Locus 4509

Sequence ID 3L_DroMel_CAF1
Location 13,003,910 – 13,004,053
Length 143
Max. P 0.722674
window7045 window7046

overview

Window 5

Location 13,003,910 – 13,004,022
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.27
Mean single sequence MFE -32.62
Consensus MFE -19.48
Energy contribution -19.64
Covariance contribution 0.16
Combinations/Pair 1.17
Mean z-score -2.05
Structure conservation index 0.60
SVM decision value 0.05
SVM RNA-class probability 0.559597
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13003910 112 - 23771897
GCUCACAA--------CCGGUGGCAGUAGAAAAAAAAGAAAAGUAUUUUUCCCACAAGAAUGCAGCUGCAUUCCGCAAACCACCACCAUGCCCAAUCGCUGGGUCAGAUCUCCUGCCGCA
........--------...(((((((.(((...........................((((((....))))))................(((((.....)))))....))).))))))). ( -28.90)
>DroSec_CAF1 10952 111 - 1
GAUCACAA--------CCGGUGGCGGUGGAAA-AAAAGAAAUGUAUUUUUCCCACAAGAAUGCAGCUGCAUUCCGCAAACCACCACCAUGCCCAAUCGCUGGGUCAGAUCUCCUGCCGCA
((((....--------..(((((.((((((((-((.(....)...))))))).....((((((....)))))).....))).)))))..(((((.....)))))..)))).......... ( -36.70)
>DroSim_CAF1 13480 112 - 1
GAUCACAA--------CCGGUGGCGGUGGAAAAAAAAGAAAAGUAUUUUUCCCACAAGAAUGCAGCUGCAUUCCGCAAACCACCACCAUGCCCAAUCGCUGGGUCAGAUCUCCUGCCGCA
((((....--------..(((((.((((((((((...........))))))).....((((((....)))))).....))).)))))..(((((.....)))))..)))).......... ( -35.90)
>DroEre_CAF1 10861 112 - 1
GCUCACAACUGCUAUAGAGCUGCUAAU-----AGAGAGAAAAGUCUUUUUCCCACAGGAAUGCAGCUGCAUUCCGCA---CACCAGCGUGCCCAAUCGCAGGGUCAGAUCUGCUGCCGCA
((......((((.((.(.((((((...-----(((((((....)))))))......(((((((....)))))))...---....)))).)).).)).))))((.(((.....))))))). ( -33.10)
>DroYak_CAF1 11369 104 - 1
GCUCACAA--------GCGGUGGUAGU-----AAAAAGAAAAGUAUUUUUCCCACAGGAAUGCAGCUGCAGUCCGCA---CAACACCGUGUCCAAUCGCAGGGUCAGAUCUCCUGCCGCA
((......--------((((((((.(.-----(((((........))))).).)).(((.(((....))).)))...---...))))))........((((((.......)))))).)). ( -28.50)
>consensus
GCUCACAA________CCGGUGGCAGU_GAAAAAAAAGAAAAGUAUUUUUCCCACAAGAAUGCAGCUGCAUUCCGCAAACCACCACCAUGCCCAAUCGCUGGGUCAGAUCUCCUGCCGCA
...................(((((((...............................((((((....))))))...............(((((.......))).))......))))))). (-19.48 = -19.64 +   0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,003,950 – 13,004,053
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.72
Mean single sequence MFE -33.46
Consensus MFE -16.22
Energy contribution -15.86
Covariance contribution -0.36
Combinations/Pair 1.13
Mean z-score -2.11
Structure conservation index 0.48
SVM decision value 0.40
SVM RNA-class probability 0.722674
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13003950 103 + 23771897
GUUUGCGGAAUGCAGCUGCAUUCUUGUGGGAAAAAUACUUUUCUUUUUUUUCUACUGCCACCGG--------UUGUGAGCCCUAAAUUGUAGG---------GUAUGAAGCCGUAGGGAC
......(((((((....))))))).((((((((((..........))))))))))..((..(((--------((....((((((.....))))---------))....)))))..))... ( -33.10)
>DroSec_CAF1 10992 102 + 1
GUUUGCGGAAUGCAGCUGCAUUCUUGUGGGAAAAAUACAUUUCUUUU-UUUCCACCGCCACCGG--------UUGUGAUCCCUAAAUUGUAGG---------GUAUGAAGCCGUAGGGAU
......(((((((....))))))).((((((((((.........)))-)))))))..((..(((--------((.....(((((.....))))---------).....)))))..))... ( -33.80)
>DroSim_CAF1 13520 103 + 1
GUUUGCGGAAUGCAGCUGCAUUCUUGUGGGAAAAAUACUUUUCUUUUUUUUCCACCGCCACCGG--------UUGUGAUCCCUAAGUUGUAGG---------GUAUGAAGCCGUAGGGAC
......(((((((....))))))).((((((((((..........))))))))))..((..(((--------((.....(((((.....))))---------).....)))))..))... ( -33.70)
>DroEre_CAF1 10901 103 + 1
---UGCGGAAUGCAGCUGCAUUCCUGUGGGAAAAAGACUUUUCUCUCU-----AUUAGCAGCUCUAUAGCAGUUGUGAGCCCUAAGUUGUAGG---------GUAUGAAAUCGUAGGGAC
---((((((((((....))))))).(.(((((((....))))))).).-----....))).((((((.((....))..((((((.....))))---------))........)))))).. ( -31.60)
>DroYak_CAF1 11409 104 + 1
---UGCGGACUGCAGCUGCAUUCCUGUGGGAAAAAUACUUUUCUUUUU-----ACUACCACCGC--------UUGUGAGCCCUAAGAUGUAGGGUAUGUAGGGUAUGAGCCCAUAGGGAC
---(((((.(....))))))((((((((((....(((((((.(.....-----.....(((...--------..))).((((((.....))))))..).)))))))...)))))))))). ( -35.10)
>consensus
GUUUGCGGAAUGCAGCUGCAUUCUUGUGGGAAAAAUACUUUUCUUUUUUUUC_ACUGCCACCGG________UUGUGAGCCCUAAGUUGUAGG_________GUAUGAAGCCGUAGGGAC
...(((((.......)))))((((((((((((((....))))).....................................((((.....)))).................))))))))). (-16.22 = -15.86 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:21 2006