Locus 2125

Sequence ID 3L_DroMel_CAF1
Location 5,809,750 – 5,809,860
Length 110
Max. P 0.995988
window3306 window3307 window3308 window3309

overview

Window 6

Location 5,809,750 – 5,809,840
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 83.17
Mean single sequence MFE -25.80
Consensus MFE -19.08
Energy contribution -18.95
Covariance contribution -0.13
Combinations/Pair 1.12
Mean z-score -3.15
Structure conservation index 0.74
SVM decision value 2.64
SVM RNA-class probability 0.995988
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5809750 90 + 23771897
GAGCACUUCAAACUGCAGAUUGGGUGCAAUUUGGCGGAUGCUUCCGCCAAUAAAACACUGCUGCUUCUGCUUCUGCUUCAUCGUAGCAGA
..(((((.(((.(....).))))))))...((((((((....)))))))).......(((((((....((....))......))))))). ( -32.80)
>DroSec_CAF1 17675 84 + 1
AAGCACUUCAAACUGCAGAUUGGGUGCAAUUUGGCGGAUGCUUCCGCUAAUAAAACACUGCUGCUUCUGCUUC------UUCGUAGCAGA
..(((((.(((.(....).))))))))...((((((((....)))))))).......(((((((.........------...))))))). ( -28.20)
>DroEre_CAF1 17843 77 + 1
AACCACUUCAAACUGCAGAUUGGGUGCAAUUUGGCGGAUGCUUCCGCCAAUAAAACACAUCUCU-------UC------UUUAUAGCGCA
..(((..((........)).)))((((....(((((((....)))))))(((((..........-------..------))))).)))). ( -20.40)
>DroYak_CAF1 18508 79 + 1
AACCACUUCAAACUGCAGAUUGGGUGCAAUUUGGCGGAUGCUUCCGCCAAUAAAACACAUCUCUU-----UUC------UUUAUAGCAGA
............(((((((..(((((....((((((((....)))))))).......)))))...-----.))------).....)))). ( -21.80)
>consensus
AACCACUUCAAACUGCAGAUUGGGUGCAAUUUGGCGGAUGCUUCCGCCAAUAAAACACAGCUCCU_____UUC______UUCAUAGCAGA
............((((((((((....))))))((((((....)))))).....................................)))). (-19.08 = -18.95 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,809,750 – 5,809,840
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 83.17
Mean single sequence MFE -26.12
Consensus MFE -17.99
Energy contribution -17.55
Covariance contribution -0.44
Combinations/Pair 1.14
Mean z-score -2.48
Structure conservation index 0.69
SVM decision value 1.48
SVM RNA-class probability 0.957800
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5809750 90 - 23771897
UCUGCUACGAUGAAGCAGAAGCAGAAGCAGCAGUGUUUUAUUGGCGGAAGCAUCCGCCAAAUUGCACCCAAUCUGCAGUUUGAAGUGCUC
((((((.......)))))).((....))...((..(((((((((((((....))))))))((((((.......)))))).)))))..)). ( -30.10)
>DroSec_CAF1 17675 84 - 1
UCUGCUACGAA------GAAGCAGAAGCAGCAGUGUUUUAUUAGCGGAAGCAUCCGCCAAAUUGCACCCAAUCUGCAGUUUGAAGUGCUU
((((((.....------..))))))...((((.(.........(((((....)))))(((((((((.......))))))))).).)))). ( -27.20)
>DroEre_CAF1 17843 77 - 1
UGCGCUAUAAA------GA-------AGAGAUGUGUUUUAUUGGCGGAAGCAUCCGCCAAAUUGCACCCAAUCUGCAGUUUGAAGUGGUU
..((((.((((------..-------(((...((((....((((((((....))))))))...))))....)))....)))).))))... ( -23.40)
>DroYak_CAF1 18508 79 - 1
UCUGCUAUAAA------GAA-----AAGAGAUGUGUUUUAUUGGCGGAAGCAUCCGCCAAAUUGCACCCAAUCUGCAGUUUGAAGUGGUU
.(..((.((((------...-----.(((...((((....((((((((....))))))))...))))....)))....)))).))..).. ( -23.80)
>consensus
UCUGCUACAAA______GAA_____AACAGAAGUGUUUUAUUGGCGGAAGCAUCCGCCAAAUUGCACCCAAUCUGCAGUUUGAAGUGCUU
..((((.(((..............................((((((((....))))))))((((((.......))))))))).))))... (-17.99 = -17.55 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,809,765 – 5,809,860
Length 95
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 79.68
Mean single sequence MFE -26.85
Consensus MFE -17.25
Energy contribution -19.50
Covariance contribution 2.25
Combinations/Pair 1.12
Mean z-score -2.31
Structure conservation index 0.64
SVM decision value 1.46
SVM RNA-class probability 0.955691
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5809765 95 + 23771897
CAGAUUGGGUGCAAUUUGGCGGAUGCUUCCGCCAAUAAAACACUGCUGCUUCUGCUUCUGCUUCAUCGUAGCAGAGC--AUAUAACA---AUUUUGAGGG
.((((((.((((...((((((((....)))))))).......(((((((....((....))......))))))).))--))....))---))))...... ( -33.70)
>DroSec_CAF1 17690 89 + 1
CAGAUUGGGUGCAAUUUGGCGGAUGCUUCCGCUAAUAAAACACUGCUGCUUCUGCUUC------UUCGUAGCAGAGC--AUACAUCA---AUUUUGAGGG
.((((((((((....((((((((....)))))))).....))))..((((.(((((..------.....))))))))--).....))---))))...... ( -28.80)
>DroEre_CAF1 17858 84 + 1
CAGAUUGGGUGCAAUUUGGCGGAUGCUUCCGCCAAUAAAACACAUCUCU-------UC------UUUAUAGCGCAGCGCAUACAUCA---CUUUUCAGGG
.(((..(((((....((((((((....)))))))).......)))))..-------))------).....(((...)))........---.......... ( -21.30)
>DroYak_CAF1 18523 88 + 1
CAGAUUGGGUGCAAUUUGGCGGAUGCUUCCGCCAAUAAAACACAUCUCUU-----UUC------UUUAUAGCAGAGCAC-UACAUCACUACUUUUCAGGG
..(((..(((((...((((((((....)))))))).........(((((.-----...------.....)).)))))))-)..))).............. ( -23.60)
>consensus
CAGAUUGGGUGCAAUUUGGCGGAUGCUUCCGCCAAUAAAACACAGCUCCU_____UUC______UUCAUAGCAGAGC__AUACAUCA___AUUUUCAGGG
..(((((.((((...((((((((....)))))))).......(((((((..................))))))).)))).)).))).............. (-17.25 = -19.50 +   2.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,809,765 – 5,809,860
Length 95
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 79.68
Mean single sequence MFE -24.93
Consensus MFE -15.20
Energy contribution -15.45
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.61
SVM decision value 0.06
SVM RNA-class probability 0.564011
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5809765 95 - 23771897
CCCUCAAAAU---UGUUAUAU--GCUCUGCUACGAUGAAGCAGAAGCAGAAGCAGCAGUGUUUUAUUGGCGGAAGCAUCCGCCAAAUUGCACCCAAUCUG
.........(---((((...(--((((((((.......))))).))))..)))))..((((....((((((((....))))))))...))))........ ( -30.90)
>DroSec_CAF1 17690 89 - 1
CCCUCAAAAU---UGAUGUAU--GCUCUGCUACGAA------GAAGCAGAAGCAGCAGUGUUUUAUUAGCGGAAGCAUCCGCCAAAUUGCACCCAAUCUG
........((---((.(((.(--((((((((.....------..))))).)))))))((((.......(((((....)))))......)))).))))... ( -24.02)
>DroEre_CAF1 17858 84 - 1
CCCUGAAAAG---UGAUGUAUGCGCUGCGCUAUAAA------GA-------AGAGAUGUGUUUUAUUGGCGGAAGCAUCCGCCAAAUUGCACCCAAUCUG
..((....))---...((((.(((...)))))))..------..-------(((...((((....((((((((....))))))))...))))....))). ( -21.60)
>DroYak_CAF1 18523 88 - 1
CCCUGAAAAGUAGUGAUGUA-GUGCUCUGCUAUAAA------GAA-----AAGAGAUGUGUUUUAUUGGCGGAAGCAUCCGCCAAAUUGCACCCAAUCUG
..((....(((((.(.....-...).)))))....)------)..-----.(((...((((....((((((((....))))))))...))))....))). ( -23.20)
>consensus
CCCUCAAAAG___UGAUGUAU__GCUCUGCUACAAA______GAA_____AACAGAAGUGUUUUAUUGGCGGAAGCAUCCGCCAAAUUGCACCCAAUCUG
.........................................................((((....((((((((....))))))))...))))........ (-15.20 = -15.45 +   0.25)

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 10:25:00 2006