Locus 6739

Sequence ID X_DroMel_CAF1
Location 16,757,457 – 16,757,636
Length 179
Max. P 0.997198
window11018 window11019 window11020

overview

Window 8

Location 16,757,457 – 16,757,575
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.12
Mean single sequence MFE -34.60
Consensus MFE -28.17
Energy contribution -28.43
Covariance contribution 0.25
Combinations/Pair 1.07
Mean z-score -1.56
Structure conservation index 0.81
SVM decision value 0.23
SVM RNA-class probability 0.645497
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16757457 118 - 22224390
GCAGUUGUGUCAACAAAAGUAUGAUGCCCGCGUUGAAGGGUAUCGCACUUGACACAUGCCUGGGUUUAUUCACAC--ACCGAUCGGCCAUAAGUCGGUUAUGAAGCUCGGAGCUUGGAGC
(((..(((((((.....(((.((((((((........)))))))).)))))))))))))(..(((((.((((...--((((((.........))))))..)))).....)))))..)... ( -40.20)
>DroSec_CAF1 44438 105 - 1
GCAGUUGUGUCAACAAAAGUAUGAUGCCCGCGUUGAAGGGUAUCGCACUUGACACAUGUCUGGGUUUAUUCACAC--ACCGAUCGGCCAUAAGUCGGCUAUGAGUCU-------------
.(((.(((((((.....(((.((((((((........)))))))).))))))))))...))).....(((((...--.(((((.........)))))...)))))..------------- ( -32.20)
>DroEre_CAF1 35779 105 - 1
GCAGUUGUGUCAACAA-AGUAUGAUGCCCGCGUCGAAGGGUAUCGCACUUGACACAUGCCUGGGUUUAUUCACACACACUGAUCGGCCAUAAGUCGGCUGUGAAGC--------------
.(((.(((((((....-(((.((((((((........)))))))).))))))))))...)))......(((((.(.....)...((((.......)))))))))..-------------- ( -33.70)
>DroYak_CAF1 36242 93 - 1
GCAGUUGUGUCAACAAAAGUAUGAUGCCCGCGUUGAAGGGUAUCGCACUUGACACAUGCCUGGGUUUAUUCACAC--ACCGAUCGG-----------CUGUGAAGC--------------
.(((.(((((((.....(((.((((((((........)))))))).))))))))))...)))......((((((.--.((....))-----------.))))))..-------------- ( -32.30)
>consensus
GCAGUUGUGUCAACAAAAGUAUGAUGCCCGCGUUGAAGGGUAUCGCACUUGACACAUGCCUGGGUUUAUUCACAC__ACCGAUCGGCCAUAAGUCGGCUAUGAAGC______________
.(((.(((((((.....(((.((((((((........)))))))).))))))))))...)))......(((((...........((((.......)))))))))................ (-28.17 = -28.43 +   0.25)

alignment

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secondary structure

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Window 9

Location 16,757,497 – 16,757,611
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.11
Mean single sequence MFE -41.25
Consensus MFE -30.95
Energy contribution -35.08
Covariance contribution 4.12
Combinations/Pair 1.03
Mean z-score -3.06
Structure conservation index 0.75
SVM decision value 2.82
SVM RNA-class probability 0.997198
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16757497 114 - 22224390
AAGCGAGUGUAUCACAGGCACCA----UUGGCUGUGCGCAGCAGUUGUGUCAACAAAAGUAUGAUGCCCGCGUUGAAGGGUAUCGCACUUGACACAUGCCUGGGUUUAUUCACAC--ACC
..(.(((((.(((.((((((...----...((((....))))...(((((((.....(((.((((((((........)))))))).))))))))))))))))))).))))).)..--... ( -45.60)
>DroSec_CAF1 44465 118 - 1
AAGCGAGUGUAUCACAGGCACCGUCAACUGGCUACGCGCAGCAGUUGUGUCAACAAAAGUAUGAUGCCCGCGUUGAAGGGUAUCGCACUUGACACAUGUCUGGGUUUAUUCACAC--ACC
..(.(((((.(((.((((((.....(((((.((......)))))))((((((.....(((.((((((((........)))))))).))))))))).))))))))).))))).)..--... ( -40.70)
>DroEre_CAF1 35805 119 - 1
AAGCGACUGCAUCACAGGCACCGCCAACUGGCUGUGCACAGCAGUUGUGUCAACAA-AGUAUGAUGCCCGCGUCGAAGGGUAUCGCACUUGACACAUGCCUGGGUUUAUUCACACACACU
..(.((.((.(((.((((((.....(((((.(((....))))))))((((((....-(((.((((((((........)))))))).))))))))).))))))))).)).)).)....... ( -43.60)
>DroYak_CAF1 36257 91 - 1
AAGCGA---------------------------GUGUGCCGCAGUUGUGUCAACAAAAGUAUGAUGCCCGCGUUGAAGGGUAUCGCACUUGACACAUGCCUGGGUUUAUUCACAC--ACC
..(.((---------------------------(((.(((.(((.(((((((.....(((.((((((((........)))))))).))))))))))...)))))).))))).)..--... ( -35.10)
>consensus
AAGCGAGUGUAUCACAGGCACCG____CUGGCUGUGCGCAGCAGUUGUGUCAACAAAAGUAUGAUGCCCGCGUUGAAGGGUAUCGCACUUGACACAUGCCUGGGUUUAUUCACAC__ACC
..(.(((((.(((.((((((..........((((....))))...(((((((.....(((.((((((((........)))))))).))))))))))))))))))).))))).)....... (-30.95 = -35.08 +   4.12)

alignment

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secondary structure

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Window 0

Location 16,757,535 – 16,757,636
Length 101
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 84.52
Mean single sequence MFE -29.13
Consensus MFE -22.85
Energy contribution -22.63
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -1.88
Structure conservation index 0.78
SVM decision value 0.32
SVM RNA-class probability 0.686622
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16757535 101 + 22224390
CCCUUCAACGCGGGCAUCAUACUUUUGUUGACACAACUGCUGCGCACAGCCAA----UGGUGCCUGUGAUACACUCGCUUUGCGACUCGCUUUUCCAAUUAUUUU
........((((((((((((......((((...)))).((((....))))..)----)))))))))))......((((...)))).................... ( -27.00)
>DroSec_CAF1 44503 100 + 1
CCCUUCAACGCGGGCAUCAUACUUUUGUUGACACAACUGCUGCGCGUAGCCAGUUGACGGUGCCUGUGAUACACUCGCUUUGC-----GCAUUUCCAAUUAUUUU
........((((((((((.......((....))(((((((((....))).))))))..))))))))))........((.....-----))............... ( -27.50)
>DroEre_CAF1 35845 99 + 1
CCCUUCGACGCGGGCAUCAUACU-UUGUUGACACAACUGCUGUGCACAGCCAGUUGGCGGUGCCUGUGAUGCAGUCGCUUUGU-----GGGUUUCCCAUUCUUUU
(((.....((((((((((.....-.((....))(((((((((....))).))))))..))))))))))..((((.....))))-----))).............. ( -32.90)
>consensus
CCCUUCAACGCGGGCAUCAUACUUUUGUUGACACAACUGCUGCGCACAGCCAGUUG_CGGUGCCUGUGAUACACUCGCUUUGC_____GCAUUUCCAAUUAUUUU
........((((((((((........((((...)))).((((....))))........))))))))))..................................... (-22.85 = -22.63 +  -0.22)

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 12:21:34 2006