Locus 8299

Sequence ID 3L_DroMel_CAF1
Location 21,745,525 – 21,745,685
Length 160
Max. P 0.988676
window13584 window13585 window13586

overview

Window 4

Location 21,745,525 – 21,745,645
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.00
Mean single sequence MFE -37.94
Consensus MFE -35.92
Energy contribution -36.32
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 0.95
SVM decision value 0.46
SVM RNA-class probability 0.744218
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21745525 120 + 23771897
CGAAAAUUGUCACGGUUUCGCGGUCGAUGGCUCGCUUGCUGUGAAGGUGCAAAUUUAAUGUUUGCCAAUUUAGCAGCGCUCUGCUGUCACCUUUGGUGUCCAUUAGCGAGCGUUUAUAUG
...(((((((((((((...(((((.....)).)))..)))))))....((((((.....))))))))))))...(((((((.((((.((((...)))).....)))))))))))...... ( -39.20)
>DroSec_CAF1 29897 120 + 1
CGAAAAUUGUCACGGUUUCGCGGUCGAUGGCUCGCUCGCUGUGAAGGUGCAAAUUUAAUGUUUGCCAAUUUAGCAGCUCUCUGCUGUCACCUUUGGUGUCCAUUAGCGAGCGUUUAUAUG
........((((((..(....)..)).)))).(((((((((.((((((((((((.....)))))).......(((((.....))))).))))))((...))..)))))))))........ ( -36.80)
>DroSim_CAF1 32145 120 + 1
CGAAAAUUGUCACGGUUUCGCGGUCGAUGGCUCGCUCGCUGUGAAGGUGCAAAUUUAAUGUUUGCCAAUUUAGCAGCGCUCUGCUGUCACCUUUGGUGUCCAUUAGCGAGCGUUUAUAUG
...(((((((((((((...(((((.....)).)))..)))))))....((((((.....))))))))))))...(((((((.((((.((((...)))).....)))))))))))...... ( -38.50)
>DroEre_CAF1 13603 120 + 1
CGAAAAUUGUCACGGUUUCGCGGUCGAUGGCUCGCUCGCUGUGAAGGUGCAAAUUUAAUGUUUGCCAAUUUAGCAGCGCUCUGCUGUCACCUUUGGUGUCCAUUAGCGAGCGUUUAUAUG
...(((((((((((((...(((((.....)).)))..)))))))....((((((.....))))))))))))...(((((((.((((.((((...)))).....)))))))))))...... ( -38.50)
>DroYak_CAF1 90597 120 + 1
CGAAAAUUGUCACGGUUUCGCGUUCGAUGGCUCGCUCGCUGUGAAGGUGCAAAUUUAAUGUUUGCCAAUUUAGCAGCGCUCUGCUGUCACCUUUGGUGUCCAUUAGCGAGCGUUUAUAUG
........(((((((........))).)))).(((((((((.((((((((((((.....)))))).....((((((....))))))..))))))((...))..)))))))))........ ( -36.70)
>consensus
CGAAAAUUGUCACGGUUUCGCGGUCGAUGGCUCGCUCGCUGUGAAGGUGCAAAUUUAAUGUUUGCCAAUUUAGCAGCGCUCUGCUGUCACCUUUGGUGUCCAUUAGCGAGCGUUUAUAUG
...(((((((((((((...(((((.....)).)))..)))))))....((((((.....))))))))))))...(((((((.((((.((((...)))).....)))))))))))...... (-35.92 = -36.32 +   0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,745,525 – 21,745,645
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.00
Mean single sequence MFE -32.78
Consensus MFE -31.88
Energy contribution -32.08
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.97
SVM decision value 2.13
SVM RNA-class probability 0.988676
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21745525 120 - 23771897
CAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGCGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCACAGCAAGCGAGCCAUCGACCGCGAAACCGUGACAAUUUUCG
.........(((((((((((....((((.(....)(((((....)))))...))))....)))))...((((.........)))))))))).......((((....)))).......... ( -31.70)
>DroSec_CAF1 29897 120 - 1
CAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGAGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCACAGCGAGCGAGCCAUCGACCGCGAAACCGUGACAAUUUUCG
........((((((((..(((...)))(((((...(((((....)))))......(((((.......))))))))))...))))))))..........((((....)))).......... ( -33.00)
>DroSim_CAF1 32145 120 - 1
CAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGCGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCACAGCGAGCGAGCCAUCGACCGCGAAACCGUGACAAUUUUCG
........((((((((..(((...)))(((((...(((((....)))))......(((((.......))))))))))...))))))))..........((((....)))).......... ( -33.00)
>DroEre_CAF1 13603 120 - 1
CAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGCGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCACAGCGAGCGAGCCAUCGACCGCGAAACCGUGACAAUUUUCG
........((((((((..(((...)))(((((...(((((....)))))......(((((.......))))))))))...))))))))..........((((....)))).......... ( -33.00)
>DroYak_CAF1 90597 120 - 1
CAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGCGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCACAGCGAGCGAGCCAUCGAACGCGAAACCGUGACAAUUUUCG
........((((((((..(((...)))(((((...(((((....)))))......(((((.......))))))))))...))))))))..........((((....)))).......... ( -33.20)
>consensus
CAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGCGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCACAGCGAGCGAGCCAUCGACCGCGAAACCGUGACAAUUUUCG
........((((((((..(((...)))(((((...(((((....)))))......(((((.......))))))))))...))))))))..........((((....)))).......... (-31.88 = -32.08 +   0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,745,565 – 21,745,685
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.92
Mean single sequence MFE -32.94
Consensus MFE -31.42
Energy contribution -31.70
Covariance contribution 0.28
Combinations/Pair 1.04
Mean z-score -1.16
Structure conservation index 0.95
SVM decision value 0.06
SVM RNA-class probability 0.563241
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21745565 120 - 23771897
UGCCAGAUCCGGAGCUGGCCUGCCAAUGCUCGGCACUUUGCAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGCGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCAC
.(((((........))))).(((((((...((((.((((((.................(((...)))..(....).)))))).))))....)))))))...................... ( -34.50)
>DroSec_CAF1 29937 120 - 1
UGCCAGAUCCGGAGCUGGCCUGCCAAUGCUCGGCACUUUGCAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGAGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCAC
.(((((........))))).(((((((...((((.((((((.................(((...)))..(....).)))))).))))....)))))))...................... ( -33.70)
>DroSim_CAF1 32185 120 - 1
UGCCAGAUCCGGAGCUGGCCUGCCAAUGCUCGGCACUUUGCAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGCGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCAC
.(((((........))))).(((((((...((((.((((((.................(((...)))..(....).)))))).))))....)))))))...................... ( -34.50)
>DroEre_CAF1 13643 120 - 1
UGGCAGAUCCGAAGCUGGCCUGCCAAUGCUCGGCACUUUGCAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGCGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCAC
((((((..((((.(((((....)))..))))))...............((((((((..(((...)))..(....)))).))))))))))).....(((((.......)))))........ ( -33.30)
>DroYak_CAF1 90637 120 - 1
UUUCAGAUCCCAAGCUGGCCUGCCAAUGCUCGGCACUUUGCAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGCGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCAC
..((((........))))..(((((((...((((.((((((.................(((...)))..(....).)))))).))))....)))))))...................... ( -28.70)
>consensus
UGCCAGAUCCGGAGCUGGCCUGCCAAUGCUCGGCACUUUGCAUAUAAACGCUCGCUAAUGGACACCAAAGGUGACAGCAGAGCGCUGCUAAAUUGGCAAACAUUAAAUUUGCACCUUCAC
.(((((........))))).(((((((...((((.((((((.................(((...)))..(....).)))))).))))....)))))))...................... (-31.42 = -31.70 +   0.28)

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 13:12:00 2006