Locus 7516

Sequence ID X_DroMel_CAF1
Location 18,779,644 – 18,779,843
Length 199
Max. P 0.973606
window12333 window12334 window12335 window12336

overview

Window 3

Location 18,779,644 – 18,779,739
Length 95
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 76.77
Mean single sequence MFE -17.76
Consensus MFE -14.92
Energy contribution -14.70
Covariance contribution -0.22
Combinations/Pair 1.10
Mean z-score -1.63
Structure conservation index 0.84
SVM decision value 1.71
SVM RNA-class probability 0.973606
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18779644 95 + 22224390
CGCUCCCGCUCCCGCUCCCAAUUCCAAUCCCGUU------------CCUGUUCCCACAACUUCCCUUUUAACCGGGAGUGCCUUUUGUGACUGGGUACUCUCAAUCA
(((((((((....))...................------------..(((....)))...............))))))).......(((.((((....)))).))) ( -16.80)
>DroSec_CAF1 26135 83 + 1
CGC------------UCCCAAUCCCAAUCCCGUU------------CCUGUUCCCACAACUUCCCUUUUACCCGGGAGUGCCUUUUGUGACUGGGUACUUUCAAUCA
.(.------------.((((.((.(((...((((------------((((......................))))))))....))).)).))))..)......... ( -14.05)
>DroEre_CAF1 24632 95 + 1
CGU------------UCCCGUUCCCGUUCCCAUUCCCGCUAGCAAUCCCGUUCCCACAACUUCCCUUUUAGCCGGGAGUGCCUUUUGUGACUGGGUACUCUCAAUCA
.((------------.((((.((.((....((((((((((((.......(((.....))).......)))).)))))))).....)).)).)))).))......... ( -22.44)
>consensus
CGC____________UCCCAAUCCCAAUCCCGUU____________CCUGUUCCCACAACUUCCCUUUUAACCGGGAGUGCCUUUUGUGACUGGGUACUCUCAAUCA
.........................................................................((((((((((.........))))))))))..... (-14.92 = -14.70 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,779,644 – 18,779,739
Length 95
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 76.77
Mean single sequence MFE -25.07
Consensus MFE -16.76
Energy contribution -16.32
Covariance contribution -0.44
Combinations/Pair 1.14
Mean z-score -1.63
Structure conservation index 0.67
SVM decision value 0.61
SVM RNA-class probability 0.798194
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18779644 95 - 22224390
UGAUUGAGAGUACCCAGUCACAAAAGGCACUCCCGGUUAAAAGGGAAGUUGUGGGAACAGG------------AACGGGAUUGGAAUUGGGAGCGGGAGCGGGAGCG
............(((.(((......))).(((((((((..((......((.((....)).)------------)......))..))))))))).))).((....)). ( -27.60)
>DroSec_CAF1 26135 83 - 1
UGAUUGAAAGUACCCAGUCACAAAAGGCACUCCCGGGUAAAAGGGAAGUUGUGGGAACAGG------------AACGGGAUUGGGAUUGGGA------------GCG
.........((.(((((((.(((.......((((........))))..((.((....)).)------------)......))).))))))).------------)). ( -23.60)
>DroEre_CAF1 24632 95 - 1
UGAUUGAGAGUACCCAGUCACAAAAGGCACUCCCGGCUAAAAGGGAAGUUGUGGGAACGGGAUUGCUAGCGGGAAUGGGAACGGGAACGGGA------------ACG
.........((.((((.((.(....((((.(((((.(((.((......)).)))...))))).))))....))).)))).)).....((...------------.)) ( -24.00)
>consensus
UGAUUGAGAGUACCCAGUCACAAAAGGCACUCCCGGCUAAAAGGGAAGUUGUGGGAACAGG____________AACGGGAUUGGGAUUGGGA____________GCG
............(((.(((......)))..(((((..............(.((....)).)..............)))))........)))................ (-16.76 = -16.32 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,779,678 – 18,779,774
Length 96
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 82.98
Mean single sequence MFE -32.65
Consensus MFE -27.31
Energy contribution -29.62
Covariance contribution 2.31
Combinations/Pair 1.04
Mean z-score -1.38
Structure conservation index 0.84
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18779678 96 + 22224390
------------------CCUGUUCCCACAACUUCCCUUUUAACCGGGAGUGCCUUUUGUGACUGGGUACUCUCAAUCAAAGCCGGCCC-----GGGCCGGGACUUUGGACUCGAGCUC
------------------...((((....................((((((((((.........))))))))))..(((((((((((..-----..)))))..))))))....)))).. ( -33.80)
>DroSec_CAF1 26157 101 + 1
------------------CCUGUUCCCACAACUUCCCUUUUACCCGGGAGUGCCUUUUGUGACUGGGUACUUUCAAUCAAAGCCGGCCCGGACCGGGCCGGGACUUUGGACUCGAGCUC
------------------...((((....................(..(((((((.........)))))))..)..((((((((((((((...))))))))..))))))....)))).. ( -37.30)
>DroEre_CAF1 24660 97 + 1
------------AGCAAUCCCGUUCCCACAACUUCCCUUUUAGCCGGGAGUGCCUUUUGUGACUGGGUACUCUCAAUCAAAGCC----------GCGCCGGGACUUUGGACUCGAGCUC
------------.........((((....................((((((((((.........))))))))))..((((((((----------......)).))))))....)))).. ( -26.30)
>DroYak_CAF1 24361 109 + 1
ACCGCUACUGCUACCAAUCCCGUUCCCACAACUUCCCUUUUAGCCGGGAGUGCCUUUUGUGACUGGGUACUCUCAAUCAAAGCC----------GGGCCGGGACUUUGGACUCGAGCUC
...(((.......(((((((((..(((....((........))..((((((((((.........))))))))))..........----------))).)))))..)))).....))).. ( -33.20)
>consensus
__________________CCCGUUCCCACAACUUCCCUUUUAGCCGGGAGUGCCUUUUGUGACUGGGUACUCUCAAUCAAAGCC__________GGGCCGGGACUUUGGACUCGAGCUC
.....................((((....................((((((((((.........))))))))))..(((((((((((((.....)))))))..))))))....)))).. (-27.31 = -29.62 +   2.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,779,739 – 18,779,843
Length 104
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 91.04
Mean single sequence MFE -28.71
Consensus MFE -22.85
Energy contribution -25.35
Covariance contribution 2.50
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.80
SVM decision value 1.12
SVM RNA-class probability 0.919032
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18779739 104 - 22224390
CUCCCCCAUUUUGGUAGUUUCUGAAACUCCCCUUCGUUUUUUUC-CCAUUUUGUUCCCUGCCAAAAAGGGGAGCUCGAGUCCAAAGUCCCGGCCC-----GGGCCGGCUU
((((((..(((((((((.....(((((........)))))....-............))))))))).))))))...............(((((..-----..)))))... ( -30.80)
>DroSec_CAF1 26218 110 - 1
CUCCCCCAUUUUGGUAGUUUCUGAAACUCCCCUUCAUUUUUUUCUCCAUUCUGCUCCCUGCCAAAAAGGGGAGCUCGAGUCCAAAGUCCCGGCCCGGUCCGGGCCGGCUU
.......(((((((.......((((.......))))...........((((.(((((((........)))))))..))))))))))).((((((((...))))))))... ( -36.20)
>DroEre_CAF1 24727 98 - 1
CUCCCCCAUUUUGGUAGUUUCUGAAACUCCCCUUCAUUUUUU-C-CCAUUUUGCUCCCUGCCAAAAAGGGGAGCUCGAGUCCAAAGUCCCGGCGC----------GGCUU
...((((.(((((((((....((((.......))))......-.-.(.....)....))))))))).))))(((.((.(.((........))).)----------)))). ( -23.60)
>DroYak_CAF1 24440 98 - 1
CUCCCCCAUUUUGGUAGUUUCUGAAACUCCCCUUCAUUUUUU-C-CCAUUUUUCUCCCUGCCAAAAAGGGGAGCUCGAGUCCAAAGUCCCGGCCC----------GGCUU
...((((.(((((((((.....((((................-.-.....))))...))))))))).))))(((.((.(.((........))).)----------)))). ( -24.25)
>consensus
CUCCCCCAUUUUGGUAGUUUCUGAAACUCCCCUUCAUUUUUU_C_CCAUUUUGCUCCCUGCCAAAAAGGGGAGCUCGAGUCCAAAGUCCCGGCCC__________GGCUU
((((((..(((((((((........................................))))))))).))))))...............(((((((.....)))))))... (-22.85 = -25.35 +   2.50)

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 12:40:57 2006