Locus 5403

Sequence ID	X_DroMel_CAF1
Location	14,055,270 – 14,055,360
Length	90
Max. P	0.646731

overview

Window 7

Location	14,055,270 – 14,055,360
Length	90
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	74.25
Mean single sequence MFE	-18.02
Consensus MFE	-3.00
Energy contribution	-3.24
Covariance contribution	0.24
Combinations/Pair	1.31
Mean z-score	-1.50
Structure conservation index	0.17
SVM decision value	0.06
SVM RNA-class probability	0.563726
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14055270 90 + 22224390
GACUAUCGUAAUUACCGUUAACGCCCACCUGACGUCAUCGGAA-GCGAUA--GCGGCACCGUUACCUUC--UCUCCGCAUCUUCUCUCUUCCGUA
.......(((((..((((((.(((....((((.....))))..-))).))--))))....)))))....--........................ ( -15.40)
>DroSec_CAF1 23924 86 + 1
GACUAUCGUAAUUACCGU-AAUUACCACCUGACGUCAUCGGCG-GAGAUA--GCGGCACCGUUACCUUC--ACUCCGCAUC---UCUCCUCCCUA
(((....(((((((...)-))))))(....)..)))...((.(-((((..--((((.............--...))))...---))))).))... ( -17.59)
>DroEre_CAF1 24248 87 + 1
GACUAUGGUAAUUACCGUUAACUCCCACCUGACGUCAUCAGCG-GAGACA--ACGGCUGCAUUAUCUCC--UCUCCGCAUC---UCUCUUCCUUA
......(((((((((((((..((((...((((.....)))).)-)))..)--)))).)).))))))...--..........---........... ( -17.20)
>DroYak_CAF1 23690 87 + 1
GACUAUCGUAAUUACCGUUAACGCCCACCUGACGUCAUCAGCG-GAGAUA--ACGACUCCGUUAUCUCC--UUUCCGCAUC---UCUCUUCCUUA
......................((....((((.....)))).(-((((((--(((....))))))))))--.....))...---........... ( -19.20)
>DroAna_CAF1 19638 80 + 1
AGCUAUCGUAAUUGCCGU-------CACCUGACGUCAUCUGCAGGUGAUAUCAAGAUUGCUUUAUCUGCGGCUUCAGCGUU---ACACUU-----
......(((....(((((-------((((((.((.....))))))))))....((((......))))..)))....)))..---......----- ( -20.70)
>consensus
GACUAUCGUAAUUACCGUUAACGCCCACCUGACGUCAUCAGCG_GAGAUA__ACGGCUCCGUUAUCUCC__UCUCCGCAUC___UCUCUUCCUUA
.......(((((..((((..........((((.....))))...........))))....))))).............................. ( -3.00 =  -3.24 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	14,055,270 – 14,055,360
Length	90
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	74.25
Mean single sequence MFE	-24.72
Consensus MFE	-5.06
Energy contribution	-4.18
Covariance contribution	-0.88
Combinations/Pair	1.50
Mean z-score	-1.63
Structure conservation index	0.20
SVM decision value	0.24
SVM RNA-class probability	0.646731
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14055270 90 - 22224390
UACGGAAGAGAGAAGAUGCGGAGA--GAAGGUAACGGUGCCGC--UAUCGC-UUCCGAUGACGUCAGGUGGGCGUUAACGGUAAUUACGAUAGUC
..((((((.((......((((...--(..(....)..).))))--..)).)-))))).(((((((.....))))))).((.......))...... ( -24.70)
>DroSec_CAF1 23924 86 - 1
UAGGGAGGAGA---GAUGCGGAGU--GAAGGUAACGGUGCCGC--UAUCUC-CGCCGAUGACGUCAGGUGGUAAUU-ACGGUAAUUACGAUAGUC
...((.(((((---...((((.((--.......))....))))--..))))-).))...(((.....((.((((((-(...))))))).)).))) ( -25.80)
>DroEre_CAF1 24248 87 - 1
UAAGGAAGAGA---GAUGCGGAGA--GGAGAUAAUGCAGCCGU--UGUCUC-CGCUGAUGACGUCAGGUGGGAGUUAACGGUAAUUACCAUAGUC
...........---((((((.((.--((((((((((....)))--))))))-).))..)).))))..((((.(((((....))))).)))).... ( -24.60)
>DroYak_CAF1 23690 87 - 1
UAAGGAAGAGA---GAUGCGGAAA--GGAGAUAACGGAGUCGU--UAUCUC-CGCUGAUGACGUCAGGUGGGCGUUAACGGUAAUUACGAUAGUC
...........---(((.((....--((((((((((....)))--))))))-)((((.(((((((.....))))))).)))).....))...))) ( -30.10)
>DroAna_CAF1 19638 80 - 1
-----AAGUGU---AACGCUGAAGCCGCAGAUAAAGCAAUCUUGAUAUCACCUGCAGAUGACGUCAGGUG-------ACGGCAAUUACGAUAGCU
-----.((((.---..))))...((((.((((......)))).....((((((((.......).))))))-------)))))............. ( -18.40)
>consensus
UAAGGAAGAGA___GAUGCGGAGA__GAAGAUAACGGAGCCGU__UAUCUC_CGCCGAUGACGUCAGGUGGGAGUUAACGGUAAUUACGAUAGUC
..............(((((((.......(((((.((....))...)))))....)))....)))).............................. ( -5.06 =  -4.18 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:07 2006