Locus 3452

Sequence ID 3R_DroMel_CAF1
Location 9,349,127 – 9,349,217
Length 90
Max. P 0.618037
window5539 window5540

overview

Window 9

Location 9,349,127 – 9,349,217
Length 90
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 78.56
Mean single sequence MFE -31.70
Consensus MFE -18.55
Energy contribution -18.72
Covariance contribution 0.17
Combinations/Pair 1.05
Mean z-score -1.59
Structure conservation index 0.59
SVM decision value 0.10
SVM RNA-class probability 0.583786
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9349127 90 + 27905053
---GAGGGGGCUUUG------GUAGUUUUAUUGGAGC--------------------ACCAUGGAGCGUCAGCUUCGACGCUGUUUCCCCUCGACGCUGACACUUGUUCAAUUCAAAUA
---((((((((((..------(((....)))..))))--------------------.......((((((......))))))....))))))((....(((....)))....))..... ( -30.80)
>DroPse_CAF1 113792 78 + 1
GCGGCGGGGGCCACG------G-----------------------------------GCUGCGGAGCGACAGCUUCGACGCUGUUUCCCCUCGACGCUGACACUUGUUCAAUUCAAAUA
(((.((((((..(((------(-----------------------------------.(..((((((....))))))..)))))..)))).)).)))...................... ( -28.60)
>DroSec_CAF1 118592 93 + 1
GUGGAGGGGGCAUCG------GUAGUUUUAUUGGAGC--------------------ACCAUGGAGCGUCAGCUUCGACGCUGUUUCCCCUCGACGCUGACACUUGUUCAAUUCAAAUA
((.((((((((((.(------((.((((.....))))--------------------)))))).((((((......))))))...))))))).))........................ ( -31.80)
>DroSim_CAF1 129847 93 + 1
GUGGAGGGGGCAUCG------GUAGUUUUAUUGGAGC--------------------ACCAUGGAGCGUCAGCUUCGACGCUGUUUCCCCUCGACGCUGACACUUGUUCAAUUCAAAUA
((.((((((((((.(------((.((((.....))))--------------------)))))).((((((......))))))...))))))).))........................ ( -31.80)
>DroEre_CAF1 118908 94 + 1
---A--GGGGCUUAUGUACGAGUAGUUCUAUUGGAGC--------------------ACCAUGGAGCGUCAGCUUCGACGCUGUUUCCCCUCGACGCUGACACUUGUUCAAUUCAAAUA
---.--........((.((((((.(((((((.((...--------------------.)))))))))((((((.((((.(........).)))).)))))))))))).))......... ( -29.70)
>DroYak_CAF1 119908 110 + 1
---ACGGGGGCUUAG------GUAGUUCCAUUGGAGCACCAUAGAGCAGCAUGGAGCACCAUGGAGCGUCAGCUUCGACGCUGUUUCCCCUCGACGCUGACACUUGUUCAAUUCAAAUA
---.((((((....(------((.(((((...))))))))...(((((((((((....))))(((((....)))))...))))))).)))))).......................... ( -37.50)
>consensus
___GAGGGGGCUUCG______GUAGUUUUAUUGGAGC____________________ACCAUGGAGCGUCAGCUUCGACGCUGUUUCCCCUCGACGCUGACACUUGUUCAAUUCAAAUA
.......((((.............((((.....))))..........................(((.((((((.((((.(........).)))).)))))).))))))).......... (-18.55 = -18.72 +   0.17)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,349,127 – 9,349,217
Length 90
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 78.56
Mean single sequence MFE -27.70
Consensus MFE -21.27
Energy contribution -21.43
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.01
Structure conservation index 0.77
SVM decision value 0.17
SVM RNA-class probability 0.618037
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9349127 90 - 27905053
UAUUUGAAUUGAACAAGUGUCAGCGUCGAGGGGAAACAGCGUCGAAGCUGACGCUCCAUGGU--------------------GCUCCAAUAAAACUAC------CAAAGCCCCCUC---
..((((.........(((((((((.((((.((....)..).)))).)))))))))...(((.--------------------...)))..........------))))........--- ( -25.40)
>DroPse_CAF1 113792 78 - 1
UAUUUGAAUUGAACAAGUGUCAGCGUCGAGGGGAAACAGCGUCGAAGCUGUCGCUCCGCAGC-----------------------------------C------CGUGGCCCCCGCCGC
((((((.......))))))...(((.((.((((..(((((......)))))....((((...-----------------------------------.------.)))))))))).))) ( -25.50)
>DroSec_CAF1 118592 93 - 1
UAUUUGAAUUGAACAAGUGUCAGCGUCGAGGGGAAACAGCGUCGAAGCUGACGCUCCAUGGU--------------------GCUCCAAUAAAACUAC------CGAUGCCCCCUCCAC
.......((((....(((((((((.((((.((....)..).)))).)))))))))...(((.--------------------...)))..........------))))........... ( -25.20)
>DroSim_CAF1 129847 93 - 1
UAUUUGAAUUGAACAAGUGUCAGCGUCGAGGGGAAACAGCGUCGAAGCUGACGCUCCAUGGU--------------------GCUCCAAUAAAACUAC------CGAUGCCCCCUCCAC
.......((((....(((((((((.((((.((....)..).)))).)))))))))...(((.--------------------...)))..........------))))........... ( -25.20)
>DroEre_CAF1 118908 94 - 1
UAUUUGAAUUGAACAAGUGUCAGCGUCGAGGGGAAACAGCGUCGAAGCUGACGCUCCAUGGU--------------------GCUCCAAUAGAACUACUCGUACAUAAGCCCC--U---
...............(((((((((.((((.((....)..).)))).)))))))))....((.--------------------(((......((.....)).......))).))--.--- ( -26.12)
>DroYak_CAF1 119908 110 - 1
UAUUUGAAUUGAACAAGUGUCAGCGUCGAGGGGAAACAGCGUCGAAGCUGACGCUCCAUGGUGCUCCAUGCUGCUCUAUGGUGCUCCAAUGGAACUAC------CUAAGCCCCCGU---
................((((((((.((((.((....)..).)))).))))))))(((((((.((.(((((......))))).)).)).))))).....------............--- ( -38.80)
>consensus
UAUUUGAAUUGAACAAGUGUCAGCGUCGAGGGGAAACAGCGUCGAAGCUGACGCUCCAUGGU____________________GCUCCAAUAAAACUAC______CGAAGCCCCCUC___
...............(((((((((.((((.((....)..).)))).)))))))))................................................................ (-21.27 = -21.43 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:21 2006