Locus 6446

Sequence ID 3L_DroMel_CAF1
Location 17,225,403 – 17,225,548
Length 145
Max. P 0.999067
window10348 window10349 window10350

overview

Window 8

Location 17,225,403 – 17,225,516
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.52
Mean single sequence MFE -25.28
Consensus MFE -19.41
Energy contribution -19.77
Covariance contribution 0.36
Combinations/Pair 1.12
Mean z-score -2.04
Structure conservation index 0.77
SVM decision value 0.92
SVM RNA-class probability 0.881767
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17225403 113 - 23771897
AAUCGAUUAACGCUUGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCUUCCUUGCUUCUCCAUCCUGAUUGUCCCACUCCCU-------GGAAUAUCCUCGAUUGUUUCUGUGACUUUC
((((((.....((..((....((((((((((...))))))))))......))..))...........(((..(((........-------)))..))).))))))............... ( -25.90)
>DroSec_CAF1 108830 113 - 1
AAUCGAUUAACGCUUGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCGUCCUUGCUCCUCCAUUCUGAUUGUCCCACUCCCU-------GGCAUAUCCUCGAUUGUUUCUGUGACUUUC
((((((.....((..((((..((((((((((...))))))))))..).).))..))...........(((((((.........-------)))).))).))))))............... ( -25.50)
>DroSim_CAF1 102571 113 - 1
AAUCGAUUAACGCUUGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCGUCCUUGCUCCUCCAUUCUGAUUGUCCCACUCCCU-------GGCAUAUCCUCGAUUGUUUCUGCGACUUUC
((((((.....((..((((..((((((((((...))))))))))..).).))..))...........(((((((.........-------)))).))).))))))............... ( -25.50)
>DroEre_CAF1 112616 116 - 1
AAUCGAUUAACGC-UGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCGUCCUUGCUCCAUCAUU---AUUGUCCCACUCCCACUCCGAGGAUAUAUCCCCGAUUGUUUCUGUGACUUUC
....(((....((-.((((..((((((((((...))))))))))..).)))...))...)))...---...(((.((....((.((.(.(((....)))).)).))....)).))).... ( -24.60)
>DroYak_CAF1 115346 110 - 1
AAUCGAUUAACGCCUGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCGUCCUUGCUCCUUCAUU---AUGCUCCCACUCCCA-------GCGAAAUCCUCGAUUGUUUCUAUGACUUUC
((((((....(((.(((....((((((((((...))))))))))....((....((.........---..))....))..)))-------)))......))))))............... ( -24.90)
>consensus
AAUCGAUUAACGCUUGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCGUCCUUGCUCCUCCAUUCUGAUUGUCCCACUCCCU_______GGCAUAUCCUCGAUUGUUUCUGUGACUUUC
((((((.....((..((....((((((((((...))))))))))......))..))..............((((................)))).....))))))............... (-19.41 = -19.77 +   0.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,225,436 – 17,225,548
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.34
Mean single sequence MFE -34.76
Consensus MFE -29.54
Energy contribution -29.98
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.94
Structure conservation index 0.85
SVM decision value 1.62
SVM RNA-class probability 0.967821
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17225436 112 + 23771897
GAGUGGGACAAUCAGGAUGGAGAAGCAAGGAAGAAGGAUGCAGCUGGAGCAGCUACAUCAAUGCCAAGCGUUAAUCGAUUAUGC--------UUACAUAAUUGCAUUUUUCCCAUCUCAG
((((((((.....((((((.....((..((......((((.(((((...))))).))))....))..))......((((((((.--------...))))))))))))))))))).))).. ( -32.90)
>DroSec_CAF1 108863 112 + 1
GAGUGGGACAAUCAGAAUGGAGGAGCAAGGACGAAGGAUGCAGCUGGAGCAGCUACAUCAAUGCCAAGCGUUAAUCGAUUAUGC--------UUACAUAAUUGUAUUUUUCCCAUCUCAA
((((((((.((.(((.(((...(((((..(.(((..((((.(((((...))))).))))(((((...)))))..))).)..)))--------)).)))..)))...)).))))).))).. ( -33.40)
>DroSim_CAF1 102604 112 + 1
GAGUGGGACAAUCAGAAUGGAGGAGCAAGGACGAAGGAUGCAGCUGGAGCAGCUACAUCAAUGCCAAGCGUUAAUCGAUUAUGC--------UUACAUAAUUGCAUUUUUCCCAUCUCAG
((((((((.....((((((.....((..((.((...((((.(((((...))))).))))..))))..))......((((((((.--------...))))))))))))))))))).))).. ( -33.70)
>DroEre_CAF1 112656 116 + 1
GAGUGGGACAAU---AAUGAUGGAGCAAGGACGAAGGAUGCAGCUGGAGCAGCUACAUCAAUGCCA-GCGUUAAUCGAUUGCGCUUGCCGACUUACAUAAUUGCAUUUUUCCCAUCUCGG
((((((((((..---..)).....((((.....(((((((.(((((...))))).))))...((.(-((((.........))))).))...)))......)))).....))))).))).. ( -34.00)
>DroYak_CAF1 115379 117 + 1
GAGUGGGAGCAU---AAUGAAGGAGCAAGGACGAAGGAUGCAGCUGGAGCAGCUACAUCAAUGCCAGGCGUUAAUCGAUUGUGCUUGCCGACUUACAUAAUUGCAUUUUUCCCAUCUCAG
(((((((((((.---.((((((..(((((.((((..((((.(((((...))))).))))(((((...)))))......)))).)))))...))).)))...))).....))))).))).. ( -39.80)
>consensus
GAGUGGGACAAUCAGAAUGGAGGAGCAAGGACGAAGGAUGCAGCUGGAGCAGCUACAUCAAUGCCAAGCGUUAAUCGAUUAUGC________UUACAUAAUUGCAUUUUUCCCAUCUCAG
((((((((.....((((((.....((..((......((((.(((((...))))).))))....))..))......((((((((............))))))))))))))))))).))).. (-29.54 = -29.98 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,225,436 – 17,225,548
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.34
Mean single sequence MFE -33.70
Consensus MFE -29.16
Energy contribution -29.04
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -2.70
Structure conservation index 0.87
SVM decision value 3.35
SVM RNA-class probability 0.999067
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17225436 112 - 23771897
CUGAGAUGGGAAAAAUGCAAUUAUGUAA--------GCAUAAUCGAUUAACGCUUGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCUUCCUUGCUUCUCCAUCCUGAUUGUCCCACUC
..(((.(((((......(.((((((...--------.)))))).)......((..((....((((((((((...))))))))))......))..))................)))))))) ( -31.40)
>DroSec_CAF1 108863 112 - 1
UUGAGAUGGGAAAAAUACAAUUAUGUAA--------GCAUAAUCGAUUAACGCUUGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCGUCCUUGCUCCUCCAUUCUGAUUGUCCCACUC
..(((.(((((......(.((((((...--------.)))))).)......((..((((..((((((((((...))))))))))..).).))..))................)))))))) ( -32.10)
>DroSim_CAF1 102604 112 - 1
CUGAGAUGGGAAAAAUGCAAUUAUGUAA--------GCAUAAUCGAUUAACGCUUGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCGUCCUUGCUCCUCCAUUCUGAUUGUCCCACUC
..(((.(((((......(.((((((...--------.)))))).)......((..((((..((((((((((...))))))))))..).).))..))................)))))))) ( -31.80)
>DroEre_CAF1 112656 116 - 1
CCGAGAUGGGAAAAAUGCAAUUAUGUAAGUCGGCAAGCGCAAUCGAUUAACGC-UGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCGUCCUUGCUCCAUCAUU---AUUGUCCCACUC
..(((.(((((..((((.......(((((.((((.((((...........)))-).))...((((((((((...))))))))))...))..))))).....))))---....)))))))) ( -36.40)
>DroYak_CAF1 115379 117 - 1
CUGAGAUGGGAAAAAUGCAAUUAUGUAAGUCGGCAAGCACAAUCGAUUAACGCCUGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCGUCCUUGCUCCUUCAUU---AUGCUCCCACUC
..(((.(((((.....(((...(((.(((..((((((.((...........((...))...((((((((((...))))))))))....)).)))))).)))))).---.))))))))))) ( -36.80)
>consensus
CUGAGAUGGGAAAAAUGCAAUUAUGUAA________GCAUAAUCGAUUAACGCUUGGCAUUGAUGUAGCUGCUCCAGCUGCAUCCUUCGUCCUUGCUCCUCCAUUCUGAUUGUCCCACUC
..(((.(((((....((((....)))).........(((....(((.....((...))...((((((((((...))))))))))..)))....)))................)))))))) (-29.16 = -29.04 +  -0.12)

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 12:19:05 2006