Locus 804

Sequence ID	3L_DroMel_CAF1
Location	2,417,604 – 2,417,701
Length	97
Max. P	0.880472

overview

Window 7

Location	2,417,604 – 2,417,701
Length	97
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	81.07
Mean single sequence MFE	-33.38
Consensus MFE	-21.38
Energy contribution	-23.05
Covariance contribution	1.67
Combinations/Pair	1.07
Mean z-score	-1.42
Structure conservation index	0.64
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2417604 97 + 23771897
UGGCUAUAAAAAGCAG----GCAACCCUCACCUCACCUUGACACGGUUGUAGGUGUUUAGUGGGUGGGG------AUGGGCAUGGGGCGUGCCAAGAUGAGGGGGCG
..(((......)))..----((..((((((((((((((.(((((........)))))....))))))))------...((((((...))))))....)))))).)). ( -40.90)
>DroSec_CAF1 50805 91 + 1
UGGCUAUAAAAUGCAG----GCAACCCUCACCUCACCUUGACACGGUUGUAGGUGUUUAGUGGGUG------------GGCAUGGGGCGGCCCAAGAUGAGGGGGCG
..((........))..----((..((((((.(((((((.(((((........)))))....)))))------------))..((((....))))...)))))).)). ( -33.40)
>DroSim_CAF1 44737 91 + 1
UGGCUAUAAAAAGCAG----GCAACCCUCACCUCACCUUGACACGGUUGUAGGUGUUUAGUGGGUG------------GGCAUGGGGCGGCCCAAGAUGAGGGGGCG
..(((......)))..----((..((((((.(((((((.(((((........)))))....)))))------------))..((((....))))...)))))).)). ( -34.20)
>DroEre_CAF1 44433 106 + 1
UGGCUAUAAAAAGCAGGCGGGCAACCCUCACCUCACCUUGACAUGGUUGUAGGUGUUUAGUGGGUGGAGAUGGGGAUGGGAAUGGGGCGGUCCAAGAUGAGG-GGCG
..((........((......))..(((((((..(((((.(((((........)))))....)))))..)....((((.(........).))))....)))))-))). ( -30.50)
>DroYak_CAF1 45499 103 + 1
UGGCUAUAAAAAGCAG----GCAACCCUCACCUCACCUUGACAUGGUUGUAGGUGUUUAGUGGGUGGGGAUUACGAUGAGGAUGGGGCGGUCCAAGAUGAGGGGGCG
..(((......)))..----((..((((((((((((((.(((((........)))))....))))))))..........((((......))))....)))))).)). ( -35.10)
>DroAna_CAF1 38543 79 + 1
U-GCUAUAAAAAGCAG----GCAACCCUCACCUCACCUUGACACGAUUGUGGGUGUUUCG--GGU---------------------GCACCCCUUGUGCAGGGGCCG
(-(((......))))(----((..((((.(((((((((..(((....))))))))....)--)))---------------------((((.....))))))))))). ( -26.20)
>consensus
UGGCUAUAAAAAGCAG____GCAACCCUCACCUCACCUUGACACGGUUGUAGGUGUUUAGUGGGUG____________GGCAUGGGGCGGCCCAAGAUGAGGGGGCG
..(((.......((......))..((((((.(((((((.(((((........)))))....)))))................((((....)))))).))))))))). (-21.38 = -23.05 +   1.67)

alignment

secondary structure

dotplot

Window 8

Location	2,417,604 – 2,417,701
Length	97
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	81.07
Mean single sequence MFE	-28.40
Consensus MFE	-18.47
Energy contribution	-20.13
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-2.43
Structure conservation index	0.65
SVM decision value	0.91
SVM RNA-class probability	0.880472
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2417604 97 - 23771897
CGCCCCCUCAUCUUGGCACGCCCCAUGCCCAU------CCCCACCCACUAAACACCUACAACCGUGUCAAGGUGAGGUGAGGGUUGC----CUGCUUUUUAUAGCCA
.(((((((((((((((((((............------........................)))))))))))))))...))))...----..(((......))).. ( -28.92)
>DroSec_CAF1 50805 91 - 1
CGCCCCCUCAUCUUGGGCCGCCCCAUGCC------------CACCCACUAAACACCUACAACCGUGUCAAGGUGAGGUGAGGGUUGC----CUGCAUUUUAUAGCCA
.((.((((((((((((((........)))------------)).........((((((((....)))..))))))))))))))..))----..((........)).. ( -30.00)
>DroSim_CAF1 44737 91 - 1
CGCCCCCUCAUCUUGGGCCGCCCCAUGCC------------CACCCACUAAACACCUACAACCGUGUCAAGGUGAGGUGAGGGUUGC----CUGCUUUUUAUAGCCA
.((.((((((((((((((........)))------------)).........((((((((....)))..))))))))))))))..))----..(((......))).. ( -31.60)
>DroEre_CAF1 44433 106 - 1
CGCC-CCUCAUCUUGGACCGCCCCAUUCCCAUCCCCAUCUCCACCCACUAAACACCUACAACCAUGUCAAGGUGAGGUGAGGGUUGCCCGCCUGCUUUUUAUAGCCA
.(((-(((((((((((......)))...........................((((((((....)))..))))))))))))))..))......(((......))).. ( -25.30)
>DroYak_CAF1 45499 103 - 1
CGCCCCCUCAUCUUGGACCGCCCCAUCCUCAUCGUAAUCCCCACCCACUAAACACCUACAACCAUGUCAAGGUGAGGUGAGGGUUGC----CUGCUUUUUAUAGCCA
.((.((((((((((((......)))...........................((((((((....)))..))))))))))))))..))----..(((......))).. ( -25.90)
>DroAna_CAF1 38543 79 - 1
CGGCCCCUGCACAAGGGGUGC---------------------ACC--CGAAACACCCACAAUCGUGUCAAGGUGAGGUGAGGGUUGC----CUGCUUUUUAUAGC-A
..((((((.....))))))((---------------------(((--(....(((((((............))).)))).))).)))----..(((......)))-. ( -28.70)
>consensus
CGCCCCCUCAUCUUGGGCCGCCCCAUGCC____________CACCCACUAAACACCUACAACCGUGUCAAGGUGAGGUGAGGGUUGC____CUGCUUUUUAUAGCCA
....((((((((((((......)))...........................((((((((....)))..))))))))))))))..........(((......))).. (-18.47 = -20.13 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:37 2006