Locus 6579

Sequence ID 2R_DroMel_CAF1
Location 20,575,129 – 20,575,302
Length 173
Max. P 0.837289
window10471 window10472 window10473

overview

Window 1

Location 20,575,129 – 20,575,246
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.49
Mean single sequence MFE -25.56
Consensus MFE -15.40
Energy contribution -15.18
Covariance contribution -0.22
Combinations/Pair 1.13
Mean z-score -1.60
Structure conservation index 0.60
SVM decision value 0.27
SVM RNA-class probability 0.661832
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20575129 117 - 20766785
AUUGAACACGGCACGUAUACUAACUACGUGCGCGCGUUUUGUAAAAUAACAUUCAAUUUGUGCAACCUGAUCAAGCCAUUGCAGCAGGACCAGAUUAUUGAUCGCCCUUCGACGAUC---
..........(((((((.......)))))))(((((..(((............)))..)))))..((((..(((....)))...))))....(((..((((.......))))..)))--- ( -28.30)
>DroVir_CAF1 40545 106 - 1
AUCGCAUAUUGCACGG---CUAGCUACGUGUGCGCAUUUUGCAAAAUAACAUUCAAUUUGUGCAACCUGAUCAAGCAAUUUCAUCAAC----------CGAUCAG-GUCCAACGAUCUCU
((((......(((((.---.......)))))(((((..(((.((.......)))))..))))).((((((((................----------.))))))-))....)))).... ( -25.13)
>DroPse_CAF1 29343 103 - 1
GUGGCAUACUGCACGUAUACUUGCUACGUGCGCGCAUUUUGCAAAAUAACAUUCAAUUUGUGCAACCUGAUCAAGCAAUUGCAUCA--------------ACCGCUGAUCGAUGAUC---
((((......(((((((.......)))))))(((((..(((.((.......)))))..)))))....(((((((....))).))))--------------.)))).((((...))))--- ( -26.50)
>DroGri_CAF1 43077 103 - 1
AUCGCAUAUUGCACGG---CUAGCUACGUGUGCGCAUUUUGCAAAAUAACAUUCAAUUUGUGCAACCUGAUCAAGCAAUUUCAUCAGG----------CAUUCAA----CCUCGAUCUAC
((((......(((((.---.......)))))(((((..(((.((.......)))))..)))))..((((((.((....))..))))))----------.......----...)))).... ( -21.20)
>DroMoj_CAF1 44442 104 - 1
AUCGCAUAUUGCACGG---CUAGGUACGUGUGCGCAUUUUGCAAAAUAACAUUCAAUUUGUGCAACCUGAUCAAGCAAUUGCAACAAC----------CGAUCGC-GUCCAAUGAUC--U
...(((.(((((..(.---.(((((.....((((((..(((.((.......)))))..)))))))))))..)..))))))))......----------.(((((.-......)))))--. ( -25.70)
>DroPer_CAF1 29279 103 - 1
GUGGCAUACUGCACGUAUACUUGCUACGUGCGCGCAUUUUGCAAAAUAACAUUCAAUUUGUGCAACCUGAUCAAGCAAUUGCAUCA--------------ACCGCUGAUCGAUGAUC---
((((......(((((((.......)))))))(((((..(((.((.......)))))..)))))....(((((((....))).))))--------------.)))).((((...))))--- ( -26.50)
>consensus
AUCGCAUACUGCACGG___CUAGCUACGUGCGCGCAUUUUGCAAAAUAACAUUCAAUUUGUGCAACCUGAUCAAGCAAUUGCAUCA____________CGAUCGC_GUUCGACGAUC___
...((.....(((((...........)))))(((((..(((............)))..)))))...........))............................................ (-15.40 = -15.18 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,575,206 – 20,575,302
Length 96
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 79.25
Mean single sequence MFE -28.52
Consensus MFE -17.63
Energy contribution -18.63
Covariance contribution 1.00
Combinations/Pair 1.22
Mean z-score -1.93
Structure conservation index 0.62
SVM decision value 0.74
SVM RNA-class probability 0.837289
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20575206 96 + 20766785
AAAACGCGCGCACGUAGUUAGUAUACGUGCCGUGUUCAAU-----UGCAGAAGACGACUAAGUCCUGACCCAGUAGAUUGGGGGGGGAAGGGUGGGUCGGG
..((((((.(((((((.......)))))))))))))....-----.........(((((...((((..(((((....)))))..))))......))))).. ( -37.70)
>DroPse_CAF1 29406 87 + 1
AAAAUGCGCGCACGUAGCAAGUAUACGUGCAGUAUGCCACAGCGUGGCAGCAGAAU--AAAGUUACCUUUCUGGGGAUAGAG------------AGAAGGG
....(((..(((((((.......)))))))....((((((...)))))))))....--........(((((((....)))))------------))..... ( -28.40)
>DroSec_CAF1 26712 85 + 1
AAAAUGCGCGCACGUAGUUAGUAUACGUGCCGUGUUCAAU-----UGCAGAAGACGACUAAGUCCUGACCCAGGAGAUGGGG-----------GGAUCGGG
.........(((((((.......)))))))(((.(((...-----....))).))).((..(((((..((((.....)))))-----------))))..)) ( -26.60)
>DroSim_CAF1 26841 85 + 1
AAAAUGCGCGCACGUAGUUAGUAUACGUGCCGUGUUCAAU-----UGCAGAAGACGACUAAGUCCUGACCCAGGAGAUGGGG-----------GGGUCGGG
..((((((.(((((((.......)))))))))))))....-----.......(((......)))(((((((...........-----------))))))). ( -28.60)
>DroEre_CAF1 27248 84 + 1
AAAAUGCGCGCACGUAGUUAGUAGACGUGCCGUGUUCAAU-----UGCAGAAGACGACCAAGUCCUGACCCAGGAGAAGGG------------GAAUCGGG
..((((((.((((((.........))))))))))))....-----.......(((......)))(((((((........))------------)..)))). ( -21.80)
>DroYak_CAF1 27686 84 + 1
AAAAUGCGCGCACGUAGUUAGUAUACGUGCCGUGUUCAAU-----UGCAGAAGACGACUAAGUCCUGACCCAGCAGAUGGG------------GGAUUGGG
..((((((.(((((((.......)))))))))))))((((-----(.(((..(((......)))))).((((.....))))------------.))))).. ( -28.00)
>consensus
AAAAUGCGCGCACGUAGUUAGUAUACGUGCCGUGUUCAAU_____UGCAGAAGACGACUAAGUCCUGACCCAGGAGAUGGGG___________GGAUCGGG
..((((((.(((((((.......)))))))))))))...........(((..(((......)))))).((((.....)))).................... (-17.63 = -18.63 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,575,206 – 20,575,302
Length 96
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 79.25
Mean single sequence MFE -21.92
Consensus MFE -15.18
Energy contribution -14.77
Covariance contribution -0.41
Combinations/Pair 1.35
Mean z-score -1.58
Structure conservation index 0.69
SVM decision value 0.64
SVM RNA-class probability 0.807341
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20575206 96 - 20766785
CCCGACCCACCCUUCCCCCCCCAAUCUACUGGGUCAGGACUUAGUCGUCUUCUGCA-----AUUGAACACGGCACGUAUACUAACUACGUGCGCGCGUUUU
...((((((....................))))))(((((......))))).....-----...((((.(((((((((.......))))))).)).)))). ( -25.95)
>DroPse_CAF1 29406 87 - 1
CCCUUCU------------CUCUAUCCCCAGAAAGGUAACUUU--AUUCUGCUGCCACGCUGUGGCAUACUGCACGUAUACUUGCUACGUGCGCGCAUUUU
.((((.(------------((........))))))).......--....(((((((((...))))))....(((((((.......)))))))..))).... ( -23.20)
>DroSec_CAF1 26712 85 - 1
CCCGAUCC-----------CCCCAUCUCCUGGGUCAGGACUUAGUCGUCUUCUGCA-----AUUGAACACGGCACGUAUACUAACUACGUGCGCGCAUUUU
((.(((((-----------...........))))).)).......(((.(((....-----...))).)))(((((((.......)))))))......... ( -20.20)
>DroSim_CAF1 26841 85 - 1
CCCGACCC-----------CCCCAUCUCCUGGGUCAGGACUUAGUCGUCUUCUGCA-----AUUGAACACGGCACGUAUACUAACUACGUGCGCGCAUUUU
((.(((((-----------...........))))).)).......(((.(((....-----...))).)))(((((((.......)))))))......... ( -22.80)
>DroEre_CAF1 27248 84 - 1
CCCGAUUC------------CCCUUCUCCUGGGUCAGGACUUGGUCGUCUUCUGCA-----AUUGAACACGGCACGUCUACUAACUACGUGCGCGCAUUUU
.((((.((------------((((......)))...))).)))).(((.(((....-----...))).)))((((((.........))))))......... ( -19.80)
>DroYak_CAF1 27686 84 - 1
CCCAAUCC------------CCCAUCUGCUGGGUCAGGACUUAGUCGUCUUCUGCA-----AUUGAACACGGCACGUAUACUAACUACGUGCGCGCAUUUU
.....(((------------((((.....))))...)))......(((.(((....-----...))).)))(((((((.......)))))))......... ( -19.60)
>consensus
CCCGACCC___________CCCCAUCUCCUGGGUCAGGACUUAGUCGUCUUCUGCA_____AUUGAACACGGCACGUAUACUAACUACGUGCGCGCAUUUU
((.(((((......................))))).)).......(((.(((............))).)))(((((((.......)))))))......... (-15.18 = -14.77 +  -0.41)

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 12:14:17 2006