Locus 251

Sequence ID 2R_DroMel_CAF1
Location 1,635,142 – 1,635,286
Length 144
Max. P 0.911634
window536 window537 window538

overview

Window 6

Location 1,635,142 – 1,635,249
Length 107
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 84.22
Mean single sequence MFE -25.15
Consensus MFE -20.67
Energy contribution -20.80
Covariance contribution 0.13
Combinations/Pair 1.04
Mean z-score -1.46
Structure conservation index 0.82
SVM decision value 0.06
SVM RNA-class probability 0.561473
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1635142 107 - 20766785
-----AGCUCCGUCAGCAGAUCUGCUUGGGAAACAAAGCAGCUGAAGGAAUACAGAGCUAAAGAAGCUUUUAAUCAAAAUGUAGAUUCCAU-------GUUAUAGCCAACUAAUUGAAA
-----.(((((.(((((.....(((((.(....).)))))))))).)))....((((((.....)))))).....................-------......))............. ( -23.20)
>DroSec_CAF1 20946 107 - 1
-----AGCUCCGUCAACAGAUCUGCUUGGGAAACGCAGCAGCUGAAGGAAUACAGAGCUGAAGAAGCUUUUAAUGAAAAUGUAGGUUCCAU-------GUUAUAGCCAACUAAUUGAAA
-----.(((....((.(((..(((((.((....).)))))))))..(((((..((((((.....))))))..((....))....))))).)-------)....)))............. ( -22.60)
>DroSim_CAF1 19378 107 - 1
-----AGCUCCGUCAACAGAUCUGCUUGGGAAACGCAGCAGCUGAAGGAAUACAGAGCUGAAGAAGCUUUUAAUGAAAAUGUAGGUUCCAU-------GUUAUAGCAAACUAAUUGAAA
-----.(((....((.(((..(((((.((....).)))))))))..(((((..((((((.....))))))..((....))....))))).)-------)....)))............. ( -23.50)
>DroEre_CAF1 23461 109 - 1
UACAUAGCUCCGUCAACAGAUCUGCUUGGGAAACUAAGCAGCUGAAGGAAUACAGAGCUGAAGAUGCUUUUAAUGAAAAUGUAGGGUCCAAUAACUUGGCUAUAACG----------AA
...((((((..((...(((..((((((((....)))))))))))..(((.((((((((.......)))))..((....)))))...)))....))..))))))....----------.. ( -31.30)
>consensus
_____AGCUCCGUCAACAGAUCUGCUUGGGAAACGAAGCAGCUGAAGGAAUACAGAGCUGAAGAAGCUUUUAAUGAAAAUGUAGGUUCCAU_______GUUAUAGCCAACUAAUUGAAA
.....(((((..((..(((..((((((.(....).)))))))))...)).....)))))...(((.((....((....))..)).)))............................... (-20.67 = -20.80 +   0.13)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,635,175 – 1,635,286
Length 111
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 91.30
Mean single sequence MFE -23.80
Consensus MFE -20.95
Energy contribution -21.57
Covariance contribution 0.62
Combinations/Pair 1.03
Mean z-score -1.89
Structure conservation index 0.88
SVM decision value 1.05
SVM RNA-class probability 0.906040
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1635175 111 + 20766785
UUUUGAUUAAAAGCUUCUUUAGCUCUGUAUUCCUUCAGCUGCUUUGUUUCCCAAGCAGAUCUGCUGACGGAGCU--------AAAUAUCCCAGAGUUUCCUUUUAAUAAUUCACAUCUU
.....((((((((.(((((((((((((.......(((((.(.((((((.....)))))).).))))))))))))--------)).......))))....))))))))............ ( -25.12)
>DroSec_CAF1 20979 111 + 1
UUUUCAUUAAAAGCUUCUUCAGCUCUGUAUUCCUUCAGCUGCUGCGUUUCCCAAGCAGAUCUGUUGACGGAGCU--------AGAUAUCCCAGAGUCUCCUUUUAAUAAUUCACAUGUU
.....((((((((.......((((((((.......(((...((((.........))))..)))...))))))))--------((((........)))).))))))))............ ( -24.50)
>DroSim_CAF1 19411 111 + 1
UUUUCAUUAAAAGCUUCUUCAGCUCUGUAUUCCUUCAGCUGCUGCGUUUCCCAAGCAGAUCUGUUGACGGAGCU--------AGAUAUCCCAGAGUCUCCUUUCAAUAAUUCACAUGUU
...........((((((.(((((.(((........)))(((((..........)))))....))))).))))))--------((((........))))..................... ( -21.10)
>DroEre_CAF1 23491 119 + 1
UUUUCAUUAAAAGCAUCUUCAGCUCUGUAUUCCUUCAGCUGCUUAGUUUCCCAAGCAGAUCUGUUGACGGAGCUAUGUAGAUAGAUAUCCCAGAGUCUCCUUUUAUUAAUUCACAUGUU
.......((((((.((((..((((((((.......(((((((((........))))))..)))...))))))))....))))((((........)))).)))))).............. ( -24.50)
>consensus
UUUUCAUUAAAAGCUUCUUCAGCUCUGUAUUCCUUCAGCUGCUGCGUUUCCCAAGCAGAUCUGUUGACGGAGCU________AGAUAUCCCAGAGUCUCCUUUUAAUAAUUCACAUGUU
.....((((((((.......((((((((.......(((((((((........))))))..)))...))))))))........((((........)))).))))))))............ (-20.95 = -21.57 +   0.62)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,635,175 – 1,635,286
Length 111
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 91.30
Mean single sequence MFE -27.70
Consensus MFE -23.15
Energy contribution -23.96
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -2.10
Structure conservation index 0.84
SVM decision value 1.08
SVM RNA-class probability 0.911634
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1635175 111 - 20766785
AAGAUGUGAAUUAUUAAAAGGAAACUCUGGGAUAUUU--------AGCUCCGUCAGCAGAUCUGCUUGGGAAACAAAGCAGCUGAAGGAAUACAGAGCUAAAGAAGCUUUUAAUCAAAA
..(((.((((.((((...((....))....))))(((--------(((((..((..(((..((((((.(....).)))))))))...)).....))))))))......))))))).... ( -27.70)
>DroSec_CAF1 20979 111 - 1
AACAUGUGAAUUAUUAAAAGGAGACUCUGGGAUAUCU--------AGCUCCGUCAACAGAUCUGCUUGGGAAACGCAGCAGCUGAAGGAAUACAGAGCUGAAGAAGCUUUUAAUGAAAA
..........((((((((((....((((((((.....--------...))).((..(((..(((((.((....).)))))))))...))...)))))((.....))))))))))))... ( -25.70)
>DroSim_CAF1 19411 111 - 1
AACAUGUGAAUUAUUGAAAGGAGACUCUGGGAUAUCU--------AGCUCCGUCAACAGAUCUGCUUGGGAAACGCAGCAGCUGAAGGAAUACAGAGCUGAAGAAGCUUUUAAUGAAAA
..........((((((((((....((((((((.....--------...))).((..(((..(((((.((....).)))))))))...))...)))))((.....))))))))))))... ( -25.80)
>DroEre_CAF1 23491 119 - 1
AACAUGUGAAUUAAUAAAAGGAGACUCUGGGAUAUCUAUCUACAUAGCUCCGUCAACAGAUCUGCUUGGGAAACUAAGCAGCUGAAGGAAUACAGAGCUGAAGAUGCUUUUAAUGAAAA
..((((((...........((((.((.((((((....)))).)).)))))).((..(((..((((((((....)))))))))))...)).)))(((((.......)))))..))).... ( -31.60)
>consensus
AACAUGUGAAUUAUUAAAAGGAGACUCUGGGAUAUCU________AGCUCCGUCAACAGAUCUGCUUGGGAAACGAAGCAGCUGAAGGAAUACAGAGCUGAAGAAGCUUUUAAUGAAAA
..........((((((((((....((((((((................))).((..(((..((((((.(....).)))))))))...))...)))))(....)...))))))))))... (-23.15 = -23.96 +   0.81)

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 09:33:35 2006