Locus 3967

Sequence ID	3R_DroMel_CAF1
Location	10,728,289 – 10,728,390
Length	101
Max. P	0.983796

overview

Window 3

Location	10,728,289 – 10,728,390
Length	101
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	78.43
Mean single sequence MFE	-33.85
Consensus MFE	-24.23
Energy contribution	-23.82
Covariance contribution	-0.41
Combinations/Pair	1.20
Mean z-score	-3.63
Structure conservation index	0.72
SVM decision value	1.95
SVM RNA-class probability	0.983796
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10728289 101 + 27905053
GA---AAUAAACAAAUCACGGUCGUUUUCACACCGUGCACACUCCACAGUCGAUUGAG---UGAUGCUGGUGACUGC--GAGCGUGCGAGGCGUGAAAACCAACUGCCA
..---.............((((.((((((((.((.(((((.(((..((((((....((---.....))..)))))).--))).))))).)).))))))))..))))... ( -35.20)
>DroPse_CAF1 3907 106 + 1
UA---CAUAAACAAAUCUUUGUCAUUUUUACACCAUGCACACUCAGCAAUCAAUUGAAAUUGGAUGCUGAUAAUUGCGCGAGUAGGCGUGGCGUAAAAAUAAACAUCUA
..---..............(((.((((((((.((((((....((((((.(((((....))))).))))))...((((....)))))))))).))))))))..))).... ( -32.80)
>DroEre_CAF1 4192 101 + 1
GA---AAUAAACAAAUCGCCGCCGUUUUCACACCAUGCACACUCCACAGUCGAUUGAG---UGAUGCUGGUGACUGC--AAGUGUGCGAGGCGUGAAAACCAACUGCCA
..---............((.(..((((((((.((.((((((((...((.((....)).---)).(((.(....).))--))))))))).)).))))))))...).)).. ( -34.30)
>DroYak_CAF1 3885 101 + 1
UA---AAUAAACAAAUCGCCGUCGUUUUCACACCGUGCACACUCCACAGUCGAUUGAG---UGAUGCUGGUGACUGC--AAGUGUGCGAGGCGUGAAAACCAACUGCCA
..---............((.((.((((((((.((.((((((((...((.((....)).---)).(((.(....).))--))))))))).)).))))))))..)).)).. ( -35.80)
>DroAna_CAF1 4859 106 + 1
AUUAUAAAAAACAAAACUCAGUCGUUUUCACAUCGGGCACACUCUGCAAUCGAUUGAG---UGAUGCUGGUGAUUGCUAAAGUGUGCGAGGCGUGAAAACUAACAGCUU
.......................((((((((..(..(((((((..(((((((....((---.....))..)))))))...)))))))..)..))))))))......... ( -32.20)
>DroPer_CAF1 3931 106 + 1
UA---CAUAAACAAAUCUUUGUCAUUUUUACACCAUGCACACUCAGCAAUCAAUUGAAAUUGGAUGCUGAUAAUUGCGCGAGUAGGCGUGGCGUAAAAAUAAACAUCUA
..---..............(((.((((((((.((((((....((((((.(((((....))))).))))))...((((....)))))))))).))))))))..))).... ( -32.80)
>consensus
UA___AAUAAACAAAUCUCCGUCGUUUUCACACCAUGCACACUCCACAAUCGAUUGAG___UGAUGCUGGUGACUGC__AAGUGUGCGAGGCGUGAAAACCAACAGCCA
.......................((((((((.((.((((((((...((((((...(..........)...))))))....)))))))).)).))))))))......... (-24.23 = -23.82 +  -0.41)

alignment

secondary structure

dotplot

Window 4

Location	10,728,289 – 10,728,390
Length	101
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	78.43
Mean single sequence MFE	-36.75
Consensus MFE	-32.99
Energy contribution	-30.88
Covariance contribution	-2.11
Combinations/Pair	1.32
Mean z-score	-3.89
Structure conservation index	0.90
SVM decision value	1.55
SVM RNA-class probability	0.963065
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10728289 101 - 27905053
UGGCAGUUGGUUUUCACGCCUCGCACGCUC--GCAGUCACCAGCAUCA---CUCAAUCGACUGUGGAGUGUGCACGGUGUGAAAACGACCGUGAUUUGUUUAUU---UC
..((.((((.((((((((((..((((((((--((((((..........---.......)))))).))))))))..)))))))))))))).))............---.. ( -40.33)
>DroPse_CAF1 3907 106 - 1
UAGAUGUUUAUUUUUACGCCACGCCUACUCGCGCAAUUAUCAGCAUCCAAUUUCAAUUGAUUGCUGAGUGUGCAUGGUGUAAAAAUGACAAAGAUUUGUUUAUG---UA
....((((.((((((((((((.((......))(((....((((((..((((....))))..))))))...))).))))))))))))))))..............---.. ( -33.30)
>DroEre_CAF1 4192 101 - 1
UGGCAGUUGGUUUUCACGCCUCGCACACUU--GCAGUCACCAGCAUCA---CUCAAUCGACUGUGGAGUGUGCAUGGUGUGAAAACGGCGGCGAUUUGUUUAUU---UC
..((.((((.((((((((((..(((((((.--.(((((..........---.......)))))..).))))))..)))))))))))))).))............---.. ( -40.73)
>DroYak_CAF1 3885 101 - 1
UGGCAGUUGGUUUUCACGCCUCGCACACUU--GCAGUCACCAGCAUCA---CUCAAUCGACUGUGGAGUGUGCACGGUGUGAAAACGACGGCGAUUUGUUUAUU---UA
..((.((((.((((((((((..(((((((.--.(((((..........---.......)))))..).))))))..)))))))))))))).))............---.. ( -40.33)
>DroAna_CAF1 4859 106 - 1
AAGCUGUUAGUUUUCACGCCUCGCACACUUUAGCAAUCACCAGCAUCA---CUCAAUCGAUUGCAGAGUGUGCCCGAUGUGAAAACGACUGAGUUUUGUUUUUUAUAAU
((((((((.(((((((((.(..(((((((((.((((((..........---.......)))))))))))))))..).))))))))))))..)))))............. ( -32.53)
>DroPer_CAF1 3931 106 - 1
UAGAUGUUUAUUUUUACGCCACGCCUACUCGCGCAAUUAUCAGCAUCCAAUUUCAAUUGAUUGCUGAGUGUGCAUGGUGUAAAAAUGACAAAGAUUUGUUUAUG---UA
....((((.((((((((((((.((......))(((....((((((..((((....))))..))))))...))).))))))))))))))))..............---.. ( -33.30)
>consensus
UAGCAGUUGGUUUUCACGCCUCGCACACUC__GCAAUCACCAGCAUCA___CUCAAUCGACUGCGGAGUGUGCACGGUGUGAAAACGACAGAGAUUUGUUUAUU___UA
.....(((.(((((((((((..((((((((..((((((....................)))))).))))))))..)))))))))))))).................... (-32.99 = -30.88 +  -2.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:47 2006