Locus 1449

Sequence ID	3L_DroMel_CAF1
Location	4,189,298 – 4,189,428
Length	130
Max. P	0.883773

overview

Window 8

Location	4,189,298 – 4,189,402
Length	104
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	81.23
Mean single sequence MFE	-27.92
Consensus MFE	-16.62
Energy contribution	-19.18
Covariance contribution	2.56
Combinations/Pair	1.25
Mean z-score	-2.17
Structure conservation index	0.60
SVM decision value	0.42
SVM RNA-class probability	0.730685
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4189298 104 + 23771897
UAUGAAAUGACGCGAAAUUCAGCAUUUUAAUUGCCCGCCUCGCAUUUGAGGCGACAAUUGUAAUCGAGCGUGCCAGCGUGCAUGGUUAUAAUAAAUACUCGCAU------
...........((((......(((.......))).(((((((....)))))))...((((((((((.(((((....))))).))))))))))......))))..------ ( -30.30)
>DroPse_CAF1 36172 94 + 1
UAUGAAAUGACGCGAAAUCCAGCAUUUUAAUUGCUC--CUC---------GCGACAAUUGUAAUCGAGCGUGCCAACGUCUAUGGUUAC-----AUACUCGUCUAAGUAC
........(((((((.....((((.......)))).--.))---------))((....(((((((((((((....))).)).)))))))-----)...)))))....... ( -22.50)
>DroSec_CAF1 34902 104 + 1
UAUGAAAUGACGAAAAAUUCAGCAUUUUAAUUGCCCGUCUCGCAUUCGAGGCGACAAUUGUAAUCGAGCGUGCCAGCGUGCACGGUUAUAAUAAAUACUCGUAU------
..(((((((..((.....))..)))))))..(((.(((((((....)))))))...((((((((((.(((((....))))).))))))))))........))).------ ( -28.10)
>DroEre_CAF1 35474 100 + 1
UAUGAAAUGACGCGAAAUUCAGCAUUUUAAUUGCCCGCCUCGCAUUUGAGGCGACAAUUGUAAUCGAGCGUGCCAGC----UCCGUUACAGUAAAUACACGUAU------
.........(((.(.......(((.......))).(((((((....)))))))...((((((((.((((......))----)).)))))))).....).)))..------ ( -28.90)
>DroYak_CAF1 39584 104 + 1
UAUGAAAUGACGCGAAAUUCAGCAUUUUAAUUGCCCGCCUCGCAUUCGAGGCGACAAUUGUAAUCGAGCGUGCCAGCGUGCACGGUUACAAUAAAUACUCGCAU------
...........((((......(((.......))).(((((((....)))))))...((((((((((.(((((....))))).))))))))))......))))..------ ( -35.20)
>DroPer_CAF1 36751 94 + 1
UAUGAAAUGACGCGAAAUCCAGCAUUUUAAUUGCUC--CUC---------GCGACAAUUGUAAUCGAGCGUGCCAACGUCUAUGGUUAC-----AUACUCGUCUAAGUAC
........(((((((.....((((.......)))).--.))---------))((....(((((((((((((....))).)).)))))))-----)...)))))....... ( -22.50)
>consensus
UAUGAAAUGACGCGAAAUUCAGCAUUUUAAUUGCCCGCCUCGCAUU_GAGGCGACAAUUGUAAUCGAGCGUGCCAGCGUGCACGGUUACAAUAAAUACUCGUAU______
...........((((......(((.......))).(((((((....)))))))...((((((((((.((((....))))...))))))))))......))))........ (-16.62 = -19.18 +   2.56)

alignment

secondary structure

dotplot

Window 9

Location	4,189,333 – 4,189,428
Length	95
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	83.09
Mean single sequence MFE	-29.38
Consensus MFE	-19.16
Energy contribution	-21.48
Covariance contribution	2.32
Combinations/Pair	1.26
Mean z-score	-2.32
Structure conservation index	0.65
SVM decision value	0.93
SVM RNA-class probability	0.883773
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4189333 95 + 23771897
--CGCCUCGCAUUUGAGGCGACAAUUGUAAUCGAGCGUGCCAGCGUGCAUGGUUAUAAUAAAUACUCGCAUUACAUGUGUGCGUGAUCACUUAAUCA
--(((((((....)))))))...((((((((((.(((((....))))).))))))))))...(((.(((((.....))))).)))............ ( -29.10)
>DroSec_CAF1 34937 95 + 1
--CGUCUCGCAUUCGAGGCGACAAUUGUAAUCGAGCGUGCCAGCGUGCACGGUUAUAAUAAAUACUCGUAUUACAUGUGUGCGUGAUCACUUAAUCA
--(((((((....)))))))...((((((((((.(((((....))))).)))))))))).....(.(((((.......))))).)............ ( -27.10)
>DroEre_CAF1 35509 91 + 1
--CGCCUCGCAUUUGAGGCGACAAUUGUAAUCGAGCGUGCCAGC----UCCGUUACAGUAAAUACACGUAUUACAUGUGUGCGUGAUCACUUAAUCA
--(((((((....)))))))...((((((((.((((......))----)).)))))))).....(((((((.......)))))))............ ( -32.80)
>DroYak_CAF1 39619 95 + 1
--CGCCUCGCAUUCGAGGCGACAAUUGUAAUCGAGCGUGCCAGCGUGCACGGUUACAAUAAAUACUCGCAUUACAUGUGUGCGUGAUCACUUAAUCA
--(((((((....)))))))...((((((((((.(((((....))))).))))))))))...(((.(((((.....))))).)))............ ( -34.00)
>DroAna_CAF1 36721 82 + 1
GCUGCCGCUCUUUUGAGGCGACAAUUGUAAUCGAGCGUGCCG-CCUGUGGGGAU--------------CAUUACAGGUGUGCGUGAUCACUUAAUCA
(.((((.(......).)))).)....((.(((..(((..(.(-(((((((....--------------..)))))))))..)))))).))....... ( -23.90)
>consensus
__CGCCUCGCAUUUGAGGCGACAAUUGUAAUCGAGCGUGCCAGCGUGCACGGUUACAAUAAAUACUCGCAUUACAUGUGUGCGUGAUCACUUAAUCA
..((((((......))))))...((((((((((.(((((....))))).)))))))))).....(.(((((.......))))).)............ (-19.16 = -21.48 +   2.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:01 2006