Locus 2112

Sequence ID	3L_DroMel_CAF1
Location	5,791,697 – 5,791,803
Length	106
Max. P	0.994847

overview

Window 8

Location	5,791,697 – 5,791,803
Length	106
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	78.23
Mean single sequence MFE	-23.02
Consensus MFE	-15.07
Energy contribution	-15.75
Covariance contribution	0.68
Combinations/Pair	1.10
Mean z-score	-1.49
Structure conservation index	0.65
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5791697 106 + 23771897
AAAUAACAAGUGAAUUGGAGCAUACCGAAUUGGCCGCAACAUAACAUCGACAUA----UCUACAGAUAUACAUUGAUGCUUGUUGCAACACCCACGCAUCACUCGCAAUG
.........((((..((..((...((.....))..((((((...((((((.(((----((....)))))...))))))..)))))).........))..)).)))).... ( -24.20)
>DroSec_CAF1 5073 94 + 1
AAAUAACAAGUGAAUUGGAGCAUACCGAAUUGGCCGCAACAUAACAUCGACA----------------UACAUUGAUGCCUGUUGCAACACCCACGCAUCACUCGCAAUG
.........((((..((..((...((.....))..((((((...((((((..----------------....))))))..)))))).........))..)).)))).... ( -20.30)
>DroSim_CAF1 4917 94 + 1
AAAUAACAAGUGAAUUGGAGCAUACCGAAUUGGCCGCAACAUAACAUCGACA----------------UACAUUGAUGCUUGUUGCAACACCCACGCAUCACUCGCAAUG
.........((((..((..((...((.....))..((((((...((((((..----------------....))))))..)))))).........))..)).)))).... ( -21.00)
>DroEre_CAF1 4981 104 + 1
AAAUACCAAGUGAAUUGGAGCAUGCCGAAUGGGCCG-AGCACAACAUCGCCAUAUACUCGCACAUGGAUGCUUGGGUGGGUGUUGCAA--CCCACGGAUCACUAGCA---
........(((((.((((......)))).....(((-((((...(((.((.........))..)))..)))))))((((((......)--)))))...)))))....--- ( -29.50)
>DroYak_CAF1 5293 109 + 1
AAAUAACAAGUGAAUUGGAGCAUACCGAAUUGGCCGCAACAUAACAUCGACUUCGACAUCGACAUAUAGAAAUACAUGCUUGUUGCAACACCCACAGAUCACUUAUA-UG
.......((((((.((((......)))).......((((((.....((((........))))(((.((....)).)))..))))))............))))))...-.. ( -20.10)
>consensus
AAAUAACAAGUGAAUUGGAGCAUACCGAAUUGGCCGCAACAUAACAUCGACAU________ACA___AUACAUUGAUGCUUGUUGCAACACCCACGCAUCACUCGCAAUG
........(((((.((((......)))).......((((((...((((((......................))))))..))))))............)))))....... (-15.07 = -15.75 +   0.68)

alignment

secondary structure

dotplot

Window 9

Location	5,791,697 – 5,791,803
Length	106
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	78.23
Mean single sequence MFE	-32.94
Consensus MFE	-22.15
Energy contribution	-23.47
Covariance contribution	1.32
Combinations/Pair	1.16
Mean z-score	-2.64
Structure conservation index	0.67
SVM decision value	2.52
SVM RNA-class probability	0.994847
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5791697 106 - 23771897
CAUUGCGAGUGAUGCGUGGGUGUUGCAACAAGCAUCAAUGUAUAUCUGUAGA----UAUGUCGAUGUUAUGUUGCGGCCAAUUCGGUAUGCUCCAAUUCACUUGUUAUUU
....((((((((....((((((((((((((((((((....((((((....))----))))..)))))).)))))))(((.....))))))).)))..))))))))..... ( -34.90)
>DroSec_CAF1 5073 94 - 1
CAUUGCGAGUGAUGCGUGGGUGUUGCAACAGGCAUCAAUGUA----------------UGUCGAUGUUAUGUUGCGGCCAAUUCGGUAUGCUCCAAUUCACUUGUUAUUU
....((((((((....((((((((((((((((((((.((...----------------.)).)))))).)))))))(((.....))))))).)))..))))))))..... ( -30.60)
>DroSim_CAF1 4917 94 - 1
CAUUGCGAGUGAUGCGUGGGUGUUGCAACAAGCAUCAAUGUA----------------UGUCGAUGUUAUGUUGCGGCCAAUUCGGUAUGCUCCAAUUCACUUGUUAUUU
....((((((((....((((((((((((((((((((.((...----------------.)).)))))).)))))))(((.....))))))).)))..))))))))..... ( -31.00)
>DroEre_CAF1 4981 104 - 1
---UGCUAGUGAUCCGUGGG--UUGCAACACCCACCCAAGCAUCCAUGUGCGAGUAUAUGGCGAUGUUGUGCU-CGGCCCAUUCGGCAUGCUCCAAUUCACUUGGUAUUU
---(((((((((...(((((--(......))))))...((((((((((.(((((((((.........))))))-).)).)))..)).))))).....)))).)))))... ( -33.30)
>DroYak_CAF1 5293 109 - 1
CA-UAUAAGUGAUCUGUGGGUGUUGCAACAAGCAUGUAUUUCUAUAUGUCGAUGUCGAAGUCGAUGUUAUGUUGCGGCCAAUUCGGUAUGCUCCAAUUCACUUGUUAUUU
..-.((((((((..((.(((((((((((((.(((((((....))))))).(((((((....))))))).)))))))(((.....)))))))))))..))))))))..... ( -34.90)
>consensus
CAUUGCGAGUGAUGCGUGGGUGUUGCAACAAGCAUCAAUGUAU___UGU________AUGUCGAUGUUAUGUUGCGGCCAAUUCGGUAUGCUCCAAUUCACUUGUUAUUU
....((((((((....((((((((((((((((((((..........................)))))).)))))))(((.....))))))).)))..))))))))..... (-22.15 = -23.47 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:41 2006