Locus 5306

Sequence ID 3L_DroMel_CAF1
Location 14,665,769 – 14,665,889
Length 120
Max. P 0.737124
window8386 window8387

overview

Window 6

Location 14,665,769 – 14,665,889
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.42
Mean single sequence MFE -28.08
Consensus MFE -20.37
Energy contribution -20.66
Covariance contribution 0.29
Combinations/Pair 1.16
Mean z-score -1.83
Structure conservation index 0.73
SVM decision value 0.44
SVM RNA-class probability 0.737124
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14665769 120 + 23771897
CGUCGUCCAGAAUUGCAGAUUCAUUUUGUAGUGUUUUCAAAUGUUCCUUCAGCUGUUCAUCUGAGGAACAGCUUGGACUACCUGGUGGACUACCAUUUUUAAUCAUUUCUGUUGUUGCCU
.(((..((((.((((((((.....))))))))...(((((.(((((((.(((........))))))))))..)))))....))))..))).............................. ( -29.40)
>DroSec_CAF1 15517 120 + 1
CGUCGUCCAGAAUUGCAGAUUCAUUUUGUAGUGUUUUCAAACGUUCCUUCAGCUGUUCAUCUGAGGAACAGCUUGGAUUACCUGGUGGACUACCACUUUUAGUCAUUUCUGUUGUUGCCU
...((.((((.((((((((.....))))))))............(((...((((((((.......)))))))).)))....))))))(((((.......)))))................ ( -29.30)
>DroSim_CAF1 16332 120 + 1
CGUCGUCCAGAAUUGCAGAUUCAUUUUGUAGUGUUUUCAAACGUUCCUUCAGCUGUUCAUCUGAGGAACAGCUUAGACUACCUGGUGGACUACCAUUUAUAGUCAUUUCUUUUGUUGCCU
(((........((((((((.....))))))))........))).......((((((((.......))))))))..(((((...(((((....)))))..)))))................ ( -27.19)
>DroEre_CAF1 16028 120 + 1
CGUCAUCCAGAAUCUUAGACUCAUUUUGAAGUGCUUUAAUACGUUCCUUCAGCUGUUCAUCUGAGGAACAGCUUUGAUUACUUGUUGAACUUUCAUUUUUAGUCAUUUCUGGUGAUGCCU
(((((.((((((.....((((.....(((((.(.(((((((.((......((((((((.......))))))))......)).))))))))))))).....))))..)))))))))))... ( -34.30)
>DroYak_CAF1 16288 105 + 1
CGUCAUCCAGAAUUUUAGAUUCGUUUUGAAGUGCUUUAAUACGUUCCUCCAGCUGUUUAUCUGAGGCACAGUUUUCAUUACU---------------UUUAGUAAUUUCUGUUGAUGCCU
(((((..(((((..(((((...((..((((((((((((..(((((.....))).)).....))))))))....))))..)).---------------)))))....))))).)))))... ( -20.20)
>consensus
CGUCGUCCAGAAUUGCAGAUUCAUUUUGUAGUGUUUUCAAACGUUCCUUCAGCUGUUCAUCUGAGGAACAGCUUGGAUUACCUGGUGGACUACCAUUUUUAGUCAUUUCUGUUGUUGCCU
.......((((((((((((.....))))))))..........((((((.(((........)))))))))......(((((...(((((....)))))..)))))...))))......... (-20.37 = -20.66 +   0.29)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,665,769 – 14,665,889
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.42
Mean single sequence MFE -26.79
Consensus MFE -16.03
Energy contribution -15.78
Covariance contribution -0.25
Combinations/Pair 1.26
Mean z-score -1.99
Structure conservation index 0.60
SVM decision value 0.11
SVM RNA-class probability 0.587925
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14665769 120 - 23771897
AGGCAACAACAGAAAUGAUUAAAAAUGGUAGUCCACCAGGUAGUCCAAGCUGUUCCUCAGAUGAACAGCUGAAGGAACAUUUGAAAACACUACAAAAUGAAUCUGCAAUUCUGGACGACG
.(....)..(((((.((.......((.(((((....(((((..(((.((((((((.......))))))))...)))..))))).....)))))...)).......)).)))))....... ( -30.24)
>DroSec_CAF1 15517 120 - 1
AGGCAACAACAGAAAUGACUAAAAGUGGUAGUCCACCAGGUAAUCCAAGCUGUUCCUCAGAUGAACAGCUGAAGGAACGUUUGAAAACACUACAAAAUGAAUCUGCAAUUCUGGACGACG
.(....)..(((((.((.......((((....))))(((((..(((.((((((((.......))))))))...))).(((((............))))).))))))).)))))....... ( -30.80)
>DroSim_CAF1 16332 120 - 1
AGGCAACAAAAGAAAUGACUAUAAAUGGUAGUCCACCAGGUAGUCUAAGCUGUUCCUCAGAUGAACAGCUGAAGGAACGUUUGAAAACACUACAAAAUGAAUCUGCAAUUCUGGACGACG
.(....).........((((((.....))))))..(((((((((.(((((.(((((((((........))).))))))))))).....)))))....((......))...))))...... ( -28.00)
>DroEre_CAF1 16028 120 - 1
AGGCAUCACCAGAAAUGACUAAAAAUGAAAGUUCAACAAGUAAUCAAAGCUGUUCCUCAGAUGAACAGCUGAAGGAACGUAUUAAAGCACUUCAAAAUGAGUCUAAGAUUCUGGAUGACG
.....(((((((((..((((.....((((.((((.............((((((((.......))))))))....))))((......))..)))).....)))).....)))))).))).. ( -27.93)
>DroYak_CAF1 16288 105 - 1
AGGCAUCAACAGAAAUUACUAAA---------------AGUAAUGAAAACUGUGCCUCAGAUAAACAGCUGGAGGAACGUAUUAAAGCACUUCAAAACGAAUCUAAAAUUCUGGAUGACG
.(.((((..((((((((((....---------------.)))))(((....((.((((((........)).)))).))((......))..)))...............))))))))).). ( -17.00)
>consensus
AGGCAACAACAGAAAUGACUAAAAAUGGUAGUCCACCAGGUAAUCAAAGCUGUUCCUCAGAUGAACAGCUGAAGGAACGUUUGAAAACACUACAAAAUGAAUCUGCAAUUCUGGACGACG
.........(((((.((........(((....)))...(((....(((((.(((((((((........))).))))))))))).....)))..............)).)))))....... (-16.03 = -15.78 +  -0.25)

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 11:46:51 2006