Locus 5512

Sequence ID 2R_DroMel_CAF1
Location 17,658,313 – 17,658,593
Length 280
Max. P 0.997573
window8825 window8826 window8827

overview

Window 5

Location 17,658,313 – 17,658,433
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.17
Mean single sequence MFE -24.64
Consensus MFE -22.06
Energy contribution -22.06
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.34
Structure conservation index 0.90
SVM decision value 2.89
SVM RNA-class probability 0.997573
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17658313 120 - 20766785
CUACAGUUCUUUUUGAACAGUUCUUAAAUCCAACCGGUUCUGAUAUGAUUAUUAUUAUGCUCCAACCGGUUUGCAAGGCAAACAUUUUAAUUUUAUUCGGUUUUAUUUUGCAUUGUUCCU
..............(((((((.(.((((.((...(((((..((((((((....)))))).)).)))))((((((...))))))...............)).))))....).))))))).. ( -23.10)
>DroSec_CAF1 11849 119 - 1
CUACAGGUCUUUUUGAACAGUUCUUAAAUCCAACCGGUUCUCAUAUGAUUAUUAUUAUGCUCGAACCGGUUUGCAAGGCAAAC-UUUUAAUUUUAUUCGGUUUUAUUUUGCAUUGUUCCU
..............(((((((.(..((((..(((((((((...((((((....))))))...)))))(((((((...))))))-).............))))..)))).).))))))).. ( -26.10)
>DroSim_CAF1 17801 120 - 1
CUACAGUUCUUUUUGAACAGUUCUUAAAUCCAACCGGUUCUGAUAUGAUUAUUAUUAUGCUCGAACCGGUUUGCAAGGCAAACAUUUUAAUUUUAUUCGGUUUUAUUUUGCAUUGUUCCU
..............(((((((.(.((((.((...((((((.((((((((....)))))).))))))))((((((...))))))...............)).))))....).))))))).. ( -27.10)
>DroEre_CAF1 12111 120 - 1
CUACAGUUCUUUUUGAACAGUUCUUAAAUCCAACCGGUUCUGAUAUGAUUAUUAUUAUGCCUCAACCGGUUUGCAAGGCAAACAUUUUAAUUUUAUUCGGUUUUAUUUUGCAUUGUUCCU
..............(((((((.(.((((.((...(((((..(.((((((....)))))).)..)))))((((((...))))))...............)).))))....).))))))).. ( -23.80)
>DroYak_CAF1 23551 120 - 1
CUACAGUUCAUUUUGAACAGUUCUUAAAUCCAACCGGUUCUGAUAUGAUUAUUAUUAUGCUCCAACCGGUUUGCAAGGCAAACAUUUUAAUUUUAUUCGGUUUUAUUUUGCAUUGUUCCC
..............(((((((.(.((((.((...(((((..((((((((....)))))).)).)))))((((((...))))))...............)).))))....).))))))).. ( -23.10)
>consensus
CUACAGUUCUUUUUGAACAGUUCUUAAAUCCAACCGGUUCUGAUAUGAUUAUUAUUAUGCUCCAACCGGUUUGCAAGGCAAACAUUUUAAUUUUAUUCGGUUUUAUUUUGCAUUGUUCCU
..............(((((((.(.((((.((...(((((....((((((....))))))....)))))((((((...))))))...............)).))))....).))))))).. (-22.06 = -22.06 +   0.00)

alignment

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secondary structure

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Window 6

Location 17,658,353 – 17,658,473
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.58
Mean single sequence MFE -31.12
Consensus MFE -24.54
Energy contribution -25.34
Covariance contribution 0.80
Combinations/Pair 1.08
Mean z-score -1.75
Structure conservation index 0.79
SVM decision value 0.50
SVM RNA-class probability 0.760273
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17658353 120 - 20766785
CUAAGCCAGAAAAACUGUGGCGACUUUAUUCUGGGUCUGACUACAGUUCUUUUUGAACAGUUCUUAAAUCCAACCGGUUCUGAUAUGAUUAUUAUUAUGCUCCAACCGGUUUGCAAGGCA
....((((((((((((((((((((((......))))).).)))))))).))))).................((((((((..((((((((....)))))).)).)))))))).....))). ( -33.40)
>DroSec_CAF1 11888 120 - 1
CUAAGGCAGAAAAGCUGUGGCGACUUUAUUCUGGGUCUGACUACAGGUCUUUUUGAACAGUUCUUAAAUCCAACCGGUUCUCAUAUGAUUAUUAUUAUGCUCGAACCGGUUUGCAAGGCA
.....(((((((((((((((((((((......))))).).))))))..)))))).................(((((((((...((((((....))))))...))))))))))))...... ( -32.70)
>DroSim_CAF1 17841 120 - 1
CUAAGGCUGAAAAGCUGUGGCGACUUUAUUCUGGGUCUGACUACAGUUCUUUUUGAACAGUUCUUAAAUCCAACCGGUUCUGAUAUGAUUAUUAUUAUGCUCGAACCGGUUUGCAAGGCA
....((((....))))((.((((........(((((.(((..((.((((.....)))).))..))).)))))((((((((.((((((((....)))))).))))))))))))))...)). ( -35.60)
>DroEre_CAF1 12151 120 - 1
CAAAGGCAGAAAAACUGUGGCGAUUUUAUUCUGGCUCUGACUACAGUUCUUUUUGAACAGUUCUUAAAUCCAACCGGUUCUGAUAUGAUUAUUAUUAUGCCUCAACCGGUUUGCAAGGCA
.....((((.....)))).((((........(((...(((..((.((((.....)))).))..)))...)))(((((((..(.((((((....)))))).)..)))))))))))...... ( -25.70)
>DroYak_CAF1 23591 120 - 1
CCAAGGCAGAAAAACUGUGGAGAUUUUAUUCUCUGUUCGACUACAGUUCAUUUUGAACAGUUCUUAAAUCCAACCGGUUCUGAUAUGAUUAUUAUUAUGCUCCAACCGGUUUGCAAGGCA
((...(((((.......((((...((((....((((((((............))))))))....)))))))).((((((..((((((((....)))))).)).)))))))))))..)).. ( -28.20)
>consensus
CUAAGGCAGAAAAACUGUGGCGACUUUAUUCUGGGUCUGACUACAGUUCUUUUUGAACAGUUCUUAAAUCCAACCGGUUCUGAUAUGAUUAUUAUUAUGCUCCAACCGGUUUGCAAGGCA
......((((((((((((((.(((((......)))))...)))))))).))))))....((.(((....(.((((((((....((((((....))))))....)))))))).).))))). (-24.54 = -25.34 +   0.80)

alignment

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secondary structure

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Window 7

Location 17,658,473 – 17,658,593
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -27.48
Consensus MFE -24.22
Energy contribution -25.30
Covariance contribution 1.08
Combinations/Pair 1.05
Mean z-score -2.04
Structure conservation index 0.88
SVM decision value 2.48
SVM RNA-class probability 0.994392
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17658473 120 - 20766785
UCUCAAUCAAGCCGCAAUCAAAUUGAAAUUAGGCUGUGAUCCGUUGGAACACUGCUUUAAAUUAAAUUAUUUUGGUUUAAAUUGUAAAAUUAAUUGCCAAAAGGUUGCGGAGAUUACAAG
....((((...((((((((...((((....((((.(((.(((...))).))).))))....))))....(((((((...(((((......)))))))))))))))))))).))))..... ( -31.90)
>DroSec_CAF1 12008 120 - 1
UCUCAAUCAAGCCGCAAUCAAAUUGAAAUUAGGCUGUGAUCCGUUUGGACACUGCCUUAAAGUGAAUUAUUUUGGUUUAAAUUGUAAAAUUAAUUGCCAAAAGGUUGCAGAGAUUACAAG
....((((...(.((((((.((((.(....((((.(((.(((....)))))).)))).....).)))).(((((((...(((((......)))))))))))))))))).).))))..... ( -29.70)
>DroSim_CAF1 17961 120 - 1
UCUCAAUCAAGCCGCAAUCAAAUUGAAAUUAGGCUGUGAUCCUUUUUGACACUGCCUUAAAUUAAAUUAUUUUGGUUUAAAUUGUAAAAUUAAUUGCCAAAAGGUUGCGGAGAUUACAAG
....((((...((((((((...((((....((((.(((.((......))))).))))....))))....(((((((...(((((......)))))))))))))))))))).))))..... ( -31.90)
>DroEre_CAF1 12271 120 - 1
UCUCAAUCAAGCCCCAAUCAAAUUGAAAUUAGGCUGUGAUCCGUUUUGACACUGCCUUAAAUUAAAUUAUUUUGGUUUAAAUUGUAAAAUUAAUUGCCAAGAGGUUGCGGAGAUUACAAG
....((((...((.(((((...((((....((((.(((.((......))))).))))....))))....(((((((...(((((......))))))))))))))))).)).))))..... ( -25.70)
>DroYak_CAF1 23711 120 - 1
UCUCAAUCAAGCGCCAAUCAAAUUGAAAUUAGGCUGUGAUCCGUUGUGACACUACCUUAAAUUAAAUUAUUUUGGUUUAAAUUGUAAAAUUAAUUGCCAAAAGGUUUCAGAGAUUACAAG
...............((((...(((((((((((..(((.((......)))))..)))............(((((((...(((((......)))))))))))))))))))).))))..... ( -18.20)
>consensus
UCUCAAUCAAGCCGCAAUCAAAUUGAAAUUAGGCUGUGAUCCGUUUUGACACUGCCUUAAAUUAAAUUAUUUUGGUUUAAAUUGUAAAAUUAAUUGCCAAAAGGUUGCGGAGAUUACAAG
....((((...((((((((.((((......((((.(((.((......))))).)))).......)))).(((((((...(((((......)))))))))))))))))))).))))..... (-24.22 = -25.30 +   1.08)

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 11:47:17 2006