAGGAGGCG
59.781
63.158
0.00
0.00
0.00
5.52
1034
1341
0.539518
GAGAAGGGTGAAGAGGAGGC
59.460
60.000
0.00
0.00
0.00
4.70
1038
1345
1.941668
GCAACGAGAAGGGTGAAGAGG
60.942
57.143
0.00
0.00
0.00
3.69
1042
1349
4.792087
GGCAACGAGAAGGGTGAA
57.208
55.556
0.00
0.00
0.00
3.18
1107
1414
4.992381
ACTAGAAACAAACATGAGACGC
57.008
40.909
0.00
0.00
0.00
5.19
1359
1677
0.326264
AATCTCCCAAACGCAGAGCT
59.674
50.000
0.00
0.00
0.00
4.09
1535
1860
6.987992
TCAAGTTTACCGTGAGATTTTGTAGT
59.012
34.615
0.00
0.00
0.00
2.73
1537
1862
7.789273
TTCAAGTTTACCGTGAGATTTTGTA
57.211
32.000
0.00
0.00
33.01
2.41
1577
1904
1.072331
ACTGTTTACTGTCCCTGCAGG
59.928
52.381
26.87
26.87
40.59
4.85
1595
1922
5.568620
AAGGTCAACAGTCCAAATCTACT
57.431
39.130
0.00
0.00
0.00
2.57
1604
1931
7.862873
CAGAAAGAAAAATAAGGTCAACAGTCC
59.137
37.037
0.00
0.00
0.00
3.85
1630
1957
5.754890
AGAACATTTCACTTCATGCCAAAAC
59.245
36.000
0.00
0.00
0.00
2.43
1661
2016
0.951040
CAGCAAAGGGAGGACACGAC
60.951
60.000
0.00
0.00
0.00
4.34
1664
2019
0.606673
GGACAGCAAAGGGAGGACAC
60.607
60.000
0.00
0.00
0.00
3.67
1674
2029
0.685785
TGGCAAGGTTGGACAGCAAA
60.686
50.000
0.00
0.00
0.00
3.68
1698
2054
8.420222
ACAAGTGATATGAGAACATAAGAGGAG
58.580
37.037
0.00
0.00
41.46
3.69
1700
2056
9.689976
CTACAAGTGATATGAGAACATAAGAGG
57.310
37.037
0.00
0.00
41.46
3.69
1771
2132
1.742761
AGAAATCACCTGGCATGACG
58.257
50.000
0.00
0.00
0.00
4.35
1808
2172
7.452880
AAACAAGTAGCAGCTGAATTATTGA
57.547
32.000
20.43
0.00
0.00
2.57
1809
2173
9.443283
GATAAACAAGTAGCAGCTGAATTATTG
57.557
33.333
20.43
16.24
0.00
1.90
1810
2174
9.177608
TGATAAACAAGTAGCAGCTGAATTATT
57.822
29.630
20.43
1.62
0.00
1.40
1820
2184
7.601073
TGAACTGATGATAAACAAGTAGCAG
57.399
36.000
0.00
0.00
0.00
4.24
1821
2185
7.823799
TGATGAACTGATGATAAACAAGTAGCA
59.176
33.333
0.00
0.00
0.00
3.49
1823
2187
8.824781
CCTGATGAACTGATGATAAACAAGTAG
58.175
37.037
0.00
0.00
0.00
2.57
1828
2192
5.748402
AGCCTGATGAACTGATGATAAACA
58.252
37.500
0.00
0.00
0.00
2.83
1969
2333
3.314913
TGACAAAGTCGATGTGCATTGTT
59.685
39.130
0.00
0.00
34.95
2.83
2071
2435
1.851304
ACTTGGTAATGGCCATGTGG
58.149
50.000
21.63
9.19
42.81
4.17
2186
2550
2.455032
GAGGATCTTCGTCATGTCACG
58.545
52.381
0.69
0.69
41.36
4.35
2494
2865
9.492973
AAGCACAAATTTCATGTTAAAGCTATT
57.507
25.926
0.00
0.00
29.45
1.73
2632
3003
5.122711
TGCTCATCACATGAACAACATACAG
59.877
40.000
0.00
0.00
39.11
2.74
2708
3079
4.469586
AGGAACTTGTTTGAACCAAATGGT
59.530
37.500
0.00
0.00
45.74
3.55
2744
3122
8.814038
ATGTTCATAAAATAACTCTGGCTTCT
57.186
30.769
0.00
0.00
0.00
2.85
2745
3123
9.860898
AAATGTTCATAAAATAACTCTGGCTTC
57.139
29.630
0.00
0.00
0.00
3.86
2949
3366
4.681483
GCAAAGTTTGAGCTTACATCAACC
59.319
41.667
19.82
0.00
36.44
3.77
2976
3393
0.179097
GTTCCCCGATGACTCTCTGC
60.179
60.000
0.00
0.00
0.00
4.26
3114
3531
8.093307
ACATACCTAGAAGCATGATATGAAGTG
58.907
37.037
0.00
0.00
0.00
3.16
3116
3533
8.309656
TCACATACCTAGAAGCATGATATGAAG
58.690
37.037
0.00
0.00
0.00
3.02
3179
3596
4.898320
TGATGAAAGAGCAGCTTGAAGTA
58.102
39.130
0.00
0.00
36.80
2.24
3264
3681
3.241868
CGCTTTATTTTACGGACTCCACG
60.242
47.826
0.00
0.00
37.36
4.94
3492
3913
5.829924
TGGGAATCTTCCTGAAATCATAAGC
59.170
40.000
8.78
0.00
46.72
3.09
3495
3916
6.779049
CCATTGGGAATCTTCCTGAAATCATA
59.221
38.462
8.78
0.00
46.72
2.15
3560
3981
3.565902
TCCATTTGCAACGACACAACATA
59.434
39.130
0.00
0.00
0.00
2.29
3561
3982
2.360483
TCCATTTGCAACGACACAACAT
59.640
40.909
0.00
0.00
0.00
2.71
3571
3992
0.319405
AGCCAGCTTCCATTTGCAAC
59.681
50.000
0.00
0.00
0.00
4.17
3624
4045
9.467258
CAAATTATATGCATCCGTTCTTCAATT
57.533
29.630
0.19
0.00
0.00
2.32
3715
4137
7.665559
AGTCAGAAAACAGAAATACCAGCAATA
59.334
33.333
0.00
0.00
0.00
1.90
3721
4143
8.463930
AATGAAGTCAGAAAACAGAAATACCA
57.536
30.769
0.00
0.00
0.00
3.25
3778
4200
3.761752
TCACTCTCACATAATCGGTGACA
59.238
43.478
0.00
0.00
40.16
3.58
3962
4384
1.870064
TGTCTGCATCAGATCCCTCA
58.130
50.000
0.00
0.00
42.73
3.86
3992
4414
0.036875
CGAAGCTCCTCTTGGGGTTT
59.963
55.000
0.00
0.00
40.10
3.27
4028
4450
2.577059
TCGGACCTCGAATGGTGC
59.423
61.111
0.26
3.12
45.86
5.01
4049
4471
1.812686
TTCTGCCCTCGTACACGCTT
61.813
55.000
0.00
0.00
39.60
4.68
4051
4473
0.947180
TTTTCTGCCCTCGTACACGC
60.947
55.000
0.00
0.00
39.60
5.34
4081
4503
1.070786
GTTGTGAGCAACGAGGGGA
59.929
57.895
0.00
0.00
44.40
4.81
4089
4511
3.496884
GTCGGATTAACAGTTGTGAGCAA
59.503
43.478
0.00
0.00
0.00
3.91
4090
4512
3.064207
GTCGGATTAACAGTTGTGAGCA
58.936
45.455
0.00
0.00
0.00
4.26
4116
4576
2.751166
CACAGGTTGGATCTCGAGTT
57.249
50.000
13.13
3.51
0.00
3.01
4149
4609
4.166144
CCTCTACCATTCCCTACACCAATT
59.834
45.833
0.00
0.00
0.00
2.32
4328
4788
2.919856
AGCAGCCTCACCACGTCT
60.920
61.111
0.00
0.00
0.00
4.18
4330
4790
4.996434
GCAGCAGCCTCACCACGT
62.996
66.667
0.00
0.00
33.58
4.49
4393
4861
8.642935
TCTTGAACCAGATAGGATAGTGATAG
57.357
38.462
0.00
0.00
41.22
2.08
4396
4864
6.667848
TGTTCTTGAACCAGATAGGATAGTGA
59.332
38.462
10.51
0.00
41.22
3.41
4533
5002
8.761575
ATGTTTGCAAGAAAATACTTGTATGG
57.238
30.769
0.00
0.00
45.98
2.74
4553
5033
9.426837
CCAATCAGAAATGTGATTTGTATGTTT
57.573
29.630
3.28
0.00
43.29
2.83
4595
5075
4.529897
TCATGATATGGCAAAGCTTGAGT
58.470
39.130
0.00
0.00
0.00
3.41
4642
5122
5.276461
TCAAGTTATCAGCGTGATATGGT
57.724
39.130
8.03
0.00
38.94
3.55
4659
5139
7.595819
TGGTAGAAAATTTGACCATTCAAGT
57.404
32.000
13.28
0.00
42.79
3.16
4701
5195
3.011257
TCCTCATTCCCTTTTTAGTGGGG
59.989
47.826
0.00
0.00
43.51
4.96
4756
5253
7.389607
TCATGGATCATGCTTCATACACTAATG
59.610
37.037
3.23
0.00
41.18
1.90
4772
5274
0.178970
GCCTGGGCTTCATGGATCAT
60.179
55.000
4.12
0.00
38.26
2.45
4864
5395
6.096846
GGCCAAGTTACTTAATGGATCATGTT
59.903
38.462
5.81
0.00
34.82
2.71
4865
5396
5.594317
GGCCAAGTTACTTAATGGATCATGT
59.406
40.000
5.81
0.00
34.82
3.21
4866
5397
5.829924
AGGCCAAGTTACTTAATGGATCATG
59.170
40.000
5.01
0.00
34.82
3.07
4894
5425
3.318017
ACATCGGTTCTGTTCTTTCGAG
58.682
45.455
0.00
0.00
0.00
4.04
4936
5467
2.840038
AGCCTGATGAGGTGACATGTTA
59.160
45.455
0.00
0.00
42.15
2.41
4974
5505
5.491323
TGTGGACTTGTGGTGTATAATCA
57.509
39.130
0.00
0.00
0.00
2.57
5164
5695
5.218885
CAATGTTGTTGTATTGGCGAGAAA
58.781
37.500
0.00
0.00
32.13
2.52
5180
5711
6.176183
ACTCCCTAGATTCTTCACAATGTTG
58.824
40.000
0.00
0.00
0.00
3.33
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.