Locus 7903

Sequence ID X_DroMel_CAF1
Location 19,682,433 – 19,682,588
Length 155
Max. P 0.913115
window12964 window12965 window12966 window12967

overview

Window 4

Location 19,682,433 – 19,682,553
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -49.05
Consensus MFE -41.79
Energy contribution -42.23
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -2.16
Structure conservation index 0.85
SVM decision value 1.00
SVM RNA-class probability 0.897289
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19682433 120 + 22224390
GCGCAGCAACUCGAACUCAAACACAACAGGCGCGAGCGAGAGCGCCGACAGCGCUGCCAACUGGACUGCAGAUGCAAGCGAGUUGGCAGCCCUGGAUGUCGGAUGCAAGUGCGUACACGG
((((((((.(.(((..((..........(((((........)))))..(((.((((((((((.(..(((....)))..).)))))))))).)))))..)))).)))...)))))...... ( -53.10)
>DroSec_CAF1 56257 120 + 1
GCGCAGCAACUCGAACUCAAAUACAACAGGAGCGAGCGAGAGCGCCGACGGCGCUGCCAACCGGACUGCAGAUGCAAGCGAGUUGGCAGCUCUGGACGUCGGAUGCAAGUGCGUACACGG
(((((....((((..(((...........)))....)))).(((((((((..(((((((((((...(((....)))..)).)))))))))......)))))).)))...)))))...... ( -47.40)
>DroSim_CAF1 43203 120 + 1
GCGCAGCAACUGGAACUCAAACACAACAGGCGCGAGCGAGAGCGCCGACGGCGCUGCCAACCGGACUGCAGAUGCAAGCGAGUUGGCAGCUCUGGACGUCGGAUGCAAGUGCAUACACGG
((((.(((.((((...((..........(((((........)))))..(((.(((((((((((...(((....)))..)).))))))))).)))))..)))).)))..))))........ ( -49.30)
>DroEre_CAF1 67452 120 + 1
GCGCAGCAACUCGAACUCAAACACAACAGGCGCGAGCGAGAGAGCCGACGGCGCUGCCAACCGGACUGCAGAUGCAGGCAAGUUGGCAGUACUGGACGUCGGAUGCAAACGCGUACACGG
(((..(((.(((...(((...(......)((....))))).)))((((((..(((((((((..(.((((....)))).)..)))))))))......)))))).)))...)))........ ( -46.40)
>consensus
GCGCAGCAACUCGAACUCAAACACAACAGGCGCGAGCGAGAGCGCCGACGGCGCUGCCAACCGGACUGCAGAUGCAAGCGAGUUGGCAGCUCUGGACGUCGGAUGCAAGUGCGUACACGG
((((.(((.(.(((..((..........(((((........)))))..(((.(((((((((..(..(((....)))..)..))))))))).)))))..)))).)))..))))........ (-41.79 = -42.23 +   0.44)

alignment

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secondary structure

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Window 5

Location 19,682,433 – 19,682,553
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.89
Mean single sequence MFE -48.88
Consensus MFE -44.49
Energy contribution -44.80
Covariance contribution 0.31
Combinations/Pair 1.10
Mean z-score -1.79
Structure conservation index 0.91
SVM decision value 0.86
SVM RNA-class probability 0.868612
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19682433 120 - 22224390
CCGUGUACGCACUUGCAUCCGACAUCCAGGGCUGCCAACUCGCUUGCAUCUGCAGUCCAGUUGGCAGCGCUGUCGGCGCUCUCGCUCGCGCCUGUUGUGUUUGAGUUCGAGUUGCUGCGC
..(((((.(((((((..((.(((((.(((.((((((((((.(.((((....)))).).)))))))))).)))..(((((........)))))....))))).))...)))).)))))))) ( -54.60)
>DroSec_CAF1 56257 120 - 1
CCGUGUACGCACUUGCAUCCGACGUCCAGAGCUGCCAACUCGCUUGCAUCUGCAGUCCGGUUGGCAGCGCCGUCGGCGCUCUCGCUCGCUCCUGUUGUAUUUGAGUUCGAGUUGCUGCGC
..(((((.(((...((..((((((......((((((((((.(.((((....)))).).))))))))))..)))))).)).((((...((((...........)))).)))).)))))))) ( -46.10)
>DroSim_CAF1 43203 120 - 1
CCGUGUAUGCACUUGCAUCCGACGUCCAGAGCUGCCAACUCGCUUGCAUCUGCAGUCCGGUUGGCAGCGCCGUCGGCGCUCUCGCUCGCGCCUGUUGUGUUUGAGUUCCAGUUGCUGCGC
..(((((.(((((.((..((((((......((((((((((.(.((((....)))).).))))))))))..)))))).)).((((..((((.....))))..))))....)).)))))))) ( -46.60)
>DroEre_CAF1 67452 120 - 1
CCGUGUACGCGUUUGCAUCCGACGUCCAGUACUGCCAACUUGCCUGCAUCUGCAGUCCGGUUGGCAGCGCCGUCGGCUCUCUCGCUCGCGCCUGUUGUGUUUGAGUUCGAGUUGCUGCGC
........((((..(((.((((((....(..(((((((((.(.((((....)))).).)))))))))..)))))))..(((..((((((((.....))))..))))..))).))).)))) ( -48.20)
>consensus
CCGUGUACGCACUUGCAUCCGACGUCCAGAGCUGCCAACUCGCUUGCAUCUGCAGUCCGGUUGGCAGCGCCGUCGGCGCUCUCGCUCGCGCCUGUUGUGUUUGAGUUCGAGUUGCUGCGC
..(((((.(((.......((((((....(.((((((((((.(.((((....)))).).)))))))))).))))))).((((..((((((((.....))))..))))..)))))))))))) (-44.49 = -44.80 +   0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,682,473 – 19,682,588
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.80
Mean single sequence MFE -45.24
Consensus MFE -33.84
Energy contribution -33.60
Covariance contribution -0.24
Combinations/Pair 1.15
Mean z-score -2.14
Structure conservation index 0.75
SVM decision value 0.98
SVM RNA-class probability 0.893651
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19682473 115 + 22224390
AGCGCCGACAGCGCUGCCAACUGGACUGCAGAUGCAAGCGAGUUGGCAGCCCUGGAUGUCGGAUGCAAGUGCGUACACGGUUAGAAAUCGGGGAUAGCA---AAACUAGUGCUGCCCG--
.(((((((((..((((((((((.(..(((....)))..).))))))))))......)))))).)))...........((((.....))))(((.(((((---.......)))))))).-- ( -49.40)
>DroSec_CAF1 56297 118 + 1
AGCGCCGACGGCGCUGCCAACCGGACUGCAGAUGCAAGCGAGUUGGCAGCUCUGGACGUCGGAUGCAAGUGCGUACACGGUUAGAAAUCAGGGAUAGCAACGAAACUAGUGCUGCCCG--
.(((((((((..(((((((((((...(((....)))..)).)))))))))......)))))).)))..(((....)))............(((.(((((.(.......))))))))).-- ( -47.20)
>DroSim_CAF1 43243 115 + 1
AGCGCCGACGGCGCUGCCAACCGGACUGCAGAUGCAAGCGAGUUGGCAGCUCUGGACGUCGGAUGCAAGUGCAUACACGGUUAGAAAUCGGGGAUAGCAACGAAACUAGUG---CCCG--
.(((((((((..(((((((((((...(((....)))..)).)))))))))......)))))).)))..(((....)))..........((((.((((........)).)).---))))-- ( -43.00)
>DroEre_CAF1 67492 120 + 1
AGAGCCGACGGCGCUGCCAACCGGACUGCAGAUGCAGGCAAGUUGGCAGUACUGGACGUCGGAUGCAAACGCGUACACGGUUAGAAAUCGGGGAUUGCAACGGUACUAGUGCUUCUCGCA
..(((((.(((..((((((((..(.((((....)))).)..))))))))..))).(((.((........)))))...)))))......((((((..(((.(.......)))))))))).. ( -43.10)
>DroYak_CAF1 69720 101 + 1
AGAGCCGACGGCGCUGCCAACCGGGCUGCAGAUGCAAGCAAGUUGGCAGCGCUGGACGACGGAUGCAAGUGCGUACACGGUUACAAAUCGGGGAUAACAAC-------------------
....(((((((((((((((((...(((((....)).)))..))))))))))))).....((.((((....))))...))........))))..........------------------- ( -43.50)
>consensus
AGCGCCGACGGCGCUGCCAACCGGACUGCAGAUGCAAGCGAGUUGGCAGCUCUGGACGUCGGAUGCAAGUGCGUACACGGUUAGAAAUCGGGGAUAGCAACGAAACUAGUGCU_CCCG__
....(((((((.(((((((((..(..(((....)))..)..))))))))).)))..(((...((((....))))..)))........))))............................. (-33.84 = -33.60 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,682,473 – 19,682,588
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.80
Mean single sequence MFE -42.64
Consensus MFE -32.18
Energy contribution -31.94
Covariance contribution -0.24
Combinations/Pair 1.11
Mean z-score -2.18
Structure conservation index 0.75
SVM decision value 1.09
SVM RNA-class probability 0.913115
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19682473 115 - 22224390
--CGGGCAGCACUAGUUU---UGCUAUCCCCGAUUUCUAACCGUGUACGCACUUGCAUCCGACAUCCAGGGCUGCCAACUCGCUUGCAUCUGCAGUCCAGUUGGCAGCGCUGUCGGCGCU
--((((.((((.......---))))...))))..........(((....)))..((..((((((....(.((((((((((.(.((((....)))).).)))))))))).))))))).)). ( -45.10)
>DroSec_CAF1 56297 118 - 1
--CGGGCAGCACUAGUUUCGUUGCUAUCCCUGAUUUCUAACCGUGUACGCACUUGCAUCCGACGUCCAGAGCUGCCAACUCGCUUGCAUCUGCAGUCCGGUUGGCAGCGCCGUCGGCGCU
--.(((.(((((.......).))))..)))............(((....)))..((..((((((......((((((((((.(.((((....)))).).))))))))))..)))))).)). ( -42.60)
>DroSim_CAF1 43243 115 - 1
--CGGG---CACUAGUUUCGUUGCUAUCCCCGAUUUCUAACCGUGUAUGCACUUGCAUCCGACGUCCAGAGCUGCCAACUCGCUUGCAUCUGCAGUCCGGUUGGCAGCGCCGUCGGCGCU
--((((---...((((......))))..))))..........(((....)))..((..((((((......((((((((((.(.((((....)))).).))))))))))..)))))).)). ( -44.40)
>DroEre_CAF1 67492 120 - 1
UGCGAGAAGCACUAGUACCGUUGCAAUCCCCGAUUUCUAACCGUGUACGCGUUUGCAUCCGACGUCCAGUACUGCCAACUUGCCUGCAUCUGCAGUCCGGUUGGCAGCGCCGUCGGCUCU
...(((..(((...(((((((((.((((...))))..))).)).)))).....)))..((((((....(..(((((((((.(.((((....)))).).)))))))))..)))))))))). ( -42.40)
>DroYak_CAF1 69720 101 - 1
-------------------GUUGUUAUCCCCGAUUUGUAACCGUGUACGCACUUGCAUCCGUCGUCCAGCGCUGCCAACUUGCUUGCAUCUGCAGCCCGGUUGGCAGCGCCGUCGGCUCU
-------------------..........(((((.(((((..(((....))))))))...........((((((((((((.(((.((....)))))..)))))))))))).))))).... ( -38.70)
>consensus
__CGGG_AGCACUAGUUUCGUUGCUAUCCCCGAUUUCUAACCGUGUACGCACUUGCAUCCGACGUCCAGAGCUGCCAACUCGCUUGCAUCUGCAGUCCGGUUGGCAGCGCCGUCGGCGCU
..........................................(((((......)))))((((((....(.((((((((((.(.((((....)))).).)))))))))).))))))).... (-32.18 = -31.94 +  -0.24)

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 12:50:25 2006