Locus 5023

Sequence ID 2R_DroMel_CAF1
Location 16,326,374 – 16,326,547
Length 173
Max. P 0.998930
window8032 window8033 window8034 window8035 window8036

overview

Window 2

Location 16,326,374 – 16,326,467
Length 93
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 97.54
Mean single sequence MFE -34.48
Consensus MFE -33.40
Energy contribution -33.28
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -2.11
Structure conservation index 0.97
SVM decision value 3.29
SVM RNA-class probability 0.998930
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16326374 93 + 20766785
-GGGUAACUUGGCUUCGUUGUGUUGCAAUUGUUGUGACACCCUGAUUGCCGUUGUUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGC
-(((((((.((((.(((..((((..((.....))..))))..)))..))))..))))).)).........(((((..(((....)))..))))) ( -35.60)
>DroSec_CAF1 29553 94 + 1
AGGGUAACUUGGCUUCGUUGUGUUGCAAUUGUUGUGACAUCCUGAUUGCCGUUGUUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGC
.(((((((.((((.(((..((((..((.....))..))))..)))..))))..))))).)).........(((((..(((....)))..))))) ( -34.60)
>DroSim_CAF1 30038 93 + 1
-GGGUAACUUGGCUUCGUUGUGUUGCAAUUGUUGUGACACCCUGAUUGCCGUUGUUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGC
-(((((((.((((.(((..((((..((.....))..))))..)))..))))..))))).)).........(((((..(((....)))..))))) ( -35.60)
>DroEre_CAF1 28752 93 + 1
-GGGUAACUUGGCUUCGUUGUGCUGCAAUUGUUGUGACACCCUGAUUGCCGUUGUUGCAUCAUCAUUGUUGCACCGGCGGCGCUUCGGAGGUGC
-.........(((........))).............((((((((.((((((((.((((.((....)).)))).))))))))..)))).)))). ( -31.40)
>DroYak_CAF1 29942 93 + 1
-GGGUAACUUGGCUUCGUUGUGUUGCAAUUGUUGUGACACCCUGAUUGCCGUUGUUGCACCAUCAUUGUUGCACCGUCGGCGCUUCGGAGGUGC
-(((((((.((((.(((..((((..((.....))..))))..)))..))))..))))).)).........(((((..(((....)))..))))) ( -35.20)
>consensus
_GGGUAACUUGGCUUCGUUGUGUUGCAAUUGUUGUGACACCCUGAUUGCCGUUGUUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGC
.(((((((.((((.(((..((((((((.....))))))))..)))..))))..))))).)).........(((((..(((....)))..))))) (-33.40 = -33.28 +  -0.12)

alignment

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secondary structure

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Window 3

Location 16,326,407 – 16,326,507
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 89.00
Mean single sequence MFE -31.67
Consensus MFE -24.94
Energy contribution -24.75
Covariance contribution -0.19
Combinations/Pair 1.21
Mean z-score -2.15
Structure conservation index 0.79
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16326407 100 + 20766785
--------UGACAC----------CCUGA--UUGCCGUUGUUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGU
--------((.(((----------(((((--.((((((((.((((.((....)).)))).))))))))..)))).))))))...........................((.....))... ( -31.60)
>DroSec_CAF1 29587 100 + 1
--------UGACAU----------CCUGA--UUGCCGUUGUUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGU
--------((.(((----------(((((--.((((((((.((((.((....)).)))).))))))))..)))).))))))...........................((.....))... ( -29.00)
>DroSim_CAF1 30071 100 + 1
--------UGACAC----------CCUGA--UUGCCGUUGUUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGU
--------((.(((----------(((((--.((((((((.((((.((....)).)))).))))))))..)))).))))))...........................((.....))... ( -31.60)
>DroEre_CAF1 28785 100 + 1
--------UGACAC----------CCUGA--UUGCCGUUGUUGCAUCAUCAUUGUUGCACCGGCGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGU
--------((.(((----------(((((--.((((((((.((((.((....)).)))).))))))))..)))).))))))...........................((.....))... ( -31.20)
>DroYak_CAF1 29975 100 + 1
--------UGACAC----------CCUGA--UUGCCGUUGUUGCACCAUCAUUGUUGCACCGUCGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGU
--------((.(((----------(((((--.(((((.((.((((.((....)).)))).)).)))))..)))).))))))...........................((.....))... ( -27.00)
>DroAna_CAF1 30419 120 + 1
GGUGCUCCUGGCACUCCUGGUACUCCUGCUGCUGCCACUGUUGUGCCAUCAUUGUUGCACUGGCGGCGCUUCGGAGGUGCAACUUUCGCCCAAGUUGCAACUUUUAACGCUUUUAGCUGU
...(((...(((.((((.((....)).((.(((((((.(((.(((....)))....))).)))))))))...)))).((((((((......)))))))).........)))...)))... ( -39.60)
>consensus
________UGACAC__________CCUGA__UUGCCGUUGUUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGU
.........................((((...((((((((.((((.((....)).)))).))))))))..)))).((.((.......)))).................((.....))... (-24.94 = -24.75 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,326,407 – 16,326,507
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 89.00
Mean single sequence MFE -33.23
Consensus MFE -27.94
Energy contribution -28.97
Covariance contribution 1.03
Combinations/Pair 1.03
Mean z-score -2.03
Structure conservation index 0.84
SVM decision value 0.58
SVM RNA-class probability 0.788779
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16326407 100 - 20766785
ACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGUCGGUGCAACAAUGAUGGUGCAACAACGGCAA--UCAGG----------GUGUCA--------
.(((((((.(((.......))).)))))))(((....)))((((((..((...(((((.(.((((.((....)).)))).).)))))..--)).))----------))))..-------- ( -33.50)
>DroSec_CAF1 29587 100 - 1
ACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGUCGGUGCAACAAUGAUGGUGCAACAACGGCAA--UCAGG----------AUGUCA--------
.(((((((.(((.......))).))))))).......((((((((((.(..(((((...)))))..)...)).))))))))...((((.--.....----------.)))).-------- ( -32.00)
>DroSim_CAF1 30071 100 - 1
ACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGUCGGUGCAACAAUGAUGGUGCAACAACGGCAA--UCAGG----------GUGUCA--------
.(((((((.(((.......))).)))))))(((....)))((((((..((...(((((.(.((((.((....)).)))).).)))))..--)).))----------))))..-------- ( -33.50)
>DroEre_CAF1 28785 100 - 1
ACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGCCGGUGCAACAAUGAUGAUGCAACAACGGCAA--UCAGG----------GUGUCA--------
.(((((((.(((.......))).)))))))(((....)))((((((..((...((((....((((.((....)).))))....))))..--)).))----------))))..-------- ( -31.60)
>DroYak_CAF1 29975 100 - 1
ACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGACGGUGCAACAAUGAUGGUGCAACAACGGCAA--UCAGG----------GUGUCA--------
.(((((((.(((.......))).))))))).......((((((((((.(..(((((...)))))..)...)).))))))))...((((.--.....----------.)))).-------- ( -32.00)
>DroAna_CAF1 30419 120 - 1
ACAGCUAAAAGCGUUAAAAGUUGCAACUUGGGCGAAAGUUGCACCUCCGAAGCGCCGCCAGUGCAACAAUGAUGGCACAACAGUGGCAGCAGCAGGAGUACCAGGAGUGCCAGGAGCACC
...(((....(((........)))..(((((((....)))((((.(((...(((((((..((((..........))))....))))).))....((....)).))))))))))))))... ( -36.80)
>consensus
ACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGUCGGUGCAACAAUGAUGGUGCAACAACGGCAA__UCAGG__________GUGUCA________
.(((((((.(((.......))).)))))))((((...((((((((..((......))..))))))))..(((...(((.......)))...))).............))))......... (-27.94 = -28.97 +   1.03)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,326,427 – 16,326,547
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 95.78
Mean single sequence MFE -35.64
Consensus MFE -33.69
Energy contribution -33.78
Covariance contribution 0.09
Combinations/Pair 1.09
Mean z-score -1.36
Structure conservation index 0.95
SVM decision value 1.57
SVM RNA-class probability 0.964864
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16326427 120 + 20766785
UUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGUUGAUAGUAGUCAGGAAAGUUUUGGGCCAACUGUUAUCGCC
..((.........((((((((..(((....)))..))))))))....((((((((.((.(((.(((((((.....)).))))).))).)).)).......))))))...........)). ( -36.01)
>DroSec_CAF1 29607 120 + 1
UUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGUUGAUAGUAGUCAGGAAAGUUUUGGGCCAACUGUUAUCGCC
..((.........((((((((..(((....)))..))))))))....((((((((.((.(((.(((((((.....)).))))).))).)).)).......))))))...........)). ( -36.01)
>DroSim_CAF1 30091 120 + 1
UUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGUUGAUAGUAGUCAGGAAAGUUUUGGGCCAACUGUUAUCGCC
..((.........((((((((..(((....)))..))))))))....((((((((.((.(((.(((((((.....)).))))).))).)).)).......))))))...........)). ( -36.01)
>DroEre_CAF1 28805 120 + 1
UUGCAUCAUCAUUGUUGCACCGGCGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGUUGAUAGUAGUCAGGAAAGUUUUGGGCCAACUGUUAUCGCC
..((.........((((((((..(((....)))..))))))))....((((((((.((.(((.(((((((.....)).))))).))).)).)).......))))))...........)). ( -34.31)
>DroYak_CAF1 29995 120 + 1
UUGCACCAUCAUUGUUGCACCGUCGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGUUGAUAGUAGUCAGGAAAGUUUUGGGCCAACUGUUAUCGCC
..((.........((((((((..(((....)))..))))))))....((((((((.((.(((.(((((((.....)).))))).))).)).)).......))))))...........)). ( -35.61)
>DroAna_CAF1 30459 119 + 1
UUGUGCCAUCAUUGUUGCACUGGCGGCGCUUCGGAGGUGCAACUUUCGCCCAAGUUGCAACUUUUAACGCUUUUAGCUGUUGAUAGUAGUGCGAAAAGUUUCGGGCCA-CCGUUAUCGCC
....((((.((....))...))))((((...(((.((((((((((......)))))))(((((((..((((.(((........))).))))..)))))))....))).-)))....)))) ( -35.90)
>consensus
UUGCACCAUCAUUGUUGCACCGACGGCGCUUCGGAGGUGCAACUUUCGCCCAACUAACAACUUUUAACGCUUUUAGCUGUUGAUAGUAGUCAGGAAAGUUUUGGGCCAACUGUUAUCGCC
..((.........((((((((..(((....)))..))))))))....((((((((.((.(((.(((((((.....)).))))).))).)).)).......))))))...........)). (-33.69 = -33.78 +   0.09)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,326,427 – 16,326,547
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 95.78
Mean single sequence MFE -36.65
Consensus MFE -32.59
Energy contribution -33.34
Covariance contribution 0.75
Combinations/Pair 1.08
Mean z-score -1.86
Structure conservation index 0.89
SVM decision value 1.53
SVM RNA-class probability 0.962063
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16326427 120 - 20766785
GGCGAUAACAGUUGGCCCAAAACUUUCCUGACUACUAUCAACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGUCGGUGCAACAAUGAUGGUGCAA
.((......(((..(............)..)))(((((((.(((((((.(((.......))).))))))).......((((((((..((......))..))))))))..))))))))).. ( -37.20)
>DroSec_CAF1 29607 120 - 1
GGCGAUAACAGUUGGCCCAAAACUUUCCUGACUACUAUCAACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGUCGGUGCAACAAUGAUGGUGCAA
.((......(((..(............)..)))(((((((.(((((((.(((.......))).))))))).......((((((((..((......))..))))))))..))))))))).. ( -37.20)
>DroSim_CAF1 30091 120 - 1
GGCGAUAACAGUUGGCCCAAAACUUUCCUGACUACUAUCAACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGUCGGUGCAACAAUGAUGGUGCAA
.((......(((..(............)..)))(((((((.(((((((.(((.......))).))))))).......((((((((..((......))..))))))))..))))))))).. ( -37.20)
>DroEre_CAF1 28805 120 - 1
GGCGAUAACAGUUGGCCCAAAACUUUCCUGACUACUAUCAACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGCCGGUGCAACAAUGAUGAUGCAA
.(((.((.((.((.((((((.......(((((.(((.(.(((.((.....))))).).))).))))))))))).)).((((((((..((......))..))))))))..)).)).))).. ( -36.11)
>DroYak_CAF1 29995 120 - 1
GGCGAUAACAGUUGGCCCAAAACUUUCCUGACUACUAUCAACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGACGGUGCAACAAUGAUGGUGCAA
.((......(((..(............)..)))(((((((.(((((((.(((.......))).))))))).......((((((((..((......))..))))))))..))))))))).. ( -36.30)
>DroAna_CAF1 30459 119 - 1
GGCGAUAACGG-UGGCCCGAAACUUUUCGCACUACUAUCAACAGCUAAAAGCGUUAAAAGUUGCAACUUGGGCGAAAGUUGCACCUCCGAAGCGCCGCCAGUGCAACAAUGAUGGCACAA
((((.....((-(((..((((....))))..)))))..............(((((...((.((((((((......)))))))).))....))))))))).((((..........)))).. ( -35.90)
>consensus
GGCGAUAACAGUUGGCCCAAAACUUUCCUGACUACUAUCAACAGCUAAAAGCGUUAAAAGUUGUUAGUUGGGCGAAAGUUGCACCUCCGAAGCGCCGUCGGUGCAACAAUGAUGGUGCAA
.(((.((.((.((.((((((.......(((((.(((.(.(((.((.....))))).).))).))))))))))).)).((((((((..((......))..))))))))..)).)).))).. (-32.59 = -33.34 +   0.75)

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 11:34:39 2006