Locus 1460

Sequence ID	3R_DroMel_CAF1
Location	4,200,618 – 4,200,787
Length	169
Max. P	0.827454

overview

Window 7

Location	4,200,618 – 4,200,717
Length	99
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	80.87
Mean single sequence MFE	-29.33
Consensus MFE	-20.57
Energy contribution	-21.93
Covariance contribution	1.37
Combinations/Pair	1.25
Mean z-score	-1.91
Structure conservation index	0.70
SVM decision value	0.70
SVM RNA-class probability	0.827454
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4200618 99 + 27905053
UGAAUUGGAUAAUAAUUUUCCAUGGCAUUUUCCGAGAUGCC---UUUUCCCACGCUCGAGUAGCAGCAGGCAAAUGUCAUGGGAGGACGCAAAAGAAGUCCA
.................(((((((((((((.((((((....---.))))....((((.....).))).)).)))))))))))))((((.........)))). ( -29.60)
>DroSec_CAF1 11985 99 + 1
UGAAUUGGAUAAUAAUUUUCCAUGGCCUUUUCCGAGUUGCC---UUCUCCCACGCUCGAGUAGCAGCAGGCCAAAGUCGUGGGAGGACGCAAAAGAAGUCCA
.....((((.........))))(((.(((((.....((((.---(((((((((((((.....).))).(((....)))))))))))).)))).))))).))) ( -33.10)
>DroSim_CAF1 12168 102 + 1
UGAAUUGGAUAAUAAUUUUCCAUGGCAUUUUCCGAGUUGCCUCCUUCUCCCACGCUCGAGUAGCAGCAGGCAAAUGUCGUGGGAGGACGCAAAAGAAGUCCA
.................(((((((((((((.((..(((((......(((........)))..))))).)).)))))))))))))((((.........)))). ( -32.10)
>DroEre_CAF1 12693 99 + 1
UGAAUUGGAUAAUAAUUUUCCCUGGCAUUUUCCGAGUUGCC---UUCUUCCACGCUCGAAUAGCAGCAGGCAAAUGUCGUGGGAGGACGCAAAAGAAGUCCA
.((((((.....))))))((((((((((((.((..(((((.---(((..........)))..))))).)).)))))))).))))((((.........)))). ( -28.80)
>DroYak_CAF1 12360 97 + 1
UGAAUGGGAUAAUAAUUUUCCAUGGCAUUUUCCGAGCUGCC---UU--UCCACGCUCGAGUAGCAGCAGGCAAAUGUCGUGGGAGGACGCAAAAGAAGUCCA
.................(((((((((((((.((..(((((.---.(--((.......)))..))))).)).)))))))))))))((((.........)))). ( -35.50)
>DroAna_CAF1 14051 79 + 1
---------------UUUUUUCU-GUAUUUUCCCC-ACACA---UUUUCCCACGCACGAGCAGCAGUAGACCAACAGCAAGAGGGGA---AAGAGAAGUCCA
---------------...(((((-...((((((((-.....---.........((....)).((.((......)).))....)))))---)))))))).... ( -16.90)
>consensus
UGAAUUGGAUAAUAAUUUUCCAUGGCAUUUUCCGAGUUGCC___UUCUCCCACGCUCGAGUAGCAGCAGGCAAAUGUCGUGGGAGGACGCAAAAGAAGUCCA
.................(((((((((((((.((..(((((......................))))).)).)))))))))))))((((.........)))). (-20.57 = -21.93 +   1.37)

alignment

secondary structure

dotplot

Window 8

Location	4,200,682 – 4,200,787
Length	105
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	86.20
Mean single sequence MFE	-30.99
Consensus MFE	-24.67
Energy contribution	-25.03
Covariance contribution	0.37
Combinations/Pair	1.25
Mean z-score	-1.79
Structure conservation index	0.80
SVM decision value	-0.03
SVM RNA-class probability	0.518485
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4200682 105 + 27905053
AGGCAAAUGUCAUGGGAGGACGCAAAAGAAGUCCAGCAGAAGACAUAAUAAAAUUAAUGCCGGGGCAUUAUGUGUCCUUUCCCGGACUCGAGAC-CGUCCGCCUGU
((((.........(((((((((((......(((........)))..........((((((....)))))))))))))..))))((((.......-.)))))))).. ( -37.70)
>DroSec_CAF1 12049 105 + 1
AGGCCAAAGUCGUGGGAGGACGCAAAAGAAGUCCAGCAGAAGACAUAAUAAAAUUAAUGCCGGAGCAUUAUGUGUUCUUUCCCGGACUCGAGAC-CGUCCGCCUGU
((((.........(((((((((((......(((........)))..........((((((....)))))))))))))..))))((((.......-.)))))))).. ( -32.00)
>DroSim_CAF1 12235 105 + 1
AGGCAAAUGUCGUGGGAGGACGCAAAAGAAGUCCAGCAGAAGACAUAAUAAAAUUAAUGCCGGAGCAUUAUGUGUUCUUUCCCGGACUCGAGAC-CGUCCGCCUGU
((((.........(((((((((((......(((........)))..........((((((....)))))))))))))..))))((((.......-.)))))))).. ( -32.90)
>DroEre_CAF1 12757 106 + 1
AGGCAAAUGUCGUGGGAGGACGCAAAAGAAGUCCAGCAGAAGACAUAAUAAAAUUAAUGCUGGGGCAUUAUGUGUUCUUUCCCUGACUCGAGACUCGUUCGCCUGU
((((....((((.(((((((((((.((....(((((((...................)))))))...)).)))))))..))))))))..(((.....))))))).. ( -32.91)
>DroYak_CAF1 12422 105 + 1
AGGCAAAUGUCGUGGGAGGACGCAAAAGAAGUCCAGCAGAAGACAUAAUAAAAUUAAUGCUGGGGCAUUAUGUGUUCUUUCCCGGACUCGAGAC-CGUUCGUCUGU
((((....(((.((((((((((((.((....(((((((...................)))))))...)).)))))))..))))))))..(((..-..))))))).. ( -30.21)
>DroAna_CAF1 14098 97 + 1
AGACCAACAGCAAGAGGGGA---AAGAGAAGUCCACCCAGAGAUGUAAUAAAAUUAAUGCCAAGGCAUUAUAUGUUCUUUUCCAAACU-GA-----GUCGUCCUGC
.(((...(((......((((---(((((..(((........)))..........((((((....))))))....)))))))))...))-).-----)))....... ( -20.20)
>consensus
AGGCAAAUGUCGUGGGAGGACGCAAAAGAAGUCCAGCAGAAGACAUAAUAAAAUUAAUGCCGGGGCAUUAUGUGUUCUUUCCCGGACUCGAGAC_CGUCCGCCUGU
((((.........(((((((((((......(((........)))..........((((((....)))))))))))))))))..((((.........)))))))).. (-24.67 = -25.03 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:07 2006