Locus 6130

Sequence ID 3L_DroMel_CAF1
Location 16,225,933 – 16,226,133
Length 200
Max. P 0.896847
window9849 window9850 window9851

overview

Window 9

Location 16,225,933 – 16,226,053
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.14
Mean single sequence MFE -40.51
Consensus MFE -31.15
Energy contribution -31.78
Covariance contribution 0.63
Combinations/Pair 1.06
Mean z-score -1.85
Structure conservation index 0.77
SVM decision value 0.45
SVM RNA-class probability 0.741921
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16225933 120 + 23771897
UUAUUAACAAUGCUAAGUAUCAAUGGCCAUAGAGCAAUCUACGCAUUUGCGUAUGUUCCAUGGGUGGAUGCCAUGUGACGGCCUCGGGUCACGUUCCGGAGCGAUUCCUUUCGGGAUCGA
...........(((..........((((.((((....)))).(((((..(.((((...)))).)..)))))........))))(((((......))))))))((((((....)))))).. ( -39.50)
>DroSec_CAF1 44729 120 + 1
UUAUUAUCCCUACUAAAUAUCAAUGGCCAUAGAACAAUCUAUGCAUUCGCGUAUGUUCCAUGGGUGGAUGCCAUGUGACGGCCUCGGGUCACGUUCCGGAGCGAUUCCUUUCGGGAUCGA
......(((...............(((((((((....)))))((((((((.((((...)))).))))))))........))))..(((......)))))).(((((((....))))))). ( -38.70)
>DroSim_CAF1 46441 120 + 1
UUAUUAUCCCUGCUAAGUAUCAAUGGCCAUAGAGCAAUCUACGCAUUCGCGUAUGUUCUAUGGGUGGAUGCCAUGUGACGGCCUCGGGUCACGUUCCGGAGCGAUUCCUUUCGGGAUCGA
......(((.......(((((...(.((((((((((...(((((....))))))))))))))).).))))).(((((((........)))))))...))).(((((((....))))))). ( -44.70)
>DroEre_CAF1 44514 120 + 1
UAACUAACCCUGCUGAGUAUCGAUGGCCAUCCAGCAAUCUACGCACUUGGGUAUCUUCCAUGGCUGGAUGCCAUGUGACAACCUCGGGUCACGUUCCGAAGCGAUUCCCUUCGGGAUCGA
......((((....(((..((((((((.(((((((............((((.....))))..)))))))))))).)))....)))))))..((((((((((.(....))))))))).)). ( -39.14)
>consensus
UUAUUAACCCUGCUAAGUAUCAAUGGCCAUAGAGCAAUCUACGCAUUCGCGUAUGUUCCAUGGGUGGAUGCCAUGUGACGGCCUCGGGUCACGUUCCGGAGCGAUUCCUUUCGGGAUCGA
................(((((...(.((((.(((((...(((((....)))))))))).)))).).))))).(((((((........))))))).......(((((((....))))))). (-31.15 = -31.78 +   0.63)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,225,933 – 16,226,053
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.14
Mean single sequence MFE -37.52
Consensus MFE -28.26
Energy contribution -28.70
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -1.53
Structure conservation index 0.75
SVM decision value 0.01
SVM RNA-class probability 0.539615
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16225933 120 - 23771897
UCGAUCCCGAAAGGAAUCGCUCCGGAACGUGACCCGAGGCCGUCACAUGGCAUCCACCCAUGGAACAUACGCAAAUGCGUAGAUUGCUCUAUGGCCAUUGAUACUUAGCAUUGUUAAUAA
..(((.((....)).)))(((.(((........))).((((((..(((((.......)))))..)).(((((....)))))...........))))..........)))........... ( -36.00)
>DroSec_CAF1 44729 120 - 1
UCGAUCCCGAAAGGAAUCGCUCCGGAACGUGACCCGAGGCCGUCACAUGGCAUCCACCCAUGGAACAUACGCGAAUGCAUAGAUUGUUCUAUGGCCAUUGAUAUUUAGUAGGGAUAAUAA
...(((((..........((..(((........)))..)).((((.(((((.((((....)))).............((((((....)))))))))))))))........)))))..... ( -35.10)
>DroSim_CAF1 46441 120 - 1
UCGAUCCCGAAAGGAAUCGCUCCGGAACGUGACCCGAGGCCGUCACAUGGCAUCCACCCAUAGAACAUACGCGAAUGCGUAGAUUGCUCUAUGGCCAUUGAUACUUAGCAGGGAUAAUAA
...(((((....(((...((..(((........)))..)).(((....))).)))..(((((((.(((((((....)))))...)).)))))))................)))))..... ( -36.10)
>DroEre_CAF1 44514 120 - 1
UCGAUCCCGAAGGGAAUCGCUUCGGAACGUGACCCGAGGUUGUCACAUGGCAUCCAGCCAUGGAAGAUACCCAAGUGCGUAGAUUGCUGGAUGGCCAUCGAUACUCAGCAGGGUUAGUUA
......((((((.(...).))))))(((.((((((..((.((((.((((((.....))))))...)))).))...(((..((((((.(((....))).)))).))..)))))))))))). ( -42.90)
>consensus
UCGAUCCCGAAAGGAAUCGCUCCGGAACGUGACCCGAGGCCGUCACAUGGCAUCCACCCAUGGAACAUACGCAAAUGCGUAGAUUGCUCUAUGGCCAUUGAUACUUAGCAGGGAUAAUAA
..(((.((....)).)))(((.(((........))).((((((..(((((.......)))))..)).(((((....)))))...........))))..........)))........... (-28.26 = -28.70 +   0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,226,013 – 16,226,133
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -49.42
Consensus MFE -45.85
Energy contribution -45.23
Covariance contribution -0.62
Combinations/Pair 1.12
Mean z-score -1.81
Structure conservation index 0.93
SVM decision value 0.99
SVM RNA-class probability 0.896847
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16226013 120 + 23771897
GCCUCGGGUCACGUUCCGGAGCGAUUCCUUUCGGGAUCGACGAGCCACUCGCCAAAGGGCAAAAAUCGGGGGAACAGCCUGUGUGAGUCACAUUGCACCUUGCGGUGGACUCUACGGCUU
(((.(((((...(((((((.((((((((....))))))).)...))....(((....)))..........))))).))))).(((((((.((((((.....))))))))))).))))).. ( -49.80)
>DroSec_CAF1 44809 120 + 1
GCCUCGGGUCACGUUCCGGAGCGAUUCCUUUCGGGAUCGACGAGCCGUUCGCCAAAGGGCACAAAUCGAGGGAGCAGCCUGUGGGAGUCACAUUGCACCUUGCGGUGGACUCUACGGCUU
(((.(((((...(((((((.((((((((....))))))).)...))....(((....)))..........))))).)))))..((((((.((((((.....))))))))))))..))).. ( -50.30)
>DroSim_CAF1 46521 120 + 1
GCCUCGGGUCACGUUCCGGAGCGAUUCCUUUCGGGAUCGACGAGCCAUUCGCCAAAGGGCAAAAAUCGAGGGAGCAGCCUGUGGGAGUCACAUUGCACCUUGCGGUGGACUCUACGGCUU
(((.(((((...(((((((.((((((((....))))))).)...))....(((....)))..........))))).)))))..((((((.((((((.....))))))))))))..))).. ( -50.30)
>DroEre_CAF1 44594 119 + 1
ACCUCGGGUCACGUUCCGAAGCGAUUCCCUUCGGGAUCGACAUGCCAUUUGCCAAAGGGCAAAAAUCG-GGGAGCAGCUUGUGGGAGUCACAUUGCACCUUGCGGUGGAUUCUACGGCUU
.(((((((((..(((((((((.(....)))))))))).)))......((((((....))))))..)))-)))...((((.((((.((((.((((((.....)))))))))))))))))). ( -47.30)
>consensus
GCCUCGGGUCACGUUCCGGAGCGAUUCCUUUCGGGAUCGACGAGCCAUUCGCCAAAGGGCAAAAAUCGAGGGAGCAGCCUGUGGGAGUCACAUUGCACCUUGCGGUGGACUCUACGGCUU
.(((((((((..(((((((((.(....)))))))))).))).........(((....))).....))))))....((((.(((.(((((.((((((.....)))))))))))))))))). (-45.85 = -45.23 +  -0.62)

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 12:10:54 2006