Locus 4176

Sequence ID 2R_DroMel_CAF1
Location 13,739,855 – 13,739,985
Length 130
Max. P 0.574079
window6714 window6715

overview

Window 4

Location 13,739,855 – 13,739,965
Length 110
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 77.97
Mean single sequence MFE -23.44
Consensus MFE -12.52
Energy contribution -12.52
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 0.53
SVM decision value 0.08
SVM RNA-class probability 0.574079
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13739855 110 + 20766785
AUCAAAAACAUGCGCUCCUUAUUUUA---CCACGCAACGGAU-UAAAGCAAAUUAAAAGUCGGAUUAAAGACGUGCAUUUUUUCAGUGUAGCCGCACAUUAACUGCCGGCUGCA
....((((.((((((...........---((.......))..-...............(((........))))))))).))))...((((((((((.......)).)))))))) ( -24.40)
>DroSec_CAF1 41210 110 + 1
AUCAAAAACAUGCACUCUUUAUUUCA---CCACCCAACCGAUUUAAAGCAAAUCAAAA-UCCGAUUGCAGACGUGAAAUUUUUCAAUGUAGCCGCACAUUAACUGCGGGCUGCA
.(((......(((...(((((..((.---..........))..)))))..((((....-...)))))))....)))..........((((((((((.......))).))))))) ( -20.50)
>DroSim_CAF1 43961 110 + 1
AUCAAAAACAUGCACUCUUUAUUUCA---CCACCCAACCGAUUUAAUGCAAAUGAAAA-UACGAUUAAAGACGUGCAUUUUUUCAGUGUAGCCGCACAUUAACUGCCGGCUGCA
....((((.((((((((((((..((.---..........(........)..((....)-)..)).)))))).)))))).))))...((((((((((.......)).)))))))) ( -23.90)
>DroEre_CAF1 41088 96 + 1
------------CACAUUUUAGGUCA---UCACCCAACGAGU-G-AAACAAAUCAAAA-ACUGAUUAUAGACGUGUAUUUUUUCAGUGUAGCCGCACAUUAACUGCCGGCUGCA
------------.......((.(((.---((((.......))-)-)....(((((...-..)))))...))).))...........((((((((((.......)).)))))))) ( -21.00)
>DroYak_CAF1 43334 111 + 1
UGCCAAAACAGGCACUCUUUAUUUCAUGAUCAGCUGGCAAAU-U-AAACAAAUCAAAA-ACCGAUUGGAGUUGAGUAUUUUUUCAGUGUAGCCGCACAUUAACUGCCGGCUGCA
((((......))))................(((((((((...-.-.......((((..-.((....))..))))...........((((....))))......))))))))).. ( -27.40)
>consensus
AUCAAAAACAUGCACUCUUUAUUUCA___CCACCCAACCGAU_UAAAGCAAAUCAAAA_UCCGAUUAAAGACGUGCAUUUUUUCAGUGUAGCCGCACAUUAACUGCCGGCUGCA
......................................................................................((((((((((.......))).))))))) (-12.52 = -12.52 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,739,889 – 13,739,985
Length 96
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 79.15
Mean single sequence MFE -24.51
Consensus MFE -15.95
Energy contribution -15.15
Covariance contribution -0.80
Combinations/Pair 1.29
Mean z-score -1.27
Structure conservation index 0.65
SVM decision value 0.00
SVM RNA-class probability 0.534075
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13739889 96 - 20766785
CAGCAGUGGCAGCAACAAGUUGCAGC-CGGCAGUUAAUGUGCGGCUACACUGAAAAAAUGCACGUCUUUAAUCCGACUUUU-AAUUU-GCUUUA-AUCCG
...((((((((((.....)))))(((-(((((.....))).))))).)))))...........(((........)))....-.....-......-..... ( -24.60)
>DroSec_CAF1 41244 96 - 1
CAGCAGUGGCAGCAACAAGUUGCAGC-CCGCAGUUAAUGUGCGGCUACAUUGAAAAAUUUCACGUCUGCAAUCGGA-UUUU-GAUUU-GCUUUAAAUCGG
..(((((((((((.....)))))(((-(((((.....)))).))))................)).)))).......-...(-(((((-(...))))))). ( -25.30)
>DroSim_CAF1 43995 96 - 1
CAGCGGUGGCAGCAACAAGUUGCAGC-CGGCAGUUAAUGUGCGGCUACACUGAAAAAAUGCACGUCUUUAAUCGUA-UUUU-CAUUU-GCAUUAAAUCGG
...((((((((((.....)))))(((-(((((.....))).))))).)))))..........((..((((((.(((-....-....)-)))))))).)). ( -26.10)
>DroEre_CAF1 41110 94 - 1
CAGCAGUGGCAGCAACAAGUUGCAGC-CGGCAGUUAAUGUGCGGCUACACUGAAAAAAUACACGUCUAUAAUCAGU-UUUU-GAUUU-GUUU-C-ACUCG
...((((((((((.....)))))(((-(((((.....))).))))).))))).......(((.(((..........-....-))).)-))..-.-..... ( -24.04)
>DroYak_CAF1 43371 94 - 1
CAGCAGUGGCAGCAACAAGUUGCAGC-CGGCAGUUAAUGUGCGGCUACACUGAAAAAAUACUCAACUCCAAUCGGU-UUUU-GAUUU-GUUU-A-AUUUG
...((((((((((.....)))))(((-(((((.....))).))))).)))))...(((((.((((..((....)).-..))-))..)-))))-.-..... ( -26.00)
>DroAna_CAF1 43334 83 - 1
CAGUAGUGGCAGCAACAAGUUGCAGGUUGCCAGUUAAUGUGGAACUACACUGAACGCAUU----------AUUGGC-UUUUUAGUUUAGUUUUA------
((..(.(((((((((....))))....))))).)...))((((((((.((((((.((...----------....))-..)))))).))))))))------ ( -21.00)
>consensus
CAGCAGUGGCAGCAACAAGUUGCAGC_CGGCAGUUAAUGUGCGGCUACACUGAAAAAAUACACGUCUUUAAUCGGA_UUUU_GAUUU_GCUUUA_AUCCG
...((((((((((.....)))))(((.(.(((.......))))))).)))))................................................ (-15.95 = -15.15 +  -0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:34 2006