Locus 133

Sequence ID 2L_DroMel_CAF1
Location 404,481 – 404,612
Length 131
Max. P 0.708082
window205 window206 window207

overview

Window 5

Location 404,481 – 404,572
Length 91
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 76.42
Mean single sequence MFE -24.07
Consensus MFE -13.43
Energy contribution -13.98
Covariance contribution 0.56
Combinations/Pair 1.26
Mean z-score -1.70
Structure conservation index 0.56
SVM decision value 0.37
SVM RNA-class probability 0.708082
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 404481 91 + 22407834
CAAUCUUGUACCUAUAGCAAGGUU-UCGUGCUAAUAGAUUUACUUCUAUGGCUAGCAUUUGGCCAAUUUGGGAGGUCCACAUGUGGAUUCCU
.....((((.......))))((((-..(((((((((((......)))))...))))))..)))).....(((((.((((....))))))))) ( -24.90)
>DroVir_CAF1 86 79 + 1
--GU----UGCCUGCCGCCAAGUAUAGACUUUAAUGUAAU-----ACUU--GCAGCAUCUGGCCAAUUUGGGUGCACCACAUGUGGACUCUU
--..----.((((((.((.((((((..((......)).))-----))))--)).)))...)))......((((.(((.....))).)))).. ( -21.40)
>DroSec_CAF1 99 91 + 1
CAAACUUGUACCUACAGCCAGGUG-UCGUGCUAAUAAAUUUCCCUCUAUGGCUAGCAUCUGGCCAAUUUGGGAGCUCCUCAUGUGGAUUCCU
((((..(((....)))((((((((-(...((((...............))))..)))))))))...))))((((.(((......))))))). ( -24.96)
>DroSim_CAF1 99 91 + 1
CAAACUUGUACCUACAGCCAGGUG-UAGUGCUAAUAAAUUUCCCUCUAUGGCUAGCAUCUGGCCAAUUUGGGAGCUCCUCAUGUGGAUUCCU
((((..(((....)))((((((((-(...((((...............))))..)))))))))...))))((((.(((......))))))). ( -24.96)
>DroEre_CAF1 99 91 + 1
CAAUUUUGUACCUGCCGUGCGGUU-UCGUGCUAAUACAUUUCUGUCUAUGGCUAGCAUCUGGCCAAUUUGGGAGCUCCACAUGUGGAUUCCU
.......((((.....))))((((-..((((((...(((........)))..))))))..)))).....(((((.((((....))))))))) ( -25.30)
>DroYak_CAF1 99 91 + 1
AAAUUUUGUACCCACCGUACGGUU-UCGUGCUCAUACACUUCUUUCUAUGGCUAGCAUUUGGCCAACUUGGGAGCUCCACAUGUGGAUUCCU
.......((.((((..(((((...-.))))).................(((((((...)))))))...)))).))((((....))))..... ( -22.90)
>consensus
CAAUCUUGUACCUACAGCCAGGUU_UCGUGCUAAUAAAUUUCCCUCUAUGGCUAGCAUCUGGCCAAUUUGGGAGCUCCACAUGUGGAUUCCU
.........((((......)))).........................(((((((...)))))))....(((((.(((......)))))))) (-13.43 = -13.98 +   0.56) 

alignment

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secondary structure

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dotplot

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Window 6

Location 404,511 – 404,612
Length 101
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 83.04
Mean single sequence MFE -31.57
Consensus MFE -22.24
Energy contribution -23.10
Covariance contribution 0.86
Combinations/Pair 1.25
Mean z-score -1.71
Structure conservation index 0.70
SVM decision value 0.09
SVM RNA-class probability 0.577742
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 404511 101 + 22407834
UAAUAGAUUUACUUCUAUGGCUAGCAUUUGGCCAAUUUGGGAGGUCCACAUGUGGAUUCCUUCGACGAGAUGCUGACCGUGGGACUGGAUAACUCGGCCAA
......(((((.((((((((.((((((((.(.(.....(((((.((((....)))))))))..).).)))))))).)))))))).)))))........... ( -31.90)
>DroVir_CAF1 111 94 + 1
UAAUGUAAU-----ACUU--GCAGCAUCUGGCCAAUUUGGGUGCACCACAUGUGGACUCUUUUGAUGAAAUGCUCAGCGUGGGCCUGGAGCAUGUGGCCAG
...((((..-----...)--)))....(((((((....((((.(((.....))).))))..........((((((.((....))...)))))).))))))) ( -30.10)
>DroSec_CAF1 129 101 + 1
UAAUAAAUUUCCCUCUAUGGCUAGCAUCUGGCCAAUUUGGGAGCUCCUCAUGUGGAUUCCUUCGACGAGAUGCUAACCGUGGGACUGGAUUACUCCGCCAA
.........((((...((((.((((((((.(.(.....(((((.(((......))))))))..).).)))))))).))))))))..(((....)))..... ( -32.30)
>DroSim_CAF1 129 101 + 1
UAAUAAAUUUCCCUCUAUGGCUAGCAUCUGGCCAAUUUGGGAGCUCCUCAUGUGGAUUCCUUCGACGAGAUGCUGACCGUGGGACUGGAUUACUCGGCCAA
.........(((.(((((((.((((((((.(.(.....(((((.(((......))))))))..).).)))))))).)))))))...)))............ ( -31.60)
>DroEre_CAF1 129 101 + 1
UAAUACAUUUCUGUCUAUGGCUAGCAUCUGGCCAAUUUGGGAGCUCCACAUGUGGAUUCCUUUGACGAGAUGUUGACCUUGGGACUGGAUAACACGGCCAA
....(((((((.(((..(((((((...)))))))....(((((.((((....)))))))))..))))))))))........((.(((.......))))).. ( -32.30)
>DroYak_CAF1 129 101 + 1
UCAUACACUUCUUUCUAUGGCUAGCAUUUGGCCAACUUGGGAGCUCCACAUGUGGAUUCCUUUGACGAGAUGCUGACCUUGGGACUGGAUAACGUGGCCAA
.....(((.((((((((.((.((((((((.(.(((...(((((.((((....)))))))))))).).)))))))).)).)))))..)))....)))..... ( -31.20)
>consensus
UAAUAAAUUUCCCUCUAUGGCUAGCAUCUGGCCAAUUUGGGAGCUCCACAUGUGGAUUCCUUCGACGAGAUGCUGACCGUGGGACUGGAUAACUCGGCCAA
.............(((((((.((((((((.(.(.....(((((.(((......))))))))..).).)))))))).)))))))..(((.........))). (-22.24 = -23.10 +   0.86) 

alignment

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secondary structure

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dotplot

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Window 7

Location 404,511 – 404,612
Length 101
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 83.04
Mean single sequence MFE -28.65
Consensus MFE -19.42
Energy contribution -20.95
Covariance contribution 1.53
Combinations/Pair 1.12
Mean z-score -1.60
Structure conservation index 0.68
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 404511 101 - 22407834
UUGGCCGAGUUAUCCAGUCCCACGGUCAGCAUCUCGUCGAAGGAAUCCACAUGUGGACCUCCCAAAUUGGCCAAAUGCUAGCCAUAGAAGUAAAUCUAUUA
(((((((((((..((........))..)))...........(((.((((....))))..)))....)))))))).........(((((......))))).. ( -24.00)
>DroVir_CAF1 111 94 - 1
CUGGCCACAUGCUCCAGGCCCACGCUGAGCAUUUCAUCAAAAGAGUCCACAUGUGGUGCACCCAAAUUGGCCAGAUGCUGC--AAGU-----AUUACAUUA
(((((((.((((((..(((....)))))))))............(((((....))).))........)))))))((((...--..))-----))....... ( -25.60)
>DroSec_CAF1 129 101 - 1
UUGGCGGAGUAAUCCAGUCCCACGGUUAGCAUCUCGUCGAAGGAAUCCACAUGAGGAGCUCCCAAAUUGGCCAGAUGCUAGCCAUAGAGGGAAAUUUAUUA
.....(((....)))..((((.((((((((((((.(((((.(((.(((......)))..)))....))))).)))))))))))...).))))......... ( -38.50)
>DroSim_CAF1 129 101 - 1
UUGGCCGAGUAAUCCAGUCCCACGGUCAGCAUCUCGUCGAAGGAAUCCACAUGAGGAGCUCCCAAAUUGGCCAGAUGCUAGCCAUAGAGGGAAAUUUAUUA
.......(((((.....((((.(((..(((((((.(((((.(((.(((......)))..)))....))))).)))))))..))...).))))...))))). ( -31.80)
>DroEre_CAF1 129 101 - 1
UUGGCCGUGUUAUCCAGUCCCAAGGUCAACAUCUCGUCAAAGGAAUCCACAUGUGGAGCUCCCAAAUUGGCCAGAUGCUAGCCAUAGACAGAAAUGUAUUA
((((((.((..((...))..)).))))))(((((.(((((.(((.((((....))))..)))....))))).)))))(((....)))(((....))).... ( -26.30)
>DroYak_CAF1 129 101 - 1
UUGGCCACGUUAUCCAGUCCCAAGGUCAGCAUCUCGUCAAAGGAAUCCACAUGUGGAGCUCCCAAGUUGGCCAAAUGCUAGCCAUAGAAAGAAGUGUAUGA
((((..((........)).))))((..(((((...(((((.(((.((((....))))..)))....)))))...)))))..)).................. ( -25.70)
>consensus
UUGGCCGAGUUAUCCAGUCCCACGGUCAGCAUCUCGUCAAAGGAAUCCACAUGUGGAGCUCCCAAAUUGGCCAGAUGCUAGCCAUAGAAGGAAAUGUAUUA
((((.........))))......(((.(((((((.(((((.(((.((((....))))..)))....))))).))))))).))).................. (-19.42 = -20.95 +   1.53) 

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 09:27:02 2006