Locus 3282

Sequence ID 3L_DroMel_CAF1
Location 9,626,182 – 9,626,317
Length 135
Max. P 0.684818
window5103 window5104

overview

Window 3

Location 9,626,182 – 9,626,290
Length 108
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 76.44
Mean single sequence MFE -28.27
Consensus MFE -13.77
Energy contribution -14.22
Covariance contribution 0.45
Combinations/Pair 1.36
Mean z-score -1.79
Structure conservation index 0.49
SVM decision value -0.04
SVM RNA-class probability 0.511537
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9626182 108 - 23771897
CAACUAACUAAAAUAGUUUA-UAGUUGUCAUGACAACAUUUCCACUGUUGUU--CUGGCCGACU--UAGAUAUGAG--CAUGGGUCAGAAAUUGAUCCGAGCUCCACCGCCAUCU
...............(((((-.((((((((.(((((((.......)))))))--.))).)))))--)))))..(((--(.((((((((...)))))))).))))........... ( -29.10)
>DroSec_CAF1 21974 108 - 1
CAACUAAGUAAAAUAGUUUA-UAGUUGUCAUGACAACAAUUCGACUGUUGUU--CUGGCCGUCU--CAGAUAUGAG--CAGGGGUCGGAAAUUGAUCCGAGCUUCACCGCCAUCU
......((...(((((((.(-(.(((((....))))).))..)))))))...--))(((.(.((--((....))))--).(((((((((......))))).))))...))).... ( -28.80)
>DroSim_CAF1 24466 108 - 1
CAACUAACUAAAAUAGUUUA-UAGUUGUCAUGACAACAUUUCGACUGUUGUU--CUGGCCGACU--CAAAUAUGAG--CAUGGGUCGGAAAUUGAUCCGAGCUUCACCGCCAUCU
((((((((((...))))...-))))))....(((((((.......)))))))--.((((.(.((--((....))))--)..((.(((((......))))).)).....))))... ( -26.10)
>DroEre_CAF1 21263 108 - 1
CAAGCAGCUAAAAUAGUUUA-UAGUUGUCAUGCCAACAUUUCCACUGUUGUU--CUGGCCAGCU--CAGAUAUGAG--CAUGGGUCAGAAAUUGAUCCCAGCUUGAACGCCAUCU
((((((((((...)))))..-..(..((((...(((((.......)))))((--((((((.(((--((....))))--)...))))))))..))))..).))))).......... ( -31.80)
>DroYak_CAF1 22018 110 - 1
CAAGCAACUAAAAUAGUUUA-UAGUUGUCAUGACGACAUUUCCACUGUUGUC--CUGGCCAGCU--CAGAUAUGAGGGUAUGGUUCAGAAAUUGAUCCGAGCCUCAACGCCAUCU
...(((((((.((....)).-)))))))...(((((((.......)))))))--.((((...((--((....))))(((.(((.((((...)))).))).))).....))))... ( -29.50)
>DroAna_CAF1 34376 93 - 1
------CUUAAAAUAGUUUGGCCGUUGGCAUGACAACUUUAUGACUCUUGUUUGUUGUCCAGCUUUUGGACGUAAG--CC-GGGCCAGC-------------AUCCCACUCAUCC
------.........(..(((..((((((..((((((.....(((....))).))))))......((((.(....)--))-))))))))-------------...)))..).... ( -24.30)
>consensus
CAACUAACUAAAAUAGUUUA_UAGUUGUCAUGACAACAUUUCCACUGUUGUU__CUGGCCAGCU__CAGAUAUGAG__CAUGGGUCAGAAAUUGAUCCGAGCUUCACCGCCAUCU
...............((((...((((((((.(((((((.......)))))))...))).)))))...))))..........((((((.....))))))................. (-13.77 = -14.22 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,626,218 – 9,626,317
Length 99
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 76.55
Mean single sequence MFE -21.82
Consensus MFE -13.10
Energy contribution -12.86
Covariance contribution -0.24
Combinations/Pair 1.18
Mean z-score -1.71
Structure conservation index 0.60
SVM decision value 0.31
SVM RNA-class probability 0.684818
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9626218 99 - 23771897
AUUGGC---------CACCAUACCCAUACUAAGCUACAACUAACUAAAAUAGUUUAUAGUUGUCAUGACAACAUUUCCACUGUUGUUCUGGCCGACUUAGAUAUGAG--C
.(((((---------((..................(((((((((((...))))...)))))))...(((((((.......))))))).)))))))((((....))))--. ( -22.20)
>DroSec_CAF1 22010 107 - 1
GUUGCC-CCCACCCCCGCCAUACUCAUACUAAACUACAACUAAGUAAAAUAGUUUAUAGUUGUCAUGACAACAAUUCGACUGUUGUUCUGGCCGUCUCAGAUAUGAG--C
......-...............((((((((.(((((.(((((.......)))))..)))))((((.(((((((.......))))))).))))......)).))))))--. ( -20.80)
>DroSim_CAF1 24502 108 - 1
GUUGUCACCCACCCCCCCCAUACUCAUACUAAACUACAACUAACUAAAAUAGUUUAUAGUUGUCAUGACAACAUUUCGACUGUUGUUCUGGCCGACUCAAAUAUGAG--C
......................((((((.(((((((.............))))))).((((((((.(((((((.......))))))).))).)))))....))))))--. ( -20.42)
>DroEre_CAF1 21299 88 - 1
GUUG----------------GCCCCAUCCU----CUCAAGCAGCUAAAAUAGUUUAUAGUUGUCAUGCCAACAUUUCCACUGUUGUUCUGGCCAGCUCAGAUAUGAG--C
..((----------------(((.......----.....(((((((.((....)).))))))).....(((((.......)))))....)))))(((((....))))--) ( -22.80)
>DroYak_CAF1 22054 103 - 1
GCAGCU-CCCGUC--CUCGAUCCCCAUCCU----CCCAAGCAACUAAAAUAGUUUAUAGUUGUCAUGACGACAUUUCCACUGUUGUCCUGGCCAGCUCAGAUAUGAGGGU
......-....((--(((((((........----.......(((((...)))))...((((((((.(((((((.......))))))).))).)))))..))).)))))). ( -22.90)
>consensus
GUUGCC_CCC__C__C_CCAUACCCAUACUAA_CUACAACUAACUAAAAUAGUUUAUAGUUGUCAUGACAACAUUUCCACUGUUGUUCUGGCCGACUCAGAUAUGAG__C
.........................................(((((.((....)).)))))((((.(((((((.......))))))).))))...((((....))))... (-13.10 = -12.86 +  -0.24)

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 10:53:49 2006