Locus 8549

Sequence ID 3R_DroMel_CAF1
Location 22,819,311 – 22,819,470
Length 159
Max. P 0.980605
window13738 window13739

overview

Window 8

Location 22,819,311 – 22,819,408
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.08
Mean single sequence MFE -20.82
Consensus MFE -13.48
Energy contribution -12.82
Covariance contribution -0.66
Combinations/Pair 1.20
Mean z-score -1.35
Structure conservation index 0.65
SVM decision value 0.00
SVM RNA-class probability 0.535948
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22819311 97 + 27905053
-------AUGCCGCUCGCUAUUCACUUUAUUUGGGUAGCUGCUGUUUUGUUUUAUUACUUAUUGUU-----UUCGUUUUCGA------CGCUUAAUGUUU-----GGCUUCAAUUUGAAA
-------..(((((..((((((((.......)))))))).)).................(((((..-----.(((....)))------....)))))...-----)))............ ( -16.40)
>DroPse_CAF1 31472 119 + 1
CGGUGCCACGCCGCAUGCUACUCACUUGAUUUGGGUGGCUGCUGUUUUGUUUUAUCAUUUAUUGUUUCGACUUGUUU-UUUUCUUUCAUGCCACAUGCUUGGCUUGGCUUCAAUUAUAAA
.((.((((.((((((.((((((((.......)))))))))))...................................-........((((...))))...))).)))).))......... ( -28.00)
>DroSec_CAF1 28191 102 + 1
-------ACGCCGCUCGCUAUUCACUUUAUUUGGGUAGCUGCUGUUUUGUUUUAUUACUUAUUGUUUCGAUUUCGUUUUCGA------CGCUUAAUGUUU-----GGCUUCAAUUUGAAA
-------..(((((..((((((((.......)))))))).)).....................((.((((........))))------.)).........-----)))............ ( -19.80)
>DroSim_CAF1 28567 100 + 1
-------ACGCCGCUCGCUAUUCACUUUAUUUGGGUAGCUGCUGUUUUGUUUUAUUACUUAUUGUUUCGAUUUCGUUUUCGA--------CUUAAUGUUU-----GGCUUCAAUUUGAAA
-------..(((((..((((((((.......)))))))).)).................(((((..((((........))))--------..)))))...-----)))............ ( -20.70)
>DroEre_CAF1 28271 102 + 1
-------ACGCCGCUCGCUAUUCACUUUAUUUGGGUAGCUGCUGUUUUGUUUUAUUACUUAUUGUUUCGAUUUCGUUUUUGA------CGUUUAAUGUUU-----GGCUUCAAUUUGAAA
-------..(((((..((((((((.......)))))))).)).................(((((..((((........))))------....)))))...-----)))............ ( -16.30)
>DroPer_CAF1 31114 115 + 1
CGGUGCCACGCCGCAUGCUACUCACUUGAUUUGGGUGGCUGCUGUUUUGUUUUAUCAUUUAUUGUUUCGACUUCUUUUUUUUCUUUCAUGCCACAUGCUU-----GGCUUCAAUUAUAAA
.((.((((.((.(((.((((((((.......)))))))))))......(((....((.....))....))).........................)).)-----))).))......... ( -23.70)
>consensus
_______ACGCCGCUCGCUAUUCACUUUAUUUGGGUAGCUGCUGUUUUGUUUUAUUACUUAUUGUUUCGAUUUCGUUUUCGA______CGCUUAAUGUUU_____GGCUUCAAUUUGAAA
.........(((((..((((((((.......)))))))).))......((......))...............................................)))............ (-13.48 = -12.82 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,819,379 – 22,819,470
Length 91
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.14
Mean single sequence MFE -11.62
Consensus MFE -5.52
Energy contribution -5.36
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -2.56
Structure conservation index 0.48
SVM decision value 1.87
SVM RNA-class probability 0.980605
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22819379 91 - 27905053
------------------ACUUUCAACACCUACGAUAACAAUUACGAAACAAUCGUAACAAAAUCAAAAUCAAAAUCAAUUUUCAAAUUGAAGCC-----AAACAUUAAGCG------UC
------------------.............(((.......((((((.....)))))).................((((((....))))))....-----..........))------). (  -8.00)
>DroPse_CAF1 31551 120 - 1
AUCCACCAUUUACCAUCCACUUUCAACACCUACGACAACAAUUACGAAACAAACGUAACAAAAUCAAAAUCAAAAUCAAUUUUAUAAUUGAAGCCAAGCCAAGCAUGUGGCAUGAAAGAA
...................((((((................(((((.......))))).................((((((....)))))).((((.((...))...)))).)))))).. ( -17.20)
>DroSec_CAF1 28264 91 - 1
------------------ACUUUCAACACCUACGACAACAAUUACGAAACAAUCGUAACAAAAUCAAAAUCAAAAUUAAUUUUCAAAUUGAAGCC-----AAACAUUAAGCG------UC
------------------...............(((.....((((((.....)))))).................((((((....))))))....-----...........)------)) (  -7.00)
>DroEre_CAF1 28344 91 - 1
------------------ACUUUCAACACCUACGACAACAAUUACGAAACAAUCGUAACAAAAUCAAAAUCGAAAUCAAUUUUCAAAUUGAAGCC-----AAACAUUAAACG------UC
------------------...............(((.....((((((.....)))))).................((((((....))))))....-----...........)------)) (  -9.20)
>DroPer_CAF1 31194 115 - 1
AUCCACCAUUUACCAUCCACUUUCAACACCUACGACAACAAUUACGAAACAAACGUAACAAAAUCAAAAUCAAAAUCAAUUUUAUAAUUGAAGCC-----AAGCAUGUGGCAUGAAAGAA
...................((((((................(((((.......))))).................((((((....)))))).(((-----(......)))).)))))).. ( -16.70)
>consensus
__________________ACUUUCAACACCUACGACAACAAUUACGAAACAAUCGUAACAAAAUCAAAAUCAAAAUCAAUUUUCAAAUUGAAGCC_____AAACAUUAAGCG______UC
.........................................(((((.......))))).................((((((....))))))............................. ( -5.52 =  -5.36 +  -0.16)

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 13:13:52 2006