Locus 267

Sequence ID	3R_DroMel_CAF1
Location	1,048,618 – 1,048,778
Length	160
Max. P	0.996533

overview

Window 3

Location	1,048,618 – 1,048,738
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.17
Mean single sequence MFE	-43.23
Consensus MFE	-40.00
Energy contribution	-40.80
Covariance contribution	0.80
Combinations/Pair	1.05
Mean z-score	-1.12
Structure conservation index	0.93
SVM decision value	0.12
SVM RNA-class probability	0.594439
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1048618 120 + 27905053
CCAUCUCAAGCAGGGAGGCCUGGUCGUUGACGUCCGCGAUGAAGAUGGGCACCUGCGAGAGGUCCUUCUUGGCCUUGGCGCCCAUCUCCUUCAACACCGCCUCCAGCUUCUCGCGGUUCC
((.....((((..((((((..(((.(((((((((...)))).((((((((.((.....((((((......)))))))).))))))))...)))))))))))))).)))).....)).... ( -48.20)
>DroSec_CAF1 20531 120 + 1
CCAUCUCCAGCAGGGAGGUCUGGUCGUUGACGUCCGCGAUGAAGAUGGGCACCUGCGAGAGGUCCUUCUUGGCCUUGGCGCCCAUCUCCUUCAACACCGCCUCCAGCUUCUCGCGGUUCC
((......(((..((((((..(((.(((((((((...)))).((((((((.((.....((((((......)))))))).))))))))...)))))))))))))).)))......)).... ( -45.70)
>DroSim_CAF1 20411 120 + 1
CCAUCUCCAGCAGGGAGGCCUGGUCGUUGACGUCCGCGAUGAAGAUGGGCACCUGCGAGAGGUCCUUCUUGGCCUUGGCGCCCAUCUCCUUCAACACCGCCUCCAGCUUCUCGCGGUUCC
((......(((..((((((..(((.(((((((((...)))).((((((((.((.....((((((......)))))))).))))))))...)))))))))))))).)))......)).... ( -47.10)
>DroEre_CAF1 20689 120 + 1
CCAUCUCCAGCAGGGAGGCCUCGUCGUUGACGUCCGCGAUGAAGAUAGGCACCUGCGACAGGUCCUUUUUGGCCUUGGCGCCCAUCUCCUUCAACACCGCCUCCAGCUUCUCGCGGUUUC
((......(((..((((((.(((((((.(....).)))))))((((.(((.((......(((((......))))).)).))).))))...........)))))).)))......)).... ( -38.60)
>DroYak_CAF1 21448 120 + 1
CCAUCUCCAGCAGGGAAGUCUCGUCGUUGACGUCCGCGAUAAAGAUGGGCACCUGUGAGAGGUCCUUCUUGGCCUUGGCGCCCAUCUCCUUUAAAACCGCCUCCAGCUUCUCACGGUUUC
((((((...((..(((.(((........))).))))).....))))))....(((((((((((......(((....((((.................)))).)))))))))))))).... ( -36.53)
>consensus
CCAUCUCCAGCAGGGAGGCCUGGUCGUUGACGUCCGCGAUGAAGAUGGGCACCUGCGAGAGGUCCUUCUUGGCCUUGGCGCCCAUCUCCUUCAACACCGCCUCCAGCUUCUCGCGGUUCC
((......(((..((((((..(((.(((((((....))....((((((((.((.....((((((......)))))))).))))))))...)))))))))))))).)))......)).... (-40.00 = -40.80 +   0.80)

alignment

secondary structure

dotplot

Window 4

Location	1,048,618 – 1,048,738
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.17
Mean single sequence MFE	-50.52
Consensus MFE	-46.06
Energy contribution	-45.38
Covariance contribution	-0.68
Combinations/Pair	1.14
Mean z-score	-1.96
Structure conservation index	0.91
SVM decision value	2.71
SVM RNA-class probability	0.996533
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1048618 120 - 27905053
GGAACCGCGAGAAGCUGGAGGCGGUGUUGAAGGAGAUGGGCGCCAAGGCCAAGAAGGACCUCUCGCAGGUGCCCAUCUUCAUCGCGGACGUCAACGACCAGGCCUCCCUGCUUGAGAUGG
....((((...((((.((((((((((((((.(((((((((((((.(((((.....)).)))......)))))))))))))..((....))))))).)))..))))))..))))..).))) ( -53.10)
>DroSec_CAF1 20531 120 - 1
GGAACCGCGAGAAGCUGGAGGCGGUGUUGAAGGAGAUGGGCGCCAAGGCCAAGAAGGACCUCUCGCAGGUGCCCAUCUUCAUCGCGGACGUCAACGACCAGACCUCCCUGCUGGAGAUGG
....((((....(((.((((((((((((((.(((((((((((((.(((((.....)).)))......)))))))))))))..((....))))))).))).).)))))..)))...).))) ( -50.50)
>DroSim_CAF1 20411 120 - 1
GGAACCGCGAGAAGCUGGAGGCGGUGUUGAAGGAGAUGGGCGCCAAGGCCAAGAAGGACCUCUCGCAGGUGCCCAUCUUCAUCGCGGACGUCAACGACCAGGCCUCCCUGCUGGAGAUGG
....((((....(((.((((((((((((((.(((((((((((((.(((((.....)).)))......)))))))))))))..((....))))))).)))..))))))..)))...).))) ( -52.90)
>DroEre_CAF1 20689 120 - 1
GAAACCGCGAGAAGCUGGAGGCGGUGUUGAAGGAGAUGGGCGCCAAGGCCAAAAAGGACCUGUCGCAGGUGCCUAUCUUCAUCGCGGACGUCAACGACGAGGCCUCCCUGCUGGAGAUGG
....((((....(((.((((((..(((((..(((((((((((((.(((((.....)).)))......)))))))))))))...((....))...)))))..))))))..)))...).))) ( -50.20)
>DroYak_CAF1 21448 120 - 1
GAAACCGUGAGAAGCUGGAGGCGGUUUUAAAGGAGAUGGGCGCCAAGGCCAAGAAGGACCUCUCACAGGUGCCCAUCUUUAUCGCGGACGUCAACGACGAGACUUCCCUGCUGGAGAUGG
....(((((((((((((....)))))))...(((((((((((((.(((((.....)).)))......))))))))))))).)))))).((((...))))...(.((((....)).)).). ( -45.90)
>consensus
GGAACCGCGAGAAGCUGGAGGCGGUGUUGAAGGAGAUGGGCGCCAAGGCCAAGAAGGACCUCUCGCAGGUGCCCAUCUUCAUCGCGGACGUCAACGACCAGGCCUCCCUGCUGGAGAUGG
....((((((...((((....))))......(((((((((((((.(((((.....)).)))......))))))))))))).))))))..(((........)))((((.....)))).... (-46.06 = -45.38 +  -0.68)

alignment

secondary structure

dotplot

Window 5

Location	1,048,658 – 1,048,778
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.33
Mean single sequence MFE	-52.00
Consensus MFE	-47.66
Energy contribution	-48.58
Covariance contribution	0.92
Combinations/Pair	1.07
Mean z-score	-1.72
Structure conservation index	0.92
SVM decision value	2.17
SVM RNA-class probability	0.989533
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1048658 120 - 27905053
GUCACGGUGCUGCGCGGCUUGCGAUGGGGCAUCGCUGGCAGGAACCGCGAGAAGCUGGAGGCGGUGUUGAAGGAGAUGGGCGCCAAGGCCAAGAAGGACCUCUCGCAGGUGCCCAUCUUC
....(((..((((...(((.((((((...)))))).))).....((((.....)).))..))))..)))..(((((((((((((.(((((.....)).)))......))))))))))))) ( -53.00)
>DroSec_CAF1 20571 120 - 1
GUCACCGUGCUGCGCGGCUUGCGAUGGGGCAUAGCGGGCAGGAACCGCGAGAAGCUGGAGGCGGUGUUGAAGGAGAUGGGCGCCAAGGCCAAGAAGGACCUCUCGCAGGUGCCCAUCUUC
..((((((.((((.(.((((((......))).))).)))))...((((.....)).))..)))))).....(((((((((((((.(((((.....)).)))......))))))))))))) ( -53.70)
>DroSim_CAF1 20451 120 - 1
GUCACCGUGCUGCGCGGCUUGCGAUGGGGCAUAGCGGGCAGGAACCGCGAGAAGCUGGAGGCGGUGUUGAAGGAGAUGGGCGCCAAGGCCAAGAAGGACCUCUCGCAGGUGCCCAUCUUC
..((((((.((((.(.((((((......))).))).)))))...((((.....)).))..)))))).....(((((((((((((.(((((.....)).)))......))))))))))))) ( -53.70)
>DroEre_CAF1 20729 120 - 1
GUCACCGUGCUGCGAGGCUUGCGAUGGGGAAUCGCGGGCAGAAACCGCGAGAAGCUGGAGGCGGUGUUGAAGGAGAUGGGCGCCAAGGCCAAAAAGGACCUGUCGCAGGUGCCUAUCUUC
..((((((.((.((..(((((((((.....))))))))).......((.....)))).)))))))).....(((((((((((((.(((((.....)).)))......))))))))))))) ( -52.40)
>DroYak_CAF1 21488 120 - 1
GUCACCGUGCUGCGAGGGUUGCGAUGGGGAAUCGCGGGCAGAAACCGUGAGAAGCUGGAGGCGGUUUUAAAGGAGAUGGGCGCCAAGGCCAAGAAGGACCUCUCACAGGUGCCCAUCUUU
.((.((((((.((....)).)).)))).)).((((((.......))))))(((((((....)))))))...(((((((((((((.(((((.....)).)))......))))))))))))) ( -47.20)
>consensus
GUCACCGUGCUGCGCGGCUUGCGAUGGGGCAUCGCGGGCAGGAACCGCGAGAAGCUGGAGGCGGUGUUGAAGGAGAUGGGCGCCAAGGCCAAGAAGGACCUCUCGCAGGUGCCCAUCUUC
(((.(((.(((.(((((((((((((.....))))))))......)))))...)))))).))).........(((((((((((((.(((((.....)).)))......))))))))))))) (-47.66 = -48.58 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:06 2006