Locus 186

Sequence ID 3R_DroMel_CAF1
Location 844,830 – 844,966
Length 136
Max. P 0.958781
window311 window312 window313

overview

Window 1

Location 844,830 – 844,926
Length 96
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.15
Mean single sequence MFE -35.09
Consensus MFE -28.26
Energy contribution -30.33
Covariance contribution 2.06
Combinations/Pair 1.04
Mean z-score -2.35
Structure conservation index 0.81
SVM decision value 1.49
SVM RNA-class probability 0.958781
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 844830 96 + 27905053
UGGCUCUUGCUGGCUAAUUUGCCGCAGCAGGCAAUGGAAAUUGUUGAUGUGCAAAAAUUUUGCUGCGU------------------------CGUUGUUGUUGUCGUGUAAAUGCCAUAA
((((..((((.(((......)))((((((((((((....))))))(((((((((.....)))).))))------------------------)..))))))......))))..))))... ( -32.50)
>DroSec_CAF1 20594 99 + 1
UGGCUCUUGCUGGCUAAUUUGCCGCAGCAGGCAAUGGAAAUUGUUGAUGUGCAAAAAUGUUGCUGCGCCGC---------------------CGUUGUUGUUGUCGUGUAAGUGCCAUAA
((((.(((((.(((......)))(((((((.((((((...........(((((..........)))))..)---------------------))))))))))))...))))).))))... ( -34.12)
>DroSim_CAF1 19821 99 + 1
UGGCUCUUGCUGGCUAAUUUGCCGCAGCAGGCAAUGGAAAUUGUUGAUGUGCAAAAAUGUUGCUGCGCCGC---------------------CGUUGUUGUUGUCGUGUAAGUGCCAUAA
((((.(((((.(((......)))(((((((.((((((...........(((((..........)))))..)---------------------))))))))))))...))))).))))... ( -34.12)
>DroEre_CAF1 21690 120 + 1
UGGCUGUUGCUGGCUAAUUUGCCGCGGCGGGCAAUGGAAAUUGUUGAUGUGCAAAAAUGUUGCUGCGCCGCUUUGUUGUUGUUGCGUUGUUGCGUUGUUGUUGUCGUGUAAAUGCCAUAA
((((..((((.(((......)))((((((((((((....)))))).....((((.(((((.((.((((.((.........)).)))).)).))))).))))))))))))))..))))... ( -39.60)
>consensus
UGGCUCUUGCUGGCUAAUUUGCCGCAGCAGGCAAUGGAAAUUGUUGAUGUGCAAAAAUGUUGCUGCGCCGC_____________________CGUUGUUGUUGUCGUGUAAAUGCCAUAA
((((.(((((.(((......)))(((((.((((((....))))))(((((......)))))))))).........................................))))).))))... (-28.26 = -30.33 +   2.06) 

alignment

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secondary structure

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dotplot

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Window 2

Location 844,830 – 844,926
Length 96
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.15
Mean single sequence MFE -23.75
Consensus MFE -19.56
Energy contribution -20.38
Covariance contribution 0.81
Combinations/Pair 1.12
Mean z-score -2.06
Structure conservation index 0.82
SVM decision value 1.12
SVM RNA-class probability 0.917693
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 844830 96 - 27905053
UUAUGGCAUUUACACGACAACAACAACG------------------------ACGCAGCAAAAUUUUUGCACAUCAACAAUUUCCAUUGCCUGCUGCGGCAAAUUAGCCAGCAAGAGCCA
...((((.....................------------------------..(((((((((((.(((.....))).)))))........))))))(((......))).......)))) ( -20.10)
>DroSec_CAF1 20594 99 - 1
UUAUGGCACUUACACGACAACAACAACG---------------------GCGGCGCAGCAACAUUUUUGCACAUCAACAAUUUCCAUUGCCUGCUGCGGCAAAUUAGCCAGCAAGAGCCA
...((((.(((.(...............---------------------((((((..((((.....(((........)))......)))).))))))(((......))).).))).)))) ( -23.70)
>DroSim_CAF1 19821 99 - 1
UUAUGGCACUUACACGACAACAACAACG---------------------GCGGCGCAGCAACAUUUUUGCACAUCAACAAUUUCCAUUGCCUGCUGCGGCAAAUUAGCCAGCAAGAGCCA
...((((.(((.(...............---------------------((((((..((((.....(((........)))......)))).))))))(((......))).).))).)))) ( -23.70)
>DroEre_CAF1 21690 120 - 1
UUAUGGCAUUUACACGACAACAACAACGCAACAACGCAACAACAACAAAGCGGCGCAGCAACAUUUUUGCACAUCAACAAUUUCCAUUGCCCGCCGCGGCAAAUUAGCCAGCAACAGCCA
...((((....................((......))............((((((..((((.....(((........)))......)))).))))))(((......))).......)))) ( -27.50)
>consensus
UUAUGGCACUUACACGACAACAACAACG_____________________GCGGCGCAGCAACAUUUUUGCACAUCAACAAUUUCCAUUGCCUGCUGCGGCAAAUUAGCCAGCAAGAGCCA
...((((.(((.(....................................((((((..((((.....(((........)))......)))).))))))(((......))).).))).)))) (-19.56 = -20.38 +   0.81) 

alignment

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secondary structure

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dotplot

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Window 3

Location 844,870 – 844,966
Length 96
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.06
Mean single sequence MFE -20.66
Consensus MFE -15.68
Energy contribution -16.93
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.03
Structure conservation index 0.76
SVM decision value 0.82
SVM RNA-class probability 0.858222
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 844870 96 - 27905053
UUUUAAUUCCGCUCCGCUGUGUCUGUUGACACAAACUAAUUUAUGGCAUUUACACGACAACAACAACG------------------------ACGCAGCAAAAUUUUUGCACAUCAACAA
...............(((((((((((((................................)))))..)------------------------)))))))..................... ( -15.45)
>DroSec_CAF1 20634 99 - 1
UUUUAAUUCCGCUCCGCUGUGUCUGUUGACACAAACUAAUUUAUGGCACUUACACGACAACAACAACG---------------------GCGGCGCAGCAACAUUUUUGCACAUCAACAA
..........((.(((((((...(((((.............................)))))...)))---------------------)))).)).((((.....)))).......... ( -21.55)
>DroSim_CAF1 19861 99 - 1
UUUUAAUUCCGCUCCGCUGUGUCUGUUGACACAAACUAAUUUAUGGCACUUACACGACAACAACAACG---------------------GCGGCGCAGCAACAUUUUUGCACAUCAACAA
..........((.(((((((...(((((.............................)))))...)))---------------------)))).)).((((.....)))).......... ( -21.55)
>DroEre_CAF1 21730 120 - 1
UUUUAAUUCCGCUCCGCUAUGUCUGUUGACACAAACUAAUUUAUGGCAUUUACACGACAACAACAACGCAACAACGCAACAACAACAAAGCGGCGCAGCAACAUUUUUGCACAUCAACAA
..........((.(((((.(((.(((((............(..((.......))..)..........((......))..)))))))).))))).)).((((.....)))).......... ( -24.10)
>consensus
UUUUAAUUCCGCUCCGCUGUGUCUGUUGACACAAACUAAUUUAUGGCACUUACACGACAACAACAACG_____________________GCGGCGCAGCAACAUUUUUGCACAUCAACAA
..........((.((((((((((....)))))).......(..((.......))..)................................)))).)).((((.....)))).......... (-15.68 = -16.93 +   1.25) 

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 09:36:36 2006