Locus 8674

Sequence ID 3R_DroMel_CAF1
Location 23,160,319 – 23,160,439
Length 120
Max. P 0.952149
window13931 window13932

overview

Window 1

Location 23,160,319 – 23,160,439
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -35.63
Consensus MFE -34.04
Energy contribution -34.27
Covariance contribution 0.23
Combinations/Pair 1.05
Mean z-score -1.98
Structure conservation index 0.96
SVM decision value 0.80
SVM RNA-class probability 0.852989
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23160319 120 + 27905053
UGGCGAAGGGUAUGGGGUGGUGUCGGAAUUGGUGUCCUGGUUGGGUGGUGAUGUUGCGUUAAUGAAAUAAAAAUUAAGCUCUGAUGCCUGCCAGGACGAAUUAAUUGUGUGUCGCCAAAG
((.(....).))...((((..(.((.(((((((((((((((.(((((..((....((.(((((.........)))))))))...)))))))))))))..))))))).)))..)))).... ( -34.10)
>DroSec_CAF1 10388 120 + 1
UGACGAAGGGUGUGGAGUGGUGGCGGAAUUGGUGUCCUGGUUGGGUGGUGUUGUUGCGUUAAUGAAAUAAAAAUUAAGCUCUGAUGCUUGCCAGGACGAAUUAAUUGUGUGUCGCCAAAG
...(....)........((((((((.(((((((((((((((.....(((((((..((.(((((.........)))))))..))))))).))))))))..)))))))...))))))))... ( -34.50)
>DroSim_CAF1 15694 120 + 1
UGACGAAGGGUAUGGAGUGGCGGCGGAAUUGGUGUCCUGGUUGGGUGGUGUUGUUGCGUUAAUGAAAUAAAAAUUAAGCUCUGAUGCCUGCCAGGACGAAUUAAUUGUGUGUCGCCAAAG
...(....)........((((((((.(((((((((((((((.....(((((((..((.(((((.........)))))))..))))))).))))))))..)))))))...))))))))... ( -38.30)
>consensus
UGACGAAGGGUAUGGAGUGGUGGCGGAAUUGGUGUCCUGGUUGGGUGGUGUUGUUGCGUUAAUGAAAUAAAAAUUAAGCUCUGAUGCCUGCCAGGACGAAUUAAUUGUGUGUCGCCAAAG
...(....)........((((((((.(((((((((((((((.....(((((((..((.(((((.........)))))))..))))))).))))))))..))))))).)))..)))))... (-34.04 = -34.27 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 23,160,319 – 23,160,439
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -20.13
Consensus MFE -19.51
Energy contribution -19.07
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -2.31
Structure conservation index 0.97
SVM decision value 1.42
SVM RNA-class probability 0.952149
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23160319 120 - 27905053
CUUUGGCGACACACAAUUAAUUCGUCCUGGCAGGCAUCAGAGCUUAAUUUUUAUUUCAUUAACGCAACAUCACCACCCAACCAGGACACCAAUUCCGACACCACCCCAUACCCUUCGCCA
...((((((..............(((((((..((.....(((((((((.........))))).))....)).....))..))))))).........(....)............)))))) ( -21.80)
>DroSec_CAF1 10388 120 - 1
CUUUGGCGACACACAAUUAAUUCGUCCUGGCAAGCAUCAGAGCUUAAUUUUUAUUUCAUUAACGCAACAACACCACCCAACCAGGACACCAAUUCCGCCACCACUCCACACCCUUCGUCA
...((((((............))(((((((.((((......)))).....(((......)))..................))))))).........)))).................... ( -19.10)
>DroSim_CAF1 15694 120 - 1
CUUUGGCGACACACAAUUAAUUCGUCCUGGCAGGCAUCAGAGCUUAAUUUUUAUUUCAUUAACGCAACAACACCACCCAACCAGGACACCAAUUCCGCCGCCACUCCAUACCCUUCGUCA
...(((((...............(((((((.((((......)))).....(((......)))..................)))))))..(......).)))))................. ( -19.50)
>consensus
CUUUGGCGACACACAAUUAAUUCGUCCUGGCAGGCAUCAGAGCUUAAUUUUUAUUUCAUUAACGCAACAACACCACCCAACCAGGACACCAAUUCCGCCACCACUCCAUACCCUUCGUCA
...((((((..............(((((((.((((......)))).....(((......)))..................))))))).........(....)............)))))) (-19.51 = -19.07 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:58 2006