Locus 6480

Sequence ID 3L_DroMel_CAF1
Location 17,250,663 – 17,250,818
Length 155
Max. P 0.984351
window10448 window10449 window10450

overview

Window 8

Location 17,250,663 – 17,250,778
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.76
Mean single sequence MFE -27.10
Consensus MFE -22.60
Energy contribution -23.08
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -2.14
Structure conservation index 0.83
SVM decision value 1.97
SVM RNA-class probability 0.984351
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17250663 115 - 23771897
UCGUCAUGGCCCAUGGUACACUGUA-----AUACACCAUUCACGGCCAUGACACGAUACGGUCAUAUAUCAAAUUGACUAGUUUAUUUUCCCUUAUAGCGAACAGUUUGCCUCAUUUUUC
..(((((((((.(((((........-----....)))))....))))))))).......(((((..........)))))..................((((.....)))).......... ( -25.90)
>DroSec_CAF1 134470 115 - 1
UCGUCAUGGCCCAUGGUCCACUGUA-----AUACACCAUUCACGGCCAUGACACGGUACGCUCAUAUAUCAAAUUGACUAGUUUAUUUUCCCUUUGAGCGAACAGUUUGCCUCAUUUUUC
..(((((((((.(((((........-----....)))))....)))))))))..((((((((((......((((.((....)).))))......)))))).......))))......... ( -30.61)
>DroSim_CAF1 129273 115 - 1
UCGUCAUGGCCCAUGGUCCACUGUA-----AUACACCAUUCACGGCCAUGACACGGUACGCUCAUAUAUCAAAUUGACUAGUUUAUUUUCCCUUUGAGCGAACAGUUUGGCUCAUUUUUC
..(((((((((.(((((........-----....)))))....)))))))))...((.((((((......((((.((....)).))))......)))))).))................. ( -30.20)
>DroEre_CAF1 137633 115 - 1
UCGUCAUGGCCCAUGCUCCACUGUA-----CUGCACCAUUCACGCCCAUGACACGGUACGGUCAUAUAUCAAAUUGACUAGUUUAUUUUCCCUUUGAGCGAACAGUUUUCCUCAUUUUUC
..(((((((....(((......)))-----..((.........)))))))))..((.(((((((..........))))).(((..(((.......)))..))).))...))......... ( -19.30)
>DroYak_CAF1 141318 120 - 1
UCGUCAUGGCCCAUGGUCCACUGUAUAGUAAUACACCAUUCACGGCCAUGACACGGUACGGUCAUAUAUCAAAUUGACUAGUUUAUUUUCCCUUUGAGCGAGCAGUUUCCCUCAUUUUUC
..(((((((((.(((((.....((((....)))))))))....)))))))))..((.(((((((..........))))).(((..(((.......)))..))).))..)).......... ( -29.50)
>consensus
UCGUCAUGGCCCAUGGUCCACUGUA_____AUACACCAUUCACGGCCAUGACACGGUACGGUCAUAUAUCAAAUUGACUAGUUUAUUUUCCCUUUGAGCGAACAGUUUGCCUCAUUUUUC
..(((((((((.((((.....((((......))))))))....)))))))))..((((........))))((((((....(((((.........)))))...))))))............ (-22.60 = -23.08 +   0.48)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,250,703 – 17,250,818
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.73
Mean single sequence MFE -31.18
Consensus MFE -27.38
Energy contribution -27.82
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.45
Structure conservation index 0.88
SVM decision value 0.75
SVM RNA-class probability 0.839682
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17250703 115 + 23771897
UAGUCAAUUUGAUAUAUGACCGUAUCGUGUCAUGGCCGUGAAUGGUGUAU-----UACAGUGUACCAUGGGCCAUGACGAACCAAUUAAAUCAACGUCUGAUUGCAAAAUGAAUGACUUG
.(((((....(((((......)))))(((((((((((....(((((((((-----....))))))))).)))))))))..........(((((.....)))))))........))))).. ( -34.10)
>DroSec_CAF1 134510 115 + 1
UAGUCAAUUUGAUAUAUGAGCGUACCGUGUCAUGGCCGUGAAUGGUGUAU-----UACAGUGGACCAUGGGCCAUGACGAACCAAUUAAAUCAACGUCUGAUUGCAAAAUGAAUGACUUG
...(((.((((....((.(((((.....(((((((((....(((((.(((-----....))).))))).)))))))))((..........)).))).)).))..)))).)))........ ( -32.40)
>DroSim_CAF1 129313 115 + 1
UAGUCAAUUUGAUAUAUGAGCGUACCGUGUCAUGGCCGUGAAUGGUGUAU-----UACAGUGGACCAUGGGCCAUGACGAACCAAUUAAAUCAACGUCUGAUUGCAAAAUGAAUGACUUG
...(((.((((....((.(((((.....(((((((((....(((((.(((-----....))).))))).)))))))))((..........)).))).)).))..)))).)))........ ( -32.40)
>DroEre_CAF1 137673 115 + 1
UAGUCAAUUUGAUAUAUGACCGUACCGUGUCAUGGGCGUGAAUGGUGCAG-----UACAGUGGAGCAUGGGCCAUGACGAACCAAUUAAAUCAACGUCUGAUUGCAAAAUGAAUGACUUG
.(((((..........((((.(((((((.((((....))))))))))).)-----).)).....((.(((..(.....)..)))....(((((.....)))))))........))))).. ( -25.10)
>DroYak_CAF1 141358 120 + 1
UAGUCAAUUUGAUAUAUGACCGUACCGUGUCAUGGCCGUGAAUGGUGUAUUACUAUACAGUGGACCAUGGGCCAUGACGAACCAAUUAAAUCAACGUCUGAUUGCAAAAUGAAUGACUUG
.(((((.....................((((((((((....(((((.((((.......)))).))))).)))))))))).........(((((.....)))))..........))))).. ( -31.90)
>consensus
UAGUCAAUUUGAUAUAUGACCGUACCGUGUCAUGGCCGUGAAUGGUGUAU_____UACAGUGGACCAUGGGCCAUGACGAACCAAUUAAAUCAACGUCUGAUUGCAAAAUGAAUGACUUG
.(((((.....................((((((((((....(((((.(((.........))).))))).)))))))))).........(((((.....)))))..........))))).. (-27.38 = -27.82 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,250,703 – 17,250,818
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.73
Mean single sequence MFE -26.45
Consensus MFE -25.19
Energy contribution -25.27
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.44
Structure conservation index 0.95
SVM decision value 1.47
SVM RNA-class probability 0.956521
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17250703 115 - 23771897
CAAGUCAUUCAUUUUGCAAUCAGACGUUGAUUUAAUUGGUUCGUCAUGGCCCAUGGUACACUGUA-----AUACACCAUUCACGGCCAUGACACGAUACGGUCAUAUAUCAAAUUGACUA
...(((................)))((..((((.........(((((((((.(((((........-----....)))))....)))))))))..((((........))))))))..)).. ( -27.89)
>DroSec_CAF1 134510 115 - 1
CAAGUCAUUCAUUUUGCAAUCAGACGUUGAUUUAAUUGGUUCGUCAUGGCCCAUGGUCCACUGUA-----AUACACCAUUCACGGCCAUGACACGGUACGCUCAUAUAUCAAAUUGACUA
...(((................)))((..((((.........(((((((((.(((((........-----....)))))....)))))))))..((((........))))))))..)).. ( -27.09)
>DroSim_CAF1 129313 115 - 1
CAAGUCAUUCAUUUUGCAAUCAGACGUUGAUUUAAUUGGUUCGUCAUGGCCCAUGGUCCACUGUA-----AUACACCAUUCACGGCCAUGACACGGUACGCUCAUAUAUCAAAUUGACUA
...(((................)))((..((((.........(((((((((.(((((........-----....)))))....)))))))))..((((........))))))))..)).. ( -27.09)
>DroEre_CAF1 137673 115 - 1
CAAGUCAUUCAUUUUGCAAUCAGACGUUGAUUUAAUUGGUUCGUCAUGGCCCAUGCUCCACUGUA-----CUGCACCAUUCACGCCCAUGACACGGUACGGUCAUAUAUCAAAUUGACUA
..(((((........(((.(((((((..((((.....)))))))).)))....)))...((((((-----(((...(((........)))...)))))))))............))))). ( -21.50)
>DroYak_CAF1 141358 120 - 1
CAAGUCAUUCAUUUUGCAAUCAGACGUUGAUUUAAUUGGUUCGUCAUGGCCCAUGGUCCACUGUAUAGUAAUACACCAUUCACGGCCAUGACACGGUACGGUCAUAUAUCAAAUUGACUA
...(((................)))((..((((.........(((((((((.(((((.....((((....)))))))))....)))))))))..((((........))))))))..)).. ( -28.69)
>consensus
CAAGUCAUUCAUUUUGCAAUCAGACGUUGAUUUAAUUGGUUCGUCAUGGCCCAUGGUCCACUGUA_____AUACACCAUUCACGGCCAUGACACGGUACGGUCAUAUAUCAAAUUGACUA
...(((................)))((..((((.........(((((((((.((((.....((((......))))))))....)))))))))..((((........))))))))..)).. (-25.19 = -25.27 +   0.08)

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 12:20:41 2006