Locus 7821

Sequence ID	2L_DroMel_CAF1
Location	22,153,929 – 22,154,037
Length	108
Max. P	0.748793

overview

Window 3

Location	22,153,929 – 22,154,037
Length	108
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	86.06
Mean single sequence MFE	-28.85
Consensus MFE	-21.81
Energy contribution	-21.00
Covariance contribution	-0.81
Combinations/Pair	1.20
Mean z-score	-1.39
Structure conservation index	0.76
SVM decision value	-0.05
SVM RNA-class probability	0.509653
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 22153929 108 + 22407834
GAAAGGACAUAUGCAGCUGAAGUGUUAACGAUGGAACAUCGUUU-UCUA--UUCUUUAAUAUCAUUGUGGUGAUAUAUGCGCCCUUAGAGAUGGUUCUGGGGCUAGCAUAG
.........(((((.(((((((.(..(((((((...))))))).-.)..--..)))))(((((((....)))))))..))(((((.((((....)))))))))..))))). ( -32.10)
>DroSim_CAF1 25922 109 + 1
GAAAGGACAUAUGCAGCUGAAGUGUUAACGAUGGAAUAUCGUUUGUCUA--UUCUUUAAUAUCAUUGUGGUGAGAUAUGCGCCCGCAGAGGUGGUUCUGGGGUUAGCAUAG
(((.(((((.....(((......)))(((((((...)))))))))))).--))).......((((....))))..(((((((((.(((((....)))))))))..))))). ( -28.30)
>DroEre_CAF1 30938 110 + 1
GAAAGAAAAUAUGCAGCUGAAGUGUUACCGAUGAAACAUCGUUUGUUUUGUUUUUUAAAUAUCUUUGUGGUGAG-AAUGUGCCCUUGGUAAUGGUUCUGGGGCUAGCAUAG
.........((((((((((((.(((((((((..(((((.....)))))..)).........((((......)))-)..........))))))).)))...)))).))))). ( -27.40)
>DroYak_CAF1 32602 109 + 1
GAAAGAAAAUAUGCAGCUGAAGUGUUAACGAUGGAACAUCGUUUAUUUU--UUUUUAAAUAUCUUUGUGGUGAGUUAUGCGCCCUCGGUGACAGUUCUGGGGCUAGCAUAG
.........((((((((((((.(((((.(((.((..(((..((((((..--.................))))))..)))..)).))).))))).)))...)))).))))). ( -27.61)
>consensus
GAAAGAAAAUAUGCAGCUGAAGUGUUAACGAUGGAACAUCGUUUGUCUA__UUCUUAAAUAUCAUUGUGGUGAGAUAUGCGCCCUCAGAGAUGGUUCUGGGGCUAGCAUAG
.........(((((.((.........(((((((...)))))))................((((.....))))......))((((.(((........)))))))..))))). (-21.81 = -21.00 +  -0.81)

alignment

secondary structure

dotplot

Window 4

Location	22,153,929 – 22,154,037
Length	108
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	86.06
Mean single sequence MFE	-20.45
Consensus MFE	-13.30
Energy contribution	-15.05
Covariance contribution	1.75
Combinations/Pair	1.00
Mean z-score	-2.15
Structure conservation index	0.65
SVM decision value	0.47
SVM RNA-class probability	0.748793
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 22153929 108 - 22407834
CUAUGCUAGCCCCAGAACCAUCUCUAAGGGCGCAUAUAUCACCACAAUGAUAUUAAAGAA--UAGA-AAACGAUGUUCCAUCGUUAACACUUCAGCUGCAUAUGUCCUUUC
.(((((..((((.(((......)))..))))((..((((((......))))))....(((--....-.(((((((...))))))).....))).)).)))))......... ( -24.50)
>DroSim_CAF1 25922 109 - 1
CUAUGCUAACCCCAGAACCACCUCUGCGGGCGCAUAUCUCACCACAAUGAUAUUAAAGAA--UAGACAAACGAUAUUCCAUCGUUAACACUUCAGCUGCAUAUGUCCUUUC
.(((((...(((((((......)))).))).(((((((..........)))))....(((--......((((((.....)))))).....))).)).)))))......... ( -21.30)
>DroEre_CAF1 30938 110 - 1
CUAUGCUAGCCCCAGAACCAUUACCAAGGGCACAUU-CUCACCACAAAGAUAUUUAAAAAACAAAACAAACGAUGUUUCAUCGGUAACACUUCAGCUGCAUAUUUUCUUUC
.(((((.(((....(((...(((((..((.......-....))............................((((...)))))))))...))).))))))))......... ( -16.50)
>DroYak_CAF1 32602 109 - 1
CUAUGCUAGCCCCAGAACUGUCACCGAGGGCGCAUAACUCACCACAAAGAUAUUUAAAAA--AAAAUAAACGAUGUUCCAUCGUUAACACUUCAGCUGCAUAUUUUCUUUC
.(((((..((((..(.........)..))))((.................(((((.....--.)))))(((((((...))))))).........)).)))))......... ( -19.50)
>consensus
CUAUGCUAGCCCCAGAACCAUCACCAAGGGCGCAUAUCUCACCACAAAGAUAUUAAAAAA__AAAACAAACGAUGUUCCAUCGUUAACACUUCAGCUGCAUAUGUCCUUUC
.(((((..(((((((........))).)))).....................................(((((((...)))))))............)))))......... (-13.30 = -15.05 +   1.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:38 2006