Locus 7620

Sequence ID 3R_DroMel_CAF1
Location 20,424,868 – 20,425,004
Length 136
Max. P 0.805022
window12295 window12296 window12297

overview

Window 5

Location 20,424,868 – 20,424,964
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.87
Mean single sequence MFE -37.00
Consensus MFE -22.60
Energy contribution -22.84
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.20
Structure conservation index 0.61
SVM decision value 0.39
SVM RNA-class probability 0.715931
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20424868 96 + 27905053
AUUGGCCAUUUGGGAUUGAGUUCGUCGAAUGCGA---CGUAUCGCAGCGGGUU---------------------UCUUCGGCUUGAACUGGCCAAGUAACACGCUAAGCUAUAGAUUCUA
..........(((((((((...(((((....)))---))..))((((((.(((---------------------.(((.((((......))))))).))).))))..))....))))))) ( -28.50)
>DroSec_CAF1 7899 99 + 1
AUUGGCCAUUUGGGAUUGAGUUCGUCGAAUGCGACGACGGAUCGCAGCGGGUU---------------------UCUUCGGCUUGAACUGGCCAAGUAACCCGCUAAGCUAUAGAUUCUA
..((((.....(.((((..((.(((((....))))))).)))).)((((((((---------------------.(((.((((......))))))).))))))))..))))......... ( -38.20)
>DroSim_CAF1 7470 96 + 1
AUUGGCCAUUUGGGAUUGAGUUCGUCGAAUGCGA---CGGAUCGCAGCGGGUU---------------------UCUUCGGCUUGAACUGGCCAAGUAACCCGCUAAGCUAUAGAUUCUA
..........(((((((((.(((((((....)))---))))))((((((((((---------------------.(((.((((......))))))).))))))))..))....))))))) ( -36.80)
>DroEre_CAF1 7409 114 + 1
AUUGGCCAUUUGGGUUCGAAUUCGUCGUAUGCGA---CGGAUCGCAGCGGGUUUCUUGAGCCG---GAGCAGUUUCUUCGGCUUGAACUGGCCAAGUAACCCGCUAAGCUAUAGUUUCUA
..((((..........(((.(((((((....)))---))))))).((((((((.((((.((((---(..(((...(....).)))..))))))))).))))))))..))))......... ( -44.80)
>DroYak_CAF1 7813 117 + 1
AUUGGCCAUUUGGGUUUGACUUCAUCGUAUGCUG---CGGAUCGCAGCGGGUUUCUUGAGCCGCCUGAGCAGUUUCUUCGGCUUGAACUGGCCAAGUAACCCGCUAAGCUAUAGAUUCUA
...((((.....)))).......(((....((((---((...)))((((((((.((((.(((((....))((((((....)...)))))))))))).)))))))).)))....))).... ( -36.70)
>consensus
AUUGGCCAUUUGGGAUUGAGUUCGUCGAAUGCGA___CGGAUCGCAGCGGGUU_____________________UCUUCGGCUUGAACUGGCCAAGUAACCCGCUAAGCUAUAGAUUCUA
..((((........................((((.......))))((((((((......................(((.((((......))))))).))))))))..))))......... (-22.60 = -22.84 +   0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,424,905 – 20,425,004
Length 99
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 89.47
Mean single sequence MFE -25.84
Consensus MFE -23.03
Energy contribution -23.36
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.89
SVM decision value 0.63
SVM RNA-class probability 0.805022
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20424905 99 + 27905053
AUCGCAGCGGGUUUCUUCGGCUUGAACUGGCCAAGUAACACGCUAAGCUAUAGAUUCUACAUACAUAUAUAUAGAUACGUACAUACCAUAUAUGGCCGG
.....((((.(((.(((.((((......))))))).))).))))..((((((.........(((.(((......))).))).........))))))... ( -21.97)
>DroSec_CAF1 7939 87 + 1
AUCGCAGCGGGUUUCUUCGGCUUGAACUGGCCAAGUAACCCGCUAAGCUAUAGAUUCUACAUGCAUAU------------ACAUACCAUAUAUGGCCGG
.....((((((((.(((.((((......))))))).))))))))..((((((........(((.....------------.)))......))))))... ( -27.14)
>DroSim_CAF1 7507 87 + 1
AUCGCAGCGGGUUUCUUCGGCUUGAACUGGCCAAGUAACCCGCUAAGCUAUAGAUUCUACGUGCAUAU------------ACAUACCAUAUAUGGCCGG
...((((((((((.(((.((((......))))))).))))))))..))...........((..(((((------------(.......))))))..)). ( -28.40)
>consensus
AUCGCAGCGGGUUUCUUCGGCUUGAACUGGCCAAGUAACCCGCUAAGCUAUAGAUUCUACAUGCAUAU____________ACAUACCAUAUAUGGCCGG
.....((((((((.(((.((((......))))))).))))))))..((((((......................................))))))... (-23.03 = -23.36 +   0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,424,905 – 20,425,004
Length 99
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 89.47
Mean single sequence MFE -27.43
Consensus MFE -23.12
Energy contribution -23.57
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.92
Structure conservation index 0.84
SVM decision value 0.20
SVM RNA-class probability 0.628963
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20424905 99 - 27905053
CCGGCCAUAUAUGGUAUGUACGUAUCUAUAUAUAUGUAUGUAGAAUCUAUAGCUUAGCGUGUUACUUGGCCAGUUCAAGCCGAAGAAACCCGCUGCGAU
..(((.(((.((..(((((((((((......)))))))))))..)).))).)))(((((.(((.((((((........))).))).))).))))).... ( -26.20)
>DroSec_CAF1 7939 87 - 1
CCGGCCAUAUAUGGUAUGU------------AUAUGCAUGUAGAAUCUAUAGCUUAGCGGGUUACUUGGCCAGUUCAAGCCGAAGAAACCCGCUGCGAU
..((((((((((.....))------------)))))..(((((...))))))))(((((((((.((((((........))).))).))))))))).... ( -27.70)
>DroSim_CAF1 7507 87 - 1
CCGGCCAUAUAUGGUAUGU------------AUAUGCACGUAGAAUCUAUAGCUUAGCGGGUUACUUGGCCAGUUCAAGCCGAAGAAACCCGCUGCGAU
.((..(((((((.....))------------)))))..))...........((..((((((((.((((((........))).))).))))))))))... ( -28.40)
>consensus
CCGGCCAUAUAUGGUAUGU____________AUAUGCAUGUAGAAUCUAUAGCUUAGCGGGUUACUUGGCCAGUUCAAGCCGAAGAAACCCGCUGCGAU
.((((((....))))....................((.(((((...))))))).(((((((((.((((((........))).))).))))))))))).. (-23.12 = -23.57 +   0.45)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:22 2006