Locus 4848

Sequence ID 3R_DroMel_CAF1
Location 12,697,237 – 12,697,377
Length 140
Max. P 0.832200
window7939 window7940 window7941

overview

Window 9

Location 12,697,237 – 12,697,327
Length 90
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 80.34
Mean single sequence MFE -21.23
Consensus MFE -15.19
Energy contribution -15.22
Covariance contribution 0.03
Combinations/Pair 1.24
Mean z-score -1.44
Structure conservation index 0.72
SVM decision value 0.38
SVM RNA-class probability 0.711034
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12697237 90 + 27905053
UGGCCCUGCCUACUGCCGGCUU-----------UUGUUGGCGGCAGUAAAAUUCGUUAAAUGCCCAACAAAUUGUUUAUUAUAGCAGUUUGGCAAUAAAUG
.(((...)))((((((((.(..-----------.....).))))))))............((((....((((((((......))))))))))))....... ( -27.30)
>DroVir_CAF1 76753 93 + 1
GC--------AGCGGCUGGCUUUGUUAUUCUUGUUACUGGCGGCAGUAAAAUUCGUUAAACGCUCAACAAAUUGUUUAUUAUAGCAAUUUGGCAAUAAAUG
((--------((((..((((....(((((.((((.....)))).))))).....))))..))))...(((((((((......)))))))))))........ ( -21.70)
>DroPse_CAF1 74631 81 + 1
A---------CGCUGACGGCUC-----------UUGUUGGCGGUAGUAAAAUUCGUUAAAUGCUCAACAAAUUGUUUAUUACAGCAGUUUGGCAAUAAAUG
.---------(((..(((....-----------.)))..)))..................(((....(((((((((......))))))))))))....... ( -17.40)
>DroGri_CAF1 125191 93 + 1
GC--------GGCGGCUGACUUUGUUAUUCUUGUUACUGGCGGCAGUAAAAUUCGUUAAACGCUCAACAAAUUGUUUAUUAUAGCAAUUUGGCAAUAAAUG
((--------((((..((((....(((((.((((.....)))).))))).....))))..))))...(((((((((......)))))))))))........ ( -22.20)
>DroAna_CAF1 60363 82 + 1
CG--------UUCUGCCGGCUU-----------UUGUUGGCGGUAGUAAAAUUCGUUAAAUGCCCAACAAAUUGUUUAUUAUAGCAGUUUGGCAAUAAAUG
..--------..((((((((..-----------..)))))))).................((((....((((((((......))))))))))))....... ( -21.40)
>DroPer_CAF1 81060 81 + 1
A---------CGCUGACGGCUC-----------UUGUUGGCGGUAGUAAAAUUCGUUAAAUGCUCAACAAAUUGUUUAUUACAGCAGUUUGGCAAUAAAUG
.---------(((..(((....-----------.)))..)))..................(((....(((((((((......))))))))))))....... ( -17.40)
>consensus
A_________CGCUGCCGGCUU___________UUGUUGGCGGCAGUAAAAUUCGUUAAAUGCUCAACAAAUUGUUUAUUAUAGCAGUUUGGCAAUAAAUG
...........(((((((.(..................).)))))))....................(((((((((......))))))))).......... (-15.19 = -15.22 +   0.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,697,258 – 12,697,367
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.40
Mean single sequence MFE -28.70
Consensus MFE -24.58
Energy contribution -24.25
Covariance contribution -0.33
Combinations/Pair 1.21
Mean z-score -1.97
Structure conservation index 0.86
SVM decision value 0.72
SVM RNA-class probability 0.832200
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12697258 109 + 27905053
U-----------UUGUUGGCGGCAGUAAAAUUCGUUAAAUGCCCAACAAAUUGUUUAUUAUAGCAGUUUGGCAAUAAAUGCGGCUAUUAACUCAUUUUAGGUGUUGCCACCGCACUUUUC
.-----------.(((((((((((.((((((..(((((..(((...(((((((((......)))))))))(((.....))))))..)))))..))))).).))))))))..)))...... ( -32.10)
>DroVir_CAF1 76766 120 + 1
UUGUUAUUCUUGUUACUGGCGGCAGUAAAAUUCGUUAAACGCUCAACAAAUUGUUUAUUAUAGCAAUUUGGCAAUAAAUGCGGCUAUUAGCUCAUUUUAGGUGUUGCCACCGCACUUUUC
..........(((...((((((((.((((((..(((((..(((...(((((((((......)))))))))(((.....))))))..)))))..))))).).))))))))..)))...... ( -29.30)
>DroGri_CAF1 125204 120 + 1
UUGUUAUUCUUGUUACUGGCGGCAGUAAAAUUCGUUAAACGCUCAACAAAUUGUUUAUUAUAGCAAUUUGGCAAUAAAUGCGGCCAUUAGCUCAUUGUAGGUGUUGCCACCGCACACUUA
...........((((.((((.(((........((.....)).....(((((((((......)))))))))........))).)))).))))......(((((((.((....))))))))) ( -30.30)
>DroWil_CAF1 99129 109 + 1
G-----------CUACUGACGGCAGUAAAAUUCGUUAAAUGCUUAACAAAUUGUUUAUUAUAGCAGUUUGGCAAUAAAUGCGGCCAUUAACUCAUUUUAGGUGUUGCCACCGCACUUUUC
(-----------((((((....)))))......(((((..(((...(((((((((......)))))))))(((.....))))))..)))))........((((....))))))....... ( -25.40)
>DroMoj_CAF1 86020 120 + 1
UUGUUAUUCUUGUUACUGGUGGCAGUAAAAUUCGUUAAACGCUAAACAAAUUGUUUAUUAUGGCAAUUUGGCAAUAAAUGCGGCCAUUAGCGCAUUUUAGGUGUUGCUACCGUACUUCUC
.............(((.((((((((((((((.((((((..(((...(((((((((......)))))))))(((.....))))))..)))))).))))))....)))))))))))...... ( -32.80)
>DroPer_CAF1 81072 109 + 1
C-----------UUGUUGGCGGUAGUAAAAUUCGUUAAAUGCUCAACAAAUUGUUUAUUACAGCAGUUUGGCAAUAAAUGCCCCCAUUAACUCAGUUUAGGUGUUGCCACCGCACUUUUC
.-----------......(((((.((((....(.((((((......(((((((((......)))))))))(((.....))).............)))))))..)))).)))))....... ( -22.30)
>consensus
U___________UUACUGGCGGCAGUAAAAUUCGUUAAACGCUCAACAAAUUGUUUAUUAUAGCAAUUUGGCAAUAAAUGCGGCCAUUAACUCAUUUUAGGUGUUGCCACCGCACUUUUC
................((((((((.((((((..(((((..(((...(((((((((......)))))))))(((.....))))))..)))))..))))).).))))))))........... (-24.58 = -24.25 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,697,287 – 12,697,377
Length 90
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 84.33
Mean single sequence MFE -18.02
Consensus MFE -16.02
Energy contribution -15.38
Covariance contribution -0.64
Combinations/Pair 1.22
Mean z-score -1.36
Structure conservation index 0.89
SVM decision value 0.06
SVM RNA-class probability 0.561534
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12697287 90 + 27905053
GCCCAACAAAUUGUUUAUUAUAGCAGUUUGGCAAUAAAUGCGGCUAUUAACUCAUUUUAGGUGUUGCCACCGCACUUUUCUGUUCGUCUC-----
(((...(((((((((......)))))))))(((.....))))))...............((((....))))...................----- ( -19.50)
>DroVir_CAF1 76806 95 + 1
GCUCAACAAAUUGUUUAUUAUAGCAAUUUGGCAAUAAAUGCGGCUAUUAGCUCAUUUUAGGUGUUGCCACCGCACUUUUCUCAUUUUUUAUCGCC
((....(((((((((......)))))))))((...(((((.(((.....))))))))..((((....))))))...................)). ( -20.90)
>DroPse_CAF1 74672 90 + 1
GCUCAACAAAUUGUUUAUUACAGCAGUUUGGCAAUAAAUGCCCCCAUUAACUCAGUUUAGGUGUUGCCACCGCACUUUUCUGUUUAUCCA-----
((..(((((((((((......))))))))((((.....))))............)))..((((....)))))).................----- ( -15.70)
>DroWil_CAF1 99158 86 + 1
GCUUAACAAAUUGUUUAUUAUAGCAGUUUGGCAAUAAAUGCGGCCAUUAACUCAUUUUAGGUGUUGCCACCGCACUUUUCCAU----CCA-----
......(((((((((......)))))))))((...(((((.(........).)))))..((((....))))))..........----...----- ( -17.30)
>DroMoj_CAF1 86060 94 + 1
GCUAAACAAAUUGUUUAUUAUGGCAAUUUGGCAAUAAAUGCGGCCAUUAGCGCAUUUUAGGUGUUGCUACCGUACUUCUCUCCUCUUUUUUU-CC
......(((((((((......)))))))))........(((((....((((((((.....))).))))))))))..................-.. ( -19.00)
>DroPer_CAF1 81101 90 + 1
GCUCAACAAAUUGUUUAUUACAGCAGUUUGGCAAUAAAUGCCCCCAUUAACUCAGUUUAGGUGUUGCCACCGCACUUUUCUGUUUAUCCA-----
((..(((((((((((......))))))))((((.....))))............)))..((((....)))))).................----- ( -15.70)
>consensus
GCUCAACAAAUUGUUUAUUAUAGCAGUUUGGCAAUAAAUGCGGCCAUUAACUCAUUUUAGGUGUUGCCACCGCACUUUUCUGUUUAUCCA_____
((....(((((((((......)))))))))(((.....)))..................((((....))))))...................... (-16.02 = -15.38 +  -0.64)

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 11:40:17 2006