Locus 6642

Sequence ID	3L_DroMel_CAF1
Location	17,682,712 – 17,682,841
Length	129
Max. P	0.980778

overview

Window 1

Location	17,682,712 – 17,682,812
Length	100
Sequences	3
Columns	106
Reading direction	forward
Mean pairwise identity	83.60
Mean single sequence MFE	-26.80
Consensus MFE	-18.78
Energy contribution	-19.89
Covariance contribution	1.11
Combinations/Pair	1.03
Mean z-score	-3.23
Structure conservation index	0.70
SVM decision value	1.78
SVM RNA-class probability	0.976684
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17682712 100 + 23771897
UAAAAACCAG------UUCUCUUUUGGAUUGUACAGAUUUGCUUAGAUUUUAAGCAUGUUUUUAUUUUUUUAAUCUGUAUGUCCAAAAGCUGUGGAUUUUGCAGUG
(((((.(((.------....(((((((((.((((((((((((((((...)))))))...............))))))))))))))))))...))).)))))..... ( -25.26)
>DroSec_CAF1 64873 105 + 1
UAACAACCAGAAUCCUUUAUCUUAAGGAUUGUACAGAUUUGCUUAGAGCUUAAGCAUUAUUUU-UUUUUGUAAUCUGUAUGCCCAAAAGCUUUGGUUGUUGUUGUG
(((((((((((((((((......)))))))((((((((((((((((...))))))).......-.......)))))))))...........))))))))))..... ( -29.83)
>DroSim_CAF1 59986 102 + 1
UAAAAACCAGAAUCCUUUAUCUCAAGGAUUGUACAGAUUUGCUUAGAGCUUAAGCAUUAUUUU---UUUGUAAUCUGUAUGUCCAAAAGCUUUGGUU-UUGUGGUG
..(((((((((((((((......)))))))((((((((((((((((...))))))).......---.....)))))))))...........))))))-))...... ( -25.30)
>consensus
UAAAAACCAGAAUCCUUUAUCUUAAGGAUUGUACAGAUUUGCUUAGAGCUUAAGCAUUAUUUU_UUUUUGUAAUCUGUAUGUCCAAAAGCUUUGGUU_UUGUAGUG
(((((((((((........))....((((.((((((((((((((((...)))))))...............)))))))))))))........)))))))))..... (-18.78 = -19.89 +   1.11)

alignment

secondary structure

dotplot

Window 2

Location	17,682,712 – 17,682,812
Length	100
Sequences	3
Columns	106
Reading direction	reverse
Mean pairwise identity	83.60
Mean single sequence MFE	-25.40
Consensus MFE	-19.86
Energy contribution	-19.87
Covariance contribution	0.01
Combinations/Pair	1.11
Mean z-score	-4.96
Structure conservation index	0.78
SVM decision value	1.87
SVM RNA-class probability	0.980778
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17682712 100 - 23771897
CACUGCAAAAUCCACAGCUUUUGGACAUACAGAUUAAAAAAAUAAAAACAUGCUUAAAAUCUAAGCAAAUCUGUACAAUCCAAAAGAGAA------CUGGUUUUUA
......((((.(((...((((((((..((((((((...............((((((.....))))))))))))))...))))))))....------.))).)))). ( -24.06)
>DroSec_CAF1 64873 105 - 1
CACAACAACAACCAAAGCUUUUGGGCAUACAGAUUACAAAAA-AAAAUAAUGCUUAAGCUCUAAGCAAAUCUGUACAAUCCUUAAGAUAAAGGAUUCUGGUUGUUA
......((((((((..(((....))).((((((((.......-.......((((((.....)))))))))))))).(((((((......))))))).)))))))). ( -28.53)
>DroSim_CAF1 59986 102 - 1
CACCACAA-AACCAAAGCUUUUGGACAUACAGAUUACAAA---AAAAUAAUGCUUAAGCUCUAAGCAAAUCUGUACAAUCCUUGAGAUAAAGGAUUCUGGUUUUUA
......((-(((((.............((((((((.....---.......((((((.....)))))))))))))).(((((((......))))))).))))))).. ( -23.60)
>consensus
CACAACAA_AACCAAAGCUUUUGGACAUACAGAUUACAAAAA_AAAAUAAUGCUUAAGCUCUAAGCAAAUCUGUACAAUCCUUAAGAUAAAGGAUUCUGGUUUUUA
......((((((((...(((..(((..((((((((...............((((((.....))))))))))))))...)))..)))...........)))))))). (-19.86 = -19.87 +   0.01)

alignment

secondary structure

dotplot

Window 3

Location	17,682,732 – 17,682,841
Length	109
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	88.96
Mean single sequence MFE	-18.06
Consensus MFE	-15.50
Energy contribution	-15.28
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-2.56
Structure conservation index	0.86
SVM decision value	1.10
SVM RNA-class probability	0.915615
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17682732 109 - 23771897
ACGAAAAAGUCGAAAAAAUUGUAGUUUAGCACUGCAAAAUCCACAGCUUUUGGACAUACAGAUUAAAAAAAUAAAAACAUGCUUAAAAUCUAAGCAAAUCUGUACAAUC
.(((.....)))......(((((((.....)))))))..((((.......))))..((((((((...............((((((.....))))))))))))))..... ( -20.16)
>DroSec_CAF1 64899 108 - 1
ACGAAAAAGUCGCUAAAAUUGUAGUUUAUCACAACAACAACCAAAGCUUUUGGGCAUACAGAUUACAAAAA-AAAAUAAUGCUUAAGCUCUAAGCAAAUCUGUACAAUC
...........((.....((((.(((......))).))))((((.....)))))).((((((((.......-.......((((((.....))))))))))))))..... ( -17.83)
>DroSim_CAF1 60012 105 - 1
ACGAAAAAGUCGCUAAAAUUGUAGUUUAUCACCACAA-AACCAAAGCUUUUGGACAUACAGAUUACAAA---AAAAUAAUGCUUAAGCUCUAAGCAAAUCUGUACAAUC
........(((((((......)))).........(((-((.......)))))))).((((((((.....---.......((((((.....))))))))))))))..... ( -16.20)
>consensus
ACGAAAAAGUCGCUAAAAUUGUAGUUUAUCACAACAA_AACCAAAGCUUUUGGACAUACAGAUUACAAAAA_AAAAUAAUGCUUAAGCUCUAAGCAAAUCUGUACAAUC
....((((((........((((.((.....)).))))........)))))).....((((((((...............((((((.....))))))))))))))..... (-15.50 = -15.28 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:20 2006