Locus 2419

Sequence ID 3L_DroMel_CAF1
Location 6,804,812 – 6,805,008
Length 196
Max. P 0.984234
window3739 window3740 window3741

overview

Window 9

Location 6,804,812 – 6,804,931
Length 119
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 90.59
Mean single sequence MFE -35.00
Consensus MFE -31.10
Energy contribution -31.32
Covariance contribution 0.21
Combinations/Pair 1.18
Mean z-score -1.51
Structure conservation index 0.89
SVM decision value 0.54
SVM RNA-class probability 0.775542
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6804812 119 + 23771897
CACUGGAGAUUUCACAGCUUUUGGCUUUGUUUGAUUUGUCAAAAUGUUAAAUGGAUCCCCGUGGAAGAUCCGUGUGUCGUAGCUGGAAAUUGGUCAGCGUGUUUGCAAGUGGCAAACGA
(.((((.((((((.(((((..((((....(((((....))))).......(((((((.(....)..)))))))..)))).)))))))))))..)))).)(((((((.....))))))). ( -36.40)
>DroSec_CAF1 65698 119 + 1
CACUGGAGAUUUCACAGCUUUUGGCUUUGUUUGAUUUGUCAAAAUGUUAAAUGGAUCCCCGAGGAAGAUCCGUCUGCCGUAGCUGGAAAUUGGUCAGCGUGUUUGCAAGUGGCAAACGA
(.((((.((((((.(((((..((((....(((((....))))).......(((((((.(....)..)))))))..)))).)))))))))))..)))).)(((((((.....))))))). ( -38.50)
>DroSim_CAF1 68308 119 + 1
CACUGGAGAUUUCACAGCUUUUGGCUUUGUUUGAUUUGCCAAAAUGUUAAAUGGAUCCCCGAGGAAGAUCCGUCUGCCGUAGCUGGAAAUUGGUCAGCGUGUUUGCAAGUGGCAAACGA
(.((((.((((((.(((((((((((............))))))(((.((.(((((((.(....)..))))))).)).))))))))))))))..)))).)(((((((.....))))))). ( -37.90)
>DroEre_CAF1 79192 119 + 1
CACUGGAGAUUUCACAGCUUUUGGCUUUGUUUGAUUUGUCAAAAUGUUAAAUGGAUCCCCGAGGAAGAUCCAUCUGCCGUAGCUGGAAAUUGGUCAGCGUGUUUGCAAGUGGCAAACGA
(.((((.((((((.(((((..((((....(((((....))))).......(((((((.(....)..)))))))..)))).)))))))))))..)))).)(((((((.....))))))). ( -38.90)
>DroYak_CAF1 70710 119 + 1
CACUGGAGAUUUCACAGCUUUUGGCUUUGUUUGAUUUGUCAAAAUGUUAAAUGGAUCCCCGAGGAAGAUCCAUCUGCCGUAGCUGGAAAUUGGUCAGCGUGUUUGCAAGUGGCAAACGA
(.((((.((((((.(((((..((((....(((((....))))).......(((((((.(....)..)))))))..)))).)))))))))))..)))).)(((((((.....))))))). ( -38.90)
>DroAna_CAF1 76680 104 + 1
CACUGGAGAUUUCACAGUUUUUGGCUUUGUUUGAUUUGUCGAAAUGUUGAUUUGAUUCCCCAGGAAGAUCCAGCUGGUGUAACUAGAAAUUGGUCAG---------------CAAAUGA
..((((.((..(((......(..((....(((((....)))))..))..)..))).)).))))...((.(((.((((.....))))....)))))..---------------....... ( -19.40)
>consensus
CACUGGAGAUUUCACAGCUUUUGGCUUUGUUUGAUUUGUCAAAAUGUUAAAUGGAUCCCCGAGGAAGAUCCAUCUGCCGUAGCUGGAAAUUGGUCAGCGUGUUUGCAAGUGGCAAACGA
..((((.((((((.(((((..((((....(((((....))))).......(((((((.(....)..)))))))..)))).)))))))))))..))))...((((((.....)))))).. (-31.10 = -31.32 +   0.21)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,804,812 – 6,804,931
Length 119
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 90.59
Mean single sequence MFE -34.73
Consensus MFE -28.06
Energy contribution -29.72
Covariance contribution 1.66
Combinations/Pair 1.08
Mean z-score -3.79
Structure conservation index 0.81
SVM decision value 1.97
SVM RNA-class probability 0.984234
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6804812 119 - 23771897
UCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUACGACACACGGAUCUUCCACGGGGAUCCAUUUAACAUUUUGACAAAUCAAACAAAGCCAAAAGCUGUGAAAUCUCCAGUG
..((((((.....)))))).(((((....((((((((((.........(((((((.....))))))).........(((((....)))))..........))))).)))))...))))) ( -33.20)
>DroSec_CAF1 65698 119 - 1
UCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUACGGCAGACGGAUCUUCCUCGGGGAUCCAUUUAACAUUUUGACAAAUCAAACAAAGCCAAAAGCUGUGAAAUCUCCAGUG
..((((((.....)))))).(((((....((((((((((..(((....(((((((.....))))))).........(((((....)))))....)))...))))).)))))...))))) ( -38.30)
>DroSim_CAF1 68308 119 - 1
UCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUACGGCAGACGGAUCUUCCUCGGGGAUCCAUUUAACAUUUUGGCAAAUCAAACAAAGCCAAAAGCUGUGAAAUCUCCAGUG
..((((((.....)))))).(((((....((((((((((..(..(((.(((((((.....))))))).)))..)..((((((............))))))))))).)))))...))))) ( -38.80)
>DroEre_CAF1 79192 119 - 1
UCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUACGGCAGAUGGAUCUUCCUCGGGGAUCCAUUUAACAUUUUGACAAAUCAAACAAAGCCAAAAGCUGUGAAAUCUCCAGUG
..((((((.....)))))).(((((....((((((((((..((((((((((((((.....))))))))))).....(((((....)))))....)))...))))).)))))...))))) ( -41.90)
>DroYak_CAF1 70710 119 - 1
UCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUACGGCAGAUGGAUCUUCCUCGGGGAUCCAUUUAACAUUUUGACAAAUCAAACAAAGCCAAAAGCUGUGAAAUCUCCAGUG
..((((((.....)))))).(((((....((((((((((..((((((((((((((.....))))))))))).....(((((....)))))....)))...))))).)))))...))))) ( -41.90)
>DroAna_CAF1 76680 104 - 1
UCAUUUG---------------CUGACCAAUUUCUAGUUACACCAGCUGGAUCUUCCUGGGGAAUCAAAUCAACAUUUCGACAAAUCAAACAAAGCCAAAAACUGUGAAAUCUCCAGUG
.......---------------..........(((((((.....))))))).....(((((((................((....))...((.((.......)).))...))))))).. ( -14.30)
>consensus
UCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUACGGCAGACGGAUCUUCCUCGGGGAUCCAUUUAACAUUUUGACAAAUCAAACAAAGCCAAAAGCUGUGAAAUCUCCAGUG
..((((((.....)))))).(((((....((((((((((..(((....(((((((.....))))))).........(((((....)))))....)))...))))).)))))...))))) (-28.06 = -29.72 +   1.66)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,804,891 – 6,805,008
Length 117
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 86.95
Mean single sequence MFE -24.58
Consensus MFE -19.68
Energy contribution -19.56
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -2.12
Structure conservation index 0.80
SVM decision value 1.32
SVM RNA-class probability 0.941800
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6804891 117 - 23771897
UUUGUCACUCACAA--CAUAAUGUGUCACCCCACAAUCCAGUGUAAUCUAGAGUCGCCAUAACCAGGCUGGAACCACUUUCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUA
...((.((((....--.....((((......))))....((......)).)))).))........((((((((........((((((.....))))))..(.....)...)))))))). ( -23.10)
>DroSec_CAF1 65777 117 - 1
UUUGUGACUCACAA--CAUAAUGUGUCCCCCCACAAUCAAGUGUAAUCUACAGUCGCCAUAACCAGGCUGGAACCACUUUCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUA
...((((((((((.--.....))))......(((......)))........))))))........((((((((........((((((.....))))))..(.....)...)))))))). ( -26.20)
>DroSim_CAF1 68387 115 - 1
UUUGUGACUCACAA--CAUAAUGUGUCC--CCACAAUCCAGUGUAAUCUAGAGUCGCCAUAACCAGGCUGGAACCACUUUCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUA
...(((((((....--.....((((...--.))))....((......)).)))))))........((((((((........((((((.....))))))..(.....)...)))))))). ( -28.40)
>DroEre_CAF1 79271 98 - 1
CC-------------------UGUGUCC--CCACAAUCCAGUGUAAUCUAAAGUCGCCUUAAACAGGCUGGAACCACUUUCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUA
..-------------------((((...--.))))...((((((.....(((((.((((.....)))).(....)))))).((((((.....))))))))))))............... ( -21.50)
>DroYak_CAF1 70789 117 - 1
UCACAAACUCACAACACAUAAUGUGUCC--CCGAAAUCGAGUGUAAUCCAAAGUCGCCAUAAACAGGCUGGAACCACUUUCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUA
.............((((.....))))..--........(((((...((((.....(((.......)))))))..)))))..((((((.....))))))..((((.........)))).. ( -23.70)
>consensus
UUUGUGACUCACAA__CAUAAUGUGUCC__CCACAAUCCAGUGUAAUCUAAAGUCGCCAUAACCAGGCUGGAACCACUUUCGUUUGCCACUUGCAAACACGCUGACCAAUUUCCAGCUA
.....................((((......))))....((((...((((.....(((.......)))))))..))))...((((((.....))))))..((((.........)))).. (-19.68 = -19.56 +  -0.12)

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 10:31:59 2006