Locus 8915

Sequence ID 3R_DroMel_CAF1
Location 23,921,592 – 23,921,712
Length 120
Max. P 0.998384
window14299 window14300 window14301

overview

Window 9

Location 23,921,592 – 23,921,693
Length 101
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 85.98
Mean single sequence MFE -35.93
Consensus MFE -33.49
Energy contribution -33.38
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -4.36
Structure conservation index 0.93
SVM decision value 3.08
SVM RNA-class probability 0.998384
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23921592 101 + 27905053
AAGCGGCAGCUGGCCAAAGUCGAAGGAAGUUGGUUGGCUGCCAUGUCAACGGCUAAAUGACACUGGCACUGGGAAUGGAAAUA------GGAAUAGGAAUAGGAAUA
..((((((((..(((((..((....))..)))))..)))))).(((((.........)))))...))................------.................. ( -34.60)
>DroSec_CAF1 123236 89 + 1
AAGCGGCAGCUGGCCAAAGUCGAAGGAAGUUGGUUGGCUGCCAUGUCAACGGCUAAAUGACACUGGCACUGGGAAUGGAAAUA------GGA------------AUA
..((((((((..(((((..((....))..)))))..)))))).(((((.........)))))...))................------...------------... ( -34.60)
>DroSim_CAF1 124970 95 + 1
AAGCGGCAGCUGGCCAAAGUCGAAGGAAGUUGGUUGGCUGCCAUGUCAACGGCUAAAUGACACUGGCACUGGGAAUGGAAAUA------GGAAUA------GGAAUA
..((((((((..(((((..((....))..)))))..)))))).(((((.........)))))...))................------......------...... ( -34.60)
>DroEre_CAF1 126663 107 + 1
AAGCGGCAGCUGGCCAAAGUCGAAGGAAGUUGGUUGGCUGCCAUGUCAACGGCUAAAUGACACUGGCACUGGGAAUGGGAAUGGGAAUGGAAAUAGGAAUAGGAAUA
..((((((((..(((((..((....))..)))))..)))))).(((((.........)))))...))........................................ ( -34.60)
>DroYak_CAF1 130461 95 + 1
AAGCGGCAGCUGGCCAAAGUCGAAGGAAGUUGGUUGGCUGCCAUGUCAACGGCUAAAUGACACUGGCACUGGGAAUGGGAAUG------GAAA------UAGGAACA
..((((((((..(((((..((....))..)))))..)))))).(((((.........)))))...))................------....------........ ( -34.60)
>DroAna_CAF1 130966 88 + 1
AAGCGGCAGCUGGCCAAAGUCGAAGGAAGUUGGCCGGCUACCAUGUCAACGGCUAAAUGACACUGGCACUGGGAUGGGUCCUG------GG-------------CCA
....((.((((((((((..((....))..)))))))))).)).(((((.........)))))..(((.(..(((....)))..------))-------------)). ( -42.60)
>consensus
AAGCGGCAGCUGGCCAAAGUCGAAGGAAGUUGGUUGGCUGCCAUGUCAACGGCUAAAUGACACUGGCACUGGGAAUGGAAAUA______GGAA________GGAAUA
..(((((((((((((((..((....))..))))))))))))).(((((.........)))))...))........................................ (-33.49 = -33.38 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 23,921,592 – 23,921,693
Length 101
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 85.98
Mean single sequence MFE -24.45
Consensus MFE -22.10
Energy contribution -21.97
Covariance contribution -0.14
Combinations/Pair 1.05
Mean z-score -2.63
Structure conservation index 0.90
SVM decision value 2.06
SVM RNA-class probability 0.986880
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23921592 101 - 27905053
UAUUCCUAUUCCUAUUCC------UAUUUCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACUUCCUUCGACUUUGGCCAGCUGCCGCUU
..................------................((..((((((.........))))))((((((...((((..((....))..))))...)))))))).. ( -22.30)
>DroSec_CAF1 123236 89 - 1
UAU------------UCC------UAUUUCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACUUCCUUCGACUUUGGCCAGCUGCCGCUU
...------------...------................((..((((((.........))))))((((((...((((..((....))..))))...)))))))).. ( -22.30)
>DroSim_CAF1 124970 95 - 1
UAUUCC------UAUUCC------UAUUUCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACUUCCUUCGACUUUGGCCAGCUGCCGCUU
......------......------................((..((((((.........))))))((((((...((((..((....))..))))...)))))))).. ( -22.30)
>DroEre_CAF1 126663 107 - 1
UAUUCCUAUUCCUAUUUCCAUUCCCAUUCCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACUUCCUUCGACUUUGGCCAGCUGCCGCUU
........................................((..((((((.........))))))((((((...((((..((....))..))))...)))))))).. ( -22.30)
>DroYak_CAF1 130461 95 - 1
UGUUCCUA------UUUC------CAUUCCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACUUCCUUCGACUUUGGCCAGCUGCCGCUU
........------....------................((..((((((.........))))))((((((...((((..((....))..))))...)))))))).. ( -22.30)
>DroAna_CAF1 130966 88 - 1
UGG-------------CC------CAGGACCCAUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGUAGCCGGCCAACUUCCUUCGACUUUGGCCAGCUGCCGCUU
(((-------------((------..(((....)))..).))))((((((.........))))))((((((.((((((..((....))..)))))).)))))).... ( -35.20)
>consensus
UAUUCC________UUCC______CAUUUCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACUUCCUUCGACUUUGGCCAGCUGCCGCUU
........................................((..((((((.........))))))((((((...((((..((....))..))))...)))))))).. (-22.10 = -21.97 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 1

Location 23,921,619 – 23,921,712
Length 93
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 87.10
Mean single sequence MFE -12.42
Consensus MFE -12.20
Energy contribution -12.20
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 0.98
SVM decision value 0.30
SVM RNA-class probability 0.679756
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23921619 93 - 27905053
CCAAUACUAAGACCAUUCCUAUUCCUAUUCCUAUUCC------UAUUUCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACU
.....................................------...............(((((.(((((.........))))))))))........... ( -12.20)
>DroSec_CAF1 123263 81 - 1
CCAAUACUAAGACCAUUCCUAU------------UCC------UAUUUCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACU
......................------------...------...............(((((.(((((.........))))))))))........... ( -12.20)
>DroSim_CAF1 124997 87 - 1
CCAAUACUAAGACCAUUCCUAUUCC------UAUUCC------UAUUUCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACU
.........................------......------...............(((((.(((((.........))))))))))........... ( -12.20)
>DroEre_CAF1 126690 99 - 1
CCAAUACUGAGAUCAUUCCUAUUCCUAUUCCUAUUUCCAUUCCCAUUCCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACU
.....((((.((........................................)).))))((((.(((((.........)))))))))............ ( -13.30)
>DroYak_CAF1 130488 87 - 1
CCAAUACUUAGACCAUUCCUGUUCCUA------UUUC------CAUUCCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACU
...........................------....------...............(((((.(((((.........))))))))))........... ( -12.20)
>consensus
CCAAUACUAAGACCAUUCCUAUUCCUA____UAUUCC______UAUUUCCAUUCCCAGUGCCAGUGUCAUUUAGCCGUUGACAUGGCAGCCAACCAACU
..........................................................(((((.(((((.........))))))))))........... (-12.20 = -12.20 +   0.00)

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 13:22:40 2006