Locus 9680

Sequence ID	3R_DroMel_CAF1
Location	25,606,835 – 25,606,935
Length	100
Max. P	0.914924

overview

Window 9

Location	25,606,835 – 25,606,935
Length	100
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	66.83
Mean single sequence MFE	-32.24
Consensus MFE	-10.64
Energy contribution	-13.24
Covariance contribution	2.60
Combinations/Pair	1.11
Mean z-score	-1.99
Structure conservation index	0.33
SVM decision value	0.48
SVM RNA-class probability	0.753218
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25606835 100 + 27905053
CGAUACGUGAUUCUGGCCAGCAAGAGCUGAUCAGACUACUCUAUCA-GCUCUAGCUUCCGAGCUGGAAGAGCUCGGAAUUCGUAUCUGAAACUGGAAGCGG
.((((((.((((((((..(((.(((((((((.(((....)))))))-))))).))).))(((((.....))))))))))))))))).....(((....))) ( -41.40)
>DroSec_CAF1 33768 92 + 1
CGAUACGUGAUUCUGGCCAGCAAGAGCUGAGCAGACUACUCUACC--GCUCCAGCUUCCGAGCUGGAAGUGCUCGCAAUCUG-------GACUGUAAGCGG
......(((..((((..((((....))))..)))).)))....((--(((((((.((.(((((.......))))).)).)))-------))......)))) ( -30.00)
>DroSim_CAF1 34635 99 + 1
UAAUACGUGAUUCUGGCCAGCAAAAGCUGAGCAGACUACUCUACC--GCUCCAGCUUCCGAGCUUGAAGUGCUCGCAAUCCGUAUCUGGAACUGGAAGCGG
......(((..((((..((((....))))..)))).)))....((--(((((((.((((((((.......))))((.....))....)))))))).))))) ( -35.10)
>DroEre_CAF1 34753 93 + 1
AGUUACGUGAUUCUGGGCUAUAAGGCAAGUGCAGAGUAAUG--CCAGUCGCUGGCUUCCGUGCUGGAAAUGCCGGC------UAUCUGGAACUGGAAGCUA
((((.(((.((((((.(((........))).)))))).)))--((((..((((((((((.....))))..))))))------...))))))))........ ( -32.10)
>DroYak_CAF1 35998 78 + 1
AGAUACGUGAUUAUGGGCUACCAG----------AAU------CCGCUCUUUGGCUUCCGAG-UGGAAGUGUCGGU------UAUCAGGAACUGGAAGCUA
.(((((.......(((....))).----------..(------((((((..........)))-)))).)))))(((------(.((((...)))).)))). ( -22.60)
>consensus
AGAUACGUGAUUCUGGCCAGCAAGAGCUGAGCAGACUACUCUACC__GCUCUAGCUUCCGAGCUGGAAGUGCUCGCAAU__GUAUCUGGAACUGGAAGCGG
...........((((..((((....))))..))))..................((((((((((.......))))...................)))))).. (-10.64 = -13.24 +   2.60)

alignment

secondary structure

dotplot

Window 0

Location	25,606,835 – 25,606,935
Length	100
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	66.83
Mean single sequence MFE	-30.44
Consensus MFE	-11.46
Energy contribution	-14.18
Covariance contribution	2.72
Combinations/Pair	1.15
Mean z-score	-2.11
Structure conservation index	0.38
SVM decision value	1.10
SVM RNA-class probability	0.914924
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25606835 100 - 27905053
CCGCUUCCAGUUUCAGAUACGAAUUCCGAGCUCUUCCAGCUCGGAAGCUAGAGC-UGAUAGAGUAGUCUGAUCAGCUCUUGCUGGCCAGAAUCACGUAUCG
...............((((((...((((((((.....))))))))(((.(((((-(((((((....))).))))))))).)))...........)))))). ( -40.60)
>DroSec_CAF1 33768 92 - 1
CCGCUUACAGUC-------CAGAUUGCGAGCACUUCCAGCUCGGAAGCUGGAGC--GGUAGAGUAGUCUGCUCAGCUCUUGCUGGCCAGAAUCACGUAUCG
..(((..((((.-------...))))..)))..((((((((....))))))))(--((((..((..((((..((((....))))..))))...)).))))) ( -34.70)
>DroSim_CAF1 34635 99 - 1
CCGCUUCCAGUUCCAGAUACGGAUUGCGAGCACUUCAAGCUCGGAAGCUGGAGC--GGUAGAGUAGUCUGCUCAGCUUUUGCUGGCCAGAAUCACGUAUUA
(((((.((((((((......)))((.(((((.......))))).))))))))))--))..((....((((..((((....))))..)))).))........ ( -39.10)
>DroEre_CAF1 34753 93 - 1
UAGCUUCCAGUUCCAGAUA------GCCGGCAUUUCCAGCACGGAAGCCAGCGACUGG--CAUUACUCUGCACUUGCCUUAUAGCCCAGAAUCACGUAACU
........(((.((((...------((.(((..((((.....))))))).))..))))--.)))..((((..((........))..))))........... ( -19.90)
>DroYak_CAF1 35998 78 - 1
UAGCUUCCAGUUCCUGAUA------ACCGACACUUCCA-CUCGGAAGCCAAAGAGCGG------AUU----------CUGGUAGCCCAUAAUCACGUAUCU
..(((.((((.(((.....------.((((........-.))))..((......))))------)..----------)))).)))................ ( -17.90)
>consensus
CCGCUUCCAGUUCCAGAUAC__AUUGCGAGCACUUCCAGCUCGGAAGCUAGAGC__GGUAGAGUAGUCUGCUCAGCUCUUGCUGGCCAGAAUCACGUAUCG
..((((((.((..............))((((.......))))))))))..................((((..((((....))))..))))........... (-11.46 = -14.18 +   2.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:39:46 2006