Locus 4207

Sequence ID 3R_DroMel_CAF1
Location 11,353,779 – 11,353,930
Length 151
Max. P 0.955069
window6786 window6787 window6788

overview

Window 6

Location 11,353,779 – 11,353,890
Length 111
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 89.97
Mean single sequence MFE -33.17
Consensus MFE -28.66
Energy contribution -28.60
Covariance contribution -0.06
Combinations/Pair 1.07
Mean z-score -1.92
Structure conservation index 0.86
SVM decision value 1.05
SVM RNA-class probability 0.906194
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11353779 111 + 27905053
CCAAUGGCAAGGACAAGCUGCUGAUGCUGGUUCGGGC------UCUGCAUCUUUGGCUGCCACUGCAGUGGCAAGCUCAAAAUUUUAAUGAUAUCAAAUACAUACAAAGCCCAGCCA
....((((..((((.(((.......))).))))((((------(.((....((((((((((((....))))).))).)))).......((....))........)).))))).)))) ( -38.00)
>DroSec_CAF1 101342 105 + 1
CCAAUGGCAAGGACAAGCUGCUGAUGCUGGGUCUGGU------------UCUUUGGCUGCCACUGCAGUGGCAAGCUCAAAAUUUUAAUGAUAUCAAAUACAUACAAAGCCGAGCCA
....((((..((((.(((.......)))..))))(((------------(.((((((((((((....))))).))).)))).......((....))...........))))..)))) ( -30.80)
>DroSim_CAF1 92118 105 + 1
CCAAUGGCAAGGACAAGCUGCUGGUGCUGGUUCUGGU------------UCUUUGGCUGCCACUGCAGUGGCAAGCUCAAAAUUUUAAUGAUAUCAAAUACAUACAAAGCCGAGCCA
....((((.(((((.(((.......))).)))))(((------------(.((((((((((((....))))).))).)))).......((....))...........))))..)))) ( -31.30)
>DroYak_CAF1 91297 117 + 1
CCAAUGGCAAGGACAAGCUGCUGGUUCUGGUUCUGGUUCUGCUUCUGCUGCUUUGGCUGCCACUGCAGUGGCAAGCUCAAAAUUUUAAUGAUAUCAAAUACAUACAAUGCCGAGCCA
(((..(((........)))..)))....(((((.(((...(((((..((((..(((...)))..))))..).))))............((....))............)))))))). ( -32.60)
>consensus
CCAAUGGCAAGGACAAGCUGCUGAUGCUGGUUCUGGU____________UCUUUGGCUGCCACUGCAGUGGCAAGCUCAAAAUUUUAAUGAUAUCAAAUACAUACAAAGCCGAGCCA
....((((..((((.(((.......))).))))((((..............((((((((((((....))))).))).)))).......((....))............)))).)))) (-28.66 = -28.60 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,353,816 – 11,353,930
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.51
Mean single sequence MFE -33.60
Consensus MFE -23.82
Energy contribution -24.62
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.17
Structure conservation index 0.71
SVM decision value 0.58
SVM RNA-class probability 0.789673
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11353816 114 + 27905053
------UCUGCAUCUUUGGCUGCCACUGCAGUGGCAAGCUCAAAAUUUUAAUGAUAUCAAAUACAUACAAAGCCCAGCCAGGACGUACCAAUAUGCACAUGUGUGUUGCUGGGCACAAUG
------........((((((((((((....))))).))).))))...........................(((((((..((.....))(((((((....))))))))))))))...... ( -34.70)
>DroSec_CAF1 101379 108 + 1
------------UCUUUGGCUGCCACUGCAGUGGCAAGCUCAAAAUUUUAAUGAUAUCAAAUACAUACAAAGCCGAGCCAGGACACACGAGUAUGCACAUGUGUGUAGCUGGGCACAAUG
------------..((((((((((((....))))).))).))))...........................(((.(((....(((((((.((....)).))))))).))).)))...... ( -34.90)
>DroSim_CAF1 92155 108 + 1
------------UCUUUGGCUGCCACUGCAGUGGCAAGCUCAAAAUUUUAAUGAUAUCAAAUACAUACAAAGCCGAGCCAGGACAUGCGAGUAUGCACAUGUGUGUAGCUGGGCACAAUG
------------..((((((((((((....))))).))).))))...........................(((.(((..(.(((((.(......).))))).)...))).)))...... ( -32.10)
>DroEre_CAF1 88869 114 + 1
GCUGGUUCUGCUUCUUUGGCUGCCACUGCAGUGGCAAGCUGAAAAUUUUAAUGAUAUCAAAUACAUACAAUGCCGAGCCAGGAC------GUAUGCACAUGUGUGUAUCUGGGCACAAUG
.(((((((.((...((..((((((((....))))).)))..))........((....))............)).)))))))..(------(.((((((....)))))).))......... ( -35.60)
>DroYak_CAF1 91337 111 + 1
---GCUUCUGCUGCUUUGGCUGCCACUGCAGUGGCAAGCUCAAAAUUUUAAUGAUAUCAAAUACAUACAAUGCCGAGCCAGGAC------GUAUGCACAUGUGUGUAUCUGGGCACAAUG
---((....))(((((((((((((((....))))).))).))))............(((.((((((((((((((......)).)------)).......))))))))).))))))..... ( -30.71)
>consensus
______UCUGC_UCUUUGGCUGCCACUGCAGUGGCAAGCUCAAAAUUUUAAUGAUAUCAAAUACAUACAAAGCCGAGCCAGGAC___C_AGUAUGCACAUGUGUGUAGCUGGGCACAAUG
..............((((((((((((....))))).))).))))...........................(((.(((...............(((((....)))))))).)))...... (-23.82 = -24.62 +   0.80)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,353,816 – 11,353,930
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.51
Mean single sequence MFE -34.58
Consensus MFE -25.92
Energy contribution -25.96
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.52
Structure conservation index 0.75
SVM decision value 1.45
SVM RNA-class probability 0.955069
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11353816 114 - 27905053
CAUUGUGCCCAGCAACACACAUGUGCAUAUUGGUACGUCCUGGCUGGGCUUUGUAUGUAUUUGAUAUCAUUAAAAUUUUGAGCUUGCCACUGCAGUGGCAGCCAAAGAUGCAGA------
......(((((((.......((((((......))))))....)))))))(((((((...((((((...)))))).(((((.(((.(((((....))))))))))))))))))))------ ( -38.90)
>DroSec_CAF1 101379 108 - 1
CAUUGUGCCCAGCUACACACAUGUGCAUACUCGUGUGUCCUGGCUCGGCUUUGUAUGUAUUUGAUAUCAUUAAAAUUUUGAGCUUGCCACUGCAGUGGCAGCCAAAGA------------
......(((.(((((.(((((((........)))))))..))))).)))..........................(((((.(((.(((((....))))))))))))).------------ ( -34.20)
>DroSim_CAF1 92155 108 - 1
CAUUGUGCCCAGCUACACACAUGUGCAUACUCGCAUGUCCUGGCUCGGCUUUGUAUGUAUUUGAUAUCAUUAAAAUUUUGAGCUUGCCACUGCAGUGGCAGCCAAAGA------------
......(((.(((((...(((((((......)))))))..))))).)))..........................(((((.(((.(((((....))))))))))))).------------ ( -33.70)
>DroEre_CAF1 88869 114 - 1
CAUUGUGCCCAGAUACACACAUGUGCAUAC------GUCCUGGCUCGGCAUUGUAUGUAUUUGAUAUCAUUAAAAUUUUCAGCUUGCCACUGCAGUGGCAGCCAAAGAAGCAGAACCAGC
..((.(((.((((((((.(((.((((....------((....))...))))))).))))))))............((((..(((.(((((....))))))))..)))).))).))..... ( -31.70)
>DroYak_CAF1 91337 111 - 1
CAUUGUGCCCAGAUACACACAUGUGCAUAC------GUCCUGGCUCGGCAUUGUAUGUAUUUGAUAUCAUUAAAAUUUUGAGCUUGCCACUGCAGUGGCAGCCAAAGCAGCAGAAGC---
..((.(((.((((((((.(((.((((....------((....))...))))))).))))))))............(((((.(((.(((((....)))))))))))))..))).))..--- ( -34.40)
>consensus
CAUUGUGCCCAGCUACACACAUGUGCAUACU_G___GUCCUGGCUCGGCUUUGUAUGUAUUUGAUAUCAUUAAAAUUUUGAGCUUGCCACUGCAGUGGCAGCCAAAGA_GCAGA______
...((((........))))((.((((((((......(((.......)))...)))))))).))............(((((.(((.(((((....)))))))))))))............. (-25.92 = -25.96 +   0.04)

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 11:21:41 2006