Locus 9687

Sequence ID	3R_DroMel_CAF1
Location	25,632,690 – 25,632,850
Length	160
Max. P	0.887510

overview

Window 8

Location	25,632,690 – 25,632,810
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-34.10
Consensus MFE	-28.88
Energy contribution	-30.12
Covariance contribution	1.24
Combinations/Pair	1.03
Mean z-score	-1.59
Structure conservation index	0.85
SVM decision value	0.95
SVM RNA-class probability	0.887510
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25632690 120 - 27905053
AAAAGAAAGCAAAACGCUUUCAAGAAGUUCGCCCCGGAUUGCCGCAACCGUCCGGCAACGACACUAGUGCUGCGCACAAGACUUCACUCUUCAGGCUGUUGAACAGUCCGCCGCGACUUU
....((((((.....))))))..(((((.(((..(((((((...((((.(((((....))...((.((((...)))).)).............))).))))..)))))))..)))))))) ( -40.80)
>DroSec_CAF1 7285 120 - 1
AAAAGAAAGCAAAACGCUUUCAAGAAGUUCGCCCCGGAUUGCCGCAACCGUCCGGCAACGCCACUCGUGCUGCGCACAAAACUUCACUCUUCAGGCUGUUAAACUGUCCACCGCGACUUU
....((((((.....))))))..(((((.(((...((((....(((.((....(((...)))....((((...))))................)).)))......))))...)))))))) ( -30.20)
>DroSim_CAF1 7643 120 - 1
AAAAGAAAGCAAAACGCUUUCAAGAAGUUCGCCCCGGAUUGCCGCAACCGUCCGGCAACGCCACUCGUGCUGCGCACAAAACUUCACUCUUCAGGCUGUUAAAUUGUCCGCCGCGACUUU
....((((((.....))))))..(((((.(((..(((((....(((.((....(((...)))....((((...))))................)).)))......)))))..)))))))) ( -33.30)
>DroEre_CAF1 7039 119 - 1
AAAACAAAGCAAACCGCCUU-AAGAAGUUCGCCCCGGAUUGCCGCAACCGUCCGGCAACGCUACUCGUGCUGCGCACAAUACUUCACUCUUCGGGCUGUUAAACAGUCCGCCGCGACUUU
..............(((...-..(((((..((.((((((.(......).))))))....)).....((((...))))...)))))......(((((((.....)))))))..)))..... ( -32.10)
>DroYak_CAF1 7084 119 - 1
AAAAGAAAGCAAACCGCUUU-AAGAAGUUCUCCCCGGAUUGUCGCAACCGUCCGGCAACGCCACUUGUGCUGCGCACAAGGCUUCACUCUUCAGGCUGUUUAACAGUCCGCCGCGACUUU
.....(((((.....)))))-..((((((.....((((((((.(((.((....(((...))).(((((((...))))))).............)).)))...))))))))....)))))) ( -34.10)
>consensus
AAAAGAAAGCAAAACGCUUUCAAGAAGUUCGCCCCGGAUUGCCGCAACCGUCCGGCAACGCCACUCGUGCUGCGCACAAAACUUCACUCUUCAGGCUGUUAAACAGUCCGCCGCGACUUU
....((((((.....))))))..(((((.(((..(((((((..(((.((...((....))......((((...))))................)).)))....)))))))..)))))))) (-28.88 = -30.12 +   1.24)

alignment

secondary structure

dotplot

Window 9

Location	25,632,730 – 25,632,850
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.91
Mean single sequence MFE	-35.32
Consensus MFE	-29.50
Energy contribution	-29.82
Covariance contribution	0.32
Combinations/Pair	1.12
Mean z-score	-1.64
Structure conservation index	0.84
SVM decision value	0.94
SVM RNA-class probability	0.885326
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25632730 120 - 27905053
CAGAAUAGCGCGGCCUUCCUUCACACCGCACAAGCUCGCAAAAAGAAAGCAAAACGCUUUCAAGAAGUUCGCCCCGGAUUGCCGCAACCGUCCGGCAACGACACUAGUGCUGCGCACAAG
.......(((((((((..((((.....((........)).....((((((.....))))))..)))).(((..((((((.(......).))))))...)))....)).)))))))..... ( -37.30)
>DroSec_CAF1 7325 120 - 1
CAGAAUAGCGCGGCCUUCCUCCGCACCGCACAAGCUCGCAAAAAGAAAGCAAAACGCUUUCAAGAAGUUCGCCCCGGAUUGCCGCAACCGUCCGGCAACGCCACUCGUGCUGCGCACAAA
.......(((((((((((....((...((....))..)).....((((((.....))))))..))))........((.((((((........))))))..))......)))))))..... ( -36.90)
>DroSim_CAF1 7683 120 - 1
CAGAAUAGCGCGGCCUUCCUCCGCACCGCACAAGCUCGCAAAAAGAAAGCAAAACGCUUUCAAGAAGUUCGCCCCGGAUUGCCGCAACCGUCCGGCAACGCCACUCGUGCUGCGCACAAA
.......(((((((((((....((...((....))..)).....((((((.....))))))..))))........((.((((((........))))))..))......)))))))..... ( -36.90)
>DroEre_CAF1 7079 119 - 1
AGAAAUAGCGCGGCCUCCCUCUGCACCGCACAAGCUCGCGAAAACAAAGCAAACCGCCUU-AAGAAGUUCGCCCCGGAUUGCCGCAACCGUCCGGCAACGCUACUCGUGCUGCGCACAAU
.......(((((((........((.((((....))..(((((......((.....))...-......)))))...)).((((((........)))))).)).......)))))))..... ( -32.12)
>DroYak_CAF1 7124 119 - 1
AAGAAUAGCGCGGCCACCCUCCGCACCGCACAAGCUCACGAAAAGAAAGCAAACCGCUUU-AAGAAGUUCUCCCCGGAUUGUCGCAACCGUCCGGCAACGCCACUUGUGCUGCGCACAAG
.......(((((((........))...(((((((.....(((...(((((.....)))))-......)))...((((((.((....)).))))))........))))))))))))..... ( -33.40)
>consensus
CAGAAUAGCGCGGCCUUCCUCCGCACCGCACAAGCUCGCAAAAAGAAAGCAAAACGCUUUCAAGAAGUUCGCCCCGGAUUGCCGCAACCGUCCGGCAACGCCACUCGUGCUGCGCACAAA
.......((((((((....((((....((....)).........((((((.....)))))).............))))((((((........))))))........).)))))))..... (-29.50 = -29.82 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:39:54 2006