Locus 5283

Sequence ID X_DroMel_CAF1
Location 13,848,739 – 13,849,014
Length 275
Max. P 0.952163
window8549 window8550 window8551 window8552

overview

Window 9

Location 13,848,739 – 13,848,857
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.39
Mean single sequence MFE -33.40
Consensus MFE -31.10
Energy contribution -31.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.93
SVM decision value 0.38
SVM RNA-class probability 0.713217
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13848739 118 + 22224390
GUAAACCAACUGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGACCGUUCUAUGCUUUUUUU--UAAUAUUCAUAUUUU
..........((((((((..((((........)))).((((((....).))))).....(((((.......)))))))))))))...................--............... ( -31.50)
>DroSim_CAF1 2641 118 + 1
UUUAAACAACUGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAUCCUUCUAUACUUUUUUU--CAAUAUUAAUAUUUU
..........((((((((..((((........)))).((((((....).))))).....(((((.......)))))))))))))...................--............... ( -31.50)
>DroYak_CAF1 75 119 + 1
GUAAAUCAACUGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAAAGUUUAACACUUUUUUUUUAAGUGUUUAUAUUU-
..........((((((((..((((........)))).((((((....).))))).....(((((.......))))))))))))).((((..(((((((.......)))))))...))))- ( -37.20)
>consensus
GUAAAACAACUGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAACGUUCUAUACUUUUUUU__AAAUAUUAAUAUUUU
..........((((((((..((((........))))...(((((.((((((.(.......).)))))))))))...)))))))).................................... (-31.10 = -31.10 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,848,739 – 13,848,857
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.39
Mean single sequence MFE -32.23
Consensus MFE -28.60
Energy contribution -28.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.67
Structure conservation index 0.89
SVM decision value 1.42
SVM RNA-class probability 0.952163
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13848739 118 - 22224390
AAAAUAUGAAUAUUA--AAAAAAAGCAUAGAACGGUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGUUGGUUUAC
...............--..........((((.(((..(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))..))).)))). ( -30.90)
>DroSim_CAF1 2641 118 - 1
AAAAUAUUAAUAUUG--AAAAAAAGUAUAGAAGGAUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGUUGUUUAAA
.........(((((.--......))))).(((.(((.(((((((.((((.......))))......((((((.....)))))).((((........))))..))))))).))).)))... ( -31.70)
>DroYak_CAF1 75 119 - 1
-AAAUAUAAACACUUAAAAAAAAAGUGUUAAACUUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGUUGAUUUAC
-.......(((((((.......)))))))........(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))........... ( -34.10)
>consensus
AAAAUAUAAAUAUUA__AAAAAAAGUAUAGAACGAUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGUUGAUUUAC
.....................................(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))........... (-28.60 = -28.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,848,857 – 13,848,974
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.31
Mean single sequence MFE -28.30
Consensus MFE -15.72
Energy contribution -17.95
Covariance contribution 2.23
Combinations/Pair 1.14
Mean z-score -1.99
Structure conservation index 0.56
SVM decision value 0.06
SVM RNA-class probability 0.565391
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13848857 117 + 22224390
UCCUUGAGCUAUGAAUAUUACAGCUUUCAUUAAUUGGCCAAGUCAAUUGCUGAAAA---AAAUAUUUAUUAGUUCUUUAAGGAACUAGAAGCUUAAAUAGUGUAUUGGGCUUGCGUAAGG
.(((((.((..((((((((.....(((((.((((((((...)))))))).))))).---.))))))))((((((((....))))))))((((((((........)))))))))).))))) ( -31.10)
>DroSim_CAF1 2759 117 + 1
UCCUUGAGCUAUGAAUAUUACAGCUUUUUUUAAUUGGCCAAGUCAAUUGUUGCCAC---AAAUAUUUAUAAGUUCUUUAAGGAACUAGAAGCCUAAAUAGUGUAUUGGGCUUGCCAAAUA
(((((((((((((((((((...((......((((((((...))))))))..))...---.))))))))).)))))...))))).....((((((((........))))))))........ ( -28.80)
>DroYak_CAF1 194 118 + 1
UGCUUGAGCUCAGAAUAUUACAGAUUUUAUUAAUUGGUCAAGCCUAUUGCUGCUAAAAAAGAGAGUUAU--GUUCGCUGAGAAGCAAGAAUCUUAACUAGCGUAUUGGGCGCCUAUAAUA
.((((((.(....((((..........))))....).))))(((((.(((.((((...(((((((....--.)))(((....))).....))))...))))))).)))))))........ ( -25.00)
>consensus
UCCUUGAGCUAUGAAUAUUACAGCUUUUAUUAAUUGGCCAAGUCAAUUGCUGCAAA___AAAUAUUUAU_AGUUCUUUAAGGAACUAGAAGCUUAAAUAGUGUAUUGGGCUUGCAUAAUA
(((((((((((((((((((...........((((((((...))))))))...........))))))))).)))))...))))).....((((((((........))))))))........ (-15.72 = -17.95 +   2.23)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,848,897 – 13,849,014
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.55
Mean single sequence MFE -31.97
Consensus MFE -21.31
Energy contribution -22.77
Covariance contribution 1.45
Combinations/Pair 1.13
Mean z-score -1.56
Structure conservation index 0.67
SVM decision value 0.03
SVM RNA-class probability 0.547837
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13848897 117 + 22224390
AGUCAAUUGCUGAAAA---AAAUAUUUAUUAGUUCUUUAAGGAACUAGAAGCUUAAAUAGUGUAUUGGGCUUGCGUAAGGACAAGUAGCAGUCGUGGCCGAGUGGUUAAGGCGUCUGACU
(((((..(((((....---.........((((((((....))))))))((((((((........)))))))).............)))))(((.(((((....))))).)))...))))) ( -30.10)
>DroSim_CAF1 2799 117 + 1
AGUCAAUUGUUGCCAC---AAAUAUUUAUAAGUUCUUUAAGGAACUAGAAGCCUAAAUAGUGUAUUGGGCUUGCCAAAUAACAAGUAGCAGUCGUGGCCGAGUGGUUAAGGCGUCUGACU
(((((..(((((((((---...........((((((....))))))..((((((((........))))))))((((....((........))..))))...)))))...))))..))))) ( -32.60)
>DroYak_CAF1 234 118 + 1
AGCCUAUUGCUGCUAAAAAAGAGAGUUAU--GUUCGCUGAGAAGCAAGAAUCUUAACUAGCGUAUUGGGCGCCUAUAAUAAUAUGCAGCAGUCGUGGCCGAGUGGUUAAGGCGUCUGACU
.((((((((((((..........(((((.--(((((((....)))..))))..))))).((((.....))))............))))))))..(((((....)))))))))........ ( -33.20)
>consensus
AGUCAAUUGCUGCAAA___AAAUAUUUAU_AGUUCUUUAAGGAACUAGAAGCUUAAAUAGUGUAUUGGGCUUGCAUAAUAACAAGUAGCAGUCGUGGCCGAGUGGUUAAGGCGUCUGACU
((((...((((((..................(((((....)))))...((((((((........))))))))............))))))(((.(((((....))))).)))....)))) (-21.31 = -22.77 +   1.45)

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 11:43:56 2006