Locus 394

Sequence ID	3L_DroMel_CAF1
Location	1,136,300 – 1,136,432
Length	132
Max. P	0.907707

overview

Window 7

Location	1,136,300 – 1,136,392
Length	92
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	80.51
Mean single sequence MFE	-21.57
Consensus MFE	-13.44
Energy contribution	-13.58
Covariance contribution	0.14
Combinations/Pair	1.27
Mean z-score	-2.51
Structure conservation index	0.62
SVM decision value	1.05
SVM RNA-class probability	0.907707
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1136300 92 - 23771897
CUAAUCCACCUGCCAACAGGUGGCCCAAUAUGCCCAACCUGAGGUCAAGGGGUAG---UCGUAGAAG---CAAAUUACACAAAUUUAAAAAUAAUAAA
(((..(((((((....))))))).......(((((.(((...)))....))))).---...)))...---............................ ( -19.10)
>DroPse_CAF1 36120 81 - 1
AG-GUGCA-GAGCC--CACGGGGCCCAAUAUGCCCCA-------UCGAGGGGUGG---GCA---AAGGCACAAAUUACACAAAUUUAAAAAUAAUAAA
..-((((.-..(((--((((((((.......))))).-------.(....)))))---)).---...))))........................... ( -26.80)
>DroSec_CAF1 29521 89 - 1
CCAAUCCACCUGCCAACAGGUGGCCCAAUAUGCCCAGCCUGAGGUCAAGGGGUAG---UCG---AAG---CAAAUUACACGAAUUUAAAAAUAAUAAA
.....(((((((....))))))).......(((((.(((...)))....))))).---...---...---............................ ( -19.00)
>DroSim_CAF1 27333 89 - 1
CUAAUCCACCUGCCCACAGGUGGCCCAAUAUGCCCAGCCUGGGGUCAAGGGGUAG---UCA---AAG---CAAAUUACACAAAUUUAAAAAUAAUAAA
........(((((((.((((((((.......)))..)))))))))..))).((((---(..---...---...))))).................... ( -22.10)
>DroEre_CAF1 27493 89 - 1
CUAAUCCGCCUGCCAACAGGUGGUCCAAAAUGCCCAGCCCGGGGUUAAUGGGUAG---UCA---GAG---CAAAUUACACAGAUUUAAAAAUAAUAAA
.....(((((((....))))))).(((....((((......))))...)))((((---(..---...---...))))).................... ( -21.20)
>DroYak_CAF1 30395 92 - 1
CUAAUCCACCUGCCAACAGGUGGUCCAAAAUGCCCAACCUCAGGUUAAGAGGUACUCCUCA---GAG---CAAAUUACACGAAUUUAAUAAUAAUAAA
.....(((((((....))))))).......(((.(((((...))))..((((....)))).---).)---)).......................... ( -21.20)
>consensus
CUAAUCCACCUGCCAACAGGUGGCCCAAUAUGCCCAACCUGAGGUCAAGGGGUAG___UCA___AAG___CAAAUUACACAAAUUUAAAAAUAAUAAA
.....(((((((....))))))).......(((((.(((...)))....)))))............................................ (-13.44 = -13.58 +   0.14)

alignment

secondary structure

dotplot

Window 8

Location	1,136,336 – 1,136,432
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.23
Mean single sequence MFE	-33.18
Consensus MFE	-20.32
Energy contribution	-19.80
Covariance contribution	-0.52
Combinations/Pair	1.39
Mean z-score	-1.62
Structure conservation index	0.61
SVM decision value	0.90
SVM RNA-class probability	0.878235
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1136336 96 + 23771897
A---CUACCCCUUGACCU------CAGG---UUGGGCAUAUUGGGCCACCUGUUGGC------------AGGUGGAUUAGGCCACGAUUCCGCCAGAUUACUGGGUAAAUUCUAGUCCAA
.---......((((.((.------((((---(.((.(......).)))))))..)))------------)))(((((((((...((....))((((....))))......))))))))). ( -31.30)
>DroSec_CAF1 29554 96 + 1
A---CUACCCCUUGACCU------CAGG---CUGGGCAUAUUGGGCCACCUGUUGGC------------AGGUGGAUUGGGCCACCAUUCCGCCAGAUCACUGGGUAAAUUCUAGUCCAA
.---.(((((..(((((.------((((---.(((.(......).)))))))..)).------------.((((((.(((....))).))))))...)))..)))))............. ( -37.10)
>DroSim_CAF1 27366 96 + 1
A---CUACCCCUUGACCC------CAGG---CUGGGCAUAUUGGGCCACCUGUGGGC------------AGGUGGAUUAGGCCACCAUUCCGCCAGAUUACUGGGUAAAUUCUAGUCCAA
.---.(((((..((.(((------((((---.(((.(......).))))))).))))------------)((((((...((...))..))))))........)))))............. ( -34.50)
>DroEre_CAF1 27526 96 + 1
A---CUACCCAUUAACCC------CGGG---CUGGGCAUUUUGGACCACCUGUUGGC------------AGGCGGAUUAGGCGACACUUCCGCCAGAUUACUGGGUAAGCAAUAGUCCAA
.---.((((((.(((((.------((((---.(((..........)))))))..)).------------.((((((...(....)...))))))...))).))))))............. ( -30.30)
>DroYak_CAF1 30428 99 + 1
AGGAGUACCUCUUAACCU------GAGG---UUGGGCAUUUUGGACCACCUGUUGGC------------AGGUGGAUUAGGCGACGAUUCCGCCAGAUUACUGGGUAACUCAUAGUUCAA
..(((((((((((((((.------..))---))))).........(((((((....)------------))))))....((((.......))))........)))).))))......... ( -33.00)
>DroAna_CAF1 32700 117 + 1
C---AUACCCCUUACUCCUAACUCUGGGAAUUGGGGUAUCUCCGGCCACCUGAAAUCCACCAAAAAAUUAGUGUGAUUAGGCCAUGAUUCUGGGCGAUUACUGGGUAAGAUAAGGUCGAG
.---(((((((....(((((....)))))...)))))))...(((((.(((((..(((((..........))).)))))))((((((((......))))).))).........))))).. ( -32.90)
>consensus
A___CUACCCCUUAACCC______CAGG___CUGGGCAUAUUGGGCCACCUGUUGGC____________AGGUGGAUUAGGCCACGAUUCCGCCAGAUUACUGGGUAAAUUAUAGUCCAA
.....(((((..(((.........((((....(((.(......).)))))))..................((((((...(....)...))))))...)))..)))))............. (-20.32 = -19.80 +  -0.52)

alignment

secondary structure

dotplot

Window 9

Location	1,136,336 – 1,136,432
Length	96
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.23
Mean single sequence MFE	-33.05
Consensus MFE	-16.20
Energy contribution	-17.29
Covariance contribution	1.09
Combinations/Pair	1.20
Mean z-score	-1.67
Structure conservation index	0.49
SVM decision value	-0.01
SVM RNA-class probability	0.527822
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1136336 96 - 23771897
UUGGACUAGAAUUUACCCAGUAAUCUGGCGGAAUCGUGGCCUAAUCCACCU------------GCCAACAGGUGGCCCAAUAUGCCCAA---CCUG------AGGUCAAGGGGUAG---U
............((((((..(.(((((((((....((((......))))))------------)))..((((((((.......)))..)---))))------)))).)..))))))---. ( -31.10)
>DroSec_CAF1 29554 96 - 1
UUGGACUAGAAUUUACCCAGUGAUCUGGCGGAAUGGUGGCCCAAUCCACCU------------GCCAACAGGUGGCCCAAUAUGCCCAG---CCUG------AGGUCAAGGGGUAG---U
............((((((..((((((((((....(((((......))))))------------)))..((((((((.......)))..)---))))------))))))..))))))---. ( -38.30)
>DroSim_CAF1 27366 96 - 1
UUGGACUAGAAUUUACCCAGUAAUCUGGCGGAAUGGUGGCCUAAUCCACCU------------GCCCACAGGUGGCCCAAUAUGCCCAG---CCUG------GGGUCAAGGGGUAG---U
..((.(((..((((..((((....))))..))))..)))))....((.(((------------((((.((((((((.......)))..)---))))------))))..)))))...---. ( -33.10)
>DroEre_CAF1 27526 96 - 1
UUGGACUAUUGCUUACCCAGUAAUCUGGCGGAAGUGUCGCCUAAUCCGCCU------------GCCAACAGGUGGUCCAAAAUGCCCAG---CCCG------GGGUUAAUGGGUAG---U
((((((.((((((.....))))))..(((((.....))))).....(((((------------(....))))))))))))..(((((((---((..------.)))...)))))).---. ( -33.00)
>DroYak_CAF1 30428 99 - 1
UUGAACUAUGAGUUACCCAGUAAUCUGGCGGAAUCGUCGCCUAAUCCACCU------------GCCAACAGGUGGUCCAAAAUGCCCAA---CCUC------AGGUUAAGAGGUACUCCU
.........((((.(((...(((((((((((.....)))))....((((((------------(....)))))))..............---....------))))))...))))))).. ( -29.80)
>DroAna_CAF1 32700 117 - 1
CUCGACCUUAUCUUACCCAGUAAUCGCCCAGAAUCAUGGCCUAAUCACACUAAUUUUUUGGUGGAUUUCAGGUGGCCGGAGAUACCCCAAUUCCCAGAGUUAGGAGUAAGGGGUAU---G
(((....................((.....))....(((((.((((.((((((....))))))))))......))))))))(((((((.(((((........)))))..)))))))---. ( -33.00)
>consensus
UUGGACUAGAAUUUACCCAGUAAUCUGGCGGAAUCGUGGCCUAAUCCACCU____________GCCAACAGGUGGCCCAAUAUGCCCAA___CCUG______AGGUCAAGGGGUAG___U
.............(((((..(((((((((.........)))....((((((..................))))))...........................))))))..)))))..... (-16.20 = -17.29 +   1.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:49 2006