Locus 4025

Sequence ID 2L_DroMel_CAF1
Location 11,679,571 – 11,679,680
Length 109
Max. P 0.730202
window6344 window6345

overview

Window 4

Location 11,679,571 – 11,679,680
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 88.52
Mean single sequence MFE -21.80
Consensus MFE -15.73
Energy contribution -16.33
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.72
SVM decision value 0.26
SVM RNA-class probability 0.659052
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11679571 109 + 22407834
AUCCUGAUUUAGGACAAACAUACAACUGCCUGCCUUAAAUUCUCCUUCGCAGCACUCACAUCAAGAUGUGUCCCCUUGGCAUUUUGGCAUUGGCCAAAAUCAAACACAU
.(((((...)))))............(((((((...............))).....(((((....))))).......))))(((((((....))))))).......... ( -19.86)
>DroSec_CAF1 140711 109 + 1
ACCCUGAUUUAGGACAAACAUACAACUGCCUGCCUAAAAUUCUCCUUCGCAGCACUCACAUCAAGAUGUGUCCCCUUGGCAUUUUGGCAUUGGCCAAAAUCAAACACAU
.......((((((.((..((......))..))))))))..........((......(((((....)))))........))((((((((....))))))))......... ( -20.84)
>DroSim_CAF1 138588 109 + 1
ACCCUGAUUUAGGACAAACAUACAACUGCCUGCCUUAAAUUCUCCUUCGCAGCACUCACAUCAAGAUGUGUCCCCUUGGCAUUUUGGCAUUGGCCAAAAUCAAACACAU
.....((((((((.((..((......))..)).)))))))).......((......(((((....)))))........))((((((((....))))))))......... ( -19.74)
>DroEre_CAF1 163961 93 + 1
AGCCUGAUUUUGGACAAACAUUCAACUGCCUGCCUUAAA---------------CUCCCAUCGAGAUGUCUC-CCUGGGCAUUCUGGCAUUGGCCAAAAUCAAACACAU
....(((((((((.(((.((......))..((((.....---------------..((((..(((....)))-..))))......))))))).)))))))))....... ( -24.82)
>DroYak_CAF1 136503 107 + 1
ACCCUGAUU-UGGCAAAACAUUCAAGUGCCUGCCUUAAAUUCUCC-UCGCAGCACUCACAUCAAGAUGUGUCCCCUUGGCAUUUUGGCAUUGGCCAAAAUCAAACACAU
....(((((-((((..........(((((.(((............-..))))))))....(((((((((.........))))))))).....))).))))))....... ( -23.74)
>consensus
ACCCUGAUUUAGGACAAACAUACAACUGCCUGCCUUAAAUUCUCCUUCGCAGCACUCACAUCAAGAUGUGUCCCCUUGGCAUUUUGGCAUUGGCCAAAAUCAAACACAU
....((((((.((.........(((.((((((((......................(((((....))))).......))))....))))))).)).))))))....... (-15.73 = -16.33 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,679,571 – 11,679,680
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 88.52
Mean single sequence MFE -32.22
Consensus MFE -22.90
Energy contribution -24.02
Covariance contribution 1.12
Combinations/Pair 1.05
Mean z-score -2.09
Structure conservation index 0.71
SVM decision value 0.42
SVM RNA-class probability 0.730202
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11679571 109 - 22407834
AUGUGUUUGAUUUUGGCCAAUGCCAAAAUGCCAAGGGGACACAUCUUGAUGUGAGUGCUGCGAAGGAGAAUUUAAGGCAGGCAGUUGUAUGUUUGUCCUAAAUCAGGAU
.(((((((.((((((((....)))))))).(....))))))))(((((((.(((((.((.(....))).)))))(((((((((......)))))).)))..))))))). ( -32.90)
>DroSec_CAF1 140711 109 - 1
AUGUGUUUGAUUUUGGCCAAUGCCAAAAUGCCAAGGGGACACAUCUUGAUGUGAGUGCUGCGAAGGAGAAUUUUAGGCAGGCAGUUGUAUGUUUGUCCUAAAUCAGGGU
.(((((((.((((((((....)))))))).(....))))))))(((((((.......((.(....)))....(((((((((((......)))))).)))))))))))). ( -31.80)
>DroSim_CAF1 138588 109 - 1
AUGUGUUUGAUUUUGGCCAAUGCCAAAAUGCCAAGGGGACACAUCUUGAUGUGAGUGCUGCGAAGGAGAAUUUAAGGCAGGCAGUUGUAUGUUUGUCCUAAAUCAGGGU
.(((((((.((((((((....)))))))).(....))))))))(((((((.(((((.((.(....))).)))))(((((((((......)))))).)))..))))))). ( -32.00)
>DroEre_CAF1 163961 93 - 1
AUGUGUUUGAUUUUGGCCAAUGCCAGAAUGCCCAGG-GAGACAUCUCGAUGGGAG---------------UUUAAGGCAGGCAGUUGAAUGUUUGUCCAAAAUCAGGCU
....((((((((((((.(((((((.((((.((((..-(((....)))..)))).)---------------)))..)))).(((......)))))).)))))))))))). ( -35.00)
>DroYak_CAF1 136503 107 - 1
AUGUGUUUGAUUUUGGCCAAUGCCAAAAUGCCAAGGGGACACAUCUUGAUGUGAGUGCUGCGA-GGAGAAUUUAAGGCAGGCACUUGAAUGUUUUGCCA-AAUCAGGGU
.(((((((.((((((((....)))))))).(....))))))))(((((((.....((..((((-((...(((((((.......))))))).))))))))-.))))))). ( -29.40)
>consensus
AUGUGUUUGAUUUUGGCCAAUGCCAAAAUGCCAAGGGGACACAUCUUGAUGUGAGUGCUGCGAAGGAGAAUUUAAGGCAGGCAGUUGUAUGUUUGUCCUAAAUCAGGGU
.(((((((.((((((((....)))))))).(....))))))))(((((((..((((.((.(....))).))))..((((((((......))))))))....))))))). (-22.90 = -24.02 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:27 2006