Locus 6754

Sequence ID	3R_DroMel_CAF1
Location	17,807,061 – 17,807,165
Length	104
Max. P	0.996793

overview

Window 1

Location	17,807,061 – 17,807,165
Length	104
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	75.95
Mean single sequence MFE	-23.92
Consensus MFE	-12.09
Energy contribution	-12.95
Covariance contribution	0.86
Combinations/Pair	1.24
Mean z-score	-3.21
Structure conservation index	0.51
SVM decision value	2.75
SVM RNA-class probability	0.996793
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17807061 104 + 27905053
GAAAAUGCAUUCGCGCAUGGAAAAUGGAAAAUGUGCUAAGCAAACGCAAAUGAAUUUUGCAAAUUCGAAAUUCAAACGUUAAGCGACAACA--UAG---CAGA--AUGCAU
....((((((((((((((............))))))...((.((((....(((((((((......)))))))))..))))..)).......--...---..))--)))))) ( -26.90)
>DroVir_CAF1 102062 85 + 1
UGCAAUGCAUUCGCGU---GA-------AAAUGUGCUAAAUAAACGCAAAUGAAUU-UGCACAUUCA-GAUUUAAACACGAAGUGACAA---CAAG---AAAA--------
.....((((((..(((---(.-------...((((.........))))..((((((-((......))-))))))..)))).)))).)).---....---....-------- ( -13.00)
>DroGri_CAF1 93905 90 + 1
UGCAA-GCAUUCGCGU--AGA-------AAAUGUGCUAAACCAACGCAAAUGAAUU-UCCAUAUU-------CAAACACGAAGCGACAACAACAAU---CAAAUUGUGCAC
(((..-((.((((.((--...-------...((((.........))))..(((((.-.....)))-------)).)).)))))).......(((((---...)))))))). ( -14.80)
>DroSec_CAF1 95649 104 + 1
GAAAAUGCAUUCGCGCAUGGAAAAUGAAAAAUGUGCUAAGCAAACGCAAAUGAAUUUUGCAAAUUCGAAAUUCAAACGUGAAGCGACAACA--UCG---CAGA--AUGCAU
....((((((((((((((............))))))........(((...(((((((((......)))))))))...)))..((((.....--)))---).))--)))))) ( -30.00)
>DroSim_CAF1 95504 104 + 1
GAAAAUGCAUUCGCGCAUGGAAAAUGGAAAAUGUGCUAAGCAAACGCAAAUGAAUUUUGCAAAUUCGAAAUUCAAACGUGAAGCGACAACA--UCG---CAGA--AUGCAU
....((((((((((((((............))))))........(((...(((((((((......)))))))))...)))..((((.....--)))---).))--)))))) ( -30.00)
>DroAna_CAF1 102892 100 + 1
GAAAAUGCAUUCGCGCAUGGAA-------AAUGUGCUAAGCAAACGCAAAUGAAUUUUGCAAAUUCGAAAUUCAAACGUGAAGCGACAACU--ACGCCACCGA--AUGCAU
....((((((((((((((....-------.))))))...((....))...(((((((((......)))))))))...(((..(((......--.)))))).))--)))))) ( -28.80)
>consensus
GAAAAUGCAUUCGCGCAUGGAA______AAAUGUGCUAAGCAAACGCAAAUGAAUUUUGCAAAUUCGAAAUUCAAACGUGAAGCGACAACA__AAG___CAGA__AUGCAU
......((.((((((................((((.........))))..(((((((((......)))))))))..))))))))........................... (-12.09 = -12.95 +   0.86)

alignment

secondary structure

dotplot

Window 2

Location	17,807,061 – 17,807,165
Length	104
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	75.95
Mean single sequence MFE	-23.09
Consensus MFE	-9.56
Energy contribution	-10.23
Covariance contribution	0.67
Combinations/Pair	1.14
Mean z-score	-2.19
Structure conservation index	0.41
SVM decision value	0.47
SVM RNA-class probability	0.749592
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17807061 104 - 27905053
AUGCAU--UCUG---CUA--UGUUGUCGCUUAACGUUUGAAUUUCGAAUUUGCAAAAUUCAUUUGCGUUUGCUUAGCACAUUUUCCAUUUUCCAUGCGCGAAUGCAUUUUC
((((((--((((---(.(--((.(((.(((.(((((.(((((((.(......).)))))))...))))).....))))))............)))))).)))))))).... ( -24.02)
>DroVir_CAF1 102062 85 - 1
--------UUUU---CUUG---UUGUCACUUCGUGUUUAAAUC-UGAAUGUGCA-AAUUCAUUUGCGUUUAUUUAGCACAUUU-------UC---ACGCGAAUGCAUUGCA
--------....---..((---(.((((.(((((((..(((((-((((((((((-((....))))))..)))))))...))))-------..---))))))))).)).))) ( -18.10)
>DroGri_CAF1 93905 90 - 1
GUGCACAAUUUG---AUUGUUGUUGUCGCUUCGUGUUUG-------AAUAUGGA-AAUUCAUUUGCGUUGGUUUAGCACAUUU-------UCU--ACGCGAAUGC-UUGCA
(((((((((...---...)))))....(((.((((..((-------(((.....-.)))))..))))..)))...))))....-------...--..((((....-)))). ( -19.70)
>DroSec_CAF1 95649 104 - 1
AUGCAU--UCUG---CGA--UGUUGUCGCUUCACGUUUGAAUUUCGAAUUUGCAAAAUUCAUUUGCGUUUGCUUAGCACAUUUUUCAUUUUCCAUGCGCGAAUGCAUUUUC
((((((--((.(---((.--(((((..((...((((.(((((((.(......).)))))))...))))..)).))))).......(((.....)))))))))))))).... ( -24.60)
>DroSim_CAF1 95504 104 - 1
AUGCAU--UCUG---CGA--UGUUGUCGCUUCACGUUUGAAUUUCGAAUUUGCAAAAUUCAUUUGCGUUUGCUUAGCACAUUUUCCAUUUUCCAUGCGCGAAUGCAUUUUC
((((((--((.(---((.--(((((..((...((((.(((((((.(......).)))))))...))))..)).))))).......(((.....)))))))))))))).... ( -24.80)
>DroAna_CAF1 102892 100 - 1
AUGCAU--UCGGUGGCGU--AGUUGUCGCUUCACGUUUGAAUUUCGAAUUUGCAAAAUUCAUUUGCGUUUGCUUAGCACAUU-------UUCCAUGCGCGAAUGCAUUUUC
((((((--(((((((((.--...)))))))..((((.(((((((.(......).)))))))...)))).......((.(((.-------....))).)))))))))).... ( -27.30)
>consensus
AUGCAU__UCUG___CGA__UGUUGUCGCUUCACGUUUGAAUUUCGAAUUUGCAAAAUUCAUUUGCGUUUGCUUAGCACAUUU______UUCCAUGCGCGAAUGCAUUUUC
...............................((.(((((.....))))).)).(((((.(((((((((...........................))))))))).))))). ( -9.56 = -10.23 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:11 2006