Locus 5246

Sequence ID X_DroMel_CAF1
Location 13,686,749 – 13,686,980
Length 231
Max. P 0.943453
window8501 window8502 window8503

overview

Window 1

Location 13,686,749 – 13,686,867
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.65
Mean single sequence MFE -34.07
Consensus MFE -33.32
Energy contribution -33.10
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.67
Structure conservation index 0.98
SVM decision value 0.45
SVM RNA-class probability 0.742488
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13686749 118 - 22224390
CCUACAAACA--AGCUAAACAGGCAAGAAUAGUUUAUAGCGAUGGCAACCAUGGCAAGCAAUAGAGAAAUUGGACGGUGCUGGCAAUCCUGCAGCUGCUGCAUCGUCCAUCCGCUGGAAA
((........--.(((....((((.......))))...((.((((...)))).)).))).....((....((((((((((.((((..........))))))))))))))....))))... ( -32.60)
>DroSim_CAF1 3945 118 - 1
CCUACAAACA--AGCUAAACAGGCAAGAAUAGUUUAUAGCGAUGGCAACCAUGGCAAGCAAUAGAGAAAUUGGACGGUGCUGGCAAUCCUGCAGCUGCCGCAUCGUCCAUCCGCUGGAAA
((........--.(((....((((.......))))...((.((((...)))).)).))).....((....((((((((((.((((..........))))))))))))))....))))... ( -34.80)
>DroYak_CAF1 4185 120 - 1
CCUACAAACAAAAGCUAAACAGGCAAGCAUAGUUUAUAGCGAUGGCAACCAUGGCAAGCAAUAGAGAAACUGGACGGUGCUGGCAACCCUGCAGCUGCUGCAUCGUCCAUCCGCUGGAAA
((...........(((.....))).(((...((((...((.((((...)))).))))))...........((((((((((.((((.(......).))))))))))))))...)))))... ( -34.80)
>consensus
CCUACAAACA__AGCUAAACAGGCAAGAAUAGUUUAUAGCGAUGGCAACCAUGGCAAGCAAUAGAGAAAUUGGACGGUGCUGGCAAUCCUGCAGCUGCUGCAUCGUCCAUCCGCUGGAAA
((...........(((....((((.......))))...((.((((...)))).)).))).....((....((((((((((.((((..........))))))))))))))....))))... (-33.32 = -33.10 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 13,686,867 – 13,686,980
Length 113
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.50
Mean single sequence MFE -24.37
Consensus MFE -23.00
Energy contribution -23.33
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.94
SVM decision value 1.03
SVM RNA-class probability 0.902915
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13686867 113 + 22224390
UUAGUUAAAACUUCAAUGUUCUUCUCUUGUUGUGAUCACAGUUAGUUUUGUGUUGUUGUAGUUGCAUGUAUGCAGUUGCAGUUUUAAUUGUAAUUGCUAUUGGUAAUUGU-------UAA
.((((((((((..(((..(......((..((((....))))..))....)..))).((((..((((....))))..))))))))))))))(((((((.....))))))).-------... ( -23.90)
>DroSim_CAF1 4063 111 + 1
UUAGUUAAAACUUCAAUGUUCUUUUCUUGUUGUGAUCACAGUUAGUUUUGUGUUGUUGUAGUUGCAU--UUGCAGUUGCAGUUUUAAUUGUAAUUGCUAUUGGUAAUUGU-------UAA
.((((((((((..(((..(......((..((((....))))..))....)..))).((((..(((..--..)))..))))))))))))))(((((((.....))))))).-------... ( -23.30)
>DroYak_CAF1 4305 119 + 1
UUAGUUAAAACUUCAAUGUUGCUUUCUUGUUGUGAUCACAGUUAGUUUUGUGUUGUUGUAGUUGCA-GUUUGCAGUUGCAGUUUAAAUUGUAAUUGCUAUUGGUAAUUGUUAAUUGUUAA
.(((((((....((((((((((...((....(..(.(((((......))))))..)...))..)))-)...(((((((((((....)))))))))))))))))......))))))).... ( -25.90)
>consensus
UUAGUUAAAACUUCAAUGUUCUUUUCUUGUUGUGAUCACAGUUAGUUUUGUGUUGUUGUAGUUGCAUGUUUGCAGUUGCAGUUUUAAUUGUAAUUGCUAUUGGUAAUUGU_______UAA
.((((((((((..(((..(......((..((((....))))..))....)..))).((((..((((....))))..))))))))))))))(((((((.....)))))))........... (-23.00 = -23.33 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,686,867 – 13,686,980
Length 113
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.50
Mean single sequence MFE -11.30
Consensus MFE -11.53
Energy contribution -11.87
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 1.02
SVM decision value 1.34
SVM RNA-class probability 0.943453
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13686867 113 - 22224390
UUA-------ACAAUUACCAAUAGCAAUUACAAUUAAAACUGCAACUGCAUACAUGCAACUACAACAACACAAAACUAACUGUGAUCACAACAAGAGAAGAACAUUGAAGUUUUAACUAA
...-------.......................((((((((.(((.((((....))))..........((((........))))....................))).)))))))).... ( -12.70)
>DroSim_CAF1 4063 111 - 1
UUA-------ACAAUUACCAAUAGCAAUUACAAUUAAAACUGCAACUGCAA--AUGCAACUACAACAACACAAAACUAACUGUGAUCACAACAAGAAAAGAACAUUGAAGUUUUAACUAA
...-------.......................((((((((.(((.(((..--..)))..........((((........))))....................))).)))))))).... ( -12.10)
>DroYak_CAF1 4305 119 - 1
UUAACAAUUAACAAUUACCAAUAGCAAUUACAAUUUAAACUGCAACUGCAAAC-UGCAACUACAACAACACAAAACUAACUGUGAUCACAACAAGAAAGCAACAUUGAAGUUUUAACUAA
.......................(((.((........)).)))((((.(((..-(((...........((((........)))).((.......))..)))...))).))))........ (  -9.10)
>consensus
UUA_______ACAAUUACCAAUAGCAAUUACAAUUAAAACUGCAACUGCAAACAUGCAACUACAACAACACAAAACUAACUGUGAUCACAACAAGAAAAGAACAUUGAAGUUUUAACUAA
.................................((((((((.(((.((((....))))..........((((........))))....................))).)))))))).... (-11.53 = -11.87 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:13 2006