Locus 5338

Sequence ID 2R_DroMel_CAF1
Location 17,278,009 – 17,278,143
Length 134
Max. P 0.961874
window8525 window8526 window8527

overview

Window 5

Location 17,278,009 – 17,278,109
Length 100
Sequences 3
Columns 100
Reading direction reverse
Mean pairwise identity 99.33
Mean single sequence MFE -17.00
Consensus MFE -17.22
Energy contribution -17.00
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.99
Structure conservation index 1.01
SVM decision value 1.12
SVM RNA-class probability 0.918934
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17278009 100 - 20766785
CAACAAAUGGUCAACAUGCAAUCGGGCAAACAUUUGCAUGCCAAAGGCAGCCGGACAACAAUUACCAUAUAAAAUUUGAAAUGAUUAAGCAACAACCACA
.......((((.....(((..((((((((....)))).((((...)))).))))..................((((......))))..)))...)))).. ( -16.40)
>DroSec_CAF1 1028 100 - 1
CAACAAAUGGUCAACAUGCAAUCGGGCAAACAUUUGCAUGCCAAAGGCAGCCGAACAACAAUUACCAUAUAAAAUUUGAAAUGAUUAAGCAACAACCACA
.......((((.....(((..((((((((....)))).((((...)))).))))..................((((......))))..)))...)))).. ( -17.30)
>DroSim_CAF1 3003 100 - 1
CAACAAAUGGUCAACAUGCAAUCGGGCAAACAUUUGCAUGCCAAAGGCAGCCGAACAACAAUUACCAUAUAAAAUUUGAAAUGAUUAAGCAACAACCACA
.......((((.....(((..((((((((....)))).((((...)))).))))..................((((......))))..)))...)))).. ( -17.30)
>consensus
CAACAAAUGGUCAACAUGCAAUCGGGCAAACAUUUGCAUGCCAAAGGCAGCCGAACAACAAUUACCAUAUAAAAUUUGAAAUGAUUAAGCAACAACCACA
.......((((.....(((..((((((((....)))).((((...)))).))))..................((((......))))..)))...)))).. (-17.22 = -17.00 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,278,036 – 17,278,143
Length 107
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 97.58
Mean single sequence MFE -31.07
Consensus MFE -30.43
Energy contribution -30.43
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.98
SVM decision value 1.53
SVM RNA-class probability 0.961874
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17278036 107 + 20766785
UUUAUAUGGUAAUUGUUGUCCGGCUGCCUUUGGCAUGCAAAUGUUUGCCCGAUUGCAUGUUGACCAUUUGUUGUUUGCAAAACAGUUGCCAUUGUGAUUCG---UAUGUC
.(((((((((((((((((..(((((((..((((((.((....)).)).))))..))).))))..))(((((.....))))))))))))))).)))))....---...... ( -30.20)
>DroSec_CAF1 1055 110 + 1
UUUAUAUGGUAAUUGUUGUUCGGCUGCCUUUGGCAUGCAAAUGUUUGCCCGAUUGCAUGUUGACCAUUUGUUGUUUGCAAAACAGUUGCCAUUGUGAUUCGUAGUAUGUC
.(((((((((((((((((.((((((((..((((((.((....)).)).))))..))).))))).))(((((.....))))))))))))))).)))))............. ( -31.50)
>DroSim_CAF1 3030 110 + 1
UUUAUAUGGUAAUUGUUGUUCGGCUGCCUUUGGCAUGCAAAUGUUUGCCCGAUUGCAUGUUGACCAUUUGUUGUUUGCAAAACAGUUGCCAUUGUGAUUCGUAGUAUGUC
.(((((((((((((((((.((((((((..((((((.((....)).)).))))..))).))))).))(((((.....))))))))))))))).)))))............. ( -31.50)
>consensus
UUUAUAUGGUAAUUGUUGUUCGGCUGCCUUUGGCAUGCAAAUGUUUGCCCGAUUGCAUGUUGACCAUUUGUUGUUUGCAAAACAGUUGCCAUUGUGAUUCGUAGUAUGUC
.((((((((((((((((((.((((.....(..((((((((.((......)).))))))))..)......))))...)))..)))))))))).)))))............. (-30.43 = -30.43 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,278,036 – 17,278,143
Length 107
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 97.58
Mean single sequence MFE -19.90
Consensus MFE -20.12
Energy contribution -19.90
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.45
Structure conservation index 1.01
SVM decision value 0.25
SVM RNA-class probability 0.652979
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17278036 107 - 20766785
GACAUA---CGAAUCACAAUGGCAACUGUUUUGCAAACAACAAAUGGUCAACAUGCAAUCGGGCAAACAUUUGCAUGCCAAAGGCAGCCGGACAACAAUUACCAUAUAAA
......---.........((((.((.(((((((((....((.....)).....)))))((((((((....)))).((((...)))).))))..)))).)).))))..... ( -19.30)
>DroSec_CAF1 1055 110 - 1
GACAUACUACGAAUCACAAUGGCAACUGUUUUGCAAACAACAAAUGGUCAACAUGCAAUCGGGCAAACAUUUGCAUGCCAAAGGCAGCCGAACAACAAUUACCAUAUAAA
..................((((.((.(((((((((....((.....)).....)))))((((((((....)))).((((...)))).))))..)))).)).))))..... ( -20.20)
>DroSim_CAF1 3030 110 - 1
GACAUACUACGAAUCACAAUGGCAACUGUUUUGCAAACAACAAAUGGUCAACAUGCAAUCGGGCAAACAUUUGCAUGCCAAAGGCAGCCGAACAACAAUUACCAUAUAAA
..................((((.((.(((((((((....((.....)).....)))))((((((((....)))).((((...)))).))))..)))).)).))))..... ( -20.20)
>consensus
GACAUACUACGAAUCACAAUGGCAACUGUUUUGCAAACAACAAAUGGUCAACAUGCAAUCGGGCAAACAUUUGCAUGCCAAAGGCAGCCGAACAACAAUUACCAUAUAAA
..................((((.((.(((((((((....((.....)).....)))))((((((((....)))).((((...)))).))))..)))).)).))))..... (-20.12 = -19.90 +  -0.22)

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 11:42:28 2006