Locus 3099

Sequence ID X_DroMel_CAF1
Location 8,272,647 – 8,272,782
Length 135
Max. P 0.989449
window5068 window5069 window5070

overview

Window 8

Location 8,272,647 – 8,272,749
Length 102
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 63.24
Mean single sequence MFE -34.30
Consensus MFE -19.68
Energy contribution -19.93
Covariance contribution 0.25
Combinations/Pair 1.42
Mean z-score -1.85
Structure conservation index 0.57
SVM decision value 2.16
SVM RNA-class probability 0.989449
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8272647 102 - 22224390
CAUUGCCAUUGCUGGCGACGGUCGGCAGA-UUAGCCUUAUUUUC-----------------GCUGCUAGUAAGGAACAUAUUUUUACUGCCGGUUGCCAGAACAAUGGUAUCCCCGUUGG
...((((((((((((((((...((((((.-....(((((((...-----------------......)))))))....((....))))))))))))))))..)))))))).......... ( -35.80)
>DroSim_CAF1 11872 102 - 1
CAUUGCCAUUGCUGGCGACGGUCGGCAGA-AUAGCCUUAUUAUC-----------------GCUGCUAGUAAGGAACAUACUUUUGCUGCCGGUUGCCAGCACAAUGGUAUCCCCGUUGG
...((((((((((((((((((.(((((((-(((.((((((((..-----------------.....))))))))....)).)))))))))).))))))))))..)))))).......... ( -43.20)
>DroWil_CAF1 16489 111 - 1
GAUUACCACCAUUGAGAAUAGUCGUUGUUCCUGUCCCCGUUACAGCUGCUGCUUGCUUCUCGGCAUUGGAAAAUAUCAUUGGUUUAUUGCCAUUUGCCAGGACA---------CCGUUGA
........((...(((((((((.(((((..(.......)..))))).)))).....)))))((((.(((..((((.........)))).)))..)))).))...---------....... ( -23.10)
>DroYak_CAF1 10059 105 - 1
CAUUGCCAUUGGUGGCGACGGUCGGCAUC-ACACCCUUGUUAUCAUU--------------ACUGCUGGUAAGGAACAUACUCUUGUUGCCGUUCGCCAGCACAAUGGUAUCGCCGUUGG
..((((((....))))))(((.((((...-(((....)))(((((((--------------..(((((((..((((((......)))).))....))))))).)))))))..))))))). ( -35.10)
>consensus
CAUUGCCAUUGCUGGCGACGGUCGGCAGA_AUAGCCUUAUUAUC_________________GCUGCUAGUAAGGAACAUACUUUUACUGCCGGUUGCCAGCACAAUGGUAUCCCCGUUGG
.........(((((((((((((.(((((..................................)))))(((((((.......))))))))))).)))))))))((((((.....)))))). (-19.68 = -19.93 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,272,687 – 8,272,782
Length 95
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 59.60
Mean single sequence MFE -29.08
Consensus MFE -13.90
Energy contribution -15.90
Covariance contribution 2.00
Combinations/Pair 1.30
Mean z-score -1.58
Structure conservation index 0.48
SVM decision value 0.79
SVM RNA-class probability 0.851009
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8272687 95 + 22224390
UAUGUUCCUUACUAGCAGC-----------------GAAAAUAAGGCUAA-UCUGCCGACCGUCGCCAGCAAUGGCAAUGGUCUGAUCACAGCCAAAAUGGAUCUAUUGGA-------GG
....((((...........-----------------........(((...-...)))((((((.((((....)))).)))))).((((.((.......))))))....)))-------). ( -29.00)
>DroSim_CAF1 11912 95 + 1
UAUGUUCCUUACUAGCAGC-----------------GAUAAUAAGGCUAU-UCUGCCGACCGUCGCCAGCAAUGGCAAUGGUCUGAUCACGGCCAAAAUGGAGCUAUUGGA-------GG
...(((((......((.(.-----------------(((.....(((...-...)))((((((.((((....)))).))))))..))).).))......))))).......-------.. ( -33.00)
>DroWil_CAF1 16520 120 + 1
AAUGAUAUUUUCCAAUGCCGAGAAGCAAGCAGCAGCUGUAACGGGGACAGGAACAACGACUAUUCUCAAUGGUGGUAAUCGAUUUAUGGUUACAAAAAUGGAACAUCCAGAUACAACAGC
.......(((((.......)))))((.....)).(((((...(....).(((...((.(((((.....))))).))..((.((((.((....)).)))).))...))).......))))) ( -22.20)
>DroYak_CAF1 10099 98 + 1
UAUGUUCCUUACCAGCAGU--------------AAUGAUAACAAGGGUGU-GAUGCCGACCGUCGCCACCAAUGGCAAUGGUUUGCUCACAGCUAAAACGGAACUAUUGGA-------GG
...(((((.......((..--------------..)).......((.(((-((.((.((((((.((((....)))).)))))).))))))).)).....))))).......-------.. ( -32.10)
>consensus
UAUGUUCCUUACCAGCAGC_________________GAUAACAAGGCUAU_UAUGCCGACCGUCGCCAGCAAUGGCAAUGGUCUGAUCACAGCCAAAAUGGAACUAUUGGA_______GG
...(((((......((............................(((.......)))((((((.((((....)))).))))))........))......)))))................ (-13.90 = -15.90 +   2.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,272,687 – 8,272,782
Length 95
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 59.60
Mean single sequence MFE -29.35
Consensus MFE -13.18
Energy contribution -14.92
Covariance contribution 1.75
Combinations/Pair 1.29
Mean z-score -1.86
Structure conservation index 0.45
SVM decision value 0.95
SVM RNA-class probability 0.887440
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8272687 95 - 22224390
CC-------UCCAAUAGAUCCAUUUUGGCUGUGAUCAGACCAUUGCCAUUGCUGGCGACGGUCGGCAGA-UUAGCCUUAUUUUC-----------------GCUGCUAGUAAGGAACAUA
..-------.......(.(((...(((((.((((...((((.((((((....)))))).))))(((...-...)))......))-----------------)).)))))...))).)... ( -32.40)
>DroSim_CAF1 11912 95 - 1
CC-------UCCAAUAGCUCCAUUUUGGCCGUGAUCAGACCAUUGCCAUUGCUGGCGACGGUCGGCAGA-AUAGCCUUAUUAUC-----------------GCUGCUAGUAAGGAACAUA
..-------.......(.(((...(((((.(((((..((((.((((((....)))))).))))(((...-...))).....)))-----------------)).)))))...))).)... ( -33.00)
>DroWil_CAF1 16520 120 - 1
GCUGUUGUAUCUGGAUGUUCCAUUUUUGUAACCAUAAAUCGAUUACCACCAUUGAGAAUAGUCGUUGUUCCUGUCCCCGUUACAGCUGCUGCUUGCUUCUCGGCAUUGGAAAAUAUCAUU
.............(((((((((.....((((.(.......).)))).....(((((((((((.(((((..(.......)..))))).)))).....)))))))...))))..)))))... ( -19.40)
>DroYak_CAF1 10099 98 - 1
CC-------UCCAAUAGUUCCGUUUUAGCUGUGAGCAAACCAUUGCCAUUGGUGGCGACGGUCGGCAUC-ACACCCUUGUUAUCAUU--------------ACUGCUGGUAAGGAACAUA
..-------.......(((((...((((((((((((..(((.((((((....)))))).)))..)).))-)))....((....))..--------------...)))))...)))))... ( -32.60)
>consensus
CC_______UCCAAUAGUUCCAUUUUGGCUGUGAUCAAACCAUUGCCAUUGCUGGCGACGGUCGGCAGA_AUAGCCUUAUUAUC_________________GCUGCUAGUAAGGAACAUA
................(.(((...(((((.((.....((((.((((((....)))))).))))(((.......))).........................)).)))))...))).)... (-13.18 = -14.92 +   1.75)

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 10:50:57 2006