Locus 7160

Sequence ID 3R_DroMel_CAF1
Location 18,873,315 – 18,873,456
Length 141
Max. P 0.999934
window11581 window11582 window11583

overview

Window 1

Location 18,873,315 – 18,873,417
Length 102
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.98
Mean single sequence MFE -24.00
Consensus MFE -20.54
Energy contribution -20.10
Covariance contribution -0.44
Combinations/Pair 1.11
Mean z-score -1.23
Structure conservation index 0.86
SVM decision value 1.65
SVM RNA-class probability 0.969662
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18873315 102 + 27905053
----------------UAC--UUAACAUGAAAUGCGACUGCAUUUUCUAAGUGCAUCCAUGUCUGAUGUGCAUCUGACUAGCCUUAUUAAUGGCUCAUUUGCCAGACGCUCAUUGCAGCC
----------------.((--(((....(((((((....))))))).)))))(((....((((((....(((..(((...(((........))))))..))))))))).....))).... ( -25.60)
>DroSim_CAF1 1101 86 + 1
----------------------------------AGACUGCAUUUUCUAAGUGCAUCCAUGUCUGAUGUGCAUCUGACUAGCCUUAUUAAUGGCUCAUUUGCCAGACGCUCAUUGCAGCC
----------------------------------.((.((((((.....))))))))...(((((....(((..(((...(((........))))))..))))))))((.....)).... ( -21.70)
>DroYak_CAF1 1138 120 + 1
CAUAAUCUAUUUUUGAUACGAUUAACGUGAAAGCAUACUGCAUUUUCCGAGUGCAUCCAAGUCCGAUGUGUAUCUGACUAGCCUUAUUAAUGGCUCAUUUGCCAGGCGUUCAUUGCAGCC
..(((((((((...)))).)))))..((....))...(((((......(((..((((.......))))..).))(((...((((.......(((......)))))))..))).))))).. ( -24.71)
>consensus
________________UAC__UUAAC_UGAAA__AGACUGCAUUUUCUAAGUGCAUCCAUGUCUGAUGUGCAUCUGACUAGCCUUAUUAAUGGCUCAUUUGCCAGACGCUCAUUGCAGCC
.....................................(((((........(..((((.......))))..).((((.(.((((........)))).....).)))).......))))).. (-20.54 = -20.10 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,873,315 – 18,873,417
Length 102
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.98
Mean single sequence MFE -30.00
Consensus MFE -26.87
Energy contribution -28.20
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.90
SVM decision value 4.65
SVM RNA-class probability 0.999934
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18873315 102 - 27905053
GGCUGCAAUGAGCGUCUGGCAAAUGAGCCAUUAAUAAGGCUAGUCAGAUGCACAUCAGACAUGGAUGCACUUAGAAAAUGCAGUCGCAUUUCAUGUUAA--GUA----------------
(((((((....(((((((((.....((((........)))).))))))))).((((.......))))...........)))))))..............--...---------------- ( -33.20)
>DroSim_CAF1 1101 86 - 1
GGCUGCAAUGAGCGUCUGGCAAAUGAGCCAUUAAUAAGGCUAGUCAGAUGCACAUCAGACAUGGAUGCACUUAGAAAAUGCAGUCU----------------------------------
(((((((....(((((((((.....((((........)))).))))))))).((((.......))))...........))))))).---------------------------------- ( -32.70)
>DroYak_CAF1 1138 120 - 1
GGCUGCAAUGAACGCCUGGCAAAUGAGCCAUUAAUAAGGCUAGUCAGAUACACAUCGGACUUGGAUGCACUCGGAAAAUGCAGUAUGCUUUCACGUUAAUCGUAUCAAAAAUAGAUUAUG
.((((((.....((....(((....((((........))))((((.(((....))).))))....)))...)).....))))))............(((((............))))).. ( -24.10)
>consensus
GGCUGCAAUGAGCGUCUGGCAAAUGAGCCAUUAAUAAGGCUAGUCAGAUGCACAUCAGACAUGGAUGCACUUAGAAAAUGCAGUCU__UUUCA_GUUAA__GUA________________
(((((((....(((((((((.....((((........)))).))))))))).((((.......))))...........)))))))................................... (-26.87 = -28.20 +   1.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,873,337 – 18,873,456
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.20
Mean single sequence MFE -39.47
Consensus MFE -33.83
Energy contribution -35.17
Covariance contribution 1.34
Combinations/Pair 1.08
Mean z-score -2.93
Structure conservation index 0.86
SVM decision value 1.22
SVM RNA-class probability 0.932362
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18873337 119 - 27905053
UGGUGAGUUGCAUUCGAGUGCCC-AUUGGGGCUAACAAAUGGCUGCAAUGAGCGUCUGGCAAAUGAGCCAUUAAUAAGGCUAGUCAGAUGCACAUCAGACAUGGAUGCACUUAGAAAAUG
...(((((.(((((((.((...(-((((.(((((.....))))).))))).(((((((((.....((((........)))).))))))))).......)).))))))))))))....... ( -45.00)
>DroSim_CAF1 1107 120 - 1
UGGUGAGUUGCAUUCGAGUGCCCAAUUGGGGCUAACAAAUGGCUGCAAUGAGCGUCUGGCAAAUGAGCCAUUAAUAAGGCUAGUCAGAUGCACAUCAGACAUGGAUGCACUUAGAAAAUG
...(((((.((((((....((((.....))))......(((.(((..(((.(((((((((.....((((........)))).))))))))).)))))).))))))))))))))....... ( -43.80)
>DroYak_CAF1 1178 119 - 1
UGGUAAGUUGCAAUCGAGUGCUU-AUUCGUGCUAACAAAUGGCUGCAAUGAACGCCUGGCAAAUGAGCCAUUAAUAAGGCUAGUCAGAUACACAUCGGACUUGGAUGCACUCGGAAAAUG
.............((((((((..-((((((((((.....)))).)).......(((((((......))).......)))).((((.(((....))).)))).))))))))))))...... ( -29.61)
>consensus
UGGUGAGUUGCAUUCGAGUGCCC_AUUGGGGCUAACAAAUGGCUGCAAUGAGCGUCUGGCAAAUGAGCCAUUAAUAAGGCUAGUCAGAUGCACAUCAGACAUGGAUGCACUUAGAAAAUG
...(((((.(((((((.((((((.....))))..........(((..(((.(((((((((.....((((........)))).))))))))).)))))))).))))))))))))....... (-33.83 = -35.17 +   1.34)

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 12:38:53 2006