Locus 192

Sequence ID	4_DroMel_CAF1
Location	1,169,633 – 1,169,753
Length	120
Max. P	0.839861

overview

Window 0

Location	1,169,633 – 1,169,727
Length	94
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	69.10
Mean single sequence MFE	-17.93
Consensus MFE	-9.21
Energy contribution	-9.27
Covariance contribution	0.06
Combinations/Pair	1.35
Mean z-score	-1.72
Structure conservation index	0.51
SVM decision value	0.44
SVM RNA-class probability	0.738250
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1169633 94 - 1281640
UAUCGGAAAACGUACAAUCAAUGUAAGUUUUAAAAAUGUUGUAGCACAAAAAGCACAAUAUUUUACCC-------UUUUCGAGCGGCAAGCAUUAUAAAAU-----------------
..(((((((((.((((.....)))).))))).((((((((((.((.......))))))))))))....-------...))))((.....))..........----------------- ( -18.60)
>DroSec_CAF1 4042 101 - 1
UAUGGGAAAACAUACAAUCAAUGUAAGUUUUAAAAAUUUUGUGGCACAAAAAGCACAAAGUUUCACUUGAACUAAUUUCCAAGUGACAAACAUUAUAAAAU-----------------
......(((((.((((.....)))).)))))...(((((((((.(.......))))))))))(((((((..........)))))))...............----------------- ( -17.90)
>DroSim_CAF1 287 101 - 1
UAUGGGAAAACAUACAAUCAAUGUAAGUUUUAAAAAUUUUGUGGCACAAAAAGCACAAAGUUUCACUUGAACUAAUUUCCAAGUGACAAGCAUUAUAAAAU-----------------
......(((((.((((.....)))).)))))...(((((((((.(.......))))))))))(((((((..........)))))))...............----------------- ( -17.90)
>DroEre_CAF1 11931 114 - 1
UAUCGGAAAAUGUAAAAUAAAUGUUAGUUUAGAAAAUAUCACAGAAUAAGGAUC--C--AUGUUACUUGAAUUACUUUCCAAGCUAUAAGCAUGCUAUAUUUCAGUUUGCUUAAGAAU
..(((((((..((((..(((((....))))).......(((.((((((.(....--)--.)))).))))).)))))))))......((((((.(((.......))).)))))).)).. ( -17.30)
>consensus
UAUCGGAAAACAUACAAUCAAUGUAAGUUUUAAAAAUUUUGUAGCACAAAAAGCACAAAAUUUCACUUGAACUAAUUUCCAAGCGACAAGCAUUAUAAAAU_________________
....(((((((((.......))))........((((((((((.((.......))))))))))))...........)))))..((.....))........................... ( -9.21 =  -9.27 +   0.06)

alignment

secondary structure

dotplot

Window 1

Location	1,169,654 – 1,169,753
Length	99
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	81.92
Mean single sequence MFE	-18.70
Consensus MFE	-15.21
Energy contribution	-13.67
Covariance contribution	-1.55
Combinations/Pair	1.18
Mean z-score	-1.83
Structure conservation index	0.81
SVM decision value	0.75
SVM RNA-class probability	0.839861
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1169654 99 - 1281640
CCGUA------------AAAUCAGAUGUUUUAAUGUAAUAUCGGAAAACGUACAAUCAAUGUAAGUUUUAAAAAUGUUGUAGCACAAAAAGCACAAUAUUUUACCC-------UUUUC
.....------------......((((((.......))))))(((((((.((((.....)))).))))).((((((((((.((.......))))))))))))..))-------..... ( -19.10)
>DroSec_CAF1 4063 118 - 1
CCGUAUCAUAUAUCUAAUAAUCAUAUAUUUUAAUGUAAUAUGGGAAAACAUACAAUCAAUGUAAGUUUUAAAAAUUUUGUGGCACAAAAAGCACAAAGUUUCACUUGAACUAAUUUCC
((((((.((((....((((......))))...)))).))))))((((...((((.....))))(((((...((((((((((.(.......))))))))))).....)))))..)))). ( -18.50)
>DroSim_CAF1 308 118 - 1
CCGUAUCAUAUAUCUAAUAAUCAUAUAUUUUAAUGUAAUAUGGGAAAACAUACAAUCAAUGUAAGUUUUAAAAAUUUUGUGGCACAAAAAGCACAAAGUUUCACUUGAACUAAUUUCC
((((((.((((....((((......))))...)))).))))))((((...((((.....))))(((((...((((((((((.(.......))))))))))).....)))))..)))). ( -18.50)
>consensus
CCGUAUCAUAUAUCUAAUAAUCAUAUAUUUUAAUGUAAUAUGGGAAAACAUACAAUCAAUGUAAGUUUUAAAAAUUUUGUGGCACAAAAAGCACAAAGUUUCACUUGAACUAAUUUCC
.......................((((((.......))))))(((((((.((((.....)))).)))))..(((((((((.((.......)))))))))))..))............. (-15.21 = -13.67 +  -1.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:53 2006