Locus 1295

Sequence ID 2L_DroMel_CAF1
Location 3,425,322 – 3,425,481
Length 159
Max. P 0.806246
window2116 window2117

overview

Window 6

Location 3,425,322 – 3,425,442
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.44
Mean single sequence MFE -34.82
Consensus MFE -30.57
Energy contribution -31.32
Covariance contribution 0.75
Combinations/Pair 1.10
Mean z-score -1.49
Structure conservation index 0.88
SVM decision value 0.43
SVM RNA-class probability 0.734631
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3425322 120 + 22407834
GCACCGCUUUCACCAUCCUGCGGAAAUGUUGAAAAUAUUGCAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUU
((((.((..(((((.(((((((...((((.....))))))).)))).).)))).))(((((((((((((((((....)))))))........)))))))))).))))............. ( -37.00)
>DroSec_CAF1 14163 120 + 1
GCACCCCUUUCACCAUCCUGCGGAAAUGUUGAAAAUAUUGCAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUU
...............((((((((............(((..(........)..))).(((((((((((((((((....)))))))........))))))))))....))))))))...... ( -35.10)
>DroAna_CAF1 16636 117 + 1
AGGCCGUAUCUACUAUCCUGCGGAAAUGUUGCAACGAUUGCAAGGAGA---GGAGCUGCCACAAAUUAGUGCAUAAUUUCAUUAGUCACUUCAUUUAUGGCAAGAGCGGCAGGAAGUGUU
..........((((.((((((.....(.(((((.....))))).)...---...(((((((.((((.((((..((((...))))..))))..)))).))))...))).)))))))))).. ( -29.50)
>DroSim_CAF1 14337 120 + 1
GCACCCCUUUCACCAUCCUGCGGAAAUGUUGAAAAUAUUGCAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUU
...............((((((((............(((..(........)..))).(((((((((((((((((....)))))))........))))))))))....))))))))...... ( -35.10)
>DroEre_CAF1 14392 120 + 1
GCACCCCUUUCACCAUCCUGCGGAAAUGUUGAAAAUAUUGCAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUU
...............((((((((............(((..(........)..))).(((((((((((((((((....)))))))........))))))))))....))))))))...... ( -35.10)
>DroYak_CAF1 15633 120 + 1
GCACCCCUUUCACUAUCCUGCGGAAAUGUGGAAAAUAUUGCAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUU
...........(((.((((((((...(((((....(((..(........)..)))...)))))...(((((((....)))))))(((((.......))))).....)))))))))))... ( -37.10)
>consensus
GCACCCCUUUCACCAUCCUGCGGAAAUGUUGAAAAUAUUGCAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUU
...............((((((((............((((((........)))))).(((((((((((((((((....)))))))........))))))))))....))))))))...... (-30.57 = -31.32 +   0.75)

alignment

Postscript

secondary structure

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dotplot

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Window 7

Location 3,425,362 – 3,425,481
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.23
Mean single sequence MFE -34.65
Consensus MFE -29.35
Energy contribution -30.13
Covariance contribution 0.78
Combinations/Pair 1.10
Mean z-score -1.94
Structure conservation index 0.85
SVM decision value 0.63
SVM RNA-class probability 0.806246
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3425362 119 + 22407834
CAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUUGCUUGCA-ACCGCCAAAAUUCGUUGCAAUUUAUAUCAAGU
(((.((((((.(.((((((((((((((((((((....)))))))........))))))))))......(((((....)))))..)))-.))))).....)).)))............... ( -36.60)
>DroSec_CAF1 14203 119 + 1
CAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUUGCUUGCA-ACCGCCGAAAUUCGUUGCAAUUUAUAUCAAGU
(((.((((((.(.((((((((((((((((((((....)))))))........))))))))))......(((((....)))))..)))-.))))).....)).)))............... ( -36.60)
>DroAna_CAF1 16676 117 + 1
CAAGGAGA---GGAGCUGCCACAAAUUAGUGCAUAAUUUCAUUAGUCACUUCAUUUAUGGCAAGAGCGGCAGGAAGUGUUUCCUGAAAAUCAUCUAAAUUUCUUGCAAUUUAUAGAGCGU
(((((((.---(((..(((((.((((.((((..((((...))))..))))..)))).))))).((....((((((....))))))....)).)))...)))))))............... ( -24.90)
>DroSim_CAF1 14377 119 + 1
CAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUUGCUUGCA-ACCGCCGAAAUUCGUUGCAAUUUAUAUCAAGU
(((.((((((.(.((((((((((((((((((((....)))))))........))))))))))......(((((....)))))..)))-.))))).....)).)))............... ( -36.60)
>DroEre_CAF1 14432 119 + 1
CAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUUGCUUGCA-ACCGCCGAAAUUCGUUGCAAUUUAUAUCAAGU
(((.((((((.(.((((((((((((((((((((....)))))))........))))))))))......(((((....)))))..)))-.))))).....)).)))............... ( -36.60)
>DroYak_CAF1 15673 119 + 1
CAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUUGCUUGCA-ACCGCCGAAAUUCGUUGCAAUUUAUAUCAAGU
(((.((((((.(.((((((((((((((((((((....)))))))........))))))))))......(((((....)))))..)))-.))))).....)).)))............... ( -36.60)
>consensus
CAAGGAGGCGUGAUGCUGCCGCAAAUUAAUGCAUAAUUGCAUUAGUCACUUCAUUUGUGGCAAGUGCUGCAGGAAGUCUUGCUUGCA_ACCGCCGAAAUUCGUUGCAAUUUAUAUCAAGU
......((((...((((((((((((((((((((....)))))))........))))))))))......(((((....)))))..)))...)))).......................... (-29.35 = -30.13 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:53 2006