Locus 6669

Sequence ID	3R_DroMel_CAF1
Location	17,544,877 – 17,545,031
Length	154
Max. P	0.999253

overview

Window 5

Location	17,544,877 – 17,544,991
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	97.72
Mean single sequence MFE	-34.08
Consensus MFE	-31.24
Energy contribution	-31.20
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-2.59
Structure conservation index	0.92
SVM decision value	3.46
SVM RNA-class probability	0.999253
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17544877 114 - 27905053
CGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCGGAGCAUCAGACAAGUGGAACCACUAGCACCAGCACUUGCAACAACAGCAAUGCAGCAAAUACGGUCAGCAACAACAAUGC
.((..(((.((((((((((.......))))))))))((........((((....)))).......(((.((((.......))))))).))...)))..)).(((.......))) ( -34.60)
>DroSec_CAF1 53918 114 - 1
CGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCGGAGCAUCAGACAAGUGGAACCACUAGCACCAUCACUUGCAACAACAGCAAUGCAGCCAAUACGGUCAGCAACAACAAUGC
...((((((((((((((((.......))))))))))..........((((....)))).......))))))((.......))..(((.(((.....)))..))).......... ( -33.00)
>DroSim_CAF1 54948 114 - 1
CGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCGGAGCAUCAGACAAGUGGAACCACUAGCACCAGCACUUGCAACAACAGCAAUGCAGCCAAUACGGUCAGCAACAACAAUGC
(....)...((((((((((.......))))))))))((((......((((....)))).((....(((.((((.......))))))).(((.....)))..)).......)))) ( -34.60)
>DroEre_CAF1 54864 114 - 1
CGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCGGAGCAUCAGACAAGUGGAACCACUAACACCAGCACUUGCAACAACAGCAAUGCAGCCAUUACGGCCAGCAACAACAAUGC
(....)...((((((((((.......))))))))))((........((((....)))).......(((.((((.......))))))).(((.....)))..))........... ( -34.10)
>DroYak_CAF1 50057 114 - 1
CGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCGGAGCAUCAGACAAGUGGAACCACUAACACCAGCACUUGCAACAACAGCAAUGCAGCCAUUACGGCCAGCAACAACAAUGC
(....)...((((((((((.......))))))))))((........((((....)))).......(((.((((.......))))))).(((.....)))..))........... ( -34.10)
>consensus
CGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCGGAGCAUCAGACAAGUGGAACCACUAGCACCAGCACUUGCAACAACAGCAAUGCAGCCAAUACGGUCAGCAACAACAAUGC
...(((((.((((((((((.......))))))))))..........((((....))))........)))))((.......))..(((.(((.....)))..))).......... (-31.24 = -31.20 +  -0.04)

alignment

secondary structure

dotplot

Window 6

Location	17,544,914 – 17,545,031
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.95
Mean single sequence MFE	-32.92
Consensus MFE	-22.70
Energy contribution	-22.45
Covariance contribution	-0.25
Combinations/Pair	1.05
Mean z-score	-1.58
Structure conservation index	0.69
SVM decision value	0.16
SVM RNA-class probability	0.611063
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17544914 117 - 27905053
AGCCCAUUCUGAGUCCAACUCGAUCCCUGGACGAAGGUUUCGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCGGAGCAUCAGACAAGUGGAACCAC---UAGCACCAGCACUUGCAACA
.((....(((((.......((((..(((......)))..))))...((.((((((((((.......)))))))))).)))))))..((((....)))---).))....((....)).... ( -39.70)
>DroVir_CAF1 67114 103 - 1
AGCCCAUACUGAGUCCAACACGAUCCCUUGACGAAGGUUUCGAAAGUGAUCCGGAUCGGGUUUCAACCGAUUCAGAGCAUCAAAUAAAUAACAACAA---CGUCAA--------------
........(((((((.....((((((...(((....))).(....)......))))))(((....))))))))))......................---......-------------- ( -23.00)
>DroPse_CAF1 65771 112 - 1
AGCCCAUACUGAGUCCAACACGAUCCCUGGACGAAGGUUUCGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCAGAGCAUCAGACAAGUGGAACCGCCACUGCCGCCAGCAG--------
.((.....(((((..(....(((..(((......)))..)))..........(((((((.......))))))).)..).))))...(((((.....))))).......))..-------- ( -31.90)
>DroGri_CAF1 56935 103 - 1
AGCCCAUACUGAGUCCAACACGAUCCCUUGACGAAGGUUUCGAAAGUGAUCCGGAUCGGGUUUCAACCGAUUCAGAGCAUCAAACAAGUGCAACUGC---CAACAA--------------
.((.....(((((((.....((((((...(((....))).(....)......))))))(((....)))))))))).((((.......))))....))---......-------------- ( -26.70)
>DroAna_CAF1 53414 111 - 1
AGCCCAUACUGAGUCCAACUCGAUCCCUGGACGAAGGUUUCGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCGGAGCAUCAGACCAGUACCAGUGC---UAAUACUA------CCAACA
((((..(((((.(((....((((..(((......)))..))))..(((.((((((((((.......)))))))))).)))..))))))))...).))---).......------...... ( -38.50)
>DroPer_CAF1 69760 112 - 1
AGCCCAUACUGAGUCCAACACGAUCCCUGGACGAAGGUUUCGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCGGAGCAUCAGACAAGUGGAACCGCCACUGCCGCCAGCAG--------
.((.....((((........(((..(((......)))..)))....((.((((((((((.......)))))))))).))))))...(((((.....))))).......))..-------- ( -37.70)
>consensus
AGCCCAUACUGAGUCCAACACGAUCCCUGGACGAAGGUUUCGAAAGUGAUCCGGAUCGGGUUUCCACCGAUUCAGAGCAUCAGACAAGUGGAACCGC___UAACACCA____________
........(((((((.....((((((...(((....))).(....)......))))))(((....))))))))))............................................. (-22.70 = -22.45 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:10 2006