Locus 5096

Sequence ID	2L_DroMel_CAF1
Location	14,524,161 – 14,524,299
Length	138
Max. P	0.895475

overview

Window 1

Location	14,524,161 – 14,524,268
Length	107
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	92.75
Mean single sequence MFE	-25.25
Consensus MFE	-22.95
Energy contribution	-22.95
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.48
Structure conservation index	0.91
SVM decision value	0.99
SVM RNA-class probability	0.895475
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14524161 107 + 22407834
UUUCAACAGUUUGUGACGUCCUCUCCCGUCUACACAUUUAUCCUCCACUCC-------ACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA-CCAACUCGACGCGA
...........(((((((........)))).))).................-------..(((((((((((((((.((((.....)))).)).)))))).-))..)))))..... ( -25.30)
>DroPse_CAF1 60587 111 + 1
UUUCAACAGUUUGUGACGUCGU----CGUCUACACAUUUAUCCUCCACUCCACACACCACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCAAACGACUCGACUCGA
.............(((.((((.----.(((..........(((((.................)))))((((((((.((((.....)))).)).))))))....))).))))))). ( -25.53)
>DroSec_CAF1 56036 106 + 1
UUUCAACAGUUUGUGACGUCCUCUC-CGUCUACACAUUUAUCCUCCACUCC-------ACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA-CCAACUCGACGCGA
...........(((((((.......-)))).))).................-------..(((((((((((((((.((((.....)))).)).)))))).-))..)))))..... ( -25.00)
>DroSim_CAF1 41414 106 + 1
UUUCAACAGUUUGUGACGUCCUCUC-CGUCUACACAUUUAUCCUCCACUCC-------ACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA-CCAACUCGACGCGA
...........(((((((.......-)))).))).................-------..(((((((((((((((.((((.....)))).)).)))))).-))..)))))..... ( -25.00)
>DroEre_CAF1 52168 106 + 1
UUUCAACAGUUUGUGACGUCGCCCC-CGUCUACACAUUUAUCCCACACUCC-------ACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA-CCAACUCGACGCGA
...........(((((((.......-)))).))).................-------..(((((((((((((((.((((.....)))).)).)))))).-))..)))))..... ( -25.00)
>DroYak_CAF1 46568 111 + 1
UUUCAACAGUUUGUGACGUCGUCUC-CGUCUACACAUUUAUCCUCCACUCCAC--UUCACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA-CCAACUCGACGCGA
...........(((((((.......-)))).)))...................--.((.((((((((((((((((.((((.....)))).)).)))))).-))..))))).).)) ( -25.70)
>consensus
UUUCAACAGUUUGUGACGUCCUCUC_CGUCUACACAUUUAUCCUCCACUCC_______ACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA_CCAACUCGACGCGA
...........(((((((........)))).)))..........................(((((..((((((((.((((.....)))).)).))))))......)))))..... (-22.95 = -22.95 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	14,524,201 – 14,524,299
Length	98
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	90.79
Mean single sequence MFE	-29.32
Consensus MFE	-22.03
Energy contribution	-22.20
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-3.10
Structure conservation index	0.75
SVM decision value	0.12
SVM RNA-class probability	0.590992
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14524201 98 + 22407834
UCCUCCACUCC-------ACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA-CCAACUCGACGCGACUC-------GACUUUCGAGACAUG--CUACCAACACUUC
...........-------..(((((((((((((((.((((.....)))).)).)))))).-))..))))).(((.(((-------(.....))))...))--)............ ( -26.40)
>DroPse_CAF1 60623 115 + 1
UCCUCCACUCCACACACCACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCAAACGACUCGACUCGACUCGAGUCGAGACUUUCAAGACAUGCGCUACCAACACUUG
...................((.(((((((((((((.((((.....)))).)).))))))......(((((((((...))))))))).))))).)).................... ( -32.10)
>DroSec_CAF1 56075 98 + 1
UCCUCCACUCC-------ACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA-CCAACUCGACGCGACUC-------GACUUUCGAGACAUG--CUACCAACACUUC
...........-------..(((((((((((((((.((((.....)))).)).)))))).-))..))))).(((.(((-------(.....))))...))--)............ ( -26.40)
>DroSim_CAF1 41453 98 + 1
UCCUCCACUCC-------ACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA-CCAACUCGACGCGACUC-------GACUUUCGAGACAUG--CUACCAACACUUC
...........-------..(((((((((((((((.((((.....)))).)).)))))).-))..))))).(((.(((-------(.....))))...))--)............ ( -26.40)
>DroEre_CAF1 52207 98 + 1
UCCCACACUCC-------ACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA-CCAACUCGACGCGAGUC-------GACUUUCGAGACAUG--CUACCAACACUUC
...........-------.((((((((((((((((.((((.....)))).)).)))))).-.....(((((....)))-------)))))))))).....--............. ( -32.30)
>DroYak_CAF1 46607 103 + 1
UCCUCCACUCCAC--UUCACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA-CCAACUCGACGCGAGUC-------GACUUUCGAGACAUG--CUACCAACACUUC
.............--....((((((((((((((((.((((.....)))).)).)))))).-.....(((((....)))-------)))))))))).....--............. ( -32.30)
>consensus
UCCUCCACUCC_______ACUCGAGGGGGCGGUUAACAAAAGCUCUUUGAUAUACCGCCA_CCAACUCGACGCGACUC_______GACUUUCGAGACAUG__CUACCAACACUUC
...................((((((((((((((((.((((.....)))).)).)))))).......(((...)))............)))))))).................... (-22.03 = -22.20 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:52 2006