Locus 1619

Sequence ID 3L_DroMel_CAF1
Location 4,746,370 – 4,746,505
Length 135
Max. P 0.897812
window2502 window2503

overview

Window 2

Location 4,746,370 – 4,746,473
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.80
Mean single sequence MFE -43.34
Consensus MFE -35.46
Energy contribution -34.54
Covariance contribution -0.92
Combinations/Pair 1.17
Mean z-score -1.42
Structure conservation index 0.82
SVM decision value 0.03
SVM RNA-class probability 0.550332
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4746370 103 - 23771897
-----GCUUCCUU------------GGAGCUUGGCUCCGGGGACAGGAGUCGCGUGCGUCGCAUCAGGUCGUAGGGAUCCUUCUGCGGAUCCAGAAUGGAGGGACGUGAUUUUUUCGUCG
-----...(((((------------(((((...)))))))))).(((((((((((.(.((.(((....((....((((((......)))))).))))))).).)))))))))))...... ( -42.90)
>DroPse_CAF1 19714 120 - 1
UGGGGGUGUCCUUGCUGGUGACACUGGCACUCGGCUCCGGCGAUAGGAGUCGCGUGCGUCGCAUCAGGUCGUAGGGAUCCUUCUGUGGAUCCAGAAUGGAGGGACGUGAUUUCUUUGUGG
.(..(.(((((((.((((((..((..((((.(((((((.......))))))).))))))..)))))).((((..((((((......))))))...)))))))))))...)..)....... ( -48.30)
>DroSec_CAF1 6605 103 - 1
-----GCUUCCUU------------GGAGCUUGGCUCUGGGGACAGGAGUCGCGUGCGUCGCAUCAGGUCGUAGGGAUCCUUCUGCGGAUCCAGAAUGGAGGGACGUGAUUUUUUCGUCG
-----...((((.------------.((((...))))..)))).(((((((((((.(.((.(((....((....((((((......)))))).))))))).).)))))))))))...... ( -41.20)
>DroSim_CAF1 7167 103 - 1
-----GCUUCCUU------------GGAGCUUGGCUCUGGGGACAGGAGUCGCGUGCGUCGCAUCAGGUCGUAGGGAUCCUUCUGCGGAUCCAGAAUGGAGGGACGUGAUUUUUUCGCCG
-----((.((((.------------.((((...))))..)))).(((((((((((.(.((.(((....((....((((((......)))))).))))))).).)))))))))))..)).. ( -42.30)
>DroYak_CAF1 5421 103 - 1
-----GCGUCCUU------------GGAGCUUGGCUCCGGCGACAGGAGUCGCGUGCGUCGCAUCAGGUCAUAGGGAUCCUUCUGCGGAUCCAGAAUGGAGGGACGUGAUUUCUUUGUCG
-----........------------(((((...)))))(((((.(((((((((((.(.((.(((....((....((((((......)))))).))))))).).)))))))))))))))). ( -42.00)
>consensus
_____GCUUCCUU____________GGAGCUUGGCUCCGGGGACAGGAGUCGCGUGCGUCGCAUCAGGUCGUAGGGAUCCUUCUGCGGAUCCAGAAUGGAGGGACGUGAUUUUUUCGUCG
.....(((((...............))))).((((((((....).)))))))...(((((.(..((..((....((((((......)))))).)).))..).)))))............. (-35.46 = -34.54 +  -0.92)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,746,410 – 4,746,505
Length 95
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.52
Mean single sequence MFE -44.74
Consensus MFE -34.47
Energy contribution -34.75
Covariance contribution 0.28
Combinations/Pair 1.10
Mean z-score -2.06
Structure conservation index 0.77
SVM decision value 1.00
SVM RNA-class probability 0.897812
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4746410 95 - 23771897
----CCGUUUCACUGCGACUACGUGACUUGCUGUCC---------GCUUCCUU------------GGAGCUUGGCUCCGGGGACAGGAGUCGCGUGCGUCGCAUCAGGUCGUAGGGAUCC
----.........((((((((((((((((.((((((---------.(......------------(((((...)))))).)))))))))))))))).))))))...((((.....)))). ( -43.40)
>DroPse_CAF1 19754 117 - 1
GUGGCCGUUUC---GCGGCUACGUGACUUUCCCUCCUUGCUGGGGGUGUCCUUGCUGGUGACACUGGCACUCGGCUCCGGCGAUAGGAGUCGCGUGCGUCGCAUCAGGUCGUAGGGAUCC
(((((((....---.)))))))(((((...(((........)))((((((((....)).)))))).((((.(((((((.......))))))).)))))))))....((((.....)))). ( -54.70)
>DroSec_CAF1 6645 95 - 1
----CCGUUUCACUGCGACUACGUGACUUGCUGUCC---------GCUUCCUU------------GGAGCUUGGCUCUGGGGACAGGAGUCGCGUGCGUCGCAUCAGGUCGUAGGGAUCC
----.........((((((((((((((((.((((((---------.(......------------(((((...)))))).)))))))))))))))).))))))...((((.....)))). ( -41.70)
>DroSim_CAF1 7207 95 - 1
----CCGUUUCACUGCGACUACGUGACUUGCUGUCC---------GCUUCCUU------------GGAGCUUGGCUCUGGGGACAGGAGUCGCGUGCGUCGCAUCAGGUCGUAGGGAUCC
----.........((((((((((((((((.((((((---------.(......------------(((((...)))))).)))))))))))))))).))))))...((((.....)))). ( -41.70)
>DroYak_CAF1 5461 95 - 1
----CCGUUUCGCUGCGACUACGUGACUUGCUGUCC---------GCGUCCUU------------GGAGCUUGGCUCCGGCGACAGGAGUCGCGUGCGUCGCAUCAGGUCAUAGGGAUCC
----.......(.((((((((((((((((.(((((.---------((.....(------------(((((...))))))))))))))))))))))).)))))).).((((.....)))). ( -42.20)
>consensus
____CCGUUUCACUGCGACUACGUGACUUGCUGUCC_________GCUUCCUU____________GGAGCUUGGCUCCGGGGACAGGAGUCGCGUGCGUCGCAUCAGGUCGUAGGGAUCC
..............(((((((((((((((.((((((.........(((((...............)))))..........)))))))))))))))).)))))....((((.....)))). (-34.47 = -34.75 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:02 2006