Locus 4245

Sequence ID 3R_DroMel_CAF1
Location 11,383,188 – 11,383,336
Length 148
Max. P 0.994195
window6884 window6885 window6886 window6887

overview

Window 4

Location 11,383,188 – 11,383,296
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.15
Mean single sequence MFE -37.20
Consensus MFE -31.89
Energy contribution -31.73
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -2.16
Structure conservation index 0.86
SVM decision value 2.46
SVM RNA-class probability 0.994195
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11383188 108 + 27905053
AUUGGCCUGACUGGCGAUU------------CGCAUUCGCUGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAAACAAAUUUCCUGCCAACGGCCACGCAAUUUAUACCCAUAUACG
..(((((....((((((..------------((((.((....)).)))).....))))))..(((..((((((((.....))))))))..))).)))))..................... ( -34.70)
>DroSec_CAF1 130910 108 + 1
AUUGGCCUGACUGGCGAUU------------CGCAUUCGCUGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAAACAAAUUUCCUGCCAACGGCCACGCAAUUUGUGCCUAUAUACG
..(((((....((((((..------------((((.((....)).)))).....))))))..(((..((((((((.....))))))))..))).))))).(((.....)))......... ( -36.00)
>DroSim_CAF1 122034 108 + 1
AUUGGCCUGACUGGCGAUU------------CGCAUUCGCUGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAAACAAAUUUCCUGCCAACGGCCACGCAAUUUGUGCCCAUAUACG
..(((((....((((((..------------((((.((....)).)))).....))))))..(((..((((((((.....))))))))..))).))))).(((.....)))......... ( -36.00)
>DroEre_CAF1 118399 120 + 1
AUUGGCCUGACUGGCGAUUCGGAUUCGGAUUCGCAUUCGGUGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAAACAAAUUUCCUGCCAGCGGCCACGCAAUUUGUGCCCAUAUACG
..(((((.(.(((((.....((....((((.((((.((....)).)))).))))...))........((((((((.....))))))))))))))))))).(((.....)))......... ( -39.70)
>DroYak_CAF1 121059 114 + 1
AUUGGCCUGACUGGCGAUUCG------GAUUCGCAUUCGGCGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAUACAAAUUUCCUGCCAACGGCCACGCAAUUUGUGCCCAUAUACG
..(((((....((((((...(------(((.((((.((....)).)))).))))))))))..(((..((((((((.....))))))))..))).))))).(((.....)))......... ( -39.60)
>consensus
AUUGGCCUGACUGGCGAUU____________CGCAUUCGCUGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAAACAAAUUUCCUGCCAACGGCCACGCAAUUUGUGCCCAUAUACG
..(((((....((((((..............((((.((....)).)))).....))))))..(((..((((((((.....))))))))..))).)))))..................... (-31.89 = -31.73 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,383,188 – 11,383,296
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.15
Mean single sequence MFE -33.52
Consensus MFE -29.43
Energy contribution -29.47
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.66
Structure conservation index 0.88
SVM decision value 1.47
SVM RNA-class probability 0.956670
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11383188 108 - 27905053
CGUAUAUGGGUAUAAAUUGCGUGGCCGUUGGCAGGAAAUUUGUUUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCAGCGAAUGCG------------AAUCGCCAGUCAGGCCAAU
((((.............))))((((((((((.(((............))).)))))..((((((((.....((((.((....)).))))------------..))))))))..))))).. ( -31.82)
>DroSec_CAF1 130910 108 - 1
CGUAUAUAGGCACAAAUUGCGUGGCCGUUGGCAGGAAAUUUGUUUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCAGCGAAUGCG------------AAUCGCCAGUCAGGCCAAU
.........(((.....))).((((((((((.(((............))).)))))..((((((((.....((((.((....)).))))------------..))))))))..))))).. ( -32.80)
>DroSim_CAF1 122034 108 - 1
CGUAUAUGGGCACAAAUUGCGUGGCCGUUGGCAGGAAAUUUGUUUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCAGCGAAUGCG------------AAUCGCCAGUCAGGCCAAU
((((..((....))...))))((((((((((.(((............))).)))))..((((((((.....((((.((....)).))))------------..))))))))..))))).. ( -33.40)
>DroEre_CAF1 118399 120 - 1
CGUAUAUGGGCACAAAUUGCGUGGCCGCUGGCAGGAAAUUUGUUUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCACCGAAUGCGAAUCCGAAUCCGAAUCGCCAGUCAGGCCAAU
((((..((....))...))))(((((((((((.(((....(((((....((((((....)))).)))))))((((.((....)).))))..)))((.......))))))))..))))).. ( -34.90)
>DroYak_CAF1 121059 114 - 1
CGUAUAUGGGCACAAAUUGCGUGGCCGUUGGCAGGAAAUUUGUAUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCGCCGAAUGCGAAUC------CGAAUCGCCAGUCAGGCCAAU
((((..((....))...))))((((((((((.(((..((....))..))).)))))..((((((((.((..((((.((....)).))))..))------....))))))))..))))).. ( -34.70)
>consensus
CGUAUAUGGGCACAAAUUGCGUGGCCGUUGGCAGGAAAUUUGUUUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCAGCGAAUGCG____________AAUCGCCAGUCAGGCCAAU
.........(((.....))).((((((((((.(((............))).)))))..((((((((.....((((.((....)).))))..............))))))))..))))).. (-29.43 = -29.47 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,383,216 – 11,383,336
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -37.76
Consensus MFE -35.26
Energy contribution -35.18
Covariance contribution -0.08
Combinations/Pair 1.08
Mean z-score -1.46
Structure conservation index 0.93
SVM decision value 1.24
SVM RNA-class probability 0.935125
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11383216 120 + 27905053
UGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAAACAAAUUUCCUGCCAACGGCCACGCAAUUUAUACCCAUAUACGCGACCUACAGGUUGGGAUCCUCGACUUUUGUCUGGAUGUC
(((((((((((.....(((...(((..((((((((.....))))))))..))).))))))))))))))..........(.(((((....))))).)((((..(((....))).))))... ( -39.90)
>DroSec_CAF1 130938 120 + 1
UGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAAACAAAUUUCCUGCCAACGGCCACGCAAUUUGUGCCUAUAUACGCGACCUACAGGUGGGGAUCCUCGACUUUUGUCUGGAUGUC
.((((((((((.....(((...(((..((((((((.....))))))))..))).)))))))))))))...........(.(.(((....))).).)((((..(((....))).))))... ( -37.50)
>DroSim_CAF1 122062 120 + 1
UGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAAACAAAUUUCCUGCCAACGGCCACGCAAUUUGUGCCCAUAUACGCGACCUACAGGUGGGGAUCCUCGACUUUUGUCUGGAUGUC
.((((((((((.....(((...(((..((((((((.....))))))))..))).)))))))))))))...........(.(.(((....))).).)((((..(((....))).))))... ( -37.50)
>DroEre_CAF1 118439 120 + 1
UGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAAACAAAUUUCCUGCCAGCGGCCACGCAAUUUGUGCCCAUAUACGCGACCUACAGGUGGGGAUCCUCGACUUUUGUCUGGCUGUC
.((((((((((.....(((...(((..((((((((.....))))))))..))).)))))))))))))..(((......(.(.(((....))).).)......(((....))).))).... ( -37.10)
>DroYak_CAF1 121093 120 + 1
CGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAUACAAAUUUCCUGCCAACGGCCACGCAAUUUGUGCCCAUAUACGCGACCUACAGGUGGGGAUCCUCUACUCUUGUCUGGAUGUC
(((((((((((.....(((...(((..((((((((.....))))))))..))).)))))))))))))).((........))(((...((((..(((.........)))..))))...))) ( -36.80)
>consensus
UGGAUUGCGUGUCUUCGCCAAUUUGUUGGGAGAUUAAACAAAUUUCCUGCCAACGGCCACGCAAUUUGUGCCCAUAUACGCGACCUACAGGUGGGGAUCCUCGACUUUUGUCUGGAUGUC
(((((((((((.....(((...(((..((((((((.....))))))))..))).))))))))))))))..........(.(.(((....))).).)((((..(((....))).))))... (-35.26 = -35.18 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,383,216 – 11,383,336
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -34.21
Consensus MFE -32.14
Energy contribution -32.62
Covariance contribution 0.48
Combinations/Pair 1.03
Mean z-score -1.11
Structure conservation index 0.94
SVM decision value 0.00
SVM RNA-class probability 0.535365
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11383216 120 - 27905053
GACAUCCAGACAAAAGUCGAGGAUCCCAACCUGUAGGUCGCGUAUAUGGGUAUAAAUUGCGUGGCCGUUGGCAGGAAAUUUGUUUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCA
...((((.(((....)))..)))).....(((((.(((((((((.............)))))))))....))))).((((((((.........)))))))).(((......)))...... ( -33.82)
>DroSec_CAF1 130938 120 - 1
GACAUCCAGACAAAAGUCGAGGAUCCCCACCUGUAGGUCGCGUAUAUAGGCACAAAUUGCGUGGCCGUUGGCAGGAAAUUUGUUUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCA
...((((.(((....)))..)))).....(((((.(((((((((.............)))))))))....))))).((((((((.........)))))))).(((......)))...... ( -33.82)
>DroSim_CAF1 122062 120 - 1
GACAUCCAGACAAAAGUCGAGGAUCCCCACCUGUAGGUCGCGUAUAUGGGCACAAAUUGCGUGGCCGUUGGCAGGAAAUUUGUUUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCA
...((((.(((....)))..)))).....(((((.(((((((((..((....))...)))))))))....))))).((((((((.........)))))))).(((......)))...... ( -35.40)
>DroEre_CAF1 118439 120 - 1
GACAGCCAGACAAAAGUCGAGGAUCCCCACCUGUAGGUCGCGUAUAUGGGCACAAAUUGCGUGGCCGCUGGCAGGAAAUUUGUUUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCA
....(((((.(........(((.......)))...(((((((((..((....))...))))))))))))))).(((((((((((.........)))))))).(((......)))..))). ( -35.90)
>DroYak_CAF1 121093 120 - 1
GACAUCCAGACAAGAGUAGAGGAUCCCCACCUGUAGGUCGCGUAUAUGGGCACAAAUUGCGUGGCCGUUGGCAGGAAAUUUGUAUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCG
....................((((.....(((((.(((((((((..((....))...)))))))))....))))).(((((((...........))))))).(((......))).)))). ( -32.10)
>consensus
GACAUCCAGACAAAAGUCGAGGAUCCCCACCUGUAGGUCGCGUAUAUGGGCACAAAUUGCGUGGCCGUUGGCAGGAAAUUUGUUUAAUCUCCCAACAAAUUGGCGAAGACACGCAAUCCA
........(((....)))..((((.....(((((.(((((((((..((....))...)))))))))....))))).((((((((.........)))))))).(((......))).)))). (-32.14 = -32.62 +   0.48)

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 11:23:19 2006