Locus 2387

Sequence ID 3L_DroMel_CAF1
Location 6,706,441 – 6,706,568
Length 127
Max. P 0.984255
window3678 window3679 window3680 window3681

overview

Window 8

Location 6,706,441 – 6,706,537
Length 96
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 79.29
Mean single sequence MFE -35.90
Consensus MFE -24.35
Energy contribution -24.43
Covariance contribution 0.09
Combinations/Pair 1.08
Mean z-score -2.48
Structure conservation index 0.68
SVM decision value 1.97
SVM RNA-class probability 0.984255
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6706441 96 + 23771897
CAUAAGUUGGUGGCGCAAUUUUCUGCU---G------CUGUUGCUGCAAAUUAUCCACGGCGUCUGCUGCGGCAGCAGCAUUUGCUGCGGCAUUAGUAGACUGAU
......((((((.((((......((((---(------(((((((.(((.((...(....).)).))).)))))))))))).....)))).))))))......... ( -35.20)
>DroSec_CAF1 2086 99 + 1
CAUAAGUUGGUGGUGCGAUUUUCUGCUGCUG------CUGUUGCUGCAAAUUAUCCACGGCGUCUGCUGCGGCAGCAGCAUUUGCUGCGGCAUUAGUAGACUGAU
.........((.(((.(((..(.(((.((..------.....)).))).)..)))))).))((((((((..((.(((((....))))).))..)))))))).... ( -37.90)
>DroYak_CAF1 2122 90 + 1
CAUAAGUUGGAGGCGCAAUUUUCUGCUGCUGUUGCUGUUG---------------CACGGCGUCUGCUGCAGCUGCAGCAUUGGCAGCGGCAUUAGUAGACUGAU
...((((((......))))))((..((((((.((((((((---------------(.(((....((((((....)))))))))))))))))).))))))...)). ( -34.60)
>consensus
CAUAAGUUGGUGGCGCAAUUUUCUGCUGCUG______CUGUUGCUGCAAAUUAUCCACGGCGUCUGCUGCGGCAGCAGCAUUUGCUGCGGCAUUAGUAGACUGAU
.....((((.....(((......)))............(((....))).........))))(((((((((.(((((.......))))).))...))))))).... (-24.35 = -24.43 +   0.09)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,706,441 – 6,706,537
Length 96
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 79.29
Mean single sequence MFE -26.40
Consensus MFE -18.34
Energy contribution -18.23
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -1.54
Structure conservation index 0.69
SVM decision value 0.16
SVM RNA-class probability 0.613631
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6706441 96 - 23771897
AUCAGUCUACUAAUGCCGCAGCAAAUGCUGCUGCCGCAGCAGACGCCGUGGAUAAUUUGCAGCAACAG------C---AGCAGAAAAUUGCGCCACCAACUUAUG
....((((.....(((.((((((.....)))))).)))..))))...((((....(((((.((....)------)---.)))))........))))......... ( -27.70)
>DroSec_CAF1 2086 99 - 1
AUCAGUCUACUAAUGCCGCAGCAAAUGCUGCUGCCGCAGCAGACGCCGUGGAUAAUUUGCAGCAACAG------CAGCAGCAGAAAAUCGCACCACCAACUUAUG
....((((.....(((.((((((.....)))))).)))..))))...((((......(((.((....)------).)))((........)).))))......... ( -28.80)
>DroYak_CAF1 2122 90 - 1
AUCAGUCUACUAAUGCCGCUGCCAAUGCUGCAGCUGCAGCAGACGCCGUG---------------CAACAGCAACAGCAGCAGAAAAUUGCGCCUCCAACUUAUG
....((((.....(((.(((((.......))))).)))..))))((..((---------------(....)))...)).((((....)))).............. ( -22.70)
>consensus
AUCAGUCUACUAAUGCCGCAGCAAAUGCUGCUGCCGCAGCAGACGCCGUGGAUAAUUUGCAGCAACAG______CAGCAGCAGAAAAUUGCGCCACCAACUUAUG
....((((.....(((.((((((.....)))))).)))..))))...................................((........)).............. (-18.34 = -18.23 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,706,469 – 6,706,568
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 88.05
Mean single sequence MFE -33.23
Consensus MFE -26.94
Energy contribution -27.75
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -1.95
Structure conservation index 0.81
SVM decision value 0.87
SVM RNA-class probability 0.871914
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6706469 99 + 23771897
CUGUUGCUGCAAAUUAUCCACGGCGUCUGCUGCGGCAGCAGCAUUUGCUGCGGCAUUAGUAGACUGAUACUGCGCAUAGGUUGGAUAUUUCGGUUUGUG
.....((((.((((.(((((.((((..((((((....))))))..))))((((.(((((....))))).))))........)))))))))))))..... ( -34.30)
>DroSec_CAF1 2117 99 + 1
CUGUUGCUGCAAAUUAUCCACGGCGUCUGCUGCGGCAGCAGCAUUUGCUGCGGCAUUAGUAGACUGAUAUUGCGCAUAGGUUGGAUAUUUCGGUUUGUG
.....((((.((((.((((((.((((..((((((((((......))))))))))(((((....)))))...))))....).)))))))))))))..... ( -32.10)
>DroEre_CAF1 2170 99 + 1
CUGUUGCUGCAAAUUAUCCACGGCAUCUGCUGCGGCUGCAGCAUUGGCUGCGGCAUUAGUAGACUGAUAUUGCGCAUAGGUUGGAUAUUUCGGUUUGUG
.....((((.((((.(((((....(((((.((((((((((((....))))))))(((((....)))))....))))))))))))))))))))))..... ( -35.20)
>DroYak_CAF1 2159 84 + 1
UUG---------------CACGGCGUCUGCUGCAGCUGCAGCAUUGGCAGCGGCAUUAGUAGACUGAUAUUGCGCAUAGGUUGGAUAUUUCGGCUUGUG
..(---------------((...(((((((((..(((((.((....)).)))))..)))))))).)....))).(((((((((((...))))))))))) ( -31.30)
>consensus
CUGUUGCUGCAAAUUAUCCACGGCGUCUGCUGCGGCAGCAGCAUUGGCUGCGGCAUUAGUAGACUGAUAUUGCGCAUAGGUUGGAUAUUUCGGUUUGUG
........................((((((((..((((((((....))))))))..))))))))..........((((((..(((...)))..)))))) (-26.94 = -27.75 +   0.81)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,706,469 – 6,706,568
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 88.05
Mean single sequence MFE -25.00
Consensus MFE -18.10
Energy contribution -20.35
Covariance contribution 2.25
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.72
SVM decision value 0.45
SVM RNA-class probability 0.740072
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6706469 99 - 23771897
CACAAACCGAAAUAUCCAACCUAUGCGCAGUAUCAGUCUACUAAUGCCGCAGCAAAUGCUGCUGCCGCAGCAGACGCCGUGGAUAAUUUGCAGCAACAG
.......((((.((((((.....(((..((((......))))..(((.((((((.....)))))).)))))).......)))))).))))......... ( -27.40)
>DroSec_CAF1 2117 99 - 1
CACAAACCGAAAUAUCCAACCUAUGCGCAAUAUCAGUCUACUAAUGCCGCAGCAAAUGCUGCUGCCGCAGCAGACGCCGUGGAUAAUUUGCAGCAACAG
.......................(((((((.....((((((...(((.((((((.....)))))).)))((....)).))))))...)))).))).... ( -27.10)
>DroEre_CAF1 2170 99 - 1
CACAAACCGAAAUAUCCAACCUAUGCGCAAUAUCAGUCUACUAAUGCCGCAGCCAAUGCUGCAGCCGCAGCAGAUGCCGUGGAUAAUUUGCAGCAACAG
.......................(((((((.....((((((....((.(((((....))))).)).(((.....))).))))))...)))).))).... ( -25.20)
>DroYak_CAF1 2159 84 - 1
CACAAGCCGAAAUAUCCAACCUAUGCGCAAUAUCAGUCUACUAAUGCCGCUGCCAAUGCUGCAGCUGCAGCAGACGCCGUG---------------CAA
.......................(((((.......((((.....(((.(((((.......))))).)))..))))...)))---------------)). ( -20.30)
>consensus
CACAAACCGAAAUAUCCAACCUAUGCGCAAUAUCAGUCUACUAAUGCCGCAGCAAAUGCUGCAGCCGCAGCAGACGCCGUGGAUAAUUUGCAGCAACAG
.......((((.((((((.....((((...(((.((....)).))).))))((...((((((....))))))...))..)))))).))))......... (-18.10 = -20.35 +   2.25)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:02 2006