Locus 5974

Sequence ID 2R_DroMel_CAF1
Location 18,808,388 – 18,808,585
Length 197
Max. P 0.862482
window9581 window9582 window9583 window9584

overview

Window 1

Location 18,808,388 – 18,808,506
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 97.74
Mean single sequence MFE -42.80
Consensus MFE -41.80
Energy contribution -42.47
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.98
SVM decision value 0.82
SVM RNA-class probability 0.859231
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18808388 118 + 20766785
GAUUGCGCGAGCUGACAACGGAAUUGAUUUAAUGCCUCUUUGCAGCAGCCACAGGUGGAGUUGUCCACAUGUCCGGAUGUCCAGCUCGGCCUGGGCUGUCGUCCGCAUCUCACAGAUU
..(((.(.((((.(((................(((......)))((((((.(((((.(((((((((........)))....)))))).))))))))))).))).)).)).).)))... ( -41.90)
>DroSec_CAF1 301 118 + 1
AAUUGCGCGAGCUGACAACGGAAUUGAUUUAAUGCCUCUUUGCAGCAGCCACAGGUGGAGUUAUCCACAUGUCCACAUGUCCAGCUCGGCCUGGGCUGUCGUCCGCAUCUCACAGAUU
..(((.(.((((.(((................(((......)))((((((.(((((.(((((....(((((....)))))..))))).))))))))))).))).)).)).).)))... ( -41.70)
>DroSim_CAF1 361 118 + 1
GAUUGCGCGAGCUGACAACGGAAUUGAUUUAAUGCCUCUUUGCAGCAGCCACAGGUGGAGUUGUCCACAUGUCCACAUGUCCAGCUCGGCCUGGGCUGUCGUCCGCAUCUCACAGAUU
..(((.(.((((.(((................(((......)))((((((.(((((.((((((...(((((....))))).)))))).))))))))))).))).)).)).).)))... ( -44.80)
>consensus
GAUUGCGCGAGCUGACAACGGAAUUGAUUUAAUGCCUCUUUGCAGCAGCCACAGGUGGAGUUGUCCACAUGUCCACAUGUCCAGCUCGGCCUGGGCUGUCGUCCGCAUCUCACAGAUU
..(((.(.((((.(((................(((......)))((((((.(((((.((((((...(((((....))))).)))))).))))))))))).))).)).)).).)))... (-41.80 = -42.47 +   0.67)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,808,388 – 18,808,506
Length 118
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 97.74
Mean single sequence MFE -40.97
Consensus MFE -40.42
Energy contribution -40.87
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.49
Structure conservation index 0.99
SVM decision value 0.17
SVM RNA-class probability 0.619274
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18808388 118 - 20766785
AAUCUGUGAGAUGCGGACGACAGCCCAGGCCGAGCUGGACAUCCGGACAUGUGGACAACUCCACCUGUGGCUGCUGCAAAGAGGCAUUAAAUCAAUUCCGUUGUCAGCUCGCGCAAUC
....((((.((.((.((((((.((...((((...((((....))))(((.(((((....))))).)))))))...)).....((.(((.....))).)))))))).)))).))))... ( -40.50)
>DroSec_CAF1 301 118 - 1
AAUCUGUGAGAUGCGGACGACAGCCCAGGCCGAGCUGGACAUGUGGACAUGUGGAUAACUCCACCUGUGGCUGCUGCAAAGAGGCAUUAAAUCAAUUCCGUUGUCAGCUCGCGCAAUU
....((((.((.((.((((((((((((((..(((.((..(((((....)))))..)).)))..)))).))))(((.......)))..............)))))).)))).))))... ( -39.90)
>DroSim_CAF1 361 118 - 1
AAUCUGUGAGAUGCGGACGACAGCCCAGGCCGAGCUGGACAUGUGGACAUGUGGACAACUCCACCUGUGGCUGCUGCAAAGAGGCAUUAAAUCAAUUCCGUUGUCAGCUCGCGCAAUC
....((((.((.((.((((((((((((((..(((.((..(((((....)))))..)).)))..)))).))))(((.......)))..............)))))).)))).))))... ( -42.50)
>consensus
AAUCUGUGAGAUGCGGACGACAGCCCAGGCCGAGCUGGACAUGUGGACAUGUGGACAACUCCACCUGUGGCUGCUGCAAAGAGGCAUUAAAUCAAUUCCGUUGUCAGCUCGCGCAAUC
....((((.((.((.((((((((((((((..(((.((..(((((....)))))..)).)))..)))).))))(((.......)))..............)))))).)))).))))... (-40.42 = -40.87 +   0.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,808,428 – 18,808,546
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 98.31
Mean single sequence MFE -47.40
Consensus MFE -46.40
Energy contribution -47.07
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.98
SVM decision value 0.83
SVM RNA-class probability 0.862482
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18808428 118 + 20766785
UGCAGCAGCCACAGGUGGAGUUGUCCACAUGUCCGGAUGUCCAGCUCGGCCUGGGCUGUCGUCCGCAUCUCACAGAUUCGACUGGCUCCUCUUAAUUGGGCCCACUUUGGCGGUAGCG
.((.((((((.(((((.(((((((((........)))....)))))).)))))))))))...(((((((.....)))......(((.((........))))).......))))..)). ( -46.50)
>DroSec_CAF1 341 118 + 1
UGCAGCAGCCACAGGUGGAGUUAUCCACAUGUCCACAUGUCCAGCUCGGCCUGGGCUGUCGUCCGCAUCUCACAGAUUCGACUGGCUCCUCUUAAUUGGGCCCACUUUGGCGGUAGCG
.((.((((((.(((((.(((((....(((((....)))))..))))).)))))))))))...(((((((.....)))......(((.((........))))).......))))..)). ( -46.30)
>DroSim_CAF1 401 118 + 1
UGCAGCAGCCACAGGUGGAGUUGUCCACAUGUCCACAUGUCCAGCUCGGCCUGGGCUGUCGUCCGCAUCUCACAGAUUCGACUGGCUCCUCUUAAUUGGGCCCACUUUGGCGGUAGCG
.((.((((((.(((((.((((((...(((((....))))).)))))).)))))))))))...(((((((.....)))......(((.((........))))).......))))..)). ( -49.40)
>consensus
UGCAGCAGCCACAGGUGGAGUUGUCCACAUGUCCACAUGUCCAGCUCGGCCUGGGCUGUCGUCCGCAUCUCACAGAUUCGACUGGCUCCUCUUAAUUGGGCCCACUUUGGCGGUAGCG
.((.((((((.(((((.((((((...(((((....))))).)))))).)))))))))))...(((((((.....)))......(((.((........))))).......))))..)). (-46.40 = -47.07 +   0.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,808,466 – 18,808,585
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -44.30
Consensus MFE -44.30
Energy contribution -44.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 1.00
SVM decision value 0.09
SVM RNA-class probability 0.578452
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18808466 119 - 20766785
GGAUCCGCAAAAAGUGGCCGAGCCACAGGCCUGAAUGAGCGCUACCGCCAAAGUGGGCCCAAUUAAGAGGAGCCAGUCGAAUCUGUGAGAUGCGGACGACAGCCCAGGCCGAGCUGGAC
...(((((.....(((((...))))).((((((..((.(((....))))).....(((((........)).))).((((..(((((.....)))))))))....))))))..)).))). ( -44.30)
>DroSec_CAF1 379 119 - 1
GGAUCCGCAAAAAGUGGCCGAGCCACAGGCCUGAAUGAGCGCUACCGCCAAAGUGGGCCCAAUUAAGAGGAGCCAGUCGAAUCUGUGAGAUGCGGACGACAGCCCAGGCCGAGCUGGAC
...(((((.....(((((...))))).((((((..((.(((....))))).....(((((........)).))).((((..(((((.....)))))))))....))))))..)).))). ( -44.30)
>DroSim_CAF1 439 119 - 1
GGAUCCGCAAAAAGUGGCCGAGCCACAGGCCUGAAUGAGCGCUACCGCCAAAGUGGGCCCAAUUAAGAGGAGCCAGUCGAAUCUGUGAGAUGCGGACGACAGCCCAGGCCGAGCUGGAC
...(((((.....(((((...))))).((((((..((.(((....))))).....(((((........)).))).((((..(((((.....)))))))))....))))))..)).))). ( -44.30)
>consensus
GGAUCCGCAAAAAGUGGCCGAGCCACAGGCCUGAAUGAGCGCUACCGCCAAAGUGGGCCCAAUUAAGAGGAGCCAGUCGAAUCUGUGAGAUGCGGACGACAGCCCAGGCCGAGCUGGAC
...(((((.....(((((...))))).((((((..((.(((....))))).....(((((........)).))).((((..(((((.....)))))))))....))))))..)).))). (-44.30 = -44.30 +   0.00)

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 11:59:26 2006