Locus 5709

Sequence ID	3L_DroMel_CAF1
Location	15,592,905 – 15,593,098
Length	193
Max. P	0.999460

overview

Window 2

Location	15,592,905 – 15,593,025
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.17
Mean single sequence MFE	-28.20
Consensus MFE	-26.50
Energy contribution	-26.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.06
Structure conservation index	0.94
SVM decision value	3.62
SVM RNA-class probability	0.999460
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15592905 120 + 23771897
CACAUGUCUAUAGCUUUACAGUUAGCCCACUACUGCUUGCCAAUGCAAAAACAGUUUCAAUUAAGCAAUUAGCGCCAUUGAAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCA
............((((..(((((((((((..(((((........)))......((((((((...((.....))...))))))))...........))..)).))))....))))))))). ( -28.00)
>DroSec_CAF1 16306 120 + 1
CACAUUUCUAUAGCUUUACAGUUAGCCCACUAGUGCUUGCCAAUGCAAAAACAGUUUCAAUUAAGCAAUUAGCGCCAUUGAAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCA
............((((..(((((((((((...(((.((((....)))).....((((((((...((.....))...))))))))........)))....)).))))....))))))))). ( -28.50)
>DroSim_CAF1 16255 120 + 1
CACAUGUCUAUAGCUUUACAGUUAGCCCACUAGUGCUUGCCAAUGCAAAAACAGUUUCAAUUAAGCAAUUAGCGCCAUUGAAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCA
............((((..(((((((((((...(((.((((....)))).....((((((((...((.....))...))))))))........)))....)).))))....))))))))). ( -28.50)
>DroEre_CAF1 16329 120 + 1
CACAUGUCUAUAGCUUUACAGUUAGCCCACUACUGCUUGCCAAUGCAAAAACAGUUUCAAUUAAGCAAUUAGCGCCAUUGAAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCA
............((((..(((((((((((..(((((........)))......((((((((...((.....))...))))))))...........))..)).))))....))))))))). ( -28.00)
>DroYak_CAF1 17518 120 + 1
CACAUGUCUAUAGCUUUACAGUUAGCCCACUACUGCUUGCCAAUGCAAAAACAGUUUCAAUUAAGCAAUUAGCGCCAUUGAAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCA
............((((..(((((((((((..(((((........)))......((((((((...((.....))...))))))))...........))..)).))))....))))))))). ( -28.00)
>consensus
CACAUGUCUAUAGCUUUACAGUUAGCCCACUACUGCUUGCCAAUGCAAAAACAGUUUCAAUUAAGCAAUUAGCGCCAUUGAAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCA
............((((..(((((((((.((....((((((....)))).....((((((((...((.....))...))))))))...........))...))))))....))))))))). (-26.50 = -26.50 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	15,592,985 – 15,593,098
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.89
Mean single sequence MFE	-34.38
Consensus MFE	-31.84
Energy contribution	-31.68
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.64
Structure conservation index	0.93
SVM decision value	1.69
SVM RNA-class probability	0.972181
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15592985 113 + 23771897
AAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCAUCAUGUCGAUUGGUUCGAACCCUGCGGUCGAUGGAAUGGAACCGGG-------AAUAGGCCAUAGGAUUGGGGAUUUUGU
..((((((((..((.((((((((((((((...(((...(((..(((((((((............)))))))))..)))....))).-------.)))))))))))))))).))).))))) ( -33.50)
>DroSec_CAF1 16386 113 + 1
AAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCAUCAUGUCGAUUGGUUCGAACCCUGCGGUCGAUGGAAUGGAACCGGG-------AAUAGGCCAUAGGAUUGGGGAUUUUGU
..((((((((..((.((((((((((((((...(((...(((..(((((((((............)))))))))..)))....))).-------.)))))))))))))))).))).))))) ( -33.50)
>DroSim_CAF1 16335 113 + 1
AAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCAUCAUGUCGAUUGGUUCGAACCCUGCGGUCGAUGGAAUGGAACCGGG-------AAUAGGCCAUAGGACUGGGGAUUUUGU
..((((((((..((.((((((((((((((...(((...(((..(((((((((............)))))))))..)))....))).-------.)))))))))))))))).))).))))) ( -35.80)
>DroEre_CAF1 16409 120 + 1
AAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCAUCAUGUCGAUUGGUUCGAAGCCUGCGGUCGAUGGAAUGGAACCGGGAACCAGGAAUAGGCCAUAGGAUUGGGGAUUUUGU
..((((((((..((.((((((((((((((...(((...(((..(((((((((((.....)))...))))))))..))).....(....))))..)))))))))))))))).))).))))) ( -35.60)
>DroYak_CAF1 17598 113 + 1
AAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCAUCAUGUCGAUUGGUUCGAACCCUGCGGUCGAUGGAAUGGAACCGGG-------AAUAGGCCAUAGGAUUGGGGAUUUUGU
..((((((((..((.((((((((((((((...(((...(((..(((((((((............)))))))))..)))....))).-------.)))))))))))))))).))).))))) ( -33.50)
>consensus
AAACAAAUCCAACACGUUUUGUGGCUUAUAAACUGAAGCAUCAUGUCGAUUGGUUCGAACCCUGCGGUCGAUGGAAUGGAACCGGG_______AAUAGGCCAUAGGAUUGGGGAUUUUGU
..((((((((..((.((((((((((((((..(((((....))).))...(((((((.(..((..........))..).))))))).........)))))))))))))))).))).))))) (-31.84 = -31.68 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:17 2006