Locus 5017

Sequence ID	3R_DroMel_CAF1
Location	13,232,517 – 13,232,671
Length	154
Max. P	0.964342

overview

Window 0

Location	13,232,517 – 13,232,636
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.14
Mean single sequence MFE	-23.79
Consensus MFE	-16.40
Energy contribution	-17.32
Covariance contribution	0.92
Combinations/Pair	1.04
Mean z-score	-2.05
Structure conservation index	0.69
SVM decision value	1.21
SVM RNA-class probability	0.931015
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13232517 119 - 27905053
AUUGAACUGGUUCUGAAUACAGCUGUUAAAAUUCAUUAACGUUUAAUAGUGUUCAGAUAAAUAUGAAUACAGUUCAACUCUUUUUUGAAUGUGAUGGAGUUCAGC-AUCCAUUACCUAUG
.((((((((..((((((((((((.(((((......)))))))).....)))))))))............)))))))).............((((((((.......-.))))))))..... ( -29.84)
>DroSec_CAF1 261211 104 - 1
AUAGAACUGGUUCUGAAUUCAGCUGUUCAAUUUCAUUAACGUUUAAUAGUGUUCAGAU-------AAUACAGUUCAACUCUUUUUUAUAUG--------UUCCGC-AGCCAUUACCUAUG
...((((((..(((((((...((((((.(((.........))).))))))))))))).-------....))))))................--------......-.............. ( -18.30)
>DroSim_CAF1 246690 104 - 1
AUAGAACUGGUUCUGAAUACAGCUGUUAAAUUUCAUUAACGUUUAAUAGUGUUCAAAA-------AAUACAGUUCAACUCUUUUUUAUAUG--------UUCCGC-AGCCAUUACCUAUG
...((((((.((.(((((...((((((((((.........))))))))))))))).))-------....))))))................--------......-.............. ( -17.70)
>DroEre_CAF1 250899 105 - 1
---GAACUGGUUCUGAUUACAGCUGUUAAACUCAAUGAACAUUUAAUAGUGUUCAGAUAA------AUACAGUUCAACCCGUUUUUGUAUGGGA------UCAGCUAUUAAUUACCUAUG
---((((((..(((((.....(((((((((...........)))))))))..)))))...------...))))))..(((((......))))).------.................... ( -24.80)
>DroYak_CAF1 261728 113 - 1
GAUGAACUGGUUCUGAAUACAGCUGUUAAAUUCCAUGAACAUUUAAUAGUGUUCAGAUAAAUAUAAAUACAGUUCAAC-UGUUUUUGUAUGUAA------UCGCUUUUUCAUUGCCUAUG
........(((..((((...(((............((((((((....))))))))(((..(((((((.((((.....)-))).)))))))...)------)))))..))))..))).... ( -28.30)
>consensus
AUAGAACUGGUUCUGAAUACAGCUGUUAAAUUUCAUUAACGUUUAAUAGUGUUCAGAUAA_____AAUACAGUUCAACUCUUUUUUGUAUG__A_____UUCAGC_AUCCAUUACCUAUG
...((((((..(((((((...((((((((((.........)))))))))))))))))............))))))............................................. (-16.40 = -17.32 +   0.92)

alignment

secondary structure

dotplot

Window 1

Location	13,232,556 – 13,232,671
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.15
Mean single sequence MFE	-23.42
Consensus MFE	-16.40
Energy contribution	-17.32
Covariance contribution	0.92
Combinations/Pair	1.04
Mean z-score	-2.38
Structure conservation index	0.70
SVM decision value	1.57
SVM RNA-class probability	0.964342
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13232556 115 - 27905053
UUAUAUAGGCAUAUAAAUACAUAU----AUAUU-AGGUAUAUUGAACUGGUUCUGAAUACAGCUGUUAAAAUUCAUUAACGUUUAAUAGUGUUCAGAUAAAUAUGAAUACAGUUCAACUC
.(((((....(((((........)----)))).-..)))))((((((((..((((((((((((.(((((......)))))))).....)))))))))............))))))))... ( -22.04)
>DroSec_CAF1 261242 113 - 1
UUAUAUAGGCAUAUAGAUAUACAUAUGUAUAUUGAGUUAUAUAGAACUGGUUCUGAAUUCAGCUGUUCAAUUUCAUUAACGUUUAAUAGUGUUCAGAU-------AAUACAGUUCAACUC
.(((((((.(.....(((((((....)))))))..))))))))((((((..(((((((...((((((.(((.........))).))))))))))))).-------....))))))..... ( -25.40)
>DroSim_CAF1 246721 113 - 1
UUAUAUAGGCAUAUAGAUAUACAUAUGUAUAUUGAGAUAUAUAGAACUGGUUCUGAAUACAGCUGUUAAAUUUCAUUAACGUUUAAUAGUGUUCAAAA-------AAUACAGUUCAACUC
.((((((........(((((((....)))))))....))))))((((((.((.(((((...((((((((((.........))))))))))))))).))-------....))))))..... ( -24.90)
>DroEre_CAF1 250933 102 - 1
UUUUAUAAGCAUUUAGAUAUA--------UAUUGAUAUA----GAACUGGUUCUGAUUACAGCUGUUAAACUCAAUGAACAUUUAAUAGUGUUCAGAUAA------AUACAGUUCAACCC
.................((((--------(....)))))----((((((..(((((.....(((((((((...........)))))))))..)))))...------...))))))..... ( -19.00)
>DroYak_CAF1 261762 111 - 1
UUAUAUAGGCAUAUAGAUAUA--------UAUUGAUAUAUGAUGAACUGGUUCUGAAUACAGCUGUUAAAUUCCAUGAACAUUUAAUAGUGUUCAGAUAAAUAUAAAUACAGUUCAAC-U
(((((((...(((((....))--------)))...)))))))(((((((..(((((((...((((((((((.........)))))))))))))))))............)))))))..-. ( -25.74)
>consensus
UUAUAUAGGCAUAUAGAUAUA_AU____AUAUUGAGAUAUAUAGAACUGGUUCUGAAUACAGCUGUUAAAUUUCAUUAACGUUUAAUAGUGUUCAGAUAA_____AAUACAGUUCAACUC
...........................................((((((..(((((((...((((((((((.........)))))))))))))))))............))))))..... (-16.40 = -17.32 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:23 2006