Locus 8182

Sequence ID 3L_DroMel_CAF1
Location 21,528,011 – 21,528,153
Length 142
Max. P 0.636962
window13388 window13389 window13390

overview

Window 8

Location 21,528,011 – 21,528,117
Length 106
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 86.75
Mean single sequence MFE -31.82
Consensus MFE -24.92
Energy contribution -24.42
Covariance contribution -0.50
Combinations/Pair 1.17
Mean z-score -1.55
Structure conservation index 0.78
SVM decision value 0.21
SVM RNA-class probability 0.636962
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21528011 106 + 23771897
UCGGUAUCUGAAACUUUGGGCUAUCUUAGGAUAAUCCUUUCACUCGAUAGUGUGUGU--GUGUGUGUGCAGGCGAGCGAUAUGCUCGCAAUUUAUGUACGCAAU------CGCA
.((.(((((((((....((..((((....))))..)))))))...)))).))..(((--(..((((((((.((((((.....))))))......))))))))..------)))) ( -34.70)
>DroSec_CAF1 33407 108 + 1
UCGGAAUCUGAAACUUUGGGCUAUCUUAGGAUAAUCCUUUCACUCGAGAGUGUGUGUGUGUGUGUGUGCAGGCGAGCGAUAUGCUCGCAAUUUAUGUACGCAAU------CGCA
((((...))))......((..((((....))))..))...(((.(....).)))..((((..((((((((.((((((.....))))))......))))))))..------)))) ( -34.50)
>DroSim_CAF1 33789 108 + 1
UCGGAAUCUGAAACUUUGGGCUAUCUUAGGAUAAUCCUUUCACUCAAGAGUGUGUGUGUGUGUGUGUGCAGGCGAGCGAUAUGCUCGCAAUUUAUGUACGCAAU------CGCA
((((...))))......((..((((....))))..))...((((....))))....((((..((((((((.((((((.....))))))......))))))))..------)))) ( -33.30)
>DroYak_CAF1 8598 100 + 1
UCGGAAUCUGGAUCUUUGGACUAUCUUAGAAUAAUCCUUUUACUCGA--------------GUGUGUGCAGGCGAGCGAUAUGUUCGCAAUUUAUGUACGCAAUCGCAAUCGCA
..(((.(((((((.........))).))))....)))........((--------------.((((((((.((((((.....))))))......)))))))).))((....)). ( -24.80)
>consensus
UCGGAAUCUGAAACUUUGGGCUAUCUUAGGAUAAUCCUUUCACUCGAGAGUGUGUGU__GUGUGUGUGCAGGCGAGCGAUAUGCUCGCAAUUUAUGUACGCAAU______CGCA
........(((......(((.((((....)))).)))......)))................((((((((.((((((.....))))))......))))))))............ (-24.92 = -24.42 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,528,050 – 21,528,153
Length 103
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 88.70
Mean single sequence MFE -32.77
Consensus MFE -26.64
Energy contribution -28.02
Covariance contribution 1.38
Combinations/Pair 1.06
Mean z-score -1.47
Structure conservation index 0.81
SVM decision value 0.13
SVM RNA-class probability 0.597139
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21528050 103 + 23771897
UCACUCGAUAGUGUGUGU--GUGUGUGUGCAGGCGAGCGAUAUGCUCGCAAUUUAUGUACGCAAU------CGCAAUCUACGGUGGGUAAACACAGCUGCAAAUGCGUUUC
((((.((.(((..((((.--...((((((((.((((((.....))))))......))))))))..------))))..)))))))))..((((.((........)).)))). ( -33.80)
>DroSec_CAF1 33446 105 + 1
UCACUCGAGAGUGUGUGUGUGUGUGUGUGCAGGCGAGCGAUAUGCUCGCAAUUUAUGUACGCAAU------CGCAAUCUACGGUGGGUAAACACAGCUGCAAAUGCGUUUC
((((.(((((.((((..((((((..((.....((((((.....))))))....))..))))))..------)))).))).))))))..((((.((........)).)))). ( -35.20)
>DroSim_CAF1 33828 105 + 1
UCACUCAAGAGUGUGUGUGUGUGUGUGUGCAGGCGAGCGAUAUGCUCGCAAUUUAUGUACGCAAU------CGCAAUCUACGGUGGGUAAACACAGCUGCAAAUGCGUUUC
..(((((...(((..((((....((((((((.((((((.....))))))......))))))))..------))))...)))..)))))((((.((........)).)))). ( -33.90)
>DroYak_CAF1 8637 97 + 1
UUACUCGA--------------GUGUGUGCAGGCGAGCGAUAUGUUCGCAAUUUAUGUACGCAAUCGCAAUCGCAAUCUACGGUGGGUAAACACAGCUGCAAAUGCGUUUC
((((((((--------------.((((((((.((((((.....))))))......)))))))).))((....))..........)))))).....((.......))..... ( -28.20)
>consensus
UCACUCGAGAGUGUGUGU__GUGUGUGUGCAGGCGAGCGAUAUGCUCGCAAUUUAUGUACGCAAU______CGCAAUCUACGGUGGGUAAACACAGCUGCAAAUGCGUUUC
(((((..(((.((((........((((((((.((((((.....))))))......))))))))........)))).)))..)))))..((((.((........)).)))). (-26.64 = -28.02 +   1.38)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,528,050 – 21,528,153
Length 103
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 88.70
Mean single sequence MFE -27.82
Consensus MFE -19.56
Energy contribution -20.81
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.70
SVM decision value 0.13
SVM RNA-class probability 0.600103
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21528050 103 - 23771897
GAAACGCAUUUGCAGCUGUGUUUACCCACCGUAGAUUGCG------AUUGCGUACAUAAAUUGCGAGCAUAUCGCUCGCCUGCACACACAC--ACACACACUAUCGAGUGA
...(((((.(((((((((((......)))...)).)))))------).))))).........((((((.....))))))............--.....((((....)))). ( -28.60)
>DroSec_CAF1 33446 105 - 1
GAAACGCAUUUGCAGCUGUGUUUACCCACCGUAGAUUGCG------AUUGCGUACAUAAAUUGCGAGCAUAUCGCUCGCCUGCACACACACACACACACACUCUCGAGUGA
...(((((.(((((((((((......)))...)).)))))------).))))).........((((((.....))))))...................((((....)))). ( -29.20)
>DroSim_CAF1 33828 105 - 1
GAAACGCAUUUGCAGCUGUGUUUACCCACCGUAGAUUGCG------AUUGCGUACAUAAAUUGCGAGCAUAUCGCUCGCCUGCACACACACACACACACACUCUUGAGUGA
...(((((.(((((((((((......)))...)).)))))------).))))).........((((((.....))))))...................((((....)))). ( -29.20)
>DroYak_CAF1 8637 97 - 1
GAAACGCAUUUGCAGCUGUGUUUACCCACCGUAGAUUGCGAUUGCGAUUGCGUACAUAAAUUGCGAACAUAUCGCUCGCCUGCACACAC--------------UCGAGUAA
...(((((.((((((.(((((((((.....))))).)))).)))))).)))))....................(((((..((....)).--------------.))))).. ( -24.30)
>consensus
GAAACGCAUUUGCAGCUGUGUUUACCCACCGUAGAUUGCG______AUUGCGUACAUAAAUUGCGAGCAUAUCGCUCGCCUGCACACACAC__ACACACACUCUCGAGUGA
...(((((......((...((((((.....)))))).)).........))))).........((((((.....))))))...................((((....)))). (-19.56 = -20.81 +   1.25)

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 13:08:49 2006