Locus 3017

Sequence ID 3L_DroMel_CAF1
Location 8,668,010 – 8,668,171
Length 161
Max. P 0.999969
window4704 window4705 window4706

overview

Window 4

Location 8,668,010 – 8,668,108
Length 98
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 92.26
Mean single sequence MFE -16.90
Consensus MFE -14.48
Energy contribution -14.32
Covariance contribution -0.16
Combinations/Pair 1.06
Mean z-score -1.29
Structure conservation index 0.86
SVM decision value 0.22
SVM RNA-class probability 0.639596
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8668010 98 + 23771897
UGAAUUCACACGCUUCGUUGUGGUUUAUUGUAU---UUUUUUCCAUAUAAUUUAUAUAUCAUUUGAUUGUAUUCCACUUCGUGGAAUUUGCGGCGACAUUC
.((((((.(.(((.(((..(((((..(((((((---........)))))))......))))).)))....(((((((...)))))))..)))).)).)))) ( -17.10)
>DroSec_CAF1 55872 98 + 1
UGAAUUCACACGCUUCGUUGUGGUUUAUUGUAU---UUUUUUCCAUAUAUUUUAUAUUUCAUUUUAUUGUAUUCCACUUCGUGGAAUUCGCGGCGACAUUC
.((((((.((((.......((((..(((.(((.---........(((.....))).........))).)))..))))..))))))))))..(....).... ( -17.07)
>DroSim_CAF1 56227 98 + 1
UGAAUUCACACGCUUCAUUGUGGUUUAUUGUAU---UUUUUUCCAUAUAUUUUAUAUUUCAUUUGAUUGUAUUCCACUUCGUGGAAUUCGCGGCGACAUUC
.((((((.(.(((.(((..((((..(((.((((---..........))))...)))..)))).)))..(.(((((((...))))))).))))).)).)))) ( -17.70)
>DroEre_CAF1 57245 100 + 1
UGAAUUCACACGCU-CAUUGUGGUUUAUUGUACGUAUUUCUUCCAUCUAUUUUUUAUUCCAUUUGAUUGUAUUCCACUUCGUGGAAUUCGCGGCGACAUUC
.((((((.(.((((-((..((((..((...........................))..)))).)))..(.(((((((...))))))).))))).)).)))) ( -17.03)
>DroYak_CAF1 57698 97 + 1
UGAAUUCACACGCUUCAUUGUGGUUUAUUGU----AUUUUUUCCAUCUAUUUUUUAUUCCAUUCGAUUGUAUUCCACUUCGUGGAAUUCGCGGCGACAUUC
.((((((.(.(((.((...((((..((....----...................))..))))..))..(.(((((((...))))))).))))).)).)))) ( -15.60)
>consensus
UGAAUUCACACGCUUCAUUGUGGUUUAUUGUAU___UUUUUUCCAUAUAUUUUAUAUUUCAUUUGAUUGUAUUCCACUUCGUGGAAUUCGCGGCGACAUUC
.((((((.((((.......((((..(((........................................)))..))))..))))))))))..(....).... (-14.48 = -14.32 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,668,010 – 8,668,108
Length 98
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 92.26
Mean single sequence MFE -19.76
Consensus MFE -18.51
Energy contribution -18.51
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.88
Structure conservation index 0.94
SVM decision value 5.03
SVM RNA-class probability 0.999969
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8668010 98 - 23771897
GAAUGUCGCCGCAAAUUCCACGAAGUGGAAUACAAUCAAAUGAUAUAUAAAUUAUAUGGAAAAAA---AUACAAUAAACCACAACGAAGCGUGUGAAUUCA
((((.(((((((..(((((((...)))))))....(((.(((((......))))).)))......---....................))).)))))))). ( -21.00)
>DroSec_CAF1 55872 98 - 1
GAAUGUCGCCGCGAAUUCCACGAAGUGGAAUACAAUAAAAUGAAAUAUAAAAUAUAUGGAAAAAA---AUACAAUAAACCACAACGAAGCGUGUGAAUUCA
((((.((((((((.(((((((...))))))).).......................(((......---..........))).......))).)))))))). ( -19.09)
>DroSim_CAF1 56227 98 - 1
GAAUGUCGCCGCGAAUUCCACGAAGUGGAAUACAAUCAAAUGAAAUAUAAAAUAUAUGGAAAAAA---AUACAAUAAACCACAAUGAAGCGUGUGAAUUCA
((((.((((((((.(((((((...))))))).).......................(((......---..........))).......))).)))))))). ( -19.09)
>DroEre_CAF1 57245 100 - 1
GAAUGUCGCCGCGAAUUCCACGAAGUGGAAUACAAUCAAAUGGAAUAAAAAAUAGAUGGAAGAAAUACGUACAAUAAACCACAAUG-AGCGUGUGAAUUCA
((((.((((((((.(((((((...))))))).)..(((..(((............(((.........)))........)))...))-)))).)))))))). ( -20.05)
>DroYak_CAF1 57698 97 - 1
GAAUGUCGCCGCGAAUUCCACGAAGUGGAAUACAAUCGAAUGGAAUAAAAAAUAGAUGGAAAAAAU----ACAAUAAACCACAAUGAAGCGUGUGAAUUCA
((((.(((((((..(((((((((..((.....)).)))..))))))..........(((.......----........))).......))).)))))))). ( -19.56)
>consensus
GAAUGUCGCCGCGAAUUCCACGAAGUGGAAUACAAUCAAAUGAAAUAUAAAAUAUAUGGAAAAAA___AUACAAUAAACCACAAUGAAGCGUGUGAAUUCA
((((.(((((((..(((((((...))))))).........................(((...................))).......))).)))))))). (-18.51 = -18.51 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,668,069 – 8,668,171
Length 102
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 81.63
Mean single sequence MFE -24.22
Consensus MFE -17.60
Energy contribution -17.52
Covariance contribution -0.08
Combinations/Pair 1.14
Mean z-score -1.54
Structure conservation index 0.73
SVM decision value 0.29
SVM RNA-class probability 0.668243
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8668069 102 - 23771897
CCCCAUUAUCCAUA----UAUCCACAUGU-CAGUAGACUACACUAUAU----------AUAUAUACGAAGUGUGCUGGGAAUGUCGCCGCAAAUUCCACGAAGUGGAAUACAAUCAA
..............----..(((((....-(((((.(((.(..((((.----------...)))).).))).)))))(((((..........))))).....))))).......... ( -20.30)
>DroSec_CAF1 55931 99 - 1
C-CCAUUAUCGAUA----UAUCUACAUGU-CAGUAGACUACACUAU------------AUAUAUACGGAGUGUGCUGGGAAUGUCGCCGCGAAUUCCACGAAGUGGAAUACAAUAAA
.-(((((.(((...----..(((((....-..))))).........------------........(((((.(((.(((.....).))))).))))).))))))))........... ( -22.80)
>DroSim_CAF1 56286 92 - 1
C-CCAUUAUCCAUA----UAUCUACAUGU-CAGUAGACU-------------------AUAUAUACGGAGUGUGCUGGGAAUGUCGCCGCGAAUUCCACGAAGUGGAAUACAAUCAA
.-(((((.((.(((----(((((((....-..))))).)-------------------))))....(((((.(((.(((.....).))))).)))))..)))))))........... ( -22.20)
>DroEre_CAF1 57306 114 - 1
C-CCAUUAUCCAUAUAUGUAUCCACAUGU-CAGUAGACUAAGCUACAUACAUACUCGUAUAUAUAC-GAGUGUGCUGGGAAUGUCGCCGCGAAUUCCACGAAGUGGAAUACAAUCAA
.-..............(((((((((...(-(.((((......))))...((((((((((....)))-)))))))...(((((.(((...))))))))..)).)))).)))))..... ( -32.30)
>DroYak_CAF1 57756 104 - 1
C-CCAUUAUCCAUACAUAUAUCCACAUGU-CAGCAGACUACAGUA-----------GACUAUAUACGGAGUGUGCUGGGAAUGUCGCCGCGAAUUCCACGAAGUGGAAUACAAUCGA
.-..................(((((....-(((((.(((...(((-----------.......)))..))).)))))(((((.(((...)))))))).....))))).......... ( -27.20)
>DroAna_CAF1 53744 98 - 1
--CCAUUAUCCAUA----UAUCCAUAAAUCCAGCAGUCUAUAUAAU------------AGGUGC-UAGAGUGUGCUGGGAAUGUCGCCGCGAAUUCCACGAAGCGGAAUACAAUCAA
--............----...........((((((.(((((((...------------..))).-))))...))))))((.(((..((((............))))...))).)).. ( -20.50)
>consensus
C_CCAUUAUCCAUA____UAUCCACAUGU_CAGUAGACUACACUAU____________AUAUAUACGGAGUGUGCUGGGAAUGUCGCCGCGAAUUCCACGAAGUGGAAUACAAUCAA
....................(((((.....(((((.(((.............................))).)))))(((((.(((...)))))))).....))))).......... (-17.60 = -17.52 +  -0.08)

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 10:47:28 2006