Locus 3679

Sequence ID 2R_DroMel_CAF1
Location 12,229,483 – 12,229,578
Length 95
Max. P 0.748755
window5983 window5984

overview

Window 3

Location 12,229,483 – 12,229,578
Length 95
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 79.25
Mean single sequence MFE -23.54
Consensus MFE -15.51
Energy contribution -15.32
Covariance contribution -0.19
Combinations/Pair 1.22
Mean z-score -1.81
Structure conservation index 0.66
SVM decision value 0.47
SVM RNA-class probability 0.748755
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12229483 95 + 20766785
AAAUUGCUUAAGCUUGCUCAAAUCCGAUUUAACUAGCUAGCAUGGGCACACUGUGAUUUUAGUGUGGCCUACUGAUUAUAAUAAGC-------------------UACCUAUAA---
.....(((((.(((.(((................))).)))..((.(((((((......))))))).))............)))))-------------------.........--- ( -23.69)
>DroSec_CAF1 90545 95 + 1
AAAUUGCUUCAGCUUGCUCAAAUCCGAUUUAACUAGCUAGCAUGGGCACACUGUGAUUUUAGUGUGGCCUACUGAUUAUAGCAAGC-------------------UACCUAUAA---
..........((((((((..((((.(.........(....)..((.(((((((......))))))).))..).))))..)))))))-------------------)........--- ( -27.20)
>DroSim_CAF1 86997 95 + 1
AAAUUGCUUCAGCUUGCUCAAAUCCGAUUGAACUAGCUAGCAUGGGCACAUUAUGAUUUUAGUGUGGACUACUGAUUAUAACAAGU-------------------UACCUAUAA---
.....(((..((((.(.((((......)))).).)))))))((((((((((((......)))))))((((.............)))-------------------).)))))..--- ( -20.22)
>DroYak_CAF1 93536 117 + 1
GAAUUGAUUCAGCUUGCCCUAAGCCCAUUUAACAAGCUAGCAAGGUCACACUGUGCUUUUAGUGUGGUCUACUGAUUAUAAUAAGCGCGCCCAAUAAUUACACGCUCCCAACAAAUU
...(((....((((((................))))))(((.((..(((((((......)))))))..))..(((((((..............)))))))...))).....)))... ( -23.03)
>consensus
AAAUUGCUUCAGCUUGCUCAAAUCCGAUUUAACUAGCUAGCAUGGGCACACUGUGAUUUUAGUGUGGCCUACUGAUUAUAACAAGC___________________UACCUAUAA___
.....((((..(((.((..................)).)))..((.(((((((......))))))).)).............))))............................... (-15.51 = -15.32 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,229,483 – 12,229,578
Length 95
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 79.25
Mean single sequence MFE -25.90
Consensus MFE -15.10
Energy contribution -15.98
Covariance contribution 0.87
Combinations/Pair 1.11
Mean z-score -1.93
Structure conservation index 0.58
SVM decision value 0.20
SVM RNA-class probability 0.629698
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12229483 95 - 20766785
---UUAUAGGUA-------------------GCUUAUUAUAAUCAGUAGGCCACACUAAAAUCACAGUGUGCCCAUGCUAGCUAGUUAAAUCGGAUUUGAGCAAGCUUAAGCAAUUU
---.........-------------------(((((........((((((.((((((........)))))).)).))))((((.(((.((......)).))).)))))))))..... ( -22.30)
>DroSec_CAF1 90545 95 - 1
---UUAUAGGUA-------------------GCUUGCUAUAAUCAGUAGGCCACACUAAAAUCACAGUGUGCCCAUGCUAGCUAGUUAAAUCGGAUUUGAGCAAGCUGAAGCAAUUU
---.......((-------------------(((((((..((((((((((.((((((........)))))).)).)))).....(......).))))..)))))))))......... ( -27.10)
>DroSim_CAF1 86997 95 - 1
---UUAUAGGUA-------------------ACUUGUUAUAAUCAGUAGUCCACACUAAAAUCAUAAUGUGCCCAUGCUAGCUAGUUCAAUCGGAUUUGAGCAAGCUGAAGCAAUUU
---.....((((-------------------....(((((.((...((((....))))..)).))))).))))..((((((((.((((((......)))))).))))..)))).... ( -20.90)
>DroYak_CAF1 93536 117 - 1
AAUUUGUUGGGAGCGUGUAAUUAUUGGGCGCGCUUAUUAUAAUCAGUAGACCACACUAAAAGCACAGUGUGACCUUGCUAGCUUGUUAAAUGGGCUUAGGGCAAGCUGAAUCAAUUC
.....(((((((((((((.........)))))))).......((((.....((((((........))))))..((((((((((..(...)..))))...)))))))))).))))).. ( -33.30)
>consensus
___UUAUAGGUA___________________GCUUAUUAUAAUCAGUAGGCCACACUAAAAUCACAGUGUGCCCAUGCUAGCUAGUUAAAUCGGAUUUGAGCAAGCUGAAGCAAUUU
........((.....................(((((((......)))))))((((((........)))))).)).((((((((.(((.((......)).))).))))..)))).... (-15.10 = -15.98 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:44 2006