Locus 5240

Sequence ID	3R_DroMel_CAF1
Location	13,692,877 – 13,692,997
Length	120
Max. P	0.996446

overview

Window 1

Location	13,692,877 – 13,692,997
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.43
Mean single sequence MFE	-53.78
Consensus MFE	-45.92
Energy contribution	-47.76
Covariance contribution	1.84
Combinations/Pair	1.03
Mean z-score	-2.32
Structure conservation index	0.85
SVM decision value	2.70
SVM RNA-class probability	0.996446
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13692877 120 + 27905053
AAUGGGCAUGGGCAUAGGUGGGGGCAUCAAUGGGGGCAUGGGCGGGACGGGCAUGGGACUGGCCGCCCAGGAGGACAUCUAUUGGCCCAAGCUGACGCCCAGUUCGCCCAAGCUGAAGGU
..(((((.(((((...(((..((((..(((((((..(.(((((((..(((........))).)))))))....)...)))))))))))..)))...)))))....))))).......... ( -55.50)
>DroSec_CAF1 2774 118 + 1
--UGGGCAUGGGCAUGGGUGGGGGCAUCAAUGGGGGCAUGGGCGGAACGGGCAUGGGACUGGCCGCCCAGGAGGACAUCUAUUGGCCCAAGCUGACGCCCAGUUCGCCCAAGCUGAAGGU
--(((((.(((((.(.(((..((((..(((((((..(.(((((((..(((........))).)))))))....)...)))))))))))..))).).)))))....))))).......... ( -55.20)
>DroSim_CAF1 2789 118 + 1
--UGGGCAUGGGCAUGGGUGGGGGCAUCAAUGGGGGCAUGGGCGGAACGGGCAUGGGACUGGCCGCCCAGGAGGACAUCUAUUGGCCCAAGCUGACGCCCAGUUCGCCCAAGCUGAAGGU
--(((((.(((((.(.(((..((((..(((((((..(.(((((((..(((........))).)))))))....)...)))))))))))..))).).)))))....))))).......... ( -55.20)
>DroEre_CAF1 2795 112 + 1
--UGGGA------UUGGGUGGGGGCAUUAAUGGGGGCAUGGGCGGCACGGGCAUGGGACUGGCCGCCCAGGAGGACAUAUACUGGCCCAAGCUGACGCCCAGUUCGCCCAAGCUGAAGGU
--(.((.------((((((((((((.(((.(..((((.((((((((.(((........)))))))))))..((........)).))))..).))).))))...)))))))).)).).... ( -50.70)
>DroYak_CAF1 2837 118 + 1
--UGGGAUUGGGAUUGGGUGGGGGCAUCAAUGGGGGCAUGGGCGGGACGGGCAUGGGACUGGCCGCCCAGGAGGACAUCUAUUGGCCCAAGCUGACACCCAGUUCGCCCAAGCUGAAGGU
--((((....((((((((((..(((..(....)((((.(((((((..(((........))).)))))))(((.....)))....))))..)))..)))))))))).)))).......... ( -52.30)
>consensus
__UGGGCAUGGGCAUGGGUGGGGGCAUCAAUGGGGGCAUGGGCGGAACGGGCAUGGGACUGGCCGCCCAGGAGGACAUCUAUUGGCCCAAGCUGACGCCCAGUUCGCCCAAGCUGAAGGU
..(((((.(((((.(.(((..((((..(((((((..(.(((((((..(((........))).)))))))....)...)))))))))))..))).).)))))....))))).......... (-45.92 = -47.76 +   1.84)

alignment

secondary structure

dotplot

Window 2

Location	13,692,877 – 13,692,997
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.43
Mean single sequence MFE	-41.20
Consensus MFE	-36.24
Energy contribution	-36.72
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-1.69
Structure conservation index	0.88
SVM decision value	1.62
SVM RNA-class probability	0.968003
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13692877 120 - 27905053
ACCUUCAGCUUGGGCGAACUGGGCGUCAGCUUGGGCCAAUAGAUGUCCUCCUGGGCGGCCAGUCCCAUGCCCGUCCCGCCCAUGCCCCCAUUGAUGCCCCCACCUAUGCCCAUGCCCAUU
.......((.((((((....((((((((((.(((((....((........))((((((.((......)).)))))).))))).))......)))))))).......)))))).))..... ( -44.90)
>DroSec_CAF1 2774 118 - 1
ACCUUCAGCUUGGGCGAACUGGGCGUCAGCUUGGGCCAAUAGAUGUCCUCCUGGGCGGCCAGUCCCAUGCCCGUUCCGCCCAUGCCCCCAUUGAUGCCCCCACCCAUGCCCAUGCCCA--
.......((.((((((....((((((((((.(((((........((((....))))((.((......)).)).....))))).))......)))))))).......)))))).))...-- ( -43.40)
>DroSim_CAF1 2789 118 - 1
ACCUUCAGCUUGGGCGAACUGGGCGUCAGCUUGGGCCAAUAGAUGUCCUCCUGGGCGGCCAGUCCCAUGCCCGUUCCGCCCAUGCCCCCAUUGAUGCCCCCACCCAUGCCCAUGCCCA--
.......((.((((((....((((((((((.(((((........((((....))))((.((......)).)).....))))).))......)))))))).......)))))).))...-- ( -43.40)
>DroEre_CAF1 2795 112 - 1
ACCUUCAGCUUGGGCGAACUGGGCGUCAGCUUGGGCCAGUAUAUGUCCUCCUGGGCGGCCAGUCCCAUGCCCGUGCCGCCCAUGCCCCCAUUAAUGCCCCCACCCAA------UCCCA--
.........(((((.(....((((((......((((((.....))......(((((((((.((.....))..).)))))))).))))......)))))).).)))))------.....-- ( -37.10)
>DroYak_CAF1 2837 118 - 1
ACCUUCAGCUUGGGCGAACUGGGUGUCAGCUUGGGCCAAUAGAUGUCCUCCUGGGCGGCCAGUCCCAUGCCCGUCCCGCCCAUGCCCCCAUUGAUGCCCCCACCCAAUCCCAAUCCCA--
.........(((((.(....((((((((((.(((((....((........))((((((.((......)).)))))).))))).))......)))))))).).)))))...........-- ( -37.20)
>consensus
ACCUUCAGCUUGGGCGAACUGGGCGUCAGCUUGGGCCAAUAGAUGUCCUCCUGGGCGGCCAGUCCCAUGCCCGUCCCGCCCAUGCCCCCAUUGAUGCCCCCACCCAUGCCCAUGCCCA__
.......((.((((.(....((((((((((.(((((........((((....))))((.((......)).)).....))))).))......)))))))).).)))).))........... (-36.24 = -36.72 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:57 2006