Locus 4182

Sequence ID 2L_DroMel_CAF1
Location 11,977,452 – 11,977,576
Length 124
Max. P 0.530736
window6610 window6611

overview

Window 0

Location 11,977,452 – 11,977,548
Length 96
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 90.10
Mean single sequence MFE -25.81
Consensus MFE -21.26
Energy contribution -20.90
Covariance contribution -0.36
Combinations/Pair 1.15
Mean z-score -1.30
Structure conservation index 0.82
SVM decision value -0.06
SVM RNA-class probability 0.505169
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11977452 96 + 22407834
----ACUUUUUGGCCUGCGGUUACGGUUGGCC-----GCUGUCUAAGCAUUAAAUCAACCAGCAGCUGUAAAAUUACAGCAAAUGUUUAACCAACCCCUUUCGGG
----.....((((..(((((((..((....))-----(((.....)))........)))).)))((((((....))))))..........)))).(((....))) ( -25.20)
>DroSec_CAF1 196873 95 + 1
----ACUUUUUGGCCUGCGGUUACGGUUGGCC-----GCUGUCUAAGCAUUAAAUCAACCAGCAGCUGUAAAAUUACAGCAAAUGUUUAACUAACCCCUU-CGGG
----.......(((..(((((((....)))))-----)).)))((((((((....(.....)..((((((....)))))).)))))))).......((..-..)) ( -24.20)
>DroSim_CAF1 163303 95 + 1
----ACUUUUUGGCCUGCGGUUACGGUUGGCC-----GCUGUCUAAGCAUUAAAUCAACCAGCAGCUGUAAAAUUACAGCAAAUGUUUAACCAACCCCUU-CGGG
----.....((((..(((((((..((....))-----(((.....)))........)))).)))((((((....))))))..........))))..((..-..)) ( -25.30)
>DroEre_CAF1 171319 98 + 1
UUCAGGUUUUUGGCCUGCGGUUACGGUUGGCC-----GCUGUCUAAGCAUUAAACCAACCAGCAGCUGUAAAAUUACGGCAAAUGUUUAACCAACCC-CG-CUGC
...((((.....))))((((....((((((..-----((((..................)))).((((((....))))))..........)))))))-))-)... ( -28.67)
>DroYak_CAF1 168316 100 + 1
----AGUUUUUGGCCUGCGGUUACGCUUGGCUGUCUAGCUGUCUAAGCAUUAAAUCAACCAGCAGCUGUAAAAUUACGGCAAAUGUUUAACCAACCCCCG-CGGC
----........(((.((((....(((.((.((....(((.....))).......)).))))).((((((....)))))).................)))-)))) ( -25.70)
>consensus
____ACUUUUUGGCCUGCGGUUACGGUUGGCC_____GCUGUCUAAGCAUUAAAUCAACCAGCAGCUGUAAAAUUACAGCAAAUGUUUAACCAACCCCUU_CGGG
..................(((((.((((((.......(((.....)))......))))))....((((((....)))))).......)))))............. (-21.26 = -20.90 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,977,480 – 11,977,576
Length 96
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 84.08
Mean single sequence MFE -27.93
Consensus MFE -19.83
Energy contribution -20.03
Covariance contribution 0.20
Combinations/Pair 1.10
Mean z-score -1.59
Structure conservation index 0.71
SVM decision value -0.01
SVM RNA-class probability 0.530736
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11977480 96 + 22407834
-----GCUGUCUAAGCAUUAAAUCAACCAGCAGCUGUAAAAUUACAGCAAAUGUUUAACCAACCCCUUUCGGGGG-G---AAAAUUGGGCAGGUG--------GGGCCAACUG
-----(((.....)))..........(((.(.((((((....))))))...(((((((....(((((....))))-)---....)))))))).))--------)......... ( -28.30)
>DroSec_CAF1 196901 97 + 1
-----GCUGUCUAAGCAUUAAAUCAACCAGCAGCUGUAAAAUUACAGCAAAUGUUUAACUAACCCCUU-CGGGGG-AAA-AAAAUUGGGCAGGUG--------GGGCCAACUG
-----(((.....)))..........(((.(.((((((....))))))...(((((((....((((..-..))))-...-....)))))))).))--------)......... ( -28.60)
>DroSim_CAF1 163331 98 + 1
-----GCUGUCUAAGCAUUAAAUCAACCAGCAGCUGUAAAAUUACAGCAAAUGUUUAACCAACCCCUU-CGGGGG-AAAAAAAAUUGGGCAGGUG--------GGGCCAACUG
-----(((.....)))......((.(((.((.((((((....))))))..........((((((((..-..))))-........)))))).))).--------))........ ( -28.60)
>DroEre_CAF1 171351 92 + 1
-----GCUGUCUAAGCAUUAAACCAACCAGCAGCUGUAAAAUUACGGCAAAUGUUUAACCAACCC-CG-CUGCGGGCCA-AAAAUUGGGGAGGUG--------GGGCG-----
-----..((..((((((((....(.....)..((((((....)))))).))))))))..)).(((-((-((.....(((-.....)))...))))--------)))..----- ( -24.70)
>DroYak_CAF1 168344 105 + 1
GUCUAGCUGUCUAAGCAUUAAAUCAACCAGCAGCUGUAAAAUUACGGCAAAUGUUUAACCAACCCCCG-CGGCGG-----AAAAUUGGGGAGGUGCUGUGGUGGGGCA--CUG
.....(((.....))).............((.((((((....))))))..............((((((-(((((.-----.............)))))))).))))).--... ( -29.44)
>consensus
_____GCUGUCUAAGCAUUAAAUCAACCAGCAGCUGUAAAAUUACAGCAAAUGUUUAACCAACCCCUU_CGGGGG_A_A_AAAAUUGGGCAGGUG________GGGCCAACUG
........((((.........(((..((((..((((((....))))))..............((((.....)))).........))))...))).........))))...... (-19.83 = -20.03 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:48 2006