Locus 9317

Sequence ID 3R_DroMel_CAF1
Location 24,782,709 – 24,782,969
Length 260
Max. P 0.881297
window14897 window14898 window14899 window14900 window14901 window14902 window14903

overview

Window 7

Location 24,782,709 – 24,782,816
Length 107
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.09
Mean single sequence MFE -31.42
Consensus MFE -22.36
Energy contribution -24.92
Covariance contribution 2.56
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.71
SVM decision value 0.23
SVM RNA-class probability 0.642167
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24782709 107 + 27905053
AAAGCA------------GCAGCAACUCCAAUAUACUUUUGUUUCUUUGCCUCUAUUGUGCUGCCGUCUCUUUCUGCCGCAGUGCAGCCGUCUCUCUCGCUCCACC-GGCUGACUGCAUG
...(((------------(((((((....((((......))))...))))........))))))..............(((((.((((((...............)-))))))))))... ( -27.96)
>DroSec_CAF1 13786 119 + 1
AAAGCAGCAAAAGCAGCAGCAGCAACUCCAAUAUACUUUUGUUUCUUUGCCUUUAUUGUGCUGCCGUCUCUUUCUGCAGCAGUGCAGCCGUCUCUCUCUCUCCCCC-AGCUGACUGCCUG
...((((..((((..((.((((((....(((((....................))))))))))).))..)))))))).(((((.((((..................-.)))))))))... ( -29.76)
>DroEre_CAF1 22841 119 + 1
AAAGCAGCAAAAGCAGCAGCAGCAACUCCAAUAUACUUUUGUUUCUUUGCCUCUAUUGUGCUGCCGUCUCUUUCUGCCGCAGUGCAGCCGUCUCUUUCGCUCCAAC-GGCUGACUGCCUG
...((((..((((..((.((((((....(((((....................))))))))))).))..)))))))).(((((.(((((((.............))-))))))))))... ( -35.67)
>DroYak_CAF1 14597 117 + 1
AAAGCAGCAAAAGCAG---CGGCAACUCCAAUAUACUUUUGUUUCUUUGCCUCUAUUGUGCUGCCGUCUCUUUCUGCCGCAGUGCAGCCGUCUCUUUCGCUCCCGCUGGCUGACUGGCUG
..((((((.((((..(---((((.....(((...((....))....))).......((..((((.((........)).))))..)))))))..)))).)))...)))((((....)))). ( -32.30)
>consensus
AAAGCAGCAAAAGCAG__GCAGCAACUCCAAUAUACUUUUGUUUCUUUGCCUCUAUUGUGCUGCCGUCUCUUUCUGCCGCAGUGCAGCCGUCUCUCUCGCUCCACC_GGCUGACUGCCUG
...((((..((((..((.((((((....(((((....................))))))))))).))..)))))))).(((((.(((((..................))))))))))... (-22.36 = -24.92 +   2.56)

alignment

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secondary structure

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Window 8

Location 24,782,709 – 24,782,816
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.09
Mean single sequence MFE -44.09
Consensus MFE -30.55
Energy contribution -32.17
Covariance contribution 1.63
Combinations/Pair 1.06
Mean z-score -3.89
Structure conservation index 0.69
SVM decision value 0.92
SVM RNA-class probability 0.881297
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24782709 107 - 27905053
CAUGCAGUCAGCC-GGUGGAGCGAGAGAGACGGCUGCACUGCGGCAGAAAGAGACGGCAGCACAAUAGAGGCAAAGAAACAAAAGUAUAUUGGAGUUGCUGC------------UGCUUU
...((((((((((-(......(....)...)))))).)))))(((((.......(((((((.(((((...((............)).)))))..))))))))------------)))).. ( -37.41)
>DroSec_CAF1 13786 119 - 1
CAGGCAGUCAGCU-GGGGGAGAGAGAGAGACGGCUGCACUGCUGCAGAAAGAGACGGCAGCACAAUAAAGGCAAAGAAACAAAAGUAUAUUGGAGUUGCUGCUGCUGCUUUUGCUGCUUU
..(((((((((((-(...............)))))).))))))((((.(((((.((((((((........((((.....(((.......)))...))))))))))))))))).))))... ( -43.16)
>DroEre_CAF1 22841 119 - 1
CAGGCAGUCAGCC-GUUGGAGCGAAAGAGACGGCUGCACUGCGGCAGAAAGAGACGGCAGCACAAUAGAGGCAAAGAAACAAAAGUAUAUUGGAGUUGCUGCUGCUGCUUUUGCUGCUUU
...((((((((((-(((....(....).)))))))).)))))(((((.(((((.(((((((.(....).(((((.....(((.......)))...))))))))))))))))).))))).. ( -51.40)
>DroYak_CAF1 14597 117 - 1
CAGCCAGUCAGCCAGCGGGAGCGAAAGAGACGGCUGCACUGCGGCAGAAAGAGACGGCAGCACAAUAGAGGCAAAGAAACAAAAGUAUAUUGGAGUUGCCG---CUGCUUUUGCUGCUUU
(((((.(((.....((....))......))))))))....(((((((((..((.(((((((.(((((...((............)).)))))..)))))))---))..)))))))))... ( -44.40)
>consensus
CAGGCAGUCAGCC_GGGGGAGCGAAAGAGACGGCUGCACUGCGGCAGAAAGAGACGGCAGCACAAUAGAGGCAAAGAAACAAAAGUAUAUUGGAGUUGCUGC__CUGCUUUUGCUGCUUU
...((((((((((....(...(....)...)))))).))))).((((.(((((.(((((((.(((((...((............)).)))))..)))))))......))))).))))... (-30.55 = -32.17 +   1.63)

alignment

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secondary structure

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Window 9

Location 24,782,737 – 24,782,856
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 95.52
Mean single sequence MFE -34.42
Consensus MFE -30.70
Energy contribution -30.59
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -1.75
Structure conservation index 0.89
SVM decision value -0.01
SVM RNA-class probability 0.527730
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24782737 119 - 27905053
CAGUUAUGCAAAUAUGAGAAAUUGCAUUUCACGCAGCCAGCAUGCAGUCAGCCGGUGGAGCGAGAGAGACGGCUGCACUGCGGCAGAAAGAGACGGCAGCACAAUAGAGGCAAAGAAAC
..(..((((((..........))))))..)..((.(((.((.((((((((((((......(....)...)))))).)))))))).(.......)))).))................... ( -34.10)
>DroSec_CAF1 13826 119 - 1
CAGUUAUGCAAAUAUGAGAAAUUGCAUUUCACGCAGCCAGCAGGCAGUCAGCUGGGGGAGAGAGAGAGACGGCUGCACUGCUGCAGAAAGAGACGGCAGCACAAUAAAGGCAAAGAAAC
..(..((((((..........))))))..)..((.(((.((((.((((((((((...............)))))).)))))))).(.......)))).))................... ( -31.16)
>DroEre_CAF1 22881 119 - 1
CAGUUAUGCAAAUAUGAGAAAUUGCAUUUCACGCAGCCAGCAGGCAGUCAGCCGUUGGAGCGAAAGAGACGGCUGCACUGCGGCAGAAAGAGACGGCAGCACAAUAGAGGCAAAGAAAC
..(..((((((..........))))))..)..((.(((.((..(((((((((((((....(....).)))))))).))))).)).(.......)))).))................... ( -38.00)
>consensus
CAGUUAUGCAAAUAUGAGAAAUUGCAUUUCACGCAGCCAGCAGGCAGUCAGCCGGUGGAGCGAGAGAGACGGCUGCACUGCGGCAGAAAGAGACGGCAGCACAAUAGAGGCAAAGAAAC
..(..((((((..........))))))..)..((.(((.((.((((((((((((...............)))))).)))))))).(.......)))).))................... (-30.70 = -30.59 +  -0.11)

alignment

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secondary structure

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Window 0

Location 24,782,777 – 24,782,896
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.68
Mean single sequence MFE -33.45
Consensus MFE -29.09
Energy contribution -29.59
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.87
SVM decision value 0.20
SVM RNA-class probability 0.629991
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24782777 119 + 27905053
AGUGCAGCCGUCUCUCUCGCUCCACC-GGCUGACUGCAUGCUGGCUGCGUGAAAUGCAAUUUCUCAUAUUUGCAUAACUGCAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCU
(((.((((((...............)-))))))))((.(((((.((((((...((((((..........)))))).)).)))).)))))..(((((........)))))........)). ( -33.36)
>DroSec_CAF1 13866 119 + 1
AGUGCAGCCGUCUCUCUCUCUCCCCC-AGCUGACUGCCUGCUGGCUGCGUGAAAUGCAAUUUCUCAUAUUUGCAUAACUGCAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCU
(((.((((..................-.)))))))((((((((.((((((...((((((..........)))))).)).)))).)))))).(((((........)))))........)). ( -29.41)
>DroEre_CAF1 22921 119 + 1
AGUGCAGCCGUCUCUUUCGCUCCAAC-GGCUGACUGCCUGCUGGCUGCGUGAAAUGCAAUUUCUCAUAUUUGCAUAACUGCAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCU
(((.(((((((.............))-))))))))((((((((.((((((...((((((..........)))))).)).)))).)))))).(((((........)))))........)). ( -36.92)
>DroYak_CAF1 14674 120 + 1
AGUGCAGCCGUCUCUUUCGCUCCCGCUGGCUGACUGGCUGCUGGCUGCGUGAAAUGCAAUUUCUCAUAUUUGCAUAACUGCAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAAUUUCGCU
...((((((.........((....)).((((....))))...))))))(((((((.((((((.........((.((.((((.....)))).))))........))))))...))))))). ( -34.13)
>consensus
AGUGCAGCCGUCUCUCUCGCUCCACC_GGCUGACUGCCUGCUGGCUGCGUGAAAUGCAAUUUCUCAUAUUUGCAUAACUGCAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCU
(((((((((..................))))).(((.((((((.((((((...((((((..........)))))).)).)))).)))))).)))......................)))) (-29.09 = -29.59 +   0.50)

alignment

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secondary structure

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Window 1

Location 24,782,816 – 24,782,929
Length 113
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 99.56
Mean single sequence MFE -32.38
Consensus MFE -31.90
Energy contribution -31.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.99
SVM decision value 0.37
SVM RNA-class probability 0.709798
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24782816 113 + 27905053
CUGGCUGCGUGAAAUGCAAUUUCUCAUAUUUGCAUAACUGCAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCUGCGGUGGCGGCAACAACAAAGCGGCAGCAACAG
...(((((((((((..((((((.........((.((.((((.....)))).))))........))))))....))))))(((..((..(....)..))..))))))))..... ( -31.93)
>DroSec_CAF1 13905 113 + 1
CUGGCUGCGUGAAAUGCAAUUUCUCAUAUUUGCAUAACUGCAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCUGCGGUGGCGGCAACAACAAAGCGGCAGCAACAG
...(((((((((((..((((((.........((.((.((((.....)))).))))........))))))....))))))(((..((..(....)..))..))))))))..... ( -31.93)
>DroEre_CAF1 22960 113 + 1
CUGGCUGCGUGAAAUGCAAUUUCUCAUAUUUGCAUAACUGCAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCUGCGGUGGCGGCAACAACAAAGCGGCAGCAACAG
...(((((((((((..((((((.........((.((.((((.....)))).))))........))))))....))))))(((..((..(....)..))..))))))))..... ( -31.93)
>DroYak_CAF1 14714 113 + 1
CUGGCUGCGUGAAAUGCAAUUUCUCAUAUUUGCAUAACUGCAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAAUUUCGCUGCGGUGGCGGCAACAACAAAGCGGCAGCAACAG
...((((((((((((.((((((.........((.((.((((.....)))).))))........))))))...)))))))(((..((..(....)..))..))))))))..... ( -33.73)
>consensus
CUGGCUGCGUGAAAUGCAAUUUCUCAUAUUUGCAUAACUGCAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCUGCGGUGGCGGCAACAACAAAGCGGCAGCAACAG
...((((((((((((((((..........))))))..((((.....)))).(((((........))))).....)))))(((..((..(....)..))..))))))))..... (-31.90 = -31.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 24,782,856 – 24,782,969
Length 113
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 98.67
Mean single sequence MFE -32.65
Consensus MFE -30.66
Energy contribution -30.72
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -1.89
Structure conservation index 0.94
SVM decision value 0.27
SVM RNA-class probability 0.660505
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24782856 113 + 27905053
CAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCUGCGGUGGCGGCAACAACAAAGCGGCAGCAACAGCAACAACUUUAAUAUUGCCUGGCCGUGCUGCGUAAUUGCC
......(((((..((((((..((((((((........(((((..((..(....)..))..))))).((....))..))))))))...)))...)))..).))))......... ( -32.10)
>DroSec_CAF1 13945 113 + 1
CAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCUGCGGUGGCGGCAACAACAAAGCGGCAGCAACAGCAACAACUUUAAUAUUGCCUAUCCGUGCUGCGUAAUUGCC
..(.((((((((((..(((..((((((((........(((((..((..(....)..))..))))).((....))..))))))))...))).)))))..))))))......... ( -34.30)
>DroEre_CAF1 23000 113 + 1
CAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCUGCGGUGGCGGCAACAACAAAGCGGCAGCAACAGCAACAACUUUAAUAUUGCCUGGCCGUGCUGCGUAAUUGCC
......(((((..((((((..((((((((........(((((..((..(....)..))..))))).((....))..))))))))...)))...)))..).))))......... ( -32.10)
>DroYak_CAF1 14754 113 + 1
CAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAAUUUCGCUGCGGUGGCGGCAACAACAAAGCGGCAGCAACAGCAACAACUUUAAUAUUGCCUGGCCGUGCUGCGUAAUUGCC
......(((((..((((((..((((((((........(((((..((..(....)..))..))))).((....))..))))))))...)))...)))..).))))......... ( -32.10)
>consensus
CAGACAGCAGAUAGCUCAAAAUAAAGUUGAAAUUUUCGCUGCGGUGGCGGCAACAACAAAGCGGCAGCAACAGCAACAACUUUAAUAUUGCCUGGCCGUGCUGCGUAAUUGCC
......(((((..((((((..((((((((........(((((..((..(....)..))..))))).((....))..))))))))...)))...)))..).))))......... (-30.66 = -30.72 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 24,782,856 – 24,782,969
Length 113
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 98.67
Mean single sequence MFE -35.35
Consensus MFE -34.55
Energy contribution -34.80
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.98
SVM decision value 0.39
SVM RNA-class probability 0.717563
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24782856 113 - 27905053
GGCAAUUACGCAGCACGGCCAGGCAAUAUUAAAGUUGUUGCUGUUGCUGCCGCUUUGUUGUUGCCGCCACCGCAGCGAAAAUUUCAACUUUAUUUUGAGCUAUCUGCUGUCUG
((((((.(((.(((.((((..(((((((.......)))))))...))))..))).))).))))))......((((((.....(((((.......))))).....))))))... ( -35.70)
>DroSec_CAF1 13945 113 - 1
GGCAAUUACGCAGCACGGAUAGGCAAUAUUAAAGUUGUUGCUGUUGCUGCCGCUUUGUUGUUGCCGCCACCGCAGCGAAAAUUUCAACUUUAUUUUGAGCUAUCUGCUGUCUG
.........((((((..(((((.(((...(((((((((((((((.((.((.((......)).)).))....)))))))......))))))))..)))..)))))))))))... ( -34.30)
>DroEre_CAF1 23000 113 - 1
GGCAAUUACGCAGCACGGCCAGGCAAUAUUAAAGUUGUUGCUGUUGCUGCCGCUUUGUUGUUGCCGCCACCGCAGCGAAAAUUUCAACUUUAUUUUGAGCUAUCUGCUGUCUG
((((((.(((.(((.((((..(((((((.......)))))))...))))..))).))).))))))......((((((.....(((((.......))))).....))))))... ( -35.70)
>DroYak_CAF1 14754 113 - 1
GGCAAUUACGCAGCACGGCCAGGCAAUAUUAAAGUUGUUGCUGUUGCUGCCGCUUUGUUGUUGCCGCCACCGCAGCGAAAUUUUCAACUUUAUUUUGAGCUAUCUGCUGUCUG
((((((.(((.(((.((((..(((((((.......)))))))...))))..))).))).))))))......((((((.....(((((.......))))).....))))))... ( -35.70)
>consensus
GGCAAUUACGCAGCACGGCCAGGCAAUAUUAAAGUUGUUGCUGUUGCUGCCGCUUUGUUGUUGCCGCCACCGCAGCGAAAAUUUCAACUUUAUUUUGAGCUAUCUGCUGUCUG
((((((.(((.(((.((((..(((((((.......)))))))...))))..))).))).))))))......((((((.....(((((.......))))).....))))))... (-34.55 = -34.80 +   0.25)

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 13:31:33 2006