Locus 8076

Sequence ID 3L_DroMel_CAF1
Location 21,268,945 – 21,269,105
Length 160
Max. P 0.972766
window13192 window13193 window13194 window13195

overview

Window 2

Location 21,268,945 – 21,269,065
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.92
Mean single sequence MFE -32.35
Consensus MFE -24.89
Energy contribution -25.82
Covariance contribution 0.94
Combinations/Pair 1.10
Mean z-score -2.90
Structure conservation index 0.77
SVM decision value 1.70
SVM RNA-class probability 0.972766
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21268945 120 + 23771897
AAUACAACAGUUGUUAGCAGCUGCUAACUCACAUACUCACCACUGCUGUUAAGCGCUACAGGCGAUGUUUUGCAAAACAUCGCCCAACAUCGAUAUCAAGAGAAACGUCGAGCUAUCGAG
.........((.((((((....))))))..))...(((......(((....)))((....((((((((((....)))))))))).....(((((.((....))...)))))))....))) ( -32.60)
>DroSec_CAF1 27233 120 + 1
AACACAACAGCUGUUAUCAGCUGCUUACUCAUAUACUCACCUCUGCUGUUAAGCGCUACAGACGAUGUUUUGCAAAAUAUCGCCCAACAUCGAUAUCAAGAGAAACGUCGUGUUAUCGAG
(((((..((((((....)))))).................(((((((....)))........(((((((..((........))..)))))))......)))).......)))))...... ( -30.40)
>DroSim_CAF1 29485 120 + 1
AACACAACAGCUGUUAUCAGCUGCUUACUCAUAUACUCACCUCUGCUGUUAAGCGCUACAGACGAUGUUUUGCAAAACAUCGCCCAACAUCGAUAUCAAGAGAAACGUCGUGUUAUCGAG
(((((..((((((....)))))).................(((((((....)))........(((((((..((........))..)))))))......)))).......)))))...... ( -30.40)
>DroEre_CAF1 28408 118 + 1
CA-AGUACCGCUGUUAGCAGCUGCGUUCCAACAUACUCACCACUGCUGUUAAGU-CUACAGGCGAUGUUUUGCAAAACAUCGCCUAACAUCGAUAUCAACAAUAACAUUGAGAUAUCGAG
..-.(((..(((..((((((.((.((........)).))...))))))...)))-.)))(((((((((((....)))))))))))....((((((((..((((...)))).)))))))). ( -36.00)
>consensus
AACACAACAGCUGUUAGCAGCUGCUUACUCACAUACUCACCACUGCUGUUAAGCGCUACAGACGAUGUUUUGCAAAACAUCGCCCAACAUCGAUAUCAAGAGAAACGUCGAGUUAUCGAG
.......((((((....)))))).....................(((....)))......((((((((((....)))))))))).....((((((.((.((......)).)).)))))). (-24.89 = -25.82 +   0.94)

alignment

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secondary structure

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Window 3

Location 21,268,945 – 21,269,065
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.92
Mean single sequence MFE -38.88
Consensus MFE -28.12
Energy contribution -29.25
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -2.55
Structure conservation index 0.72
SVM decision value 1.08
SVM RNA-class probability 0.912590
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21268945 120 - 23771897
CUCGAUAGCUCGACGUUUCUCUUGAUAUCGAUGUUGGGCGAUGUUUUGCAAAACAUCGCCUGUAGCGCUUAACAGCAGUGGUGAGUAUGUGAGUUAGCAGCUGCUAACAACUGUUGUAUU
......(((((((..((......))..)))).((((((((((((((....)))))))))))..))))))..((((((((.((.(((((((......)))..)))).)).))))))))... ( -38.20)
>DroSec_CAF1 27233 120 - 1
CUCGAUAACACGACGUUUCUCUUGAUAUCGAUGUUGGGCGAUAUUUUGCAAAACAUCGUCUGUAGCGCUUAACAGCAGAGGUGAGUAUAUGAGUAAGCAGCUGAUAACAGCUGUUGUGUU
......(((((((((((((((...(((((((((((..((((....))))..)))))))(((((.(.......).))))).....))))..))).))))(((((....))))))))))))) ( -38.90)
>DroSim_CAF1 29485 120 - 1
CUCGAUAACACGACGUUUCUCUUGAUAUCGAUGUUGGGCGAUGUUUUGCAAAACAUCGUCUGUAGCGCUUAACAGCAGAGGUGAGUAUAUGAGUAAGCAGCUGAUAACAGCUGUUGUGUU
......(((((((((((((((...((((..((.(((((((((((((....))))))))))).....(((....))).)).))..))))..))).))))(((((....))))))))))))) ( -39.00)
>DroEre_CAF1 28408 118 - 1
CUCGAUAUCUCAAUGUUAUUGUUGAUAUCGAUGUUAGGCGAUGUUUUGCAAAACAUCGCCUGUAG-ACUUAACAGCAGUGGUGAGUAUGUUGGAACGCAGCUGCUAACAGCGGUACU-UG
.(((((((((((....((((((((.((.......((((((((((((....))))))))))))...-...)).)))))))).)))).)))))))......(((((.....)))))...-.. ( -39.42)
>consensus
CUCGAUAACACGACGUUUCUCUUGAUAUCGAUGUUGGGCGAUGUUUUGCAAAACAUCGCCUGUAGCGCUUAACAGCAGAGGUGAGUAUAUGAGUAAGCAGCUGAUAACAGCUGUUGUGUU
.((((((.((.((......)).)).))))))....(((((((((((....))))))))))).....(((((.(......).))))).........((((((((....))))))))..... (-28.12 = -29.25 +   1.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,268,985 – 21,269,105
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.32
Mean single sequence MFE -29.51
Consensus MFE -19.83
Energy contribution -20.95
Covariance contribution 1.12
Combinations/Pair 1.08
Mean z-score -2.30
Structure conservation index 0.67
SVM decision value 0.42
SVM RNA-class probability 0.729985
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21268985 120 + 23771897
CACUGCUGUUAAGCGCUACAGGCGAUGUUUUGCAAAACAUCGCCCAACAUCGAUAUCAAGAGAAACGUCGAGCUAUCGAGAAAAAUAUUGAAUCGACAGAACAUGUGCUCUAGCUCCAGC
..(((..(((((((((....((((((((((....)))))))))).....(((((.((((........((((....))))........)))))))))........))))).))))..))). ( -37.19)
>DroSec_CAF1 27273 114 + 1
CUCUGCUGUUAAGCGCUACAGACGAUGUUUUGCAAAAUAUCGCCCAACAUCGAUAUCAAGAGAAACGUCGUGUUAUCGAGAAAAAUAUUAAAUCGACAGAACAUGUGCUCUAUC------
....(((....)))((.(((.((((((((((.....((((((........)))))).....))))))))))(((.((((.............))))...))).)))))......------ ( -25.92)
>DroSim_CAF1 29525 114 + 1
CUCUGCUGUUAAGCGCUACAGACGAUGUUUUGCAAAACAUCGCCCAACAUCGAUAUCAAGAGAAACGUCGUGUUAUCGAGAAAAAUAUUAAAUCGACAGAACAUGUGCUCUAUC------
(((((((....)))........(((((((..((........))..)))))))......))))....((((((((.((((.............))))...)))))).))......------ ( -24.72)
>DroEre_CAF1 28447 113 + 1
CACUGCUGUUAAGU-CUACAGGCGAUGUUUUGCAAAACAUCGCCUAACAUCGAUAUCAACAAUAACAUUGAGAUAUCGAGAAAAACAUUGCAUCGUCAGAACAUGUGCUCUAGG------
((((((((((...(-(...(((((((((((....)))))))))))....((((((((..((((...)))).))))))))))..))))..)))((....))....))).......------ ( -30.20)
>consensus
CACUGCUGUUAAGCGCUACAGACGAUGUUUUGCAAAACAUCGCCCAACAUCGAUAUCAAGAGAAACGUCGAGUUAUCGAGAAAAAUAUUAAAUCGACAGAACAUGUGCUCUAGC______
...........(((((....((((((((((....)))))))))).....((((((.((.((......)).)).)))))).........................)))))........... (-19.83 = -20.95 +   1.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,268,985 – 21,269,105
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.32
Mean single sequence MFE -35.05
Consensus MFE -25.89
Energy contribution -27.20
Covariance contribution 1.31
Combinations/Pair 1.06
Mean z-score -2.65
Structure conservation index 0.74
SVM decision value 1.21
SVM RNA-class probability 0.931348
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21268985 120 - 23771897
GCUGGAGCUAGAGCACAUGUUCUGUCGAUUCAAUAUUUUUCUCGAUAGCUCGACGUUUCUCUUGAUAUCGAUGUUGGGCGAUGUUUUGCAAAACAUCGCCUGUAGCGCUUAACAGCAGUG
((((((((.(((((....)))))((((((((((........((((....))))........)))).))))))((((((((((((((....)))))))))))..)))))))..)))).... ( -40.09)
>DroSec_CAF1 27273 114 - 1
------GAUAGAGCACAUGUUCUGUCGAUUUAAUAUUUUUCUCGAUAACACGACGUUUCUCUUGAUAUCGAUGUUGGGCGAUAUUUUGCAAAACAUCGUCUGUAGCGCUUAACAGCAGAG
------((((((((....))))))))..............(((((((.((.((......)).)).))))((((((..((((....))))..))))))(.((((........))))).))) ( -30.90)
>DroSim_CAF1 29525 114 - 1
------GAUAGAGCACAUGUUCUGUCGAUUUAAUAUUUUUCUCGAUAACACGACGUUUCUCUUGAUAUCGAUGUUGGGCGAUGUUUUGCAAAACAUCGUCUGUAGCGCUUAACAGCAGAG
------((((((((....))))))))...............((((((.((.((......)).)).)))))).((((((((((((((....)))))))))))..)))(((....))).... ( -33.00)
>DroEre_CAF1 28447 113 - 1
------CCUAGAGCACAUGUUCUGACGAUGCAAUGUUUUUCUCGAUAUCUCAAUGUUAUUGUUGAUAUCGAUGUUAGGCGAUGUUUUGCAAAACAUCGCCUGUAG-ACUUAACAGCAGUG
------..((((((....))))))....(((..((((..((((((((((.((((...))))..))))))))...((((((((((((....))))))))))))..)-)...)))))))... ( -36.20)
>consensus
______GAUAGAGCACAUGUUCUGUCGAUUCAAUAUUUUUCUCGAUAACACGACGUUUCUCUUGAUAUCGAUGUUGGGCGAUGUUUUGCAAAACAUCGCCUGUAGCGCUUAACAGCAGAG
......((((((((....))))))))...............((((((.((.((......)).)).))))))(((((((((((((((....)))))))))))((........))))))... (-25.89 = -27.20 +   1.31)

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 13:05:33 2006