Locus 9661

Sequence ID 3R_DroMel_CAF1
Location 25,548,436 – 25,548,540
Length 104
Max. P 0.934087
window15440 window15441

overview

Window 0

Location 25,548,436 – 25,548,540
Length 104
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 75.28
Mean single sequence MFE -34.98
Consensus MFE -14.28
Energy contribution -16.65
Covariance contribution 2.37
Combinations/Pair 1.41
Mean z-score -2.09
Structure conservation index 0.41
SVM decision value 0.31
SVM RNA-class probability 0.681045
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25548436 104 + 27905053
AUAGCUUGCGUUGGAGGAAGACAACCACUGUGGCGCCUGAAGUGGUCACUGGAUCCAGUGGAUCAACCGUUAACACGGUCACCACCACCGACCAUCCCAAGCUG
.(((((((.(((((.((..((..((((((..(....)...))))))(((((....)))))..)).(((((....))))).....)).))))).....))))))) ( -35.10)
>DroPse_CAF1 29658 95 + 1
ACAGCCUUCGCUGGCGGAAAACAACCCCAGCAGCCACAGAGGCAACCACUG---------GACACCCCAUGGACCUGGCCACCUCCACGGAGCAUCCCAAGAUG
...(((...(((((.((.......))))))).(((.....)))..(((.((---------(.....))))))....)))...(((....)))((((....)))) ( -28.60)
>DroSec_CAF1 32036 104 + 1
ACAGCUUGCGUUGGAGGAAGACAACCAGUGUGGCGCCUGAGGUGGUCACUGGAUCCAGUGGACCCACCAUUCACACUGUCACCACCACCGACCAUCCCAAGCUG
.(((((((.(((((.((........((((((((.......(((((((((((....))))))..)))))..))))))))......)).))))).....))))))) ( -40.04)
>DroEre_CAF1 32872 101 + 1
ACAGCUUGCGUUGGAAGAAGACAACCUCUGUGGCGCCUGAGGUGGUCACUGCU---GAUGGACCCACCGUUCACACAGUCACCACCACCGACCAUCCCAAGCUG
.(((((((.((((........))))....((((((...(.((((((.((((.(---(.(((((.....))))))))))).)))))).))).))))..))))))) ( -36.50)
>DroYak_CAF1 35174 104 + 1
ACAGCUUGCGUUGGAAGAAGACAACCUCUGUGGCGCCGGAGGUGGUCACUGCUUCCGGUGGGGCCAUCAUUCACACAGUCACCACCACCGACCAUCCCAAGCUG
.(((((((....(((((..(((.(((((((......))))))).)))....)))))((((((((.............))).)))))...........))))))) ( -41.02)
>DroPer_CAF1 29228 95 + 1
ACAGCCUUCGCUGGCGGAAAACAACCCCAGCAGCCACAGAGGCAACCACUG---------GACACCCCAUGGACCUGGCCACCUCCACGGAGCAUCCCAAGAUG
...(((...(((((.((.......))))))).(((.....)))..(((.((---------(.....))))))....)))...(((....)))((((....)))) ( -28.60)
>consensus
ACAGCUUGCGUUGGAGGAAGACAACCACUGUGGCGCCUGAGGUGGUCACUG______GUGGACCCACCAUUCACACGGUCACCACCACCGACCAUCCCAAGCUG
.((((((((((((..((........))...))))))....((((((.((((.....(((((.....)))))....)))).))))))............)))))) (-14.28 = -16.65 +   2.37)

alignment

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secondary structure

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dotplot

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Window 1

Location 25,548,436 – 25,548,540
Length 104
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 75.28
Mean single sequence MFE -43.82
Consensus MFE -20.04
Energy contribution -19.41
Covariance contribution -0.63
Combinations/Pair 1.36
Mean z-score -2.31
Structure conservation index 0.46
SVM decision value 1.23
SVM RNA-class probability 0.934087
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25548436 104 - 27905053
CAGCUUGGGAUGGUCGGUGGUGGUGACCGUGUUAACGGUUGAUCCACUGGAUCCAGUGACCACUUCAGGCGCCACAGUGGUUGUCUUCCUCCAACGCAAGCUAU
.((((((.(.(((..((.((((((((((((....))))))....(((((....)))))))))))..(((((((.....)).))))).)).))).).)))))).. ( -42.90)
>DroPse_CAF1 29658 95 - 1
CAUCUUGGGAUGCUCCGUGGAGGUGGCCAGGUCCAUGGGGUGUC---------CAGUGGUUGCCUCUGUGGCUGCUGGGGUUGUUUUCCGCCAGCGAAGGCUGU
.......((((((((((((((..(....)..)))))))))))))---------).((((..(((((.((....)).)))))......))))((((....)))). ( -40.90)
>DroSec_CAF1 32036 104 - 1
CAGCUUGGGAUGGUCGGUGGUGGUGACAGUGUGAAUGGUGGGUCCACUGGAUCCAGUGACCACCUCAGGCGCCACACUGGUUGUCUUCCUCCAACGCAAGCUGU
(((((((.(.(((...((((((....).((.(((..(((((...(((((....))))).)))))))).)))))))...((.......)).))).).))))))). ( -45.80)
>DroEre_CAF1 32872 101 - 1
CAGCUUGGGAUGGUCGGUGGUGGUGACUGUGUGAACGGUGGGUCCAUC---AGCAGUGACCACCUCAGGCGCCACAGAGGUUGUCUUCUUCCAACGCAAGCUGU
(((((((.(.(((..((.((((((.((((((....)((((....))))---.))))).)))))).)(((((((.....)).))))).)..))).).))))))). ( -45.10)
>DroYak_CAF1 35174 104 - 1
CAGCUUGGGAUGGUCGGUGGUGGUGACUGUGUGAAUGAUGGCCCCACCGGAAGCAGUGACCACCUCCGGCGCCACAGAGGUUGUCUUCUUCCAACGCAAGCUGU
(((((((.(.(((((((.((((((.(((((.....((.((....)).))...))))).)))))).))))).....(((((....)))))..)).).))))))). ( -47.30)
>DroPer_CAF1 29228 95 - 1
CAUCUUGGGAUGCUCCGUGGAGGUGGCCAGGUCCAUGGGGUGUC---------CAGUGGUUGCCUCUGUGGCUGCUGGGGUUGUUUUCCGCCAGCGAAGGCUGU
.......((((((((((((((..(....)..)))))))))))))---------).((((..(((((.((....)).)))))......))))((((....)))). ( -40.90)
>consensus
CAGCUUGGGAUGGUCGGUGGUGGUGACCGUGUGAAUGGUGGGUCCAC______CAGUGACCACCUCAGGCGCCACAGAGGUUGUCUUCCUCCAACGCAAGCUGU
(((((((((...(((.(.((((((.((............................)).)))))).).))).))......((((........)))).))))))). (-20.04 = -19.41 +  -0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:39:21 2006