Locus 6818

Sequence ID 3R_DroMel_CAF1
Location 18,031,149 – 18,031,287
Length 138
Max. P 0.892178
window11067 window11068 window11069

overview

Window 7

Location 18,031,149 – 18,031,247
Length 98
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 91.63
Mean single sequence MFE -18.02
Consensus MFE -15.36
Energy contribution -15.32
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.54
Structure conservation index 0.85
SVM decision value 0.85
SVM RNA-class probability 0.867167
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18031149 98 + 27905053
AGAUACUAACGCACAC------------UCGCAUGCAUGCAGUCGGAUGCAAAUAAAAAUAAAUAUUUACAUUCAAUUUCGACAAACGCGCCAGCCACUGAGCGCCAACU
..........(((..(------------......)..))).((((((((.(((((........))))).))))......))))....(((((((...))).))))..... ( -17.10)
>DroSec_CAF1 73793 94 + 1
AGAUACUGACGCACAC------------UCGCA----UGCAGUCGGAUGCAAAUAAAAAUAAAUAUUUACAUUCAAUUUCGACAAACGCGCCAGCCACUGAGCGCCAACU
.......((((((...------------.....----))).)))(((((.(((((........))))).))))).............(((((((...))).))))..... ( -19.00)
>DroSim_CAF1 75698 94 + 1
AGAUACUAACGCACAC------------UCGCA----UGCAGUCGGAUGCAAAUAAAAAUAAAUAUUUACAUUCAAUUUCGACAAACGCGCCAGCCACUGAGCGCCAACU
..........(((...------------.....----))).((((((((.(((((........))))).))))......))))....(((((((...))).))))..... ( -16.60)
>DroEre_CAF1 75607 94 + 1
AGAUACUAACGCAUAC------------UCGCA----UGCAGUCGAAUGCAAAUAAAAAUAAAUAUUUACAUUCAAUUUCGACAAACGCGCCAGCCACUGAGCGCCAACU
..........((((..------------....)----))).((((((((.(((((........))))).)))......)))))....(((((((...))).))))..... ( -18.70)
>DroYak_CAF1 77376 106 + 1
AGAUACUAACGCAUACUCUCGCACUCACUCGCA----UGCAGUCGAAUGCAAAUAAAAAUAAAUAUUUACAUUCAAUUUCGACAAACGCGGCAGCCACUGAGCGCCAACU
....................((.((((...((.----(((....(((((.(((((........))))).))))).....((.(....))))))))...)))).))..... ( -18.70)
>consensus
AGAUACUAACGCACAC____________UCGCA____UGCAGUCGGAUGCAAAUAAAAAUAAAUAUUUACAUUCAAUUUCGACAAACGCGCCAGCCACUGAGCGCCAACU
..............................(((....))).((((((((.(((((........))))).))......))))))....(((((((...))).))))..... (-15.36 = -15.32 +  -0.04)

alignment

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secondary structure

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Window 8

Location 18,031,149 – 18,031,247
Length 98
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 91.63
Mean single sequence MFE -28.74
Consensus MFE -22.48
Energy contribution -22.28
Covariance contribution -0.20
Combinations/Pair 1.07
Mean z-score -1.99
Structure conservation index 0.78
SVM decision value 0.97
SVM RNA-class probability 0.892178
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18031149 98 - 27905053
AGUUGGCGCUCAGUGGCUGGCGCGUUUGUCGAAAUUGAAUGUAAAUAUUUAUUUUUAUUUGCAUCCGACUGCAUGCAUGCGA------------GUGUGCGUUAGUAUCU
..(((((((.((.(.((..(((.((..((((.....((.((((((((........)))))))))))))).)).)))..)).)------------.)).)))))))..... ( -28.80)
>DroSec_CAF1 73793 94 - 1
AGUUGGCGCUCAGUGGCUGGCGCGUUUGUCGAAAUUGAAUGUAAAUAUUUAUUUUUAUUUGCAUCCGACUGCA----UGCGA------------GUGUGCGUCAGUAUCU
..(((((((.((.(.((..((.((.....))...(((.(((((((((........))))))))).)))..)).----.)).)------------.)).)))))))..... ( -27.10)
>DroSim_CAF1 75698 94 - 1
AGUUGGCGCUCAGUGGCUGGCGCGUUUGUCGAAAUUGAAUGUAAAUAUUUAUUUUUAUUUGCAUCCGACUGCA----UGCGA------------GUGUGCGUUAGUAUCU
..(((((((.((.(.((..((.((.....))...(((.(((((((((........))))))))).)))..)).----.)).)------------.)).)))))))..... ( -25.00)
>DroEre_CAF1 75607 94 - 1
AGUUGGCGCUCAGUGGCUGGCGCGUUUGUCGAAAUUGAAUGUAAAUAUUUAUUUUUAUUUGCAUUCGACUGCA----UGCGA------------GUAUGCGUUAGUAUCU
...............((((((((((...(((...(((((((((((((........))))))))))))).....----..)))------------..)))))))))).... ( -27.90)
>DroYak_CAF1 77376 106 - 1
AGUUGGCGCUCAGUGGCUGCCGCGUUUGUCGAAAUUGAAUGUAAAUAUUUAUUUUUAUUUGCAUUCGACUGCA----UGCGAGUGAGUGCGAGAGUAUGCGUUAGUAUCU
..((.(((((((.(.(((((..((.....))...(((((((((((((........)))))))))))))..)))----.)).).))))))).))((.((((....)))))) ( -34.90)
>consensus
AGUUGGCGCUCAGUGGCUGGCGCGUUUGUCGAAAUUGAAUGUAAAUAUUUAUUUUUAUUUGCAUCCGACUGCA____UGCGA____________GUGUGCGUUAGUAUCU
...............(((((((((...((((.....((.((((((((........))))))))))))))((((....))))................))))))))).... (-22.48 = -22.28 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,031,176 – 18,031,287
Length 111
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 76.98
Mean single sequence MFE -24.82
Consensus MFE -8.54
Energy contribution -8.40
Covariance contribution -0.14
Combinations/Pair 1.08
Mean z-score -2.48
Structure conservation index 0.34
SVM decision value 0.29
SVM RNA-class probability 0.669110
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18031176 111 - 27905053
CUGUUCCCGCUGCUUUUUACGCACAAUUUUCCUUUGGCAAAGUUGGCGCUCAGUGGCUGGCGCGUUUGUCGAAAUUGAAUGUAAAUAUUUAUUU-UUAUUUGCAUCC---GACUG
..((.((.((..((.....(((.(((((((((...)).))))))))))...))..)).)).))....((((.....((.((((((((.......-.)))))))))))---))).. ( -29.40)
>DroVir_CAF1 84763 89 - 1
-------CAACGCUUUUUACGCACAAUUUUCCUUUGGCAA-GCAG-C------------GCGCGUUUGCC-AAAUGGAAUGUAAAUAUUUAUUU-UUAUUUGCAGUC---AGCCG
-------....(((..............((((((((((((-((..-.------------....)))))))-))).))))((((((((.......-.))))))))...---))).. ( -25.30)
>DroPse_CAF1 95944 95 - 1
--------CCUCCUUUUUACGCACAAUUUUCCUUUGGCAAAGUUUGCGCUCC-------GCGCGUUUGCC-AAAUUGAAUGUAAAUAUUUAUUU-UUAUUUGCAUCC---GAAUG
--------........................(((((((((...(((((...-------)))))))))))-)))(((.(((((((((.......-.))))))))).)---))... ( -24.00)
>DroWil_CAF1 79590 88 - 1
-------CGAUGCUUUUUACGCACAAUUUUCCUUUGGCAA-GUUG--------------GCGCGUUUG-CGAAAUUGAAUGCAAAUAUUUAUUUUUUAUUUGCAGCC---GCA-A
-------...(((.....((((.((((((.((...)).))-))))--------------..))))...-.......(..((((((((.........))))))))..)---)))-. ( -20.20)
>DroAna_CAF1 70428 105 - 1
CCGCUCCCCCUGCUUUUUACGCACAAUUUUCCUUUGGCA-AGUUGGCGCUCGCUG--------GUUUGUCGAAAUUGAAUGUAAAUAUUUAUUU-UUAUUUGCAUCUGUUGGCUG
..((.......)).......((.((((.....(((((((-((..(((....))).--------.))))))))).....(((((((((.......-.)))))))))..)))))).. ( -26.00)
>DroPer_CAF1 92319 98 - 1
-----CUGCCUCCUUUUUACGCACAAUUUUCCUUUGGCAAAGUUUGCGCUCC-------GCGCGUUUGCC-AAAUUGAAUGUAAAUAUUUAUUU-UUAUUUGCAUCC---GAAUG
-----...........................(((((((((...(((((...-------)))))))))))-)))(((.(((((((((.......-.))))))))).)---))... ( -24.00)
>consensus
_______CCCUGCUUUUUACGCACAAUUUUCCUUUGGCAAAGUUGGCGCUC________GCGCGUUUGCC_AAAUUGAAUGUAAAUAUUUAUUU_UUAUUUGCAUCC___GAAUG
....................((.(((.......))))).........................................((((((((.........))))))))........... ( -8.54 =  -8.40 +  -0.14)

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 12:30:43 2006