Multiple sequence alignment - TraesCS4B01G157400
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
TraesCS4B01G157400
chr4B
100.000
5693
0
0
1
5693
296299182
296293490
0.000000e+00
10514.0
1
TraesCS4B01G157400
chr4B
76.206
601
90
30
3716
4269
34729730
34729136
9.400000e-68
268.0
2
TraesCS4B01G157400
chr4B
72.032
497
108
19
3753
4221
139630915
139630422
1.000000e-22
119.0
3
TraesCS4B01G157400
chr4A
92.374
3252
164
39
4
3223
346058926
346062125
0.000000e+00
4554.0
4
TraesCS4B01G157400
chr4A
90.033
913
54
6
3682
4583
346063084
346063970
0.000000e+00
1147.0
5
TraesCS4B01G157400
chr4A
91.569
510
19
8
4591
5083
346064103
346064605
0.000000e+00
682.0
6
TraesCS4B01G157400
chr4A
95.779
308
8
5
3219
3526
346062254
346062556
5.120000e-135
492.0
7
TraesCS4B01G157400
chr4A
78.707
634
93
23
3673
4266
578216575
578217206
8.950000e-103
385.0
8
TraesCS4B01G157400
chr4A
79.123
570
84
18
3727
4266
579425779
579426343
1.510000e-95
361.0
9
TraesCS4B01G157400
chr4A
79.392
296
39
15
3897
4172
24941407
24941700
7.530000e-44
189.0
10
TraesCS4B01G157400
chr4A
80.282
142
21
4
5538
5674
122255190
122255329
3.630000e-17
100.0
11
TraesCS4B01G157400
chr4D
98.141
2152
32
3
903
3054
204734335
204732192
0.000000e+00
3746.0
12
TraesCS4B01G157400
chr4D
93.004
1558
53
13
3639
5142
204731662
204730107
0.000000e+00
2222.0
13
TraesCS4B01G157400
chr4D
88.262
886
69
17
44
910
204855556
204854687
0.000000e+00
1027.0
14
TraesCS4B01G157400
chr4D
92.632
475
20
9
5220
5683
204724279
204723809
0.000000e+00
669.0
15
TraesCS4B01G157400
chr4D
95.935
246
10
0
3334
3579
204731907
204731662
3.200000e-107
399.0
16
TraesCS4B01G157400
chr4D
79.022
634
92
25
3673
4266
25211276
25211908
4.130000e-106
396.0
17
TraesCS4B01G157400
chr4D
96.651
209
7
0
3053
3261
204732110
204731902
1.170000e-91
348.0
18
TraesCS4B01G157400
chr4D
96.000
50
2
0
315
364
109367411
109367460
1.310000e-11
82.4
19
TraesCS4B01G157400
chr4D
100.000
38
0
0
5141
5178
204724816
204724779
2.850000e-08
71.3
20
TraesCS4B01G157400
chr2B
79.708
616
87
20
3681
4266
87357341
87357948
1.480000e-110
411.0
21
TraesCS4B01G157400
chr2B
86.093
151
9
7
4122
4260
397053632
397053782
9.880000e-33
152.0
22
TraesCS4B01G157400
chr3D
78.806
670
96
28
3630
4269
416142092
416141439
5.310000e-110
409.0
23
TraesCS4B01G157400
chr3D
77.445
634
94
21
3673
4272
348146080
348146698
3.290000e-87
333.0
24
TraesCS4B01G157400
chr3D
79.389
393
47
22
3788
4151
448291100
448291487
4.410000e-61
246.0
25
TraesCS4B01G157400
chr2D
79.158
499
68
24
3812
4281
55160166
55160657
4.280000e-81
313.0
26
TraesCS4B01G157400
chr3A
82.410
307
28
14
3984
4266
272796320
272796624
1.580000e-60
244.0
27
TraesCS4B01G157400
chr6B
77.839
361
54
16
3745
4086
198404579
198404932
3.480000e-47
200.0
28
TraesCS4B01G157400
chr2A
83.598
189
17
9
4086
4260
433394860
433395048
1.270000e-36
165.0
29
TraesCS4B01G157400
chr5D
80.729
192
34
3
3897
4086
396416165
396416355
4.600000e-31
147.0
30
TraesCS4B01G157400
chr5A
86.719
128
17
0
5216
5343
702190758
702190885
5.950000e-30
143.0
31
TraesCS4B01G157400
chr5A
94.286
35
2
0
5552
5586
593099653
593099687
3.000000e-03
54.7
32
TraesCS4B01G157400
chr5B
73.409
440
85
26
329
747
73469876
73469448
9.950000e-28
135.0
33
TraesCS4B01G157400
chr1B
79.720
143
21
6
5538
5674
432461863
432461723
4.700000e-16
97.1
34
TraesCS4B01G157400
chr7D
76.033
121
27
2
5550
5668
38640856
38640976
1.710000e-05
62.1
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
TraesCS4B01G157400
chr4B
296293490
296299182
5692
True
10514.00
10514
100.00000
1
5693
1
chr4B.!!$R3
5692
1
TraesCS4B01G157400
chr4B
34729136
34729730
594
True
268.00
268
76.20600
3716
4269
1
chr4B.!!$R1
553
2
TraesCS4B01G157400
chr4A
346058926
346064605
5679
False
1718.75
4554
92.43875
4
5083
4
chr4A.!!$F5
5079
3
TraesCS4B01G157400
chr4A
578216575
578217206
631
False
385.00
385
78.70700
3673
4266
1
chr4A.!!$F3
593
4
TraesCS4B01G157400
chr4A
579425779
579426343
564
False
361.00
361
79.12300
3727
4266
1
chr4A.!!$F4
539
5
TraesCS4B01G157400
chr4D
204730107
204734335
4228
True
1678.75
3746
95.93275
903
5142
4
chr4D.!!$R3
4239
6
TraesCS4B01G157400
chr4D
204854687
204855556
869
True
1027.00
1027
88.26200
44
910
1
chr4D.!!$R1
866
7
TraesCS4B01G157400
chr4D
25211276
25211908
632
False
396.00
396
79.02200
3673
4266
1
chr4D.!!$F1
593
8
TraesCS4B01G157400
chr4D
204723809
204724816
1007
True
370.15
669
96.31600
5141
5683
2
chr4D.!!$R2
542
9
TraesCS4B01G157400
chr2B
87357341
87357948
607
False
411.00
411
79.70800
3681
4266
1
chr2B.!!$F1
585
10
TraesCS4B01G157400
chr3D
416141439
416142092
653
True
409.00
409
78.80600
3630
4269
1
chr3D.!!$R1
639
11
TraesCS4B01G157400
chr3D
348146080
348146698
618
False
333.00
333
77.44500
3673
4272
1
chr3D.!!$F1
599
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
828
876
0.035439
AGTATTTGTGTCCCGCCTGG
60.035
55.000
0.00
0.0
0.00
4.45
F
829
877
0.035820
GTATTTGTGTCCCGCCTGGA
60.036
55.000
0.00
0.0
42.41
3.86
F
871
931
0.608035
TTAAAGTCTGCAAGCGGGGG
60.608
55.000
0.37
0.0
0.00
5.40
F
1638
1700
1.514443
GCAGAGACAGTACGCCGAC
60.514
63.158
0.00
0.0
0.00
4.79
F
3608
4009
0.108992
TGGACGTGTCTGCGGATAAC
60.109
55.000
0.00
0.0
35.98
1.89
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1842
1904
0.032515
TGATCGCTGAGACCCCCTTA
60.033
55.0
0.0
0.0
0.00
2.69
R
1869
1931
1.056660
ATAGATGGCCGTACTTGGGG
58.943
55.0
0.0
0.0
0.00
4.96
R
1878
1940
1.224075
CAGACAGCAATAGATGGCCG
58.776
55.0
0.0
0.0
41.11
6.13
R
3627
4028
0.846427
AGAGTTGGATGGCTCCCCAA
60.846
55.0
0.0
0.0
46.14
4.12
R
5355
6699
0.038310
GGCAAGCCCTGTAGTTTCCT
59.962
55.0
0.0
0.0
0.00
3.36
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
20
21
3.644966
TGTTTTCAACTGGGACACTCT
57.355
42.857
0.00
0.00
0.00
3.24
21
22
3.278574
TGTTTTCAACTGGGACACTCTG
58.721
45.455
0.00
0.00
0.00
3.35
22
23
3.279434
GTTTTCAACTGGGACACTCTGT
58.721
45.455
0.00
0.00
0.00
3.41
23
24
2.910688
TTCAACTGGGACACTCTGTC
57.089
50.000
0.00
0.00
46.23
3.51
73
75
0.322816
AACCGCTGGCATCTGAACAT
60.323
50.000
0.00
0.00
0.00
2.71
96
98
4.284550
GGGTTCAGGTGCCAGCCA
62.285
66.667
0.00
0.00
0.00
4.75
155
157
0.681564
ACCGACGAGCTCATCTCCTT
60.682
55.000
15.40
0.00
38.62
3.36
219
221
1.189524
CCGGGACACCTAGTTCACCA
61.190
60.000
0.00
0.00
33.28
4.17
226
228
0.038526
ACCTAGTTCACCAACGAGCG
60.039
55.000
0.00
0.00
37.61
5.03
227
229
0.242825
CCTAGTTCACCAACGAGCGA
59.757
55.000
0.00
0.00
37.61
4.93
238
240
4.103103
CGAGCGAGACCAGCGACA
62.103
66.667
0.00
0.00
40.04
4.35
298
300
0.616111
GAGCTGGTGAAGGAGGAGGA
60.616
60.000
0.00
0.00
0.00
3.71
299
301
0.617249
AGCTGGTGAAGGAGGAGGAG
60.617
60.000
0.00
0.00
0.00
3.69
306
308
0.930726
GAAGGAGGAGGAGGAGGAGA
59.069
60.000
0.00
0.00
0.00
3.71
313
315
0.634465
GAGGAGGAGGAGAAGGAGGT
59.366
60.000
0.00
0.00
0.00
3.85
420
422
1.022735
CAGAGTATAGGTCGCCGTGT
58.977
55.000
0.00
0.00
0.00
4.49
481
483
2.261671
GCACTCGTGGTCGTGGAT
59.738
61.111
0.00
0.00
38.33
3.41
509
511
3.345808
CCGTGCACGTCCAAGTGG
61.346
66.667
34.81
15.31
42.09
4.00
538
540
1.276415
GAGCTGAAGCAACTAGAGCG
58.724
55.000
4.90
0.00
45.16
5.03
582
590
2.050351
ACGAGCCGACGACAGTTG
60.050
61.111
0.00
0.00
37.03
3.16
615
653
1.134901
CTCTTCGTCGACCTCACCG
59.865
63.158
10.58
0.00
0.00
4.94
616
654
1.296755
CTCTTCGTCGACCTCACCGA
61.297
60.000
10.58
0.00
0.00
4.69
620
658
2.479650
GTCGACCTCACCGACGAG
59.520
66.667
3.51
0.00
45.23
4.18
621
659
2.031516
GTCGACCTCACCGACGAGA
61.032
63.158
3.51
0.00
45.23
4.04
622
660
1.301953
TCGACCTCACCGACGAGAA
60.302
57.895
0.00
0.00
34.79
2.87
623
661
0.886043
TCGACCTCACCGACGAGAAA
60.886
55.000
0.00
0.00
34.79
2.52
624
662
0.454620
CGACCTCACCGACGAGAAAG
60.455
60.000
0.00
0.00
34.79
2.62
625
663
0.879765
GACCTCACCGACGAGAAAGA
59.120
55.000
0.00
0.00
34.79
2.52
626
664
0.882474
ACCTCACCGACGAGAAAGAG
59.118
55.000
0.00
0.00
34.79
2.85
627
665
0.171455
CCTCACCGACGAGAAAGAGG
59.829
60.000
0.00
1.66
36.98
3.69
628
666
1.166129
CTCACCGACGAGAAAGAGGA
58.834
55.000
0.00
0.00
34.79
3.71
629
667
0.879765
TCACCGACGAGAAAGAGGAC
59.120
55.000
0.00
0.00
0.00
3.85
630
668
0.109226
CACCGACGAGAAAGAGGACC
60.109
60.000
0.00
0.00
0.00
4.46
631
669
0.538977
ACCGACGAGAAAGAGGACCA
60.539
55.000
0.00
0.00
0.00
4.02
632
670
0.109226
CCGACGAGAAAGAGGACCAC
60.109
60.000
0.00
0.00
0.00
4.16
633
671
0.109226
CGACGAGAAAGAGGACCACC
60.109
60.000
0.00
0.00
0.00
4.61
653
694
7.565680
ACCACCAGATCTAGGTTTTACTTATG
58.434
38.462
12.50
1.75
37.23
1.90
654
695
7.182206
ACCACCAGATCTAGGTTTTACTTATGT
59.818
37.037
12.50
0.00
37.23
2.29
655
696
8.047310
CCACCAGATCTAGGTTTTACTTATGTT
58.953
37.037
12.50
0.00
37.23
2.71
656
697
9.449719
CACCAGATCTAGGTTTTACTTATGTTT
57.550
33.333
12.50
0.00
37.23
2.83
696
737
8.637281
TTAATATATGAACAGACTTTTCGCGA
57.363
30.769
3.71
3.71
0.00
5.87
697
738
4.842139
ATATGAACAGACTTTTCGCGAC
57.158
40.909
9.15
0.00
0.00
5.19
799
847
7.933577
AGAAAAACATTGATCGCATCTATAGGA
59.066
33.333
0.00
0.00
0.00
2.94
812
860
4.406648
TCTATAGGACGACGGACAAGTA
57.593
45.455
0.00
0.00
0.00
2.24
813
861
4.965814
TCTATAGGACGACGGACAAGTAT
58.034
43.478
0.00
0.00
0.00
2.12
814
862
5.371526
TCTATAGGACGACGGACAAGTATT
58.628
41.667
0.00
0.00
0.00
1.89
815
863
4.996788
ATAGGACGACGGACAAGTATTT
57.003
40.909
0.00
0.00
0.00
1.40
816
864
2.955614
AGGACGACGGACAAGTATTTG
58.044
47.619
0.00
0.00
40.24
2.32
826
874
1.073284
ACAAGTATTTGTGTCCCGCCT
59.927
47.619
2.38
0.00
45.54
5.52
828
876
0.035439
AGTATTTGTGTCCCGCCTGG
60.035
55.000
0.00
0.00
0.00
4.45
829
877
0.035820
GTATTTGTGTCCCGCCTGGA
60.036
55.000
0.00
0.00
42.41
3.86
849
909
2.590092
GGCCCGTTGGAGTAGCAT
59.410
61.111
0.00
0.00
0.00
3.79
869
929
4.601019
CATAATTAAAGTCTGCAAGCGGG
58.399
43.478
0.37
0.00
0.00
6.13
870
930
1.463674
ATTAAAGTCTGCAAGCGGGG
58.536
50.000
0.37
0.00
0.00
5.73
871
931
0.608035
TTAAAGTCTGCAAGCGGGGG
60.608
55.000
0.37
0.00
0.00
5.40
872
932
1.774894
TAAAGTCTGCAAGCGGGGGT
61.775
55.000
0.37
0.00
0.00
4.95
886
946
2.793288
GGGGGTCCGTCTTTTCATTA
57.207
50.000
0.00
0.00
0.00
1.90
891
951
5.407502
GGGGTCCGTCTTTTCATTATTTTG
58.592
41.667
0.00
0.00
0.00
2.44
953
1015
1.841450
CGGCCTCGTAGACAAATCTC
58.159
55.000
0.00
0.00
36.29
2.75
1638
1700
1.514443
GCAGAGACAGTACGCCGAC
60.514
63.158
0.00
0.00
0.00
4.79
1790
1852
3.134127
GGATGCCAAGGCGACCAC
61.134
66.667
17.30
3.75
45.51
4.16
1869
1931
2.869192
GGTCTCAGCGATCAGATTTTCC
59.131
50.000
0.00
0.00
0.00
3.13
1878
1940
3.877508
CGATCAGATTTTCCCCCAAGTAC
59.122
47.826
0.00
0.00
0.00
2.73
2490
2552
3.584733
AAGAAGAAGAGGTTTGCAGGT
57.415
42.857
0.00
0.00
0.00
4.00
2745
2807
9.774742
GACAAGATAAACATATGAAAACACCTC
57.225
33.333
10.38
0.00
0.00
3.85
2807
2869
5.678921
GCACCATTGCTGTTTAAATTGTTC
58.321
37.500
0.00
0.00
46.17
3.18
2871
2933
9.846248
GATTTAGATTGTGCAGTATGTCTTTTT
57.154
29.630
0.00
0.00
39.31
1.94
2958
3020
5.880887
GCTAGAAGGGTAGTTTAGTTTGCAT
59.119
40.000
0.00
0.00
0.00
3.96
3019
3081
6.324819
CACACAAACTTGATTATGATGTCCC
58.675
40.000
0.00
0.00
0.00
4.46
3174
3319
4.085357
TGTTACTGATTGTGTTGGCTCT
57.915
40.909
0.00
0.00
0.00
4.09
3182
3327
0.682532
TGTGTTGGCTCTTTGGTGCA
60.683
50.000
0.00
0.00
34.07
4.57
3267
3545
1.610522
CCTGGACCACTGCTCTTTTTG
59.389
52.381
0.00
0.00
0.00
2.44
3272
3550
3.003793
GGACCACTGCTCTTTTTGTCTTC
59.996
47.826
0.00
0.00
0.00
2.87
3273
3551
2.952310
ACCACTGCTCTTTTTGTCTTCC
59.048
45.455
0.00
0.00
0.00
3.46
3274
3552
2.951642
CCACTGCTCTTTTTGTCTTCCA
59.048
45.455
0.00
0.00
0.00
3.53
3275
3553
3.571401
CCACTGCTCTTTTTGTCTTCCAT
59.429
43.478
0.00
0.00
0.00
3.41
3276
3554
4.320788
CCACTGCTCTTTTTGTCTTCCATC
60.321
45.833
0.00
0.00
0.00
3.51
3400
3678
2.133553
CATCTTCTACATGCCGCTGAG
58.866
52.381
0.00
0.00
0.00
3.35
3458
3736
6.308766
CCCATTCAAAAGAACTCGCAAATTAG
59.691
38.462
0.00
0.00
0.00
1.73
3573
3974
2.288152
CCATCAAAACGGACACCCAAAG
60.288
50.000
0.00
0.00
0.00
2.77
3593
3994
1.507141
CGTTTGTGGGCAGTCTGGAC
61.507
60.000
1.14
0.00
0.00
4.02
3608
4009
0.108992
TGGACGTGTCTGCGGATAAC
60.109
55.000
0.00
0.00
35.98
1.89
3611
4012
0.885879
ACGTGTCTGCGGATAACAGA
59.114
50.000
0.00
0.00
41.78
3.41
3612
4013
1.476891
ACGTGTCTGCGGATAACAGAT
59.523
47.619
0.00
0.00
45.40
2.90
3613
4014
2.686405
ACGTGTCTGCGGATAACAGATA
59.314
45.455
0.00
0.00
45.40
1.98
3614
4015
3.243101
ACGTGTCTGCGGATAACAGATAG
60.243
47.826
0.00
0.00
45.40
2.08
3615
4016
3.643763
GTGTCTGCGGATAACAGATAGG
58.356
50.000
0.00
0.00
45.40
2.57
3616
4017
2.628178
TGTCTGCGGATAACAGATAGGG
59.372
50.000
0.00
0.00
45.40
3.53
3617
4018
2.028930
GTCTGCGGATAACAGATAGGGG
60.029
54.545
0.00
0.00
45.40
4.79
3618
4019
1.276421
CTGCGGATAACAGATAGGGGG
59.724
57.143
0.00
0.00
37.32
5.40
3619
4020
1.132977
TGCGGATAACAGATAGGGGGA
60.133
52.381
0.00
0.00
0.00
4.81
3620
4021
1.550976
GCGGATAACAGATAGGGGGAG
59.449
57.143
0.00
0.00
0.00
4.30
3621
4022
2.180276
CGGATAACAGATAGGGGGAGG
58.820
57.143
0.00
0.00
0.00
4.30
3622
4023
2.552367
GGATAACAGATAGGGGGAGGG
58.448
57.143
0.00
0.00
0.00
4.30
3623
4024
2.552367
GATAACAGATAGGGGGAGGGG
58.448
57.143
0.00
0.00
0.00
4.79
3624
4025
1.336347
TAACAGATAGGGGGAGGGGT
58.664
55.000
0.00
0.00
0.00
4.95
3625
4026
0.327576
AACAGATAGGGGGAGGGGTG
60.328
60.000
0.00
0.00
0.00
4.61
3626
4027
1.462238
CAGATAGGGGGAGGGGTGG
60.462
68.421
0.00
0.00
0.00
4.61
3627
4028
1.952766
AGATAGGGGGAGGGGTGGT
60.953
63.158
0.00
0.00
0.00
4.16
3628
4029
1.005690
GATAGGGGGAGGGGTGGTT
59.994
63.158
0.00
0.00
0.00
3.67
3629
4030
1.308746
ATAGGGGGAGGGGTGGTTG
60.309
63.158
0.00
0.00
0.00
3.77
3630
4031
2.876033
ATAGGGGGAGGGGTGGTTGG
62.876
65.000
0.00
0.00
0.00
3.77
3634
4035
3.339093
GGAGGGGTGGTTGGGGAG
61.339
72.222
0.00
0.00
0.00
4.30
3651
4052
3.305398
GGAGCCATCCAACTCTATACG
57.695
52.381
0.00
0.00
45.87
3.06
3671
4072
1.080569
CAAATGCCCGCACCTGTTC
60.081
57.895
0.00
0.00
0.00
3.18
4063
4746
0.524414
TGCATGATCACACAAGCTGC
59.476
50.000
0.00
2.51
0.00
5.25
4128
4826
2.481289
AAACAGGCTTAGAGCACTCC
57.519
50.000
2.04
0.00
44.75
3.85
4131
4829
1.699634
ACAGGCTTAGAGCACTCCAAA
59.300
47.619
2.04
0.00
44.75
3.28
4132
4830
2.307098
ACAGGCTTAGAGCACTCCAAAT
59.693
45.455
2.04
0.00
44.75
2.32
4133
4831
2.681848
CAGGCTTAGAGCACTCCAAATG
59.318
50.000
2.04
0.00
44.75
2.32
4134
4832
1.403323
GGCTTAGAGCACTCCAAATGC
59.597
52.381
2.04
0.00
44.75
3.56
4153
4853
2.032620
GCCCTCGACATCCTTTCTAGA
58.967
52.381
0.00
0.00
0.00
2.43
4350
5079
3.996921
AGATTCTCATGTCAACCTGCT
57.003
42.857
0.00
0.00
0.00
4.24
4394
5123
9.423061
GTTTTCCTGTAAAATTGCTCATATGTT
57.577
29.630
1.90
0.00
39.22
2.71
4444
5173
7.462109
TTGTTGAGTTCATTACATTTGCAAC
57.538
32.000
0.00
0.00
35.10
4.17
4491
5220
8.455598
TTTGTTCTTAAGTTGTGTTAAAGTGC
57.544
30.769
1.63
0.00
0.00
4.40
4492
5221
6.557110
TGTTCTTAAGTTGTGTTAAAGTGCC
58.443
36.000
1.63
0.00
0.00
5.01
4504
5246
2.674796
AAAGTGCCTATCGTGGAGAC
57.325
50.000
0.00
0.00
0.00
3.36
4585
5327
8.387354
CCGAATAACTATATGCATATTTTCGCA
58.613
33.333
23.71
4.58
43.45
5.10
4659
5526
6.930731
ACAATTTTCTTTACTTGTGGTGTGT
58.069
32.000
0.00
0.00
31.00
3.72
4679
5546
8.349983
GGTGTGTCATTAACTCTTTTGTACAAT
58.650
33.333
9.56
0.00
0.00
2.71
4883
5754
4.713824
TCCAACTACCGTCTAGTTCATG
57.286
45.455
0.81
0.00
35.76
3.07
4884
5755
3.119245
TCCAACTACCGTCTAGTTCATGC
60.119
47.826
0.81
0.00
35.76
4.06
4931
5816
5.486526
TGCACCATTCAGTTTTTCAACTTT
58.513
33.333
0.00
0.00
40.66
2.66
4954
5839
4.974399
ACTTCTAGGACTTTGGTTTCAGG
58.026
43.478
0.00
0.00
0.00
3.86
4959
5844
6.192044
TCTAGGACTTTGGTTTCAGGTTTTT
58.808
36.000
0.00
0.00
0.00
1.94
4960
5845
5.339008
AGGACTTTGGTTTCAGGTTTTTC
57.661
39.130
0.00
0.00
0.00
2.29
4962
5847
5.483937
AGGACTTTGGTTTCAGGTTTTTCTT
59.516
36.000
0.00
0.00
0.00
2.52
4963
5848
6.013725
AGGACTTTGGTTTCAGGTTTTTCTTT
60.014
34.615
0.00
0.00
0.00
2.52
5104
5989
3.802685
ACTATTTGATTCTTCGGCTACGC
59.197
43.478
0.00
0.00
40.69
4.42
5132
6017
0.523519
CTCCCTGCGCTTTCCTTTTC
59.476
55.000
9.73
0.00
0.00
2.29
5178
6063
4.868171
GTCAAACTTCCCAACTTTCCAAAC
59.132
41.667
0.00
0.00
0.00
2.93
5179
6064
4.528596
TCAAACTTCCCAACTTTCCAAACA
59.471
37.500
0.00
0.00
0.00
2.83
5181
6066
3.708451
ACTTCCCAACTTTCCAAACACT
58.292
40.909
0.00
0.00
0.00
3.55
5182
6067
4.093743
ACTTCCCAACTTTCCAAACACTT
58.906
39.130
0.00
0.00
0.00
3.16
5183
6068
4.159693
ACTTCCCAACTTTCCAAACACTTC
59.840
41.667
0.00
0.00
0.00
3.01
5184
6069
3.702792
TCCCAACTTTCCAAACACTTCA
58.297
40.909
0.00
0.00
0.00
3.02
5212
6130
4.022589
ACAGTCTTTGATGCATGACTTTGG
60.023
41.667
13.22
6.84
37.64
3.28
5214
6132
3.057033
GTCTTTGATGCATGACTTTGGCT
60.057
43.478
2.46
0.00
0.00
4.75
5217
6135
6.038603
GTCTTTGATGCATGACTTTGGCTATA
59.961
38.462
2.46
0.00
0.00
1.31
5218
6136
6.774170
TCTTTGATGCATGACTTTGGCTATAT
59.226
34.615
2.46
0.00
0.00
0.86
5257
6600
7.764695
TGAACATGTATAAATGGTGTAGTCG
57.235
36.000
7.81
0.00
31.46
4.18
5366
6710
6.693315
TCTTTTTGACCAAGGAAACTACAG
57.307
37.500
0.00
0.00
42.68
2.74
5386
6731
1.037579
GGCTTGCCCCCTCAACATAC
61.038
60.000
0.00
0.00
0.00
2.39
5460
6805
9.634021
TGGCATATGTACATAAATAAAGTTCCA
57.366
29.630
19.11
8.37
0.00
3.53
5461
6806
9.893305
GGCATATGTACATAAATAAAGTTCCAC
57.107
33.333
19.11
0.00
0.00
4.02
5474
6823
8.474006
AATAAAGTTCCACAAGTGAAACAAAC
57.526
30.769
5.14
1.20
41.43
2.93
5617
6969
6.831868
ACTTGGTTGGTATTGTAGAAGTTTGT
59.168
34.615
0.00
0.00
0.00
2.83
5675
7027
5.010012
AGTTTGACCTGAAACAAGCCTATTG
59.990
40.000
0.00
0.00
38.14
1.90
5679
7031
4.980573
ACCTGAAACAAGCCTATTGTGTA
58.019
39.130
0.00
0.00
32.22
2.90
5680
7032
5.003804
ACCTGAAACAAGCCTATTGTGTAG
58.996
41.667
0.00
0.00
32.22
2.74
5681
7033
5.003804
CCTGAAACAAGCCTATTGTGTAGT
58.996
41.667
0.00
0.00
32.22
2.73
5682
7034
6.170506
CCTGAAACAAGCCTATTGTGTAGTA
58.829
40.000
0.00
0.00
32.22
1.82
5683
7035
6.092259
CCTGAAACAAGCCTATTGTGTAGTAC
59.908
42.308
0.00
0.00
32.22
2.73
5684
7036
6.765403
TGAAACAAGCCTATTGTGTAGTACT
58.235
36.000
0.00
0.00
32.22
2.73
5685
7037
6.872020
TGAAACAAGCCTATTGTGTAGTACTC
59.128
38.462
0.00
0.00
32.22
2.59
5686
7038
5.340439
ACAAGCCTATTGTGTAGTACTCC
57.660
43.478
0.00
0.00
0.00
3.85
5687
7039
4.161754
ACAAGCCTATTGTGTAGTACTCCC
59.838
45.833
0.00
0.00
0.00
4.30
5688
7040
4.267341
AGCCTATTGTGTAGTACTCCCT
57.733
45.455
0.00
0.00
0.00
4.20
5689
7041
4.216708
AGCCTATTGTGTAGTACTCCCTC
58.783
47.826
0.00
0.00
0.00
4.30
5690
7042
3.321396
GCCTATTGTGTAGTACTCCCTCC
59.679
52.174
0.00
0.00
0.00
4.30
5691
7043
3.568853
CCTATTGTGTAGTACTCCCTCCG
59.431
52.174
0.00
0.00
0.00
4.63
5692
7044
2.592102
TTGTGTAGTACTCCCTCCGT
57.408
50.000
0.00
0.00
0.00
4.69
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
5.161249
GACAGAGTGTCCCAGTTGAAAACA
61.161
45.833
0.00
0.00
44.88
2.83
2
3
3.541632
GACAGAGTGTCCCAGTTGAAAA
58.458
45.455
0.00
0.00
41.37
2.29
16
17
2.118513
ACGGCAGGAGGACAGAGT
59.881
61.111
0.00
0.00
0.00
3.24
17
18
2.575993
CACGGCAGGAGGACAGAG
59.424
66.667
0.00
0.00
0.00
3.35
18
19
2.997315
CCACGGCAGGAGGACAGA
60.997
66.667
0.00
0.00
0.00
3.41
19
20
4.767255
GCCACGGCAGGAGGACAG
62.767
72.222
2.36
0.00
41.49
3.51
24
25
4.162690
GTAGGGCCACGGCAGGAG
62.163
72.222
10.83
0.00
44.11
3.69
42
44
4.778143
GCGGTTCAGCGGGTGGAT
62.778
66.667
7.42
0.00
0.00
3.41
73
75
0.116342
TGGCACCTGAACCCTCTCTA
59.884
55.000
0.00
0.00
0.00
2.43
96
98
0.178970
GCATGATGGGAGGCCAGAAT
60.179
55.000
5.01
0.00
0.00
2.40
155
157
0.952280
GGTCGTAGCGGAGATCATCA
59.048
55.000
0.00
0.00
0.00
3.07
219
221
3.362797
TCGCTGGTCTCGCTCGTT
61.363
61.111
0.00
0.00
0.00
3.85
226
228
1.226717
GATCGGTGTCGCTGGTCTC
60.227
63.158
0.00
0.00
36.13
3.36
227
229
2.885861
GATCGGTGTCGCTGGTCT
59.114
61.111
0.00
0.00
36.13
3.85
298
300
0.257616
CTCGACCTCCTTCTCCTCCT
59.742
60.000
0.00
0.00
0.00
3.69
299
301
0.753848
CCTCGACCTCCTTCTCCTCC
60.754
65.000
0.00
0.00
0.00
4.30
306
308
0.252103
TTGTAGGCCTCGACCTCCTT
60.252
55.000
9.68
0.00
41.50
3.36
459
461
4.742201
CGACCACGAGTGCCCCAG
62.742
72.222
0.00
0.00
42.66
4.45
489
491
2.047274
CTTGGACGTGCACGGGAT
60.047
61.111
39.21
21.97
44.95
3.85
501
503
4.263572
CACGCCCACCCACTTGGA
62.264
66.667
0.00
0.00
39.24
3.53
509
511
4.329545
TTCAGCTCCACGCCCACC
62.330
66.667
0.00
0.00
40.39
4.61
525
527
2.353208
CCTCTTGACGCTCTAGTTGCTT
60.353
50.000
8.36
0.36
0.00
3.91
596
616
1.296755
CGGTGAGGTCGACGAAGAGA
61.297
60.000
9.92
0.00
0.00
3.10
615
653
0.966920
TGGTGGTCCTCTTTCTCGTC
59.033
55.000
0.00
0.00
34.23
4.20
616
654
0.969894
CTGGTGGTCCTCTTTCTCGT
59.030
55.000
0.00
0.00
34.23
4.18
617
655
1.257743
TCTGGTGGTCCTCTTTCTCG
58.742
55.000
0.00
0.00
34.23
4.04
618
656
3.103742
AGATCTGGTGGTCCTCTTTCTC
58.896
50.000
0.00
0.00
34.23
2.87
619
657
3.197927
AGATCTGGTGGTCCTCTTTCT
57.802
47.619
0.00
0.00
34.23
2.52
620
658
3.386402
CCTAGATCTGGTGGTCCTCTTTC
59.614
52.174
5.18
0.00
34.23
2.62
621
659
3.246167
ACCTAGATCTGGTGGTCCTCTTT
60.246
47.826
13.91
0.00
36.30
2.52
622
660
2.316372
ACCTAGATCTGGTGGTCCTCTT
59.684
50.000
13.91
0.00
36.30
2.85
623
661
1.933765
ACCTAGATCTGGTGGTCCTCT
59.066
52.381
13.91
0.00
36.30
3.69
624
662
2.463047
ACCTAGATCTGGTGGTCCTC
57.537
55.000
13.91
0.00
36.30
3.71
625
663
2.950990
AACCTAGATCTGGTGGTCCT
57.049
50.000
15.00
1.64
37.93
3.85
626
664
4.470304
AGTAAAACCTAGATCTGGTGGTCC
59.530
45.833
15.00
6.82
37.93
4.46
627
665
5.678955
AGTAAAACCTAGATCTGGTGGTC
57.321
43.478
15.00
5.57
37.93
4.02
628
666
7.182206
ACATAAGTAAAACCTAGATCTGGTGGT
59.818
37.037
15.00
12.51
37.93
4.16
629
667
7.565680
ACATAAGTAAAACCTAGATCTGGTGG
58.434
38.462
15.00
11.97
37.93
4.61
630
668
9.449719
AAACATAAGTAAAACCTAGATCTGGTG
57.550
33.333
15.00
5.56
37.93
4.17
684
725
8.589335
AATATATACATTGTCGCGAAAAGTCT
57.411
30.769
18.02
10.35
0.00
3.24
728
769
5.618236
TGTTGGGATGCATTTCAAATTTCA
58.382
33.333
14.46
7.95
0.00
2.69
771
812
9.941664
CTATAGATGCGATCAATGTTTTTCTTT
57.058
29.630
0.00
0.00
0.00
2.52
772
813
8.562892
CCTATAGATGCGATCAATGTTTTTCTT
58.437
33.333
0.00
0.00
0.00
2.52
785
833
1.738350
CCGTCGTCCTATAGATGCGAT
59.262
52.381
0.00
0.00
34.80
4.58
799
847
3.054878
GACACAAATACTTGTCCGTCGT
58.945
45.455
0.00
0.00
44.15
4.34
812
860
3.166434
TCCAGGCGGGACACAAAT
58.834
55.556
0.91
0.00
42.15
2.32
824
872
4.856801
CCAACGGGCCGATCCAGG
62.857
72.222
35.78
21.00
36.21
4.45
826
874
3.781307
CTCCAACGGGCCGATCCA
61.781
66.667
35.78
12.53
36.21
3.41
828
876
1.067582
CTACTCCAACGGGCCGATC
59.932
63.158
35.78
0.00
0.00
3.69
829
877
3.090219
GCTACTCCAACGGGCCGAT
62.090
63.158
35.78
20.37
0.00
4.18
849
909
3.013921
CCCCGCTTGCAGACTTTAATTA
58.986
45.455
0.00
0.00
0.00
1.40
869
929
6.262193
TCAAAATAATGAAAAGACGGACCC
57.738
37.500
0.00
0.00
0.00
4.46
891
951
5.294552
CGGGAGGAGATTTGTATCTTGTTTC
59.705
44.000
0.00
0.00
41.23
2.78
953
1015
2.047560
GTTTCGTCGGGACAGGGG
60.048
66.667
0.00
0.00
0.00
4.79
1157
1219
4.452733
GACGGGAGGTGGAAGCGG
62.453
72.222
0.00
0.00
40.95
5.52
1158
1220
4.452733
GGACGGGAGGTGGAAGCG
62.453
72.222
0.00
0.00
40.95
4.68
1159
1221
3.003763
AGGACGGGAGGTGGAAGC
61.004
66.667
0.00
0.00
0.00
3.86
1790
1852
1.270094
TGGGAATATAACAGCGCTCGG
60.270
52.381
7.13
0.00
0.00
4.63
1842
1904
0.032515
TGATCGCTGAGACCCCCTTA
60.033
55.000
0.00
0.00
0.00
2.69
1869
1931
1.056660
ATAGATGGCCGTACTTGGGG
58.943
55.000
0.00
0.00
0.00
4.96
1878
1940
1.224075
CAGACAGCAATAGATGGCCG
58.776
55.000
0.00
0.00
41.11
6.13
2490
2552
1.818060
GCATAACCTGCCACAATGTGA
59.182
47.619
15.91
0.00
45.66
3.58
2937
2999
6.516693
GCAAATGCAAACTAAACTACCCTTCT
60.517
38.462
0.00
0.00
41.59
2.85
2958
3020
2.591923
TGTAATGGACCTTGCTGCAAA
58.408
42.857
16.74
1.02
0.00
3.68
2965
3027
8.681486
TGATAATCTGAATGTAATGGACCTTG
57.319
34.615
0.00
0.00
0.00
3.61
2968
3030
8.778358
GTCTTGATAATCTGAATGTAATGGACC
58.222
37.037
0.00
0.00
0.00
4.46
3019
3081
6.259550
AGTTCTAGCCATAAGTTTTTGCAG
57.740
37.500
0.00
0.00
0.00
4.41
3174
3319
2.645297
TGGTAGATAAGGGTGCACCAAA
59.355
45.455
35.78
20.94
43.89
3.28
3182
3327
6.064717
GCATCAAGAAATGGTAGATAAGGGT
58.935
40.000
0.00
0.00
0.00
4.34
3272
3550
5.180271
ACAAAGCCTTGCATTTTATGATGG
58.820
37.500
0.00
0.00
35.84
3.51
3273
3551
6.539324
CAACAAAGCCTTGCATTTTATGATG
58.461
36.000
0.00
0.00
35.84
3.07
3274
3552
5.122711
GCAACAAAGCCTTGCATTTTATGAT
59.877
36.000
0.00
0.00
43.04
2.45
3275
3553
4.451774
GCAACAAAGCCTTGCATTTTATGA
59.548
37.500
0.00
0.00
43.04
2.15
3276
3554
4.714851
GCAACAAAGCCTTGCATTTTATG
58.285
39.130
0.00
0.00
43.04
1.90
3573
3974
2.639286
CAGACTGCCCACAAACGC
59.361
61.111
0.00
0.00
0.00
4.84
3583
3984
2.024319
GCAGACACGTCCAGACTGC
61.024
63.158
11.63
11.63
44.88
4.40
3593
3994
2.209838
ATCTGTTATCCGCAGACACG
57.790
50.000
0.00
0.00
44.52
4.49
3608
4009
1.462238
CCACCCCTCCCCCTATCTG
60.462
68.421
0.00
0.00
0.00
2.90
3611
4012
1.308746
CAACCACCCCTCCCCCTAT
60.309
63.158
0.00
0.00
0.00
2.57
3612
4013
2.126372
CAACCACCCCTCCCCCTA
59.874
66.667
0.00
0.00
0.00
3.53
3617
4018
3.339093
CTCCCCAACCACCCCTCC
61.339
72.222
0.00
0.00
0.00
4.30
3618
4019
4.048470
GCTCCCCAACCACCCCTC
62.048
72.222
0.00
0.00
0.00
4.30
3621
4022
3.662117
GATGGCTCCCCAACCACCC
62.662
68.421
0.00
0.00
46.14
4.61
3622
4023
2.043953
GATGGCTCCCCAACCACC
60.044
66.667
0.00
0.00
46.14
4.61
3627
4028
0.846427
AGAGTTGGATGGCTCCCCAA
60.846
55.000
0.00
0.00
46.14
4.12
3629
4030
1.439543
ATAGAGTTGGATGGCTCCCC
58.560
55.000
1.34
0.00
41.29
4.81
3630
4031
2.028930
CGTATAGAGTTGGATGGCTCCC
60.029
54.545
1.34
0.00
41.29
4.30
3631
4032
2.628657
ACGTATAGAGTTGGATGGCTCC
59.371
50.000
0.00
0.00
42.45
4.70
3632
4033
3.318275
TGACGTATAGAGTTGGATGGCTC
59.682
47.826
0.00
0.00
0.00
4.70
3633
4034
3.296854
TGACGTATAGAGTTGGATGGCT
58.703
45.455
0.00
0.00
0.00
4.75
3634
4035
3.728076
TGACGTATAGAGTTGGATGGC
57.272
47.619
0.00
0.00
0.00
4.40
3651
4052
1.805428
AACAGGTGCGGGCATTTGAC
61.805
55.000
12.34
0.00
0.00
3.18
4063
4746
0.673644
GACGTTGTGGGAGGTGATGG
60.674
60.000
0.00
0.00
0.00
3.51
4119
4815
4.751431
GGGCATTTGGAGTGCTCT
57.249
55.556
0.00
0.00
39.95
4.09
4128
4826
1.755179
AAGGATGTCGAGGGCATTTG
58.245
50.000
0.00
0.00
0.00
2.32
4131
4829
1.207791
AGAAAGGATGTCGAGGGCAT
58.792
50.000
0.00
0.00
0.00
4.40
4132
4830
1.757118
CTAGAAAGGATGTCGAGGGCA
59.243
52.381
0.00
0.00
0.00
5.36
4133
4831
2.032620
TCTAGAAAGGATGTCGAGGGC
58.967
52.381
0.00
0.00
0.00
5.19
4134
4832
4.586841
AGAATCTAGAAAGGATGTCGAGGG
59.413
45.833
0.00
0.00
0.00
4.30
4350
5079
9.619316
CAGGAAAACAAATACATTAACGAATCA
57.381
29.630
0.00
0.00
0.00
2.57
4394
5123
7.102993
TCATCAAATTGTCGAGGTAAGATTCA
58.897
34.615
0.00
0.00
0.00
2.57
4490
5219
2.380084
TGTTTGTCTCCACGATAGGC
57.620
50.000
0.00
0.00
43.77
3.93
4491
5220
5.631026
CATTTTGTTTGTCTCCACGATAGG
58.369
41.667
0.00
0.00
43.77
2.57
4492
5221
5.088739
GCATTTTGTTTGTCTCCACGATAG
58.911
41.667
0.00
0.00
46.19
2.08
4504
5246
8.600625
CAATAGATCCTTCATGCATTTTGTTTG
58.399
33.333
0.00
0.00
0.00
2.93
4635
5502
6.930731
ACACACCACAAGTAAAGAAAATTGT
58.069
32.000
0.00
0.00
36.34
2.71
4659
5526
9.462174
CTGCAAATTGTACAAAAGAGTTAATGA
57.538
29.630
13.23
0.00
0.00
2.57
4679
5546
4.285517
TGCCAAATCTTTAATCCCTGCAAA
59.714
37.500
0.00
0.00
0.00
3.68
4931
5816
5.605488
ACCTGAAACCAAAGTCCTAGAAGTA
59.395
40.000
0.00
0.00
0.00
2.24
4954
5839
4.402583
GCACCAGCAAAACAAAGAAAAAC
58.597
39.130
0.00
0.00
41.58
2.43
5104
5989
2.604046
AGCGCAGGGAGTATAACAAG
57.396
50.000
11.47
0.00
0.00
3.16
5132
6017
9.961265
TGACTGAAGACAAACCTATATTATACG
57.039
33.333
0.00
0.00
0.00
3.06
5178
6063
5.333645
GCATCAAAGACTGTACAGTGAAGTG
60.334
44.000
32.51
21.94
42.66
3.16
5179
6064
4.752101
GCATCAAAGACTGTACAGTGAAGT
59.248
41.667
32.51
8.97
42.66
3.01
5181
6066
4.702831
TGCATCAAAGACTGTACAGTGAA
58.297
39.130
32.51
8.59
42.66
3.18
5182
6067
4.335400
TGCATCAAAGACTGTACAGTGA
57.665
40.909
32.51
22.38
42.66
3.41
5183
6068
4.692155
TCATGCATCAAAGACTGTACAGTG
59.308
41.667
32.51
17.92
42.66
3.66
5184
6069
4.692625
GTCATGCATCAAAGACTGTACAGT
59.307
41.667
28.27
28.27
45.84
3.55
5212
6130
9.251792
TGTTCAATTCATGCATTTTGATATAGC
57.748
29.630
14.10
0.00
0.00
2.97
5217
6135
7.915293
ACATGTTCAATTCATGCATTTTGAT
57.085
28.000
14.10
1.79
44.26
2.57
5343
6687
5.592688
CCTGTAGTTTCCTTGGTCAAAAAGA
59.407
40.000
0.00
0.00
0.00
2.52
5344
6688
5.221244
CCCTGTAGTTTCCTTGGTCAAAAAG
60.221
44.000
0.00
0.00
0.00
2.27
5355
6699
0.038310
GGCAAGCCCTGTAGTTTCCT
59.962
55.000
0.00
0.00
0.00
3.36
5435
6780
9.893305
GTGGAACTTTATTTATGTACATATGCC
57.107
33.333
16.16
8.20
0.00
4.40
5453
6798
5.461032
TGTTTGTTTCACTTGTGGAACTT
57.539
34.783
21.20
0.00
38.04
2.66
5455
6800
6.532365
TTTTGTTTGTTTCACTTGTGGAAC
57.468
33.333
15.82
15.82
37.35
3.62
5456
6801
7.736447
ATTTTTGTTTGTTTCACTTGTGGAA
57.264
28.000
0.64
0.00
0.00
3.53
5458
6803
8.472683
TCTATTTTTGTTTGTTTCACTTGTGG
57.527
30.769
0.64
0.00
0.00
4.17
5649
7001
3.769300
AGGCTTGTTTCAGGTCAAACTTT
59.231
39.130
0.00
0.00
37.20
2.66
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.