Locus 2916

Sequence ID	3L_DroMel_CAF1
Location	8,307,779 – 8,307,965
Length	186
Max. P	0.872776

overview

Window 2

Location	8,307,779 – 8,307,869
Length	90
Sequences	4
Columns	90
Reading direction	forward
Mean pairwise identity	85.37
Mean single sequence MFE	-18.30
Consensus MFE	-12.88
Energy contribution	-11.62
Covariance contribution	-1.25
Combinations/Pair	1.20
Mean z-score	-2.17
Structure conservation index	0.70
SVM decision value	0.88
SVM RNA-class probability	0.872776
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8307779 90 + 23771897
GGUUCCUUAAUACAUUAACAAACAGAGAAAUGUUUCUUGAUAUUUUUUGCAGUGUGACAAACUUUUUGUCCGAUUGCUUUGUUUUAUUUU
................((((((..((((((((((....))))))))))(((((..(((((.....)))))..)))))))))))....... ( -16.80)
>DroSec_CAF1 14095 90 + 1
AGUUAAUUAAUACAUGAAUAAACAGAGCAAUGCUGCUUGAUAUUUUUUGCAGUGUGACAAACUUUUUGUCCGAUUGCUUUGUUUUAUUUU
...............(((((((((((((((((((((..((....))..)))))(.(((((.....)))))).))))))))).))))))). ( -24.70)
>DroSim_CAF1 12734 90 + 1
AGUUAAUUAAUACAUUAAUAAACAGAGCAAUGUUGCUUGGUAUUUUUUGCAGUGUGACAAACUUUUUGUCCGAUUGCUUUGUUUUAUUUU
.((((((......))))))((((((((((((.((((..((....))..))))((.(((((.....)))))))))))))))))))...... ( -20.00)
>DroEre_CAF1 13326 86 + 1
AGUUUCUUUAUAAAUUAAUAAACAGAAAAAGGUUUU---CCUCUUUUUGCAGUGUGGCAAACUU-UUGUCCAAUUGUUUUGUUUUAUUUU
...........((((.((((((((((((.(((....---))).))))))((((.((((((....-))).))))))).))))))..)))). ( -11.70)
>consensus
AGUUAAUUAAUACAUUAAUAAACAGAGAAAUGUUGCUUGAUAUUUUUUGCAGUGUGACAAACUUUUUGUCCGAUUGCUUUGUUUUAUUUU
...................((((((((((....)))............(((((..(((((.....)))))..))))))))))))...... (-12.88 = -11.62 +  -1.25)

alignment

secondary structure

dotplot

Window 3

Location	8,307,869 – 8,307,965
Length	96
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	81.97
Mean single sequence MFE	-32.80
Consensus MFE	-22.47
Energy contribution	-24.55
Covariance contribution	2.08
Combinations/Pair	1.09
Mean z-score	-2.10
Structure conservation index	0.68
SVM decision value	0.55
SVM RNA-class probability	0.777074
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8307869 96 + 23771897
---GUUUGGCCGAUGUCGCAAAUGUACACCAGAAAUAGCU-AUAGCUUCGGCUUUUGCUGUA------GCGGCAGGAGGACUUCAACUGCUUUUGGCCAAGUUAAU
---.(((((((((((((((...((.....))...(((((.-..(((....)))...))))).------))))))(.((........)).)..)))))))))..... ( -33.30)
>DroSec_CAF1 14185 96 + 1
---GUUUGGCCGAUGUCGCAAAUGUACACAAGAAAUAGCU-AGAGCUGCGGCUUUUGCUGUG------GCGGCAGGAGCACUUCAACUGCUUUUGGCCAAGUUAAU
---.(((((((((((((((...((....))....(((((.-(((((....))))).))))).------)))))).(((((.......))))))))))))))..... ( -35.00)
>DroSim_CAF1 12824 96 + 1
---GUUUGGCCGAUGUCGCAAAUGUACACCAGAAAUAGCU-AGAGCUGCCGCUUUUGCUGUG------GCGGCAGGAGCACUUCAACUGCUUUUGGCCAAGUUAAU
---.(((((((((((((((...((.....))...(((((.-(((((....))))).))))).------)))))).(((((.......))))))))))))))..... ( -33.70)
>DroEre_CAF1 13412 102 + 1
---GUUUGGCCGAUGUCGCAAAUGUACACCAGAAAUAGCU-AUAGCAGUGGCUUUUGCUGUGGCCGCGGCGGCAGGAGCACUUCAACUGCUUUUGGCCAAGUUAAU
---.(((((((((.(((((...((.....))......(((-(((((((......)))))))))).)))))(((((...........))))).)))))))))..... ( -38.50)
>DroYak_CAF1 13384 105 + 1
UUUUUUUCGCCGAUGUCGCAAAUGUACACCAGAAAUAGCU-AAAGCUGCGGCUUUGGCUGUGGCCGCGGCGGCAGGAGCACUUCAACUGCUUUUGGCCAAGUUAAU
........((((..(((((...((.....)).....((((-(((((....))))))))))))))..))))((((((((((.......))))))).)))........ ( -37.00)
>DroPer_CAF1 15065 82 + 1
---GUUUGGACGAUGUCGCAAAUGUACGGCAGAAACCUCAGAAAG------C---AGCAGCA------GCAGCAGGAGCAGUUCAG------UCGGCCAAGUUAAU
---.(((((.((((((((........)))).(((..(((.....(------(---.((....------)).))..)))...))).)------))).)))))..... ( -19.30)
>consensus
___GUUUGGCCGAUGUCGCAAAUGUACACCAGAAAUAGCU_AAAGCUGCGGCUUUUGCUGUG______GCGGCAGGAGCACUUCAACUGCUUUUGGCCAAGUUAAU
....((((((((((((.((....)))))...(((.((((.....))))..(((((((((((.......)))))))))))..)))........)))))))))..... (-22.47 = -24.55 +   2.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:57 2006