Locus 7963

Sequence ID 3L_DroMel_CAF1
Location 21,093,734 – 21,093,931
Length 197
Max. P 0.993362
window12990 window12991 window12992

overview

Window 0

Location 21,093,734 – 21,093,853
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.48
Mean single sequence MFE -28.64
Consensus MFE -24.36
Energy contribution -24.60
Covariance contribution 0.24
Combinations/Pair 1.14
Mean z-score -2.18
Structure conservation index 0.85
SVM decision value 2.39
SVM RNA-class probability 0.993362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21093734 119 - 23771897
UAGACUUGUUCAAGGGGAA-AAGCCUUUAAACGACUCCAAAUGAGUGUGAGAAAAAUGCCAGAAAAUGUGGACAGAUCAAACAUUAUUUUACUACAUUCAAGUGCCUGGGAAAUUGCACA
..((.(((((.(((((...-...))))).))))).))....((((((((((((.((((...((...((....))..))...)))).))))..)))))))).((((..........)))). ( -22.60)
>DroSec_CAF1 143974 119 - 1
UAGACUCGUUCAAGGGGAA-AAGCCUUUAAACGACUCCAAAUGAGUGUGUGAAAAAUGCCAGAAAAUGUGGACAGAUCAAACAUUAUUUUACUACAUUCAAGUGCCUGGAAAAUUGCACA
..((.(((((.(((((...-...))))).))))).))....(((((((((((((((((...((...((....))..))...)))).)))))).))))))).((((..........)))). ( -28.10)
>DroSim_CAF1 51024 119 - 1
UAGACUCGUUCAAGGGGAA-AAGCCUUUAAACGACUCCAAAUGAGUGUGUGAAAAAUGCCAGAAAAUGUGGACAGAUCAAACAUUAUUUUACUACAUUCAAGUGCCUGGGAAAUUGCACA
..((.(((((.(((((...-...))))).))))).))....(((((((((((((((((...((...((....))..))...)))).)))))).))))))).((((..........)))). ( -28.10)
>DroEre_CAF1 66360 120 - 1
UAGACUCGUUCGAGGGGAAAAAACCUUUAAGCGAUUCCAAAUGAGUGUGUGAACAAUGUCAGAAAAUGUGGGCAGAUCAAACAUUAUUUUACUACAUUCAAGUGUCUGUUAAAUUGCACA
((((((((((..((((.......))))..))))).......((((((((((((.(((((..((...((....))..))..)))))..))))).)))))))...)))))............ ( -30.10)
>DroYak_CAF1 38177 119 - 1
UAGACUCGUUUAAGGGGAAAAAACCUUUAAACGACUCCAAAUGAAUGUGUGAAAUAUGUCAGAAAAUGUGAGCAGAUCAAACAUUAUUUUUCUACAUUCAAGUG-CUAGGAAAUUGCACA
..((.(((((((((((.......))))))))))).))....((((((((.((((.((((..((...((....))..))..))))....)))))))))))).(((-(.........)))). ( -34.30)
>consensus
UAGACUCGUUCAAGGGGAA_AAGCCUUUAAACGACUCCAAAUGAGUGUGUGAAAAAUGCCAGAAAAUGUGGACAGAUCAAACAUUAUUUUACUACAUUCAAGUGCCUGGGAAAUUGCACA
..((.(((((.(((((.......))))).))))).))....(((((((((((((((((...((...((....))..))...)))).)))))).))))))).((((..........)))). (-24.36 = -24.60 +   0.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,093,774 – 21,093,893
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.16
Mean single sequence MFE -28.46
Consensus MFE -22.69
Energy contribution -22.65
Covariance contribution -0.04
Combinations/Pair 1.17
Mean z-score -1.89
Structure conservation index 0.80
SVM decision value 1.00
SVM RNA-class probability 0.898221
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21093774 119 - 23771897
GACAAAGAUGCUGUUGAGAGAACUCAAGUUCUUAGCUCAAUAGACUUGUUCAAGGGGAA-AAGCCUUUAAACGACUCCAAAUGAGUGUGAGAAAAAUGCCAGAAAAUGUGGACAGAUCAA
......(((.((((((((....)))...(((((((((((...((.(((((.(((((...-...))))).))))).))....))))).)))))).................)))))))).. ( -27.80)
>DroSec_CAF1 144014 116 - 1
GACAAAGAUGCUGUCUU---CUCUUAAGUUCUAAGCUCAAUAGACUCGUUCAAGGGGAA-AAGCCUUUAAACGACUCCAAAUGAGUGUGUGAAAAAUGCCAGAAAAUGUGGACAGAUCAA
......(((.((((((.---..(.....((((..(((((...((.(((((.(((((...-...))))).))))).))....)))))((((.....)))).))))...).))))))))).. ( -28.20)
>DroSim_CAF1 51064 116 - 1
GACAAAGAUGCUGUCUU---CUCUCAAGUUCUAAGCUCAAUAGACUCGUUCAAGGGGAA-AAGCCUUUAAACGACUCCAAAUGAGUGUGUGAAAAAUGCCAGAAAAUGUGGACAGAUCAA
......(((.((((((.---....((..((((..(((((...((.(((((.(((((...-...))))).))))).))....)))))((((.....)))).))))..)).))))))))).. ( -29.70)
>DroEre_CAF1 66400 116 - 1
GACAAAUAUGCUGUCUU---CUC-CAAGUUCUUAGCUCAAUAGACUCGUUCGAGGGGAAAAAACCUUUAAGCGAUUCCAAAUGAGUGUGUGAACAAUGUCAGAAAAUGUGGGCAGAUCAA
..........((((((.---...-...((((...(((((...((.(((((..((((.......))))..))))).))....)))))....)))).....((.....)).))))))..... ( -28.20)
>DroYak_CAF1 38216 117 - 1
GACAAAGAUGCUGUCUU---CACUCAAGUUCUAAGCUCAAUAGACUCGUUUAAGGGGAAAAAACCUUUAAACGACUCCAAAUGAAUGUGUGAAAUAUGUCAGAAAAUGUGAGCAGAUCAA
......(((.((((..(---(((.....((((..........((.(((((((((((.......))))))))))).)).....((((((.....)))).))))))...))))))))))).. ( -28.40)
>consensus
GACAAAGAUGCUGUCUU___CUCUCAAGUUCUAAGCUCAAUAGACUCGUUCAAGGGGAA_AAGCCUUUAAACGACUCCAAAUGAGUGUGUGAAAAAUGCCAGAAAAUGUGGACAGAUCAA
......(((.((((((............(((...(((((...((.(((((.(((((.......))))).))))).))....)))))....)))................))))))))).. (-22.69 = -22.65 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,093,814 – 21,093,931
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.01
Mean single sequence MFE -28.38
Consensus MFE -22.14
Energy contribution -22.30
Covariance contribution 0.16
Combinations/Pair 1.15
Mean z-score -1.92
Structure conservation index 0.78
SVM decision value 0.85
SVM RNA-class probability 0.865661
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21093814 117 - 23771897
CAAAUUUCAAUUAUGCUUUAUGGCAACAGACGACGC--CUGACAAAGAUGCUGUUGAGAGAACUCAAGUUCUUAGCUCAAUAGACUUGUUCAAGGGGAA-AAGCCUUUAAACGACUCCAA
..............(((((.((....)).....(.(--((((..(((...(((((((((((((....)))))...)))))))).)))..)).))).).)-))))................ ( -26.40)
>DroSec_CAF1 144054 116 - 1
CAUAUUUCAAUUAUGCUUUAUGGCAGCAGACGACGCGUCUGACAAAGAUGCUGUCUU---CUCUUAAGUUCUAAGCUCAAUAGACUCGUUCAAGGGGAA-AAGCCUUUAAACGACUCCAA
.........(((..((((.((...((.(((.(((((((((.....)))))).))).)---))))...))...))))..))).((.(((((.(((((...-...))))).))))).))... ( -28.70)
>DroSim_CAF1 51104 116 - 1
CAUAUUUCAAUUAUGCUUUAUGGCAACAGACGACGCGUCUGACAAAGAUGCUGUCUU---CUCUCAAGUUCUAAGCUCAAUAGACUCGUUCAAGGGGAA-AAGCCUUUAAACGACUCCAA
.........(((..((((..((....))((.(((((((((.....)))))).))).)---)...........))))..))).((.(((((.(((((...-...))))).))))).))... ( -28.10)
>DroEre_CAF1 66440 116 - 1
CAUAUUUCAAUUAUGCUUUAUGGCAACAGACGUCGCGUCUGACAAAUAUGCUGUCUU---CUC-CAAGUUCUUAGCUCAAUAGACUCGUUCGAGGGGAAAAAACCUUUAAGCGAUUCCAA
(((((((......((((....)))).((((((...))))))..)))))))..((((.---...-..(((.....)))....))))(((((..((((.......))))..)))))...... ( -28.00)
>DroYak_CAF1 38256 117 - 1
CAUAUUUCAAUUAUGCUUUAUGGCAACAGACGUCGCGUCUGACAAAGAUGCUGUCUU---CACUCAAGUUCUAAGCUCAAUAGACUCGUUUAAGGGGAAAAAACCUUUAAACGACUCCAA
.........(((..((((..((....))((((..((((((.....))))))))))..---............))))..))).((.(((((((((((.......))))))))))).))... ( -30.70)
>consensus
CAUAUUUCAAUUAUGCUUUAUGGCAACAGACGACGCGUCUGACAAAGAUGCUGUCUU___CUCUCAAGUUCUAAGCUCAAUAGACUCGUUCAAGGGGAA_AAGCCUUUAAACGACUCCAA
.............((((....))))..(((((..((((((.....)))))))))))..........................((.(((((.(((((.......))))).))))).))... (-22.14 = -22.30 +   0.16)

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 13:02:12 2006