Locus 249

Sequence ID 3L_DroMel_CAF1
Location 678,303 – 678,485
Length 182
Max. P 0.874367
window373 window374 window375

overview

Window 3

Location 678,303 – 678,418
Length 115
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 82.93
Mean single sequence MFE -44.02
Consensus MFE -30.44
Energy contribution -30.08
Covariance contribution -0.36
Combinations/Pair 1.21
Mean z-score -2.08
Structure conservation index 0.69
SVM decision value 0.31
SVM RNA-class probability 0.684055
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 678303 115 + 23771897
GGGUUCUCCGGCCGGGGAAACGCAAAGAACUGCAUACUCGGGUGCUGACGCGAAUUGGACAAGCAUCCGAUGAUGCAGCACCGCCGGAUGGUCGGCAUCUCGACCUGCGGAUGAG
..((((((((((.(((....)........((((((..(((((((((....(......)...)))))))))..))))))..)))))))).((((((....))))))...))))... ( -47.80)
>DroVir_CAF1 40695 103 + 1
GGAUUGUCCGGCCUGGGAAAGGCGAAGAACUGCAUGCUCGGAUGCUGCCGCGAAUUCGACAAGCAUCCGAUGAUGCAGCAUCGCCGGAUAGUCGGCAUAACGG------------
.(((((((((((((.....))))...((.((((((..(((((((((....((....))...)))))))))..))))))..))..)))))))))..........------------ ( -46.60)
>DroPse_CAF1 40694 108 + 1
GGACUCUCCGGCCGUGGAAAGGCGAAGAACUGCAUGCUCGGAUGCUGCCGGGAAUUGGACAUGCAGCCGAUGAUGCAGCAACGCCGAAUGGUCGGCAUUCCG-------GAAACG
(((....((((((((.....((((..(..((((((..((((.((((((((.....))).)).))).))))..)))))))..))))..))))))))...)))(-------....). ( -45.20)
>DroSec_CAF1 33927 102 + 1
GGGUUCUCCGGCCGGGGAAACGCAAAGAACUGCAUACUCGGGUGCUGACGCGAAUUGGACAGGCAUCCGAUGAUGCAGCACCGCCGGAUGGUCGGCAUCUCG-------------
.(..(.((((((.(((....)........((((((..(((((((((....(......)...)))))))))..))))))..)))))))).)..).........------------- ( -40.40)
>DroWil_CAF1 13215 106 + 1
GGAUUCUCUGGCCUGGGAAACGCAAAGAACUGCAUGCUCGGAUGCUGUCGCGAAUUGGACAGGCAGCCGAUAAUGCAGCAUCGCCGAAUGGUCGGCAUUUCGGC-------AA--
...(((((......)))))..((...(((((((((..((((.(((((((........)))).))).))))..))))))....(((((....)))))..))).))-------..-- ( -38.90)
>DroPer_CAF1 45120 108 + 1
GGACUUUCCGGCCGUGGAAAGGCGAAGAACUGCAUGCUCGGAUGCUGCCGGGAAUUGGACAUGCAGCCGAUGAUGCAGCAACGCCGAAUGGUCGGCAUUCCG-------GAAACG
(((....((((((((.....((((..(..((((((..((((.((((((((.....))).)).))).))))..)))))))..))))..))))))))...)))(-------....). ( -45.20)
>consensus
GGAUUCUCCGGCCGGGGAAACGCAAAGAACUGCAUGCUCGGAUGCUGCCGCGAAUUGGACAAGCAGCCGAUGAUGCAGCAACGCCGAAUGGUCGGCAUUUCG_________AA__
(((....((((((........(((......)))....((((((((((.((...(((((........)))))..))))))))..))))..))))))...))).............. (-30.44 = -30.08 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 678,303 – 678,418
Length 115
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 82.93
Mean single sequence MFE -41.75
Consensus MFE -32.37
Energy contribution -32.57
Covariance contribution 0.20
Combinations/Pair 1.10
Mean z-score -2.49
Structure conservation index 0.78
SVM decision value 0.89
SVM RNA-class probability 0.874367
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 678303 115 - 23771897
CUCAUCCGCAGGUCGAGAUGCCGACCAUCCGGCGGUGCUGCAUCAUCGGAUGCUUGUCCAAUUCGCGUCAGCACCCGAGUAUGCAGUUCUUUGCGUUUCCCCGGCCGGAGAACCC
.((.......(((((......))))).((((((((((((((......((((....)))).......).))))))).(((.((((((....)))))))))....)))))))).... ( -41.72)
>DroVir_CAF1 40695 103 - 1
------------CCGUUAUGCCGACUAUCCGGCGAUGCUGCAUCAUCGGAUGCUUGUCGAAUUCGCGGCAGCAUCCGAGCAUGCAGUUCUUCGCCUUUCCCAGGCCGGACAAUCC
------------..(((..(((........(((((.(((((((..(((((((((.((((......)))))))))))))..)))))))...))))).......)))..)))..... ( -47.26)
>DroPse_CAF1 40694 108 - 1
CGUUUC-------CGGAAUGCCGACCAUUCGGCGUUGCUGCAUCAUCGGCUGCAUGUCCAAUUCCCGGCAGCAUCCGAGCAUGCAGUUCUUCGCCUUUCCACGGCCGGAGAGUCC
..((((-------(((((((((((....))))))))(((((((..((((.(((.((((........))))))).))))..))))))).................))))))).... ( -43.70)
>DroSec_CAF1 33927 102 - 1
-------------CGAGAUGCCGACCAUCCGGCGGUGCUGCAUCAUCGGAUGCCUGUCCAAUUCGCGUCAGCACCCGAGUAUGCAGUUCUUUGCGUUUCCCCGGCCGGAGAACCC
-------------......((((......))))((((((((((..((((.(((.((.((.....).).))))).))))..)))))))((((((.(((.....)))))))))))). ( -34.50)
>DroWil_CAF1 13215 106 - 1
--UU-------GCCGAAAUGCCGACCAUUCGGCGAUGCUGCAUUAUCGGCUGCCUGUCCAAUUCGCGACAGCAUCCGAGCAUGCAGUUCUUUGCGUUUCCCAGGCCAGAGAAUCC
--((-------((((((.((.....)))))))))).(((((((..((((.(((.(((((.....).))))))).))))..)))))))((((((.(((.....))))))))).... ( -39.70)
>DroPer_CAF1 45120 108 - 1
CGUUUC-------CGGAAUGCCGACCAUUCGGCGUUGCUGCAUCAUCGGCUGCAUGUCCAAUUCCCGGCAGCAUCCGAGCAUGCAGUUCUUCGCCUUUCCACGGCCGGAAAGUCC
..((((-------(((((((((((....))))))))(((((((..((((.(((.((((........))))))).))))..))))))).................))))))).... ( -43.60)
>consensus
__UU_________CGAAAUGCCGACCAUCCGGCGAUGCUGCAUCAUCGGAUGCAUGUCCAAUUCGCGGCAGCAUCCGAGCAUGCAGUUCUUCGCCUUUCCCCGGCCGGAGAAUCC
..................(((((......)))))..(((((((..((((.(((.((((........))))))).))))..)))))))(((((((.........).)))))).... (-32.37 = -32.57 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 678,383 – 678,485
Length 102
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 72.79
Mean single sequence MFE -30.89
Consensus MFE -20.42
Energy contribution -19.95
Covariance contribution -0.47
Combinations/Pair 1.15
Mean z-score -1.34
Structure conservation index 0.66
SVM decision value 0.83
SVM RNA-class probability 0.860557
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 678383 102 - 23771897
ACCUGGCGAAGCGU-GAGCAACGCCAGCACUCCA-GCAUUUAAGAUUCGGGGCCAACAGCAAUUUCAUCCUCA--UCCGCAGGUCGAGAUGCCGACCAUCCGGCGG
..((((((..((..-..))..))))))..((((.-.............))))((.......(((((..((((.--...).)))..)))))((((......)))))) ( -32.54)
>DroPse_CAF1 40774 92 - 1
GCUUGGCGGCGCAUUUAGCAACGCCAAGACAAAAUUCAUUAAAAAUUCGGGGCAUACAGAACAA-----CGUU--UC-------CGGAAUGCCGACCAUUCGGCGU
.(((((((..((.....))..))))))).................(((((((...((.......-----.)))--))-------))))(((((((....))))))) ( -28.40)
>DroSec_CAF1 34007 84 - 1
GCCUGGCGAAGCGU-GAGCAACGCCAGCACUCCA-GCAUUUAAGAUUCGGGGCCAACAGCAAUU--------------------CGAGAUGCCGACCAUCCGGCGG
((.(((((..((..-..))..)))))))...((.-..........(((((.((.....))...)--------------------))))..((((......)))))) ( -28.80)
>DroYak_CAF1 36067 102 - 1
GCCUGGCGAAGCGU-GAGCAACGCCAGCACACCA-GCAUUUAAGAUUCGGGGCCAACAGCAAUUCCAUCCGCA--UCCGCAGGUCGAGAUGCCGACCAUCCGGCGG
((((((((..((..-..))..)))).((......-))............)))).....((..........)).--.((((.(((((......))))).....)))) ( -33.30)
>DroAna_CAF1 35268 96 - 1
GCUUGGCGAAGCGU-CAGCAACGCCAGCUCCUAA-AGAUUUAAAAUUCGGGGCCAUCAGCA--------CGCAAUUCCGCAGCCCGAGAUGCCGACCAUUCGGCGU
(((.((((..((..-..))..)))))))......-..........((((((((.....)).--------.((......))..))))))(((((((....))))))) ( -33.90)
>DroPer_CAF1 45200 92 - 1
GCUUGGCGGCGCAUUUAGCAACGCCAAGACAAAAUUCAUUAAAAAUUCGGGGCAUACAGAACAA-----CGUU--UC-------CGGAAUGCCGACCAUUCGGCGU
.(((((((..((.....))..))))))).................(((((((...((.......-----.)))--))-------))))(((((((....))))))) ( -28.40)
>consensus
GCCUGGCGAAGCGU_GAGCAACGCCAGCACACAA_GCAUUUAAAAUUCGGGGCCAACAGCAAUU_____CGCA__UC_______CGAGAUGCCGACCAUCCGGCGG
..((((((..((.....))..))))))..............................................................(((((......))))). (-20.42 = -19.95 +  -0.47)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:29 2006