Locus 8510

Sequence ID 3L_DroMel_CAF1
Location 22,301,523 – 22,301,658
Length 135
Max. P 0.691655
window13928 window13929

overview

Window 8

Location 22,301,523 – 22,301,628
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.90
Mean single sequence MFE -30.02
Consensus MFE -17.62
Energy contribution -19.82
Covariance contribution 2.20
Combinations/Pair 1.14
Mean z-score -1.91
Structure conservation index 0.59
SVM decision value 0.13
SVM RNA-class probability 0.596362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22301523 105 + 23771897
ACUUCGUACACCCUGCAGCCUGGCAUCCC-GGGGCUUUUAGCUAUGGCACUUGAGUCAUGUUAAUGAGUCUAAUAUUGAAAUUAAUAUAAAUAUCAAUAGCCGCAA--------------
.............(((..(((((....))-)))((.....))...(((....((.((((....)))).))...((((((.(((......))).)))))))))))).-------------- ( -25.20)
>DroSec_CAF1 60128 119 + 1
ACUUCGUACACCCUGCAGCCUGGCAUCCC-GUGGCUUUUAGCUAUGUCACUUGAGUCAUGUUAAUGAGUCUAAUAUUGAAAUUAAUAUAAAUUUCAAUGGCCGCAAUUUGAGCGGUGAGG
........((((((.(((..((((....(-(((((.....))))))......((.((((....)))).))...((((((((((......))))))))))))))....))))).))))... ( -31.20)
>DroSim_CAF1 42193 119 + 1
ACUUCGUACACCCUGCAGCCUGGCAUCCC-GUGGCUUUUAGCUAUGGCACUUGAGUCAUGUUAAUGAGUCUAAUAUUGAAAUUAAUAUAAAUUUCAAUGGCCGCAAUUUGAGCGGUGAGG
........((((((.(((..((((...((-(((((.....))))))).....((.((((....)))).))...((((((((((......))))))))))))))....))))).))))... ( -34.30)
>DroEre_CAF1 58633 95 + 1
-CUUCCUACACCCUGCCGCCUGGUAGCCC-GGGGCUUUUAGCUAUGGCACUUGAGUCAUGCUAAUGAGUCUAGUAUUGCAAUUAAUAUAAAUUUC------------------GG-----
-...........(((((....))))).((-((((((((((((.(((((......)))))))))).)))))).((((((....))))))......)------------------))----- ( -24.90)
>DroYak_CAF1 24920 114 + 1
-CUUCCUACACCCUGCCGCCUGGCCUCCCAGGGACUUUUAGCUAUGGCACUUUAGUCAUGCUAAUUAGUCCAAUAUUGAAAUUAAUACAAAUUUCAAUGCCCGCAAUUUGAGCGG-----
-..............((((((((....))))(((((.(((((.(((((......))))))))))..)))))..((((((((((......))))))))))............))))----- ( -34.50)
>consensus
ACUUCGUACACCCUGCAGCCUGGCAUCCC_GGGGCUUUUAGCUAUGGCACUUGAGUCAUGUUAAUGAGUCUAAUAUUGAAAUUAAUAUAAAUUUCAAUGGCCGCAAUUUGAGCGG_____
.....................(((.......(((((((((((.(((((......)))))))))).))))))..((((((((((......))))))))))))).................. (-17.62 = -19.82 +   2.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,301,562 – 22,301,658
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.12
Mean single sequence MFE -24.20
Consensus MFE -10.50
Energy contribution -13.56
Covariance contribution 3.06
Combinations/Pair 1.10
Mean z-score -1.94
Structure conservation index 0.43
SVM decision value 0.33
SVM RNA-class probability 0.691655
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22301562 96 + 23771897
GCUAUGGCACUUGAGUCAUGUUAAUGAGUCUAAUAUUGAAAUUAAUAUAAAUAUCAAUAGCCGCAA---------------------GAGAAACAUGCAGUUAAGUAAACAA---GAACA
(((..(((....((.((((....)))).))...((((((.(((......))).)))))))))(((.---------------------(.....).))).....)))......---..... ( -17.50)
>DroSec_CAF1 60167 117 + 1
GCUAUGUCACUUGAGUCAUGUUAAUGAGUCUAAUAUUGAAAUUAAUAUAAAUUUCAAUGGCCGCAAUUUGAGCGGUGAGGUGGCAGAGGAGAACAUACAGUUAAGUAAACGA---GAACA
.((.((((((((((.((((....)))).))...((((((((((......))))))))))(((((.......))))).)))))))).))...........(((..(....)..---.))). ( -31.30)
>DroSim_CAF1 42232 117 + 1
GCUAUGGCACUUGAGUCAUGUUAAUGAGUCUAAUAUUGAAAUUAAUAUAAAUUUCAAUGGCCGCAAUUUGAGCGGUGAGGGGGCAGAGGAGAACAUGCAGUUAAGUAAACAA---GAACA
((....))((((((.(((((((.....((((..((((((((((......))))))))))(((((.......)))))....)))).......)))))).).))))))......---..... ( -30.30)
>DroEre_CAF1 58671 89 + 1
GCUAUGGCACUUGAGUCAUGCUAAUGAGUCUAGUAUUGCAAUUAAUAUAAAUUUC------------------GG--------AA--GAGGAACAUGCAGUUAAGUACACAA---GAACA
((.((((((((.((.((((....)))).)).)))...))............((((------------------..--------..--))))..)))))..............---..... ( -16.30)
>DroYak_CAF1 24959 110 + 1
GCUAUGGCACUUUAGUCAUGCUAAUUAGUCCAAUAUUGAAAUUAAUACAAAUUUCAAUGCCCGCAAUUUGAGCGG--------AG--GAGGAACAUGCAGUUAGGCAAACAAGAAGAACA
((((((((......)))))((...((..(((..((((((((((......)))))))))).((((.......))))--------.)--))..))...)).....))).............. ( -25.60)
>consensus
GCUAUGGCACUUGAGUCAUGUUAAUGAGUCUAAUAUUGAAAUUAAUAUAAAUUUCAAUGGCCGCAAUUUGAGCGG________AA__GAGGAACAUGCAGUUAAGUAAACAA___GAACA
....((..((((((.(((((((...........((((((((((......)))))))))).((((.......))))................)))))).).))))))...))......... (-10.50 = -13.56 +   3.06)

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 13:17:28 2006