Locus 857

Sequence ID	3R_DroMel_CAF1
Location	2,901,858 – 2,901,991
Length	133
Max. P	0.991979

overview

Window 6

Location	2,901,858 – 2,901,967
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.43
Mean single sequence MFE	-46.70
Consensus MFE	-30.34
Energy contribution	-31.34
Covariance contribution	1.00
Combinations/Pair	1.23
Mean z-score	-2.58
Structure conservation index	0.65
SVM decision value	1.67
SVM RNA-class probability	0.970990
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2901858 109 - 27905053
UCGCCUCCCAGGCGAUGACAUCUGAGGCAAGUGCGGUGAAGAAGCAUUUGUAAUGAUGCGUCAUCCGCUGGGGGA--GGCACAUUCCGCCCAACUCC---------CGCCUGGGGUGUAU
(((((.....)))))..((((((.((((.((((.(((((....(((((......))))).)))))))))(((((.--(((.......)))...))))---------))))).)))))).. ( -50.60)
>DroSec_CAF1 8611 109 - 1
UCGCCUCCCAGGCGAUGACAUCUGAGGCAAGUGCGGUGAAGAAGCAUUUGUAAUGAUGCGUCAUCCGCUGGGGGA--GGCACAUGCCGCCCAACUCC---------CGCCCGGGGUGUAU
..(((((((.((((((((((((....((((((((.........))))))))...)))..))))).))))..))))--)))((((.(((..(......---------.)..))).)))).. ( -47.80)
>DroSim_CAF1 9627 109 - 1
UCGCCUCCCAGGCGAUGACAUCUGAGGCAAGUGCGGUGAAGAAGCAUUUGUAAUGAUGCGUCAUCCGCUGGGGGA--GGCACAUGCCGCCCAACUCC---------CGCCCGGGGUGUAU
..(((((((.((((((((((((....((((((((.........))))))))...)))..))))).))))..))))--)))((((.(((..(......---------.)..))).)))).. ( -47.80)
>DroYak_CAF1 9548 105 - 1
UCGCCUCCUAAGCGAUGACCUCUGAGGCAAGUGCUGUAA---AGCAUUUGUAAUGAUGCGUCAUCCACUGG-GGA--GGCACUUUCAGCCCAACUCC---------CGCUCAGGGUGUAU
..(((((((.((.(((((((((....(((((((((....---)))))))))...)).).))))))..)).)-)))--)))............((.((---------(.....))).)).. ( -42.70)
>DroAna_CAF1 8704 117 - 1
UCGCCAGAGAGGCGAUGACAUCUGCCAGAAGUGCUGUAG---AAUGUUUGUAAUAAUGCGUCAUCCGCUGGGGGGGUGGCAUUGUCAACCCGAUGCCCCAACCAGUCCCCGGGGGUGUAU
(((((.....))))).(((((((((.((.....))))))---.))))).............(((((.((((((.((((((((((......)))))))...)))...)))))))))))... ( -44.60)
>consensus
UCGCCUCCCAGGCGAUGACAUCUGAGGCAAGUGCGGUGAAGAAGCAUUUGUAAUGAUGCGUCAUCCGCUGGGGGA__GGCACAUUCCGCCCAACUCC_________CGCCCGGGGUGUAU
(((((.....)))))..((((((..(((.((((.(((((....(((((......))))).)))))))))((((....(((.......)))...))))..........)))..)))))).. (-30.34 = -31.34 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	2,901,889 – 2,901,991
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.69
Mean single sequence MFE	-32.52
Consensus MFE	-19.16
Energy contribution	-19.84
Covariance contribution	0.68
Combinations/Pair	1.21
Mean z-score	-1.88
Structure conservation index	0.59
SVM decision value	0.33
SVM RNA-class probability	0.692540
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2901889 102 + 27905053
GCC--UCCCCCAGCGGAUGACGCAUCAUUACAAAUGCUUCUUCACCGCACUUGCCUCAGAUGUCAUCGCCUGGGAGGCGACCUCUUUUCCGCCAU---AAGCGAGGC-------------
(((--((.(((((.(((((((((((........)))).........((....)).......)))))).)))))).((((..........))))..---....)))))------------- ( -35.60)
>DroSec_CAF1 8642 115 + 1
GCC--UCCCCCAGCGGAUGACGCAUCAUUACAAAUGCUUCUUCACCGCACUUGCCUCAGAUGUCAUCGCCUGGGAGGCGACCUCUUUUCCGCCAU---AAGCGAGGCAUAAAUAGAUGGA
(((--((.(((((.(((((((((((........)))).........((....)).......)))))).)))))).((((..........))))..---....)))))............. ( -37.30)
>DroSim_CAF1 9658 115 + 1
GCC--UCCCCCAGCGGAUGACGCAUCAUUACAAAUGCUUCUUCACCGCACUUGCCUCAGAUGUCAUCGCCUGGGAGGCGACCUCUUUUCCGCCAU---AAGCGAGGCAUAAAUAGAUGGA
(((--((.(((((.(((((((((((........)))).........((....)).......)))))).)))))).((((..........))))..---....)))))............. ( -37.30)
>DroYak_CAF1 9579 110 + 1
GCC--UCC-CCAGUGGAUGACGCAUCAUUACAAAUGCU---UUACAGCACUUGCCUCAGAGGUCAUCGCUUAGGAGGCGACCUCUUUU-CGCCAU---AAUCAAGGCAUAAAUAGAUGGA
(((--(((-..((((.(((((.(.((....(((.((((---....)))).))).....))))))))))))..))))))..(((((...-.(((..---......)))......))).)). ( -34.20)
>DroAna_CAF1 8744 112 + 1
GCCACCCCCCCAGCGGAUGACGCAUUAUUACAAACAUU---CUACAGCACUUCUGGCAGAUGUCAUCGCCUCUCUGGCGACCUCUUUUCCACUUUCCCAAGUACAAUAUAAGUAG-----
............(((.....)))...............---((((........((((....))))(((((.....)))))...............................))))----- ( -18.20)
>consensus
GCC__UCCCCCAGCGGAUGACGCAUCAUUACAAAUGCUUCUUCACCGCACUUGCCUCAGAUGUCAUCGCCUGGGAGGCGACCUCUUUUCCGCCAU___AAGCGAGGCAUAAAUAGAUGGA
(((..((((...(((.(((((((((........)))).........((....)).......))))))))..)))))))............(((...........)))............. (-19.16 = -19.84 +   0.68)

alignment

secondary structure

dotplot

Window 8

Location	2,901,889 – 2,901,991
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.69
Mean single sequence MFE	-42.82
Consensus MFE	-27.58
Energy contribution	-27.42
Covariance contribution	-0.16
Combinations/Pair	1.31
Mean z-score	-2.73
Structure conservation index	0.64
SVM decision value	2.30
SVM RNA-class probability	0.991979
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2901889 102 - 27905053
-------------GCCUCGCUU---AUGGCGGAAAAGAGGUCGCCUCCCAGGCGAUGACAUCUGAGGCAAGUGCGGUGAAGAAGCAUUUGUAAUGAUGCGUCAUCCGCUGGGGGA--GGC
-------------(((((.(((---..((((((.........(((.....)))((((.((((....((((((((.........))))))))...)))))))).))))))))).))--))) ( -45.70)
>DroSec_CAF1 8642 115 - 1
UCCAUCUAUUUAUGCCUCGCUU---AUGGCGGAAAAGAGGUCGCCUCCCAGGCGAUGACAUCUGAGGCAAGUGCGGUGAAGAAGCAUUUGUAAUGAUGCGUCAUCCGCUGGGGGA--GGC
.((.(((.(((.((((......---..)))).))))))))..(((((((.((((((((((((....((((((((.........))))))))...)))..))))).))))..))))--))) ( -47.10)
>DroSim_CAF1 9658 115 - 1
UCCAUCUAUUUAUGCCUCGCUU---AUGGCGGAAAAGAGGUCGCCUCCCAGGCGAUGACAUCUGAGGCAAGUGCGGUGAAGAAGCAUUUGUAAUGAUGCGUCAUCCGCUGGGGGA--GGC
.((.(((.(((.((((......---..)))).))))))))..(((((((.((((((((((((....((((((((.........))))))))...)))..))))).))))..))))--))) ( -47.10)
>DroYak_CAF1 9579 110 - 1
UCCAUCUAUUUAUGCCUUGAUU---AUGGCG-AAAAGAGGUCGCCUCCUAAGCGAUGACCUCUGAGGCAAGUGCUGUAA---AGCAUUUGUAAUGAUGCGUCAUCCACUGG-GGA--GGC
...((((.(((.((((......---..))))-.))).)))).(((((((.((.(((((((((....(((((((((....---)))))))))...)).).))))))..)).)-)))--))) ( -42.60)
>DroAna_CAF1 8744 112 - 1
-----CUACUUAUAUUGUACUUGGGAAAGUGGAAAAGAGGUCGCCAGAGAGGCGAUGACAUCUGCCAGAAGUGCUGUAG---AAUGUUUGUAAUAAUGCGUCAUCCGCUGGGGGGGUGGC
-----.(((..(((((.(((..(.(....(((...(((.((((((.....))))))....))).)))....).).))).---)))))..))).......(((((((.(...).))))))) ( -31.60)
>consensus
UCCAUCUAUUUAUGCCUCGCUU___AUGGCGGAAAAGAGGUCGCCUCCCAGGCGAUGACAUCUGAGGCAAGUGCGGUGAAGAAGCAUUUGUAAUGAUGCGUCAUCCGCUGGGGGA__GGC
............(((((((((......))).....(((.((((((.....))))))....)))))))))((((.(((((....(((((......))))).)))))))))........... (-27.58 = -27.42 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:58 2006