Locus 4966

Sequence ID 3R_DroMel_CAF1
Location 13,067,022 – 13,067,152
Length 130
Max. P 0.940614
window8127 window8128

overview

Window 7

Location 13,067,022 – 13,067,120
Length 98
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 69.36
Mean single sequence MFE -15.38
Consensus MFE -6.64
Energy contribution -6.96
Covariance contribution 0.32
Combinations/Pair 1.25
Mean z-score -1.95
Structure conservation index 0.43
SVM decision value 1.01
SVM RNA-class probability 0.898870
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13067022 98 + 27905053
UCUAAUCCAUUUUGGCUUC-UUGGGGAAAUAU------------ACUUUAUCCAACUAACUGAUUUUAAAUUCUUAGAGAGAUUUUCUGAUCUCUCUCCAAAUAACUUCUG-----
..........(((((....-((((..(((...------------..)))..))))....................(((((((((....)))))))))))))).........----- ( -17.10)
>DroSec_CAF1 86987 89 + 1
UCUAAUCCAUUCUG----------GAAAAUAU------------ACUUUAUCCAACUAACUGAUUUUAAAUUCUUAGAGAGAUUUUCUGAUUUCUCUCUAAAUACCUUCUG-----
............((----------((.((...------------...)).))))...................(((((((((..........)))))))))..........----- ( -13.80)
>DroSim_CAF1 79369 89 + 1
UCUAAUCCAUUCUG----------GAAAAUAU------------ACUUUAUCCAACUAACUGAUUUUAAAUUCUUAGAGAGAUUUUCUGAUCUUUCUCUAAAUACCUUCUG-----
............((----------((.((...------------...)).)))).....................(((((((((....)))))))))..............----- ( -11.40)
>DroEre_CAF1 87493 96 + 1
UCGCAUCCAUCUUGGCUUC-UUGGAAAAAGAUUCUCGAG-------------CAACUGAUUGAUUUUAGAUUCCUAGAGAGAUUUUCCGAUCUCUCCAUAAAUACCAUCC------
....(((.(((...((((.-..((((.....)))).)))-------------)....))).)))............((((((((....))))))))..............------ ( -17.00)
>DroYak_CAF1 89783 113 + 1
---AGUCCAUUUUGACUUUUUUGGAUAAAUAUUUCCGGGUAUAAACUUAAACCAACUUUUUGAUUUUAAAUUCCCAGAGAUAUUUUCUUAUCUCUGUACAAAUACUUUCUGCUUUU
---((((......)))).....(((........)))(((..((((.(((((.......))))).))))....)))(((((((......)))))))..................... ( -17.60)
>consensus
UCUAAUCCAUUUUG_CUU__UUGGGAAAAUAU____________ACUUUAUCCAACUAACUGAUUUUAAAUUCUUAGAGAGAUUUUCUGAUCUCUCUCUAAAUACCUUCUG_____
............................................................................((((((((....)))))))).................... ( -6.64 =  -6.96 +   0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 13,067,053 – 13,067,152
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -15.53
Consensus MFE -10.36
Energy contribution -10.43
Covariance contribution 0.06
Combinations/Pair 1.25
Mean z-score -2.44
Structure conservation index 0.67
SVM decision value 1.29
SVM RNA-class probability 0.940614
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13067053 99 + 27905053
ACUUUAUCCAACUAACUGAUUUUAAAUUCUUAGAGAGAUUUUCUGAUCUCUCUCCAAAUAACUUCUGGAUUAUUUUAUAAAUUCGACAUACAUCCAGAC
...............................(((((((((....)))))))))..........((((((((((.((........)).))).))))))). ( -18.30)
>DroSec_CAF1 87009 99 + 1
ACUUUAUCCAACUAACUGAUUUUAAAUUCUUAGAGAGAUUUUCUGAUUUCUCUCUAAAUACCUUCUGGUUUAUUGUAUAAAUUCGACAUAAAUCUAGAU
.............................(((((((((..........)))))))))......((((((((((.((.........))))))).))))). ( -15.90)
>DroSim_CAF1 79391 99 + 1
ACUUUAUCCAACUAACUGAUUUUAAAUUCUUAGAGAGAUUUUCUGAUCUUUCUCUAAAUACCUUCUGGUUUAUUGUAUAAAUUCGACAUAAAUCCAGAU
...............................(((((((((....)))))))))..........((((((((((.((.........))))))).))))). ( -15.80)
>DroEre_CAF1 87531 89 + 1
--------CAACUGAUUGAUUUUAGAUUCCUAGAGAGAUUUUCCGAUCUCUCCAUAAAUACCAUCC--CUUGUUUUAUAAACACGACAUAAUUCCAGAU
--------...(((..................((((((((....))))))))..............--(.((((.....)))).).........))).. ( -12.10)
>consensus
ACUUUAUCCAACUAACUGAUUUUAAAUUCUUAGAGAGAUUUUCUGAUCUCUCUCUAAAUACCUUCUGGUUUAUUGUAUAAAUUCGACAUAAAUCCAGAU
...............(((..............((((((((....))))))))...........((.(((((((...))))))).))........))).. (-10.36 = -10.43 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:14 2006