Locus 359

Sequence ID 3L_DroMel_CAF1
Location 1,043,895 – 1,044,026
Length 131
Max. P 0.931470
window529 window530 window531

overview

Window 9

Location 1,043,895 – 1,043,987
Length 92
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 81.72
Mean single sequence MFE -30.40
Consensus MFE -23.19
Energy contribution -23.50
Covariance contribution 0.31
Combinations/Pair 1.12
Mean z-score -2.80
Structure conservation index 0.76
SVM decision value 1.21
SVM RNA-class probability 0.931470
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1043895 92 + 23771897
GGCGACAC-UGGAACGACCCCAUCCUGCAUC---------------------CGGAAUCGUGCAACUGCAUCCUGCAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAA
.(((....-(((.......)))...)))...---------------------..(((((((((((.(((.....((((.(((........))).)))))))))))))))))).. ( -27.80)
>DroSec_CAF1 18564 88 + 1
GGCGACAC-UGGAA----CCCAUCCUGCAUG---------------------CCGAAUCGUGCAACUGCAUCCUGCAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAA
((((....-.(((.----....)))....))---------------------))(((((((((((.(((.....((((.(((........))).)))))))))))))))))).. ( -32.00)
>DroSim_CAF1 19325 88 + 1
GGCGACAC-UGGAA----CCCAUCCUGCAUC---------------------CCGAAUCGUGCAACUGCAUCCUGCAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAA
((.((..(-.(((.----....))).)..))---------------------))(((((((((((.(((.....((((.(((........))).)))))))))))))))))).. ( -30.00)
>DroEre_CAF1 21670 88 + 1
GGCGACAC-UGGAG----CCCAUCCUGCAUC---------------------CCGAAUCCUGCAACUGCAUCCUGCAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAA
((.((..(-.(((.----....))).)..))---------------------))(((((.(((((.(((.....((((.(((........))).)))))))))))).))))).. ( -26.90)
>DroYak_CAF1 19358 109 + 1
GGCGACAC-UGGAA----CCCAUCCUGCAUCCUGCAUCCUGCAUCCCGAGUCCCGAAUCGUGCAACUGCAUCCUGCAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAA
((.(((.(-.(((.----..((...(((.....)))...))..))).).)))))(((((((((((.(((.....((((.(((........))).)))))))))))))))))).. ( -36.10)
>DroAna_CAF1 17205 79 + 1
AGAGGCAGUUGCAG----CAGAUGCU----------------------------GA--GAUGCAGAUGCAUC-UACAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAA
....(((((.((.(----((((((((----------------------------((--(((((....)))))-).)))).((........)))))))))))))))......... ( -29.60)
>consensus
GGCGACAC_UGGAA____CCCAUCCUGCAUC_____________________CCGAAUCGUGCAACUGCAUCCUGCAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAA
..........(((.........))).............................(((((((((((.(((.....((((.(((........))).)))))))))))))))))).. (-23.19 = -23.50 +   0.31) 

alignment

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secondary structure

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Window 0

Location 1,043,895 – 1,043,987
Length 92
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 81.72
Mean single sequence MFE -33.50
Consensus MFE -23.34
Energy contribution -23.45
Covariance contribution 0.11
Combinations/Pair 1.15
Mean z-score -2.41
Structure conservation index 0.70
SVM decision value 0.84
SVM RNA-class probability 0.864619
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1043895 92 - 23771897
UUGAAUCAUGCAAUGCGCAAAUGCGAAACGUUGCAGCUGCAGGAUGCAGUUGCACGAUUCCG---------------------GAUGCAGGAUGGGGUCGUUCCA-GUGUCGCC
........(((.....)))...((((.((...((((((((.....))))))))(((((((((---------------------.........)))))))))....-)).)))). ( -32.40)
>DroSec_CAF1 18564 88 - 1
UUGAAUCAUGCAAUGCGCAAAUGCGAAACGUUGCAGCUGCAGGAUGCAGUUGCACGAUUCGG---------------------CAUGCAGGAUGGG----UUCCA-GUGUCGCC
..(((((.((((.(((((....))(((.(((.((((((((.....))))))))))).))).)---------------------)))))).....))----)))..-........ ( -33.10)
>DroSim_CAF1 19325 88 - 1
UUGAAUCAUGCAAUGCGCAAAUGCGAAACGUUGCAGCUGCAGGAUGCAGUUGCACGAUUCGG---------------------GAUGCAGGAUGGG----UUCCA-GUGUCGCC
..(((((........(((....)))....((.((((((((.....)))))))))))))))((---------------------(((((.(((....----.))).-))))).)) ( -33.30)
>DroEre_CAF1 21670 88 - 1
UUGAAUCAUGCAAUGCGCAAAUGCGAAACGUUGCAGCUGCAGGAUGCAGUUGCAGGAUUCGG---------------------GAUGCAGGAUGGG----CUCCA-GUGUCGCC
..(((((........(((....))).....((((((((((.....)))))))))))))))((---------------------(((((.(((....----.))).-))))).)) ( -32.90)
>DroYak_CAF1 19358 109 - 1
UUGAAUCAUGCAAUGCGCAAAUGCGAAACGUUGCAGCUGCAGGAUGCAGUUGCACGAUUCGGGACUCGGGAUGCAGGAUGCAGGAUGCAGGAUGGG----UUCCA-GUGUCGCC
..(((((........(((....)))....((.((((((((.....)))))))))))))))(((((.((((((.((...(((.....)))...)).)----)))).-).))).)) ( -41.80)
>DroAna_CAF1 17205 79 - 1
UUGAAUCAUGCAAUGCGCAAAUGCGAAACGUUGCAGCUGUA-GAUGCAUCUGCAUC--UC----------------------------AGCAUCUG----CUGCAACUGCCUCU
.........(((...(((....)))....((((((((((((-(((((....)))))--).----------------------------.)))...)----)))))))))).... ( -27.50)
>consensus
UUGAAUCAUGCAAUGCGCAAAUGCGAAACGUUGCAGCUGCAGGAUGCAGUUGCACGAUUCGG_____________________GAUGCAGGAUGGG____UUCCA_GUGUCGCC
..(((((........(((....)))......(((((((((.....))))))))).))))).............................(((.........))).......... (-23.34 = -23.45 +   0.11) 

alignment

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secondary structure

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dotplot

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Window 1

Location 1,043,925 – 1,044,026
Length 101
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 80.20
Mean single sequence MFE -25.79
Consensus MFE -13.29
Energy contribution -13.10
Covariance contribution -0.19
Combinations/Pair 1.09
Mean z-score -2.19
Structure conservation index 0.52
SVM decision value 0.21
SVM RNA-class probability 0.633909
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1043925 101 + 23771897
------------CGGAAUCGUGC---AACUGCAUCCUGCAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAAUAAUGAUUGAAUUAAUUGCGUUAAUAACUGACACUAGCC
------------.((((.(((((---(.((((.....)))).))).)))))))((....))((...((((((((((((....)))))))))..)))((((.....))))....)). ( -29.20)
>DroVir_CAF1 28814 87 + 1
-----------------UCGUGUUUGAAGUGCG--C----------CCAUUUUGCAUUUGCGCAUUGCAUGAUUCAAUAAUGAUUGAAUUAAUUGCGUUAAUAACUGACACUAGCC
-----------------..(((((.(.((((((--(----------.............)))))))((((((((((((....)))))))))..)))........).)))))..... ( -22.22)
>DroGri_CAF1 23874 89 + 1
-----------------UCGUGCUUGAAGUGCGUAC----------CCAUUUUGCAUUUGCGCAUUGCAUGAUUCAAUAAUGAUUGAAUUAAUUGCGUUAAUAACUGACACUAGCA
-----------------...((((.(.((((((((.----------............))))))))((((((((((((....)))))))))..)))((((.....)))).).)))) ( -20.72)
>DroEre_CAF1 21696 101 + 1
------------CCGAAUCCUGC---AACUGCAUCCUGCAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAAUAAUGAUUGAAUUAAUUGCGUUAAUAACUGACACUAGCC
------------..(((...(((---(.((((.....)))).))))....)))((....))((...((((((((((((....)))))))))..)))((((.....))))....)). ( -26.20)
>DroYak_CAF1 19393 113 + 1
GCAUCCCGAGUCCCGAAUCGUGC---AACUGCAUCCUGCAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAAUAAUGAUUGAAUUAAUUGCGUUAAUAACUGACACUAGCC
.........(((.((((.(((((---(.((((.....)))).))).))).)))).(((.(((((.....(((((((((....)))))))))..))))).)))....)))....... ( -31.80)
>DroAna_CAF1 17227 96 + 1
--------------GA--GAUGC---AGAUGCAUC-UACAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAAUAAUGAUUGAAUUAAUUGCGUUAAUAACUGACACUAGGC
--------------.(--(((((---....)))))-)...(((((((.((..(((....)))....)).(((((((((....))))))))).))))((((.....))))....))) ( -24.60)
>consensus
______________GA_UCGUGC___AACUGCAUCCUGCAGCUGCAACGUUUCGCAUUUGCGCAUUGCAUGAUUCAAUAAUGAUUGAAUUAAUUGCGUUAAUAACUGACACUAGCC
....................(((.......)))....................((....))((...((((((((((((....)))))))))..)))((((.....))))....)). (-13.29 = -13.10 +  -0.19) 

alignment

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secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:02 2006