Locus 4933

Sequence ID 3R_DroMel_CAF1
Location 12,970,554 – 12,970,699
Length 145
Max. P 0.716085
window8073 window8074

overview

Window 3

Location 12,970,554 – 12,970,666
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.96
Mean single sequence MFE -24.28
Consensus MFE -14.18
Energy contribution -14.55
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -1.80
Structure conservation index 0.58
SVM decision value 0.38
SVM RNA-class probability 0.714017
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12970554 112 + 27905053
AACACGCGUGCUAAACGAACUCAAGCCAUCGGUCUCACAGAAACGAUUGUUAAAAUACUUGCUGUAGGCCAAGAUAAUAAUGUUAAGUAUAAUGACCCACACA--UAGU------AGUAC
.......((((((.................(((((.((((.....(((.....))).....))))))))).........((((...((......))....)))--)..)------))))) ( -17.30)
>DroSim_CAF1 10740 101 + 1
AACACGCGUGCUAAACGAACU--------------CACAGAAAUGAUUGUUAAAAUACUUGCUGUGGGCCAAGACAAUAAUGUUAAGUAUAAUGGCCCACACA--UAGUA---GUAGUAC
.......((((((....(((.--------------..((....))...)))....((((((.(((((((((..((...........))....)))))))))))--.))))---.)))))) ( -26.70)
>DroEre_CAF1 10526 107 + 1
AACACACGUGCUAUACGAACUCAAUCCAUCGGUCUCACAGAAAUGGUUGUUAAAAUACUUGCUGUGGGCCAAGGCAGU----------UAAUUGGCCCACACACAUACAC---GUAGUAC
.......(((((((.......(((.((((...((.....)).)))))))..........((.((((((((((......----------...)))))))))))).......---))))))) ( -28.90)
>DroYak_CAF1 10679 110 + 1
AACACGCGUGCUAUACCAACUUAAUCCAUCGGUCUCACAGAAAUGGUUGUUAAAAUACUUUCUUUGGGCCAAGACAAU----------AUAAAGGCCCAAACACAUACACGACGUAGUAC
.(((((((((.(((......(((((((((...((.....)).))))..))))).........((((((((........----------.....))))))))...))))))).))).)).. ( -24.22)
>consensus
AACACGCGUGCUAAACGAACUCAAUCCAUCGGUCUCACAGAAAUGAUUGUUAAAAUACUUGCUGUGGGCCAAGACAAU__________AUAAUGGCCCACACA__UACAC___GUAGUAC
.......((((((.......................((((......))))............((((((((.......................)))))))).............)))))) (-14.18 = -14.55 +   0.37)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 12,970,594 – 12,970,699
Length 105
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 80.21
Mean single sequence MFE -21.60
Consensus MFE -14.48
Energy contribution -15.47
Covariance contribution 1.00
Combinations/Pair 1.14
Mean z-score -1.78
Structure conservation index 0.67
SVM decision value 0.39
SVM RNA-class probability 0.716085
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12970594 105 - 27905053
ACUUCUUAUGAAUGCCGCGCUUUCUAGACCUAUGUACU------ACUA--UGUGUGGGUCAUUAUACUUAACAUUAUUAUCUUGGCCUACAGCAAGUAUUUUAACAAUCGUUU
...(((...(((.((...)).))).))).........(------(((.--(((((((((((..(((...........)))..))))))))).))))))............... ( -17.40)
>DroSim_CAF1 10766 108 - 1
ACUUCUUAUGAAUGCCACGCUUUCUAGACCUAUGUACUAC---UACUA--UGUGUGGGCCAUUAUACUUAACAUUAUUGUCUUGGCCCACAGCAAGUAUUUUAACAAUCAUUU
...(((...(((.((...)).))).)))....(((.....---((((.--(((((((((((..(((...........)))..))))))))).)))))).....)))....... ( -23.20)
>DroEre_CAF1 10566 100 - 1
ACUUCUUAUGAUUACCACGCUUUCUAGACCUAUGUACUAC---GUGUAUGUGUGUGGGCCAAUUA----------ACUGCCUUGGCCCACAGCAAGUAUUUUAACAACCAUUU
..................((..........(((((((...---..)))))))((((((((((...----------......)))))))))))).................... ( -22.90)
>DroYak_CAF1 10719 103 - 1
ACUUCUUAUGAUUACCACGCUUUCUAGACCUAUGUACUACGUCGUGUAUGUGUUUGGGCCUUUAU----------AUUGUCUUGGCCCAAAGAAAGUAUUUUAACAACCAUUU
..................(((((((.....(((((((........))))))).(((((((.....----------........))))))))))))))................ ( -22.92)
>consensus
ACUUCUUAUGAAUACCACGCUUUCUAGACCUAUGUACUAC___GACUA__UGUGUGGGCCAUUAU__________AUUGUCUUGGCCCACAGCAAGUAUUUUAACAACCAUUU
..................((((.((.....(((((((........))))))).((((((((.....................)))))))))).))))................ (-14.48 = -15.47 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:24 2006