Locus 4467

Sequence ID 3R_DroMel_CAF1
Location 11,814,840 – 11,815,093
Length 253
Max. P 0.887900
window7304 window7305 window7306 window7307 window7308

overview

Window 4

Location 11,814,840 – 11,814,959
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.13
Mean single sequence MFE -23.36
Consensus MFE -19.30
Energy contribution -19.94
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -1.73
Structure conservation index 0.83
SVM decision value 0.95
SVM RNA-class probability 0.887900
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11814840 119 + 27905053
AGCU-CUAGGUACACACGUGGCUAACGACGAAAAGUAAAAACAUAUUUUCGAAAAUUAUAUAACCCAACAAUGGAAGGGACAAUAUUUUCCCUGACGUUGUCAGCGAAAACAAAUUCAUA
.(((-...(((.....(((.....))).((((((...........))))))...........)))..((((((..(((((........)))))..)))))).)))(((......)))... ( -25.40)
>DroSec_CAF1 19176 120 + 1
AGCGCCUAGGUACAUACGUGGCUAACGACGAAAAGUAAAAACAUAUUUUCGAAAAUUAUAUAACCCAAAAAUGGAAGGGACAAUAUUUUCCCUGACGUUGUCAGCGAAAACAAAUUCAUA
..(((.(((.(((....))).)))..((((((((...........)))))...................((((..(((((........)))))..))))))).))).............. ( -23.50)
>DroSim_CAF1 20169 120 + 1
AGCGCCUAGGUACAUACGUGUCUAACGACGAAAAGUAAAAACAUAUUUUCGAAAAUUAUAUAACCCAACAAUGGAAGGGACAAUAUUUUCCCUGACGUUGUCAGCGAAAACAAAUUCAUA
..(((...(((........(((....)))(((((...........)))))............)))..((((((..(((((........)))))..))))))..))).............. ( -26.10)
>DroEre_CAF1 19477 115 + 1
AGCG-CUAGGU----ACGUGGCAAAUGACGAAAAGUAAAAACAUAUUUUCCAAAAUUAUAUAACCCAACAAUGGAAGGGACAAUAUUUUCACUGGCGUUGUCAGCGAAAACAAAUUCAUA
((((-((((((----.(((.....)))))(((((...........(((((((...................))))))).......))))).))))))))......(((......)))... ( -18.48)
>DroYak_CAF1 19516 115 + 1
AGCG-CUAGGU----ACGUGGCAAACGACGAAAAGUAAAAACAUAUUUUCCAAAAUUAUAUAACCCAACAAUGGAAGGGACAAUAUUUUCCCUGGCGUUGUCAGCGAAAACAAAUUCAUA
..((-((.(((----.(((.....)))..(.((((((......)))))).)...........)))..((((((..(((((........)))))..)))))).)))).............. ( -23.30)
>consensus
AGCG_CUAGGUACA_ACGUGGCUAACGACGAAAAGUAAAAACAUAUUUUCGAAAAUUAUAUAACCCAACAAUGGAAGGGACAAUAUUUUCCCUGACGUUGUCAGCGAAAACAAAUUCAUA
.((.....(((.....(((.....))).((((((...........))))))...........)))..((((((..(((((........)))))..))))))..))(((......)))... (-19.30 = -19.94 +   0.64)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,814,879 – 11,814,999
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.67
Mean single sequence MFE -26.58
Consensus MFE -24.38
Energy contribution -23.82
Covariance contribution -0.56
Combinations/Pair 1.10
Mean z-score -1.42
Structure conservation index 0.92
SVM decision value 0.72
SVM RNA-class probability 0.833850
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11814879 120 + 27905053
ACAUAUUUUCGAAAAUUAUAUAACCCAACAAUGGAAGGGACAAUAUUUUCCCUGACGUUGUCAGCGAAAACAAAUUCAUAAUUCUGUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUUG
........................(((((((((..(((((........)))))..)))))).((((((((((............))))..)))))))))..(((((.(....)..))))) ( -26.40)
>DroSec_CAF1 19216 120 + 1
ACAUAUUUUCGAAAAUUAUAUAACCCAAAAAUGGAAGGGACAAUAUUUUCCCUGACGUUGUCAGCGAAAACAAAUUCAUAAUUCUGUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUCG
........................((((.((((..(((((........)))))..))))....(((((((((............))))..)))))))))..(((((.(....)..))))) ( -25.00)
>DroSim_CAF1 20209 120 + 1
ACAUAUUUUCGAAAAUUAUAUAACCCAACAAUGGAAGGGACAAUAUUUUCCCUGACGUUGUCAGCGAAAACAAAUUCAUAAUUCUGUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUCG
........................(((((((((..(((((........)))))..)))))).((((((((((............))))..)))))))))..(((((.(....)..))))) ( -28.50)
>DroEre_CAF1 19512 120 + 1
ACAUAUUUUCCAAAAUUAUAUAACCCAACAAUGGAAGGGACAAUAUUUUCACUGGCGUUGUCAGCGAAAACAAAUUCAUAAUUCUAUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUCG
......((((((...................))))))((((....(((((.(((((...))))).)))))(((((..(((....)))..)))))....))))((((.(....)..)))). ( -26.11)
>DroYak_CAF1 19551 120 + 1
ACAUAUUUUCCAAAAUUAUAUAACCCAACAAUGGAAGGGACAAUAUUUUCCCUGGCGUUGUCAGCGAAAACAAAUUCAUAAUUCUGUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUCG
........................(((((((((..(((((........)))))..)))))).((((((((((............))))..)))))))))..(((((.(....)..))))) ( -26.90)
>consensus
ACAUAUUUUCGAAAAUUAUAUAACCCAACAAUGGAAGGGACAAUAUUUUCCCUGACGUUGUCAGCGAAAACAAAUUCAUAAUUCUGUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUCG
........................(((....)))...((((....(((((.(((((...))))).)))))(((((..(((....)))..)))))....))))((((.(....)..)))). (-24.38 = -23.82 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,814,959 – 11,815,053
Length 94
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.42
Mean single sequence MFE -30.50
Consensus MFE -24.59
Energy contribution -24.67
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.77
Structure conservation index 0.81
SVM decision value 0.58
SVM RNA-class probability 0.788425
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11814959 94 + 27905053
AUUCUGUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUUGAAGGAC--------------------------AUCGAAGGGAUCGAGGGAACCAAGUGAGCACGAGAUGCGGCAAUAACA
.(((((((((((((((((((((((((.(....)..))))((.....--------------------------.))....)))))))).....)))))))))).))).............. ( -24.20)
>DroSec_CAF1 19296 94 + 1
AUUCUGUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUCGAAGGAC--------------------------AUCGAAGGGACCGAGAGAACCAAGUGAGCACGAGAUGCGGCAAUAACA
.(((((((((((((((((((((((((.(....)..))))((.....--------------------------.))....)))))))).....)))))))))).))).............. ( -29.70)
>DroSim_CAF1 20289 94 + 1
AUUCUGUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUCGAAGGAC--------------------------AUCGAAGGGACCGAGGGAACCAAGUGAGCACGAGAUGCGGCAAUAACA
.(((((((((((((((((((((((((.(....)..))))((.....--------------------------.))....)))))))).....)))))))))).))).............. ( -29.70)
>DroEre_CAF1 19592 120 + 1
AUUCUAUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUCGAAGGACGUUGAGAGGAUAGACGUCGAAGGGACGUCGGAGGGACCGAGGGAACCAAGUGAGCACGAGAUGCGGCAAUAACA
....(((((.(((.((((((((((((.(....)..))))...................((((((.....))))))....)))))))).)))..))))).((.((.....))))....... ( -36.70)
>DroYak_CAF1 19631 105 + 1
AUUCUGUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUCGAAGGACG---------------UGGAAGGGACGUCGAAGGGUCCGAGGGAACCAAGUGAGCACGAGAUGCGGCAAUAACA
.((((((((((((((((((.((((((.(....)..))))....((((---------------(.......)))))....)).))))).....)))))))))).))).............. ( -32.20)
>consensus
AUUCUGUUUAUUUGCUUGGUCCGAGAGCGAAAGGAUCUCGAAGGAC__________________________AUCGAAGGGACCGAGGGAACCAAGUGAGCACGAGAUGCGGCAAUAACA
.(((((((((((((((((((((((((.(....)..))))....((............................))....)))))))).....)))))))))).))).............. (-24.59 = -24.67 +   0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,814,999 – 11,815,093
Length 94
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.92
Mean single sequence MFE -37.08
Consensus MFE -26.02
Energy contribution -26.26
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.19
Structure conservation index 0.70
SVM decision value 0.89
SVM RNA-class probability 0.874745
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11814999 94 + 27905053
AAGGAC--------------------------AUCGAAGGGAUCGAGGGAACCAAGUGAGCACGAGAUGCGGCAAUAACAAUAACAACCGCAUCCCCUGGGUGUCCUGUCUGUUGUCCGC
..((((--------------------------(.((.(((((((.((((......((....))..(((((((...............))))))))))).))).))))...)).))))).. ( -32.66)
>DroSec_CAF1 19336 94 + 1
AAGGAC--------------------------AUCGAAGGGACCGAGAGAACCAAGUGAGCACGAGAUGCGGCAAUAACAAUAACAACCGCAUCCCCUGGGUGUCCUGUCCGCUGUCCCC
..((((--------------------------(.((.(((((((.((........((....))..(((((((...............)))))))..)).))).))))...)).))))).. ( -29.36)
>DroSim_CAF1 20329 94 + 1
AAGGAC--------------------------AUCGAAGGGACCGAGGGAACCAAGUGAGCACGAGAUGCGGCAAUAACAAUAACAACCGCAUCCCCUGGGUGUCCUGUCCGCUGUCCCC
..((((--------------------------(.((.(((((((.((((......((....))..(((((((...............))))))))))).))).))))...)).))))).. ( -35.96)
>DroEre_CAF1 19632 119 + 1
AAGGACGUUGAGAGGAUAGACGUCGAAGGGACGUCGGAGGGACCGAGGGAACCAAGUGAGCACGAGAUGCGGCAAUAACAAUAACAACCGCAUCCCCUGGGUGUCCUGUCCGCUU-CCCC
..(((.((.((.(((((.((((((.....))))))......(((.((((......((....))..(((((((...............))))))))))).)))))))).)).)).)-)).. ( -46.46)
>DroYak_CAF1 19671 104 + 1
AAGGACG---------------UGGAAGGGACGUCGAAGGGUCCGAGGGAACCAAGUGAGCACGAGAUGCGGCAAUAACAAUAACAACCGCAUCCCCUGGGUGUCCUGUCCGCUU-CCCC
..(((.(---------------((((.((((((((....)).((.((((......((....))..(((((((...............))))))))))).)))))))).))))).)-)).. ( -40.96)
>consensus
AAGGAC__________________________AUCGAAGGGACCGAGGGAACCAAGUGAGCACGAGAUGCGGCAAUAACAAUAACAACCGCAUCCCCUGGGUGUCCUGUCCGCUGUCCCC
.(((((...........................((....))(((.((((......((....))..(((((((...............))))))))))).))))))))............. (-26.02 = -26.26 +   0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,814,999 – 11,815,093
Length 94
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.92
Mean single sequence MFE -37.96
Consensus MFE -31.01
Energy contribution -30.73
Covariance contribution -0.28
Combinations/Pair 1.11
Mean z-score -1.93
Structure conservation index 0.82
SVM decision value 0.91
SVM RNA-class probability 0.880790
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11814999 94 - 27905053
GCGGACAACAGACAGGACACCCAGGGGAUGCGGUUGUUAUUGUUAUUGCCGCAUCUCGUGCUCACUUGGUUCCCUCGAUCCCUUCGAU--------------------------GUCCUU
..(((((.......(((.(((((.((((((((((.((.......)).)))))))))).)).......)))))).((((.....)))))--------------------------)))).. ( -33.61)
>DroSec_CAF1 19336 94 - 1
GGGGACAGCGGACAGGACACCCAGGGGAUGCGGUUGUUAUUGUUAUUGCCGCAUCUCGUGCUCACUUGGUUCUCUCGGUCCCUUCGAU--------------------------GUCCUU
.((((((.((((..((((...((.((((((((((.((.......)).)))))))))).))(......).........)))).)))).)--------------------------))))). ( -35.50)
>DroSim_CAF1 20329 94 - 1
GGGGACAGCGGACAGGACACCCAGGGGAUGCGGUUGUUAUUGUUAUUGCCGCAUCUCGUGCUCACUUGGUUCCCUCGGUCCCUUCGAU--------------------------GUCCUU
.((((((.((((..((((....((((((((((((.((.......)).))))))))..((....))......))))..)))).)))).)--------------------------))))). ( -36.30)
>DroEre_CAF1 19632 119 - 1
GGGG-AAGCGGACAGGACACCCAGGGGAUGCGGUUGUUAUUGUUAUUGCCGCAUCUCGUGCUCACUUGGUUCCCUCGGUCCCUCCGACGUCCCUUCGACGUCUAUCCUCUCAACGUCCUU
((((-(((.((((.(((.(((((.((((((((((.((.......)).)))))))))).)).......))))))....))))))..((((((.....))))))..)))))........... ( -44.31)
>DroYak_CAF1 19671 104 - 1
GGGG-AAGCGGACAGGACACCCAGGGGAUGCGGUUGUUAUUGUUAUUGCCGCAUCUCGUGCUCACUUGGUUCCCUCGGACCCUUCGACGUCCCUUCCA---------------CGUCCUU
.(((-(.(.(((..((((...((.((((((((((.((.......)).)))))))))).)).......(((((....))))).......))))..))).---------------).)))). ( -40.10)
>consensus
GGGGACAGCGGACAGGACACCCAGGGGAUGCGGUUGUUAUUGUUAUUGCCGCAUCUCGUGCUCACUUGGUUCCCUCGGUCCCUUCGAU__________________________GUCCUU
.........((((.(((.(((((.((((((((((.((.......)).)))))))))).)).......)))))).((((.....))))...........................)))).. (-31.01 = -30.73 +  -0.28)

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 11:30:07 2006