Locus 6674

Sequence ID	3R_DroMel_CAF1
Location	17,555,595 – 17,555,738
Length	143
Max. P	0.856223

overview

Window 1

Location	17,555,595 – 17,555,705
Length	110
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	92.00
Mean single sequence MFE	-36.73
Consensus MFE	-32.59
Energy contribution	-32.70
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.07
Structure conservation index	0.89
SVM decision value	0.57
SVM RNA-class probability	0.783879
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17555595 110 + 27905053
GAGCUUGAUGGACCCCUCUCAUCAAUUGAGAUAUUAUGAAAUCCACUGCACUCC--CCGCUUCCCCC-GCGAGUGCGUGCGGUCCGCGCUCGCUAAUAGAGACGCAUUCAUGU-------
..((.(((.(((((..(((((.....)))))............(((.((((((.--..((.......-))))))))))).)))))((((((.......))).)))..))).))------- ( -35.20)
>DroSim_CAF1 3569 113 + 1
GAGCUUGAUGGACCCCUCUCAUCAAUUGAGAUAUUAUGAAAUCCACUGCACUCCCCCCGCUUCCCCCAGCGAGUGCGUGCGGUCCGCGCUCGCUAAUAGAGACGCAUUCAUGU-------
..((.(((.(((((..(((((.....)))))............(((.((((((.....(((......)))))))))))).)))))((((((.......))).)))..))).))------- ( -35.70)
>DroEre_CAF1 7867 117 + 1
GAGCUUGAUGGACCCCUCUCAUCAAUUGAGAUAUUAUGAAAUCCACUGCACGCC--GCGCUUCCCCA-GCGAGUGCGUGCGGUCCGCGUUCGCUAAUAGAGACGCAUUCAUGUACAUUCA
(.((.(((.(((((..(((((.....)))))................(((((((--.((((.....)-))).).)))))))))))((((((.......)).))))..))).)).)..... ( -39.30)
>consensus
GAGCUUGAUGGACCCCUCUCAUCAAUUGAGAUAUUAUGAAAUCCACUGCACUCC__CCGCUUCCCCC_GCGAGUGCGUGCGGUCCGCGCUCGCUAAUAGAGACGCAUUCAUGU_______
..((.(((.(((((..(((((.....)))))............(((.(((((.....(((........))))))))))).)))))((((((.......))).)))..))).))....... (-32.59 = -32.70 +   0.11)

alignment

secondary structure

dotplot

Window 2

Location	17,555,595 – 17,555,705
Length	110
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.00
Mean single sequence MFE	-40.97
Consensus MFE	-36.57
Energy contribution	-37.23
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.68
Structure conservation index	0.89
SVM decision value	0.04
SVM RNA-class probability	0.554061
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17555595 110 - 27905053
-------ACAUGAAUGCGUCUCUAUUAGCGAGCGCGGACCGCACGCACUCGC-GGGGGAAGCGG--GGAGUGCAGUGGAUUUCAUAAUAUCUCAAUUGAUGAGAGGGGUCCAUCAAGCUC
-------.......(((.(((((....(((((.(((.......))).)))))-.))))).))).--.((((...((((((..(......(((((.....))))))..))))))...)))) ( -41.20)
>DroSim_CAF1 3569 113 - 1
-------ACAUGAAUGCGUCUCUAUUAGCGAGCGCGGACCGCACGCACUCGCUGGGGGAAGCGGGGGGAGUGCAGUGGAUUUCAUAAUAUCUCAAUUGAUGAGAGGGGUCCAUCAAGCUC
-------.......(((.(((((..(((((((.(((.......))).)))))))))))).)))....((((...((((((..(......(((((.....))))))..))))))...)))) ( -42.30)
>DroEre_CAF1 7867 117 - 1
UGAAUGUACAUGAAUGCGUCUCUAUUAGCGAACGCGGACCGCACGCACUCGC-UGGGGAAGCGC--GGCGUGCAGUGGAUUUCAUAAUAUCUCAAUUGAUGAGAGGGGUCCAUCAAGCUC
....(((((.....((((..(((.(((((((..(((.......)))..))))-))))))..)))--)..)))))((((((..(......(((((.....))))))..))))))....... ( -39.40)
>consensus
_______ACAUGAAUGCGUCUCUAUUAGCGAGCGCGGACCGCACGCACUCGC_GGGGGAAGCGG__GGAGUGCAGUGGAUUUCAUAAUAUCUCAAUUGAUGAGAGGGGUCCAUCAAGCUC
..............(((.(((((....(((((.(((.......))).)))))..))))).)))....((((...((((((..(......(((((.....))))))..))))))...)))) (-36.57 = -37.23 +   0.67)

alignment

secondary structure

dotplot

Window 3

Location	17,555,635 – 17,555,738
Length	103
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	84.26
Mean single sequence MFE	-34.27
Consensus MFE	-33.05
Energy contribution	-33.50
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-0.87
Structure conservation index	0.96
SVM decision value	0.81
SVM RNA-class probability	0.856223
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17555635 103 + 27905053
AUCCACUGCACUCC--CCGCUUCCCCC-GCGAGUGCGUGCGGUCCGCGCUCGCUAAUAGAGACGCAUUCAUGU--------------ACAUCCUUCUGGACCUCGCGCUGAGCUCCACGG
.......((.....--..)).....((-(.(((((((((.(((((((((((.......))).)))((....))--------------..........))))).)))))...))))..))) ( -30.60)
>DroSim_CAF1 3609 106 + 1
AUCCACUGCACUCCCCCCGCUUCCCCCAGCGAGUGCGUGCGGUCCGCGCUCGCUAAUAGAGACGCAUUCAUGU--------------ACAUCCUUCUGGACCUCGCGCUGAGCUCCACGG
................(((((......)))(((((((((.(((((((((((.......))).)))((....))--------------..........))))).)))))...))))...)) ( -30.90)
>DroEre_CAF1 7907 113 + 1
AUCCACUGCACGCC--GCGCUUCCCCA-GCGAGUGCGUGCGGUCCGCGUUCGCUAAUAGAGACGCAUUCAUGUACAUUCAUGUAUGUACAUCCCUCUGGACCUCGCGCUGAGCCC----G
.......(((((((--.((((.....)-))).).))))))(((((((((((.......)).))))....((((((((......))))))))......)))))..((.....))..----. ( -41.30)
>consensus
AUCCACUGCACUCC__CCGCUUCCCCC_GCGAGUGCGUGCGGUCCGCGCUCGCUAAUAGAGACGCAUUCAUGU______________ACAUCCUUCUGGACCUCGCGCUGAGCUCCACGG
.......((........(((........)))...(((((.(((((((((((.......))).)))....((((((((......))))))))......))))).)))))...))....... (-33.05 = -33.50 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:17 2006