Locus 3965

Sequence ID	2R_DroMel_CAF1
Location	13,097,103 – 13,097,318
Length	215
Max. P	0.853792

overview

Window 1

Location	13,097,103 – 13,097,198
Length	95
Sequences	3
Columns	95
Reading direction	reverse
Mean pairwise identity	92.98
Mean single sequence MFE	-30.90
Consensus MFE	-27.93
Energy contribution	-28.27
Covariance contribution	0.34
Combinations/Pair	1.12
Mean z-score	-1.91
Structure conservation index	0.90
SVM decision value	0.41
SVM RNA-class probability	0.724716
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13097103 95 - 20766785
CCUUCGUGGUCACGCUGCUCUUCCCAAUCCUCAAGAGCUCGAUCGGGCCGGGUCCGACCUUUUGGAUCUUUACCGCGAUCGCGGUCAUCGCCUUC
.....(((((..(((.((((((..........))))))..(((((((..((((((((....))))))))...)).))))))))...))))).... ( -32.50)
>DroSim_CAF1 8304 95 - 1
CCUUCAUGGUCACGCUGCUCUUCCCAAUCCUCAAGAGCGCGAUCGGGCCGGGUCCAACCUUCUGGAUCUUCACCGUGAUCGCGGUCAUCGCCUUC
.....(((..(.....((((((..........))))))(((((((((..(((((((......)))))))...)).))))))))..)))....... ( -32.40)
>DroYak_CAF1 8478 95 - 1
CCUUCAUGGUCACGCUGCUCUUCCCAAUCCUCAAGAACGCGAUCGGGGCGGGUCCAACCUUCUGGAUCUUCACCGUGAUCGCGGUCCUCUCCUUC
.......((.(.......((((..........)))).((((((((.((.(((((((......)))))))...)).))))))))).))........ ( -27.80)
>consensus
CCUUCAUGGUCACGCUGCUCUUCCCAAUCCUCAAGAGCGCGAUCGGGCCGGGUCCAACCUUCUGGAUCUUCACCGUGAUCGCGGUCAUCGCCUUC
.....(((..(.....((((((..........))))))(((((((((..(((((((......)))))))...)).))))))))..)))....... (-27.93 = -28.27 +   0.34)

alignment

secondary structure

dotplot

Window 2

Location	13,097,158 – 13,097,278
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-50.50
Consensus MFE	-47.67
Energy contribution	-48.67
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	0.94
SVM decision value	0.33
SVM RNA-class probability	0.692205
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13097158 120 - 20766785
GCUGGUGAUGGCGGAACUCUUCUCGGAGGAUGUGAAGAGUGUGGCAGGAUCGAUUGCCGGCACCAGCAACUGGCUGUCGGCCUUCGUGGUCACGCUGCUCUUCCCAAUCCUCAAGAGCUC
(((......))).((.(((((....((((((..((((((((((((.....(((..(((((((((((...)))).)))))))..)))..)))))...)))))))...))))))))))).)) ( -50.90)
>DroSim_CAF1 8359 120 - 1
GCUGGUGAUGGCGGAGCUCUUCUCGGAGGAUGUGAAGAGUGUGGCAGGAUCGAUUGCCGGCACCAGCAACUGGCUGUCGGCCUUCAUGGUCACGCUGCUCUUCCCAAUCCUCAAGAGCGC
(((......)))...((((((....((((((..(((((((..(((..((((((..(((((((((((...)))).)))))))..))..))))..))))))))))...)))))))))))).. ( -53.40)
>DroYak_CAF1 8533 120 - 1
GCUGGUGAUGGCGGAGCUCUUCUCGGAGGAUGUGAAGAGUGUGGCAGGAUCUAUUGCCGGCACCAGCAACUGGCUGUCGGCCUUCAUGGUCACGCUGCUCUUCCCAAUCCUCAAGAACGC
(((......)))...((..((((..((((((..(((((((..(((..((((....(((((((((((...)))).)))))))......))))..))))))))))...)))))).)))).)) ( -47.20)
>consensus
GCUGGUGAUGGCGGAGCUCUUCUCGGAGGAUGUGAAGAGUGUGGCAGGAUCGAUUGCCGGCACCAGCAACUGGCUGUCGGCCUUCAUGGUCACGCUGCUCUUCCCAAUCCUCAAGAGCGC
(((......)))...((((((....((((((..(((((((..(((..((((((..(((((((((((...)))).)))))))..))..))))..))))))))))...)))))))))))).. (-47.67 = -48.67 +   1.00)

alignment

secondary structure

dotplot

Window 3

Location	13,097,198 – 13,097,318
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.56
Mean single sequence MFE	-34.90
Consensus MFE	-33.97
Energy contribution	-33.97
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.97
SVM decision value	0.80
SVM RNA-class probability	0.853792
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13097198 120 + 20766785
CCGACAGCCAGUUGCUGGUGCCGGCAAUCGAUCCUGCCACACUCUUCACAUCCUCCGAGAAGAGUUCCGCCAUCACCAGCCACGGCACCGGUCCGAAUCCAAUCGAGAAGAAGAUUAUGA
(((...(((.((.(((((((..((((........))))..(((((((.(.......).)))))))........))))))).)))))..)))(((((......))).))............ ( -36.50)
>DroSim_CAF1 8399 120 + 1
CCGACAGCCAGUUGCUGGUGCCGGCAAUCGAUCCUGCCACACUCUUCACAUCCUCCGAGAAGAGCUCCGCCAUCACCAGCCACGGCACCGGUCCAAAUCCAAUCGAGAAGAAUAUAAUGA
.(((..(((.((.(((((((..((((........))))...((((((.(.......).)))))).........))))))).)))))...((.......))..)))............... ( -33.90)
>DroYak_CAF1 8573 120 + 1
CCGACAGCCAGUUGCUGGUGCCGGCAAUAGAUCCUGCCACACUCUUCACAUCCUCCGAGAAGAGCUCCGCCAUCACCAGCCACGGCACCGGUCCGAAUCCAAUCGAAAAGAAGACAAUAA
(((...(((.((.(((((((..((((........))))...((((((.(.......).)))))).........))))))).)))))..)))..(((......)))............... ( -34.30)
>consensus
CCGACAGCCAGUUGCUGGUGCCGGCAAUCGAUCCUGCCACACUCUUCACAUCCUCCGAGAAGAGCUCCGCCAUCACCAGCCACGGCACCGGUCCGAAUCCAAUCGAGAAGAAGAUAAUGA
.(((..(((.((.(((((((..((((........))))...((((((.(.......).)))))).........))))))).)))))...((.......))..)))............... (-33.97 = -33.97 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:30 2006