Locus 6689

Sequence ID 3L_DroMel_CAF1
Location 17,818,056 – 17,818,216
Length 160
Max. P 0.712511
window10885 window10886 window10887

overview

Window 5

Location 17,818,056 – 17,818,176
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.33
Mean single sequence MFE -39.20
Consensus MFE -21.05
Energy contribution -21.67
Covariance contribution 0.62
Combinations/Pair 1.25
Mean z-score -2.68
Structure conservation index 0.54
SVM decision value 0.24
SVM RNA-class probability 0.648957
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17818056 120 + 23771897
GCCAUAGGCCAGGAAGAUUGCCAGGCCUAUGGCGAUCCAUAUACUGAAGCGAAUCCAUGUGAGAAUGUCCAACUUGAUCAUCAGGUAAAUGUUGAUCAAAAUGGAAAUGCCGGGUAGCCA
((((((((((.((.......)).)))))))))).((((.................(((......)))((((..(((((((.((......)).)))))))..))))......))))..... ( -40.40)
>DroPse_CAF1 148 120 + 1
GCCGUAGGCCAGAAAGAUCGCCAGACCUAUGGUGAGCCAAAUACAAAAACGCACCCAGGUGAGGAUGUCCAAUUUGAUCAUCAGGUAUAUGUUGAUCAAUAUGGAUAUGCCUGGGAGCCA
......(((........((((((......)))))))))............((.(((((((....(((((((..(((((((.((......)).)))))))..)))))))))))))).)).. ( -43.30)
>DroEre_CAF1 153 120 + 1
GCCGUAGGCCAGAAAGAUAGUCAGGCCUAUUGCGAUCCAUAUGCUAAAGCGCACCCAUGUGAGAAUAUCCAACUUGAUCAUCAGGUAAAUGUUAAUCAGAAUGGAAAUGCCCGGUAGCCA
((.(((((((.((.......)).))))))).)).........((((..(.(((.((((.(((.(((((...(((((.....)))))..)))))..)))..))))...))).)..)))).. ( -33.60)
>DroWil_CAF1 2637 120 + 1
GCUAUAGGAGAAAAAGAUGGCCAAACCGAUGGCAAUCCAAAUGCUAAAGCGCACCCAUGUUAGGAUAUCCAAUUUGAUCAUUAAGUAUAUAUUGAUCAGGAUGGAUAUGCCUGGUAGCCA
(((((.((.......(((.((((......)))).)))....(((......))).))....(((((((((((.((((((((.((......)).)))))))).))))))).))))))))).. ( -37.20)
>DroAna_CAF1 151 120 + 1
GCCGUAGGACAGGAAGAUGGACAGGCCGAUGGCCAGCCAUAUGCUGAAGCGCACCCAGGUGAGAAUGUCGAGCUUGAUCAUCAGGUAGAUGUUGAUCAGAAUGGAAAUGCCCGGCAGCCA
((((.....(((.(..((((...((((...))))..)))).).)))....(((.(((..(((.((((((..(((((.....))))).))))))..)))...)))...))).))))..... ( -36.40)
>DroPer_CAF1 163 120 + 1
GCCGUUGGCCAUGAAGAUCGCCAGACCUAUGGUGAGCCAAAUACAAAAACGCACCCAGGUGAGGAUGUCCAAUUUGAUCAUCAGGUAUAUGUUGAUCAAUACGGAUACGCCUGGGAGCCA
....(((((........((((((......)))))))))))..........((.((((((((....(((((...(((((((.((......)).)))))))...))))))))))))).)).. ( -44.30)
>consensus
GCCGUAGGCCAGAAAGAUCGCCAGACCUAUGGCGAGCCAAAUACUAAAGCGCACCCAGGUGAGAAUGUCCAACUUGAUCAUCAGGUAUAUGUUGAUCAAAAUGGAAAUGCCUGGUAGCCA
......(((........((((((......)))))).((...........(.(((....))).)....((((..(((((((.((......)).)))))))..)))).......))..))). (-21.05 = -21.67 +   0.62)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,818,056 – 17,818,176
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.33
Mean single sequence MFE -35.88
Consensus MFE -23.86
Energy contribution -23.95
Covariance contribution 0.09
Combinations/Pair 1.32
Mean z-score -2.10
Structure conservation index 0.67
SVM decision value 0.38
SVM RNA-class probability 0.712511
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17818056 120 - 23771897
UGGCUACCCGGCAUUUCCAUUUUGAUCAACAUUUACCUGAUGAUCAAGUUGGACAUUCUCACAUGGAUUCGCUUCAGUAUAUGGAUCGCCAUAGGCCUGGCAAUCUUCCUGGCCUAUGGC
..(((....)))...((((.((((((((.((......)).)))))))).))))............((((((..........))))))((((((((((.((.......)).)))))))))) ( -39.80)
>DroPse_CAF1 148 120 - 1
UGGCUCCCAGGCAUAUCCAUAUUGAUCAACAUAUACCUGAUGAUCAAAUUGGACAUCCUCACCUGGGUGCGUUUUUGUAUUUGGCUCACCAUAGGUCUGGCGAUCUUUCUGGCCUACGGC
..((.((((((.((.((((..(((((((.((......)).)))))))..)))).)).....)))))).))....(((((...(((.((....(((((....)))))...)))))))))). ( -36.20)
>DroEre_CAF1 153 120 - 1
UGGCUACCGGGCAUUUCCAUUCUGAUUAACAUUUACCUGAUGAUCAAGUUGGAUAUUCUCACAUGGGUGCGCUUUAGCAUAUGGAUCGCAAUAGGCCUGACUAUCUUUCUGGCCUACGGC
..((((..(.(((..((((...((((((.((......)).))))))...))))....(((....)))))).)..)))).........((..((((((.((.......)).))))))..)) ( -31.90)
>DroWil_CAF1 2637 120 - 1
UGGCUACCAGGCAUAUCCAUCCUGAUCAAUAUAUACUUAAUGAUCAAAUUGGAUAUCCUAACAUGGGUGCGCUUUAGCAUUUGGAUUGCCAUCGGUUUGGCCAUCUUUUUCUCCUAUAGC
..((((..(((.(((((((...((((((.((......)).))))))...))))))))))....(((((((......)))...((((.((((......)))).))))......)))))))) ( -35.30)
>DroAna_CAF1 151 120 - 1
UGGCUGCCGGGCAUUUCCAUUCUGAUCAACAUCUACCUGAUGAUCAAGCUCGACAUUCUCACCUGGGUGCGCUUCAGCAUAUGGCUGGCCAUCGGCCUGUCCAUCUUCCUGUCCUACGGC
..((((..(((((.........((((((.((......)).)))))).(((((.(((((......)))))))....)))..(((((.((((...)))).).)))).....)))))..)))) ( -33.90)
>DroPer_CAF1 163 120 - 1
UGGCUCCCAGGCGUAUCCGUAUUGAUCAACAUAUACCUGAUGAUCAAAUUGGACAUCCUCACCUGGGUGCGUUUUUGUAUUUGGCUCACCAUAGGUCUGGCGAUCUUCAUGGCCAACGGC
..((.((((((.(..((((..(((((((.((......)).)))))))..))))......).)))))).))..........(((((.((....(((((....)))))...))))))).... ( -38.20)
>consensus
UGGCUACCAGGCAUAUCCAUUCUGAUCAACAUAUACCUGAUGAUCAAAUUGGACAUCCUCACAUGGGUGCGCUUUAGCAUAUGGAUCGCCAUAGGCCUGGCCAUCUUCCUGGCCUACGGC
.(((((((((((...((((...((((((.((......)).))))))...))))(((((......)))))............(((....)))...)))))).........)))))...... (-23.86 = -23.95 +   0.09)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,818,096 – 17,818,216
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.17
Mean single sequence MFE -35.55
Consensus MFE -20.26
Energy contribution -20.02
Covariance contribution -0.25
Combinations/Pair 1.38
Mean z-score -2.18
Structure conservation index 0.57
SVM decision value 0.31
SVM RNA-class probability 0.683615
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17818096 120 - 23771897
AUCAGGGGUGAAAUUGUCGUUCAAGGUGCCCUUGGUUCCCUGGCUACCCGGCAUUUCCAUUUUGAUCAACAUUUACCUGAUGAUCAAGUUGGACAUUCUCACAUGGAUUCGCUUCAGUAU
....((((((((..(((((.....((((((...((...)).))).))))))))..((((.((((((((.((......)).)))))))).))))..............))))))))..... ( -33.90)
>DroPse_CAF1 188 120 - 1
AUCCGCAGUGAAUCUCUCCUUUAAGGUGCCCUUGGUUCCUUGGCUCCCAGGCAUAUCCAUAUUGAUCAACAUAUACCUGAUGAUCAAAUUGGACAUCCUCACCUGGGUGCGUUUUUGUAU
....((((.............(((((.(((...))).)))))((.((((((.((.((((..(((((((.((......)).)))))))..)))).)).....)))))).))....)))).. ( -34.40)
>DroEre_CAF1 193 120 - 1
AUCAGGGGUGAAAUUGUCGUUCAAGGUUCCCUUGGUACCCUGGCUACCGGGCAUUUCCAUUCUGAUUAACAUUUACCUGAUGAUCAAGUUGGAUAUUCUCACAUGGGUGCGCUUUAGCAU
..((((((.((..(((.....)))..))))))))(((((((((((....)))...((((...((((((.((......)).))))))...))))........)).))))))((....)).. ( -34.90)
>DroWil_CAF1 2677 120 - 1
UUCAGGUGUGAAGCUCUCAUUCAAAGUUCCUCUAGUACCCUGGCUACCAGGCAUAUCCAUCCUGAUCAAUAUAUACUUAAUGAUCAAAUUGGAUAUCCUAACAUGGGUGCGCUUUAGCAU
.....(((((((((..........((.....)).((((((((......(((.(((((((...((((((.((......)).))))))...))))))))))..)).)))))))))))).))) ( -34.60)
>DroAna_CAF1 191 120 - 1
GUCGGGAGUUAAGCUGUCCUUCAAGGUGCCAUUGGUACCAUGGCUGCCGGGCAUUUCCAUUCUGAUCAACAUCUACCUGAUGAUCAAGCUCGACAUUCUCACCUGGGUGCGCUUCAGCAU
...((((((..((((((((.....((((((((.(....)))))).)))))))..........((((((.((......)).))))))))))..))..))))......((((......)))) ( -34.80)
>DroPer_CAF1 203 120 - 1
AUCCGCAGGGAAUCUCUGCUUUAAGGUGCCCUUGGUUCCUUGGCUCCCAGGCGUAUCCGUAUUGAUCAACAUAUACCUGAUGAUCAAAUUGGACAUCCUCACCUGGGUGCGUUUUUGUAU
....((((((...))))))..(((((.(((...))).)))))((.((((((.(..((((..(((((((.((......)).)))))))..))))......).)))))).)).......... ( -40.70)
>consensus
AUCAGGAGUGAAACUCUCCUUCAAGGUGCCCUUGGUACCCUGGCUACCAGGCAUAUCCAUUCUGAUCAACAUAUACCUGAUGAUCAAAUUGGACAUCCUCACAUGGGUGCGCUUUAGCAU
....((((((...............(((((..((((......))))...))))).((((...((((((.((......)).))))))...))))(((((......)))))))))))..... (-20.26 = -20.02 +  -0.25)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:40 2006