Locus 3833

Sequence ID	3R_DroMel_CAF1
Location	10,459,886 – 10,460,014
Length	128
Max. P	0.891571

overview

Window 9

Location	10,459,886 – 10,459,987
Length	101
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	81.68
Mean single sequence MFE	-20.73
Consensus MFE	-13.88
Energy contribution	-13.77
Covariance contribution	-0.11
Combinations/Pair	1.20
Mean z-score	-2.22
Structure conservation index	0.67
SVM decision value	0.65
SVM RNA-class probability	0.812989
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10459886 101 + 27905053
GCGAACAAAAUAACAAUCAAAACCCAAAGGCAGCUGUGAAGAAACCCAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAA
............................((...(((((((((((.........)))))))).)))....))..((((((.....))))))........... ( -21.30)
>DroPse_CAF1 5707 77 + 1
UUGCAAGA---AACACACAAAAA-CAAAGUC---------------AAUAAAAUUUCUUCAGCGGAAUUCCAGGCUAGUGCUGAGCCAGCA-----GCAGA
((((((((---((..........-.......---------------.......))))))..((((....)).((((.......)))).)).-----)))). ( -13.26)
>DroSec_CAF1 5948 89 + 1
ACGUACAAAAUAACAAUCAAAACCCAAAGGCAGC------------CAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAA
...(((......................(.((((------------(....((((((......))))))...))))).)((((...))))......))).. ( -18.40)
>DroSim_CAF1 5989 89 + 1
ACGUACAAAAUAACAAUCAAAACCCAAAGGCAGC------------CAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAA
...(((......................(.((((------------(....((((((......))))))...))))).)((((...))))......))).. ( -18.40)
>DroEre_CAF1 5819 101 + 1
ACAUACAAAAUAACAAUCAAAACCCGAAGGCAGCCGCGAAGAAACCCAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAA
...(((......................((...(((((((((((.........))))))).))))....))..((((((.....))))))......))).. ( -26.50)
>DroYak_CAF1 6187 101 + 1
ACAUACAAAAUAACAAUCAAAACCCGAAGGCAGCCGCGAAGAAACCCAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAA
...(((......................((...(((((((((((.........))))))).))))....))..((((((.....))))))......))).. ( -26.50)
>consensus
ACGUACAAAAUAACAAUCAAAACCCAAAGGCAGC____________CAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAA
.............................................................((((....))..((((((.....))))))......))... (-13.88 = -13.77 +  -0.11)

alignment

secondary structure

dotplot

Window 0

Location	10,459,921 – 10,460,014
Length	93
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	86.13
Mean single sequence MFE	-20.54
Consensus MFE	-18.80
Energy contribution	-18.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.92
SVM decision value	0.97
SVM RNA-class probability	0.891571
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10459921 93 + 27905053
GUGAAGAAACCCAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAACUCAACUGAAGUAU---------AAAGCCAAUAAAG
.((((((((.........))))))))((((....))..((((((.....))))))((((.(((.......))).))))..---------...))........ ( -20.00)
>DroSec_CAF1 5982 82 + 1
-----------CAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAACUCAACUGAAGUAU---------AAAGCCAAUAAAG
-----------..........((((((.((....))..((((((.....))))))................))))))...---------............. ( -18.80)
>DroSim_CAF1 6023 82 + 1
-----------CAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAACUCAACUGAAGUAU---------AAAGCCAAUAAAG
-----------..........((((((.((....))..((((((.....))))))................))))))...---------............. ( -18.80)
>DroEre_CAF1 5854 99 + 1
GCGAAGAAACCCAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAACUGUACUGAAGUACG---AGUAUAAAGCCAAUAAAG
(((((((((.........))))))).))((........((((((.....))))))..........(((((((....)))).---)))......))....... ( -24.40)
>DroYak_CAF1 6222 101 + 1
GCGAAGAAACCCAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAACUGAACUGAAGUAUAAAAAGUAUA-AGCCAAUAAAG
(((((((((.........))))))).))((.....(((((((((.....)))))).....((....))...)))..((((.....)))).-..))....... ( -20.70)
>consensus
G_GAAGAAACCCAUAAAAUUUCUUUAGCGGAAUUCCAGGCUGGCGCUGAGCCAGCAUUUAAGUAAACUCAACUGAAGUAU_________AAAGCCAAUAAAG
.....................((((((.((....))..((((((.....))))))................))))))......................... (-18.80 = -18.80 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	10,459,921 – 10,460,014
Length	93
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	86.13
Mean single sequence MFE	-21.72
Consensus MFE	-17.60
Energy contribution	-18.20
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.81
SVM decision value	0.55
SVM RNA-class probability	0.778669
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10459921 93 - 27905053
CUUUAUUGGCUUU---------AUACUUCAGUUGAGUUUACUUAAAUGCUGGCUCAGCGCCAGCCUGGAAUUCCGCUAAAGAAAUUUUAUGGGUUUCUUCAC
.....(((((...---------....((((((((((....)))))..((((((.....))))))))))).....)))))(((((((.....))))))).... ( -23.00)
>DroSec_CAF1 5982 82 - 1
CUUUAUUGGCUUU---------AUACUUCAGUUGAGUUUACUUAAAUGCUGGCUCAGCGCCAGCCUGGAAUUCCGCUAAAGAAAUUUUAUG-----------
.(((.(((((...---------....((((((((((....)))))..((((((.....))))))))))).....))))).)))........----------- ( -20.20)
>DroSim_CAF1 6023 82 - 1
CUUUAUUGGCUUU---------AUACUUCAGUUGAGUUUACUUAAAUGCUGGCUCAGCGCCAGCCUGGAAUUCCGCUAAAGAAAUUUUAUG-----------
.(((.(((((...---------....((((((((((....)))))..((((((.....))))))))))).....))))).)))........----------- ( -20.20)
>DroEre_CAF1 5854 99 - 1
CUUUAUUGGCUUUAUACU---CGUACUUCAGUACAGUUUACUUAAAUGCUGGCUCAGCGCCAGCCUGGAAUUCCGCUAAAGAAAUUUUAUGGGUUUCUUCGC
.....(((((..((.(((---.((((....))))))).)).......((((((.....))))))..((....)))))))(((((((.....))))))).... ( -24.40)
>DroYak_CAF1 6222 101 - 1
CUUUAUUGGCU-UAUACUUUUUAUACUUCAGUUCAGUUUACUUAAAUGCUGGCUCAGCGCCAGCCUGGAAUUCCGCUAAAGAAAUUUUAUGGGUUUCUUCGC
((..(((((..-((((.....))))..)))))..))...........((((((.....))))))..((((..(((..(((....)))..)))..)))).... ( -20.80)
>consensus
CUUUAUUGGCUUU_________AUACUUCAGUUGAGUUUACUUAAAUGCUGGCUCAGCGCCAGCCUGGAAUUCCGCUAAAGAAAUUUUAUGGGUUUCUUC_C
.(((.(((((.....................(((((....)))))..((((((.....))))))..((....))))))).)))................... (-17.60 = -18.20 +   0.60)

alignment

secondary structure

dotplot

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