Locus 3609

Sequence ID X_DroMel_CAF1
Location 9,665,538 – 9,665,631
Length 93
Max. P 0.804552
window5905 window5906

overview

Window 5

Location 9,665,538 – 9,665,631
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.71
Mean single sequence MFE -23.10
Consensus MFE -17.00
Energy contribution -17.53
Covariance contribution 0.53
Combinations/Pair 1.05
Mean z-score -1.93
Structure conservation index 0.74
SVM decision value 0.63
SVM RNA-class probability 0.804552
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9665538 93 + 22224390
--------------------G------UUUUCAUUUGCAGGCCAAUUACGAUUUGUUGGGGCCAUCAUUUAUGCAGCAUUAUGCUGCAUUAUUAACCGAUUCAAUUAUUAAGUGAGCUC-
--------------------.------..((((((((..((((....((.....))...)))).......(((((((.....)))))))...................))))))))...- ( -23.00)
>DroSec_CAF1 1203 93 + 1
--------------------G------UUUUCAUUUGCAGGCCAAUUACGAUUUGUUAGGGCCAUCAUUUAUGCAGCAUUAUGCUGCAUUAUUAACCGAUUCAAUUAUUAAGUGAGCAC-
--------------------.------........(((.((((....((.....))...)))).(((((((((((((.....)))))))........(((......)))))))))))).- ( -23.30)
>DroAna_CAF1 29511 120 + 1
CGUUCUCAGUUUAAUUUUCGGUUUCCAUUUUCGCUUUCGGGCCAAUUACGUUUUGUUAGGGCCAUAAUUUAUGCAGCAUUAUGCUGCAUUAUUAACCGAUUCAAUUAUUGAGUGCCCCCC
.((.((((((.......(((((.................((((....((.....))...)))).((((..(((((((.....))))))).))))))))).......)))))).))..... ( -33.24)
>DroSim_CAF1 15607 93 + 1
--------------------G------UUUUCAUUUGCAGGCCAAUUACGAUUUGUUAGGGCCAUCAUUUAUGCAGCAUUAUGCUGCAUUAUUAACCGAUUCAAUUAUUAAGUGAGCAC-
--------------------.------........(((.((((....((.....))...)))).(((((((((((((.....)))))))........(((......)))))))))))).- ( -23.30)
>DroEre_CAF1 8020 96 + 1
-----------------UUGG------UUUCCAUUUGCAGGCCAAUUACGAUUUGUUAGGGCCAUCAUUUAUGCAGCAUUAUGCUGCAUUAUUAACCGAUUCAAUUAUUAAGUGAACAG-
-----------------((((------((..........((((....((.....))...)))).......(((((((.....)))))))....))))))....................- ( -22.60)
>DroYak_CAF1 12261 83 + 1
------------------------------------GCUGGCCAAUUACGAUUUGUUAGGGCCAUCAUUUAUGAAACAUUAUGCUGCAUUAUUAACCGAUUCAAUUAUUAAGUGAGCAG-
------------------------------------(((((((....((.....))...)))))(((((((((((.(....................).)))).....)))))))))..- ( -13.15)
>consensus
____________________G______UUUUCAUUUGCAGGCCAAUUACGAUUUGUUAGGGCCAUCAUUUAUGCAGCAUUAUGCUGCAUUAUUAACCGAUUCAAUUAUUAAGUGAGCAC_
.......................................((((....((.....))...)))).(((((((((((((.....)))))))........(((......)))))))))..... (-17.00 = -17.53 +   0.53)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,665,538 – 9,665,631
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.71
Mean single sequence MFE -20.78
Consensus MFE -16.72
Energy contribution -17.08
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -1.68
Structure conservation index 0.80
SVM decision value 0.55
SVM RNA-class probability 0.777555
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9665538 93 - 22224390
-GAGCUCACUUAAUAAUUGAAUCGGUUAAUAAUGCAGCAUAAUGCUGCAUAAAUGAUGGCCCCAACAAAUCGUAAUUGGCCUGCAAAUGAAAA------C--------------------
-..(((((.........)))...(((((((.(((((((.....)))))))..(((((...........))))).))))))).)).........------.-------------------- ( -19.80)
>DroSec_CAF1 1203 93 - 1
-GUGCUCACUUAAUAAUUGAAUCGGUUAAUAAUGCAGCAUAAUGCUGCAUAAAUGAUGGCCCUAACAAAUCGUAAUUGGCCUGCAAAUGAAAA------C--------------------
-.((((((.........)))...(((((((.(((((((.....)))))))..(((((...........))))).))))))).)))........------.-------------------- ( -20.50)
>DroAna_CAF1 29511 120 - 1
GGGGGGCACUCAAUAAUUGAAUCGGUUAAUAAUGCAGCAUAAUGCUGCAUAAAUUAUGGCCCUAACAAAACGUAAUUGGCCCGAAAGCGAAAAUGGAAACCGAAAAUUAAACUGAGAACG
........((((.(((((...((((((....(((((((.....))))))).......((((...((.....))....))))................)))))).)))))...)))).... ( -28.80)
>DroSim_CAF1 15607 93 - 1
-GUGCUCACUUAAUAAUUGAAUCGGUUAAUAAUGCAGCAUAAUGCUGCAUAAAUGAUGGCCCUAACAAAUCGUAAUUGGCCUGCAAAUGAAAA------C--------------------
-.((((((.........)))...(((((((.(((((((.....)))))))..(((((...........))))).))))))).)))........------.-------------------- ( -20.50)
>DroEre_CAF1 8020 96 - 1
-CUGUUCACUUAAUAAUUGAAUCGGUUAAUAAUGCAGCAUAAUGCUGCAUAAAUGAUGGCCCUAACAAAUCGUAAUUGGCCUGCAAAUGGAAA------CCAA-----------------
-..(((((.........))))).((((....(((((((.....)))))))...((..((((...((.....))....))))..))......))------))..----------------- ( -21.60)
>DroYak_CAF1 12261 83 - 1
-CUGCUCACUUAAUAAUUGAAUCGGUUAAUAAUGCAGCAUAAUGUUUCAUAAAUGAUGGCCCUAACAAAUCGUAAUUGGCCAGC------------------------------------
-.((((((.(((.((((((...)))))).))))).)))).................(((((...((.....))....)))))..------------------------------------ ( -13.50)
>consensus
_GUGCUCACUUAAUAAUUGAAUCGGUUAAUAAUGCAGCAUAAUGCUGCAUAAAUGAUGGCCCUAACAAAUCGUAAUUGGCCUGCAAAUGAAAA______C____________________
.......................(((((((.(((((((.....)))))))..(((((...........))))).)))))))....................................... (-16.72 = -17.08 +   0.36)

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 11:03:38 2006