Locus 10221

Sequence ID	3R_DroMel_CAF1
Location	27,404,774 – 27,404,913
Length	139
Max. P	0.921050

overview

Window 3

Location	27,404,774 – 27,404,873
Length	99
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	85.72
Mean single sequence MFE	-37.78
Consensus MFE	-26.82
Energy contribution	-27.73
Covariance contribution	0.92
Combinations/Pair	1.21
Mean z-score	-2.93
Structure conservation index	0.71
SVM decision value	0.19
SVM RNA-class probability	0.625533
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27404774 99 - 27905053
CCAUAUGCACCCGCAUCAUCCAGGCGGACCUAUGGGUCACCCACAUGGCCCACAUCCGCACAUGGGUGGUCCACCUCCAAUGCGAGGAAUGAGCCCCAU
......((....(.((((((((.(((((....(((((((......)))))))..)))))...)))))))).).((((......)))).....))..... ( -36.00)
>DroSec_CAF1 6900 99 - 1
CCAUAUGCACCCGCAUCAUCCAGGCGGACCCAUGGGUCACCCACAUGGCCCACAUCCGCACAUGAGUGGUCCGCCUCCAAUGCGAGGCAUGAGCCCCAU
...(((((.(.(((((.....((((((((((.(((((((......)))))))(((......))).).)))))))))...))))).))))))........ ( -40.20)
>DroEre_CAF1 7156 99 - 1
CCAUAUGCACCCGCAUCAUCCAGGCGGACCCAUGGGUCACCCACAUGGUCCACAUCCGCACAUGGGUGGUCCGCCUCCGAUGCGUGGCAUGAGCCCCAU
...(((((.(.((((((....(((((((((((((((....)).)))))....((((((....))))))))))))))..)))))).))))))........ ( -43.90)
>DroWil_CAF1 6802 93 - 1
UCACAUGCAUCCACAUCAUCCAGGCGGUCCGAUGGGACAUCCACAUGGACCACAU---CAUAUGGGUGGACCG---CCCAUGCGCGGCAUGAGUCCAAU
...(((((.(((((.((((....(.(((((.(((((....)).)))))))).)..---...))))))))).((---(......))))))))........ ( -33.50)
>DroYak_CAF1 6456 99 - 1
CCAUAUGCACCCGCAUCAUCCAGGCGGACCCAUGGGUCAUCCACAUGGUCCCCAUCCGCACAUGGGUGGUCCGCCUCCAAUGCGAGGCAUGAGCCCCAU
...(((((.(.(((((.....(((((((((((((((....)).))))...(((((......))))).)))))))))...))))).))))))........ ( -41.30)
>DroAna_CAF1 6773 99 - 1
GCACAUGCAUCCCCAUCAUCCAGGUGGUCCAAUGGGUCAUCCCCACGGUCCCCAUCCGCACAUGGGAGGGCCUCCGCCAAUGCGAGGAAUGAGUCCGAU
((....))(((....((((((.((.(((((..((((.....)))).....(((((......))))).))))).))((....))..)).))))....))) ( -31.80)
>consensus
CCAUAUGCACCCGCAUCAUCCAGGCGGACCCAUGGGUCACCCACAUGGUCCACAUCCGCACAUGGGUGGUCCGCCUCCAAUGCGAGGCAUGAGCCCCAU
...(((((...(((((.....(((((((((..((((...))))((((((........)).))))...)))))))))...)))))..)))))........ (-26.82 = -27.73 +   0.92)

alignment

secondary structure

dotplot

Window 4

Location	27,404,811 – 27,404,913
Length	102
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	81.92
Mean single sequence MFE	-39.00
Consensus MFE	-25.32
Energy contribution	-26.35
Covariance contribution	1.03
Combinations/Pair	1.08
Mean z-score	-3.21
Structure conservation index	0.65
SVM decision value	1.14
SVM RNA-class probability	0.921050
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27404811 102 - 27905053
GCAUGGGCGGUGGACCUCCUCCCCCGCCUCACAUGCAUCCCCAUAUGCACCCGCAUCAUCCAGGCGGACCUAUGGGUCACCCACAUGGCCCACAUCCGCACA
((((((((((.(((.....))).)))))...)))))........((((....)))).......(((((....(((((((......)))))))..)))))... ( -40.00)
>DroPse_CAF1 7506 93 - 1
GCAUGGGCGGUGGG---------CCGCCGCAUAUGCAUCCCCACAUGCAUCCGCACCAUCCGGGCGGACCGAUGGGACAUCCCCAUGGACCCCCGCAUCACA
((((((((((....---------)))))((....)).......))))).(((((.((....)))))))((.(((((.....))))))).............. ( -39.30)
>DroSec_CAF1 6937 102 - 1
GCAUGGGCGGUGGACCUCCUCCCCCGCCGCACAUGCAUCCCCAUAUGCACCCGCAUCAUCCAGGCGGACCCAUGGGUCACCCACAUGGCCCACAUCCGCACA
(((((.(((((((..........))))))).)))))........((((....)))).......(((((....(((((((......)))))))..)))))... ( -41.90)
>DroYak_CAF1 6493 102 - 1
GCAUGGGUGGUGGACCUCCUCCCCCGCCUCACAUGCAUCCCCAUAUGCACCCGCAUCAUCCAGGCGGACCCAUGGGUCAUCCACAUGGUCCCCAUCCGCACA
((..((((((.(((((........(((((...(((.........((((....)))))))..)))))((((....))))........)))))))))))))... ( -37.60)
>DroAna_CAF1 6810 102 - 1
GCAUGGGUGGAGCACCACCGCCGCCGCCGCACAUGCACCCGCACAUGCAUCCCCAUCAUCCAGGUGGUCCAAUGGGUCAUCCCCACGGUCCCCAUCCGCACA
((..((((((.(.(((((((((((....))..(((((........)))))............))))))....((((.....)))).))).)))))))))... ( -33.30)
>DroPer_CAF1 6951 93 - 1
GCAUGGGCGGUGGC---------CCGCCGCAUAUGCAUCCCCACAUGCAUCCGCACCAUCCGGGCGGACCGAUGGGUCAUCCCCAUGGACCCCCGCAUCACA
(((((((.((((((---------(((.((....(((((......)))))(((((.((....))))))).)).))))))))))))))((....))))...... ( -41.90)
>consensus
GCAUGGGCGGUGGACCUCCUCCCCCGCCGCACAUGCAUCCCCACAUGCACCCGCAUCAUCCAGGCGGACCCAUGGGUCAUCCACAUGGACCCCAUCCGCACA
(((((.(((((((..........))))))).))))).........(((..((((.........)))).((.(((((....)).))))).........))).. (-25.32 = -26.35 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:51 2006