Locus 4633

Sequence ID X_DroMel_CAF1
Location 12,109,268 – 12,109,406
Length 138
Max. P 0.942138
window7612 window7613 window7614

overview

Window 2

Location 12,109,268 – 12,109,373
Length 105
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 89.81
Mean single sequence MFE -20.17
Consensus MFE -16.83
Energy contribution -17.07
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.83
SVM decision value 0.32
SVM RNA-class probability 0.685325
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12109268 105 + 22224390
-AGAAACUUUUUUACGCAGUUCAGAGCUCCCUAGUUAGUGCCUAACUCCAUAAGGAAUUUUCCCCCGA-GGAGAUUUCCACUCUUUUUCCCCUGUUGCUUUUUAUUU-----
-..............((((..(((........((((((...))))))......((((.(((((.....-))))).))))............))))))).........----- ( -18.30)
>DroSec_CAF1 21479 104 + 1
-AGAAACUUUUUUGUGCAGUUCAGAGUUCCCUAGUUAGUGCCUAACUCCAUAAGGAAUUUUCCCCCCAGGGAGAUUUCCACUCUUUU--CCCUGUUGCUUUUUAUUU-----
-..............((((...(((((.....((((((...))))))......((((.((((((....)))))).)))))))))...--..))))............----- ( -22.90)
>DroEre_CAF1 32998 102 + 1
-AGAAACUUUUUUGUGCAGCUCACAGUUUCCUAGUUAGUGCCUAACUCCAUAGGGAAUUUUCCC-CGA-GGAGAUUUCCACUCUUUU--CCCUGUUGCUUUUUAUUU-----
-..............(((((....(((((((((...(((.....)))...))))))))).....-.((-(((((.......))))))--)...))))).........----- ( -21.30)
>DroYak_CAF1 34220 110 + 1
CAAAAACUUUUUUGUGCAGUUCAGAGUUCCCUUGUUAGUGCCUAACUCCAUAAGGAAUUUUCCC-CGA-GGAGAUUUCCACUCUUUUUCCCCUGUUGCUUUUUUUUUUUAUU
.(((((.........((((...(((((......(((((...))))).......((((.(((((.-...-))))).))))))))).......)))).........)))))... ( -18.17)
>consensus
_AGAAACUUUUUUGUGCAGUUCAGAGUUCCCUAGUUAGUGCCUAACUCCAUAAGGAAUUUUCCC_CGA_GGAGAUUUCCACUCUUUU__CCCUGUUGCUUUUUAUUU_____
...............((((..(((.........(((((...))))).......((((.(((((......))))).))))............))))))).............. (-16.83 = -17.07 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,109,268 – 12,109,373
Length 105
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 89.81
Mean single sequence MFE -23.82
Consensus MFE -18.64
Energy contribution -19.20
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.01
Structure conservation index 0.78
SVM decision value 0.74
SVM RNA-class probability 0.839450
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12109268 105 - 22224390
-----AAAUAAAAAGCAACAGGGGAAAAAGAGUGGAAAUCUCC-UCGGGGGAAAAUUCCUUAUGGAGUUAGGCACUAACUAGGGAGCUCUGAACUGCGUAAAAAAGUUUCU-
-----.........(((.(((((.......((((.....((((-...(((((....)))))..)))).....))))..........)))))...)))..............- ( -21.83)
>DroSec_CAF1 21479 104 - 1
-----AAAUAAAAAGCAACAGGG--AAAAGAGUGGAAAUCUCCCUGGGGGGAAAAUUCCUUAUGGAGUUAGGCACUAACUAGGGAACUCUGAACUGCACAAAAAAGUUUCU-
-----.........(((.(((((--....((.......))(((((((..((..((((((....)))))).....))..))))))).)))))...)))..............- ( -26.00)
>DroEre_CAF1 32998 102 - 1
-----AAAUAAAAAGCAACAGGG--AAAAGAGUGGAAAUCUCC-UCG-GGGAAAAUUCCCUAUGGAGUUAGGCACUAACUAGGAAACUGUGAGCUGCACAAAAAAGUUUCU-
-----........(((.((((..--.....((((.....((((-..(-((((....)))))..)))).....))))..........))))..)))................- ( -24.53)
>DroYak_CAF1 34220 110 - 1
AAUAAAAAAAAAAAGCAACAGGGGAAAAAGAGUGGAAAUCUCC-UCG-GGGAAAAUUCCUUAUGGAGUUAGGCACUAACAAGGGAACUCUGAACUGCACAAAAAAGUUUUUG
..............(((.(((((.......((((.....((((-..(-((((....)))))..)))).....))))..........)))))...)))............... ( -22.93)
>consensus
_____AAAUAAAAAGCAACAGGG__AAAAGAGUGGAAAUCUCC_UCG_GGGAAAAUUCCUUAUGGAGUUAGGCACUAACUAGGGAACUCUGAACUGCACAAAAAAGUUUCU_
..............(((.(((((.......((((.....((((....(((((....)))))..)))).....))))..........)))))...)))............... (-18.64 = -19.20 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,109,302 – 12,109,406
Length 104
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 93.02
Mean single sequence MFE -26.00
Consensus MFE -22.49
Energy contribution -22.80
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -2.24
Structure conservation index 0.86
SVM decision value 1.32
SVM RNA-class probability 0.942138
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12109302 104 - 22224390
CCUUCAAAGGUGAUUCAACUCGGUGAAGGGGAA-------AAAUAAAAAGCAACAGGGGAAAAAGAGUGGAAAUCUCC-UCGGGGGAAAAUUCCUUAUGGAGUUAGGCACUA
((((((..(((......)).)..))))))....-------.........................((((.....((((-...(((((....)))))..)))).....)))). ( -24.80)
>DroSec_CAF1 21513 103 - 1
CCUUCAAAGGUGAUUCAACUCGGUGAAGGGGAA-------AAAUAAAAAGCAACAGGG--AAAAGAGUGGAAAUCUCCCUGGGGGGAAAAUUCCUUAUGGAGUUAGGCACUA
((((((..(((......)).)..))))))....-------.........((..(((((--(...((.......)))))))).......((((((....))))))..)).... ( -26.80)
>DroEre_CAF1 33032 101 - 1
CCUUCAAAGGUGAUUCAACUCGGUGAAGGGGAA-------AAAUAAAAAGCAACAGGG--AAAAGAGUGGAAAUCUCC-UCG-GGGAAAAUUCCCUAUGGAGUUAGGCACUA
((((((..(((......)).)..))))))....-------..................--.....((((.....((((-..(-((((....)))))..)))).....)))). ( -27.60)
>DroYak_CAF1 34255 110 - 1
CCUUCAAAGGUGAUUCAACUCGGUGAAGGGGAAUAAAUAAAAAAAAAAAGCAACAGGGGAAAAAGAGUGGAAAUCUCC-UCG-GGGAAAAUUCCUUAUGGAGUUAGGCACUA
((((((..(((......)).)..))))))....................................((((.....((((-..(-((((....)))))..)))).....)))). ( -24.80)
>consensus
CCUUCAAAGGUGAUUCAACUCGGUGAAGGGGAA_______AAAUAAAAAGCAACAGGG__AAAAGAGUGGAAAUCUCC_UCG_GGGAAAAUUCCUUAUGGAGUUAGGCACUA
((((((..(((......)).)..))))))....................................((((.....((((....(((((....)))))..)))).....)))). (-22.49 = -22.80 +   0.31)

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 11:29:51 2006