Locus 3929

Sequence ID	3L_DroMel_CAF1
Location	11,402,463 – 11,402,596
Length	133
Max. P	0.953374

overview

Window 6

Location	11,402,463 – 11,402,565
Length	102
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	81.22
Mean single sequence MFE	-26.10
Consensus MFE	-18.98
Energy contribution	-19.10
Covariance contribution	0.12
Combinations/Pair	1.32
Mean z-score	-2.26
Structure conservation index	0.73
SVM decision value	1.43
SVM RNA-class probability	0.953374
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11402463 102 + 23771897
AG-ACAUAGUUCUCGAGCGCUGAGAACUAAGAGAUCAGCUUUCUCUUGAGUGAUCGCGGCAAGCUCAAGAGUGUCAAAAAAUUGAAAAAAAAGAGAGCAACAA
..-.....((((((((((((((.(((((((((((.......)))))).)))..)).))))..)))).......((((....)))).......))))))..... ( -29.40)
>DroSec_CAF1 122674 101 + 1
AG-ACAUAGUUCUUGAGCGCUGAGAACUAAGAGAUCGGCUUUCUCUUGAGUGAUCGCCGCUAACUCAAAAGAGUCAAAAAAUUUAAA-AAAAGAGAGCAACAA
..-.....((((((.((((.(((..(((((((((.......)))))).)))..))).)))).((((....)))).............-....))))))..... ( -26.80)
>DroSim_CAF1 134791 101 + 1
AG-ACAUAGUUCUUGAGCGCUGAGAACUAAGAGAUCGGCUUUCUCUUGAGUGAUCGCGGCAAACUCAAGAGAGUCAAAAAAUUGUAA-AAAAGAGAGCAACAA
..-.....((((((....(((((...........))))).(((((((((((...........)))))))))))..............-....))))))..... ( -26.40)
>DroEre_CAF1 129571 98 + 1
AGCACAUAGUUCUUGAGCUCUGAGAACUAAGAGUUCAGGUUUCUCUUGAGUGAUCGCGG----CUUAAGAGUGUCGGUAAACCAAGU-GUAAGAGAGCCACAC
.((((......((((((((((........))))))))))...(((((((((.......)----))))))))....((....))..))-))............. ( -28.70)
>DroYak_CAF1 120357 98 + 1
GGCACAUAGUUCUUGAGUUCUGAGAAAUAAGAGUUCAGCUUUCUCUUGAGUGAUCGCGU----UUUAAGAGAGUCAAAAAACCGAGU-UAAAGAGAUUCAAUU
(((.........((((..(((........)))..))))...(((((((((.........----))))))))))))........((((-(.....))))).... ( -19.20)
>consensus
AG_ACAUAGUUCUUGAGCGCUGAGAACUAAGAGAUCAGCUUUCUCUUGAGUGAUCGCGGC_A_CUCAAGAGAGUCAAAAAAUUGAAA_AAAAGAGAGCAACAA
........((((((....(((((...........))))).(((((((((((...........)))))))))))...................))))))..... (-18.98 = -19.10 +   0.12)

alignment

secondary structure

dotplot

Window 7

Location	11,402,499 – 11,402,596
Length	97
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	81.05
Mean single sequence MFE	-22.39
Consensus MFE	-15.70
Energy contribution	-16.70
Covariance contribution	1.00
Combinations/Pair	1.23
Mean z-score	-1.59
Structure conservation index	0.70
SVM decision value	0.12
SVM RNA-class probability	0.593444
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11402499 97 + 23771897
GCUUUCUCUUGAGUGAUCGCGGCAAGCUCAAGAGUGUCAAAAAAUUGAAAAAAAAGAGAGCAACAAUUUCCACUCAAUUGCUCUUAAAU--UGGCGUGA
((((((((((((((...........))))))))...((((....)))).......)))))).........(((((((((.......)))--))).))). ( -24.00)
>DroSec_CAF1 122710 96 + 1
GCUUUCUCUUGAGUGAUCGCCGCUAACUCAAAAGAGUCAAAAAAUUUAAA-AAAAGAGAGCAACAAUUUUCACUCAAUUGCUCUUAAAU--UGGCGUGA
(((((((....((((.....)))).((((....)))).............-...)))))))........((((((((((.......)))--))).)))) ( -20.60)
>DroSim_CAF1 134827 96 + 1
GCUUUCUCUUGAGUGAUCGCGGCAAACUCAAGAGAGUCAAAAAAUUGUAA-AAAAGAGAGCAACAAAUUCCACUCAAUUGCUCUUAAAU--UGGCGUGA
((((((((((((((...........)))))))))))..............-....((((((((..............))))))))....--.))).... ( -24.84)
>DroEre_CAF1 129608 94 + 1
GGUUUCUCUUGAGUGAUCGCGG----CUUAAGAGUGUCGGUAAACCAAGU-GUAAGAGAGCCACACUUUUCACUCAAUUGCUCUUAAAUUGUGGCGUGA
((((.((....)).))))((.(----(((((((((...((....)).(((-(.(((((.......))))))))).....))))))))...)).)).... ( -22.30)
>DroYak_CAF1 120394 93 + 1
GCUUUCUCUUGAGUGAUCGCGU----UUUAAGAGAGUCAAAAAACCGAGU-UAAAGAGAUUCAAUUUUCUCACUCAAUUGCUCUUAAAC-AUAGCGUGA
((((......))))..((((((----((((((((.((......)).((((-....((((........)))))))).....)))))))).-...)))))) ( -20.20)
>consensus
GCUUUCUCUUGAGUGAUCGCGGC_A_CUCAAGAGAGUCAAAAAAUUGAAA_AAAAGAGAGCAACAAUUUUCACUCAAUUGCUCUUAAAU__UGGCGUGA
((((((((((((((...........)))))))))))...................((((((((..............)))))))).......))).... (-15.70 = -16.70 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:14 2006