Locus 1648

Sequence ID 3L_DroMel_CAF1
Location 4,770,419 – 4,770,535
Length 116
Max. P 0.894689
window2551 window2552

overview

Window 1

Location 4,770,419 – 4,770,535
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 96.02
Mean single sequence MFE -36.70
Consensus MFE -31.29
Energy contribution -31.99
Covariance contribution 0.70
Combinations/Pair 1.03
Mean z-score -1.94
Structure conservation index 0.85
SVM decision value 0.78
SVM RNA-class probability 0.848651
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4770419 116 + 23771897
--GCCAGCUAGUGGGCCACAGAAUGUCAUUUUAAAUUUUAAGGACACAAUGGCGCUGCGCAUAAAAAGCAACCGCAGCGACUCGAGAGAUUUAUUUCAAAGGCGGCCCACGGAGCCAC--
--....(((.(((((((.((...((((.(((........)))))))...))((((((((.............)))))).....((((......))))....)))))))))..)))...-- ( -37.12)
>DroSec_CAF1 33176 116 + 1
--GCCAGCCAGUGGGCCACAGAAUGUCAUUUUAAAUUUUAAGGACACAAUGGCGCUGCGCAUAAAAAGCAACCGCAGCGACUCGAGAGAUUUAUUUCAAAGGCGGCCCACGGAGCCAC--
--((...((.(((((((.((...((((.(((........)))))))...))((((((((.............)))))).....((((......))))....))))))))))).))...-- ( -36.32)
>DroSim_CAF1 32115 116 + 1
--GCCAGCCAGUGGGCCACAGAAUGUCAUUUUAAAUUUUAAGGACACAAUGGCGCUGCGCAUAAAAAGCAACCGCAGCGACUCGAGAGAUUUAUUUCAAAGGCGGCCCACGGAGCCAC--
--((...((.(((((((.((...((((.(((........)))))))...))((((((((.............)))))).....((((......))))....))))))))))).))...-- ( -36.32)
>DroEre_CAF1 22470 116 + 1
--GCCAGCCAGUGGGCCACAGAAUGUCAUUUUAAAUUUUAAGGACACAAUGGCGCUGCGCAUAAAAAGCAACCGCAGCGACUCGAGAGAUUUAUUUCAAAGGCGGCCCACGGAGCCAC--
--((...((.(((((((.((...((((.(((........)))))))...))((((((((.............)))))).....((((......))))....))))))))))).))...-- ( -36.32)
>DroYak_CAF1 29663 116 + 1
--GGCAGCCAGUGGGCCACAGAAUGUCAUUUUAAAUUUUAAGGACACAAUGGCGCUGCGCAUAAAAAGCAACCGCAGCGACUCGAGAGAUUUAUUUCAAAGGCGGCCCACGGAGCCAC--
--(((..((.(((((((.((...((((.(((........)))))))...))((((((((.............)))))).....((((......))))....))))))))))).)))..-- ( -40.02)
>DroAna_CAF1 23383 120 + 1
ACUCCAGCCAGCGGGCCGGCGAAUGUCAUUUUAAAUUUUAAGGACACAAUGGCACUGCGCAUAAAAAGCAACCGCAGCGACUCGAGAGAUUUAUUUCAAAGGCGGCCAACGGAGCCGCCU
......((..((((((((.....((((.(((........)))))))...))))..(((.........))).)))).)).....((((......))))..((((((((....).))))))) ( -34.10)
>consensus
__GCCAGCCAGUGGGCCACAGAAUGUCAUUUUAAAUUUUAAGGACACAAUGGCGCUGCGCAUAAAAAGCAACCGCAGCGACUCGAGAGAUUUAUUUCAAAGGCGGCCCACGGAGCCAC__
......(((.(((((((.((...((((.(((........)))))))...))((((((((.............)))))).....((((......))))....))))))))).).))..... (-31.29 = -31.99 +   0.70)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 4,770,419 – 4,770,535
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.02
Mean single sequence MFE -37.03
Consensus MFE -35.35
Energy contribution -34.99
Covariance contribution -0.36
Combinations/Pair 1.17
Mean z-score -1.09
Structure conservation index 0.95
SVM decision value 0.98
SVM RNA-class probability 0.894689
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4770419 116 - 23771897
--GUGGCUCCGUGGGCCGCCUUUGAAAUAAAUCUCUCGAGUCGCUGCGGUUGCUUUUUAUGCGCAGCGCCAUUGUGUCCUUAAAAUUUAAAAUGACAUUCUGUGGCCCACUAGCUGGC--
--..((((..(((((((((....................(.(((((((.............))))))).)...(((((.((.........)).)))))...))))))))).))))...-- ( -36.42)
>DroSec_CAF1 33176 116 - 1
--GUGGCUCCGUGGGCCGCCUUUGAAAUAAAUCUCUCGAGUCGCUGCGGUUGCUUUUUAUGCGCAGCGCCAUUGUGUCCUUAAAAUUUAAAAUGACAUUCUGUGGCCCACUGGCUGGC--
--..((((..(((((((((....................(.(((((((.............))))))).)...(((((.((.........)).)))))...))))))))).))))...-- ( -36.42)
>DroSim_CAF1 32115 116 - 1
--GUGGCUCCGUGGGCCGCCUUUGAAAUAAAUCUCUCGAGUCGCUGCGGUUGCUUUUUAUGCGCAGCGCCAUUGUGUCCUUAAAAUUUAAAAUGACAUUCUGUGGCCCACUGGCUGGC--
--..((((..(((((((((....................(.(((((((.............))))))).)...(((((.((.........)).)))))...))))))))).))))...-- ( -36.42)
>DroEre_CAF1 22470 116 - 1
--GUGGCUCCGUGGGCCGCCUUUGAAAUAAAUCUCUCGAGUCGCUGCGGUUGCUUUUUAUGCGCAGCGCCAUUGUGUCCUUAAAAUUUAAAAUGACAUUCUGUGGCCCACUGGCUGGC--
--..((((..(((((((((....................(.(((((((.............))))))).)...(((((.((.........)).)))))...))))))))).))))...-- ( -36.42)
>DroYak_CAF1 29663 116 - 1
--GUGGCUCCGUGGGCCGCCUUUGAAAUAAAUCUCUCGAGUCGCUGCGGUUGCUUUUUAUGCGCAGCGCCAUUGUGUCCUUAAAAUUUAAAAUGACAUUCUGUGGCCCACUGGCUGCC--
--(..(((..(((((((((....................(.(((((((.............))))))).)...(((((.((.........)).)))))...))))))))).)))..).-- ( -39.12)
>DroAna_CAF1 23383 120 - 1
AGGCGGCUCCGUUGGCCGCCUUUGAAAUAAAUCUCUCGAGUCGCUGCGGUUGCUUUUUAUGCGCAGUGCCAUUGUGUCCUUAAAAUUUAAAAUGACAUUCGCCGGCCCGCUGGCUGGAGU
((((((((.....)))))))).............(((.(((((..((((((((.........)))).(((...(((((.((.........)).))))).....)))))))))))).))). ( -37.40)
>consensus
__GUGGCUCCGUGGGCCGCCUUUGAAAUAAAUCUCUCGAGUCGCUGCGGUUGCUUUUUAUGCGCAGCGCCAUUGUGUCCUUAAAAUUUAAAAUGACAUUCUGUGGCCCACUGGCUGGC__
...(((((..(((((((((....................(.(((((((.............))))))).)...(((((.((.........)).)))))...))))))))).))))).... (-35.35 = -34.99 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:50 2006