Locus 1492

Sequence ID X_DroMel_CAF1
Location 4,423,437 – 4,423,674
Length 237
Max. P 0.999824
window2393 window2394 window2395 window2396 window2397

overview

Window 3

Location 4,423,437 – 4,423,554
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.97
Mean single sequence MFE -31.58
Consensus MFE -31.54
Energy contribution -31.54
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 1.00
SVM decision value 4.17
SVM RNA-class probability 0.999824
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4423437 117 + 22224390
---AUGCAUUCACAAUUGCCCACUGGUGACAUAAUCCACUGGCAGCAGCCAACACAUUUUCUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAAUAUCCUGAAAGAGGUCAAGUG
---..(((........)))...(..((((((.(((....((((....))))....)))...))))))..).....(((((((.((((...((............))...))))))))))) ( -31.40)
>DroSec_CAF1 25832 120 + 1
CAUAUGCAUUCACAAUUGCCCACUGGUGACAUAAUCCACUGGCAGCAGCCAACACAUUUUCUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAACAUCCUGAAAGAGGUCAAGUG
.....(((........)))...(..((((((.(((....((((....))))....)))...))))))..).....(((((((.((((...((............))...))))))))))) ( -31.40)
>DroSim_CAF1 27161 117 + 1
---AUGCAUUCACAAUUGCCCACUGGUGACAUAAUCCACUGGCAGCAGCCAACACAUUUUCUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAACAUCCUGAAAGAGGUCAAGUG
---..(((........)))...(..((((((.(((....((((....))))....)))...))))))..).....(((((((.((((...((............))...))))))))))) ( -31.40)
>DroEre_CAF1 26767 117 + 1
---AUGCAUUCACAAUUGCCCACUGGUGACAUAAUCCACUGGCAGCAGCCAACACAUUUUCUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAACAUCCUGAAAGAGGUCAAGUG
---..(((........)))...(..((((((.(((....((((....))))....)))...))))))..).....(((((((.((((...((............))...))))))))))) ( -31.40)
>DroYak_CAF1 26418 117 + 1
---AUGCAUUCGCAAUUGCCCACUGGUGACAUAAUCCACUGGCAGCAGCCAACACAUUUUUUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAACAUCCUGAAAGAGGUCAAGUG
---.(((....)))........(..((((((.(((....((((....))))....)))...))))))..).....(((((((.((((...((............))...))))))))))) ( -32.30)
>consensus
___AUGCAUUCACAAUUGCCCACUGGUGACAUAAUCCACUGGCAGCAGCCAACACAUUUUCUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAACAUCCUGAAAGAGGUCAAGUG
.....(((........)))...(..((((((.(((....((((....))))....)))...))))))..).....(((((((.((((...((............))...))))))))))) (-31.54 = -31.54 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,423,437 – 4,423,554
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.97
Mean single sequence MFE -39.68
Consensus MFE -39.70
Energy contribution -39.54
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.92
Structure conservation index 1.00
SVM decision value 2.90
SVM RNA-class probability 0.997630
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4423437 117 - 22224390
CACUUGACCUCUUUCAGGAUAUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAGAAAAUGUGUUGGCUGCUGCCAGUGGAUUAUGUCACCAGUGGGCAAUUGUGAAUGCAU---
((((((((((((..(((.(......).)))..))))).))))))).(((..(.((((((...(((.(..((((....))))..).))).))))))..)..)))..............--- ( -39.50)
>DroSec_CAF1 25832 120 - 1
CACUUGACCUCUUUCAGGAUGUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAGAAAAUGUGUUGGCUGCUGCCAGUGGAUUAUGUCACCAGUGGGCAAUUGUGAAUGCAUAUG
((((((((((((..(((.(......).)))..))))).))))))).(((..(.((((((...(((.(..((((....))))..).))).))))))..)..)))...((((....)))).. ( -40.00)
>DroSim_CAF1 27161 117 - 1
CACUUGACCUCUUUCAGGAUGUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAGAAAAUGUGUUGGCUGCUGCCAGUGGAUUAUGUCACCAGUGGGCAAUUGUGAAUGCAU---
((((((((((((..(((.(......).)))..))))).))))))).(((..(.((((((...(((.(..((((....))))..).))).))))))..)..)))..............--- ( -39.50)
>DroEre_CAF1 26767 117 - 1
CACUUGACCUCUUUCAGGAUGUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAGAAAAUGUGUUGGCUGCUGCCAGUGGAUUAUGUCACCAGUGGGCAAUUGUGAAUGCAU---
((((((((((((..(((.(......).)))..))))).))))))).(((..(.((((((...(((.(..((((....))))..).))).))))))..)..)))..............--- ( -39.50)
>DroYak_CAF1 26418 117 - 1
CACUUGACCUCUUUCAGGAUGUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAAAAAAUGUGUUGGCUGCUGCCAGUGGAUUAUGUCACCAGUGGGCAAUUGCGAAUGCAU---
..(((((......)))))......((((..(((((((..(....)..)))))))..))))...(((((((.((...(((((.(((.........))).).))))...)).)))))))--- ( -39.90)
>consensus
CACUUGACCUCUUUCAGGAUGUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAGAAAAUGUGUUGGCUGCUGCCAGUGGAUUAUGUCACCAGUGGGCAAUUGUGAAUGCAU___
((((((((((((..(((.(......).)))..))))).))))))).(((..(.((((((...(((.(..((((....))))..).))).))))))..)..)))...(((....))).... (-39.70 = -39.54 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,423,474 – 4,423,594
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.97
Mean single sequence MFE -32.84
Consensus MFE -29.52
Energy contribution -30.86
Covariance contribution 1.34
Combinations/Pair 1.03
Mean z-score -1.44
Structure conservation index 0.90
SVM decision value 0.50
SVM RNA-class probability 0.760162
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4423474 120 + 22224390
GGCAGCAGCCAACACAUUUUCUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAAUAUCCUGAAAGAGGUCAAGUGAUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGCACCU
(((....)))((((((.....(((..((((((...(....)...))))))..))).............(((((((((....)))))).)))...))))))........((((....)))) ( -33.00)
>DroSec_CAF1 25872 117 + 1
GGCAGCAGCCAACACAUUUUCUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAACAUCCUGAAAGAGGUCAAGUGAUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGC---U
(((.(((.((...........(((..((((((...(....)...))))))..)))..(((((..(((..((((((((....)))))).)))))..))))).........)))))))---) ( -32.20)
>DroSim_CAF1 27198 117 + 1
GGCAGCAGCCAACACAUUUUCUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAACAUCCUGAAAGAGGUCAAGUGAUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGC---U
(((.(((.((...........(((..((((((...(....)...))))))..)))..(((((..(((..((((((((....)))))).)))))..))))).........)))))))---) ( -32.20)
>DroEre_CAF1 26804 117 + 1
GGCAGCAGCCAACACAUUUUCUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAACAUCCUGAAAGAGGUCAAGUGAUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGC---U
(((.(((.((...........(((..((((((...(....)...))))))..)))..(((((..(((..((((((((....)))))).)))))..))))).........)))))))---) ( -32.20)
>DroYak_CAF1 26455 117 + 1
GGCAGCAGCCAACACAUUUUUUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAACAUCCUGAAAGAGGUCAAGUGAUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGC---C
(((.(((.((..........((((..((((((...(....)...))))))..)))).(((((..(((..((((((((....)))))).)))))..))))).........)))))))---) ( -34.60)
>consensus
GGCAGCAGCCAACACAUUUUCUGUCACUGGAGACGCACUUGAACCUCCAGCAACAACAACAUCCUGAAAGAGGUCAAGUGAUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGC___U
(((....))).......(((((......)))))(((((((((......((((.(((((......))..(((((((((....)))))).)))..)))))))......)))))))))..... (-29.52 = -30.86 +   1.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,423,474 – 4,423,594
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.97
Mean single sequence MFE -37.08
Consensus MFE -35.96
Energy contribution -35.80
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.20
Structure conservation index 0.97
SVM decision value 0.30
SVM RNA-class probability 0.677919
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4423474 120 - 22224390
AGGUGCGCACCUGAUGAGAAAACACAAUGAGAUGGCCAAUCACUUGACCUCUUUCAGGAUAUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAGAAAAUGUGUUGGCUGCUGCC
.((((.((..((.((...........)).))..(((((((..(((((......)))))(((((.((((..(((((((..(....)..)))))))..))))..)))))))))))))))))) ( -36.50)
>DroSec_CAF1 25872 117 - 1
A---GCGCACCUGAUGAGAAAACACAAUGAGAUGGCCAAUCACUUGACCUCUUUCAGGAUGUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAGAAAAUGUGUUGGCUGCUGCC
(---((((((((((.((((.....(((.(.(((.....))).))))...)))))))))......((((..(((((((..(....)..)))))))..))))....))))))(((....))) ( -36.90)
>DroSim_CAF1 27198 117 - 1
A---GCGCACCUGAUGAGAAAACACAAUGAGAUGGCCAAUCACUUGACCUCUUUCAGGAUGUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAGAAAAUGUGUUGGCUGCUGCC
(---((((((((((.((((.....(((.(.(((.....))).))))...)))))))))......((((..(((((((..(....)..)))))))..))))....))))))(((....))) ( -36.90)
>DroEre_CAF1 26804 117 - 1
A---GCGCACCUGAUGAGAAAACACAAUGAGAUGGCCAAUCACUUGACCUCUUUCAGGAUGUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAGAAAAUGUGUUGGCUGCUGCC
(---((((((((((.((((.....(((.(.(((.....))).))))...)))))))))......((((..(((((((..(....)..)))))))..))))....))))))(((....))) ( -36.90)
>DroYak_CAF1 26455 117 - 1
G---GCGCACCUGAUGAGAAAACACAAUGAGAUGGCCAAUCACUUGACCUCUUUCAGGAUGUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAAAAAAUGUGUUGGCUGCUGCC
(---((((..((.((...........)).))..((((((.(((..(((.(((....))).))).((((..(((((((..(....)..)))))))..)))).....))))))))))).))) ( -38.20)
>consensus
A___GCGCACCUGAUGAGAAAACACAAUGAGAUGGCCAAUCACUUGACCUCUUUCAGGAUGUUGUUGUUGCUGGAGGUUCAAGUGCGUCUCCAGUGACAGAAAAUGUGUUGGCUGCUGCC
....((((((((((.((((.....(((.(.(((.....))).))))...)))))))))......((((..(((((((..(....)..)))))))..))))....))))).(((....))) (-35.96 = -35.80 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 4,423,554 – 4,423,674
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.12
Mean single sequence MFE -33.56
Consensus MFE -33.10
Energy contribution -33.34
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.12
Structure conservation index 0.99
SVM decision value 0.27
SVM RNA-class probability 0.662094
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4423554 120 + 22224390
AUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGCACCUGAGAGGGCCUAAAGUCCAAAAACUCCGAGUGCCAAGUGGUUGGGCCCAAAGAAAUAUGAUACGCAACAUUGUGUAUGCAU
...((((...(((((.......(((.((((((....)))))))))(((((..(((......)))...)).))).)))))...)))).........((((((((((....))))))).))) ( -35.90)
>DroSec_CAF1 25952 117 + 1
AUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGC---UCAGAGGGCCUAAAGCCCAAAAACUCCGAGUGCCAAGUGGUUGGGCCCAAAGAAAUAUGAUACGCAACAUUGUGUAUGCAU
...((((...((((((((......)))...(.((((---((.((((((.....))))......)).))))))).)))))...)))).........((((((((((....))))))).))) ( -32.40)
>DroSim_CAF1 27278 117 + 1
AUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGC---UGAGAGGGCCUAAAGUCCAAAAACUCCGAGUGCCAAGUGGUUGGGCCCAAAGAAAUAUGAUACGCAACAUUGUGUAUGCAU
...((((.(((((.((..(((.......)))..)).---))))).))))....((((((..(((..(....)..)))..))))))..........((((((((((....))))))).))) ( -33.40)
>DroEre_CAF1 26884 117 + 1
AUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGC---UGAGAGGGCCUAAAGUCCAAAAACUCCGAGUGCAAAGUGGUUGGGCCCAAAGAAAUAUGAUACGCAACAUUGUGUAUGCAU
...((((.(((((.((..(((.......)))..)).---))))).))))....((((((..(((..(....)..)))..))))))..........((((((((((....))))))).))) ( -33.30)
>DroYak_CAF1 26535 117 + 1
AUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGC---CGAGAGGGCCUAAAGUCCAAAAACUCCGAGUGCAAAGUGGUUGGGCUCAAAGAAAUAUGAUACGCAACAUUGUGUAUGCAU
...((((.((((...((((..(((....))).))))---.)))).))))...(((((((..(((..(....)..)))..))))))).........((((((((((....))))))).))) ( -32.80)
>consensus
AUUGGCCAUCUCAUUGUGUUUUCUCAUCAGGUGCGC___UGAGAGGGCCUAAAGUCCAAAAACUCCGAGUGCCAAGUGGUUGGGCCCAAAGAAAUAUGAUACGCAACAUUGUGUAUGCAU
...((((.(((((..((((..(((....))).))))...))))).))))....((((((..(((..(....)..)))..))))))..........((((((((((....))))))).))) (-33.10 = -33.34 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:58 2006