Locus 7572

Sequence ID 3R_DroMel_CAF1
Location 20,302,829 – 20,302,932
Length 103
Max. P 0.957955
window12225 window12226

overview

Window 5

Location 20,302,829 – 20,302,932
Length 103
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 82.79
Mean single sequence MFE -38.26
Consensus MFE -28.88
Energy contribution -29.25
Covariance contribution 0.38
Combinations/Pair 1.08
Mean z-score -2.29
Structure conservation index 0.75
SVM decision value 1.48
SVM RNA-class probability 0.957955
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20302829 103 + 27905053
GGAUGGGAUGGAUGGCUGAAGGAU-----GGCCGAGGUGCUGAGGGGCGUGGCAGCUGAAGAUGGGUCAGCUAAUAAAGCGCCACUCGGUACGGUUUGCCUGGAAGCC
.............((((..(((..-----((((...((((((((.(((((...((((((.......))))))......))))).))))))))))))..)))...)))) ( -41.30)
>DroSec_CAF1 111654 99 + 1
---------GGAUGGCUGAAGGAACGAGGUGCUGAGGUGCUGAGGGGCGUGGCAGCUGAAGAUGGGUCAGCUAAUAAAGCGCCACUCGGUACUGUUUGGCUGGAAGCC
---------....((((.............((..((((((((((.(((((...((((((.......))))))......))))).)))))))))..)..))....)))) ( -36.23)
>DroSim_CAF1 120081 99 + 1
---------GGAUUGCUGAAGGGCCGAGGUGCUGAGGUGCUGAGGGGCGUGGCAGCUGAAGAUGGGUCAGCUAAUAAAGCGCCACUCGGUACUGUUUGGCUGGAAGCC
---------.....(((....(((((((.......(((((((((.(((((...((((((.......))))))......))))).))))))))).)))))))...))). ( -39.10)
>DroEre_CAF1 115452 87 + 1
---------GGAUG----AAGG--------GCCGACCUGCUGAGGGGCGUGGCAGCUGAGGAUGGGUCAGCUAAUAAAGCGCCACUCGGUACAGGCUGCCUGGAAGCC
---------((...----..((--------((.(.(((((((((.(((((...((((((.......))))))......))))).)))))..))))).)))).....)) ( -36.40)
>consensus
_________GGAUGGCUGAAGGA______UGCCGAGGUGCUGAGGGGCGUGGCAGCUGAAGAUGGGUCAGCUAAUAAAGCGCCACUCGGUACUGUUUGCCUGGAAGCC
..............................((((((((((((((.(((((...((((((.......))))))......))))).))))))))..))))))........ (-28.88 = -29.25 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 20,302,829 – 20,302,932
Length 103
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 82.79
Mean single sequence MFE -27.70
Consensus MFE -19.73
Energy contribution -20.72
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.71
SVM decision value 1.11
SVM RNA-class probability 0.916630
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20302829 103 - 27905053
GGCUUCCAGGCAAACCGUACCGAGUGGCGCUUUAUUAGCUGACCCAUCUUCAGCUGCCACGCCCCUCAGCACCUCGGCC-----AUCCUUCAGCCAUCCAUCCCAUCC
((((...(((....(((..(.(((.((((......(((((((.......)))))))...)))).))).).....)))..-----..)))..))))............. ( -28.10)
>DroSec_CAF1 111654 99 - 1
GGCUUCCAGCCAAACAGUACCGAGUGGCGCUUUAUUAGCUGACCCAUCUUCAGCUGCCACGCCCCUCAGCACCUCAGCACCUCGUUCCUUCAGCCAUCC---------
((((...((...(((......(((.((((......(((((((.......)))))))...)))).))).((......)).....))).))..))))....--------- ( -25.30)
>DroSim_CAF1 120081 99 - 1
GGCUUCCAGCCAAACAGUACCGAGUGGCGCUUUAUUAGCUGACCCAUCUUCAGCUGCCACGCCCCUCAGCACCUCAGCACCUCGGCCCUUCAGCAAUCC---------
(((.....)))....((..(((((.((((......(((((((.......)))))))...)))).....((......))..)))))..))..........--------- ( -27.10)
>DroEre_CAF1 115452 87 - 1
GGCUUCCAGGCAGCCUGUACCGAGUGGCGCUUUAUUAGCUGACCCAUCCUCAGCUGCCACGCCCCUCAGCAGGUCGGC--------CCUU----CAUCC---------
........(((.((((((...(((.((((......(((((((.......)))))))...)))).))).))))))..))--------)...----.....--------- ( -30.30)
>consensus
GGCUUCCAGCCAAACAGUACCGAGUGGCGCUUUAUUAGCUGACCCAUCUUCAGCUGCCACGCCCCUCAGCACCUCAGCA______UCCUUCAGCCAUCC_________
((((.................(((.((((......(((((((.......)))))))...)))).))).((......)).............))))............. (-19.73 = -20.72 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:15 2006