Locus 3064

Sequence ID X_DroMel_CAF1
Location 8,191,030 – 8,191,172
Length 142
Max. P 0.837764
window5011 window5012 window5013

overview

Window 1

Location 8,191,030 – 8,191,137
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.97
Mean single sequence MFE -41.16
Consensus MFE -30.72
Energy contribution -31.48
Covariance contribution 0.76
Combinations/Pair 1.09
Mean z-score -1.76
Structure conservation index 0.75
SVM decision value 0.33
SVM RNA-class probability 0.689962
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8191030 107 + 22224390
---CCCCUUC--CGUUAUCCGGUAGCCA-----UUUGCAUGCCGUCCACGAGGCG-GUGGCACAGAUUUCUGGACUCGAAGUCUGAGCCUGCGACUGAGCCACCACUAGAAUCUGGCC--
---.......--........(((.((((-----.(((((.((((((.....))))-))(((.((((((((.......)))))))).)))))))).)).)).))).((((...))))..-- ( -36.80)
>DroSec_CAF1 93496 110 + 1
CCCCCCCUUC--CGCCAUCCGGUGGCCA-----UUUGCAUGCCGUCCACGAGGCG-GUGGCACAGAUUUCUGGACUCGAAGUCUGAGCCUGCGACUGAGCCACCACUAGAAUCUGGCC--
..........--.((((((.((((((((-----.(((((.((((((.....))))-))(((.((((((((.......)))))))).)))))))).)).))))))....))...)))).-- ( -45.70)
>DroEre_CAF1 83706 107 + 1
---CCCUUAC--CGCCUUCCGGUGGCCA-----UUUGCAUGCCGUCCACGAGGCG-GUGGCACAGAUUUCUGGACCCGAAGUCUGAGCCUGCGACUGAGCCGCCACUAGAAUCUGGCC--
---.......--.((((((.((((((((-----.(((((.((((((.....))))-))(((.((((((((.(....))))))))).)))))))).)).))))))....)))...))).-- ( -45.00)
>DroYak_CAF1 82139 108 + 1
---CCCUUUC--CGCCUUCCGGUGGCCA-----UUUGCAUGCCGUCCACGAGGCGGGUGGCACAGAUUUCUGGACUCGAAGUCUGAGCCUGCGACUGAGCCAGCACUAGAAUCUGGCC--
---.....((--((((((..((((((..-----.......)))).))..)))))))).(((.(((((((((((.(((..((((.........))))))))))).....))))))))))-- ( -41.30)
>DroAna_CAF1 128434 114 + 1
---CACUUGCCACGUUAUCCAAUGGCCACUGUAUUUGCAUGCAGUUCACG--GCU-GUGGCACAGAUUUCUGGACUUGAAGUCUGAGCCUGCGACUGAGCCACCACUAGAAUCUGGCCUU
---.....((((.(((......((((.(((((((....)))))))...((--(.(-(((((.((((((((.......)))))))).))).))).))).)))).......))).))))... ( -37.02)
>consensus
___CCCUUUC__CGCCAUCCGGUGGCCA_____UUUGCAUGCCGUCCACGAGGCG_GUGGCACAGAUUUCUGGACUCGAAGUCUGAGCCUGCGACUGAGCCACCACUAGAAUCUGGCC__
.............((((((.((((((((......(((((.(((........)))....(((.((((((((.......)))))))).)))))))).)).))))))....))...))))... (-30.72 = -31.48 +   0.76)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,191,060 – 8,191,172
Length 112
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 95.11
Mean single sequence MFE -44.45
Consensus MFE -39.76
Energy contribution -39.45
Covariance contribution -0.31
Combinations/Pair 1.06
Mean z-score -1.86
Structure conservation index 0.89
SVM decision value 0.71
SVM RNA-class probability 0.829594
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8191060 112 + 22224390
GCCGUCCACGAGGCG-GUGGCACAGAUUUCUGGACUCGAAGUCUGAGCCUGCGACUGAGCCACCACUAGAAUCUGGCCAAGGACUCGGCCAAAAGCUGGAGGCUGAAGGCACA
(((((((....((((-(((((.(((.((.(.((.((((.....)))))).).))))).)))))).(........))))..))))((((((..........)))))).)))... ( -44.10)
>DroSec_CAF1 93529 112 + 1
GCCGUCCACGAGGCG-GUGGCACAGAUUUCUGGACUCGAAGUCUGAGCCUGCGACUGAGCCACCACUAGAAUCUGGCCAAGGACUCGGCCAAAAGCUGAAGGCUGAAGGCGCA
(((((((....((((-(((((.(((.((.(.((.((((.....)))))).).))))).)))))).(........))))..))))((((((..........)))))).)))... ( -44.10)
>DroEre_CAF1 83736 112 + 1
GCCGUCCACGAGGCG-GUGGCACAGAUUUCUGGACCCGAAGUCUGAGCCUGCGACUGAGCCGCCACUAGAAUCUGGCCAAGGACUUGGCCAAAAGCUGAACGCUAAAGGCUGA
(((.....((.((((-(((((.((((((((.(....))))))))).))).........))))))..(((....(((((((....)))))))....)))..)).....)))... ( -43.80)
>DroYak_CAF1 82169 113 + 1
GCCGUCCACGAGGCGGGUGGCACAGAUUUCUGGACUCGAAGUCUGAGCCUGCGACUGAGCCAGCACUAGAAUCUGGCCAAGGACUCGGCCAAAAGCUGAAGGCUGAAGGCUGA
(((((((.....((((((....((((((((.......)))))))).))))))...((.(((((.........))))))).))))((((((..........)))))).)))... ( -45.80)
>consensus
GCCGUCCACGAGGCG_GUGGCACAGAUUUCUGGACUCGAAGUCUGAGCCUGCGACUGAGCCACCACUAGAAUCUGGCCAAGGACUCGGCCAAAAGCUGAAGGCUGAAGGCUCA
(((((((.....(((...(((.((((((((.......)))))))).))))))...((.((((...........)))))).))))((((((..........)))))).)))... (-39.76 = -39.45 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,191,060 – 8,191,172
Length 112
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 95.11
Mean single sequence MFE -44.38
Consensus MFE -40.06
Energy contribution -39.75
Covariance contribution -0.31
Combinations/Pair 1.09
Mean z-score -1.84
Structure conservation index 0.90
SVM decision value 0.74
SVM RNA-class probability 0.837764
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8191060 112 - 22224390
UGUGCCUUCAGCCUCCAGCUUUUGGCCGAGUCCUUGGCCAGAUUCUAGUGGUGGCUCAGUCGCAGGCUCAGACUUCGAGUCCAGAAAUCUGUGCCAC-CGCCUCGUGGACGGC
..........((((((((..(((((((((....)))))))))..)).((((((((.(((((...(((((.......)))))..))...))).)))))-))).....))).))) ( -47.40)
>DroSec_CAF1 93529 112 - 1
UGCGCCUUCAGCCUUCAGCUUUUGGCCGAGUCCUUGGCCAGAUUCUAGUGGUGGCUCAGUCGCAGGCUCAGACUUCGAGUCCAGAAAUCUGUGCCAC-CGCCUCGUGGACGGC
...(((.((.((....((..(((((((((....)))))))))..)).((((((((.(((((...(((((.......)))))..))...))).)))))-)))...)).)).))) ( -45.60)
>DroEre_CAF1 83736 112 - 1
UCAGCCUUUAGCGUUCAGCUUUUGGCCAAGUCCUUGGCCAGAUUCUAGUGGCGGCUCAGUCGCAGGCUCAGACUUCGGGUCCAGAAAUCUGUGCCAC-CGCCUCGUGGACGGC
...........(((((((..(((((((((....)))))))))..)).(.((((((......)).(((.((((.(((.......))).)))).)))..-)))).)..))))).. ( -43.20)
>DroYak_CAF1 82169 113 - 1
UCAGCCUUCAGCCUUCAGCUUUUGGCCGAGUCCUUGGCCAGAUUCUAGUGCUGGCUCAGUCGCAGGCUCAGACUUCGAGUCCAGAAAUCUGUGCCACCCGCCUCGUGGACGGC
...(((.(((((((..((..(((((((((....)))))))))..)))).)))))....(((...(((.((((.(((.......))).)))).)))...(((...))))))))) ( -41.30)
>consensus
UCAGCCUUCAGCCUUCAGCUUUUGGCCGAGUCCUUGGCCAGAUUCUAGUGGUGGCUCAGUCGCAGGCUCAGACUUCGAGUCCAGAAAUCUGUGCCAC_CGCCUCGUGGACGGC
...(((.((.((....((..(((((((((....)))))))))..)).(.((((((......)).(((.((((.(((.......))).)))).)))...)))).))).)).))) (-40.06 = -39.75 +  -0.31)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:07 2006