Locus 108

Sequence ID Eco_1
Location 4,178,949 – 4,179,268
Length 319
Max. P 0.992563
window381 window382 window383 window384 window385 window386 window387

overview

Window 1

Location 4,178,949 – 4,179,069
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -56.70
Consensus MFE -54.70
Energy contribution -56.70
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -5.76
Structure conservation index 0.96
SVM decision value 0.85
SVM RNA-class probability 0.865581
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4178949 120 + 1
GCCAACCCUUCCGGUUGCAGCCUGAGAAAUCAGGCUGAUGGCUGGUGACUUUUUAGUCACCAGCCUUUUUGCGCUGUAAGGCGCCAGUAGCGUUUCACACUGUUUGACUACUGCUGUGCC
(((((((.....)))))((((((((....))))))))..(((((((((((....))))))))))).....)).......(((((((((((((...(.....)..)).))))))..))))) ( -56.70)
>Sfl_1 1 120 + 1
GCCAACCCUUCCGGUUGCAGCCUGAGAAAUCAGGCUGAUGGCUGGUGACUUUUUAGUCACCAGCCUUUUUGCGCUGUAAGGCGCCAGUAGCGUUUCACACUGUUUGACUACUGCUGUGCC
(((((((.....)))))((((((((....))))))))..(((((((((((....))))))))))).....)).......(((((((((((((...(.....)..)).))))))..))))) ( -56.70)
>Sty_1 1 120 + 1
GCCAACCCUUCCGGUUGCAGCCUGAGAAAUCAGGCUGAUGGCUGGUGACUUUUUAGUCACCAGCCUUUUUGCGCUGUAAGGCGCCAGUAGCGUUUCACACUGUUUGACUACUGCUGUGCC
(((((((.....)))))((((((((....))))))))..(((((((((((....))))))))))).....)).......(((((((((((((...(.....)..)).))))))..))))) ( -56.70)
>consensus
GCCAACCCUUCCGGUUGCAGCCUGAGAAAUCAGGCUGAUGGCUGGUGACUUUUUAGUCACCAGCCUUUUUGCGCUGUAAGGCGCCAGUAGCGUUUCACACUGUUUGACUACUGCUGUGCC
(((((((.....)))))((((((((....))))))))..(((((((((((....))))))))))).....)).......(((((((((((((...(.....)..)).))))))..))))) (-54.70 = -56.70 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,178,949 – 4,179,069
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -55.20
Consensus MFE -55.20
Energy contribution -55.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -5.73
Structure conservation index 1.00
SVM decision value 1.05
SVM RNA-class probability 0.906145
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4178949 120 - 1
GGCACAGCAGUAGUCAAACAGUGUGAAACGCUACUGGCGCCUUACAGCGCAAAAAGGCUGGUGACUAAAAAGUCACCAGCCAUCAGCCUGAUUUCUCAGGCUGCAACCGGAAGGGUUGGC
(((.(((.(((..(((.......)))...))).)))..)))...((((((.....(((((((((((....)))))))))))...(((((((....)))))))))..((....)))))).. ( -55.20)
>Sfl_1 1 120 - 1
GGCACAGCAGUAGUCAAACAGUGUGAAACGCUACUGGCGCCUUACAGCGCAAAAAGGCUGGUGACUAAAAAGUCACCAGCCAUCAGCCUGAUUUCUCAGGCUGCAACCGGAAGGGUUGGC
(((.(((.(((..(((.......)))...))).)))..)))...((((((.....(((((((((((....)))))))))))...(((((((....)))))))))..((....)))))).. ( -55.20)
>Sty_1 1 120 - 1
GGCACAGCAGUAGUCAAACAGUGUGAAACGCUACUGGCGCCUUACAGCGCAAAAAGGCUGGUGACUAAAAAGUCACCAGCCAUCAGCCUGAUUUCUCAGGCUGCAACCGGAAGGGUUGGC
(((.(((.(((..(((.......)))...))).)))..)))...((((((.....(((((((((((....)))))))))))...(((((((....)))))))))..((....)))))).. ( -55.20)
>consensus
GGCACAGCAGUAGUCAAACAGUGUGAAACGCUACUGGCGCCUUACAGCGCAAAAAGGCUGGUGACUAAAAAGUCACCAGCCAUCAGCCUGAUUUCUCAGGCUGCAACCGGAAGGGUUGGC
(((.(((.(((..(((.......)))...))).)))..)))...((((((.....(((((((((((....)))))))))))...(((((((....)))))))))..((....)))))).. (-55.20 = -55.20 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 4,178,989 – 4,179,109
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -40.60
Consensus MFE -40.60
Energy contribution -40.60
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.80
Structure conservation index 1.00
SVM decision value 2.18
SVM RNA-class probability 0.989713
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4178989 120 + 1
GCUGGUGACUUUUUAGUCACCAGCCUUUUUGCGCUGUAAGGCGCCAGUAGCGUUUCACACUGUUUGACUACUGCUGUGCCUUUCAAUGCUUGUUUCUAUCGACGACUUAAUAUACUGCGA
((((((((((....))))))))))....((((((((.(((((((((((((((...(.....)..)).))))))..))))))).))..))(((((......)))))...........)))) ( -40.60)
>Sfl_1 41 120 + 1
GCUGGUGACUUUUUAGUCACCAGCCUUUUUGCGCUGUAAGGCGCCAGUAGCGUUUCACACUGUUUGACUACUGCUGUGCCUUUCAAUGCUUGUUUCUAUCGACGACUUAAUAUACUGCGA
((((((((((....))))))))))....((((((((.(((((((((((((((...(.....)..)).))))))..))))))).))..))(((((......)))))...........)))) ( -40.60)
>Sty_1 41 120 + 1
GCUGGUGACUUUUUAGUCACCAGCCUUUUUGCGCUGUAAGGCGCCAGUAGCGUUUCACACUGUUUGACUACUGCUGUGCCUUUCAAUGCUUGUUUCUAUCGACGACUUAAUAUACUGCGA
((((((((((....))))))))))....((((((((.(((((((((((((((...(.....)..)).))))))..))))))).))..))(((((......)))))...........)))) ( -40.60)
>consensus
GCUGGUGACUUUUUAGUCACCAGCCUUUUUGCGCUGUAAGGCGCCAGUAGCGUUUCACACUGUUUGACUACUGCUGUGCCUUUCAAUGCUUGUUUCUAUCGACGACUUAAUAUACUGCGA
((((((((((....))))))))))....((((((((.(((((((((((((((...(.....)..)).))))))..))))))).))..))(((((......)))))...........)))) (-40.60 = -40.60 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,178,989 – 4,179,109
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -38.20
Consensus MFE -38.20
Energy contribution -38.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.51
Structure conservation index 1.00
SVM decision value 2.21
SVM RNA-class probability 0.990463
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4178989 120 - 1
UCGCAGUAUAUUAAGUCGUCGAUAGAAACAAGCAUUGAAAGGCACAGCAGUAGUCAAACAGUGUGAAACGCUACUGGCGCCUUACAGCGCAAAAAGGCUGGUGACUAAAAAGUCACCAGC
..((.((....((((.(((((.(((......((((((...(((((....)).)))...))))))......))).))))).))))..))))......((((((((((....)))))))))) ( -38.20)
>Sfl_1 41 120 - 1
UCGCAGUAUAUUAAGUCGUCGAUAGAAACAAGCAUUGAAAGGCACAGCAGUAGUCAAACAGUGUGAAACGCUACUGGCGCCUUACAGCGCAAAAAGGCUGGUGACUAAAAAGUCACCAGC
..((.((....((((.(((((.(((......((((((...(((((....)).)))...))))))......))).))))).))))..))))......((((((((((....)))))))))) ( -38.20)
>Sty_1 41 120 - 1
UCGCAGUAUAUUAAGUCGUCGAUAGAAACAAGCAUUGAAAGGCACAGCAGUAGUCAAACAGUGUGAAACGCUACUGGCGCCUUACAGCGCAAAAAGGCUGGUGACUAAAAAGUCACCAGC
..((.((....((((.(((((.(((......((((((...(((((....)).)))...))))))......))).))))).))))..))))......((((((((((....)))))))))) ( -38.20)
>consensus
UCGCAGUAUAUUAAGUCGUCGAUAGAAACAAGCAUUGAAAGGCACAGCAGUAGUCAAACAGUGUGAAACGCUACUGGCGCCUUACAGCGCAAAAAGGCUGGUGACUAAAAAGUCACCAGC
..((.((....((((.(((((.(((......((((((...(((((....)).)))...))))))......))).))))).))))..))))......((((((((((....)))))))))) (-38.20 = -38.20 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,179,069 – 4,179,189
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -39.53
Consensus MFE -38.83
Energy contribution -38.73
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -3.65
Structure conservation index 0.98
SVM decision value 2.34
SVM RNA-class probability 0.992563
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4179069 120 + 1
UUUCAAUGCUUGUUUCUAUCGACGACUUAAUAUACUGCGACAGGACGUCCGUUCUGUGUAAAUCGCAAUGAAAUGGUUUAAGCGUGAUAGCAACAGGCAUUGCGGAAAGUGUUCCAUUUU
...(((((((((((.(((((.(((.(((((.....(((((((((((....))))))......)))))..........))))))))))))).))))))))))).((((....))))..... ( -39.66)
>Sfl_1 121 120 + 1
UUUCAAUGCUUGUUUCUAUCGACGACUUAAUAUACUGCGACAGGACGUCCGUUCUGUGUAAAUCGCAAUGAAAUGGUUUAAGCGUGAUAGCAACAGGCAUUGCGGAAAGUGUUCCAUUUU
...(((((((((((.(((((.(((.(((((.....(((((((((((....))))))......)))))..........))))))))))))).))))))))))).((((....))))..... ( -39.66)
>Sty_1 121 119 + 1
UUUCAAUGCUUGUUUCUAUCGACGACUUAAUAUACUGCGACAGAGCGUACGUUCUGUGUAAAUCGCAAUGAAAUGGUUUAAGCGUGAUAGCAACAGGCAUUGCGGAAAGUAU-CCAUUUU
...(((((((((((.(((((.(((.(((((.....(((((((((((....))))))......)))))..........))))))))))))).))))))))))).(((.....)-))..... ( -39.26)
>consensus
UUUCAAUGCUUGUUUCUAUCGACGACUUAAUAUACUGCGACAGGACGUCCGUUCUGUGUAAAUCGCAAUGAAAUGGUUUAAGCGUGAUAGCAACAGGCAUUGCGGAAAGUGUUCCAUUUU
...(((((((((((.(((((.(((.(((((.....(((((((((((....))))))......)))))..........))))))))))))).))))))))))).((((....))))..... (-38.83 = -38.73 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,179,069 – 4,179,189
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -34.07
Consensus MFE -31.80
Energy contribution -32.47
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.49
Structure conservation index 0.93
SVM decision value 1.87
SVM RNA-class probability 0.980693
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4179069 120 - 1
AAAAUGGAACACUUUCCGCAAUGCCUGUUGCUAUCACGCUUAAACCAUUUCAUUGCGAUUUACACAGAACGGACGUCCUGUCGCAGUAUAUUAAGUCGUCGAUAGAAACAAGCAUUGAAA
.....((((....)))).((((((.((((.(((((((((((((........(((((((......(((.((....)).))))))))))...))))).))).))))).)))).))))))... ( -34.00)
>Sfl_1 121 120 - 1
AAAAUGGAACACUUUCCGCAAUGCCUGUUGCUAUCACGCUUAAACCAUUUCAUUGCGAUUUACACAGAACGGACGUCCUGUCGCAGUAUAUUAAGUCGUCGAUAGAAACAAGCAUUGAAA
.....((((....)))).((((((.((((.(((((((((((((........(((((((......(((.((....)).))))))))))...))))).))).))))).)))).))))))... ( -34.00)
>Sty_1 121 119 - 1
AAAAUGG-AUACUUUCCGCAAUGCCUGUUGCUAUCACGCUUAAACCAUUUCAUUGCGAUUUACACAGAACGUACGCUCUGUCGCAGUAUAUUAAGUCGUCGAUAGAAACAAGCAUUGAAA
.....((-(.....))).((((((.((((.(((((((((((((........(((((((......((((.(....).)))))))))))...))))).))).))))).)))).))))))... ( -34.20)
>consensus
AAAAUGGAACACUUUCCGCAAUGCCUGUUGCUAUCACGCUUAAACCAUUUCAUUGCGAUUUACACAGAACGGACGUCCUGUCGCAGUAUAUUAAGUCGUCGAUAGAAACAAGCAUUGAAA
.....((((....)))).((((((.((((.(((((((((((((........(((((((......(((.((....)).))))))))))...))))).))).))))).)))).))))))... (-31.80 = -32.47 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 4,179,148 – 4,179,268
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -37.53
Consensus MFE -36.27
Energy contribution -36.60
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.97
SVM decision value 0.02
SVM RNA-class probability 0.546187
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4179148 120 + 1
AAGCGUGAUAGCAACAGGCAUUGCGGAAAGUGUUCCAUUUUCCGGUCAACAAAAUAGUGUUGCACAAACUGUCCGCUCAAUGGACAGAUGGGUCGACUUGUCAGCGAGCUGAGGAACCCU
..((.((.......)).))....(((((((((...)))))))))(((((((......))))).))...(((((((.....)))))))..((((....((.((((....)))).)))))). ( -38.20)
>Sfl_1 200 120 + 1
AAGCGUGAUAGCAACAGGCAUUGCGGAAAGUGUUCCAUUUUCCGGUCAACAAAAUAGUGUUGCACAAACUGUCCGCUCAAUGGACAGAUGGGUCGACUUGUCAGCGAGCUGAGGAACCCU
..((.((.......)).))....(((((((((...)))))))))(((((((......))))).))...(((((((.....)))))))..((((....((.((((....)))).)))))). ( -38.20)
>Sty_1 200 118 + 1
AAGCGUGAUAGCAACAGGCAUUGCGGAAAGUAU-CCAUUUUCCGGUCAACAAAAUAGUGUUGCACAAACUGUCC-CCCGCAGGACAGAUGGGUCGACUUGUCAGCGAGCUGAGGAACCCU
..((.((.......)).))....((((((((..-..))))))))(((((((......))))).))...((((((-......))))))..((((....((.((((....)))).)))))). ( -36.20)
>consensus
AAGCGUGAUAGCAACAGGCAUUGCGGAAAGUGUUCCAUUUUCCGGUCAACAAAAUAGUGUUGCACAAACUGUCCGCUCAAUGGACAGAUGGGUCGACUUGUCAGCGAGCUGAGGAACCCU
..((.((.......)).))....((((((((.....))))))))(((((((......))))).))...(((((((.....)))))))..((((....((.((((....)))).)))))). (-36.27 = -36.60 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:07:37 2006