Locus 7648

Sequence ID	3L_DroMel_CAF1
Location	20,562,244 – 20,562,459
Length	215
Max. P	0.688886

overview

Window 5

Location	20,562,244 – 20,562,350
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.06
Mean single sequence MFE	-31.26
Consensus MFE	-26.20
Energy contribution	-26.28
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.42
Structure conservation index	0.84
SVM decision value	0.32
SVM RNA-class probability	0.688886
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20562244 106 + 23771897
AAACGUUGUUAAUGACAGUCCACGUCGACUUCGA----------GCCGAGUGUUGAGCUGAAAAGAUGGCGAUAGAUGCACUUUGGGUGUGUCGGCUGUUUGUCUAAUAGAAAAA----A
.....((((((..(((((((..(((((.(((..(----------(((((...))).)))...))).)))))...(((((((.....))))))))))))))....)))))).....----. ( -27.70)
>DroSec_CAF1 7275 103 + 1
AAACGUUGUUAAUGACAGUCGACGUCGACUUCGA----------GCCGAGUGUUGAGCUGAAAAGAUGGCGAUAGAUGCACUUUGGGUGUGUCGGCUGUUUGUCUAAUAGAAA-------
.....((((((..((((((((((((((....)))----------(((((((((...(((........))).......))))))..))).)))))))))))....))))))...------- ( -30.00)
>DroAna_CAF1 28296 120 + 1
AAACGUUGUUAAUGACAGUCGAUGUCGACGACGACGAUGCCGCCGCCGAGCGUUGAGCUGAAAAGAUGGCGAUAGAUGCACUUUGGGUGUGUCGAUUGUUUGUCUAAUAGAAAAAUUGAA
...(((((((...((((.....))))))))))).((((((((....)).))))))..(((...(((..(((((.(((((((.....))))))).)))).)..)))..))).......... ( -34.00)
>DroSim_CAF1 792 103 + 1
AAACGUUGUUAAUGACAGUCGACGUCGACUUCGA----------GCCGAGUGUUGAGCUGAAAAGAUGGCGAUAGAUGCACUUUGGGUGUGUCGGCUGUUUGUCUAAUAGAAU-------
.....((((((..((((((((((((((....)))----------(((((((((...(((........))).......))))))..))).)))))))))))....))))))...------- ( -30.00)
>DroEre_CAF1 791 103 + 1
AAACGUUGUUAAUGACAGUCGCCGUCGACUUCGA----------GCCGAGUGUUGAGCUGAAAAGAUGGCGAUAGAUGCACUUUGGGUGUGUCGGCUGUUUGUCUAAUAGAAA-------
.....((((((..(((((((((((((...(((.(----------(((((...))).))))))..))))))....(((((((.....))))))))))))))....))))))...------- ( -34.60)
>consensus
AAACGUUGUUAAUGACAGUCGACGUCGACUUCGA__________GCCGAGUGUUGAGCUGAAAAGAUGGCGAUAGAUGCACUUUGGGUGUGUCGGCUGUUUGUCUAAUAGAAA_______
.....((((((..(((((((....(((((((((.............)))).)))))(((........)))....(((((((.....))))))))))))))....)))))).......... (-26.20 = -26.28 +   0.08)

alignment

secondary structure

dotplot

Window 6

Location	20,562,350 – 20,562,459
Length	109
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	93.91
Mean single sequence MFE	-21.30
Consensus MFE	-18.15
Energy contribution	-18.52
Covariance contribution	0.38
Combinations/Pair	1.03
Mean z-score	-1.70
Structure conservation index	0.85
SVM decision value	0.32
SVM RNA-class probability	0.688136
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20562350 109 + 23771897
AAAAAAAAACGCAAUCAAUAUAUUUGUAUAUUAUAUAGACAAUAAUUGCAAAAUAAACGAUCGGGCGAUUGUGGGGUUAAUUGUUCGAUGUCG---AAUAUGAACACGUACA
........(((...(((.....((((((.(((((.......))))))))))).....((((((((((((((......)))))))))))..)))---....)))...)))... ( -20.30)
>DroSec_CAF1 7378 107 + 1
-----AAAACGCAAUCAAUAUAUUUGUAUAUUAUAUAGACAAUAAUUGCAAAAUAAACGAUCGGACGAUUGUGUGGUUAAUUGUUCGAUGUCGUCAAAUAUGAACACGUACA
-----...(((...(((.....((((((.(((((.......)))))))))))....(((((((((((((((......)))))))))))..))))......)))...)))... ( -21.30)
>DroSim_CAF1 895 107 + 1
-----AAAACGCAAUCAAUAUAUUUGUAUAUUAUAUAGACAAUAAUUGCAAAAUAAACGAUCGGACGAUUGUGUGGUUAAUUGUUCGAUGUCGUCAAAUAUGAACACGUACA
-----...(((...(((.....((((((.(((((.......)))))))))))....(((((((((((((((......)))))))))))..))))......)))...)))... ( -21.30)
>DroEre_CAF1 894 107 + 1
-----AAAACGCAAUCAAUAUAUUUGUAUAUUAUAUAGACAAUAAUUGCAAAAUAAACGAUCGCUCGAUUGUGUGGUUAAUUGUUCGAUGCCGUCGAAUAUGAACACGUACA
-----...((((((((......((((((.(((((.......)))))))))))......((....)))))))))).(((...((((((((...))))))))..)))....... ( -22.30)
>consensus
_____AAAACGCAAUCAAUAUAUUUGUAUAUUAUAUAGACAAUAAUUGCAAAAUAAACGAUCGGACGAUUGUGUGGUUAAUUGUUCGAUGUCGUCAAAUAUGAACACGUACA
........(((...(((.....((((((.(((((.......))))))))))).......((((((((((((......))))))))))))...........)))...)))... (-18.15 = -18.52 +   0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:52:38 2006