Locus 4765

Sequence ID 3R_DroMel_CAF1
Location 12,495,958 – 12,496,077
Length 119
Max. P 0.999819
window7814 window7815 window7816

overview

Window 4

Location 12,495,958 – 12,496,048
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 96.89
Mean single sequence MFE -24.80
Consensus MFE -23.14
Energy contribution -22.82
Covariance contribution -0.32
Combinations/Pair 1.09
Mean z-score -1.95
Structure conservation index 0.93
SVM decision value 2.68
SVM RNA-class probability 0.996287
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12495958 90 - 27905053
UCGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAAGCAAAAGGAAAAGCACUGGCAGAGGAAAGCGUACAACAAUUGAAACGCCAA
..((((((.((.((....(((...(((((....))))).)))...))....))))))))........((((............))))... ( -24.10)
>DroSec_CAF1 17452 90 - 1
UCGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAAGCAAAAGGAAAAGCACUGGCAGAGGAAAGCGUACAGCAAUUGAAACGCCAA
..((((((.((.((....(((...(((((....))))).)))...))....))))))))........((((............))))... ( -24.10)
>DroSim_CAF1 16766 90 - 1
UCGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAAGCAAAAGGAAAAGCACUGGCAGAGGAAAGCGUACAACAAUUGAAACGCCAA
..((((((.((.((....(((...(((((....))))).)))...))....))))))))........((((............))))... ( -24.10)
>DroEre_CAF1 17801 90 - 1
CUGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAACCAAAAGGAAAAGCGCUGGCAGAGGAAAGCGUACAACAAUUGAAACUCCAA
((((((((((..(....)..))..(((((((.((.....))...)))))))..)))))))).(((...((.........))....))).. ( -28.00)
>DroYak_CAF1 17730 90 - 1
UUGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAAGCAAAAGGAAAAGCACUGGCAGAGGAAAGCGUACAACAAUUGAAACUCCAA
((((((((.((.((....(((...(((((....))))).)))...))....)))))))))).(((...((.........))....))).. ( -23.70)
>consensus
UCGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAAGCAAAAGGAAAAGCACUGGCAGAGGAAAGCGUACAACAAUUGAAACGCCAA
......(((((((...(((((...(((((((..(......)...)))))))))))).((........))))))))).............. (-23.14 = -22.82 +  -0.32)

alignment

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secondary structure

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Window 5

Location 12,495,979 – 12,496,077
Length 98
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 96.94
Mean single sequence MFE -23.42
Consensus MFE -20.26
Energy contribution -20.42
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -1.89
Structure conservation index 0.87
SVM decision value 1.48
SVM RNA-class probability 0.957559
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12495979 98 + 27905053
GCUUUCCUCUGCCAGUGCUUUUCCUUUUGCUUUUCCCCAGGAAAACAUGCACUUCGGCACAACUGGCGAAAGAAACCGCAGCUUAUGCUACCCCUCUU
((((((...(((((((..(((((((.............)))))))..(((......)))..)))))))...))))..))(((....)))......... ( -21.82)
>DroSec_CAF1 17473 98 + 1
GCUUUCCUCUGCCAGUGCUUUUCCUUUUGCUUUUCCCCAGGAAAACAUGCACUUCGGCACAACUGGCGAAAGAAACCGCAGCUUAUGCUACCCCUCUG
((((((...(((((((..(((((((.............)))))))..(((......)))..)))))))...))))..))(((....)))......... ( -21.82)
>DroSim_CAF1 16787 98 + 1
GCUUUCCUCUGCCAGUGCUUUUCCUUUUGCUUUUCCCCAGGAAAACAUGCACUUCGGCACAACUGGCGAAAGAAACCGCAGCUUAUGGUACCCCUCUU
(((......((((((((((((((((.............)))))))...)))))..))))......(((........))))))................ ( -20.92)
>DroEre_CAF1 17822 98 + 1
GCUUUCCUCUGCCAGCGCUUUUCCUUUUGGUUUUCCCCAGGAAAACAUGCACUUCGGCACAACUGGCAGAAGAAACCGCAGCUUAUGCUACCCCUCGU
((((((.((((((((.(.(((((((...((....))..)))))))).(((......)))...)))))))).))))..))(((....)))......... ( -30.00)
>DroYak_CAF1 17751 98 + 1
GCUUUCCUCUGCCAGUGCUUUUCCUUUUGCUUUUCCCCAGGAAAACAUGCACUUCGGCACAACUGGCAAAAGAAACCGCAGCUUAUGCUACCCCUCUU
((((((...(((((((..(((((((.............)))))))..(((......)))..)))))))...))))..))(((....)))......... ( -22.52)
>consensus
GCUUUCCUCUGCCAGUGCUUUUCCUUUUGCUUUUCCCCAGGAAAACAUGCACUUCGGCACAACUGGCGAAAGAAACCGCAGCUUAUGCUACCCCUCUU
((((((...((((((((.(((((((.............)))))))).(((......)))..)))))))...))))..))(((....)))......... (-20.26 = -20.42 +   0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,495,979 – 12,496,077
Length 98
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 96.94
Mean single sequence MFE -35.96
Consensus MFE -32.54
Energy contribution -32.62
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -3.63
Structure conservation index 0.90
SVM decision value 4.16
SVM RNA-class probability 0.999819
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12495979 98 - 27905053
AAGAGGGGUAGCAUAAGCUGCGGUUUCUUUCGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAAGCAAAAGGAAAAGCACUGGCAGAGGAAAGC
.......(((((....)))))(.((((((..((((((.((.((....(((...(((((....))))).)))...))....))))))))..)))))).) ( -34.50)
>DroSec_CAF1 17473 98 - 1
CAGAGGGGUAGCAUAAGCUGCGGUUUCUUUCGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAAGCAAAAGGAAAAGCACUGGCAGAGGAAAGC
.......(((((....)))))(.((((((..((((((.((.((....(((...(((((....))))).)))...))....))))))))..)))))).) ( -34.50)
>DroSim_CAF1 16787 98 - 1
AAGAGGGGUACCAUAAGCUGCGGUUUCUUUCGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAAGCAAAAGGAAAAGCACUGGCAGAGGAAAGC
....(.(((.......))).)(.((((((..((((((.((.((....(((...(((((....))))).)))...))....))))))))..)))))).) ( -30.00)
>DroEre_CAF1 17822 98 - 1
ACGAGGGGUAGCAUAAGCUGCGGUUUCUUCUGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAACCAAAAGGAAAAGCGCUGGCAGAGGAAAGC
.......(((((....)))))(.((((((((((((((((..(....)..))..(((((((.((.....))...)))))))..)))))))))))))).) ( -42.70)
>DroYak_CAF1 17751 98 - 1
AAGAGGGGUAGCAUAAGCUGCGGUUUCUUUUGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAAGCAAAAGGAAAAGCACUGGCAGAGGAAAGC
.......(((((....)))))(.((((((((((((((.((.((....(((...(((((....))))).)))...))....)))))))))))))))).) ( -38.10)
>consensus
AAGAGGGGUAGCAUAAGCUGCGGUUUCUUUCGCCAGUUGUGCCGAAGUGCAUGUUUUCCUGGGGAAAAGCAAAAGGAAAAGCACUGGCAGAGGAAAGC
.......(((((....)))))(.(((((((.((((((.((.((....(((...(((((....))))).)))...))....)))))))).))))))).) (-32.54 = -32.62 +   0.08)

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 11:38:19 2006