Locus 5679

Sequence ID	3R_DroMel_CAF1
Location	14,902,989 – 14,903,128
Length	139
Max. P	0.990334

overview

Window 2

Location	14,902,989 – 14,903,102
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	81.07
Mean single sequence MFE	-31.30
Consensus MFE	-16.20
Energy contribution	-17.40
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-3.21
Structure conservation index	0.52
SVM decision value	2.21
SVM RNA-class probability	0.990334
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14902989 113 + 27905053
AGCCAAGAUCGCUUGUAUGUAAGUAAGUAUGUCCCAUGGGAAGGGGGUGAACCAUUGUGUGUAUAUUGUACAUACGAAUAUGAUGUAUAGUGUGCGCAUAUGUUGGGCAUAAA
.(((....((((((((((........)))).(((....)))...))))))..((.((((((((((((((((((.(......)))))))))))))))))))...)))))..... ( -35.10)
>DroSec_CAF1 30448 109 + 1
AGCCAAGAUCGCUUGUAUGUAU----GGAUGUACCAUGGGAAGGGGGUGAACCAUUGUGUGUAUAUUGUACAUACGAGUAUGAUGUAUAGUGUGUGCAUAUGUUGGGCAUAAA
.(((......(((((((((((.----.(.(((((((..(....((......)).)..)).))))))..)))))))))))...((((((.....))))))......)))..... ( -35.90)
>DroSim_CAF1 30345 109 + 1
AGCCAAGAUCGCUUGUAUGUGC----GUAUGUCCCAUGGGAAGGGGGUGAACCAUUGUGUGUAUAUUGUACAUACGAGUAUGAUGUAUAGUGUGUGCAUAUGUUGGGCAUAAA
.(((......((((((((((((----(((((.(((.......)))((....))........)))).)))))))))))))...((((((.....))))))......)))..... ( -34.00)
>DroEre_CAF1 29976 85 + 1
AGCCAAGAUCGUUUGUAA------------GUCCCAUGGGAAGG-GGUAAACCAUUGUGUGUAUAUUGUACAUAU-------------A--GUGUGCAUAUGUUGGGCAUAAA
.(((.....(((.((((.------------.((((.......))-)).....((((((((((((...))))))))-------------)--))))))).)))...)))..... ( -24.50)
>DroYak_CAF1 36947 86 + 1
AGCCAAGAUCGUUUGUAA------------GCCCCAUGGGAAGGGGGUAAACCAUUGGGUGUAUAUUGUACAUAC-------------A--GUGUGCAUAUGUUGGGCAUAAA
.(((.....(((.((((.------------(((((........)))))....(((((..(((((...)))))..)-------------)--))))))).)))...)))..... ( -27.00)
>consensus
AGCCAAGAUCGCUUGUAUGU______G_AUGUCCCAUGGGAAGGGGGUGAACCAUUGUGUGUAUAUUGUACAUACGA_UAUGAUGUAUAGUGUGUGCAUAUGUUGGGCAUAAA
.(((..............................((((.((.((.......)).)).))))(((((.((((((((..............)))))))))))))...)))..... (-16.20 = -17.40 +   1.20)

alignment

secondary structure

dotplot

Window 3

Location	14,903,026 – 14,903,128
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	88.66
Mean single sequence MFE	-29.04
Consensus MFE	-20.60
Energy contribution	-21.44
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-2.40
Structure conservation index	0.71
SVM decision value	0.73
SVM RNA-class probability	0.836338
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14903026 102 + 27905053
GGGAAGGGGGUGAACCAUUGUGUGUAUAUUGUACAUACGAAUAUGAUGUAUAGUGUGCGCAUAUGUUGGGCAUAAAGCUGCUUUAUCCUGGGGAUGCGGUCU
......(((((((((((.((((((((((((((((((.(......)))))))))))))))))))...)))(((......)))))))))))............. ( -33.40)
>DroSec_CAF1 30481 102 + 1
GGGAAGGGGGUGAACCAUUGUGUGUAUAUUGUACAUACGAGUAUGAUGUAUAGUGUGUGCAUAUGUUGGGCAUAAAGCUGCUUUAUCCUGGGGAUGCGGUCU
......(((((((((((.((((..((((((((((((.(......)))))))))))))..))))...)))(((......)))))))))))............. ( -30.50)
>DroSim_CAF1 30378 102 + 1
GGGAAGGGGGUGAACCAUUGUGUGUAUAUUGUACAUACGAGUAUGAUGUAUAGUGUGUGCAUAUGUUGGGCAUAAAGCUGCUUUAUCCUGGGGAUGCGGUCU
......(((((((((((.((((..((((((((((((.(......)))))))))))))..))))...)))(((......)))))))))))............. ( -30.50)
>DroEre_CAF1 30001 86 + 1
GGGAAGG-GGUAAACCAUUGUGUGUAUAUUGUACAUAU-------------A--GUGUGCAUAUGUUGGGCAUAAAGCUGCUUUAUCCUGGGGAUGCGGUCU
((((..(-((((..(((..(((((((((((((....))-------------)--))))))))))..)))((.....)))))))..))))............. ( -25.80)
>DroYak_CAF1 36972 87 + 1
GGGAAGGGGGUAAACCAUUGGGUGUAUAUUGUACAUAC-------------A--GUGUGCAUAUGUUGGGCAUAAAGCUGCUUUAUCCUGGGGAUGCGGUCU
......(((((((((((....(((((((((((....))-------------)--))))))))....)))(((......)))))))))))............. ( -25.00)
>consensus
GGGAAGGGGGUGAACCAUUGUGUGUAUAUUGUACAUACGA_UAUGAUGUAUAGUGUGUGCAUAUGUUGGGCAUAAAGCUGCUUUAUCCUGGGGAUGCGGUCU
.............(((.((((((((((...))))))))))..................((((.(.(..((.((((((...))))))))..).)))))))).. (-20.60 = -21.44 +   0.84)

alignment

secondary structure

dotplot

Window 4

Location	14,903,026 – 14,903,128
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	88.66
Mean single sequence MFE	-13.96
Consensus MFE	-12.70
Energy contribution	-12.90
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.77
Structure conservation index	0.91
SVM decision value	1.61
SVM RNA-class probability	0.967163
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14903026 102 - 27905053
AGACCGCAUCCCCAGGAUAAAGCAGCUUUAUGCCCAACAUAUGCGCACACUAUACAUCAUAUUCGUAUGUACAAUAUACACACAAUGGUUCACCCCCUUCCC
.((((((((((...))))......((..((((.....)))).))))..................((((((...)))))).......))))............ ( -14.30)
>DroSec_CAF1 30481 102 - 1
AGACCGCAUCCCCAGGAUAAAGCAGCUUUAUGCCCAACAUAUGCACACACUAUACAUCAUACUCGUAUGUACAAUAUACACACAAUGGUUCACCCCCUUCCC
.((((((((.....((((((((...)))))).))......))))....................((((((...)))))).......))))............ ( -13.90)
>DroSim_CAF1 30378 102 - 1
AGACCGCAUCCCCAGGAUAAAGCAGCUUUAUGCCCAACAUAUGCACACACUAUACAUCAUACUCGUAUGUACAAUAUACACACAAUGGUUCACCCCCUUCCC
.((((((((.....((((((((...)))))).))......))))....................((((((...)))))).......))))............ ( -13.90)
>DroEre_CAF1 30001 86 - 1
AGACCGCAUCCCCAGGAUAAAGCAGCUUUAUGCCCAACAUAUGCACAC--U-------------AUAUGUACAAUAUACACACAAUGGUUUACC-CCUUCCC
(((((((((.....((((((((...)))))).))......))))....--(-------------((((.....)))))........)))))...-....... ( -12.70)
>DroYak_CAF1 36972 87 - 1
AGACCGCAUCCCCAGGAUAAAGCAGCUUUAUGCCCAACAUAUGCACAC--U-------------GUAUGUACAAUAUACACCCAAUGGUUUACCCCCUUCCC
(((((((((.....((((((((...)))))).))......))))....--(-------------((((((...)))))))......)))))........... ( -15.00)
>consensus
AGACCGCAUCCCCAGGAUAAAGCAGCUUUAUGCCCAACAUAUGCACACACUAUACAUCAUA_UCGUAUGUACAAUAUACACACAAUGGUUCACCCCCUUCCC
.((((((((.....((((((((...)))))).))......))))....................((((((...)))))).......))))............ (-12.70 = -12.90 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:33 2006