Locus 400

Sequence ID 2R_DroMel_CAF1
Location 2,394,924 – 2,395,069
Length 145
Max. P 0.968281
window783 window784 window785

overview

Window 3

Location 2,394,924 – 2,395,044
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.50
Mean single sequence MFE -31.46
Consensus MFE -26.64
Energy contribution -26.68
Covariance contribution 0.04
Combinations/Pair 1.09
Mean z-score -1.42
Structure conservation index 0.85
SVM decision value 0.49
SVM RNA-class probability 0.756190
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2394924 120 - 20766785
CCUACUGGCGAUACUUCAUUACGUUACUGAGAACUGCGCACACAGCUCUCUCGGAUUGAAAUCCAAUGACGUCUAGUGGGAUUUCAUAGCUGAGUUCUAUUCGGUCUCACUGCUGUUCUU
((((((((.((....))...((((((..((((.(((......))).))))..((((....))))..)))))))))))))).....(((((((((..(.....)..))))..))))).... ( -33.10)
>DroSec_CAF1 50651 120 - 1
CCUACUGGCGAUACUUCAUUACGUUACUGAGAACUGCGCACACAGCUCUCUCGGAUUGAAAUCCAAUGACGUCUAGUGGGAUUUCAUAGCUGAGUUCUAUUCGGUCUCACUACUGUUCUU
((((((((.((....))...((((((..((((.(((......))).))))..((((....))))..))))))))))))))......(((.((((..(.....)..)))))))........ ( -30.70)
>DroSim_CAF1 8030 120 - 1
CCUACUGGCGAUACUUCAUUACGUUACUGAGAACUGCGCACACAGCUCUCUCGGAUUGAAAUCCAAUGACGUCUAGUGGGAUUUCAUAGCUGAGUUCUAUUCGGUCUCACUGCUGUUCUU
((((((((.((....))...((((((..((((.(((......))).))))..((((....))))..)))))))))))))).....(((((((((..(.....)..))))..))))).... ( -33.10)
>DroEre_CAF1 8278 120 - 1
CCUACUGGCAAUACUUUACUUCGCUACUGAGAACCGCGCACACAGCUCUCUCAGAUUGAAAUCCAAUGACGUCUAGUGGGAUUUCAUAGCUGCGUUCUAUUCGGUCUCACUGCUGCUCCU
......((((............((...(((((.(((.(.((.(((((.........((((((((....((.....)).)))))))).))))).)).)....))))))))..))))))... ( -26.70)
>DroYak_CAF1 7934 120 - 1
CCUACUGGCAAACCUUUAUUACGCUACUGAGAACUGCGCACACAGCUCUCUCAGAUUGAAAUCCAAUGAGGUUUAGUGGGAUUUCAUAGCUGAGUUCCAUUUGGUCUCACUGCUGUUCCU
(((((((...((((((..........((((((...((.......))..))))))((((.....))))))))))))))))).....(((((((((..((....)).))))..))))).... ( -33.70)
>consensus
CCUACUGGCGAUACUUCAUUACGUUACUGAGAACUGCGCACACAGCUCUCUCGGAUUGAAAUCCAAUGACGUCUAGUGGGAUUUCAUAGCUGAGUUCUAUUCGGUCUCACUGCUGUUCUU
(((((((((.................((((((...((.......))..))))))((((.....))))...).)))))))).....(((((((((..((....)).))))..))))).... (-26.64 = -26.68 +   0.04) 

alignment

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secondary structure

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dotplot

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Window 4

Location 2,394,964 – 2,395,069
Length 105
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 88.57
Mean single sequence MFE -32.46
Consensus MFE -27.82
Energy contribution -27.10
Covariance contribution -0.72
Combinations/Pair 1.19
Mean z-score -1.96
Structure conservation index 0.86
SVM decision value 1.62
SVM RNA-class probability 0.968281
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2394964 105 + 20766785
CCCACUAGACGUCAUUGGAUUUCAAUCCGAGAGAGCUGUGUGCGCAGUUCUCAGUAACGUAAUGAAGUAUCGCCAGUAGGUACAUA----------UAUGUCCAGUGCAUAUAUG
..((((.(((((((((((((....))))..(((((((((....)))))))))........))))).(((((.......)))))...----------..)))).))))........ ( -32.60)
>DroSec_CAF1 50691 105 + 1
CCCACUAGACGUCAUUGGAUUUCAAUCCGAGAGAGCUGUGUGCGCAGUUCUCAGUAACGUAAUGAAGUAUCGCCAGUAGGUACAUA----------UAUGUCCAGUGCAUAUAUG
..((((.(((((((((((((....))))..(((((((((....)))))))))........))))).(((((.......)))))...----------..)))).))))........ ( -32.60)
>DroSim_CAF1 8070 105 + 1
CCCACUAGACGUCAUUGGAUUUCAAUCCGAGAGAGCUGUGUGCGCAGUUCUCAGUAACGUAAUGAAGUAUCGCCAGUAGGUACAUA----------UAUGUCCAGUGCAUAUAUG
..((((.(((((((((((((....))))..(((((((((....)))))))))........))))).(((((.......)))))...----------..)))).))))........ ( -32.60)
>DroEre_CAF1 8318 115 + 1
CCCACUAGACGUCAUUGGAUUUCAAUCUGAGAGAGCUGUGUGCGCGGUUCUCAGUAGCGAAGUAAAGUAUUGCCAGUAGGUACAUAUAGGUACAUAUGAGUCCAGUGCAUAUAUG
..........(.(((((((((.((......(((((((((....))))))))).........(((..((((((((....)))).))))...)))...))))))))))))....... ( -32.10)
>DroYak_CAF1 7974 107 + 1
CCCACUAAACCUCAUUGGAUUUCAAUCUGAGAGAGCUGUGUGCGCAGUUCUCAGUAGCGUAAUAAAGGUUUGCCAGUAGGUACA--------CAUAUGUGUUCGGUGCAUAUAUG
((.(((((((((..(..(((....)))..)(((((((((....))))))))).............))))))...))).))....--------(((((((((.....))))))))) ( -32.40)
>consensus
CCCACUAGACGUCAUUGGAUUUCAAUCCGAGAGAGCUGUGUGCGCAGUUCUCAGUAACGUAAUGAAGUAUCGCCAGUAGGUACAUA__________UAUGUCCAGUGCAUAUAUG
..((((.(((....((((((....))))))(((((((((....)))))))))..............(((((.......)))))................))).))))........ (-27.82 = -27.10 +  -0.72) 

alignment

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secondary structure

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dotplot

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Window 5

Location 2,394,964 – 2,395,069
Length 105
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 88.57
Mean single sequence MFE -30.06
Consensus MFE -22.46
Energy contribution -22.10
Covariance contribution -0.36
Combinations/Pair 1.09
Mean z-score -2.25
Structure conservation index 0.75
SVM decision value 1.01
SVM RNA-class probability 0.898976
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2394964 105 - 20766785
CAUAUAUGCACUGGACAUA----------UAUGUACCUACUGGCGAUACUUCAUUACGUUACUGAGAACUGCGCACACAGCUCUCUCGGAUUGAAAUCCAAUGACGUCUAGUGGG
(((((((((....).))))----------))))..((((((((.((....))...((((((..((((.(((......))).))))..((((....))))..)))))))))))))) ( -31.20)
>DroSec_CAF1 50691 105 - 1
CAUAUAUGCACUGGACAUA----------UAUGUACCUACUGGCGAUACUUCAUUACGUUACUGAGAACUGCGCACACAGCUCUCUCGGAUUGAAAUCCAAUGACGUCUAGUGGG
(((((((((....).))))----------))))..((((((((.((....))...((((((..((((.(((......))).))))..((((....))))..)))))))))))))) ( -31.20)
>DroSim_CAF1 8070 105 - 1
CAUAUAUGCACUGGACAUA----------UAUGUACCUACUGGCGAUACUUCAUUACGUUACUGAGAACUGCGCACACAGCUCUCUCGGAUUGAAAUCCAAUGACGUCUAGUGGG
(((((((((....).))))----------))))..((((((((.((....))...((((((..((((.(((......))).))))..((((....))))..)))))))))))))) ( -31.20)
>DroEre_CAF1 8318 115 - 1
CAUAUAUGCACUGGACUCAUAUGUACCUAUAUGUACCUACUGGCAAUACUUUACUUCGCUACUGAGAACCGCGCACACAGCUCUCUCAGAUUGAAAUCCAAUGACGUCUAGUGGG
........((((((((((((..((((......))))....((((.............))))((((((...((.......))..))))))...........)))).)))))))).. ( -27.62)
>DroYak_CAF1 7974 107 - 1
CAUAUAUGCACCGAACACAUAUG--------UGUACCUACUGGCAAACCUUUAUUACGCUACUGAGAACUGCGCACACAGCUCUCUCAGAUUGAAAUCCAAUGAGGUUUAGUGGG
((((((((.........))))))--------))..(((((((...((((((..........((((((...((.......))..))))))((((.....))))))))))))))))) ( -29.10)
>consensus
CAUAUAUGCACUGGACAUA__________UAUGUACCUACUGGCGAUACUUCAUUACGUUACUGAGAACUGCGCACACAGCUCUCUCGGAUUGAAAUCCAAUGACGUCUAGUGGG
........((((((((...................((....))..................((((((...((.......))..))))))((((.....))))...)))))))).. (-22.46 = -22.10 +  -0.36) 

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 09:37:38 2006