Locus 5438

Sequence ID 2L_DroMel_CAF1
Location 15,486,416 – 15,486,522
Length 106
Max. P 0.990426
window8634 window8635

overview

Window 4

Location 15,486,416 – 15,486,522
Length 106
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 88.66
Mean single sequence MFE -36.56
Consensus MFE -33.62
Energy contribution -34.46
Covariance contribution 0.84
Combinations/Pair 1.09
Mean z-score -1.95
Structure conservation index 0.92
SVM decision value 2.21
SVM RNA-class probability 0.990426
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15486416 106 + 22407834
GGGAUGCCGAGGAUUCCAAGGAUACC-------------ACGGAAUACCAAGCAUUCCAACGAUAUAUGAACCAGCAGCUCAGUGCGCACGCUUAUGUUGGCCUGGAACUUUUGGCAUU
..(((((((((..(((((.((.....-------------..(((((.......))))).............((((((....((((....))))..)))))))))))))..))))))))) ( -34.10)
>DroSec_CAF1 225095 106 + 1
GGGAUGCCGAGGAUUCCAAGGAUACC-------------AAGGAAUGCCAAGCAUUCCAACGAUAUAUGAACCAGCAGCUCAGUGCGCACGCUUAUGUUGGCCUGGAACUUUUGGCAUU
..(((((((((..(((((.((.....-------------..(((((((...))))))).............((((((....((((....))))..)))))))))))))..))))))))) ( -39.40)
>DroSim_CAF1 231492 106 + 1
GGGAUGCCGAGGAUUCCAAGGAUACC-------------AAGGAAUGCCAAGCAUUCCAACGAUAUAUGAACCAGCAGCUCAGUGCGCACGCUUAUGUUGGCCUGGAACUUUUGGCAUU
..(((((((((..(((((.((.....-------------..(((((((...))))))).............((((((....((((....))))..)))))))))))))..))))))))) ( -39.40)
>DroEre_CAF1 234947 105 + 1
GGGAUGCCAAGGAUUCCAAGGAUACC-------------GAGG-CAGCCUGGCAUUCCAACCAUAUAGGAACCAGCAGCUCAGUGCGCACGCUUAUGUUGGCCUGGAACUUUUGGCAUU
..(((((((((..((((..((...))-------------.(((-(...((((..((((.........))))))))((((..((((....))))...))))))))))))..))))))))) ( -35.80)
>DroYak_CAF1 234132 118 + 1
GGGAUACCACGGAUUCCGAGGAUACCAACCAAGGCUUCCAAGG-AUGCCAGGCAUUCCAACGAUACUUGAAUCAGCAGCUCAGUGCGCACGCUUAUGUUGGCCUGGAACUUUUGGCAUU
(((((.(....))))))..(((..((......))..)))...(-((((((((..(((((..(((......)))..((((..((((....))))...))))...)))))..))))))))) ( -34.10)
>consensus
GGGAUGCCGAGGAUUCCAAGGAUACC_____________AAGGAAUGCCAAGCAUUCCAACGAUAUAUGAACCAGCAGCUCAGUGCGCACGCUUAUGUUGGCCUGGAACUUUUGGCAUU
..(((((((((..(((((.((....................(((((((...))))))).............((((((....((((....))))..)))))))))))))..))))))))) (-33.62 = -34.46 +   0.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,486,416 – 15,486,522
Length 106
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 88.66
Mean single sequence MFE -35.54
Consensus MFE -27.06
Energy contribution -26.90
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -1.72
Structure conservation index 0.76
SVM decision value 0.35
SVM RNA-class probability 0.701871
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15486416 106 - 22407834
AAUGCCAAAAGUUCCAGGCCAACAUAAGCGUGCGCACUGAGCUGCUGGUUCAUAUAUCGUUGGAAUGCUUGGUAUUCCGU-------------GGUAUCCUUGGAAUCCUCGGCAUCCC
.(((((....(((((((((((((....((....))..(((((.....)))))......))))).((((((((....))).-------------))))).))))))))....)))))... ( -32.50)
>DroSec_CAF1 225095 106 - 1
AAUGCCAAAAGUUCCAGGCCAACAUAAGCGUGCGCACUGAGCUGCUGGUUCAUAUAUCGUUGGAAUGCUUGGCAUUCCUU-------------GGUAUCCUUGGAAUCCUCGGCAUCCC
.(((((....((((((((..(((...((((.((.......)))))).)))...((((((..(((((((...))))))).)-------------))))).))))))))....)))))... ( -34.40)
>DroSim_CAF1 231492 106 - 1
AAUGCCAAAAGUUCCAGGCCAACAUAAGCGUGCGCACUGAGCUGCUGGUUCAUAUAUCGUUGGAAUGCUUGGCAUUCCUU-------------GGUAUCCUUGGAAUCCUCGGCAUCCC
.(((((....((((((((..(((...((((.((.......)))))).)))...((((((..(((((((...))))))).)-------------))))).))))))))....)))))... ( -34.40)
>DroEre_CAF1 234947 105 - 1
AAUGCCAAAAGUUCCAGGCCAACAUAAGCGUGCGCACUGAGCUGCUGGUUCCUAUAUGGUUGGAAUGCCAGGCUG-CCUC-------------GGUAUCCUUGGAAUCCUUGGCAUCCC
.(((((((..((((((((.........((....))(((((((.(((((((((.........)))..)))).)).)-.)))-------------)))...))))))))..)))))))... ( -38.20)
>DroYak_CAF1 234132 118 - 1
AAUGCCAAAAGUUCCAGGCCAACAUAAGCGUGCGCACUGAGCUGCUGAUUCAAGUAUCGUUGGAAUGCCUGGCAU-CCUUGGAAGCCUUGGUUGGUAUCCUCGGAAUCCGUGGUAUCCC
.((((((...(((((((((((((...((((.((.......))))))(((......)))))))).(((((.(((.(-(....)).)))......)))))))).)))))...))))))... ( -38.20)
>consensus
AAUGCCAAAAGUUCCAGGCCAACAUAAGCGUGCGCACUGAGCUGCUGGUUCAUAUAUCGUUGGAAUGCUUGGCAUUCCUU_____________GGUAUCCUUGGAAUCCUCGGCAUCCC
.(((((....(((((((((((((...((((.((.......))))))(((......)))))))).(((((........................))))).))))))))....)))))... (-27.06 = -26.90 +  -0.16)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:12 2006