Locus 3250

Sequence ID	3R_DroMel_CAF1
Location	8,675,881 – 8,675,984
Length	103
Max. P	0.999953

overview

Window 5

Location	8,675,881 – 8,675,984
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	91.50
Mean single sequence MFE	-26.30
Consensus MFE	-20.92
Energy contribution	-21.52
Covariance contribution	0.60
Combinations/Pair	1.12
Mean z-score	-2.26
Structure conservation index	0.80
SVM decision value	1.63
SVM RNA-class probability	0.968701
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8675881 103 + 27905053
CUCGCAAAAAACUGCAGACUUUUAUCUACCGCUUGCAUAUUCGUAUGCAAAGGUUGUUUGGUUGAAAAUAUCAACCCCAGAGCUCUGAAAUAAAUUUUUUCCG
..((.((((((...((((((((.....(((..(((((((....))))))).))).....((((((.....))))))..)))).)))).......)))))).)) ( -22.30)
>DroSec_CAF1 102823 102 + 1
CUCGCAAAAAACUGCAGACUUUUAUCUACCGCUUGCAUAUUCGUAUGCAAAGGUUGU-UGGUUGAAAAUAUCAACCCUAGAGCUCUGGAAUACAUUUUUUGCG
..(((((((((.(.((((.(((((...(((..(((((((....))))))).)))...-.((((((.....)))))).))))).)))).).....))))))))) ( -28.60)
>DroSim_CAF1 119452 102 + 1
CUCGCAAAAAACUGCAGACUUUUAUCUACCGCUUGCAUAUUCGUAUGCAAAGGUUGU-UGGUUGAAAAUAUCAACCCUAGAGCUCUGGAAUAAAUUUUUUGCG
..(((((((((.(.((((.(((((...(((..(((((((....))))))).)))...-.((((((.....)))))).))))).)))).).....))))))))) ( -28.60)
>DroEre_CAF1 116240 101 + 1
CUCGCAAAA-ACUGCAGACUUUUAUCUACUACUUGCAUAUUCCUAUGCAAAGGUUGU-UGGCUGAAUAUACCAACCCUAGAGCUGUGGAAUAAAUUGUUUGUG
.........-...((((((.(((((((((..((((((((....)))))..(((..((-(((.........)))))))).)))..)))).)))))..)))))). ( -24.80)
>DroYak_CAF1 108920 102 + 1
CUCGCAAAAUGCUGCAGACUUUUAUCUGCUGCUUGCAUAUUCGUAUGCAAAGGUUGU-UGGUUGAAUAUACCAACCUCAGAGCUCUGGAAUAAAUUGUUUGUG
..((((((..((.(((((......))))).))(((((((....))))))).....((-((((.......)))))).((((....)))).........)))))) ( -27.20)
>consensus
CUCGCAAAAAACUGCAGACUUUUAUCUACCGCUUGCAUAUUCGUAUGCAAAGGUUGU_UGGUUGAAAAUAUCAACCCUAGAGCUCUGGAAUAAAUUUUUUGCG
..(((((((((.(.((((((((.....(((..(((((((....))))))).))).....(((((.......)))))..)))).)))).).....))))))))) (-20.92 = -21.52 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	8,675,881 – 8,675,984
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	91.50
Mean single sequence MFE	-29.70
Consensus MFE	-26.74
Energy contribution	-27.82
Covariance contribution	1.08
Combinations/Pair	1.12
Mean z-score	-3.29
Structure conservation index	0.90
SVM decision value	4.82
SVM RNA-class probability	0.999953
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8675881 103 - 27905053
CGGAAAAAAUUUAUUUCAGAGCUCUGGGGUUGAUAUUUUCAACCAAACAACCUUUGCAUACGAAUAUGCAAGCGGUAGAUAAAAGUCUGCAGUUUUUUGCGAG
((.((((((((....((((....))))((((((.....))))))......(.((((((((....)))))))).)((((((....)))))))))))))).)).. ( -29.00)
>DroSec_CAF1 102823 102 - 1
CGCAAAAAAUGUAUUCCAGAGCUCUAGGGUUGAUAUUUUCAACCA-ACAACCUUUGCAUACGAAUAUGCAAGCGGUAGAUAAAAGUCUGCAGUUUUUUGCGAG
((((((((((..........((.....((((((.....)))))).-.......(((((((....))))))))).((((((....)))))).)))))))))).. ( -32.90)
>DroSim_CAF1 119452 102 - 1
CGCAAAAAAUUUAUUCCAGAGCUCUAGGGUUGAUAUUUUCAACCA-ACAACCUUUGCAUACGAAUAUGCAAGCGGUAGAUAAAAGUCUGCAGUUUUUUGCGAG
(((((((((((.........((.....((((((.....)))))).-.......(((((((....))))))))).((((((....))))))))))))))))).. ( -32.90)
>DroEre_CAF1 116240 101 - 1
CACAAACAAUUUAUUCCACAGCUCUAGGGUUGGUAUAUUCAGCCA-ACAACCUUUGCAUAGGAAUAUGCAAGUAGUAGAUAAAAGUCUGCAGU-UUUUGCGAG
...........((((((...((...(((((((((.......))))-))..)))..))...))))))((((((..((((((....))))))...-.)))))).. ( -27.60)
>DroYak_CAF1 108920 102 - 1
CACAAACAAUUUAUUCCAGAGCUCUGAGGUUGGUAUAUUCAACCA-ACAACCUUUGCAUACGAAUAUGCAAGCAGCAGAUAAAAGUCUGCAGCAUUUUGCGAG
(.((((..........(((....))).((((((.....)))))).-.......(((((((....)))))))((.((((((....)))))).))..)))).).. ( -26.10)
>consensus
CGCAAAAAAUUUAUUCCAGAGCUCUAGGGUUGAUAUUUUCAACCA_ACAACCUUUGCAUACGAAUAUGCAAGCGGUAGAUAAAAGUCUGCAGUUUUUUGCGAG
(((((((((((.........((.....((((((.....)))))).........(((((((....))))))))).((((((....))))))))))))))))).. (-26.74 = -27.82 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:43 2006