Locus 6210

Sequence ID	3R_DroMel_CAF1
Location	16,199,105 – 16,199,265
Length	160
Max. P	0.962627

overview

Window 1

Location	16,199,105 – 16,199,225
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.36
Mean single sequence MFE	-24.61
Consensus MFE	-20.00
Energy contribution	-20.13
Covariance contribution	0.13
Combinations/Pair	1.06
Mean z-score	-2.64
Structure conservation index	0.81
SVM decision value	1.29
SVM RNA-class probability	0.940577
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16199105 120 + 27905053
UUGCAUAUGUUCGCUUAGUUUCAGUCUGGCUCUUUUUCAUGCCCCUCUUCGCACUCAUCGGACCUAUACAUUAUGAUUUAUUUUAAUCAUGAUGCUAAAUGAUUUUUUCUGGGAUCAUCU
....(((.(((((...(((...((...(((..........)))...))....)))...))))).))).((((((((((......))))))))))....((((((((....)))))))).. ( -23.20)
>DroSec_CAF1 28304 119 + 1
UUGCAUAUGUUCGCUUAGUUUCACUCUGGCUCUUUUUCAUGCCCCUCUUCGCACUCAUCGGACCUAUACAUUAUGAUUUAUUUUAAUCAUGAUGCUAAAUGAUUUUUUUU-GGAUCAUCU
....(((.(((((...(((........(((..........))).........)))...))))).))).((((((((((......))))))))))....(((((((.....-))))))).. ( -21.73)
>DroEre_CAF1 28516 120 + 1
UUGCAUAUGUUCGCUUAGUUUCACUCUGGCCCUUUUCCAGACCCCUCUGCUUACUCAUCGGGCCUAUACAUUAUGAUUUAUUUUAAUCAUGAUGCUAAAUGAUUUUUUCUGGGAUCAUCU
..((........))((((.........(((((.....((((....))))..........)))))....((((((((((......))))))))))))))((((((((....)))))))).. ( -25.16)
>DroYak_CAF1 30714 119 + 1
UUGCAUAUGUUCGCUUAGUUUUACUCUGGUCCUCUUCCAGGCCCC-CUACUCACUCAUCGGGCCUAUACAUUAUGAUUUAUUUUAAUCAUGAUGCUAAAUGAUUUUUUCAGGGAUCAUCU
..((........))............(((((((.....((((((.-.............))))))...((((((((((......)))))))))).....(((.....))))))))))... ( -28.34)
>consensus
UUGCAUAUGUUCGCUUAGUUUCACUCUGGCCCUUUUCCAGGCCCCUCUUCGCACUCAUCGGACCUAUACAUUAUGAUUUAUUUUAAUCAUGAUGCUAAAUGAUUUUUUCUGGGAUCAUCU
....(((.(((((...(((........(((..........))).........)))...))))).))).((((((((((......))))))))))....((((((((....)))))))).. (-20.00 = -20.13 +   0.13)

alignment

secondary structure

dotplot

Window 2

Location	16,199,145 – 16,199,265
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.86
Mean single sequence MFE	-23.71
Consensus MFE	-20.86
Energy contribution	-20.93
Covariance contribution	0.06
Combinations/Pair	1.06
Mean z-score	-3.92
Structure conservation index	0.88
SVM decision value	1.54
SVM RNA-class probability	0.962627
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16199145 120 + 27905053
GCCCCUCUUCGCACUCAUCGGACCUAUACAUUAUGAUUUAUUUUAAUCAUGAUGCUAAAUGAUUUUUUCUGGGAUCAUCUUUCACUUUUAUGACCUCUGACAAAAUUAUUUUCCUGCUUA
..........(((......(((......((((((((((......))))))))))..((((((((((.((.(((.((((...........)))).))).)).))))))))))))))))... ( -23.40)
>DroSec_CAF1 28344 119 + 1
GCCCCUCUUCGCACUCAUCGGACCUAUACAUUAUGAUUUAUUUUAAUCAUGAUGCUAAAUGAUUUUUUUU-GGAUCAUCUUUCACUUUUAUGACCUCUGACAAAAUUAUAUUCCUGCUUA
..........(((......(((......((((((((((......))))))))))....((((((((.((.-((.((((...........))))))...)).))))))))..))))))... ( -18.80)
>DroEre_CAF1 28556 120 + 1
ACCCCUCUGCUUACUCAUCGGGCCUAUACAUUAUGAUUUAUUUUAAUCAUGAUGCUAAAUGAUUUUUUCUGGGAUCAUCUUUCACUUUUAUGACCUCUGACAAAAUUAUUUUCCUGCUUA
..................((((......((((((((((......))))))))))..((((((((((.((.(((.((((...........)))).))).)).)))))))))).)))).... ( -23.20)
>DroYak_CAF1 30754 119 + 1
GCCCC-CUACUCACUCAUCGGGCCUAUACAUUAUGAUUUAUUUUAAUCAUGAUGCUAAAUGAUUUUUUCAGGGAUCAUCUUUCACUUUUAUGACCUCUGACAAAAUUAUUUUCCUUCUUA
((((.-.............)))).....((((((((((......))))))))))..((((((((((.((((((.((((...........)))).)))))).))))))))))......... ( -29.44)
>consensus
GCCCCUCUUCGCACUCAUCGGACCUAUACAUUAUGAUUUAUUUUAAUCAUGAUGCUAAAUGAUUUUUUCUGGGAUCAUCUUUCACUUUUAUGACCUCUGACAAAAUUAUUUUCCUGCUUA
...................(((......((((((((((......))))))))))..((((((((((.((.(((.((((...........)))).))).)).)))))))))))))...... (-20.86 = -20.93 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:42 2006