Locus 4398

Sequence ID 3L_DroMel_CAF1
Location 12,879,560 – 12,879,754
Length 194
Max. P 0.832845
window6819 window6820 window6821

overview

Window 9

Location 12,879,560 – 12,879,664
Length 104
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 93.40
Mean single sequence MFE -27.02
Consensus MFE -23.51
Energy contribution -23.27
Covariance contribution -0.25
Combinations/Pair 1.12
Mean z-score -1.43
Structure conservation index 0.87
SVM decision value 0.20
SVM RNA-class probability 0.632679
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12879560 104 - 23771897
UACAGCAAUGGAUGUGGAGUAUCCUGUGGAUACAUGUGUAUGGGAUGGCAUUGGAUAAUAGUGUCUUGCAGUCAAAGUGCGUGUAUGCAAGGAAUUAUCAAGUG
((((........))))((...((((.((.(((((((..(....(((.(((..(((((....)))))))).)))...)..))))))).))))))....))..... ( -26.90)
>DroSec_CAF1 6487 104 - 1
UACAGCAAUGGAAGUGGAGUAUCCUGUGGAUACAUGUGUAUGGGAUGGCAUUGGAUAAUAGUGUCUUGCAGUCAAAGUGCGUGUAUGCAAGGAAUUAUCAAGUG
..((....))......((...((((.((.(((((((..(....(((.(((..(((((....)))))))).)))...)..))))))).))))))....))..... ( -26.70)
>DroSim_CAF1 4046 104 - 1
UACAGCAAUGGAAGUGGAGUAUCCUGUGGAUACAUGUGUAUGGGAUGGCAUUGGAUAAUAGUGUCUUGCAGUCAAAGUGCGUGUAUGCAAGGAAUUAUCAAGUG
..((....))......((...((((.((.(((((((..(....(((.(((..(((((....)))))))).)))...)..))))))).))))))....))..... ( -26.70)
>DroEre_CAF1 9254 104 - 1
CACAGCAAUGGAAGUGGCGUAUCCUGUGGAUACAUGUGUAUGGGAUGGCAUUGGAUAAUAGUGUCUUGCAGUCAAAGUGCGUGUAUGCAAGGAAUUAUCAAGUG
(((.((.((....)).))...((((.((.(((((((..(....(((.(((..(((((....)))))))).)))...)..))))))).))))))........))) ( -27.70)
>DroYak_CAF1 5924 104 - 1
CACGGCAAUGGAAGUGGAGUAUCCUGUGGAUACAUGUGUACGGGAUGGCAUUGGAUAAUAGUGUCUUGCAGUCAAAGUGCGUGUAUGCAAGGAAUUAUCAAGUG
(((..(....)..)))((...((((.((.(((((((..(....(((.(((..(((((....)))))))).)))...)..))))))).))))))....))..... ( -27.70)
>DroAna_CAF1 31301 102 - 1
CAGAGCA--GGAGGUCGAGUAUCUGGCGGAUACAUGCGAAUACGAUGGCAAUGGAUAAUAGUGUCUUGCAGUCAAAGUGCGUGUAUGCAGGGAAUUACCAAGUG
....((.--(((.........))).))(.(((((((((.....(((.(((..(((((....)))))))).)))....))))))))).).((......))..... ( -26.40)
>consensus
CACAGCAAUGGAAGUGGAGUAUCCUGUGGAUACAUGUGUAUGGGAUGGCAUUGGAUAAUAGUGUCUUGCAGUCAAAGUGCGUGUAUGCAAGGAAUUAUCAAGUG
....(((...........((((((...))))))(..(((((..(((.(((..(((((....)))))))).)))...)))))..).)))................ (-23.51 = -23.27 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,879,624 – 12,879,719
Length 95
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 82.74
Mean single sequence MFE -27.30
Consensus MFE -20.30
Energy contribution -22.30
Covariance contribution 2.00
Combinations/Pair 1.12
Mean z-score -2.37
Structure conservation index 0.74
SVM decision value 0.72
SVM RNA-class probability 0.832845
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12879624 95 + 23771897
UACACAUGUAUCCACAGGAUACUCCACAUCCAUUGCUGUACGUACUCUGAUGCCCCUGGGCAUCUGGAGGCUUCUCGUCUGCGGCUUUGAAUUAU
.......((((((...))))))........((..((((((((..((((((((((....)))))).))))......)))..)))))..))...... ( -30.70)
>DroSec_CAF1 6551 95 + 1
UACACAUGUAUCCACAGGAUACUCCACUUCCAUUGCUGUACGUACUCUGAUGCCCCUGGGCAUAUGGAGCCUUCUCGUCUGCGGCUUUGAAUUAU
.......((((((...))))))........((..((((((((..((((((((((....))))).)))))......)))..)))))..))...... ( -26.80)
>DroSim_CAF1 4110 95 + 1
UACACAUGUAUCCACAGGAUACUCCACUUCCAUUGCUGUACGUACUCUGAUGCCCCUGGGCAUCUGGAGGCUUCCCGUCUGCGGCUUUGAAUUAU
.......((((((...))))))........((..((((((((..((((((((((....)))))).))))......)))..)))))..))...... ( -30.00)
>DroEre_CAF1 9318 95 + 1
UACACAUGUAUCCACAGGAUACGCCACUUCCAUUGCUGUGCGUACUCUGAUGCCCCUGGGCAUCUGGAGGCUGCUCGUCUGCGGCUUUGAAUUAU
..........((((.((..((((((((.......).)).)))))..))((((((....))))))))))((((((......))))))......... ( -32.50)
>DroYak_CAF1 5988 95 + 1
UACACAUGUAUCCACAGGAUACUCCACUUCCAUUGCCGUGAGUACUCUGAUGCCCCUGGGCAUCUGGAGGCUGUUCGGCUGCGGCUUUGAAUUAU
.......((((((...))))))........((..(((((.....((((((((((....)))))).))))(((....))).)))))..))...... ( -34.50)
>DroAna_CAF1 31365 73 + 1
UUCGCAUGUAUCCGCCAGAUACUCGACCUCC--UGCUCUG------CUCAUCCUCCUGA------------UUUUAUUC--UGGCUUUGAAUUAU
.............((((((.....((.(...--.).))..------.(((......)))------------......))--)))).......... (  -9.30)
>consensus
UACACAUGUAUCCACAGGAUACUCCACUUCCAUUGCUGUACGUACUCUGAUGCCCCUGGGCAUCUGGAGGCUUCUCGUCUGCGGCUUUGAAUUAU
.......(((((.....)))))........((..((((((((..((((((((((....)))))).))))......)))..)))))..))...... (-20.30 = -22.30 +   2.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,879,664 – 12,879,754
Length 90
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 78.83
Mean single sequence MFE -27.91
Consensus MFE -13.16
Energy contribution -13.75
Covariance contribution 0.59
Combinations/Pair 1.31
Mean z-score -2.14
Structure conservation index 0.47
SVM decision value 0.12
SVM RNA-class probability 0.593137
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12879664 90 + 23771897
CGUACUCUGAUGCCCCUGGGCAUCUGGAGGCUUCUCGUCUGCGGCUUUGAAUUAUUUAAAAUUGUUUUCUCACGC---C-CGCUUUUGCGGGUG
....((((((((((....)))))).))))(((.(......).)))...........................(((---(-(((....))))))) ( -31.00)
>DroSec_CAF1 6591 90 + 1
CGUACUCUGAUGCCCCUGGGCAUAUGGAGCCUUCUCGUCUGCGGCUUUGAAUUAUUUAAAAUUGUUUUCUCACGC---C-CGCUCUUGCGGGUG
.........(((((....)))))..((((((...........))))))........................(((---(-(((....))))))) ( -26.80)
>DroSim_CAF1 4150 90 + 1
CGUACUCUGAUGCCCCUGGGCAUCUGGAGGCUUCCCGUCUGCGGCUUUGAAUUAUUUAAAAUUGUUUUCUCACGC---C-CGCUCCUGCGGGUG
....((((((((((....)))))).)))).....(((....)))............................(((---(-(((....))))))) ( -31.80)
>DroEre_CAF1 9358 90 + 1
CGUACUCUGAUGCCCCUGGGCAUCUGGAGGCUGCUCGUCUGCGGCUUUGAAUUAUUUAAAAUUGUUUCCUCAUAC---C-CGCUCUUGUGGGUG
....((((((((((....)))))).))))(((((......)))))...........................(((---(-(((....))))))) ( -33.60)
>DroYak_CAF1 6028 93 + 1
AGUACUCUGAUGCCCCUGGGCAUCUGGAGGCUGUUCGGCUGCGGCUUUGAAUUAUUUAAAACUGUUUCGCCACACCCCC-CGCUCUUCUGGGUG
(((.((((((((((....)))))).)))))))....(((.((((.(((((.....))))).))))...))).(((((..-.........))))) ( -31.60)
>DroAna_CAF1 31403 71 + 1
------CUCAUCCUCCUGA------------UUUUAUUC--UGGCUUUGAAUUAUUUAAAAUUGUUUCUUGCCGC---CACACUUUGUUGGGGG
------......((((..(------------(.......--((((...(((.((........)).)))..)))).---........))..)))) ( -12.69)
>consensus
CGUACUCUGAUGCCCCUGGGCAUCUGGAGGCUUCUCGUCUGCGGCUUUGAAUUAUUUAAAAUUGUUUCCUCACGC___C_CGCUCUUGCGGGUG
....((((((((((....)))))).))))....(((((..(((..(((((.....)))))..(((......)))......)))....))))).. (-13.16 = -13.75 +   0.59)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:41 2006