Locus 9372

Sequence ID 3R_DroMel_CAF1
Location 24,898,787 – 24,899,020
Length 233
Max. P 0.876187
window14998 window14999 window15000

overview

Window 8

Location 24,898,787 – 24,898,907
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.92
Mean single sequence MFE -31.16
Consensus MFE -26.52
Energy contribution -27.56
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -1.31
Structure conservation index 0.85
SVM decision value 0.23
SVM RNA-class probability 0.644141
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24898787 120 + 27905053
AUCUUGCGGAUAAUAACACAUUGCUUAUCUGUCGCCUGAGAUCUAUUCUCUUGAAGACAGCUGUAUGCCUAGAAGGAUAACACACGCUGUUUUGUUACUUUGGCAGUACAGGUAGCAUCA
.....................((((.((((((((((.((((.....))))...(((((((((((.(.((.....))...).))).))))))))........))).).))))))))))... ( -31.10)
>DroSec_CAF1 11790 120 + 1
AUCUUGCGGAUAAUAAAACAUUGCUAAUCUGUCGUCUGAGAUCUAUUCUCUUGAAGACAGAUGUAUGCCUAGAAGGAUAACACACGCUGUUUUGUUGCUUUGGCAGUACAGGUAGCAUCA
.....................((((((((((((.((.((((.....))))..)).)))))))(((((((..(((((((((.((.....)).))))).)))))))).)))...)))))... ( -31.70)
>DroSim_CAF1 11245 120 + 1
AUCUUGCGGAUAAUAACACAUUGCUAAUCUGUCGCCUGAGAUCUAUCCUCUUGAAGACAGCUGUAUGCCUAGAAGGAUAACACACGCUGUUUGGUUGCUUUGGCAGUACAGGUAGCAUCA
.....................(((((.(((((((((.(((......((......((((((((((.(.((.....))...).))).)))))))))...))).))).).))))))))))... ( -28.00)
>DroEre_CAF1 11852 120 + 1
AUCUUGUGGAUAAUAAUACAUUGCUAAUCUGUCGCUUAAGAUCUAUUCUCUUGAAGACAGCUGUAUGCCUAGAAGGAUAACACACGCUGUUUUGUUGCUUUGGCAGUACAGGUAGCAUCC
....((((........)))).(((((..(((((..((((((.......)))))).)))))(((((((((..(((((((((.((.....)).))))).)))))))).))))).)))))... ( -31.30)
>DroYak_CAF1 11978 119 + 1
AUU-UUAGGGUAAUAAUACAUUGCUAAUCUGUCGCUUAAGAUCUAUUCUGUUGAAGACAGCUGUAUGCCUAGAAGGAUAACACACGCUGUUUUGUUGUUCUGGCAGUACAGGUAGCAUCC
...-...(((((....)))..(((((..(((((.....(((.....)))......)))))(((((((((.((((.(((((.((.....)).))))).)))))))).))))).))))).)) ( -33.70)
>consensus
AUCUUGCGGAUAAUAACACAUUGCUAAUCUGUCGCCUGAGAUCUAUUCUCUUGAAGACAGCUGUAUGCCUAGAAGGAUAACACACGCUGUUUUGUUGCUUUGGCAGUACAGGUAGCAUCA
.....................(((((..(((((....((((.....)))).....)))))(((((((((.(((..(((((.((.....)).)))))..))))))).))))).)))))... (-26.52 = -27.56 +   1.04)

alignment

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secondary structure

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Window 9

Location 24,898,867 – 24,898,980
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 95.66
Mean single sequence MFE -33.70
Consensus MFE -30.60
Energy contribution -30.24
Covariance contribution -0.36
Combinations/Pair 1.16
Mean z-score -1.39
Structure conservation index 0.91
SVM decision value 0.89
SVM RNA-class probability 0.876187
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24898867 113 + 27905053
CACACGCUGUUUUGUUACUUUGGCAGUACAGGUAGCAUCAAUAUCCCAUCUACUUUUUGGUAUGUCUGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCC
.....((((...((((((((.(......)))))))))........(((((((((........((((.....))))((((((.....))))))...))))))...))).)))). ( -32.70)
>DroSec_CAF1 11870 113 + 1
CACACGCUGUUUUGUUGCUUUGGCAGUACAGGUAGCAUCAAUAUCCCAUCUACUUUUUGGUCCGUCUGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCC
.....((((...((((((((.(......)))))))))........(((((((((.....(((((.....))))).((((((.....))))))...))))))...))).)))). ( -34.90)
>DroSim_CAF1 11325 113 + 1
CACACGCUGUUUGGUUGCUUUGGCAGUACAGGUAGCAUCAAUAUCCCAUCUACUUUUUGGUCCGUCGGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCC
.....((((..((..(((....)))...))..)))).........(((((((((.....(((((.....))))).((((((.....))))))...))))))...)))...... ( -34.40)
>DroEre_CAF1 11932 113 + 1
CACACGCUGUUUUGUUGCUUUGGCAGUACAGGUAGCAUCCAUAUCCCAUCUACUCUUUGGUCCGUCUGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCC
.....((((...((((((((.(......)))))))))........(((((((((((...(((((.....))))).((((((.....)))))))).))))))...))).)))). ( -35.60)
>DroYak_CAF1 12057 113 + 1
CACACGCUGUUUUGUUGUUCUGGCAGUACAGGUAGCAUCCAUAUCCCAUCUAGUUUUUGGUUCUUCUGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCC
...((.((((.(((((.....))))).)))))).......................((((((.((((((((....((((((.....))))))..))))))))...)))))).. ( -30.90)
>consensus
CACACGCUGUUUUGUUGCUUUGGCAGUACAGGUAGCAUCAAUAUCCCAUCUACUUUUUGGUCCGUCUGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCC
.....((((....(((((.(((......)))))))).........(((((((((.....((((.......)))).((((((.....))))))...))))))...))).)))). (-30.60 = -30.24 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 24,898,907 – 24,899,020
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 95.66
Mean single sequence MFE -28.47
Consensus MFE -25.62
Energy contribution -25.90
Covariance contribution 0.28
Combinations/Pair 1.04
Mean z-score -1.17
Structure conservation index 0.90
SVM decision value 0.06
SVM RNA-class probability 0.562542
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24898907 113 + 27905053
AUAUCCCAUCUACUUUUUGGUAUGUCUGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCCACUUACCAACGCUCUUCUCUUCAGUUCGAGUUCCUUUGAG
................((((((.((..(((((.(.((((((.....))))))..((((....)))))))))).)).)))))).((((..((....))...))))......... ( -28.00)
>DroSec_CAF1 11910 113 + 1
AUAUCCCAUCUACUUUUUGGUCCGUCUGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCCACUUACCAACGCUCUCCUCUUCAGUUCGAGUUCCUUUGAG
................((((((..(((((((....((((((.....))))))..)))))))....))))))...((((.....((((.............)))).....)))) ( -27.42)
>DroSim_CAF1 11365 113 + 1
AUAUCCCAUCUACUUUUUGGUCCGUCGGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCCACUUACCAACGCUCUUCUCUUCAGUUCGAGUUCCUUUGAG
................(((((..((.((((((.(.((((((.....))))))..((((....)))))))))))))..))))).((((..((....))...))))......... ( -30.60)
>DroEre_CAF1 11972 113 + 1
AUAUCCCAUCUACUCUUUGGUCCGUCUGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCCACUUACCUACGCUCUUUACUUCAGUUCGAGUUGCUUUGAG
............(((..(((((..(((((((....((((((.....))))))..)))))))....)))))((.((((....((.............))..)))).))...))) ( -29.32)
>DroYak_CAF1 12097 113 + 1
AUAUCCCAUCUAGUUUUUGGUUCUUCUGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCCACUUACCAACGCUCUUCACUUCAGUUCGAGUUCCUUUGAG
................(((((..((((((((....((((((.....))))))..))))))))..(((....)))...))))).((((...((....))..))))......... ( -27.00)
>consensus
AUAUCCCAUCUACUUUUUGGUCCGUCUGCUGGACAGCUGCAAAAACUGCAGCAGCAGUAGAAAUUGGCCAGCCACUUACCAACGCUCUUCUCUUCAGUUCGAGUUCCUUUGAG
................((((((..(((((((....((((((.....))))))..)))))))....))))))...((((.....((((.............)))).....)))) (-25.62 = -25.90 +   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 13:32:57 2006