Locus 5949

Sequence ID 3L_DroMel_CAF1
Location 15,933,347 – 15,933,489
Length 142
Max. P 0.969256
window9501 window9502 window9503 window9504

overview

Window 1

Location 15,933,347 – 15,933,461
Length 114
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 89.28
Mean single sequence MFE -33.80
Consensus MFE -28.46
Energy contribution -28.90
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -2.40
Structure conservation index 0.84
SVM decision value 1.64
SVM RNA-class probability 0.969256
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15933347 114 + 23771897
AUAAUUCUCAUAAUUGAGAUAUAUCUAGUAUAUUUUAAGUUCCGAACUGCGGC-UUCGGUCACACUGGCGGCGACGUCGGCAGCGAUGCCGACGUCUAUUUACAACGCAUCGUUU
.............(((((((((((...)))))))))))....(((..((((((-(((((.....)))).)))((((((((((....)))))))))).........)))))))... ( -37.70)
>DroSec_CAF1 35155 115 + 1
AUAAUUCCCAUAAUUGAGAUAUUUCUAGUAUAUUUUAUGUUCCGAACUGUGGCCUUCGGUCACACUGGUUGCGACGUCGGCAGCGAUGCCGACGUCUAUUUACAACGCAUCGUUU
..............((((((((.......)))))))).((.(((...(((((((...))))))).)))..))((((((((((....))))))))))................... ( -33.50)
>DroSim_CAF1 35418 115 + 1
AUAAUUCCCAUAAUUGAGAUAUUUCUAGUAUAUUUUAAGUUCCGAACUGCGGCCUUCGGUCACACUGGCUGCGACGUCGGCAGCGAUGCCGACGUCUAUUUACAACGCAUCGUUU
.............(((((((((.......)))))))))....(((...((((((...(....)...))))))((((((((((....)))))))))).............)))... ( -36.40)
>DroEre_CAF1 32749 114 + 1
AUCAUUAAUAGAAUUGAGGUUUUUCUAGUAUAUUUAAA-CUCUGAAUUGUCCCCCUUGGUCACACUGGCAGCGACGUCGGCAGAGAUGCCGACGUCUAUUUACAACGCAUCGUUU
........(((((.........)))))........(((-(..((..((((........(((.....)))...((((((((((....)))))))))).....))))..))..)))) ( -27.60)
>consensus
AUAAUUCCCAUAAUUGAGAUAUUUCUAGUAUAUUUUAAGUUCCGAACUGCGGCCUUCGGUCACACUGGCUGCGACGUCGGCAGCGAUGCCGACGUCUAUUUACAACGCAUCGUUU
.............(((((((((.......)))))))))....(((..((((((..((((.....))))..))((((((((((....)))))))))).........)))))))... (-28.46 = -28.90 +   0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,933,347 – 15,933,461
Length 114
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 89.28
Mean single sequence MFE -32.55
Consensus MFE -26.45
Energy contribution -27.95
Covariance contribution 1.50
Combinations/Pair 1.10
Mean z-score -2.03
Structure conservation index 0.81
SVM decision value 0.96
SVM RNA-class probability 0.890649
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15933347 114 - 23771897
AAACGAUGCGUUGUAAAUAGACGUCGGCAUCGCUGCCGACGUCGCCGCCAGUGUGACCGAA-GCCGCAGUUCGGAACUUAAAAUAUACUAGAUAUAUCUCAAUUAUGAGAAUUAU
...(((((((.........((((((((((....))))))))))..(((....)))......-..))))..))).......................(((((....)))))..... ( -31.20)
>DroSec_CAF1 35155 115 - 1
AAACGAUGCGUUGUAAAUAGACGUCGGCAUCGCUGCCGACGUCGCAACCAGUGUGACCGAAGGCCACAGUUCGGAACAUAAAAUAUACUAGAAAUAUCUCAAUUAUGGGAAUUAU
......((.(((((.....((((((((((....)))))))))))))))))((((..(((((........))))).)))).................(((((....)))))..... ( -34.30)
>DroSim_CAF1 35418 115 - 1
AAACGAUGCGUUGUAAAUAGACGUCGGCAUCGCUGCCGACGUCGCAGCCAGUGUGACCGAAGGCCGCAGUUCGGAACUUAAAAUAUACUAGAAAUAUCUCAAUUAUGGGAAUUAU
...(((.((..........((((((((((....))))))))))((.(((..((....))..))).)).))))).......................(((((....)))))..... ( -33.70)
>DroEre_CAF1 32749 114 - 1
AAACGAUGCGUUGUAAAUAGACGUCGGCAUCUCUGCCGACGUCGCUGCCAGUGUGACCAAGGGGGACAAUUCAGAG-UUUAAAUAUACUAGAAAAACCUCAAUUCUAUUAAUGAU
((((..((.(((((.....((((((((((....)))))))))).((.((..((....)).)).))))))).))..)-)))........(((((.........)))))........ ( -31.00)
>consensus
AAACGAUGCGUUGUAAAUAGACGUCGGCAUCGCUGCCGACGUCGCAGCCAGUGUGACCGAAGGCCACAGUUCGGAACUUAAAAUAUACUAGAAAUAUCUCAAUUAUGGGAAUUAU
..(((.((.(((((.....((((((((((....))))))))))))))))).)))..(((((........)))))......................(((((....)))))..... (-26.45 = -27.95 +   1.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,933,387 – 15,933,489
Length 102
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 93.69
Mean single sequence MFE -35.45
Consensus MFE -30.40
Energy contribution -31.53
Covariance contribution 1.13
Combinations/Pair 1.06
Mean z-score -2.33
Structure conservation index 0.86
SVM decision value 1.27
SVM RNA-class probability 0.938343
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15933387 102 + 23771897
UCCGAACUGCGGC-UUCGGUCACACUGGCGGCGACGUCGGCAGCGAUGCCGACGUCUAUUUACAACGCAUCGUUUUGUUUAUUGUUCAGUCAGAUCAGAGUAA
......(((.(((-....)))...(((((...((((((((((....)))))))))).....((((.(((......)))...))))...)))))..)))..... ( -35.00)
>DroSec_CAF1 35195 103 + 1
UCCGAACUGUGGCCUUCGGUCACACUGGUUGCGACGUCGGCAGCGAUGCCGACGUCUAUUUACAACGCAUCGUUUUGUUUAUUGUUCAGUCAGAUCAGAGUAA
((.((..(((((((...)))))))(((..((.((((((((((....)))))))))).....((((.(((......)))...)))).))..))).)).)).... ( -35.70)
>DroSim_CAF1 35458 103 + 1
UCCGAACUGCGGCCUUCGGUCACACUGGCUGCGACGUCGGCAGCGAUGCCGACGUCUAUUUACAACGCAUCGUUUUGUUUAUUGUUCAGUCAGAUCAGAGUAA
......(((.((((...))))...(((((((.((((((((((....)))))))))).....((((.(((......)))...)))).)))))))..)))..... ( -36.20)
>DroEre_CAF1 32788 103 + 1
UCUGAAUUGUCCCCCUUGGUCACACUGGCAGCGACGUCGGCAGAGAUGCCGACGUCUAUUUACAACGCAUCGUUUUGUUUAUUGUUUAGUCAGAUCAGAGUAA
(((((..((.((.....)).))..(((((...((((((((((....)))))))))).....((((.(((......)))...))))...))))).))))).... ( -34.90)
>consensus
UCCGAACUGCGGCCUUCGGUCACACUGGCUGCGACGUCGGCAGCGAUGCCGACGUCUAUUUACAACGCAUCGUUUUGUUUAUUGUUCAGUCAGAUCAGAGUAA
((.((..((((((.....))))))(((((((.((((((((((....)))))))))).....((((.(((......)))...)))).))))))).)).)).... (-30.40 = -31.53 +   1.13)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,933,387 – 15,933,489
Length 102
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 93.69
Mean single sequence MFE -32.42
Consensus MFE -29.12
Energy contribution -29.75
Covariance contribution 0.62
Combinations/Pair 1.11
Mean z-score -1.93
Structure conservation index 0.90
SVM decision value 1.05
SVM RNA-class probability 0.906740
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15933387 102 - 23771897
UUACUCUGAUCUGACUGAACAAUAAACAAAACGAUGCGUUGUAAAUAGACGUCGGCAUCGCUGCCGACGUCGCCGCCAGUGUGACCGAA-GCCGCAGUUCGGA
((((.(((..........(((((...((......)).))))).....((((((((((....)))))))))).....))).))))(((((-.......))))). ( -30.80)
>DroSec_CAF1 35195 103 - 1
UUACUCUGAUCUGACUGAACAAUAAACAAAACGAUGCGUUGUAAAUAGACGUCGGCAUCGCUGCCGACGUCGCAACCAGUGUGACCGAAGGCCACAGUUCGGA
..............((((((..............((.(((((.....((((((((((....))))))))))))))))).((((.((...)).)))))))))). ( -34.90)
>DroSim_CAF1 35458 103 - 1
UUACUCUGAUCUGACUGAACAAUAAACAAAACGAUGCGUUGUAAAUAGACGUCGGCAUCGCUGCCGACGUCGCAGCCAGUGUGACCGAAGGCCGCAGUUCGGA
..............((((((..........((((....)))).....((((((((((....))))))))))((.(((..((....))..))).)).)))))). ( -35.00)
>DroEre_CAF1 32788 103 - 1
UUACUCUGAUCUGACUAAACAAUAAACAAAACGAUGCGUUGUAAAUAGACGUCGGCAUCUCUGCCGACGUCGCUGCCAGUGUGACCAAGGGGGACAAUUCAGA
....(((((.(((.....(((((...((......)).))))).....((((((((((....)))))))))).....)))(((..((...))..)))..))))) ( -29.00)
>consensus
UUACUCUGAUCUGACUGAACAAUAAACAAAACGAUGCGUUGUAAAUAGACGUCGGCAUCGCUGCCGACGUCGCAGCCAGUGUGACCGAAGGCCACAGUUCGGA
..............((((((..............((.(((((.....((((((((((....))))))))))))))))).((((.(.....).)))))))))). (-29.12 = -29.75 +   0.62)

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 12:04:57 2006