Locus 8983

Sequence ID	3R_DroMel_CAF1
Location	24,095,310 – 24,095,470
Length	160
Max. P	0.997623

overview

Window 0

Location	24,095,310 – 24,095,408
Length	98
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	79.39
Mean single sequence MFE	-30.90
Consensus MFE	-25.32
Energy contribution	-25.06
Covariance contribution	-0.26
Combinations/Pair	1.14
Mean z-score	-2.92
Structure conservation index	0.82
SVM decision value	2.90
SVM RNA-class probability	0.997623
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24095310 98 + 27905053
AACAAUGGGCCAA--GAAUUGGCAGCAGAGAAUUCAGCAGGAUGCAGAAGGAUGCAGAAGAACGCAGGAGGAUGCAAGAG---CUGCUGCUGCUCGUUGUUAU
(((((((.((((.--....))))(((((......((((((..((((......)))).......(((......))).....---)))))))))))))))))).. ( -32.10)
>DroSec_CAF1 282663 98 + 1
AACAAUGGGCCAA--GAAUCGGCAGCAGAGGAUUCAGCAGGAUGCAGAAGGAUGCAGAAGGACGCAGAAGGAUGCAGGAG---UUGCUGCUGCCCGUUGUUAU
((((((((((...--.....((((((((....(((.((....((((......))))....).)(((......))).))).---)))))))))))))))))).. ( -34.50)
>DroSim_CAF1 282384 98 + 1
AACAAUGGGCCAA--GAAUCGGCAGCAGAGGAUUCAGCAGGAUGCAAAAGGAUGCAGAAGGACGCAGAAGGAUGCAGGAG---UUGCUGCUGCCCGUUGUUAU
((((((((((...--.....((((((((....(((.((....((((......))))....).)(((......))).))).---)))))))))))))))))).. ( -33.70)
>DroEre_CAF1 296038 78 + 1
AACAAUGGGCCAA--GAAUCGGCAGCAGAGGAUUCGGCAGGAUGCAG--------------------GAUGAUGCAAGAG---CUGCUACUGCCCGUUGUUAU
((((((((((...--(((((..(....)..)))))(((((..((((.--------------------.....))))....---)))))...)))))))))).. ( -29.90)
>DroYak_CAF1 294885 83 + 1
AACAAUGGGCCAAGAGAAUCGACAGCAGAGGAUUCGGCAGGAUGCAG--------------------GAGGAUGAAAGAGUUGCUGCUGCUGCCCCUUGUUAU
(((((.((((.....(((((..........)))))(((((.(.((((--------------------.............))))).))))))))).))))).. ( -24.32)
>consensus
AACAAUGGGCCAA__GAAUCGGCAGCAGAGGAUUCAGCAGGAUGCAGAAGGAUGCAGAAG_ACGCAGGAGGAUGCAAGAG___CUGCUGCUGCCCGUUGUUAU
((((((((((.....(((((..(....)..)))))(((((..((((......(((........)))......)))).......)))))...)))))))))).. (-25.32 = -25.06 +  -0.26)

alignment

secondary structure

dotplot

Window 1

Location	24,095,310 – 24,095,408
Length	98
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	79.39
Mean single sequence MFE	-24.71
Consensus MFE	-18.32
Energy contribution	-19.04
Covariance contribution	0.72
Combinations/Pair	1.10
Mean z-score	-2.76
Structure conservation index	0.74
SVM decision value	2.62
SVM RNA-class probability	0.995847
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24095310 98 - 27905053
AUAACAACGAGCAGCAGCAG---CUCUUGCAUCCUCCUGCGUUCUUCUGCAUCCUUCUGCAUCCUGCUGAAUUCUCUGCUGCCAAUUC--UUGGCCCAUUGUU
..(((((.((((((((((((---....((((......((((......))))......))))..))))))......)))))((((....--.)))).).))))) ( -25.80)
>DroSec_CAF1 282663 98 - 1
AUAACAACGGGCAGCAGCAA---CUCCUGCAUCCUUCUGCGUCCUUCUGCAUCCUUCUGCAUCCUGCUGAAUCCUCUGCUGCCGAUUC--UUGGCCCAUUGUU
..(((((.(((((((((...---.....(((......))).......((((......))))..)))))(((((..(....)..)))))--...)))).))))) ( -25.90)
>DroSim_CAF1 282384 98 - 1
AUAACAACGGGCAGCAGCAA---CUCCUGCAUCCUUCUGCGUCCUUCUGCAUCCUUUUGCAUCCUGCUGAAUCCUCUGCUGCCGAUUC--UUGGCCCAUUGUU
..(((((.(((((((((...---.....(((......))).......((((......))))..)))))(((((..(....)..)))))--...)))).))))) ( -26.70)
>DroEre_CAF1 296038 78 - 1
AUAACAACGGGCAGUAGCAG---CUCUUGCAUCAUC--------------------CUGCAUCCUGCCGAAUCCUCUGCUGCCGAUUC--UUGGCCCAUUGUU
..(((((.((((....((((---....((((.....--------------------.))))..)))).(((((..(....)..)))))--...)))).))))) ( -23.20)
>DroYak_CAF1 294885 83 - 1
AUAACAAGGGGCAGCAGCAGCAACUCUUUCAUCCUC--------------------CUGCAUCCUGCCGAAUCCUCUGCUGUCGAUUCUCUUGGCCCAUUGUU
..(((((.((((.((((..(((..............--------------------.)))...)))).(((((..(....)..))))).....)))).))))) ( -21.96)
>consensus
AUAACAACGGGCAGCAGCAG___CUCUUGCAUCCUCCUGCGU_CUUCUGCAUCCUUCUGCAUCCUGCUGAAUCCUCUGCUGCCGAUUC__UUGGCCCAUUGUU
..(((((.((((.(((((((.......((((......((((......))))......))))((.....)).....)))))))(((.....))))))).))))) (-18.32 = -19.04 +   0.72)

alignment

secondary structure

dotplot

Window 2

Location	24,095,376 – 24,095,470
Length	94
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	85.79
Mean single sequence MFE	-33.54
Consensus MFE	-23.24
Energy contribution	-23.27
Covariance contribution	0.03
Combinations/Pair	1.19
Mean z-score	-2.90
Structure conservation index	0.69
SVM decision value	0.03
SVM RNA-class probability	0.547053
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24095376 94 - 27905053
CGGCUG---CCGUUGCCGUUGUACUUAGGCCUAAUGCCUUGCACUUGUUUGCAAAUUGCAUUGGGAUAACAACG--AGCAGCAGCAG---CUCUUGCAUCCU
.(((((---(.(((((((((((...((..((((((((.(((((......)))))...)))))))).))))))))--.))))).))))---)).......... ( -40.20)
>DroSec_CAF1 282729 94 - 1
CGGCUG---ACGUUGCCGUUGUACUUAGGCCUAAUGCCUUGCACUUGUUUGCAAAUUGCAUUGGGAUAACAACG--GGCAGCAGCAA---CUCCUGCAUCCU
.((...---..(((((((((((...((..((((((((.(((((......)))))...)))))))).))))))).--)))))).(((.---....)))..)). ( -32.60)
>DroSim_CAF1 282450 94 - 1
CGGCUG---ACGUUGCCGUUGUACUUAGGCCUAAUGCCUUGCACUUGUUUGCAAAUUGCAUUGGGAUAACAACG--GGCAGCAGCAA---CUCCUGCAUCCU
.((...---..(((((((((((...((..((((((((.(((((......)))))...)))))))).))))))).--)))))).(((.---....)))..)). ( -32.60)
>DroEre_CAF1 296084 88 - 1
---------CCGUUGCCGUUGUACUUAGGCCUAAUGCCUUGCACUUGUUUGCAAAUUGCAUUGGGAUAACAACG--GGCAGUAGCAG---CUCUUGCAUCAU
---------(..((((((((((...((..((((((((.(((((......)))))...)))))))).))))))).--)))))..)..(---(....))..... ( -27.70)
>DroYak_CAF1 294933 97 - 1
CGGCUG---CUGUUGCCGUUGUACUUAGGCCUAAUGCCUUGCACUUGUUUGCAAAUUGCAUUGGGAUAACAAGG--GGCAGCAGCAGCAACUCUUUCAUCCU
..((((---((((((((.((....(((..((((((((.(((((......)))))...)))))))).)))..)).--)))))))))))).............. ( -41.90)
>DroAna_CAF1 291757 97 - 1
CACUUGAAGCCUUUGCCGUUGUACUUAGGCCUAAUGCCCUGUGCUUGUUUGCAAAUUGCAUUGGGAUAACGACACAAGCCGGCGCUG---CUCUC-CAUCG-
.....(((((...(((((((((.......((((((((....(((......)))....))))))))........))))..)))))..)---)).))-.....- ( -26.26)
>consensus
CGGCUG___CCGUUGCCGUUGUACUUAGGCCUAAUGCCUUGCACUUGUUUGCAAAUUGCAUUGGGAUAACAACG__GGCAGCAGCAG___CUCUUGCAUCCU
...........(((((((((((...((..((((((((.(((((......)))))...)))))))).)))))))...)))))).................... (-23.24 = -23.27 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:24:12 2006