Locus 8312

Sequence ID	X_DroMel_CAF1
Location	20,663,411 – 20,663,549
Length	138
Max. P	0.651359

overview

Window 0

Location	20,663,411 – 20,663,509
Length	98
Sequences	3
Columns	111
Reading direction	forward
Mean pairwise identity	88.59
Mean single sequence MFE	-21.65
Consensus MFE	-16.18
Energy contribution	-16.40
Covariance contribution	0.22
Combinations/Pair	1.03
Mean z-score	-2.32
Structure conservation index	0.75
SVM decision value	0.25
SVM RNA-class probability	0.651359
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20663411 98 + 22224390
GAAAAUUU-------------UGGUAGUUGUAAGGAUAUUCGUAUAAAACAUUACAGCUCCCUAAAUGUCGUGAUACUCAUAUACAAUAUAUAUGUAUAUACACAUAUAUA
((..((((-------------.((.(((((((((..(((....)))...).)))))))).)).)))).))((((((..((((((.....))))))..))).)))....... ( -18.40)
>DroSec_CAF1 65086 111 + 1
GAAAAUUGUAUAAAAACACAGUGGUAGUUGUAGGGAUAUUCGUAUAAAAGAUUACAGCUCCCCAAAUGUCGUGAUACUCAUAUACAAUAUAUAUGUAUAUACACAUAUAUA
....((((((((...(((((..((.((((((((...(((....))).....)))))))).))....))).))(.....).))))))))((((((((......)))))))). ( -20.50)
>DroSim_CAF1 42526 111 + 1
GAAAAUUGUAUAAAAACACAGUGGUAGUUGUAUGGAUAUUCGUAUAAAAGAUUACAGCUCCCAAAAUGUCGUGAUACUCAUAUACAAUAUAUAUGUGUAUACACAUAUAUA
....((((((((...(((((.(((.(((((((....................))))))).)))...))).))(.....).))))))))(((((((((....))))))))). ( -26.05)
>consensus
GAAAAUUGUAUAAAAACACAGUGGUAGUUGUAAGGAUAUUCGUAUAAAAGAUUACAGCUCCCAAAAUGUCGUGAUACUCAUAUACAAUAUAUAUGUAUAUACACAUAUAUA
......................((.((((((((...(((....))).....)))))))).))...((((.((((((..((((((.....))))))..))).)))))))... (-16.18 = -16.40 +   0.22)

alignment

secondary structure

dotplot

Window 1

Location	20,663,411 – 20,663,509
Length	98
Sequences	3
Columns	111
Reading direction	reverse
Mean pairwise identity	88.59
Mean single sequence MFE	-20.82
Consensus MFE	-15.94
Energy contribution	-16.17
Covariance contribution	0.23
Combinations/Pair	1.11
Mean z-score	-2.02
Structure conservation index	0.77
SVM decision value	0.02
SVM RNA-class probability	0.542596
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20663411 98 - 22224390
UAUAUAUGUGUAUAUACAUAUAUAUUGUAUAUGAGUAUCACGACAUUUAGGGAGCUGUAAUGUUUUAUACGAAUAUCCUUACAACUACCA-------------AAAUUUUC
((((((((((....))))))))))((((((((..((((...(((((((((....))).))))))..))))..)))....)))))......-------------........ ( -18.30)
>DroSec_CAF1 65086 111 - 1
UAUAUAUGUGUAUAUACAUAUAUAUUGUAUAUGAGUAUCACGACAUUUGGGGAGCUGUAAUCUUUUAUACGAAUAUCCCUACAACUACCACUGUGUUUUUAUACAAUUUUC
((((((((((....))))))))))(((((((.((((((.........((((((.((((((....))))).)....))))))...........)))))).)))))))..... ( -20.95)
>DroSim_CAF1 42526 111 - 1
UAUAUAUGUGUAUACACAUAUAUAUUGUAUAUGAGUAUCACGACAUUUUGGGAGCUGUAAUCUUUUAUACGAAUAUCCAUACAACUACCACUGUGUUUUUAUACAAUUUUC
((((((((((....))))))))))(((((((((.....)).(((((..(((.((.((((......(((....)))....)))).)).)))..)))))..)))))))..... ( -23.20)
>consensus
UAUAUAUGUGUAUAUACAUAUAUAUUGUAUAUGAGUAUCACGACAUUUAGGGAGCUGUAAUCUUUUAUACGAAUAUCCAUACAACUACCACUGUGUUUUUAUACAAUUUUC
......((((.((((.(((((((...))))))).)))))))).....((((((.((((((....))))).)....)))))).............................. (-15.94 = -16.17 +   0.23)

alignment

secondary structure

dotplot

Window 2

Location	20,663,431 – 20,663,549
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	73.65
Mean single sequence MFE	-26.10
Consensus MFE	-14.30
Energy contribution	-16.46
Covariance contribution	2.16
Combinations/Pair	1.30
Mean z-score	-1.62
Structure conservation index	0.55
SVM decision value	0.03
SVM RNA-class probability	0.547205
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20663431 118 - 22224390
AGCAACCCCAAAUAGUGUGGCAUAUUCAAGGCAAAGAUGUUAUAUAUGUGUAUAUACAUAUAUAUUGUA--UAUGAGUAUCACGACAUUUAGGGAGCUGUAAUGUUUUAUACGAAUAUCC
(((..(((.((((..((((..(((((((..((((......((((((((((....)))))))))))))).--..)))))))))))..)))).))).)))...((((((.....)))))).. ( -26.20)
>DroSec_CAF1 65119 118 - 1
AGCAACCCCAAAUAGUGUGGCAUGUUCAAGGCAAAGAUGGUAUAUAUGUGUAUAUACAUAUAUAUUGUA--UAUGAGUAUCACGACAUUUGGGGAGCUGUAAUCUUUUAUACGAAUAUCC
(((..((((((((..(((((..(((.....)))...(..(((((((((((....)))))))))))..).--........)))))..)))))))).)))...................... ( -31.40)
>DroSim_CAF1 42559 118 - 1
AGCAACCCCAAAUAGUGUGGCAUGUUCAAGGCAAAGAUGGUAUAUAUGUGUAUACACAUAUAUAUUGUA--UAUGAGUAUCACGACAUUUUGGGAGCUGUAAUCUUUUAUACGAAUAUCC
.(((.(((((((...(((((..(((.....)))...(..(((((((((((....)))))))))))..).--........)))))....)))))).).))).................... ( -29.20)
>DroEre_CAF1 60722 95 - 1
AGCAACCCCAAAUAGUGUGGCAUAUUCGAAGCAAAGAUGUUCUAUACAGG-----------GUGCUGUUCUAAUGGGUAUCACCACAUUUAAGGAUGUAU----------CCAAAU----
..............((((((.((((.(........))))).)))))).((-----------((((.(((((((((((.....)).))))..)))))))))----------))....---- ( -22.10)
>DroYak_CAF1 62013 95 - 1
AGCAACCCCAAAUAGUGUGGCAUAUUCGAAGCAAAGACCGCAUAUACAGG-----------GUGCUGUACUAAUGGGUAUCACCGCAUUUAAGGAGCCCU----------ACGAAU----
.((...((((..(((((..((((..((........))((.........))-----------))))..))))).)))).....((........)).))...----------......---- ( -21.60)
>consensus
AGCAACCCCAAAUAGUGUGGCAUAUUCAAGGCAAAGAUGGUAUAUAUGUGUAUA_ACAUAUAUAUUGUA__UAUGAGUAUCACGACAUUUAGGGAGCUGUAAU_UUUUAUACGAAUAUCC
.....(((.((((.(((((..(((((((........((((((((((((((....)))))))))))))).....)))))))))).)))))).))).......................... (-14.30 = -16.46 +   2.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:53 2006