Locus 5966

Sequence ID X_DroMel_CAF1
Location 15,371,719 – 15,372,013
Length 294
Max. P 0.954959
window9688 window9689 window9690 window9691

overview

Window 8

Location 15,371,719 – 15,371,839
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.08
Mean single sequence MFE -40.64
Consensus MFE -29.38
Energy contribution -28.90
Covariance contribution -0.48
Combinations/Pair 1.26
Mean z-score -2.85
Structure conservation index 0.72
SVM decision value 1.20
SVM RNA-class probability 0.929891
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15371719 120 + 22224390
AUUUUUAUCGACGAAAAUGUAGUAGCUAUUAAACAACAUUUUCAUUGCGCUUUUCUCGCAGUGCAGGAGCAUUGGAGCGCUGGAAGUGGCGUUCCUUGGCUUCUGUGCAACUCGGACGUG
.......((((.((((((((.((.........)).))))))))..((((.......))))(..(((((((...((((((((......))))))))...)))))))..)...))))..... ( -43.80)
>DroSec_CAF1 13709 120 + 1
AUUUUUAUCGGCGAAAAUGUAGUGGCUAUUAAACUACAUUUUCAUUGCUAUUUUCUCGCAGUGCACGAGCAUUGGAGCGCUGGAAGUGGCGUUCCUUGGCUUCUGUGCAACGCGGACUUG
.........((((((((((((((.........)))))))))))...)))....((.(((..(((((((((...((((((((......))))))))...))))..)))))..))))).... ( -45.80)
>DroSim_CAF1 6874 120 + 1
AUUUUUAUCGGCGAAAAUAUAGUGGCUAUUAAACUACAUUUUCAUUGCUAUUUUCUCGCAGUGCACGAGCAUUGGAGCGCUGGAAGUGGCGUUCCUUGGCUUCUGUGCAACGCGGACGUG
.........(((((((((.((((.........)))).))))))...)))....((.(((..(((((((((...((((((((......))))))))...))))..)))))..))))).... ( -39.80)
>DroEre_CAF1 11811 120 + 1
AUUUUUAUCGGUGGAAAUAUGGUCGCUAUUAAACUACAUUUUCAUAGCUCUUUUCUCACAGUGCAGGAGUUUUGGAGCGCUGGAAGUUGCGUUCCUUGGCUUCUGUGCAACUCGGACGUG
.......((((((((((...((..(((((.(((......))).))))).)))))).))).(..((((((((..(((((((........)))))))..))))))))..)....)))..... ( -39.60)
>DroYak_CAF1 3783 120 + 1
AUUUUUAUUGGUGAGAAUAGAGUCGCUAUUAAACUACAUUUUCAUGGCUAUUUUCUCGUAGUGCAUUAGCUUUGGAGCGCUGGAAGUUGCGUUCUUUGGCUUCUGUGCAACUUGGACGUG
...((((.((((((........)))))).))))...(((.((((.((((((......)))))((((.((((..(((((((........)))))))..))))...))))..).)))).))) ( -34.20)
>consensus
AUUUUUAUCGGCGAAAAUAUAGUCGCUAUUAAACUACAUUUUCAUUGCUAUUUUCUCGCAGUGCACGAGCAUUGGAGCGCUGGAAGUGGCGUUCCUUGGCUUCUGUGCAACUCGGACGUG
.......(((..((((((.((((.........)))).)))))).................(..((.((((...(((((((........)))))))...)))).))..)....)))..... (-29.38 = -28.90 +  -0.48)

alignment

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secondary structure

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Window 9

Location 15,371,759 – 15,371,873
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.69
Mean single sequence MFE -43.54
Consensus MFE -37.14
Energy contribution -36.98
Covariance contribution -0.16
Combinations/Pair 1.24
Mean z-score -1.91
Structure conservation index 0.85
SVM decision value 1.37
SVM RNA-class probability 0.947179
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15371759 114 + 22224390
UUCAUUGCGCUUUUCUCGCAGUGCAGGAGCAUUGGAGCGCUGGAAGUGGCGUUCCUUGGCUUCUGUGCAACUCGGACGUGGCUGAACAUGUGGAAUGUAUGGAUGUGCCUGUG------C
..(((.((((..(((..((((..(((((((...((((((((......))))))))...)))))))..).......(((((......)))))....)))..))).))))..)))------. ( -45.20)
>DroSec_CAF1 13749 119 + 1
UUCAUUGCUAUUUUCUCGCAGUGCACGAGCAUUGGAGCGCUGGAAGUGGCGUUCCUUGGCUUCUGUGCAACGCGGACUUGGACGAACAUGUGG-AUGUAUAGAUGUGCCUGUGGACGUGG
.......((((..((.(((((.((((((((...((((((((......))))))))...)))((((((((.((((...((....))...)))).-.)))))))))))))))))))).)))) ( -43.80)
>DroSim_CAF1 6914 119 + 1
UUCAUUGCUAUUUUCUCGCAGUGCACGAGCAUUGGAGCGCUGGAAGUGGCGUUCCUUGGCUUCUGUGCAACGCGGACGUGGCGGAACAUGUGG-AUGUAUGGAUGUGCCUGUGGACGUGG
....(((((((..((.(((..(((((((((...((((((((......))))))))...))))..)))))..))))).)))))))..(((((..-((((((....))))..))..))))). ( -43.90)
>DroEre_CAF1 11851 119 + 1
UUCAUAGCUCUUUUCUCACAGUGCAGGAGUUUUGGAGCGCUGGAAGUUGCGUUCCUUGGCUUCUGUGCAACUCGGACGUGAAUGAGCACGUGG-AUGUAUGGAUGUGCCUGUGAAUAUGG
((((((((.(..(((..((((..((((((((..(((((((........)))))))..))))))))..).......(((((......)))))..-.)))..))).).).)))))))..... ( -44.80)
>DroYak_CAF1 3823 119 + 1
UUCAUGGCUAUUUUCUCGUAGUGCAUUAGCUUUGGAGCGCUGGAAGUUGCGUUCUUUGGCUUCUGUGCAACUUGGACGUGAAUGAGCACGUGG-AUGUAUGGAUGUGCCUGUGGACGUGG
(((((((((...(((.(((..(((((.((((..(((((((........)))))))..))))...)))))......))).)))..))).)))))-).......((((.((...)))))).. ( -40.00)
>consensus
UUCAUUGCUAUUUUCUCGCAGUGCACGAGCAUUGGAGCGCUGGAAGUGGCGUUCCUUGGCUUCUGUGCAACUCGGACGUGGAUGAACAUGUGG_AUGUAUGGAUGUGCCUGUGGACGUGG
...............((((((.((((((((...(((((((........)))))))...)))((((((((......(((((......)))))....)))))))))))))))))))...... (-37.14 = -36.98 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,371,873 – 15,371,975
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.37
Mean single sequence MFE -38.34
Consensus MFE -29.54
Energy contribution -29.94
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.77
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15371873 102 + 22224390
AUG------UG------------GCCAUGGUCGACCCAUUUAGGAGUGCUCGCGAUGGAGACGCCGUCGUGGUUGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGCCAAAAGCACAAAGU
...------((------------((((((((...........((((((((((((((((.....))))))))).....)))))))((.....))....)))))).))))............ ( -36.50)
>DroSec_CAF1 13868 102 + 1
AUG------UG------------GACAUGGUCGACCCAUUUAGGAGUGCUCGCUAUGGAGACGCCGUCGUGGUUGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGCCAAAAACACAAAGU
.((------((------------...((((.....))))...(((((((..((((((..(....)..))))))....))))))).((((.(((((.....))))).))))..)))).... ( -30.50)
>DroSim_CAF1 7033 102 + 1
AUG------UG------------GACAUGGUCGACCCAUUUAGGAGUGCUCGCGAUGGAGACGCCGUCGUGGUUGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGCCAAAAGCACAAAGU
..(------..------------(((((((.....))))...((((((((((((((((.....))))))))).....))))))))))..).((((.....))))((.....))....... ( -36.10)
>DroEre_CAF1 11970 108 + 1
AUGUGAGUGUG------------GACAUGGUCGACCCACUUAGGAGUGCUCGCGAUGGAGACGCCGUCGUGGUCGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGGCAAAAGCACAAAGU
.((((((((.(------------(.(......).))))))..((((((((((((((((.....))))))))).....))))))).((((((((((.....))))))))))..)))).... ( -44.90)
>DroYak_CAF1 3942 120 + 1
AUGUGGAUGUGGAUGUGGAUACGGACAUGGUCGACCCACUUAGGAGUGCUCGCGAUGGAGACGCCGGCGUGGUUGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGGCAAAAGCACAAAGU
..((((..((.((((((........))).))).))))))......(((((...(((((((.(((.((((....))))))))))))))((((((((.....))))))))..)))))..... ( -43.70)
>consensus
AUG______UG____________GACAUGGUCGACCCAUUUAGGAGUGCUCGCGAUGGAGACGCCGUCGUGGUUGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGCCAAAAGCACAAAGU
...........................(((.....)))....((((((((((((((((.....))))))))).....))))))).((((.(((((.....))))).)))).......... (-29.54 = -29.94 +   0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,371,895 – 15,372,013
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.23
Mean single sequence MFE -46.18
Consensus MFE -37.64
Energy contribution -37.56
Covariance contribution -0.08
Combinations/Pair 1.15
Mean z-score -2.02
Structure conservation index 0.82
SVM decision value 1.45
SVM RNA-class probability 0.954959
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15371895 118 + 22224390
UAGGAGUGCUCGCGAUGGAGACGCCGUCGUGGUUGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGCCAAAAGCACAAAGUCCUGCCAGGACGCGAAAUUGCUAGAUGGAGUGGG--AAAG
.......((.((((((((.....))))))))))..((.((((((((((((.((((.....))))))....((((....((((.....)))).......)))))))))))))).)--)... ( -41.60)
>DroSec_CAF1 13890 117 + 1
UAGGAGUGCUCGCUAUGGAGACGCCGUCGUGGUUGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGCCAAAAACACAAAGUCCUGCCAGGACGCGAAAUGGUUCGAUGGAGUGGG--A-AG
..(((((((..((((((..(....)..))))))....))))))).((..((.(((.((((((.(((............((((.....)))))))..))))))..))).))..))--.-.. ( -36.20)
>DroSim_CAF1 7055 117 + 1
UAGGAGUGCUCGCGAUGGAGACGCCGUCGUGGUUGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGCCAAAAGCACAAAGUCCUGCCAGGACGCGAAAUGGUUAGAUGGAGUGGG--A-AG
..((((((((((((((((.....))))))))).....))))))).((..((.(((.((((((((((.....)).....((((.....))))))...))))))..))).))..))--.-.. ( -43.40)
>DroEre_CAF1 11998 117 + 1
UAGGAGUGCUCGCGAUGGAGACGCCGUCGUGGUCGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGGCAAAAGCACAAAGUCCUGCCAGGACGCGAAAUGGCAGGACGGGGCGGG--U-AG
......((((((((((((..(((....)))..)))))))(((((.((((((((((.....))))))))))........(((((((((..........)))))))))))))))))--)-). ( -57.80)
>DroYak_CAF1 3982 119 + 1
UAGGAGUGCUCGCGAUGGAGACGCCGGCGUGGUUGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGGCAAAAGCACAAAGUCCUGCCAGGACGCAAAAUGGCAGGAUGGAGUGGGGUU-AG
.......((((((((..(..(((....)))..)..))))(((((.((((((((((.....))))))))))........(((((((((..........)))))))))))))).)))).-.. ( -51.90)
>consensus
UAGGAGUGCUCGCGAUGGAGACGCCGUCGUGGUUGUCGCGCUCCGUUUGCUGCAUAAAUCAUGCGCCAAAAGCACAAAGUCCUGCCAGGACGCGAAAUGGCUAGAUGGAGUGGG__A_AG
...((..((.((((((((.....))))))))))..)).(((((((((((((((((.....))))..............((((.....)))).......))).))))))))))........ (-37.64 = -37.56 +  -0.08)

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 12:00:50 2006