Locus 4306

Sequence ID	3R_DroMel_CAF1
Location	11,424,027 – 11,424,267
Length	240
Max. P	0.997965

overview

Window 7

Location	11,424,027 – 11,424,147
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.17
Mean single sequence MFE	-37.00
Consensus MFE	-33.38
Energy contribution	-34.22
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-2.33
Structure conservation index	0.90
SVM decision value	2.97
SVM RNA-class probability	0.997965
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11424027 120 + 27905053
CGAGUGUUUGCUCUGCCAACUUCGGCCAGCCAGGAUAUUCCCUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUUGCGCCAUAGGUAGUCU
((((((...(((..(((......))).)))((((((.........)))))).)))))).......((((((((((((......(((.......))).......))))))...)))))).. ( -36.72)
>DroSec_CAF1 171566 120 + 1
CGAGUGUUUGCUCUGCCAACUCCGGCCAGCCAGGAUAUUCCCUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUUGCGCCAUAGGUAGUCU
((((((...(((..(((......))).)))((((((.........)))))).)))))).......((((((((((((......(((.......))).......))))))...)))))).. ( -36.72)
>DroSim_CAF1 165404 120 + 1
CGAGUGUUUGCUCCGCCAACUCCGGCCAGGCCGGAUAUUCCCUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUUGCGCCAUAGGUAGUCU
(((((.........(((......)))..(((.((((.........)))).)))))))).......((((((((((((......(((.......))).......))))))...)))))).. ( -35.32)
>DroEre_CAF1 161270 120 + 1
CGAGUGUUUGCUCUGCCAACUCCGACCAGGCAGGAUAUUCCUUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUCGCGCCAUAGGUAGUCU
((((((((.((...)).)))........((((((((.........))))))))))))).......((((((((((((......(((.......))).......))))))...)))))).. ( -38.62)
>DroYak_CAF1 163842 120 + 1
CGAGUGUUUGCUCUACCAACUCCGGCCAGGCAGGAUAUUCCCUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUUGCGCCAUAGGUAGUCU
.((((....))))((((......(((..((((((((.........))))))))..(((.....)))..)))((((((......(((.......))).......))))))...)))).... ( -37.62)
>consensus
CGAGUGUUUGCUCUGCCAACUCCGGCCAGGCAGGAUAUUCCCUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUUGCGCCAUAGGUAGUCU
(((((.........(((......)))..((((((((.........))))))))))))).......((((((((((((......(((.......))).......))))))...)))))).. (-33.38 = -34.22 +   0.84)

alignment

secondary structure

dotplot

Window 8

Location	11,424,067 – 11,424,187
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.17
Mean single sequence MFE	-31.02
Consensus MFE	-28.38
Energy contribution	-28.62
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.01
Structure conservation index	0.91
SVM decision value	2.50
SVM RNA-class probability	0.994714
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11424067 120 + 27905053
CCUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUUGCGCCAUAGGUAGUCUCGCCAGUCUAUUAAGUGGCGCUCCCCAUAAUUCACAACAC
..........((((((((((.((.(((((((((((((......(((.......))).......))))))...))))).)).....))..))))))))))..................... ( -30.52)
>DroSec_CAF1 171606 120 + 1
CCUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUUGCGCCAUAGGUAGUCUCGCCAGUCUAUUAAGUGGCGCUCCCCAUAAUUCACAACAC
..........((((((((((.((.(((((((((((((......(((.......))).......))))))...))))).)).....))..))))))))))..................... ( -30.52)
>DroSim_CAF1 165444 120 + 1
CCUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUUGCGCCAUAGGUAGUCUCGCCAGUCUAUUAAGUGGCGCUCCCCAUAAUUCACAACAC
..........((((((((((.((.(((((((((((((......(((.......))).......))))))...))))).)).....))..))))))))))..................... ( -30.52)
>DroEre_CAF1 161310 120 + 1
CUUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUCGCGCCAUAGGUAGUCUCGCCGGUCUAUUAAGUGGGGCUGGCCAUAAUUCACAACAC
...........(((((((((.((((((((((((((((......(((.......))).......))))))...))))).))....)))..)))))))))((....)).............. ( -34.32)
>DroYak_CAF1 163882 120 + 1
CCUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUUGCGCCAUAGGUAGUCUCGCCAGUCUAUUAAGUGGGCCUGGCCAUAAUUCACAACAC
................(((......((((((((((((......(((.......))).......))))))...))))))...((((((((((...))))).)))))......)))...... ( -29.22)
>consensus
CCUUAAUCCUGCCACUUGAUCACCAGCUGCCGGCGCGUUUCAAGUCCCCAAUCGACAAUCCUUUGCGCCAUAGGUAGUCUCGCCAGUCUAUUAAGUGGCGCUCCCCAUAAUUCACAACAC
..........((((((((((.((.(((((((((((((......(((.......))).......))))))...))))).)).....))..))))))))))..................... (-28.38 = -28.62 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	11,424,147 – 11,424,267
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.58
Mean single sequence MFE	-39.90
Consensus MFE	-33.52
Energy contribution	-33.76
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.84
SVM decision value	1.58
SVM RNA-class probability	0.965260
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11424147 120 + 27905053
CGCCAGUCUAUUAAGUGGCGCUCCCCAUAAUUCACAACACUUUCGGUCCAUCAAGGACCAAAGGGAUGCAGAGCGUCCAGCUGAGGCCAGCAUAAGGCGCAUUUCGCAAACAAAAAGCGA
((((...........((((((((..(((...........((((.(((((.....))))).)))).)))..))))).)))((((....))))....))))....((((.........)))) ( -38.60)
>DroSec_CAF1 171686 120 + 1
CGCCAGUCUAUUAAGUGGCGCUCCCCAUAAUUCACAACACUUUCGGUCCAUCAAGGACGAAAGGGAUGCAGAGCGUCCAGCUGAGGCCAGCAUAAGGCGCAUUUCGCAAACAAAAAGCGA
((((...........((((((((..(((...........((((((.(((.....)))))))))..)))..))))).)))((((....))))....))))....((((.........)))) ( -37.62)
>DroSim_CAF1 165524 120 + 1
CGCCAGUCUAUUAAGUGGCGCUCCCCAUAAUUCACAACACUUUCGGUCCAUCAAGGACGAAAGGGAUGCAGAGCGUCCAGCUGAGGCCAGCAUAGGGCGCAUUUCGCAAACAAAAAGCGA
.((((.(......).))))((.(((..............((((((.(((.....)))))))))((((((...)))))).((((....))))...))).))...((((.........)))) ( -40.80)
>DroEre_CAF1 161390 120 + 1
CGCCGGUCUAUUAAGUGGGGCUGGCCAUAAUUCACAACACUUUCGGUCCAUCAAGGACGAUGGGGAUGCAGAGCGUCCAGCUGAGGCCAGCAUAAGGCGCAUUUCGCAAACACAAAGCGA
((((..(((((...)))))(((((((.............((.(((.(((.....)))))).))((((((...))))))......)))))))....))))....((((.........)))) ( -41.60)
>DroYak_CAF1 163962 120 + 1
CGCCAGUCUAUUAAGUGGGCCUGGCCAUAAUUCACAACACUUUCGGUCCAUCAAGGACGAGGGGGCUGCAGAGCGUCCAGCUGGGGCCAGCAUAAGGCGCAUUUCGCAAACACAAUGCGA
((((.((((((...))))))((((((.............((((((.(((.....)))))))))(((((.........)))))..)))))).....))))....(((((.......))))) ( -40.90)
>consensus
CGCCAGUCUAUUAAGUGGCGCUCCCCAUAAUUCACAACACUUUCGGUCCAUCAAGGACGAAAGGGAUGCAGAGCGUCCAGCUGAGGCCAGCAUAAGGCGCAUUUCGCAAACAAAAAGCGA
((((..........((((......))))...........((((((.(((.....)))))))))((((((...)))))).((((....))))....))))....((((.........)))) (-33.52 = -33.76 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:28 2006