Locus 2169

Sequence ID 3R_DroMel_CAF1
Location 6,224,911 – 6,225,063
Length 152
Max. P 0.823146
window3530 window3531 window3532

overview

Window 0

Location 6,224,911 – 6,225,001
Length 90
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 86.52
Mean single sequence MFE -41.72
Consensus MFE -34.72
Energy contribution -35.34
Covariance contribution 0.61
Combinations/Pair 1.15
Mean z-score -1.59
Structure conservation index 0.83
SVM decision value -0.02
SVM RNA-class probability 0.522140
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6224911 90 + 27905053
UUGGCAAGCAACAGCAACAACAGGCUGUGGUGGCCGCCGG---AGCGGGACUUCCGCUGUCCACCAACUCGGCGGCGGCUCAGGCAGCCGCUG
..(((..((....)).......(((((((((.((((((((---(((((.....)))))((......)))))))))).)))...))))))))). ( -42.30)
>DroSec_CAF1 42125 90 + 1
UUGGCAAGCAACAGCAACAACAGGCUGUGGUGGCCGCCGG---AGCGGGACUUCCGCUGUCCACCAACUCGGCGGCGGCUCAGGCGGCCGCUG
..........(((((........)))))((((((((((.(---(((.((....))((((.((........)))))).)))).)))))))))). ( -45.40)
>DroSim_CAF1 43862 90 + 1
UUGGCAAGCAACAGCAACAACAGGCUGUGGUGGCCGCCGG---AGCGGGACAUCCGCUGUCCACCAACUCGGCGGCGGCUCAGGCGGCCGCUG
..........(((((........)))))((((((((((.(---(((.((....))((((.((........)))))).)))).)))))))))). ( -45.40)
>DroEre_CAF1 42454 90 + 1
UUGGCAAGCAACAGCAACAGCAAGCUGUGGUGGCCGCCGG---AGCGGGACAUCCCCUGUCCACCAACUCGGCGGCGGCUCAGGCAGCCGCUG
.......((....))..((((..((((((((.((((((((---.(..(((((.....)))))..)...)))))))).)))...))))).)))) ( -40.10)
>DroYak_CAF1 39498 90 + 1
UUGGCAAGCAACAGCAACAACAGGCUGUGGUGGCCGCCGG---AGCGGGACCUCCCCUGUCCACCAACUCGGCGGCGGCUCAGGCAGCCGCUG
..(((..((....)).......(((((((((.((((((((---.(..((((.......))))..)...)))))))).)))...))))))))). ( -40.90)
>DroAna_CAF1 47287 84 + 1
CCGGAAAGCAA---------CAGGCGGUGGUGGCCGCUGGAGGAGCUGGUGUCCCACUCUCCACGAGUUCGGCCGCUGCCCAGGCAGCCGCAG
.(((...((..---------..((((((((((((((.(((((.((.(((....)))))))))))).)))..)))))))))...))..)))... ( -36.20)
>consensus
UUGGCAAGCAACAGCAACAACAGGCUGUGGUGGCCGCCGG___AGCGGGACUUCCGCUGUCCACCAACUCGGCGGCGGCUCAGGCAGCCGCUG
..(((..((....)).......(((((((((.((((((((.......((((.......))))......)))))))).)))...))))))))). (-34.72 = -35.34 +   0.61)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,224,971 – 6,225,063
Length 92
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 83.77
Mean single sequence MFE -45.12
Consensus MFE -33.40
Energy contribution -34.52
Covariance contribution 1.11
Combinations/Pair 1.24
Mean z-score -2.72
Structure conservation index 0.74
SVM decision value 0.69
SVM RNA-class probability 0.823146
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6224971 92 + 27905053
CCAACUCGGCGGCGGCUCAGGCAGCCGCUGUGGCCGCCGCAGCGGUGGCUAAGGCCAAACUGGAGCAGGCCAUGAACCAGAGCUGGUAAAGC
(((.(((((((((.((....)).))))))((((((((..(((...((((....))))..)))..)).))))))......))).)))...... ( -43.30)
>DroVir_CAF1 42017 86 + 1
CUAGCUCAGCAGCCGUGCAGGCGGCUGCUGCUG------CCGCUGUGGCUAAGGCCAAGCUGGAGCAGGCCAUUAGCAACAGCUGGUAAGCU
..((((((((((((((....)))))))))).((------(((((((.(((((((((..((....)).)))).))))).))))).)))))))) ( -48.80)
>DroSec_CAF1 42185 92 + 1
CCAACUCGGCGGCGGCUCAGGCGGCCGCUGUGGCCGCCGCAGCGGUGGCCAAGGCCAAACUGGAGCAGGCCAUGAACCAGAGCUGGUAAAGC
...((.((((...((((..(((.((((((((((...)))))))))).)))..))))...((((..((.....))..)))).))))))..... ( -47.20)
>DroSim_CAF1 43922 92 + 1
CCAACUCGGCGGCGGCUCAGGCGGCCGCUGUGGCCGCCGCAGCGGUGGCCAAGGCCAAACUGGAGCAGGCCAUGAACCAGAGCUGGUAAAGC
...((.((((...((((..(((.((((((((((...)))))))))).)))..))))...((((..((.....))..)))).))))))..... ( -47.20)
>DroYak_CAF1 39558 92 + 1
CCAACUCGGCGGCGGCUCAGGCAGCCGCUGUGGCCGCCGCUGCGGUGGCCAAGGCCAAACUGGAGCAGGCCAUGAACCAGAGCUGGUAAGGC
(((.(((((((((.((....)).))))))((((((...(((.(((((((....)))..)))).))).))))))......))).)))...... ( -46.20)
>DroAna_CAF1 47341 92 + 1
CGAGUUCGGCCGCUGCCCAGGCAGCCGCAGCAGCCGCCGCCGCAGUGGCUAAGGCCAAACUAGAGCAGGCCAUCAACCAGGGAUGGUGAAGU
...(((((((((((((...(((.((.((....)).)).)))))))))))).((......)).))))..((((((.......))))))..... ( -38.00)
>consensus
CCAACUCGGCGGCGGCUCAGGCAGCCGCUGUGGCCGCCGCAGCGGUGGCCAAGGCCAAACUGGAGCAGGCCAUGAACCAGAGCUGGUAAAGC
......(((((((.((....)).)))))))((((((((.....)))))))).((((...........))))....((((....))))..... (-33.40 = -34.52 +   1.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,224,971 – 6,225,063
Length 92
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 83.77
Mean single sequence MFE -45.77
Consensus MFE -32.46
Energy contribution -33.88
Covariance contribution 1.42
Combinations/Pair 1.21
Mean z-score -2.82
Structure conservation index 0.71
SVM decision value 0.59
SVM RNA-class probability 0.793602
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6224971 92 - 27905053
GCUUUACCAGCUCUGGUUCAUGGCCUGCUCCAGUUUGGCCUUAGCCACCGCUGCGGCGGCCACAGCGGCUGCCUGAGCCGCCGCCGAGUUGG
......(((((((.(((...(((((.(((.((((.((((....))))..)))).))))))))..((((((.....)))))).)))))))))) ( -46.50)
>DroVir_CAF1 42017 86 - 1
AGCUUACCAGCUGUUGCUAAUGGCCUGCUCCAGCUUGGCCUUAGCCACAGCGG------CAGCAGCAGCCGCCUGCACGGCUGCUGAGCUAG
((((..((.(((((.(((((.((((.((....))..))))))))).)))))))------...(((((((((......))))))))))))).. ( -46.90)
>DroSec_CAF1 42185 92 - 1
GCUUUACCAGCUCUGGUUCAUGGCCUGCUCCAGUUUGGCCUUGGCCACCGCUGCGGCGGCCACAGCGGCCGCCUGAGCCGCCGCCGAGUUGG
......(((((((.(((....(((..((((((((.((((....))))..)))).(((((((.....))))))).)))).))))))))))))) ( -48.70)
>DroSim_CAF1 43922 92 - 1
GCUUUACCAGCUCUGGUUCAUGGCCUGCUCCAGUUUGGCCUUGGCCACCGCUGCGGCGGCCACAGCGGCCGCCUGAGCCGCCGCCGAGUUGG
......(((((((.(((....(((..((((((((.((((....))))..)))).(((((((.....))))))).)))).))))))))))))) ( -48.70)
>DroYak_CAF1 39558 92 - 1
GCCUUACCAGCUCUGGUUCAUGGCCUGCUCCAGUUUGGCCUUGGCCACCGCAGCGGCGGCCACAGCGGCUGCCUGAGCCGCCGCCGAGUUGG
......(((((((.(((....((((.((....))..)))).(((((.(((...))).)))))..((((((.....)))))).)))))))))) ( -44.00)
>DroAna_CAF1 47341 92 - 1
ACUUCACCAUCCCUGGUUGAUGGCCUGCUCUAGUUUGGCCUUAGCCACUGCGGCGGCGGCUGCUGCGGCUGCCUGGGCAGCGGCCGAACUCG
...((((((....))).)))((((((((((..((.((((....))))..))((((((.((....)).)))))).)))))..)))))...... ( -39.80)
>consensus
GCUUUACCAGCUCUGGUUCAUGGCCUGCUCCAGUUUGGCCUUAGCCACCGCUGCGGCGGCCACAGCGGCCGCCUGAGCCGCCGCCGAGUUGG
......((((((((((((...((((.((....))..))))..)))))..((.(((((((((.....)))))))...)).))....))))))) (-32.46 = -33.88 +   1.42)

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 10:29:01 2006