Locus 6518

Sequence ID 3R_DroMel_CAF1
Location 17,189,741 – 17,189,835
Length 94
Max. P 0.765013
window10603 window10604

overview

Window 3

Location 17,189,741 – 17,189,835
Length 94
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 81.32
Mean single sequence MFE -29.42
Consensus MFE -15.26
Energy contribution -18.04
Covariance contribution 2.78
Combinations/Pair 1.19
Mean z-score -2.35
Structure conservation index 0.52
SVM decision value 0.13
SVM RNA-class probability 0.596630
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17189741 94 + 27905053
AAAUCGAUGAGUAUAUUAUA---UUAACUGCUGGUCCU---CCGGAGCUUACUGCAGCUCCGGAAAUUCGUCCAGCAGGUCAGUCGUGAGAUCCAUCGAG
...((((((...........---....(((((((.(.(---((((((((......))))))))).....).)))))))....(((....))).)))))). ( -40.10)
>DroPse_CAF1 13262 90 + 1
----------GUAAAUUAUAAGUUUGGCUACUGCUCAACGAUGGACGACUACUGCAACUCGGGAAAAUCAUCCAGCAGGUCGGCCGAAAGGUCCAGCGAA
----------...........(((.(((....))).)))(.(((.((((..((((......(((......))).))))))))(((....)))))).)... ( -24.10)
>DroSec_CAF1 11210 94 + 1
AAAUCUAUGAGUAUAUUAUA---UUAACUGCUGGUCCU---CCGGAGCCUACUGCAGCUCCGGAAAUUCGUCCAGCAGGUCAGUCGUGAGAUCCAUCGAG
...((.(((...........---....(((((((.(.(---(((((((........)))))))).....).)))))))....(((....))).))).)). ( -32.80)
>DroSim_CAF1 12080 94 + 1
AAAUCUAUGAGUAUAUUAUA---UUAACUGCUGGUCCU---CCGGAGCCUACUGCAGCUCCGGAAAUUCGUCCAGCAGGUCAGUCGUGAGAUCCAUCGAG
...((.(((...........---....(((((((.(.(---(((((((........)))))))).....).)))))))....(((....))).))).)). ( -32.80)
>DroEre_CAF1 13230 94 + 1
AAAUCUAUGAGUAAAUUAUA---UUAACUGCUGGUCGU---AUAGAGCCUAUUGCAGCUCCGGAAAUUCGUCCAGCAGUUCAGUCGCGAGAUCCAUUGAG
...((.(((...........---..(((((((((.((.---...((((........))))........)).)))))))))..(((....))).))).)). ( -25.10)
>DroYak_CAF1 13024 94 + 1
AAAUCUAUGAGUAAAUUAUA---UUAACUGCUGGUUGA---UCAGAGCCUACUGCAGCUCCGGGAAUUCGUCCAGCAAGUCAGUCGUGAGAUCCAUCGAG
...((.(((...........---.....((((((.(((---((.((((........))))...))..))).)))))).....(((....))).))).)). ( -21.60)
>consensus
AAAUCUAUGAGUAAAUUAUA___UUAACUGCUGGUCCU___CCGGAGCCUACUGCAGCUCCGGAAAUUCGUCCAGCAGGUCAGUCGUGAGAUCCAUCGAG
...........................(((((((.......((.((((........)))).))........)))))))....(((....)))........ (-15.26 = -18.04 +   2.78)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,189,741 – 17,189,835
Length 94
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 81.32
Mean single sequence MFE -27.89
Consensus MFE -18.35
Energy contribution -18.21
Covariance contribution -0.14
Combinations/Pair 1.39
Mean z-score -1.98
Structure conservation index 0.66
SVM decision value 0.51
SVM RNA-class probability 0.765013
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17189741 94 - 27905053
CUCGAUGGAUCUCACGACUGACCUGCUGGACGAAUUUCCGGAGCUGCAGUAAGCUCCGG---AGGACCAGCAGUUAA---UAUAAUAUACUCAUCGAUUU
.(((((((...(((....))).(((((((.....(((((((((((......))))))))---))).)))))))....---..........)))))))... ( -36.90)
>DroPse_CAF1 13262 90 - 1
UUCGCUGGACCUUUCGGCCGACCUGCUGGAUGAUUUUCCCGAGUUGCAGUAGUCGUCCAUCGUUGAGCAGUAGCCAAACUUAUAAUUUAC----------
...(((((.((....))))...(((((.((((((.....(((.(......).)))...)))))).))))).)))................---------- ( -21.30)
>DroSec_CAF1 11210 94 - 1
CUCGAUGGAUCUCACGACUGACCUGCUGGACGAAUUUCCGGAGCUGCAGUAGGCUCCGG---AGGACCAGCAGUUAA---UAUAAUAUACUCAUAGAUUU
.(((.((.....))))).((((.((((((.....(((((((((((......))))))))---))).)))))))))).---.................... ( -30.40)
>DroSim_CAF1 12080 94 - 1
CUCGAUGGAUCUCACGACUGACCUGCUGGACGAAUUUCCGGAGCUGCAGUAGGCUCCGG---AGGACCAGCAGUUAA---UAUAAUAUACUCAUAGAUUU
.(((.((.....))))).((((.((((((.....(((((((((((......))))))))---))).)))))))))).---.................... ( -30.40)
>DroEre_CAF1 13230 94 - 1
CUCAAUGGAUCUCGCGACUGAACUGCUGGACGAAUUUCCGGAGCUGCAAUAGGCUCUAU---ACGACCAGCAGUUAA---UAUAAUUUACUCAUAGAUUU
.((.((((............(((((((((.((.((....((((((......))))))))---.)).)))))))))..---..........)))).))... ( -25.15)
>DroYak_CAF1 13024 94 - 1
CUCGAUGGAUCUCACGACUGACUUGCUGGACGAAUUCCCGGAGCUGCAGUAGGCUCUGA---UCAACCAGCAGUUAA---UAUAAUUUACUCAUAGAUUU
.(((.((.....))))).(((((.(((((..((.....(((((((......))))))).---))..)))))))))).---.................... ( -23.20)
>consensus
CUCGAUGGAUCUCACGACUGACCUGCUGGACGAAUUUCCGGAGCUGCAGUAGGCUCCGG___AGGACCAGCAGUUAA___UAUAAUAUACUCAUAGAUUU
......((.((....))))...(((((((.........(((((((......)))))))........)))))))........................... (-18.35 = -18.21 +  -0.14)

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 12:23:19 2006