Locus 4862

Sequence ID 3R_DroMel_CAF1
Location 12,778,366 – 12,778,473
Length 107
Max. P 0.996263
window7964 window7965

overview

Window 4

Location 12,778,366 – 12,778,473
Length 107
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -34.92
Consensus MFE -33.78
Energy contribution -33.20
Covariance contribution -0.58
Combinations/Pair 1.08
Mean z-score -1.74
Structure conservation index 0.97
SVM decision value 2.67
SVM RNA-class probability 0.996263
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12778366 107 + 27905053
CUAUAAAUCCAUCGAAAUAAUGGAUCGGAUAAGAGGCGCGCAUUCGAGAUGAGUUCCAGUCGCGCC-GUCAAGUGGGUUGAGUGCCCACACGAUGGCCAUUCCCAUUC--
........((((((..................((((((((.(((.(((.....))).)))))))))-.))..((((((.....)))))).))))))............-- ( -34.00)
>DroPse_CAF1 161892 98 + 1
CUAUAAAUCCAUCGAAAUAAUGGAUCGGAUAAGGGGCGCGCAUUCGAGAUGAGUUCCAGUCGCGCC-GCCAAGUGGGUUGAGUGCCCACACGAUGGCCG-----------
........((((((..................((((((((.(((.(((.....))).)))))))))-.))..((((((.....)))))).))))))...----------- ( -36.10)
>DroSec_CAF1 153200 101 + 1
CUAUAAAUCCAUCGAAAUAAUGGAUCGGAUAAGAGGCGCGCAUUCGAGAUGAGUUCCAGUCGCGCC-GUCAAGUGGGUUGAGUGCCCACACGAUGGUCAUUC--------
........((((((..................((((((((.(((.(((.....))).)))))))))-.))..((((((.....)))))).))))))......-------- ( -34.20)
>DroEre_CAF1 160450 109 + 1
CUAUAAAUCCAUCGAAAUAAUGGAUCGGAUAAGAGGCGCGCAUUCGAGAUGAGUUCCAGUCGCGCC-GUCAAGUGGGUAGAGUGCCCACACGAUGGCCAUUCCCAUUCCC
........((((((..................((((((((.(((.(((.....))).)))))))))-.))..((((((.....)))))).)))))).............. ( -33.70)
>DroAna_CAF1 140007 103 + 1
CUAUAAAUCCAUCGAAAUAAUGGAUCGGAUAAGAGGCGCGCAUUCGAGAUGAGUUCCAGUCGCGCCAGUCAAGUGGGCUGAGUGCCCACACGAUGGCCAUUCC-------
........((((((....................((((((.(((.(((.....))).)))))))))......((((((.....)))))).)))))).......------- ( -35.40)
>DroPer_CAF1 169002 98 + 1
CUAUAAAUCCAUCGAAAUAAUGGAUCGGAUAAGGGGCGCGCAUUCGAGAUGAGUUCCAGUCGCGCC-GCCAAGUGGGUUGAGUGCCCACACGAUGGCCA-----------
........((((((..................((((((((.(((.(((.....))).)))))))))-.))..((((((.....)))))).))))))...----------- ( -36.10)
>consensus
CUAUAAAUCCAUCGAAAUAAUGGAUCGGAUAAGAGGCGCGCAUUCGAGAUGAGUUCCAGUCGCGCC_GUCAAGUGGGUUGAGUGCCCACACGAUGGCCAUUC________
........((((((..................((((((((.(((.(((.....))).)))))))))..))..((((((.....)))))).)))))).............. (-33.78 = -33.20 +  -0.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 12,778,366 – 12,778,473
Length 107
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 92.17
Mean single sequence MFE -33.23
Consensus MFE -28.57
Energy contribution -28.52
Covariance contribution -0.06
Combinations/Pair 1.04
Mean z-score -1.48
Structure conservation index 0.86
SVM decision value 0.08
SVM RNA-class probability 0.572965
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12778366 107 - 27905053
--GAAUGGGAAUGGCCAUCGUGUGGGCACUCAACCCACUUGAC-GGCGCGACUGGAACUCAUCUCGAAUGCGCGCCUCUUAUCCGAUCCAUUAUUUCGAUGGAUUUAUAG
--(.((((((.......(((.(((((.......))))).))).-((((((..(.((.......)).)...)))))))))))).)((((((((.....))))))))..... ( -32.30)
>DroPse_CAF1 161892 98 - 1
-----------CGGCCAUCGUGUGGGCACUCAACCCACUUGGC-GGCGCGACUGGAACUCAUCUCGAAUGCGCGCCCCUUAUCCGAUCCAUUAUUUCGAUGGAUUUAUAG
-----------..((((....(((((.......))))).))))-((((((..(.((.......)).)...))))))........((((((((.....))))))))..... ( -33.30)
>DroSec_CAF1 153200 101 - 1
--------GAAUGACCAUCGUGUGGGCACUCAACCCACUUGAC-GGCGCGACUGGAACUCAUCUCGAAUGCGCGCCUCUUAUCCGAUCCAUUAUUUCGAUGGAUUUAUAG
--------......((((((.(((((.......)))))..((.-((((((..(.((.......)).)...))))))))..................))))))........ ( -29.20)
>DroEre_CAF1 160450 109 - 1
GGGAAUGGGAAUGGCCAUCGUGUGGGCACUCUACCCACUUGAC-GGCGCGACUGGAACUCAUCUCGAAUGCGCGCCUCUUAUCCGAUCCAUUAUUUCGAUGGAUUUAUAG
.(((.(((((.......(((.(((((.......))))).))).-((((((..(.((.......)).)...))))))))))))))((((((((.....))))))))..... ( -35.30)
>DroAna_CAF1 140007 103 - 1
-------GGAAUGGCCAUCGUGUGGGCACUCAGCCCACUUGACUGGCGCGACUGGAACUCAUCUCGAAUGCGCGCCUCUUAUCCGAUCCAUUAUUUCGAUGGAUUUAUAG
-------(((.......(((.((((((.....)))))).)))..((((((..(.((.......)).)...)))))).....)))((((((((.....))))))))..... ( -36.00)
>DroPer_CAF1 169002 98 - 1
-----------UGGCCAUCGUGUGGGCACUCAACCCACUUGGC-GGCGCGACUGGAACUCAUCUCGAAUGCGCGCCCCUUAUCCGAUCCAUUAUUUCGAUGGAUUUAUAG
-----------..((((....(((((.......))))).))))-((((((..(.((.......)).)...))))))........((((((((.....))))))))..... ( -33.30)
>consensus
________GAAUGGCCAUCGUGUGGGCACUCAACCCACUUGAC_GGCGCGACUGGAACUCAUCUCGAAUGCGCGCCUCUUAUCCGAUCCAUUAUUUCGAUGGAUUUAUAG
............((...(((.(((((.......))))).)))..((((((..(.((.......)).)...))))))......))((((((((.....))))))))..... (-28.57 = -28.52 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:40 2006