Locus 305

Sequence ID	3R_DroMel_CAF1
Location	1,162,690 – 1,162,858
Length	168
Max. P	0.898028

overview

Window 5

Location	1,162,690 – 1,162,795
Length	105
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	95.24
Mean single sequence MFE	-23.75
Consensus MFE	-19.42
Energy contribution	-20.43
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.82
SVM decision value	0.02
SVM RNA-class probability	0.543579
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1162690 105 + 27905053
CGACACAACAACAUCGAUUGCCAGGGAGCUCAAAAUAUGUCUUCAUAAAUGCUCGCCGCUCGAUGGACAGAAAUGCAUUUUAGCCAUCAAAAUAAACGCACUCAA
...............((.(((..((((((......((((....))))...)))).))....(((((..((((.....))))..))))).........))).)).. ( -21.50)
>DroSec_CAF1 98335 105 + 1
CGACACAACAACAUCGAUUGCCAGGGAGCUCGAAAGAUGUCUUUAUAAAUGCUCGCUGCUCGAUGGACAGAAAUGCAUUUUAGCCAUCAAAAUAAACGCACUCAA
...............((.((((((.((((...((((....))))......)))).)))...(((((..((((.....))))..))))).........))).)).. ( -24.50)
>DroSim_CAF1 94616 105 + 1
CGACACAACAACAUCGAUUGCCAGGGAGCUCGAAAGAUGUCUUUAUAAAUGCUCGCUGCUCGAUGGACAGAAAUGCAUUUUAGCCAUCAAAAUAAACGCACUCAA
...............((.((((((.((((...((((....))))......)))).)))...(((((..((((.....))))..))))).........))).)).. ( -24.50)
>DroEre_CAF1 96194 105 + 1
CGACACAACAACAUCGAUUGCCAGAGAGCUCGAAAGAUGUCUUUAUAAAUGCUCACUGCUUGAUGGACAGAAAUGCAUUUAAGCCAUCGAUAUAAACGCACUCAA
............((((((.((.(((((..((....))..))))).(((((((...(((((....)).)))....))))))).)).)))))).............. ( -24.50)
>consensus
CGACACAACAACAUCGAUUGCCAGGGAGCUCGAAAGAUGUCUUUAUAAAUGCUCGCUGCUCGAUGGACAGAAAUGCAUUUUAGCCAUCAAAAUAAACGCACUCAA
...............((.((((((.((((...((((....))))......)))).)))...(((((.(.((((....)))).)))))).........))).)).. (-19.42 = -20.43 +   1.00)

alignment

secondary structure

dotplot

Window 6

Location	1,162,766 – 1,162,858
Length	92
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	77.69
Mean single sequence MFE	-17.10
Consensus MFE	-6.96
Energy contribution	-7.08
Covariance contribution	0.12
Combinations/Pair	1.30
Mean z-score	-2.22
Structure conservation index	0.41
SVM decision value	1.00
SVM RNA-class probability	0.898028
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1162766 92 + 27905053
AUUUU-AGCCAUCAA---------AAUAAACGCACUCAAUGCCAUUCCGAAGUGGGAAUGUUCGGAACA-------CCCGACACUUUUCCCCAUUUCCCGCUAACUU-UU
...((-(((......---------.......(((.....)))......((((((((((.((((((....-------.)))).))..)).))))))))..)))))...-.. ( -21.40)
>DroSec_CAF1 98411 92 + 1
AUUUU-AGCCAUCAA---------AAUAAACGCACUCAAUGCCAUUCCGAAAUGGGCAUGUUCGGAAAA-------CCCGACACUUUUCCCCAUUUCCCGCUGACUU-UU
...((-(((......---------.......(((.....)))......((((((((...((((((....-------.)))).)).....))))))))..)))))...-.. ( -21.40)
>DroSim_CAF1 94692 92 + 1
AUUUU-AGCCAUCAA---------AAUAAACGCACUCAAUGCCAUUCCGAAAUGGGCAUGUUCGGAAAA-------CCCGACACUUUUCCCCAUUUCCCGCUGACUU-UU
...((-(((......---------.......(((.....)))......((((((((...((((((....-------.)))).)).....))))))))..)))))...-.. ( -21.40)
>DroEre_CAF1 96270 92 + 1
AUUUA-AGCCAUCGA---------UAUAAACGCACUCAAUGCCAUCCCAAAAUGGGCUUGUUCGAAAAA-------CCCGACGAU-UUCCACAUUCCCCACUCACUUUUU
...((-((((.....---------.......(((.....)))(((......))))))))).(((.....-------..)))....-........................ (  -9.40)
>DroAna_CAF1 92558 110 + 1
AUUUUGAACCAUCAAAUUCCGUAAAAUAAACGCACUCAAUGCCAUUCAAAAUUGUGCAUGUUCAAAAAAAAAUCCUUUCGAUGAUUUCCACCACUUUUCGUUUACAUUGC
.((((((((..........(((.......)))......((((((........)).))))))))))))............(((((.............)))))........ ( -11.92)
>consensus
AUUUU_AGCCAUCAA_________AAUAAACGCACUCAAUGCCAUUCCGAAAUGGGCAUGUUCGGAAAA_______CCCGACACUUUUCCCCAUUUCCCGCUGACUU_UU
......(((......................(((.....)))......((((((((...((((((............)))).))....)).))))))..)))........ ( -6.96 =  -7.08 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:57 2006