Locus 4870

Sequence ID 3R_DroMel_CAF1
Location 12,816,601 – 12,816,801
Length 200
Max. P 0.999096
window7974 window7975 window7976

overview

Window 4

Location 12,816,601 – 12,816,721
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.75
Mean single sequence MFE -34.98
Consensus MFE -30.38
Energy contribution -30.82
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.40
Structure conservation index 0.87
SVM decision value 0.64
SVM RNA-class probability 0.808941
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12816601 120 - 27905053
GAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGCUGCACAAUCCGCAUAGCCAUCUAAUACACCAGCGUUUGGCAGAAAUACGAUACACAAUGGUGAGCUAUAUAAGCCCACUA
...((((.(((((((((((((.....))))).((((.(((..........))).))))...........)))).)))).))))..............(((((.(((.....))).))))) ( -32.90)
>DroSec_CAF1 191457 120 - 1
GAGUUUGGCAAAGCUGCUUUUUGUAUGGAGGAGGUUUUGCUGCACAAUCCCCAUAGCCAUCUAAUACACCAGCGCUUGGCGGAAAUACGGUACACAAUGGUGAGCUAUAUAACCCCGCUA
.....((((.((((.(((...((((((((((.((..(((.....)))..)).....)).))).)))))..)))))))((.((..(((..((.(((....))).))..)))..)))))))) ( -30.50)
>DroSim_CAF1 193371 120 - 1
GAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGCUGCACAAUCCCCAUAGCCAUCUAAUACACCAGCGCUUGGCAGAAAUACGCUACACAAUGGUGAGCUAUAUAACCUCGCUA
(((...(((((((((.(((((.....))))).)))))))))...........(((((.........(((((..(..((((........))))..)..))))).))))).....))).... ( -33.30)
>DroEre_CAF1 200084 120 - 1
GAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGCUGCACAAUCCCCAUAGCCAUUUAAUACACCAGCGCCUGGCGGAAAUACGCUAUACAAUGGUGAGCUAUAUAAGCAAGCUA
..((.((((((((((.(((((.....))))).)))))))))).))........((((.........(((((..(..(((((......)))))..)..))))).(((.....)))..)))) ( -40.00)
>DroYak_CAF1 192660 120 - 1
GAGUUUGGCAAAGCCGCUUUCUGCAUGGAGGAGGUUUUGCUCCACAAUCCCCAUAGCCAUCUAAUACACCAGCGCUUGGCGGAAAUACGCUACACAAUGGUGAGCUAUAAAAGCAAGAUA
..((..(((((((((.(((((.....))))).)))))))))..)).............((((....(((((..(..(((((......)))))..)..))))).(((.....))).)))). ( -38.20)
>consensus
GAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGCUGCACAAUCCCCAUAGCCAUCUAAUACACCAGCGCUUGGCGGAAAUACGCUACACAAUGGUGAGCUAUAUAAGCACGCUA
..((.((((((((((.(((((.....))))).)))))))))).)).......(((((.........(((((..(..(((((......)))))..)..))))).)))))............ (-30.38 = -30.82 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,816,641 – 12,816,761
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -44.16
Consensus MFE -42.96
Energy contribution -43.24
Covariance contribution 0.28
Combinations/Pair 1.09
Mean z-score -1.69
Structure conservation index 0.97
SVM decision value 2.62
SVM RNA-class probability 0.995805
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12816641 120 - 27905053
GGCAUGGCAUGAGCUGUGCAACAUGUAUCUGGCUGAAGGCGAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGCUGCACAAUCCGCAUAGCCAUCUAAUACACCAGCGUUUGGC
.(((((((....)))))))....(((((.((((((...(((..((((((((((((.(((((.....))))).))))))))))...))..))).))))))....)))))((((...)))). ( -43.20)
>DroSec_CAF1 191497 120 - 1
GACAUGGCACGAGCUGUGCAACAUGUAUCUGGCUGAGGGCGAGUUUGGCAAAGCUGCUUUUUGUAUGGAGGAGGUUUUGCUGCACAAUCCCCAUAGCCAUCUAAUACACCAGCGCUUGGC
......((.(((((.((......(((((.((((((.(((.((((.((((((((((.(((((.....))))).)))))))))).))..))))).))))))....)))))...))))))))) ( -39.40)
>DroSim_CAF1 193411 120 - 1
GGCAUGGCACGAGCUGUGCAACAUGUAUCUGGCUGAGGGCGAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGCUGCACAAUCCCCAUAGCCAUCUAAUACACCAGCGCUUGGC
.(((((((....)))))))....(((((.((((((.(((.((((.((((((((((.(((((.....))))).)))))))))).))..))))).))))))....)))))((((...)))). ( -47.00)
>DroEre_CAF1 200124 120 - 1
GGCAUGGCACGAGCUGUGCAACAUGUAUCUGGCUGAGGGUGAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGCUGCACAAUCCCCAUAGCCAUUUAAUACACCAGCGCCUGGC
.(((((((....)))))))....(((((.((((((.(((.((((.((((((((((.(((((.....))))).)))))))))).))..))))).))))))....)))))((((...)))). ( -49.00)
>DroYak_CAF1 192700 120 - 1
GGCAUGGCACGAGCUGUGCAACAUGUAUCUGGCCGAGGGUGAGUUUGGCAAAGCCGCUUUCUGCAUGGAGGAGGUUUUGCUCCACAAUCCCCAUAGCCAUCUAAUACACCAGCGCUUGGC
.(((((((....)))))))....(((((.((((...(((.((((..(((((((((.(((((.....))))).)))))))))..))..)))))...))))....)))))((((...)))). ( -42.20)
>consensus
GGCAUGGCACGAGCUGUGCAACAUGUAUCUGGCUGAGGGCGAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGCUGCACAAUCCCCAUAGCCAUCUAAUACACCAGCGCUUGGC
.(((((((....)))))))....(((((.((((((.(((.((((.((((((((((.(((((.....))))).)))))))))).))..))))).))))))....)))))((((...)))). (-42.96 = -43.24 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,816,681 – 12,816,801
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.83
Mean single sequence MFE -40.52
Consensus MFE -38.08
Energy contribution -37.00
Covariance contribution -1.08
Combinations/Pair 1.19
Mean z-score -2.04
Structure conservation index 0.94
SVM decision value 3.37
SVM RNA-class probability 0.999096
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12816681 120 - 27905053
UAACUAUUUAAUAUUCCUUCAGGUUUAUGUCUGACCAGGAGGCAUGGCAUGAGCUGUGCAACAUGUAUCUGGCUGAAGGCGAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGC
.............((((((((((((((((((((.((....)))).))))))))))((((.....))))...((.((((((.(((((....))))))))))).)).))))))))....... ( -41.80)
>DroSec_CAF1 191537 120 - 1
UAAAUAUGUAAUAUUCCUUCAGAUUUAUGUCUGACCAGGAGACAUGGCACGAGCUGUGCAACAUGUAUCUGGCUGAGGGCGAGUUUGGCAAAGCUGCUUUUUGUAUGGAGGAGGUUUUGC
.......((((..(((((((((((....))))))((((((.(((((((((.....))))..))))).))).((.((((((.(((((....))))))))))).)).))))))))...)))) ( -36.40)
>DroSim_CAF1 193451 120 - 1
UAAAUAUGUAAUAUUCCUUCAGGUUUAUGUCUGACCAGGAGGCAUGGCACGAGCUGUGCAACAUGUAUCUGGCUGAGGGCGAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGC
.......((((..((((((((((((.......)))).(((.(((((((((.....))))..))))).))).((.((((((.(((((....))))))))))).)).))))))))...)))) ( -43.20)
>DroEre_CAF1 200164 120 - 1
AAAACAUUUAUAAUUCCUUCAGGUUCAUGUCUGACCAGGAGGCAUGGCACGAGCUGUGCAACAUGUAUCUGGCUGAGGGUGAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGC
...............(((((((..(((....)))(((((..(((((((((.....))))..))))).))))))))))))........((((((((.(((((.....))))).)))))))) ( -40.60)
>DroYak_CAF1 192740 120 - 1
UAAACAUUUUUAAUUCCUUCAGGUUCAUGUCUGACCAGGAGGCAUGGCACGAGCUGUGCAACAUGUAUCUGGCCGAGGGUGAGUUUGGCAAAGCCGCUUUCUGCAUGGAGGAGGUUUUGC
...................((..(((((.(.((.(((((..(((((((((.....))))..))))).))))).)).).)))))..))((((((((.(((((.....))))).)))))))) ( -40.60)
>consensus
UAAAUAUUUAAUAUUCCUUCAGGUUUAUGUCUGACCAGGAGGCAUGGCACGAGCUGUGCAACAUGUAUCUGGCUGAGGGCGAGUUUGGCAAAGCUGCCUUCUGCAUGGAGGAGGUUUUGC
...............(((((((..(((....)))(((((..(((((((((.....))))..))))).))))))))))))........((((((((.(((((.....))))).)))))))) (-38.08 = -37.00 +  -1.08)

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 11:40:51 2006