Locus 1655

Sequence ID 3R_DroMel_CAF1
Location 4,786,399 – 4,786,630
Length 231
Max. P 0.999140
window2731 window2732 window2733

overview

Window 1

Location 4,786,399 – 4,786,515
Length 116
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 77.05
Mean single sequence MFE -20.73
Consensus MFE -17.70
Energy contribution -17.37
Covariance contribution -0.33
Combinations/Pair 1.17
Mean z-score -1.14
Structure conservation index 0.85
SVM decision value 0.77
SVM RNA-class probability 0.846688
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4786399 116 - 27905053
-AAAAAUUAAAAAACUCCAGCAACAAUGGCAACAACAACAGUAGCGGCUGUUUGUACCGUUAGAUGACGCAAAAUUACGCUUACUCAUUCGGCAAGCGGCAGUUCCCUC--AAAAACAA
-...........((((((.((.....((....))((((((((....)))).))))...((..(((((.((........))....)))))..))..)))).)))).....--........ ( -20.90)
>DroEre_CAF1 21915 115 - 1
--AAAAUUUUAAAACACCAGCAACAAUGGCAACAACAACAGUAGCGGCCGUAUGUACCGUUAGAUGACGCAAAAUUACGCUUACUCAUUCGGCAAGCGGCAGUUCCCCC--AAAAACAA
--..............((.((.((((((((..(.((....)).)..))))).)))...((..(((((.((........))....)))))..))..))))..........--........ ( -19.80)
>DroAna_CAF1 21237 93 - 1
G--------------------------AACAACAACAACAGUAGCGGCUGCUUGUACCGUUAGAUGACGCAAAAUUACGCUUACUCAUUCGGCAAGCAGCGUUCCCCCCCAAAAAACAA
(--------------------------(((....((....))....((((((((..(((...(((((.((........))....))))))))))))))))))))............... ( -21.50)
>consensus
__AAAAUU__AAAAC_CCAGCAACAAUGGCAACAACAACAGUAGCGGCUGUUUGUACCGUUAGAUGACGCAAAAUUACGCUUACUCAUUCGGCAAGCGGCAGUUCCCCC__AAAAACAA
..............................................((((((((..(((...(((((.((........))....))))))))))))))))................... (-17.70 = -17.37 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,786,515 – 4,786,630
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.83
Mean single sequence MFE -24.60
Consensus MFE -23.41
Energy contribution -23.38
Covariance contribution -0.02
Combinations/Pair 1.09
Mean z-score -1.25
Structure conservation index 0.95
SVM decision value 1.34
SVM RNA-class probability 0.943597
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4786515 115 + 27905053
-----UUUUUUGGCUGGCAUUGCCAUUCCGUUCUUACCAGCCGAUUGUUGUUGUAUUUUAGACCAUUUUUGUCAGACAAACAAACGGUUUUAUGGUUUAUUUUUAGCCCGUCCAACGGCU
-----....((((((((....((......)).....))))))))..(((((((......(((((...(((((.......))))).))))).((((.(((....))).)))).))))))). ( -25.80)
>DroSec_CAF1 21773 116 + 1
----UUUUUUUGGCUGGCAUUGCCAUUCCGUUCUUACCAACCGAUUGUUGUUGUAUUUUAGACCAUUUUUGUCAGACAAACAAACGGUUUUAUGGUUUAUUUUUAGCCCGUCCAACGGCU
----......((((.......))))..(((((......(((((.((((((((........(((.......))).))).))))).)))))..((((.(((....))).))))..))))).. ( -22.00)
>DroSim_CAF1 17237 119 + 1
UUUUUUUUUUUGGCUGGCAUUGCCAUUCCGUUCUUACCAGCCGAU-GUUGUUGUAUUUUAGACCAUUUUUGUCAGACAAACAAACGGUUUUAUGGUUUAUUUUUAGCCCGUCCAACGGCU
.........((((((((....((......)).....)))))))).-(((((((......(((((...(((((.......))))).))))).((((.(((....))).)))).))))))). ( -25.80)
>DroEre_CAF1 22030 115 + 1
-----UUUUUUGGCUGGCAUUGCCAUUCCGUUCUUACCAGCCGAUUGUUGUUGUAUUUUAGACCAUUUUUGUCAGACAAACAAACGGUUUUAUGGUUUAUUUUUAGCCCGUCCAACGGCU
-----....((((((((....((......)).....))))))))..(((((((......(((((...(((((.......))))).))))).((((.(((....))).)))).))))))). ( -25.80)
>DroYak_CAF1 22387 118 + 1
--UUUUUUUUUGGCUGGCAUUGCCAUUCCGUUCUUACCAGCCUAUUGUUGUUGUAUUUUAGACCAUUUUUGUCAGACAAACAAACGGUUUUAUGGUUUAUUUUUAGCCCGUCCAACGGCU
--.........((((((....((......)).....))))))....(((((((......(((((...(((((.......))))).))))).((((.(((....))).)))).))))))). ( -24.00)
>DroAna_CAF1 21330 119 + 1
UUUUUUUUUUUGGCCGCCAUUGCCAUUCCGUUCUUAC-GGCCGAUUGUUGUUGUAUUUUAGACCAUUUUUGUCAGACAAGCAAACGGUUUUAUGAUUUAUUUUUAGCUCGUCCAACGGCU
.........(((((((.....((......)).....)-))))))..(((((((.......(((.......))).(((.(((.((..((..........))..)).))).)))))))))). ( -24.20)
>consensus
____UUUUUUUGGCUGGCAUUGCCAUUCCGUUCUUACCAGCCGAUUGUUGUUGUAUUUUAGACCAUUUUUGUCAGACAAACAAACGGUUUUAUGGUUUAUUUUUAGCCCGUCCAACGGCU
.........((((((((....((......)).....))))))))..(((((((......(((((...(((((.......))))).))))).((((.(((....))).)))).))))))). (-23.41 = -23.38 +  -0.02)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,786,515 – 4,786,630
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.83
Mean single sequence MFE -26.74
Consensus MFE -24.43
Energy contribution -24.08
Covariance contribution -0.36
Combinations/Pair 1.22
Mean z-score -2.57
Structure conservation index 0.91
SVM decision value 3.39
SVM RNA-class probability 0.999140
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4786515 115 - 27905053
AGCCGUUGGACGGGCUAAAAAUAAACCAUAAAACCGUUUGUUUGUCUGACAAAAAUGGUCUAAAAUACAACAACAAUCGGCUGGUAAGAACGGAAUGGCAAUGCCAGCCAAAAAA-----
.((((((.(.(((((...((((((((.........))))))))))))).)...))))))...................((((((((....(.....)....))))))))......----- ( -27.20)
>DroSec_CAF1 21773 116 - 1
AGCCGUUGGACGGGCUAAAAAUAAACCAUAAAACCGUUUGUUUGUCUGACAAAAAUGGUCUAAAAUACAACAACAAUCGGUUGGUAAGAACGGAAUGGCAAUGCCAGCCAAAAAAA----
.((((((.(.(((((...((((((((.........))))))))))))).)...))))))...................((((((((....(.....)....)))))))).......---- ( -24.80)
>DroSim_CAF1 17237 119 - 1
AGCCGUUGGACGGGCUAAAAAUAAACCAUAAAACCGUUUGUUUGUCUGACAAAAAUGGUCUAAAAUACAACAAC-AUCGGCUGGUAAGAACGGAAUGGCAAUGCCAGCCAAAAAAAAAAA
.((((((.(.(((((...((((((((.........))))))))))))).)...))))))...............-...((((((((....(.....)....))))))))........... ( -27.20)
>DroEre_CAF1 22030 115 - 1
AGCCGUUGGACGGGCUAAAAAUAAACCAUAAAACCGUUUGUUUGUCUGACAAAAAUGGUCUAAAAUACAACAACAAUCGGCUGGUAAGAACGGAAUGGCAAUGCCAGCCAAAAAA-----
.((((((.(.(((((...((((((((.........))))))))))))).)...))))))...................((((((((....(.....)....))))))))......----- ( -27.20)
>DroYak_CAF1 22387 118 - 1
AGCCGUUGGACGGGCUAAAAAUAAACCAUAAAACCGUUUGUUUGUCUGACAAAAAUGGUCUAAAAUACAACAACAAUAGGCUGGUAAGAACGGAAUGGCAAUGCCAGCCAAAAAAAAA--
.((((((.(.(((((...((((((((.........))))))))))))).)...))))))...................((((((((....(.....)....)))))))).........-- ( -27.10)
>DroAna_CAF1 21330 119 - 1
AGCCGUUGGACGAGCUAAAAAUAAAUCAUAAAACCGUUUGCUUGUCUGACAAAAAUGGUCUAAAAUACAACAACAAUCGGCC-GUAAGAACGGAAUGGCAAUGGCGGCCAAAAAAAAAAA
....((..(((((((........................)))))))..)).....(((((....................((-((....))))....((....))))))).......... ( -26.96)
>consensus
AGCCGUUGGACGGGCUAAAAAUAAACCAUAAAACCGUUUGUUUGUCUGACAAAAAUGGUCUAAAAUACAACAACAAUCGGCUGGUAAGAACGGAAUGGCAAUGCCAGCCAAAAAAA____
....((..(((((((........................)))))))..))............................((((((((....(.....)....))))))))........... (-24.43 = -24.08 +  -0.36)

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 10:16:04 2006