Locus 5662

Sequence ID	3L_DroMel_CAF1
Location	15,540,934 – 15,541,043
Length	109
Max. P	0.618821

overview

Window 3

Location	15,540,934 – 15,541,043
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	78.81
Mean single sequence MFE	-41.08
Consensus MFE	-26.24
Energy contribution	-28.50
Covariance contribution	2.26
Combinations/Pair	1.15
Mean z-score	-1.57
Structure conservation index	0.64
SVM decision value	-0.03
SVM RNA-class probability	0.518551
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15540934 109 + 23771897
ACAUCGGCUGUGACCGGUGGAGGAUCCUCUGGAUCAGGAGGAUCUGCAGCCACUUCUGCUGCCAAGCAGAGGAAGUAGCGCCAGAGUAGCCGCGGUGGAUAUGGAUGCU
.....((((((..((...)).(((((((((......))))))))))))))).((((((((....))))))))....(((((((.....((....)).....))).)))) ( -45.20)
>DroSec_CAF1 3671 109 + 1
ACAUCGGUUGCGACCGGUGGAGGAACCUCUGGACCUGGAGGAUCUGCAGCCACUUCUGCUGCCAAGCAGAGGAAGUAGCGCCAGAGUAGCCGCGGUGGAUAUGGAUGCU
.((((.((..(.((((.(((......((((((.((....))....((.((..((((((((....))))))))..)).)).))))))...))))))).)..)).)))).. ( -42.20)
>DroSim_CAF1 3676 109 + 1
ACAUCGGUUGCGACCGGUGGAGGAACCUCUGGACCAGGAGGAUCUGCAGCCACUUCUGCUGCCAAGCAGAGGAAGUAGCGCCAGAGUAGCCGCGGUGGAUAUGGAUGCU
.((((.((..(.((((.(((......((((((.((....))....((.((..((((((((....))))))))..)).)).))))))...))))))).)..)).)))).. ( -42.00)
>DroEre_CAF1 3734 109 + 1
ACAACGGUUGGGAUCGGUGGAGGGACCUCUGGACCAGGAGGACCUGCAGCCACUUCUUCUGCCAAGCAGAGGAAGUAGCGCCAGAGCAGCCGCGGUGGAUAUGGAUGCU
((..((((((...((((((.(((..(((((......))))).))).).((.(((((((((((...))))))))))).))))).)).))))))..))............. ( -45.60)
>DroAna_CAF1 3672 82 + 1
UCCUCGGCGGC------AGGAGCAGCUCCUG------------CUUUGGGCAGUUCUGUUGCCAAACAGAGAAAGUAGCGCCAG---------GAUGGCUACGGAUGUU
((((.((((((------(((((...))))))------------).....((..(((((((....)))))))...))..))))))---------)).............. ( -30.40)
>consensus
ACAUCGGUUGCGACCGGUGGAGGAACCUCUGGACCAGGAGGAUCUGCAGCCACUUCUGCUGCCAAGCAGAGGAAGUAGCGCCAGAGUAGCCGCGGUGGAUAUGGAUGCU
.((((.(((((....(((...(((.(((((......))))).)))...))).((((((((....))))))))..))))).(((..((....))..))).....)))).. (-26.24 = -28.50 +   2.26)

alignment

secondary structure

dotplot

Window 4

Location	15,540,934 – 15,541,043
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	78.81
Mean single sequence MFE	-36.22
Consensus MFE	-19.72
Energy contribution	-22.36
Covariance contribution	2.64
Combinations/Pair	1.14
Mean z-score	-1.86
Structure conservation index	0.54
SVM decision value	0.17
SVM RNA-class probability	0.618821
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15540934 109 - 23771897
AGCAUCCAUAUCCACCGCGGCUACUCUGGCGCUACUUCCUCUGCUUGGCAGCAGAAGUGGCUGCAGAUCCUCCUGAUCCAGAGGAUCCUCCACCGGUCACAGCCGAUGU
.................(((((...((((.((((((((..((((...))))..))))))))....(((((((........))))))).....))))....))))).... ( -39.40)
>DroSec_CAF1 3671 109 - 1
AGCAUCCAUAUCCACCGCGGCUACUCUGGCGCUACUUCCUCUGCUUGGCAGCAGAAGUGGCUGCAGAUCCUCCAGGUCCAGAGGUUCCUCCACCGGUCGCAACCGAUGU
.......(((((....((((((..((((((((((((((..((((...))))..)))))))).)).((((.....))))))))(((......)))))))))....))))) ( -37.60)
>DroSim_CAF1 3676 109 - 1
AGCAUCCAUAUCCACCGCGGCUACUCUGGCGCUACUUCCUCUGCUUGGCAGCAGAAGUGGCUGCAGAUCCUCCUGGUCCAGAGGUUCCUCCACCGGUCGCAACCGAUGU
.......(((((....((((((..((((((((((((((..((((...))))..))))))))..(((......)))).)))))(((......)))))))))....))))) ( -38.50)
>DroEre_CAF1 3734 109 - 1
AGCAUCCAUAUCCACCGCGGCUGCUCUGGCGCUACUUCCUCUGCUUGGCAGAAGAAGUGGCUGCAGGUCCUCCUGGUCCAGAGGUCCCUCCACCGAUCCCAACCGUUGU
.............((.((((.(((((((((((((((((.(((((...))))).))))))))..((((....))))).))))))(((........)))..)).)))).)) ( -39.20)
>DroAna_CAF1 3672 82 - 1
AACAUCCGUAGCCAUC---------CUGGCGCUACUUUCUCUGUUUGGCAACAGAACUGCCCAAAG------------CAGGAGCUGCUCCU------GCCGCCGAGGA
..............((---------((((((........((((((....))))))..........(------------((((((...)))))------)))))).)))) ( -26.40)
>consensus
AGCAUCCAUAUCCACCGCGGCUACUCUGGCGCUACUUCCUCUGCUUGGCAGCAGAAGUGGCUGCAGAUCCUCCUGGUCCAGAGGUUCCUCCACCGGUCGCAACCGAUGU
..................((...((((((.((((((((..((((...))))..))))))))..(((......)))..))))))...))..((.((((....)))).)). (-19.72 = -22.36 +   2.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:59 2006