Locus 2968

Sequence ID	3R_DroMel_CAF1
Location	7,929,014 – 7,929,167
Length	153
Max. P	0.998271

overview

Window 1

Location	7,929,014 – 7,929,127
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	98.05
Mean single sequence MFE	-25.80
Consensus MFE	-25.54
Energy contribution	-25.54
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.51
Structure conservation index	0.99
SVM decision value	1.51
SVM RNA-class probability	0.960199
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7929014 113 + 27905053
GCCGCCAUUUUGUCCUUCCAAACAACCAUGACAUUUUAUUGGACAUGUAAUUACUGCGUGUGUUUUCGGCUCGCGGGCCCACGCAUAUUUUUUAUAAUUACAUGAAAAAUGAA
.....((((((.....(((((.................)))))((((((((((.((((((.......((((....)))))))))).........)))))))))).)))))).. ( -25.54)
>DroSec_CAF1 60191 113 + 1
GCCGCCAUUUUGUCCUUCCAAACAACCAUGAAUUUUUAUUGGACAUGUAAUUACUGCGUGUGUUUUCGGCUCGUGGGCCCACGCAUAUUUUUUAUAAUUACAUGAAAAAUGAA
.....((((((.....(((((.................)))))((((((((((.((((((.......((((....)))))))))).........)))))))))).)))))).. ( -25.54)
>DroSim_CAF1 62002 113 + 1
GCCGCCAUUUUGUCCUUCCAAACAACCAUGACUUUUUAUUGGACAUGUAAUUACUGCGUGUGUUUUCGGCUCGCGGGCCCACGCAUAUUUUUUAUAAUUACAUGAAAAAUGAA
.....((((((.....(((((.................)))))((((((((((.((((((.......((((....)))))))))).........)))))))))).)))))).. ( -25.54)
>DroEre_CAF1 61077 112 + 1
GCCGCCAUUUUGUCCUUCCAAACAACCAUGACUUUUUAUUGGACAUGUAAUUACUGCGUGCGUUUUCGGCUCGUGGGCCCACGCAUAUUU-UUAUAAUUACAUGAAAAAUGAA
.....((((((.....(((((.................)))))((((((((((....((((((....((((....)))).))))))....-...)))))))))).)))))).. ( -26.83)
>DroYak_CAF1 62387 113 + 1
GCCGCCAUUUUGUCCUUCCAAACAACCAUGACUUUUUAUUGGACAUGUAAUUACUGCGUGUGUUUUCGGCUCGUGGGCCCACGCAUAUUUUUUAUAAUUACAUGAAAAAUGAA
.....((((((.....(((((.................)))))((((((((((.((((((.......((((....)))))))))).........)))))))))).)))))).. ( -25.54)
>consensus
GCCGCCAUUUUGUCCUUCCAAACAACCAUGACUUUUUAUUGGACAUGUAAUUACUGCGUGUGUUUUCGGCUCGUGGGCCCACGCAUAUUUUUUAUAAUUACAUGAAAAAUGAA
.....((((((.....(((((.................)))))((((((((((.((((((.......((((....)))))))))).........)))))))))).)))))).. (-25.54 = -25.54 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	7,929,014 – 7,929,127
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	98.05
Mean single sequence MFE	-29.16
Consensus MFE	-28.42
Energy contribution	-28.62
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.06
Structure conservation index	0.97
SVM decision value	3.05
SVM RNA-class probability	0.998271
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7929014 113 - 27905053
UUCAUUUUUCAUGUAAUUAUAAAAAAUAUGCGUGGGCCCGCGAGCCGAAAACACACGCAGUAAUUACAUGUCCAAUAAAAUGUCAUGGUUGUUUGGAAGGACAAAAUGGCGGC
.........(((((((((((........(((((((((......)))(....).)))))))))))))))))..........((((((..((((((....)))))).)))))).. ( -29.80)
>DroSec_CAF1 60191 113 - 1
UUCAUUUUUCAUGUAAUUAUAAAAAAUAUGCGUGGGCCCACGAGCCGAAAACACACGCAGUAAUUACAUGUCCAAUAAAAAUUCAUGGUUGUUUGGAAGGACAAAAUGGCGGC
.(((((((.(((((((((((........(((((((((......)))(....).)))))))))))))))))(((((....(((.....)))..))))).....))))))).... ( -27.10)
>DroSim_CAF1 62002 113 - 1
UUCAUUUUUCAUGUAAUUAUAAAAAAUAUGCGUGGGCCCGCGAGCCGAAAACACACGCAGUAAUUACAUGUCCAAUAAAAAGUCAUGGUUGUUUGGAAGGACAAAAUGGCGGC
.........(((((((((((........(((((((((......)))(....).)))))))))))))))))...........(((((..((((((....)))))).)))))... ( -29.70)
>DroEre_CAF1 61077 112 - 1
UUCAUUUUUCAUGUAAUUAUAA-AAAUAUGCGUGGGCCCACGAGCCGAAAACGCACGCAGUAAUUACAUGUCCAAUAAAAAGUCAUGGUUGUUUGGAAGGACAAAAUGGCGGC
.........(((((((((((..-.....(((((((((......)))(....).)))))))))))))))))...........(((((..((((((....)))))).)))))... ( -29.51)
>DroYak_CAF1 62387 113 - 1
UUCAUUUUUCAUGUAAUUAUAAAAAAUAUGCGUGGGCCCACGAGCCGAAAACACACGCAGUAAUUACAUGUCCAAUAAAAAGUCAUGGUUGUUUGGAAGGACAAAAUGGCGGC
.........(((((((((((........(((((((((......)))(....).)))))))))))))))))...........(((((..((((((....)))))).)))))... ( -29.70)
>consensus
UUCAUUUUUCAUGUAAUUAUAAAAAAUAUGCGUGGGCCCACGAGCCGAAAACACACGCAGUAAUUACAUGUCCAAUAAAAAGUCAUGGUUGUUUGGAAGGACAAAAUGGCGGC
.........(((((((((((........(((((((((......)))(....).)))))))))))))))))...........(((((..((((((....)))))).)))))... (-28.42 = -28.62 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	7,929,049 – 7,929,167
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	96.19
Mean single sequence MFE	-32.12
Consensus MFE	-30.30
Energy contribution	-30.62
Covariance contribution	0.32
Combinations/Pair	1.06
Mean z-score	-1.80
Structure conservation index	0.94
SVM decision value	2.50
SVM RNA-class probability	0.994678
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7929049 118 - 27905053
ACACUCAGGAUGCUCGGGAAAUUCGCAUCAGCUGGGGGUCUUCAUUUUUCAUGUAAUUAUAAAAAAUAUGCGUGGGCCCGCGAGCCGAAAACACACGCAGUAAUUACAUGUCCAAUAA
...((((((((((...........)))))..))))).............(((((((((((........(((((((((......)))(....).)))))))))))))))))........ ( -30.90)
>DroSec_CAF1 60226 118 - 1
ACAGUCAGGAUGCUCCGGAAAUUCGCAUCAGCUGCGGGUCUUCAUUUUUCAUGUAAUUAUAAAAAAUAUGCGUGGGCCCACGAGCCGAAAACACACGCAGUAAUUACAUGUCCAAUAA
.......(((......(((.(((((((.....))))))).)))......(((((((((((........(((((((((......)))(....).))))))))))))))))))))..... ( -32.70)
>DroSim_CAF1 62037 118 - 1
ACACUCAGGAUGCUCGGGAAAUUCGCAUCAGCUGCGGGUCUUCAUUUUUCAUGUAAUUAUAAAAAAUAUGCGUGGGCCCGCGAGCCGAAAACACACGCAGUAAUUACAUGUCCAAUAA
.......(((......(((.(((((((.....))))))).)))......(((((((((((........(((((((((......)))(....).))))))))))))))))))))..... ( -32.40)
>DroEre_CAF1 61112 116 - 1
ACACUCAGGAUGCUCGGGAAG-UCGCAUCAGCUGCGGGUCUUCAUUUUUCAUGUAAUUAUAA-AAAUAUGCGUGGGCCCACGAGCCGAAAACGCACGCAGUAAUUACAUGUCCAAUAA
.......(((.......((((-(((((.....)))))..))))......(((((((((((..-.....(((((((((......)))(....).))))))))))))))))))))..... ( -31.31)
>DroYak_CAF1 62422 118 - 1
UCACUCAGGAUGCUCGGGAAACGCGCAUCAGCUGCGGGUCUUCAUUUUUCAUGUAAUUAUAAAAAAUAUGCGUGGGCCCACGAGCCGAAAACACACGCAGUAAUUACAUGUCCAAUAA
.......(((.....((((..(((((....)).)))..)))).......(((((((((((........(((((((((......)))(....).))))))))))))))))))))..... ( -33.30)
>consensus
ACACUCAGGAUGCUCGGGAAAUUCGCAUCAGCUGCGGGUCUUCAUUUUUCAUGUAAUUAUAAAAAAUAUGCGUGGGCCCACGAGCCGAAAACACACGCAGUAAUUACAUGUCCAAUAA
.......(((......(((.(((((((.....))))))).)))......(((((((((((........(((((((((......)))(....).))))))))))))))))))))..... (-30.30 = -30.62 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:57 2006