Locus 2654

Sequence ID X_DroMel_CAF1
Location 7,109,715 – 7,109,821
Length 106
Max. P 0.988810
window4345 window4346 window4347 window4348

overview

Window 5

Location 7,109,715 – 7,109,807
Length 92
Sequences 3
Columns 92
Reading direction forward
Mean pairwise identity 87.27
Mean single sequence MFE -24.80
Consensus MFE -18.69
Energy contribution -18.70
Covariance contribution 0.01
Combinations/Pair 1.15
Mean z-score -2.05
Structure conservation index 0.75
SVM decision value 0.12
SVM RNA-class probability 0.593502
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7109715 92 + 22224390
ACGACUGCUAAAAGCUGGGAGGGCGUGGGUGGAUGGAUGGUAGCAAUGUCCAAAGGGAAUGCUAAGGGAAAUGGCCAAAAUUCAAAAUGGCC
.((.(..((....(((.....)))...))..).)).....(((((...(((....))).)))))........(((((..........))))) ( -21.40)
>DroSec_CAF1 100946 88 + 1
ACGACUGCUAAAAGCAGGGAGGGCGUGGGUGG----AUGGUGGCAAUGUCCAAAGGGAAUGCUAAGGGAAAUGGCCAAAAUUCAAAAUGGCC
....((((.....))))...((.(((...(((----((..((((....(((....((....))...)))....))))..)))))..))).)) ( -28.20)
>DroEre_CAF1 103256 89 + 1
GCGACUGCCAGGAGCAGGAAAGGCGUGGGC---UUGAAGGUGGCAAUGUCCAAGGGGAAUGCUAAGGGAAAUGGCCAAAAUUCAAAAUGGCC
(((.((((.....))))......))).(((---(((((..((((....(((...((.....))...)))....))))...))))....)))) ( -24.80)
>consensus
ACGACUGCUAAAAGCAGGGAGGGCGUGGGUGG_U_GAUGGUGGCAAUGUCCAAAGGGAAUGCUAAGGGAAAUGGCCAAAAUUCAAAAUGGCC
....(((((....((.......))...)))))........(((((...(((....))).)))))........(((((..........))))) (-18.69 = -18.70 +   0.01)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,109,715 – 7,109,807
Length 92
Sequences 3
Columns 92
Reading direction reverse
Mean pairwise identity 87.27
Mean single sequence MFE -17.40
Consensus MFE -15.43
Energy contribution -15.77
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.89
SVM decision value 0.50
SVM RNA-class probability 0.760709
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7109715 92 - 22224390
GGCCAUUUUGAAUUUUGGCCAUUUCCCUUAGCAUUCCCUUUGGACAUUGCUACCAUCCAUCCACCCACGCCCUCCCAGCUUUUAGCAGUCGU
(((((..........)))))........(((((.(((....)))...))))).........................((.....))...... ( -16.40)
>DroSec_CAF1 100946 88 - 1
GGCCAUUUUGAAUUUUGGCCAUUUCCCUUAGCAUUCCCUUUGGACAUUGCCACCAU----CCACCCACGCCCUCCCUGCUUUUAGCAGUCGU
(((((..........)))))..........(((.(((....)))...)))......----...............((((.....)))).... ( -17.00)
>DroEre_CAF1 103256 89 - 1
GGCCAUUUUGAAUUUUGGCCAUUUCCCUUAGCAUUCCCCUUGGACAUUGCCACCUUCAA---GCCCACGCCUUUCCUGCUCCUGGCAGUCGC
(((...((((((...((((.((.(((...((.......)).))).)).))))..)))))---).....)))....((((.....)))).... ( -18.80)
>consensus
GGCCAUUUUGAAUUUUGGCCAUUUCCCUUAGCAUUCCCUUUGGACAUUGCCACCAUC_A_CCACCCACGCCCUCCCUGCUUUUAGCAGUCGU
(((((..........)))))..........(((.(((....)))...))).........................((((.....)))).... (-15.43 = -15.77 +   0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,109,729 – 7,109,821
Length 92
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 88.89
Mean single sequence MFE -24.10
Consensus MFE -18.02
Energy contribution -18.13
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -2.17
Structure conservation index 0.75
SVM decision value 0.07
SVM RNA-class probability 0.567677
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7109729 92 + 22224390
CUGGGAGGGCGUGGGUGGAUGGAUGGUAGCAAUGUCCAAAGGGAAUGCUAAGGGAAAUGGCCAAAAUUCAAAAUGGCCACUUGAGGGGUG--AG
((..((((((.....(((((...((((((((...(((....))).))))..........))))..))))).....))).)))..))....--.. ( -21.30)
>DroSec_CAF1 100960 90 + 1
CAGGGAGGGCGUGGGUGG----AUGGUGGCAAUGUCCAAAGGGAAUGCUAAGGGAAAUGGCCAAAAUUCAAAAUGGCCACUUGAGGGGUGAGAG
((((..((.(((...(((----((..((((....(((....((....))...)))....))))..)))))..))).)).))))........... ( -27.60)
>DroEre_CAF1 103270 89 + 1
CAGGAAAGGCGUGGGC---UUGAAGGUGGCAAUGUCCAAGGGGAAUGCUAAGGGAAAUGGCCAAAAUUCAAAAUGGCCACUUGAGGGGUG--AG
..........((((.(---(((((..((((....(((...((.....))...)))....))))...)))))...).))))..........--.. ( -23.40)
>consensus
CAGGGAGGGCGUGGGUGG_U_GAUGGUGGCAAUGUCCAAAGGGAAUGCUAAGGGAAAUGGCCAAAAUUCAAAAUGGCCACUUGAGGGGUG__AG
((((......................(((((...(((....))).))))).......((((((..........))))))))))........... (-18.02 = -18.13 +   0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,109,729 – 7,109,821
Length 92
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 88.89
Mean single sequence MFE -16.50
Consensus MFE -15.73
Energy contribution -15.73
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.67
Structure conservation index 0.95
SVM decision value 2.14
SVM RNA-class probability 0.988810
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7109729 92 - 22224390
CU--CACCCCUCAAGUGGCCAUUUUGAAUUUUGGCCAUUUCCCUUAGCAUUCCCUUUGGACAUUGCUACCAUCCAUCCACCCACGCCCUCCCAG
..--........(((((((((..........)))))))))....(((((.(((....)))...))))).......................... ( -18.20)
>DroSec_CAF1 100960 90 - 1
CUCUCACCCCUCAAGUGGCCAUUUUGAAUUUUGGCCAUUUCCCUUAGCAUUCCCUUUGGACAUUGCCACCAU----CCACCCACGCCCUCCCUG
............(((((((((..........)))))))))......(((.(((....)))...)))......----.................. ( -15.60)
>DroEre_CAF1 103270 89 - 1
CU--CACCCCUCAAGUGGCCAUUUUGAAUUUUGGCCAUUUCCCUUAGCAUUCCCCUUGGACAUUGCCACCUUCAA---GCCCACGCCUUUCCUG
..--..........((((....((((((...((((.((.(((...((.......)).))).)).))))..)))))---).)))).......... ( -15.70)
>consensus
CU__CACCCCUCAAGUGGCCAUUUUGAAUUUUGGCCAUUUCCCUUAGCAUUCCCUUUGGACAUUGCCACCAUC_A_CCACCCACGCCCUCCCUG
............(((((((((..........)))))))))......(((.(((....)))...)))............................ (-15.73 = -15.73 +  -0.00)

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 10:40:11 2006