Locus 2027

Sequence ID	2R_DroMel_CAF1
Location	7,656,973 – 7,657,133
Length	160
Max. P	0.839184

overview

Window 4

Location	7,656,973 – 7,657,093
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.39
Mean single sequence MFE	-34.99
Consensus MFE	-20.38
Energy contribution	-21.66
Covariance contribution	1.28
Combinations/Pair	1.37
Mean z-score	-1.66
Structure conservation index	0.58
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7656973 120 + 20766785
CGUGAUGCGCGCUCUUAUUGACUUCAAGUACAUUGAAAAGAUAUUCCUGAAUGUAACGCUUCGAGAGGACAAGUGCAACAAGCGGAGCGUGGAGUUCCGUAUGCUGGGCAACGAGCAGUU
..((.(((((..((((.((((.(((((.....)))))...(((((....)))))......)))).))))...))))).)).(((((((.....))))))).((((.(....).))))... ( -35.20)
>DroVir_CAF1 117 120 + 1
CGUUGAACAUGCAUUGAUUGACUUCAAGUACAUGGAGAAGAUAUUCCUAAAUGUAACGCUACGCGAGAACAAAUGCAACAAGCGCAGCGUCGAAUUCCGCAUGCUGGGCAACGAGCAGUU
(((((..((.((((.(...((.(((...(((((((((......))))...)))))(((((.(((.................))).))))).))).))..)))))))..)))))....... ( -30.13)
>DroGri_CAF1 117 120 + 1
UGUGGAGCACGCCCUGAUCGACUUCAAAUACAUGGAAAAGAUAUUCUUAACUGUGUCGCUGCGCGAGAAUAAAUGCAAUAAGCGCAGCGUCGAAUUUCGCAUGCUUGGCAACGAGCAAUU
(((((((((.....)).(((((.......((((((..(((.....)))..)))))).(((((((.................)))))))))))).)))))))((((((....))))))... ( -38.93)
>DroWil_CAF1 1363 120 + 1
UGUGGAACAUGCCCUGAUUGACUUUAAAUACAUGGAGAAGAUCUAUUUAAAUGUGGUCAUGCGGGAGGAUAAAUCGAAUAAACGAAGCGUUGAGUUCCGUAUGCUUGGCAAUGAGCAGUU
...(((((((((((((..(((((.....((.(((((.....))))).)).....)))))..))))........(((......))).))))...)))))...(((((......)))))... ( -29.30)
>DroMoj_CAF1 117 120 + 1
CGUGGAGCAUGCAUUGAUUGACUUCAAGUACAUGGAAAAAAUAUUCCUAAAUGUAACGUUGCGCGAAAGUAAAUGCAACAAGCGCAGUGUCGAAUUUCGCAUGCUUGGCAACGAGCAGUU
.((.((((((((.....(((((......(((((((((......))))...)))))..(((((((....))....))))).........))))).....)))))))).))........... ( -34.70)
>DroAna_CAF1 117 120 + 1
UGUGGAGCAUGCGCUAAUUGACUUCAAGUACAUGGAAAAGAUCUUCCUGAACGUAACGCUGCGGGAGGACAAGUGCAAUAAGCGCAGUGUGGAGUUCAGGAUGCUUGGCAACGAGCAAUU
.......((((..((...((....))))..))))..........((((((((...((((((((......)....((.....)))))))))...))))))))((((((....))))))... ( -41.70)
>consensus
CGUGGAGCAUGCACUGAUUGACUUCAAGUACAUGGAAAAGAUAUUCCUAAAUGUAACGCUGCGCGAGAACAAAUGCAACAAGCGCAGCGUCGAAUUCCGCAUGCUUGGCAACGAGCAGUU
.((.((((((((.....(((((......(((((((((......))))...)))))..((((((...................))))))))))).....)))))))).))........... (-20.38 = -21.66 +   1.28)

alignment

secondary structure

dotplot

Window 5

Location	7,657,013 – 7,657,133
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.67
Mean single sequence MFE	-34.82
Consensus MFE	-21.05
Energy contribution	-21.24
Covariance contribution	0.20
Combinations/Pair	1.38
Mean z-score	-2.07
Structure conservation index	0.60
SVM decision value	0.74
SVM RNA-class probability	0.839184
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7657013 120 + 20766785
AUAUUCCUGAAUGUAACGCUUCGAGAGGACAAGUGCAACAAGCGGAGCGUGGAGUUCCGUAUGCUGGGCAACGAGCAGUUUUCGCUCAAGAACAGGAAUUACUUCCAGGUAAUCAUUGCC
..(((((((........(.(((....)))).((((.(((..(((((((.....))))))).((((.(....).)))))))..))))......)))))))........((((.....)))) ( -34.80)
>DroVir_CAF1 157 118 + 1
AUAUUCCUAAAUGUAACGCUACGCGAGAACAAAUGCAACAAGCGCAGCGUCGAAUUCCGCAUGCUGGGCAACGAGCAGUUUUCCCUGAAGAACAGGAAAUACUUUCAGGCAAGUGG--GC
.................(((.(((((((((...(((.....((.((((((((.....)).)))))).)).....)))))))))((((((....((......))))))))...))))--)) ( -30.90)
>DroGri_CAF1 157 118 + 1
AUAUUCUUAACUGUGUCGCUGCGCGAGAAUAAAUGCAAUAAGCGCAGCGUCGAAUUUCGCAUGCUUGGCAACGAGCAAUUCUCGCUAAAAAACAGGAAAUAUUUUCAGGCAAGUAA--CC
..............((..((((((((((((...(((.......)))(((........))).((((((....)))))))))))))).........((((....))))..)).))..)--). ( -32.90)
>DroMoj_CAF1 157 115 + 1
AUAUUCCUAAAUGUAACGUUGCGCGAAAGUAAAUGCAACAAGCGCAGUGUCGAAUUUCGCAUGCUUGGCAACGAGCAGUUCUCCCUAAAGAAUAGAAAAUACUUUCAGGCAAGUA-----
...............((.((((..(((((((..........(((.(((.....))).))).((((((....))))))(((((......)))))......)))))))..)))))).----- ( -28.10)
>DroAna_CAF1 157 117 + 1
AUCUUCCUGAACGUAACGCUGCGGGAGGACAAGUGCAAUAAGCGCAGUGUGGAGUUCAGGAUGCUUGGCAACGAGCAAUUCUCUCUGAAGAACCGAAAAUAUUUUCAGGUAAGAGGA---
....((((((((...((((((((......)....((.....)))))))))...))))))))((((((....)))))).(((((((((((((..........)))))))...))))))--- ( -45.20)
>DroPer_CAF1 157 117 + 1
AUCUUCCUGAACGUGACCCUGCGAGAGGACAAGUGCAACAAGAGGAGUGUCGAAUUCCGCAUGCUUGGAAACGAGCAGUUCUCCCUAAAGAACAGGAAAUACUUUCAGGUGAGUCAA---
.((..((((((.(((..((((...((((((...........(.(((((.....))))).).((((((....)))))))))))).(....)..))))...))).)))))).)).....--- ( -37.00)
>consensus
AUAUUCCUAAAUGUAACGCUGCGCGAGAACAAAUGCAACAAGCGCAGCGUCGAAUUCCGCAUGCUUGGCAACGAGCAGUUCUCCCUAAAGAACAGGAAAUACUUUCAGGCAAGUAA____
.....((((((.(((((((((((...................))))))))....((((...((((((....))))))(((((......))))).)))).)))))).)))........... (-21.05 = -21.24 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:15 2006