Locus 308

Sequence ID	3R_DroMel_CAF1
Location	1,188,789 – 1,188,945
Length	156
Max. P	0.644650

overview

Window 0

Location	1,188,789 – 1,188,905
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.18
Mean single sequence MFE	-23.42
Consensus MFE	-17.56
Energy contribution	-17.38
Covariance contribution	-0.19
Combinations/Pair	1.21
Mean z-score	-1.41
Structure conservation index	0.75
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1188789 116 + 27905053
AGUUAUAAAAUACUUCUUAAAGU----ACUCAACAACUGCAGUGUGUAUCAUAGCGCACUUAGCCAGAACCAAACUGGUUCUGAACUCAAUUCACGUUCCGAUCGUAAACUUUACGGCAC
.((..((((.(((((....))))----)...(((..(((.(((((((......)))))))))).(((((((.....)))))))............)))............))))..)).. ( -25.40)
>DroSec_CAF1 4776 116 + 1
AGUUAUAAAAUACUUCUUAAAGU----ACUCAACAACUGCAGUGUGAAUCAUGGCGCACUCAGCCAGAACCAAACUGGUUCUGAACUCAAUUCACGUUCCGAUCGUAAACUUUACGGCAC
.((..((((.(((((....))))----)...(((..(((.((((((........))))))))).(((((((.....)))))))............)))............))))..)).. ( -25.70)
>DroSim_CAF1 3717 116 + 1
GGUUAUAAAAUACUUCUUAAAGU----ACUCAACAACUGCAGUGUGAAUCAUGGCGCACUUGGCCAGAACCAAACUGGUUCUGAACUCAAUUCACGUUCCGAUCGUAAACUUUACGGCAC
((((......(((((....))))----)......))))((...((((((...(((.......)))((((((.....)))))).......))))))........((((.....)))))).. ( -24.00)
>DroEre_CAF1 3599 109 + 1
AGCUAUAAAAUACUACUUAAAGUAUGUACUUAAAAGUUCCAGUGUGAAUCAUAGCACACUUAGUCAGAACCAAACAGGUUCCGAUUUAUAUUCCUGUUCCGAUCGUAAA-----------
.(((((...(((((((((.((((....))))..))))...))))).....)))))......((((.(((((.....))))).)))).......................----------- ( -18.60)
>consensus
AGUUAUAAAAUACUUCUUAAAGU____ACUCAACAACUGCAGUGUGAAUCAUAGCGCACUUAGCCAGAACCAAACUGGUUCUGAACUCAAUUCACGUUCCGAUCGUAAACUUUACGGCAC
..........(((.......................(((.((((((........))))))))).(((((((.....))))))).....................)))............. (-17.56 = -17.38 +  -0.19)

alignment

secondary structure

dotplot

Window 1

Location	1,188,825 – 1,188,945
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.83
Mean single sequence MFE	-26.43
Consensus MFE	-18.20
Energy contribution	-17.83
Covariance contribution	-0.37
Combinations/Pair	1.08
Mean z-score	-1.68
Structure conservation index	0.69
SVM decision value	0.23
SVM RNA-class probability	0.644650
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1188825 120 + 27905053
AGUGUGUAUCAUAGCGCACUUAGCCAGAACCAAACUGGUUCUGAACUCAAUUCACGUUCCGAUCGUAAACUUUACGGCACCUCAUUUACUAACAAUGUACAAUUGCUUUGAACUUGGCCA
(((((((......)))))))..(((((((((.....)))))).............((((.(.(((((.....))))))..............((((.....))))....))))..))).. ( -26.70)
>DroSec_CAF1 4812 120 + 1
AGUGUGAAUCAUGGCGCACUCAGCCAGAACCAAACUGGUUCUGAACUCAAUUCACGUUCCGAUCGUAAACUUUACGGCACCUCAUUUACUAACAAUGAACAAUUGCUUUGAACUUGGCCA
...((((((...(((.......)))((((((.....)))))).......))))))((((....((((.....))))(((..(((((.......))))).....)))...))))....... ( -25.50)
>DroSim_CAF1 3753 120 + 1
AGUGUGAAUCAUGGCGCACUUGGCCAGAACCAAACUGGUUCUGAACUCAAUUCACGUUCCGAUCGUAAACUUUACGGCACCUCAUUUACUAACAAUGAACAAUUGCUUUGAACUUGGCCA
((((((........))))))(((((((((((.....)))))).............((((....((((.....))))(((..(((((.......))))).....)))...))))..))))) ( -29.60)
>DroEre_CAF1 3639 90 + 1
AGUGUGAAUCAUAGCACACUUAGUCAGAACCAAACAGGUUCCGAUUUAUAUUCCUGUUCCGAUCGUAAA------------------------------CGAUUGCUUUGAACUUGGCCA
((((((........)))))).((((.(((((.....))))).))))......((.((((((((((....------------------------------))))))....))))..))... ( -23.90)
>consensus
AGUGUGAAUCAUAGCGCACUUAGCCAGAACCAAACUGGUUCUGAACUCAAUUCACGUUCCGAUCGUAAACUUUACGGCACCUCAUUUACUAACAAUGAACAAUUGCUUUGAACUUGGCCA
((((((........))))))..(((((((((.....)))))..............((((.((..((((..................................)))))).)))).)))).. (-18.20 = -17.83 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:02 2006