Locus 5368

Sequence ID	3L_DroMel_CAF1
Location	14,778,112 – 14,778,292
Length	180
Max. P	0.765169

overview

Window 7

Location	14,778,112 – 14,778,212
Length	100
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	83.09
Mean single sequence MFE	-29.18
Consensus MFE	-19.29
Energy contribution	-19.35
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.66
SVM decision value	-0.03
SVM RNA-class probability	0.520583
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14778112 100 + 23771897
AAAGGGGUAU--CAAAUGGGGGAGGGGGGUGGUGUGUAGGGCACUGUGCGGUUGCGGCCUGAAGAUUUUGAAGUUUUUGCGGUGGCCGCUGCUCUUUUCGUU
..........--.........((((((((..(((..(((....)))..)(((..(.((..(((((((....))))))))).)..)))))..))))))))... ( -33.30)
>DroSec_CAF1 20974 80 + 1
AAAGGGGUAU--CAAAGGGGGG--------------------ACCGUGCUGUUGCGGCCUGAAGAUUUUGAAGUUUUUGCGGUGGCCGCUGCUCGUUUCGUU
(((.(((((.--.....((...--------------------.))........((((((.(((((((....))))))).....))))))))))).))).... ( -23.70)
>DroEre_CAF1 20329 82 + 1
AAAGGGGUUUUCCAAGGGGGGG--------------------GCUGUGCGGUUGCGGCCUGAAGAUUUUGAAGUUUUUGCGGUGGCCGCUGCUCGUUUCGUU
...(((....)))..(..(.((--------------------((...(((((..(.((..(((((((....))))))))).)..))))).)))).)..)... ( -31.00)
>DroYak_CAF1 21123 82 + 1
AAAGGGGUUUUCCAAAGGGGGG--------------------ACUGUGCGGUUGCGGCCUGAAGAUUUCGAAGUUUUUGCGGUGGCCGCUGCUCGUUUCGUU
...((((((..((....))..)--------------------))...(((((..(.((..(((((((....))))))))).)..)))))..)))........ ( -28.70)
>consensus
AAAGGGGUAU__CAAAGGGGGG____________________ACUGUGCGGUUGCGGCCUGAAGAUUUUGAAGUUUUUGCGGUGGCCGCUGCUCGUUUCGUU
(((.((((.........(.((......................)).)(((((..(.((..(((((((....))))))))).)..))))).)))).))).... (-19.29 = -19.35 +   0.06)

alignment

secondary structure

dotplot

Window 8

Location	14,778,150 – 14,778,252
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.50
Mean single sequence MFE	-27.73
Consensus MFE	-22.32
Energy contribution	-22.40
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-1.62
Structure conservation index	0.80
SVM decision value	0.39
SVM RNA-class probability	0.715084
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14778150 102 - 23771897
UUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUGAAGCGAAACGAAAAGAGCAGCGG------------------CCACCGCAAAAACUUCAAAAUCUUCAGGCCGCAACCGCACAGUGC
((((((....)))))).....(((.((((((((....((...))..))))...((((------------------((........................))))))...)))).))).. ( -28.06)
>DroSec_CAF1 20994 100 - 1
UUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUCAAGCGAAACGAAACGAGCAGCGG------------------CCACCGCAAAAACUUCAAAAUCUUCAGGCCGCAACAGCACGGU--
((((((....)))))).......(((((........)))))......((.((.((((------------------((........................))))))....)).))..-- ( -25.66)
>DroEre_CAF1 20351 100 - 1
CUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUGAAGCGAAACGAAACGAGCAGCGG------------------CCACCGCAAAAACUUCAAAAUCUUCAGGCCGCAACCGCACAGC--
.(((((....))))).........(((((.(((((((((........))....((((------------------...))))..............))))))).))))).........-- ( -26.30)
>DroYak_CAF1 21145 100 - 1
CUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUGAAGCGAAACGAAACGAGCAGCGG------------------CCACCGCAAAAACUUCGAAAUCUUCAGGCCGCAACCGCACAGU--
.(((((....))))).........(((((.(((((((.....((((.......((((------------------...))))......))))....))))))).))))).........-- ( -28.12)
>DroAna_CAF1 21073 118 - 1
UUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUGAAGCGAAACGAAACGAACAGCGGCGGCCCAGAUGCCGGCGACCACCGCAAAAACUUCAAAAUCUUCAACCCGUAACCGCACCAC--
((((((....))))))........(((((..((((((((........))....((((.(((((.......)).).)).))))..............))))))..))))).........-- ( -30.50)
>consensus
UUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUGAAGCGAAACGAAACGAGCAGCGG__________________CCACCGCAAAAACUUCAAAAUCUUCAGGCCGCAACCGCACAGU__
.(((((....))))).........(((((.(((((((......(((.......((((.....................))))......))).....))))))).)))))........... (-22.32 = -22.40 +   0.08)

alignment

secondary structure

dotplot

Window 9

Location	14,778,190 – 14,778,292
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.93
Mean single sequence MFE	-37.40
Consensus MFE	-28.70
Energy contribution	-28.42
Covariance contribution	-0.28
Combinations/Pair	1.14
Mean z-score	-1.79
Structure conservation index	0.77
SVM decision value	0.51
SVM RNA-class probability	0.765169
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14778190 102 - 23771897
GAUCCUUUGAGAUGAAGCCAUCGGUUGCAACUCGCGACCGUUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUGAAGCGAAACGAAAAGAGCAGCGG------------------CCACC
..........((((....))))((((((..(((.....((((.(((.((((((((((......)))))).))))..))).))))....)))..))))------------------))... ( -33.30)
>DroSec_CAF1 21032 102 - 1
GAUCCUUUGAGAUGAAGCCAUCGGUUGCAACUCGCGGCCGUUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUCAAGCGAAACGAAACGAGCAGCGG------------------CCACC
........(((.((.((((...)))).)).)))..(((((((((((..(((((((((......)))))).)))...))....((...)).)))))))------------------))... ( -34.90)
>DroEre_CAF1 20389 102 - 1
GAUCCUUUGAGAUGAAGCCAUCGGUUGCAACUCGCGGCCGCUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUGAAGCGAAACGAAACGAGCAGCGG------------------CCACC
........(((.((.((((...)))).)).)))..(((((((((((.((((((((((......)))))).))))..))....((...)).)))))))------------------))... ( -38.20)
>DroYak_CAF1 21183 102 - 1
GAUCCUUUGAGAUGAAGCCAUCGGUUGCAACUCGCGGCCGCUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUGAAGCGAAACGAAACGAGCAGCGG------------------CCACC
........(((.((.((((...)))).)).)))..(((((((((((.((((((((((......)))))).))))..))....((...)).)))))))------------------))... ( -38.20)
>DroAna_CAF1 21111 120 - 1
GACCCUUUGAGAUGAAGCCGUUGGCUGCAACUCGCGGCCGUUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUGAAGCGAAACGAAACGAACAGCGGCGGCCCAGAUGCCGGCGACCACC
..(((...........((((((((((((.....)))))((((.(((.((((((((((......)))))).))))..))).)))).......)))))))(((......))))).)...... ( -42.40)
>consensus
GAUCCUUUGAGAUGAAGCCAUCGGUUGCAACUCGCGGCCGUUGCGCCUAAGCGCAAGAUAAACUUUGCGUCUUGAAGCGAAACGAAACGAGCAGCGG__________________CCACC
..(((((..(((((.......(((((((.....))))))).(((((....)))))............)))))..))).))........................................ (-28.70 = -28.42 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:29 2006