Locus 9759

Sequence ID 3R_DroMel_CAF1
Location 25,851,604 – 25,851,757
Length 153
Max. P 0.797144
window15590 window15591 window15592

overview

Window 0

Location 25,851,604 – 25,851,724
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.84
Mean single sequence MFE -41.32
Consensus MFE -28.28
Energy contribution -29.88
Covariance contribution 1.60
Combinations/Pair 1.22
Mean z-score -1.56
Structure conservation index 0.68
SVM decision value -0.05
SVM RNA-class probability 0.510228
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25851604 120 + 27905053
CGCGCCCAAGUGCAUCCUUCGGGUCCUUCGGUGUCCUUGUAAUGGGCGUUGCACCUGAAAAGUAGGCGCUUCCGCGCUGAACUUUUCCGCCUGUGCUGGCAACUUUUGCCGCGCACAAAG
.(((((((..((((......(((..(....)..))).)))).))))))).((....(((((((.(((((....)))))..))))))).)).((((((((((.....))))).)))))... ( -47.50)
>DroSec_CAF1 2827 120 + 1
CGCGCCCAAGUGCAUACUUCGGGUCCUUCGGUGUCCUUGCAAUGGGCGUUGCACCUGAAAAGUGGGCGCUUCCGCGCUGAACUUUUCCGCCUAUGCUGGCAACUUUUGCCGCGCACAAAG
.(((((((..((((......(((..(....)..))).)))).)))))))(((....(((((((.(((((....)))))..))))))).......((.((((.....)))))))))..... ( -46.50)
>DroSim_CAF1 2920 111 + 1
CGCGCCCAAGUGCAU---------CCUUCGGUGUCCUUGCAAUGGGCGUUGCACCUGAAAAGUGGGCGCUUCCGCGCUGAACUUUUCCGCCUAUGCUGGCAACUUUUGCCGCGCACAAAG
.((((..(((..(((---------(....))))..)))(((.((((((........(((((((.(((((....)))))..)))))))))))))))).((((.....))))))))...... ( -43.90)
>DroEre_CAF1 3413 111 + 1
CGCGCCCAAGUGCAU---------CCUUCGGUGUCCUUGCACUGGGCGUUGCACCUGAAAAGUGGGCGCUUCCGCGCUGAACUUUUCCGGCUUUGCUGGCAACUUUUGCCGCGUACAAAG
.(((((((.(((((.---------((....).)....))))))))))))(((.((.(((((((.(((((....)))))..))))))).))....((.((((.....)))))))))..... ( -47.40)
>DroAna_CAF1 1940 93 + 1
--------AGAGCCU---------CCUCCGAUGGCAUUGCAGUGGGCUUUGCACCUGAAAAGUGAGUGUUUCCGUGCUGAACUUU---------GCCGGCAACUUUU-CCGUAGACAAAG
--------((((((.---------.((.((((...)))).))..))))))....(((....(.(((.(((.(((.((........---------))))).)))..))-)).)))...... ( -21.30)
>consensus
CGCGCCCAAGUGCAU_________CCUUCGGUGUCCUUGCAAUGGGCGUUGCACCUGAAAAGUGGGCGCUUCCGCGCUGAACUUUUCCGCCUAUGCUGGCAACUUUUGCCGCGCACAAAG
.((((......((((..............(((((...(((.....)))..))))).(((((((.(((((....)))))..))))))).....)))).((((.....))))))))...... (-28.28 = -29.88 +   1.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 25,851,604 – 25,851,724
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.84
Mean single sequence MFE -41.68
Consensus MFE -26.98
Energy contribution -29.90
Covariance contribution 2.92
Combinations/Pair 1.06
Mean z-score -1.75
Structure conservation index 0.65
SVM decision value 0.14
SVM RNA-class probability 0.603580
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25851604 120 - 27905053
CUUUGUGCGCGGCAAAAGUUGCCAGCACAGGCGGAAAAGUUCAGCGCGGAAGCGCCUACUUUUCAGGUGCAACGCCCAUUACAAGGACACCGAAGGACCCGAAGGAUGCACUUGGGCGCG
..((((((..((((.....)))).))))))((((((((((...((((....))))..)))))))(((((((..(.((.......)).).((...(....)...)).)))))))...))). ( -47.70)
>DroSec_CAF1 2827 120 - 1
CUUUGUGCGCGGCAAAAGUUGCCAGCAUAGGCGGAAAAGUUCAGCGCGGAAGCGCCCACUUUUCAGGUGCAACGCCCAUUGCAAGGACACCGAAGGACCCGAAGUAUGCACUUGGGCGCG
.....(((((((((.....)))).((....)).(((((((...((((....))))..)))))))..))))).((((((.((((...((..((.......))..)).))))..)))))).. ( -46.40)
>DroSim_CAF1 2920 111 - 1
CUUUGUGCGCGGCAAAAGUUGCCAGCAUAGGCGGAAAAGUUCAGCGCGGAAGCGCCCACUUUUCAGGUGCAACGCCCAUUGCAAGGACACCGAAGG---------AUGCACUUGGGCGCG
.....(((((((((.....)))).((....)).(((((((...((((....))))..)))))))..))))).((((((.((((.(....)(....)---------.))))..)))))).. ( -44.00)
>DroEre_CAF1 3413 111 - 1
CUUUGUACGCGGCAAAAGUUGCCAGCAAAGCCGGAAAAGUUCAGCGCGGAAGCGCCCACUUUUCAGGUGCAACGCCCAGUGCAAGGACACCGAAGG---------AUGCACUUGGGCGCG
..((((((((((((.....)))).)).......(((((((...((((....))))..)))))))..))))))(((((((((((.(....)(....)---------.))))).)))))).. ( -47.60)
>DroAna_CAF1 1940 93 - 1
CUUUGUCUACGG-AAAAGUUGCCGGC---------AAAGUUCAGCACGGAAACACUCACUUUUCAGGUGCAAAGCCCACUGCAAUGCCAUCGGAGG---------AGGCUCU--------
((((((...(((-........)))))---------))))...(((..(....).....((((((.((((((..((.....))..)).)))).))))---------)))))..-------- ( -22.70)
>consensus
CUUUGUGCGCGGCAAAAGUUGCCAGCAUAGGCGGAAAAGUUCAGCGCGGAAGCGCCCACUUUUCAGGUGCAACGCCCAUUGCAAGGACACCGAAGG_________AUGCACUUGGGCGCG
..((((((((((((.....)))).)).......(((((((...((((....))))..)))))))..))))))((((((..(((.......................)))...)))))).. (-26.98 = -29.90 +   2.92)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,851,644 – 25,851,757
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.74
Mean single sequence MFE -43.60
Consensus MFE -30.04
Energy contribution -32.04
Covariance contribution 2.00
Combinations/Pair 1.09
Mean z-score -2.40
Structure conservation index 0.69
SVM decision value 0.60
SVM RNA-class probability 0.797144
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25851644 113 - 27905053
G------GCUGC-GAGUAUUGCCGAAGGUCAAUAGUGGCACUUUGUGCGCGGCAAAAGUUGCCAGCACAGGCGGAAAAGUUCAGCGCGGAAGCGCCUACUUUUCAGGUGCAACGCCCAUU
(------(((((-(.....((((((((((((....)))).))))((((..((((.....)))).)))).))))(((((((...((((....))))..)))))))...))))..))).... ( -47.90)
>DroSec_CAF1 2867 113 - 1
G------GCUGC-GAGUAUUGCCGAAGGUCAAUAGUGGCACUUUGUGCGCGGCAAAAGUUGCCAGCAUAGGCGGAAAAGUUCAGCGCGGAAGCGCCCACUUUUCAGGUGCAACGCCCAUU
(------((...-...(((((.(....).)))))((.(((((((((((..((((.....)))).)))))....(((((((...((((....))))..))))))))))))).))))).... ( -45.30)
>DroSim_CAF1 2951 113 - 1
G------GCUGG-GAGUAUUGCCGAAGGUCAAUAGUGGCACUUUGUGCGCGGCAAAAGUUGCCAGCAUAGGCGGAAAAGUUCAGCGCGGAAGCGCCCACUUUUCAGGUGCAACGCCCAUU
.------..(((-(..(((((.(....).)))))((.(((((((((((..((((.....)))).)))))....(((((((...((((....))))..))))))))))))).)).)))).. ( -46.50)
>DroEre_CAF1 3444 113 - 1
G------GCUGC-GAGUAUUGCCGAAGGUCAAUAGUGGCACUUUGUACGCGGCAAAAGUUGCCAGCAAAGCCGGAAAAGUUCAGCGCGGAAGCGCCCACUUUUCAGGUGCAACGCCCAGU
(------(((((-.(.(((((.(....).))))).).)))..((((((((((((.....)))).)).......(((((((...((((....))))..)))))))..)))))).))).... ( -45.30)
>DroAna_CAF1 1963 110 - 1
CGCCAGAGCUGCUGGUUAUUGCCGAAGGUCAAUAGUGGCACUUUGUCUACGG-AAAAGUUGCCGGC---------AAAGUUCAGCACGGAAACACUCACUUUUCAGGUGCAAAGCCCACU
.(((.((.((..((((....)))).)).))......((((((((.((....)-))))).)))))))---------...(((..((((.((((........))))..))))..)))..... ( -33.00)
>consensus
G______GCUGC_GAGUAUUGCCGAAGGUCAAUAGUGGCACUUUGUGCGCGGCAAAAGUUGCCAGCAUAGGCGGAAAAGUUCAGCGCGGAAGCGCCCACUUUUCAGGUGCAACGCCCAUU
.......((.....(.(((((.(....).))))).).(((((((((((..((((.....)))).)))))....(((((((...((((....))))..)))))))))))))...))..... (-30.04 = -32.04 +   2.00)

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 13:41:35 2006