Locus 9824

Sequence ID	3R_DroMel_CAF1
Location	26,132,163 – 26,132,255
Length	92
Max. P	0.963958

overview

Window 9

Location	26,132,163 – 26,132,255
Length	92
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	72.36
Mean single sequence MFE	-13.70
Consensus MFE	-4.80
Energy contribution	-4.83
Covariance contribution	0.03
Combinations/Pair	1.14
Mean z-score	-2.03
Structure conservation index	0.35
SVM decision value	0.27
SVM RNA-class probability	0.662042
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26132163 92 + 27905053
AAUAUUAUAACCAAUAUAUU-AACCAAUUUAUAUUCUCUAAAUUAGAAGAGAAUAAAAGCAGAGCUUACCUCUGCUU---ACCUUCGCCAACAAAG
....................-..........((((((((........)))))))).((((((((.....))))))))---................ ( -18.50)
>DroSec_CAF1 122724 83 + 1
AAUAUAA--------AGAUU-AACCAAUUUAUAUUCUCUAAAUUAUGA-AAAAUAAAAGCAGAGCUUACCUCCGCUU---ACCUUCGCCAACAAAG
(((((((--------(....-......)))))))).............-.......((((.(((.....))).))))---................ (  -7.80)
>DroSim_CAF1 128619 83 + 1
AAUAUAA--------AGAUU-AACCAAUUUAUAUUCUCUAGAUUAUGA-AAAAUAAAAGCAGAGCUUACCUCCGCUU---ACCUUCGCCAACAAAG
.......--------.....-......((((((.((....)).)))))-)......((((.(((.....))).))))---................ (  -9.60)
>DroEre_CAF1 131407 84 + 1
CAAGUAA--------UGUUUAAACCAAUUUAAAUCCUCUAUAUCAGAG-AAAAUAAAAGCUGAGCUUACCACUGCUU---ACCUUCGCCAACAAAG
.......--------((((................((((.....))))-.......(((.(((((........))))---).)))....))))... (  -9.80)
>DroYak_CAF1 130173 84 + 1
AAAAUAU--------AGUUUAAAUCAAUACGAAGCUUUUAAAUCAGAG-AAAAUAAAAGCAGAGCUUACCUCUGCUU---ACCUUCGCCAACAAAG
.......--------..............(((((((((......))))-.......((((((((.....))))))))---..)))))......... ( -15.50)
>DroAna_CAF1 134692 77 + 1
GAUGGGA--------GGAUUUCAAUAAUUUAGGAUUGCUGU-----------UGAAGAGCAGAGCUUACCUCUGCUUAUUACCUUCGGCCACGAAG
....(((--------((..(((((((............)))-----------))))((((((((.....))))))))....))))).......... ( -21.00)
>consensus
AAUAUAA________AGAUU_AACCAAUUUAUAUUCUCUAAAUUAGAA_AAAAUAAAAGCAGAGCUUACCUCUGCUU___ACCUUCGCCAACAAAG
........................................................((((.(((.....))).))))................... ( -4.80 =  -4.83 +   0.03)

alignment

secondary structure

dotplot

Window 0

Location	26,132,163 – 26,132,255
Length	92
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	72.36
Mean single sequence MFE	-18.47
Consensus MFE	-12.20
Energy contribution	-12.40
Covariance contribution	0.20
Combinations/Pair	1.15
Mean z-score	-1.70
Structure conservation index	0.66
SVM decision value	1.56
SVM RNA-class probability	0.963958
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26132163 92 - 27905053
CUUUGUUGGCGAAGGU---AAGCAGAGGUAAGCUCUGCUUUUAUUCUCUUCUAAUUUAGAGAAUAUAAAUUGGUU-AAUAUAUUGGUUAUAAUAUU
(((((....)))))..---((((((((.....)))))))).((((((((........))))))))..(((..((.-.....))..)))........ ( -24.60)
>DroSec_CAF1 122724 83 - 1
CUUUGUUGGCGAAGGU---AAGCGGAGGUAAGCUCUGCUUUUAUUUU-UCAUAAUUUAGAGAAUAUAAAUUGGUU-AAUCU--------UUAUAUU
....(((((((((((.---((((((((.....))))))))....)))-)).(((((((.......))))))))))-)))..--------....... ( -18.40)
>DroSim_CAF1 128619 83 - 1
CUUUGUUGGCGAAGGU---AAGCGGAGGUAAGCUCUGCUUUUAUUUU-UCAUAAUCUAGAGAAUAUAAAUUGGUU-AAUCU--------UUAUAUU
....(((((((((((.---((((((((.....))))))))....)))-))(((.((....)).)))......)))-)))..--------....... ( -16.20)
>DroEre_CAF1 131407 84 - 1
CUUUGUUGGCGAAGGU---AAGCAGUGGUAAGCUCAGCUUUUAUUUU-CUCUGAUAUAGAGGAUUUAAAUUGGUUUAAACA--------UUACUUG
(((((....))))).(---(((.((((.(((((.(((..((((..((-(((((...)))))))..))))))))))))..))--------)).)))) ( -18.20)
>DroYak_CAF1 130173 84 - 1
CUUUGUUGGCGAAGGU---AAGCAGAGGUAAGCUCUGCUUUUAUUUU-CUCUGAUUUAAAAGCUUCGUAUUGAUUUAAACU--------AUAUUUU
((((((..(.((((((---((((((((.....)))))))..))))))-).)..))...))))...................--------....... ( -18.30)
>DroAna_CAF1 134692 77 - 1
CUUCGUGGCCGAAGGUAAUAAGCAGAGGUAAGCUCUGCUCUUCA-----------ACAGCAAUCCUAAAUUAUUGAAAUCC--------UCCCAUC
....((((..((((......(((((((.....))))))))))).-----------....((((........))))......--------..)))). ( -15.10)
>consensus
CUUUGUUGGCGAAGGU___AAGCAGAGGUAAGCUCUGCUUUUAUUUU_UUCUAAUUUAGAGAAUAUAAAUUGGUU_AAUCU________UUAUAUU
(((((....))))).....((((((((.....))))))))........................................................ (-12.20 = -12.40 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:43:01 2006