Locus 2056

Sequence ID 2R_DroMel_CAF1
Location 7,729,141 – 7,729,233
Length 92
Max. P 0.956807
window3409 window3410

overview

Window 9

Location 7,729,141 – 7,729,233
Length 92
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 78.61
Mean single sequence MFE -27.45
Consensus MFE -14.22
Energy contribution -14.50
Covariance contribution 0.28
Combinations/Pair 1.33
Mean z-score -2.09
Structure conservation index 0.52
SVM decision value 0.46
SVM RNA-class probability 0.745102
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7729141 92 + 20766785
GAAAUGAGAAUCCGUAAUUUGCUUUUGGAUA---------CGGAUUUGGCUGUACGCCCAAGACAAAUGCUCGCAAUUAUCCGAGCAUAAAG--UA--GGUGCGU
.......(((((((((.(((......)))))---------)))))))......((((((...((..(((((((........)))))))...)--).--)).)))) ( -25.80)
>DroSec_CAF1 19111 91 + 1
GAAAUGCGAAUCCGUAAUUUGCUU-UGGAUU---------CGGAUUUGGCUCUACGCCCAAGACAAAUGCUCGCAAUUAUCCGAGCAUAAAG--UA--GGUGCGU
.((((.((((((((..........-))))))---------)).))))......((((((...((..(((((((........)))))))...)--).--)).)))) ( -29.00)
>DroSim_CAF1 17483 91 + 1
GAAAUGCGAAUCCGUAAUUUGCUU-UGGAUU---------CGGAUUUGGCUCUACGCCCAAGACAAAUGCUCGCAAUUAUCCGAGCAUAAAG--UA--GGUGCGU
.((((.((((((((..........-))))))---------)).))))......((((((...((..(((((((........)))))))...)--).--)).)))) ( -29.00)
>DroEre_CAF1 12580 91 + 1
GGCAUCCGAAUCCGUAAUUUGGUA-UGGAUU---------UGGAUUUGGCUAUACGCCCAAGACAAAUGCUCGCAAUUAUCCAGGCAUAAAG--UA--GGUGCGU
((((((((((((((((......))-))))))---------)))))...)))..((((((...((..((((..(........)..))))...)--).--)).)))) ( -28.40)
>DroYak_CAF1 12977 91 + 1
GAAAUCCGAGUCCGUAAUUUGGCU-UGAAUU---------UGGAUUCGGCUGUACGCCCAAGACAAAUGCUCGCAAUUAUCCGAGCAUAAAG--UG--GGUGCGU
.....(((((((((.(((((....-.)))))---------))))))))).....((((((......(((((((........)))))))....--))--))))... ( -32.80)
>DroAna_CAF1 9736 104 + 1
GAAAUUGGAAUUGGUAGCUUAGUU-UAUAUUGUAGAUACAUACAUUUUAUUAUCUGGGAAAGACAAAUGCUAGCAAUUAUUUGGGCAUAUAAGCCAGGGGUGGAA
........(((((.((((((.(((-(...((.((((((.(((.....))))))))).)).)))).)).)))).))))).....(((......))).......... ( -19.70)
>consensus
GAAAUGCGAAUCCGUAAUUUGCUU_UGGAUU_________CGGAUUUGGCUAUACGCCCAAGACAAAUGCUCGCAAUUAUCCGAGCAUAAAG__UA__GGUGCGU
......((((((((..........................)))))))).....((((((.......(((((((........)))))))..........)).)))) (-14.22 = -14.50 +   0.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,729,141 – 7,729,233
Length 92
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 78.61
Mean single sequence MFE -25.36
Consensus MFE -12.27
Energy contribution -12.33
Covariance contribution 0.06
Combinations/Pair 1.29
Mean z-score -2.84
Structure conservation index 0.48
SVM decision value 1.47
SVM RNA-class probability 0.956807
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7729141 92 - 20766785
ACGCACC--UA--CUUUAUGCUCGGAUAAUUGCGAGCAUUUGUCUUGGGCGUACAGCCAAAUCCG---------UAUCCAAAAGCAAAUUACGGAUUCUCAUUUC
((((.((--.(--(...(((((((.(....).)))))))..))...)))))).......((((((---------((.............))))))))........ ( -26.72)
>DroSec_CAF1 19111 91 - 1
ACGCACC--UA--CUUUAUGCUCGGAUAAUUGCGAGCAUUUGUCUUGGGCGUAGAGCCAAAUCCG---------AAUCCA-AAGCAAAUUACGGAUUCGCAUUUC
..((...--..--((((((((((((((((.((....)).))))).)))))))))))........(---------(((((.-...........))))))))..... ( -28.80)
>DroSim_CAF1 17483 91 - 1
ACGCACC--UA--CUUUAUGCUCGGAUAAUUGCGAGCAUUUGUCUUGGGCGUAGAGCCAAAUCCG---------AAUCCA-AAGCAAAUUACGGAUUCGCAUUUC
..((...--..--((((((((((((((((.((....)).))))).)))))))))))........(---------(((((.-...........))))))))..... ( -28.80)
>DroEre_CAF1 12580 91 - 1
ACGCACC--UA--CUUUAUGCCUGGAUAAUUGCGAGCAUUUGUCUUGGGCGUAUAGCCAAAUCCA---------AAUCCA-UACCAAAUUACGGAUUCGGAUGCC
..((...--..--((.(((((((((((((.((....)).))))).)))))))).))....((((.---------(((((.-((......)).))))).)))))). ( -26.30)
>DroYak_CAF1 12977 91 - 1
ACGCACC--CA--CUUUAUGCUCGGAUAAUUGCGAGCAUUUGUCUUGGGCGUACAGCCGAAUCCA---------AAUUCA-AGCCAAAUUACGGACUCGGAUUUC
((((.((--.(--(...(((((((.(....).)))))))..))...))))))....((((.(((.---------......-...........))).))))..... ( -25.97)
>DroAna_CAF1 9736 104 - 1
UUCCACCCCUGGCUUAUAUGCCCAAAUAAUUGCUAGCAUUUGUCUUUCCCAGAUAAUAAAAUGUAUGUAUCUACAAUAUA-AACUAAGCUACCAAUUCCAAUUUC
..........(((......))).....(((((.((((..((((((.....)))))).....((((......)))).....-......)))).)))))........ ( -15.60)
>consensus
ACGCACC__UA__CUUUAUGCUCGGAUAAUUGCGAGCAUUUGUCUUGGGCGUACAGCCAAAUCCA_________AAUCCA_AACCAAAUUACGGAUUCGCAUUUC
.............((.(((((((((((((.((....)).))))).)))))))).))................................................. (-12.27 = -12.33 +   0.06)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:09 2006