Locus 4578

Sequence ID 2L_DroMel_CAF1
Location 13,125,788 – 13,125,934
Length 146
Max. P 0.959571
window7217 window7218

overview

Window 7

Location 13,125,788 – 13,125,906
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 89.68
Mean single sequence MFE -35.23
Consensus MFE -25.06
Energy contribution -28.14
Covariance contribution 3.08
Combinations/Pair 1.06
Mean z-score -2.85
Structure conservation index 0.71
SVM decision value 1.07
SVM RNA-class probability 0.910045
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13125788 118 + 22407834
UCAAUUUGCCUUUACUUUGAGCGGGCAGCAUGGGUUUUCUUUUUCUCUGGCCGGCUUUUCAUCGAAGUCUGACAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCAGCA
......(((((...........)))))((.((((..................((((((.....))))))..........(((((...)))))((((((....))))))...)))))). ( -29.20)
>DroSec_CAF1 18791 117 + 1
UCAAUUUGCCUUUACUUUGAGCUGGCAGCAUGUGGUUU-UUUUCCUCUGGCCGGCUUCUCAUCGAAGUCUGCCAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCAGCA
((((............))))(((((..((((((((...-....))..((((.((((((.....)))))).))))........)).))))...((((((....))))))....))))). ( -38.10)
>DroSim_CAF1 19882 117 + 1
UCAAUUUGCCUUUACUUUGAGCUGGCAGCAUGUGGUUU-UUUUUCUCUGGCCGGCUUCUCAUCGAAGUCUGCCAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCAGCA
((((............))))(((((..((((...((..-........((((.((((((.....)))))).))))........)).))))...((((((....))))))....))))). ( -37.67)
>DroEre_CAF1 20339 115 + 1
UCAAUUUGCCCUUACUUCGAGCGGGCAGCAUGGGGUUU-UU--GCUCUGGCCGGCUGCUCAUCGAAGUCUGCCAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCGCCA
....(((((....(((((((..(((((((.((((((..-..--))))))....))))))).))))))).(((.(......).)))..)))))((((((....)))))).......... ( -41.10)
>DroYak_CAF1 19208 105 + 1
UCAAUUUGCCUUUACUUUGAGCUGACAGGAUGGGGUUU-UUU-GCC-----------CUCAUCGAAGUCUGCCAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCAGCA
.....((((........((.((.(((..((((((((..-...-)))-----------).))))...))).))))........))))......((((((....)))))).......... ( -30.09)
>consensus
UCAAUUUGCCUUUACUUUGAGCUGGCAGCAUGGGGUUU_UUUUGCUCUGGCCGGCUUCUCAUCGAAGUCUGCCAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCAGCA
......((((.............))))((.(((((((..........((((.((((((.....)))))).)))).....(((((...)))))((((((....))))))))))))))). (-25.06 = -28.14 +   3.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,125,828 – 13,125,934
Length 106
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 85.30
Mean single sequence MFE -35.50
Consensus MFE -21.94
Energy contribution -24.42
Covariance contribution 2.48
Combinations/Pair 1.11
Mean z-score -3.45
Structure conservation index 0.62
SVM decision value 1.50
SVM RNA-class probability 0.959571
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13125828 106 + 22407834
UUUUCUCUGGCCGGCUUUUCAUCGAAGUCUGACAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCAGCAACAGCAUAUAUGCGAAAAAAAAAAAAA-----A
(((((.((((..((((((.....))))))..........(((((...)))))((((((....))))))....)))).....(((....)))))))).........-----. ( -24.40)
>DroSec_CAF1 18830 111 + 1
UUUCCUCUGGCCGGCUUCUCAUCGAAGUCUGCCAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCAGCAACAGCAUAUAUGCUGGAAUUAUAAUGGAGGGCG
..(((((((((.((((((.....)))))).))).(((((((...........((((((....))))))....((((((..........)))))))))))))..)))))).. ( -41.50)
>DroSim_CAF1 19921 111 + 1
UUUUCUCUGGCCGGCUUCUCAUCGAAGUCUGCCAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCAGCAACAGCAUAUAUGCUGGAAUUAUAAUGGAGGGCG
..(((((((((.((((((.....)))))).))).(((((((...........((((((....))))))....((((((..........)))))))))))))..)))))).. ( -38.70)
>DroEre_CAF1 20378 109 + 1
U--GCUCUGGCCGGCUGCUCAUCGAAGUCUGCCAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCGCCAACAGCAUACGUGGUGGAAUUAUAAUGGAGGGCG
.--((((((((.((((.........)))).))).(((((((...........((((((....))))))....((((((...(....).)))))))))))))....))))). ( -36.90)
>DroYak_CAF1 19247 99 + 1
UU-GCC-----------CUCAUCGAAGUCUGCCAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCAGCAACAGCAUACGUGGUGGAAUUAUAAUGGAGGGCG
..-(((-----------(((.......((..((((....(((((...)))))((((((....)))))).......((....))....))))..)).........)))))). ( -35.99)
>consensus
UUUGCUCUGGCCGGCUUCUCAUCGAAGUCUGCCAUAUAAUUUGCAAUGCAAACAGGACUCAUGUCCUGAAUCCCAGCAACAGCAUAUAUGCUGGAAUUAUAAUGGAGGGCG
.......((((.((((((.....)))))).)))).....(((((...)))))((((((....))))))....((((((..........))))))................. (-21.94 = -24.42 +   2.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:33 2006