Locus 3526

Sequence ID 2R_DroMel_CAF1
Location 11,800,863 – 11,801,063
Length 200
Max. P 0.817257
window5739 window5740

overview

Window 9

Location 11,800,863 – 11,800,983
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -40.37
Consensus MFE -38.11
Energy contribution -37.67
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.75
Structure conservation index 0.94
SVM decision value 0.30
SVM RNA-class probability 0.677636
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11800863 120 + 20766785
UUAGUUCUUAUAUUCAAGCGCGCUAAUCGCGGCGUGGCCAGGAUUUGUGAGAAGAUCUGCGGCACUUGUCUGCUGCAUUUUGCAUUUUCCGGCUCCGUGGAUAUAUCUGUGUUCCAACAG
........(((((((...((((.....))))(((..(((.(((..((..(((.....(((((((......))))))))))..))...))))))..)))))))))).((((......)))) ( -40.10)
>DroSec_CAF1 5003 120 + 1
UUAGUUCUUAUAUUCAAGCGAGCUAAUCGCGGCGUGGCCAGGAUUUGUGAGAAGAUCUGCGGCACUUGCCUGCUGCACUUUGCAUUUUCCGGCUCCGUGGAUAUAUCUGUGUUCCAGCAG
........(((((((..((((.....)))).(((..(((.(((...(((..(((...(((((((......))))))))))..)))..))))))..)))))))))).((((......)))) ( -41.00)
>DroSim_CAF1 4999 120 + 1
UUAGUUCUUAUAUUCAAGCGCGCUAAUCGCGGCGUGGCCAGGAUUUGUGAGAAGAUCUGCGGCACUUGCCUGCUGCACUUUGCAUUUUCCGGCUCCGUGGAUAUAUCUGUGUUCCAGCAG
........(((((((...((((.....))))(((..(((.(((...(((..(((...(((((((......))))))))))..)))..))))))..)))))))))).((((......)))) ( -40.00)
>consensus
UUAGUUCUUAUAUUCAAGCGCGCUAAUCGCGGCGUGGCCAGGAUUUGUGAGAAGAUCUGCGGCACUUGCCUGCUGCACUUUGCAUUUUCCGGCUCCGUGGAUAUAUCUGUGUUCCAGCAG
........(((((((..(((.......))).(((..(((.(((...(((..(((...(((((((......))))))))))..)))..))))))..)))))))))).((((......)))) (-38.11 = -37.67 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 11,800,943 – 11,801,063
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -42.23
Consensus MFE -40.28
Energy contribution -40.17
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -1.92
Structure conservation index 0.95
SVM decision value 0.67
SVM RNA-class probability 0.817257
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11800943 120 + 20766785
UGCAUUUUCCGGCUCCGUGGAUAUAUCUGUGUUCCAACAGCAGUUGUCCAGCAGGCUGAGUUCCUCCGGUGACAUCUUAAGGAGCUACUACAGUCAUGUAGUGGAGCUACUGUCAGCCUU
(((......((....))((((((...((((......))))....)))))))))((((((((((((..((......))..))))))(((((((....))))))).........)))))).. ( -39.70)
>DroSec_CAF1 5083 120 + 1
UGCAUUUUCCGGCUCCGUGGAUAUAUCUGUGUUCCAGCAGCAGUUGUCCAGCAGGCUGAGCUCCUCCGGUGACAUCUUAAGGAGGUACUACAGCCAUGUAGUGGAGCUACUUUCAGCCUU
.((.......(((((((((((((...((((((....))).))).))))))((((((((((..(((((..(((....))).)))))..)).))))).)))..))))))).......))... ( -43.54)
>DroSim_CAF1 5079 120 + 1
UGCAUUUUCCGGCUCCGUGGAUAUAUCUGUGUUCCAGCAGCAGUUGUCCAGCAGGCUGAGCUCCUCCGGUGACAUCUUGAGGAGGUACUACAGCCAUGUAGUGGAGCUACUGUCAGCCUU
.((.......(((((((((((((...((((((....))).))).))))))((((((((((..(((((...(....)....)))))..)).))))).)))..))))))).......))... ( -43.44)
>consensus
UGCAUUUUCCGGCUCCGUGGAUAUAUCUGUGUUCCAGCAGCAGUUGUCCAGCAGGCUGAGCUCCUCCGGUGACAUCUUAAGGAGGUACUACAGCCAUGUAGUGGAGCUACUGUCAGCCUU
.((.......(((((((((((((...((((((....))).))).))))))((((((((((..(((((...(....)....)))))..)).))))).)))..))))))).......))... (-40.28 = -40.17 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:38 2006