Multiple sequence alignment - TraesCS6D01G361800
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
TraesCS6D01G361800
chr6D
100.000
2534
0
0
1
2534
452710810
452708277
0.000000e+00
4680.0
1
TraesCS6D01G361800
chr6D
83.837
563
45
22
1074
1614
452623536
452622998
6.300000e-136
494.0
2
TraesCS6D01G361800
chr6D
86.217
341
31
8
1292
1624
452641652
452641320
3.100000e-94
355.0
3
TraesCS6D01G361800
chr6D
83.268
257
28
7
1647
1901
452592602
452592359
3.280000e-54
222.0
4
TraesCS6D01G361800
chr6D
82.353
255
18
9
1030
1280
452641985
452641754
1.990000e-46
196.0
5
TraesCS6D01G361800
chr6B
90.899
1736
72
45
861
2534
687413703
687411992
0.000000e+00
2252.0
6
TraesCS6D01G361800
chr6B
86.756
521
40
13
1015
1507
687372435
687371916
1.020000e-153
553.0
7
TraesCS6D01G361800
chr6B
92.032
251
15
3
1058
1303
687367117
687366867
5.190000e-92
348.0
8
TraesCS6D01G361800
chr6B
87.823
271
26
4
1009
1278
687108210
687108474
6.810000e-81
311.0
9
TraesCS6D01G361800
chr6B
82.721
272
27
9
1292
1563
687317749
687317498
9.120000e-55
224.0
10
TraesCS6D01G361800
chr6B
94.118
68
4
0
861
928
687318423
687318356
1.240000e-18
104.0
11
TraesCS6D01G361800
chr6B
92.647
68
5
0
861
928
687108039
687108106
5.770000e-17
99.0
12
TraesCS6D01G361800
chr6A
78.252
1407
181
64
1044
2372
598326993
598325634
0.000000e+00
787.0
13
TraesCS6D01G361800
chr6A
78.252
1407
181
65
1044
2372
598461077
598459718
0.000000e+00
787.0
14
TraesCS6D01G361800
chr6A
78.196
1408
181
67
1044
2372
598253709
598252349
0.000000e+00
784.0
15
TraesCS6D01G361800
chr6A
77.983
1408
184
66
1044
2372
598521008
598519648
0.000000e+00
767.0
16
TraesCS6D01G361800
chr6A
84.364
825
79
26
1
809
598597965
598597175
0.000000e+00
763.0
17
TraesCS6D01G361800
chr6A
77.825
1407
188
70
1044
2372
598568796
598567436
0.000000e+00
756.0
18
TraesCS6D01G361800
chr6A
83.654
624
56
29
1009
1614
598576250
598575655
1.710000e-151
545.0
19
TraesCS6D01G361800
chr6A
77.711
664
75
34
1292
1901
598212506
598211862
3.120000e-89
339.0
20
TraesCS6D01G361800
chr6A
81.979
283
21
15
1375
1638
598207504
598207233
1.970000e-51
213.0
21
TraesCS6D01G361800
chr6A
80.357
224
27
7
1647
1869
598207189
598206982
1.210000e-33
154.0
22
TraesCS6D01G361800
chrUn
94.286
210
9
1
1041
1250
341387582
341387788
4.070000e-83
318.0
23
TraesCS6D01G361800
chr7A
83.333
78
9
3
782
859
71161839
71161912
4.520000e-08
69.4
24
TraesCS6D01G361800
chr7A
88.679
53
6
0
808
860
37236564
37236512
5.850000e-07
65.8
25
TraesCS6D01G361800
chr7A
94.737
38
2
0
808
845
37210332
37210295
2.720000e-05
60.2
26
TraesCS6D01G361800
chr7A
94.737
38
2
0
808
845
37351162
37351125
2.720000e-05
60.2
27
TraesCS6D01G361800
chr4A
89.091
55
6
0
806
860
686565894
686565948
4.520000e-08
69.4
28
TraesCS6D01G361800
chr4A
86.207
58
8
0
808
865
686585159
686585216
2.100000e-06
63.9
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
TraesCS6D01G361800
chr6D
452708277
452710810
2533
True
4680.0
4680
100.000
1
2534
1
chr6D.!!$R3
2533
1
TraesCS6D01G361800
chr6D
452622998
452623536
538
True
494.0
494
83.837
1074
1614
1
chr6D.!!$R2
540
2
TraesCS6D01G361800
chr6D
452641320
452641985
665
True
275.5
355
84.285
1030
1624
2
chr6D.!!$R4
594
3
TraesCS6D01G361800
chr6B
687411992
687413703
1711
True
2252.0
2252
90.899
861
2534
1
chr6B.!!$R3
1673
4
TraesCS6D01G361800
chr6B
687371916
687372435
519
True
553.0
553
86.756
1015
1507
1
chr6B.!!$R2
492
5
TraesCS6D01G361800
chr6A
598325634
598326993
1359
True
787.0
787
78.252
1044
2372
1
chr6A.!!$R3
1328
6
TraesCS6D01G361800
chr6A
598459718
598461077
1359
True
787.0
787
78.252
1044
2372
1
chr6A.!!$R4
1328
7
TraesCS6D01G361800
chr6A
598252349
598253709
1360
True
784.0
784
78.196
1044
2372
1
chr6A.!!$R2
1328
8
TraesCS6D01G361800
chr6A
598519648
598521008
1360
True
767.0
767
77.983
1044
2372
1
chr6A.!!$R5
1328
9
TraesCS6D01G361800
chr6A
598597175
598597965
790
True
763.0
763
84.364
1
809
1
chr6A.!!$R8
808
10
TraesCS6D01G361800
chr6A
598567436
598568796
1360
True
756.0
756
77.825
1044
2372
1
chr6A.!!$R6
1328
11
TraesCS6D01G361800
chr6A
598575655
598576250
595
True
545.0
545
83.654
1009
1614
1
chr6A.!!$R7
605
12
TraesCS6D01G361800
chr6A
598211862
598212506
644
True
339.0
339
77.711
1292
1901
1
chr6A.!!$R1
609
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
971
990
0.321653
CGGTAACCTCTTTGCCAGCT
60.322
55.0
0.0
0.0
39.94
4.24
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1968
2222
1.277842
TGCTAAAATGGGTCAGCGAGA
59.722
47.619
0.0
0.0
36.81
4.04
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
51
53
6.875972
AGTCCATACTTGAACTATTCACCT
57.124
37.500
0.00
0.00
39.87
4.00
55
57
6.051717
CCATACTTGAACTATTCACCTCCTG
58.948
44.000
0.00
0.00
39.87
3.86
56
58
4.559862
ACTTGAACTATTCACCTCCTGG
57.440
45.455
0.00
0.00
39.87
4.45
69
71
5.145564
TCACCTCCTGGTATCCTAACATAC
58.854
45.833
0.00
0.00
46.60
2.39
112
114
3.998099
GGAGTACCCGATAGTAACCAC
57.002
52.381
0.00
0.00
0.00
4.16
148
150
7.504926
TTACCCAGTCATTATTAGGAAGTGT
57.495
36.000
0.00
0.00
0.00
3.55
170
172
6.609616
GTGTTATCAAAATCCCCCAATTCCTA
59.390
38.462
0.00
0.00
0.00
2.94
174
176
9.959693
TTATCAAAATCCCCCAATTCCTATTTA
57.040
29.630
0.00
0.00
0.00
1.40
179
181
1.886542
CCCCAATTCCTATTTAGCGCC
59.113
52.381
2.29
0.00
0.00
6.53
197
199
3.831715
GCCTTAAGCGCCATTTATAGG
57.168
47.619
2.29
7.59
0.00
2.57
211
215
7.610305
CGCCATTTATAGGATATTGGGTTAACT
59.390
37.037
5.42
0.00
0.00
2.24
212
216
8.739972
GCCATTTATAGGATATTGGGTTAACTG
58.260
37.037
5.42
0.00
0.00
3.16
213
217
9.243105
CCATTTATAGGATATTGGGTTAACTGG
57.757
37.037
5.42
0.00
0.00
4.00
214
218
9.807921
CATTTATAGGATATTGGGTTAACTGGT
57.192
33.333
5.42
0.00
0.00
4.00
219
223
1.627864
ATTGGGTTAACTGGTGCACC
58.372
50.000
29.67
29.67
0.00
5.01
235
239
2.750237
CCAGGTAGCAAACGGGCC
60.750
66.667
0.00
0.00
0.00
5.80
252
256
1.687563
GCCGGGCCATGTAAGTATTT
58.312
50.000
8.12
0.00
0.00
1.40
282
286
2.807837
CGGTTTTGTAGGTTCGGAAGGT
60.808
50.000
0.00
0.00
0.00
3.50
295
299
0.826256
GGAAGGTTTCTTTGGGCGGT
60.826
55.000
0.00
0.00
32.52
5.68
309
313
1.411246
GGGCGGTTTTTCCTTCTGTTT
59.589
47.619
0.00
0.00
0.00
2.83
321
325
3.070446
TCCTTCTGTTTTTCTAGTGCGGA
59.930
43.478
0.00
0.00
0.00
5.54
329
333
4.419522
TTTTCTAGTGCGGATTTTGCTC
57.580
40.909
0.00
0.00
0.00
4.26
330
334
2.760634
TCTAGTGCGGATTTTGCTCA
57.239
45.000
0.00
0.00
0.00
4.26
331
335
3.052455
TCTAGTGCGGATTTTGCTCAA
57.948
42.857
0.00
0.00
0.00
3.02
339
343
4.389382
TGCGGATTTTGCTCAATTTTCATG
59.611
37.500
0.00
0.00
0.00
3.07
342
346
6.256321
GCGGATTTTGCTCAATTTTCATGTAT
59.744
34.615
0.00
0.00
0.00
2.29
400
404
6.473758
ACTTAGTTCCTAATCCACAAACTCC
58.526
40.000
0.00
0.00
32.71
3.85
408
412
7.010160
TCCTAATCCACAAACTCCTTTTCAAT
58.990
34.615
0.00
0.00
0.00
2.57
413
417
9.492973
AATCCACAAACTCCTTTTCAATTTATG
57.507
29.630
0.00
0.00
0.00
1.90
415
419
7.288852
TCCACAAACTCCTTTTCAATTTATGGA
59.711
33.333
0.00
0.00
0.00
3.41
416
420
7.384932
CCACAAACTCCTTTTCAATTTATGGAC
59.615
37.037
0.00
0.00
0.00
4.02
421
429
9.764363
AACTCCTTTTCAATTTATGGACTTTTC
57.236
29.630
0.00
0.00
0.00
2.29
426
434
9.336171
CTTTTCAATTTATGGACTTTTCCCAAA
57.664
29.630
0.00
0.00
42.01
3.28
464
472
6.148645
TCAAATGCATGAACTTTTAGCTCGTA
59.851
34.615
0.00
0.00
0.00
3.43
469
477
7.367285
TGCATGAACTTTTAGCTCGTAATTTT
58.633
30.769
0.00
0.00
0.00
1.82
664
678
7.532682
TTTTCCAATTCAAGAACCTTTTTCG
57.467
32.000
0.00
0.00
0.00
3.46
669
683
6.019075
CCAATTCAAGAACCTTTTTCGTTTCC
60.019
38.462
0.00
0.00
0.00
3.13
670
684
4.281525
TCAAGAACCTTTTTCGTTTCCG
57.718
40.909
0.00
0.00
0.00
4.30
671
685
2.768833
AGAACCTTTTTCGTTTCCGC
57.231
45.000
0.00
0.00
0.00
5.54
673
687
2.424246
AGAACCTTTTTCGTTTCCGCAA
59.576
40.909
0.00
0.00
0.00
4.85
674
688
2.943449
ACCTTTTTCGTTTCCGCAAA
57.057
40.000
0.00
0.00
0.00
3.68
675
689
3.233684
ACCTTTTTCGTTTCCGCAAAA
57.766
38.095
0.00
0.00
36.96
2.44
679
694
4.960953
CCTTTTTCGTTTCCGCAAAATTTG
59.039
37.500
0.57
0.57
38.24
2.32
823
838
9.956720
GTAGTACTCCGTATATGTTAATGTTGT
57.043
33.333
0.00
0.00
0.00
3.32
825
840
9.956720
AGTACTCCGTATATGTTAATGTTGTAC
57.043
33.333
0.00
0.00
0.00
2.90
826
841
9.956720
GTACTCCGTATATGTTAATGTTGTACT
57.043
33.333
0.00
0.00
0.00
2.73
837
852
7.970102
TGTTAATGTTGTACTAGAAGAAGGGT
58.030
34.615
0.00
0.00
0.00
4.34
838
853
7.876068
TGTTAATGTTGTACTAGAAGAAGGGTG
59.124
37.037
0.00
0.00
0.00
4.61
839
854
6.681729
AATGTTGTACTAGAAGAAGGGTGA
57.318
37.500
0.00
0.00
0.00
4.02
840
855
6.681729
ATGTTGTACTAGAAGAAGGGTGAA
57.318
37.500
0.00
0.00
0.00
3.18
841
856
6.488769
TGTTGTACTAGAAGAAGGGTGAAA
57.511
37.500
0.00
0.00
0.00
2.69
842
857
7.074653
TGTTGTACTAGAAGAAGGGTGAAAT
57.925
36.000
0.00
0.00
0.00
2.17
843
858
8.197592
TGTTGTACTAGAAGAAGGGTGAAATA
57.802
34.615
0.00
0.00
0.00
1.40
844
859
8.311836
TGTTGTACTAGAAGAAGGGTGAAATAG
58.688
37.037
0.00
0.00
0.00
1.73
845
860
6.875076
TGTACTAGAAGAAGGGTGAAATAGC
58.125
40.000
0.00
0.00
0.00
2.97
846
861
5.012328
ACTAGAAGAAGGGTGAAATAGCG
57.988
43.478
0.00
0.00
0.00
4.26
847
862
4.710375
ACTAGAAGAAGGGTGAAATAGCGA
59.290
41.667
0.00
0.00
0.00
4.93
848
863
4.762289
AGAAGAAGGGTGAAATAGCGAT
57.238
40.909
0.00
0.00
0.00
4.58
849
864
4.446371
AGAAGAAGGGTGAAATAGCGATG
58.554
43.478
0.00
0.00
0.00
3.84
850
865
3.914426
AGAAGGGTGAAATAGCGATGT
57.086
42.857
0.00
0.00
0.00
3.06
851
866
4.222124
AGAAGGGTGAAATAGCGATGTT
57.778
40.909
0.00
0.00
0.00
2.71
852
867
4.589908
AGAAGGGTGAAATAGCGATGTTT
58.410
39.130
0.00
0.00
0.00
2.83
853
868
4.636206
AGAAGGGTGAAATAGCGATGTTTC
59.364
41.667
14.96
14.96
35.45
2.78
854
869
3.279434
AGGGTGAAATAGCGATGTTTCC
58.721
45.455
18.32
10.54
34.29
3.13
855
870
3.054361
AGGGTGAAATAGCGATGTTTCCT
60.054
43.478
18.32
7.91
34.29
3.36
856
871
3.065371
GGGTGAAATAGCGATGTTTCCTG
59.935
47.826
18.32
0.00
34.29
3.86
857
872
3.938963
GGTGAAATAGCGATGTTTCCTGA
59.061
43.478
18.32
0.00
34.29
3.86
858
873
4.576463
GGTGAAATAGCGATGTTTCCTGAT
59.424
41.667
18.32
0.00
34.29
2.90
859
874
5.758296
GGTGAAATAGCGATGTTTCCTGATA
59.242
40.000
18.32
0.00
34.29
2.15
879
894
3.677648
GGTGTGCCTTGCCTGCAG
61.678
66.667
6.78
6.78
39.87
4.41
889
904
0.321919
TTGCCTGCAGAGCTACAAGG
60.322
55.000
17.39
0.00
0.00
3.61
907
922
4.184629
CAAGGTACTGATTCCTCCTTTCG
58.815
47.826
0.00
0.00
40.86
3.46
928
943
3.417069
TGTGCTACACATTTACTGCCT
57.583
42.857
0.00
0.00
39.62
4.75
944
963
1.320507
GCCTCGCCTAACTAGCTAGT
58.679
55.000
20.95
20.95
38.39
2.57
945
964
2.158711
TGCCTCGCCTAACTAGCTAGTA
60.159
50.000
26.29
13.46
34.99
1.82
946
965
3.083293
GCCTCGCCTAACTAGCTAGTAT
58.917
50.000
26.29
17.69
34.99
2.12
947
966
3.119779
GCCTCGCCTAACTAGCTAGTATG
60.120
52.174
26.29
19.86
34.99
2.39
948
967
3.119779
CCTCGCCTAACTAGCTAGTATGC
60.120
52.174
26.29
24.09
34.99
3.14
949
968
3.483421
TCGCCTAACTAGCTAGTATGCA
58.517
45.455
26.29
15.24
34.99
3.96
950
969
3.502595
TCGCCTAACTAGCTAGTATGCAG
59.497
47.826
26.29
20.60
34.99
4.41
951
970
3.580731
GCCTAACTAGCTAGTATGCAGC
58.419
50.000
26.29
19.32
39.41
5.25
952
971
3.615351
GCCTAACTAGCTAGTATGCAGCC
60.615
52.174
26.29
8.13
39.99
4.85
953
972
2.802787
AACTAGCTAGTATGCAGCCG
57.197
50.000
26.29
0.00
39.99
5.52
954
973
0.962489
ACTAGCTAGTATGCAGCCGG
59.038
55.000
24.97
0.00
39.99
6.13
955
974
0.962489
CTAGCTAGTATGCAGCCGGT
59.038
55.000
12.92
0.00
39.99
5.28
956
975
2.160205
CTAGCTAGTATGCAGCCGGTA
58.840
52.381
12.92
0.00
39.99
4.02
957
976
1.410004
AGCTAGTATGCAGCCGGTAA
58.590
50.000
1.90
0.00
39.99
2.85
958
977
1.068741
AGCTAGTATGCAGCCGGTAAC
59.931
52.381
1.90
0.00
39.99
2.50
959
978
1.872653
GCTAGTATGCAGCCGGTAACC
60.873
57.143
1.90
0.00
32.68
2.85
960
979
1.687123
CTAGTATGCAGCCGGTAACCT
59.313
52.381
1.90
0.00
0.00
3.50
961
980
0.464452
AGTATGCAGCCGGTAACCTC
59.536
55.000
1.90
0.00
0.00
3.85
962
981
0.464452
GTATGCAGCCGGTAACCTCT
59.536
55.000
1.90
0.00
0.00
3.69
963
982
1.134491
GTATGCAGCCGGTAACCTCTT
60.134
52.381
1.90
0.00
0.00
2.85
964
983
0.328258
ATGCAGCCGGTAACCTCTTT
59.672
50.000
1.90
0.00
0.00
2.52
965
984
0.605319
TGCAGCCGGTAACCTCTTTG
60.605
55.000
1.90
0.00
0.00
2.77
966
985
1.923227
GCAGCCGGTAACCTCTTTGC
61.923
60.000
1.90
0.00
0.00
3.68
967
986
1.002502
AGCCGGTAACCTCTTTGCC
60.003
57.895
1.90
0.00
36.63
4.52
968
987
1.302993
GCCGGTAACCTCTTTGCCA
60.303
57.895
1.90
0.00
39.94
4.92
969
988
1.305930
GCCGGTAACCTCTTTGCCAG
61.306
60.000
1.90
0.00
39.94
4.85
970
989
1.305930
CCGGTAACCTCTTTGCCAGC
61.306
60.000
0.00
0.00
39.94
4.85
971
990
0.321653
CGGTAACCTCTTTGCCAGCT
60.322
55.000
0.00
0.00
39.94
4.24
972
991
1.454201
GGTAACCTCTTTGCCAGCTC
58.546
55.000
0.00
0.00
39.72
4.09
973
992
1.079503
GTAACCTCTTTGCCAGCTCG
58.920
55.000
0.00
0.00
0.00
5.03
974
993
0.685097
TAACCTCTTTGCCAGCTCGT
59.315
50.000
0.00
0.00
0.00
4.18
975
994
0.886490
AACCTCTTTGCCAGCTCGTG
60.886
55.000
0.00
0.00
0.00
4.35
976
995
2.684843
CCTCTTTGCCAGCTCGTGC
61.685
63.158
0.07
0.07
40.05
5.34
977
996
1.962822
CTCTTTGCCAGCTCGTGCA
60.963
57.895
12.58
0.00
42.74
4.57
978
997
2.180131
CTCTTTGCCAGCTCGTGCAC
62.180
60.000
12.58
6.82
42.74
4.57
979
998
3.584250
CTTTGCCAGCTCGTGCACG
62.584
63.158
32.76
32.76
42.74
5.34
1028
1083
1.617850
ACAGCACAGAGACAGAGAAGG
59.382
52.381
0.00
0.00
0.00
3.46
1055
1111
2.434428
CAGCCAAGCAAAGTGAGAGAT
58.566
47.619
0.00
0.00
0.00
2.75
1070
1129
1.340889
AGAGATCAAGAGAGATGGCGC
59.659
52.381
0.00
0.00
0.00
6.53
1195
1257
1.075970
AGGATCTGCTGCCGGACTA
60.076
57.895
5.05
0.00
0.00
2.59
1213
1275
0.251922
TACAGCCACCGACTTACCCT
60.252
55.000
0.00
0.00
0.00
4.34
1214
1276
1.218316
CAGCCACCGACTTACCCTC
59.782
63.158
0.00
0.00
0.00
4.30
1255
1317
7.739444
TCCTCCACCATTGGTAATCTATCTATT
59.261
37.037
8.31
0.00
44.35
1.73
1262
1327
9.376075
CCATTGGTAATCTATCTATTGCTGTAG
57.624
37.037
0.00
0.00
0.00
2.74
1629
1827
4.690748
ACAACGAATGATGTACTGTTGAGG
59.309
41.667
9.59
0.00
39.11
3.86
1719
1943
1.540707
ACCAAACGGTTCACAAACGTT
59.459
42.857
6.25
6.25
36.16
3.99
1735
1960
5.518487
ACAAACGTTTTTCGATCTTGCATTT
59.482
32.000
11.66
0.00
42.86
2.32
1837
2072
5.209818
TCGCGAGTATATCCCAAAAGAAT
57.790
39.130
3.71
0.00
0.00
2.40
1886
2130
1.540267
TTGGCCAGATACCAAAACCG
58.460
50.000
5.11
0.00
44.11
4.44
1962
2216
9.790389
ACGTTTCTAGTATTAGAGACAGAAATG
57.210
33.333
13.95
10.85
39.69
2.32
1963
2217
8.747666
CGTTTCTAGTATTAGAGACAGAAATGC
58.252
37.037
13.95
0.00
39.69
3.56
1966
2220
7.640852
TCTAGTATTAGAGACAGAAATGCGAC
58.359
38.462
0.00
0.00
32.21
5.19
1968
2222
6.868622
AGTATTAGAGACAGAAATGCGACTT
58.131
36.000
0.00
0.00
0.00
3.01
1969
2223
6.975772
AGTATTAGAGACAGAAATGCGACTTC
59.024
38.462
0.00
0.00
0.00
3.01
1971
2225
3.843999
AGAGACAGAAATGCGACTTCTC
58.156
45.455
0.00
0.00
30.58
2.87
2022
2290
7.861176
TTCTCGTTTTATGTAAAAACATGGC
57.139
32.000
12.34
0.00
39.42
4.40
2333
2617
4.335735
AATGAAGGACCCATTTGGATCA
57.664
40.909
0.00
0.00
37.39
2.92
2419
2704
6.041423
AGGAAGTTTGAATTAAAGGCATGG
57.959
37.500
0.00
0.00
0.00
3.66
2518
2803
1.015607
GCAAAAGCTTTGCCCCATCG
61.016
55.000
13.54
0.00
39.38
3.84
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
22
23
9.739276
TGAATAGTTCAAGTATGGACTTCAATT
57.261
29.630
0.00
0.00
43.16
2.32
33
34
6.240549
CCAGGAGGTGAATAGTTCAAGTAT
57.759
41.667
0.00
0.00
42.15
2.12
51
53
7.073208
TGATCAAGTATGTTAGGATACCAGGA
58.927
38.462
0.00
0.00
30.20
3.86
95
97
3.290710
TCTGGTGGTTACTATCGGGTAC
58.709
50.000
0.00
0.00
0.00
3.34
101
103
5.871396
TGAAGGATCTGGTGGTTACTATC
57.129
43.478
0.00
0.00
0.00
2.08
112
114
3.455910
TGACTGGGTAATGAAGGATCTGG
59.544
47.826
0.00
0.00
0.00
3.86
148
150
8.868404
AAATAGGAATTGGGGGATTTTGATAA
57.132
30.769
0.00
0.00
0.00
1.75
179
181
7.201732
CCCAATATCCTATAAATGGCGCTTAAG
60.202
40.741
7.64
0.00
0.00
1.85
190
192
7.722285
GCACCAGTTAACCCAATATCCTATAAA
59.278
37.037
0.88
0.00
0.00
1.40
197
199
3.380320
GGTGCACCAGTTAACCCAATATC
59.620
47.826
31.23
0.00
35.64
1.63
211
215
0.821711
GTTTGCTACCTGGTGCACCA
60.822
55.000
35.49
35.49
45.30
4.17
212
216
1.852067
CGTTTGCTACCTGGTGCACC
61.852
60.000
29.67
29.67
39.05
5.01
213
217
1.574428
CGTTTGCTACCTGGTGCAC
59.426
57.895
19.02
8.80
39.05
4.57
214
218
1.599518
CCGTTTGCTACCTGGTGCA
60.600
57.895
10.23
14.10
37.42
4.57
219
223
3.124921
CGGCCCGTTTGCTACCTG
61.125
66.667
0.00
0.00
0.00
4.00
235
239
3.945285
ACAAGAAATACTTACATGGCCCG
59.055
43.478
0.00
0.00
37.03
6.13
238
242
6.422223
CGATGACAAGAAATACTTACATGGC
58.578
40.000
0.00
0.00
37.03
4.40
252
256
4.345859
ACCTACAAAACCGATGACAAGA
57.654
40.909
0.00
0.00
0.00
3.02
282
286
2.112190
AGGAAAAACCGCCCAAAGAAA
58.888
42.857
0.00
0.00
44.74
2.52
295
299
6.262601
CGCACTAGAAAAACAGAAGGAAAAA
58.737
36.000
0.00
0.00
0.00
1.94
309
313
3.407698
TGAGCAAAATCCGCACTAGAAA
58.592
40.909
0.00
0.00
0.00
2.52
361
365
7.694093
AGGAACTAAGTTCTGGAATCTGAAAT
58.306
34.615
0.00
0.00
41.70
2.17
380
384
5.584551
AAGGAGTTTGTGGATTAGGAACT
57.415
39.130
0.00
0.00
46.37
3.01
413
417
7.566760
AAAAACATGAATTTGGGAAAAGTCC
57.433
32.000
0.00
0.00
44.10
3.85
439
447
5.048782
ACGAGCTAAAAGTTCATGCATTTGA
60.049
36.000
0.00
0.00
0.00
2.69
440
448
5.156355
ACGAGCTAAAAGTTCATGCATTTG
58.844
37.500
0.00
0.00
0.00
2.32
477
485
7.890127
ACTCATGAATCTGGAAAAGTTTATGGA
59.110
33.333
0.00
0.00
0.00
3.41
478
486
8.059798
ACTCATGAATCTGGAAAAGTTTATGG
57.940
34.615
0.00
0.00
0.00
2.74
645
659
6.933130
GGAAACGAAAAAGGTTCTTGAATTG
58.067
36.000
0.00
0.00
37.91
2.32
811
826
8.603304
ACCCTTCTTCTAGTACAACATTAACAT
58.397
33.333
0.00
0.00
0.00
2.71
812
827
7.876068
CACCCTTCTTCTAGTACAACATTAACA
59.124
37.037
0.00
0.00
0.00
2.41
813
828
8.092687
TCACCCTTCTTCTAGTACAACATTAAC
58.907
37.037
0.00
0.00
0.00
2.01
814
829
8.197592
TCACCCTTCTTCTAGTACAACATTAA
57.802
34.615
0.00
0.00
0.00
1.40
815
830
7.786046
TCACCCTTCTTCTAGTACAACATTA
57.214
36.000
0.00
0.00
0.00
1.90
816
831
6.681729
TCACCCTTCTTCTAGTACAACATT
57.318
37.500
0.00
0.00
0.00
2.71
817
832
6.681729
TTCACCCTTCTTCTAGTACAACAT
57.318
37.500
0.00
0.00
0.00
2.71
818
833
6.488769
TTTCACCCTTCTTCTAGTACAACA
57.511
37.500
0.00
0.00
0.00
3.33
819
834
7.278203
GCTATTTCACCCTTCTTCTAGTACAAC
59.722
40.741
0.00
0.00
0.00
3.32
820
835
7.328737
GCTATTTCACCCTTCTTCTAGTACAA
58.671
38.462
0.00
0.00
0.00
2.41
821
836
6.405508
CGCTATTTCACCCTTCTTCTAGTACA
60.406
42.308
0.00
0.00
0.00
2.90
822
837
5.978322
CGCTATTTCACCCTTCTTCTAGTAC
59.022
44.000
0.00
0.00
0.00
2.73
823
838
5.889853
TCGCTATTTCACCCTTCTTCTAGTA
59.110
40.000
0.00
0.00
0.00
1.82
824
839
4.710375
TCGCTATTTCACCCTTCTTCTAGT
59.290
41.667
0.00
0.00
0.00
2.57
825
840
5.263968
TCGCTATTTCACCCTTCTTCTAG
57.736
43.478
0.00
0.00
0.00
2.43
826
841
5.128827
ACATCGCTATTTCACCCTTCTTCTA
59.871
40.000
0.00
0.00
0.00
2.10
827
842
4.080863
ACATCGCTATTTCACCCTTCTTCT
60.081
41.667
0.00
0.00
0.00
2.85
828
843
4.192317
ACATCGCTATTTCACCCTTCTTC
58.808
43.478
0.00
0.00
0.00
2.87
829
844
4.222124
ACATCGCTATTTCACCCTTCTT
57.778
40.909
0.00
0.00
0.00
2.52
830
845
3.914426
ACATCGCTATTTCACCCTTCT
57.086
42.857
0.00
0.00
0.00
2.85
831
846
4.201920
GGAAACATCGCTATTTCACCCTTC
60.202
45.833
0.00
0.00
36.69
3.46
832
847
3.694566
GGAAACATCGCTATTTCACCCTT
59.305
43.478
0.00
0.00
36.69
3.95
833
848
3.054361
AGGAAACATCGCTATTTCACCCT
60.054
43.478
0.00
0.00
36.69
4.34
834
849
3.065371
CAGGAAACATCGCTATTTCACCC
59.935
47.826
0.00
0.00
36.69
4.61
835
850
3.938963
TCAGGAAACATCGCTATTTCACC
59.061
43.478
0.00
0.00
36.69
4.02
836
851
5.741388
ATCAGGAAACATCGCTATTTCAC
57.259
39.130
0.00
0.00
36.69
3.18
837
852
6.479990
CACTATCAGGAAACATCGCTATTTCA
59.520
38.462
0.00
0.00
36.69
2.69
838
853
6.073548
CCACTATCAGGAAACATCGCTATTTC
60.074
42.308
0.00
0.00
34.65
2.17
839
854
5.760253
CCACTATCAGGAAACATCGCTATTT
59.240
40.000
0.00
0.00
0.00
1.40
840
855
5.163301
ACCACTATCAGGAAACATCGCTATT
60.163
40.000
0.00
0.00
0.00
1.73
841
856
4.345257
ACCACTATCAGGAAACATCGCTAT
59.655
41.667
0.00
0.00
0.00
2.97
842
857
3.704566
ACCACTATCAGGAAACATCGCTA
59.295
43.478
0.00
0.00
0.00
4.26
843
858
2.501723
ACCACTATCAGGAAACATCGCT
59.498
45.455
0.00
0.00
0.00
4.93
844
859
2.609459
CACCACTATCAGGAAACATCGC
59.391
50.000
0.00
0.00
0.00
4.58
845
860
3.618594
CACACCACTATCAGGAAACATCG
59.381
47.826
0.00
0.00
0.00
3.84
846
861
3.375299
GCACACCACTATCAGGAAACATC
59.625
47.826
0.00
0.00
0.00
3.06
847
862
3.347216
GCACACCACTATCAGGAAACAT
58.653
45.455
0.00
0.00
0.00
2.71
848
863
2.552155
GGCACACCACTATCAGGAAACA
60.552
50.000
0.00
0.00
35.26
2.83
849
864
2.084546
GGCACACCACTATCAGGAAAC
58.915
52.381
0.00
0.00
35.26
2.78
850
865
1.985159
AGGCACACCACTATCAGGAAA
59.015
47.619
0.00
0.00
39.06
3.13
851
866
1.656587
AGGCACACCACTATCAGGAA
58.343
50.000
0.00
0.00
39.06
3.36
852
867
1.278985
CAAGGCACACCACTATCAGGA
59.721
52.381
0.00
0.00
39.06
3.86
853
868
1.742761
CAAGGCACACCACTATCAGG
58.257
55.000
0.00
0.00
39.06
3.86
854
869
1.089920
GCAAGGCACACCACTATCAG
58.910
55.000
0.00
0.00
39.06
2.90
855
870
0.322456
GGCAAGGCACACCACTATCA
60.322
55.000
0.00
0.00
39.06
2.15
856
871
0.035056
AGGCAAGGCACACCACTATC
60.035
55.000
0.00
0.00
39.06
2.08
857
872
0.322816
CAGGCAAGGCACACCACTAT
60.323
55.000
0.00
0.00
39.06
2.12
858
873
1.073025
CAGGCAAGGCACACCACTA
59.927
57.895
0.00
0.00
39.06
2.74
859
874
2.203394
CAGGCAAGGCACACCACT
60.203
61.111
0.00
0.00
39.06
4.00
879
894
4.202172
GGAGGAATCAGTACCTTGTAGCTC
60.202
50.000
0.00
0.00
36.57
4.09
889
904
3.927142
CACACGAAAGGAGGAATCAGTAC
59.073
47.826
0.00
0.00
0.00
2.73
921
936
1.030457
GCTAGTTAGGCGAGGCAGTA
58.970
55.000
0.00
0.00
0.00
2.74
924
939
1.319541
CTAGCTAGTTAGGCGAGGCA
58.680
55.000
12.92
0.00
34.52
4.75
927
942
3.502595
TGCATACTAGCTAGTTAGGCGAG
59.497
47.826
30.40
13.66
37.73
5.03
928
943
3.483421
TGCATACTAGCTAGTTAGGCGA
58.517
45.455
30.40
12.74
37.73
5.54
944
963
1.200519
AAGAGGTTACCGGCTGCATA
58.799
50.000
0.00
0.00
0.00
3.14
945
964
0.328258
AAAGAGGTTACCGGCTGCAT
59.672
50.000
0.00
0.00
0.00
3.96
946
965
0.605319
CAAAGAGGTTACCGGCTGCA
60.605
55.000
0.00
0.00
0.00
4.41
947
966
1.923227
GCAAAGAGGTTACCGGCTGC
61.923
60.000
0.00
0.44
0.00
5.25
948
967
1.305930
GGCAAAGAGGTTACCGGCTG
61.306
60.000
0.00
0.00
0.00
4.85
949
968
1.002502
GGCAAAGAGGTTACCGGCT
60.003
57.895
0.00
0.00
0.00
5.52
950
969
1.302993
TGGCAAAGAGGTTACCGGC
60.303
57.895
0.00
0.00
0.00
6.13
951
970
1.305930
GCTGGCAAAGAGGTTACCGG
61.306
60.000
0.00
0.00
0.00
5.28
952
971
0.321653
AGCTGGCAAAGAGGTTACCG
60.322
55.000
0.00
0.00
0.00
4.02
953
972
1.454201
GAGCTGGCAAAGAGGTTACC
58.546
55.000
0.00
0.00
0.00
2.85
954
973
1.079503
CGAGCTGGCAAAGAGGTTAC
58.920
55.000
0.00
0.00
0.00
2.50
955
974
0.685097
ACGAGCTGGCAAAGAGGTTA
59.315
50.000
0.00
0.00
0.00
2.85
956
975
0.886490
CACGAGCTGGCAAAGAGGTT
60.886
55.000
0.00
0.00
0.00
3.50
957
976
1.302033
CACGAGCTGGCAAAGAGGT
60.302
57.895
0.00
0.00
0.00
3.85
958
977
2.684843
GCACGAGCTGGCAAAGAGG
61.685
63.158
0.00
0.00
37.91
3.69
959
978
1.962822
TGCACGAGCTGGCAAAGAG
60.963
57.895
6.36
0.00
42.74
2.85
960
979
2.110835
TGCACGAGCTGGCAAAGA
59.889
55.556
6.36
0.00
42.74
2.52
961
980
2.253452
GTGCACGAGCTGGCAAAG
59.747
61.111
0.00
0.00
42.45
2.77
962
981
3.648982
CGTGCACGAGCTGGCAAA
61.649
61.111
34.93
0.00
42.45
3.68
975
994
2.652548
GCATAATTGTGCACCGTGC
58.347
52.632
20.86
16.93
44.43
5.34
1003
1022
6.488344
CCTTCTCTGTCTCTGTGCTGTATATA
59.512
42.308
0.00
0.00
0.00
0.86
1011
1030
0.390998
GCCCTTCTCTGTCTCTGTGC
60.391
60.000
0.00
0.00
0.00
4.57
1055
1111
1.552799
TTGGGCGCCATCTCTCTTGA
61.553
55.000
30.85
0.00
31.53
3.02
1070
1129
4.447342
AGCGGGGAATGCCTTGGG
62.447
66.667
0.00
0.00
0.00
4.12
1195
1257
1.535687
AGGGTAAGTCGGTGGCTGT
60.536
57.895
0.00
0.00
0.00
4.40
1213
1275
3.731728
GAGTGGGCATGGGCAGGA
61.732
66.667
0.00
0.00
43.71
3.86
1214
1276
4.828296
GGAGTGGGCATGGGCAGG
62.828
72.222
0.00
0.00
43.71
4.85
1255
1317
6.416631
AATCATGAGAGATTAGCTACAGCA
57.583
37.500
0.09
0.00
37.44
4.41
1262
1327
5.537188
ACGGAGAAATCATGAGAGATTAGC
58.463
41.667
0.09
0.00
37.24
3.09
1467
1631
2.997315
CTGCCTGGACCTGGACGA
60.997
66.667
21.06
3.18
0.00
4.20
1530
1700
8.902806
TGACAACTTCACACAGATTTTATTCTT
58.097
29.630
0.00
0.00
0.00
2.52
1629
1827
8.837389
GGATAAACTTGTATATGTCCCAACTTC
58.163
37.037
0.00
0.00
0.00
3.01
1701
1925
4.620248
GAAAAACGTTTGTGAACCGTTTG
58.380
39.130
15.46
0.00
39.73
2.93
1709
1933
4.032355
GCAAGATCGAAAAACGTTTGTGA
58.968
39.130
15.46
12.83
43.13
3.58
1719
1943
6.073494
TCAGTACGAAAATGCAAGATCGAAAA
60.073
34.615
20.55
6.93
38.59
2.29
1735
1960
6.693978
CGACCATGTACATTTATCAGTACGAA
59.306
38.462
5.37
0.00
42.62
3.85
1837
2072
2.319025
TGGGATGTAGATATCGGCCA
57.681
50.000
2.24
0.00
0.00
5.36
1966
2220
2.352960
GCTAAAATGGGTCAGCGAGAAG
59.647
50.000
0.00
0.00
0.00
2.85
1968
2222
1.277842
TGCTAAAATGGGTCAGCGAGA
59.722
47.619
0.00
0.00
36.81
4.04
1969
2223
1.737838
TGCTAAAATGGGTCAGCGAG
58.262
50.000
0.00
0.00
36.81
5.03
1971
2225
3.296322
TTTTGCTAAAATGGGTCAGCG
57.704
42.857
0.00
0.00
36.81
5.18
2333
2617
7.068702
TGCATAATTCATATGAAACTCCCCTT
58.931
34.615
21.50
11.85
43.52
3.95
2419
2704
4.701956
ATACATAAGTTTGCAGTGTGCC
57.298
40.909
0.00
0.00
44.23
5.01
2504
2789
2.172717
ACTAATACGATGGGGCAAAGCT
59.827
45.455
0.00
0.00
0.00
3.74
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.