Locus 7493

Sequence ID 3R_DroMel_CAF1
Location 20,009,991 – 20,010,122
Length 131
Max. P 0.954330
window12104 window12105

overview

Window 4

Location 20,009,991 – 20,010,107
Length 116
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 74.93
Mean single sequence MFE -16.97
Consensus MFE -9.88
Energy contribution -9.77
Covariance contribution -0.11
Combinations/Pair 1.13
Mean z-score -1.94
Structure conservation index 0.58
SVM decision value 0.86
SVM RNA-class probability 0.868679
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20009991 116 + 27905053
AUAUUCUAUCUGCUGUUUUAUUUAUAUAUAAUUUUCCUUACAAUGUGCAUAAGC---UAUUCUUUACUAGGAAACAAGCAGUUCAGUCACAAUAUGAAAUAAUUAUGAUUGAAACUAAC
.........(((((...((((......)))).((((((...((((.((....))---)))).......))))))..)))))((((((((.(((........))).))))))))...... ( -18.10)
>DroSec_CAF1 4004 101 + 1
AUAUUCUAUCUGCUGUUUUAUUUACAUAUGAUUUUCCUUA---UGU---------------CUUUACUAGCAAACAAACAGCUCAGUCAUAAUAUGAAAUAAUUAUGAUUGAAACUAAC
...........(((((((.....(((((.(......).))---)))---------------((.....)).....)))))))(((((((((((........)))))))))))....... ( -18.10)
>DroSim_CAF1 3962 100 + 1
----------------AUCAUUUACAUAUGAUUUUCCUUA---UGUAUUUAUGCACUUAUUCUUUACUAGCAAACAAACAGCUCAGUCAUAAUAUGAAAUAAUUAUGAUUGAAACUAAC
----------------..(((.((((((.(......).))---))))...))).............................(((((((((((........)))))))))))....... ( -14.70)
>consensus
AUAUUCUAUCUGCUGUUUUAUUUACAUAUGAUUUUCCUUA___UGU___UA_GC___UAUUCUUUACUAGCAAACAAACAGCUCAGUCAUAAUAUGAAAUAAUUAUGAUUGAAACUAAC
.................((((......))))...................................................(((((((((((........)))))))))))....... ( -9.88 =  -9.77 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 20,010,031 – 20,010,122
Length 91
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 66.00
Mean single sequence MFE -11.44
Consensus MFE -6.28
Energy contribution -7.52
Covariance contribution 1.24
Combinations/Pair 1.09
Mean z-score -1.90
Structure conservation index 0.55
SVM decision value 1.44
SVM RNA-class probability 0.954330
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20010031 91 + 27905053
CAAUGUGCAUAAGC---UAUUCUUUA-CUAGGAAACAAGCAGUUCAGUCACAAUAUGAAAUAAUUAUGAUUGAAACUAACAAGCAAUCAA--CUGAC
.....(((....((---(.(((((..-..)))))...)))((((((((((.(((........))).)))))).)))).....))).....--..... ( -15.90)
>DroSec_CAF1 4044 76 + 1
---UGU---------------CUUUA-CUAGCAAACAAACAGCUCAGUCAUAAUAUGAAAUAAUUAUGAUUGAAACUAACAAGCAAUCAA--CUGAC
---.((---------------(....-...((.........))(((((((((((........))))))))))).................--..))) ( -11.80)
>DroSim_CAF1 3986 91 + 1
---UGUAUUUAUGCACUUAUUCUUUA-CUAGCAAACAAACAGCUCAGUCAUAAUAUGAAAUAAUUAUGAUUGAAACUAACAAGCAAUCAA--CUGAC
---........(((............-...((.........))(((((((((((........))))))))))).........))).....--..... ( -14.00)
>DroEre_CAF1 5893 85 + 1
GCAUUUAUUUAUCC--------UACA-CUAACCACCAAGC-UCUCAGUCAUAAUAUUAAAUAAUUAUGAUUGAAACUAACAAGCAAUCAA--CUGAC
((............--------....-((........)).-..(((((((((((........))))))))))).........))......--..... ( -11.00)
>DroAna_CAF1 4393 74 + 1
----------------------UACAAAUUGCCAAAAAUU-ACUUAGUACAAACACUAAAAAAUCAUAAAUGAAAAUUCCCAAGAGUUAGCGCCGAC
----------------------........((........-..(((((......)))))...............(((((....))))).))...... (  -4.50)
>consensus
___UGU___UA__C_______CUUUA_CUAGCAAACAAACAGCUCAGUCAUAAUAUGAAAUAAUUAUGAUUGAAACUAACAAGCAAUCAA__CUGAC
...........................................(((((((((((........)))))))))))........................ ( -6.28 =  -7.52 +   1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:18 2006