Locus 4198

Sequence ID X_DroMel_CAF1
Location 11,016,714 – 11,016,870
Length 156
Max. P 0.724516
window6901 window6902

overview

Window 1

Location 11,016,714 – 11,016,833
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 89.44
Mean single sequence MFE -33.72
Consensus MFE -26.97
Energy contribution -28.17
Covariance contribution 1.20
Combinations/Pair 1.20
Mean z-score -2.35
Structure conservation index 0.80
SVM decision value 0.28
SVM RNA-class probability 0.667536
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11016714 119 - 22224390
GCUUAUUUUGCUUUCGCCUUCGUUUUCACUCAGUUCAAGUGUUUUGCAUUUUAUGCUUGGCACAAGAAUCAAGUGGAA-UGUGAAUGGCCAAGAGGGUGAGAACCUUAAAAAUACCGUAU
.....(((..(((((((((((..(((((((..((((..(((((..((((...))))..)))))..))))..)))))))-...))).)))...)))))..))).................. ( -33.80)
>DroSec_CAF1 9469 119 - 1
GCUUAUUUUACUGUCGCCUUCGUUUCCACUCAGUUCAAGUGUUUUGCAUUUUAUGCUUGGCACAAGAAUCAAGUGGAA-UGUGAAUGGACAACAGAGUGAGAACCUUAAAAAUACCGUAU
.((((((((..((((.(.(((..(((((((..((((..(((((..((((...))))..)))))..))))..)))))))-...))).)))))..))))))))................... ( -35.00)
>DroSim_CAF1 5173 118 - 1
GCUUAUUUUGCUUUCGCCUUCGUUUCCACUCAGUUCAAGUGUUUUGCAUUUUAUGCUUGGCACAAGAAUCAAGUGGAA-UGUGAAUGGACAAAAGAGUGAGAACCUUAAAAA-ACCGUAU
.((((((((.......(((((..(((((((..((((..(((((..((((...))))..)))))..))))..)))))))-...))).)).....))))))))...........-....... ( -31.90)
>DroEre_CAF1 3329 119 - 1
GCUUAUUUUGCUUUCGCCUUCGUUUCCACUCAGUUCAAGUGUUUUGCAUUUUAUGCUUGGCACGAGGAGCAAGUGGAA-UGCGAAUGGCCAAGAGGGUGAGAACCUAAAAAAUACCCUAU
.....(((..((((((((((((((((((((..((((..(((((..((((...))))..)))))...)))).)))))))-.))))).)))...)))))..))).................. ( -41.70)
>DroYak_CAF1 4622 119 - 1
GCUUAUUUUGCUUUCGCCUUCGUUUCCACUCAGUUCAAGUGUUUUGCAUUUUAUGCUUGGCACAAGAAACAAGUGGAA-UGUGAAUGGCCAGGAGGGUGAGAACCUUAAAAAUACCCUAU
.....(((..(((((((((((..(((((((...(((..(((((..((((...))))..)))))..)))...)))))))-...))).)))...)))))..))).................. ( -34.90)
>DroAna_CAF1 4108 120 - 1
GCUUAUUUUGCUUUCGCCUUCGUUUCCACUCAGUUCAAGUGUUUUGCAUUUUCUGCUUGGCACAAGAAUCAAGUGAGACCAUAAAUUGGAGAGUGUGUUUUGACUUUAUUAAUACCCUGU
.........((((((......(((((.(((..((((..(((((..(((.....)))..)))))..))))..))))))))((.....))))))))(((((...........)))))..... ( -25.00)
>consensus
GCUUAUUUUGCUUUCGCCUUCGUUUCCACUCAGUUCAAGUGUUUUGCAUUUUAUGCUUGGCACAAGAAUCAAGUGGAA_UGUGAAUGGCCAAGAGGGUGAGAACCUUAAAAAUACCCUAU
.....((((((((((.((((((.(((((((..((((..(((((..(((.....)))..)))))..))))..)))))))...)))).))....)))))))))).................. (-26.97 = -28.17 +   1.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,016,754 – 11,016,870
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.85
Mean single sequence MFE -22.02
Consensus MFE -17.59
Energy contribution -18.45
Covariance contribution 0.86
Combinations/Pair 1.11
Mean z-score -1.74
Structure conservation index 0.80
SVM decision value 0.41
SVM RNA-class probability 0.724516
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11016754 116 + 22224390
A-UUCCACUUGAUUCUUGUGCCAAGCAUAAAAUGCAAAACACUUGAACUGAGUGAAAACGAAGGCGAAAGCAAAAUAAGCAACAACAAAAUGUCUCA-UAAACCAAC--CAGAUGCAGUG
.-...(((((..(((..(((....((((...))))....)))..)))..))))).........((....))..............((...(((.((.-.........--..)).))).)) ( -19.70)
>DroSec_CAF1 9509 118 + 1
A-UUCCACUUGAUUCUUGUGCCAAGCAUAAAAUGCAAAACACUUGAACUGAGUGGAAACGAAGGCGACAGUAAAAUAAGCAACAACAAAAUGUCUCA-UAAACCAAACCAAGAUGCAGUG
.-((((((((..(((..(((....((((...))))....)))..)))..))))))))......(.((((.....................)))).).-...................... ( -22.20)
>DroEre_CAF1 3369 115 + 1
A-UUCCACUUGCUCCUCGUGCCAAGCAUAAAAUGCAAAACACUUGAACUGAGUGGAAACGAAGGCGAAAGCAAAAUAAGCAGCAACAAAAUGUCUCA-UAAACCAA---CAGAUGCAGUG
.-...((((((((.(((((..(..((((...))))....(((((.....))))))..))))..((....)).......).))))).....(((.((.-........---..)).)))))) ( -21.80)
>DroYak_CAF1 4662 115 + 1
A-UUCCACUUGUUUCUUGUGCCAAGCAUAAAAUGCAAAACACUUGAACUGAGUGGAAACGAAGGCGAAAGCAAAAUAAGCAACAACAAAAUGUCUCA-UAAACCAA---CAGAUGCACUG
.-((((((((..(((..(((....((((...))))....)))..)))..))))))))......((....))...................(((.((.-........---..)).)))... ( -24.30)
>DroMoj_CAF1 4304 99 + 1
--GUUGUCUUUUAUCUUGUGAAAAGCAUGAAAUGCAAAACACUUGAACUGAGUGGAAAUGAAGGCGAAAGCAAAAUAAGUAACAAAACAA----------------GACAAGAAG---CG
--...(..((((.((((((.....((((...)))).....(((((..((..((....))..))((....))....)))))......))))----------------)).))))..---). ( -21.20)
>DroAna_CAF1 4148 120 + 1
GGUCUCACUUGAUUCUUGUGCCAAGCAGAAAAUGCAAAACACUUGAACUGAGUGGAAACGAAGGCGAAAGCAAAAUAAGCAACAACAAAAUGUCUUUCUUAACAAACACCAGAAGCACUG
(((.((((((..(((..(((....(((.....)))....)))..)))..))))))........((....))....((((.((..((.....))..))))))......))).......... ( -22.90)
>consensus
A_UUCCACUUGAUUCUUGUGCCAAGCAUAAAAUGCAAAACACUUGAACUGAGUGGAAACGAAGGCGAAAGCAAAAUAAGCAACAACAAAAUGUCUCA_UAAACCAA___CAGAUGCAGUG
..((((((((..(((..(((....(((.....)))....)))..)))..))))))))......((....))................................................. (-17.59 = -18.45 +   0.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:58 2006