Multiple sequence alignment - TraesCS1D01G087000
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
TraesCS1D01G087000
chr1D
100.000
3044
0
0
1
3044
72436751
72433708
0.000000e+00
5622.0
1
TraesCS1D01G087000
chr1D
81.806
1484
210
36
1575
3044
72443223
72441786
0.000000e+00
1190.0
2
TraesCS1D01G087000
chr1D
81.781
1482
213
34
1575
3044
72459630
72458194
0.000000e+00
1188.0
3
TraesCS1D01G087000
chr1D
74.667
1425
267
59
1224
2612
71639738
71638372
2.060000e-151
545.0
4
TraesCS1D01G087000
chr1D
76.984
882
187
13
3
879
441653559
441654429
9.810000e-135
490.0
5
TraesCS1D01G087000
chr1D
77.250
589
119
13
2207
2785
25140039
25140622
6.290000e-87
331.0
6
TraesCS1D01G087000
chr1B
93.642
2029
92
14
1023
3044
113499199
113497201
0.000000e+00
2998.0
7
TraesCS1D01G087000
chr1B
93.494
2029
98
13
1023
3044
113316411
113314410
0.000000e+00
2985.0
8
TraesCS1D01G087000
chr1B
93.988
1863
85
11
1182
3044
113213884
113212049
0.000000e+00
2795.0
9
TraesCS1D01G087000
chr1B
86.176
1794
203
23
1229
3006
113516577
113514813
0.000000e+00
1897.0
10
TraesCS1D01G087000
chr1B
93.519
324
20
1
2721
3044
113407767
113407445
5.900000e-132
481.0
11
TraesCS1D01G087000
chr1B
91.391
151
12
1
1023
1172
113214294
113214144
3.980000e-49
206.0
12
TraesCS1D01G087000
chr1B
94.643
56
2
1
1023
1077
113409188
113409133
5.410000e-13
86.1
13
TraesCS1D01G087000
chr1B
94.118
51
2
1
1023
1072
113211252
113211302
3.250000e-10
76.8
14
TraesCS1D01G087000
chr1B
92.593
54
3
1
1020
1072
113406649
113406702
3.250000e-10
76.8
15
TraesCS1D01G087000
chr1B
92.593
54
3
1
1020
1072
113496401
113496454
3.250000e-10
76.8
16
TraesCS1D01G087000
chrUn
93.958
1804
76
12
1079
2876
372932431
372934207
0.000000e+00
2697.0
17
TraesCS1D01G087000
chrUn
82.837
705
117
3
3
706
257143896
257144597
1.990000e-176
628.0
18
TraesCS1D01G087000
chrUn
82.837
705
117
3
3
706
318231798
318231097
1.990000e-176
628.0
19
TraesCS1D01G087000
chr7D
82.854
869
146
3
3
870
619117981
619118847
0.000000e+00
776.0
20
TraesCS1D01G087000
chr5B
77.496
1222
221
35
1629
2838
411744253
411743074
0.000000e+00
684.0
21
TraesCS1D01G087000
chr1A
74.917
1503
290
55
1224
2687
71724976
71723522
9.330000e-170
606.0
22
TraesCS1D01G087000
chr1A
76.508
796
176
11
84
873
12226177
12226967
1.010000e-114
424.0
23
TraesCS1D01G087000
chr1A
75.463
216
44
6
1247
1456
570787915
570787703
2.500000e-16
97.1
24
TraesCS1D01G087000
chr3D
79.603
755
128
23
138
879
32136137
32136878
4.500000e-143
518.0
25
TraesCS1D01G087000
chr3B
79.470
755
129
23
138
879
54703157
54703898
2.090000e-141
512.0
26
TraesCS1D01G087000
chr6B
76.362
863
187
15
6
861
254080367
254079515
5.990000e-122
448.0
27
TraesCS1D01G087000
chr6B
82.222
135
24
0
1231
1365
82958228
82958094
1.920000e-22
117.0
28
TraesCS1D01G087000
chr6B
80.734
109
16
5
773
879
674968095
674968200
2.520000e-11
80.5
29
TraesCS1D01G087000
chr2B
76.382
796
177
11
84
873
691408996
691409786
4.690000e-113
418.0
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
TraesCS1D01G087000
chr1D
72433708
72436751
3043
True
5622.00
5622
100.0000
1
3044
1
chr1D.!!$R2
3043
1
TraesCS1D01G087000
chr1D
72441786
72443223
1437
True
1190.00
1190
81.8060
1575
3044
1
chr1D.!!$R3
1469
2
TraesCS1D01G087000
chr1D
72458194
72459630
1436
True
1188.00
1188
81.7810
1575
3044
1
chr1D.!!$R4
1469
3
TraesCS1D01G087000
chr1D
71638372
71639738
1366
True
545.00
545
74.6670
1224
2612
1
chr1D.!!$R1
1388
4
TraesCS1D01G087000
chr1D
441653559
441654429
870
False
490.00
490
76.9840
3
879
1
chr1D.!!$F2
876
5
TraesCS1D01G087000
chr1D
25140039
25140622
583
False
331.00
331
77.2500
2207
2785
1
chr1D.!!$F1
578
6
TraesCS1D01G087000
chr1B
113497201
113499199
1998
True
2998.00
2998
93.6420
1023
3044
1
chr1B.!!$R2
2021
7
TraesCS1D01G087000
chr1B
113314410
113316411
2001
True
2985.00
2985
93.4940
1023
3044
1
chr1B.!!$R1
2021
8
TraesCS1D01G087000
chr1B
113514813
113516577
1764
True
1897.00
1897
86.1760
1229
3006
1
chr1B.!!$R3
1777
9
TraesCS1D01G087000
chr1B
113212049
113214294
2245
True
1500.50
2795
92.6895
1023
3044
2
chr1B.!!$R4
2021
10
TraesCS1D01G087000
chr1B
113407445
113409188
1743
True
283.55
481
94.0810
1023
3044
2
chr1B.!!$R5
2021
11
TraesCS1D01G087000
chrUn
372932431
372934207
1776
False
2697.00
2697
93.9580
1079
2876
1
chrUn.!!$F2
1797
12
TraesCS1D01G087000
chrUn
257143896
257144597
701
False
628.00
628
82.8370
3
706
1
chrUn.!!$F1
703
13
TraesCS1D01G087000
chrUn
318231097
318231798
701
True
628.00
628
82.8370
3
706
1
chrUn.!!$R1
703
14
TraesCS1D01G087000
chr7D
619117981
619118847
866
False
776.00
776
82.8540
3
870
1
chr7D.!!$F1
867
15
TraesCS1D01G087000
chr5B
411743074
411744253
1179
True
684.00
684
77.4960
1629
2838
1
chr5B.!!$R1
1209
16
TraesCS1D01G087000
chr1A
71723522
71724976
1454
True
606.00
606
74.9170
1224
2687
1
chr1A.!!$R1
1463
17
TraesCS1D01G087000
chr1A
12226177
12226967
790
False
424.00
424
76.5080
84
873
1
chr1A.!!$F1
789
18
TraesCS1D01G087000
chr3D
32136137
32136878
741
False
518.00
518
79.6030
138
879
1
chr3D.!!$F1
741
19
TraesCS1D01G087000
chr3B
54703157
54703898
741
False
512.00
512
79.4700
138
879
1
chr3B.!!$F1
741
20
TraesCS1D01G087000
chr6B
254079515
254080367
852
True
448.00
448
76.3620
6
861
1
chr6B.!!$R2
855
21
TraesCS1D01G087000
chr2B
691408996
691409786
790
False
418.00
418
76.3820
84
873
1
chr2B.!!$F1
789
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
942
946
0.323725
AGACCCGCAAGATGCCAATT
60.324
50.0
0.00
0.00
41.12
2.32
F
1002
1006
0.169672
CAACAAGCCGAGCAGGAATG
59.830
55.0
2.12
2.89
45.00
2.67
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2004
2260
1.538687
AAAGGCCCAACATCTGCAGC
61.539
55.0
9.47
0.0
0.00
5.25
R
2649
2955
2.284263
TCTAGCAGCGTGAGTTGATG
57.716
50.0
0.00
0.0
46.01
3.07
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
49
50
4.263331
CCTCTCTTGCTACCCTACCAAAAA
60.263
45.833
0.00
0.00
0.00
1.94
74
75
6.768381
AGCTTTAATCATAGAAGTTAGGTGCC
59.232
38.462
0.00
0.00
0.00
5.01
76
77
4.755266
AATCATAGAAGTTAGGTGCCGT
57.245
40.909
0.00
0.00
0.00
5.68
77
78
5.864418
AATCATAGAAGTTAGGTGCCGTA
57.136
39.130
0.00
0.00
0.00
4.02
79
80
5.864418
TCATAGAAGTTAGGTGCCGTAAT
57.136
39.130
0.00
0.00
0.00
1.89
82
83
4.667519
AGAAGTTAGGTGCCGTAATAGG
57.332
45.455
0.00
0.00
0.00
2.57
109
110
5.238650
ACGAGGGAGTTTAAAACAAGACATG
59.761
40.000
0.00
0.00
0.00
3.21
115
116
7.229907
GGGAGTTTAAAACAAGACATGGAGTAA
59.770
37.037
0.00
0.00
0.00
2.24
118
119
9.185680
AGTTTAAAACAAGACATGGAGTAAACT
57.814
29.630
0.00
0.00
37.60
2.66
133
134
3.388350
AGTAAACTGGTATAGCCTGAGCC
59.612
47.826
0.00
0.00
41.25
4.70
159
160
9.007901
CACTGATTTTATCAAGACTTCCTTTCT
57.992
33.333
0.00
0.00
39.11
2.52
256
257
1.002069
TCTTTGATGCCCCCACATCT
58.998
50.000
6.13
0.00
45.51
2.90
397
400
8.321353
TCTTTATTTATTCTCTGACCAGAAGCA
58.679
33.333
1.08
0.00
35.83
3.91
452
455
2.169352
TCAGCTCCCTCTGTATTTGCTC
59.831
50.000
0.00
0.00
35.63
4.26
541
544
6.718454
CCTTAATGCCACCAAGATTAGATGAT
59.282
38.462
0.00
0.00
0.00
2.45
546
549
5.951148
TGCCACCAAGATTAGATGATTGAAA
59.049
36.000
0.00
0.00
0.00
2.69
548
551
7.779326
TGCCACCAAGATTAGATGATTGAAATA
59.221
33.333
0.00
0.00
0.00
1.40
614
617
7.698163
AAGAGGTATGGTGAAATAGGATCTT
57.302
36.000
0.00
0.00
0.00
2.40
628
631
1.619332
GGATCTTCCTGACGGATACCC
59.381
57.143
0.00
0.00
39.58
3.69
629
632
2.317040
GATCTTCCTGACGGATACCCA
58.683
52.381
0.00
0.00
39.58
4.51
654
658
7.552687
CAGTGTAGGGTTAAATTCATCAGCTTA
59.447
37.037
0.00
0.00
0.00
3.09
717
721
6.262273
CCATGTCCATAACTATGTTAACCCAC
59.738
42.308
2.48
0.00
31.82
4.61
738
742
2.768527
CCTCTCAGTGAATCCCAGCTTA
59.231
50.000
0.00
0.00
0.00
3.09
747
751
5.767168
AGTGAATCCCAGCTTAAGCATAATC
59.233
40.000
28.39
17.53
45.16
1.75
803
807
5.382616
TGCCTTCATCATATCAAGCTTCAT
58.617
37.500
0.00
0.00
0.00
2.57
804
808
5.240844
TGCCTTCATCATATCAAGCTTCATG
59.759
40.000
0.00
0.71
0.00
3.07
824
828
2.626088
GCACAATGCCTGTTTCTCTC
57.374
50.000
0.00
0.00
37.42
3.20
826
830
2.294233
GCACAATGCCTGTTTCTCTCAA
59.706
45.455
0.00
0.00
37.42
3.02
838
842
6.372937
CCTGTTTCTCTCAACCTTATTTCTCC
59.627
42.308
0.00
0.00
0.00
3.71
875
879
7.674120
AGACACTCATAAGCAGCAATGATATA
58.326
34.615
10.08
0.00
31.95
0.86
876
880
8.319881
AGACACTCATAAGCAGCAATGATATAT
58.680
33.333
10.08
0.00
31.95
0.86
877
881
9.591792
GACACTCATAAGCAGCAATGATATATA
57.408
33.333
10.08
0.00
31.95
0.86
934
938
8.918202
ATATATTTTAAATGAGACCCGCAAGA
57.082
30.769
0.00
0.00
43.02
3.02
935
939
7.823745
ATATTTTAAATGAGACCCGCAAGAT
57.176
32.000
0.00
0.00
43.02
2.40
936
940
4.963276
TTTAAATGAGACCCGCAAGATG
57.037
40.909
0.00
0.00
43.02
2.90
937
941
1.098050
AAATGAGACCCGCAAGATGC
58.902
50.000
0.00
0.00
40.69
3.91
938
942
0.749454
AATGAGACCCGCAAGATGCC
60.749
55.000
0.00
0.00
41.12
4.40
939
943
1.913951
ATGAGACCCGCAAGATGCCA
61.914
55.000
0.00
0.00
41.12
4.92
940
944
1.377202
GAGACCCGCAAGATGCCAA
60.377
57.895
0.00
0.00
41.12
4.52
941
945
0.749454
GAGACCCGCAAGATGCCAAT
60.749
55.000
0.00
0.00
41.12
3.16
942
946
0.323725
AGACCCGCAAGATGCCAATT
60.324
50.000
0.00
0.00
41.12
2.32
943
947
0.532115
GACCCGCAAGATGCCAATTT
59.468
50.000
0.00
0.00
41.12
1.82
944
948
0.975887
ACCCGCAAGATGCCAATTTT
59.024
45.000
0.00
0.00
41.12
1.82
945
949
1.347378
ACCCGCAAGATGCCAATTTTT
59.653
42.857
0.00
0.00
41.12
1.94
975
979
3.544772
AAAAACAACCAGGCCCGG
58.455
55.556
2.45
2.45
0.00
5.73
976
980
1.382009
AAAAACAACCAGGCCCGGT
60.382
52.632
4.23
4.23
42.71
5.28
977
981
1.396607
AAAAACAACCAGGCCCGGTC
61.397
55.000
12.19
0.00
38.76
4.79
978
982
3.802852
AAACAACCAGGCCCGGTCC
62.803
63.158
12.19
0.00
38.76
4.46
980
984
4.722700
CAACCAGGCCCGGTCCAG
62.723
72.222
12.19
0.00
38.76
3.86
988
992
4.278513
CCCGGTCCAGCCCAACAA
62.279
66.667
0.00
0.00
0.00
2.83
989
993
2.672996
CCGGTCCAGCCCAACAAG
60.673
66.667
0.00
0.00
0.00
3.16
990
994
3.365265
CGGTCCAGCCCAACAAGC
61.365
66.667
0.00
0.00
0.00
4.01
991
995
2.991540
GGTCCAGCCCAACAAGCC
60.992
66.667
0.00
0.00
0.00
4.35
992
996
3.365265
GTCCAGCCCAACAAGCCG
61.365
66.667
0.00
0.00
0.00
5.52
993
997
3.565214
TCCAGCCCAACAAGCCGA
61.565
61.111
0.00
0.00
0.00
5.54
994
998
3.058160
CCAGCCCAACAAGCCGAG
61.058
66.667
0.00
0.00
0.00
4.63
995
999
3.741476
CAGCCCAACAAGCCGAGC
61.741
66.667
0.00
0.00
0.00
5.03
996
1000
4.269523
AGCCCAACAAGCCGAGCA
62.270
61.111
0.00
0.00
0.00
4.26
997
1001
3.741476
GCCCAACAAGCCGAGCAG
61.741
66.667
0.00
0.00
0.00
4.24
998
1002
3.058160
CCCAACAAGCCGAGCAGG
61.058
66.667
0.00
0.00
44.97
4.85
999
1003
2.032528
CCAACAAGCCGAGCAGGA
59.967
61.111
2.12
0.00
45.00
3.86
1000
1004
1.600636
CCAACAAGCCGAGCAGGAA
60.601
57.895
2.12
0.00
45.00
3.36
1001
1005
0.962356
CCAACAAGCCGAGCAGGAAT
60.962
55.000
2.12
0.00
45.00
3.01
1002
1006
0.169672
CAACAAGCCGAGCAGGAATG
59.830
55.000
2.12
2.89
45.00
2.67
1003
1007
0.250901
AACAAGCCGAGCAGGAATGT
60.251
50.000
2.12
3.47
45.00
2.71
1004
1008
0.957395
ACAAGCCGAGCAGGAATGTG
60.957
55.000
2.12
0.00
45.00
3.21
1005
1009
2.042831
AAGCCGAGCAGGAATGTGC
61.043
57.895
2.12
0.00
45.00
4.57
1006
1010
3.512516
GCCGAGCAGGAATGTGCC
61.513
66.667
2.12
0.00
45.20
5.01
1007
1011
2.046023
CCGAGCAGGAATGTGCCA
60.046
61.111
0.00
0.00
45.20
4.92
1008
1012
1.452651
CCGAGCAGGAATGTGCCAT
60.453
57.895
0.00
0.00
45.20
4.40
1009
1013
1.442526
CCGAGCAGGAATGTGCCATC
61.443
60.000
0.00
0.00
45.20
3.51
1010
1014
1.769098
CGAGCAGGAATGTGCCATCG
61.769
60.000
0.00
0.00
45.20
3.84
1011
1015
0.745845
GAGCAGGAATGTGCCATCGT
60.746
55.000
0.00
0.00
45.20
3.73
1012
1016
0.322816
AGCAGGAATGTGCCATCGTT
60.323
50.000
0.00
0.00
45.20
3.85
1013
1017
0.179156
GCAGGAATGTGCCATCGTTG
60.179
55.000
0.00
0.00
37.49
4.10
1014
1018
0.452987
CAGGAATGTGCCATCGTTGG
59.547
55.000
8.23
8.23
46.66
3.77
1015
1019
0.327924
AGGAATGTGCCATCGTTGGA
59.672
50.000
16.83
0.00
46.92
3.53
1016
1020
1.173043
GGAATGTGCCATCGTTGGAA
58.827
50.000
16.83
2.29
46.92
3.53
1017
1021
1.133025
GGAATGTGCCATCGTTGGAAG
59.867
52.381
16.83
0.00
46.92
3.46
1018
1022
0.527565
AATGTGCCATCGTTGGAAGC
59.472
50.000
16.83
5.71
46.92
3.86
1019
1023
0.322816
ATGTGCCATCGTTGGAAGCT
60.323
50.000
16.83
0.00
46.92
3.74
1020
1024
1.236616
TGTGCCATCGTTGGAAGCTG
61.237
55.000
16.83
0.00
46.92
4.24
1021
1025
1.675310
TGCCATCGTTGGAAGCTGG
60.675
57.895
16.83
0.00
46.92
4.85
1028
1032
1.202879
TCGTTGGAAGCTGGAACCAAT
60.203
47.619
14.70
0.00
43.89
3.16
1033
1037
1.285078
GGAAGCTGGAACCAATACCCT
59.715
52.381
0.00
0.00
0.00
4.34
1092
1097
1.218047
CTCGCCGGACATGAAGGAA
59.782
57.895
5.05
0.00
0.00
3.36
1216
1471
1.870402
CACACAAACTGGCACGTGATA
59.130
47.619
22.23
5.82
33.56
2.15
1256
1511
2.945008
TCATCAACAATCTTCCGGATGC
59.055
45.455
4.15
0.00
34.45
3.91
1303
1558
2.654877
CCACCAAGTACGGCGTCT
59.345
61.111
19.21
11.21
0.00
4.18
1305
1560
1.736645
CACCAAGTACGGCGTCTGG
60.737
63.158
25.36
25.36
0.00
3.86
1372
1627
3.358076
CTCAACCTCGACGCCTCCC
62.358
68.421
0.00
0.00
0.00
4.30
1522
1777
4.810661
AAGCCGCTGAGCTCGAGC
62.811
66.667
30.01
30.01
44.11
5.03
1564
1819
1.056660
GGACAACCTCCAGGAACTCA
58.943
55.000
0.00
0.00
39.21
3.41
1584
1839
5.527951
ACTCAATATCGTCTTCTCGCTCTTA
59.472
40.000
0.00
0.00
0.00
2.10
1595
1850
6.575942
GTCTTCTCGCTCTTAGAATATTCGTC
59.424
42.308
9.78
0.00
32.72
4.20
1767
2023
1.883084
GCGCGTTTCCATCTCCGAT
60.883
57.895
8.43
0.00
0.00
4.18
1878
2134
1.833630
TCGCCAACTCTCAGGATCATT
59.166
47.619
0.00
0.00
0.00
2.57
1903
2159
3.691049
TCTCTTGTTTGTTTGAAGGCG
57.309
42.857
0.00
0.00
0.00
5.52
1905
2161
3.312421
TCTCTTGTTTGTTTGAAGGCGAG
59.688
43.478
0.00
0.00
0.00
5.03
2004
2260
1.084289
GGGTTGTTAGCGCACCTAAG
58.916
55.000
11.47
0.00
36.72
2.18
2041
2297
0.911769
TTTGTCTCCCCGCATCTCAT
59.088
50.000
0.00
0.00
0.00
2.90
2084
2340
4.223923
AGTCTTCTAGGTAACAGCTGCATT
59.776
41.667
15.27
3.96
41.41
3.56
2094
2350
5.163499
GGTAACAGCTGCATTAGTCTCTAGT
60.163
44.000
15.27
0.00
0.00
2.57
2095
2351
6.039493
GGTAACAGCTGCATTAGTCTCTAGTA
59.961
42.308
15.27
0.00
0.00
1.82
2096
2352
5.766150
ACAGCTGCATTAGTCTCTAGTAG
57.234
43.478
15.27
0.00
0.00
2.57
2097
2353
4.582656
ACAGCTGCATTAGTCTCTAGTAGG
59.417
45.833
15.27
0.00
0.00
3.18
2098
2354
3.572255
AGCTGCATTAGTCTCTAGTAGGC
59.428
47.826
1.02
0.00
0.00
3.93
2100
2356
4.320935
GCTGCATTAGTCTCTAGTAGGCTC
60.321
50.000
0.00
0.00
40.17
4.70
2101
2357
5.055265
TGCATTAGTCTCTAGTAGGCTCT
57.945
43.478
0.00
0.00
40.17
4.09
2102
2358
5.450453
TGCATTAGTCTCTAGTAGGCTCTT
58.550
41.667
0.00
0.00
40.17
2.85
2104
2360
7.061054
TGCATTAGTCTCTAGTAGGCTCTTAA
58.939
38.462
0.00
0.00
40.17
1.85
2246
2520
4.097892
GGTTTTGGCTCTCAAGTTTTCTGA
59.902
41.667
0.00
0.00
36.62
3.27
2575
2881
4.520743
GCTTTGCCAAGTTCTTTGTTTC
57.479
40.909
0.00
0.00
34.87
2.78
2649
2955
4.872691
ACATCGACAAGAAATGGATGACTC
59.127
41.667
6.35
0.00
38.24
3.36
2687
2993
3.467803
AGAAGTGGAAACAAGACCTTCG
58.532
45.455
0.00
0.00
46.06
3.79
2771
3082
1.881252
CTTATCCGTTGCCGACCCG
60.881
63.158
0.00
0.00
35.63
5.28
2785
3096
0.307760
GACCCGTTCAGCTGTTGTTG
59.692
55.000
14.67
3.78
0.00
3.33
2845
3161
3.638627
TGATCTGTCAATGGCGTATCTCT
59.361
43.478
0.00
0.00
0.00
3.10
2861
3177
2.912771
TCTCTTTGGTTGCTTCGTTCA
58.087
42.857
0.00
0.00
0.00
3.18
2862
3178
3.476552
TCTCTTTGGTTGCTTCGTTCAT
58.523
40.909
0.00
0.00
0.00
2.57
2863
3179
3.250762
TCTCTTTGGTTGCTTCGTTCATG
59.749
43.478
0.00
0.00
0.00
3.07
2880
3200
7.496747
TCGTTCATGAATTATGTACCTGATGA
58.503
34.615
12.12
0.00
38.01
2.92
2989
3310
1.803334
TTGCTAGTTTCAATCGGCGT
58.197
45.000
6.85
0.00
0.00
5.68
2992
3313
2.550606
TGCTAGTTTCAATCGGCGTTTT
59.449
40.909
6.85
0.00
0.00
2.43
3006
3327
3.672867
CGGCGTTTTATGCTTGTTTTGAT
59.327
39.130
0.00
0.00
0.00
2.57
3009
3330
6.034470
CGGCGTTTTATGCTTGTTTTGATAAT
59.966
34.615
0.00
0.00
0.00
1.28
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
16
17
4.218417
GGTAGCAAGAGAGGCAAATGAAAA
59.782
41.667
0.00
0.00
0.00
2.29
21
22
1.918957
AGGGTAGCAAGAGAGGCAAAT
59.081
47.619
0.00
0.00
0.00
2.32
49
50
6.768381
GGCACCTAACTTCTATGATTAAAGCT
59.232
38.462
0.00
0.00
0.00
3.74
74
75
0.314302
CTCCCTCGTGGCCTATTACG
59.686
60.000
3.32
5.50
41.38
3.18
76
77
2.170012
AACTCCCTCGTGGCCTATTA
57.830
50.000
3.32
0.00
0.00
0.98
77
78
1.286248
AAACTCCCTCGTGGCCTATT
58.714
50.000
3.32
0.00
0.00
1.73
79
80
1.941377
TTAAACTCCCTCGTGGCCTA
58.059
50.000
3.32
0.00
0.00
3.93
82
83
2.223745
TGTTTTAAACTCCCTCGTGGC
58.776
47.619
9.33
0.00
0.00
5.01
85
86
4.773013
TGTCTTGTTTTAAACTCCCTCGT
58.227
39.130
9.33
0.00
0.00
4.18
109
110
4.501743
GCTCAGGCTATACCAGTTTACTCC
60.502
50.000
0.00
0.00
43.14
3.85
115
116
1.486726
GTGGCTCAGGCTATACCAGTT
59.513
52.381
0.00
0.00
43.14
3.16
118
119
1.123077
CAGTGGCTCAGGCTATACCA
58.877
55.000
0.00
0.00
43.14
3.25
133
134
9.007901
AGAAAGGAAGTCTTGATAAAATCAGTG
57.992
33.333
0.00
0.00
40.94
3.66
159
160
7.826252
GGATGGAGAAATTATTATCTGCAGCTA
59.174
37.037
9.47
0.00
45.82
3.32
256
257
4.298626
AGAAGTATCTTGGGATGCCTACA
58.701
43.478
4.35
0.00
35.59
2.74
397
400
4.460382
CACCTTCTGGAAACATATGCACTT
59.540
41.667
1.58
0.00
41.51
3.16
546
549
7.277396
CCTTTCATGCCTTTTGAAATCCATAT
58.723
34.615
0.00
0.00
41.03
1.78
548
551
5.493809
CCTTTCATGCCTTTTGAAATCCAT
58.506
37.500
0.00
0.00
41.03
3.41
565
568
0.840288
TGGTAGCAGAGGGCCTTTCA
60.840
55.000
7.89
0.00
46.50
2.69
628
631
5.882557
AGCTGATGAATTTAACCCTACACTG
59.117
40.000
0.00
0.00
0.00
3.66
629
632
6.067217
AGCTGATGAATTTAACCCTACACT
57.933
37.500
0.00
0.00
0.00
3.55
654
658
9.753674
TCATTCTTAGTCCTTTTTAATGGTCAT
57.246
29.630
0.00
0.00
0.00
3.06
717
721
1.202330
AGCTGGGATTCACTGAGAGG
58.798
55.000
0.00
0.00
0.00
3.69
747
751
5.973565
GGTTGAATGGAATTATTTGAGAGCG
59.026
40.000
0.00
0.00
36.07
5.03
818
822
6.935240
TGAGGAGAAATAAGGTTGAGAGAA
57.065
37.500
0.00
0.00
0.00
2.87
820
824
6.882656
TCATGAGGAGAAATAAGGTTGAGAG
58.117
40.000
0.00
0.00
0.00
3.20
824
828
8.059798
ACATTTCATGAGGAGAAATAAGGTTG
57.940
34.615
0.00
0.00
42.17
3.77
826
830
8.772250
TCTACATTTCATGAGGAGAAATAAGGT
58.228
33.333
0.00
0.00
42.17
3.50
838
842
7.493645
TGCTTATGAGTGTCTACATTTCATGAG
59.506
37.037
18.05
18.05
38.25
2.90
909
913
8.918202
TCTTGCGGGTCTCATTTAAAATATAT
57.082
30.769
0.00
0.00
0.00
0.86
910
914
8.783093
CATCTTGCGGGTCTCATTTAAAATATA
58.217
33.333
0.00
0.00
0.00
0.86
911
915
7.651808
CATCTTGCGGGTCTCATTTAAAATAT
58.348
34.615
0.00
0.00
0.00
1.28
912
916
6.459573
GCATCTTGCGGGTCTCATTTAAAATA
60.460
38.462
0.00
0.00
31.71
1.40
913
917
5.679638
GCATCTTGCGGGTCTCATTTAAAAT
60.680
40.000
0.00
0.00
31.71
1.82
914
918
4.380444
GCATCTTGCGGGTCTCATTTAAAA
60.380
41.667
0.00
0.00
31.71
1.52
915
919
3.128589
GCATCTTGCGGGTCTCATTTAAA
59.871
43.478
0.00
0.00
31.71
1.52
916
920
2.682856
GCATCTTGCGGGTCTCATTTAA
59.317
45.455
0.00
0.00
31.71
1.52
917
921
2.288666
GCATCTTGCGGGTCTCATTTA
58.711
47.619
0.00
0.00
31.71
1.40
918
922
1.098050
GCATCTTGCGGGTCTCATTT
58.902
50.000
0.00
0.00
31.71
2.32
919
923
0.749454
GGCATCTTGCGGGTCTCATT
60.749
55.000
0.00
0.00
46.21
2.57
920
924
1.153086
GGCATCTTGCGGGTCTCAT
60.153
57.895
0.00
0.00
46.21
2.90
921
925
2.123248
TTGGCATCTTGCGGGTCTCA
62.123
55.000
0.00
0.00
46.21
3.27
922
926
0.749454
ATTGGCATCTTGCGGGTCTC
60.749
55.000
0.00
0.00
46.21
3.36
923
927
0.323725
AATTGGCATCTTGCGGGTCT
60.324
50.000
0.00
0.00
46.21
3.85
924
928
0.532115
AAATTGGCATCTTGCGGGTC
59.468
50.000
0.00
0.00
46.21
4.46
925
929
0.975887
AAAATTGGCATCTTGCGGGT
59.024
45.000
0.00
0.00
46.21
5.28
926
930
2.097680
AAAAATTGGCATCTTGCGGG
57.902
45.000
0.00
0.00
46.21
6.13
958
962
1.382009
ACCGGGCCTGGTTGTTTTT
60.382
52.632
31.91
6.05
39.99
1.94
959
963
1.830847
GACCGGGCCTGGTTGTTTT
60.831
57.895
36.96
13.91
44.01
2.43
960
964
2.203437
GACCGGGCCTGGTTGTTT
60.203
61.111
36.96
14.77
44.01
2.83
961
965
4.280019
GGACCGGGCCTGGTTGTT
62.280
66.667
36.96
15.21
44.01
2.83
963
967
4.722700
CTGGACCGGGCCTGGTTG
62.723
72.222
36.96
24.51
44.01
3.77
971
975
4.278513
TTGTTGGGCTGGACCGGG
62.279
66.667
6.32
0.00
40.62
5.73
972
976
2.672996
CTTGTTGGGCTGGACCGG
60.673
66.667
0.00
0.00
40.62
5.28
973
977
3.365265
GCTTGTTGGGCTGGACCG
61.365
66.667
0.00
0.00
40.62
4.79
974
978
2.991540
GGCTTGTTGGGCTGGACC
60.992
66.667
0.00
0.00
37.93
4.46
975
979
3.365265
CGGCTTGTTGGGCTGGAC
61.365
66.667
0.00
0.00
32.91
4.02
976
980
3.551496
CTCGGCTTGTTGGGCTGGA
62.551
63.158
0.00
0.00
36.77
3.86
977
981
3.058160
CTCGGCTTGTTGGGCTGG
61.058
66.667
0.00
0.00
36.77
4.85
978
982
3.741476
GCTCGGCTTGTTGGGCTG
61.741
66.667
0.00
0.00
37.41
4.85
979
983
4.269523
TGCTCGGCTTGTTGGGCT
62.270
61.111
0.00
0.00
0.00
5.19
980
984
3.741476
CTGCTCGGCTTGTTGGGC
61.741
66.667
0.00
0.00
0.00
5.36
981
985
3.058160
CCTGCTCGGCTTGTTGGG
61.058
66.667
0.00
0.00
0.00
4.12
982
986
0.962356
ATTCCTGCTCGGCTTGTTGG
60.962
55.000
0.00
0.00
0.00
3.77
983
987
0.169672
CATTCCTGCTCGGCTTGTTG
59.830
55.000
0.00
0.00
0.00
3.33
984
988
0.250901
ACATTCCTGCTCGGCTTGTT
60.251
50.000
0.00
0.00
0.00
2.83
985
989
0.957395
CACATTCCTGCTCGGCTTGT
60.957
55.000
0.00
0.00
0.00
3.16
986
990
1.798735
CACATTCCTGCTCGGCTTG
59.201
57.895
0.00
0.00
0.00
4.01
987
991
2.042831
GCACATTCCTGCTCGGCTT
61.043
57.895
0.00
0.00
34.06
4.35
988
992
2.437359
GCACATTCCTGCTCGGCT
60.437
61.111
0.00
0.00
34.06
5.52
989
993
3.512516
GGCACATTCCTGCTCGGC
61.513
66.667
0.00
0.00
37.33
5.54
990
994
2.046023
TGGCACATTCCTGCTCGG
60.046
61.111
0.00
0.00
37.33
4.63
1006
1010
0.804989
GGTTCCAGCTTCCAACGATG
59.195
55.000
0.00
0.00
0.00
3.84
1007
1011
0.400213
TGGTTCCAGCTTCCAACGAT
59.600
50.000
0.00
0.00
0.00
3.73
1008
1012
0.181587
TTGGTTCCAGCTTCCAACGA
59.818
50.000
0.00
0.00
36.48
3.85
1009
1013
1.247567
ATTGGTTCCAGCTTCCAACG
58.752
50.000
10.33
0.00
42.75
4.10
1010
1014
2.492088
GGTATTGGTTCCAGCTTCCAAC
59.508
50.000
10.33
2.08
42.75
3.77
1011
1015
2.556559
GGGTATTGGTTCCAGCTTCCAA
60.557
50.000
10.47
10.47
43.83
3.53
1012
1016
1.005450
GGGTATTGGTTCCAGCTTCCA
59.995
52.381
0.00
0.00
0.00
3.53
1013
1017
1.285078
AGGGTATTGGTTCCAGCTTCC
59.715
52.381
0.00
0.00
0.00
3.46
1014
1018
2.808906
AGGGTATTGGTTCCAGCTTC
57.191
50.000
0.00
0.00
0.00
3.86
1015
1019
2.241430
GGTAGGGTATTGGTTCCAGCTT
59.759
50.000
0.00
0.00
0.00
3.74
1016
1020
1.844497
GGTAGGGTATTGGTTCCAGCT
59.156
52.381
0.00
0.00
0.00
4.24
1017
1021
1.133884
GGGTAGGGTATTGGTTCCAGC
60.134
57.143
0.00
0.00
0.00
4.85
1018
1022
2.201830
TGGGTAGGGTATTGGTTCCAG
58.798
52.381
0.00
0.00
0.00
3.86
1019
1023
2.362797
TGGGTAGGGTATTGGTTCCA
57.637
50.000
0.00
0.00
0.00
3.53
1020
1024
3.743092
TTTGGGTAGGGTATTGGTTCC
57.257
47.619
0.00
0.00
0.00
3.62
1021
1025
4.647853
GGAATTTGGGTAGGGTATTGGTTC
59.352
45.833
0.00
0.00
0.00
3.62
1028
1032
1.215140
CGGGGAATTTGGGTAGGGTA
58.785
55.000
0.00
0.00
0.00
3.69
1033
1037
0.917333
AGGAGCGGGGAATTTGGGTA
60.917
55.000
0.00
0.00
0.00
3.69
1110
1115
1.150567
CCTCATTCTTCTCGGCAGCG
61.151
60.000
0.00
0.00
0.00
5.18
1113
1118
1.153568
CGCCTCATTCTTCTCGGCA
60.154
57.895
0.00
0.00
40.72
5.69
1115
1120
0.108138
AACCGCCTCATTCTTCTCGG
60.108
55.000
0.00
0.00
42.24
4.63
1167
1416
4.373116
GACCCAGCCGCTTCGTCA
62.373
66.667
10.47
0.00
0.00
4.35
1177
1426
3.721706
CCTGGACCTGGACCCAGC
61.722
72.222
24.40
0.00
46.52
4.85
1256
1511
2.280389
CGATGGTGGCGAGGATGG
60.280
66.667
0.00
0.00
0.00
3.51
1372
1627
1.734477
CGTTGGAGCAGAGGTCGTG
60.734
63.158
0.00
0.00
0.00
4.35
1522
1777
2.742372
CGGGGAGTTGAACCAGCG
60.742
66.667
0.00
0.00
0.00
5.18
1564
1819
6.621316
TTCTAAGAGCGAGAAGACGATATT
57.379
37.500
0.00
0.00
37.00
1.28
1584
1839
4.950475
TCAGACTGTCCAGACGAATATTCT
59.050
41.667
13.45
0.93
0.00
2.40
1595
1850
2.801483
TCTCCTTCTCAGACTGTCCAG
58.199
52.381
3.76
1.09
0.00
3.86
1767
2023
1.899437
GCACCCCGGAGAAGACATCA
61.899
60.000
0.73
0.00
0.00
3.07
1878
2134
5.450412
GCCTTCAAACAAACAAGAGATGACA
60.450
40.000
0.00
0.00
0.00
3.58
1903
2159
5.310409
TCCATAATGACCAATTCTCCCTC
57.690
43.478
0.00
0.00
0.00
4.30
1905
2161
4.401925
CCTCCATAATGACCAATTCTCCC
58.598
47.826
0.00
0.00
0.00
4.30
2004
2260
1.538687
AAAGGCCCAACATCTGCAGC
61.539
55.000
9.47
0.00
0.00
5.25
2068
2324
4.956700
AGAGACTAATGCAGCTGTTACCTA
59.043
41.667
16.64
0.00
0.00
3.08
2095
2351
8.907885
GTGAGAATTCCATTTAATTAAGAGCCT
58.092
33.333
0.65
0.00
0.00
4.58
2096
2352
8.907885
AGTGAGAATTCCATTTAATTAAGAGCC
58.092
33.333
0.65
0.00
0.00
4.70
2471
2776
4.166725
AGGCATTTGATTGGATCTAGTGGA
59.833
41.667
0.00
0.00
0.00
4.02
2575
2881
4.497473
TCCTTTACCACTTTTGCATTCG
57.503
40.909
0.00
0.00
0.00
3.34
2649
2955
2.284263
TCTAGCAGCGTGAGTTGATG
57.716
50.000
0.00
0.00
46.01
3.07
2687
2993
5.412594
TCTGAATTTGAATACAGTGTCTGGC
59.587
40.000
0.00
0.00
35.51
4.85
2771
3082
4.728608
CGTCTAAAACAACAACAGCTGAAC
59.271
41.667
23.35
0.00
0.00
3.18
2845
3161
4.582701
ATTCATGAACGAAGCAACCAAA
57.417
36.364
11.07
0.00
0.00
3.28
2861
3177
8.985315
ACACAATCATCAGGTACATAATTCAT
57.015
30.769
0.00
0.00
0.00
2.57
2862
3178
8.676401
CAACACAATCATCAGGTACATAATTCA
58.324
33.333
0.00
0.00
0.00
2.57
2863
3179
8.677300
ACAACACAATCATCAGGTACATAATTC
58.323
33.333
0.00
0.00
0.00
2.17
2880
3200
3.469008
TCAGACGGAAGACAACACAAT
57.531
42.857
0.00
0.00
0.00
2.71
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.