Multiple sequence alignment - TraesCS2A01G471900
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
TraesCS2A01G471900
chr2A
100.000
2339
0
0
1
2339
713914027
713916365
0.000000e+00
4320.0
1
TraesCS2A01G471900
chr2A
94.933
1046
48
5
320
1362
742308988
742307945
0.000000e+00
1633.0
2
TraesCS2A01G471900
chr7D
96.842
1045
31
2
320
1363
232925266
232926309
0.000000e+00
1746.0
3
TraesCS2A01G471900
chr7D
96.743
1044
33
1
320
1362
497912164
497911121
0.000000e+00
1738.0
4
TraesCS2A01G471900
chr7D
96.648
1044
34
1
320
1362
149106659
149105616
0.000000e+00
1733.0
5
TraesCS2A01G471900
chr2D
96.555
1045
34
2
320
1362
273018230
273019274
0.000000e+00
1729.0
6
TraesCS2A01G471900
chr2D
90.705
312
28
1
1364
1675
575759485
575759795
4.650000e-112
414.0
7
TraesCS2A01G471900
chr2D
86.850
327
25
8
8
319
575759163
575759486
1.330000e-92
350.0
8
TraesCS2A01G471900
chr2D
90.574
244
20
3
2095
2336
575690327
575690569
1.040000e-83
320.0
9
TraesCS2A01G471900
chr2D
88.163
245
20
5
2095
2336
575760155
575760393
1.370000e-72
283.0
10
TraesCS2A01G471900
chr2D
84.472
161
17
4
169
323
575759795
575759953
4.030000e-33
152.0
11
TraesCS2A01G471900
chr2D
75.401
374
36
21
5
323
575689464
575689836
1.890000e-26
130.0
12
TraesCS2A01G471900
chr2D
88.235
68
2
2
262
323
575690060
575690127
2.490000e-10
76.8
13
TraesCS2A01G471900
chr3D
96.077
1045
39
2
320
1363
87390355
87391398
0.000000e+00
1701.0
14
TraesCS2A01G471900
chr5A
95.881
1044
41
2
320
1362
635794214
635793172
0.000000e+00
1688.0
15
TraesCS2A01G471900
chr6A
94.556
1047
50
5
318
1362
35542769
35543810
0.000000e+00
1611.0
16
TraesCS2A01G471900
chr6D
94.163
1045
59
2
320
1362
413277146
413278190
0.000000e+00
1591.0
17
TraesCS2A01G471900
chr2B
93.750
240
11
2
2097
2336
691776907
691777142
7.950000e-95
357.0
18
TraesCS2A01G471900
chr7A
97.059
34
1
0
1530
1563
127083459
127083492
9.030000e-05
58.4
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
TraesCS2A01G471900
chr2A
713914027
713916365
2338
False
4320.00
4320
100.0000
1
2339
1
chr2A.!!$F1
2338
1
TraesCS2A01G471900
chr2A
742307945
742308988
1043
True
1633.00
1633
94.9330
320
1362
1
chr2A.!!$R1
1042
2
TraesCS2A01G471900
chr7D
232925266
232926309
1043
False
1746.00
1746
96.8420
320
1363
1
chr7D.!!$F1
1043
3
TraesCS2A01G471900
chr7D
497911121
497912164
1043
True
1738.00
1738
96.7430
320
1362
1
chr7D.!!$R2
1042
4
TraesCS2A01G471900
chr7D
149105616
149106659
1043
True
1733.00
1733
96.6480
320
1362
1
chr7D.!!$R1
1042
5
TraesCS2A01G471900
chr2D
273018230
273019274
1044
False
1729.00
1729
96.5550
320
1362
1
chr2D.!!$F1
1042
6
TraesCS2A01G471900
chr2D
575759163
575760393
1230
False
299.75
414
87.5475
8
2336
4
chr2D.!!$F3
2328
7
TraesCS2A01G471900
chr3D
87390355
87391398
1043
False
1701.00
1701
96.0770
320
1363
1
chr3D.!!$F1
1043
8
TraesCS2A01G471900
chr5A
635793172
635794214
1042
True
1688.00
1688
95.8810
320
1362
1
chr5A.!!$R1
1042
9
TraesCS2A01G471900
chr6A
35542769
35543810
1041
False
1611.00
1611
94.5560
318
1362
1
chr6A.!!$F1
1044
10
TraesCS2A01G471900
chr6D
413277146
413278190
1044
False
1591.00
1591
94.1630
320
1362
1
chr6D.!!$F1
1042
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
940
961
1.204146
GGGGGCAGTATTGAGAGACA
58.796
55.0
0.0
0.0
0.0
3.41
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1749
1772
0.03779
AGCCGAAGAAGCACTCAGAC
60.038
55.0
0.0
0.0
0.0
3.51
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
22
1.370437
CATGCTGATCTCCCTCGGG
59.630
63.158
0.00
0.00
0.00
5.14
22
24
3.157252
GCTGATCTCCCTCGGGCA
61.157
66.667
0.00
0.00
34.68
5.36
23
25
3.136750
CTGATCTCCCTCGGGCAG
58.863
66.667
0.00
0.00
34.68
4.85
34
36
2.249413
CTCGGGCAGCTCTGGTGAAT
62.249
60.000
0.66
0.00
32.22
2.57
40
42
2.559440
GCAGCTCTGGTGAATCTAAGG
58.441
52.381
0.66
0.00
32.22
2.69
53
55
5.411669
GTGAATCTAAGGGTCGTTGTTTGAT
59.588
40.000
0.00
0.00
0.00
2.57
55
57
6.148811
TGAATCTAAGGGTCGTTGTTTGATTC
59.851
38.462
0.00
0.00
40.15
2.52
57
59
2.951229
AGGGTCGTTGTTTGATTCCT
57.049
45.000
0.00
0.00
0.00
3.36
58
60
4.360951
AAGGGTCGTTGTTTGATTCCTA
57.639
40.909
0.00
0.00
0.00
2.94
59
61
3.671716
AGGGTCGTTGTTTGATTCCTAC
58.328
45.455
0.00
0.00
0.00
3.18
60
62
2.414138
GGGTCGTTGTTTGATTCCTACG
59.586
50.000
0.00
0.00
0.00
3.51
62
64
3.930848
GGTCGTTGTTTGATTCCTACGAT
59.069
43.478
0.00
0.00
39.73
3.73
63
65
5.104374
GGTCGTTGTTTGATTCCTACGATA
58.896
41.667
0.00
0.00
39.73
2.92
64
66
5.577945
GGTCGTTGTTTGATTCCTACGATAA
59.422
40.000
0.00
0.00
39.73
1.75
81
83
9.916397
CCTACGATAAACTGCTATTTACTTTTG
57.084
33.333
0.00
0.00
0.00
2.44
90
92
7.488322
ACTGCTATTTACTTTTGCTTTTGTCA
58.512
30.769
0.00
0.00
0.00
3.58
94
96
6.833342
ATTTACTTTTGCTTTTGTCAGCTG
57.167
33.333
7.63
7.63
40.79
4.24
95
97
2.543641
ACTTTTGCTTTTGTCAGCTGC
58.456
42.857
9.47
4.92
40.79
5.25
138
140
7.036220
GCTTGAGCTCAACTACTCTTGTATTA
58.964
38.462
25.16
0.00
38.21
0.98
142
144
5.958987
AGCTCAACTACTCTTGTATTAGGGT
59.041
40.000
0.00
0.00
32.47
4.34
187
190
6.477033
CCGTAAGCCATCTATATGCATCTTAC
59.523
42.308
0.19
11.05
36.63
2.34
193
196
8.105197
AGCCATCTATATGCATCTTACATGAAA
58.895
33.333
0.19
0.00
0.00
2.69
195
198
8.671921
CCATCTATATGCATCTTACATGAAACC
58.328
37.037
0.19
0.00
0.00
3.27
207
210
6.759827
TCTTACATGAAACCGTAGCTAATTCC
59.240
38.462
0.00
0.00
0.00
3.01
263
271
7.857569
TGCATATTTAATAGCACGGTAAGTTC
58.142
34.615
5.46
0.00
31.05
3.01
284
292
8.747538
AGTTCAGTTAAACTCCAAACTTGTAT
57.252
30.769
0.00
0.00
34.37
2.29
289
303
7.012894
CAGTTAAACTCCAAACTTGTATGGACA
59.987
37.037
0.00
0.00
40.74
4.02
310
324
1.680735
GAGTGTTGAATGGTGGCACAA
59.319
47.619
20.82
9.03
44.16
3.33
322
336
4.148079
TGGTGGCACAATACTTCATTTCA
58.852
39.130
20.82
0.00
44.16
2.69
384
398
8.200792
GTGTCAGATATGGAAGTTATCTTGTCT
58.799
37.037
0.00
0.00
34.85
3.41
398
412
5.948992
ATCTTGTCTGGCTAAAGTCAAAC
57.051
39.130
0.00
0.00
0.00
2.93
497
512
2.532250
TGTCCTACATGCTCTCAGGA
57.468
50.000
0.00
0.00
34.79
3.86
653
669
5.878406
TTACTCCTTCCAGATCAAGATCC
57.122
43.478
6.45
0.00
38.58
3.36
700
716
5.950758
TCGAGAAATGGTAGCTATCTCTC
57.049
43.478
15.78
13.16
35.50
3.20
886
906
5.101628
GCTTTGTGAAACTCAATGTTGACA
58.898
37.500
0.00
0.00
39.13
3.58
925
946
2.041301
TGGAGGGTACGATGGGGG
60.041
66.667
0.00
0.00
0.00
5.40
940
961
1.204146
GGGGGCAGTATTGAGAGACA
58.796
55.000
0.00
0.00
0.00
3.41
965
986
5.222048
ACAAAGGTAGGTTTATTGCAGGAGA
60.222
40.000
0.00
0.00
0.00
3.71
1009
1030
1.215647
GACGTTCTCATGGCGGAGT
59.784
57.895
5.98
0.00
36.30
3.85
1050
1071
2.288666
CTAGATTTAGCGCAAAGGGCA
58.711
47.619
11.47
0.00
44.06
5.36
1203
1224
9.988350
ATCATGACTAAATTCGAACATTGTAAC
57.012
29.630
0.00
0.00
0.00
2.50
1283
1305
2.644676
GGATTGGTTTGAGGAGCCTAC
58.355
52.381
0.00
0.00
0.00
3.18
1393
1416
9.343539
CTCCTTATAAAGTTCTTTATGGAAGGG
57.656
37.037
26.31
19.65
35.41
3.95
1418
1441
4.520492
TCCTCTGCAATTCTTTGAACTTCC
59.480
41.667
0.00
0.00
34.60
3.46
1424
1447
4.676924
GCAATTCTTTGAACTTCCACTTCG
59.323
41.667
0.00
0.00
34.60
3.79
1431
1454
4.139420
CTTCCACTTCGCGCGCTG
62.139
66.667
30.48
22.06
0.00
5.18
1501
1524
5.481105
TGCTAGGCAAATCAAGGAAATTTG
58.519
37.500
0.00
4.61
43.69
2.32
1502
1525
5.011943
TGCTAGGCAAATCAAGGAAATTTGT
59.988
36.000
0.00
0.00
43.09
2.83
1516
1539
4.039124
GGAAATTTGTCTTCAAGCCCAAGA
59.961
41.667
0.00
0.00
34.88
3.02
1522
1545
3.632145
TGTCTTCAAGCCCAAGAAAGAAC
59.368
43.478
0.00
0.00
31.60
3.01
1524
1547
1.604604
TCAAGCCCAAGAAAGAACGG
58.395
50.000
0.00
0.00
0.00
4.44
1525
1548
0.598065
CAAGCCCAAGAAAGAACGGG
59.402
55.000
0.00
0.00
42.03
5.28
1565
1588
7.946207
AGAAAAGGAAGGAAAGAGAATTTCAC
58.054
34.615
0.00
0.00
0.00
3.18
1588
1611
3.875727
CCAGAAGACATGCTTACATCAGG
59.124
47.826
0.00
0.00
36.83
3.86
1613
1636
4.201812
CGCAACCCTACAAACATGAGTATG
60.202
45.833
0.00
0.00
40.24
2.39
1623
1646
1.340017
ACATGAGTATGCACCACCACC
60.340
52.381
0.00
0.00
37.85
4.61
1626
1649
0.324943
GAGTATGCACCACCACCTGT
59.675
55.000
0.00
0.00
0.00
4.00
1629
1652
2.081462
GTATGCACCACCACCTGTAAC
58.919
52.381
0.00
0.00
0.00
2.50
1643
1666
6.102663
CCACCTGTAACTTCACTCTAGATTG
58.897
44.000
3.74
3.74
0.00
2.67
1650
1673
8.570488
TGTAACTTCACTCTAGATTGTACGAAA
58.430
33.333
9.66
0.00
0.00
3.46
1652
1675
7.216973
ACTTCACTCTAGATTGTACGAAACT
57.783
36.000
9.66
0.00
0.00
2.66
1653
1676
7.085116
ACTTCACTCTAGATTGTACGAAACTG
58.915
38.462
9.66
0.00
0.00
3.16
1675
1698
2.280524
TGTCCTTGAACGCGTGGG
60.281
61.111
14.98
13.38
0.00
4.61
1678
1701
3.283684
CCTTGAACGCGTGGGCAA
61.284
61.111
14.98
16.75
39.92
4.52
1680
1703
2.824489
TTGAACGCGTGGGCAACA
60.824
55.556
14.98
3.93
39.92
3.33
1681
1704
2.128853
CTTGAACGCGTGGGCAACAT
62.129
55.000
14.98
0.00
39.92
2.71
1682
1705
2.126888
GAACGCGTGGGCAACATG
60.127
61.111
14.98
0.00
39.92
3.21
1683
1706
3.609214
GAACGCGTGGGCAACATGG
62.609
63.158
14.98
0.00
39.92
3.66
1686
1709
3.762247
GCGTGGGCAACATGGCAT
61.762
61.111
6.25
0.00
45.76
4.40
1687
1710
2.972267
CGTGGGCAACATGGCATT
59.028
55.556
0.00
0.00
45.76
3.56
1690
1713
0.391528
GTGGGCAACATGGCATTTCC
60.392
55.000
0.00
0.00
45.76
3.13
1693
1716
2.041701
GGGCAACATGGCATTTCCTAT
58.958
47.619
0.00
0.00
45.76
2.57
1694
1717
2.036346
GGGCAACATGGCATTTCCTATC
59.964
50.000
0.00
0.00
45.76
2.08
1696
1719
4.144297
GGCAACATGGCATTTCCTATCTA
58.856
43.478
0.00
0.00
43.14
1.98
1697
1720
4.217118
GGCAACATGGCATTTCCTATCTAG
59.783
45.833
0.00
0.00
43.14
2.43
1698
1721
4.823989
GCAACATGGCATTTCCTATCTAGT
59.176
41.667
0.00
0.00
35.26
2.57
1700
1723
6.486657
GCAACATGGCATTTCCTATCTAGTAA
59.513
38.462
0.00
0.00
35.26
2.24
1702
1725
6.223852
ACATGGCATTTCCTATCTAGTAACG
58.776
40.000
0.00
0.00
35.26
3.18
1703
1726
4.628074
TGGCATTTCCTATCTAGTAACGC
58.372
43.478
0.00
0.00
35.26
4.84
1705
1728
4.448060
GGCATTTCCTATCTAGTAACGCAC
59.552
45.833
0.00
0.00
0.00
5.34
1706
1729
5.047847
GCATTTCCTATCTAGTAACGCACA
58.952
41.667
0.00
0.00
0.00
4.57
1708
1731
6.346919
GCATTTCCTATCTAGTAACGCACATG
60.347
42.308
0.00
0.00
0.00
3.21
1710
1733
5.690997
TCCTATCTAGTAACGCACATGAG
57.309
43.478
0.00
0.00
0.00
2.90
1723
1746
3.818961
CACATGAGTGCTAACTGTTGG
57.181
47.619
0.00
0.69
39.21
3.77
1726
1749
0.472044
TGAGTGCTAACTGTTGGGCA
59.528
50.000
15.38
15.38
36.52
5.36
1742
1765
1.228657
GGCAGTCCCAGTTCGACAAC
61.229
60.000
0.00
0.00
32.41
3.32
1743
1766
0.249911
GCAGTCCCAGTTCGACAACT
60.250
55.000
0.00
0.00
44.26
3.16
1745
1768
1.341531
CAGTCCCAGTTCGACAACTCT
59.658
52.381
0.00
0.00
41.24
3.24
1746
1769
1.341531
AGTCCCAGTTCGACAACTCTG
59.658
52.381
0.00
0.00
41.24
3.35
1747
1770
1.068741
GTCCCAGTTCGACAACTCTGT
59.931
52.381
0.00
0.00
41.24
3.41
1749
1772
1.867233
CCCAGTTCGACAACTCTGTTG
59.133
52.381
8.66
8.66
41.24
3.33
1750
1773
2.550978
CCAGTTCGACAACTCTGTTGT
58.449
47.619
14.80
14.80
41.24
3.32
1751
1774
2.540101
CCAGTTCGACAACTCTGTTGTC
59.460
50.000
25.02
25.02
41.24
3.18
1752
1775
3.448686
CAGTTCGACAACTCTGTTGTCT
58.551
45.455
28.91
15.51
44.79
3.41
1753
1776
3.243877
CAGTTCGACAACTCTGTTGTCTG
59.756
47.826
28.91
23.71
44.79
3.51
1757
1780
2.791560
CGACAACTCTGTTGTCTGAGTG
59.208
50.000
28.91
16.41
46.80
3.51
1758
1781
2.541762
GACAACTCTGTTGTCTGAGTGC
59.458
50.000
26.60
7.92
46.80
4.40
1760
1783
3.201290
CAACTCTGTTGTCTGAGTGCTT
58.799
45.455
8.13
0.00
46.80
3.91
1761
1784
3.104843
ACTCTGTTGTCTGAGTGCTTC
57.895
47.619
6.90
0.00
46.12
3.86
1762
1785
2.697751
ACTCTGTTGTCTGAGTGCTTCT
59.302
45.455
6.90
0.00
46.12
2.85
1763
1786
3.133721
ACTCTGTTGTCTGAGTGCTTCTT
59.866
43.478
6.90
0.00
46.12
2.52
1764
1787
3.722147
TCTGTTGTCTGAGTGCTTCTTC
58.278
45.455
0.00
0.00
0.00
2.87
1765
1788
2.473816
TGTTGTCTGAGTGCTTCTTCG
58.526
47.619
0.00
0.00
0.00
3.79
1766
1789
1.795286
GTTGTCTGAGTGCTTCTTCGG
59.205
52.381
0.00
0.00
0.00
4.30
1768
1791
0.037790
GTCTGAGTGCTTCTTCGGCT
60.038
55.000
0.00
0.00
0.00
5.52
1769
1792
0.681733
TCTGAGTGCTTCTTCGGCTT
59.318
50.000
0.00
0.00
0.00
4.35
1770
1793
1.070758
TCTGAGTGCTTCTTCGGCTTT
59.929
47.619
0.00
0.00
0.00
3.51
1771
1794
1.196354
CTGAGTGCTTCTTCGGCTTTG
59.804
52.381
0.00
0.00
0.00
2.77
1773
1796
1.462670
GAGTGCTTCTTCGGCTTTGAG
59.537
52.381
0.00
0.00
0.00
3.02
1774
1797
0.110010
GTGCTTCTTCGGCTTTGAGC
60.110
55.000
0.00
0.00
41.46
4.26
1775
1798
0.250467
TGCTTCTTCGGCTTTGAGCT
60.250
50.000
0.00
0.00
41.99
4.09
1776
1799
1.001974
TGCTTCTTCGGCTTTGAGCTA
59.998
47.619
0.00
0.00
41.99
3.32
1777
1800
2.284190
GCTTCTTCGGCTTTGAGCTAT
58.716
47.619
0.00
0.00
41.99
2.97
1778
1801
2.680339
GCTTCTTCGGCTTTGAGCTATT
59.320
45.455
0.00
0.00
41.99
1.73
1779
1802
3.127721
GCTTCTTCGGCTTTGAGCTATTT
59.872
43.478
0.00
0.00
41.99
1.40
1780
1803
4.379918
GCTTCTTCGGCTTTGAGCTATTTT
60.380
41.667
0.00
0.00
41.99
1.82
1781
1804
5.703876
CTTCTTCGGCTTTGAGCTATTTTT
58.296
37.500
0.00
0.00
41.99
1.94
1782
1805
6.622896
GCTTCTTCGGCTTTGAGCTATTTTTA
60.623
38.462
0.00
0.00
41.99
1.52
1785
1808
7.826690
TCTTCGGCTTTGAGCTATTTTTATTT
58.173
30.769
0.00
0.00
41.99
1.40
1786
1809
7.968405
TCTTCGGCTTTGAGCTATTTTTATTTC
59.032
33.333
0.00
0.00
41.99
2.17
1787
1810
7.391148
TCGGCTTTGAGCTATTTTTATTTCT
57.609
32.000
0.00
0.00
41.99
2.52
1790
1921
8.925700
CGGCTTTGAGCTATTTTTATTTCTTTT
58.074
29.630
0.00
0.00
41.99
2.27
1931
2082
9.567776
TGACAAACATTTTTAGATACCTTCTGA
57.432
29.630
0.00
0.00
35.79
3.27
2029
2180
8.568732
AAATACATGTTTTCGTGAAAATTCGT
57.431
26.923
2.30
9.99
41.64
3.85
2030
2181
9.666626
AAATACATGTTTTCGTGAAAATTCGTA
57.333
25.926
2.30
11.47
41.64
3.43
2031
2182
9.666626
AATACATGTTTTCGTGAAAATTCGTAA
57.333
25.926
2.30
0.00
41.64
3.18
2032
2183
9.834628
ATACATGTTTTCGTGAAAATTCGTAAT
57.165
25.926
2.30
0.34
41.64
1.89
2033
2184
8.568732
ACATGTTTTCGTGAAAATTCGTAATT
57.431
26.923
10.64
0.00
41.64
1.40
2034
2185
9.026074
ACATGTTTTCGTGAAAATTCGTAATTT
57.974
25.926
10.64
0.00
41.64
1.82
2127
2278
2.330924
ATCTAAGCTCCTTGGGCCGC
62.331
60.000
0.00
0.00
0.00
6.53
2149
2300
2.436115
GTGACCGGCCCAGTTAGC
60.436
66.667
0.00
0.00
0.00
3.09
2177
2328
2.358737
CTCCCAGGCCACACGTTC
60.359
66.667
5.01
0.00
0.00
3.95
2178
2329
2.847234
TCCCAGGCCACACGTTCT
60.847
61.111
5.01
0.00
0.00
3.01
2179
2330
1.534476
TCCCAGGCCACACGTTCTA
60.534
57.895
5.01
0.00
0.00
2.10
2180
2331
1.079127
CCCAGGCCACACGTTCTAG
60.079
63.158
5.01
0.00
0.00
2.43
2181
2332
1.079127
CCAGGCCACACGTTCTAGG
60.079
63.158
5.01
0.00
0.00
3.02
2222
2373
2.601562
GTGGGCGACGATTCCATAC
58.398
57.895
0.00
0.00
32.71
2.39
2228
2379
0.462375
CGACGATTCCATACCCACCA
59.538
55.000
0.00
0.00
0.00
4.17
2243
2394
1.384525
CACCAACGGTTTTCCACTCA
58.615
50.000
0.00
0.00
40.70
3.41
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
1.370437
CGAGGGAGATCAGCATGGG
59.630
63.158
0.00
0.00
36.16
4.00
1
2
1.370437
CCGAGGGAGATCAGCATGG
59.630
63.158
0.00
0.00
36.16
3.66
2
3
1.370437
CCCGAGGGAGATCAGCATG
59.630
63.158
0.84
0.00
37.50
4.06
3
4
2.515071
GCCCGAGGGAGATCAGCAT
61.515
63.158
13.28
0.00
37.50
3.79
4
5
3.157252
GCCCGAGGGAGATCAGCA
61.157
66.667
13.28
0.00
37.50
4.41
5
6
3.157252
TGCCCGAGGGAGATCAGC
61.157
66.667
13.28
0.00
37.50
4.26
6
7
3.136750
CTGCCCGAGGGAGATCAG
58.863
66.667
13.28
5.76
44.17
2.90
20
22
2.559440
CCTTAGATTCACCAGAGCTGC
58.441
52.381
0.00
0.00
0.00
5.25
22
24
2.769095
GACCCTTAGATTCACCAGAGCT
59.231
50.000
0.00
0.00
0.00
4.09
23
25
2.482142
CGACCCTTAGATTCACCAGAGC
60.482
54.545
0.00
0.00
0.00
4.09
29
31
4.753107
TCAAACAACGACCCTTAGATTCAC
59.247
41.667
0.00
0.00
0.00
3.18
34
36
4.041198
AGGAATCAAACAACGACCCTTAGA
59.959
41.667
0.00
0.00
0.00
2.10
40
42
3.319755
TCGTAGGAATCAAACAACGACC
58.680
45.455
0.00
0.00
34.74
4.79
53
55
9.880157
AAAGTAAATAGCAGTTTATCGTAGGAA
57.120
29.630
0.00
0.00
0.00
3.36
55
57
9.916397
CAAAAGTAAATAGCAGTTTATCGTAGG
57.084
33.333
0.00
0.00
0.00
3.18
57
59
9.158233
AGCAAAAGTAAATAGCAGTTTATCGTA
57.842
29.630
0.00
0.00
0.00
3.43
58
60
8.040716
AGCAAAAGTAAATAGCAGTTTATCGT
57.959
30.769
0.00
0.00
0.00
3.73
59
61
8.895932
AAGCAAAAGTAAATAGCAGTTTATCG
57.104
30.769
0.00
0.00
0.00
2.92
62
64
9.810545
ACAAAAGCAAAAGTAAATAGCAGTTTA
57.189
25.926
0.00
0.00
0.00
2.01
63
65
8.716646
ACAAAAGCAAAAGTAAATAGCAGTTT
57.283
26.923
0.00
0.00
0.00
2.66
64
66
7.978975
TGACAAAAGCAAAAGTAAATAGCAGTT
59.021
29.630
0.00
0.00
0.00
3.16
81
83
1.605710
TCTCTTGCAGCTGACAAAAGC
59.394
47.619
20.43
0.00
43.88
3.51
90
92
2.753452
CCAATTCATGTCTCTTGCAGCT
59.247
45.455
0.00
0.00
0.00
4.24
94
96
3.015327
AGCTCCAATTCATGTCTCTTGC
58.985
45.455
0.00
0.00
0.00
4.01
95
97
4.698780
TCAAGCTCCAATTCATGTCTCTTG
59.301
41.667
0.00
0.00
32.46
3.02
142
144
2.299867
GGAACACGACAACTAGGGGTAA
59.700
50.000
0.00
0.00
0.00
2.85
155
157
8.925039
GCATATAGATGGCTTACGGAACACGA
62.925
46.154
0.00
0.00
38.64
4.35
187
190
3.564225
GGGGAATTAGCTACGGTTTCATG
59.436
47.826
0.00
0.00
0.00
3.07
193
196
1.343681
TGGAGGGGAATTAGCTACGGT
60.344
52.381
0.00
0.00
0.00
4.83
195
198
3.118371
ACTTTGGAGGGGAATTAGCTACG
60.118
47.826
0.00
0.00
0.00
3.51
254
262
6.259387
AGTTTGGAGTTTAACTGAACTTACCG
59.741
38.462
0.93
0.00
39.84
4.02
255
263
7.563888
AGTTTGGAGTTTAACTGAACTTACC
57.436
36.000
0.93
0.00
39.84
2.85
263
271
7.012894
TGTCCATACAAGTTTGGAGTTTAACTG
59.987
37.037
11.84
0.00
40.50
3.16
284
292
2.487086
CCACCATTCAACACTCTGTCCA
60.487
50.000
0.00
0.00
0.00
4.02
289
303
1.133823
TGTGCCACCATTCAACACTCT
60.134
47.619
0.00
0.00
32.49
3.24
310
324
4.644685
CCCATCCCGTTTGAAATGAAGTAT
59.355
41.667
0.00
0.00
0.00
2.12
322
336
2.987125
CTCCGTCCCATCCCGTTT
59.013
61.111
0.00
0.00
0.00
3.60
497
512
4.806247
GCAAGTGCTTCGTATCTTCTACAT
59.194
41.667
0.00
0.00
38.21
2.29
653
669
1.018148
TTTGTACCCCATAATGCGCG
58.982
50.000
0.00
0.00
0.00
6.86
700
716
4.412199
TCTTTCCCACCATAGATACCAAGG
59.588
45.833
0.00
0.00
0.00
3.61
842
862
1.408822
CCCTAGGAGGACATTGCCAAC
60.409
57.143
11.48
0.00
37.67
3.77
886
906
2.887152
GCAAGTCATGGTCAAAAGAGGT
59.113
45.455
0.00
0.00
0.00
3.85
925
946
4.757149
ACCTTTGTTGTCTCTCAATACTGC
59.243
41.667
0.00
0.00
38.38
4.40
940
961
5.390387
TCCTGCAATAAACCTACCTTTGTT
58.610
37.500
0.00
0.00
0.00
2.83
965
986
6.155221
TGCACAGTAGTCTATCTTTCCATTCT
59.845
38.462
0.00
0.00
0.00
2.40
1009
1030
3.010584
AGGCCAAATTTGAGAGCTAAGGA
59.989
43.478
19.86
0.00
0.00
3.36
1050
1071
5.745312
TGATGATTAGGCGATTACATCCT
57.255
39.130
0.00
0.00
34.97
3.24
1203
1224
4.937620
TGTGCTACTTTATTTGCCTCTCTG
59.062
41.667
0.00
0.00
0.00
3.35
1387
1410
2.174424
AGAATTGCAGAGGATCCCTTCC
59.826
50.000
8.55
0.00
45.85
3.46
1393
1416
5.893897
AGTTCAAAGAATTGCAGAGGATC
57.106
39.130
0.00
0.00
36.45
3.36
1400
1423
5.591099
GAAGTGGAAGTTCAAAGAATTGCA
58.409
37.500
5.01
0.00
45.59
4.08
1401
1424
4.676924
CGAAGTGGAAGTTCAAAGAATTGC
59.323
41.667
5.01
0.00
46.63
3.56
1405
1428
2.286833
CGCGAAGTGGAAGTTCAAAGAA
59.713
45.455
0.00
0.00
46.63
2.52
1431
1454
0.871722
TGTAGTTCACATGCGTTGCC
59.128
50.000
0.00
0.00
30.04
4.52
1501
1524
3.304057
CGTTCTTTCTTGGGCTTGAAGAC
60.304
47.826
0.00
0.00
0.00
3.01
1502
1525
2.878406
CGTTCTTTCTTGGGCTTGAAGA
59.122
45.455
0.00
0.00
0.00
2.87
1516
1539
4.546829
TTAGCATAGTGTCCCGTTCTTT
57.453
40.909
0.00
0.00
0.00
2.52
1522
1545
6.202954
CCTTTTCTTATTAGCATAGTGTCCCG
59.797
42.308
0.00
0.00
0.00
5.14
1524
1547
8.732746
TTCCTTTTCTTATTAGCATAGTGTCC
57.267
34.615
0.00
0.00
0.00
4.02
1525
1548
8.831550
CCTTCCTTTTCTTATTAGCATAGTGTC
58.168
37.037
0.00
0.00
0.00
3.67
1565
1588
3.875727
CTGATGTAAGCATGTCTTCTGGG
59.124
47.826
5.78
0.00
36.25
4.45
1588
1611
0.109319
CATGTTTGTAGGGTTGCGGC
60.109
55.000
0.00
0.00
0.00
6.53
1613
1636
1.235724
GAAGTTACAGGTGGTGGTGC
58.764
55.000
0.00
0.00
0.00
5.01
1623
1646
7.749808
TCGTACAATCTAGAGTGAAGTTACAG
58.250
38.462
25.87
13.07
0.00
2.74
1626
1649
8.790718
AGTTTCGTACAATCTAGAGTGAAGTTA
58.209
33.333
25.87
5.72
0.00
2.24
1629
1652
7.085116
ACAGTTTCGTACAATCTAGAGTGAAG
58.915
38.462
25.87
15.40
0.00
3.02
1643
1666
3.366440
AGGACACAGACAGTTTCGTAC
57.634
47.619
0.00
0.00
0.00
3.67
1650
1673
1.806623
GCGTTCAAGGACACAGACAGT
60.807
52.381
0.00
0.00
0.00
3.55
1652
1675
0.874175
CGCGTTCAAGGACACAGACA
60.874
55.000
0.00
0.00
0.00
3.41
1653
1676
0.874607
ACGCGTTCAAGGACACAGAC
60.875
55.000
5.58
0.00
0.00
3.51
1675
1698
4.823989
ACTAGATAGGAAATGCCATGTTGC
59.176
41.667
0.00
0.00
40.02
4.17
1678
1701
6.223852
CGTTACTAGATAGGAAATGCCATGT
58.776
40.000
0.00
0.00
40.02
3.21
1680
1703
5.221641
TGCGTTACTAGATAGGAAATGCCAT
60.222
40.000
0.00
0.00
40.02
4.40
1681
1704
4.100344
TGCGTTACTAGATAGGAAATGCCA
59.900
41.667
0.00
5.19
40.02
4.92
1682
1705
4.448060
GTGCGTTACTAGATAGGAAATGCC
59.552
45.833
0.00
0.00
35.88
4.40
1683
1706
5.047847
TGTGCGTTACTAGATAGGAAATGC
58.952
41.667
0.00
11.53
36.59
3.56
1685
1708
7.050970
TCATGTGCGTTACTAGATAGGAAAT
57.949
36.000
0.00
0.00
0.00
2.17
1686
1709
6.096423
ACTCATGTGCGTTACTAGATAGGAAA
59.904
38.462
0.00
0.00
0.00
3.13
1687
1710
5.593095
ACTCATGTGCGTTACTAGATAGGAA
59.407
40.000
0.00
0.00
0.00
3.36
1703
1726
2.485426
CCCAACAGTTAGCACTCATGTG
59.515
50.000
0.00
0.00
46.37
3.21
1705
1728
1.470098
GCCCAACAGTTAGCACTCATG
59.530
52.381
3.16
0.00
0.00
3.07
1706
1729
1.073763
TGCCCAACAGTTAGCACTCAT
59.926
47.619
6.15
0.00
0.00
2.90
1708
1731
1.160137
CTGCCCAACAGTTAGCACTC
58.840
55.000
6.15
0.00
41.86
3.51
1723
1746
1.070786
TTGTCGAACTGGGACTGCC
59.929
57.895
0.00
0.00
35.45
4.85
1726
1749
1.341531
CAGAGTTGTCGAACTGGGACT
59.658
52.381
0.00
0.00
42.80
3.85
1727
1750
1.068741
ACAGAGTTGTCGAACTGGGAC
59.931
52.381
0.00
0.00
42.80
4.46
1729
1752
1.867233
CAACAGAGTTGTCGAACTGGG
59.133
52.381
0.00
0.00
42.80
4.45
1730
1753
2.540101
GACAACAGAGTTGTCGAACTGG
59.460
50.000
22.41
0.00
42.80
4.00
1731
1754
3.843426
GACAACAGAGTTGTCGAACTG
57.157
47.619
22.41
0.00
42.80
3.16
1737
1760
2.541762
GCACTCAGACAACAGAGTTGTC
59.458
50.000
26.94
26.94
46.71
3.18
1738
1761
2.169352
AGCACTCAGACAACAGAGTTGT
59.831
45.455
14.68
14.68
40.09
3.32
1739
1762
2.831333
AGCACTCAGACAACAGAGTTG
58.169
47.619
8.24
8.24
40.09
3.16
1742
1765
3.383620
AGAAGCACTCAGACAACAGAG
57.616
47.619
0.00
0.00
36.06
3.35
1743
1766
3.722147
GAAGAAGCACTCAGACAACAGA
58.278
45.455
0.00
0.00
0.00
3.41
1745
1768
2.473816
CGAAGAAGCACTCAGACAACA
58.526
47.619
0.00
0.00
0.00
3.33
1746
1769
1.795286
CCGAAGAAGCACTCAGACAAC
59.205
52.381
0.00
0.00
0.00
3.32
1747
1770
1.873903
GCCGAAGAAGCACTCAGACAA
60.874
52.381
0.00
0.00
0.00
3.18
1749
1772
0.037790
AGCCGAAGAAGCACTCAGAC
60.038
55.000
0.00
0.00
0.00
3.51
1750
1773
0.681733
AAGCCGAAGAAGCACTCAGA
59.318
50.000
0.00
0.00
0.00
3.27
1751
1774
1.196354
CAAAGCCGAAGAAGCACTCAG
59.804
52.381
0.00
0.00
0.00
3.35
1752
1775
1.202639
TCAAAGCCGAAGAAGCACTCA
60.203
47.619
0.00
0.00
0.00
3.41
1753
1776
1.462670
CTCAAAGCCGAAGAAGCACTC
59.537
52.381
0.00
0.00
0.00
3.51
1756
1779
0.250467
AGCTCAAAGCCGAAGAAGCA
60.250
50.000
0.00
0.00
43.77
3.91
1757
1780
1.726853
TAGCTCAAAGCCGAAGAAGC
58.273
50.000
0.00
0.00
43.77
3.86
1758
1781
4.954092
AAATAGCTCAAAGCCGAAGAAG
57.046
40.909
0.00
0.00
43.77
2.85
1760
1783
7.391148
AATAAAAATAGCTCAAAGCCGAAGA
57.609
32.000
0.00
0.00
43.77
2.87
1761
1784
7.970614
AGAAATAAAAATAGCTCAAAGCCGAAG
59.029
33.333
0.00
0.00
43.77
3.79
1762
1785
7.826690
AGAAATAAAAATAGCTCAAAGCCGAA
58.173
30.769
0.00
0.00
43.77
4.30
1763
1786
7.391148
AGAAATAAAAATAGCTCAAAGCCGA
57.609
32.000
0.00
0.00
43.77
5.54
1764
1787
8.466086
AAAGAAATAAAAATAGCTCAAAGCCG
57.534
30.769
0.00
0.00
43.77
5.52
1905
2056
9.567776
TCAGAAGGTATCTAAAAATGTTTGTCA
57.432
29.630
0.00
0.00
36.32
3.58
2003
2154
9.666626
ACGAATTTTCACGAAAACATGTATTTA
57.333
25.926
7.09
0.00
42.32
1.40
2004
2155
8.568732
ACGAATTTTCACGAAAACATGTATTT
57.431
26.923
7.09
2.16
42.32
1.40
2005
2156
9.666626
TTACGAATTTTCACGAAAACATGTATT
57.333
25.926
7.09
0.00
42.32
1.89
2006
2157
9.834628
ATTACGAATTTTCACGAAAACATGTAT
57.165
25.926
7.09
0.00
42.32
2.29
2007
2158
9.666626
AATTACGAATTTTCACGAAAACATGTA
57.333
25.926
7.09
7.40
42.32
2.29
2008
2159
8.568732
AATTACGAATTTTCACGAAAACATGT
57.431
26.923
7.09
0.00
42.32
3.21
2009
2160
9.842444
AAAATTACGAATTTTCACGAAAACATG
57.158
25.926
7.09
0.00
45.32
3.21
2104
2255
3.099905
GGCCCAAGGAGCTTAGATTTTT
58.900
45.455
0.00
0.00
0.00
1.94
2105
2256
2.739943
GGCCCAAGGAGCTTAGATTTT
58.260
47.619
0.00
0.00
0.00
1.82
2106
2257
1.408822
CGGCCCAAGGAGCTTAGATTT
60.409
52.381
0.00
0.00
0.00
2.17
2107
2258
0.181350
CGGCCCAAGGAGCTTAGATT
59.819
55.000
0.00
0.00
0.00
2.40
2108
2259
1.832912
CGGCCCAAGGAGCTTAGAT
59.167
57.895
0.00
0.00
0.00
1.98
2110
2261
2.514824
GCGGCCCAAGGAGCTTAG
60.515
66.667
0.00
0.00
0.00
2.18
2130
2281
1.079127
CTAACTGGGCCGGTCACAG
60.079
63.158
20.44
21.80
38.19
3.66
2135
2286
2.928396
AGTGCTAACTGGGCCGGT
60.928
61.111
13.59
13.59
34.48
5.28
2165
2316
2.955881
GCCCTAGAACGTGTGGCCT
61.956
63.158
3.32
0.00
36.07
5.19
2181
2332
3.697439
TAACGCTCATGGGCCAGCC
62.697
63.158
13.12
0.00
31.37
4.85
2222
2373
0.753848
AGTGGAAAACCGTTGGTGGG
60.754
55.000
0.00
0.00
35.34
4.61
2228
2379
0.256464
TGGGTGAGTGGAAAACCGTT
59.744
50.000
0.00
0.00
34.62
4.44
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.