Locus 4217

Sequence ID 3R_DroMel_CAF1
Location 11,359,964 – 11,360,324
Length 360
Max. P 0.971390
window6812 window6813 window6814 window6815 window6816

overview

Window 2

Location 11,359,964 – 11,360,084
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.25
Mean single sequence MFE -40.82
Consensus MFE -36.98
Energy contribution -37.42
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.60
Structure conservation index 0.91
SVM decision value 1.67
SVM RNA-class probability 0.971390
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11359964 120 + 27905053
AGGGUAGUAUUUCUUCCGCUCCGCCCUCGUAGGUCAGUUUCACCAGCUCUGCUGCCCGAUUGGCCAGCGAAUUGGAGUUGGCUAGGAUUAUGCCCACGGGCUGACCAUAAAACUUAAUCU
.(((((....((((.((((((((...((((.((((((((....((((...))))...)))))))).))))..))))).)))..))))...)))))..((.....)).............. ( -40.90)
>DroSec_CAF1 107512 120 + 1
UGGGUAGUAUUUCUUCCGCUCCGCCUUCGUAGGUCAGUUUCACCAGCUCUGCUGCCCGAUUGGCCAGCGAAUUGGAGUUGGCUAGGAUUAUGCCCACGGGUUGACCAUAAAACUUAAUCU
((((((....((((.((((((((..(((((.((((((((....((((...))))...)))))))).))))).))))).)))..))))...)))))).((.....)).............. ( -42.00)
>DroSim_CAF1 98294 120 + 1
UGGGUAGUAUCUCUUCCGCUCCGCCCUCGUAGGUCAGUUUCACCAGCUCUGCUGCCCGAUUGGCCAGCGAAUUGGAGUUGGCUAGAAUUAUGCCCACAGGCUGACCAUAAAACUUAAUCA
((((((.((..(((.((((((((...((((.((((((((....((((...))))...)))))))).))))..))))).)))..)))..))))))))..((....)).............. ( -38.70)
>DroEre_CAF1 94942 120 + 1
UGGGCAGUAUUUCUUCCGCUCCGCCCUCGUAGGUCAGUUUCACCAGCUCUGCGGCCCGAUUGGCCAGCGAAUUGGAGUUGGCUAGGAUCAUGCCCACGGGCUGACCAUAGAACAUAAUUU
((((((....((((.((((((((...((((.((((((((...((.((...))))...)))))))).))))..))))).)))..))))...)))))).((.....)).............. ( -41.50)
>DroYak_CAF1 97617 120 + 1
UGGGCAGUACUUCUUCCGCUCCACCCUCGUAGCUCAGUUUCACCAGCUCUGCGGCCCGAUUGGCCAGCGAAUUGGAGUUGGCUAGGAUCAUGCCCACGGGCUGACCAUAGAACGAAAUUU
((((((....((((.((((((((...((((.((..((((.....))))..))((((.....)))).))))..))))).)))..))))...))))))((..(((....)))..))...... ( -41.00)
>consensus
UGGGUAGUAUUUCUUCCGCUCCGCCCUCGUAGGUCAGUUUCACCAGCUCUGCUGCCCGAUUGGCCAGCGAAUUGGAGUUGGCUAGGAUUAUGCCCACGGGCUGACCAUAAAACUUAAUCU
.(((((....((((.((((((((...((((.((((((((....((((...))))...)))))))).))))..))))).)))..))))...)))))..((.....)).............. (-36.98 = -37.42 +   0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,360,084 – 11,360,204
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.50
Mean single sequence MFE -44.74
Consensus MFE -33.90
Energy contribution -34.66
Covariance contribution 0.76
Combinations/Pair 1.15
Mean z-score -1.55
Structure conservation index 0.76
SVM decision value 0.04
SVM RNA-class probability 0.555187
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11360084 120 - 27905053
AUCUACCCGGGGUGGUGGCGUACCUCGAUGCCAAGGACAUUCCGGGACCGAACUACGUUGGGCCCAAAAUCCGGGACCAGUUUUUCUUCCCCAAGGAUGAGGAACUAUUCGCCACGGGAG
.....(((((((((.((((((......))))))....))))))))).(((..........(((((.......))).))((((((((.(((....))).))))))))........)))... ( -46.20)
>DroSec_CAF1 107632 120 - 1
AUCUACCCGGGGUGGUGGCGUAUCUCGACGCCAAGGACAUUCCGGGACCCAACUACGUUGGGCCCAAAAUCCGCGACACUCAUUUCUUCCCCAAGGAUGAGGAACUAUUCGCCACAGGAG
.....(((((((((.((((((......))))))....))))))))).((((((...)))))).......(((((((..((((((.(((....))))))))).......))))....))). ( -43.80)
>DroSim_CAF1 98414 120 - 1
AUCUACCCGGGGUGGUGGCGUACCUCGACGCCAAGGACAUUCCGGGACCCAACUACGUUGGGCCCAAAAUCCGCGACGACUUUUUCUUCCCCAAUGAUGAGGAACUAUUCGCCACAGGAG
.....(((((((((.((((((......))))))....))))))))).((((((...)))))).......(((((((....((((((.((......)).))))))....))))....))). ( -42.80)
>DroEre_CAF1 95062 120 - 1
AUCUACCCGGAGUGGUGGCAUACCUCGAUGCCAAGGACAUUCCGGGACCCAAUUAUGUGGGGCCCAAAUUAAGGGACGCGCACUUCUUCCCACAGGAUGAGGAACUGUUCGCCGCAGGUC
.....(((((((((.((((((......))))))....))))))))).........((((.(.(((.......))).).))))((((.(((....))).))))..((((.....))))... ( -45.30)
>DroYak_CAF1 97737 120 - 1
AUCUACCCGGCGUGGUGGCGUACCUCGAUGCCAAGGACAUUCCGGGACCCAACUACGUCGGCCCCAAGGUCAGGGACGCGUUCUUCUUCCCGCAGGACGAGCAACUGUUCGCCACGGGUC
.....(((((((((((((.((.(((.(((((....).)).)).))))))).))))))))((((....)))).))).............((((..((.(((((....))))))).)))).. ( -45.60)
>consensus
AUCUACCCGGGGUGGUGGCGUACCUCGAUGCCAAGGACAUUCCGGGACCCAACUACGUUGGGCCCAAAAUCCGGGACGCGUUUUUCUUCCCCAAGGAUGAGGAACUAUUCGCCACAGGAG
.....(((((((((.((((((......))))))....))))))))).((((((...)))))).((.......((((...........))))...((.((((......))))))...)).. (-33.90 = -34.66 +   0.76)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,360,124 – 11,360,244
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.92
Mean single sequence MFE -46.80
Consensus MFE -38.74
Energy contribution -39.22
Covariance contribution 0.48
Combinations/Pair 1.15
Mean z-score -1.58
Structure conservation index 0.83
SVM decision value 0.61
SVM RNA-class probability 0.798826
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11360124 120 - 27905053
GGCGCAAAAGUCACCAAGGUGGAUACGCAACCGGCUCUGGAUCUACCCGGGGUGGUGGCGUACCUCGAUGCCAAGGACAUUCCGGGACCGAACUACGUUGGGCCCAAAAUCCGGGACCAG
.(((......((((....))))...)))....((..((((((...(((((((((.((((((......))))))....))))))))).((((......)))).......))))))..)).. ( -46.60)
>DroSec_CAF1 107672 120 - 1
GGCGCCAAUGUAACCAAAGUGGAUACGCAACCAGCUCUGGAUCUACCCGGGGUGGUGGCGUAUCUCGACGCCAAGGACAUUCCGGGACCCAACUACGUUGGGCCCAAAAUCCGCGACACU
.................(((((((((((.((((.((((((......)))))))))).)))))))....(((...((.....))(((.((((((...))))))))).......))).)))) ( -48.70)
>DroSim_CAF1 98454 120 - 1
GGCGCCAAAGUCACCAAAGUGGAUACGCAACCAGCUCUGGAUCUACCCGGGGUGGUGGCGUACCUCGACGCCAAGGACAUUCCGGGACCCAACUACGUUGGGCCCAAAAUCCGCGACGAC
(((......)))........((.(((((.((((.((((((......)))))))))).)))))))(((.(((...((.....))(((.((((((...))))))))).......))).))). ( -48.50)
>DroEre_CAF1 95102 120 - 1
GGCGCCAAGGUCACCAAAGUGGAUACGCAGCCAGCUCUGGAUCUACCCGGAGUGGUGGCAUACCUCGAUGCCAAGGACAUUCCGGGACCCAAUUAUGUGGGGCCCAAAUUAAGGGACGCG
.(((((...(((......(((....))).((((.((((((......))))))))))(((((......)))))...))).....(((.((((......)))).)))........)).))). ( -45.90)
>DroYak_CAF1 97777 120 - 1
GGCGCCAAGGUCACCAAAGUGGAUACGCAGCCAGCUCUGGAUCUACCCGGCGUGGUGGCGUACCUCGAUGCCAAGGACAUUCCGGGACCCAACUACGUCGGCCCCAAGGUCAGGGACGCG
.(((((..((((.((...(.((.(((((.((((.(.((((......)))).))))).))))))).)........((.....))))))))..........((((....))))..)).))). ( -44.30)
>consensus
GGCGCCAAAGUCACCAAAGUGGAUACGCAACCAGCUCUGGAUCUACCCGGGGUGGUGGCGUACCUCGAUGCCAAGGACAUUCCGGGACCCAACUACGUUGGGCCCAAAAUCCGGGACGCG
((((......((((....)))).(((((.((((.((((((......)))))))))).)))))......))))..((.....))(((.((((((...)))))))))............... (-38.74 = -39.22 +   0.48)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,360,164 – 11,360,284
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.75
Mean single sequence MFE -46.44
Consensus MFE -40.26
Energy contribution -40.02
Covariance contribution -0.24
Combinations/Pair 1.15
Mean z-score -1.32
Structure conservation index 0.87
SVM decision value 0.31
SVM RNA-class probability 0.683507
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11360164 120 - 27905053
CAACCAGUUGUGGGCUGCGUUUGUCAUCGCGAAGAAGGUGGGCGCAAAAGUCACCAAGGUGGAUACGCAACCGGCUCUGGAUCUACCCGGGGUGGUGGCGUACCUCGAUGCCAAGGACAU
......(((.(.(((((((((..((.((.....)).))..))))))...(((((....))((.(((((.((((.((((((......)))))))))).)))))))..)))))).).))).. ( -46.10)
>DroSec_CAF1 107712 120 - 1
CAACCAGUUGUGGGCUGCAUUUGUCACCGCGAAGAAGGUGGGCGCCAAUGUAACCAAAGUGGAUACGCAACCAGCUCUGGAUCUACCCGGGGUGGUGGCGUAUCUCGACGCCAAGGACAU
......(((.(.(((((((((.((..((((.......))))..)).))))))......((((((((((.((((.((((((......)))))))))).))))))))..))))).).))).. ( -46.10)
>DroSim_CAF1 98494 120 - 1
CAACCAGUUGUGGGCUGCGUUUGUCACCGCGAAGAAGGUGGGCGCCAAAGUCACCAAAGUGGAUACGCAACCAGCUCUGGAUCUACCCGGGGUGGUGGCGUACCUCGACGCCAAGGACAU
......(((.(.(((.((((...(((((........)))))))))....(((.((.....)).(((((.((((.((((((......)))))))))).)))))....)))))).).))).. ( -44.90)
>DroEre_CAF1 95142 120 - 1
CAACCAGUUGUGGGCUGCGUUCGUCACCGCGAAGAAGGUGGGCGCCAAGGUCACCAAAGUGGAUACGCAGCCAGCUCUGGAUCUACCCGGAGUGGUGGCAUACCUCGAUGCCAAGGACAU
..(((.......((((((((...(((((.....)..(((((.(.....).)))))...))))..)))))))).(((((((......))))))))))(((((......)))))........ ( -47.80)
>DroYak_CAF1 97817 120 - 1
CAACCAGUUGUGGGCUGCGUUUGUCACCGCGAAGAAGGUGGGCGCCAAGGUCACCAAAGUGGAUACGCAGCCAGCUCUGGAUCUACCCGGCGUGGUGGCGUACCUCGAUGCCAAGGACAU
...((((..((.((((((((...(((((.....)..(((((.(.....).)))))...))))..)))))))).)).)))).....((.(((((.(.((....)).).)))))..)).... ( -47.30)
>consensus
CAACCAGUUGUGGGCUGCGUUUGUCACCGCGAAGAAGGUGGGCGCCAAAGUCACCAAAGUGGAUACGCAACCAGCUCUGGAUCUACCCGGGGUGGUGGCGUACCUCGAUGCCAAGGACAU
......(((.(.(((.((((...(((((........))))))))).............(.((.(((((.((((.((((((......)))))))))).))))))).)...))).).))).. (-40.26 = -40.02 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,360,204 – 11,360,324
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.50
Mean single sequence MFE -48.92
Consensus MFE -47.18
Energy contribution -47.62
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.16
Structure conservation index 0.96
SVM decision value 0.42
SVM RNA-class probability 0.729437
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11360204 120 + 27905053
CCAGAGCCGGUUGCGUAUCCACCUUGGUGACUUUUGCGCCCACCUUCUUCGCGAUGACAAACGCAGCCCACAACUGGUUGUGCUGGGUGGGCAGAUCGUUGGAGUAGGUGGCUUCGCCAG
...(((((((..(((((..(((....))).....)))))))((((.(((((((........))).((((((..(..(.....)..)))))))........)))).)))))))))...... ( -43.30)
>DroSec_CAF1 107752 120 + 1
CCAGAGCUGGUUGCGUAUCCACUUUGGUUACAUUGGCGCCCACCUUCUUCGCGGUGACAAAUGCAGCCCACAACUGGUUGUGCUGGGUGGGCAGAUCGUUGGAGUAGGUGGCUUCGCCAG
((((((.(((........)))))))))......(((((.((((((.(((((((....).......((((((..(..(.....)..))))))).....).))))).))))))...))))). ( -49.00)
>DroSim_CAF1 98534 120 + 1
CCAGAGCUGGUUGCGUAUCCACUUUGGUGACUUUGGCGCCCACCUUCUUCGCGGUGACAAACGCAGCCCACAACUGGUUGUGCUGGGUGGGCAGAUCGUUGGAGUAGGUGGCUUCGCCAG
((((((.(((........)))))))))......(((((.((((((.(((((((........))).((((((..(..(.....)..)))))))........)))).))))))...))))). ( -51.40)
>DroEre_CAF1 95182 120 + 1
CCAGAGCUGGCUGCGUAUCCACUUUGGUGACCUUGGCGCCCACCUUCUUCGCGGUGACGAACGCAGCCCACAACUGGUUGUGCUGGGUGGGCAGAUCGUUGGAGUAGGUGGCUUCGCCAG
((((((.(((........)))))))))......(((((.((((((.((((.((....))((((..((((((..(..(.....)..)))))))....)))))))).))))))...))))). ( -50.50)
>DroYak_CAF1 97857 120 + 1
CCAGAGCUGGCUGCGUAUCCACUUUGGUGACCUUGGCGCCCACCUUCUUCGCGGUGACAAACGCAGCCCACAACUGGUUGUGCUGGGUGGGCAGAUCGUUGGAGUAGGUGGCUUCGCCAG
((((((.(((........)))))))))......(((((.((((((.(((((((........))).((((((..(..(.....)..)))))))........)))).))))))...))))). ( -50.40)
>consensus
CCAGAGCUGGUUGCGUAUCCACUUUGGUGACCUUGGCGCCCACCUUCUUCGCGGUGACAAACGCAGCCCACAACUGGUUGUGCUGGGUGGGCAGAUCGUUGGAGUAGGUGGCUUCGCCAG
((((((.(((........)))))))))......(((((.((((((.(((((((........))).((((((..(..(.....)..)))))))........)))).))))))...))))). (-47.18 = -47.62 +   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 11:22:09 2006