Locus 7206

Sequence ID 2L_DroMel_CAF1
Location 20,246,009 – 20,246,145
Length 136
Max. P 0.967604
window11509 window11510 window11511 window11512

overview

Window 9

Location 20,246,009 – 20,246,105
Length 96
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.72
Mean single sequence MFE -47.67
Consensus MFE -37.87
Energy contribution -38.23
Covariance contribution 0.37
Combinations/Pair 1.08
Mean z-score -1.85
Structure conservation index 0.79
SVM decision value 0.29
SVM RNA-class probability 0.670409
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20246009 96 + 22407834
UGCCGGGCUGC------------------------UGGGAUGGAGGAUUAUUCUAGUGGAUGGAGCGACACACCCCGGCACAUCCACAUGUCUGACAUGACAGUUGGUUAUGCCGGGGCC
..(((..(..(------------------------((((((((....)))))))))..).))).........((((((((...(((..((((......))))..)))...)))))))).. ( -40.50)
>DroSec_CAF1 4569 120 + 1
UGCCGGGAUGCCGGGUUGCUGGGAUGGUGGGAUGGUGGGAUGGAGGACCAUUCUAGUGGAUGGAGCGACACACCCCGGCACAUCCACAUGUCUGACAUGACAGUUGGUUAUGCCGGGGCC
..((((....))))((((((....((.(((((((((..........))))))))).)).....))))))...((((((((...(((..((((......))))..)))...)))))))).. ( -50.60)
>DroSim_CAF1 4991 120 + 1
UGCCGGGAUGCCGGGUUGCCGGGAUGGUGGGAUGGUGGGAUGGAGGACCAUUCUAGUGGAUGGAGCGACACACCCCGGCACAUCCACAUGUCUGACAUGACAGUUGGUUAUGCCGGGGCC
..((((....))))((((((.(..((.(((((((((..........))))))))).))..).).)))))...((((((((...(((..((((......))))..)))...)))))))).. ( -51.90)
>consensus
UGCCGGGAUGCCGGGUUGC_GGGAUGGUGGGAUGGUGGGAUGGAGGACCAUUCUAGUGGAUGGAGCGACACACCCCGGCACAUCCACAUGUCUGACAUGACAGUUGGUUAUGCCGGGGCC
..(((...(((((..(((((.....)))))..)))))...))).((.((((((....)))))).........((((((((...(((..((((......))))..)))...)))))))))) (-37.87 = -38.23 +   0.37)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,246,009 – 20,246,105
Length 96
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 84.72
Mean single sequence MFE -38.86
Consensus MFE -33.53
Energy contribution -34.20
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.86
SVM decision value 1.10
SVM RNA-class probability 0.915212
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20246009 96 - 22407834
GGCCCCGGCAUAACCAACUGUCAUGUCAGACAUGUGGAUGUGCCGGGGUGUGUCGCUCCAUCCACUAGAAUAAUCCUCCAUCCCA------------------------GCAGCCCGGCA
.(((((((((((.(((..((((......))))..))).))))))))))).(((((((.(..........................------------------------).)))..)))) ( -32.87)
>DroSec_CAF1 4569 120 - 1
GGCCCCGGCAUAACCAACUGUCAUGUCAGACAUGUGGAUGUGCCGGGGUGUGUCGCUCCAUCCACUAGAAUGGUCCUCCAUCCCACCAUCCCACCAUCCCAGCAACCCGGCAUCCCGGCA
.(((((((((((.(((..((((......))))..))).))))))))))).....(((............(((((..........)))))...........)))...((((....)))).. ( -40.80)
>DroSim_CAF1 4991 120 - 1
GGCCCCGGCAUAACCAACUGUCAUGUCAGACAUGUGGAUGUGCCGGGGUGUGUCGCUCCAUCCACUAGAAUGGUCCUCCAUCCCACCAUCCCACCAUCCCGGCAACCCGGCAUCCCGGCA
.(((((((((((.(((..((((......))))..))).))))))))))).(((((..............((((....)))).................((((....)))).....))))) ( -42.90)
>consensus
GGCCCCGGCAUAACCAACUGUCAUGUCAGACAUGUGGAUGUGCCGGGGUGUGUCGCUCCAUCCACUAGAAUGGUCCUCCAUCCCACCAUCCCACCAUCCC_GCAACCCGGCAUCCCGGCA
.(((((((((((.(((..((((......))))..))).))))))))))).(((((.....((.....))((((....))))..................................))))) (-33.53 = -34.20 +   0.67)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,246,025 – 20,246,145
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -45.40
Consensus MFE -45.84
Energy contribution -45.40
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -2.20
Structure conservation index 1.01
SVM decision value 1.43
SVM RNA-class probability 0.953368
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20246025 120 + 22407834
UGGAGGAUUAUUCUAGUGGAUGGAGCGACACACCCCGGCACAUCCACAUGUCUGACAUGACAGUUGGUUAUGCCGGGGCCACAAGGCACGUAGCGCAGUGCAGUUAAGAUUUGGAUUUCC
....(((....((((((((.((......))..((((((((...(((..((((......))))..)))...))))))))))))...((((........))))..........))))..))) ( -42.40)
>DroSec_CAF1 4609 120 + 1
UGGAGGACCAUUCUAGUGGAUGGAGCGACACACCCCGGCACAUCCACAUGUCUGACAUGACAGUUGGUUAUGCCGGGGCCACAAGGCACGUAGCGCAGUGCAGUUAAGAUUUGGAUUUCC
.(((((.(((.(((.((((.((......))..((((((((...(((..((((......))))..)))...))))))))))))...((((........)))).....)))..))).))))) ( -46.90)
>DroSim_CAF1 5031 120 + 1
UGGAGGACCAUUCUAGUGGAUGGAGCGACACACCCCGGCACAUCCACAUGUCUGACAUGACAGUUGGUUAUGCCGGGGCCACAAGGCACGUAGCGCAGUGCAGUUAAGAUUUGGAUUUCC
.(((((.(((.(((.((((.((......))..((((((((...(((..((((......))))..)))...))))))))))))...((((........)))).....)))..))).))))) ( -46.90)
>consensus
UGGAGGACCAUUCUAGUGGAUGGAGCGACACACCCCGGCACAUCCACAUGUCUGACAUGACAGUUGGUUAUGCCGGGGCCACAAGGCACGUAGCGCAGUGCAGUUAAGAUUUGGAUUUCC
.(((((.(((.(((.((((.((......))..((((((((...(((..((((......))))..)))...))))))))))))...((((........)))).....)))..))).))))) (-45.84 = -45.40 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,246,025 – 20,246,145
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -44.00
Consensus MFE -42.43
Energy contribution -43.10
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.67
Structure conservation index 0.96
SVM decision value 1.61
SVM RNA-class probability 0.967604
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20246025 120 - 22407834
GGAAAUCCAAAUCUUAACUGCACUGCGCUACGUGCCUUGUGGCCCCGGCAUAACCAACUGUCAUGUCAGACAUGUGGAUGUGCCGGGGUGUGUCGCUCCAUCCACUAGAAUAAUCCUCCA
(((................((((........))))((.((((((((((((((.(((..((((......))))..))).)))))))))))(((......))).))).))........))). ( -41.60)
>DroSec_CAF1 4609 120 - 1
GGAAAUCCAAAUCUUAACUGCACUGCGCUACGUGCCUUGUGGCCCCGGCAUAACCAACUGUCAUGUCAGACAUGUGGAUGUGCCGGGGUGUGUCGCUCCAUCCACUAGAAUGGUCCUCCA
(((...(((..........((((........))))((.((((((((((((((.(((..((((......))))..))).)))))))))))(((......))).))).))..)))...))). ( -45.20)
>DroSim_CAF1 5031 120 - 1
GGAAAUCCAAAUCUUAACUGCACUGCGCUACGUGCCUUGUGGCCCCGGCAUAACCAACUGUCAUGUCAGACAUGUGGAUGUGCCGGGGUGUGUCGCUCCAUCCACUAGAAUGGUCCUCCA
(((...(((..........((((........))))((.((((((((((((((.(((..((((......))))..))).)))))))))))(((......))).))).))..)))...))). ( -45.20)
>consensus
GGAAAUCCAAAUCUUAACUGCACUGCGCUACGUGCCUUGUGGCCCCGGCAUAACCAACUGUCAUGUCAGACAUGUGGAUGUGCCGGGGUGUGUCGCUCCAUCCACUAGAAUGGUCCUCCA
(((...(((..........((((........))))((.((((((((((((((.(((..((((......))))..))).)))))))))))(((......))).))).))..)))...))). (-42.43 = -43.10 +   0.67)

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 12:30:08 2006