Locus 8685

Sequence ID 3R_DroMel_CAF1
Location 23,188,949 – 23,189,144
Length 195
Max. P 0.998381
window13947 window13948 window13949

overview

Window 7

Location 23,188,949 – 23,189,053
Length 104
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 89.92
Mean single sequence MFE -40.20
Consensus MFE -33.40
Energy contribution -33.60
Covariance contribution 0.20
Combinations/Pair 1.17
Mean z-score -2.85
Structure conservation index 0.83
SVM decision value 3.08
SVM RNA-class probability 0.998381
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23188949 104 + 27905053
AGGAGGCCGCAAAGCCA---CCAAGUGCCGCAGAACAACCACAACCUAAUGCCAACACAGUGGAAGGGAUGGAAUCUGCGGCGGCAGAGCCAGCGUCUGUUGGCAAA
.((.(((......))).---))..((((((((((....(((...(((....(((......))).)))..)))..)))))))).))...((((((....))))))... ( -40.10)
>DroSec_CAF1 3893 100 + 1
----GGCCGCAAAGCCA---CCAAGUGCCGCAGAACAACCACAGCCUAAUGCCAACACGGUGGAAGGGAUGGAAUCUGCGGCUGCAGAGCCAGCGUCUGUUGGCAAA
----(((......))).---....((((((((((....(((...(((..((((.....))))..)))..)))..)))))))).))...((((((....))))))... ( -38.40)
>DroSim_CAF1 4158 104 + 1
AGGAGGCCACAAAGCCA---CCAAGUGCCGCAGAACAACCACCGCCUAAUGCCAACACGGUGGAAGGGAUGGAAUCUGCGGCUGCAGAGCCAGCGUCUGUUGGCAAA
.((.(((......))).---))..((((((((((.((.((.(((((............)))))...)).))...)))))))).))...((((((....))))))... ( -43.10)
>DroEre_CAF1 4146 104 + 1
AGGAGGCCGCAAAGCCA---CCAAGUGCCGCAGAGCAACCACAGCCUAAUGCCAACACGGUCGAAGGGGCGGAAUCUGUGGCUACAGAGCCAGCUUCUGUUGGCAAA
.((.(((......))).---))..((((((((((....((...((((...(((.....))).....))))))..)))))))).))...((((((....))))))... ( -41.30)
>DroYak_CAF1 3500 107 + 1
AGGAAGCCGCAAAGCCACCACCAAGUGCCGCAGAACAACCACAGCCUAAUGCCAACAAGGCCGACGGGAUGGAAUCUGCGGCUGUGGAGCCAGUGUCUGUUGGCAAA
.((..((......))..)).(((...((((((((....(((...(((...(((.....)))....))).)))..))))))))..))).(((((......)))))... ( -38.10)
>consensus
AGGAGGCCGCAAAGCCA___CCAAGUGCCGCAGAACAACCACAGCCUAAUGCCAACACGGUGGAAGGGAUGGAAUCUGCGGCUGCAGAGCCAGCGUCUGUUGGCAAA
....(((......)))........((((((((((....(((...(((..((((.....))))...))).)))..)))))))).))...((((((....))))))... (-33.40 = -33.60 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 23,188,949 – 23,189,053
Length 104
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 89.92
Mean single sequence MFE -39.26
Consensus MFE -31.42
Energy contribution -31.18
Covariance contribution -0.24
Combinations/Pair 1.16
Mean z-score -1.68
Structure conservation index 0.80
SVM decision value 0.62
SVM RNA-class probability 0.803575
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23188949 104 - 27905053
UUUGCCAACAGACGCUGGCUCUGCCGCCGCAGAUUCCAUCCCUUCCACUGUGUUGGCAUUAGGUUGUGGUUGUUCUGCGGCACUUGG---UGGCUUUGCGGCCUCCU
...((((........))))......((((((((..((((.(((.(((......)))....)))..))))....))))))))....((---.((((....)))).)). ( -37.90)
>DroSec_CAF1 3893 100 - 1
UUUGCCAACAGACGCUGGCUCUGCAGCCGCAGAUUCCAUCCCUUCCACCGUGUUGGCAUUAGGCUGUGGUUGUUCUGCGGCACUUGG---UGGCUUUGCGGCC----
...(((((((((.(....)))))..((((((((..((((.(((.(((......)))....)))..))))....))))))))..))))---)((((....))))---- ( -35.40)
>DroSim_CAF1 4158 104 - 1
UUUGCCAACAGACGCUGGCUCUGCAGCCGCAGAUUCCAUCCCUUCCACCGUGUUGGCAUUAGGCGGUGGUUGUUCUGCGGCACUUGG---UGGCUUUGUGGCCUCCU
...((((........))))......((((((((..((((((((.(((......)))....))).)))))....))))))))....((---.((((....)))).)). ( -42.50)
>DroEre_CAF1 4146 104 - 1
UUUGCCAACAGAAGCUGGCUCUGUAGCCACAGAUUCCGCCCCUUCGACCGUGUUGGCAUUAGGCUGUGGUUGCUCUGCGGCACUUGG---UGGCUUUGCGGCCUCCU
..((((((((((((..((((((((....)))))....))).)))).....))))))))....((((..(.....)..))))....((---.((((....)))).)). ( -38.20)
>DroYak_CAF1 3500 107 - 1
UUUGCCAACAGACACUGGCUCCACAGCCGCAGAUUCCAUCCCGUCGGCCUUGUUGGCAUUAGGCUGUGGUUGUUCUGCGGCACUUGGUGGUGGCUUUGCGGCUUCCU
...((((........)))).....(((((((((..((((((((...(((.....))).....((((..(.....)..))))...))).))))).))))))))).... ( -42.30)
>consensus
UUUGCCAACAGACGCUGGCUCUGCAGCCGCAGAUUCCAUCCCUUCCACCGUGUUGGCAUUAGGCUGUGGUUGUUCUGCGGCACUUGG___UGGCUUUGCGGCCUCCU
...((((........))))......((((((((..((((.(((....((.....))....)))..))))....))))))))..........((((....)))).... (-31.42 = -31.18 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 23,189,053 – 23,189,144
Length 91
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 86.60
Mean single sequence MFE -38.10
Consensus MFE -28.53
Energy contribution -28.91
Covariance contribution 0.38
Combinations/Pair 1.16
Mean z-score -2.86
Structure conservation index 0.75
SVM decision value 1.73
SVM RNA-class probability 0.974655
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23189053 91 - 27905053
GACCGGGUGGAG------------CAGCGGUGGGCGGAGGUAUGGGAGUAGGAUUGGUAUUUGGUUUCGGCUUGGCUUCAGCCAGCUCCAUCUGUUCUGUUUU
((.(((((((((------------(...(((.(((.(((...((..(.((((.......)))).)..)).))).)))...))).)))))))))).))...... ( -31.20)
>DroSec_CAF1 3993 91 - 1
GAGCGGGUGGAA------------CAGCGGUGGGCGGAGGUGUGGGAGUAGGAUUGGUAUUUGGUUUAGGCUUGGCUUCAGCCUGCUCCAUCUGUUCGGUUUU
(((((((((((.------------.....(..(((.(((((....((((.((((..(...)..))))..)))).))))).)))..))))))))))))...... ( -32.80)
>DroSim_CAF1 4262 91 - 1
GAGCGGGUGGAG------------CAGCGGUGGGCGGAGGUGUGGGAGUAGGAUUGGUAUUUGGUUUCGGCUUGGCUUCAGCCUGCUCCAUCUGUUCGGUUUU
((((((((((((------------(((.(.(((((.((...((.((((..((((....))))..)))).)))).)).))).))))))))))))))))...... ( -39.40)
>DroEre_CAF1 4250 103 - 1
GAGCAGGUGGAGCAGCGGCUGGAGCAGCGGUGGGUGGAGGUGUGGGACUAGGACUGGUAUUUGGUUUCGGCAUGACUGCAGCCUGCUCCAUCUGCUCGGUUUU
((((((((((((((((.((((...)))).))((.((.(((((((..((((((.......))))))..).))))..)).)).))))))))))))))))...... ( -49.00)
>consensus
GAGCGGGUGGAG____________CAGCGGUGGGCGGAGGUGUGGGAGUAGGAUUGGUAUUUGGUUUCGGCUUGGCUUCAGCCUGCUCCAUCUGUUCGGUUUU
(((((((((((..................((((((.(((((....((((.((((..(...)..))))..)))).))))).)))))))))))))))))...... (-28.53 = -28.91 +   0.38)

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 13:17:13 2006