Locus 5710

Sequence ID 2R_DroMel_CAF1
Location 18,082,239 – 18,082,369
Length 130
Max. P 0.993993
window9144 window9145 window9146

overview

Window 4

Location 18,082,239 – 18,082,342
Length 103
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 62.19
Mean single sequence MFE -25.56
Consensus MFE -7.94
Energy contribution -9.18
Covariance contribution 1.24
Combinations/Pair 1.28
Mean z-score -2.48
Structure conservation index 0.31
SVM decision value 0.61
SVM RNA-class probability 0.800245
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18082239 103 + 20766785
AUAUUUUUUAUAUAUAUUGUAGGUUGGUUG-GUAUACGUACAUAUGUAUACGUACUGUAUGUACCGUAUAUAC--CGAUGCCUGUUGCCAGGUGCCAACUUGGCUC
...................(((((..((((-(((((.(((((((((((....))).))))))))....)))))--)))))))))..(((((((....))))))).. ( -33.10)
>DroSec_CAF1 39813 84 + 1
AUAUCUAUAAUAUAUA---------GGAUG-GUGUACGUACGUAC------GUCCCGUAUG--CAG--UAUAC--CGAUGACUGUGACCAGGUGCCAACUUAGCUC
............((((---------(..((-((((((...(((((------(...))))))--..)--)))))--))....)))))...((((....))))..... ( -19.30)
>DroSim_CAF1 40467 84 + 1
AUAUUUUUUAUAUAUA---------GGUUG-GUGUACGUACGUAU------GUACCGUAUA--CCG--UAUAC--CGAUGCCUGUUGCCAGGUGCCAACUUGGCUC
.............(((---------(((((-(((((((((((...------....))))..--.))--)))))--))..)))))).(((((((....))))))).. ( -29.50)
>DroYak_CAF1 41231 79 + 1
AUAUUUUGU---------------------UUUAUACUUGUAUUUAGGUAGG---AGUAUGUA-UGUAUAUGC--CGAUGCCUGUUGCCAGGUGCCAACUUGGCUC
.........---------------------..............((((((..---.((((((.-...))))))--...))))))..(((((((....))))))).. ( -21.20)
>DroAna_CAF1 39013 82 + 1
AUAUUUUUUAUAU----------------------ACCUACAUAUAUAGAGGUA-UGUGAGUG-AGUGGGGCGGGGAAGGCCUGUUGCCAGGUGCCAGGUUGGCUC
......(((((((----------------------((((.(.......))))))-)))))).(-(((.((.(..((...(((((....))))).)).).)).)))) ( -24.70)
>consensus
AUAUUUUUUAUAUAUA_________GG_UG_GUAUACGUACAUAU____A_GUACCGUAUGU_CAGU_UAUAC__CGAUGCCUGUUGCCAGGUGCCAACUUGGCUC
...................................((((((((((......))).))))))).................(((((....)))))(((.....))).. ( -7.94 =  -9.18 +   1.24)

alignment

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secondary structure

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Window 5

Location 18,082,239 – 18,082,342
Length 103
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 62.19
Mean single sequence MFE -19.64
Consensus MFE -10.52
Energy contribution -10.56
Covariance contribution 0.04
Combinations/Pair 1.14
Mean z-score -2.43
Structure conservation index 0.54
SVM decision value 2.44
SVM RNA-class probability 0.993993
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18082239 103 - 20766785
GAGCCAAGUUGGCACCUGGCAACAGGCAUCG--GUAUAUACGGUACAUACAGUACGUAUACAUAUGUACGUAUAC-CAACCAACCUACAAUAUAUAUAAAAAAUAU
.......(((((..((((....))))....(--((((((...(((((((..(((....))).)))))))))))))-)..)))))...................... ( -27.70)
>DroSec_CAF1 39813 84 - 1
GAGCUAAGUUGGCACCUGGUCACAGUCAUCG--GUAUA--CUG--CAUACGGGAC------GUACGUACGUACAC-CAUCC---------UAUAUAUUAUAGAUAU
(((((.....)))..(((....)))...))(--((.((--(((--(.((((...)------))).))).))).))-)...(---------((((...))))).... ( -15.50)
>DroSim_CAF1 40467 84 - 1
GAGCCAAGUUGGCACCUGGCAACAGGCAUCG--GUAUA--CGG--UAUACGGUAC------AUACGUACGUACAC-CAACC---------UAUAUAUAAAAAAUAU
(((((.....))).((((....))))..))(--((...--.((--(.((((.(((------....))))))).))-).)))---------................ ( -23.10)
>DroYak_CAF1 41231 79 - 1
GAGCCAAGUUGGCACCUGGCAACAGGCAUCG--GCAUAUACA-UACAUACU---CCUACCUAAAUACAAGUAUAAA---------------------ACAAAAUAU
.......(((((..((((....))))..)))--)).......-...(((((---..((......))..)))))...---------------------......... ( -14.20)
>DroAna_CAF1 39013 82 - 1
GAGCCAACCUGGCACCUGGCAACAGGCCUUCCCCGCCCCACU-CACUCACA-UACCUCUAUAUAUGUAGGU----------------------AUAUAAAAAAUAU
..(((.....))).((((....))))................-.......(-((((((.......).))))----------------------))........... ( -17.70)
>consensus
GAGCCAAGUUGGCACCUGGCAACAGGCAUCG__GUAUA_ACGG_ACAUACAGUAC_U____AUAUGUACGUACAC_CA_CC_________UAUAUAUAAAAAAUAU
..(((.....))).((((....))))................................................................................ (-10.52 = -10.56 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,082,276 – 18,082,369
Length 93
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 74.40
Mean single sequence MFE -19.34
Consensus MFE -11.44
Energy contribution -11.36
Covariance contribution -0.08
Combinations/Pair 1.18
Mean z-score -1.86
Structure conservation index 0.59
SVM decision value 0.99
SVM RNA-class probability 0.895210
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18082276 93 - 20766785
AAGAAAAUCAAUACGAGGCAGACACAAGAGCCAAGUUGGCACCUGGCAACAGGCAUCG--GUAUAUACGGUACAUACAGUACGUAUACAUAUGUA
.............(((.((..........(((.....)))..(((....))))).)))--((((((...((((.....))))))))))....... ( -22.80)
>DroSec_CAF1 39841 81 - 1
AAGAAAAUCAAUACGAGGCAGA--CUAGAGCUAAGUUGGCACCUGGUCACAGUCAUCG--GUAUA--CUG--CAUACGGGAC------GUACGUA
.............((((((.((--((((.(((.....)))..))))))...))).)))--((((.--(((--....)))...------))))... ( -17.50)
>DroSim_CAF1 40495 81 - 1
AAGAAAAUCAAUACGAGGCAGA--CAAGAGCCAAGUUGGCACCUGGCAACAGGCAUCG--GUAUA--CGG--UAUACGGUAC------AUACGUA
.............(((.((...--.....(((.....)))..(((....))))).)))--((((.--((.--....))))))------....... ( -19.40)
>DroYak_CAF1 41248 87 - 1
AAGAAAAUCAAUACGAGGCAGA--CAAGAGCCAAGUUGGCACCUGGCAACAGGCAUCG--GCAUAUACA-UACAUACU---CCUACCUAAAUACA
................(((...--.....)))..(((((..((((....))))..)))--)).......-........---.............. ( -17.50)
>DroAna_CAF1 39029 91 - 1
AAUAAAAUCAAUACAAGGCAGA--CAAGAGCCAACCUGGCACCUGGCAACAGGCCUUCCCCGCCCCACU-CACUCACA-UACCUCUAUAUAUGUA
................(((.(.--.(((.(((.....))).((((....)))).)))..).))).....-.....(((-((........))))). ( -19.50)
>consensus
AAGAAAAUCAAUACGAGGCAGA__CAAGAGCCAAGUUGGCACCUGGCAACAGGCAUCG__GUAUA_ACGG_ACAUACAGUAC_U____AUAUGUA
.............(((.((..........(((.....)))..(((....))))).)))..................................... (-11.44 = -11.36 +  -0.08)

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 11:52:25 2006