Locus 8734

Sequence ID	3R_DroMel_CAF1
Location	23,321,434 – 23,321,529
Length	95
Max. P	0.973295

overview

Window 0

Location	23,321,434 – 23,321,529
Length	95
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	79.24
Mean single sequence MFE	-26.82
Consensus MFE	-16.28
Energy contribution	-16.62
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.90
Structure conservation index	0.61
SVM decision value	1.71
SVM RNA-class probability	0.973295
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23321434 95 + 27905053
AG-------------UAGG---------GCAUCAAAUUGCCGCCUAAUGGUAAUUUGAUGAAACUAAUUUGAUAACAAAUUCAAUUUGAGAAUACCCAAACUCUAGACAUUGCCCAA
..-------------..((---------((((((((((((((.....))))))))))))....((...((((........))))....)).....................)))).. ( -23.90)
>DroPse_CAF1 120900 117 + 1
GGAGCAGAACAGUCGCAGGGUAGUGGCAUCAUCAAAUUGCCGCCUAAUGGUAAUUUGAUGCAACUAAUUUGAUAACAAAUUCAAUUUCAAAGUACCAGAACUGUGGACGAACCCCAA
...........(((.((.(((..(((...(((((((((((((.....))))))))))))).....((((((....)))))).............)))..))).)))))......... ( -28.30)
>DroSim_CAF1 123135 95 + 1
AG-------------UAGG---------GCAUCAAAAUGCCGCCUUAUGGUAAUUUGAUGAAACUAAUUUGAUAACAAAUUCAAUUUGAGAGUACCCAAACUCCAGACGUUGCCCAA
..-------------..((---------((((((((.(((((.....))))).))))))..(((.((((((....))))))...((((.((((......)))))))).))))))).. ( -25.20)
>DroYak_CAF1 130139 95 + 1
AG-------------UAGG---------GCAUCAAAUUGCCGCCUAAUGGUAAUUUGAUGAAACUAAUUUGAUAACAAAUUCAAUUUGAGAGUACCCAAACUCUAGACGUUGGCCAA
..-------------...(---------((((((((((((((.....))))))))))))......((((((....))))))((((...(((((......)))))....))))))).. ( -25.60)
>DroAna_CAF1 114500 94 + 1
-G-------------UAGA---------GCAUCAAAUUGCCGCCUAAUGGUAAUUUGAUGCAACUAAUUUGAUAACAAAUUCAAUUUCAAAGUGACAAAACUGUAGACGUUGGCCAA
-.-------------....---------((((((((((((((.....))))))))))))))....((((((....))))))((((.((..(((......)))...)).))))..... ( -25.60)
>DroPer_CAF1 121383 117 + 1
GGAGCAGAACAGUCGCAGGGUGGUGGCAUCAUCAAAUUGCCGCCUAAUGGUAAUUUGAUGCAACUAAUUUGAUAACAAAUUCAAUUUCAAAGUGCCAGAACUGUAGACGAACCCCAA
...........(((..(.(((..(((((((((((((((((((.....))))))))))))).....((((((....))))))..........))))))..))).).)))......... ( -32.30)
>consensus
AG_____________UAGG_________GCAUCAAAUUGCCGCCUAAUGGUAAUUUGAUGAAACUAAUUUGAUAACAAAUUCAAUUUCAAAGUACCAAAACUCUAGACGUUGCCCAA
.................((..........(((((((((((((.....))))))))))))).....((((((....))))))................................)).. (-16.28 = -16.62 +   0.33)

alignment

secondary structure

dotplot

Window 1

Location	23,321,434 – 23,321,529
Length	95
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	79.24
Mean single sequence MFE	-24.13
Consensus MFE	-15.02
Energy contribution	-14.88
Covariance contribution	-0.14
Combinations/Pair	1.11
Mean z-score	-1.43
Structure conservation index	0.62
SVM decision value	0.04
SVM RNA-class probability	0.555893
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23321434 95 - 27905053
UUGGGCAAUGUCUAGAGUUUGGGUAUUCUCAAAUUGAAUUUGUUAUCAAAUUAGUUUCAUCAAAUUACCAUUAGGCGGCAAUUUGAUGC---------CCUA-------------CU
..((((.........((((((((....)))))))).((((((....))))))......((((((((.((.......)).))))))))))---------))..-------------.. ( -24.00)
>DroPse_CAF1 120900 117 - 1
UUGGGGUUCGUCCACAGUUCUGGUACUUUGAAAUUGAAUUUGUUAUCAAAUUAGUUGCAUCAAAUUACCAUUAGGCGGCAAUUUGAUGAUGCCACUACCCUGCGACUGUUCUGCUCC
..(((((.((((((..((..(((((......((((((.((((....)))))))))).(((((((((.((.......)).))))))))).)))))..))..)).))).)....))))) ( -28.60)
>DroSim_CAF1 123135 95 - 1
UUGGGCAACGUCUGGAGUUUGGGUACUCUCAAAUUGAAUUUGUUAUCAAAUUAGUUUCAUCAAAUUACCAUAAGGCGGCAUUUUGAUGC---------CCUA-------------CU
..(((((.(((((((((((((((....)))))))).((((((....))))))...............))...))))).(.....).)))---------))..-------------.. ( -22.10)
>DroYak_CAF1 130139 95 - 1
UUGGCCAACGUCUAGAGUUUGGGUACUCUCAAAUUGAAUUUGUUAUCAAAUUAGUUUCAUCAAAUUACCAUUAGGCGGCAAUUUGAUGC---------CCUA-------------CU
..(((.(((......((((((((....)))))))).((((((....)))))).)))..((((((((.((.......)).))))))))))---------)...-------------.. ( -20.10)
>DroAna_CAF1 114500 94 - 1
UUGGCCAACGUCUACAGUUUUGUCACUUUGAAAUUGAAUUUGUUAUCAAAUUAGUUGCAUCAAAUUACCAUUAGGCGGCAAUUUGAUGC---------UCUA-------------C-
((((..((((....((((((((......))))))))....)))).))))..(((..((((((((((.((.......)).))))))))))---------.)))-------------.- ( -21.50)
>DroPer_CAF1 121383 117 - 1
UUGGGGUUCGUCUACAGUUCUGGCACUUUGAAAUUGAAUUUGUUAUCAAAUUAGUUGCAUCAAAUUACCAUUAGGCGGCAAUUUGAUGAUGCCACCACCCUGCGACUGUUCUGCUCC
..(((((......((((((.(((((......((((((.((((....)))))))))).(((((((((.((.......)).))))))))).))))).........))))))...))))) ( -28.50)
>consensus
UUGGGCAACGUCUACAGUUUGGGUACUCUCAAAUUGAAUUUGUUAUCAAAUUAGUUGCAUCAAAUUACCAUUAGGCGGCAAUUUGAUGC_________CCUA_____________CU
..((...........((((((((....)))))))).((((((....)))))).....(((((((((.((.......)).)))))))))..........))................. (-15.02 = -14.88 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:28 2006