Locus 2000

Sequence ID	3R_DroMel_CAF1
Location	5,676,699 – 5,676,804
Length	105
Max. P	0.906011

overview

Window 4

Location	5,676,699 – 5,676,804
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.65
Mean single sequence MFE	-27.85
Consensus MFE	-19.67
Energy contribution	-19.45
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-2.11
Structure conservation index	0.71
SVM decision value	0.93
SVM RNA-class probability	0.883865
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5676699 105 + 27905053
GGC---------------ACAUACGAAUAAAUCGAGAAUAUUGCGCAUAAAUGUAUUUAAAAUUACGCAUUGCUCAUACGCAGCGUAUGGCAAUAUUUCCGCUUGACGGCGCCUUUUGUG
(((---------------...............(..(((((((((((....((((........))))...))).((((((...))))))))))))))..)(((....))))))....... ( -27.00)
>DroVir_CAF1 19828 105 + 1
AGC---------------GCAAUGAUAUAAAUCGACAAUAUUGCGCAUAAAUGUGUUUAAAAUUACGCAUUGCUCAUACGCAGCGUAUGGCAAUAUUUCCGCUUCAUGGCACAUUAUAUG
.((---------------((((((..............))))))))...((((((((...........(((((.((((((...))))))))))).............))))))))..... ( -26.29)
>DroPse_CAF1 10555 101 + 1
-------------------ACAAUAAAUAAAUCGAGAAUAUUGCGCAUAAAUGUAUUUAAAAUUACGCAUUGCUCAUACGCAACGUAUGGCAAUAUUUCCGCUCGACGGCGUCUUUUGUG
-------------------((((........((((((((((((((((....((((........))))...))).((((((...))))))))))))))....))))).........)))). ( -23.03)
>DroGri_CAF1 30166 103 + 1
AGC---------------GCGAUGAAGUAAAUCGACAAUAUUGCGCACAAAUGUGUUUAAAAUUACGCAUUGCUCAUACGCAGCGUAUGGCAAUAUUUCCGCUUGAUCGCAUUUUUG--U
...---------------(((((.((((.....((.(((((((((((...((((((........))))))))).((((((...)))))))))))))))).)))).))))).......--. ( -32.00)
>DroWil_CAF1 26352 104 + 1
G-A---------------AUCGGCAAAUAAAUCGAGAAUAUUGCGCAUAAAUGUAUUUAAAAUUACGCAUUGCUCAUACGCAGCGUAUGGCAAUAUUUCCGCUUCAUAGGGUUUUAUAUA
(-(---------------(.(((............((((((((((((....((((........))))...))).((((((...)))))))))))))))))).)))............... ( -22.00)
>DroPer_CAF1 6707 120 + 1
GGCCGAAAGGGUGGCUGGAGAGACAAAUAAAUCGAGAAUAUUGCGCAUAAAUGUAUUUAAAAUUACGCAUUGCUCAUACGCAACGUAUGGCAAUAUUUCCGCUCGACGGCGCCUUUUGUG
.....((((((((.(((..(((..........((..(((((((((((....((((........))))...))).((((((...))))))))))))))..)))))..)))))))))))... ( -36.80)
>consensus
GGC_______________ACAAACAAAUAAAUCGAGAAUAUUGCGCAUAAAUGUAUUUAAAAUUACGCAUUGCUCAUACGCAGCGUAUGGCAAUAUUUCCGCUUGACGGCGCCUUUUGUG
................................((..(((((((((((....((((........))))...))).((((((...))))))))))))))..))................... (-19.67 = -19.45 +  -0.22)

alignment

secondary structure

dotplot

Window 5

Location	5,676,699 – 5,676,804
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.65
Mean single sequence MFE	-27.02
Consensus MFE	-20.64
Energy contribution	-20.50
Covariance contribution	-0.14
Combinations/Pair	1.05
Mean z-score	-2.11
Structure conservation index	0.76
SVM decision value	1.04
SVM RNA-class probability	0.906011
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5676699 105 - 27905053
CACAAAAGGCGCCGUCAAGCGGAAAUAUUGCCAUACGCUGCGUAUGAGCAAUGCGUAAUUUUAAAUACAUUUAUGCGCAAUAUUCUCGAUUUAUUCGUAUGU---------------GCC
.......(((((((.....((..((((((((((((((...))))))......((((((............))))))))))))))..)).......))...))---------------))) ( -28.20)
>DroVir_CAF1 19828 105 - 1
CAUAUAAUGUGCCAUGAAGCGGAAAUAUUGCCAUACGCUGCGUAUGAGCAAUGCGUAAUUUUAAACACAUUUAUGCGCAAUAUUGUCGAUUUAUAUCAUUGC---------------GCU
........((((.((((..((..((((((((((((((...))))))......((((((............))))))))))))))..)).......)))).))---------------)). ( -27.40)
>DroPse_CAF1 10555 101 - 1
CACAAAAGACGCCGUCGAGCGGAAAUAUUGCCAUACGUUGCGUAUGAGCAAUGCGUAAUUUUAAAUACAUUUAUGCGCAAUAUUCUCGAUUUAUUUAUUGU-------------------
.((((.(((....((((((....((((((((((((((((((......)))))).(((........)))...)))).))))))))))))))...))).))))------------------- ( -25.20)
>DroGri_CAF1 30166 103 - 1
A--CAAAAAUGCGAUCAAGCGGAAAUAUUGCCAUACGCUGCGUAUGAGCAAUGCGUAAUUUUAAACACAUUUGUGCGCAAUAUUGUCGAUUUACUUCAUCGC---------------GCU
.--.......(((((.(((((..((((((((..((((((((......)))..)))))........(((....))).))))))))..)).....))).)))))---------------... ( -28.20)
>DroWil_CAF1 26352 104 - 1
UAUAUAAAACCCUAUGAAGCGGAAAUAUUGCCAUACGCUGCGUAUGAGCAAUGCGUAAUUUUAAAUACAUUUAUGCGCAAUAUUCUCGAUUUAUUUGCCGAU---------------U-C
.............(((((.((..((((((((((((((...))))))......((((((............))))))))))))))..)).)))))........---------------.-. ( -23.10)
>DroPer_CAF1 6707 120 - 1
CACAAAAGGCGCCGUCGAGCGGAAAUAUUGCCAUACGUUGCGUAUGAGCAAUGCGUAAUUUUAAAUACAUUUAUGCGCAAUAUUCUCGAUUUAUUUGUCUCUCCAGCCACCCUUUCGGCC
......(((((..((((((....((((((((((((((((((......)))))).(((........)))...)))).)))))))))))))).....))))).....(((........))). ( -30.00)
>consensus
CACAAAAGACGCCAUCAAGCGGAAAUAUUGCCAUACGCUGCGUAUGAGCAAUGCGUAAUUUUAAAUACAUUUAUGCGCAAUAUUCUCGAUUUAUUUGUUUGU_______________GCC
...................((..((((((((((((((...))))))......((((((............))))))))))))))..))................................ (-20.64 = -20.50 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:50 2006