Locus 6349

Sequence ID 3L_DroMel_CAF1
Location 16,991,379 – 16,991,539
Length 160
Max. P 0.982637
window10174 window10175 window10176 window10177

overview

Window 4

Location 16,991,379 – 16,991,499
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -51.10
Consensus MFE -49.78
Energy contribution -48.90
Covariance contribution -0.88
Combinations/Pair 1.12
Mean z-score -2.69
Structure conservation index 0.97
SVM decision value 1.92
SVM RNA-class probability 0.982637
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16991379 120 + 23771897
UAUCAACAGUGAGGUGUGGGUGCGCUGCGAGAACGAGCAGCAGUACGCCAAGUGGAUGGCUGCUUGUCGUUUGGCGGCCAAGGGAAGAUCCCUGGCGGAUAGCUCGUACGAGAGUGAAGU
..........(((.(((..(((((((((........))))).))))(((.......((((((((........))))))))((((.....)))))))..))).))).(((....))).... ( -46.60)
>DroSim_CAF1 2941 120 + 1
UACCAACAGCGAGGUGUGGGUGCGCUGCGAGAACGAGCAGCAGUACGCCAAGUGGAUGGCUGCCUGUCGUUUGGCGGCCAAGGGAAGAUCCCUGGCGGACAGCUCGUACGAGAGUGAAGU
........(((((.(((..(((((((((........))))).))))(((.......((((((((........))))))))((((.....)))))))..))).)))))((....))..... ( -53.50)
>DroYak_CAF1 3134 120 + 1
AACCAACAGCGAGGUGUGGGUGCGCUGCGAGAACGAGCAGCAGUACGCCAAGUGGAUGGCCGCUUGUCGUUUGGCGGCCAAGGGAAGAUCCCUGGCGGAUAGCUCGUACGAGGGUGAAGU
.(((....(((((.(((..(((((((((........))))).))))(((.......((((((((........))))))))((((.....)))))))..))).))))).....)))..... ( -53.20)
>consensus
UACCAACAGCGAGGUGUGGGUGCGCUGCGAGAACGAGCAGCAGUACGCCAAGUGGAUGGCUGCUUGUCGUUUGGCGGCCAAGGGAAGAUCCCUGGCGGAUAGCUCGUACGAGAGUGAAGU
........(((((.(((..(((((((((........))))).))))(((.......((((((((........))))))))((((.....)))))))..))).)))))((....))..... (-49.78 = -48.90 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,991,379 – 16,991,499
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -39.37
Consensus MFE -35.89
Energy contribution -36.00
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.27
Structure conservation index 0.91
SVM decision value 0.85
SVM RNA-class probability 0.865263
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16991379 120 - 23771897
ACUUCACUCUCGUACGAGCUAUCCGCCAGGGAUCUUCCCUUGGCCGCCAAACGACAAGCAGCCAUCCACUUGGCGUACUGCUGCUCGUUCUCGCAGCGCACCCACACCUCACUGUUGAUA
...(((.....((((..(((....(((((((......)))))))((.....))...))).((((......)))))))).(((((........)))))..................))).. ( -34.50)
>DroSim_CAF1 2941 120 - 1
ACUUCACUCUCGUACGAGCUGUCCGCCAGGGAUCUUCCCUUGGCCGCCAAACGACAGGCAGCCAUCCACUUGGCGUACUGCUGCUCGUUCUCGCAGCGCACCCACACCUCGCUGUUGGUA
.............((((((.((.((((((((.....))).((((.(((........))).))))......))))).))....)))))).((.((((((...........)))))).)).. ( -41.90)
>DroYak_CAF1 3134 120 - 1
ACUUCACCCUCGUACGAGCUAUCCGCCAGGGAUCUUCCCUUGGCCGCCAAACGACAAGCGGCCAUCCACUUGGCGUACUGCUGCUCGUUCUCGCAGCGCACCCACACCUCGCUGUUGGUU
.....(((...(.((((((....((((((((.....))).(((((((..........)))))))......))))).......)))))).)..((((((...........)))))).))). ( -41.70)
>consensus
ACUUCACUCUCGUACGAGCUAUCCGCCAGGGAUCUUCCCUUGGCCGCCAAACGACAAGCAGCCAUCCACUUGGCGUACUGCUGCUCGUUCUCGCAGCGCACCCACACCUCGCUGUUGGUA
...........((((..(((....(((((((......)))))))((.....))...))).((((......)))))))).(((((........)))))..(((.(((......))).))). (-35.89 = -36.00 +   0.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,991,419 – 16,991,539
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -48.10
Consensus MFE -46.56
Energy contribution -45.90
Covariance contribution -0.66
Combinations/Pair 1.09
Mean z-score -1.71
Structure conservation index 0.97
SVM decision value 0.47
SVM RNA-class probability 0.750378
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16991419 120 + 23771897
CAGUACGCCAAGUGGAUGGCUGCUUGUCGUUUGGCGGCCAAGGGAAGAUCCCUGGCGGAUAGCUCGUACGAGAGUGAAGUGGACAGCAUACUCUCGCUACUGCAGAUGCAGCGACCCGCA
(((.(((.((((..(....)..)))).))))))(((((((.(((.....)))))))((...((..(((((((((((..((.....)).)))))))).)))(((....)))))..))))). ( -45.30)
>DroSim_CAF1 2981 120 + 1
CAGUACGCCAAGUGGAUGGCUGCCUGUCGUUUGGCGGCCAAGGGAAGAUCCCUGGCGGACAGCUCGUACGAGAGUGAAGUGGACAGCAUACUCUCGCUACUGCAGAUGCAGCGACCUGCA
..((.((((.......((((((((........))))))))((((.....)))))))).)).((..(((((((((((..((.....)).)))))))).))).))...(((((....))))) ( -50.10)
>DroYak_CAF1 3174 120 + 1
CAGUACGCCAAGUGGAUGGCCGCUUGUCGUUUGGCGGCCAAGGGAAGAUCCCUGGCGGAUAGCUCGUACGAGGGUGAAGUGGAUAGCAUACUCUCGUUACUGCAGAUGCAGCGACCAGCA
.....((((.......((((((((........))))))))((((.....))))))))....(((.(((((((((((..((.....)).)))))))))..((((....))))..)).))). ( -48.90)
>consensus
CAGUACGCCAAGUGGAUGGCUGCUUGUCGUUUGGCGGCCAAGGGAAGAUCCCUGGCGGAUAGCUCGUACGAGAGUGAAGUGGACAGCAUACUCUCGCUACUGCAGAUGCAGCGACCAGCA
.....((((.......((((((((........))))))))((((.....))))))))....(((((..((((((((..((.....)).))))))))...((((....)))))))...)). (-46.56 = -45.90 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,991,419 – 16,991,539
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -44.56
Consensus MFE -40.65
Energy contribution -40.54
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.02
Structure conservation index 0.91
SVM decision value 0.52
SVM RNA-class probability 0.767118
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16991419 120 - 23771897
UGCGGGUCGCUGCAUCUGCAGUAGCGAGAGUAUGCUGUCCACUUCACUCUCGUACGAGCUAUCCGCCAGGGAUCUUCCCUUGGCCGCCAAACGACAAGCAGCCAUCCACUUGGCGUACUG
(((..((((((((....))))).((((((((..............))))))))...........(((((((......)))))))........)))..)))((((......))))...... ( -43.34)
>DroSim_CAF1 2981 120 - 1
UGCAGGUCGCUGCAUCUGCAGUAGCGAGAGUAUGCUGUCCACUUCACUCUCGUACGAGCUGUCCGCCAGGGAUCUUCCCUUGGCCGCCAAACGACAGGCAGCCAUCCACUUGGCGUACUG
.((((.(((((((....))))).((((((((..............))))))))..)).)))).((((((((.....))).((((.(((........))).))))......)))))..... ( -47.94)
>DroYak_CAF1 3174 120 - 1
UGCUGGUCGCUGCAUCUGCAGUAACGAGAGUAUGCUAUCCACUUCACCCUCGUACGAGCUAUCCGCCAGGGAUCUUCCCUUGGCCGCCAAACGACAAGCGGCCAUCCACUUGGCGUACUG
..((.((..((((....))))..)).))(((((((((.........((((.((..((....)).)).)))).........(((((((..........)))))))......))))))))). ( -42.40)
>consensus
UGCAGGUCGCUGCAUCUGCAGUAGCGAGAGUAUGCUGUCCACUUCACUCUCGUACGAGCUAUCCGCCAGGGAUCUUCCCUUGGCCGCCAAACGACAAGCAGCCAUCCACUUGGCGUACUG
(((..((((((((....))))).((((((((..............))))))))...........(((((((......)))))))........)))..)))((((......))))...... (-40.65 = -40.54 +  -0.11)

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 12:16:16 2006