Locus 2823

Sequence ID 3L_DroMel_CAF1
Location 8,044,074 – 8,044,314
Length 240
Max. P 0.997774
window4409 window4410 window4411 window4412 window4413

overview

Window 9

Location 8,044,074 – 8,044,194
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.67
Mean single sequence MFE -32.18
Consensus MFE -29.56
Energy contribution -32.20
Covariance contribution 2.64
Combinations/Pair 1.03
Mean z-score -2.29
Structure conservation index 0.92
SVM decision value 2.63
SVM RNA-class probability 0.995948
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8044074 120 + 23771897
AGAUAUUGACACGCCCCGUCAAUAUAAAUAAUUGCUAAUUGCUAGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUACGGCUCCGAAAACAUUUGACUCGCUCAAUU
..((((((((.......))))))))........((....((((((.(((.....))).)))))).......(((((.((((...((((....))))...))))....)))))))...... ( -33.10)
>DroSec_CAF1 15171 120 + 1
AGAUAUUGACACGCCCCGUCAAUAUAAAUAAUUGCUAAUUGCUAGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUUCGGCUCCGAAAACAUUCGACUCGCUCAAUU
..((((((((.......))))))))........((....((((((.(((.....))).)))))).......(((((.((((...((((....))))...))))....)))))))...... ( -33.60)
>DroSim_CAF1 15174 120 + 1
AGAUAUUGACACGCCCCGUCAAUAUAAAUAAUUGCUAAUUGCUAGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUU
..((((((((.......))))))))........((....((((((.(((.....))).)))))).......(((((.((((...((((....))))...))))....)))))))...... ( -33.10)
>DroEre_CAF1 15000 120 + 1
AGAUAUUGACACGCCCCAUCAAUAUAAAUAAUUGCUAAUUGCUGGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUU
..(((((((.........)))))))........((....(((..(.(((.....))).)..))).......(((((.((((...((((....))))...))))....)))))))...... ( -28.00)
>DroYak_CAF1 15472 120 + 1
AGAUAUUGACACGCCCCGUCAAUAUAAAUAAUUGCUAAUUGCUAGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUU
..((((((((.......))))))))........((....((((((.(((.....))).)))))).......(((((.((((...((((....))))...))))....)))))))...... ( -33.10)
>consensus
AGAUAUUGACACGCCCCGUCAAUAUAAAUAAUUGCUAAUUGCUAGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUU
..((((((((.......))))))))........((....((((((.(((.....))).)))))).......(((((.((((...((((....))))...))))....)))))))...... (-29.56 = -32.20 +   2.64)

alignment

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secondary structure

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Window 0

Location 8,044,114 – 8,044,234
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -34.38
Consensus MFE -31.52
Energy contribution -34.52
Covariance contribution 3.00
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.92
SVM decision value 2.93
SVM RNA-class probability 0.997774
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8044114 120 + 23771897
GCUAGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUACGGCUCCGAAAACAUUUGACUCGCUCAAUUUGCAUAAUUGCAAUUUAUUGUAAAUCCGUGUGCAAAUAUG
((..((((.(((....)))))))........(((((.((((...((((....))))...))))....)))))))...(((((((((.((((((....)))))).....)))))))))... ( -35.40)
>DroSec_CAF1 15211 120 + 1
GCUAGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUUCGGCUCCGAAAACAUUCGACUCGCUCAAUUUGCAUAAUUGCAAUUUAUUGUAAAUCCGUGUGCAAAUAUG
((..((((.(((....)))))))........(((((.((((...((((....))))...))))....)))))))...(((((((((.((((((....)))))).....)))))))))... ( -35.90)
>DroSim_CAF1 15214 120 + 1
GCUAGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUUUGCAUAAUUGCACUUUAUUGUAAAUCCGUGUGCAAAUAUG
((..((((.(((....)))))))........(((((.((((...((((....))))...))))....)))))))...(((((((((.(((((......))))).....)))))))))... ( -34.60)
>DroEre_CAF1 15040 120 + 1
GCUGGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUUUGCAUAAUUGCAAUUUAUUGUAAAUCCGUGCGCAAAUAUG
((..((((.(((....)))))))........(((((.((((...((((....))))...))))....)))))))...((((((.((.((((((....)))))).....)).))))))... ( -30.60)
>DroYak_CAF1 15512 120 + 1
GCUAGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUUUGCAUAAUUGCAAUUUAUUGUAAAUCCGUGUGCAAAUAUG
((..((((.(((....)))))))........(((((.((((...((((....))))...))))....)))))))...(((((((((.((((((....)))))).....)))))))))... ( -35.40)
>consensus
GCUAGCCAUGAUUAAUGUCUGGCAUCUUUUGGAGUUCGUUUGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUUUGCAUAAUUGCAAUUUAUUGUAAAUCCGUGUGCAAAUAUG
((..((((.(((....)))))))........(((((.((((...((((....))))...))))....)))))))...(((((((((.((((((....)))))).....)))))))))... (-31.52 = -34.52 +   3.00)

alignment

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secondary structure

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Window 1

Location 8,044,154 – 8,044,274
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.67
Mean single sequence MFE -32.17
Consensus MFE -30.20
Energy contribution -30.44
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -2.14
Structure conservation index 0.94
SVM decision value 2.61
SVM RNA-class probability 0.995729
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8044154 120 + 23771897
UGAAGAGCUACGGCUCCGAAAACAUUUGACUCGCUCAAUUUGCAUAAUUGCAAUUUAUUGUAAAUCCGUGUGCAAAUAUGCAAGAAAUUUGCAGCAGCUCUUUAUGGCAAACCAGAGGCC
(((((((((.((....))..............((...(((((((((.((((((....)))))).....))))))))).((((((...))))))))))))))))).(((.........))) ( -31.20)
>DroSec_CAF1 15251 120 + 1
UGAAGAGCUUCGGCUCCGAAAACAUUCGACUCGCUCAAUUUGCAUAAUUGCAAUUUAUUGUAAAUCCGUGUGCAAAUAUGCAAGAAAUUUGCAGCAGCUCUUUAUGGCAAACCAGAGGCC
....((((....))))((((....)))).(((((((.(((((((((.((((((....)))))).....))))))))).((((((...))))))).)))......(((....))))))... ( -32.60)
>DroSim_CAF1 15254 120 + 1
UGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUUUGCAUAAUUGCACUUUAUUGUAAAUCCGUGUGCAAAUAUGCAAGAAAUUUGCAGCAGCUCUUUAUGGCAAACCAGAGGCC
....((((....))))((((....)))).(((((((((((((((((.((((((................)))))).))))))))....))).))).(((......)))......)))... ( -34.99)
>DroEre_CAF1 15080 120 + 1
UGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUUUGCAUAAUUGCAAUUUAUUGUAAAUCCGUGCGCAAAUAUGCAAGAAAUUUGCAGCAGCUCUUUAUGGCAAACCAGAGGCC
....((((....))))((((....)))).(((((((((((((((((.((((....................)))).))))))))....))).))).(((......)))......)))... ( -29.95)
>DroYak_CAF1 15552 120 + 1
UGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUUUGCAUAAUUGCAAUUUAUUGUAAAUCCGUGUGCAAAUAUGCAAGAAAUUUGCAGCAGCUCUUUAUGGCAAACCAGAGGCC
....((((....))))((((....)))).(((((((.(((((((((.((((((....)))))).....))))))))).((((((...))))))).)))......(((....))))))... ( -32.10)
>consensus
UGAAGAGCUACGGCUCCGAAAACAUUCGACUCGCUCAAUUUGCAUAAUUGCAAUUUAUUGUAAAUCCGUGUGCAAAUAUGCAAGAAAUUUGCAGCAGCUCUUUAUGGCAAACCAGAGGCC
(((((((((.(.((..((((....)))).((.((...(((((((((.((((((....)))))).....)))))))))..)).))......)).).))))))))).(((.........))) (-30.20 = -30.44 +   0.24)

alignment

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secondary structure

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Window 2

Location 8,044,154 – 8,044,274
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.67
Mean single sequence MFE -34.02
Consensus MFE -32.59
Energy contribution -32.83
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.95
Structure conservation index 0.96
SVM decision value 2.37
SVM RNA-class probability 0.993096
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8044154 120 - 23771897
GGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCACACGGAUUUACAAUAAAUUGCAAUUAUGCAAAUUGAGCGAGUCAAAUGUUUUCGGAGCCGUAGCUCUUCA
(((.........)))...(((((((((.((.......(((((((.(((((..................))))).)))))))......((((.........))))..)).))))))))).. ( -32.77)
>DroSec_CAF1 15251 120 - 1
GGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCACACGGAUUUACAAUAAAUUGCAAUUAUGCAAAUUGAGCGAGUCGAAUGUUUUCGGAGCCGAAGCUCUUCA
(((.........)))...(((((((............(((((((.(((((..................))))).))))))).(((.((...(((((....))))).)))))))))))).. ( -30.97)
>DroSim_CAF1 15254 120 - 1
GGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCACACGGAUUUACAAUAAAGUGCAAUUAUGCAAAUUGAGCGAGUCGAAUGUUUUCGGAGCCGUAGCUCUUCA
(((.........)))...(((((((((.((.......(((((((.((((((................)))))).)))))))..........(((((....))))).)).))))))))).. ( -37.99)
>DroEre_CAF1 15080 120 - 1
GGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCGCACGGAUUUACAAUAAAUUGCAAUUAUGCAAAUUGAGCGAGUCGAAUGUUUUCGGAGCCGUAGCUCUUCA
(((.........)))...(((((((((.((.......(((((((.((((.....((((((...)))))))))).)))))))..........(((((....))))).)).))))))))).. ( -34.00)
>DroYak_CAF1 15552 120 - 1
GGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCACACGGAUUUACAAUAAAUUGCAAUUAUGCAAAUUGAGCGAGUCGAAUGUUUUCGGAGCCGUAGCUCUUCA
(((.........)))...(((((((((.((.......(((((((.(((((..................))))).)))))))..........(((((....))))).)).))))))))).. ( -34.37)
>consensus
GGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCACACGGAUUUACAAUAAAUUGCAAUUAUGCAAAUUGAGCGAGUCGAAUGUUUUCGGAGCCGUAGCUCUUCA
(((.........)))...(((((((((.((.......(((((((.(((((..................))))).)))))))..........(((((....))))).)).))))))))).. (-32.59 = -32.83 +   0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,044,194 – 8,044,314
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.67
Mean single sequence MFE -27.22
Consensus MFE -25.30
Energy contribution -25.74
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.60
Structure conservation index 0.93
SVM decision value 1.43
SVM RNA-class probability 0.952803
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8044194 120 - 23771897
GGAUUGAACAAAUCCAAUAUUCAAAUUGUGAAAAGCCGUUGGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCACACGGAUUUACAAUAAAUUGCAAUUAUGCA
(((((.....))))).........((((((((...((((.(((((.(((....)))...)).)))..(((((((.........))))))).)))).))))))))....((((....)))) ( -28.50)
>DroSec_CAF1 15291 120 - 1
GGAUUGAACAAAUCCAAAAUUCAAAUUGUGAAAAGCCGUUGGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCACACGGAUUUACAAUAAAUUGCAAUUAUGCA
(((((.....))))).........((((((((...((((.(((((.(((....)))...)).)))..(((((((.........))))))).)))).))))))))....((((....)))) ( -28.50)
>DroSim_CAF1 15294 120 - 1
GGAUUGAACAAAUCCAAAAUUCAAAUUGUGAAAAGCCGUUGGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCACACGGAUUUACAAUAAAGUGCAAUUAUGCA
(((((.....)))))..........(((((..((((((........))))))..)))))...((....))........((((((.((((((................)))))).)))))) ( -29.19)
>DroEre_CAF1 15120 120 - 1
AGAUUGAAAAAAUCCAAAAUUCAAAUUGUGAAAAGCCGUUGGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCGCACGGAUUUACAAUAAAUUGCAAUUAUGCA
.((((.....))))..........((((((((...((((.(((((.(((....)))...)).)))((.((((((.........)))))))))))).))))))))....((((....)))) ( -26.00)
>DroYak_CAF1 15592 120 - 1
AGAUUGAAAAAAUACAAAAUUCAAAUUGUGAAAAGCCGUUGGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCACACGGAUUUACAAUAAAUUGCAAUUAUGCA
...(((((...........)))))((((((((...((((.(((((.(((....)))...)).)))..(((((((.........))))))).)))).))))))))....((((....)))) ( -23.90)
>consensus
GGAUUGAACAAAUCCAAAAUUCAAAUUGUGAAAAGCCGUUGGCCUCUGGUUUGCCAUAAAGAGCUGCUGCAAAUUUCUUGCAUAUUUGCACACGGAUUUACAAUAAAUUGCAAUUAUGCA
(((((.....))))).........((((((((...((((.(((((.(((....)))...)).)))(.(((((((.........)))))))))))).))))))))....((((....)))) (-25.30 = -25.74 +   0.44)

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 10:42:39 2006