Locus 1227

Sequence ID 2R_DroMel_CAF1
Location 4,840,340 – 4,840,500
Length 160
Max. P 0.981009
window2132 window2133

overview

Window 2

Location 4,840,340 – 4,840,460
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.00
Mean single sequence MFE -29.35
Consensus MFE -24.50
Energy contribution -24.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.17
Structure conservation index 0.83
SVM decision value 1.88
SVM RNA-class probability 0.981009
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4840340 120 - 20766785
UGCGCAAGCGGUGAAGUUAUUUCCUAUUCAUAAUUUCACUGCGACUCCAAGUCUACCAUCAGUUUAUCCGCUUCUAAGUGCACUGAAAAAAUAUAAAGAGUAAUUCAUAAAAUAUGCAAA
...(((.(((((((((((((.........))))))))))))).((((...........(((((.....((((....)))).)))))...........)))).............)))... ( -26.95)
>DroSim_CAF1 994 120 - 1
UGCGCAAGCGGUGAAGUUAUUUCCUAUUCAUAAUUUCACUGCGACUCCAAGUCGACCAUCAGUACAUCCGCUUCUAAGUGCACUGAAAAAAUAUUAAGAGUUAUUCAUAAAAUAUGCACA
.(.(((.(((((((((((((.........)))))))))))))(((((..(((......(((((.(((..........))).)))))......)))..)))))............))).). ( -28.40)
>DroYak_CAF1 1322 114 - 1
UGCGCAAGCGGUGAAGUUAUUUCCUAUUCAUAAUUUCACUGCGACUCCAGGUCUACCAUUUGUAUAUUCUAUUCUAAGUGCACUGUAAAAAG-UGUACAGUUAUUGCAAAAUUCU-----
...(((((((((((((((((.........)))))))))))))((((...((....))....................(((((((......))-))))))))).))))........----- ( -32.70)
>consensus
UGCGCAAGCGGUGAAGUUAUUUCCUAUUCAUAAUUUCACUGCGACUCCAAGUCUACCAUCAGUAUAUCCGCUUCUAAGUGCACUGAAAAAAUAUAAAGAGUUAUUCAUAAAAUAUGCA_A
(((((..(((((((((((((.........)))))))))))))(((.....)))........................)))))...................................... (-24.50 = -24.50 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 4,840,380 – 4,840,500
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.13
Mean single sequence MFE -35.43
Consensus MFE -28.95
Energy contribution -29.07
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.11
Structure conservation index 0.82
SVM decision value 0.12
SVM RNA-class probability 0.592269
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4840380 120 - 20766785
GGAUUGAUAUAGGGGGGGUGUAGUCGACGCAUACAAAACGUGCGCAAGCGGUGAAGUUAUUUCCUAUUCAUAAUUUCACUGCGACUCCAAGUCUACCAUCAGUUUAUCCGCUUCUAAGUG
((((((((...((..((.((.(((((.(((((.......))))))..(((((((((((((.........))))))))))))))))).))..))..))))))))))...((((....)))) ( -36.80)
>DroSim_CAF1 1034 116 - 1
GGAUUGAUAU----GGGGUGUAGUCGACGCAUACAAAACGUGCGCAAGCGGUGAAGUUAUUUCCUAUUCAUAAUUUCACUGCGACUCCAAGUCGACCAUCAGUACAUCCGCUUCUAAGUG
((.(((((.(----(((((......(.(((((.......))))))..(((((((((((((.........))))))))))))).)))))).)))))))...........((((....)))) ( -37.10)
>DroYak_CAF1 1356 115 - 1
GGAUUGAUAU-----GGGUGUAGUCGACGCAUACAAAACGUGCGCAAGCGGUGAAGUUAUUUCCUAUUCAUAAUUUCACUGCGACUCCAGGUCUACCAUUUGUAUAUUCUAUUCUAAGUG
(((...((((-----..(((.(((((.(((((.......))))))..(((((((((((((.........))))))))))))))))).).((....))))..))))..))).......... ( -32.40)
>consensus
GGAUUGAUAU____GGGGUGUAGUCGACGCAUACAAAACGUGCGCAAGCGGUGAAGUUAUUUCCUAUUCAUAAUUUCACUGCGACUCCAAGUCUACCAUCAGUAUAUCCGCUUCUAAGUG
((((...(((.....((.((.(((((.(((((.......))))))..(((((((((((((.........))))))))))))))))).))......))....))).))))........... (-28.95 = -29.07 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:31 2006