Locus 3826

Sequence ID 3R_DroMel_CAF1
Location 10,433,415 – 10,433,560
Length 145
Max. P 0.998097
window6127 window6128 window6129

overview

Window 7

Location 10,433,415 – 10,433,528
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 91.42
Mean single sequence MFE -32.26
Consensus MFE -26.56
Energy contribution -26.68
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -2.88
Structure conservation index 0.82
SVM decision value 3.00
SVM RNA-class probability 0.998097
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10433415 113 + 27905053
UAUGUUUAAGAUAUUCGAAAGAGUGCCUUGGGCCUUUGAAGUUUUUGAAACGGAAAUUGGACAGUUAGAACAUCAGAGGUCUCAAGAUCACUUCGGAUUACUUGUAUUAUCUC
......((((..((((((...((((.(((((((((((((.(((((...(((............)))))))).))))))))).))))..))))))))))..))))......... ( -29.40)
>DroSec_CAF1 96843 113 + 1
UAUGGUUAAGAUAUUCAAAAGAGUGCCUUGUGCCUUUGAAGUUUUUGAAACUGAAAUUGGACAGUUAGAACAUCAGAGGUCUCAAGAUCACUUCGGAUUACUUGUAUUAUCUC
.(((((((((.((.((....(((((.((((.((((((((.(((((...(((((........)))))))))).))))))))..))))..)))))..)).)))))).)))))... ( -28.90)
>DroSim_CAF1 85010 112 + 1
UAUGUUUAAGAUAUUCGAAAGAGUGCCUUGGGCCUUUGAAGUUUUUGAAACUGAAAUUGAACAGUUAGAACAUCAGAGGUCUCAAGAUCCCUUCGGAUUAC-UGUAUUAUCUC
........(((((.((....))(((((((((((((((((.(((((...(((((........)))))))))).))))))))).))))((((....))))...-.))))))))). ( -32.40)
>DroEre_CAF1 93923 113 + 1
UAUGCUUAAGAUAUUCGAGCAGAUACCUUGGGCCUUUGAAGUUUUAGAAACUGAAAUUGGACAGUGAAAACAUCAGAGGUCUCAAGAUCACUUCGGAUUACUUGUAUUAUCUC
......((((..(((((((..(((..(((((((((((((.(((((....((((........)))).))))).))))))))).)))))))..)))))))..))))......... ( -32.80)
>DroYak_CAF1 95367 113 + 1
UAUGUUUAAGAUAUUCGAGCAAGUACCUUGGGCCUUUGAAGUUUUACACACUGAAAUUGGACAGUGAAAACAUCAGAGGUCUCAGGAUCACUUCGGAUUACUUGUAUUAUCUG
........(((((.....((((((((((.((((((((((.(((((...(((((........)))))))))).)))))))))).)))....(....)..)))))))..))))). ( -37.80)
>consensus
UAUGUUUAAGAUAUUCGAAAGAGUGCCUUGGGCCUUUGAAGUUUUUGAAACUGAAAUUGGACAGUUAGAACAUCAGAGGUCUCAAGAUCACUUCGGAUUACUUGUAUUAUCUC
......((((..(((((((.......(((((((((((((.(((((...(((((........)))))))))).))))))))).)))).....)))))))..))))......... (-26.56 = -26.68 +   0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,433,415 – 10,433,528
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 91.42
Mean single sequence MFE -22.48
Consensus MFE -18.28
Energy contribution -18.68
Covariance contribution 0.40
Combinations/Pair 1.11
Mean z-score -1.35
Structure conservation index 0.81
SVM decision value 0.05
SVM RNA-class probability 0.556798
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10433415 113 - 27905053
GAGAUAAUACAAGUAAUCCGAAGUGAUCUUGAGACCUCUGAUGUUCUAACUGUCCAAUUUCCGUUUCAAAAACUUCAAAGGCCCAAGGCACUCUUUCGAAUAUCUUAAACAUA
((((((.((....))...(((((((.(((((.(.(((.(((.(((..(((.(........).))).....))).))).)))).)))))))))...)))..))))))....... ( -19.60)
>DroSec_CAF1 96843 113 - 1
GAGAUAAUACAAGUAAUCCGAAGUGAUCUUGAGACCUCUGAUGUUCUAACUGUCCAAUUUCAGUUUCAAAAACUUCAAAGGCACAAGGCACUCUUUUGAAUAUCUUAACCAUA
((((((...((((......((.(((.(((((.(.(((.(((.(((..(((((........))))).....))).))).)))).)))))))))).))))..))))))....... ( -22.80)
>DroSim_CAF1 85010 112 - 1
GAGAUAAUACA-GUAAUCCGAAGGGAUCUUGAGACCUCUGAUGUUCUAACUGUUCAAUUUCAGUUUCAAAAACUUCAAAGGCCCAAGGCACUCUUUCGAAUAUCUUAAACAUA
((((((.....-...((((....))))((((.(.(((.(((.(((..(((((........))))).....))).))).)))).)))).............))))))....... ( -24.40)
>DroEre_CAF1 93923 113 - 1
GAGAUAAUACAAGUAAUCCGAAGUGAUCUUGAGACCUCUGAUGUUUUCACUGUCCAAUUUCAGUUUCUAAAACUUCAAAGGCCCAAGGUAUCUGCUCGAAUAUCUUAAGCAUA
((((((.((....))...(((.((.((((((.(.(((.(((.(((((.((((........))))....))))).))).)))).))))))....)))))..))))))....... ( -22.50)
>DroYak_CAF1 95367 113 - 1
CAGAUAAUACAAGUAAUCCGAAGUGAUCCUGAGACCUCUGAUGUUUUCACUGUCCAAUUUCAGUGUGUAAAACUUCAAAGGCCCAAGGUACUUGCUCGAAUAUCUUAAACAUA
.(((((.((....))...(((.(..(.(((..(.(((.(((.((((((((((........)))))...))))).))).))).)..)))...)..))))..)))))........ ( -23.10)
>consensus
GAGAUAAUACAAGUAAUCCGAAGUGAUCUUGAGACCUCUGAUGUUCUAACUGUCCAAUUUCAGUUUCAAAAACUUCAAAGGCCCAAGGCACUCUUUCGAAUAUCUUAAACAUA
((((((.((....))...(((((((.(((((.(.(((.(((.(((..(((((........))))).....))).))).)))).)))))))))...)))..))))))....... (-18.28 = -18.68 +   0.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,433,454 – 10,433,560
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 95.28
Mean single sequence MFE -26.64
Consensus MFE -22.08
Energy contribution -24.16
Covariance contribution 2.08
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.83
SVM decision value 1.05
SVM RNA-class probability 0.906580
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10433454 106 + 27905053
AGUUUUUGAAACGGAAAUUGGACAGUUAGAACAUCAGAGGUCUCAAGAUCACUUCGGAUUACUUGUAUUAUCUCUGUAGUCUUCGGUUUCAGCGACUAAUUGUACA
((((.(((((((.((....((((.((....))..(((((((..((((....(....)....))))....)))))))..)))))).))))))).))))......... ( -26.50)
>DroSec_CAF1 96882 106 + 1
AGUUUUUGAAACUGAAAUUGGACAGUUAGAACAUCAGAGGUCUCAAGAUCACUUCGGAUUACUUGUAUUAUCUCUGUAGUCUUCGGUUUCAGCGACUAAUUGUACA
((((.((((((((((....((((.((....))..(((((((..((((....(....)....))))....)))))))..)))))))))))))).))))......... ( -28.60)
>DroSim_CAF1 85049 105 + 1
AGUUUUUGAAACUGAAAUUGAACAGUUAGAACAUCAGAGGUCUCAAGAUCCCUUCGGAUUAC-UGUAUUAUCUCUGUAGUCUUCGGUUUCAGCGACUAAUUGUACA
((((.(((((((((((..(..((((..(((....(((..((((.(((....))).))))..)-)).....))))))).)..))))))))))).))))......... ( -27.70)
>DroEre_CAF1 93962 106 + 1
AGUUUUAGAAACUGAAAUUGGACAGUGAAAACAUCAGAGGUCUCAAGAUCACUUCGGAUUACUUGUAUUAUCUCUGUAGUCUUCGGUUUCAGCGACUAAUUGUACA
((((...((((((((....((((.((....))..(((((((..((((....(....)....))))....)))))))..))))))))))))...))))......... ( -27.50)
>DroYak_CAF1 95406 106 + 1
AGUUUUACACACUGAAAUUGGACAGUGAAAACAUCAGAGGUCUCAGGAUCACUUCGGAUUACUUGUAUUAUCUGUGUAGUCUUCGGUUUCAGCGACUAAUUGUACA
.........(.(((((((((((....((..(((.((((.....((((....(....)....)))).....)))))))..))))))))))))).)............ ( -22.90)
>consensus
AGUUUUUGAAACUGAAAUUGGACAGUUAGAACAUCAGAGGUCUCAAGAUCACUUCGGAUUACUUGUAUUAUCUCUGUAGUCUUCGGUUUCAGCGACUAAUUGUACA
((((.((((((((((....((((.((....))..(((((((..(((((((......)))..))))....)))))))..)))))))))))))).))))......... (-22.08 = -24.16 +   2.08)

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 11:11:00 2006