Locus 422

Sequence ID 2L_DroMel_CAF1
Location 1,239,412 – 1,239,516
Length 104
Max. P 0.870516
window685 window686

overview

Window 5

Location 1,239,412 – 1,239,516
Length 104
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 88.99
Mean single sequence MFE -23.23
Consensus MFE -16.65
Energy contribution -18.15
Covariance contribution 1.50
Combinations/Pair 1.10
Mean z-score -2.57
Structure conservation index 0.72
SVM decision value 0.87
SVM RNA-class probability 0.870516
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1239412 104 + 22407834
ACAA-------UAAUAAAGUAAUUCAGCAAAUUGUCUCCGUUUAAUUGCCUUUAAGCAAAUCGAGAGAUGAGCAGAGGCAUCAAUCAUGAAAGUAAGCAAUGUUGAAUUCU
....-------......((.(((((((((...((((((.(((((.((((......)))).((....))))))).))))))(((....)))..........))))))))))) ( -24.80)
>DroSec_CAF1 16881 104 + 1
UUAA-------UAAUAAAAUAAUUCAGCAAAUUGUCUCCGAUUAAUUGCCUUUAAGCAAAUCAAGAGAUGAGCAGAGGCAUCAAUCAUGGAAAUAAGCAAAGUUGAAUUCU
....-------.........((((((((...((((.(((((((...(((((((..((..(((....)))..)))))))))..))))..))).)))).....)))))))).. ( -24.60)
>DroSim_CAF1 13059 104 + 1
ACAA-------UAAUAAAGUAAUUCAGCAAAUUGUCUCUGAUUAAUUGCCUUUAAACAAAUCAAGAGAUGAUCAGAGGCAUCAAUCAUGGAAAUAAGCAAAGUUGAAUUCU
....-------......((.((((((((....((((((((((((.((..(((..........))).))))))))))))))(((....)))...........)))))))))) ( -21.90)
>DroYak_CAF1 12956 111 + 1
ACAAUGAUAAGUAAUAAAGUAAUUCAGCAAAUUGUCUCCGAUUAAUUGCCUGUAAGCAAAUGUAGAGAUGAGCAGAGGCUUCAAUCUUGGAAAUAAUCAAAGUUGAAUUCU
.................((.((((((((..(((((.(((......((((......)))).....(((((((((....))))..)))))))).)))))....)))))))))) ( -21.60)
>consensus
ACAA_______UAAUAAAGUAAUUCAGCAAAUUGUCUCCGAUUAAUUGCCUUUAAGCAAAUCAAGAGAUGAGCAGAGGCAUCAAUCAUGGAAAUAAGCAAAGUUGAAUUCU
....................((((((((...((((.(((((.....(((((((..((..(((....)))..)))))))))......))))).)))).....)))))))).. (-16.65 = -18.15 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 1,239,412 – 1,239,516
Length 104
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 88.99
Mean single sequence MFE -20.16
Consensus MFE -14.62
Energy contribution -15.75
Covariance contribution 1.12
Combinations/Pair 1.06
Mean z-score -1.52
Structure conservation index 0.73
SVM decision value 0.00
SVM RNA-class probability 0.535056
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1239412 104 - 22407834
AGAAUUCAACAUUGCUUACUUUCAUGAUUGAUGCCUCUGCUCAUCUCUCGAUUUGCUUAAAGGCAAUUAAACGGAGACAAUUUGCUGAAUUACUUUAUUA-------UUGU
..((((((.((((((((....(((....)))(((((..((..(((....)))..))....)))))........))).)))..)).)))))).........-------.... ( -17.50)
>DroSec_CAF1 16881 104 - 1
AGAAUUCAACUUUGCUUAUUUCCAUGAUUGAUGCCUCUGCUCAUCUCUUGAUUUGCUUAAAGGCAAUUAAUCGGAGACAAUUUGCUGAAUUAUUUUAUUA-------UUAA
..((((((.....((..(((((..((((((((((((..((..(((....)))..))....)))).))))))))..)).)))..)))))))).........-------.... ( -22.80)
>DroSim_CAF1 13059 104 - 1
AGAAUUCAACUUUGCUUAUUUCCAUGAUUGAUGCCUCUGAUCAUCUCUUGAUUUGUUUAAAGGCAAUUAAUCAGAGACAAUUUGCUGAAUUACUUUAUUA-------UUGU
..((((((.....((..(((((..(((((((((((((.(((((.....))))).).....)))).))))))))..)).)))..)))))))).........-------.... ( -21.20)
>DroYak_CAF1 12956 111 - 1
AGAAUUCAACUUUGAUUAUUUCCAAGAUUGAAGCCUCUGCUCAUCUCUACAUUUGCUUACAGGCAAUUAAUCGGAGACAAUUUGCUGAAUUACUUUAUUACUUAUCAUUGU
..((((((.(...((((.(((((..((((((.((((..((..............))....))))..))))))))))).)))).).)))))).................... ( -19.14)
>consensus
AGAAUUCAACUUUGCUUAUUUCCAUGAUUGAUGCCUCUGCUCAUCUCUUGAUUUGCUUAAAGGCAAUUAAUCGGAGACAAUUUGCUGAAUUACUUUAUUA_______UUGU
..((((((.(.(((....(((((..(((((((((((..((..(((....)))..))....)))).)))))))))))))))...).)))))).................... (-14.62 = -15.75 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:50 2006