Locus 5497

Sequence ID 2R_DroMel_CAF1
Location 17,652,481 – 17,652,675
Length 194
Max. P 0.936198
window8775 window8776 window8777

overview

Window 5

Location 17,652,481 – 17,652,597
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.39
Mean single sequence MFE -25.32
Consensus MFE -20.70
Energy contribution -20.30
Covariance contribution -0.40
Combinations/Pair 1.15
Mean z-score -1.95
Structure conservation index 0.82
SVM decision value 1.25
SVM RNA-class probability 0.936198
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17652481 116 + 20766785
GAUUUGCAUUUAAUUGCGUAUAAUUGGAAAACCCAAUAUGUAUUAUUUUCA----CUUAAUUUUAUUUCACAAAUGCAGCUCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCG
((.((((((((...(((((((...(((.....))))))))))(((......----..)))...........)))))))).)).......(((((((.((....)).)))))))....... ( -23.20)
>DroSec_CAF1 6093 116 + 1
GAUUUGCAUUUAAUUGCGUAUAAUUGGAAAACCAAAUAUGUAUUAUUUUCA----CUUAAUUUUAUUUCGCAAAUGCAGCUCGAAAAACGUUUGCUGUCCAGCGAAAGUAAACAAAAACG
..(((((.......(((((((..((((....))))))))))).........----..........((((((....(((((.((.....))...)))))...)))))))))))........ ( -23.80)
>DroSim_CAF1 11991 116 + 1
GAUUUGCAUUUAAUUGCGUAUAAUUGGAAAACCAAAUAUGUAUUUUUUUCA----CUUAAUUUUAUUUCGCAAAUGCAGCUCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCG
..(((((.......(((((((..((((....))))))))))).........----..........((((((....(((((.((.....))...)))))...)))))))))))........ ( -25.80)
>DroEre_CAF1 6226 116 + 1
GAUUUGCAUUUAAUUGCGUAUAAUUGGAAAACCAAUUAUGUAUUAUUUUCA----CUUAAUUUUAUUUGGCAAAUGCAGCUCGAAAAACGCUUGCUGUCCAGCGAAAGCAAACAGAAGUG
((.(((((((....(((.(((((((((....))))))))).((((......----..))))........)))))))))).))......(((((.((((...((....))..))))))))) ( -29.10)
>DroYak_CAF1 17549 120 + 1
GAUUUGCAUUUAAUUGCGUAUAAUUGGAAAACCAAAUAUGUAUUAUUUUCACUCACUUAACUUUAUUUGGCAAAUGCAACUCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCG
((.((((((((...(((((((..((((....)))))))))))..................((......)).)))))))).)).......(((((((.((....)).)))))))....... ( -24.70)
>consensus
GAUUUGCAUUUAAUUGCGUAUAAUUGGAAAACCAAAUAUGUAUUAUUUUCA____CUUAAUUUUAUUUCGCAAAUGCAGCUCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCG
((.((((((((...(((((((..((((....)))))))))))................((......))...)))))))).))......(((((..(((...((....))..))).))))) (-20.70 = -20.30 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,652,521 – 17,652,637
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.84
Mean single sequence MFE -26.64
Consensus MFE -20.60
Energy contribution -20.92
Covariance contribution 0.32
Combinations/Pair 1.14
Mean z-score -2.17
Structure conservation index 0.77
SVM decision value 1.10
SVM RNA-class probability 0.915762
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17652521 116 + 20766785
UAUUAUUUUCA----CUUAAUUUUAUUUCACAAAUGCAGCUCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCGCGCAACUGAGGUAACGAGUGCAAUAAAAACCAUUUGUUAA
..(((((..((----(((....((((((((.....(((((.((.....))...)))))...(((...((........)).)))...)))))))).))))).))))).............. ( -22.50)
>DroSec_CAF1 6133 116 + 1
UAUUAUUUUCA----CUUAAUUUUAUUUCGCAAAUGCAGCUCGAAAAACGUUUGCUGUCCAGCGAAAGUAAACAAAAACGAGCAACUGAGCUAACGAGUGCAAUAAAAACCAUUUGUUGA
.........((----(((...........((....))((((((.....(((((..(((...((....))..))).)))))......))))))...)))))(((((((.....))))))). ( -24.00)
>DroSim_CAF1 12031 116 + 1
UAUUUUUUUCA----CUUAAUUUUAUUUCGCAAAUGCAGCUCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCGAGCAACUGAGGUAACGAGUGCAAUAAAAACCAUUUGUUAA
..((((.((((----(((....(((((((((....)).(((((......(((((((.((....)).))))))).....)))))....))))))).))))).)).))))............ ( -27.90)
>DroEre_CAF1 6266 116 + 1
UAUUAUUUUCA----CUUAAUUUUAUUUGGCAAAUGCAGCUCGAAAAACGCUUGCUGUCCAGCGAAAGCAAACAGAAGUGAGCGACUGAGGCAAUGAGUGCAAUAAAAAGCAUUUGUUAA
...........----...........(((((((((((..((((.....((((..((.....((....)).......))..))))..))))(((.....)))........))))))))))) ( -30.90)
>DroYak_CAF1 17589 120 + 1
UAUUAUUUUCACUCACUUAACUUUAUUUGGCAAAUGCAACUCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCGAGAGACUGAGGUAAUGAGUGCAAUAAAAAGCAUUUGUUAA
...........((((.((...........((....))..((((......(((((((.((....)).))))))).....)))).)).)))).(((..(((((........)))))..))). ( -27.90)
>consensus
UAUUAUUUUCA____CUUAAUUUUAUUUCGCAAAUGCAGCUCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCGAGCAACUGAGGUAACGAGUGCAAUAAAAACCAUUUGUUAA
...............((((..........((....)).(((((......(((((((.((....)).))))))).....)))))...)))).(((((((((..........))))))))). (-20.60 = -20.92 +   0.32)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,652,557 – 17,652,675
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.73
Mean single sequence MFE -29.88
Consensus MFE -26.30
Energy contribution -26.22
Covariance contribution -0.08
Combinations/Pair 1.15
Mean z-score -1.28
Structure conservation index 0.88
SVM decision value 0.37
SVM RNA-class probability 0.708315
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17652557 118 + 20766785
UCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCGCGCAACUGAGGUAACGAGUGCAAUAAAAACCAUUUGUUAAUGACUUUUGAAUACGCAAUUUGCUGUUGUUGCUUGGGA--
.........(((((((.((....)).)))))))..(((((.(((((.(((.(((((((((..........)))))))))....)))........((.....)).))))))))))....-- ( -26.80)
>DroSec_CAF1 6169 120 + 1
UCGAAAAACGUUUGCUGUCCAGCGAAAGUAAACAAAAACGAGCAACUGAGCUAACGAGUGCAAUAAAAACCAUUUGUUGAUGACUUUUGAAUACGCAAUUUGCUGUUGUUGCUUGGGUCC
.........(((((((.((....)).))))))).....((((((((..((((((((((((..........))))))))).......(((......)))...)))...))))))))..... ( -27.30)
>DroSim_CAF1 12067 120 + 1
UCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCGAGCAACUGAGGUAACGAGUGCAAUAAAAACCAUUUGUUAAUGACUUUUGAAUACGCAAUUUGCUGUUGUUGCUUGGGUUC
.........(((((((.....((....)).......)))))))((((.(((((((((..((((.......((((....))))....(((......))).))))..))))))))).)))). ( -31.00)
>DroEre_CAF1 6302 119 + 1
UCGAAAAACGCUUGCUGUCCAGCGAAAGCAAACAGAAGUGAGCGACUGAGGCAAUGAGUGCAAUAAAAAGCAUUUGUUAAUGACUUUUGAAUACGCAAUUUGCUGUUGUUGCUUGGGUU-
........(((((.((((...((....))..)))))))))((((((...(((((...(((.....(((((((((....)))).))))).....)))...)))))...))))))......- ( -35.00)
>DroYak_CAF1 17629 119 + 1
UCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCGAGAGACUGAGGUAAUGAGUGCAAUAAAAAGCAUUUGUUAAUGACUUUUGAAUACGCAAUUUGCUGUUGUUGCUUGGGUU-
(((......(((((((.((....)).))))))).....)))..((((.((((((..(..((((..(((((((((....)))).)))))...........))))..)..)))))).))))- ( -29.32)
>consensus
UCGAAAAACGUUUGCUGUCCAGCGAAAGCAAACAAAAGCGAGCAACUGAGGUAACGAGUGCAAUAAAAACCAUUUGUUAAUGACUUUUGAAUACGCAAUUUGCUGUUGUUGCUUGGGUU_
.........(((((((.((....)).))))))).....((((((((...(((((...(((...(((((..((((....))))..)))))....)))...)))))...))))))))..... (-26.30 = -26.22 +  -0.08)

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 11:46:28 2006