Locus 4681

Sequence ID	3R_DroMel_CAF1
Location	12,334,812 – 12,335,000
Length	188
Max. P	0.879664

overview

Window 4

Location	12,334,812 – 12,334,930
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.86
Mean single sequence MFE	-24.17
Consensus MFE	-10.91
Energy contribution	-11.80
Covariance contribution	0.89
Combinations/Pair	1.17
Mean z-score	-1.85
Structure conservation index	0.45
SVM decision value	0.07
SVM RNA-class probability	0.568847
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12334812 118 + 27905053
AACAACGUAAACAGUAAAAUAAACAAUAGCAACAACAAGGCUUGC--CAAUGAAUUGCACUAAUAGUUUGUGUGUAAAAGCUGCCUGUUGUAAAAGCAGGCACAUAAAAAGAAAAUCCCC
......((...................(((........((....)--)......(((((((((....))).))))))..)))(((((((.....)))))))))................. ( -21.80)
>DroPse_CAF1 6318 106 + 1
-------------GGUGGAUACAUAAAAGUACAAAGACGCCUUCCAACAAUGAGUUGCACUAAUAGUUUGUAUGUGGCAGGGGCA-GGGGCAGCAGCAGCCUGGGGGCAAGAAAACGACA
-------------.((.(.(((......))).......((((((.........((..((.(((....)))..))..))..((((.-...((....)).)))))))))).......).)). ( -21.10)
>DroSec_CAF1 3605 118 + 1
AACAACGCAAACAGUAAAAUAAACAAUAGCAACAACAAGGCUUGC--CAAUGAAUUGCACUAAUAGUUUGUGUGUAAAAGCUGCCUGUUGUAAAAGCAGGCACAUAAAAAGAAAAUCCCC
.(((.(((((((.((.......))....((((......((....)--)......)))).......))))))))))....(.((((((((.....)))))))))................. ( -26.40)
>DroSim_CAF1 2817 118 + 1
AACAACGCAAACAGUAAAAUAAACAAUAGCAACAACAAGGCUUGC--CAAUGAAUUGCACUAAUAGUUUGUGUGUAAAAGCUGCCUGUUGUAAAAGCAGGCACAUAAAAAGAAAAUCCCC
.(((.(((((((.((.......))....((((......((....)--)......)))).......))))))))))....(.((((((((.....)))))))))................. ( -26.40)
>DroEre_CAF1 2937 118 + 1
AAGAACACAAACAGUAAAAUAAACAAUAGCAACAACAAGGCUUGC--CAAUGAAUUGCACUAAUAGUUUGUGUGUAAAAGCUGCCUGUUGUAAAAGCAGGCACAUAAAAAGAAAAUCCCC
....((((((((.((.......))....((((......((....)--)......)))).......))))))))......(.((((((((.....)))))))))................. ( -26.30)
>DroPer_CAF1 2036 106 + 1
-------------GUUGGAUACAUAAAAGUACAAAGACGCCUUCCAACAAUGAGUUGCACUAAUAGUUUGUAUGUGGCAGGGGCA-GGGGCAGCAGCAGCCUGGGGGCAAGAAAACGACA
-------------((((..(((......))).......((((((.........((..((.(((....)))..))..))..((((.-...((....)).)))))))))).......)))). ( -23.00)
>consensus
AACAACGCAAACAGUAAAAUAAACAAUAGCAACAACAAGGCUUGC__CAAUGAAUUGCACUAAUAGUUUGUGUGUAAAAGCUGCCUGUUGUAAAAGCAGGCACAUAAAAAGAAAAUCCCC
.......................................((((......(..(((((......)))))..)......))))((((((((.....)))))))).................. (-10.91 = -11.80 +   0.89)

alignment

secondary structure

dotplot

Window 5

Location	12,334,890 – 12,335,000
Length	110
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	99.55
Mean single sequence MFE	-24.62
Consensus MFE	-24.62
Energy contribution	-24.62
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.40
Structure conservation index	1.00
SVM decision value	0.91
SVM RNA-class probability	0.879664
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12334890 110 + 27905053
CUGCCUGUUGUAAAAGCAGGCACAUAAAAAGAAAAUCCCCAAACUGUUUGGAGUAGCAGCAACCGCAUCUACAUGAGAACAAGCUGUAAAAAUUAUAGGGAAAUAGCAAA
.((((((((.....)))))))).............((((...(((......))).(((((.......((.....))......)))))..........))))......... ( -24.62)
>DroSec_CAF1 3683 110 + 1
CUGCCUGUUGUAAAAGCAGGCACAUAAAAAGAAAAUCCCCAAACUGUUUGGAGUAGCAGCAACCGCAUCUACAUGAGAACAAGCUGUAAAAAUUAUAGGGAAAUAGCAAA
.((((((((.....)))))))).............((((...(((......))).(((((.......((.....))......)))))..........))))......... ( -24.62)
>DroSim_CAF1 2895 110 + 1
CUGCCUGUUGUAAAAGCAGGCACAUAAAAAGAAAAUCCCCAAACUGUUUGGAGUAGCAGCAACCGCAUCUACAUGAGAACAAGCUGUAAAAAUUAUAGGGAAAUAGCAAA
.((((((((.....)))))))).............((((...(((......))).(((((.......((.....))......)))))..........))))......... ( -24.62)
>DroEre_CAF1 3015 110 + 1
CUGCCUGUUGUAAAAGCAGGCACAUAAAAAGAAAAUCCCCAAACUGUUUGGAGUAGCAGCAACCGCAUCUACAUGAGAACAAGCUGUAAAAAUUAUAGGGAAAUAGUAAA
.((((((((.....)))))))).............((((...(((......))).(((((.......((.....))......)))))..........))))......... ( -24.62)
>consensus
CUGCCUGUUGUAAAAGCAGGCACAUAAAAAGAAAAUCCCCAAACUGUUUGGAGUAGCAGCAACCGCAUCUACAUGAGAACAAGCUGUAAAAAUUAUAGGGAAAUAGCAAA
.((((((((.....)))))))).............((((...(((......))).(((((.......((.....))......)))))..........))))......... (-24.62 = -24.62 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:17 2006