Locus 3297

Sequence ID 3R_DroMel_CAF1
Location 8,829,014 – 8,829,106
Length 92
Max. P 0.964186
window5324 window5325

overview

Window 4

Location 8,829,014 – 8,829,106
Length 92
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 79.70
Mean single sequence MFE -46.20
Consensus MFE -34.03
Energy contribution -35.40
Covariance contribution 1.37
Combinations/Pair 1.06
Mean z-score -2.01
Structure conservation index 0.74
SVM decision value 1.18
SVM RNA-class probability 0.927114
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8829014 92 + 27905053
GAGGAC---GACAGUCUACUGCGUCUGGACAGCCUCUGCAAGAGCCUGCAGAGGCACACGGAUGCCACAGACGCCUCGGCUGCG------------------GCUGCUGCUCU
((((..---....((((...(((((((....(((((((((......)))))))))...)))))))...)))).))))(((.((.------------------...)).))).. ( -41.40)
>DroSec_CAF1 3358 95 + 1
GAGGACGACGACAGUCUACUGCGUCUGGACAGCCUCUGCAAGAGCCUGCAGAGGCACACGGAUGCCACAGACGCCUCGGCUGCG------------------GCUGCUGCUCU
(((.(((.((.(((((....(((((((....(((((((((......)))))))))....((...)).)))))))...)))))))------------------..)).).))). ( -41.90)
>DroEre_CAF1 3495 113 + 1
GAGGGUGAUAACAGUCUUUUGCGUCUGGACAGCCUCUGCAAGCGGCUGCAGAUGCACACGGAUGCCACAGAUGCCUCGACUGCGGCAACGGCGGCCGAAGCGGCCGCUGCUGU
((((((....)).((((...(((((((....((.((((((......)))))).))...)))))))...)))).))))....((((((...(((((((...))))))))))))) ( -49.80)
>DroYak_CAF1 3420 113 + 1
GAGGGCGACAACAGUCUAUUGCGUCUGGACAGCCUCUGCAAGAGGCUGCAGAUGCACACCGAUGCCACGGACGCCUCGACUGCGGCAACGGCGGCCGAAGCGGCAGCUGCUGU
...((((((....)))...((((((((..(((((((.....)))))))))))))))(.(((.((((.(((.((...)).))).)))).))).))))...(((((....))))) ( -51.70)
>consensus
GAGGACGACAACAGUCUACUGCGUCUGGACAGCCUCUGCAAGAGCCUGCAGAGGCACACGGAUGCCACAGACGCCUCGACUGCG__________________GCUGCUGCUCU
((((.........((((...(((((((....(((((((((......)))))))))...)))))))...)))).))))(((.((.((..((.....))..)).)).)))..... (-34.03 = -35.40 +   1.37)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 5

Location 8,829,014 – 8,829,106
Length 92
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 79.70
Mean single sequence MFE -47.12
Consensus MFE -33.66
Energy contribution -35.16
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.71
SVM decision value 1.56
SVM RNA-class probability 0.964186
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8829014 92 - 27905053
AGAGCAGCAGC------------------CGCAGCCGAGGCGUCUGUGGCAUCCGUGUGCCUCUGCAGGCUCUUGCAGAGGCUGUCCAGACGCAGUAGACUGUC---GUCCUC
.(..((((.((------------------(((((.((...)).)))))))..........((((((((....))))))))))))..).(((((((....))).)---)))... ( -41.60)
>DroSec_CAF1 3358 95 - 1
AGAGCAGCAGC------------------CGCAGCCGAGGCGUCUGUGGCAUCCGUGUGCCUCUGCAGGCUCUUGCAGAGGCUGUCCAGACGCAGUAGACUGUCGUCGUCCUC
.(..((((.((------------------(((((.((...)).)))))))..........((((((((....))))))))))))..).(((((((....))).))))...... ( -42.50)
>DroEre_CAF1 3495 113 - 1
ACAGCAGCGGCCGCUUCGGCCGCCGUUGCCGCAGUCGAGGCAUCUGUGGCAUCCGUGUGCAUCUGCAGCCGCUUGCAGAGGCUGUCCAGACGCAAAAGACUGUUAUCACCCUC
...((((((((.((....)).)))))))).((((((...((.((((.((((.(((....).(((((((....))))))))).)))))))).))....)))))).......... ( -52.10)
>DroYak_CAF1 3420 113 - 1
ACAGCAGCUGCCGCUUCGGCCGCCGUUGCCGCAGUCGAGGCGUCCGUGGCAUCGGUGUGCAUCUGCAGCCUCUUGCAGAGGCUGUCCAGACGCAAUAGACUGUUGUCGCCCUC
((((((((((..((....))(((((.((((((.(.((...)).).)))))).)))))(((.(((((((((((.....)))))))..)))).))).))).)))))))....... ( -52.30)
>consensus
ACAGCAGCAGC__________________CGCAGCCGAGGCGUCUGUGGCAUCCGUGUGCAUCUGCAGCCUCUUGCAGAGGCUGUCCAGACGCAAUAGACUGUCGUCGCCCUC
..............................((((((...(((((((.((((.......((((((((((....)))))))))))))))))))))....)))))).......... (-33.66 = -35.16 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:53 2006