Locus 1591

Sequence ID 3R_DroMel_CAF1
Location 4,566,166 – 4,566,360
Length 194
Max. P 0.950038
window2625 window2626 window2627

overview

Window 5

Location 4,566,166 – 4,566,281
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 93.54
Mean single sequence MFE -27.72
Consensus MFE -22.84
Energy contribution -22.88
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.30
Structure conservation index 0.82
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4566166 115 + 27905053
UCAAUUUCAAUCUGAUGGCCCCAAGAUGCGCGAUUUCUUGGCAAUUGCUGGGCACUGAUCCGAUUGCCACCACACCCGCAUUCCUUGCGGCAAAGCAUUAAAAUCAAAUUAACCC
.......(((((.(((.(((((((((.........)))))((....)).))))....))).))))).........(((((.....)))))......................... ( -25.40)
>DroSec_CAF1 23025 111 + 1
UCAAUUU----CUGAUGGCCACAAGAUGCGCGAUUUCUUGGCAAUUGCUGUGCACUGAUCUGAUUGCCACCACACCCGCAUUCCUUGCGGCAAGGCAUUAAAAUGAAAUUAACCC
..(((((----(((((((((.(((((((((.(......((((((((...............))))))))......))))))..)))).)))....)))))....))))))..... ( -26.46)
>DroSim_CAF1 23733 111 + 1
UCAAUUU----CUGAUGGCCACAAGAUGCACGAUUUCUUGGCAAUUGCUGUGCACUGAUCUGAUUGCCACCACACCCGCAUUCCUUGCGGCAGGGCAUUAAAAUCAAAUUAACCC
.....((----(((.((((....(((((((((....)..(((....))))))))....)))....))))......(((((.....)))))))))).................... ( -24.60)
>DroEre_CAF1 23538 115 + 1
UGAAUUUCAAUCUGAUGGCCACAAGAUGUGCGAUUUCUUGGCAAUUGCUGGGCACUGAUCUGAUUGCCACCACACCCGCAUUCCUUGUGGCAAAGCAUUAAAAUCAAAUUAACCC
(((.(((.(((((....((((((((..(((((......((((((((...(((......))))))))))).......)))))..))))))))..)).)))))).)))......... ( -32.32)
>DroYak_CAF1 23281 115 + 1
UCAAUUUCAAUCUGAUGGCCACAAGAUGCGCGAUUUCUUGGCAAUUGUUGGGCACUGAUCUGAUUGCCACCACACCCGCAUUCCUUGUGGCAAGGCAUUAAAAUCAAAUUAACCC
............((((((((((((((((((.(......((((((((((..(...)..))..))))))))......))))))..))))))))....)))))............... ( -29.80)
>consensus
UCAAUUUCAAUCUGAUGGCCACAAGAUGCGCGAUUUCUUGGCAAUUGCUGGGCACUGAUCUGAUUGCCACCACACCCGCAUUCCUUGCGGCAAGGCAUUAAAAUCAAAUUAACCC
..(((((.....((((((((.(((((((((........((((((((...............)))))))).......)))))..)))).)))....))))).....)))))..... (-22.84 = -22.88 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,566,166 – 4,566,281
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 93.54
Mean single sequence MFE -33.93
Consensus MFE -28.87
Energy contribution -28.59
Covariance contribution -0.28
Combinations/Pair 1.11
Mean z-score -1.32
Structure conservation index 0.85
SVM decision value 0.25
SVM RNA-class probability 0.655144
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4566166 115 - 27905053
GGGUUAAUUUGAUUUUAAUGCUUUGCCGCAAGGAAUGCGGGUGUGGUGGCAAUCGGAUCAGUGCCCAGCAAUUGCCAAGAAAUCGCGCAUCUUGGGGCCAUCAGAUUGAAAUUGA
........(..((((((((.((..(((.((((..((((((((....(((((((.((........))....)))))))....))).))))))))).)))....))))))))))..) ( -35.00)
>DroSec_CAF1 23025 111 - 1
GGGUUAAUUUCAUUUUAAUGCCUUGCCGCAAGGAAUGCGGGUGUGGUGGCAAUCAGAUCAGUGCACAGCAAUUGCCAAGAAAUCGCGCAUCUUGUGGCCAUCAG----AAAUUGA
...((((((((......((((((..((....)).....))))))((((((.((.((((..((((...((....))...(....))))))))).)).)))))).)----))))))) ( -32.60)
>DroSim_CAF1 23733 111 - 1
GGGUUAAUUUGAUUUUAAUGCCCUGCCGCAAGGAAUGCGGGUGUGGUGGCAAUCAGAUCAGUGCACAGCAAUUGCCAAGAAAUCGUGCAUCUUGUGGCCAUCAG----AAAUUGA
........(..(((((.((((((..((....)).....))))))((((((...(((....((((((.((....))...(....))))))).)))..)))))).)----))))..) ( -32.20)
>DroEre_CAF1 23538 115 - 1
GGGUUAAUUUGAUUUUAAUGCUUUGCCACAAGGAAUGCGGGUGUGGUGGCAAUCAGAUCAGUGCCCAGCAAUUGCCAAGAAAUCGCACAUCUUGUGGCCAUCAGAUUGAAAUUCA
...((((((((((...........(((((((((..(((((......(((((((........(((...)))))))))).....)))))..))))))))).))))))))))...... ( -35.10)
>DroYak_CAF1 23281 115 - 1
GGGUUAAUUUGAUUUUAAUGCCUUGCCACAAGGAAUGCGGGUGUGGUGGCAAUCAGAUCAGUGCCCAACAAUUGCCAAGAAAUCGCGCAUCUUGUGGCCAUCAGAUUGAAAUUGA
........(..((((((((.....((((((((..((((((((....(((((((.................)))))))....))).)))))))))))))......))))))))..) ( -34.73)
>consensus
GGGUUAAUUUGAUUUUAAUGCCUUGCCGCAAGGAAUGCGGGUGUGGUGGCAAUCAGAUCAGUGCCCAGCAAUUGCCAAGAAAUCGCGCAUCUUGUGGCCAUCAGAUUGAAAUUGA
(.(((((.......))))).)...(((((((((..(((((......(((((((.................))))))).....)))))..)))))))))................. (-28.87 = -28.59 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,566,241 – 4,566,360
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 95.55
Mean single sequence MFE -21.60
Consensus MFE -22.10
Energy contribution -21.46
Covariance contribution -0.64
Combinations/Pair 1.11
Mean z-score -1.30
Structure conservation index 1.02
SVM decision value 1.40
SVM RNA-class probability 0.950038
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4566241 119 + 27905053
CCGCAUUCCUUGCGGCAAAGCAUUAAAAUCAAAUUAACCCACAUAACCAUUAAGUGCAGGAGUGGGAGAUUUCCCAUUACCAUAUCCACAUUUCCCAGAUACAAAUCAAAUGAAUUGAA
(((((.....)))))(((..((((.............................(((..((((((((......)))))).)).....)))........(((....))).))))..))).. ( -22.80)
>DroSec_CAF1 23096 119 + 1
CCGCAUUCCUUGCGGCAAGGCAUUAAAAUGAAAUUAACCCAUAUAACCAUUAAGUGCAGGAGUGGGAGCUUUUCCAUUACCAUAUCCACAUCUCUCAGAUACAAAUCAAAUGAAUUGAA
(((((.....)))))(((..((((.............................(((..(((((((((....))))))).)).....)))........(((....))).))))..))).. ( -21.00)
>DroSim_CAF1 23804 119 + 1
CCGCAUUCCUUGCGGCAGGGCAUUAAAAUCAAAUUAACCCACAUAACCAUUAAGUGCAGGAGUGGGAGAUUUUCCAUUACCAUAUCCACAUAUCCCAGAUACAAAUCAAAUGAAUUGAA
(((((.....)))))..(((...................(((...........)))..(((((((((....))))))).))............))).....(((.((....)).))).. ( -21.10)
>DroEre_CAF1 23613 119 + 1
CCGCAUUCCUUGUGGCAAAGCAUUAAAAUCAAAUUAACCCACAUAACCAUUACGUGCAGGAGUGGGAGAUUUCCCAUUACCAUAUCCACAUCUCCCAGAUACAAAUCAAAUGAAUUGAA
(((((.....)))))(((..((((.............................(((..((((((((......)))))).)).....)))........(((....))).))))..))).. ( -21.00)
>DroYak_CAF1 23356 119 + 1
CCGCAUUCCUUGUGGCAAGGCAUUAAAAUCAAAUUAACCCACAUAAUCAUUAAGUGCAGGAGUGGGAGAUUUCCCAUUACCAUAUCCACAUCUCCCAGAUACAAAUCAAAUGAAUUGAA
(((((.....)))))(((..((((.............................(((..((((((((......)))))).)).....)))........(((....))).))))..))).. ( -22.10)
>consensus
CCGCAUUCCUUGCGGCAAGGCAUUAAAAUCAAAUUAACCCACAUAACCAUUAAGUGCAGGAGUGGGAGAUUUCCCAUUACCAUAUCCACAUCUCCCAGAUACAAAUCAAAUGAAUUGAA
(((((.....)))))(((..((((.............................(((..(((((((((....))))))).)).....)))........(((....))).))))..))).. (-22.10 = -21.46 +  -0.64)

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 10:14:22 2006