Locus 4180

Sequence ID 3R_DroMel_CAF1
Location 11,338,205 – 11,338,456
Length 251
Max. P 0.903095
window6716 window6717 window6718

overview

Window 6

Location 11,338,205 – 11,338,313
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.74
Mean single sequence MFE -26.30
Consensus MFE -23.86
Energy contribution -24.66
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 0.91
SVM decision value 0.43
SVM RNA-class probability 0.734319
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11338205 108 + 27905053
CGU------------UCUCAUCCUUUAUUGUUUUCCGUGUUCAGUAGCUGUCUUCUACUCCUGGUCCUCGAGGGUGCGAGUGCGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAUUCU
...------------.....................((((.(((((...(....(((....)))....)((((((((((((((...))))))))))))))........)))))))))... ( -28.40)
>DroSec_CAF1 77028 108 + 1
CGU------------CCUCAUCCUUUAUUGUUUUCCGUGUUCAGUAGCUGUCUUCUACUCGUGGUUCUCGAGGGAGCGAGUGCGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAGUCU
...------------..........(((((..(.....)..)))))((((((..(((....))).....(((((.((((((((...)))))))).)))))............)))))).. ( -25.90)
>DroSim_CAF1 75617 108 + 1
CGU------------CCUCAUCCUUUAUUGUUUUCCGUGUUCAGUAGCUGUCUUCUACUCCUGGUCCUCGAGGGUGCGAGUGCGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAGUCU
...------------..........(((((..(.....)..)))))((((((..(((....))).....((((((((((((((...))))))))))))))............)))))).. ( -29.30)
>DroEre_CAF1 72913 120 + 1
CAUCCUCGUCCUCAUGCUCAUCCUUUAUUGUUUUCCUUUCUCAGUAGCUGUCUGUUUCUCCUGGUCCUCGAGGGUGCGAGUACGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAGUCU
.........................(((((...........)))))((((((.(..((....))..)..((((((((((((.......))))))))))))............)))))).. ( -24.50)
>DroYak_CAF1 74640 108 + 1
CAC------------UCUCAUCCUUUAUUGUUUUCCAUUCUCAGUAGCUGUCUUUUUCUCCUGGUCUUCGAGGGUGCGAGUACGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAGUCU
...------------..........(((((...........)))))((((((....((....)).....((((((((((((.......))))))))))))............)))))).. ( -23.40)
>consensus
CGU____________CCUCAUCCUUUAUUGUUUUCCGUGUUCAGUAGCUGUCUUCUACUCCUGGUCCUCGAGGGUGCGAGUGCGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAGUCU
.........................(((((...........)))))((((((.....(....)......((((((((((((((...))))))))))))))............)))))).. (-23.86 = -24.66 +   0.80)

alignment

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secondary structure

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Window 7

Location 11,338,233 – 11,338,353
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -34.20
Consensus MFE -28.77
Energy contribution -29.57
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.84
SVM decision value 1.03
SVM RNA-class probability 0.903095
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11338233 120 + 27905053
UCAGUAGCUGUCUUCUACUCCUGGUCCUCGAGGGUGCGAGUGCGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAUUCUGAGUCCGGAACUUCAACCCUCGUUCCCCUGACUUUUGCUC
.(((((...(....(((....)))....)((((((((((((((...))))))))))))))........)))))(((....(((((.(((((..........)))))...))))).))).. ( -38.60)
>DroSec_CAF1 77056 120 + 1
UCAGUAGCUGUCUUCUACUCGUGGUUCUCGAGGGAGCGAGUGCGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAGUCUGAGUCCGGAACUUCAACCCUCGUCCCCCUGACUUUUGCUC
..(((((..(((.......((.((((...(((((.((((((((...)))))))).)))))..........(((((.......).))))......))))..)).......)))..))))). ( -32.74)
>DroSim_CAF1 75645 120 + 1
UCAGUAGCUGUCUUCUACUCCUGGUCCUCGAGGGUGCGAGUGCGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAGUCUGAGUCCGGAACUUCAACCCUCGUCCCCCCGACUUUUGCUC
((((..((((((..(((....))).....((((((((((((((...))))))))))))))............))))))))))(((.((..................)).)))........ ( -35.17)
>DroEre_CAF1 72953 119 + 1
UCAGUAGCUGUCUGUUUCUCCUGGUCCUCGAGGGUGCGAGUACGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAGUCUGCGUCCGGAACAUCAACCCUCGUUC-CCCGACUUUUGCUC
...(((((((((.(..((....))..)..((((((((((((.......))))))))))))............))))).))))(((.(((((..........))))-)..)))........ ( -35.80)
>DroYak_CAF1 74668 120 + 1
UCAGUAGCUGUCUUUUUCUCCUGGUCUUCGAGGGUGCGAGUACGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAGUCUGCGUCCUGAACUUCAACCCUCGUCCCCCCGACUUUUGCUC
...(((((((((....((....)).....((((((((((((.......))))))))))))............))))).))))...................(((.....)))........ ( -28.70)
>consensus
UCAGUAGCUGUCUUCUACUCCUGGUCCUCGAGGGUGCGAGUGCGUCGCAUUUGCACCUUCAAUUAAUAUACUGGCAGUCUGAGUCCGGAACUUCAACCCUCGUCCCCCCGACUUUUGCUC
..(((((..(((..........((.....((((((((((((((...))))))))))))))..........(((((.......).)))).........))..........)))..))))). (-28.77 = -29.57 +   0.80)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,338,353 – 11,338,456
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.26
Mean single sequence MFE -32.78
Consensus MFE -32.06
Energy contribution -31.58
Covariance contribution -0.48
Combinations/Pair 1.07
Mean z-score -1.26
Structure conservation index 0.98
SVM decision value 0.82
SVM RNA-class probability 0.857870
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11338353 103 + 27905053
UU-------UUUGUGAUUUAUGAGGGUGCGCUGGCAAAACAAAAUUAAGCCGGCGGACGAACGACAUUUGGCGUCAGCAUCUUAGCCGGGCUUUCCCAGC------AACCACAUCC----
..-------..((((.......(((((((((((((.............)))))).((((..(((...))).)))).))))))).((.(((....))).))------...))))...---- ( -32.72)
>DroSec_CAF1 77176 103 + 1
UU-------UUUGUGAUUUAUGAGGGUGCGCUGGCAAAACAAAAUUAAGCCGGCGGACGAACGACAUUCGGCGUCAGCAUCUUAGCGGGGCUUUCCCAGU------AACCACAUCC----
..-------..((((.......(((((((((((((.............)))))).((((..((.....)).)))).)))))))...(((.....)))...------...))))...---- ( -32.92)
>DroSim_CAF1 75765 103 + 1
UU-------UUUGUGAUUUAUGAGGGUGCGCUGGCAAAACAAAAUUAAGCCGGCGGACGAACGACAUUCGGCGUCAGCAUCUUAGCCGGGCUUUCCCAGU------AACCACAUCC----
..-------..((((.......(((((((((((((.............)))))).((((..((.....)).)))).))))))).((.(((....))).))------...))))...---- ( -32.82)
>DroEre_CAF1 73072 103 + 1
CU-------UUUGUGAUUUAUGAGGGUGCGCUGGCAAAACAAAAUUAAGCCGGCGGACGAACGACACUUGGCGUCAGCAUCUUAGCCGGGCUUUCCCAGC------AACCACAUCC----
..-------..((((.......(((((((((((((.............)))))).((((..(((...))).)))).))))))).((.(((....))).))------...))))...---- ( -32.72)
>DroYak_CAF1 74788 120 + 1
UUUUCGCUUUUUGUGAUUUAUGAGGGUGCGCUGGCAAAACAAAAUUAAGCCGGCGGACGAACGACAUUUGGCGUCAGCAUCUUAGCCGGGCUCUCCCAGCUUUUCCAACCACAUCCCAUC
...........((((.......(((((((((((((.............)))))).((((..(((...))).)))).)))))))(((.(((....))).)))........))))....... ( -32.72)
>consensus
UU_______UUUGUGAUUUAUGAGGGUGCGCUGGCAAAACAAAAUUAAGCCGGCGGACGAACGACAUUUGGCGUCAGCAUCUUAGCCGGGCUUUCCCAGC______AACCACAUCC____
...........((((.......(((((((((((((.............)))))).((((..(((...))).)))).))))))).((.(((....))).)).........))))....... (-32.06 = -31.58 +  -0.48)

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 11:20:35 2006