Locus 7732

Sequence ID 3L_DroMel_CAF1
Location 20,627,933 – 20,628,051
Length 118
Max. P 0.979023
window12590 window12591

overview

Window 0

Location 20,627,933 – 20,628,031
Length 98
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 83.01
Mean single sequence MFE -24.69
Consensus MFE -20.64
Energy contribution -20.45
Covariance contribution -0.19
Combinations/Pair 1.17
Mean z-score -1.69
Structure conservation index 0.84
SVM decision value 0.52
SVM RNA-class probability 0.767748
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20627933 98 - 23771897
-AAAUGUUCGAGGAACAGGCCAUCGGCGAUUCAAAUCGUUGU----ACCAUUGGCCUUAAGU-UCUUGAAUGAAUUUCUGCUCUUCUUUUGCUAAUGAGUUGCA
-....(((((((((..((((((.(((((((....))))))).----.....))))))....)-))))))))........((..(((..........)))..)). ( -27.30)
>DroSec_CAF1 1252 100 - 1
UACAUGUUCGAGGAACAGGCCAUCGGCGAUUCAAAUCGUUGUCUAAAACAUUGGCCUUAAGU-UCUUGAAUGAAUUUCUGCUCUGCC---CCUAAUCAGUUUCA
.....(((((((((..((((((.(((((((....)))))))..........))))))....)-))))))))(((...(((.......---......))).))). ( -24.62)
>DroSim_CAF1 2880 100 - 1
UACAUGUUCGAGGAACAGGCCAUCGGCGAUUCAAAUCGUUGUCUAAAACAUUGGCCUUAAGU-UCCUGAAUGAAUUUCUGCUCUGCC---CCUAAUCAGUUUCA
.....((((.((((((((((((.(((((((....)))))))..........))))))...))-))))))))(((...(((.......---......))).))). ( -25.82)
>DroYak_CAF1 180984 101 - 1
UACAUAUUCAACGAACAGGCAAUCGGCGAUCGAAAUCGCUGUGUAUAAUUUUUGCCCUAAGUUUCUUGAAUGAAUUUGUGCACUUCC---UUUAAUCAGUUGCC
....(((((((.((((.(((((.(((((((....)))))))..........)))))....)))).))))))).......(((((...---.......)).))). ( -21.00)
>consensus
UACAUGUUCGAGGAACAGGCCAUCGGCGAUUCAAAUCGUUGUCUAAAACAUUGGCCUUAAGU_UCUUGAAUGAAUUUCUGCUCUGCC___CCUAAUCAGUUGCA
....(((((((((.((((((((.(((((((....)))))))..........))))))...)).)))))))))................................ (-20.64 = -20.45 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,627,961 – 20,628,051
Length 90
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 81.46
Mean single sequence MFE -28.50
Consensus MFE -25.14
Energy contribution -24.95
Covariance contribution -0.19
Combinations/Pair 1.15
Mean z-score -2.20
Structure conservation index 0.88
SVM decision value 1.83
SVM RNA-class probability 0.979023
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20627961 90 - 23771897
CCCCAAGGGGUUAGU----------UUU-AG--AAAUGUUCGAGGAACAGGCCAUCGGCGAUUCAAAUCGUUGU----ACCAUUGGCCUUAAGU-UCUUGAAUGAAUU
(((....))).....----------...-..--....(((((((((..((((((.(((((((....))))))).----.....))))))....)-))))))))..... ( -29.10)
>DroSec_CAF1 1277 97 - 1
CCCCAAGGGGUUAGG----------UUUCAGAUACAUGUUCGAGGAACAGGCCAUCGGCGAUUCAAAUCGUUGUCUAAAACAUUGGCCUUAAGU-UCUUGAAUGAAUU
(((....))).....----------............(((((((((..((((((.(((((((....)))))))..........))))))....)-))))))))..... ( -28.20)
>DroSim_CAF1 2905 97 - 1
CCCCAAGGGGUUAGG----------UUUCAGAUACAUGUUCGAGGAACAGGCCAUCGGCGAUUCAAAUCGUUGUCUAAAACAUUGGCCUUAAGU-UCCUGAAUGAAUU
(((....))).....----------............((((.((((((((((((.(((((((....)))))))..........))))))...))-))))))))..... ( -29.40)
>DroYak_CAF1 181009 108 - 1
CCCCAAGGGGUUAUGGAAUUACUUCUUGUAAAUACAUAUUCAACGAACAGGCAAUCGGCGAUCGAAAUCGCUGUGUAUAAUUUUUGCCCUAAGUUUCUUGAAUGAAUU
...((((((((.........))))))))........(((((((.((((.(((((.(((((((....)))))))..........)))))....)))).))))))).... ( -27.30)
>consensus
CCCCAAGGGGUUAGG__________UUUCAGAUACAUGUUCGAGGAACAGGCCAUCGGCGAUUCAAAUCGUUGUCUAAAACAUUGGCCUUAAGU_UCUUGAAUGAAUU
(((....)))..........................(((((((((.((((((((.(((((((....)))))))..........))))))...)).))))))))).... (-25.14 = -24.95 +  -0.19)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:25 2006