Locus 1848

Sequence ID	3L_DroMel_CAF1
Location	5,187,801 – 5,187,903
Length	102
Max. P	0.977322

overview

Window 3

Location	5,187,801 – 5,187,903
Length	102
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	77.68
Mean single sequence MFE	-33.18
Consensus MFE	-20.01
Energy contribution	-20.61
Covariance contribution	0.60
Combinations/Pair	1.10
Mean z-score	-2.34
Structure conservation index	0.60
SVM decision value	1.79
SVM RNA-class probability	0.977322
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5187801 102 + 23771897
GUGCGGCAAUUGCCGCAGUUGCAGCAACGUCGCAACUCGCUGCUCGCCACCCCGCAGCAACAUC---------ACCACCAGCGGCUGGAACUGAAAAAGCAGCAGUGGCUU
.((((((....))))))(((((.((...)).)))))..(((((..........)))))......---------......(((.((((...(((......))))))).))). ( -34.90)
>DroSec_CAF1 53020 79 + 1
GUGCGGCAAUUGCCGCAGUUCC-----------------------UCCACCCAGCAGCAACAUC---------ACCACCAGCGGCUGGGACUGAAAAAGCAGCAGUGGCUU
.((((((....))))))((..(-----------------------(...((((((.((......---------.......)).)))))).(((......))).))..)).. ( -28.02)
>DroSim_CAF1 53909 79 + 1
GUGCGGCAAUUGCCGCAGUUGC-----------------------UCCACCCAGCAGCAACAUC---------ACCACCAGCGGCUGGAACUGAAAAAGCAGCAGUGGCUU
.((((((....))))))(((((-----------------------(.(.....).))))))...---------......(((.((((...(((......))))))).))). ( -28.70)
>DroEre_CAF1 52013 81 + 1
GUGCGGCAAUUGCUGCAGUU------------------GCUGC--CCCA-CCAGCAGCAACAUC---------ACCACCAGCGGCUCGAACUGAAAAAGCAGCAGUGGCUU
.((((((....))))))(((------------------(((((--....-...))))))))...---------.((((..((.(((...........))).)).))))... ( -30.80)
>DroYak_CAF1 52607 108 + 1
GUGCGGCAAUUGCUGCAGUUGCAGCAACGUCGCAACUUGCUGC--UCCA-UCAGCAGCAACAUCAUCACCGCCACCACCAGGGGCUGGAACUGAAAAAGCAGCAGUGGCUU
.((((((..(((((((....))))))).))))))..(((((((--(...-..))))))))..........(((((..((((...))))..(((......)))..))))).. ( -43.50)
>consensus
GUGCGGCAAUUGCCGCAGUUGC________________GCUGC__UCCACCCAGCAGCAACAUC_________ACCACCAGCGGCUGGAACUGAAAAAGCAGCAGUGGCUU
.((((((....)))))).............................(((((((((.((......................)).)))))..(((......)))..))))... (-20.01 = -20.61 +   0.60)

alignment

secondary structure

dotplot

Window 4

Location	5,187,801 – 5,187,903
Length	102
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	77.68
Mean single sequence MFE	-37.20
Consensus MFE	-19.77
Energy contribution	-19.73
Covariance contribution	-0.04
Combinations/Pair	1.05
Mean z-score	-1.98
Structure conservation index	0.53
SVM decision value	0.59
SVM RNA-class probability	0.791992
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5187801 102 - 23771897
AAGCCACUGCUGCUUUUUCAGUUCCAGCCGCUGGUGGU---------GAUGUUGCUGCGGGGUGGCGAGCAGCGAGUUGCGACGUUGCUGCAACUGCGGCAAUUGCCGCAC
..((((((((.((....(((.(.((((...)))).).)---------))....)).))..))))))..(((((((((....)).)))))))...((((((....)))))). ( -44.00)
>DroSec_CAF1 53020 79 - 1
AAGCCACUGCUGCUUUUUCAGUCCCAGCCGCUGGUGGU---------GAUGUUGCUGCUGGGUGGA-----------------------GGAACUGCGGCAAUUGCCGCAC
.(((....)))..((((((...((((((.((.......---------......)).))))))..))-----------------------)))).((((((....)))))). ( -29.82)
>DroSim_CAF1 53909 79 - 1
AAGCCACUGCUGCUUUUUCAGUUCCAGCCGCUGGUGGU---------GAUGUUGCUGCUGGGUGGA-----------------------GCAACUGCGGCAAUUGCCGCAC
..((((((((.(((...........))).)).))))))---------...((((((.(.....).)-----------------------)))))((((((....)))))). ( -32.50)
>DroEre_CAF1 52013 81 - 1
AAGCCACUGCUGCUUUUUCAGUUCGAGCCGCUGGUGGU---------GAUGUUGCUGCUGG-UGGG--GCAGC------------------AACUGCAGCAAUUGCCGCAC
..((((((((.((((.........)))).)).))))))---------...(((((((((..-...)--)))))------------------)))(((.((....)).))). ( -32.80)
>DroYak_CAF1 52607 108 - 1
AAGCCACUGCUGCUUUUUCAGUUCCAGCCCCUGGUGGUGGCGGUGAUGAUGUUGCUGCUGA-UGGA--GCAGCAAGUUGCGACGUUGCUGCAACUGCAGCAAUUGCCGCAC
.......((((((((..(((((....(((((....)).)))((..((...))..)))))))-..))--))))))...((((.(((((((((....))))))).)).)))). ( -46.90)
>consensus
AAGCCACUGCUGCUUUUUCAGUUCCAGCCGCUGGUGGU_________GAUGUUGCUGCUGGGUGGA__GCAGC________________GCAACUGCGGCAAUUGCCGCAC
..((((((((.(((...........))).)).))))))............((((((((.(.................................).))))))))........ (-19.77 = -19.73 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:15 2006