Locus 1826

Sequence ID X_DroMel_CAF1
Location 5,046,070 – 5,046,221
Length 151
Max. P 0.856920
window2973 window2974 window2975

overview

Window 3

Location 5,046,070 – 5,046,187
Length 117
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 79.49
Mean single sequence MFE -24.34
Consensus MFE -14.07
Energy contribution -14.88
Covariance contribution 0.81
Combinations/Pair 1.16
Mean z-score -2.24
Structure conservation index 0.58
SVM decision value 0.81
SVM RNA-class probability 0.856920
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5046070 117 - 22224390
UAUUAUAUAGCUAAAUUUCAGUGCGCGAAAGCCACAAGAAAUUCAACUAUUUAAAAUAUAAUAA-AGAAAAGUGGGUGGAAAAAAUAGAGGAGUGCUGUGGGGGAUGGGG-GGAUGGCA
.........((((..(..(.((.(((....))((((....((((..((((((....(((.((..-......))..)))....))))))..))))..))))..).)).)..-)..)))). ( -22.50)
>DroSec_CAF1 4958 119 - 1
UAUAAUAUAGCUAAAUUUCAGUGCGCGAAAGCCACAAGAAAUUCAUCUAUUUAAAACAUAAUAAAAGAAAAGUGGAUGGCGAAACUAGGGGACUGGUGUGUGGGGGGGGGGGAGUGGCA
.........((((..(..(.(((.((....))))).......((((((((((.................))))))))))((..(((((....)))))...))......)..)..)))). ( -31.13)
>DroSim_CAF1 4961 110 - 1
UAUAAUAUAGGUACAUUUCAGUGCGCGAAAGCCACAAGAAAUUCAUCUAUUUAAAACAUAAUAAAAGAAAAGUGGGUGGCGAAACUAGAGGAGUAUUGCG---------GGGGGUGGCA
..........((.(((..(.(((.((....)))))........(((((((((.................)))))))))((((.(((.....))).)))).---------.)..))))). ( -25.53)
>DroYak_CAF1 10280 107 - 1
UGUUAUAUAGCGAAAUUCCAUUGCGCGAAAGCCACAAGAAAUUAAUCCAUUUAAAACAUAAUAAAAGA-AAGUGGAAAGAAAAAAUAGAGGAGGGUUGAGGGG----------G-UGCA
.((....(..(((..((((..((.((....))))...........(((((((................-))))))).............))))..)))..)..----------.-.)). ( -18.19)
>consensus
UAUAAUAUAGCUAAAUUUCAGUGCGCGAAAGCCACAAGAAAUUCAUCUAUUUAAAACAUAAUAAAAGAAAAGUGGAUGGAAAAAAUAGAGGAGUGUUGUGGGG______G_GGGUGGCA
.........((((.......(((.((....))))).......((((((((((.................))))))))))...................................)))). (-14.07 = -14.88 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,046,109 – 5,046,221
Length 112
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 85.88
Mean single sequence MFE -17.69
Consensus MFE -11.69
Energy contribution -12.50
Covariance contribution 0.81
Combinations/Pair 1.22
Mean z-score -2.01
Structure conservation index 0.66
SVM decision value 0.42
SVM RNA-class probability 0.730512
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5046109 112 + 22224390
CCACCCACUUUUCU-UUAUUAUAUUUUAAAUAGUUGAAUUUCUUGUGGCUUUCGCGCACUGAAAUUUAGCUAUAUAAUAAGUUUUUCAAACAUU---UUUUAGCUUAUUUAUAAUU
..............-..((((((......(((((((((((((..(((((....)).))).)))))))))))))..((((((((...........---....)))))))))))))). ( -22.66)
>DroSec_CAF1 4998 113 + 1
CCAUCCACUUUUCUUUUAUUAUGUUUUAAAUAGAUGAAUUUCUUGUGGCUUUCGCGCACUGAAAUUUAGCUAUAUUAUAAGUUUUUCAUCCAUU---UUUUAGCCUAUUUAAAAUU
......................(((((((((((.((((((((..(((((....)).))).))))))))((((......................---...))))))))))))))). ( -20.61)
>DroSim_CAF1 4992 113 + 1
CCACCCACUUUUCUUUUAUUAUGUUUUAAAUAGAUGAAUUUCUUGUGGCUUUCGCGCACUGAAAUGUACCUAUAUUAUAAGUUUUUCAUCCAUU---UUUUAGCCUAUUUAAAAUU
.............(((((.((.(((..((((.((((((...((((((((....))(((......)))........))))))...)))))).)))---)...))).))..))))).. ( -14.90)
>DroYak_CAF1 10309 115 + 1
CUUUCCACUU-UCUUUUAUUAUGUUUUAAAUGGAUUAAUUUCUUGUGGCUUUCGCGCAAUGGAAUUUCGCUAUAUAACAAGUUCUUCACCAAUUAAGUUUUAAAUUAUAUACGACU
..(((((..(-((.((((........)))).)))........(((((.......))))))))))..(((.(((((((..((..(((........)))..))...)))))))))).. ( -12.60)
>consensus
CCACCCACUUUUCUUUUAUUAUGUUUUAAAUAGAUGAAUUUCUUGUGGCUUUCGCGCACUGAAAUUUAGCUAUAUAAUAAGUUUUUCAUCCAUU___UUUUAGCCUAUUUAAAAUU
......................(((((((((((.((((((((..(((((....)).))).))))))))(((........)))......................))))))))))). (-11.69 = -12.50 +   0.81)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,046,109 – 5,046,221
Length 112
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 85.88
Mean single sequence MFE -19.65
Consensus MFE -11.90
Energy contribution -12.40
Covariance contribution 0.50
Combinations/Pair 1.12
Mean z-score -2.20
Structure conservation index 0.61
SVM decision value 0.16
SVM RNA-class probability 0.610827
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5046109 112 - 22224390
AAUUAUAAAUAAGCUAAAA---AAUGUUUGAAAAACUUAUUAUAUAGCUAAAUUUCAGUGCGCGAAAGCCACAAGAAAUUCAACUAUUUAAAAUAUAAUAA-AGAAAAGUGGGUGG
.((((((..(((((.....---...))))).........(((.((((...((((((.(((.((....)))))..))))))...)))).)))..))))))..-.............. ( -17.90)
>DroSec_CAF1 4998 113 - 1
AAUUUUAAAUAGGCUAAAA---AAUGGAUGAAAAACUUAUAAUAUAGCUAAAUUUCAGUGCGCGAAAGCCACAAGAAAUUCAUCUAUUUAAAACAUAAUAAAAGAAAAGUGGAUGG
...........(((((...---...((.(....).)).......))))).((((((.(((.((....)))))..))))))(((((((((.................))))))))). ( -20.65)
>DroSim_CAF1 4992 113 - 1
AAUUUUAAAUAGGCUAAAA---AAUGGAUGAAAAACUUAUAAUAUAGGUACAUUUCAGUGCGCGAAAGCCACAAGAAAUUCAUCUAUUUAAAACAUAAUAAAAGAAAAGUGGGUGG
............(((...(---((((((((((..((((((...))))))...((((.(((.((....)))))..)))))))))))))))....(((............)))))).. ( -22.30)
>DroYak_CAF1 10309 115 - 1
AGUCGUAUAUAAUUUAAAACUUAAUUGGUGAAGAACUUGUUAUAUAGCGAAAUUCCAUUGCGCGAAAGCCACAAGAAAUUAAUCCAUUUAAAACAUAAUAAAAGA-AAGUGGAAAG
..(((((((((((.....(((.....))).........))))))).))))..((((((((.((....)))........((((.....))))..............-.))))))).. ( -17.74)
>consensus
AAUUUUAAAUAAGCUAAAA___AAUGGAUGAAAAACUUAUAAUAUAGCUAAAUUUCAGUGCGCGAAAGCCACAAGAAAUUCAUCUAUUUAAAACAUAAUAAAAGAAAAGUGGAUGG
......................((((((((((...((........))..........(((.((....)))))......))))))))))............................ (-11.90 = -12.40 +   0.50)

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 10:19:42 2006