Locus 6241

Sequence ID	3L_DroMel_CAF1
Location	16,605,473 – 16,605,616
Length	143
Max. P	0.940783

overview

Window 7

Location	16,605,473 – 16,605,586
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	94.31
Mean single sequence MFE	-29.74
Consensus MFE	-25.36
Energy contribution	-25.04
Covariance contribution	-0.32
Combinations/Pair	1.10
Mean z-score	-1.72
Structure conservation index	0.85
SVM decision value	1.31
SVM RNA-class probability	0.940783
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16605473 113 - 23771897
AGAAUCGGAUUCCAAUACCGAUUUCGAGUCGGCUUCUCUCUUCUCGGUUGCAGUGCCUGCCUUCUAUCUGCAGGUUGAAUUGCAUUCGCUCCAAUCACGUUCGCAAUUGCAAC
.(((((((.........)))))))((((..((......))..))))(((((...((((((.........))))))..((((((...((.........))...))))))))))) ( -28.30)
>DroSec_CAF1 13503 112 - 1
AGAAUCGGAUUCCAAUACCGAUUCCGAGUCGGCUUCUCUCUUCUCGGUUGCAGUGCCAGC-UUCUAUCUGCAGGUUGAAUUGCAUUCGCUCCAAUCACGUUCGCAAUUGCAAC
.(((((((.........)))))))((((..((......))..))))((((((((((..((-........)).(((((....((....))..)))))......)).)))))))) ( -30.00)
>DroSim_CAF1 12694 112 - 1
AGAAUCGGAUUCCAAUACCGAUUCCGAGUCGGCUUCUCUCUUCUCGGUUGCAGUGCCAGC-UUCUAUCUGCAGGUUGAAUUGCAUUCGCUCCAAUCACGUUCGCAAUUGCAAC
.(((((((.........)))))))((((..((......))..))))((((((((((..((-........)).(((((....((....))..)))))......)).)))))))) ( -30.00)
>DroEre_CAF1 13519 112 - 1
AGAAUCGGAUUCCGAUUCCGAUUCCGAAUCGGCUUCUCACUUCUCGUUUGCAGUACCUGU-CUCUAUCUGCAGGUUGAAUUGCAUUCGCUCCAAUCACGUUCGCAAUUGCAAC
.(((.((((..(((((((.......)))))))..))........((..((((((((((((-........))))))...))))))..)).........)))))((....))... ( -30.00)
>DroYak_CAF1 13558 112 - 1
AGAAUCGGAUUCCAAUUCCGAUUCCGAAUCGGCUUCUCACUUCUCGUUUGCAGUACCUGU-CUCUAUCUGCAGGUUGGAUUGCAUUCGCUCCAAUCACGUUCGCAAUUGCAAC
.((((((((.......)))))))).(((.((.................(((((.......-......)))))(((((((..((....))))))))).)))))((....))... ( -30.42)
>consensus
AGAAUCGGAUUCCAAUACCGAUUCCGAGUCGGCUUCUCUCUUCUCGGUUGCAGUGCCUGC_UUCUAUCUGCAGGUUGAAUUGCAUUCGCUCCAAUCACGUUCGCAAUUGCAAC
.(((.((((((......(((((.....)))))............((..((((((((((((.........))))))...))))))..))....)))).)))))((....))... (-25.36 = -25.04 +  -0.32)

alignment

secondary structure

dotplot

Window 8

Location	16,605,507 – 16,605,616
Length	109
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	91.70
Mean single sequence MFE	-32.71
Consensus MFE	-22.86
Energy contribution	-22.54
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-2.23
Structure conservation index	0.70
SVM decision value	-0.03
SVM RNA-class probability	0.520065
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16605507 109 - 23771897
GAAUCCAUCAUUGAGCCAUGAGAA------GUAUAAAGAAUCGGAUUCCAAUACCGAUUUCGAGUCGGCUUCUCUCUUCUCGGUUGCAGUGCCUGCCUUCUAUCUGCAGGUUGAA
........(((((((((..(((((------(.....((((.(.(((((.((.......)).))))).).))))..)))))))))).)))))(((((.........)))))..... ( -28.70)
>DroSec_CAF1 13537 108 - 1
GAAUCCAUCAUUGAGCCAUGAGAA------GUAUAAAGAAUCGGAUUCCAAUACCGAUUCCGAGUCGGCUUCUCUCUUCUCGGUUGCAGUGCCAGC-UUCUAUCUGCAGGUUGAA
...((.(((((((((....(((((------((.....((.(((((.((.......)).))))).)).)))))))....))))))(((((.......-......)))))))).)). ( -30.42)
>DroSim_CAF1 12728 108 - 1
GAAUCCAUCAUUGAGCCAUGAGAA------GUAUAAAGAAUCGGAUUCCAAUACCGAUUCCGAGUCGGCUUCUCUCUUCUCGGUUGCAGUGCCAGC-UUCUAUCUGCAGGUUGAA
...((.(((((((((....(((((------((.....((.(((((.((.......)).))))).)).)))))))....))))))(((((.......-......)))))))).)). ( -30.42)
>DroEre_CAF1 13553 108 - 1
GAAUCCAUCACUGAGCCAUGAGAA------GUAUAAAGAAUCGGAUUCCGAUUCCGAUUCCGAAUCGGCUUCUCACUUCUCGUUUGCAGUACCUGU-CUCUAUCUGCAGGUUGAA
.......((((((....(((((((------((.....(((((((...))))))).((..(((...)))..))..)))))))))...))))((((((-........)))))).)). ( -32.80)
>DroYak_CAF1 13592 114 - 1
GAAUCCAUCAUUGAGCCAUGAGAAGUAGAAGUAUAAAGAAUCGGAUUCCAAUUCCGAUUCCGAAUCGGCUUCUCACUUCUCGUUUGCAGUACCUGU-CUCUAUCUGCAGGUUGGA
...((((.......((.(((((((((((((((.....((((((((.......)))))))).......)))))).)))))))))..))...((((((-........)))))))))) ( -41.20)
>consensus
GAAUCCAUCAUUGAGCCAUGAGAA______GUAUAAAGAAUCGGAUUCCAAUACCGAUUCCGAGUCGGCUUCUCUCUUCUCGGUUGCAGUGCCUGC_UUCUAUCUGCAGGUUGAA
...........(.((((.((((((......((.....((.(((((.((.......)).))))).)).)).......))))))..(((((..............))))))))).). (-22.86 = -22.54 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:30 2006