Locus 7840

Sequence ID 3L_DroMel_CAF1
Location 20,984,746 – 20,984,881
Length 135
Max. P 0.857612
window12762 window12763 window12764

overview

Window 2

Location 20,984,746 – 20,984,865
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.80
Mean single sequence MFE -20.49
Consensus MFE -13.50
Energy contribution -13.99
Covariance contribution 0.49
Combinations/Pair 1.12
Mean z-score -1.84
Structure conservation index 0.66
SVM decision value 0.09
SVM RNA-class probability 0.579458
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20984746 119 + 23771897
CGCUUUACGAAACAAAUUUAAUAAACAAUAAUUGUUAAUAUUUAUCCAGACAAUGCAAGGUUCGAAAUAUACAAGCAUCGAAAACUUGCAUAAU-UUUUGUUUGCGAUCAAUAUUCGAAU
.......((((......(((((((.......)))))))((((.((((((((((((((((.(((((............)))))..)))))))...-...)))))).))).))))))))... ( -23.20)
>DroSec_CAF1 2425 119 + 1
CGCUUUACAAAACAUAUUUAAUAAACAAUAAUUGUUAAUGUUUAUUCAGACAAUGCAAGGUUCGAAAUAUACAAGCAUCGAAAACUUGCAUAAU-UUUUGUUUGCGAUCAAUAUUCGAAA
(((...((((((.......((((((((.((.....)).))))))))......(((((((.(((((............)))))..)))))))...-))))))..))).............. ( -22.80)
>DroSim_CAF1 9823 119 + 1
CGCUUUACAAAACAUAUUUAAUAAACAAUAAUUGUUAAUGUUUAUCCAGACAAUGCAAGGUUCGAAAUAUACAAGCAUCGAAAACUUGCAUAAU-UUUUGUUUGCGAUCAAUAUUCGAAA
(((...((((((........(((((((.((.....)).))))))).......(((((((.(((((............)))))..)))))))...-))))))..))).............. ( -22.00)
>DroEre_CAF1 10845 95 + 1
CUCUAUACAAAACAUAUUUAAUAAACGAUAAUUGUUAAUAUUUAUCCAGACAAUGGAAGG-------------------------UUGCAUAACUUUUUAUUUGCGAUCAAUAUUCGGAU
.........................(((....((((........((((.....)))).((-------------------------(((((............))))))))))).)))... ( -13.80)
>DroYak_CAF1 8535 120 + 1
CGCUUUACAAAACAUAUUUAAUAAACGAUAAUUGUUAAUAUAUAUCCAGACAAUGCAAGGUUCAAAAUAAACCAACAUCGGAAGCUUGCAUAAUUUUUUGUUUGCGAUCAAUAUUCGAAU
(((...((((((.(((((((((((.......))))))).)))).........(((((((.(((.................))).)))))))....))))))..))).............. ( -20.63)
>consensus
CGCUUUACAAAACAUAUUUAAUAAACAAUAAUUGUUAAUAUUUAUCCAGACAAUGCAAGGUUCGAAAUAUACAAGCAUCGAAAACUUGCAUAAU_UUUUGUUUGCGAUCAAUAUUCGAAU
.......................(((((...)))))((((((.((((((((((((((((.(((((............)))))..))))))).......)))))).))).))))))..... (-13.50 = -13.99 +   0.49)

alignment

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secondary structure

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Window 3

Location 20,984,786 – 20,984,881
Length 95
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 85.11
Mean single sequence MFE -19.63
Consensus MFE -17.45
Energy contribution -17.23
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.81
Structure conservation index 0.89
SVM decision value 0.81
SVM RNA-class probability 0.857612
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20984786 95 + 23771897
UUUAUCCAGACAAUGCAAGGUUCGAAAUAUACAAGCAUCGAAAACUUGCAUAAUUUUUGUUUGCGAUCAAUAUUCGAAUAUCGACUCCAA------------AACUU
...((((((((((((((((.(((((............)))))..)))))))......)))))).)))......(((.....)))......------------..... ( -18.10)
>DroSec_CAF1 2465 95 + 1
UUUAUUCAGACAAUGCAAGGUUCGAAAUAUACAAGCAUCGAAAACUUGCAUAAUUUUUGUUUGCGAUCAAUAUUCGAAACUCGACUGUAU------------AUAUG
..(((.(((...(((((((.(((((............)))))..))))))).......((((.(((.......)))))))....))).))------------).... ( -18.00)
>DroSim_CAF1 9863 107 + 1
UUUAUCCAGACAAUGCAAGGUUCGAAAUAUACAAGCAUCGAAAACUUGCAUAAUUUUUGUUUGCGAUCAAUAUUCGAAACUCGAAUGUAUUUAGCUAUACUUAUAAG
...((((((((((((((((.(((((............)))))..)))))))......)))))).)))..(((((((.....)))))))................... ( -22.80)
>consensus
UUUAUCCAGACAAUGCAAGGUUCGAAAUAUACAAGCAUCGAAAACUUGCAUAAUUUUUGUUUGCGAUCAAUAUUCGAAACUCGACUGUAU____________AUAUG
...((((((((((((((((.(((((............)))))..)))))))......)))))).)))......(((.....)))....................... (-17.45 = -17.23 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,984,786 – 20,984,881
Length 95
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 85.11
Mean single sequence MFE -20.41
Consensus MFE -17.32
Energy contribution -18.10
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -1.47
Structure conservation index 0.85
SVM decision value 0.03
SVM RNA-class probability 0.548114
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20984786 95 - 23771897
AAGUU------------UUGGAGUCGAUAUUCGAAUAUUGAUCGCAAACAAAAAUUAUGCAAGUUUUCGAUGCUUGUAUAUUUCGAACCUUGCAUUGUCUGGAUAAA
....(------------(..((((((((((....)))))))).((((........(((((((((.......))))))))).........))))....))..)).... ( -20.53)
>DroSec_CAF1 2465 95 - 1
CAUAU------------AUACAGUCGAGUUUCGAAUAUUGAUCGCAAACAAAAAUUAUGCAAGUUUUCGAUGCUUGUAUAUUUCGAACCUUGCAUUGUCUGAAUAAA
....(------------(.(((((((((.((((((..(((....)))........(((((((((.......))))))))).)))))).)))).))))).))...... ( -21.20)
>DroSim_CAF1 9863 107 - 1
CUUAUAAGUAUAGCUAAAUACAUUCGAGUUUCGAAUAUUGAUCGCAAACAAAAAUUAUGCAAGUUUUCGAUGCUUGUAUAUUUCGAACCUUGCAUUGUCUGGAUAAA
.......((((......))))(((((.....)))))....(((.((.(((......(((((((..(((((............))))).)))))))))).)))))... ( -19.50)
>consensus
CAUAU____________AUACAGUCGAGUUUCGAAUAUUGAUCGCAAACAAAAAUUAUGCAAGUUUUCGAUGCUUGUAUAUUUCGAACCUUGCAUUGUCUGGAUAAA
...................(((((((((.((((((..(((....)))........(((((((((.......))))))))).)))))).)))).)))))......... (-17.32 = -18.10 +   0.78)

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 12:58:22 2006