Locus 6704

Sequence ID	3R_DroMel_CAF1
Location	17,637,185 – 17,637,311
Length	126
Max. P	0.769664

overview

Window 5

Location	17,637,185 – 17,637,275
Length	90
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	80.87
Mean single sequence MFE	-25.56
Consensus MFE	-16.42
Energy contribution	-17.34
Covariance contribution	0.92
Combinations/Pair	1.13
Mean z-score	-1.95
Structure conservation index	0.64
SVM decision value	0.53
SVM RNA-class probability	0.769664
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17637185 90 + 27905053
AGUGCAUG-AAAAGAGUGAAAGCAAUUUGGCACGAAUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC-------------------AGCAGCAACAAUG
.((((...-.(((..((....))..))).))))....((((((..((...))..))))))........(((((.....-------------------.)))))....... ( -23.10)
>DroPse_CAF1 26928 107 + 1
AGAGCGAGAACGAGAGUGAAAGCAAUUUGGCACGAAUUUGUCAUGCCAUCGAAGUGGCAACAAAUUUGGCUGCAACACUGCCACCACC---ACCACCAGCAGCAACAGCA
...((....((....))....))......((.(((((((((..((((((....)))))))))))))))(((((...............---.......)))))....)). ( -30.25)
>DroSec_CAF1 32057 90 + 1
AGUGGAUG-AAAAGAGUGAAAGCAAUUUGGCACGAAUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC-------------------AGCAGCAACAAUG
.(((((((-(...((((....((......))....)))).))))).)))((((.((....))..))))(((((.....-------------------.)))))....... ( -21.80)
>DroYak_CAF1 36682 91 + 1
AGUGCAUGGAAAAGAGUGAAAGCAAUUUGGCACGAAUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC-------------------AGCAGCAACAAUG
.((((.....(((..((....))..))).))))....((((((..((...))..))))))........(((((.....-------------------.)))))....... ( -22.40)
>DroAna_CAF1 41004 90 + 1
AGUGCAGC-UAGAGAGUGAAAACAAUUUGGCACGAAUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC-------------------AAUGGCAGUGGCA
..((((((-((((((((....))....(((((......))))))))).......((....))....)))))))).(((-------------------.......)))... ( -25.70)
>DroPer_CAF1 22055 110 + 1
AGAGCGAGAACGAGAGUGAAAGCAAUUUGGCACGAAUUUGUCAUGCCAUCGAAGUGGCAACAAAUUUGGCUGCAACACUGCCACCACCACCACCACCAGCAGCAACAGCA
...((....((....))....))......((.(((((((((..((((((....)))))))))))))))(((((.........................)))))....)). ( -30.11)
>consensus
AGUGCAUG_AAAAGAGUGAAAGCAAUUUGGCACGAAUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC___________________AGCAGCAACAACA
...............((.(((....))).)).(((((((((....((((....))))..)))))))))(((((.........................)))))....... (-16.42 = -17.34 +   0.92)

alignment

secondary structure

dotplot

Window 6

Location	17,637,219 – 17,637,311
Length	92
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	82.97
Mean single sequence MFE	-22.41
Consensus MFE	-15.15
Energy contribution	-15.23
Covariance contribution	0.08
Combinations/Pair	1.17
Mean z-score	-1.63
Structure conservation index	0.68
SVM decision value	-0.04
SVM RNA-class probability	0.510838
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17637219 92 + 27905053
AUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC----------------AGCAGCAACAAUGGCAAUAACAAUAACAAGGAUGAUGGCAGUUACAGA----G
..((((((((((..((((.((....))..))))(((((.....----------------.)))))........................)).)))))))).......----. ( -22.40)
>DroPse_CAF1 26963 105 + 1
AUUUGUCAUGCCAUCGAAGUGGCAACAAAUUUGGCUGCAACACUGCCACCACCACCACCAGCAGCAACAGCAACAGCAACAAUGACAGGAAUGA---AAGGUACAGG----C
.(((((((((((((....))))))......((((((((......................)))))....((....))..)))))))))).....---..........----. ( -22.35)
>DroSim_CAF1 31905 92 + 1
AUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC----------------AGCAGCAACAAUGGCAAUAACAAUAACAAGGAUGAUGGCAGUUACAGA----G
..((((((((((..((((.((....))..))))(((((.....----------------.)))))........................)).)))))))).......----. ( -22.40)
>DroEre_CAF1 33986 92 + 1
AUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC----------------AGCAGCAACAAUGGCAAUAACAAUAACAAGGAUGAUGGCAGUUACAGA----G
..((((((((((..((((.((....))..))))(((((.....----------------.)))))........................)).)))))))).......----. ( -22.40)
>DroYak_CAF1 36717 92 + 1
AUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC----------------AGCAGCAACAAUGGCAAUAACAAUAACAAGGAUGAUGGCAGUUACAGA----G
..((((((((((..((((.((....))..))))(((((.....----------------.)))))........................)).)))))))).......----. ( -22.40)
>DroAna_CAF1 41038 96 + 1
AUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC----------------AAUGGCAGUGGCAACAAUGACAAUAACAAGGAUGAUGGCAGUCGCCGAGCCAG
..(((((((.....((((.((....))..))))(((((.....----------------....)))))(....).)))))))......((....((((....))))..)).. ( -22.50)
>consensus
AUUUGUCAUCUCAUCGAAGUGGCAACAAAUUUGGCUGCAACAC________________AGCAGCAACAAUGGCAAUAACAAUAACAAGGAUGAUGGCAGUUACAGA____G
..(..((((((...((((.((....))..))))(((((......................))))).......................))))))..)............... (-15.15 = -15.23 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:59 2006