Locus 1864

Sequence ID	2R_DroMel_CAF1
Location	6,997,219 – 6,997,314
Length	95
Max. P	0.955502

overview

Window 3

Location	6,997,219 – 6,997,314
Length	95
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	76.51
Mean single sequence MFE	-28.86
Consensus MFE	-13.46
Energy contribution	-13.88
Covariance contribution	0.42
Combinations/Pair	1.27
Mean z-score	-2.52
Structure conservation index	0.47
SVM decision value	1.46
SVM RNA-class probability	0.955502
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6997219 95 + 20766785
AGAAAGCUCUAUUCGUGGA--UAGUGAGUGGUUAGAUAGG----------UGAAAACUAUUAAACGAGCGCACUUUAAACGCUCACUCAAUCACUUUUUGGUGCU-CC
....(((.(((...((((.--...(((((.(((.(((((.----------......))))).)))(((((.........)))))))))).))))....))).)))-.. ( -25.40)
>DroSec_CAF1 25823 92 + 1
AGAAAACUCCAUCCGUGGA--U---GAGUGGUUAGAUAGG----------UGAAAACUAUUAAACGAGCGCACUUUAAGCGCUCACUCAAUCACUUUUCGGUGCU-AC
.(((((.((((....))))--(---((((.(((.(((((.----------......))))).)))((((((.......))))))))))).....)))))......-.. ( -27.50)
>DroSim_CAF1 24053 95 + 1
AGAAAGCUCUAUCCGUGGA--UAGUGAGUGGUUAGAUAGG----------UGAAAACUAUUAAACGAGCGCACUUUAAGCGCUCACUCAAUCACUUUUUGGUGCU-AC
....(((.(((...((((.--...(((((.(((.(((((.----------......))))).)))((((((.......))))))))))).))))....))).)))-.. ( -30.30)
>DroEre_CAF1 28305 94 + 1
AGAAAGCUCUAUCCGCGGA--UAGUGAGUGCUUAGAUGGC----------UAAAACC-AUUAAACCAGCGCACUUUAAGCGCUCACUCAAUCACUUUCUGGUGCU-AC
....(((.(((......((--(((((((((((((((((((----------(......-........))).)).))))))))))))))..)))......))).)))-.. ( -29.04)
>DroYak_CAF1 26266 95 + 1
AGAAAGCUCUAUCCGUGGA--UAGUGAGUGGUUAGAUGGG----------UAAGACCUAUUAAACGAGCGCACUUUAAGCGCUCACUCAAUCACUUGCCGGUGCU-GC
....(((.(((((....))--).(..(((((((.((((((----------.....))))))....((((((.......))))))....)))))))..).)).)))-.. ( -33.40)
>DroAna_CAF1 28559 108 + 1
GGAAAGUUCUUGCCACUCACCUGGCGAGAGAUAUGAAGGUAGAAAAAAUAAGGAAACUAUUAAAUCAAUGGGCUUUAAGUGCACUCUCUAGCACUUUCUAUUGGAGGA
......(((((((((......))))))))).......((((((((...(((((...(((((.....))))).))))).((((........))))))))))))...... ( -27.50)
>consensus
AGAAAGCUCUAUCCGUGGA__UAGUGAGUGGUUAGAUAGG__________UGAAAACUAUUAAACGAGCGCACUUUAAGCGCUCACUCAAUCACUUUCUGGUGCU_AC
.........................((((((((.(((((.................))))).))).(((((.......))))))))))...((((....))))..... (-13.46 = -13.88 +   0.42)

alignment

secondary structure

dotplot

Window 4

Location	6,997,219 – 6,997,314
Length	95
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	76.51
Mean single sequence MFE	-26.00
Consensus MFE	-11.81
Energy contribution	-12.98
Covariance contribution	1.17
Combinations/Pair	1.29
Mean z-score	-1.96
Structure conservation index	0.45
SVM decision value	0.08
SVM RNA-class probability	0.572586
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6997219 95 - 20766785
GG-AGCACCAAAAAGUGAUUGAGUGAGCGUUUAAAGUGCGCUCGUUUAAUAGUUUUCA----------CCUAUCUAACCACUCACUA--UCCACGAAUAGAGCUUUCU
((-(((.............(((((((((((.......))))))(((..((((......----------.))))..))).)))))(((--(......)))).))))).. ( -21.70)
>DroSec_CAF1 25823 92 - 1
GU-AGCACCGAAAAGUGAUUGAGUGAGCGCUUAAAGUGCGCUCGUUUAAUAGUUUUCA----------CCUAUCUAACCACUC---A--UCCACGGAUGGAGUUUUCU
..-(((.(((....(((..(((((((((((.......))))))(((..((((......----------.))))..))).))))---)--..)))...))).))).... ( -27.00)
>DroSim_CAF1 24053 95 - 1
GU-AGCACCAAAAAGUGAUUGAGUGAGCGCUUAAAGUGCGCUCGUUUAAUAGUUUUCA----------CCUAUCUAACCACUCACUA--UCCACGGAUAGAGCUUUCU
..-(((.............(((((((((((.......))))))(((..((((......----------.))))..))).)))))(((--((....))))).))).... ( -27.10)
>DroEre_CAF1 28305 94 - 1
GU-AGCACCAGAAAGUGAUUGAGUGAGCGCUUAAAGUGCGCUGGUUUAAU-GGUUUUA----------GCCAUCUAAGCACUCACUA--UCCGCGGAUAGAGCUUUCU
..-......(((((((...(((((.(((((.......))))).(((((((-(((....----------))))).))))))))))(((--((....))))).))))))) ( -33.40)
>DroYak_CAF1 26266 95 - 1
GC-AGCACCGGCAAGUGAUUGAGUGAGCGCUUAAAGUGCGCUCGUUUAAUAGGUCUUA----------CCCAUCUAACCACUCACUA--UCCACGGAUAGAGCUUUCU
..-......(((.(((((((((((((((((.......))))))))))))).((.....----------.)).......))))..(((--((....))))).))).... ( -27.80)
>DroAna_CAF1 28559 108 - 1
UCCUCCAAUAGAAAGUGCUAGAGAGUGCACUUAAAGCCCAUUGAUUUAAUAGUUUCCUUAUUUUUUCUACCUUCAUAUCUCUCGCCAGGUGAGUGGCAAGAACUUUCC
..........((((((.((.(((((.((.......)).....((...(((((.....)))))...))...........)))))((((......)))).)).)))))). ( -19.00)
>consensus
GU_AGCACCAAAAAGUGAUUGAGUGAGCGCUUAAAGUGCGCUCGUUUAAUAGUUUUCA__________CCCAUCUAACCACUCACUA__UCCACGGAUAGAGCUUUCU
...........(((((.(((((((((((((.......)))))))))))))......................((((.((...............)).))))))))).. (-11.81 = -12.98 +   1.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:05 2006