Locus 3969

Sequence ID	3L_DroMel_CAF1
Location	11,526,384 – 11,526,520
Length	136
Max. P	0.995118

overview

Window 4

Location	11,526,384 – 11,526,487
Length	103
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	83.15
Mean single sequence MFE	-42.05
Consensus MFE	-31.17
Energy contribution	-32.92
Covariance contribution	1.75
Combinations/Pair	1.00
Mean z-score	-3.06
Structure conservation index	0.74
SVM decision value	2.54
SVM RNA-class probability	0.995118
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11526384 103 + 23771897
GACGC------UGGAGUAGCAGCUUUGCUGCAGCGUUGCAGUUGUUGCUGGUGUGCCAAUUCUAAGCGCUGCAUUGGCAACAGUCGCGCUUCGCCGGUUUCGCAACUGA
(((((------((.(((((.....))))).))))))).(((((((.(((((((..........((((((.(.((((....))))))))))))))))))...))))))). ( -45.90)
>DroSec_CAF1 32556 98 + 1
GCCGCUGCUGCUGGAGUAGCA-----------GCAUUGCAGUUGUUGCUGGUGUGCCAAUUCUAAGCGCUGCAUUGGCAACAGUCGCGCUUCGCCGGUUUCGCAACUGA
...((((((((....))))))-----------))....(((((((.(((((((..........((((((.(.((((....))))))))))))))))))...))))))). ( -45.10)
>DroSim_CAF1 31928 98 + 1
GCCGCUGCUGCUGGAGUAGCA-----------GCAUUGCAGUUGUUGCUGGUGUGCCAAUUCUAAGCGCUGCAUUGGCAACAGUCGCGCUUCGCCGGUUUCGCAACUGA
...((((((((....))))))-----------))....(((((((.(((((((..........((((((.(.((((....))))))))))))))))))...))))))). ( -45.10)
>DroYak_CAF1 31074 86 + 1
GCUGC-----------------------AGCAGUGUUGCAGUUGUUGCUGGUGUGCCAAUUCUAAGCGCUGCAUUGGCAACAGUCGCGCUUCGCCGGUUUCGCAACUGA
...((-----------------------(((...)))))((((((.(((((((..........((((((.(.((((....))))))))))))))))))...)))))).. ( -32.10)
>consensus
GCCGC______UGGAGUAGCA___________GCAUUGCAGUUGUUGCUGGUGUGCCAAUUCUAAGCGCUGCAUUGGCAACAGUCGCGCUUCGCCGGUUUCGCAACUGA
...((((((.....))))))..................(((((((.(((((((..........((((((.(.((((....))))))))))))))))))...))))))). (-31.17 = -32.92 +   1.75)

alignment

secondary structure

dotplot

Window 5

Location	11,526,410 – 11,526,520
Length	110
Sequences	3
Columns	111
Reading direction	forward
Mean pairwise identity	98.19
Mean single sequence MFE	-38.23
Consensus MFE	-37.17
Energy contribution	-37.50
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.97
SVM decision value	0.72
SVM RNA-class probability	0.832338
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11526410 110 + 23771897
GCGUUGCAGUUGUUGCUGGUGUGCCAAUUCUAAGCGCUGCAUUGGCAACAGUCGCGCUUCGCCGGUUUCGCAACUGAACUCUCAGCUGCUAUUGCUCCUCUGCAGUUAGU-
..(((.(((((((.(((((((..........((((((.(.((((....))))))))))))))))))...))))))))))....((((((............))))))...- ( -38.80)
>DroSec_CAF1 32577 110 + 1
GCAUUGCAGUUGUUGCUGGUGUGCCAAUUCUAAGCGCUGCAUUGGCAACAGUCGCGCUUCGCCGGUUUCGCAACUGAACUCUCAGCUGCUAUUGCUCCUCUGCAGUUAGU-
..(((((((..(..(((((((..........((((((.(.((((....))))))))))))))))))..)(((.((((....)))).)))..........)))))))....- ( -37.10)
>DroYak_CAF1 31083 111 + 1
GUGUUGCAGUUGUUGCUGGUGUGCCAAUUCUAAGCGCUGCAUUGGCAACAGUCGCGCUUCGCCGGUUUCGCAACUGAACUCUCAGCUGCUAUUGCUCCUCUGCAGUUAGUU
(.(((.(((((((.(((((((..........((((((.(.((((....))))))))))))))))))...)))))))))).)..((((((............)))))).... ( -38.80)
>consensus
GCGUUGCAGUUGUUGCUGGUGUGCCAAUUCUAAGCGCUGCAUUGGCAACAGUCGCGCUUCGCCGGUUUCGCAACUGAACUCUCAGCUGCUAUUGCUCCUCUGCAGUUAGU_
(.(((.(((((((.(((((((..........((((((.(.((((....))))))))))))))))))...)))))))))).)..((((((............)))))).... (-37.17 = -37.50 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:19 2006