Locus 176

Sequence ID	3L_DroMel_CAF1
Location	529,658 – 529,767
Length	109
Max. P	0.886724

overview

Window 3

Location	529,658 – 529,767
Length	109
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	97.27
Mean single sequence MFE	-24.34
Consensus MFE	-19.86
Energy contribution	-20.46
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.13
Structure conservation index	0.82
SVM decision value	0.94
SVM RNA-class probability	0.886724
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 529658 109 + 23771897
GAAGUGGCAGCUACAGAAAGCCAAGAUAUAUAUCUGCAUAUACAUAUGACUG--GCGAAGCUGCUGCGAAAAAGGUGCAAAACAAAUUAAGAUGCAUAAAUAAACACCGGA
...(..((((((.......((((((((....)))).((((....))))..))--))..))))))..).......(((((.............))))).............. ( -24.12)
>DroSec_CAF1 3890 109 + 1
GAAGUGGCAGCUACAGAAAGCCAAGAUAUAUAUCUGCAUAUACAUAUGAGUG--GCGAAGCUGCUGCGAAAAAGGUGCAAAACAAAUUAAGAUGCAUAAAUAAACACCGGA
...(..((((((.......((((((((....)))).((((....))))..))--))..))))))..).......(((((.............))))).............. ( -24.22)
>DroSim_CAF1 4716 109 + 1
GAAGUGGCAGCUACAGAAAGCCAAGAUAUAUAUCUGCAUAUACAUAUGAGUG--GCGAAGCUGCUGCGAAAAAGGUGCAAAACAAAUUAAGAUGCAUAAAUAAACACCGGA
...(..((((((.......((((((((....)))).((((....))))..))--))..))))))..).......(((((.............))))).............. ( -24.22)
>DroEre_CAF1 4014 108 + 1
GAAGUGGCAGCUACAGAAAGCCAAGAUAUAUAUCUGCAUAUACAUAUGAGUG--GCGAAGCUGCUGCGAA-AAGGUGCAAAACAAAUUAAGAUGCAUAAAUAAACACCGGA
...(..((((((.......((((((((....)))).((((....))))..))--))..))))))..)...-...(((((.............))))).............. ( -24.22)
>DroYak_CAF1 4097 110 + 1
GAAGUGGCAGCUACAGAAAGCCAAGUCAUAUAUCUGCAUAUACAUAUGAGUGAGGCGAAGCUGCUGCGAA-AAGGUGCAAAACAAAUUAAGAUGCAUAAAUAAACACCGCA
...(..((((((.......(((.(.((((((............)))))).)..)))..))))))..)...-...(((((.............))))).............. ( -24.92)
>consensus
GAAGUGGCAGCUACAGAAAGCCAAGAUAUAUAUCUGCAUAUACAUAUGAGUG__GCGAAGCUGCUGCGAAAAAGGUGCAAAACAAAUUAAGAUGCAUAAAUAAACACCGGA
...(..((((((.(.........((((....))))((...(((......)))..))).))))))..).......(((((.............))))).............. (-19.86 = -20.46 +   0.60)

alignment

secondary structure

dotplot

Window 4

Location	529,658 – 529,767
Length	109
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	97.27
Mean single sequence MFE	-26.44
Consensus MFE	-19.64
Energy contribution	-19.68
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.99
Structure conservation index	0.74
SVM decision value	0.19
SVM RNA-class probability	0.624531
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 529658 109 - 23771897
UCCGGUGUUUAUUUAUGCAUCUUAAUUUGUUUUGCACCUUUUUCGCAGCAGCUUCGC--CAGUCAUAUGUAUAUGCAGAUAUAUAUCUUGGCUUUCUGUAGCUGCCACUUC
...(((((........(((........)))...)))))......(((((.((...((--(((..((((((((......)))))))).))))).....)).)))))...... ( -27.00)
>DroSec_CAF1 3890 109 - 1
UCCGGUGUUUAUUUAUGCAUCUUAAUUUGUUUUGCACCUUUUUCGCAGCAGCUUCGC--CACUCAUAUGUAUAUGCAGAUAUAUAUCUUGGCUUUCUGUAGCUGCCACUUC
...(((((........(((........)))...)))))......(((((.((...((--((...((((((((......))))))))..)))).....)).)))))...... ( -26.10)
>DroSim_CAF1 4716 109 - 1
UCCGGUGUUUAUUUAUGCAUCUUAAUUUGUUUUGCACCUUUUUCGCAGCAGCUUCGC--CACUCAUAUGUAUAUGCAGAUAUAUAUCUUGGCUUUCUGUAGCUGCCACUUC
...(((((........(((........)))...)))))......(((((.((...((--((...((((((((......))))))))..)))).....)).)))))...... ( -26.10)
>DroEre_CAF1 4014 108 - 1
UCCGGUGUUUAUUUAUGCAUCUUAAUUUGUUUUGCACCUU-UUCGCAGCAGCUUCGC--CACUCAUAUGUAUAUGCAGAUAUAUAUCUUGGCUUUCUGUAGCUGCCACUUC
...(((((........(((........)))...)))))..-...(((((.((...((--((...((((((((......))))))))..)))).....)).)))))...... ( -26.10)
>DroYak_CAF1 4097 110 - 1
UGCGGUGUUUAUUUAUGCAUCUUAAUUUGUUUUGCACCUU-UUCGCAGCAGCUUCGCCUCACUCAUAUGUAUAUGCAGAUAUAUGACUUGGCUUUCUGUAGCUGCCACUUC
...(((((........(((........)))...)))))..-...(((((.((...(((....((((((((........))))))))...))).....)).)))))...... ( -26.90)
>consensus
UCCGGUGUUUAUUUAUGCAUCUUAAUUUGUUUUGCACCUUUUUCGCAGCAGCUUCGC__CACUCAUAUGUAUAUGCAGAUAUAUAUCUUGGCUUUCUGUAGCUGCCACUUC
...(((((........(((........)))...))))).........((((((.((......(((.((((((((....))))))))..))).....)).))))))...... (-19.64 = -19.68 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:45 2006