Locus 3467

Sequence ID	2L_DroMel_CAF1
Location	10,082,069 – 10,082,202
Length	133
Max. P	0.999200

overview

Window 9

Location	10,082,069 – 10,082,162
Length	93
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	84.89
Mean single sequence MFE	-21.76
Consensus MFE	-16.60
Energy contribution	-17.28
Covariance contribution	0.68
Combinations/Pair	1.18
Mean z-score	-2.57
Structure conservation index	0.76
SVM decision value	1.77
SVM RNA-class probability	0.976295
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10082069 93 - 22407834
AUAUUAUUUCCACUUACAGUCGUGGCUAUGGCUUGU-CAUUGUUUUCCUGACCACGACUGUGUCUUUCUGUUGAUAUGAGUAACCAAAACCGAU
((((((........((((((((((((...(((....-....))).....).))))))))))).........))))))................. ( -20.83)
>DroSec_CAF1 8796 94 - 1
AUAUUAUUUCCACUUACAGUCGUGGUUAUAACUAGCACAUUGUUUUUCUGACCACGACUGUGUCUUUCUGUUGAUAUGAGUAACCAAAACCAAU
((((((........((((((((((((((.((..(((.....))).)).)))))))))))))).........))))))................. ( -24.63)
>DroSim_CAF1 8792 94 - 1
AUAUUAUUUCCAUUUACAGUCUUGGUUAUAACUAGCACAUAGUUUUUCUGACCACGACUGUGUCUUUCUGUUUAUUCUACUCACCAAAACCGAU
..............(((((((.((((((.(((((.....)))))....)))))).)))))))....((.((((.............)))).)). ( -19.12)
>DroEre_CAF1 7590 94 - 1
AUACUAUUUCCAUUCACAGUGGUGCUGAUAGCUAGUAUAUCGUUUUUCUGACCACGACUGUGUCUUUCUAUUGAUUUGAGUAACCACAACCGAU
.((((.........((((((.(((..((((.......))))(((.....)))))).))))))....((....))....))))............ ( -15.60)
>DroYak_CAF1 8640 94 - 1
CUUUUAUUUCAAUUUACAGUCGUGGUUAUGGCUAGUAUAUAGUAUUCCUGACCACGACUGUGGCUUUCUGUUGAUAUGAGUAACCCAAACCGAU
..(((((.((((((((((((((((((((..((((.....)))).....)))))))))))))))......))))).))))).............. ( -28.60)
>consensus
AUAUUAUUUCCAUUUACAGUCGUGGUUAUAGCUAGUACAUAGUUUUUCUGACCACGACUGUGUCUUUCUGUUGAUAUGAGUAACCAAAACCGAU
..............((((((((((((((.(((.........)))....))))))))))))))................................ (-16.60 = -17.28 +   0.68)

alignment

secondary structure

dotplot

Window 0

Location	10,082,093 – 10,082,202
Length	109
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	76.76
Mean single sequence MFE	-23.75
Consensus MFE	-14.03
Energy contribution	-13.99
Covariance contribution	-0.04
Combinations/Pair	1.29
Mean z-score	-2.34
Structure conservation index	0.59
SVM decision value	1.92
SVM RNA-class probability	0.982644
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10082093 109 + 22407834
CAGAAAGACACAGUCGUGGUCAGGAAAACAAUG-ACAAGCCAUAGCCACGACUGUAAGUGGAAAUAAUAUCUACAGUAGCUUUAGUUACUUAUUUAGUUACUCUCUACUG
.(((..((((((((((((((..((.........-.....))...)))))))))))..(((((.......)))))((((((....))))))......)))..)))...... ( -29.64)
>DroSec_CAF1 8820 100 + 1
CAGAAAGACACAGUCGUGGUCAGAAAAACAAUGUGCUAGUUAUAACCACGACUGUAAGUGGAAAUAAUAUCUACAGUAGCU----------AUUUAGUUACUCUGUAUUG
((((.....(((((((((((.(....(((.........))).).)))))))))))..(((((.......))))).((((((----------....))))))))))..... ( -28.20)
>DroSim_CAF1 8816 100 + 1
CAGAAAGACACAGUCGUGGUCAGAAAAACUAUGUGCUAGUUAUAACCAAGACUGUAAAUGGAAAUAAUAUCUACAGUAGCU----------AUUUAGUUACUCUGUAUUG
((((.....((((((.((((.(....(((((.....))))).).)))).))))))....................((((((----------....))))))))))..... ( -21.90)
>DroEre_CAF1 7614 95 + 1
UAGAAAGACACAGUCGUGGUCAGAAAAACGAUAUACUAGCUAUCAGCACCACUGUGAAUGGAAAUAGUAUCCGCAAUGUA-------------AUACUC--AGUGCAUUG
........((((((.(((((.......))((((.......))))..))).))))))...(((.......))).(((((((-------------......--..))))))) ( -18.20)
>DroYak_CAF1 8664 97 + 1
CAGAAAGCCACAGUCGUGGUCAGGAAUACUAUAUACUAGCCAUAACCACGACUGUAAAUUGAAAUAAAAGCUACAAUAUA-------------AUAUUCACACUGUAUUG
.........(((((((((((..((....(((.....)))))...)))))))))))..................(((((((-------------..........))))))) ( -20.80)
>consensus
CAGAAAGACACAGUCGUGGUCAGAAAAACAAUGUACUAGCUAUAACCACGACUGUAAAUGGAAAUAAUAUCUACAGUAGCU__________AUUUAGUUACUCUGUAUUG
.........(((((((((((........................)))))))))))..................((((((.........................)))))) (-14.03 = -13.99 +  -0.04)

alignment

secondary structure

dotplot

Window 1

Location	10,082,093 – 10,082,202
Length	109
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	76.76
Mean single sequence MFE	-26.70
Consensus MFE	-16.95
Energy contribution	-17.43
Covariance contribution	0.48
Combinations/Pair	1.27
Mean z-score	-3.03
Structure conservation index	0.63
SVM decision value	3.43
SVM RNA-class probability	0.999200
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10082093 109 - 22407834
CAGUAGAGAGUAACUAAAUAAGUAACUAAAGCUACUGUAGAUAUUAUUUCCACUUACAGUCGUGGCUAUGGCUUGU-CAUUGUUUUCCUGACCACGACUGUGUCUUUCUG
((((((..(((.(((.....))).)))....)))))).................((((((((((((...(((....-....))).....).)))))))))))........ ( -29.40)
>DroSec_CAF1 8820 100 - 1
CAAUACAGAGUAACUAAAU----------AGCUACUGUAGAUAUUAUUUCCACUUACAGUCGUGGUUAUAACUAGCACAUUGUUUUUCUGACCACGACUGUGUCUUUCUG
...((((((((........----------.))).)))))...............((((((((((((((.((..(((.....))).)).))))))))))))))........ ( -28.10)
>DroSim_CAF1 8816 100 - 1
CAAUACAGAGUAACUAAAU----------AGCUACUGUAGAUAUUAUUUCCAUUUACAGUCUUGGUUAUAACUAGCACAUAGUUUUUCUGACCACGACUGUGUCUUUCUG
...((((((((........----------.))).)))))...............(((((((.((((((.(((((.....)))))....)))))).)))))))........ ( -24.70)
>DroEre_CAF1 7614 95 - 1
CAAUGCACU--GAGUAU-------------UACAUUGCGGAUACUAUUUCCAUUCACAGUGGUGCUGAUAGCUAGUAUAUCGUUUUUCUGACCACGACUGUGUCUUUCUA
....(((.(--(.....-------------..)).)))(((.......)))...((((((.(((..((((.......))))(((.....)))))).))))))........ ( -20.00)
>DroYak_CAF1 8664 97 - 1
CAAUACAGUGUGAAUAU-------------UAUAUUGUAGCUUUUAUUUCAAUUUACAGUCGUGGUUAUGGCUAGUAUAUAGUAUUCCUGACCACGACUGUGGCUUUCUG
...((((((((((...)-------------)))))))))..............(((((((((((((((..((((.....)))).....)))))))))))))))....... ( -31.30)
>consensus
CAAUACAGAGUAACUAAAU__________AGCUACUGUAGAUAUUAUUUCCAUUUACAGUCGUGGUUAUAGCUAGUACAUAGUUUUUCUGACCACGACUGUGUCUUUCUG
...(((((..........................)))))...............((((((((((((((.(((.........)))....))))))))))))))........ (-16.95 = -17.43 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:10 2006