Locus 1763

Sequence ID	3L_DroMel_CAF1
Location	5,054,936 – 5,055,072
Length	136
Max. P	0.769745

overview

Window 3

Location	5,054,936 – 5,055,035
Length	99
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	93.12
Mean single sequence MFE	-24.26
Consensus MFE	-23.04
Energy contribution	-22.88
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.05
Structure conservation index	0.95
SVM decision value	-0.00
SVM RNA-class probability	0.533008
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5054936 99 - 23771897
AGGCGAAACGAGCGCUUAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAAACCAU-------UUCCCAUUUUCCAGCGACACC-------CUCUGCAA
..((((.......((((....))))......(((((.((((......)))).))))).))))........-------.............(((.....-------...))).. ( -23.80)
>DroSec_CAF1 261398 99 - 1
AGGCGAAACGAGCGCUUAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAUCCCAU-------UUCCCAUUUUCCAGCGACACC-------CUCUGCAA
..((((.......((((....))))......(((((.((((......)))).))))).))))........-------.............(((.....-------...))).. ( -23.80)
>DroSim_CAF1 282708 99 - 1
AGGCGAAACGAGCGCUUAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAUCCCAU-------UUCCCAUUUUCCAGCGACACC-------CUCUGCAA
..((((.......((((....))))......(((((.((((......)))).))))).))))........-------.............(((.....-------...))).. ( -23.80)
>DroEre_CAF1 268227 99 - 1
AGGCGAAACGAGCGCUCAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAUCCCAU-------UUCCCAUUUUCCAGCGACACC-------CUCUGCAA
..((((.......((((....))))......(((((.((((......)))).))))).))))........-------.............(((.....-------...))).. ( -26.10)
>DroYak_CAF1 271789 113 - 1
AGGCGAAACGAGCGCUUAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAUCCCAUUUCACAUUUCCCAUUUUCCAGCGACACCACCCAAACUGUGCAA
..((((.......((((....))))......(((((.((((......)))).))))).))))............................((.(((..........))))).. ( -23.80)
>consensus
AGGCGAAACGAGCGCUUAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAUCCCAU_______UUCCCAUUUUCCAGCGACACC_______CUCUGCAA
..((((.......((((....))))......(((((.((((......)))).))))).))))............................(((...............))).. (-23.04 = -22.88 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	5,054,965 – 5,055,072
Length	107
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-31.44
Consensus MFE	-30.72
Energy contribution	-30.56
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.24
Structure conservation index	0.98
SVM decision value	0.53
SVM RNA-class probability	0.769745
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5054965 107 - 23771897
UGAUUACUUAAUCAGGCUGCCAGGAUAAGGCCAGAUGAGGCGAAACGAGCGCUUAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAAACCAU---
......((((.((.((((..........)))).))))))((((.......((((....))))......(((((.((((......)))).))))).))))........--- ( -30.10)
>DroSec_CAF1 261427 107 - 1
UGAUUACUUAAUCAGGCUGCCAGGAUAAGGCCAGAUGAGGCGAAACGAGCGCUUAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAUCCCAU---
.((((.((((.((.((((..........)))).))))))((((.......((((....))))......(((((.((((......)))).))))).))))))))....--- ( -31.20)
>DroSim_CAF1 282737 107 - 1
UGAUUACUUAAUCAGGCUGCCAGGAUAAGGCCAGAUGAGGCGAAACGAGCGCUUAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAUCCCAU---
.((((.((((.((.((((..........)))).))))))((((.......((((....))))......(((((.((((......)))).))))).))))))))....--- ( -31.20)
>DroEre_CAF1 268256 107 - 1
UGAUUACUUAAUCAGGCUGCCAGGAUAAGGCCAGAUGAGGCGAAACGAGCGCUCAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAUCCCAU---
.((((.((((.((.((((..........)))).))))))((((.......((((....))))......(((((.((((......)))).))))).))))))))....--- ( -33.50)
>DroYak_CAF1 271829 110 - 1
UGAUUACUUAAUCAGGCUGCCAGGAUAAGGCCAGAUGAGGCGAAACGAGCGCUUAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAUCCCAUUUC
.((((.((((.((.((((..........)))).))))))((((.......((((....))))......(((((.((((......)))).))))).))))))))....... ( -31.20)
>consensus
UGAUUACUUAAUCAGGCUGCCAGGAUAAGGCCAGAUGAGGCGAAACGAGCGCUUAAACGAGCUUUAAAUGUGCCCCUGAGUCAGCAGGCGCACAAUCGCAAUCCCAU___
......((((.((.((((..........)))).))))))((((.......((((....))))......(((((.((((......)))).))))).))))........... (-30.72 = -30.56 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:38 2006