Locus 1092

Sequence ID	3R_DroMel_CAF1
Location	3,308,615 – 3,308,735
Length	120
Max. P	0.980078

overview

Window 2

Location	3,308,615 – 3,308,735
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.53
Mean single sequence MFE	-29.50
Consensus MFE	-28.39
Energy contribution	-28.45
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.59
Structure conservation index	0.96
SVM decision value	1.85
SVM RNA-class probability	0.980078
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3308615 120 + 27905053
AAUAUGUAGCAUGCAAACAAGCGCAAACUACAUUGCUCAUUGUCUGCGUCUAAUUUAUGUUGCUGUUGGUCAGCCAGCACCAAUAAAUAAUAGUUCUUUGCUCAAACAAUUUCUGAAGUA
....((.((((((((.(((((.((((......)))).).)))).)))))........(((((.((((((....)))))).)))))..............)))))................ ( -27.30)
>DroSec_CAF1 12879 120 + 1
AAUAUGUAGCAUGCAAACAAGCGCAAACUACAUUGCUCAUUGUCUGCGUCUAAUUUAUGUUGCUGUUGGUCAGCCAGCACCAAUAAAUAAUAGUUCUUUGCUCAGACAAUUUCUGAAAAA
......(((.(((((.(((((.((((......)))).).)))).)))))))).....(((((.((((((....)))))).)))))................(((((.....))))).... ( -30.00)
>DroSim_CAF1 17074 120 + 1
AAUAUGUAGCAUGCAAACAAGCGCAAACUACAUUGCUCAUUGUCUGCGUCUAAUUUAUGUUGCUGUUGGUCAGCCAGCACCAAUAAAUAAUAGUUCUUUGCUCAGACAAUUUCUGAAAAA
......(((.(((((.(((((.((((......)))).).)))).)))))))).....(((((.((((((....)))))).)))))................(((((.....))))).... ( -30.00)
>DroYak_CAF1 23158 120 + 1
UAUAUGUAGCAUGCAAACAAGCGCAAACUACAUUGCUCAUUGUCUGCGUCUAAUUUAUGUUGCUGUUGGUCAGCCAGCACUAAUAAAUAUAAGUUCUUUGCUCAGACAAGUUCUGAAAUA
...((((((..(((........)))..))))))......(((((((.((..((((((((((..((((((....))))))......))))))))))....)).)))))))........... ( -30.70)
>consensus
AAUAUGUAGCAUGCAAACAAGCGCAAACUACAUUGCUCAUUGUCUGCGUCUAAUUUAUGUUGCUGUUGGUCAGCCAGCACCAAUAAAUAAUAGUUCUUUGCUCAGACAAUUUCUGAAAAA
......(((.(((((.(((((.((((......)))).).)))).)))))))).....(((((.((((((....)))))).)))))................(((((.....))))).... (-28.39 = -28.45 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	3,308,615 – 3,308,735
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.53
Mean single sequence MFE	-31.12
Consensus MFE	-30.76
Energy contribution	-30.82
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.24
Structure conservation index	0.99
SVM decision value	1.60
SVM RNA-class probability	0.966947
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3308615 120 - 27905053
UACUUCAGAAAUUGUUUGAGCAAAGAACUAUUAUUUAUUGGUGCUGGCUGACCAACAGCAACAUAAAUUAGACGCAGACAAUGAGCAAUGUAGUUUGCGCUUGUUUGCAUGCUACAUAUU
................((((((.....(((..((((((...(((((.........)))))..)))))))))..((((((((.(.((((......)))).))))))))).)))).)).... ( -29.30)
>DroSec_CAF1 12879 120 - 1
UUUUUCAGAAAUUGUCUGAGCAAAGAACUAUUAUUUAUUGGUGCUGGCUGACCAACAGCAACAUAAAUUAGACGCAGACAAUGAGCAAUGUAGUUUGCGCUUGUUUGCAUGCUACAUAUU
....(((((.....)))))(((.....(((..((((((...(((((.........)))))..)))))))))..((((((((.(.((((......)))).))))))))).)))........ ( -31.80)
>DroSim_CAF1 17074 120 - 1
UUUUUCAGAAAUUGUCUGAGCAAAGAACUAUUAUUUAUUGGUGCUGGCUGACCAACAGCAACAUAAAUUAGACGCAGACAAUGAGCAAUGUAGUUUGCGCUUGUUUGCAUGCUACAUAUU
....(((((.....)))))(((.....(((..((((((...(((((.........)))))..)))))))))..((((((((.(.((((......)))).))))))))).)))........ ( -31.80)
>DroYak_CAF1 23158 120 - 1
UAUUUCAGAACUUGUCUGAGCAAAGAACUUAUAUUUAUUAGUGCUGGCUGACCAACAGCAACAUAAAUUAGACGCAGACAAUGAGCAAUGUAGUUUGCGCUUGUUUGCAUGCUACAUAUA
....(((((.....)))))(((.....((...((((((...(((((.........)))))..)))))).))..((((((((.(.((((......)))).))))))))).)))........ ( -31.60)
>consensus
UAUUUCAGAAAUUGUCUGAGCAAAGAACUAUUAUUUAUUGGUGCUGGCUGACCAACAGCAACAUAAAUUAGACGCAGACAAUGAGCAAUGUAGUUUGCGCUUGUUUGCAUGCUACAUAUU
....(((((.....)))))(((.....(((..((((((...(((((.........)))))..)))))))))..((((((((.(.((((......)))).))))))))).)))........ (-30.76 = -30.82 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:37 2006