Locus 3467

Sequence ID	2R_DroMel_CAF1
Location	11,642,523 – 11,642,639
Length	116
Max. P	0.986487

overview

Window 8

Location	11,642,523 – 11,642,639
Length	116
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	88.52
Mean single sequence MFE	-31.12
Consensus MFE	-26.34
Energy contribution	-26.74
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.85
SVM decision value	2.04
SVM RNA-class probability	0.986487
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11642523 116 + 20766785
CACAUAGACGUGUGUAUCAGCUGAUGUCUGCCCAACCUAAUGGAAUGCAUUUAAUUAUAAUUUUAAGUGCGUCUCGGCCUUUGGCUUCGACCUCCGACUUUGCUGAAAUUCGCCUG
(((((....)))))..(((((....(((...(((......)))...((((((((........))))))))(((..((((...))))..)))....)))...))))).......... ( -29.70)
>DroSec_CAF1 14900 114 + 1
CACAUAGACG--UGUAUCAGCUGAUGUCUGGCCAACCUAAUGGAAUGCAUUUAAUUAUAAUUUUAAGUGCGUCUCGGCCUUUGGCUUCGACCUCCGACUUUGCUGAAAUUCGCCUG
....(((.((--.((.(((((....(((.((((..((....)).((((((((((........))))))))))...))))...((......))...)))...))))).)).)).))) ( -32.60)
>DroSim_CAF1 15159 104 + 1
------------UGUAUCAGCUGAUGUCUGGCCAACCUAAUGGAAUGCAUUUAAUUAUAAUUUUAAGUGCGUCUCGGCCUUUGGCUGCGACCUCCGACUUUGCUGAAAUUCGCCUG
------------....(((((....(((.((....))....(((..((((((((........))))))))(((.(((((...))))).))).))))))...))))).......... ( -32.00)
>DroEre_CAF1 14963 103 + 1
-------------AUGUCAGCUGAUGUCUGGCCAACCUAAUUGAGUGCAUUUAAUUAUAAUUUUAAGUGCGUCUCGGCCUUUGGCUUCGACCUCCGACUUUGCUGAAUUUUGCAUG
-------------...(((((.((.(((.((((((.....((((((((((((((........))))))))).)))))...))))))..))).)).......))))).......... ( -29.00)
>DroYak_CAF1 15215 106 + 1
----------UUUGUAUCAGCUGAUGUCUGGUUAGCCUAAUGGAAUGCAUUUAAUUAUAAUUUUAAGUGCGUCUCGGCCUUUGGCUUCGACCUCCGACUUUGCUGAAUUUCGCAUG
----------......(((((....(((.((((((((...((..((((((((((........))))))))))..))......))))..))))...)))...))))).......... ( -32.30)
>consensus
____________UGUAUCAGCUGAUGUCUGGCCAACCUAAUGGAAUGCAUUUAAUUAUAAUUUUAAGUGCGUCUCGGCCUUUGGCUUCGACCUCCGACUUUGCUGAAAUUCGCCUG
................(((((....(((.((....))....(((..((((((((........))))))))(((..((((...))))..))).))))))...))))).......... (-26.34 = -26.74 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	11,642,523 – 11,642,639
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	88.52
Mean single sequence MFE	-27.16
Consensus MFE	-23.40
Energy contribution	-23.64
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.46
Structure conservation index	0.86
SVM decision value	0.39
SVM RNA-class probability	0.715499
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11642523 116 - 20766785
CAGGCGAAUUUCAGCAAAGUCGGAGGUCGAAGCCAAAGGCCGAGACGCACUUAAAAUUAUAAUUAAAUGCAUUCCAUUAGGUUGGGCAGACAUCAGCUGAUACACACGUCUAUGUG
.(((((....(((((...(((...((((.........))))..)))(((.((((........)))).)))..((((......)))).........)))))......)))))..... ( -28.30)
>DroSec_CAF1 14900 114 - 1
CAGGCGAAUUUCAGCAAAGUCGGAGGUCGAAGCCAAAGGCCGAGACGCACUUAAAAUUAUAAUUAAAUGCAUUCCAUUAGGUUGGCCAGACAUCAGCUGAUACA--CGUCUAUGUG
.(((((....(((((...(((...(((....)))...((((((...(((.((((........)))).)))...((....)))))))).)))....)))))....--)))))..... ( -32.20)
>DroSim_CAF1 15159 104 - 1
CAGGCGAAUUUCAGCAAAGUCGGAGGUCGCAGCCAAAGGCCGAGACGCACUUAAAAUUAUAAUUAAAUGCAUUCCAUUAGGUUGGCCAGACAUCAGCUGAUACA------------
..........(((((...((((((((((.(.(((...))).).)))(((.((((........)))).))).))))....((....)).)))....)))))....------------ ( -26.20)
>DroEre_CAF1 14963 103 - 1
CAUGCAAAAUUCAGCAAAGUCGGAGGUCGAAGCCAAAGGCCGAGACGCACUUAAAAUUAUAAUUAAAUGCACUCAAUUAGGUUGGCCAGACAUCAGCUGACAU-------------
..........(((((...(((.((((((...(((...)))...)))(((.((((........)))).))).))).....((....)).)))....)))))...------------- ( -24.60)
>DroYak_CAF1 15215 106 - 1
CAUGCGAAAUUCAGCAAAGUCGGAGGUCGAAGCCAAAGGCCGAGACGCACUUAAAAUUAUAAUUAAAUGCAUUCCAUUAGGCUAACCAGACAUCAGCUGAUACAAA----------
..........(((((...((((((((((...(((...)))...)))(((.((((........)))).))).))))....((....)).)))....)))))......---------- ( -24.50)
>consensus
CAGGCGAAUUUCAGCAAAGUCGGAGGUCGAAGCCAAAGGCCGAGACGCACUUAAAAUUAUAAUUAAAUGCAUUCCAUUAGGUUGGCCAGACAUCAGCUGAUACA____________
..........(((((...((((((((((...(((...)))...)))(((.((((........)))).))).))))....((....)).)))....)))))................ (-23.40 = -23.64 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:17 2006