Locus 9184

Sequence ID 3R_DroMel_CAF1
Location 24,495,138 – 24,495,442
Length 304
Max. P 0.973836
window14689 window14690 window14691 window14692 window14693

overview

Window 9

Location 24,495,138 – 24,495,258
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.11
Mean single sequence MFE -38.35
Consensus MFE -33.33
Energy contribution -33.20
Covariance contribution -0.13
Combinations/Pair 1.13
Mean z-score -2.39
Structure conservation index 0.87
SVM decision value 1.72
SVM RNA-class probability 0.973836
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24495138 120 + 27905053
GUUAACAAUCGCUACGAGCUCUUGCUCACGGAUUAAUUGCAACCAAAUCAGCAAAUAAGUUUGCUGUGCGAUGGUAAUGCGCAGGUGUUCACCUCCACCUGUCGGAAUAAUGGCCAGUUC
..........((((.((((....)))).((........(((((((...(((((((....))))))).....))))..)))(((((((........)))))))))......))))...... ( -34.40)
>DroSec_CAF1 38115 120 + 1
GUUAACAAUCGCUAUGAGCUCUUGCUCACGGAUCAAUUGCAACCAAAUCAGCAAAUAAGUUUGCUGUGCGAUGAAAAUGCGCAGGUGUUCACCUCCACCUGCGGGAAUAAUGGUCACUUC
..............(((((....)))))..(((((((((((.......(((((((....))))))))))))).....(.((((((((........)))))))).).....)))))..... ( -37.61)
>DroSim_CAF1 49971 120 + 1
GUUAACAAUCGCUAUGAGCUCUUGCUCACGGAUCACUUGCAACCAAGUCAGCAAAUAAGUUUGCUGUGCGAUGGUAAUGCGCAGGUGUUCACCUCCACCUGCGGUAGUAAUGGUCGAUUC
......((((....(((((....)))))..(((((.((((.((((.(((((((((....))))))).))..))))....((((((((........))))))))...))))))))))))). ( -44.00)
>DroEre_CAF1 44523 120 + 1
GUUCAAAAUCGCUACGAGCUCUUGCUUACGGAUCGAUUGCAACCAAAUCAGCAAAUAAGUUUGCUGUGCGAUGGUAAUGCGCAGGUGUUCACCUCCACCUGCCAGACUAGUGGCCAAUUC
..........(((((((((....))))..((.((....(((((((...(((((((....))))))).....))))..)))(((((((........)))))))..)))).)))))...... ( -37.40)
>consensus
GUUAACAAUCGCUACGAGCUCUUGCUCACGGAUCAAUUGCAACCAAAUCAGCAAAUAAGUUUGCUGUGCGAUGGUAAUGCGCAGGUGUUCACCUCCACCUGCCGGAAUAAUGGCCAAUUC
..........(((((((((....))))...........(((((((...(((((((....))))))).....))))..)))(((((((........))))))).......)))))...... (-33.33 = -33.20 +  -0.13)

alignment

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secondary structure

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Window 0

Location 24,495,138 – 24,495,258
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.11
Mean single sequence MFE -38.27
Consensus MFE -34.19
Energy contribution -34.75
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.96
Structure conservation index 0.89
SVM decision value 1.27
SVM RNA-class probability 0.938113
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24495138 120 - 27905053
GAACUGGCCAUUAUUCCGACAGGUGGAGGUGAACACCUGCGCAUUACCAUCGCACAGCAAACUUAUUUGCUGAUUUGGUUGCAAUUAAUCCGUGAGCAAGAGCUCGUAGCGAUUGUUAAC
.....(((((......((.((((((........)))))))).............(((((((....)))))))...)))))((((((...(..(((((....)))))..).)))))).... ( -33.40)
>DroSec_CAF1 38115 120 - 1
GAAGUGACCAUUAUUCCCGCAGGUGGAGGUGAACACCUGCGCAUUUUCAUCGCACAGCAAACUUAUUUGCUGAUUUGGUUGCAAUUGAUCCGUGAGCAAGAGCUCAUAGCGAUUGUUAAC
...(..((((.......((((((((........)))))))).............(((((((....)))))))...))))..)(((((....((((((....))))))..)))))...... ( -41.70)
>DroSim_CAF1 49971 120 - 1
GAAUCGACCAUUACUACCGCAGGUGGAGGUGAACACCUGCGCAUUACCAUCGCACAGCAAACUUAUUUGCUGACUUGGUUGCAAGUGAUCCGUGAGCAAGAGCUCAUAGCGAUUGUUAAC
.(((((...((((((...(((((((........)))))))(((..((((.....(((((((....)))))))...))))))).))))))..((((((....))))))..)))))...... ( -43.40)
>DroEre_CAF1 44523 120 - 1
GAAUUGGCCACUAGUCUGGCAGGUGGAGGUGAACACCUGCGCAUUACCAUCGCACAGCAAACUUAUUUGCUGAUUUGGUUGCAAUCGAUCCGUAAGCAAGAGCUCGUAGCGAUUUUGAAC
.....(((.....)))..(((((((........)))))))(((..((((.....(((((((....)))))))...)))))))(((((...((..(((....)))))...)))))...... ( -34.60)
>consensus
GAAUUGACCAUUAUUCCCGCAGGUGGAGGUGAACACCUGCGCAUUACCAUCGCACAGCAAACUUAUUUGCUGAUUUGGUUGCAAUUGAUCCGUGAGCAAGAGCUCAUAGCGAUUGUUAAC
.....(((((........(((((((........)))))))((.........)).(((((((....)))))))...)))))(((((((..(..(((((....)))))..)))))))).... (-34.19 = -34.75 +   0.56)

alignment

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secondary structure

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Window 1

Location 24,495,178 – 24,495,298
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.56
Mean single sequence MFE -36.27
Consensus MFE -27.75
Energy contribution -29.00
Covariance contribution 1.25
Combinations/Pair 1.18
Mean z-score -2.14
Structure conservation index 0.76
SVM decision value 0.69
SVM RNA-class probability 0.823720
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24495178 120 + 27905053
AACCAAAUCAGCAAAUAAGUUUGCUGUGCGAUGGUAAUGCGCAGGUGUUCACCUCCACCUGUCGGAAUAAUGGCCAGUUCUCUCCACCAUUGCCCAGGACGAACUGCUCAAAGGCAAUCC
..((....(((((((....))))))).((((((((....((((((((........)))))).))((((........)))).....))))))))...))......((((....)))).... ( -35.00)
>DroSec_CAF1 38155 120 + 1
AACCAAAUCAGCAAAUAAGUUUGCUGUGCGAUGAAAAUGCGCAGGUGUUCACCUCCACCUGCGGGAAUAAUGGUCACUUCUCUCCACCGUUGCCCAGGACAAACUGCUCAAAGGCCAUUC
..((....(((((((....))))))).((((((......((((((((........))))))))(((.....(....).....)))..))))))...)).......(((....)))..... ( -33.00)
>DroSim_CAF1 50011 120 + 1
AACCAAGUCAGCAAAUAAGUUUGCUGUGCGAUGGUAAUGCGCAGGUGUUCACCUCCACCUGCGGUAGUAAUGGUCGAUUCUCUCCACCGUUGCCCAGGACAAACUGCUCAAAGACCAUUC
.((((.(((((((((....))))))).))..)))).....(((((((........)))))))(((.((((((((.((.....)).)))))))).(((......))).......))).... ( -40.70)
>DroEre_CAF1 44563 120 + 1
AACCAAAUCAGCAAAUAAGUUUGCUGUGCGAUGGUAAUGCGCAGGUGUUCACCUCCACCUGCCAGACUAGUGGCCAAUUCUCUCCAGCGCUGCCCAGCACAAACUGCUCAAAGGCAAUCC
.((((...(((((((....))))))).....))))...(((((((((........)))))((((......))))............))))((((.((((.....))))....)))).... ( -36.40)
>consensus
AACCAAAUCAGCAAAUAAGUUUGCUGUGCGAUGGUAAUGCGCAGGUGUUCACCUCCACCUGCCGGAAUAAUGGCCAAUUCUCUCCACCGUUGCCCAGGACAAACUGCUCAAAGGCAAUCC
.........((((.....((((((((.((((((((.....(((((((........)))))))((((((........))))))...)))))))).)))..)))))))))............ (-27.75 = -29.00 +   1.25)

alignment

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secondary structure

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Window 2

Location 24,495,218 – 24,495,338
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.81
Mean single sequence MFE -35.34
Consensus MFE -23.75
Energy contribution -24.00
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -2.28
Structure conservation index 0.67
SVM decision value 0.65
SVM RNA-class probability 0.810947
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24495218 120 + 27905053
GCAGGUGUUCACCUCCACCUGUCGGAAUAAUGGCCAGUUCUCUCCACCAUUGCCCAGGACGAACUGCUCAAAGGCAAUCCCGCCUUCCGUUGUUCCAACUUCGAGUAAUAUCUGUCCACA
(((((((((...(((.....((.((((((((((.((((((..(((...........))).))))))....(((((......))))))))))))))).))...))).)))))))))..... ( -38.00)
>DroSec_CAF1 38195 120 + 1
GCAGGUGUUCACCUCCACCUGCGGGAAUAAUGGUCACUUCUCUCCACCGUUGCCCAGGACAAACUGCUCAAAGGCCAUUCCGCCUUCUGUGGUUCCAACUGCGAGUAAUAUCUGCCCACA
(((((((........)))))))(((..(((((((...........)))))))))).((.((...(((((.(((((......)))))..(..((....))..)))))).....)).))... ( -37.00)
>DroSim_CAF1 50051 120 + 1
GCAGGUGUUCACCUCCACCUGCGGUAGUAAUGGUCGAUUCUCUCCACCGUUGCCCAGGACAAACUGCUCAAAGACCAUUCCGCCUUCUGUGGUUCCAACUGCGAGUAAUAUCUGCCCACA
(((((((........)))))))((((((((((((.((.....)).))))))))...........(((((..((......((((.....))))......))..))))).....)))).... ( -35.30)
>DroEre_CAF1 44603 120 + 1
GCAGGUGUUCACCUCCACCUGCCAGACUAGUGGCCAAUUCUCUCCAGCGCUGCCCAGCACAAACUGCUCAAAGGCAAUCCAGCCAUCUGUGGUUCCAACUGUUAGUUCUACGUGCCCACA
(((((((........))))))).......((((.((.......(.((((((....)))...(((..(.....(((......)))....)..)))......))).).......)).)))). ( -31.04)
>consensus
GCAGGUGUUCACCUCCACCUGCCGGAAUAAUGGCCAAUUCUCUCCACCGUUGCCCAGGACAAACUGCUCAAAGGCAAUCCCGCCUUCUGUGGUUCCAACUGCGAGUAAUAUCUGCCCACA
(((((((........)))))))........(((.((.....(((..((........))...((((((...(((((......)))))..))))))........))).......)).))).. (-23.75 = -24.00 +   0.25)

alignment

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secondary structure

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Window 3

Location 24,495,338 – 24,495,442
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 90.54
Mean single sequence MFE -34.95
Consensus MFE -27.67
Energy contribution -29.17
Covariance contribution 1.50
Combinations/Pair 1.11
Mean z-score -2.73
Structure conservation index 0.79
SVM decision value 1.41
SVM RNA-class probability 0.950989
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24495338 104 - 27905053
CCGUGUUGAUGGAGAAAUACGCCUUCAUGGUUCUCGCGUCGUAGCAGCUGCGAUAGAGCUCCAUGAACGUAUUUCCGUAUUUGAAACCAACCAAAUACAUGGUG
((((((...(((.((((((((..(((((((..(((..(((((((...))))))).)))..))))))))))))))).....(((....))))))...)))))).. ( -39.50)
>DroSec_CAF1 38315 104 - 1
CCGUGUUGAUGGAAAAAUACGCCUUCAUGGUUCUCGCGUCGUAGCAGCUGCGAUAGAGCUCCAUGAACGUAUUUCCAUACCUGAAACCAACCAAAUACAUGGUG
((((((..((((((..(((((..(((((((..(((..(((((((...))))))).)))..))))))))))))))))))...((....)).......)))))).. ( -35.70)
>DroSim_CAF1 50171 104 - 1
CCGUGUUGAUGGAGAAAUACGCCUUCAUGGUUCUCGCGUCGUAGCAGCUGCGAUAGAGCUCCAUGAAAGUAUUUCCAUACCUGAAACCAACCAAAUACAUGGUG
((((((...(((.(((((((...(((((((..(((..(((((((...))))))).)))..))))))).)))))))......((....)).)))...)))))).. ( -37.40)
>DroEre_CAF1 44723 104 - 1
CCAAGCUGAUGGAGAAAUAUGCCGUCAUGGUGGUGGCGUCGUAGCAGUUUCGAUAGAGCUCCAUGAACGCAUUUCCGAACUGGAAACCAACCGAAUACAUGGUG
(((...((((((.........))))))(((((((.(((((((.(.(((((.....)))))).))).))))..((((.....))))))).))))......))).. ( -27.20)
>consensus
CCGUGUUGAUGGAGAAAUACGCCUUCAUGGUUCUCGCGUCGUAGCAGCUGCGAUAGAGCUCCAUGAACGUAUUUCCAUACCUGAAACCAACCAAAUACAUGGUG
((((((...(((.((((((((..(((((((..(((..(((((((...))))))).)))..))))))))))))))).......(....)..)))...)))))).. (-27.67 = -29.17 +   1.50)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:28:27 2006