Locus 4075

Sequence ID 3L_DroMel_CAF1
Location 11,874,883 – 11,875,022
Length 139
Max. P 0.905209
window6343 window6344 window6345

overview

Window 3

Location 11,874,883 – 11,874,985
Length 102
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 85.47
Mean single sequence MFE -31.77
Consensus MFE -26.69
Energy contribution -27.17
Covariance contribution 0.47
Combinations/Pair 1.14
Mean z-score -2.42
Structure conservation index 0.84
SVM decision value 1.04
SVM RNA-class probability 0.905209
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11874883 102 + 23771897
GACCACAGGGUCAAAGUUGUUUUCUAUAUGAAAUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAUCGGCCAACAUGUCCUGCACACAAUGCGUCCGCACU
((((....))))..(((.((((((.....))))....(((((((...(((....))).(((((((((.(.....))))))))))...)))))))...))))) ( -36.10)
>DroSec_CAF1 50331 86 + 1
GACCACAGGGUCAAAGUUGUUUUCUAUAUGAAAUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAUCGGCCAACAUGUCCUGCAC----------------
(.((((((((((((.((...((((.....)))).....)).)))))..)))).))).)(((((((((.(.....))))))))))..---------------- ( -31.20)
>DroSim_CAF1 50819 86 + 1
GACCACAGGGUCAAAGUUGUUUUCUAUAUGAAGUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAUCGGCCAACAUGUCCUGCAC----------------
(.((((((((((((.((...((((.....)))).....)).)))))..)))).))).)(((((((((.(.....))))))))))..---------------- ( -30.90)
>DroEre_CAF1 52387 101 + 1
GACCACGGGGUCAAAGUUGUUUUCUAUAUGAAAUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAUC-GCCAACAUGUCCUGCACACAAUGCGUACGCACU
((((....))))..((((((((((.....))))....(((((((...(((....))).(((((((((.-......)))))))))...))))))).))).))) ( -35.40)
>DroYak_CAF1 52254 102 + 1
GACCACAGGGUCAAAGUUGUUUUCUAUAUGGAAUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAACGGCCAACAUGUCCUGCACACAAUGCGUCCGCACU
((((....)))).................(((.....(((((((...(((....))).((((((((..........))))))))...))))))))))..... ( -34.80)
>DroAna_CAF1 48812 94 + 1
GUCCGCAGGGUCAAAGUUGUUUUCUAUAUGAAAUAUUCGCAUUGACAGCCAGUUGGCCGCAGGACA-CGGCAAACAUGAACCGCACACUCGGCGC-------
((((((...(((((.((...((((.....)))).....)).))))).(((....))).)).)))).-..............(((.......))).------- ( -22.20)
>consensus
GACCACAGGGUCAAAGUUGUUUUCUAUAUGAAAUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAUCGGCCAACAUGUCCUGCACACAAUGCGU_______
(.((((((((((((.((...((((.....)))).....)).)))))..)))).))).)(((((((((........))))))))).................. (-26.69 = -27.17 +   0.47)

alignment

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secondary structure

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Window 4

Location 11,874,907 – 11,875,022
Length 115
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 81.25
Mean single sequence MFE -34.43
Consensus MFE -21.99
Energy contribution -23.22
Covariance contribution 1.22
Combinations/Pair 1.11
Mean z-score -1.82
Structure conservation index 0.64
SVM decision value 0.30
SVM RNA-class probability 0.679046
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11874907 115 + 23771897
UAUAUGAAAUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAUCGGCCAACAUGUCCUGCACACAAUGCGUCCGCACUUCCGCAGGACAGCGAGGGUCGGCACAGUAAACAA--ACG
..............((((((...(((....))).(((((((((.(.....))))))))))...))))))(((((.(((..(((......)))..)))))).)).........--... ( -42.80)
>DroSec_CAF1 50355 96 + 1
UAUAUGAAAUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAUCGGCCAACAUGUCCUGCAC-------------------GCAGGACAGCGAGGGUCGGCACAGUAAACAA--ACG
.................(((...((.(((((((((((((((((.(.....)))))))))).(-------------------((......)))..))))))))..))...)))--... ( -33.10)
>DroSim_CAF1 50843 96 + 1
UAUAUGAAGUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAUCGGCCAACAUGUCCUGCAC-------------------GCAGGACAGCGAGGGUCGGCACAGUAAACAA--ACG
.................(((...((.(((((((((((((((((.(.....)))))))))).(-------------------((......)))..))))))))..))...)))--... ( -33.10)
>DroEre_CAF1 52411 114 + 1
UAUAUGAAAUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAUC-GCCAACAUGUCCUGCACACAAUGCGUACGCACUUCCGCAGGACGACGAGGGUAGGCACAGUAAACAA--ACG
.............(((((((...(((....))).(((((((((.-......)))))))))...)))))))...((.(((((...(.....)..))).))))...........--... ( -34.70)
>DroYak_CAF1 52278 115 + 1
UAUAUGGAAUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAACGGCCAACAUGUCCUGCACACAAUGCGUCCGCACUUCCGCAGGACAACGAGGGUAGGCACAGUAAACAA--ACG
....(((..(((((((((((...(((....))).((((((((..........))))))))...))))))((((((......)).)))).....)))))..).))........--... ( -38.80)
>DroAna_CAF1 48836 102 + 1
UAUAUGAAAUAUUCGCAUUGACAGCCAGUUGGCCGCAGGACA-CGGCAAACAUGAACCGCACACUCGGCGC--------------CAGAACGAGGGUAGGCCCGUCAAACAACAACA
.................(((((.(((.(((.((((.......-)))).))).......((...((((....--------------.....)))).)).)))..)))))......... ( -24.10)
>consensus
UAUAUGAAAUAUUCGCAUUGACAGCCUGCUGGCCGCAGGACAUCGGCCAACAUGUCCUGCACACAAUGCGU__________GCAGGACAACGAGGGUAGGCACAGUAAACAA__ACG
.......................(((.((((((((........)))))....((((((((.....................)))))))).....))).)))................ (-21.99 = -23.22 +   1.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,874,907 – 11,875,022
Length 115
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 81.25
Mean single sequence MFE -40.14
Consensus MFE -28.54
Energy contribution -30.87
Covariance contribution 2.33
Combinations/Pair 1.07
Mean z-score -2.17
Structure conservation index 0.71
SVM decision value 0.84
SVM RNA-class probability 0.865055
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11874907 115 - 23771897
CGU--UUGUUUACUGUGCCGACCCUCGCUGUCCUGCGGAAGUGCGGACGCAUUGUGUGCAGGACAUGUUGGCCGAUGUCCUGCGGCCAGCAGGCUGUCAAUGCGAAUAUUUCAUAUA
.((--((((.......(((.........(((((((((.((((((....))))).).)))))))))(((((((((........)))))))))))).......)))))).......... ( -46.44)
>DroSec_CAF1 50355 96 - 1
CGU--UUGUUUACUGUGCCGACCCUCGCUGUCCUGC-------------------GUGCAGGACAUGUUGGCCGAUGUCCUGCGGCCAGCAGGCUGUCAAUGCGAAUAUUUCAUAUA
.((--((((.......(((.........(((((((.-------------------...)))))))(((((((((........)))))))))))).......)))))).......... ( -37.04)
>DroSim_CAF1 50843 96 - 1
CGU--UUGUUUACUGUGCCGACCCUCGCUGUCCUGC-------------------GUGCAGGACAUGUUGGCCGAUGUCCUGCGGCCAGCAGGCUGUCAAUGCGAAUACUUCAUAUA
.((--((((.......(((.........(((((((.-------------------...)))))))(((((((((........)))))))))))).......)))))).......... ( -37.04)
>DroEre_CAF1 52411 114 - 1
CGU--UUGUUUACUGUGCCUACCCUCGUCGUCCUGCGGAAGUGCGUACGCAUUGUGUGCAGGACAUGUUGGC-GAUGUCCUGCGGCCAGCAGGCUGUCAAUGCGAAUAUUUCAUAUA
.((--((((.......(((......(((.((((((((.((((((....))))).).)))))))))))..)))-((((.(((((.....))))).))))...)))))).......... ( -40.00)
>DroYak_CAF1 52278 115 - 1
CGU--UUGUUUACUGUGCCUACCCUCGUUGUCCUGCGGAAGUGCGGACGCAUUGUGUGCAGGACAUGUUGGCCGUUGUCCUGCGGCCAGCAGGCUGUCAAUGCGAAUAUUCCAUAUA
.((--((((.......((((........(((((((((.((((((....))))).).))))))))).(((((((((......))))))))))))).......)))))).......... ( -48.44)
>DroAna_CAF1 48836 102 - 1
UGUUGUUGUUUGACGGGCCUACCCUCGUUCUG--------------GCGCCGAGUGUGCGGUUCAUGUUUGCCG-UGUCCUGCGGCCAACUGGCUGUCAAUGCGAAUAUUUCAUAUA
..((((...((((((((((.((....))...)--------------))((((((..((((((........))))-))..)).)))).......))))))).))))............ ( -31.90)
>consensus
CGU__UUGUUUACUGUGCCGACCCUCGCUGUCCUGC__________ACGCAUUGUGUGCAGGACAUGUUGGCCGAUGUCCUGCGGCCAGCAGGCUGUCAAUGCGAAUAUUUCAUAUA
.....((((.......(((..........(((((((...(((((....)))))....))))))).(((((((((........)))))))))))).......))))............ (-28.54 = -30.87 +   2.33)

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 11:13:55 2006