Locus 186

Sequence ID	3R_DroMel_CAF1
Location	844,830 – 844,966
Length	136
Max. P	0.958781

overview

Window 1

Location	844,830 – 844,926
Length	96
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.15
Mean single sequence MFE	-35.09
Consensus MFE	-28.26
Energy contribution	-30.33
Covariance contribution	2.06
Combinations/Pair	1.04
Mean z-score	-2.35
Structure conservation index	0.81
SVM decision value	1.49
SVM RNA-class probability	0.958781
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 844830 96 + 27905053
UGGCUCUUGCUGGCUAAUUUGCCGCAGCAGGCAAUGGAAAUUGUUGAUGUGCAAAAAUUUUGCUGCGU------------------------CGUUGUUGUUGUCGUGUAAAUGCCAUAA
((((..((((.(((......)))((((((((((((....))))))(((((((((.....)))).))))------------------------)..))))))......))))..))))... ( -32.50)
>DroSec_CAF1 20594 99 + 1
UGGCUCUUGCUGGCUAAUUUGCCGCAGCAGGCAAUGGAAAUUGUUGAUGUGCAAAAAUGUUGCUGCGCCGC---------------------CGUUGUUGUUGUCGUGUAAGUGCCAUAA
((((.(((((.(((......)))(((((((.((((((...........(((((..........)))))..)---------------------))))))))))))...))))).))))... ( -34.12)
>DroSim_CAF1 19821 99 + 1
UGGCUCUUGCUGGCUAAUUUGCCGCAGCAGGCAAUGGAAAUUGUUGAUGUGCAAAAAUGUUGCUGCGCCGC---------------------CGUUGUUGUUGUCGUGUAAGUGCCAUAA
((((.(((((.(((......)))(((((((.((((((...........(((((..........)))))..)---------------------))))))))))))...))))).))))... ( -34.12)
>DroEre_CAF1 21690 120 + 1
UGGCUGUUGCUGGCUAAUUUGCCGCGGCGGGCAAUGGAAAUUGUUGAUGUGCAAAAAUGUUGCUGCGCCGCUUUGUUGUUGUUGCGUUGUUGCGUUGUUGUUGUCGUGUAAAUGCCAUAA
((((..((((.(((......)))((((((((((((....)))))).....((((.(((((.((.((((.((.........)).)))).)).))))).))))))))))))))..))))... ( -39.60)
>consensus
UGGCUCUUGCUGGCUAAUUUGCCGCAGCAGGCAAUGGAAAUUGUUGAUGUGCAAAAAUGUUGCUGCGCCGC_____________________CGUUGUUGUUGUCGUGUAAAUGCCAUAA
((((.(((((.(((......)))(((((.((((((....))))))(((((......)))))))))).........................................))))).))))... (-28.26 = -30.33 +   2.06)

alignment

secondary structure

dotplot

Window 2

Location	844,830 – 844,926
Length	96
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.15
Mean single sequence MFE	-23.75
Consensus MFE	-19.56
Energy contribution	-20.38
Covariance contribution	0.81
Combinations/Pair	1.12
Mean z-score	-2.06
Structure conservation index	0.82
SVM decision value	1.12
SVM RNA-class probability	0.917693
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 844830 96 - 27905053
UUAUGGCAUUUACACGACAACAACAACG------------------------ACGCAGCAAAAUUUUUGCACAUCAACAAUUUCCAUUGCCUGCUGCGGCAAAUUAGCCAGCAAGAGCCA
...((((.....................------------------------..(((((((((((.(((.....))).)))))........))))))(((......))).......)))) ( -20.10)
>DroSec_CAF1 20594 99 - 1
UUAUGGCACUUACACGACAACAACAACG---------------------GCGGCGCAGCAACAUUUUUGCACAUCAACAAUUUCCAUUGCCUGCUGCGGCAAAUUAGCCAGCAAGAGCCA
...((((.(((.(...............---------------------((((((..((((.....(((........)))......)))).))))))(((......))).).))).)))) ( -23.70)
>DroSim_CAF1 19821 99 - 1
UUAUGGCACUUACACGACAACAACAACG---------------------GCGGCGCAGCAACAUUUUUGCACAUCAACAAUUUCCAUUGCCUGCUGCGGCAAAUUAGCCAGCAAGAGCCA
...((((.(((.(...............---------------------((((((..((((.....(((........)))......)))).))))))(((......))).).))).)))) ( -23.70)
>DroEre_CAF1 21690 120 - 1
UUAUGGCAUUUACACGACAACAACAACGCAACAACGCAACAACAACAAAGCGGCGCAGCAACAUUUUUGCACAUCAACAAUUUCCAUUGCCCGCCGCGGCAAAUUAGCCAGCAACAGCCA
...((((....................((......))............((((((..((((.....(((........)))......)))).))))))(((......))).......)))) ( -27.50)
>consensus
UUAUGGCACUUACACGACAACAACAACG_____________________GCGGCGCAGCAACAUUUUUGCACAUCAACAAUUUCCAUUGCCUGCUGCGGCAAAUUAGCCAGCAAGAGCCA
...((((.(((.(....................................((((((..((((.....(((........)))......)))).))))))(((......))).).))).)))) (-19.56 = -20.38 +   0.81)

alignment

secondary structure

dotplot

Window 3

Location	844,870 – 844,966
Length	96
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.06
Mean single sequence MFE	-20.66
Consensus MFE	-15.68
Energy contribution	-16.93
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.76
SVM decision value	0.82
SVM RNA-class probability	0.858222
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 844870 96 - 27905053
UUUUAAUUCCGCUCCGCUGUGUCUGUUGACACAAACUAAUUUAUGGCAUUUACACGACAACAACAACG------------------------ACGCAGCAAAAUUUUUGCACAUCAACAA
...............(((((((((((((................................)))))..)------------------------)))))))..................... ( -15.45)
>DroSec_CAF1 20634 99 - 1
UUUUAAUUCCGCUCCGCUGUGUCUGUUGACACAAACUAAUUUAUGGCACUUACACGACAACAACAACG---------------------GCGGCGCAGCAACAUUUUUGCACAUCAACAA
..........((.(((((((...(((((.............................)))))...)))---------------------)))).)).((((.....)))).......... ( -21.55)
>DroSim_CAF1 19861 99 - 1
UUUUAAUUCCGCUCCGCUGUGUCUGUUGACACAAACUAAUUUAUGGCACUUACACGACAACAACAACG---------------------GCGGCGCAGCAACAUUUUUGCACAUCAACAA
..........((.(((((((...(((((.............................)))))...)))---------------------)))).)).((((.....)))).......... ( -21.55)
>DroEre_CAF1 21730 120 - 1
UUUUAAUUCCGCUCCGCUAUGUCUGUUGACACAAACUAAUUUAUGGCAUUUACACGACAACAACAACGCAACAACGCAACAACAACAAAGCGGCGCAGCAACAUUUUUGCACAUCAACAA
..........((.(((((.(((.(((((............(..((.......))..)..........((......))..)))))))).))))).)).((((.....)))).......... ( -24.10)
>consensus
UUUUAAUUCCGCUCCGCUGUGUCUGUUGACACAAACUAAUUUAUGGCACUUACACGACAACAACAACG_____________________GCGGCGCAGCAACAUUUUUGCACAUCAACAA
..........((.((((((((((....)))))).......(..((.......))..)................................)))).)).((((.....)))).......... (-15.68 = -16.93 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:36 2006