Locus 6566

Sequence ID 2R_DroMel_CAF1
Location 20,525,135 – 20,525,264
Length 129
Max. P 0.618190
window10452 window10453

overview

Window 2

Location 20,525,135 – 20,525,238
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.07
Mean single sequence MFE -32.48
Consensus MFE -15.05
Energy contribution -14.42
Covariance contribution -0.63
Combinations/Pair 1.68
Mean z-score -1.81
Structure conservation index 0.46
SVM decision value 0.17
SVM RNA-class probability 0.618190
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20525135 103 - 20766785
AUAAAGCUGGCUAGCAACUCAGACAAUUACCAGGAAA-AAUCUUGGCAGGACUCUUCUGAAGCUGGCUAG--UUUUC--------------UGUGGGCAGUCACAUGGAAAAUUCAUAUU
.....((((((((((...(((((...((.((((((..-..)))))).))......))))).)))))))))--)((((--------------((((........))))))))......... ( -32.50)
>DroSec_CAF1 26914 102 - 1
AUAGAGCUGGCUGGCAACUCGGACAACUACCAGAAAA-AAUCUUGGCAGGACUCUUCUGAAGCUGGCUAG--UUUUC--------------UGUGGCCAGUCACAUGGAAAGUUCAUAU-
...((((((((((((....((((.(((((((((....-........(((((...)))))...)))).)))--)).))--------------))..)))))))........)))))....- ( -31.66)
>DroSim_CAF1 26848 102 - 1
AUAGAGCUGGCUGGCAACUCGGACAAUUUGCAGGAAA-AAUCUUGGCAGGACUCUUCUGAAGCUGGCUAG--UUUUC--------------UGUGACCAGUCACAUGGAAAGUUCAUUU-
...((((((((..((...(((((...(((((((((..-..)))).))))).....))))).))..)))).--(((((--------------(((((....))))).)))))))))....- ( -31.70)
>DroEre_CAF1 27248 103 - 1
AUGGAGCCAACGUGCAACCCGGACAAUUACCAGGAAAGAAACUUGGCAGGACUCUUCUGAAGCUGGCUAG--UUUUC--------------GGUGGCCAGCCACAUGGAAAAUUCGUAU-
((((((((((.((....((.((.......)).))......))))))).....(((..((..((((((((.--(....--------------).))))))))..)).)))...)))))..- ( -27.00)
>DroYak_CAF1 27289 102 - 1
AUAGGGCUAACUGGCAACCCUGGCAACUACCAGGAAA-AAACUUGGCAGGACCCUUCUAAAGCUGGCUAG--UUUUC--------------GGUGGCCAGCCAUAUGGAAAAUUCGUAU-
...(((....(((.(((.(((((......)))))...-....))).)))..)))(((((..((((((((.--(....--------------).))))))))....))))).........- ( -31.30)
>DroAna_CAF1 26993 107 - 1
CUAGAGGAAG--UG----CCGGCCAAUUAUGGG---C-AGCCCUGGCAGGACUCUCGCAGGGCUUUCCAGGGUUUUCGUGGAGCAACAAUUGGUGGGCAGCCGCAUGGAAAAUUGGU---
(((..((...--((----((.(((((((...((---.-((((((((.(((.(((.....)))))).)))))))).))((......))))))))).)))).))...))).........--- ( -40.70)
>consensus
AUAGAGCUAGCUGGCAACCCGGACAAUUACCAGGAAA_AAUCUUGGCAGGACUCUUCUGAAGCUGGCUAG__UUUUC______________GGUGGCCAGCCACAUGGAAAAUUCAUAU_
....((((((((........(((...((.(((((.......))))).))...))).....))))))))........................((((....))))................ (-15.05 = -14.42 +  -0.63)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,525,164 – 20,525,264
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.92
Mean single sequence MFE -29.18
Consensus MFE -11.03
Energy contribution -11.95
Covariance contribution 0.92
Combinations/Pair 1.38
Mean z-score -1.95
Structure conservation index 0.38
SVM decision value 0.16
SVM RNA-class probability 0.610071
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20525164 100 - 20766785
CAUUAGCCAGAAUAAAAUA-----CGCG---------ACCAUAAAGCUGGCUAGCAACUCAGACAAUUACCAGGAAA-AAUCUUGGCAGGACUCUUCUGAAGCUGGCUAG--UUUUC---
...................-----....---------.....(((((((((((((...(((((...((.((((((..-..)))))).))......))))).)))))))))--)))).--- ( -28.00)
>DroSec_CAF1 26942 100 - 1
CAUUAGCCAGAAUCAAAUA-----CGCA---------ACAAUAGAGCUGGCUGGCAACUCGGACAACUACCAGAAAA-AAUCUUGGCAGGACUCUUCUGAAGCUGGCUAG--UUUUC---
...................-----....---------.....(((((((((..((...(((((...((.((((....-....)))).))......))))).))..)))))--)))).--- ( -24.30)
>DroSim_CAF1 26876 100 - 1
CAUUAGCCAGAAUCAAAUA-----CGAA---------ACAAUAGAGCUGGCUGGCAACUCGGACAAUUUGCAGGAAA-AAUCUUGGCAGGACUCUUCUGAAGCUGGCUAG--UUUUC---
...................-----....---------.....(((((((((..((...(((((...(((((((((..-..)))).))))).....))))).))..)))))--)))).--- ( -25.90)
>DroEre_CAF1 27276 104 - 1
CAUUAUCCAGAGUCAAACA--GCCCACU---------ACAAUGGAGCCAACGUGCAACCCGGACAAUUACCAGGAAAGAAACUUGGCAGGACUCUUCUGAAGCUGGCUAG--UUUUC---
..............(((((--(((..((---------.((..((((((...((.(.....).)).....(((((.......)))))..)).))))..)).))..)))).)--)))..--- ( -23.20)
>DroYak_CAF1 27317 103 - 1
CAUUAGCCAGAAUCAAACA--GCCCACU---------ACAAUAGGGCUAACUGGCAACCCUGGCAACUACCAGGAAA-AAACUUGGCAGGACCCUUCUAAAGCUGGCUAG--UUUUC---
.(((((((((........(--((((...---------......)))))..(((.(((.(((((......)))))...-....))).))).............))))))))--)....--- ( -32.20)
>DroAna_CAF1 27030 110 - 1
CAUUAGCCAGAAUAAUGGAAGGCCCACUUCCCACAUCCCACUAGAGGAAG--UG----CCGGCCAAUUAUGGG---C-AGCCCUGGCAGGACUCUCGCAGGGCUUUCCAGGGUUUUCGUG
.....(((...(((((....((((((((((((...........).)))))--))----..)))).))))).))---)-((((((((.(((.(((.....)))))).))))))))...... ( -41.50)
>consensus
CAUUAGCCAGAAUCAAAUA_____CACU_________ACAAUAGAGCUAGCUGGCAACCCGGACAAUUACCAGGAAA_AAUCUUGGCAGGACUCUUCUGAAGCUGGCUAG__UUUUC___
..((((((((...................................(((....))).....(((...((.(((((.......))))).))...))).......)))))))).......... (-11.03 = -11.95 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:58 2006