Locus 8072

Sequence ID 3L_DroMel_CAF1
Location 21,265,106 – 21,265,266
Length 160
Max. P 0.901332
window13186 window13187 window13188

overview

Window 6

Location 21,265,106 – 21,265,226
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.42
Mean single sequence MFE -32.27
Consensus MFE -29.70
Energy contribution -29.58
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -1.97
Structure conservation index 0.92
SVM decision value 1.02
SVM RNA-class probability 0.901332
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21265106 120 + 23771897
GCGUUUGGCGUUUCCUUGACUUUAAAUUGUUGCCAUGUUUUCUAUAUUAAAUGUGUCGACUCUGCCAUUGUCUAACCGUGGCCUCGGGGAUGCACCUCAUCCCCAUAGAGUCACUCACAC
.....(((((....................)))))................((((..(((((((((((.(.....).)))))...(((((((.....)))))))..))))))...)))). ( -35.05)
>DroSec_CAF1 23224 120 + 1
GCGUUUGGCGUUUCCUUGACUUUAAAUUGUUGCCAUGUUUUCUAUAUUAAAUGUGUCGACUUUGCCAUUGUCUAACCGUGGCCUCGGGGAUGCACUCCCUCCCCAUAGAGUCACUCACAC
((.....)).......((((((((....((((.(((((((........))))))).))))...(((((.(.....).)))))...(((((.(.....).))))).))))))))....... ( -30.70)
>DroSim_CAF1 24714 120 + 1
GCGUUUGGCGUUUCCUUGACUUUAAAUUGUUGCCAUGUUUUCUAUAUUAAAUGUGUCGACUCUGCCAUUGUCUAACCGUGGCCUCGGGGAUGCACUCCCUCCCCAUAGAGUCACUCACAC
.....(((((....................)))))................((((..(((((((((((.(.....).)))))...(((((.(.....).)))))..))))))...)))). ( -30.95)
>DroEre_CAF1 24316 120 + 1
GCGUUUGGCGUUUCCUUGACUUUAAAUUGUUGCCAUGUUUCCUAUAUUAAAUAUGUCGACUCUGCCAUUGUCUAACUGUGGCCUCGGGGAAGCACCACCUCCUCAUUGAGUCACUCACAC
.....(((.((((((((((.........((((.(((((((........))))))).))))...(((((.(.....).))))).)))))))))).))).........((((...))))... ( -32.40)
>consensus
GCGUUUGGCGUUUCCUUGACUUUAAAUUGUUGCCAUGUUUUCUAUAUUAAAUGUGUCGACUCUGCCAUUGUCUAACCGUGGCCUCGGGGAUGCACCCCCUCCCCAUAGAGUCACUCACAC
((.....)).......((((((((....((((.(((((((........))))))).))))...(((((.(.....).)))))...(((((.(.....).))))).))))))))....... (-29.70 = -29.58 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,265,106 – 21,265,226
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.42
Mean single sequence MFE -33.95
Consensus MFE -32.54
Energy contribution -33.47
Covariance contribution 0.94
Combinations/Pair 1.06
Mean z-score -1.81
Structure conservation index 0.96
SVM decision value 0.95
SVM RNA-class probability 0.887437
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21265106 120 - 23771897
GUGUGAGUGACUCUAUGGGGAUGAGGUGCAUCCCCGAGGCCACGGUUAGACAAUGGCAGAGUCGACACAUUUAAUAUAGAAAACAUGGCAACAAUUUAAAGUCAAGGAAACGCCAAACGC
(((((..(((((((.((((((((.....))))))))..((((..(.....)..))))))))))).)))))...............((((.((........))...(....)))))..... ( -39.20)
>DroSec_CAF1 23224 120 - 1
GUGUGAGUGACUCUAUGGGGAGGGAGUGCAUCCCCGAGGCCACGGUUAGACAAUGGCAAAGUCGACACAUUUAAUAUAGAAAACAUGGCAACAAUUUAAAGUCAAGGAAACGCCAAACGC
(((((..(((((((.((((((.........))))))))((((..(.....)..))))..))))).)))))...............((((.((........))...(....)))))..... ( -30.30)
>DroSim_CAF1 24714 120 - 1
GUGUGAGUGACUCUAUGGGGAGGGAGUGCAUCCCCGAGGCCACGGUUAGACAAUGGCAGAGUCGACACAUUUAAUAUAGAAAACAUGGCAACAAUUUAAAGUCAAGGAAACGCCAAACGC
(((((..(((((((.((((((.........))))))..((((..(.....)..))))))))))).)))))...............((((.((........))...(....)))))..... ( -35.00)
>DroEre_CAF1 24316 120 - 1
GUGUGAGUGACUCAAUGAGGAGGUGGUGCUUCCCCGAGGCCACAGUUAGACAAUGGCAGAGUCGACAUAUUUAAUAUAGGAAACAUGGCAACAAUUUAAAGUCAAGGAAACGCCAAACGC
((((..(((((((..((.(((((.....))))).))..((((..(.....)..)))).)))))(((............(....).((....)).......)))..(....)))...)))) ( -31.30)
>consensus
GUGUGAGUGACUCUAUGGGGAGGGAGUGCAUCCCCGAGGCCACGGUUAGACAAUGGCAGAGUCGACACAUUUAAUAUAGAAAACAUGGCAACAAUUUAAAGUCAAGGAAACGCCAAACGC
(((((..(((((((.((((((((.....))))))))..((((..(.....)..))))))))))).)))))...............((((.((........))...(....)))))..... (-32.54 = -33.47 +   0.94)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,265,146 – 21,265,266
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.92
Mean single sequence MFE -38.67
Consensus MFE -35.97
Energy contribution -35.73
Covariance contribution -0.25
Combinations/Pair 1.12
Mean z-score -1.73
Structure conservation index 0.93
SVM decision value 0.94
SVM RNA-class probability 0.885347
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21265146 120 + 23771897
UCUAUAUUAAAUGUGUCGACUCUGCCAUUGUCUAACCGUGGCCUCGGGGAUGCACCUCAUCCCCAUAGAGUCACUCACACCCACUUCGCCGGCUUCCAAGUGGGGCAUUGGGGAAUGAAC
...........((((..(((((((((((.(.....).)))))...(((((((.....)))))))..))))))...))))((((...(.((.(((....))).)))...))))........ ( -41.60)
>DroSec_CAF1 23264 120 + 1
UCUAUAUUAAAUGUGUCGACUUUGCCAUUGUCUAACCGUGGCCUCGGGGAUGCACUCCCUCCCCAUAGAGUCACUCACACCCACCUCGCCGGCUUCCAAGUGGGGCAUUGGGGAAUGAAC
...........((((..(((((((((((.(.....).)))))...(((((.(.....).)))))..))))))...))))((((((((((.((...))..))))))...))))........ ( -36.90)
>DroSim_CAF1 24754 120 + 1
UCUAUAUUAAAUGUGUCGACUCUGCCAUUGUCUAACCGUGGCCUCGGGGAUGCACUCCCUCCCCAUAGAGUCACUCACACCCACCUCGCCGGCUUCCAAGUGGGGCAUUGGGGAAUGAAC
...........((((..(((((((((((.(.....).)))))...(((((.(.....).)))))..))))))...))))((((((((((.((...))..))))))...))))........ ( -39.50)
>DroEre_CAF1 24356 120 + 1
CCUAUAUUAAAUAUGUCGACUCUGCCAUUGUCUAACUGUGGCCUCGGGGAAGCACCACCUCCUCAUUGAGUCACUCACACCCACCUCACCGGUUUCCAAGUGGGGCACUGGGGAUUGAGC
.................(((((.(((((.(.....).)))))...(((((.(.....).)))))...))))).((((..((((((((((.((...))..))))))...))))...)))). ( -36.70)
>consensus
UCUAUAUUAAAUGUGUCGACUCUGCCAUUGUCUAACCGUGGCCUCGGGGAUGCACCCCCUCCCCAUAGAGUCACUCACACCCACCUCGCCGGCUUCCAAGUGGGGCAUUGGGGAAUGAAC
...........((((..(((((((((((.(.....).)))))...(((((.(.....).)))))..))))))...))))((((((((((.((...))..))))))...))))........ (-35.97 = -35.73 +  -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 13:05:27 2006