Multiple sequence alignment - TraesCS3B01G150000
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
TraesCS3B01G150000
chr3B
100.000
2996
0
0
1
2996
141136108
141133113
0.000000e+00
5533
1
TraesCS3B01G150000
chr3B
82.100
1000
132
25
993
1964
141285605
141286585
0.000000e+00
811
2
TraesCS3B01G150000
chr3B
82.091
966
143
16
1022
1963
141735411
141736370
0.000000e+00
798
3
TraesCS3B01G150000
chr3B
81.474
1004
147
20
987
1963
141288915
141289906
0.000000e+00
787
4
TraesCS3B01G150000
chr3D
93.050
1367
64
6
909
2251
91683105
91681746
0.000000e+00
1969
5
TraesCS3B01G150000
chr3D
89.886
702
69
1
1
700
596069593
596070294
0.000000e+00
902
6
TraesCS3B01G150000
chr3D
81.747
767
117
9
1219
1963
91797729
91798494
1.180000e-173
619
7
TraesCS3B01G150000
chr3D
86.334
461
44
10
2549
2996
91679666
91679212
4.490000e-133
484
8
TraesCS3B01G150000
chr3D
84.759
374
43
9
989
1361
91690874
91691234
2.200000e-96
363
9
TraesCS3B01G150000
chr3A
91.005
1423
76
20
841
2236
107757245
107755848
0.000000e+00
1871
10
TraesCS3B01G150000
chr3A
82.435
1002
142
14
987
1963
545281334
545282326
0.000000e+00
845
11
TraesCS3B01G150000
chr3A
82.010
995
143
18
993
1964
545257489
545258470
0.000000e+00
813
12
TraesCS3B01G150000
chr3A
81.056
966
150
16
1022
1963
545331387
545332343
0.000000e+00
739
13
TraesCS3B01G150000
chr3A
87.188
601
47
12
2419
2996
107755571
107754978
0.000000e+00
656
14
TraesCS3B01G150000
chrUn
92.170
728
51
5
1
724
90094658
90093933
0.000000e+00
1024
15
TraesCS3B01G150000
chr2D
92.181
729
49
7
1
724
59840953
59840228
0.000000e+00
1024
16
TraesCS3B01G150000
chr2D
87.010
816
86
14
1
800
43734451
43735262
0.000000e+00
902
17
TraesCS3B01G150000
chr7B
91.322
726
59
3
1
724
229198322
229199045
0.000000e+00
989
18
TraesCS3B01G150000
chr4D
90.883
702
62
1
1
700
72576484
72575783
0.000000e+00
941
19
TraesCS3B01G150000
chr6B
87.623
816
85
11
1
803
84669584
84670396
0.000000e+00
933
20
TraesCS3B01G150000
chr4B
90.741
702
62
2
1
700
628584429
628583729
0.000000e+00
933
21
TraesCS3B01G150000
chr2B
89.889
722
64
7
2
716
107037350
107038069
0.000000e+00
920
22
TraesCS3B01G150000
chr6A
88.372
731
75
9
1
724
162548325
162549052
0.000000e+00
870
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
TraesCS3B01G150000
chr3B
141133113
141136108
2995
True
5533.0
5533
100.0000
1
2996
1
chr3B.!!$R1
2995
1
TraesCS3B01G150000
chr3B
141285605
141289906
4301
False
799.0
811
81.7870
987
1964
2
chr3B.!!$F2
977
2
TraesCS3B01G150000
chr3B
141735411
141736370
959
False
798.0
798
82.0910
1022
1963
1
chr3B.!!$F1
941
3
TraesCS3B01G150000
chr3D
91679212
91683105
3893
True
1226.5
1969
89.6920
909
2996
2
chr3D.!!$R1
2087
4
TraesCS3B01G150000
chr3D
596069593
596070294
701
False
902.0
902
89.8860
1
700
1
chr3D.!!$F3
699
5
TraesCS3B01G150000
chr3D
91797729
91798494
765
False
619.0
619
81.7470
1219
1963
1
chr3D.!!$F2
744
6
TraesCS3B01G150000
chr3A
107754978
107757245
2267
True
1263.5
1871
89.0965
841
2996
2
chr3A.!!$R1
2155
7
TraesCS3B01G150000
chr3A
545281334
545282326
992
False
845.0
845
82.4350
987
1963
1
chr3A.!!$F2
976
8
TraesCS3B01G150000
chr3A
545257489
545258470
981
False
813.0
813
82.0100
993
1964
1
chr3A.!!$F1
971
9
TraesCS3B01G150000
chr3A
545331387
545332343
956
False
739.0
739
81.0560
1022
1963
1
chr3A.!!$F3
941
10
TraesCS3B01G150000
chrUn
90093933
90094658
725
True
1024.0
1024
92.1700
1
724
1
chrUn.!!$R1
723
11
TraesCS3B01G150000
chr2D
59840228
59840953
725
True
1024.0
1024
92.1810
1
724
1
chr2D.!!$R1
723
12
TraesCS3B01G150000
chr2D
43734451
43735262
811
False
902.0
902
87.0100
1
800
1
chr2D.!!$F1
799
13
TraesCS3B01G150000
chr7B
229198322
229199045
723
False
989.0
989
91.3220
1
724
1
chr7B.!!$F1
723
14
TraesCS3B01G150000
chr4D
72575783
72576484
701
True
941.0
941
90.8830
1
700
1
chr4D.!!$R1
699
15
TraesCS3B01G150000
chr6B
84669584
84670396
812
False
933.0
933
87.6230
1
803
1
chr6B.!!$F1
802
16
TraesCS3B01G150000
chr4B
628583729
628584429
700
True
933.0
933
90.7410
1
700
1
chr4B.!!$R1
699
17
TraesCS3B01G150000
chr2B
107037350
107038069
719
False
920.0
920
89.8890
2
716
1
chr2B.!!$F1
714
18
TraesCS3B01G150000
chr6A
162548325
162549052
727
False
870.0
870
88.3720
1
724
1
chr6A.!!$F1
723
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
829
856
0.106335
ATCCTCTCATGCGCTTCCAG
59.894
55.0
9.73
0.35
0.0
3.86
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2342
7559
0.251787
TGGTGACAGCAGCTAGAGGA
60.252
55.0
2.5
0.0
42.84
3.71
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
53
54
8.793592
ACTTTAACCAGACCAGATATTTGTTTC
58.206
33.333
0.00
0.00
0.00
2.78
75
76
5.487433
TCTCAGTCAACAAAGTTTGTCAGA
58.513
37.500
21.10
18.04
44.59
3.27
93
94
1.069823
AGATCCTTCATGCGCCTACTG
59.930
52.381
4.18
0.00
0.00
2.74
94
95
1.069204
GATCCTTCATGCGCCTACTGA
59.931
52.381
4.18
0.00
0.00
3.41
324
330
6.542735
AGCTATTGTGTCTAGATCGAGTACAA
59.457
38.462
20.73
20.73
32.97
2.41
423
429
2.341257
GTCACTCATCTGCAACGTCAT
58.659
47.619
0.00
0.00
0.00
3.06
493
499
4.988065
TGCTAGGACGAAGCACAC
57.012
55.556
0.00
0.00
44.78
3.82
498
504
0.888619
TAGGACGAAGCACACTGAGG
59.111
55.000
0.00
0.00
0.00
3.86
550
556
7.315890
GTGGCTAACAAGCTTTTGAATATTCT
58.684
34.615
16.24
0.00
34.73
2.40
559
565
9.252962
CAAGCTTTTGAATATTCTGTTTGTTCT
57.747
29.630
16.24
1.75
0.00
3.01
599
605
3.621715
CGGATGGCTTTACTAAACCACTC
59.378
47.826
5.49
5.41
34.36
3.51
618
624
2.031012
CACTGCGGCAACTGGAGA
59.969
61.111
3.44
0.00
33.99
3.71
629
635
3.368531
GGCAACTGGAGATCTTTAGACGT
60.369
47.826
12.51
0.00
0.00
4.34
676
687
4.400120
TGAGGGGGTGTTAAACATTGTAC
58.600
43.478
0.00
0.00
0.00
2.90
689
706
4.260139
ACATTGTACATCACGGTGTGTA
57.740
40.909
8.17
12.47
34.79
2.90
707
724
6.536224
GGTGTGTATATAAACCGTGCTAGTTT
59.464
38.462
0.43
5.02
40.43
2.66
708
725
7.706179
GGTGTGTATATAAACCGTGCTAGTTTA
59.294
37.037
0.43
8.34
42.25
2.01
724
742
1.463444
GTTTAGGATGTGGCGTGTGTC
59.537
52.381
0.00
0.00
0.00
3.67
725
743
0.973632
TTAGGATGTGGCGTGTGTCT
59.026
50.000
0.00
0.00
0.00
3.41
726
744
0.530744
TAGGATGTGGCGTGTGTCTC
59.469
55.000
0.00
0.00
0.00
3.36
727
745
1.741770
GGATGTGGCGTGTGTCTCC
60.742
63.158
0.00
0.00
0.00
3.71
730
757
0.108585
ATGTGGCGTGTGTCTCCTTT
59.891
50.000
0.00
0.00
0.00
3.11
731
758
0.531974
TGTGGCGTGTGTCTCCTTTC
60.532
55.000
0.00
0.00
0.00
2.62
735
762
1.000506
GGCGTGTGTCTCCTTTCTGTA
59.999
52.381
0.00
0.00
0.00
2.74
738
765
3.368236
GCGTGTGTCTCCTTTCTGTAATC
59.632
47.826
0.00
0.00
0.00
1.75
746
773
8.470805
GTGTCTCCTTTCTGTAATCTGATCTTA
58.529
37.037
0.00
0.00
0.00
2.10
747
774
8.470805
TGTCTCCTTTCTGTAATCTGATCTTAC
58.529
37.037
0.00
0.00
0.00
2.34
791
818
1.904537
CACCTAACCGAACCCTAACCT
59.095
52.381
0.00
0.00
0.00
3.50
792
819
2.303890
CACCTAACCGAACCCTAACCTT
59.696
50.000
0.00
0.00
0.00
3.50
793
820
2.981784
ACCTAACCGAACCCTAACCTTT
59.018
45.455
0.00
0.00
0.00
3.11
803
830
6.171213
CGAACCCTAACCTTTCTGTAATCTT
58.829
40.000
0.00
0.00
0.00
2.40
804
831
6.313164
CGAACCCTAACCTTTCTGTAATCTTC
59.687
42.308
0.00
0.00
0.00
2.87
805
832
5.731591
ACCCTAACCTTTCTGTAATCTTCG
58.268
41.667
0.00
0.00
0.00
3.79
806
833
4.571176
CCCTAACCTTTCTGTAATCTTCGC
59.429
45.833
0.00
0.00
0.00
4.70
807
834
4.571176
CCTAACCTTTCTGTAATCTTCGCC
59.429
45.833
0.00
0.00
0.00
5.54
808
835
3.695830
ACCTTTCTGTAATCTTCGCCA
57.304
42.857
0.00
0.00
0.00
5.69
809
836
3.335579
ACCTTTCTGTAATCTTCGCCAC
58.664
45.455
0.00
0.00
0.00
5.01
810
837
3.244422
ACCTTTCTGTAATCTTCGCCACA
60.244
43.478
0.00
0.00
0.00
4.17
811
838
3.941483
CCTTTCTGTAATCTTCGCCACAT
59.059
43.478
0.00
0.00
0.00
3.21
812
839
4.034510
CCTTTCTGTAATCTTCGCCACATC
59.965
45.833
0.00
0.00
0.00
3.06
813
840
3.179443
TCTGTAATCTTCGCCACATCC
57.821
47.619
0.00
0.00
0.00
3.51
814
841
2.766263
TCTGTAATCTTCGCCACATCCT
59.234
45.455
0.00
0.00
0.00
3.24
815
842
3.126831
CTGTAATCTTCGCCACATCCTC
58.873
50.000
0.00
0.00
0.00
3.71
816
843
2.766263
TGTAATCTTCGCCACATCCTCT
59.234
45.455
0.00
0.00
0.00
3.69
817
844
2.611225
AATCTTCGCCACATCCTCTC
57.389
50.000
0.00
0.00
0.00
3.20
818
845
1.489481
ATCTTCGCCACATCCTCTCA
58.511
50.000
0.00
0.00
0.00
3.27
819
846
1.489481
TCTTCGCCACATCCTCTCAT
58.511
50.000
0.00
0.00
0.00
2.90
820
847
1.137675
TCTTCGCCACATCCTCTCATG
59.862
52.381
0.00
0.00
0.00
3.07
821
848
0.462581
TTCGCCACATCCTCTCATGC
60.463
55.000
0.00
0.00
0.00
4.06
822
849
2.242572
CGCCACATCCTCTCATGCG
61.243
63.158
0.00
0.00
0.00
4.73
823
850
2.541120
GCCACATCCTCTCATGCGC
61.541
63.158
0.00
0.00
0.00
6.09
824
851
1.145598
CCACATCCTCTCATGCGCT
59.854
57.895
9.73
0.00
0.00
5.92
825
852
0.463295
CCACATCCTCTCATGCGCTT
60.463
55.000
9.73
0.00
0.00
4.68
826
853
0.935898
CACATCCTCTCATGCGCTTC
59.064
55.000
9.73
0.00
0.00
3.86
827
854
0.179062
ACATCCTCTCATGCGCTTCC
60.179
55.000
9.73
0.00
0.00
3.46
828
855
0.179065
CATCCTCTCATGCGCTTCCA
60.179
55.000
9.73
0.00
0.00
3.53
829
856
0.106335
ATCCTCTCATGCGCTTCCAG
59.894
55.000
9.73
0.35
0.00
3.86
830
857
2.178890
CCTCTCATGCGCTTCCAGC
61.179
63.158
9.73
0.00
38.02
4.85
831
858
2.124983
TCTCATGCGCTTCCAGCC
60.125
61.111
9.73
0.00
38.18
4.85
832
859
2.124819
CTCATGCGCTTCCAGCCT
60.125
61.111
9.73
0.00
38.18
4.58
833
860
2.124983
TCATGCGCTTCCAGCCTC
60.125
61.111
9.73
0.00
38.18
4.70
834
861
2.124819
CATGCGCTTCCAGCCTCT
60.125
61.111
9.73
0.00
38.18
3.69
835
862
1.748122
CATGCGCTTCCAGCCTCTT
60.748
57.895
9.73
0.00
38.18
2.85
836
863
1.001641
ATGCGCTTCCAGCCTCTTT
60.002
52.632
9.73
0.00
38.18
2.52
837
864
1.028868
ATGCGCTTCCAGCCTCTTTC
61.029
55.000
9.73
0.00
38.18
2.62
838
865
1.672356
GCGCTTCCAGCCTCTTTCA
60.672
57.895
0.00
0.00
38.18
2.69
839
866
1.916697
GCGCTTCCAGCCTCTTTCAC
61.917
60.000
0.00
0.00
38.18
3.18
844
871
0.687354
TCCAGCCTCTTTCACACCTC
59.313
55.000
0.00
0.00
0.00
3.85
867
894
2.046507
GACCAGAGCTGCCACCAG
60.047
66.667
0.00
0.00
42.13
4.00
892
919
1.869574
CGTGCCGTCTGATCGACAG
60.870
63.158
14.90
8.24
46.97
3.51
906
933
1.009389
CGACAGGAACCTTCGTGAGC
61.009
60.000
13.31
5.44
43.66
4.26
918
945
8.086522
GGAACCTTCGTGAGCACTAATAATATA
58.913
37.037
0.00
0.00
0.00
0.86
940
967
3.524095
ATAAATCCGATGCCCCATTGA
57.476
42.857
0.00
0.00
0.00
2.57
1048
1075
2.038813
TCATGGAGGACCTGCCGA
59.961
61.111
10.94
4.33
43.43
5.54
1156
1183
3.555324
TGCAGTGGAAGGACGCCA
61.555
61.111
0.00
0.00
0.00
5.69
1263
1305
2.341176
GTGTACTTCCACGGCGGT
59.659
61.111
13.24
0.64
35.57
5.68
1426
1468
1.682257
GCTTTCCTCTCCTGGCTGT
59.318
57.895
0.00
0.00
0.00
4.40
1584
1628
4.388499
GACGTCCACCCGGTGCAT
62.388
66.667
12.54
0.00
31.34
3.96
1620
1664
0.888619
TCATCTCTGCGTTCTTCGGT
59.111
50.000
0.00
0.00
40.26
4.69
1623
1667
1.006102
CTCTGCGTTCTTCGGTGGT
60.006
57.895
0.00
0.00
40.26
4.16
1627
1671
2.280524
CGTTCTTCGGTGGTGCCA
60.281
61.111
0.00
0.00
36.97
4.92
1695
5061
1.191535
TCGAGGGATCCGACATGTTT
58.808
50.000
5.45
0.00
0.00
2.83
1967
5396
0.386476
AAGCGGTTCGTGTACACAGA
59.614
50.000
24.98
18.92
0.00
3.41
1997
5426
3.624861
CGTAATAGTACGTCCCACTGAGT
59.375
47.826
14.24
0.00
46.49
3.41
2028
5457
4.043310
TGTTTGGTGATCTCCTGATCCTTT
59.957
41.667
14.65
0.00
46.34
3.11
2036
5466
3.415212
TCTCCTGATCCTTTTGTGCAAG
58.585
45.455
0.00
0.00
0.00
4.01
2042
5473
3.380004
TGATCCTTTTGTGCAAGTCGTTT
59.620
39.130
0.00
0.00
0.00
3.60
2074
5508
4.566545
TGCAATAATGTAAATCCAGCCG
57.433
40.909
0.00
0.00
0.00
5.52
2085
5519
0.676782
ATCCAGCCGCACAACCTAAC
60.677
55.000
0.00
0.00
0.00
2.34
2158
5592
2.604914
CCGTATGTGAGATGTTCTGTGC
59.395
50.000
0.00
0.00
0.00
4.57
2181
5615
5.482006
CTGTCTCATTAGTGATGTTGTGGA
58.518
41.667
0.00
0.00
37.06
4.02
2196
5630
5.132502
TGTTGTGGATGTGTTGAGATCTTT
58.867
37.500
0.00
0.00
0.00
2.52
2197
5631
5.239306
TGTTGTGGATGTGTTGAGATCTTTC
59.761
40.000
0.00
0.00
0.00
2.62
2198
5632
3.996363
TGTGGATGTGTTGAGATCTTTCG
59.004
43.478
0.00
0.00
0.00
3.46
2215
5649
5.853936
TCTTTCGACTTTCTCCAGATTTCA
58.146
37.500
0.00
0.00
0.00
2.69
2258
5753
5.816919
ACTATTTCAACACAAAAGGACACG
58.183
37.500
0.00
0.00
0.00
4.49
2267
5762
6.445357
ACACAAAAGGACACGAAAACTAAT
57.555
33.333
0.00
0.00
0.00
1.73
2275
5770
8.732746
AAGGACACGAAAACTAATATAAGCAT
57.267
30.769
0.00
0.00
0.00
3.79
2323
5820
9.736023
AAATAATTTATGAGCAATTCGACTTCC
57.264
29.630
0.00
0.00
0.00
3.46
2330
7547
3.600388
AGCAATTCGACTTCCCTAACAG
58.400
45.455
0.00
0.00
0.00
3.16
2331
7548
2.096013
GCAATTCGACTTCCCTAACAGC
59.904
50.000
0.00
0.00
0.00
4.40
2333
7550
0.245539
TTCGACTTCCCTAACAGCCG
59.754
55.000
0.00
0.00
0.00
5.52
2334
7551
1.810030
CGACTTCCCTAACAGCCGC
60.810
63.158
0.00
0.00
0.00
6.53
2336
7553
2.511600
CTTCCCTAACAGCCGCCG
60.512
66.667
0.00
0.00
0.00
6.46
2337
7554
3.310860
CTTCCCTAACAGCCGCCGT
62.311
63.158
0.00
0.00
0.00
5.68
2338
7555
3.305177
TTCCCTAACAGCCGCCGTC
62.305
63.158
0.00
0.00
0.00
4.79
2341
7558
4.796231
CTAACAGCCGCCGTCGCT
62.796
66.667
0.00
0.00
0.00
4.93
2342
7559
4.367023
TAACAGCCGCCGTCGCTT
62.367
61.111
0.00
0.00
0.00
4.68
2362
7579
0.829333
CCTCTAGCTGCTGTCACCAT
59.171
55.000
13.43
0.00
0.00
3.55
2366
7583
1.607801
TAGCTGCTGTCACCATCGCT
61.608
55.000
13.43
0.00
0.00
4.93
2387
7604
4.196971
CTGGTTTAAAATCCCTACCTCGG
58.803
47.826
0.00
0.00
0.00
4.63
2392
7619
1.109609
AAATCCCTACCTCGGTCGAC
58.890
55.000
7.13
7.13
0.00
4.20
2443
7705
2.642129
CCGGACGCATTTTGCACA
59.358
55.556
0.00
0.00
45.36
4.57
2445
7707
0.388391
CCGGACGCATTTTGCACAAT
60.388
50.000
0.00
0.00
45.36
2.71
2450
7712
2.663119
GACGCATTTTGCACAATTCCTC
59.337
45.455
0.00
0.00
45.36
3.71
2451
7713
2.297033
ACGCATTTTGCACAATTCCTCT
59.703
40.909
0.00
0.00
45.36
3.69
2485
7747
4.769488
GGGCTGACTCATCTATCTATGTCA
59.231
45.833
0.00
0.00
34.04
3.58
2502
7764
7.410174
TCTATGTCAAATTAACAATGGACCCT
58.590
34.615
0.00
0.00
0.00
4.34
2504
7766
7.645058
ATGTCAAATTAACAATGGACCCTAG
57.355
36.000
0.00
0.00
0.00
3.02
2508
7770
6.435904
TCAAATTAACAATGGACCCTAGTTGG
59.564
38.462
0.00
0.00
0.00
3.77
2514
7776
0.690762
TGGACCCTAGTTGGCAGAAC
59.309
55.000
0.00
0.00
0.00
3.01
2565
7827
5.242795
AGACCAACTTGCTTAACTATGGT
57.757
39.130
0.00
0.00
42.09
3.55
2567
7829
6.958767
AGACCAACTTGCTTAACTATGGTAT
58.041
36.000
0.00
0.00
39.65
2.73
2628
7890
9.793252
CAAGAAATATCCCAAATTGACACTTAG
57.207
33.333
0.00
0.00
0.00
2.18
2653
7915
8.971073
AGGGAGTAAAATTTGGAATTCACTATG
58.029
33.333
7.93
0.00
0.00
2.23
2654
7916
8.966868
GGGAGTAAAATTTGGAATTCACTATGA
58.033
33.333
7.93
0.00
0.00
2.15
2666
7938
9.066892
TGGAATTCACTATGAATAACTTATGGC
57.933
33.333
7.93
0.00
45.57
4.40
2674
7946
9.547753
ACTATGAATAACTTATGGCAGTAAGTG
57.452
33.333
17.26
8.99
42.48
3.16
2678
7950
8.946085
TGAATAACTTATGGCAGTAAGTGAAAG
58.054
33.333
17.26
4.52
42.48
2.62
2683
7955
7.450903
ACTTATGGCAGTAAGTGAAAGTAGTT
58.549
34.615
16.36
0.00
41.90
2.24
2696
7968
5.234543
GTGAAAGTAGTTCCAAGTCACTCAC
59.765
44.000
5.25
0.00
35.12
3.51
2700
7972
6.859112
AGTAGTTCCAAGTCACTCACATAT
57.141
37.500
0.00
0.00
0.00
1.78
2701
7973
6.634805
AGTAGTTCCAAGTCACTCACATATG
58.365
40.000
0.00
0.00
0.00
1.78
2702
7974
5.745312
AGTTCCAAGTCACTCACATATGA
57.255
39.130
10.38
0.00
0.00
2.15
2767
8039
5.044476
TGGAATTCTAAAATAGGGAGCACCA
60.044
40.000
5.23
0.00
43.89
4.17
2775
8047
5.653255
AAATAGGGAGCACCAAGTCATAT
57.347
39.130
1.58
0.00
43.89
1.78
2776
8048
4.630644
ATAGGGAGCACCAAGTCATATG
57.369
45.455
1.58
0.00
43.89
1.78
2791
8063
4.590850
TCATATGTGAATGACTCCCTCG
57.409
45.455
1.90
0.00
30.92
4.63
2827
8099
0.741221
GGCGAGCATTCTTCTTCGGT
60.741
55.000
0.00
0.00
0.00
4.69
2923
8196
7.611467
AGAATCCATACATACACAAACACACAT
59.389
33.333
0.00
0.00
0.00
3.21
2928
8201
9.684448
CCATACATACACAAACACACATAAAAA
57.316
29.630
0.00
0.00
0.00
1.94
2961
8245
2.143876
ACTTGAGCAAAACCACCACT
57.856
45.000
0.00
0.00
0.00
4.00
2979
8263
6.318900
CCACCACTTAAAAGTTCAAAGACTCT
59.681
38.462
4.62
0.00
37.08
3.24
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
53
54
5.801350
TCTGACAAACTTTGTTGACTGAG
57.199
39.130
8.56
0.32
45.52
3.35
75
76
1.123077
TCAGTAGGCGCATGAAGGAT
58.877
50.000
10.83
0.00
0.00
3.24
93
94
8.999431
TCTTTTTACTGTTGTCCAATGAGTATC
58.001
33.333
0.00
0.00
0.00
2.24
94
95
8.918202
TCTTTTTACTGTTGTCCAATGAGTAT
57.082
30.769
0.00
0.00
0.00
2.12
304
306
5.862323
GCTTTTGTACTCGATCTAGACACAA
59.138
40.000
0.47
7.89
0.00
3.33
324
330
2.959465
AAGGCCTTGTACTCAGCTTT
57.041
45.000
19.73
0.00
0.00
3.51
423
429
3.430098
GCACCAAGATTGTCACACCAAAA
60.430
43.478
0.00
0.00
0.00
2.44
493
499
7.482743
CACGAACAAAATGATAATCAACCTCAG
59.517
37.037
0.00
0.00
0.00
3.35
498
504
7.693951
CCTCTCACGAACAAAATGATAATCAAC
59.306
37.037
0.00
0.00
0.00
3.18
550
556
6.038161
CACTTGATCACCAGTAAGAACAAACA
59.962
38.462
0.00
0.00
0.00
2.83
559
565
2.894765
TCCGTCACTTGATCACCAGTAA
59.105
45.455
0.00
0.00
0.00
2.24
599
605
2.031012
TCCAGTTGCCGCAGTGAG
59.969
61.111
0.00
0.00
0.00
3.51
676
687
5.570262
CGGTTTATATACACACCGTGATG
57.430
43.478
5.28
2.73
45.85
3.07
689
706
7.656137
CACATCCTAAACTAGCACGGTTTATAT
59.344
37.037
8.56
4.89
38.12
0.86
707
724
0.530744
GAGACACACGCCACATCCTA
59.469
55.000
0.00
0.00
0.00
2.94
708
725
1.293498
GAGACACACGCCACATCCT
59.707
57.895
0.00
0.00
0.00
3.24
725
743
9.702253
ACTAGTAAGATCAGATTACAGAAAGGA
57.298
33.333
0.00
0.00
35.92
3.36
730
757
9.854668
AGCTAACTAGTAAGATCAGATTACAGA
57.145
33.333
0.00
0.00
35.92
3.41
746
773
7.665559
TGTGGATTGATTTTCAAGCTAACTAGT
59.334
33.333
5.59
0.00
42.01
2.57
747
774
7.965107
GTGTGGATTGATTTTCAAGCTAACTAG
59.035
37.037
5.59
0.00
42.01
2.57
759
786
4.658063
TCGGTTAGGTGTGGATTGATTTT
58.342
39.130
0.00
0.00
0.00
1.82
761
788
3.992943
TCGGTTAGGTGTGGATTGATT
57.007
42.857
0.00
0.00
0.00
2.57
791
818
3.938963
GGATGTGGCGAAGATTACAGAAA
59.061
43.478
0.00
0.00
0.00
2.52
792
819
3.197766
AGGATGTGGCGAAGATTACAGAA
59.802
43.478
0.00
0.00
0.00
3.02
793
820
2.766263
AGGATGTGGCGAAGATTACAGA
59.234
45.455
0.00
0.00
0.00
3.41
803
830
1.144716
GCATGAGAGGATGTGGCGA
59.855
57.895
0.00
0.00
0.00
5.54
804
831
2.242572
CGCATGAGAGGATGTGGCG
61.243
63.158
0.00
0.00
36.93
5.69
805
832
2.541120
GCGCATGAGAGGATGTGGC
61.541
63.158
0.30
0.00
34.89
5.01
806
833
0.463295
AAGCGCATGAGAGGATGTGG
60.463
55.000
11.47
0.00
34.89
4.17
807
834
0.935898
GAAGCGCATGAGAGGATGTG
59.064
55.000
11.47
0.00
36.99
3.21
808
835
0.179062
GGAAGCGCATGAGAGGATGT
60.179
55.000
11.47
0.00
0.00
3.06
809
836
0.179065
TGGAAGCGCATGAGAGGATG
60.179
55.000
11.47
0.00
0.00
3.51
810
837
0.106335
CTGGAAGCGCATGAGAGGAT
59.894
55.000
11.47
0.00
0.00
3.24
811
838
1.519246
CTGGAAGCGCATGAGAGGA
59.481
57.895
11.47
0.00
0.00
3.71
812
839
4.121691
CTGGAAGCGCATGAGAGG
57.878
61.111
11.47
0.00
0.00
3.69
823
850
1.072965
AGGTGTGAAAGAGGCTGGAAG
59.927
52.381
0.00
0.00
0.00
3.46
824
851
1.072331
GAGGTGTGAAAGAGGCTGGAA
59.928
52.381
0.00
0.00
0.00
3.53
825
852
0.687354
GAGGTGTGAAAGAGGCTGGA
59.313
55.000
0.00
0.00
0.00
3.86
826
853
0.671781
CGAGGTGTGAAAGAGGCTGG
60.672
60.000
0.00
0.00
0.00
4.85
827
854
0.318441
TCGAGGTGTGAAAGAGGCTG
59.682
55.000
0.00
0.00
0.00
4.85
828
855
0.605589
CTCGAGGTGTGAAAGAGGCT
59.394
55.000
3.91
0.00
0.00
4.58
829
856
0.603569
TCTCGAGGTGTGAAAGAGGC
59.396
55.000
13.56
0.00
0.00
4.70
830
857
2.558795
TCTTCTCGAGGTGTGAAAGAGG
59.441
50.000
13.56
0.00
30.27
3.69
831
858
3.570559
GTCTTCTCGAGGTGTGAAAGAG
58.429
50.000
13.56
0.00
30.27
2.85
832
859
2.296471
GGTCTTCTCGAGGTGTGAAAGA
59.704
50.000
13.56
10.09
30.27
2.52
833
860
2.035961
TGGTCTTCTCGAGGTGTGAAAG
59.964
50.000
13.56
7.75
30.27
2.62
834
861
2.035961
CTGGTCTTCTCGAGGTGTGAAA
59.964
50.000
13.56
0.00
30.27
2.69
835
862
1.613925
CTGGTCTTCTCGAGGTGTGAA
59.386
52.381
13.56
0.00
0.00
3.18
836
863
1.202891
TCTGGTCTTCTCGAGGTGTGA
60.203
52.381
13.56
3.19
0.00
3.58
837
864
1.201181
CTCTGGTCTTCTCGAGGTGTG
59.799
57.143
13.56
0.70
0.00
3.82
838
865
1.540267
CTCTGGTCTTCTCGAGGTGT
58.460
55.000
13.56
0.00
0.00
4.16
839
866
0.172352
GCTCTGGTCTTCTCGAGGTG
59.828
60.000
13.56
5.92
0.00
4.00
844
871
1.153667
GGCAGCTCTGGTCTTCTCG
60.154
63.158
0.00
0.00
0.00
4.04
892
919
2.450609
TTAGTGCTCACGAAGGTTCC
57.549
50.000
0.00
0.00
36.20
3.62
918
945
5.191727
TCAATGGGGCATCGGATTTATAT
57.808
39.130
0.00
0.00
0.00
0.86
940
967
1.066143
AGGTTGTCGCGATTCCTGAAT
60.066
47.619
22.24
5.31
0.00
2.57
1048
1075
1.603236
CTGAGGAGCTTGAGGACGCT
61.603
60.000
0.00
0.00
39.61
5.07
1263
1305
2.501128
GAGCCGATGCAGTAGCCA
59.499
61.111
0.00
0.00
41.13
4.75
1446
1488
4.988598
CACGGGTCAGCGCCAACT
62.989
66.667
2.29
0.00
0.00
3.16
1583
1627
1.228367
AGGACGTACCCGGCGATAT
60.228
57.895
9.30
0.00
45.55
1.63
1584
1628
1.893808
GAGGACGTACCCGGCGATA
60.894
63.158
9.30
0.00
45.55
2.92
1836
5265
0.327000
CCTTCCCCATCTCCCTCAGT
60.327
60.000
0.00
0.00
0.00
3.41
1923
5352
2.816958
CGCATCAGCTCGTTGGCT
60.817
61.111
0.00
0.00
44.10
4.75
1997
5426
3.882888
GGAGATCACCAAACACTTCAACA
59.117
43.478
4.05
0.00
0.00
3.33
2028
5457
6.326375
AGTAAAAATCAAACGACTTGCACAA
58.674
32.000
0.00
0.00
34.76
3.33
2036
5466
9.726034
CATTATTGCAAGTAAAAATCAAACGAC
57.274
29.630
4.94
0.00
0.00
4.34
2074
5508
3.003897
TCAAATGGTTCGTTAGGTTGTGC
59.996
43.478
0.00
0.00
0.00
4.57
2119
5553
3.349022
ACGGTTTTCACTTTTCAGACCA
58.651
40.909
0.00
0.00
0.00
4.02
2158
5592
5.482006
TCCACAACATCACTAATGAGACAG
58.518
41.667
0.00
0.00
38.57
3.51
2181
5615
6.226787
AGAAAGTCGAAAGATCTCAACACAT
58.773
36.000
0.00
0.00
45.19
3.21
2196
5630
5.793817
TCAATGAAATCTGGAGAAAGTCGA
58.206
37.500
0.00
0.00
0.00
4.20
2197
5631
6.486253
TTCAATGAAATCTGGAGAAAGTCG
57.514
37.500
0.00
0.00
0.00
4.18
2198
5632
7.880105
AGTTTCAATGAAATCTGGAGAAAGTC
58.120
34.615
11.87
0.00
33.97
3.01
2236
5670
6.055231
TCGTGTCCTTTTGTGTTGAAATAG
57.945
37.500
0.00
0.00
0.00
1.73
2238
5672
4.974368
TCGTGTCCTTTTGTGTTGAAAT
57.026
36.364
0.00
0.00
0.00
2.17
2239
5673
4.768130
TTCGTGTCCTTTTGTGTTGAAA
57.232
36.364
0.00
0.00
0.00
2.69
2240
5674
4.768130
TTTCGTGTCCTTTTGTGTTGAA
57.232
36.364
0.00
0.00
0.00
2.69
2242
5676
4.481463
AGTTTTCGTGTCCTTTTGTGTTG
58.519
39.130
0.00
0.00
0.00
3.33
2243
5677
4.776795
AGTTTTCGTGTCCTTTTGTGTT
57.223
36.364
0.00
0.00
0.00
3.32
2247
5681
9.274065
GCTTATATTAGTTTTCGTGTCCTTTTG
57.726
33.333
0.00
0.00
0.00
2.44
2248
5682
9.005777
TGCTTATATTAGTTTTCGTGTCCTTTT
57.994
29.630
0.00
0.00
0.00
2.27
2312
5809
2.677037
CGGCTGTTAGGGAAGTCGAATT
60.677
50.000
0.00
0.00
44.07
2.17
2317
5814
1.449778
GGCGGCTGTTAGGGAAGTC
60.450
63.158
0.00
0.00
0.00
3.01
2331
7548
3.471244
CTAGAGGAAGCGACGGCGG
62.471
68.421
15.06
0.00
46.35
6.13
2333
7550
2.278923
GCTAGAGGAAGCGACGGC
60.279
66.667
0.00
0.00
40.37
5.68
2339
7556
0.534412
TGACAGCAGCTAGAGGAAGC
59.466
55.000
0.00
0.00
43.11
3.86
2340
7557
1.134848
GGTGACAGCAGCTAGAGGAAG
60.135
57.143
0.00
0.00
39.38
3.46
2341
7558
0.898320
GGTGACAGCAGCTAGAGGAA
59.102
55.000
0.00
0.00
39.38
3.36
2342
7559
0.251787
TGGTGACAGCAGCTAGAGGA
60.252
55.000
2.50
0.00
42.84
3.71
2343
7560
2.280835
TGGTGACAGCAGCTAGAGG
58.719
57.895
2.50
0.00
42.84
3.69
2362
7579
3.264964
AGGTAGGGATTTTAAACCAGCGA
59.735
43.478
0.00
0.00
32.43
4.93
2366
7583
3.588396
ACCGAGGTAGGGATTTTAAACCA
59.412
43.478
0.00
0.00
35.02
3.67
2368
7585
3.867493
CGACCGAGGTAGGGATTTTAAAC
59.133
47.826
0.00
0.00
35.02
2.01
2371
7588
2.689983
GTCGACCGAGGTAGGGATTTTA
59.310
50.000
3.51
0.00
35.02
1.52
2372
7589
1.479730
GTCGACCGAGGTAGGGATTTT
59.520
52.381
3.51
0.00
35.02
1.82
2387
7604
2.045143
AGTCCCCTCTCCGTCGAC
60.045
66.667
5.18
5.18
0.00
4.20
2392
7619
3.151022
GAGCCAGTCCCCTCTCCG
61.151
72.222
0.00
0.00
0.00
4.63
2443
7705
2.322355
CTCACATCGGCAGAGGAATT
57.678
50.000
5.30
0.00
31.71
2.17
2485
7747
5.186992
GCCAACTAGGGTCCATTGTTAATTT
59.813
40.000
3.05
0.00
38.09
1.82
2498
7760
1.066143
CATCGTTCTGCCAACTAGGGT
60.066
52.381
0.00
0.00
38.09
4.34
2502
7764
2.177394
TTGCATCGTTCTGCCAACTA
57.823
45.000
0.00
0.00
41.58
2.24
2504
7766
1.786579
GTTTTGCATCGTTCTGCCAAC
59.213
47.619
0.00
5.03
41.58
3.77
2508
7770
5.820926
TTTAATGTTTTGCATCGTTCTGC
57.179
34.783
0.00
1.35
42.62
4.26
2541
7803
6.407202
ACCATAGTTAAGCAAGTTGGTCTAG
58.593
40.000
8.24
0.00
29.70
2.43
2600
7862
5.812127
GTGTCAATTTGGGATATTTCTTGCC
59.188
40.000
0.00
0.00
0.00
4.52
2628
7890
8.966868
TCATAGTGAATTCCAAATTTTACTCCC
58.033
33.333
2.27
0.00
0.00
4.30
2653
7915
8.947115
ACTTTCACTTACTGCCATAAGTTATTC
58.053
33.333
6.92
0.00
41.62
1.75
2654
7916
8.863872
ACTTTCACTTACTGCCATAAGTTATT
57.136
30.769
6.92
0.00
41.62
1.40
2666
7938
6.984474
TGACTTGGAACTACTTTCACTTACTG
59.016
38.462
0.00
0.00
35.70
2.74
2674
7946
5.357257
TGTGAGTGACTTGGAACTACTTTC
58.643
41.667
0.00
0.00
0.00
2.62
2678
7950
6.531948
GTCATATGTGAGTGACTTGGAACTAC
59.468
42.308
1.90
0.00
41.10
2.73
2701
7973
9.743057
CGATATCATATTTATGAGGAAGGAGTC
57.257
37.037
3.12
0.00
45.01
3.36
2702
7974
9.480861
TCGATATCATATTTATGAGGAAGGAGT
57.519
33.333
3.12
0.00
45.01
3.85
2744
8016
5.445964
TGGTGCTCCCTATTTTAGAATTCC
58.554
41.667
0.65
0.00
0.00
3.01
2759
8031
3.266510
TCACATATGACTTGGTGCTCC
57.733
47.619
10.38
0.00
0.00
4.70
2760
8032
4.877823
TCATTCACATATGACTTGGTGCTC
59.122
41.667
10.38
0.00
33.38
4.26
2775
8047
0.252057
TCCCGAGGGAGTCATTCACA
60.252
55.000
6.80
0.00
39.76
3.58
2776
8048
2.591915
TCCCGAGGGAGTCATTCAC
58.408
57.895
6.80
0.00
39.76
3.18
2791
8063
1.472376
CGCCTCAAGAGAGAACATCCC
60.472
57.143
0.00
0.00
44.98
3.85
2827
8099
2.422479
CGTCCTGTCGGATGTCTTTCTA
59.578
50.000
0.00
0.00
42.43
2.10
2898
8170
7.139896
TGTGTGTTTGTGTATGTATGGATTC
57.860
36.000
0.00
0.00
0.00
2.52
2928
8201
6.463995
TTGCTCAAGTTGGTGATTTACTTT
57.536
33.333
2.34
0.00
30.08
2.66
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.