Locus 6890

Sequence ID	3R_DroMel_CAF1
Location	18,197,666 – 18,197,810
Length	144
Max. P	0.999648

overview

Window 6

Location	18,197,666 – 18,197,770
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	98.08
Mean single sequence MFE	-46.51
Consensus MFE	-44.57
Energy contribution	-44.61
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.54
Structure conservation index	0.96
SVM decision value	3.83
SVM RNA-class probability	0.999648
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18197666 104 + 27905053
GGCGCUGGUACCAUCGAUGCCUCUCACGCGGCUGCCAUCGCUGCCGUUGAGGCUGCCACCAAGGCCAAGGCCUCCGCCAUCGUGGUGAUCACCACCAGCGGCAA
(.(((((((((((.(((((((((....(((((.((....)).))))).))))).(((.....)))...(((....))))))))))).......))))))).).. ( -47.41)
>DroSec_CAF1 5742 104 + 1
GGCGCUGGUACCAUCGAUGCCUCUCACGCGGCUGCCAUCGCUGCCGUUGAGGCUGCCACCAAGGCCAAGGCCUCCGCCAUCGUGGUGAUCACCACCAGCGGCAA
(.(((((((((((.(((((((((....(((((.((....)).))))).))))).(((.....)))...(((....))))))))))).......))))))).).. ( -47.41)
>DroSim_CAF1 5790 104 + 1
GGCGCUGGUACCAUCGAUGCCUCUCACGCGGCUGCCAUCGCUGCCGUUGAAGCUGCCGCCAAGGCCAAGGCCUCCGCCAUCGUGGUUAUCACCACCAGCGGCAA
(.(((((((((((.(((((....(((.(((((.((....)).)))))))).......((..((((....))))..))))))))))).......))))))).).. ( -44.21)
>DroEre_CAF1 5976 104 + 1
GGCGCUGGUACCAUCGAUGCCCCUCACGCAGCUGCCAUCGCUGCCGUUGAGGCUGCCACCAAGGCCAAGGCCUCCGCCAUCGUGGUGAUCACCACCAGCGGCAA
(.(((((((((((.(((((........(((((.......))))).((.(((((((((.....)))...)))))).))))))))))).......))))))).).. ( -46.11)
>DroYak_CAF1 5868 104 + 1
GGCGCUGGUACCAUCGAUGCCUCUCACGCGGCUGCCAUCGCUGCCGUUGAGGCUGCCACCAAGGCCAAGGCCUCCGCCAUCGUGGUGAUCACCACCAGCGGCAA
(.(((((((((((.(((((((((....(((((.((....)).))))).))))).(((.....)))...(((....))))))))))).......))))))).).. ( -47.41)
>consensus
GGCGCUGGUACCAUCGAUGCCUCUCACGCGGCUGCCAUCGCUGCCGUUGAGGCUGCCACCAAGGCCAAGGCCUCCGCCAUCGUGGUGAUCACCACCAGCGGCAA
(.(((((((((((.(((((........(((((.......))))).((.(((((((((.....)))...)))))).))))))))))).......))))))).).. (-44.57 = -44.61 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	18,197,666 – 18,197,770
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	98.08
Mean single sequence MFE	-47.61
Consensus MFE	-47.05
Energy contribution	-46.57
Covariance contribution	-0.48
Combinations/Pair	1.09
Mean z-score	-1.10
Structure conservation index	0.99
SVM decision value	-0.02
SVM RNA-class probability	0.523866
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18197666 104 - 27905053
UUGCCGCUGGUGGUGAUCACCACGAUGGCGGAGGCCUUGGCCUUGGUGGCAGCCUCAACGGCAGCGAUGGCAGCCGCGUGAGAGGCAUCGAUGGUACCAGCGCC
....(((((((.......(((((((((.(.(((((....))))).(((((.(((.....))).((....)).)))))......).))))).))))))))))).. ( -47.31)
>DroSec_CAF1 5742 104 - 1
UUGCCGCUGGUGGUGAUCACCACGAUGGCGGAGGCCUUGGCCUUGGUGGCAGCCUCAACGGCAGCGAUGGCAGCCGCGUGAGAGGCAUCGAUGGUACCAGCGCC
....(((((((.......(((((((((.(.(((((....))))).(((((.(((.....))).((....)).)))))......).))))).))))))))))).. ( -47.31)
>DroSim_CAF1 5790 104 - 1
UUGCCGCUGGUGGUGAUAACCACGAUGGCGGAGGCCUUGGCCUUGGCGGCAGCUUCAACGGCAGCGAUGGCAGCCGCGUGAGAGGCAUCGAUGGUACCAGCGCC
....(((((((.......(((((((((.(.(((((....))))).(((((.(((.....))).((....)).)))))......).))))).))))))))))).. ( -46.71)
>DroEre_CAF1 5976 104 - 1
UUGCCGCUGGUGGUGAUCACCACGAUGGCGGAGGCCUUGGCCUUGGUGGCAGCCUCAACGGCAGCGAUGGCAGCUGCGUGAGGGGCAUCGAUGGUACCAGCGCC
....(((((((.......(((((((((((.(((((....))))).)).....(((((...(((((.......))))).)))))..))))).))))))))))).. ( -49.41)
>DroYak_CAF1 5868 104 - 1
UUGCCGCUGGUGGUGAUCACCACGAUGGCGGAGGCCUUGGCCUUGGUGGCAGCCUCAACGGCAGCGAUGGCAGCCGCGUGAGAGGCAUCGAUGGUACCAGCGCC
....(((((((.......(((((((((.(.(((((....))))).(((((.(((.....))).((....)).)))))......).))))).))))))))))).. ( -47.31)
>consensus
UUGCCGCUGGUGGUGAUCACCACGAUGGCGGAGGCCUUGGCCUUGGUGGCAGCCUCAACGGCAGCGAUGGCAGCCGCGUGAGAGGCAUCGAUGGUACCAGCGCC
....(((((((.......(((((((((.(.(((((....))))).(((((.(((.....))).((....)).)))))......).))))).))))))))))).. (-47.05 = -46.57 +  -0.48)

alignment

secondary structure

dotplot

Window 8

Location	18,197,690 – 18,197,810
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.67
Mean single sequence MFE	-48.48
Consensus MFE	-47.74
Energy contribution	-47.78
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.22
Structure conservation index	0.98
SVM decision value	0.26
SVM RNA-class probability	0.656632
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18197690 120 + 27905053
CACGCGGCUGCCAUCGCUGCCGUUGAGGCUGCCACCAAGGCCAAGGCCUCCGCCAUCGUGGUGAUCACCACCAGCGGCAAGUCGGCCUUCCAGGUGAGCAAGUACCGCCCACGCUGCCCC
...(((((.(((..(..((((((((((((((((.....)))...)))))).......(((((....))))).))))))).)..))).......(((.((.......)).))))))))... ( -48.80)
>DroSec_CAF1 5766 120 + 1
CACGCGGCUGCCAUCGCUGCCGUUGAGGCUGCCACCAAGGCCAAGGCCUCCGCCAUCGUGGUGAUCACCACCAGCGGCAAGUCGGCCUUCCAGGUGAGCAAGUACCGCCCACGCUGCCCC
...(((((.(((..(..((((((((((((((((.....)))...)))))).......(((((....))))).))))))).)..))).......(((.((.......)).))))))))... ( -48.80)
>DroSim_CAF1 5814 120 + 1
CACGCGGCUGCCAUCGCUGCCGUUGAAGCUGCCGCCAAGGCCAAGGCCUCCGCCAUCGUGGUUAUCACCACCAGCGGCAAGUCGGCCUUCCAGGUGAGCAAGUACCGCCCACGCUGCCCC
...(((((.(((..(..((((((((........((..((((....))))..))....(((((....))))))))))))).)..))).......(((.((.......)).))))))))... ( -46.50)
>DroEre_CAF1 6000 120 + 1
CACGCAGCUGCCAUCGCUGCCGUUGAGGCUGCCACCAAGGCCAAGGCCUCCGCCAUCGUGGUGAUCACCACCAGCGGCAAGUCGGCCUUCCAGGUGAGCAAGUACCGCCCACGCUGCCCC
...(((((.(((..(..((((((((((((((((.....)))...)))))).......(((((....))))).))))))).)..))).......(((.((.......)).))))))))... ( -49.50)
>DroYak_CAF1 5892 120 + 1
CACGCGGCUGCCAUCGCUGCCGUUGAGGCUGCCACCAAGGCCAAGGCCUCCGCCAUCGUGGUGAUCACCACCAGCGGCAAGUCGGCCUUCCAGGUGAGCAAGUACCGCCCACGCUGCCCC
...(((((.(((..(..((((((((((((((((.....)))...)))))).......(((((....))))).))))))).)..))).......(((.((.......)).))))))))... ( -48.80)
>consensus
CACGCGGCUGCCAUCGCUGCCGUUGAGGCUGCCACCAAGGCCAAGGCCUCCGCCAUCGUGGUGAUCACCACCAGCGGCAAGUCGGCCUUCCAGGUGAGCAAGUACCGCCCACGCUGCCCC
...(((((.(((..(..((((((((((((((((.....)))...)))))).......(((((....))))).))))))).)..))).......(((.((.......)).))))))))... (-47.74 = -47.78 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:37 2006