Locus 8783

Sequence ID 3R_DroMel_CAF1
Location 23,468,917 – 23,469,054
Length 137
Max. P 0.995829
window14109 window14110 window14111 window14112

overview

Window 9

Location 23,468,917 – 23,469,016
Length 99
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 81.52
Mean single sequence MFE -27.40
Consensus MFE -20.04
Energy contribution -20.38
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -3.29
Structure conservation index 0.73
SVM decision value 2.56
SVM RNA-class probability 0.995273
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23468917 99 + 27905053
AUGGUAGCUACGGAACUUCAAGAGGUUUGCAAUCACUUCAACAAAUGUCUAAAGGUAUGC-----------AGCUACUUUCUAUUUUUCAAAGCAUACUUUUAGACACUU
.((((.((....((((((....)))))))).))))..........(((((((((((((((-----------.....................)))))))))))))))... ( -25.40)
>DroSec_CAF1 68351 110 + 1
AAGGUAGCUAACCAACUUCAAGAGGUUUGCAAUCACUUCAAAAAAUGUCUAAAAGUAAGCAGCGAACUAGCAGCUACUUUCUAUUUUCCAAAGCAUACUUUUAGACACUU
..(((.((.((((..........)))).)).)))...........(((((((((((((((.((......)).))).((((.........))))..))))))))))))... ( -25.70)
>DroEre_CAF1 58994 108 + 1
A-GGUAGCUACGCUACUACAAGGGGUUUGCAAUCACUUGCA-ACAUGUCUGAAAGUAUGCAGCGAAUUACAAGCUACUUUCUAUUUUUCAUAGCAUACUUUUGGACACUU
.-((((((...)))))).........((((((....)))))-)..((((..((((((((((((.........)))......(((.....))))))))))))..))))... ( -31.10)
>consensus
A_GGUAGCUACGCAACUUCAAGAGGUUUGCAAUCACUUCAA_AAAUGUCUAAAAGUAUGCAGCGAA_UA__AGCUACUUUCUAUUUUUCAAAGCAUACUUUUAGACACUU
..(((.((.....(((((....))))).)).)))...........(((((((((((((((................................)))))))))))))))... (-20.04 = -20.38 +   0.34)

alignment

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secondary structure

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dotplot

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Window 0

Location 23,468,917 – 23,469,016
Length 99
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 81.52
Mean single sequence MFE -26.90
Consensus MFE -16.48
Energy contribution -20.37
Covariance contribution 3.89
Combinations/Pair 1.03
Mean z-score -2.10
Structure conservation index 0.61
SVM decision value 0.25
SVM RNA-class probability 0.652476
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23468917 99 - 27905053
AAGUGUCUAAAAGUAUGCUUUGAAAAAUAGAAAGUAGCU-----------GCAUACCUUUAGACAUUUGUUGAAGUGAUUGCAAACCUCUUGAAGUUCCGUAGCUACCAU
(((((((((((.((((((.....................-----------)))))).)))))))))))......(((.((((.(((........)))..)))).)))... ( -21.30)
>DroSec_CAF1 68351 110 - 1
AAGUGUCUAAAAGUAUGCUUUGGAAAAUAGAAAGUAGCUGCUAGUUCGCUGCUUACUUUUAGACAUUUUUUGAAGUGAUUGCAAACCUCUUGAAGUUGGUUAGCUACCUU
(((((((((((((((.((..((((...(((..........))).))))..)).)))))))))))))))............((.((((..........)))).))...... ( -28.20)
>DroEre_CAF1 58994 108 - 1
AAGUGUCCAAAAGUAUGCUAUGAAAAAUAGAAAGUAGCUUGUAAUUCGCUGCAUACUUUCAGACAUGU-UGCAAGUGAUUGCAAACCCCUUGUAGUAGCGUAGCUACC-U
..(((((..(((((((((..((((..((((........))))..))))..)))))))))..))))).(-(((((....))))))..........(((((...))))).-. ( -31.20)
>consensus
AAGUGUCUAAAAGUAUGCUUUGAAAAAUAGAAAGUAGCU__UA_UUCGCUGCAUACUUUUAGACAUUU_UUGAAGUGAUUGCAAACCUCUUGAAGUUGCGUAGCUACC_U
((((((((((((((((((..((((....((.......)).....))))..))))))))))))))))))......((((((.(((.....))).))))))........... (-16.48 = -20.37 +   3.89)

alignment

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secondary structure

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dotplot

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Window 1

Location 23,468,947 – 23,469,054
Length 107
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 82.49
Mean single sequence MFE -27.30
Consensus MFE -25.03
Energy contribution -25.15
Covariance contribution 0.12
Combinations/Pair 1.21
Mean z-score -2.86
Structure conservation index 0.92
SVM decision value 2.62
SVM RNA-class probability 0.995829
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23468947 107 + 27905053
AAUCACUUCAACAAAUGUCUAAAGGUAUGC-----------AGCUACUUUCUAUUUUUCAAAGCAUACUUUUAGACACUUCAUAGAUGGUUUCAAAUCUCUAAAGAUUUCGGUGGCUC
..(((((........(((((((((((((((-----------.....................)))))))))))))))(((.(.((((........)))).).))).....)))))... ( -25.30)
>DroSec_CAF1 68381 118 + 1
AAUCACUUCAAAAAAUGUCUAAAAGUAAGCAGCGAACUAGCAGCUACUUUCUAUUUUCCAAAGCAUACUUUUAGACACUUUAUAGAUGGUUUCAAGUCUCCAAAGAUUUCGGUGGCUC
..(((((........(((((((((((((((.((......)).))).((((.........))))..))))))))))))((((..((((........))))..)))).....)))))... ( -25.90)
>DroEre_CAF1 59023 117 + 1
AAUCACUUGCA-ACAUGUCUGAAAGUAUGCAGCGAAUUACAAGCUACUUUCUAUUUUUCAUAGCAUACUUUUGGACACUUCGCAGAUGCUUUCAAAUCUCUGUAGAUUUCGGUGGCUC
......((((.-...((((..((((((((((((.........)))......(((.....))))))))))))..))))....))))..(((.((((((((....)))))).)).))).. ( -30.70)
>consensus
AAUCACUUCAA_AAAUGUCUAAAAGUAUGCAGCGAA_UA__AGCUACUUUCUAUUUUUCAAAGCAUACUUUUAGACACUUCAUAGAUGGUUUCAAAUCUCUAAAGAUUUCGGUGGCUC
..(((((........(((((((((((((((................................)))))))))))))))(((((.((((........)))).))))).....)))))... (-25.03 = -25.15 +   0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 23,468,947 – 23,469,054
Length 107
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 82.49
Mean single sequence MFE -28.60
Consensus MFE -20.38
Energy contribution -23.60
Covariance contribution 3.22
Combinations/Pair 1.03
Mean z-score -2.16
Structure conservation index 0.71
SVM decision value 0.78
SVM RNA-class probability 0.847976
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23468947 107 - 27905053
GAGCCACCGAAAUCUUUAGAGAUUUGAAACCAUCUAUGAAGUGUCUAAAAGUAUGCUUUGAAAAAUAGAAAGUAGCU-----------GCAUACCUUUAGACAUUUGUUGAAGUGAUU
....(((..((((((....)))))).............(((((((((((.((((((.....................-----------)))))).)))))))))))......)))... ( -24.10)
>DroSec_CAF1 68381 118 - 1
GAGCCACCGAAAUCUUUGGAGACUUGAAACCAUCUAUAAAGUGUCUAAAAGUAUGCUUUGGAAAAUAGAAAGUAGCUGCUAGUUCGCUGCUUACUUUUAGACAUUUUUUGAAGUGAUU
....(((.....((...(....)..)).....((...((((((((((((((((.((..((((...(((..........))).))))..)).))))))))))))))))..)).)))... ( -29.50)
>DroEre_CAF1 59023 117 - 1
GAGCCACCGAAAUCUACAGAGAUUUGAAAGCAUCUGCGAAGUGUCCAAAAGUAUGCUAUGAAAAAUAGAAAGUAGCUUGUAAUUCGCUGCAUACUUUCAGACAUGU-UGCAAGUGAUU
.........((((((....)))))).....((..(((((.(((((..(((((((((..((((..((((........))))..))))..)))))))))..))))).)-))))..))... ( -32.20)
>consensus
GAGCCACCGAAAUCUUUAGAGAUUUGAAACCAUCUAUGAAGUGUCUAAAAGUAUGCUUUGAAAAAUAGAAAGUAGCU__UA_UUCGCUGCAUACUUUUAGACAUUU_UUGAAGUGAUU
....(((..((((((....)))))).............((((((((((((((((((..((((....((.......)).....))))..))))))))))))))))))......)))... (-20.38 = -23.60 +   3.22)

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 13:19:43 2006