Locus 2887

Sequence ID 3R_DroMel_CAF1
Location 7,742,029 – 7,742,127
Length 98
Max. P 0.827723
window4658 window4659

overview

Window 8

Location 7,742,029 – 7,742,127
Length 98
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 80.60
Mean single sequence MFE -28.43
Consensus MFE -17.64
Energy contribution -18.50
Covariance contribution 0.86
Combinations/Pair 1.06
Mean z-score -2.07
Structure conservation index 0.62
SVM decision value 0.61
SVM RNA-class probability 0.800237
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7742029 98 + 27905053
-----CUACUGCUACUCCUGCCGCA--------------GGCUGUUGCUGCCACAAAUUAAAAUGUGGCCGCGCUUAAAUUCCGCACACACAAUUUAUUGUUUGCCGCCGCCUGUUU
-----.....((.......)).(((--------------(((.((.((.((((((........)))))).))...........(((.(((........))).))).)).)))))).. ( -27.30)
>DroSec_CAF1 39134 98 + 1
-----CUACUGCUAUUCCUGCCGCA--------------GGCUGUUGCUGCCACAAAUUAAAAUGUGUCCGCGCUUAAAUUCCGCACACAAAAUUUAUUGUUUGCCGCCGCCUGUUU
-----.....((.......)).(((--------------(((.((.((.(.((((........)))).).))...........(((.((((......)))).))).)).)))))).. ( -21.40)
>DroSim_CAF1 41054 98 + 1
-----CUACUGCUACUCCUGCCGCA--------------GGCUGUUGCUGCCACAAAUUAAAAUGUGGCCGCGCUUAAAUUCCGCACACAAAAUUUAUUGUUUGCCGCCGCCUGUUU
-----.....((.......)).(((--------------(((.((.((.((((((........)))))).))...........(((.((((......)))).))).)).)))))).. ( -28.50)
>DroEre_CAF1 39148 109 + 1
-----CUCCUGUUACUCCUGCGGCAGCGCCAGCGGCGGCGGCUGUUGCUGCCACAAAUUAAAAUGUGGCUGCGCUUAAAUUCCCCACACAAAAUUUAUUGUUUGCC---GCCUGUUU
-----..............(((((((((((((((((....)))))))..((((((........)))))).)))).............((((......)))).))))---))...... ( -35.90)
>DroYak_CAF1 39414 111 + 1
UACUACUACCGUUACUCCUGCGGC---GACGGCGGCGGCGGCUGUUGCUGCCACAAAUUAAAAUGUGGCCGCGCUUAAAUUCCCCACACAAAAUUUAUUGUUUGCC---GCCUGUUU
........((((.......)))).---(((((((((((((((....))))))...........(((((...............)))))...............)))---))).))). ( -34.66)
>DroAna_CAF1 52841 80 + 1
--------------CUCCUGC------------------GGCUGUUGCUGCCACAAAUUAAAAUGUGGCCGCGCUUAAAUUCUGC-CGC-AAAUUUAUUGUCUGCC---GCCAGCUU
--------------...((((------------------(((....((.((((((........)))))).))((.........))-...-.............)))---).)))... ( -22.80)
>consensus
_____CUACUGCUACUCCUGCCGCA______________GGCUGUUGCUGCCACAAAUUAAAAUGUGGCCGCGCUUAAAUUCCGCACACAAAAUUUAUUGUUUGCC___GCCUGUUU
.......................................(((....((.((((((........)))))).))...........(((.((((......)))).)))....)))..... (-17.64 = -18.50 +   0.86)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,742,029 – 7,742,127
Length 98
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 80.60
Mean single sequence MFE -32.68
Consensus MFE -19.97
Energy contribution -20.80
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.61
SVM decision value 0.70
SVM RNA-class probability 0.827723
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7742029 98 - 27905053
AAACAGGCGGCGGCAAACAAUAAAUUGUGUGUGCGGAAUUUAAGCGCGGCCACAUUUUAAUUUGUGGCAGCAACAGCC--------------UGCGGCAGGAGUAGCAGUAG-----
...(..((.(((((......((((((.((....)).))))))...((.((((((........)))))).))....)))--------------.)).))..)...........----- ( -30.80)
>DroSec_CAF1 39134 98 - 1
AAACAGGCGGCGGCAAACAAUAAAUUUUGUGUGCGGAAUUUAAGCGCGGACACAUUUUAAUUUGUGGCAGCAACAGCC--------------UGCGGCAGGAAUAGCAGUAG-----
...(..((.(((((......(((((((((....)))))))))...((...((((........))))...))....)))--------------.)).))..)...........----- ( -26.10)
>DroSim_CAF1 41054 98 - 1
AAACAGGCGGCGGCAAACAAUAAAUUUUGUGUGCGGAAUUUAAGCGCGGCCACAUUUUAAUUUGUGGCAGCAACAGCC--------------UGCGGCAGGAGUAGCAGUAG-----
...(..((.(((((......(((((((((....)))))))))...((.((((((........)))))).))....)))--------------.)).))..)...........----- ( -32.20)
>DroEre_CAF1 39148 109 - 1
AAACAGGC---GGCAAACAAUAAAUUUUGUGUGGGGAAUUUAAGCGCAGCCACAUUUUAAUUUGUGGCAGCAACAGCCGCCGCCGCUGGCGCUGCCGCAGGAGUAACAGGAG-----
...(..((---(((......((((((((......))))))))(((((.((((((........)))))).....((((.......))))))))))))))..)...........----- ( -38.10)
>DroYak_CAF1 39414 111 - 1
AAACAGGC---GGCAAACAAUAAAUUUUGUGUGGGGAAUUUAAGCGCGGCCACAUUUUAAUUUGUGGCAGCAACAGCCGCCGCCGCCGUC---GCCGCAGGAGUAACGGUAGUAGUA
.....(((---(((......((((((((......))))))))...((.((((((........)))))).))....))))))((..((((.---.((....).)..))))..)).... ( -40.80)
>DroAna_CAF1 52841 80 - 1
AAGCUGGC---GGCAGACAAUAAAUUU-GCG-GCAGAAUUUAAGCGCGGCCACAUUUUAAUUUGUGGCAGCAACAGCC------------------GCAGGAG--------------
...((.((---(((......(((((((-...-...)))))))...((.((((((........)))))).))....)))------------------)).))..-------------- ( -28.10)
>consensus
AAACAGGC___GGCAAACAAUAAAUUUUGUGUGCGGAAUUUAAGCGCGGCCACAUUUUAAUUUGUGGCAGCAACAGCC______________UGCGGCAGGAGUAGCAGUAG_____
...........(((......(((((((((....)))))))))...((.((((((........)))))).))....)))....................................... (-19.97 = -20.80 +   0.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:06 2006