Locus 1031

Sequence ID 3L_DroMel_CAF1
Location 3,062,513 – 3,062,666
Length 153
Max. P 0.976119
window1591 window1592 window1593

overview

Window 1

Location 3,062,513 – 3,062,603
Length 90
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 74.44
Mean single sequence MFE -21.85
Consensus MFE -10.79
Energy contribution -10.60
Covariance contribution -0.19
Combinations/Pair 1.33
Mean z-score -2.37
Structure conservation index 0.49
SVM decision value 1.76
SVM RNA-class probability 0.976119
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3062513 90 + 23771897
GUGUGUACAUAUUUACACACAAUUUACAUUUCGUACGAUU-UCG------UUUUCGUAGUGGCUGUUG---CCAUUGCUAGUCAAGUUGAGUUUGCAGA-------U
(((((((......)))))))(((((((.....(.(((...-.))------)...)((((((((....)---)))))))..)).)))))...........-------. ( -23.20)
>DroSec_CAF1 23257 85 + 1
GUGUGUACAUAUUUACACACAAUUUACAUUUCGUACGAUU-UCG------UUUUCGUA-----CGAUU---UCAUUGCUCGUCAAGUUGAGUUUGCAGA-------U
(((((((......)))))))..........((((((((..-...------...)))))-----)))((---(((..(((((......))))).)).)))-------. ( -24.10)
>DroSim_CAF1 22827 85 + 1
GUGUGUACAUAUUUACACACAAUUUACAUUUCGUACGAUU-UCG------UUUUCGUA-----CGAUU---UCAUUGCUCGUCAAGUUGAGUUUGCAGA-------U
(((((((......)))))))..........((((((((..-...------...)))))-----)))((---(((..(((((......))))).)).)))-------. ( -24.10)
>DroEre_CAF1 23971 100 + 1
GUGUGUACAUAUUUACACACAAUUUACAUUUCGUACGUUU-UCAUUUUCGUUUUGGUAGUGCCUUUUG---CCAUUGCUCGUUAAGUUGGGUUUGAAGAUAUG---U
(((((((......)))))))................((((-(((..(((((..((((((......)))---)))..)).(.....)..)))..)))))))...---. ( -22.00)
>DroYak_CAF1 23447 100 + 1
GUGUGUACAUAUUUACACACAAUUUACAUUUCGUACGUUU-UCG------UUUGCGUAGUGCCUGUUGUUACCAUUGCUCGUCAAGUUGGGCUUGAAGUUAUAUGAU
(((((((......)))))))......((((.((((((...-.))------)..))).))))...........(((.(((..(((((.....))))))))...))).. ( -20.90)
>DroAna_CAF1 23772 70 + 1
AUGUGUACAUAUUUACACACAAUUUACAUUUCGGACGCUUGUGG------CUUUCGCA---------------AUUGUUUUGU---GUGAGCUU-------------
...............(((((((...(((.((((((.((.....)------).)))).)---------------).))).))))---))).....------------- ( -16.80)
>consensus
GUGUGUACAUAUUUACACACAAUUUACAUUUCGUACGAUU_UCG______UUUUCGUA_____UGUUG___CCAUUGCUCGUCAAGUUGAGUUUGCAGA_______U
(((((((......)))))))........................................................(((((......)))))............... (-10.79 = -10.60 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,062,513 – 3,062,603
Length 90
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 74.44
Mean single sequence MFE -16.48
Consensus MFE -6.95
Energy contribution -6.82
Covariance contribution -0.14
Combinations/Pair 1.14
Mean z-score -1.87
Structure conservation index 0.42
SVM decision value -0.05
SVM RNA-class probability 0.509292
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3062513 90 - 23771897
A-------UCUGCAAACUCAACUUGACUAGCAAUGG---CAACAGCCACUACGAAAA------CGA-AAUCGUACGAAAUGUAAAUUGUGUGUAAAUAUGUACACAC
.-------..((((...((..............(((---(....)))).(((((...------...-..))))).))..))))....(((((((......))))))) ( -17.20)
>DroSec_CAF1 23257 85 - 1
A-------UCUGCAAACUCAACUUGACGAGCAAUGA---AAUCG-----UACGAAAA------CGA-AAUCGUACGAAAUGUAAAUUGUGUGUAAAUAUGUACACAC
.-------..((((..(((........)))......---..(((-----(((((...------...-..))))))))..))))....(((((((......))))))) ( -20.90)
>DroSim_CAF1 22827 85 - 1
A-------UCUGCAAACUCAACUUGACGAGCAAUGA---AAUCG-----UACGAAAA------CGA-AAUCGUACGAAAUGUAAAUUGUGUGUAAAUAUGUACACAC
.-------..((((..(((........)))......---..(((-----(((((...------...-..))))))))..))))....(((((((......))))))) ( -20.90)
>DroEre_CAF1 23971 100 - 1
A---CAUAUCUUCAAACCCAACUUAACGAGCAAUGG---CAAAAGGCACUACCAAAACGAAAAUGA-AAACGUACGAAAUGUAAAUUGUGUGUAAAUAUGUACACAC
(---(((.((...................((....)---)....((.....)).............-........)).)))).....(((((((......))))))) ( -12.00)
>DroYak_CAF1 23447 100 - 1
AUCAUAUAACUUCAAGCCCAACUUGACGAGCAAUGGUAACAACAGGCACUACGCAAA------CGA-AAACGUACGAAAUGUAAAUUGUGUGUAAAUAUGUACACAC
....((((...(((((.....)))))((.((..((((..(....)..)))).))..(------((.-...))).))...))))....(((((((......))))))) ( -15.40)
>DroAna_CAF1 23772 70 - 1
-------------AAGCUCAC---ACAAAACAAU---------------UGCGAAAG------CCACAAGCGUCCGAAAUGUAAAUUGUGUGUAAAUAUGUACACAU
-------------.....(((---((((......---------------.((....)------).....((((.....))))...)))))))............... ( -12.50)
>consensus
A_______UCUGCAAACUCAACUUGACGAGCAAUGG___CAACA_____UACGAAAA______CGA_AAUCGUACGAAAUGUAAAUUGUGUGUAAAUAUGUACACAC
.......................................................................................(((((((......))))))) ( -6.95 =  -6.82 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,062,573 – 3,062,666
Length 93
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 83.72
Mean single sequence MFE -25.32
Consensus MFE -15.00
Energy contribution -15.44
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -2.27
Structure conservation index 0.59
SVM decision value 0.39
SVM RNA-class probability 0.717122
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3062573 93 + 23771897
G---CCAUUGCUAGUCAAGUUGAGUUUGCAGA-------UACAUGGAUGUAUUUCCAGCUAUGUAGAUGUUAUCUAGCGCAUGAA--AACCCCCCGACUUGACCU
.---.........(((((((((.(((((((..-------....((((......))))....)))))))(((.((........)).--)))....))))))))).. ( -23.60)
>DroSec_CAF1 23312 95 + 1
U---UCAUUGCUCGUCAAGUUGAGUUUGCAGA-------UACAUGGAUGUAUUUCCAGCUUUGUAGAUAUUAUCUAGCGCCUGAAAAAACCCCCCGACUUGACCU
.---.........(((((((((.(((((((((-------....((((......))))..)))))))))....((........))..........))))))))).. ( -23.40)
>DroSim_CAF1 22882 95 + 1
U---UCAUUGCUCGUCAAGUUGAGUUUGCAGA-------UACAUGGAUGUAUUUCCAGCUUUGUAGAUAUUAUCUAGCGCCUGAAAAAACCCCCCGACUUGACCU
.---.........(((((((((.(((((((((-------....((((......))))..)))))))))....((........))..........))))))))).. ( -23.40)
>DroEre_CAF1 24037 94 + 1
G---CCAUUGCUCGUUAAGUUGGGUUUGAAGAUAUG---UAUAUGCAUGUAUUUCCAGCU----AGAUAUUAUCUAGCACCUGAA-AAACCCCCCGACUUGACCU
.---.........(((((((((((...(((((((((---(....)))))).))))..(((----((((...))))))).......-......))))))))))).. ( -29.70)
>DroYak_CAF1 23507 99 + 1
GUUACCAUUGCUCGUCAAGUUGGGCUUGAAGUUAUAUGAUAUAUGAAUGUAUUUCCAGCU----AGAUAUUAACUAGCGUCU-AA-AAACCCCCCGACUUGACCU
.............(((((((((((...(((((.((((.........)))))))))..(((----((.......)))))....-..-......))))))))))).. ( -26.50)
>consensus
G___CCAUUGCUCGUCAAGUUGAGUUUGCAGA_______UACAUGGAUGUAUUUCCAGCU_UGUAGAUAUUAUCUAGCGCCUGAA_AAACCCCCCGACUUGACCU
.............(((((((((.....................((((......))))(((....((((...)))))))................))))))))).. (-15.00 = -15.44 +   0.44)

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 09:57:17 2006