Locus 9747

Sequence ID	3R_DroMel_CAF1
Location	25,794,971 – 25,795,075
Length	104
Max. P	0.813088

overview

Window 9

Location	25,794,971 – 25,795,075
Length	104
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	87.64
Mean single sequence MFE	-22.76
Consensus MFE	-17.04
Energy contribution	-17.52
Covariance contribution	0.48
Combinations/Pair	1.12
Mean z-score	-1.68
Structure conservation index	0.75
SVM decision value	0.21
SVM RNA-class probability	0.635501
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25794971 104 + 27905053
UUCAAUUACGUUUACGGAUCGACUGCCGGCGGCAUUUCAGCCAGCUCUAAGCUGAUUUUCCAGCAUUUU-UCCAACACUUCUCCGCCAGCUUC------AGCUAUCACCUA
........((....))(((.(...((.((((((......)))........((((......)))).....-..............))).))...------..).)))..... ( -20.60)
>DroSec_CAF1 38338 104 + 1
UUCAAUUACGUUUACGGAUCGACUGCCGGCGGCAUUUCAGCCCGCUCUAAGCUGACUUUCCAGCAUUUU-UCCAACACUUCUCGGCCAGCUUC------AGCUAUCACCUA
...............((.......(((((((((......).)))).....((((......)))).....-............)))).(((...------.)))....)).. ( -22.20)
>DroSim_CAF1 38700 104 + 1
UUCAAUUACGUUUACGGAUCGACUGCCGGCGGCAUUUCAGCCCGCUCUAAGCUGACUUUCCAGCAUUUU-UCCAACACUUCUCGGCCAGCUUC------AGCUAUCACCUA
...............((.......(((((((((......).)))).....((((......)))).....-............)))).(((...------.)))....)).. ( -22.20)
>DroEre_CAF1 39857 110 + 1
UUCAAUUACGA-UACGGAUCGACUGCCGGCGGCAUUUCAGCCAGUUCUAAGCUGAUUUUCCAGCAUUUUUUCCAACACUUCUUCGCCAGCUUCAGCUUCUGCUAUCACCUA
.........((-((((((......((.((((((......)))........((((......))))....................))).)).......)))).))))..... ( -26.02)
>DroYak_CAF1 38160 101 + 1
UUCAAUUACGA-UACGGUUCGACAGCCGGCGGCAUUUCAGCCGAGUCUAAGCUGAUUUUCCGGCAUUUUUUCAAACACUUCUUUGCUA---------UCACCUAUCACCUA
.........((-((.(((......(((((((((......))))((((......))))..))))).......((((......))))...---------..)))))))..... ( -22.80)
>consensus
UUCAAUUACGUUUACGGAUCGACUGCCGGCGGCAUUUCAGCCAGCUCUAAGCUGAUUUUCCAGCAUUUU_UCCAACACUUCUCCGCCAGCUUC______AGCUAUCACCUA
...............((..........((((((......)))........((((......))))....................)))((((........))))....)).. (-17.04 = -17.52 +   0.48)

alignment

secondary structure

dotplot

Window 0

Location	25,794,971 – 25,795,075
Length	104
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	87.64
Mean single sequence MFE	-30.72
Consensus MFE	-23.00
Energy contribution	-23.80
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.75
SVM decision value	0.65
SVM RNA-class probability	0.813088
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25794971 104 - 27905053
UAGGUGAUAGCU------GAAGCUGGCGGAGAAGUGUUGGA-AAAAUGCUGGAAAAUCAGCUUAGAGCUGGCUGAAAUGCCGCCGGCAGUCGAUCCGUAAACGUAAUUGAA
..(((....)))------...((((((((...((((((...-..))))))......((((((.......))))))....))))))))..(((((.((....))..))))). ( -30.80)
>DroSec_CAF1 38338 104 - 1
UAGGUGAUAGCU------GAAGCUGGCCGAGAAGUGUUGGA-AAAAUGCUGGAAAGUCAGCUUAGAGCGGGCUGAAAUGCCGCCGGCAGUCGAUCCGUAAACGUAAUUGAA
..((((((.(((------(((((((((.....((((((...-..)))))).....))))))))...((((.(......))))))))).))))..))............... ( -31.50)
>DroSim_CAF1 38700 104 - 1
UAGGUGAUAGCU------GAAGCUGGCCGAGAAGUGUUGGA-AAAAUGCUGGAAAGUCAGCUUAGAGCGGGCUGAAAUGCCGCCGGCAGUCGAUCCGUAAACGUAAUUGAA
..((((((.(((------(((((((((.....((((((...-..)))))).....))))))))...((((.(......))))))))).))))..))............... ( -31.50)
>DroEre_CAF1 39857 110 - 1
UAGGUGAUAGCAGAAGCUGAAGCUGGCGAAGAAGUGUUGGAAAAAAUGCUGGAAAAUCAGCUUAGAACUGGCUGAAAUGCCGCCGGCAGUCGAUCCGUA-UCGUAAUUGAA
..(((((((((....)))...((((((.....((((((......))))))((....((((((.......))))))....)))))))).))))..))...-........... ( -30.90)
>DroYak_CAF1 38160 101 - 1
UAGGUGAUAGGUGA---------UAGCAAAGAAGUGUUUGAAAAAAUGCCGGAAAAUCAGCUUAGACUCGGCUGAAAUGCCGCCGGCUGUCGAACCGUA-UCGUAAUUGAA
.....(((((((((---------((((......((((((....))))))(((....((((((.......))))))....)))...))))))..))).))-))......... ( -28.90)
>consensus
UAGGUGAUAGCU______GAAGCUGGCCGAGAAGUGUUGGA_AAAAUGCUGGAAAAUCAGCUUAGAGCGGGCUGAAAUGCCGCCGGCAGUCGAUCCGUAAACGUAAUUGAA
.....................((((((.....((((((......))))))((....((((((.......))))))....))))))))..((((..((....))...)))). (-23.00 = -23.80 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:41:15 2006