Locus 5708

Sequence ID	3R_DroMel_CAF1
Location	14,932,763 – 14,932,923
Length	160
Max. P	0.999171

overview

Window 0

Location	14,932,763 – 14,932,883
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.00
Mean single sequence MFE	-31.92
Consensus MFE	-28.80
Energy contribution	-29.04
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.43
Structure conservation index	0.90
SVM decision value	0.73
SVM RNA-class probability	0.834229
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14932763 120 + 27905053
UACAACGAAGGCUAAGGCCAUCCGCGGAGAAAGAGACGGCAUGCGUGGGCGCUGUUAAGUCAAUGUUAAAAGCGCAUGUUGGGCCAAUGUUAAGUGCUAAUAAGUAAACACUGCAAAAAA
......((.(((....))).)).((((.........((((((((((.((((.((......)).))))....))))))))))......((((...((((....))))))))))))...... ( -31.20)
>DroSec_CAF1 62633 120 + 1
UACAACGAAGGCUAAGGCCAUCCGCGGAGAAAGAGACGGCAUGCGUGGGCGCUGUUAAGUCAAUGUUAAAAGCGCAUGUUGGGCCAAUGUUAAGUGCUAAUAAGUAAACACUGCAAAAAA
......((.(((....))).)).((((.........((((((((((.((((.((......)).))))....))))))))))......((((...((((....))))))))))))...... ( -31.20)
>DroSim_CAF1 61332 120 + 1
UACAACGAAGGCUAAGGCCAUCCGCGGAGAAAGAGACGGCAUGCGUGGGCGCUGUUAAGUCAAUGUUAAAAGCGCAUGUUGGGCCAAUGUUAAGUGCUAAUAAGUAAACACUGCAAAAAA
......((.(((....))).)).((((.........((((((((((.((((.((......)).))))....))))))))))......((((...((((....))))))))))))...... ( -31.20)
>DroEre_CAF1 59182 119 + 1
UACAACGAAGGCUAAGGCCAUCCGCGGAGAAAGAGACGGCAUGCGUGGGCGCUGUUAAGUCAAUGUUA-AAGCGCAUGUUGGGCCAAUGUUAAGUGCUAAUAAGUAAACACUGCAAAAAA
......((.(((....))).)).((((.........((((((((((.((((.((......)).)))).-..))))))))))......((((...((((....))))))))))))...... ( -31.80)
>DroYak_CAF1 66176 119 + 1
UACAACGAAGGCUAAGGCCAUCCGCGGAGAAAGAGACGGCGUGCGUGGGCGCUGUUAAGUCAAUGUUAAAAGCGCAGGCUG-GCCAAUACUUAGUGCUAAUAAGUAAACACUCCAAAAAA
......((.(((....))).))...((((.......((((.(((((.((((.((......)).))))....))))).))))-.....((((((.......))))))....))))...... ( -34.20)
>consensus
UACAACGAAGGCUAAGGCCAUCCGCGGAGAAAGAGACGGCAUGCGUGGGCGCUGUUAAGUCAAUGUUAAAAGCGCAUGUUGGGCCAAUGUUAAGUGCUAAUAAGUAAACACUGCAAAAAA
......((.(((....))).)).((((.........((((((((((.((((.((......)).))))....)))))))))).............((((....))))....))))...... (-28.80 = -29.04 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	14,932,803 – 14,932,923
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.11
Mean single sequence MFE	-25.06
Consensus MFE	-21.83
Energy contribution	-22.35
Covariance contribution	0.52
Combinations/Pair	1.10
Mean z-score	-2.70
Structure conservation index	0.87
SVM decision value	3.41
SVM RNA-class probability	0.999171
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14932803 120 - 27905053
AGCGUGCCUUCCAUUGUCAAUGUUUUCUCUAUUCUCUUUUUUUUUUGCAGUGUUUACUUAUUAGCACUUAACAUUGGCCCAACAUGCGCUUUUAACAUUGACUUAACAGCGCCCACGCAU
.(((((.........(((((((((........................((((((........)))))).))))))))).......(((((.((((.......)))).))))).))))).. ( -27.51)
>DroSec_CAF1 62673 115 - 1
AGCGUGUCUUCCAUUGUCAAUGUUUUCUCUA-----UUUUUUUUUUGCAGUGUUUACUUAUUAGCACUUAACAUUGGCCCAACAUGCGCUUUUAACAUUGACUUAACAGCGCCCACGCAU
.(((((.........(((((((((.......-----............((((((........)))))).))))))))).......(((((.((((.......)))).))))).))))).. ( -27.95)
>DroSim_CAF1 61372 114 - 1
AGCGUGCCUU-CAUUGUCAAUGUUUUCUCUC-----UUCUUUUUUUGCAGUGUUUACUUAUUAGCACUUAACAUUGGCCCAACAUGCGCUUUUAACAUUGACUUAACAGCGCCCACGCAU
.(((((....-....(((((((((.......-----............((((((........)))))).))))))))).......(((((.((((.......)))).))))).))))).. ( -27.75)
>DroEre_CAF1 59222 110 - 1
AGAGUGUCUUCCAUUGUCAAUGUUUUCUCU---------UUUUUUUGCAGUGUUUACUUAUUAGCACUUAACAUUGGCCCAACAUGCGCUU-UAACAUUGACUUAACAGCGCCCACGCAU
...((((........(((((((((......---------.........((((((........)))))).))))))))).......((((((-(((.......)))).)))))..)))).. ( -21.99)
>DroYak_CAF1 66216 108 - 1
AGAGUUCAUUUCAUU-UUAAUGUUUUCUU----------UUUUUUUGGAGUGUUUACUUAUUAGCACUAAGUAUUGGC-CAGCCUGCGCUUUUAACAUUGACUUAACAGCGCCCACGCAC
((((..((((.....-..))))..)))).----------......(((((((((........)))))).......((.-...)).(((((.((((.......)))).))))))))..... ( -20.10)
>consensus
AGCGUGCCUUCCAUUGUCAAUGUUUUCUCU______UU_UUUUUUUGCAGUGUUUACUUAUUAGCACUUAACAUUGGCCCAACAUGCGCUUUUAACAUUGACUUAACAGCGCCCACGCAU
.(((((.........(((((((((........................((((((........)))))).))))))))).......(((((.((((.......)))).))))).))))).. (-21.83 = -22.35 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:28 2006