Locus 7953

Sequence ID 3L_DroMel_CAF1
Location 21,081,103 – 21,081,383
Length 280
Max. P 0.815357
window12973 window12974 window12975

overview

Window 3

Location 21,081,103 – 21,081,223
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.00
Mean single sequence MFE -43.68
Consensus MFE -42.76
Energy contribution -42.68
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -1.15
Structure conservation index 0.98
SVM decision value 0.16
SVM RNA-class probability 0.610782
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21081103 120 - 23771897
CCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACAAUGGCUCUGGCGACCUGCCGCCAUCGCUGCGUGCCUCCACCACAUCAAUUUUGUCCAAUUUGCGCAAGAAACAGCAGGGCGGCC
.((......(((....))).((((...((((((.((..(((..(((((......)))))..)))...)))))))).........((((((.(.....).)))))).......)))))).. ( -42.00)
>DroSec_CAF1 136453 120 - 1
CCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACACUGGCACUGGUGACCUGCCGCCAUCGCUGCGUGCCUCCACCACAUCAAUUUUGUCCAAUUUGCGCAAGAAACAGCAGGGCGGCC
.((......(((....))).((((...((((((.(((((((..(((((......)))))..)))).))))))))).........((((((.(.....).)))))).......)))))).. ( -42.60)
>DroSim_CAF1 42559 120 - 1
CCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACACUGGCACUGGCGACCUGCCGCCAUCGCUGCGUGCCUCCACCACAUCAAUUUUGUCCAAUUUGCGCAAGAAACAGCAUGGCGGCC
...........((((.(((((((....((.....))..))))))).)).)).((((((((.((((.(((.......))).....((((((.(.....).))))))..)))))))))))). ( -42.30)
>DroEre_CAF1 58552 120 - 1
CCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACGCCGGCACUGGCGACCUGCCGCCAUCGCUGCGUGCCUCCACCACAUCAAUUUUGUCCAAUUUGCGCAAGAAACAGCAGGGCGGCC
.((......(((....))).((((...((((((.(((((((..(((((......)))))..)))).))))))))).........((((((.(.....).)))))).......)))))).. ( -47.00)
>DroYak_CAF1 30634 120 - 1
CCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACACUGGCACUGGCGACCUGCCGCCAUCGCUGCGUGCCUCCACCACAUCAAUUUUGUCCAAUUUGCGCAAGAAACAGCAGGGCGGCC
.((......(((....))).((((...((((((.(((((((..(((((......)))))..)))).))))))))).........((((((.(.....).)))))).......)))))).. ( -44.50)
>consensus
CCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACACUGGCACUGGCGACCUGCCGCCAUCGCUGCGUGCCUCCACCACAUCAAUUUUGUCCAAUUUGCGCAAGAAACAGCAGGGCGGCC
.((......(((....))).((((...((((((.(((((((..(((((......)))))..)))).))))))))).........((((((.(.....).)))))).......)))))).. (-42.76 = -42.68 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,081,143 – 21,081,263
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.42
Mean single sequence MFE -43.92
Consensus MFE -40.16
Energy contribution -40.08
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -1.34
Structure conservation index 0.91
SVM decision value 0.66
SVM RNA-class probability 0.815357
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21081143 120 - 23771897
GCCAGCACAGCAAUGGCCACUCCGGACAUGUCUAAAAUACCCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACAAUGGCUCUGGCGACCUGCCGCCAUCGCUGCGUGCCUCCACCACA
((.......))..(((.((((((((....(((...........)))...))))....)))).)))..((((((.((..(((..(((((......)))))..)))...))))))))..... ( -38.10)
>DroSec_CAF1 136493 120 - 1
GCCAGCACAGCGAUGGUCACUCCGGACAUGUCCAAAAUACCCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACACUGGCACUGGUGACCUGCCGCCAUCGCUGCGUGCCUCCACCACA
((..((.((((((((((..(((((((....)))....(((((((......)))....)))).......))))......((((..(....).)))))))))))))).)))).......... ( -43.10)
>DroSim_CAF1 42599 120 - 1
GCCAGCACAGCGAUGGCCACUCCGGACAUGUCCAAAAUACCCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACACUGGCACUGGCGACCUGCCGCCAUCGCUGCGUGCCUCCACCACA
((..((.((((((((((..(((((((....)))....(((((((......)))....)))).......))))......((((..(....).)))))))))))))).)))).......... ( -43.70)
>DroEre_CAF1 58592 120 - 1
GCCGGCACAGCGAUGGCCACUCCGGACAUGUCCAACAUACCCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACGCCGGCACUGGCGACCUGCCGCCAUCGCUGCGUGCCUCCACCACA
...((((((((((((((..(.((((....(((...........)))...)))).)..(((..((....))(((.(((((....))))).)))))))))))))))..)))))......... ( -49.10)
>DroYak_CAF1 30674 120 - 1
GCCAGCACAGCGAUGGCCACUCCGGACAUGUCGAAAAUACCCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACACUGGCACUGGCGACCUGCCGCCAUCGCUGCGUGCCUCCACCACA
((..((.((((((((((..(.((((....((((.........))))...)))).)..((((((....((.....))..))))))(((.....))))))))))))).)))).......... ( -45.60)
>consensus
GCCAGCACAGCGAUGGCCACUCCGGACAUGUCCAAAAUACCCCGACUUCCCGGCGACGGUGCCCAAAUGGAGGACACUGGCACUGGCGACCUGCCGCCAUCGCUGCGUGCCUCCACCACA
((..((.((((((((((..(.((((....(((...........)))...)))).)..((((((....((.....))..))))))(((.....))))))))))))).)))).......... (-40.16 = -40.08 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,081,263 – 21,081,383
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.82
Mean single sequence MFE -38.30
Consensus MFE -32.12
Energy contribution -32.76
Covariance contribution 0.64
Combinations/Pair 1.09
Mean z-score -1.41
Structure conservation index 0.84
SVM decision value 0.27
SVM RNA-class probability 0.662380
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21081263 120 - 23771897
GGAGCAGCGGCCACAUCCUCAGUGGCAGCCGAUGCCGCGUCCUCCGAGGUAAGCUAAUGUGUGCGCCCACGCACUUAGGACUAAUUAAAGCCAAGCUAAAACCAAAAACAGCAGGAUGCA
((..(.((.(((((.......))))).)).)...))(((((((.(..(((.((((.....(((((....)))))...((.((......)))).))))...))).......).))))))). ( -38.90)
>DroSec_CAF1 136613 120 - 1
GGAGCAGCGGCCACAUCCUCGGUGGCAGCCGAUGCCGCGUCCUCCGAGGUAAGCUAAUGUGUGCGCCCACGCACUUAGGAUUAAUUAAAGCCAAGCUAAAACCAAAAACAGCAGGAUGCA
((..(.((.(((((.......))))).)).)...))(((((((.(..(((.((((.....(((((....)))))...((...........)).))))...))).......).))))))). ( -36.70)
>DroSim_CAF1 42719 120 - 1
GGAGCAGCGGCCACAUCCUCGGUGGCAGCCGAUGCCGCGUCCUCCGAGGUAAGCUAAUGUGUGCGCCCACGCACUUAGGACUAAUUAAAGCCAAGCUAAAACCAAAAACAGCAGGAUGCA
((..(.((.(((((.......))))).)).)...))(((((((.(..(((.((((.....(((((....)))))...((.((......)))).))))...))).......).))))))). ( -38.80)
>DroEre_CAF1 58712 116 - 1
GGAGCAGCGGCCACAUCCUCGGUGGCAGCAGAUGCCGCGUCCUCCGAGGUAAGUCAAUG--UGCGCCCACGCACUUAGGACUAAUUAAAGACUAGCUAAAACCAA--ACAGCAGGACGCA
((..(.((.(((((.......))))).)).)...))(((((((....(((.((((...(--((((....)))))....)))).)))........(((........--..)))))))))). ( -39.70)
>DroYak_CAF1 30794 118 - 1
GGAGCAGCGGCCACAUCCUCGGUGGCAGCAGAUGGCGCGUCCUCCGAGGUAAGUCAAUG--UGCGCCCACGCACUUAGGACUAAUUAAAGCCAAGCUAAAACCAAAAACAGCAGGAUGCA
...(((.((((.....((((((.(((.((.....))..).)).))))))..((((...(--((((....)))))....)))).......)))..(((............)))..).))). ( -37.40)
>consensus
GGAGCAGCGGCCACAUCCUCGGUGGCAGCCGAUGCCGCGUCCUCCGAGGUAAGCUAAUGUGUGCGCCCACGCACUUAGGACUAAUUAAAGCCAAGCUAAAACCAAAAACAGCAGGAUGCA
((..(.((.(((((.......))))).)).)...))(((((((.(..(((.((((.....(((((....)))))...((.((......)))).))))...))).......).))))))). (-32.12 = -32.76 +   0.64)

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 13:01:55 2006