Locus 3863

Sequence ID	3L_DroMel_CAF1
Location	11,179,218 – 11,179,317
Length	99
Max. P	0.803009

overview

Window 2

Location	11,179,218 – 11,179,317
Length	99
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	91.19
Mean single sequence MFE	-25.30
Consensus MFE	-19.78
Energy contribution	-20.22
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.78
Structure conservation index	0.78
SVM decision value	0.62
SVM RNA-class probability	0.803009
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11179218 99 + 23771897
UGCUGUUUGAGAACCAUUUUGUAUCUUUCAUCUCAGAUGCAGAUGCAUCUGAACACUUGAAUCUGCAUCU------GCUCCGUUUUCCGAGCAAUUCCAG-AGUAA
((((..(((.(((......((((...((((..((((((((....)))))))).....))))..))))..(------((((.(....).))))).))))))-)))). ( -24.90)
>DroSec_CAF1 39211 100 + 1
UGCUGUUUGAGAACCAUUUUGUAUCUUUCAUCUCAGAUGCAGAUGCAUCUGAACACUUGAAUCUGCAUCUG----UGCUCCGUU-UCCGAGCAAUUCCAG-AGUAA
(((.(((..((.((......))..........((((((((....))))))))...))..)))..)))((((----(((((....-...)))))....)))-).... ( -26.20)
>DroSim_CAF1 39029 101 + 1
UGCUGUUUGAGAACCAUUUUGUAUCUUUCAUCUCUGAUGCAGAUGCAUCUGAACACUUGAAGCUGCAUCUG----UGCUCCGUG-UCCGAGCAAUUCCAGAAGUAA
((((...(((((.............)))))..((((..(((((((((.((..........)).))))))))----)((((....-...)))).....)))))))). ( -24.72)
>DroEre_CAF1 40718 98 + 1
GGCUAUUUGAGAACCAUUUUGUAUCUUGCAUCUCAGAUGCAGAUGCAUCUGAGUACUUGAAUCUGCAUCU------GCUCCGUU-UCCGAGCAAUUCCAG-AGUAA
.....((..((.((((...(((((((.(((((...))))))))))))..)).)).))..))((((.(..(------((((....-...)))))..).)))-).... ( -28.40)
>DroYak_CAF1 41968 104 + 1
GGCUAUUUGAGAACCACUUUGUAUCUUUCAUCUGAGAUGCAGAUGUAUCUGAAUACUUGAAUCUGCAUCUGCAACUGCUCCGUU-UCCCAGCAAUUCCAG-AGUAA
...(((((.(((..((.((((((((((......))))))))))))..))))))))........(((.((((.((.((((.....-....)))).)).)))-)))). ( -22.30)
>consensus
UGCUGUUUGAGAACCAUUUUGUAUCUUUCAUCUCAGAUGCAGAUGCAUCUGAACACUUGAAUCUGCAUCUG____UGCUCCGUU_UCCGAGCAAUUCCAG_AGUAA
.(((...((.(((.....................((((((((((.((..........)).))))))))))......((((.(....).))))..)))))..))).. (-19.78 = -20.22 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	11,179,218 – 11,179,317
Length	99
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	91.19
Mean single sequence MFE	-28.27
Consensus MFE	-19.66
Energy contribution	-20.06
Covariance contribution	0.40
Combinations/Pair	1.08
Mean z-score	-2.33
Structure conservation index	0.70
SVM decision value	0.09
SVM RNA-class probability	0.580859
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11179218 99 - 23771897
UUACU-CUGGAAUUGCUCGGAAAACGGAGC------AGAUGCAGAUUCAAGUGUUCAGAUGCAUCUGCAUCUGAGAUGAAAGAUACAAAAUGGUUCUCAAACAGCA
....(-(((.(.((((((.(....).))))------)).).))))((((....(((((((((....))))))))).)))).......................... ( -28.40)
>DroSec_CAF1 39211 100 - 1
UUACU-CUGGAAUUGCUCGGA-AACGGAGCA----CAGAUGCAGAUUCAAGUGUUCAGAUGCAUCUGCAUCUGAGAUGAAAGAUACAAAAUGGUUCUCAAACAGCA
.....-(((....((((((..-..).)))))----(((((((((((.((..........)).))))))))))).((.(((..((.....))..)))))...))).. ( -28.40)
>DroSim_CAF1 39029 101 - 1
UUACUUCUGGAAUUGCUCGGA-CACGGAGCA----CAGAUGCAGCUUCAAGUGUUCAGAUGCAUCUGCAUCAGAGAUGAAAGAUACAAAAUGGUUCUCAAACAGCA
.............((((.(((-((((((((.----........)))))..)))))).(((((....))))).((((..................))))....)))) ( -23.97)
>DroEre_CAF1 40718 98 - 1
UUACU-CUGGAAUUGCUCGGA-AACGGAGC------AGAUGCAGAUUCAAGUACUCAGAUGCAUCUGCAUCUGAGAUGCAAGAUACAAAAUGGUUCUCAAAUAGCC
....(-(((.(.(((((((..-..).))))------)).).)))).....((((((((((((....))))))))).)))............((((.......)))) ( -33.30)
>DroYak_CAF1 41968 104 - 1
UUACU-CUGGAAUUGCUGGGA-AACGGAGCAGUUGCAGAUGCAGAUUCAAGUAUUCAGAUACAUCUGCAUCUCAGAUGAAAGAUACAAAGUGGUUCUCAAAUAGCC
.....-.((((((..((.(..-..)....((.(((.((((((((((....((((....))))))))))))))))).))..........))..)))).))....... ( -27.30)
>consensus
UUACU_CUGGAAUUGCUCGGA_AACGGAGCA____CAGAUGCAGAUUCAAGUGUUCAGAUGCAUCUGCAUCUGAGAUGAAAGAUACAAAAUGGUUCUCAAACAGCA
.......(((((((((((.(....).))))......((((((((((....((((....))))))))))))))...................))))).))....... (-19.66 = -20.06 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:36 2006