Locus 3236

Sequence ID	3L_DroMel_CAF1
Location	9,474,628 – 9,474,758
Length	130
Max. P	0.979426

overview

Window 4

Location	9,474,628 – 9,474,727
Length	99
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	76.58
Mean single sequence MFE	-19.90
Consensus MFE	-11.75
Energy contribution	-12.37
Covariance contribution	0.61
Combinations/Pair	1.19
Mean z-score	-2.41
Structure conservation index	0.59
SVM decision value	1.84
SVM RNA-class probability	0.979426
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9474628 99 + 23771897
AUUUGCUCUUAUCAUACAUACAUACCUUUUGCACUAUUUUCGCCCCGAAAAACCAGUGCAAACUGGUUCAUCCGAUUUAUCGGAAGAUAUAC--UACACCU
.........((((..........(((.((((((((.((((((...))))))...))))))))..)))...(((((....))))).))))...--....... ( -22.80)
>DroSec_CAF1 12305 98 + 1
GUUUGCUCUUAUCA--CAUACAUAGCUUUUGCACUAUUUUCGCCCCGAA-AACCAGUGCAAACUGGUUCAUCCGAUAGAUCGGAAGAUAUACCCCACACCU
((.((....((((.--.......((((((((((((.((((((...))))-))..))))))))..))))..(((((....))))).)))).....)).)).. ( -21.90)
>DroSim_CAF1 12911 98 + 1
GUUUGCUCUUAUCA--CAUACAUAGCUUUUGCACUAUUUUCGCCCCGAA-AACCAGUGCAAACUGGUUCAUCCGAUAGAUCGGAAGAUAUACCCCACACCU
((.((....((((.--.......((((((((((((.((((((...))))-))..))))))))..))))..(((((....))))).)))).....)).)).. ( -21.90)
>DroEre_CAF1 12334 82 + 1
GUUUGCUCUUAUCG--C----AUAGUUUUUGCACUAUUUUAGCCCCAAA-AACCAGUGCAAACUGGUUCACCCGAUUUAUCGGAAGAUA------------
.........(((((--(----(.......))).................-(((((((....)))))))...((((....))))..))))------------ ( -16.80)
>DroYak_CAF1 12432 85 + 1
GUUUGCUCUUAUCG--CACACAUAGUUUUUGCACUAUUUUUGCCCCAAA-AACCAGUGCAAACUGGCUCAUCCGAUUUAUCGGAU-CUA------------
((.(((.......)--)).)).(((((..((((((.((((((...))))-))..)))))))))))....((((((....))))))-...------------ ( -21.10)
>DroAna_CAF1 12741 77 + 1
GUUUGCCCUUAUCA--C----AUAGUU--UUCACUGUUUUUCCCC--GA-AACUAGUGCGAACUGGUUUAUCUGAACAAUCGGUCGGU-------------
....(((...(((.--.----.(((((--(.(((((((((.....--))-))).)))).))))))((((....))))....))).)))------------- ( -14.90)
>consensus
GUUUGCUCUUAUCA__CAUACAUAGCUUUUGCACUAUUUUCGCCCCGAA_AACCAGUGCAAACUGGUUCAUCCGAUUUAUCGGAAGAUA____________
.........((((.....................................(((((((....)))))))..(((((....))))).))))............ (-11.75 = -12.37 +   0.61)

alignment

secondary structure

dotplot

Window 5

Location	9,474,667 – 9,474,758
Length	91
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	71.22
Mean single sequence MFE	-20.38
Consensus MFE	-11.36
Energy contribution	-11.58
Covariance contribution	0.22
Combinations/Pair	1.17
Mean z-score	-1.91
Structure conservation index	0.56
SVM decision value	1.47
SVM RNA-class probability	0.956939
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9474667 91 + 23771897
UCGCCCCGAAAAACCAGUGCAAACUGGUUCAUCCGAUUUAUCGGAAGAUAUAC--UACACCUAUUCAUAUAU-AUACAUAUAUAUAGUUGC-UCG
..((...(((..((((((....))))))((.(((((....))))).)).....--........))).(((((-((....)))))))...))-... ( -19.50)
>DroSec_CAF1 12342 93 + 1
UCGCCCCGAA-AACCAGUGCAAACUGGUUCAUCCGAUAGAUCGGAAGAUAUACCCCACACCUAUUCAUAUAU-AUCUAUAUAGGUGGUCGUGUCG
..........-(((((((....)))))))..(((((....))))).(((((..((...((((((........-......))))))))..))))). ( -25.04)
>DroSim_CAF1 12948 93 + 1
UCGCCCCGAA-AACCAGUGCAAACUGGUUCAUCCGAUAGAUCGGAAGAUAUACCCCACACCUAUUCAUAUAU-AUCUAUAUAGGUGGUCGUGUCG
..........-(((((((....)))))))..(((((....))))).(((((..((...((((((........-......))))))))..))))). ( -25.04)
>DroEre_CAF1 12367 74 + 1
UAGCCCCAAA-AACCAGUGCAAACUGGUUCACCCGAUUUAUCGGAAGAUA-------------------UAU-AUAUAUAUAUGUGGUCGUGUCG
..........-(((((((....)))))))(((((((....))))..((((-------------------(((-((....)))))).))))))... ( -17.90)
>DroYak_CAF1 12469 74 + 1
UUGCCCCAAA-AACCAGUGCAAACUGGCUCAUCCGAUUUAUCGGAU-CUA-------------------UAUCAUAUAUAUAGGUAGUCGUGUCG
(((((.....-..(((((....)))))...((((((....))))))-...-------------------.............)))))........ ( -16.50)
>DroAna_CAF1 12772 73 + 1
UUCCCC--GA-AACUAGUGCGAACUGGUUUAUCUGAACAAUCGGUCGGU----------------CGG--AU-AUAUAUAUAUGUGCAUGUCCCG
....((--((-(((((((....)))))))...((((....)))))))).----------------.((--((-((.(((....))).)))))).. ( -18.30)
>consensus
UCGCCCCGAA_AACCAGUGCAAACUGGUUCAUCCGAUUUAUCGGAAGAUA_______________CAU_UAU_AUAUAUAUAGGUGGUCGUGUCG
...........(((((((....)))))))..(((((....))))).................................................. (-11.36 = -11.58 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:42 2006