Locus 6061

Sequence ID 3L_DroMel_CAF1
Location 16,141,193 – 16,141,458
Length 265
Max. P 0.883910
window9722 window9723 window9724

overview

Window 2

Location 16,141,193 – 16,141,313
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -41.50
Consensus MFE -40.90
Energy contribution -41.03
Covariance contribution 0.12
Combinations/Pair 1.05
Mean z-score -1.93
Structure conservation index 0.99
SVM decision value 0.93
SVM RNA-class probability 0.883910
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16141193 120 + 23771897
GCACAUCUGCAAGCAGCCUAUCAAUUUUUGACGAGACAAUCUCAGAGUCCAAAGGGGCACUGCAAAAAAAUGCAGUCGGAGCAAUUGGCUGGCGGAUCAGGGGUCGCUCGAGAGGUGAGC
((.(((((.(.(((.(((..(((((((((((((((.....)))...((((....))))..((((......))))))))))..))))))..))).(((.....)))))).)..))))).)) ( -37.90)
>DroSec_CAF1 3460 120 + 1
GCACAUCUGCAAGCAGCCUAUCAAUUUUUGACGAGACAAUCUCAGAGUCCAAAGGGGCACUGCAAAAAAAUGCAGUCGGAGCAAUUGGCUGGCGGACCAGGGGUCGCUCGAGAGGUGAGC
((.(((((.(.(((.(((..(((((((((((((((.....)))...((((....))))..((((......))))))))))..))))))..))).((((...))))))).)..))))).)) ( -40.20)
>DroEre_CAF1 2823 119 + 1
GCACAUCUGCAAGCAGCCUAUCAAUUUUUGACGAGACAAUCUCAGAGUCCAAAGGGGCACUGCAAA-AAAUGCAGUCGGAGCAAUUGGCUGGCGGACCAGGGGUCGCUUGAGAGGUGAGC
((.(((((.(((((.(((..(((((((((((((((.....)))...((((....))))..((((..-...))))))))))..))))))..))).((((...)))))))))..))))).)) ( -44.10)
>DroYak_CAF1 3482 119 + 1
UCACAUCUGCAAGCAGCCUAUCAAUUUUUGACGAGACAAUCUCAGAGUCCAAAGGGGCACUGCAAA-AAUUGCAGUCGGGGCAAUUGGCUGGCGGACCAGGGGUCGCUUGAGAGGUGAGC
((((.(((.(((((.(((..(((((((((((((((.....)))...((((....))))..((((..-...))))))))))..))))))..))).((((...)))))))))))).)))).. ( -43.80)
>consensus
GCACAUCUGCAAGCAGCCUAUCAAUUUUUGACGAGACAAUCUCAGAGUCCAAAGGGGCACUGCAAA_AAAUGCAGUCGGAGCAAUUGGCUGGCGGACCAGGGGUCGCUCGAGAGGUGAGC
.(((.(((.(((((.(((..(((((((((((((((.....)))...((((....))))..((((......))))))))))..))))))..))).((((...)))))))))))).)))... (-40.90 = -41.03 +   0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,141,233 – 16,141,353
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.73
Mean single sequence MFE -44.62
Consensus MFE -39.15
Energy contribution -38.77
Covariance contribution -0.38
Combinations/Pair 1.14
Mean z-score -1.43
Structure conservation index 0.88
SVM decision value 0.18
SVM RNA-class probability 0.621624
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16141233 120 + 23771897
CUCAGAGUCCAAAGGGGCACUGCAAAAAAAUGCAGUCGGAGCAAUUGGCUGGCGGAUCAGGGGUCGCUCGAGAGGUGAGCUCACUUCGGCCAGGGGCAUGGGGCAGCAGCAGCGCUGCAA
((((..((((......((((((((......))))))....))......(((((.((...(((.((((.(....))))).)))...)).))))))))).))))(((((......))))).. ( -49.40)
>DroSec_CAF1 3500 114 + 1
CUCAGAGUCCAAAGGGGCACUGCAAAAAAAUGCAGUCGGAGCAAUUGGCUGGCGGACCAGGGGUCGCUCGAGAGGUGAGCUUACUGCGGCCAGGGGCGUGGGGCA------GUGCUGCAA
......((((....))))((((((......)))))).(.((((.(((.((.(((..((...((((((.....(((....)))...)))))).))..))).)).))------))))).).. ( -44.90)
>DroEre_CAF1 2863 113 + 1
CUCAGAGUCCAAAGGGGCACUGCAAA-AAAUGCAGUCGGAGCAAUUGGCUGGCGGACCAGGGGUCGCUUGAGAGGUGAGCUCAGUGCGGCCAGGGGCGUGGGGCA------GCACUGCAA
..(((.((((....)))).)))....-...((((((....((...((.((.(((..((...(((((((((((.......))))).)))))).))..))).)).))------)))))))). ( -43.70)
>DroYak_CAF1 3522 113 + 1
CUCAGAGUCCAAAGGGGCACUGCAAA-AAUUGCAGUCGGGGCAAUUGGCUGGCGGACCAGGGGUCGCUUGAGAGGUGAGCUCACUGUGGCCAGGGGCGUGGGGAA------UCGCUACAA
(((...((((....))))((((((..-...)))))).)))((..(((((((.(((....(((.(((((.....))))).))).))))))))))..))((((.(..------.).)))).. ( -40.50)
>consensus
CUCAGAGUCCAAAGGGGCACUGCAAA_AAAUGCAGUCGGAGCAAUUGGCUGGCGGACCAGGGGUCGCUCGAGAGGUGAGCUCACUGCGGCCAGGGGCGUGGGGCA______GCGCUGCAA
......((((....))))((((((......))))))....((..(((((((.(((....(((.(((((.....))))).))).))))))))))..))((((.((.......)).)))).. (-39.15 = -38.77 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,141,353 – 16,141,458
Length 105
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 90.85
Mean single sequence MFE -33.33
Consensus MFE -28.75
Energy contribution -29.06
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -1.36
Structure conservation index 0.86
SVM decision value -0.01
SVM RNA-class probability 0.529966
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16141353 105 + 23771897
GAGGGGCAGGGGGGUGUUUGAGGGGAUGGGGGCUGGGCAGACGUCUGCGGUCUGUGCAUAAAAUUACGAUAAGUGCAGGCGAGGCCACAGUCCAGAGGGCUCAGA
...........((((.(((....((((...((((..((((....)))).(((((..(...............)..)))))..))))...)))).))).))))... ( -34.76)
>DroSec_CAF1 3614 102 + 1
GAGGGGCAGG-GGGUGUUUGAGGGGAUGGGGGCCGGGCAGACGUCUGCGGUCUGUGCAUGAAAUUACGAUAAGUGCAGGCGAGGCCGCAGUCCAGAGGGC--AGA
..........-...(((((....((((.(.((((..((((....)))).(((((..(...............)..)))))..)))).).))))...))))--).. ( -35.06)
>DroEre_CAF1 2976 101 + 1
GGGGGGGCAGG-GGUGUUUGAAGGGAAG-GGGCUGGGCAGACGUCUGCGGUCUGUGCAUAAAAUUACGAUAAGUGCAGGCGAGGCCGCAGUCCAGAGGGC--AGA
....(((((..-..))))).........-(((((((((...(((((((((((.(((........))))))...))))))))..))).)))))).......--... ( -30.40)
>DroYak_CAF1 3635 102 + 1
UCGGGGACAGGAGGUGUUUGAAGGGAAG-GGGCUGGGCAGACGUCUGCGGUCUGUGCAUAAAAUUACGAUAAGUGCAGGCGAGGCCACAGUCCAGAGGGC--AGA
(((((.((.....)).))))).......-(((((((((...(((((((((((.(((........))))))...))))))))..))).)))))).......--... ( -33.10)
>consensus
GAGGGGCAAGGGGGUGUUUGAAGGGAAG_GGGCUGGGCAGACGUCUGCGGUCUGUGCAUAAAAUUACGAUAAGUGCAGGCGAGGCCACAGUCCAGAGGGC__AGA
.............((.(((....((((...((((..((((....)))).(((((..(...............)..)))))..))))...)))).))).))..... (-28.75 = -29.06 +   0.31)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:47 2006