Locus 3030

Sequence ID	3L_DroMel_CAF1
Location	8,700,817 – 8,700,916
Length	99
Max. P	0.873061

overview

Window 5

Location	8,700,817 – 8,700,916
Length	99
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	73.05
Mean single sequence MFE	-17.56
Consensus MFE	-0.52
Energy contribution	-0.88
Covariance contribution	0.36
Combinations/Pair	1.20
Mean z-score	-1.82
Structure conservation index	0.03
SVM decision value	0.88
SVM RNA-class probability	0.873061
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8700817 99 + 23771897
UGUUUCUAUUGACACCUCAACUGAGU----------CCAGUAUGAUCCUUUCAAUAAAAUA--UAACUAC--AUAUUAUAAUAAUUGGAUAAUAUGAUUGGAUCUUUCUUUUC--
....((..((((....))))..))((----------(((((.(((.....)))........--......(--(((((((.........)))))))))))))))..........-- ( -14.40)
>DroSec_CAF1 6453 103 + 1
UGUUUCUAUUGACACCUCAACUGAGU----------CCAGUAUGAUCCUUUCAAUGAAAUAUAUAUCUAC--ACAUUAUUAUAAUUGGAAAAUAUGAUUGGAUCUUUCUUUUCUU
((((((.(((((....(((((((...----------.)))).))).....))))))))))).........--.......................((..(((....)))..)).. ( -13.90)
>DroSim_CAF1 7235 103 + 1
UGUUUCUAUUGACACCUCAACUGAGU----------CCAGUAUGAUCCUUUCAAUGAAAUAUAUAUCUAC--AUAUUAUUAUAAUUGAAUAAUAUGAUUGGAUCUUUCUUUUCUU
((((((.(((((....(((((((...----------.)))).))).....)))))))))))...((((((--((((((((.......)))))))))..)))))............ ( -18.70)
>DroEre_CAF1 6288 107 + 1
----UUUACAGACACCCCAAAUGAUUCUUUGGUUAUCCAGAAUGAUCCCUCCAAUGGUAUA--UCACUAAAUAUAGAGUUGUAAAUGA--UACAUCAUUGGAGUUUUAAUUUCUU
----..................((((.(((((....)))))..)))).((((((((((.((--(((....(((......)))...)))--)).))))))))))............ ( -22.10)
>DroYak_CAF1 6384 107 + 1
----UCUACUGACACCCCAAAUGAUUCUUUGGUAAUUCAGAAUGAUCCUUACAAUGGUAUA--UCACUAAAUAUAUUUUUAUAAAUGA--UAUAUCAUUCGAGUUUUCUUUUCUU
----....((((....(((((......)))))....))))...((..(((..(((((((((--(((.((((......))))....)))--))))))))).)))..))........ ( -18.70)
>consensus
UGUUUCUAUUGACACCUCAACUGAGU__________CCAGUAUGAUCCUUUCAAUGAAAUA__UAACUAC__AUAUUAUUAUAAUUGAA_AAUAUGAUUGGAUCUUUCUUUUCUU
...........................................(((((...................................................)))))........... ( -0.52 =  -0.88 +   0.36)

alignment

secondary structure

dotplot

Window 6

Location	8,700,817 – 8,700,916
Length	99
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	73.05
Mean single sequence MFE	-19.28
Consensus MFE	-3.54
Energy contribution	-3.98
Covariance contribution	0.44
Combinations/Pair	1.31
Mean z-score	-1.59
Structure conservation index	0.18
SVM decision value	0.18
SVM RNA-class probability	0.619702
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8700817 99 - 23771897
--GAAAAGAAAGAUCCAAUCAUAUUAUCCAAUUAUUAUAAUAU--GUAGUUA--UAUUUUAUUGAAAGGAUCAUACUGG----------ACUCAGUUGAGGUGUCAAUAGAAACA
--.................((((((((.........)))))))--)......--..(((((((((.....(((.((((.----------...)))))))....)))))))))... ( -15.90)
>DroSec_CAF1 6453 103 - 1
AAGAAAAGAAAGAUCCAAUCAUAUUUUCCAAUUAUAAUAAUGU--GUAGAUAUAUAUUUCAUUGAAAGGAUCAUACUGG----------ACUCAGUUGAGGUGUCAAUAGAAACA
...........(((((..........(((..(((....(((((--((....)))))))....)))..)))(((.((((.----------...))))))))).))).......... ( -13.90)
>DroSim_CAF1 7235 103 - 1
AAGAAAAGAAAGAUCCAAUCAUAUUAUUCAAUUAUAAUAAUAU--GUAGAUAUAUAUUUCAUUGAAAGGAUCAUACUGG----------ACUCAGUUGAGGUGUCAAUAGAAACA
.......((((.(((....(((((((((.......))))))))--)..))).....))))(((((.....(((.((((.----------...)))))))....)))))....... ( -16.50)
>DroEre_CAF1 6288 107 - 1
AAGAAAUUAAAACUCCAAUGAUGUA--UCAUUUACAACUCUAUAUUUAGUGA--UAUACCAUUGGAGGGAUCAUUCUGGAUAACCAAAGAAUCAUUUGGGGUGUCUGUAAA----
.((((.......((((((((.((((--(((((...............)))))--)))).))))))))......))))(((((.(((((......)))))..))))).....---- ( -30.08)
>DroYak_CAF1 6384 107 - 1
AAGAAAAGAAAACUCGAAUGAUAUA--UCAUUUAUAAAAAUAUAUUUAGUGA--UAUACCAUUGUAAGGAUCAUUCUGAAUUACCAAAGAAUCAUUUGGGGUGUCAGUAGA----
...............((((((((((--(((((.(((......)))..)))))--))).((.......)))))))))(((....(((((......)))))....))).....---- ( -20.00)
>consensus
AAGAAAAGAAAGAUCCAAUCAUAUU_UUCAAUUAUAAUAAUAU__GUAGUUA__UAUUUCAUUGAAAGGAUCAUACUGG__________ACUCAGUUGAGGUGUCAAUAGAAACA
............................................................(((((.....(((.(((((............))))))))....)))))....... ( -3.54 =  -3.98 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:56 2006