Locus 2746

Sequence ID	3R_DroMel_CAF1
Location	7,353,145 – 7,353,294
Length	149
Max. P	0.988149

overview

Window 1

Location	7,353,145 – 7,353,255
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.15
Mean single sequence MFE	-33.42
Consensus MFE	-15.99
Energy contribution	-17.33
Covariance contribution	1.34
Combinations/Pair	1.29
Mean z-score	-2.65
Structure conservation index	0.48
SVM decision value	2.11
SVM RNA-class probability	0.988149
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7353145 110 + 27905053
GUGCUCGUGCAUAUUCAAACGGAAUUCGGCAAUGCAUUGCCAACUUGCAACA---UGCAACUCGCAACUUGCAGCUGGCAGCUA-------GCAGCUAGCCGGUUGCCAUUCUUGAAUAA
.(((....)))((((((...(((((..((((.((((((((....((((....---.))))...))))..))))(((((((((..-------...))).))))))))))))))))))))). ( -36.80)
>DroSec_CAF1 29171 103 + 1
GUGCUCUUGCAUAUUUGAUCGGAAUUCGGCAAUGCAUUGCCAACUUGCAACA---UGCAA-------CUUGCAGCUGGCAGCUA-------GCAUCUAGCCGGUUGCCAUUCUUGAAUAA
((((....))))...........(((((((((((((((((......)))..)---)))).-------.))))...(((((((..-------((.....))..)))))))....))))).. ( -30.80)
>DroSim_CAF1 34637 110 + 1
GUGCUCUUGCAUAUUCGACCGGAAUUCGGCAAUGCAUUGCCAACUUGCAACA---UGCAACUUGCAACUUGCAGCUGGCAGCUA-------GCAGCUAGCCGGUUGCCAUUCUUGAAUAA
.(((....)))((((((...(((((..(((((....)))))...((((((..---......))))))...((((((((((((..-------...))).))))))))).))))))))))). ( -37.10)
>DroEre_CAF1 33004 103 + 1
GUGCUCUUGCAUAUUCAACCGGAAUUCGGCAAUGCAUUGCCAACUUGCCACA---UGCAACUUGCAACUUGCAGCUGGCAGCUUG--------------CCGUUUGCCAUUCUUGAAUAA
.(((....)))(((((((..((....((((((.((..(((((.((.((....---(((.....)))....)))).))))))))))--------------)))....))....))))))). ( -33.40)
>DroYak_CAF1 33956 117 + 1
GUGCUCCUGCAUAUUCAACCGAAAUUCGGCAAUGCAUUGCCAACUUGCCACA---UGCAACUUGCAACUUGCAGCUUGCAGCUUGCAACUUGCAGCUGGCCGUUUGCCAUUCUUGAAUAA
.(((....)))(((((((..(((....(((((....))))).....((((..---(((((.((((((.((((.....)))).)))))).)))))..)))).........)))))))))). ( -38.10)
>DroAna_CAF1 31570 101 + 1
GUGCACUUGCAUAUUCAACGGAAAAUUU---UUGUAUUUC-AGGAUGCUAGAAUCCUCAAAUCGGAAUGCGUGUCC-----CU----------CGUUUGCAGACUGCAUCUAUUGAAUAA
.(((....)))(((((((..((....((---(((.((((.-(((((......))))).)))))))))((((.(((.-----..----------........)))))))))..))))))). ( -24.30)
>consensus
GUGCUCUUGCAUAUUCAACCGGAAUUCGGCAAUGCAUUGCCAACUUGCAACA___UGCAACUUGCAACUUGCAGCUGGCAGCUA_______GCAGCUAGCCGGUUGCCAUUCUUGAAUAA
.(((....)))(((((((..((...(((((...(((((((....((((........))))...))))..)))(((.....)))...............)))))...))....))))))). (-15.99 = -17.33 +   1.34)

alignment

secondary structure

dotplot

Window 2

Location	7,353,145 – 7,353,255
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.15
Mean single sequence MFE	-35.65
Consensus MFE	-15.86
Energy contribution	-18.38
Covariance contribution	2.52
Combinations/Pair	1.26
Mean z-score	-2.58
Structure conservation index	0.44
SVM decision value	1.79
SVM RNA-class probability	0.977359
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7353145 110 - 27905053
UUAUUCAAGAAUGGCAACCGGCUAGCUGC-------UAGCUGCCAGCUGCAAGUUGCGAGUUGCA---UGUUGCAAGUUGGCAAUGCAUUGCCGAAUUCCGUUUGAAUAUGCACGAGCAC
.(((((((..((((....((((....(((-------....((((((((((((..(((.....)))---..)))).))))))))..)))..))))....)))))))))))(((....))). ( -39.10)
>DroSec_CAF1 29171 103 - 1
UUAUUCAAGAAUGGCAACCGGCUAGAUGC-------UAGCUGCCAGCUGCAAG-------UUGCA---UGUUGCAAGUUGGCAAUGCAUUGCCGAAUUCCGAUCAAAUAUGCAAGAGCAC
........((.(((....((((..(((((-------....((((((((((((.-------.....---..)))).))))))))..)))))))))....))).)).....(((....))). ( -32.80)
>DroSim_CAF1 34637 110 - 1
UUAUUCAAGAAUGGCAACCGGCUAGCUGC-------UAGCUGCCAGCUGCAAGUUGCAAGUUGCA---UGUUGCAAGUUGGCAAUGCAUUGCCGAAUUCCGGUCGAAUAUGCAAGAGCAC
.(((((.......(((...((((((...)-------)))))(((((((((((..(((.....)))---..)))).)))))))..)))...((((.....)))).)))))(((....))). ( -38.10)
>DroEre_CAF1 33004 103 - 1
UUAUUCAAGAAUGGCAAACGG--------------CAAGCUGCCAGCUGCAAGUUGCAAGUUGCA---UGUGGCAAGUUGGCAAUGCAUUGCCGAAUUCCGGUUGAAUAUGCAAGAGCAC
.(((((((...(((....(((--------------(((((((((((((((....(((.....)))---....)).))))))))..)).))))))....))).)))))))(((....))). ( -38.90)
>DroYak_CAF1 33956 117 - 1
UUAUUCAAGAAUGGCAAACGGCCAGCUGCAAGUUGCAAGCUGCAAGCUGCAAGUUGCAAGUUGCA---UGUGGCAAGUUGGCAAUGCAUUGCCGAAUUUCGGUUGAAUAUGCAGGAGCAC
...(((.....((.(((...((((..(((((.((((((..(((.....)))..)))))).)))))---..))))...))).)).(((((.((((.....)))).....)))))))).... ( -42.50)
>DroAna_CAF1 31570 101 - 1
UUAUUCAAUAGAUGCAGUCUGCAAACG----------AG-----GGACACGCAUUCCGAUUUGAGGAUUCUAGCAUCCU-GAAAUACAA---AAAUUUUCCGUUGAAUAUGCAAGUGCAC
.((((((((.((((((((((.((((..----------.(-----(((......))))..)))).)))))...)))))..-((((.....---....)))).))))))))(((....))). ( -22.50)
>consensus
UUAUUCAAGAAUGGCAACCGGCUAGCUGC_______UAGCUGCCAGCUGCAAGUUGCAAGUUGCA___UGUUGCAAGUUGGCAAUGCAUUGCCGAAUUCCGGUUGAAUAUGCAAGAGCAC
.((((((((((((((((.(((....)))..........(((((((((((((...(((.....)))...)))....))))))))..)).)))))..))))...)))))))(((....))). (-15.86 = -18.38 +   2.52)

alignment

secondary structure

dotplot

Window 3

Location	7,353,185 – 7,353,294
Length	109
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	77.95
Mean single sequence MFE	-31.17
Consensus MFE	-14.52
Energy contribution	-16.17
Covariance contribution	1.64
Combinations/Pair	1.22
Mean z-score	-1.98
Structure conservation index	0.47
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7353185 109 + 27905053
CAACUUGCAACA---UGCAACUCGCAACUUGCAGCUGGCAGCUA-------GCAGCUAGCCGGUUGCCAUUCUUGAAUAAUUAACCGAAUCCUGAUGGUCCUCGAAUGGGCAAUCAGCU
....((((((..---(((.....)))..)))))).(((((((..-------((.....))..)))))))......................(((((.((((......)))).))))).. ( -33.70)
>DroSec_CAF1 29211 102 + 1
CAACUUGCAACA---UGCAA-------CUUGCAGCUGGCAGCUA-------GCAUCUAGCCGGUUGCCAUUCUUGAAUAAUUAACCGCAUCCUGAUGGUCCUCGAAUGGGCAAUCAGCU
.....(((....---(((..-------...)))..(((((((..-------((.....))..))))))).................)))..(((((.((((......)))).))))).. ( -31.70)
>DroSim_CAF1 34677 109 + 1
CAACUUGCAACA---UGCAACUUGCAACUUGCAGCUGGCAGCUA-------GCAGCUAGCCGGUUGCCAUUCUUGAAUAAUUAACCGCAUCCUGAUGGUCCUCGAAUGGGCAAUCAGCU
.....(((....---(((.....)))....((((((((((((..-------...))).)))))))))...................)))..(((((.((((......)))).))))).. ( -36.20)
>DroEre_CAF1 33044 102 + 1
CAACUUGCCACA---UGCAACUUGCAACUUGCAGCUGGCAGCUUG--------------CCGUUUGCCAUUCUUGAAUAAUUAACCGAAUCCUGAUGGUCCUCGAAUGGGCAAUCAGCU
(((.((((((..---(((((........)))))..)))))).)))--------------................................(((((.((((......)))).))))).. ( -25.30)
>DroYak_CAF1 33996 116 + 1
CAACUUGCCACA---UGCAACUUGCAACUUGCAGCUUGCAGCUUGCAACUUGCAGCUGGCCGUUUGCCAUUCUUGAAUAAUUAACCGAACCCUGAUGGUCCUCGAAUGGGCAAUCAGCU
......((((..---(((((.((((((.((((.....)))).)))))).)))))..)))).(((((...................))))).(((((.((((......)))).))))).. ( -35.81)
>DroAna_CAF1 31607 103 + 1
-AGGAUGCUAGAAUCCUCAAAUCGGAAUGCGUGUCC-----CU----------CGUUUGCAGACUGCAUCUAUUGAAUAAUUAACCGAUUUCUGAUUGUUUUCGAAUGGGCAAUCAACU
-(((((......))))).(((((((..((((.(((.-----..----------........)))))))((....))........))))))).(((((((((......)))))))))... ( -24.30)
>consensus
CAACUUGCAACA___UGCAACUUGCAACUUGCAGCUGGCAGCUA_______GCAGCUAGCCGGUUGCCAUUCUUGAAUAAUUAACCGAAUCCUGAUGGUCCUCGAAUGGGCAAUCAGCU
.....(((........)))...........((((.(((((((............))).)))).))))........................(((((.((((......)))).))))).. (-14.52 = -16.17 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:53 2006