Multiple sequence alignment - TraesCS3B01G278900
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
TraesCS3B01G278900
chr3B
100.000
2687
0
0
1
2687
448772594
448775280
0.000000e+00
4963
1
TraesCS3B01G278900
chr3B
94.203
759
44
0
1929
2687
439336806
439336048
0.000000e+00
1158
2
TraesCS3B01G278900
chr3B
88.038
627
72
1
995
1618
449156866
449156240
0.000000e+00
739
3
TraesCS3B01G278900
chr3D
94.208
1174
36
9
645
1801
349860107
349861265
0.000000e+00
1762
4
TraesCS3B01G278900
chr3D
89.608
664
29
7
1
647
349855389
349856029
0.000000e+00
808
5
TraesCS3B01G278900
chr3D
88.379
654
76
0
1929
2582
433871353
433870700
0.000000e+00
787
6
TraesCS3B01G278900
chr3D
87.836
633
68
4
995
1618
350735956
350735324
0.000000e+00
734
7
TraesCS3B01G278900
chr3D
93.233
133
9
0
1797
1929
263400869
263401001
2.110000e-46
196
8
TraesCS3B01G278900
chr3A
91.524
1109
57
19
645
1728
468002944
468004040
0.000000e+00
1493
9
TraesCS3B01G278900
chr3A
88.296
675
26
15
1
647
468001917
468002566
0.000000e+00
760
10
TraesCS3B01G278900
chr3A
88.192
542
59
2
1080
1618
468317361
468316822
2.260000e-180
641
11
TraesCS3B01G278900
chr5A
94.730
759
38
2
1929
2687
328957971
328958727
0.000000e+00
1179
12
TraesCS3B01G278900
chr7D
94.350
761
42
1
1928
2687
206612153
206612913
0.000000e+00
1166
13
TraesCS3B01G278900
chr1A
94.211
760
44
0
1928
2687
179529701
179528942
0.000000e+00
1160
14
TraesCS3B01G278900
chr2B
91.974
760
61
0
1928
2687
313424536
313423777
0.000000e+00
1066
15
TraesCS3B01G278900
chr2B
90.436
596
57
0
2092
2687
215506290
215505695
0.000000e+00
785
16
TraesCS3B01G278900
chr2B
77.248
734
167
0
1944
2677
507823725
507822992
5.310000e-117
431
17
TraesCS3B01G278900
chr5D
93.883
703
43
0
1985
2687
271703515
271704217
0.000000e+00
1061
18
TraesCS3B01G278900
chr7B
77.381
756
171
0
1932
2687
234378284
234379039
1.470000e-122
449
19
TraesCS3B01G278900
chr6D
96.403
139
4
1
1791
1929
17368593
17368456
7.480000e-56
228
20
TraesCS3B01G278900
chr7A
93.233
133
7
2
1797
1929
267193798
267193668
7.590000e-46
195
21
TraesCS3B01G278900
chr5B
93.182
132
9
0
1795
1926
611822823
611822954
7.590000e-46
195
22
TraesCS3B01G278900
chr6A
92.481
133
10
0
1797
1929
13092840
13092972
9.820000e-45
191
23
TraesCS3B01G278900
chr6A
92.481
133
10
0
1797
1929
13150751
13150883
9.820000e-45
191
24
TraesCS3B01G278900
chr2A
91.971
137
8
2
1795
1929
121134114
121134249
3.530000e-44
189
25
TraesCS3B01G278900
chr2A
91.111
135
12
0
1795
1929
75644925
75644791
1.640000e-42
183
26
TraesCS3B01G278900
chr1D
90.511
137
13
0
1794
1930
409959405
409959541
5.910000e-42
182
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
TraesCS3B01G278900
chr3B
448772594
448775280
2686
False
4963.0
4963
100.000
1
2687
1
chr3B.!!$F1
2686
1
TraesCS3B01G278900
chr3B
439336048
439336806
758
True
1158.0
1158
94.203
1929
2687
1
chr3B.!!$R1
758
2
TraesCS3B01G278900
chr3B
449156240
449156866
626
True
739.0
739
88.038
995
1618
1
chr3B.!!$R2
623
3
TraesCS3B01G278900
chr3D
349860107
349861265
1158
False
1762.0
1762
94.208
645
1801
1
chr3D.!!$F3
1156
4
TraesCS3B01G278900
chr3D
349855389
349856029
640
False
808.0
808
89.608
1
647
1
chr3D.!!$F2
646
5
TraesCS3B01G278900
chr3D
433870700
433871353
653
True
787.0
787
88.379
1929
2582
1
chr3D.!!$R2
653
6
TraesCS3B01G278900
chr3D
350735324
350735956
632
True
734.0
734
87.836
995
1618
1
chr3D.!!$R1
623
7
TraesCS3B01G278900
chr3A
468001917
468004040
2123
False
1126.5
1493
89.910
1
1728
2
chr3A.!!$F1
1727
8
TraesCS3B01G278900
chr3A
468316822
468317361
539
True
641.0
641
88.192
1080
1618
1
chr3A.!!$R1
538
9
TraesCS3B01G278900
chr5A
328957971
328958727
756
False
1179.0
1179
94.730
1929
2687
1
chr5A.!!$F1
758
10
TraesCS3B01G278900
chr7D
206612153
206612913
760
False
1166.0
1166
94.350
1928
2687
1
chr7D.!!$F1
759
11
TraesCS3B01G278900
chr1A
179528942
179529701
759
True
1160.0
1160
94.211
1928
2687
1
chr1A.!!$R1
759
12
TraesCS3B01G278900
chr2B
313423777
313424536
759
True
1066.0
1066
91.974
1928
2687
1
chr2B.!!$R2
759
13
TraesCS3B01G278900
chr2B
215505695
215506290
595
True
785.0
785
90.436
2092
2687
1
chr2B.!!$R1
595
14
TraesCS3B01G278900
chr2B
507822992
507823725
733
True
431.0
431
77.248
1944
2677
1
chr2B.!!$R3
733
15
TraesCS3B01G278900
chr5D
271703515
271704217
702
False
1061.0
1061
93.883
1985
2687
1
chr5D.!!$F1
702
16
TraesCS3B01G278900
chr7B
234378284
234379039
755
False
449.0
449
77.381
1932
2687
1
chr7B.!!$F1
755
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
678
1089
0.46546
AGTGGTGTCGTTGCCATTGT
60.465
50.0
0.0
0.0
37.09
2.71
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1896
2355
0.179
ATCCACCAGCTCCACGAATC
59.821
55.0
0.0
0.0
0.0
2.52
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
81
84
1.335810
ACAAACTGTGTGCATGCTCAG
59.664
47.619
22.00
23.71
39.72
3.35
107
129
4.638865
GTGGTGTCTTAAACAGGTGTCTTT
59.361
41.667
0.00
0.00
38.97
2.52
108
130
5.124936
GTGGTGTCTTAAACAGGTGTCTTTT
59.875
40.000
0.00
0.00
38.97
2.27
110
132
6.885376
TGGTGTCTTAAACAGGTGTCTTTTTA
59.115
34.615
0.00
0.00
38.97
1.52
111
133
7.393796
TGGTGTCTTAAACAGGTGTCTTTTTAA
59.606
33.333
0.00
0.00
38.97
1.52
112
134
7.699391
GGTGTCTTAAACAGGTGTCTTTTTAAC
59.301
37.037
0.00
0.00
38.97
2.01
126
148
8.615585
GTGTCTTTTTAACGTTCATGTAAATCG
58.384
33.333
2.82
0.00
0.00
3.34
155
177
7.655328
CAGGATACCATTCTCAATAGTGACTTC
59.345
40.741
0.00
0.00
37.17
3.01
156
178
7.566879
AGGATACCATTCTCAATAGTGACTTCT
59.433
37.037
0.00
0.00
37.17
2.85
157
179
7.655328
GGATACCATTCTCAATAGTGACTTCTG
59.345
40.741
0.00
0.00
0.00
3.02
158
180
6.611613
ACCATTCTCAATAGTGACTTCTGA
57.388
37.500
0.00
0.00
0.00
3.27
159
181
7.009179
ACCATTCTCAATAGTGACTTCTGAA
57.991
36.000
0.00
0.00
0.00
3.02
160
182
6.876257
ACCATTCTCAATAGTGACTTCTGAAC
59.124
38.462
0.00
0.00
0.00
3.18
161
183
6.875726
CCATTCTCAATAGTGACTTCTGAACA
59.124
38.462
0.00
0.00
0.00
3.18
162
184
7.388776
CCATTCTCAATAGTGACTTCTGAACAA
59.611
37.037
0.00
0.00
0.00
2.83
163
185
8.944029
CATTCTCAATAGTGACTTCTGAACAAT
58.056
33.333
0.00
0.00
0.00
2.71
164
186
8.539770
TTCTCAATAGTGACTTCTGAACAATC
57.460
34.615
0.00
0.00
0.00
2.67
165
187
7.901029
TCTCAATAGTGACTTCTGAACAATCT
58.099
34.615
0.00
0.00
0.00
2.40
166
188
9.025041
TCTCAATAGTGACTTCTGAACAATCTA
57.975
33.333
0.00
0.00
0.00
1.98
167
189
9.299963
CTCAATAGTGACTTCTGAACAATCTAG
57.700
37.037
0.00
0.00
0.00
2.43
168
190
8.807118
TCAATAGTGACTTCTGAACAATCTAGT
58.193
33.333
0.00
0.00
0.00
2.57
169
191
8.867935
CAATAGTGACTTCTGAACAATCTAGTG
58.132
37.037
0.00
0.00
0.00
2.74
170
192
6.656632
AGTGACTTCTGAACAATCTAGTGA
57.343
37.500
0.00
0.00
0.00
3.41
171
193
6.451393
AGTGACTTCTGAACAATCTAGTGAC
58.549
40.000
0.00
0.00
0.00
3.67
172
194
6.266558
AGTGACTTCTGAACAATCTAGTGACT
59.733
38.462
0.00
0.00
29.44
3.41
173
195
6.926272
GTGACTTCTGAACAATCTAGTGACTT
59.074
38.462
0.00
0.00
0.00
3.01
174
196
7.115663
GTGACTTCTGAACAATCTAGTGACTTC
59.884
40.741
0.00
0.00
0.00
3.01
195
217
6.429385
ACTTCTCAAGTTCCTGAACAATCATC
59.571
38.462
12.21
0.00
43.47
2.92
215
237
1.474077
CTTGTGCTGTATTTGGGGAGC
59.526
52.381
0.00
0.00
0.00
4.70
254
276
3.713858
TTGTGATGCTGAAACACAAGG
57.286
42.857
7.33
0.00
45.35
3.61
255
277
1.955778
TGTGATGCTGAAACACAAGGG
59.044
47.619
0.00
0.00
40.72
3.95
275
297
1.260544
GGGGCATGGATTCTTATGGC
58.739
55.000
14.87
14.87
45.83
4.40
321
345
1.263217
GGTGGTCACGTGTGTCATTTC
59.737
52.381
16.51
1.62
0.00
2.17
431
462
4.377021
CCGGCAAAGCTTATATAGTCACA
58.623
43.478
0.00
0.00
0.00
3.58
466
497
3.578716
GGATCCCAATCGATTGACCTCTA
59.421
47.826
34.21
15.44
40.14
2.43
562
593
1.209261
TCTTGTAATGATGCTCGGCCA
59.791
47.619
2.24
0.00
0.00
5.36
580
611
1.303309
CAGGATGATGAAAGCCGTCC
58.697
55.000
0.00
0.00
39.69
4.79
655
1066
0.610174
GTCCAGTGCATGAGAGACCA
59.390
55.000
0.00
0.00
0.00
4.02
658
1069
1.485480
CCAGTGCATGAGAGACCAGAT
59.515
52.381
0.00
0.00
0.00
2.90
678
1089
0.465460
AGTGGTGTCGTTGCCATTGT
60.465
50.000
0.00
0.00
37.09
2.71
801
1247
2.159226
CCTCACACACGGATTAGAGTCC
60.159
54.545
0.00
0.00
34.82
3.85
848
1294
4.635765
TGGCACAAATAGCACAAGAGATAC
59.364
41.667
0.00
0.00
31.92
2.24
855
1302
8.292448
ACAAATAGCACAAGAGATACTGTTTTG
58.708
33.333
0.00
0.00
0.00
2.44
950
1397
4.332543
CAGCCTACATATTCGCAAAACAGA
59.667
41.667
0.00
0.00
0.00
3.41
1227
1683
1.346395
AGTACCGCCTTCAACATCACA
59.654
47.619
0.00
0.00
0.00
3.58
1514
1970
2.261361
CAGACCGACGTGGATGCA
59.739
61.111
10.46
0.00
42.00
3.96
1602
2058
1.149101
ATTGGGCCTCGGATATTGGT
58.851
50.000
4.53
0.00
0.00
3.67
1695
2151
7.167535
TCAATCAGTTTGGTTGATGATCACTA
58.832
34.615
0.00
0.00
42.07
2.74
1737
2193
8.984112
ATATGTAATATTGGGTGTAGTAGGGT
57.016
34.615
0.00
0.00
35.58
4.34
1738
2194
7.701257
ATGTAATATTGGGTGTAGTAGGGTT
57.299
36.000
0.00
0.00
0.00
4.11
1739
2195
6.891388
TGTAATATTGGGTGTAGTAGGGTTG
58.109
40.000
0.00
0.00
0.00
3.77
1740
2196
6.444493
TGTAATATTGGGTGTAGTAGGGTTGT
59.556
38.462
0.00
0.00
0.00
3.32
1741
2197
3.713826
ATTGGGTGTAGTAGGGTTGTG
57.286
47.619
0.00
0.00
0.00
3.33
1742
2198
2.106187
TGGGTGTAGTAGGGTTGTGT
57.894
50.000
0.00
0.00
0.00
3.72
1746
2202
2.036346
GGTGTAGTAGGGTTGTGTTCGT
59.964
50.000
0.00
0.00
0.00
3.85
1758
2214
2.004017
TGTGTTCGTCTGTTTGTGACC
58.996
47.619
0.00
0.00
0.00
4.02
1766
2222
3.668491
CGTCTGTTTGTGACCGTGTTTTT
60.668
43.478
0.00
0.00
0.00
1.94
1804
2263
4.617808
TGAGTACTCGATGACTTAGTGC
57.382
45.455
17.85
0.00
0.00
4.40
1805
2264
3.377485
TGAGTACTCGATGACTTAGTGCC
59.623
47.826
17.85
0.00
0.00
5.01
1806
2265
2.688958
AGTACTCGATGACTTAGTGCCC
59.311
50.000
0.00
0.00
0.00
5.36
1807
2266
0.456221
ACTCGATGACTTAGTGCCCG
59.544
55.000
0.00
0.00
0.00
6.13
1808
2267
0.456221
CTCGATGACTTAGTGCCCGT
59.544
55.000
0.00
0.00
0.00
5.28
1809
2268
0.892755
TCGATGACTTAGTGCCCGTT
59.107
50.000
0.00
0.00
0.00
4.44
1810
2269
1.135199
TCGATGACTTAGTGCCCGTTC
60.135
52.381
0.00
0.00
0.00
3.95
1811
2270
1.403647
CGATGACTTAGTGCCCGTTCA
60.404
52.381
0.00
0.00
0.00
3.18
1812
2271
2.271800
GATGACTTAGTGCCCGTTCAG
58.728
52.381
0.00
0.00
0.00
3.02
1813
2272
1.334160
TGACTTAGTGCCCGTTCAGA
58.666
50.000
0.00
0.00
0.00
3.27
1814
2273
1.272490
TGACTTAGTGCCCGTTCAGAG
59.728
52.381
0.00
0.00
0.00
3.35
1815
2274
0.608640
ACTTAGTGCCCGTTCAGAGG
59.391
55.000
0.00
0.00
0.00
3.69
1820
2279
4.475135
GCCCGTTCAGAGGCCCTC
62.475
72.222
1.26
1.26
43.76
4.30
1821
2280
3.787001
CCCGTTCAGAGGCCCTCC
61.787
72.222
7.26
0.00
0.00
4.30
1822
2281
4.148825
CCGTTCAGAGGCCCTCCG
62.149
72.222
7.26
3.48
37.47
4.63
1823
2282
4.821589
CGTTCAGAGGCCCTCCGC
62.822
72.222
7.26
0.00
37.47
5.54
1824
2283
3.394836
GTTCAGAGGCCCTCCGCT
61.395
66.667
7.26
0.00
43.70
5.52
1825
2284
3.077556
TTCAGAGGCCCTCCGCTC
61.078
66.667
7.26
0.00
40.76
5.03
1832
2291
4.021925
GCCCTCCGCTCCACAACT
62.022
66.667
0.00
0.00
0.00
3.16
1833
2292
2.266055
CCCTCCGCTCCACAACTC
59.734
66.667
0.00
0.00
0.00
3.01
1834
2293
2.286523
CCCTCCGCTCCACAACTCT
61.287
63.158
0.00
0.00
0.00
3.24
1835
2294
1.079543
CCTCCGCTCCACAACTCTG
60.080
63.158
0.00
0.00
0.00
3.35
1836
2295
1.739562
CTCCGCTCCACAACTCTGC
60.740
63.158
0.00
0.00
0.00
4.26
1837
2296
2.743928
CCGCTCCACAACTCTGCC
60.744
66.667
0.00
0.00
0.00
4.85
1838
2297
2.031012
CGCTCCACAACTCTGCCA
59.969
61.111
0.00
0.00
0.00
4.92
1839
2298
2.320587
CGCTCCACAACTCTGCCAC
61.321
63.158
0.00
0.00
0.00
5.01
1840
2299
2.320587
GCTCCACAACTCTGCCACG
61.321
63.158
0.00
0.00
0.00
4.94
1841
2300
1.669115
CTCCACAACTCTGCCACGG
60.669
63.158
0.00
0.00
0.00
4.94
1842
2301
2.099652
CTCCACAACTCTGCCACGGA
62.100
60.000
0.00
0.00
0.00
4.69
1843
2302
1.669115
CCACAACTCTGCCACGGAG
60.669
63.158
1.86
1.86
42.15
4.63
1844
2303
2.031163
ACAACTCTGCCACGGAGC
59.969
61.111
3.33
0.00
40.26
4.70
1845
2304
3.114616
CAACTCTGCCACGGAGCG
61.115
66.667
3.33
0.00
40.26
5.03
1846
2305
4.379243
AACTCTGCCACGGAGCGG
62.379
66.667
3.33
1.55
40.26
5.52
1866
2325
3.900446
GCAGGCTGCAGTTCAAATT
57.100
47.368
33.33
0.00
44.26
1.82
1867
2326
2.159327
GCAGGCTGCAGTTCAAATTT
57.841
45.000
33.33
0.00
44.26
1.82
1868
2327
2.486918
GCAGGCTGCAGTTCAAATTTT
58.513
42.857
33.33
0.00
44.26
1.82
1869
2328
2.477754
GCAGGCTGCAGTTCAAATTTTC
59.522
45.455
33.33
0.00
44.26
2.29
1870
2329
3.719924
CAGGCTGCAGTTCAAATTTTCA
58.280
40.909
16.64
0.00
0.00
2.69
1871
2330
3.739300
CAGGCTGCAGTTCAAATTTTCAG
59.261
43.478
16.64
0.00
0.00
3.02
1872
2331
3.638160
AGGCTGCAGTTCAAATTTTCAGA
59.362
39.130
16.64
0.00
0.00
3.27
1873
2332
3.985925
GGCTGCAGTTCAAATTTTCAGAG
59.014
43.478
16.64
0.00
0.00
3.35
1874
2333
4.500375
GGCTGCAGTTCAAATTTTCAGAGT
60.500
41.667
16.64
0.00
0.00
3.24
1875
2334
4.443394
GCTGCAGTTCAAATTTTCAGAGTG
59.557
41.667
16.64
0.00
0.00
3.51
1876
2335
4.935702
TGCAGTTCAAATTTTCAGAGTGG
58.064
39.130
0.00
0.00
0.00
4.00
1877
2336
4.402155
TGCAGTTCAAATTTTCAGAGTGGT
59.598
37.500
0.00
0.00
0.00
4.16
1878
2337
4.741676
GCAGTTCAAATTTTCAGAGTGGTG
59.258
41.667
0.00
0.00
0.00
4.17
1879
2338
5.284079
CAGTTCAAATTTTCAGAGTGGTGG
58.716
41.667
0.00
0.00
0.00
4.61
1880
2339
5.067674
CAGTTCAAATTTTCAGAGTGGTGGA
59.932
40.000
0.00
0.00
0.00
4.02
1881
2340
5.656416
AGTTCAAATTTTCAGAGTGGTGGAA
59.344
36.000
0.00
0.00
0.00
3.53
1882
2341
6.324770
AGTTCAAATTTTCAGAGTGGTGGAAT
59.675
34.615
0.00
0.00
0.00
3.01
1883
2342
7.505585
AGTTCAAATTTTCAGAGTGGTGGAATA
59.494
33.333
0.00
0.00
0.00
1.75
1884
2343
7.452880
TCAAATTTTCAGAGTGGTGGAATAG
57.547
36.000
0.00
0.00
0.00
1.73
1885
2344
6.434028
TCAAATTTTCAGAGTGGTGGAATAGG
59.566
38.462
0.00
0.00
0.00
2.57
1886
2345
4.993705
TTTTCAGAGTGGTGGAATAGGT
57.006
40.909
0.00
0.00
0.00
3.08
1887
2346
3.981071
TTCAGAGTGGTGGAATAGGTG
57.019
47.619
0.00
0.00
0.00
4.00
1888
2347
1.555075
TCAGAGTGGTGGAATAGGTGC
59.445
52.381
0.00
0.00
0.00
5.01
1889
2348
1.556911
CAGAGTGGTGGAATAGGTGCT
59.443
52.381
0.00
0.00
0.00
4.40
1890
2349
1.834263
AGAGTGGTGGAATAGGTGCTC
59.166
52.381
0.00
0.00
0.00
4.26
1891
2350
0.912486
AGTGGTGGAATAGGTGCTCC
59.088
55.000
0.00
0.00
0.00
4.70
1892
2351
0.462047
GTGGTGGAATAGGTGCTCCG
60.462
60.000
0.00
0.00
39.05
4.63
1893
2352
1.523938
GGTGGAATAGGTGCTCCGC
60.524
63.158
0.00
0.00
40.81
5.54
1894
2353
1.523938
GTGGAATAGGTGCTCCGCC
60.524
63.158
0.00
1.09
36.41
6.13
1895
2354
1.992834
TGGAATAGGTGCTCCGCCA
60.993
57.895
0.00
3.68
36.32
5.69
1896
2355
1.227674
GGAATAGGTGCTCCGCCAG
60.228
63.158
0.00
0.00
36.32
4.85
1897
2356
1.686325
GGAATAGGTGCTCCGCCAGA
61.686
60.000
0.00
0.00
36.32
3.86
1898
2357
0.394565
GAATAGGTGCTCCGCCAGAT
59.605
55.000
0.00
0.00
36.32
2.90
1899
2358
0.839946
AATAGGTGCTCCGCCAGATT
59.160
50.000
0.00
0.00
36.32
2.40
1900
2359
0.394565
ATAGGTGCTCCGCCAGATTC
59.605
55.000
0.00
0.00
36.32
2.52
1901
2360
2.016393
TAGGTGCTCCGCCAGATTCG
62.016
60.000
0.00
0.00
36.32
3.34
1902
2361
2.125512
GTGCTCCGCCAGATTCGT
60.126
61.111
0.00
0.00
0.00
3.85
1903
2362
2.125552
TGCTCCGCCAGATTCGTG
60.126
61.111
0.00
0.00
0.00
4.35
1904
2363
2.892425
GCTCCGCCAGATTCGTGG
60.892
66.667
0.00
0.00
41.01
4.94
1905
2364
2.892640
CTCCGCCAGATTCGTGGA
59.107
61.111
6.40
1.24
40.44
4.02
1906
2365
2.892640
TCCGCCAGATTCGTGGAG
59.107
61.111
6.40
3.60
40.44
3.86
1907
2366
2.892425
CCGCCAGATTCGTGGAGC
60.892
66.667
6.40
0.00
40.44
4.70
1908
2367
2.185350
CGCCAGATTCGTGGAGCT
59.815
61.111
0.00
0.00
40.44
4.09
1909
2368
2.169789
CGCCAGATTCGTGGAGCTG
61.170
63.158
0.00
0.00
40.44
4.24
1910
2369
4.528674
CCAGATTCGTGGAGCTGG
57.471
61.111
0.00
0.00
40.44
4.85
1911
2370
1.599047
CCAGATTCGTGGAGCTGGT
59.401
57.895
4.21
0.00
42.26
4.00
1912
2371
0.742281
CCAGATTCGTGGAGCTGGTG
60.742
60.000
4.21
0.00
42.26
4.17
1913
2372
0.742281
CAGATTCGTGGAGCTGGTGG
60.742
60.000
0.00
0.00
0.00
4.61
1914
2373
0.904865
AGATTCGTGGAGCTGGTGGA
60.905
55.000
0.00
0.00
0.00
4.02
1915
2374
0.179000
GATTCGTGGAGCTGGTGGAT
59.821
55.000
0.00
0.00
0.00
3.41
1916
2375
0.620556
ATTCGTGGAGCTGGTGGATT
59.379
50.000
0.00
0.00
0.00
3.01
1917
2376
1.271856
TTCGTGGAGCTGGTGGATTA
58.728
50.000
0.00
0.00
0.00
1.75
1918
2377
0.535335
TCGTGGAGCTGGTGGATTAC
59.465
55.000
0.00
0.00
0.00
1.89
1938
2397
2.158475
ACCAAACAGGCCTCAAAGATGA
60.158
45.455
0.00
0.00
43.14
2.92
1952
2411
4.828939
TCAAAGATGAAGATGCCAACACTT
59.171
37.500
0.00
0.00
30.99
3.16
2098
2557
3.971702
GCCAAGAGGGGTGTGCCT
61.972
66.667
0.00
0.00
37.04
4.75
2118
2577
4.814234
GCCTCGTACCATTGACATCAATTA
59.186
41.667
4.32
0.00
43.48
1.40
2330
2790
0.819259
GAGCTTGCACACCTCCAACA
60.819
55.000
0.00
0.00
0.00
3.33
2388
2848
1.580059
AAGAAAGATGGGGCGGAGTA
58.420
50.000
0.00
0.00
0.00
2.59
2394
2854
0.759346
GATGGGGCGGAGTACATCTT
59.241
55.000
0.00
0.00
37.37
2.40
2425
2885
4.503123
CGTCCCATTAGTCTTATCCATGCA
60.503
45.833
0.00
0.00
0.00
3.96
2532
2993
5.627182
ATCAAGAAGAGGAGCATACATGT
57.373
39.130
2.69
2.69
0.00
3.21
2628
3089
6.100004
TCGATATCAAGAAAGCTTTCGACTT
58.900
36.000
28.67
17.56
41.92
3.01
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
12
13
7.618019
AATGGTATCAGAATAGCAAGGAGTA
57.382
36.000
1.89
0.00
46.01
2.59
68
71
1.209383
CACAGCTGAGCATGCACAC
59.791
57.895
23.35
13.96
0.00
3.82
81
84
2.290641
CACCTGTTTAAGACACCACAGC
59.709
50.000
0.00
0.00
36.16
4.40
107
129
4.454847
TGCCCGATTTACATGAACGTTAAA
59.545
37.500
0.00
0.00
0.00
1.52
108
130
4.001652
TGCCCGATTTACATGAACGTTAA
58.998
39.130
0.00
0.00
0.00
2.01
110
132
2.418628
CTGCCCGATTTACATGAACGTT
59.581
45.455
0.00
0.00
0.00
3.99
111
133
2.006888
CTGCCCGATTTACATGAACGT
58.993
47.619
0.00
0.00
0.00
3.99
112
134
1.330521
CCTGCCCGATTTACATGAACG
59.669
52.381
0.00
0.00
0.00
3.95
126
148
3.515602
ATTGAGAATGGTATCCTGCCC
57.484
47.619
0.00
0.00
0.00
5.36
155
177
7.151308
ACTTGAGAAGTCACTAGATTGTTCAG
58.849
38.462
0.00
0.00
37.02
3.02
156
178
7.055667
ACTTGAGAAGTCACTAGATTGTTCA
57.944
36.000
0.00
0.00
37.02
3.18
157
179
7.117092
GGAACTTGAGAAGTCACTAGATTGTTC
59.883
40.741
0.00
0.00
41.91
3.18
158
180
6.931840
GGAACTTGAGAAGTCACTAGATTGTT
59.068
38.462
0.00
0.00
41.91
2.83
159
181
6.268847
AGGAACTTGAGAAGTCACTAGATTGT
59.731
38.462
0.00
0.00
41.91
2.71
160
182
6.589523
CAGGAACTTGAGAAGTCACTAGATTG
59.410
42.308
0.00
0.00
41.91
2.67
161
183
6.495181
TCAGGAACTTGAGAAGTCACTAGATT
59.505
38.462
0.00
0.00
41.91
2.40
162
184
6.013379
TCAGGAACTTGAGAAGTCACTAGAT
58.987
40.000
0.00
0.00
41.91
1.98
163
185
5.386060
TCAGGAACTTGAGAAGTCACTAGA
58.614
41.667
0.00
0.00
41.91
2.43
164
186
5.713792
TCAGGAACTTGAGAAGTCACTAG
57.286
43.478
0.00
0.00
41.91
2.57
165
187
5.362717
TGTTCAGGAACTTGAGAAGTCACTA
59.637
40.000
12.86
0.00
41.91
2.74
166
188
4.162320
TGTTCAGGAACTTGAGAAGTCACT
59.838
41.667
12.86
0.00
41.91
3.41
167
189
4.442706
TGTTCAGGAACTTGAGAAGTCAC
58.557
43.478
12.86
0.00
41.91
3.67
168
190
4.753516
TGTTCAGGAACTTGAGAAGTCA
57.246
40.909
12.86
0.00
41.91
3.41
169
191
5.760253
TGATTGTTCAGGAACTTGAGAAGTC
59.240
40.000
12.86
0.08
41.91
3.01
170
192
5.684704
TGATTGTTCAGGAACTTGAGAAGT
58.315
37.500
12.86
0.00
45.46
3.01
171
193
6.654161
AGATGATTGTTCAGGAACTTGAGAAG
59.346
38.462
12.86
0.00
41.67
2.85
172
194
6.537355
AGATGATTGTTCAGGAACTTGAGAA
58.463
36.000
12.86
0.00
41.67
2.87
173
195
6.119240
AGATGATTGTTCAGGAACTTGAGA
57.881
37.500
12.86
0.00
41.67
3.27
174
196
6.206243
ACAAGATGATTGTTCAGGAACTTGAG
59.794
38.462
12.86
0.00
41.67
3.02
195
217
1.474077
GCTCCCCAAATACAGCACAAG
59.526
52.381
0.00
0.00
0.00
3.16
215
237
6.033341
TCACAAATCTCAACAAAAGTTTCCG
58.967
36.000
0.00
0.00
0.00
4.30
255
277
1.928868
CCATAAGAATCCATGCCCCC
58.071
55.000
0.00
0.00
0.00
5.40
321
345
3.806316
AGCGGAACAAATAAACGAGTG
57.194
42.857
0.00
0.00
0.00
3.51
368
392
2.202770
ACACCGTCGCGTGTTTCA
60.203
55.556
5.77
0.00
44.57
2.69
466
497
4.058817
GAGATGTGAAGTTCGGTCTGTTT
58.941
43.478
8.62
0.00
0.00
2.83
562
593
0.911769
TGGACGGCTTTCATCATCCT
59.088
50.000
0.00
0.00
0.00
3.24
580
611
0.107508
AACATGGAGCTCCGGTGATG
60.108
55.000
32.73
27.94
39.43
3.07
655
1066
0.973632
TGGCAACGACACCACTATCT
59.026
50.000
0.00
0.00
42.51
1.98
658
1069
1.202710
ACAATGGCAACGACACCACTA
60.203
47.619
0.00
0.00
39.19
2.74
678
1089
4.728102
CTCCGCCGCCGTGTTGTA
62.728
66.667
0.00
0.00
0.00
2.41
696
1120
0.811616
GGACCATCATCGCCTGACAC
60.812
60.000
0.00
0.00
36.48
3.67
801
1247
3.722780
GGTTGTTACTCGATCGATACGTG
59.277
47.826
19.78
9.07
0.00
4.49
950
1397
4.142093
GGTGATGCATGACCTATTTTGCTT
60.142
41.667
26.10
0.00
36.10
3.91
1514
1970
2.029073
CCGTCGTCACCTTGCACT
59.971
61.111
0.00
0.00
0.00
4.40
1728
2184
3.005155
ACAGACGAACACAACCCTACTAC
59.995
47.826
0.00
0.00
0.00
2.73
1729
2185
3.225104
ACAGACGAACACAACCCTACTA
58.775
45.455
0.00
0.00
0.00
1.82
1730
2186
2.037144
ACAGACGAACACAACCCTACT
58.963
47.619
0.00
0.00
0.00
2.57
1731
2187
2.521105
ACAGACGAACACAACCCTAC
57.479
50.000
0.00
0.00
0.00
3.18
1732
2188
3.199677
CAAACAGACGAACACAACCCTA
58.800
45.455
0.00
0.00
0.00
3.53
1733
2189
2.014128
CAAACAGACGAACACAACCCT
58.986
47.619
0.00
0.00
0.00
4.34
1734
2190
1.741145
ACAAACAGACGAACACAACCC
59.259
47.619
0.00
0.00
0.00
4.11
1735
2191
2.417239
TCACAAACAGACGAACACAACC
59.583
45.455
0.00
0.00
0.00
3.77
1736
2192
3.413558
GTCACAAACAGACGAACACAAC
58.586
45.455
0.00
0.00
0.00
3.32
1737
2193
2.417239
GGTCACAAACAGACGAACACAA
59.583
45.455
0.00
0.00
36.87
3.33
1738
2194
2.004017
GGTCACAAACAGACGAACACA
58.996
47.619
0.00
0.00
36.87
3.72
1739
2195
1.005347
CGGTCACAAACAGACGAACAC
60.005
52.381
0.00
0.00
36.87
3.32
1740
2196
1.282817
CGGTCACAAACAGACGAACA
58.717
50.000
0.00
0.00
36.87
3.18
1741
2197
1.005347
CACGGTCACAAACAGACGAAC
60.005
52.381
0.00
0.00
36.87
3.95
1742
2198
1.282817
CACGGTCACAAACAGACGAA
58.717
50.000
0.00
0.00
36.87
3.85
1746
2202
3.754323
AGAAAAACACGGTCACAAACAGA
59.246
39.130
0.00
0.00
0.00
3.41
1803
2262
4.475135
GAGGGCCTCTGAACGGGC
62.475
72.222
26.44
0.00
46.89
6.13
1804
2263
3.787001
GGAGGGCCTCTGAACGGG
61.787
72.222
31.39
0.00
0.00
5.28
1805
2264
4.148825
CGGAGGGCCTCTGAACGG
62.149
72.222
34.54
9.38
39.05
4.44
1806
2265
4.821589
GCGGAGGGCCTCTGAACG
62.822
72.222
40.18
30.14
39.05
3.95
1807
2266
3.378399
GAGCGGAGGGCCTCTGAAC
62.378
68.421
40.18
28.32
45.17
3.18
1808
2267
3.077556
GAGCGGAGGGCCTCTGAA
61.078
66.667
40.18
0.00
45.17
3.02
1815
2274
3.959991
GAGTTGTGGAGCGGAGGGC
62.960
68.421
0.00
0.00
44.05
5.19
1816
2275
2.266055
GAGTTGTGGAGCGGAGGG
59.734
66.667
0.00
0.00
0.00
4.30
1817
2276
1.079543
CAGAGTTGTGGAGCGGAGG
60.080
63.158
0.00
0.00
0.00
4.30
1818
2277
1.739562
GCAGAGTTGTGGAGCGGAG
60.740
63.158
0.00
0.00
0.00
4.63
1819
2278
2.343758
GCAGAGTTGTGGAGCGGA
59.656
61.111
0.00
0.00
0.00
5.54
1820
2279
2.743928
GGCAGAGTTGTGGAGCGG
60.744
66.667
0.00
0.00
0.00
5.52
1821
2280
2.031012
TGGCAGAGTTGTGGAGCG
59.969
61.111
0.00
0.00
0.00
5.03
1822
2281
2.320587
CGTGGCAGAGTTGTGGAGC
61.321
63.158
0.00
0.00
0.00
4.70
1823
2282
1.669115
CCGTGGCAGAGTTGTGGAG
60.669
63.158
0.00
0.00
0.00
3.86
1824
2283
2.099652
CTCCGTGGCAGAGTTGTGGA
62.100
60.000
0.00
0.00
0.00
4.02
1825
2284
1.669115
CTCCGTGGCAGAGTTGTGG
60.669
63.158
0.00
0.00
0.00
4.17
1826
2285
2.320587
GCTCCGTGGCAGAGTTGTG
61.321
63.158
5.74
0.00
33.69
3.33
1827
2286
2.031163
GCTCCGTGGCAGAGTTGT
59.969
61.111
5.74
0.00
33.69
3.32
1828
2287
3.114616
CGCTCCGTGGCAGAGTTG
61.115
66.667
5.74
0.00
33.69
3.16
1829
2288
4.379243
CCGCTCCGTGGCAGAGTT
62.379
66.667
5.74
0.00
33.69
3.01
1831
2290
4.504916
CTCCGCTCCGTGGCAGAG
62.505
72.222
0.00
0.00
32.51
3.35
1844
2303
3.123620
GAACTGCAGCCTGCTCCG
61.124
66.667
18.96
8.81
45.31
4.63
1845
2304
1.174712
TTTGAACTGCAGCCTGCTCC
61.175
55.000
18.96
4.89
45.31
4.70
1846
2305
0.886563
ATTTGAACTGCAGCCTGCTC
59.113
50.000
18.96
7.87
45.31
4.26
1847
2306
1.335145
AATTTGAACTGCAGCCTGCT
58.665
45.000
18.96
0.00
45.31
4.24
1848
2307
2.159327
AAATTTGAACTGCAGCCTGC
57.841
45.000
15.27
10.45
45.29
4.85
1849
2308
3.719924
TGAAAATTTGAACTGCAGCCTG
58.280
40.909
15.27
0.00
0.00
4.85
1850
2309
3.638160
TCTGAAAATTTGAACTGCAGCCT
59.362
39.130
15.27
0.00
0.00
4.58
1851
2310
3.981211
TCTGAAAATTTGAACTGCAGCC
58.019
40.909
15.27
6.70
0.00
4.85
1852
2311
4.443394
CACTCTGAAAATTTGAACTGCAGC
59.557
41.667
15.27
0.00
0.00
5.25
1853
2312
4.980434
CCACTCTGAAAATTTGAACTGCAG
59.020
41.667
13.48
13.48
0.00
4.41
1854
2313
4.402155
ACCACTCTGAAAATTTGAACTGCA
59.598
37.500
0.00
0.00
0.00
4.41
1855
2314
4.741676
CACCACTCTGAAAATTTGAACTGC
59.258
41.667
0.00
0.00
0.00
4.40
1856
2315
5.067674
TCCACCACTCTGAAAATTTGAACTG
59.932
40.000
0.00
0.00
0.00
3.16
1857
2316
5.200483
TCCACCACTCTGAAAATTTGAACT
58.800
37.500
0.00
0.00
0.00
3.01
1858
2317
5.514274
TCCACCACTCTGAAAATTTGAAC
57.486
39.130
0.00
0.00
0.00
3.18
1859
2318
6.729690
ATTCCACCACTCTGAAAATTTGAA
57.270
33.333
0.00
0.00
0.00
2.69
1860
2319
6.434028
CCTATTCCACCACTCTGAAAATTTGA
59.566
38.462
0.00
0.00
0.00
2.69
1861
2320
6.209391
ACCTATTCCACCACTCTGAAAATTTG
59.791
38.462
0.00
0.00
0.00
2.32
1862
2321
6.209391
CACCTATTCCACCACTCTGAAAATTT
59.791
38.462
0.00
0.00
0.00
1.82
1863
2322
5.711976
CACCTATTCCACCACTCTGAAAATT
59.288
40.000
0.00
0.00
0.00
1.82
1864
2323
5.256474
CACCTATTCCACCACTCTGAAAAT
58.744
41.667
0.00
0.00
0.00
1.82
1865
2324
4.651778
CACCTATTCCACCACTCTGAAAA
58.348
43.478
0.00
0.00
0.00
2.29
1866
2325
3.559171
GCACCTATTCCACCACTCTGAAA
60.559
47.826
0.00
0.00
0.00
2.69
1867
2326
2.027192
GCACCTATTCCACCACTCTGAA
60.027
50.000
0.00
0.00
0.00
3.02
1868
2327
1.555075
GCACCTATTCCACCACTCTGA
59.445
52.381
0.00
0.00
0.00
3.27
1869
2328
1.556911
AGCACCTATTCCACCACTCTG
59.443
52.381
0.00
0.00
0.00
3.35
1870
2329
1.834263
GAGCACCTATTCCACCACTCT
59.166
52.381
0.00
0.00
0.00
3.24
1871
2330
1.134371
GGAGCACCTATTCCACCACTC
60.134
57.143
0.00
0.00
33.55
3.51
1872
2331
0.912486
GGAGCACCTATTCCACCACT
59.088
55.000
0.00
0.00
33.55
4.00
1873
2332
0.462047
CGGAGCACCTATTCCACCAC
60.462
60.000
0.00
0.00
32.87
4.16
1874
2333
1.904771
CGGAGCACCTATTCCACCA
59.095
57.895
0.00
0.00
32.87
4.17
1875
2334
4.857251
CGGAGCACCTATTCCACC
57.143
61.111
0.00
0.00
32.87
4.61
1888
2347
1.227089
CTCCACGAATCTGGCGGAG
60.227
63.158
1.04
0.00
37.52
4.63
1889
2348
2.892640
CTCCACGAATCTGGCGGA
59.107
61.111
0.00
0.00
0.00
5.54
1890
2349
2.892425
GCTCCACGAATCTGGCGG
60.892
66.667
0.00
0.00
0.00
6.13
1891
2350
2.169789
CAGCTCCACGAATCTGGCG
61.170
63.158
0.00
0.00
0.00
5.69
1892
2351
1.817099
CCAGCTCCACGAATCTGGC
60.817
63.158
0.00
0.00
39.53
4.85
1893
2352
4.528674
CCAGCTCCACGAATCTGG
57.471
61.111
0.00
0.00
39.95
3.86
1894
2353
0.742281
CCACCAGCTCCACGAATCTG
60.742
60.000
0.00
0.00
0.00
2.90
1895
2354
0.904865
TCCACCAGCTCCACGAATCT
60.905
55.000
0.00
0.00
0.00
2.40
1896
2355
0.179000
ATCCACCAGCTCCACGAATC
59.821
55.000
0.00
0.00
0.00
2.52
1897
2356
0.620556
AATCCACCAGCTCCACGAAT
59.379
50.000
0.00
0.00
0.00
3.34
1898
2357
1.066430
GTAATCCACCAGCTCCACGAA
60.066
52.381
0.00
0.00
0.00
3.85
1899
2358
0.535335
GTAATCCACCAGCTCCACGA
59.465
55.000
0.00
0.00
0.00
4.35
1900
2359
3.065575
GTAATCCACCAGCTCCACG
57.934
57.895
0.00
0.00
0.00
4.94
1910
2369
2.092323
GAGGCCTGTTTGGTAATCCAC
58.908
52.381
12.00
0.00
44.22
4.02
1911
2370
1.707989
TGAGGCCTGTTTGGTAATCCA
59.292
47.619
12.00
0.00
42.66
3.41
1912
2371
2.507407
TGAGGCCTGTTTGGTAATCC
57.493
50.000
12.00
0.00
38.35
3.01
1913
2372
4.079253
TCTTTGAGGCCTGTTTGGTAATC
58.921
43.478
12.00
0.00
38.35
1.75
1914
2373
4.112634
TCTTTGAGGCCTGTTTGGTAAT
57.887
40.909
12.00
0.00
38.35
1.89
1915
2374
3.586470
TCTTTGAGGCCTGTTTGGTAA
57.414
42.857
12.00
0.00
38.35
2.85
1916
2375
3.073798
TCATCTTTGAGGCCTGTTTGGTA
59.926
43.478
12.00
0.00
38.35
3.25
1917
2376
2.158475
TCATCTTTGAGGCCTGTTTGGT
60.158
45.455
12.00
0.00
38.35
3.67
1918
2377
2.517959
TCATCTTTGAGGCCTGTTTGG
58.482
47.619
12.00
0.00
39.35
3.28
1919
2378
3.822735
TCTTCATCTTTGAGGCCTGTTTG
59.177
43.478
12.00
0.00
32.27
2.93
1920
2379
4.104383
TCTTCATCTTTGAGGCCTGTTT
57.896
40.909
12.00
0.00
32.27
2.83
1921
2380
3.795688
TCTTCATCTTTGAGGCCTGTT
57.204
42.857
12.00
0.00
32.27
3.16
1922
2381
3.618351
CATCTTCATCTTTGAGGCCTGT
58.382
45.455
12.00
0.00
32.27
4.00
1923
2382
2.358267
GCATCTTCATCTTTGAGGCCTG
59.642
50.000
12.00
0.00
32.27
4.85
1924
2383
2.652590
GCATCTTCATCTTTGAGGCCT
58.347
47.619
3.86
3.86
32.27
5.19
1925
2384
1.680207
GGCATCTTCATCTTTGAGGCC
59.320
52.381
0.00
0.00
32.97
5.19
1926
2385
2.372264
TGGCATCTTCATCTTTGAGGC
58.628
47.619
0.00
0.00
32.27
4.70
1938
2397
5.360714
TGAAAGAAGAAAGTGTTGGCATCTT
59.639
36.000
0.00
0.00
33.28
2.40
2081
2540
3.927481
GAGGCACACCCCTCTTGGC
62.927
68.421
1.07
0.00
46.39
4.52
2098
2557
6.228616
TCCTAATTGATGTCAATGGTACGA
57.771
37.500
8.86
0.00
45.06
3.43
2128
2587
2.244117
GATCGCAAGCAGGGACAGGA
62.244
60.000
0.00
0.00
42.47
3.86
2330
2790
1.760192
GCTGAGTTGAGCCAATGGAT
58.240
50.000
2.05
0.00
32.35
3.41
2388
2848
1.553248
TGGGACGGAAATCGAAGATGT
59.447
47.619
0.00
0.00
45.12
3.06
2394
2854
3.028850
AGACTAATGGGACGGAAATCGA
58.971
45.455
0.00
0.00
42.43
3.59
2425
2885
9.664332
ATCATCTTAGCTATAATCTTCGCAATT
57.336
29.630
0.00
0.00
0.00
2.32
2532
2993
7.067372
CCAAGCCTCTCACATACATGAAATTAA
59.933
37.037
0.00
0.00
0.00
1.40
2628
3089
4.527816
CCAAAAGGAAATCCCATCTCACAA
59.472
41.667
0.00
0.00
37.41
3.33
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.