Locus 6018

Sequence ID 2L_DroMel_CAF1
Location 16,948,842 – 16,948,959
Length 117
Max. P 0.990679
window9555 window9556

overview

Window 5

Location 16,948,842 – 16,948,937
Length 95
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 84.55
Mean single sequence MFE -28.08
Consensus MFE -20.18
Energy contribution -20.78
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.72
SVM decision value -0.05
SVM RNA-class probability 0.510450
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16948842 95 + 22407834
CCCAUUCCUUCAA---GAAACGCACUUCCG-----------CACUUGAGUUCAAGUCAAGGCUGUCCGUGGCA-GCAACUUUUUGAAGCUUGCCAACACUUUGGCCUCCC
.......((((((---(((..((......)-----------)(((((....)))))....(((((.....)))-))...)))))))))...(((((....)))))..... ( -25.50)
>DroSec_CAF1 61357 96 + 1
CCCAUGCCUUCAA---GAAACGCACUUCCG-----------CACUUGAGUUCAAGUCAAGGCUGUCCGUGGCAGGCAACUUUUUGAAGCUUGCCAACACUUUGGCCUCCC
.....(((...((---(..(((.((..((.-----------.(((((....)))))...))..)).)))(((((((..(.....)..)))))))....))).)))..... ( -28.40)
>DroEre_CAF1 64240 96 + 1
GCCACUUCUUCUA---GAAACGCACUUCCG-----------CACUCGAGUUCAAGUCAAGGCUGUUCGUGGCAGGCAACUUUUUGAAGCUUGCCAACACUUUGGCCGCCC
((((.........---...(((.((..((.-----------.(((.(....).)))...))..)).)))(((((((..(.....)..))))))).......))))..... ( -24.70)
>DroYak_CAF1 62804 96 + 1
GCCAUUUCUUCUG---GAAACGCACUUCCG-----------CACUCGAGUUCAAGUCAAGGCUGUCCGUGGCAGGCAACUUUUUGAAGCUUGCCAACACUUUGGCCUCCC
............(---(((......)))).-----------.....(((.....(((((((.(((...((((((((..(.....)..))))))))))))))))))))).. ( -26.10)
>DroAna_CAF1 56307 105 + 1
GCCAU---AUCAAGCUAAAACGCACAUCCGUUUCGGGGCGGCACUC-UGCUCAAGUCAAGGCUGUCCGCGGCAGGCAACUUUCAGAAGCUUGCCAACACU-UGGCCUCGC
((((.---.....((..(((((......)))))..(((((((.((.-.((....))..)))))))))))(((((((..(.....)..)))))))......-))))..... ( -35.70)
>consensus
GCCAUUCCUUCAA___GAAACGCACUUCCG___________CACUCGAGUUCAAGUCAAGGCUGUCCGUGGCAGGCAACUUUUUGAAGCUUGCCAACACUUUGGCCUCCC
......................................................(((((((.(((...((((((((..(.....)..))))))))))))))))))..... (-20.18 = -20.78 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 16,948,869 – 16,948,959
Length 90
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 82.72
Mean single sequence MFE -28.58
Consensus MFE -24.56
Energy contribution -25.32
Covariance contribution 0.76
Combinations/Pair 1.04
Mean z-score -2.52
Structure conservation index 0.86
SVM decision value 2.23
SVM RNA-class probability 0.990679
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16948869 90 + 22407834
--CACUUGAGUUCAAGUCAAGGCUGUCCGUGGCA-GCAACUUUUUGAAGCUUGCCAACACUUUGGCCUCCCCUUGGGAAAAUCAAAAA--------AAA---AA---
--.(((((....)))))....(((((.....)))-))...(((((((.....(((((....))))).((((...))))...)))))))--------...---..--- ( -24.90)
>DroSec_CAF1 61384 92 + 1
--CACUUGAGUUCAAGUCAAGGCUGUCCGUGGCAGGCAACUUUUUGAAGCUUGCCAACACUUUGGCCUCCCCUUGGGAAAAUCAAAAA--------AAA---AAA--
--...((((.((((((...((((((....((((((((..(.....)..))))))))......))))))...))))))....))))...--------...---...-- ( -28.10)
>DroEre_CAF1 64267 90 + 1
--CACUCGAGUUCAAGUCAAGGCUGUUCGUGGCAGGCAACUUUUUGAAGCUUGCCAACACUUUGGCCGCCCCUUGGGGAAAAAAAAAA-------AGAA--------
--..((((((.....(((((((.(((...((((((((..(.....)..)))))))))))))))))).....))))))...........-------....-------- ( -28.80)
>DroYak_CAF1 62831 89 + 1
--CACUCGAGUUCAAGUCAAGGCUGUCCGUGGCAGGCAACUUUUUGAAGCUUGCCAACACUUUGGCCUCCCCUUGGGAAAAUCAAAAA--------AAA--------
--..((((((.....(((((((.(((...((((((((..(.....)..)))))))))))))))))).....))))))...........--------...-------- ( -28.60)
>DroAna_CAF1 56343 105 + 1
GGCACUC-UGCUCAAGUCAAGGCUGUCCGCGGCAGGCAACUUUCAGAAGCUUGCCAACACU-UGGCCUCGCCUUGGGGGAGAAAAAAUCCCAUCCAGAAAAAAUCGU
.....((-((.(((((.(.((((((.....(((((((..(.....)..)))))))......-)))))).).)))))((((.......))))...))))......... ( -32.50)
>consensus
__CACUCGAGUUCAAGUCAAGGCUGUCCGUGGCAGGCAACUUUUUGAAGCUUGCCAACACUUUGGCCUCCCCUUGGGAAAAUCAAAAA________AAA___A____
....((((((.....(((((((.(((...((((((((..(.....)..)))))))))))))))))).....)))))).............................. (-24.56 = -25.32 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:57 2006