Locus 8550

Sequence ID 3R_DroMel_CAF1
Location 22,820,044 – 22,820,153
Length 109
Max. P 0.916075
window13740 window13741

overview

Window 0

Location 22,820,044 – 22,820,153
Length 109
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 89.69
Mean single sequence MFE -34.86
Consensus MFE -30.00
Energy contribution -29.60
Covariance contribution -0.40
Combinations/Pair 1.13
Mean z-score -1.68
Structure conservation index 0.86
SVM decision value 1.11
SVM RNA-class probability 0.916075
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22820044 109 + 27905053
-----AGCCAGCAAUUUAAGUGCGCUCCAAUUGUGAAAAUAACACUUGGCGCACUUGGCCGAAGGUUGCGGCUGCUGCAUCUUUCAGAUGCGAGAUAUGAGAUACGAGCUACGA
-----((((((((...((((((((((....((((....)))).....))))))))))((((.......))))))))(((((.....)))))..............).))).... ( -35.40)
>DroSec_CAF1 28935 109 + 1
-----AGCCAGCGAUUUAAGUGCGCUCCAAUUGUGAAAAUAACACUUGGCGCACUUGGCCGAAGGUUGCGGCUGCUGCAUCUUUCAGAUGCGAGAUAUGAGAUACGAGAUGCGA
-----((((.((((((((((((((((....((((....)))).....))))))))))......))))))))))..(((((((((((...........))).....)))))))). ( -34.30)
>DroSim_CAF1 29248 109 + 1
-----AGCCAGCGAUUUAAGUGCGCUCCAAUUGUGAAAAUAACACUUGGCGUACUUGGCCGAAGGUUGCGGCUGCUGCAUCUCUCAGAUGCGAGAUAUGAGAUACGAGAUGCGA
-----((((.((((((((((((((((....((((....)))).....))))))))))......))))))))))..(((((((((((...........))).....)))))))). ( -33.90)
>DroEre_CAF1 29030 99 + 1
-----AGCCAGUGAUUUAAGUGCGCUCCAAUUGUGAAAAUAACACUUGGCGCACUUGGCCGAAGGUUGCGGCUGCUGCAUCUUUC------GAGAUGCGAGAUACGAGAU----
-----(((.........(((((((((....((((....)))).....)))))))))(((((.......))))))))((((((...------.))))))............---- ( -31.90)
>DroYak_CAF1 29265 110 + 1
UUUCAAGCCAGCGAUUUAAGUGCGCUCCAAUUGUGAAAAUAACACUUGGCGCACUUGGCCGAAGGUUGCGGCUGCUGCAUCUUUCAGAUGCUAGAUGCGCGAUAUGAGAU----
(((((((((.((((((((((((((((....((((....)))).....))))))))))......))))))))))((.((((((..(....)..))))))))....))))).---- ( -38.80)
>consensus
_____AGCCAGCGAUUUAAGUGCGCUCCAAUUGUGAAAAUAACACUUGGCGCACUUGGCCGAAGGUUGCGGCUGCUGCAUCUUUCAGAUGCGAGAUAUGAGAUACGAGAU_CGA
......((.((((...(((((((((..(((.(((.......))).))))))))))))((((.......))))))))))(((((........))))).................. (-30.00 = -29.60 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 22,820,044 – 22,820,153
Length 109
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 89.69
Mean single sequence MFE -30.77
Consensus MFE -24.46
Energy contribution -24.82
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.68
Structure conservation index 0.79
SVM decision value 0.56
SVM RNA-class probability 0.780821
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22820044 109 - 27905053
UCGUAGCUCGUAUCUCAUAUCUCGCAUCUGAAAGAUGCAGCAGCCGCAACCUUCGGCCAAGUGCGCCAAGUGUUAUUUUCACAAUUGGAGCGCACUUAAAUUGCUGGCU-----
....((((...............(((((.....)))))((((((((.......)))).(((((((((((.(((.......))).)))..))))))))....))))))))----- ( -32.30)
>DroSec_CAF1 28935 109 - 1
UCGCAUCUCGUAUCUCAUAUCUCGCAUCUGAAAGAUGCAGCAGCCGCAACCUUCGGCCAAGUGCGCCAAGUGUUAUUUUCACAAUUGGAGCGCACUUAAAUCGCUGGCU-----
..((...................(((((.....)))))(((.((((.......)))).(((((((((((.(((.......))).)))..)))))))).....))).)).----- ( -31.20)
>DroSim_CAF1 29248 109 - 1
UCGCAUCUCGUAUCUCAUAUCUCGCAUCUGAGAGAUGCAGCAGCCGCAACCUUCGGCCAAGUACGCCAAGUGUUAUUUUCACAAUUGGAGCGCACUUAAAUCGCUGGCU-----
..(((((((......................)))))))...((((((.......(((.......)))((((((...(((((....))))).)))))).....)).))))----- ( -28.35)
>DroEre_CAF1 29030 99 - 1
----AUCUCGUAUCUCGCAUCUC------GAAAGAUGCAGCAGCCGCAACCUUCGGCCAAGUGCGCCAAGUGUUAUUUUCACAAUUGGAGCGCACUUAAAUCACUGGCU-----
----............((((((.------...))))))(((.((((.......)))).(((((((((((.(((.......))).)))..)))))))).........)))----- ( -28.80)
>DroYak_CAF1 29265 110 - 1
----AUCUCAUAUCGCGCAUCUAGCAUCUGAAAGAUGCAGCAGCCGCAACCUUCGGCCAAGUGCGCCAAGUGUUAUUUUCACAAUUGGAGCGCACUUAAAUCGCUGGCUUGAAA
----...(((....((((((((..(....)..)))))).))((((((...(....)..(((((((((((.(((.......))).)))..)))))))).....)).))))))).. ( -33.20)
>consensus
UCG_AUCUCGUAUCUCAUAUCUCGCAUCUGAAAGAUGCAGCAGCCGCAACCUUCGGCCAAGUGCGCCAAGUGUUAUUUUCACAAUUGGAGCGCACUUAAAUCGCUGGCU_____
.................(((((..(....)..)))))((((.((((.......)))).(((((((((((.(((.......))).)))..)))))))).....))))........ (-24.46 = -24.82 +   0.36)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:54 2006