Locus 3959

Sequence ID 3L_DroMel_CAF1
Location 11,494,423 – 11,494,578
Length 155
Max. P 0.945685
window6165 window6166 window6167

overview

Window 5

Location 11,494,423 – 11,494,538
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.52
Mean single sequence MFE -28.87
Consensus MFE -19.97
Energy contribution -20.80
Covariance contribution 0.83
Combinations/Pair 1.11
Mean z-score -1.78
Structure conservation index 0.69
SVM decision value 1.19
SVM RNA-class probability 0.928116
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11494423 115 + 23771897
UUUAUUUCGGAUUGCUAAU---CAAACAUUCAUACUUU-UCCAGUUGGUCCAGAACCACUCGGAACCAAAACUGGGCACCGAGUAAACGCCGUAGUGCAGAAAGAUGCC-CACCUUGGCA
((((((.(((..(((....---...............(-((((((.(((.....)))))).))))(((....))))))))))))))).((((..(((((......))).-.))..)))). ( -27.50)
>DroSec_CAF1 9515 103 + 1
------------UGCCAAU---CAAGCAUUCAUACUUU-UCCAGUUGGUCCAGAACCACUCGGAUCCAAAACUGGGCACCGAGUAAACGCCGUAGUGCAGAAAGAUGCC-CACCUUGGCA
------------.(((((.---...(((((........-.(((((((((((((.....)).)))))...))))))((((((.((....))))..)))).....))))).-....))))). ( -29.50)
>DroSim_CAF1 4248 103 + 1
------------UGCCAAU---CAAGCAUUCAUACUUU-UCCAGUUGGUCCAGAACCACUCGGAUCCAAAACUGGGCACCGAGUAAACGCCGUAGUGCAGAAAGAUGCC-CACCUUGGCA
------------.(((((.---...(((((........-.(((((((((((((.....)).)))))...))))))((((((.((....))))..)))).....))))).-....))))). ( -29.50)
>DroPer_CAF1 8752 117 + 1
NNNNNNNNNNNNNNNNNNN---NNNNNNNNNUCACUUAACCCAAUUAUGCCAGAGCCAUUCGGAGCCGAAGCUCGGCACCGAAUAUACGCCGUAGUGCAAAAAAAUGCCCCACUUUGGCC
...................---..........................(((((((..((((((.((((.....)))).))))))............(((......)))....))))))). ( -26.90)
>DroEre_CAF1 5411 113 + 1
U-----AUCGAUUCACAUUCUUCGAACAUUCAUACUUU-UCCAGUUGGUCCAGAACCACUCGGAUCCGAAACUGGGCACAGAGUAAACGCCGUAGUGCAGAAAGAUGCC-CACCUUGGCA
.-----.((((..........)))).......((((((-((((((((((((((.....)).)))))...)))))))...))))))...((((..(((((......))).-.))..)))). ( -28.60)
>DroYak_CAF1 6019 110 + 1
U-----UUCGAUUGCCAAU---CAGGCAUUCAUACUUU-UCCAGUUAGUCCAGAACCACUCGGAUCCAAAACUGGGCACUGAGUAAACGCCGUAGUGCAGAAAGAUGCC-CACCUUGGCC
.-----.......(((((.---..((((((........-.((((((.((((((.....)).))))....))))))((((((.((....))..)))))).....))))))-....))))). ( -31.20)
>consensus
____________UGCCAAU___CAAGCAUUCAUACUUU_UCCAGUUGGUCCAGAACCACUCGGAUCCAAAACUGGGCACCGAGUAAACGCCGUAGUGCAGAAAGAUGCC_CACCUUGGCA
................................(((((..((((((((((((.((.....)))))))...)))))))....)))))...((((..(((((......)))...))..)))). (-19.97 = -20.80 +   0.83)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,494,459 – 11,494,578
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.11
Mean single sequence MFE -49.35
Consensus MFE -39.97
Energy contribution -40.95
Covariance contribution 0.98
Combinations/Pair 1.18
Mean z-score -3.19
Structure conservation index 0.81
SVM decision value 1.36
SVM RNA-class probability 0.945685
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11494459 119 + 23771897
CCAGUUGGUCCAGAACCACUCGGAACCAAAACUGGGCACCGAGUAAACGCCGUAGUGCAGAAAGAUGCC-CACCUUGGCAUCGUCGUACCAUUGGGGCAAUGGUCUCUGGUCCAAACUGG
((((((((.((((((((((((((..(((....)))...))))))....(((.(((((..((..((((((-......)))))).))....))))).)))...))).))))).)).)))))) ( -55.00)
>DroSec_CAF1 9539 119 + 1
CCAGUUGGUCCAGAACCACUCGGAUCCAAAACUGGGCACCGAGUAAACGCCGUAGUGCAGAAAGAUGCC-CACCUUGGCAUCGUCGUACCAUUGGGGCAGUGGCCUCUGGUCCAAACUGG
((((((((.(((((.((((((((.((((....))))..))))))....(((.(((((..((..((((((-......)))))).))....))))).)))...))..))))).)).)))))) ( -53.00)
>DroSim_CAF1 4272 119 + 1
CCAGUUGGUCCAGAACCACUCGGAUCCAAAACUGGGCACCGAGUAAACGCCGUAGUGCAGAAAGAUGCC-CACCUUGGCAUUGUCGUACCAUUGGGGCAGUGGCCUCUGGUCCAAACUGG
((((((((.(((((.((((((((.((((....))))..))))))....(((.(((((..((..((((((-......)))))).))....))))).)))...))..))))).)).)))))) ( -51.20)
>DroPer_CAF1 8789 120 + 1
CCAAUUAUGCCAGAGCCAUUCGGAGCCGAAGCUCGGCACCGAAUAUACGCCGUAGUGCAAAAAAAUGCCCCACUUUGGCCUCAUCAUACCAACGGGGCAGGGGCCGCUGGUCCAGACUGG
(((.((..(((((.(((((((((.((((.....)))).)))))).....(((.....).......((((((...((((..........)))).)))))))))))..)))))...)).))) ( -43.50)
>DroEre_CAF1 5445 119 + 1
CCAGUUGGUCCAGAACCACUCGGAUCCGAAACUGGGCACAGAGUAAACGCCGUAGUGCAGAAAGAUGCC-CACCUUGGCAUCGUCGUACCACUGGGGCAGUGGUCUCUGGUCCAAGCUGC
.(((((((.(((((((((((((....)))..(((....))).......(((.(((((..((..((((((-......)))))).))....))))).))).))))).))))).)).))))). ( -51.40)
>DroYak_CAF1 6050 119 + 1
CCAGUUAGUCCAGAACCACUCGGAUCCAAAACUGGGCACUGAGUAAACGCCGUAGUGCAGAAAGAUGCC-CACCUUGGCCUCGUCGUACCAUUGGGGCAGUGGCCUCUGGUCCAAGCUGG
((((((.(.(((((.((((((((.((((....))))..))))))....(((.(((((..((..((.(((-......))).)).))....))))).)))...))..))))).)..)))))) ( -42.00)
>consensus
CCAGUUGGUCCAGAACCACUCGGAUCCAAAACUGGGCACCGAGUAAACGCCGUAGUGCAGAAAGAUGCC_CACCUUGGCAUCGUCGUACCAUUGGGGCAGUGGCCUCUGGUCCAAACUGG
((((((((.(((((.((((((((..(((....)))...))))))....(((.(((((......((((((.......)))))).......))))).)))...))..))))).)).)))))) (-39.97 = -40.95 +   0.98)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,494,459 – 11,494,578
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.11
Mean single sequence MFE -49.64
Consensus MFE -39.72
Energy contribution -39.95
Covariance contribution 0.23
Combinations/Pair 1.16
Mean z-score -2.44
Structure conservation index 0.80
SVM decision value 0.35
SVM RNA-class probability 0.702350
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11494459 119 - 23771897
CCAGUUUGGACCAGAGACCAUUGCCCCAAUGGUACGACGAUGCCAAGGUG-GGCAUCUUUCUGCACUACGGCGUUUACUCGGUGCCCAGUUUUGGUUCCGAGUGGUUCUGGACCAACUGG
((((((.((.((((((.((((((((.....)))....((..(((((((((-((((((.....((.(....).))......)))))))).)))))))..))))))))))))).)))))))) ( -51.50)
>DroSec_CAF1 9539 119 - 1
CCAGUUUGGACCAGAGGCCACUGCCCCAAUGGUACGACGAUGCCAAGGUG-GGCAUCUUUCUGCACUACGGCGUUUACUCGGUGCCCAGUUUUGGAUCCGAGUGGUUCUGGACCAACUGG
((((((.((.((((((.((((((((.....))).((..(((.((((((((-((((((.....((.(....).))......)))))))).)))))))))))))))))))))).)))))))) ( -51.60)
>DroSim_CAF1 4272 119 - 1
CCAGUUUGGACCAGAGGCCACUGCCCCAAUGGUACGACAAUGCCAAGGUG-GGCAUCUUUCUGCACUACGGCGUUUACUCGGUGCCCAGUUUUGGAUCCGAGUGGUUCUGGACCAACUGG
((((((.((.((((((.((((((((.....))).........((((((((-((((((.....((.(....).))......)))))))).)))))).....))))))))))).)))))))) ( -49.60)
>DroPer_CAF1 8789 120 - 1
CCAGUCUGGACCAGCGGCCCCUGCCCCGUUGGUAUGAUGAGGCCAAAGUGGGGCAUUUUUUUGCACUACGGCGUAUAUUCGGUGCCGAGCUUCGGCUCCGAAUGGCUCUGGCAUAAUUGG
(((((...(.((((.((((..((((((.(((((........)))))...))))))......(((.(....).))).((((((.((((.....)))).)))))))))))))))...))))) ( -51.60)
>DroEre_CAF1 5445 119 - 1
GCAGCUUGGACCAGAGACCACUGCCCCAGUGGUACGACGAUGCCAAGGUG-GGCAUCUUUCUGCACUACGGCGUUUACUCUGUGCCCAGUUUCGGAUCCGAGUGGUUCUGGACCAACUGG
.(((.((((.((((((.((((((((((..(((((......)))))..).)-)))((((..(((...(((((.(....).)))))..)))....))))...))))))))))).))))))). ( -46.20)
>DroYak_CAF1 6050 119 - 1
CCAGCUUGGACCAGAGGCCACUGCCCCAAUGGUACGACGAGGCCAAGGUG-GGCAUCUUUCUGCACUACGGCGUUUACUCAGUGCCCAGUUUUGGAUCCGAGUGGUUCUGGACUAACUGG
((((.((((.((((((.((((((((.....)))....((.((((((((((-(((((......((.(....).)).......))))))).)))))).))))))))))))))).)))))))) ( -47.32)
>consensus
CCAGUUUGGACCAGAGGCCACUGCCCCAAUGGUACGACGAUGCCAAGGUG_GGCAUCUUUCUGCACUACGGCGUUUACUCGGUGCCCAGUUUUGGAUCCGAGUGGUUCUGGACCAACUGG
((((.((((.((((.((((...(((......(((.((.((((((.......)))))).)).))).....)))....((((((..((.......))..)))))))))))))).)))))))) (-39.72 = -39.95 +   0.23)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:02 2006