Locus 3840

Sequence ID 3L_DroMel_CAF1
Location 11,095,458 – 11,095,600
Length 142
Max. P 0.999204
window5978 window5979 window5980

overview

Window 8

Location 11,095,458 – 11,095,560
Length 102
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 74.02
Mean single sequence MFE -25.80
Consensus MFE -21.25
Energy contribution -21.03
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -1.38
Structure conservation index 0.82
SVM decision value 1.63
SVM RNA-class probability 0.968802
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11095458 102 + 23771897
GAAA-------------CAACCAGUUAUGCCAAUAUAAUUUUUUUUUUUUGUAUGAUCCCAUAGUGCGUCCCAACGAAGGCGAUGCCUAUCCAUUGGGCGCCUUGCCCGUGGGCA
....-------------..........((((.((((((..........))))))......((((.(((((((......)).))))))))).(((.((((.....))))))))))) ( -25.70)
>DroEre_CAF1 6626 109 + 1
GAAAUACACUGUAACACUAAAAUAUUA--AAAAUA---UUCAU-UAUUUUGUAUAUUCCCGAAGUGCGUCCCAACGAAGGCGAUGCCUAUCCACUGGGCGCUCUGCCCGUGGGCA
((((((((..((((......(((((..--...)))---))..)-)))..))))).)))....((.(((((((......)).))))))).(((((.((((.....))))))))).. ( -26.40)
>DroYak_CAF1 6594 97 + 1
---------------ACUAAAAUAUUA--AACAUAUAAUUCAU-UAUUUUGUGUAUUCCCAAAGUGCGACCCAACGAAGGCGAUGCCUAUCCAUUGGGCGCCCUGCCCGUGGGCA
---------------............--.(((((.(((....-.))).)))))........((.(((.(((((.((((((...)))).))..)))))))).))(((....))). ( -25.30)
>consensus
GAAA___________ACUAAAAUAUUA__AAAAUAUAAUUCAU_UAUUUUGUAUAUUCCCAAAGUGCGUCCCAACGAAGGCGAUGCCUAUCCAUUGGGCGCCCUGCCCGUGGGCA
..............................................................((.(((.((((..((((((...)))).))...))))))).))(((....))). (-21.25 = -21.03 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,095,458 – 11,095,560
Length 102
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 74.02
Mean single sequence MFE -30.93
Consensus MFE -25.99
Energy contribution -25.77
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -2.02
Structure conservation index 0.84
SVM decision value 3.43
SVM RNA-class probability 0.999204
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11095458 102 - 23771897
UGCCCACGGGCAAGGCGCCCAAUGGAUAGGCAUCGCCUUCGUUGGGACGCACUAUGGGAUCAUACAAAAAAAAAAAAUUAUAUUGGCAUAACUGGUUG-------------UUUC
..((((..(.....(((((((((((..((((...)))))))))))).))).)..))))................((((...((..(.....)..)).)-------------))). ( -28.50)
>DroEre_CAF1 6626 109 - 1
UGCCCACGGGCAGAGCGCCCAGUGGAUAGGCAUCGCCUUCGUUGGGACGCACUUCGGGAAUAUACAAAAUA-AUGAA---UAUUUU--UAAUAUUUUAGUGUUACAGUGUAUUUC
((((....))))..(((((((((((..((((...)))))))))))).)))......(((((((((..((((-..(((---(((...--..))))))...))))...))))))))) ( -33.40)
>DroYak_CAF1 6594 97 - 1
UGCCCACGGGCAGGGCGCCCAAUGGAUAGGCAUCGCCUUCGUUGGGUCGCACUUUGGGAAUACACAAAAUA-AUGAAUUAUAUGUU--UAAUAUUUUAGU---------------
..((((.((.....(((((((((((..((((...)))))))))))).))).)).)))).......((((((-.(((((.....)))--)).))))))...--------------- ( -30.90)
>consensus
UGCCCACGGGCAGGGCGCCCAAUGGAUAGGCAUCGCCUUCGUUGGGACGCACUUUGGGAAUAUACAAAAUA_AUGAAUUAUAUUUU__UAAUAUUUUAGU___________UUUC
((((....))))..(((((((((((..((((...)))))))))))).)))................................................................. (-25.99 = -25.77 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,095,485 – 11,095,600
Length 115
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 77.78
Mean single sequence MFE -40.95
Consensus MFE -27.51
Energy contribution -27.85
Covariance contribution 0.34
Combinations/Pair 1.29
Mean z-score -1.36
Structure conservation index 0.67
SVM decision value 0.42
SVM RNA-class probability 0.731335
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11095485 115 - 23771897
CACAUCUGGCCGGGGUUCUUCUCCAGACAGUGAAUGCGUGUGCCCACGGGCAAGGCGCCCAAUGGAUAGGCAUCGCCUUCGUUGGGACGCACUAUGGGAUCAUACAAAAAAAAAA
..((.(((.(.((((.....)))).).))))).....(((((((((..(.....(((((((((((..((((...)))))))))))).))).)..))))..))))).......... ( -40.60)
>DroPse_CAF1 10726 110 - 1
CACUGCUGGCCGGGAUUCUUCUCGAGGCAGUGGAUUCGAGUGCCUACGGGCAGGGCGCCCAAUGGGUAGGCAUCGCCUUCAUUGGGACGCACUGCGGGAGA---GAAAAAA--UU
(((((((...(((((....))))).)))))))..((((((((((....)))...(((((((((((..((((...)))))))))))).)))))).))))...---.......--.. ( -48.50)
>DroGri_CAF1 7009 100 - 1
CACAGUUGGCCGGGAUUCUUUUCUAGGCAAUGGAUGCGUGUGCCGACGGGCAAAGCGCCUAGCGGAUAAGCAUCGCCAUCAUUGGGACGCACUGCAGCAU---------------
....(((((((.(((......))).)))....(((((.(((.(((..((((.....))))..)))))).))))).(((....))).........))))..--------------- ( -33.80)
>DroEre_CAF1 6661 114 - 1
CACAUCUGACCGGGAUUCUUCUCCAGGCAGUGGAUGCGGGUGCCCACGGGCAGAGCGCCCAGUGGAUAGGCAUCGCCUUCGUUGGGACGCACUUCGGGAAUAUACAAAAUA-AUG
..((.(((.((.(((......))).)))))))..(((((((((((((((((.....)))).)))....)))))).(((.....))).))))(....)..............-... ( -36.50)
>DroYak_CAF1 6617 114 - 1
CACAUCUGCCCGGGGUUCUUCUCCAGGCAGUGGAUGCGGGUGCCCACGGGCAGGGCGCCCAAUGGAUAGGCAUCGCCUUCGUUGGGUCGCACUUUGGGAAUACACAAAAUA-AUG
....(((((((((((((((.(((((.....)))).).))).)))).))))))))(((((((((((..((((...)))))))))))).)))..((((........))))...-... ( -48.60)
>DroAna_CAF1 6886 104 - 1
CACUGCUGACCGGGAUUCUUCUCCAGACAGUGGAUGCGUGUGCCGACGGGCAGAGCGCCAAGAGGGUAAGCAUCGCCCUCAUUGGGACGCACUAUUGAAAA------UCA-----
((((((((...((((....))))))).)))))..(((((.((((....)))).....((((((((((.......)))))).)))).)))))..........------...----- ( -37.70)
>consensus
CACAGCUGGCCGGGAUUCUUCUCCAGGCAGUGGAUGCGUGUGCCCACGGGCAGAGCGCCCAAUGGAUAGGCAUCGCCUUCAUUGGGACGCACUACGGGAAA___CAAAAAA__U_
..(..(((.((.(((......))).)))))..).......((((....))))..((((((((((((..(((...)))))))))))).)))......................... (-27.51 = -27.85 +   0.34)

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 11:08:04 2006