Locus 7128

Sequence ID	3L_DroMel_CAF1
Location	19,176,551 – 19,176,711
Length	160
Max. P	0.706668

overview

Window 1

Location	19,176,551 – 19,176,671
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.64
Mean single sequence MFE	-32.92
Consensus MFE	-29.28
Energy contribution	-29.12
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.22
Structure conservation index	0.89
SVM decision value	0.12
SVM RNA-class probability	0.593978
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19176551 120 - 23771897
CCCCUUUUGUGAGUGAGUGAGUGACAUUUGCCAGAGCGCCUAAUUGUAGGCAAUUAAUUUCUGGCACAUCAAAGCGGCGGAAGGAAGCUUAACUGGCAGGAAGAGCAAACAAGGAAGACA
..((((((((......((.....)).((((((((((((((((....)))))......((((((.(.(......).).))))))...)))...))))))))....))))..))))...... ( -31.70)
>DroSec_CAF1 5069 120 - 1
CCCCUUUUGUGAGUGAGUGAGUGACAUUUGCCAGAGCGCCUAAUUGUAGGCAAUUAAUUUCUGGCACAUCAAAGCGGCGGAAGGAAGCUUAACUGGCAGGAAGAGCAAACAAGGAAGACA
..((((((((......((.....)).((((((((((((((((....)))))......((((((.(.(......).).))))))...)))...))))))))....))))..))))...... ( -31.70)
>DroSim_CAF1 8106 120 - 1
CCCCUUUUUUGAGUGAGUGAGUGACAUUUGCCAGAGCGCCUAAUUGUAGGCAAUUAAUUUCUGGCACAUCAAAGCGGCGGAAGGAAGCUUAACUGGCAGGAAGAGCAAACAAGGAAGACA
...((((((((..((.((.....)).((((((((((((((((....)))))......((((((.(.(......).).))))))...)))...)))))))).....))..))))))))... ( -34.10)
>DroEre_CAF1 7815 114 - 1
CCCUUU------GUGAGUGAGUGACAUUUGCCAGAGCGCCUAAUUGUAGGCAAUUAAUUUCUGGCACAUCAAAGCGGCGGAAGGAAGCUUAACUGGCAGGAAGAGCAAACAAGGAAGACA
..((((------((...((..(....((((((((((((((((....)))))......((((((.(.(......).).))))))...)))...))))))))..)..)).))))))...... ( -33.30)
>DroYak_CAF1 9898 114 - 1
CCCUUU------CUGAGUGAGUGACAUUUGCCAGAGCGCCUAAUUGUAGGCAAUUAAUUUCUGGCACAUCAAAGCGGCGGAAGGAAGUUUAACUGGCAGGAAGAGCAAACAAGGAAGACA
..((((------((..((..((....((((((((...(((((....)))))((((..((((((.(.(......).).))))))..))))...))))))))....))..)).))))))... ( -33.80)
>consensus
CCCCUUUU_UGAGUGAGUGAGUGACAUUUGCCAGAGCGCCUAAUUGUAGGCAAUUAAUUUCUGGCACAUCAAAGCGGCGGAAGGAAGCUUAACUGGCAGGAAGAGCAAACAAGGAAGACA
................((..((....((((((((((((((((....)))))......((((((.(.(......).).))))))...)))...))))))))....))..)).......... (-29.28 = -29.12 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	19,176,591 – 19,176,711
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.71
Mean single sequence MFE	-29.84
Consensus MFE	-24.46
Energy contribution	-24.22
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-1.47
Structure conservation index	0.82
SVM decision value	0.37
SVM RNA-class probability	0.706668
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19176591 120 + 23771897
CCGCCGCUUUGAUGUGCCAGAAAUUAAUUGCCUACAAUUAGGCGCUCUGGCAAAUGUCACUCACUCACUCACAAAAGGGGAGCAUCGACCACCCUACUGUUUGCUAAGAAGUAAUAACCA
.....((((((((.(((((((.......((((((....)))))).)))))))...)))............(((..((((..(......)..))))..))).......)))))........ ( -27.20)
>DroSec_CAF1 5109 120 + 1
CCGCCGCUUUGAUGUGCCAGAAAUUAAUUGCCUACAAUUAGGCGCUCUGGCAAAUGUCACUCACUCACUCACAAAAGGGGAGCAUCGACCACCCUACUGUUUGCUAAGAAGCACUAACCA
.....((((((((.(((((((.......((((((....)))))).)))))))...)))............(((..((((..(......)..))))..))).......)))))........ ( -29.60)
>DroSim_CAF1 8146 120 + 1
CCGCCGCUUUGAUGUGCCAGAAAUUAAUUGCCUACAAUUAGGCGCUCUGGCAAAUGUCACUCACUCACUCAAAAAAGGGGAGCAUCGACCACCCAACUGUUUGCUAAGAAGCACUAACCA
.....((((((((.(((((((.......((((((....)))))).)))))))...)))..................(((..(......)..))).............)))))........ ( -27.80)
>DroEre_CAF1 7855 114 + 1
CCGCCGCUUUGAUGUGCCAGAAAUUAAUUGCCUACAAUUAGGCGCUCUGGCAAAUGUCACUCACUCAC------AAAGGGGGCAUCGACCACCCUUCUGCUUCGUAAGAAGUACUAACAA
.........((((.(((((((.......((((((....)))))).)))))))...)))).........------.(((((((......)).))))).((((((....))))))....... ( -33.50)
>DroYak_CAF1 9938 113 + 1
CCGCCGCUUUGAUGUGCCAGAAAUUAAUUGCCUACAAUUAGGCGCUCUGGCAAAUGUCACUCACUCAG------AAAGGGGGUAUCGACCACCC-UCUGUUUCCUAAGAAGUACUAACCA
.....((((((((.(((((((.......((((((....)))))).)))))))...))).......(((------(..((((((....))).)))-))))........)))))........ ( -31.10)
>consensus
CCGCCGCUUUGAUGUGCCAGAAAUUAAUUGCCUACAAUUAGGCGCUCUGGCAAAUGUCACUCACUCACUCA_AAAAGGGGAGCAUCGACCACCCUACUGUUUGCUAAGAAGUACUAACCA
.....((((((((.(((((((.......((((((....)))))).)))))))...)))...................(((...........))).............)))))........ (-24.46 = -24.22 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:42 2006