Locus 3720

Sequence ID	3R_DroMel_CAF1
Location	10,102,499 – 10,102,641
Length	142
Max. P	0.578435

overview

Window 1

Location	10,102,499 – 10,102,601
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	93.73
Mean single sequence MFE	-34.73
Consensus MFE	-29.61
Energy contribution	-30.25
Covariance contribution	0.64
Combinations/Pair	1.12
Mean z-score	-1.21
Structure conservation index	0.85
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10102499 102 - 27905053
AGCGUCGACUUCUGUAACUUCCUCUGGACGGUCGUCUGGCUCCUCUCCAGAUGGCAAUUCCGGAGCGUCUUCCGAUGGAGCAUCUUCCGGAAUAUCAUGCGG
.((((.((.............(((((((..(((((((((.......)))))))))...)))))))....(((((..((.....))..)))))..)))))).. ( -35.10)
>DroSec_CAF1 11832 102 - 1
AGCGUCGACUUCUGGAACAUCCUCAGGACGGUCGUCUGGCUCCUCUCCAGAAGGAAAUUCCGGAGCCUCUUCCGAUGGAGCAUCUUCCGGAAUAUCCUGCGG
.((..((((((((((.......)))))..)))))(((((.......)))))((((.(((((((((.((((......))))....))))))))).)))))).. ( -35.80)
>DroSim_CAF1 8030 102 - 1
AACGUCGACUUCUGGAACAUCCUCAGGACGGUCGUCUGGCUCCUCUCCAGAAGGAAAUUCCGGAGCAUCUUCCGAUGGGGCAUCUUCCGGAAUAUCCUGCGG
..(((((((((((((.......)))))..)))))(((((.......)))))((((.(((((((((.((((((....)))).)).))))))))).))))))). ( -34.60)
>DroEre_CAF1 11912 102 - 1
AGCGUCGAUUUCUGGAACAUCCUCAGGACGAUCGUCUGGCUCCUCUCCAGAAGGUAAUUCCGGGGCAUCUUCCGAUGGAGCAUCUUCCGGAAUAUCUUGCGG
.(((..(((((((((((........((((....)))).(((((.((((.(((.....))).)))).(((....))))))))...)))))))).))).))).. ( -32.40)
>DroYak_CAF1 11923 102 - 1
AGCGUCGAAUUCUGGAUCAUCCUCAGGACGGUCGUCUGGCUCCUCUCCAGAAGGAAAUUCCGGAGCAUCUUCCGAUGGAGCAUCUUCCGGAAUAUCCUGCGG
.((.......((((((.........((((....))))........))))))((((.(((((((((.((.((((...)))).)).))))))))).)))))).. ( -35.73)
>consensus
AGCGUCGACUUCUGGAACAUCCUCAGGACGGUCGUCUGGCUCCUCUCCAGAAGGAAAUUCCGGAGCAUCUUCCGAUGGAGCAUCUUCCGGAAUAUCCUGCGG
..(((.....((((((.........((((....))))........))))))((((.(((((((((.((.((((...)))).)).))))))))).))))))). (-29.61 = -30.25 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	10,102,521 – 10,102,641
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.42
Mean single sequence MFE	-41.26
Consensus MFE	-36.44
Energy contribution	-37.08
Covariance contribution	0.64
Combinations/Pair	1.08
Mean z-score	-1.18
Structure conservation index	0.88
SVM decision value	0.09
SVM RNA-class probability	0.578435
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10102521 120 + 27905053
CUCCAUCGGAAGACGCUCCGGAAUUGCCAUCUGGAGAGGAGCCAGACGACCGUCCAGAGGAAGUUACAGAAGUCGACGCUGAGAAAGUUCUGGAGGACUUGCUCAAGGCUUUUCCAGAAG
.....(((((......)))))........((((((((..((((.(((....)))..(((.(((((.(((((.((........))...)))))...))))).)))..)))))))))))).. ( -40.60)
>DroSec_CAF1 11854 120 + 1
CUCCAUCGGAAGAGGCUCCGGAAUUUCCUUCUGGAGAGGAGCCAGACGACCGUCCUGAGGAUGUUCCAGAAGUCGACGCUGAGAAAGUUCUGGAGGACUUGCUCAAGGCUUUUCCAGAAG
.....(((((......)))))......((((((((((..((((...(((((((((...)))))........))))....((((.((((((....)))))).)))).)))))))))))))) ( -41.80)
>DroSim_CAF1 8052 120 + 1
CCCCAUCGGAAGAUGCUCCGGAAUUUCCUUCUGGAGAGGAGCCAGACGACCGUCCUGAGGAUGUUCCAGAAGUCGACGUUGAGAAAGUUCUGGAGGACUUGCUCAAGGUUUUUCCAGAAG
.((((((....))))....))......((((((((((((((((((((....)).))).....))))).......(((.(((((.((((((....)))))).))))).))))))))))))) ( -42.70)
>DroEre_CAF1 11934 120 + 1
CUCCAUCGGAAGAUGCCCCGGAAUUACCUUCUGGAGAGGAGCCAGACGAUCGUCCUGAGGAUGUUCCAGAAAUCGACGCUGAGAAAGUUCUGGGGGACUUGCCCAAGGCUUUUCCAGAAG
...((((....))))............((((((((((..((((.......(((((...)))))..((((((.((........))...))))))(((.....)))..)))))))))))))) ( -41.00)
>DroYak_CAF1 11945 120 + 1
CUCCAUCGGAAGAUGCUCCGGAAUUUCCUUCUGGAGAGGAGCCAGACGACCGUCCUGAGGAUGAUCCAGAAUUCGACGCUGAGAAAGUUCUGGGAGACUUGCUCGAGGCUUUUCCAGAAG
...((((....))))............((((((((((..((((.......(((((...)))))..(((((((((........))..)))))))(((.....)))..)))))))))))))) ( -40.20)
>consensus
CUCCAUCGGAAGAUGCUCCGGAAUUUCCUUCUGGAGAGGAGCCAGACGACCGUCCUGAGGAUGUUCCAGAAGUCGACGCUGAGAAAGUUCUGGAGGACUUGCUCAAGGCUUUUCCAGAAG
.....(((((......)))))......((((((((((..((((...(((((((((...)))))........))))....((((.((((((....)))))).)))).)))))))))))))) (-36.44 = -37.08 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:22 2006