Locus 6007

Sequence ID	2R_DroMel_CAF1
Location	18,866,636 – 18,866,776
Length	140
Max. P	0.521576

overview

Window 5

Location	18,866,636 – 18,866,746
Length	110
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	79.32
Mean single sequence MFE	-33.60
Consensus MFE	-19.43
Energy contribution	-20.20
Covariance contribution	0.77
Combinations/Pair	1.26
Mean z-score	-1.61
Structure conservation index	0.58
SVM decision value	-0.02
SVM RNA-class probability	0.521576
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18866636 110 - 20766785
GCCUAACCAUAGUUAAGCUAGUGGAGUUCAAAGCUCCUGGUUG--GGCUCACUUCUUGGGAGCCUCUGGUGCCUUAGGCUCCGUCUUGGUCUUCAGGUUCUUCAGUUGCUCC
((((((((((((.....)))..(((((.....)))))))))))--)))..........(((((..((((.((((.(((((.......)))))..))))...))))..))))) ( -43.20)
>DroSec_CAF1 209 110 - 1
GCCUAACUAUAGUUAAGCUAGUGGAGAUCCAAGCUCCUGGUUG--GGCUCACUUCUUGGGAGCCUCUGGUGCCUUAGGCUCCGUCUUGGUCUUCAGGUUCUUCAGCUGCUCC
((((((((((((.....)))..((((.......))))))))))--)))..........(((((..((((.((((.(((((.......)))))..))))...))))..))))) ( -37.80)
>DroSim_CAF1 209 110 - 1
GCCUAACUAUAGUUAAGCUAGUGGAGAUCCAAGCUCCUGGUUG--GGCUCACUUCUUGGGAGCCUCUGGUGCCUUAGGCUCCGUCUUGGUCUUCAGGUUCUUCAGCUGCUCC
((((((((((((.....)))..((((.......))))))))))--)))..........(((((..((((.((((.(((((.......)))))..))))...))))..))))) ( -37.80)
>DroEre_CAF1 671 104 - 1
------UAAUAGUUAAGCUACUGGAGUUCCAGACUCCUAGUUG--GGCUCACUUCUUGGGAGCCUCUGGUGCCUUGGGUUCCGUCUUGGCCUUCAGGUUCUUCAGCUGCUCC
------.........(((..((((((..((((((((((((..(--(.....))..)))))))..))))).((((.(((((.......)))))..)))).))))))..))).. ( -33.40)
>DroYak_CAF1 213 110 - 1
GUCAUGUAACAGUUAAGCUAGUGGAGUUCCACACUCCUAGUUG--GGCUUACUUCUUGGGAGCCUCUGGUGCCUUGGGUUCCGUUUUCGUCUUCAGGUUCUUCAGCUGCUCC
.....(((..(((..(((((..(((((.....)))))))))).--.))))))......(((((..((((.((((..((...((....)).))..))))...))))..))))) ( -30.80)
>DroAna_CAF1 11335 91 - 1
---------UUUUUAAGGUAUUCAA------------UAGGUGACAGAUCACUUCUUUUUAGUCUCAGGUGCCUUAGUGUCUGUCUUGGUCUUGAGAUUCUUCAGUUGUUCC
---------.......((....(((------------(((((((....))))))......(((((((((.(((..((.......)).)))))))))))).....))))..)) ( -18.60)
>consensus
GCCUAACAAUAGUUAAGCUAGUGGAGUUCCAAGCUCCUAGUUG__GGCUCACUUCUUGGGAGCCUCUGGUGCCUUAGGCUCCGUCUUGGUCUUCAGGUUCUUCAGCUGCUCC
..........((((.(((((..((((.......)))))))))...)))).........(((((..((((.((((.(((((.......)))))..))))...))))..))))) (-19.43 = -20.20 +   0.77)

alignment

secondary structure

dotplot

Window 6

Location	18,866,676 – 18,866,776
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	86.10
Mean single sequence MFE	-25.84
Consensus MFE	-19.26
Energy contribution	-19.06
Covariance contribution	-0.20
Combinations/Pair	1.10
Mean z-score	-1.52
Structure conservation index	0.75
SVM decision value	-0.05
SVM RNA-class probability	0.509563
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18866676 100 - 20766785
AUUCCCAUUAAAUACAAUUCAGACAAUCCAGCCUAACCAUAGUUAAGCUAGUGGAGUUCAAAGCUCCUGGUUGGGCUCACUUCUUGGGAGCCUCUGGUGC
..................(((((...((((((((((((((((.....)))..(((((.....)))))))))))))))..(.....))))...)))))... ( -30.10)
>DroSec_CAF1 249 100 - 1
AUUCAUAUUAAAUACAAUUCAGACAAUCCAGCCUAACUAUAGUUAAGCUAGUGGAGAUCCAAGCUCCUGGUUGGGCUCACUUCUUGGGAGCCUCUGGUGC
..................((((((((((.(((.((((....)))).)))...((((.......)))).)))))(((((.((....))))))))))))... ( -26.80)
>DroSim_CAF1 249 100 - 1
AUUCGUAUUAAAUACAAUUCAGACAAUCCAGCCUAACUAUAGUUAAGCUAGUGGAGAUCCAAGCUCCUGGUUGGGCUCACUUCUUGGGAGCCUCUGGUGC
....((((...))))...((((((((((.(((.((((....)))).)))...((((.......)))).)))))(((((.((....))))))))))))... ( -27.20)
>DroEre_CAF1 711 86 - 1
AUUCCCAUUAAAUACAAUUCAG--------------UAAUAGUUAAGCUACUGGAGUUCCAGACUCCUAGUUGGGCUCACUUCUUGGGAGCCUCUGGUGC
.................(((((--------------((..........)))))))((.((((((((((((..((.....))..)))))))..))))).)) ( -22.10)
>DroYak_CAF1 253 100 - 1
AUUCCCAUUAAAUACAAUUCAGACAAUGCAGUCAUGUAACAGUUAAGCUAGUGGAGUUCCACACUCCUAGUUGGGCUUACUUCUUGGGAGCCUCUGGUGC
..(((((..............(((......)))..(((..(((..(((((..(((((.....))))))))))..))))))....)))))(((...))).. ( -23.00)
>consensus
AUUCCCAUUAAAUACAAUUCAGACAAUCCAGCCUAACAAUAGUUAAGCUAGUGGAGUUCCAAGCUCCUGGUUGGGCUCACUUCUUGGGAGCCUCUGGUGC
..................(((((......................(((((..((((.......))))))))).(((((.((....))))))))))))... (-19.26 = -19.06 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:17 2006