Locus 3979

Sequence ID 2R_DroMel_CAF1
Location 13,131,608 – 13,131,799
Length 191
Max. P 0.854332
window6420 window6421 window6422

overview

Window 0

Location 13,131,608 – 13,131,698
Length 90
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 79.62
Mean single sequence MFE -23.08
Consensus MFE -18.48
Energy contribution -18.70
Covariance contribution 0.23
Combinations/Pair 1.20
Mean z-score -1.58
Structure conservation index 0.80
SVM decision value 0.80
SVM RNA-class probability 0.854332
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13131608 90 + 20766785
------------AUAUGACAUUUUUCCUUCUGCACUGUGGCAAGAGUAGCUAC-UGUAUCC--AGCGUAGCUCGCUCUAAUCCGCUGAAGGUAGAUCAAAUCGUU
------------..((((....((((((((......((((..(((((((((((-.((....--.)))))))).)))))...)))).))))).))).....)))). ( -24.90)
>DroPse_CAF1 25453 100 + 1
UAAAAUAU--UUA--UAUAGUUUUUCCUUCUGCGAUUGGGCAAGAGUUGUUGUGUAUUUCCCAAGCCUA-CAAACUCUAAUCCGCAAAAGGUAGAUCAAAUCGUU
........--...--....(.(((.((((.(((....(((..((((((((.(.((.........))).)-).))))))..)))))).)))).))).)........ ( -15.70)
>DroSec_CAF1 25474 102 + 1
UGAAAUUCUAUUAUAUAACAUUUUUCCUUCUGCACUGUGGCAAGAGUGGCUAC-UAUUUCC--AGCGUAGCUCGCUCUAAUCCGCAGAAGGUAGAUCAAAUCGUU
............................(((((.((((((..(((((((((((-.......--...))))).))))))...))))))...))))).......... ( -29.00)
>DroSim_CAF1 27362 102 + 1
UAAAAUUCUAUUAUAUAACAUUUUUCCUUCUGCACUGUGGCAAGAGUGGUUAC-UAUUUCC--AGCGUAGCUCGCUCUAAUCCGCAGAAGGUAGAUCAAAUCGUU
............................(((((.((((((..(((((((((((-.......--...))))).))))))...))))))...))))).......... ( -26.60)
>DroYak_CAF1 25821 90 + 1
UGA------------AAACAUUUUUCCUUCUGCACUGUGGCAAGAGUGGUUAC-UAUUUCC--AGCGUAGCUCGCUCUAAUCCGCAGAAGGUAGAUCAAAUCGUU
...------------.............(((((.((((((..(((((((((((-.......--...))))).))))))...))))))...))))).......... ( -26.60)
>DroPer_CAF1 25393 100 + 1
UAAAAUAU--UUA--UAUAGUUUUUCCUUCUGCGAUUGGGCAAGAGUUGUUGUGUAUUUCCCAAGCCUA-CAAACUCUAAUCCGCAAAAGGUAGAUCAAAUCGUU
........--...--....(.(((.((((.(((....(((..((((((((.(.((.........))).)-).))))))..)))))).)))).))).)........ ( -15.70)
>consensus
UAAAAU____UUA__UAACAUUUUUCCUUCUGCACUGUGGCAAGAGUGGUUAC_UAUUUCC__AGCGUAGCUCGCUCUAAUCCGCAGAAGGUAGAUCAAAUCGUU
...................((((..((((((((.....((..(((((((((((.............))))).))))))...)))))))))).))))......... (-18.48 = -18.70 +   0.23)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,131,608 – 13,131,698
Length 90
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 79.62
Mean single sequence MFE -22.09
Consensus MFE -16.55
Energy contribution -15.50
Covariance contribution -1.05
Combinations/Pair 1.35
Mean z-score -1.16
Structure conservation index 0.75
SVM decision value 0.21
SVM RNA-class probability 0.633375
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13131608 90 - 20766785
AACGAUUUGAUCUACCUUCAGCGGAUUAGAGCGAGCUACGCU--GGAUACA-GUAGCUACUCUUGCCACAGUGCAGAAGGAAAAAUGUCAUAU------------
...(((........(((((.((((...((((..((((..(((--(....))-)))))).))))..)).....)).)))))......)))....------------ ( -22.54)
>DroPse_CAF1 25453 100 - 1
AACGAUUUGAUCUACCUUUUGCGGAUUAGAGUUUG-UAGGCUUGGGAAAUACACAACAACUCUUGCCCAAUCGCAGAAGGAAAAACUAUA--UAA--AUAUUUUA
..............((((((((((...((((((((-((..(....)...))))....)))))).......))))))))))..........--...--........ ( -20.10)
>DroSec_CAF1 25474 102 - 1
AACGAUUUGAUCUACCUUCUGCGGAUUAGAGCGAGCUACGCU--GGAAAUA-GUAGCCACUCUUGCCACAGUGCAGAAGGAAAAAUGUUAUAUAAUAGAAUUUCA
..............((((((((((...((((.(.(((((...--.......-)))))).))))..)).....))))))))......................... ( -27.20)
>DroSim_CAF1 27362 102 - 1
AACGAUUUGAUCUACCUUCUGCGGAUUAGAGCGAGCUACGCU--GGAAAUA-GUAACCACUCUUGCCACAGUGCAGAAGGAAAAAUGUUAUAUAAUAGAAUUUUA
..............(((((((((......((((.....))))--((.((.(-((....))).)).))....)))))))))......................... ( -21.30)
>DroYak_CAF1 25821 90 - 1
AACGAUUUGAUCUACCUUCUGCGGAUUAGAGCGAGCUACGCU--GGAAAUA-GUAACCACUCUUGCCACAGUGCAGAAGGAAAAAUGUUU------------UCA
..............(((((((((......((((.....))))--((.((.(-((....))).)).))....)))))))))..........------------... ( -21.30)
>DroPer_CAF1 25393 100 - 1
AACGAUUUGAUCUACCUUUUGCGGAUUAGAGUUUG-UAGGCUUGGGAAAUACACAACAACUCUUGCCCAAUCGCAGAAGGAAAAACUAUA--UAA--AUAUUUUA
..............((((((((((...((((((((-((..(....)...))))....)))))).......))))))))))..........--...--........ ( -20.10)
>consensus
AACGAUUUGAUCUACCUUCUGCGGAUUAGAGCGAGCUACGCU__GGAAAUA_GUAACCACUCUUGCCACAGUGCAGAAGGAAAAAUGUUA__UAA____AUUUUA
..............(((((((((......((((.....))))..........((((......)))).....)))))))))......................... (-16.55 = -15.50 +  -1.05)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,131,698 – 13,131,799
Length 101
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 78.46
Mean single sequence MFE -21.85
Consensus MFE -16.20
Energy contribution -15.95
Covariance contribution -0.25
Combinations/Pair 1.23
Mean z-score -0.98
Structure conservation index 0.74
SVM decision value 0.06
SVM RNA-class probability 0.565772
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13131698 101 + 20766785
CAUCCUCCAUUGCCGUUGAC-ACUGCACUAGUGUUCCAUAUAUCUAAGUGGGCAUUGCAGUU-CGUAUGUGGGUGAAUACACUUUGUUUUUCUU-----U-UCCAACUA-------
..((.(((((......(((.-((((((...((((.((((........)))))))))))))))-))...))))).))..................-----.-........------- ( -20.30)
>DroVir_CAF1 31297 112 + 1
CAUUCUCAUCUGCCGUUGAC-UCUGCACUAUUGUUCCAUU-UCAUAAGUGAGCAUUGCAGAU-CUGACGUGAGUGAAUACAUUUUUUUUUUUUGCUAUUA-CGUAAAUGAGUGAAU
((((((((.((..(((((..-((((((....(((((.(((-.....)))))))).)))))).-.)))))..)))))..............(((((.....-.))))).)))))... ( -24.40)
>DroSim_CAF1 27464 101 + 1
CAUCCUCCAUUGCCGUUGAC-ACUGCACUAGUGUUCCAUAUAACUAAGUGGGCAUUGCAGUU-CGUAUGUGGGUGAAUACACUUUGUUUUUAUU-----U-UCCAACUA-------
..((.(((((......(((.-((((((...((((.((((........)))))))))))))))-))...))))).))..................-----.-........------- ( -20.30)
>DroEre_CAF1 25894 103 + 1
CAUCCUCCAUUGCCGUUGAC-GCUGCACUAGUGUUCCAUAUAUCUAAGUGGGCAUUGCAGUU-CG-ACCUGGCUGAAUACACUUCUUUUUUCUUCU--UU-UGCAACUA-------
...........((((((((.-((((((...((((.((((........)))))))))))))))-))-))..))).......................--..-........------- ( -22.60)
>DroYak_CAF1 25911 105 + 1
CAUCCUCCAUUGCCGUUGAC-ACUGCACUAGUGUUCCAUAUAUCUAAGUGGGCAUUGCAGUU-CGUAUGUGGGUGAAUACACUUUGUUUUUCUUCU--UGCCACAACUA-------
..............((((..-((((((...((((.((((........)))))))))))))).-.....(..((.(((.((.....))..)))..))--..)..))))..------- ( -21.30)
>DroAna_CAF1 25864 95 + 1
CAUCCU----UUCCGUUGACCGCUGCACUA-UGUUCCAUCCA--UAAGUGGACAUUGCAGUUUCUGAUGUGGGUGAAUACACUUU-UAUAUAUU-----U-UGUAAGUA-------
(((((.----...(((((...((((((..(-(((.((((...--...))))))))))))))...))))).)))))........((-((((....-----.-))))))..------- ( -22.20)
>consensus
CAUCCUCCAUUGCCGUUGAC_ACUGCACUAGUGUUCCAUAUAUCUAAGUGGGCAUUGCAGUU_CGUAUGUGGGUGAAUACACUUUGUUUUUCUU_____U_UGCAACUA_______
(((((........(((.....((((((...((((.((((........)))))))))))))).....))).)))))......................................... (-16.20 = -15.95 +  -0.25)

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 11:08:49 2006