Locus 2431

Sequence ID 2R_DroMel_CAF1
Location 8,734,581 – 8,734,789
Length 208
Max. P 0.940506
window4022 window4023 window4024 window4025

overview

Window 2

Location 8,734,581 – 8,734,681
Length 100
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 89.00
Mean single sequence MFE -23.90
Consensus MFE -22.20
Energy contribution -21.45
Covariance contribution -0.75
Combinations/Pair 1.15
Mean z-score -1.87
Structure conservation index 0.93
SVM decision value 1.31
SVM RNA-class probability 0.940506
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8734581 100 - 20766785
UUACGGCACUUGGAAGACGUAUUC------CCAUUACAACACUCUACGCUUUCCAAGAUGCAGCAUUCUAUCUCAAUUGACACUGAUUGGAUUGCGUGCAUGCAUA
........(((((((..((((...------..............))))..)))))))(((((((((.(.(((.(((((......)))))))).).)))).))))). ( -28.03)
>DroSec_CAF1 3693 100 - 1
CUACGGCUCUUGGAAGACAUAUUC------CCAUUACAACACUCUACGCUUUCCAAGAUGCAGCAUUCUAUCUCAAUUGACAAUGAUUGGAUUGCGUGCAUGCAUA
.......((((((((..(......------.................)..))))))))((((((((.(.(((.(((((......)))))))).).)))).)))).. ( -22.70)
>DroSim_CAF1 7196 100 - 1
CUACGGCACUUGGAAGACAUAUUC------CCAUUACAACACUCUACGCUUUCCAAGAUGCAGCAUUCUAUCUCAAUUGACAAUGAUUGGAUUGCGUGCAUGCAUA
........(((((((..(......------.................)..)))))))(((((((((.(.(((.(((((......)))))))).).)))).))))). ( -23.00)
>DroYak_CAF1 4598 104 - 1
CUGGAACACUUGGAAGACUUAUUCCCAUUCCCAUUACAACACU--UCGCUUUCUGGGAUGCAGCAUUUUAUCUCAAUUGACAAUGAUUGGAUUGCGUGCCUGCAUA
...........((((......))))...(((((..........--........)))))((((((((...(((.(((((......))))))))...))).))))).. ( -21.87)
>consensus
CUACGGCACUUGGAAGACAUAUUC______CCAUUACAACACUCUACGCUUUCCAAGAUGCAGCAUUCUAUCUCAAUUGACAAUGAUUGGAUUGCGUGCAUGCAUA
........(((((((..(.............................)..)))))))(((((((((.(.(((.(((((......)))))))).).)))).))))). (-22.20 = -21.45 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,734,621 – 8,734,721
Length 100
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 87.22
Mean single sequence MFE -22.60
Consensus MFE -17.39
Energy contribution -17.20
Covariance contribution -0.19
Combinations/Pair 1.21
Mean z-score -1.41
Structure conservation index 0.77
SVM decision value 0.00
SVM RNA-class probability 0.535495
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8734621 100 - 20766785
GGCUGGCACGCAUCAGUCAUGCAUCUUCUCCAUUUGUCAAUUACGGCACUUGGAAGACGUAUUC------CCAUUACAACACUCUACGCUUUCCAAGAUGCAGCAU
((((((......)))))).((((((((.((((..((((......))))..))))((.((((...------..............))))))....)))))))).... ( -25.83)
>DroSec_CAF1 3733 100 - 1
AGCUGGCACGCAUCAAUCAUGCAUCUUCUCCGUUUGUCAACUACGGCUCUUGGAAGACAUAUUC------CCAUUACAACACUCUACGCUUUCCAAGAUGCAGCAU
.((((.((.((((.....)))).......((((.........)))).((((((((..(......------.................)..)))))))))))))).. ( -20.40)
>DroSim_CAF1 7236 100 - 1
GGCUGGCACGCAUCAGUCAUGCAUCUUCUCCGUUUGUCAACUACGGCACUUGGAAGACAUAUUC------CCAUUACAACACUCUACGCUUUCCAAGAUGCAGCAU
((((((......)))))).((((((((.((((..((((......))))..))))(((.......------............))).........)))))))).... ( -22.41)
>DroYak_CAF1 4638 104 - 1
GGCUGGCACGCUUCAAUCAUGCAUCUUCUCCAGUUGUUAACUGGAACACUUGGAAGACUUAUUCCCAUUCCCAUUACAACACU--UCGCUUUCUGGGAUGCAGCAU
.((((.((.((.........))......((((((.....))))))......((((......))))...(((((..........--........))))))))))).. ( -21.77)
>consensus
GGCUGGCACGCAUCAAUCAUGCAUCUUCUCCAUUUGUCAACUACGGCACUUGGAAGACAUAUUC______CCAUUACAACACUCUACGCUUUCCAAGAUGCAGCAU
((((((......)))))).((((((((.((((..((((......))))..)))).((.....))..............................)))))))).... (-17.39 = -17.20 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,734,647 – 8,734,750
Length 103
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 72.06
Mean single sequence MFE -24.01
Consensus MFE -6.42
Energy contribution -8.14
Covariance contribution 1.72
Combinations/Pair 1.27
Mean z-score -1.89
Structure conservation index 0.27
SVM decision value 0.78
SVM RNA-class probability 0.847976
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8734647 103 - 20766785
ACACGGUUCAUCCAUAAUGCAU----GAUUCUAGGCUGGCACGCAUCAGUCAUGCAUCUUCUCCAUUUGUCAAUUACGGCACUUGGAAGACGUAUUC------CCAUUACAAC
..(((...........((((((----((((....((......))...))))))))))..((((((..((((......))))..))).))))))....------.......... ( -25.10)
>DroSec_CAF1 3759 103 - 1
ACACGGUUCAUCCAUAAUGCAU----GAUUCUAAGCUGGCACGCAUCAAUCAUGCAUCUUCUCCGUUUGUCAACUACGGCUCUUGGAAGACAUAUUC------CCAUUACAAC
....((...........(((((----((((....((......))...)))))))))((((((((((.........)))).....)))))).......------))........ ( -21.20)
>DroSim_CAF1 7262 103 - 1
ACACGGUUCAUCCAUAAUGCAU----GAUUCUAGGCUGGCACGCAUCAGUCAUGCAUCUUCUCCGUUUGUCAACUACGGCACUUGGAAGACAUAUUC------CCAUUACAAC
....((..........((((((----((((....((......))...))))))))))..((((((..((((......))))..))).))).......------))........ ( -23.70)
>DroYak_CAF1 4662 109 - 1
ACACGGUUCAUCCAUUAUGCAU----GAUUCUAGGCUGGCACGCUUCAAUCAUGCAUCUUCUCCAGUUGUUAACUGGAACACUUGGAAGACUUAUUCCCAUUCCCAUUACAAC
....((((..((((..((((((----((((..((((......)))).))))))))))....((((((.....)))))).....)))).))))..................... ( -27.10)
>DroPer_CAF1 3282 87 - 1
CCAUGGCUCAUCCAUAAUGCAGUCAUAUUGCAUAGUCAGCACGCAUCAAUCAUCUAGAGCUGGCCUGCGGCAGCUACUGC-----------------------CCGAU---GC
..(((((((((.....))).))))))...(((..((((((.(..............).)))))).)))(((((...))))-----------------------)....---.. ( -22.94)
>consensus
ACACGGUUCAUCCAUAAUGCAU____GAUUCUAGGCUGGCACGCAUCAAUCAUGCAUCUUCUCCAUUUGUCAACUACGGCACUUGGAAGACAUAUUC______CCAUUACAAC
....((..........((((((....((((....((......))...))))))))))....((((..((((......))))..))))................))........ ( -6.42 =  -8.14 +   1.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,734,681 – 8,734,789
Length 108
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 94.14
Mean single sequence MFE -24.26
Consensus MFE -19.66
Energy contribution -20.23
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -1.75
Structure conservation index 0.81
SVM decision value 0.08
SVM RNA-class probability 0.575575
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8734681 108 - 20766785
GAAUACUCAUAUCAAGCGGUCUACCCCUGGCCACUUCCCACACGGUUCAUCCAUAAUGCAUGAUUCUAGGCUGGCACGCAUCAGUCAUGCAUCUUCUCCAUUUGUCAA
((((.........(((.((((.......)))).)))........)))).......((((((((((....((......))...))))))))))................ ( -22.63)
>DroSec_CAF1 3793 108 - 1
GAAUACUCAUAUCAAGCGGUCUACCCCUGGACACUUCCCACACGGUUCAUCCAUAAUGCAUGAUUCUAAGCUGGCACGCAUCAAUCAUGCAUCUUCUCCGUUUGUCAA
............(((((((........((((.....((.....))....))))..((((((((((....((......))...)))))))))).....))))))).... ( -24.50)
>DroSim_CAF1 7296 108 - 1
GAAUACUCAUAUCAAGCGGUCUACCCCUGGCCACUUCCCACACGGUUCAUCCAUAAUGCAUGAUUCUAGGCUGGCACGCAUCAGUCAUGCAUCUUCUCCGUUUGUCAA
............(((((((...(((..(((.......)))...))).........((((((((((....((......))...)))))))))).....))))))).... ( -24.40)
>DroYak_CAF1 4702 108 - 1
GAAUGCUCAUAUCGAGCGCUUUACCCCUGGCCACUUCCCACACGGUUCAUCCAUUAUGCAUGAUUCUAGGCUGGCACGCUUCAAUCAUGCAUCUUCUCCAGUUGUUAA
....((((.....)))).........((((.............((.....))...((((((((((..((((......)))).)))))))))).....))))....... ( -25.50)
>consensus
GAAUACUCAUAUCAAGCGGUCUACCCCUGGCCACUUCCCACACGGUUCAUCCAUAAUGCAUGAUUCUAGGCUGGCACGCAUCAAUCAUGCAUCUUCUCCAUUUGUCAA
............(((((((...(((..(((.......)))...))).........((((((((((....((......))...)))))))))).....))))))).... (-19.66 = -20.23 +   0.56)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:00 2006