Locus 2007

Sequence ID	3L_DroMel_CAF1
Location	5,516,582 – 5,516,681
Length	99
Max. P	0.990240

overview

Window 1

Location	5,516,582 – 5,516,681
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	60.08
Mean single sequence MFE	-41.80
Consensus MFE	-21.54
Energy contribution	-21.55
Covariance contribution	0.01
Combinations/Pair	1.43
Mean z-score	-2.99
Structure conservation index	0.52
SVM decision value	2.20
SVM RNA-class probability	0.990240
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5516582 99 + 23771897
AACAGCGCCACCGUUUCCGGUGUUAUAGCG---------------ACC---GCCGUUUCCGGCGGUAUAACGAUCGCCAGAG---CCGGCGGCACCACCGUUUCCGGUGGUGUAACGGUC
....((..(((((....))))).....))(---------------(((---((((.(((.((((((......)))))).)))---.)))).(((((((((....)))))))))...)))) ( -49.60)
>DroVir_CAF1 62020 117 + 1
AACACCGGAACCUUUGCCGGGAGGAUAGACGCCAACACCGCCAGGGCCGGAACCGCUGCCGGUGUGGUAA---GCGCCACCAUCACCAGAUCCGGUACCAGUGCCAGGACGGUAUUUGCC
....((((........))))..........((.((.((((((..((((((.((((...(.((((((((..---.....)))).)))).)...)))).)).).))).)).)))).)).)). ( -39.90)
>DroSim_CAF1 79803 99 + 1
AACAGCGCCACCGUUUCCGGUGGUAUAGCG---------------ACC---ACCGUUUCCGGCGGUAUAACGAUCGCCAGAG---CCGGCGGCACCACCGUUUCCGGUGGUGUAACGGUC
....(((((((((....)))))))...))(---------------(((---.(((.(((.((((((......)))))).)))---.)))..(((((((((....)))))))))...)))) ( -49.80)
>DroEre_CAF1 79163 75 + 1
AAUGGCGCCACCGC------------------------------------------UUCCGGUGGUAUAACGGUCGCCGGAG---CCGGCGGCACCACCGCUUCCGGUGGUGUAACGGUC
....(((((((((.------------------------------------------...(((((((......(((((((...---.))))))))))))))....)))))))))....... ( -41.40)
>DroYak_CAF1 67259 75 + 1
AACGGCGCCACCGU------------------------------------------UUCCGGUGGUAUAGCGAUCGCCGGAA---CCGGCAGCACCACCGUUUCCGGUGGUGUAACGGUC
....(((((((((.------------------------------------------...)))))))...))((((((((...---.)))).(((((((((....)))))))))...)))) ( -40.00)
>DroAna_CAF1 40584 75 + 1
GACUCCGCCACCGU------------------------------------------UUCCGGUGGUAUAACGAUCGCCGGAG---CCAACUCCGCCACCGUUUCCGGUGGUAUAACGACC
......(((((((.------------------------------------------...))))))).......(((..((((---....))))(((((((....)))))))....))).. ( -30.10)
>consensus
AACAGCGCCACCGU__________________________________________UUCCGGUGGUAUAACGAUCGCCAGAG___CCGGCGGCACCACCGUUUCCGGUGGUGUAACGGUC
........................................................(((.((((((......)))))).)))...(((...(((((((((....)))))))))..))).. (-21.54 = -21.55 +   0.01)

alignment

secondary structure

dotplot

Window 2

Location	5,516,582 – 5,516,681
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	60.08
Mean single sequence MFE	-49.62
Consensus MFE	-26.36
Energy contribution	-26.52
Covariance contribution	0.16
Combinations/Pair	1.43
Mean z-score	-4.70
Structure conservation index	0.53
SVM decision value	1.48
SVM RNA-class probability	0.957920
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5516582 99 - 23771897
GACCGUUACACCACCGGAAACGGUGGUGCCGCCGG---CUCUGGCGAUCGUUAUACCGCCGGAAACGGC---GGU---------------CGCUAUAACACCGGAAACGGUGGCGCUGUU
((((....((((((((....))))))))..((((.---.(((((((..........)))))))..))))---)))---------------)((.....(((((....)))))..)).... ( -58.50)
>DroVir_CAF1 62020 117 - 1
GGCAAAUACCGUCCUGGCACUGGUACCGGAUCUGGUGAUGGUGGCGC---UUACCACACCGGCAGCGGUUCCGGCCCUGGCGGUGUUGGCGUCUAUCCUCCCGGCAAAGGUUCCGGUGUU
((......)).....((((((((.(((....((((.((.((((((((---(....((((((.(((.(((....)))))).)))))).)))).))))).))))))....))).)))))))) ( -53.60)
>DroSim_CAF1 79803 99 - 1
GACCGUUACACCACCGGAAACGGUGGUGCCGCCGG---CUCUGGCGAUCGUUAUACCGCCGGAAACGGU---GGU---------------CGCUAUACCACCGGAAACGGUGGCGCUGUU
((((....((((((((....))))))))..((((.---.(((((((..........)))))))..))))---)))---------------)((....((((((....)))))).)).... ( -58.40)
>DroEre_CAF1 79163 75 - 1
GACCGUUACACCACCGGAAGCGGUGGUGCCGCCGG---CUCCGGCGACCGUUAUACCACCGGAA------------------------------------------GCGGUGGCGCCAUU
(((.(((.((((((((....))))))))..((((.---...))))))).)))...((((((...------------------------------------------.))))))....... ( -38.40)
>DroYak_CAF1 67259 75 - 1
GACCGUUACACCACCGGAAACGGUGGUGCUGCCGG---UUCCGGCGAUCGCUAUACCACCGGAA------------------------------------------ACGGUGGCGCCGUU
(((((.((((((((((....)))))))).)).)))---)).(((((.........((((((...------------------------------------------.))))))))))).. ( -45.20)
>DroAna_CAF1 40584 75 - 1
GGUCGUUAUACCACCGGAAACGGUGGCGGAGUUGG---CUCCGGCGAUCGUUAUACCACCGGAA------------------------------------------ACGGUGGCGGAGUC
((((((....((((((....))))))(((((....---)))))))))))......((((((...------------------------------------------.))))))....... ( -43.60)
>consensus
GACCGUUACACCACCGGAAACGGUGGUGCCGCCGG___CUCCGGCGAUCGUUAUACCACCGGAA__________________________________________ACGGUGGCGCUGUU
........((((((((....)))))))).((((((.....)))))).........((((((....(((................................)))....))))))....... (-26.36 = -26.52 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:20 2006