Locus 6847

Sequence ID 3R_DroMel_CAF1
Location 18,117,887 – 18,117,977
Length 90
Max. P 0.991550
window11112 window11113

overview

Window 2

Location 18,117,887 – 18,117,977
Length 90
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 77.65
Mean single sequence MFE -34.72
Consensus MFE -15.93
Energy contribution -16.52
Covariance contribution 0.59
Combinations/Pair 1.18
Mean z-score -3.33
Structure conservation index 0.46
SVM decision value 2.27
SVM RNA-class probability 0.991550
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18117887 90 + 27905053
GGAUGUUUGUCCAUA-GU-AAAUUCCUUG-GGUCCU---------GCGGCUAAUUGGCUGUGGGCGCAUUAAUUGGAAAUUUG-CCAGGACAAACUUUGGCCC
((..((((((((...-((-(((((((.((-.((((.---------((((((....)))))))))).))......)).))))))-)..)))))))).....)). ( -34.20)
>DroVir_CAF1 164342 88 + 1
GUAUUUUGGGCACUG-CC-AAAUUCUUUA-G-CCC----------UUGGCUAAUUGGCUGUGGGCGCAUUAAUUGGAAAAUUU-UCUGGGCAAACUUCCAUCG
......(((((((.(-((-((.....(((-(-((.----------..))))))))))).))).((.((..((((....)))).-..)).)).....))))... ( -24.30)
>DroPse_CAF1 151127 103 + 1
GCAUGUUUGUCUAGGGGAAAAAUUCCUUGAGGUCCUCUGCUGCCGGCGGCUAAUUGGCUGUGGGCCCAUUAAUUGGAAAUUUUCCCCAGACAAACUUUGAUCC
.((.((((((((.((((((((.((((..(((...)))....(((.((((((....)))))).))).........)))).))))))))))))))))..)).... ( -43.90)
>DroYak_CAF1 156967 90 + 1
GGAUGUUUGUCCCUA-GU-AAAUUCCUUG-GGUCCU---------GCGGCUAAUUGGCUGUGGGCGCAUUAAUUGGAAAUUUG-CCAGGACAAACUUUGGCCC
((..((((((((...-((-(((((((.((-.((((.---------((((((....)))))))))).))......)).))))))-)..)))))))).....)). ( -34.20)
>DroAna_CAF1 144081 90 + 1
AAGUGUUUGUCCUUA-GU-AAAUUCCCAG-GGUCCU---------GCGGCUAAUUGGCUGUGGGCGCAUUAAUUGGAAAUUCG-CCAGGACAAACUUUGAACC
....(((((((((..-(.-.((((.((((-.((((.---------.(((((....)))))..)).)).....)))).))))..-).)))))))))........ ( -32.60)
>DroPer_CAF1 176781 102 + 1
GCAUGUUUGUCCAGG-GAAAAAUUCCUUGAGGUCCUCUGCUGCCGGCGGCUAAUUGGCUGUGGGCCCAUUAAUUGGAAAUUUUCCCCAGACAAACUUUGAUCC
.((.(((((((..((-(((((.((((..(((...)))....(((.((((((....)))))).))).........)))).)))))))..)))))))..)).... ( -39.10)
>consensus
GCAUGUUUGUCCAUA_GU_AAAUUCCUUG_GGUCCU_________GCGGCUAAUUGGCUGUGGGCGCAUUAAUUGGAAAUUUG_CCAGGACAAACUUUGAUCC
....((((((((..........((((.....((((..........((((((....)))))))))).........)))).........))))))))........ (-15.93 = -16.52 +   0.59)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,117,887 – 18,117,977
Length 90
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 77.65
Mean single sequence MFE -28.32
Consensus MFE -13.32
Energy contribution -13.96
Covariance contribution 0.64
Combinations/Pair 1.21
Mean z-score -2.54
Structure conservation index 0.47
SVM decision value 1.20
SVM RNA-class probability 0.929593
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18117887 90 - 27905053
GGGCCAAAGUUUGUCCUGG-CAAAUUUCCAAUUAAUGCGCCCACAGCCAAUUAGCCGC---------AGGACC-CAAGGAAUUU-AC-UAUGGACAAACAUCC
........(((((((((((-.(((((((.......((((......((......)))))---------).....-...)))))))-.)-)).)))))))).... ( -22.26)
>DroVir_CAF1 164342 88 - 1
CGAUGGAAGUUUGCCCAGA-AAAUUUUCCAAUUAAUGCGCCCACAGCCAAUUAGCCAA----------GGG-C-UAAAGAAUUU-GG-CAGUGCCCAAAAUAC
...((((((.((.......-.)).))))))........(..(((.(((((((((((..----------.))-)-))).....))-))-).)))..)....... ( -19.10)
>DroPse_CAF1 151127 103 - 1
GGAUCAAAGUUUGUCUGGGGAAAAUUUCCAAUUAAUGGGCCCACAGCCAAUUAGCCGCCGGCAGCAGAGGACCUCAAGGAAUUUUUCCCCUAGACAAACAUGC
........((((((((((((((((.((((...((((.(((.....))).))))(((...)))....(((...)))..)))).)))))))).)))))))).... ( -38.70)
>DroYak_CAF1 156967 90 - 1
GGGCCAAAGUUUGUCCUGG-CAAAUUUCCAAUUAAUGCGCCCACAGCCAAUUAGCCGC---------AGGACC-CAAGGAAUUU-AC-UAGGGACAAACAUCC
........(((((((((((-.(((((((.......((((......((......)))))---------).....-...)))))))-.)-)).)))))))).... ( -22.26)
>DroAna_CAF1 144081 90 - 1
GGUUCAAAGUUUGUCCUGG-CGAAUUUCCAAUUAAUGCGCCCACAGCCAAUUAGCCGC---------AGGACC-CUGGGAAUUU-AC-UAAGGACAAACACUU
........(((((((((((-..((((((((.....((((......((......)))))---------).....-.)))))))).-.)-).))))))))).... ( -28.40)
>DroPer_CAF1 176781 102 - 1
GGAUCAAAGUUUGUCUGGGGAAAAUUUCCAAUUAAUGGGCCCACAGCCAAUUAGCCGCCGGCAGCAGAGGACCUCAAGGAAUUUUUC-CCUGGACAAACAUGC
........(((((((..(((((((.((((...((((.(((.....))).))))(((...)))....(((...)))..)))).)))))-))..))))))).... ( -39.20)
>consensus
GGAUCAAAGUUUGUCCUGG_AAAAUUUCCAAUUAAUGCGCCCACAGCCAAUUAGCCGC_________AGGACC_CAAGGAAUUU_AC_CAUGGACAAACAUCC
........(((((((((........((((......((.((.....)))).....((............)).......)))).........))))))))).... (-13.32 = -13.96 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:24 2006