Locus 2015

Sequence ID 3R_DroMel_CAF1
Location 5,713,201 – 5,713,292
Length 91
Max. P 0.999466
window3301 window3302

overview

Window 1

Location 5,713,201 – 5,713,292
Length 91
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.78
Mean single sequence MFE -38.82
Consensus MFE -22.08
Energy contribution -21.89
Covariance contribution -0.19
Combinations/Pair 1.14
Mean z-score -3.39
Structure conservation index 0.57
SVM decision value 3.63
SVM RNA-class probability 0.999466
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5713201 91 + 27905053
GCCCAAUUUGACCCAGUUGCUC--------------GA------ACAAAACAAAAUGUU---UCACUCGGUUGGCAGGC----AAAAUGGGUCAAAUGGUUCGAU--GCCGGCAGGGCAA
((((.((((((((((.((((((--------------.(------((.((((.....)))---)......))).)..)))----))..))))))))))(((.....--)))....)))).. ( -32.50)
>DroEre_CAF1 12803 91 + 1
GCCCUAUUUGACCCAGUUGCUC--------------GA------ACCAAACAAAAUGUU---UCACUCGGUUGGCAGGC----GAAAUGGGUCAAAUGGUUCGAU--GCCGGCAGGGCAA
(((((((((((((((.((((((--------------.(------(((((((.....)))---).....)))).)..)))----))..))))))))))(((.....--)))...))))).. ( -35.90)
>DroYak_CAF1 17172 91 + 1
GCCCCAUUUGACCCAGUUGCUC--------------GA------ACCAAACAAAAUGUU---UCACUCGGUUGGCAGGC----GAAAUGGGUCAAAUGGUUCGAU--GCCGGCGGGGCAA
(((((((((((((((.((((((--------------.(------(((((((.....)))---).....)))).)..)))----))..))))))))))(((.....--)))...))))).. ( -38.70)
>DroAna_CAF1 13566 119 + 1
GCCCUAGUUGACCCAGUUGCAGUAGCCGGGCCAGGCGAGCAGCUACCAAACAAAACACUGCCAUGCUCGGUUGGCAAGGAACGAAAAUGGGUCAAACA-CUCGAUGUGCCGGCAGGGCAA
(((((..((((((((.((...((..((..(((((.((((((((................))..)))))).)))))..)).))..)).)))))))).((-(.....))).....))))).. ( -48.19)
>consensus
GCCCUAUUUGACCCAGUUGCUC______________GA______ACCAAACAAAAUGUU___UCACUCGGUUGGCAGGC____AAAAUGGGUCAAAUGGUUCGAU__GCCGGCAGGGCAA
(((((((((((((((.(((((...........................(((....((......))....))))))))..........))))))))))...(((......))).))))).. (-22.08 = -21.89 +  -0.19)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 5,713,201 – 5,713,292
Length 91
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.78
Mean single sequence MFE -35.85
Consensus MFE -23.67
Energy contribution -23.80
Covariance contribution 0.13
Combinations/Pair 1.12
Mean z-score -2.65
Structure conservation index 0.66
SVM decision value 2.98
SVM RNA-class probability 0.997980
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5713201 91 - 27905053
UUGCCCUGCCGGC--AUCGAACCAUUUGACCCAUUUU----GCCUGCCAACCGAGUGA---AACAUUUUGUUUUGU------UC--------------GAGCAACUGGGUCAAAUUGGGC
.((((.....)))--).....((((((((((((..((----((........((((..(---(((.....))))..)------))--------------).)))).))))))))).))).. ( -31.50)
>DroEre_CAF1 12803 91 - 1
UUGCCCUGCCGGC--AUCGAACCAUUUGACCCAUUUC----GCCUGCCAACCGAGUGA---AACAUUUUGUUUGGU------UC--------------GAGCAACUGGGUCAAAUAGGGC
..(((((...((.--......))((((((((((.((.----((...(.(((((((..(---(....))..))))))------).--------------).)))).))))))))))))))) ( -33.20)
>DroYak_CAF1 17172 91 - 1
UUGCCCCGCCGGC--AUCGAACCAUUUGACCCAUUUC----GCCUGCCAACCGAGUGA---AACAUUUUGUUUGGU------UC--------------GAGCAACUGGGUCAAAUGGGGC
.((((.....)))--)..(..((((((((((((.((.----((...(.(((((((..(---(....))..))))))------).--------------).)))).))))))))))))..) ( -36.30)
>DroAna_CAF1 13566 119 - 1
UUGCCCUGCCGGCACAUCGAG-UGUUUGACCCAUUUUCGUUCCUUGCCAACCGAGCAUGGCAGUGUUUUGUUUGGUAGCUGCUCGCCUGGCCCGGCUACUGCAACUGGGUCAACUAGGGC
..((((((...((((.....)-)))((((((((.((.(((.((..((((..((((((((.(((........))).))..))))))..))))..))..)).).)).)))))))).)))))) ( -42.40)
>consensus
UUGCCCUGCCGGC__AUCGAACCAUUUGACCCAUUUC____GCCUGCCAACCGAGUGA___AACAUUUUGUUUGGU______UC______________GAGCAACUGGGUCAAAUAGGGC
..(((((..(((....)))....((((((((((............((((((.(((((......))))).).)))))........(((......))).........))))))))))))))) (-23.67 = -23.80 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:16 2006