Locus 47

Sequence ID	3R_DroMel_CAF1
Location	306,870 – 306,990
Length	120
Max. P	0.983364

overview

Window 4

Location	306,870 – 306,990
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.25
Mean single sequence MFE	-46.46
Consensus MFE	-40.30
Energy contribution	-40.30
Covariance contribution	0.00
Combinations/Pair	1.11
Mean z-score	-1.88
Structure conservation index	0.87
SVM decision value	1.94
SVM RNA-class probability	0.983364
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 306870 120 + 27905053
AAGCGGCAUCUUCCAAAGGACGUCGAAGUGGAUCGGAGGCGUCGUCAGUACCAGAAGAUUAACUUGGUGAAUGAGCUGGCCAAGGCGGGCCUCACUGACGACGUGCUGCAGCCCACCGAG
...((((.(((......))).))))..((((.((((..((((((((((((((((.........))))))..((((((.((....)).)).)))))))))))))).))).)..)))).... ( -45.30)
>DroSec_CAF1 43272 120 + 1
AAGCGGCAUCUUCCAAAGGACGUCGAAGUGGAUCGGAGGCGUCGUCAGUACCAGAAGAUUAACUUGGUGAACGAGCUGGCCAAGGCGGGCCUCACUGACGACGUGCUGCAGCCCACCGAG
...((((.(((......))).))))..((((.((((..((((((((((((((((.........)))))....(((((.((....)).)).)))))))))))))).))).)..)))).... ( -45.40)
>DroSim_CAF1 44119 120 + 1
AAGCGGCAUCUUCCAAAGGACGUCGAAGUGGAUCGGAGGCGUCGUCAGUACCAGAAGAUUAACUUGGUGAACGAGCUGGCCAAGGCGGGCCUCACUGACGACGUGCUGCAGCCCACCGAG
...((((.(((......))).))))..((((.((((..((((((((((((((((.........)))))....(((((.((....)).)).)))))))))))))).))).)..)))).... ( -45.40)
>DroEre_CAF1 46192 120 + 1
AAGCGGCAUCUUCCCAAGGACGUCGAGGUGGACCGGAGGCGUCGUCAGUACCAGAAGAUCAACCUAGAGAAGGAGCUGGCCAGGGCAGGACUCACUGACGACGUGCUCCAGCCCACCGAA
...((((.(((......))).)))).(((((.(.(((((((((((((((.........((......))....(((((.((....)).)).)))))))))))))).)))).).)))))... ( -49.20)
>DroYak_CAF1 46008 120 + 1
AAGCGUCAUCUUCCAAAGGACGUUGAAGUGGACCGGAGGCGUCGUCAGUACCAGAAGAUCAACCUAGUAAAAGAGCUUGCCAAGGCGGGACUUACUGACGACGUCCUCCAGCCCACCGAG
.((((((...........))))))...((((.(.(((((((((((((((......((......)).......((((((((....))))).))))))))))))).))))).).)))).... ( -47.00)
>consensus
AAGCGGCAUCUUCCAAAGGACGUCGAAGUGGAUCGGAGGCGUCGUCAGUACCAGAAGAUUAACUUGGUGAACGAGCUGGCCAAGGCGGGCCUCACUGACGACGUGCUGCAGCCCACCGAG
...((((.(((......))).))))..((((.(.(.((((((((((((((((((.........)))))....(((((.((....)).)).)))))))))))))).)).).).)))).... (-40.30 = -40.30 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	306,870 – 306,990
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.25
Mean single sequence MFE	-45.32
Consensus MFE	-33.72
Energy contribution	-33.72
Covariance contribution	-0.00
Combinations/Pair	1.11
Mean z-score	-1.68
Structure conservation index	0.74
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 306870 120 - 27905053
CUCGGUGGGCUGCAGCACGUCGUCAGUGAGGCCCGCCUUGGCCAGCUCAUUCACCAAGUUAAUCUUCUGGUACUGACGACGCCUCCGAUCCACUUCGACGUCCUUUGGAAGAUGCCGCUU
.((((.((((....)).((((((((((..((((......)))).........((((((.....))..)))))))))))))))).)))).......((.((((........)))).))... ( -39.80)
>DroSec_CAF1 43272 120 - 1
CUCGGUGGGCUGCAGCACGUCGUCAGUGAGGCCCGCCUUGGCCAGCUCGUUCACCAAGUUAAUCUUCUGGUACUGACGACGCCUCCGAUCCACUUCGACGUCCUUUGGAAGAUGCCGCUU
.((((.((((....)).((((((((((..((((......)))).........((((((.....))..)))))))))))))))).)))).......((.((((........)))).))... ( -39.80)
>DroSim_CAF1 44119 120 - 1
CUCGGUGGGCUGCAGCACGUCGUCAGUGAGGCCCGCCUUGGCCAGCUCGUUCACCAAGUUAAUCUUCUGGUACUGACGACGCCUCCGAUCCACUUCGACGUCCUUUGGAAGAUGCCGCUU
.((((.((((....)).((((((((((..((((......)))).........((((((.....))..)))))))))))))))).)))).......((.((((........)))).))... ( -39.80)
>DroEre_CAF1 46192 120 - 1
UUCGGUGGGCUGGAGCACGUCGUCAGUGAGUCCUGCCCUGGCCAGCUCCUUCUCUAGGUUGAUCUUCUGGUACUGACGACGCCUCCGGUCCACCUCGACGUCCUUGGGAAGAUGCCGCUU
...((((((((((((..((((((((((((((...((....))..)))).....(((((.......))))).)))))))))).)))))))))))).((.((((........)))).))... ( -52.90)
>DroYak_CAF1 46008 120 - 1
CUCGGUGGGCUGGAGGACGUCGUCAGUAAGUCCCGCCUUGGCAAGCUCUUUUACUAGGUUGAUCUUCUGGUACUGACGACGCCUCCGGUCCACUUCAACGUCCUUUGGAAGAUGACGCUU
...(((((((((((((.((((((((((.......((....))..........((((((.......)))))))))))))))))))))))))))))....((((.((.....)).))))... ( -54.30)
>consensus
CUCGGUGGGCUGCAGCACGUCGUCAGUGAGGCCCGCCUUGGCCAGCUCGUUCACCAAGUUAAUCUUCUGGUACUGACGACGCCUCCGAUCCACUUCGACGUCCUUUGGAAGAUGCCGCUU
...((((((.((.((..(((((((((((.((((......))))..........(((((.....))..)))))))))))))).)).)).)))))).((.((((........)))).))... (-33.72 = -33.72 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:17 2006