Locus 3461

Sequence ID	3R_DroMel_CAF1
Location	9,361,233 – 9,361,365
Length	132
Max. P	0.581553

overview

Window 3

Location	9,361,233 – 9,361,340
Length	107
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	77.61
Mean single sequence MFE	-15.57
Consensus MFE	-8.73
Energy contribution	-9.15
Covariance contribution	0.42
Combinations/Pair	1.04
Mean z-score	-1.56
Structure conservation index	0.56
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9361233 107 + 27905053
GAAGACGCAAGCAGC------AGCAUC-ACAUCACCAACAGCGGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGCAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAA
(((((((.(((((((------.((...-............)).)).........))))).)))))))..........((.((..(((....)))..))....)).......... ( -15.76)
>DroPse_CAF1 126062 83 + 1
-------------------------------GCGGCAGCAACAGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGAAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAA
-------------------------------((..((((((.((((........))))..(((((((............))))))).....))).)))....)).......... ( -14.50)
>DroSec_CAF1 130842 107 + 1
GAAAACACAAGCAGC------AGCAUC-ACAUCAGCAACAGCGGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGCAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAA
(((((((.((((((.------......-......((....))...........)))))).)))))))..........((.((..(((....)))..))....)).......... ( -16.55)
>DroWil_CAF1 131219 83 + 1
----------------------------GCGUCAGCUAG---AGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGCAAACAAUUUUUCCACUGAAAAGCAUAAUAAAAA
----------------------------((.((((...(---((((........))))).(((((((((...)))))).))).............))))...)).......... ( -14.50)
>DroAna_CAF1 125964 106 + 1
GA--------GCAACAGCAACAGCUCGAGCACCAGCAACAGCGGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGCAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAA
((--------((..........))))..((.((.((....))))((((((((((((.((.((((((........)))))).)).))).))))))).))....)).......... ( -17.60)
>DroPer_CAF1 131638 83 + 1
-------------------------------GCGGCAGCAACAGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGAAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAA
-------------------------------((..((((((.((((........))))..(((((((............))))))).....))).)))....)).......... ( -14.50)
>consensus
_____________________________CAUCAGCAACAGCAGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGCAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAA
..................................((.....(((((..((((((((.((.((((((........)))))).)).)))))))))).)))....)).......... ( -8.73 =  -9.15 +   0.42)

alignment

secondary structure

dotplot

Window 4

Location	9,361,260 – 9,361,365
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.93
Mean single sequence MFE	-12.38
Consensus MFE	-8.63
Energy contribution	-9.05
Covariance contribution	0.42
Combinations/Pair	1.04
Mean z-score	-1.33
Structure conservation index	0.70
SVM decision value	0.10
SVM RNA-class probability	0.581553
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9361260 105 + 27905053
CCAACAGCGGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGCAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAACAACAA--------AAUUCCA----CACACAAAAACA---
......((..((((((((((((.((.((((((........)))))).)).))).))))))).))....))................--------.......----............--- ( -11.50)
>DroPse_CAF1 126065 114 + 1
GCAGCAACAGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGAAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAAGGCAGAAACAAAAACAAGACA----GA--CAAAAAGAGAG
((((((..((((........))))..))))(((((...)))))))........(((((((.(((....((...........)).....(........).))----).--))))))).... ( -12.90)
>DroWil_CAF1 131225 102 + 1
GCUAG---AGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGCAAACAAUUUUUCCACUGAAAAGCAUAAUAAAAACAAAAA--------AAAUACA--ACAA--CAGCAACA---
(((.(---((((........))))).(((((((((...)))))).))).....((((((....)))))).................--------.......--....--.)))....--- ( -11.60)
>DroYak_CAF1 131516 103 + 1
GCAACAGCGGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGCAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAACAACAA--------AAUUCCG----CA--CAAAAACA---
......((((....((((((((.((.((((((........)))))).)).))))))))((.((....))))...............--------....)))----).--........--- ( -15.10)
>DroAna_CAF1 125990 105 + 1
GCAACAGCGGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGCAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAACAAAAA----------UACAGAAACAA--CAACAACA---
((.....(((((..((((((((.((.((((((........)))))).)).)))))))))).)))....))................----------...........--........--- ( -11.60)
>DroPer_CAF1 131641 113 + 1
GCAGCAACAGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGAAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAAGACAGAAACAAAAACAAGACA----GA--CAAAAAGAGA-
((((((..((((........))))..))))(((((...)))))))........(((((((.(((...................................))----).--)))))))...- ( -11.55)
>consensus
GCAACAGCAGCAUCAAAAAUUGCUUAUGUUUUCAUAAAAUGAAGCGCAAACAAUUUUUUGACUGAAAAGCAUAAUAAAAACAAAAA________AAAUACA____AA__CAAAAACA___
((.....(((((..((((((((.((.((((((........)))))).)).)))))))))).)))....)).................................................. ( -8.63 =  -9.05 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:34 2006