Locus 2147

Sequence ID	3R_DroMel_CAF1
Location	6,129,715 – 6,129,889
Length	174
Max. P	0.684768

overview

Window 9

Location	6,129,715 – 6,129,815
Length	100
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	78.75
Mean single sequence MFE	-43.38
Consensus MFE	-25.84
Energy contribution	-25.27
Covariance contribution	-0.58
Combinations/Pair	1.36
Mean z-score	-1.50
Structure conservation index	0.60
SVM decision value	-0.00
SVM RNA-class probability	0.531247
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6129715 100 - 27905053
UGCGAUGAACGUCCAGCCCUCAAGGAACUUGUGCCCUCAGUGGCAG-----CAACUUGCGGCAAUUGCGGUGGAGGCGAGAGACAGCCACUCGGGGGACGUCCUA
((.(((....))))).......((((...(((.((((.((((((.(-----(...(..(.((....)).)..)..))(.....).)))))).)))).))))))). ( -33.20)
>DroGri_CAF1 47861 100 - 1
UGCGAGGAGCGUCCA---CGCAGGGAGCUGCUGCCAUCGGUGACGG-UGG-CACCACCGGGUGCCUGUGGCGGCGGCGAUAGGUAGCCACUCGGUGGACGCCCCA
.....((.(((((((---(((((....))))((((((((....)))-)))-)).....((.(((((((.((....)).))))))).)).....)))))))).)). ( -60.10)
>DroSec_CAF1 41657 100 - 1
UGCGAGGAACGUCCAACCCUUAGGGAACUGGUGCCCUCAGUGGCAG-----CAACUUGCGGCAAUUGCGGUGGAGGCGAGAGACAGCCACUCGGAGGACGUCCUA
....((((.(((((.(((...((....)))))..((..((((((.(-----(...(..(.((....)).)..)..))(.....).)))))).)).))))))))). ( -35.30)
>DroSim_CAF1 42701 100 - 1
UGCGAGGAACGUCCAACCCUCAGGGAACUUGUGCCCUCAGUGGCUG-----CAACUUGCGGCAAUUGCGGUGGAGGCGAGAGACAGCCACUCGGAGGACGUCCUA
....((((.(((((.......((((........))))((((.((((-----(.....))))).))))((((((..((....).)..)))).))..))))))))). ( -38.20)
>DroEre_CAF1 42150 100 - 1
UGCGAGGAACGUCCAACCCUCAGGGAACUGGUGCCUUCAGUGGCAG-----CCACUUGUGGCAGUUGCGGUGGAGGCGAGAGGCAGCCACUCGGAGGACGUCCUA
....((((.(((((...((((((....)))).((((((((..((.(-----(((....)))).))..)..)))))))(((.((...)).))))).))))))))). ( -44.20)
>DroWil_CAF1 44758 100 - 1
UGCGAGGUGCGUCUA---CGCAGGGAGCUGCUGCCAUCGG--GCAAACUGCCAAUGUUUGGCAAUUGCGGCGGCGGCGAGAGGCAACCACUUGGUGGACGCCCCA
.....((.(((((((---(.((((..(((((((((.....--((((..(((((.....))))).)))))))))))))..(.(....)).)))))))))))).)). ( -49.30)
>consensus
UGCGAGGAACGUCCAACCCUCAGGGAACUGGUGCCCUCAGUGGCAG_____CAACUUGCGGCAAUUGCGGUGGAGGCGAGAGACAGCCACUCGGAGGACGUCCUA
.....((.((((((...((((.....((((.((((...(((............)))...))))....)))).))))((((.(.....).))))..)))))))).. (-25.84 = -25.27 +  -0.58)

alignment

secondary structure

dotplot

Window 0

Location	6,129,777 – 6,129,889
Length	112
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	78.01
Mean single sequence MFE	-45.97
Consensus MFE	-29.68
Energy contribution	-30.27
Covariance contribution	0.59
Combinations/Pair	1.42
Mean z-score	-1.41
Structure conservation index	0.65
SVM decision value	0.31
SVM RNA-class probability	0.684768
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6129777 112 - 27905053
UGAGCAUGCUCUGGGUUUCCCGAUCC------CUAGGUUCGUCAAAGAAGUCGGGACGCAGGAAGCGGGAAAUCCGACGCUGCGAUGAACGUCCAGCCCUCAAGGAACUUGUGCCCUC
...((((....(((((((((((...(------((.(..(((.(......).)))..)..)))...)))))))))))..((((.(((....)))))))((....)).....)))).... ( -36.20)
>DroVir_CAF1 41458 109 - 1
GUAGGGCACUUUGAGAGUCACGCUCG------CGUGGUUCAUCAAAGAAGUCGGGCCGCAGAAAGCGUGAGAUUCGACGCUGCGAGGAGCGUCUA---CGCAAGGAGCUACUGCCGUC
(((((((.(((((.((((((((((..------((((((((..(......)..))))))).)..)))))))..)))((((((......))))))..---..))))).))).)))).... ( -42.70)
>DroGri_CAF1 47926 109 - 1
GCAGCACACUUUGAGAGUCGCGCUCG------CGUGGCUCGUCGAAGAAGUCGGGCCGCAGAAAGCGUGAGAUUCGGCGCUGCGAGGAGCGUCCA---CGCAGGGAGCUGCUGCCAUC
(((((.......(((..(((((((..------(((((((((.(......).)))))))).)..)))))))..)))(((.(((((.((.....)).---)))))...)))))))).... ( -51.90)
>DroWil_CAF1 44823 115 - 1
GAAGCAUGCUCUGGGUUUCACGUUCACGAUCGCGCGGCUCGUCAAAGAAGUCGGGCCGCAGAAAACGUGAGAUUCGGCGUUGCGAGGUGCGUCUA---CGCAGGGAGCUGCUGCCAUC
..((((.(((((((((((((((((.....((..((((((((.(......).)))))))).)).)))))))))))).((((.(((.....)))..)---)))..)))))))))...... ( -50.80)
>DroMoj_CAF1 53803 109 - 1
GCAGCACGCUUUGGGAGUCGCGCUCG------CGUGGCUCGUCGAAGAAGUCGGGCCGCAGAAAGCGUGAGAUUCGACGCUGCGAGGAGCGUCUA---CGCAACGAGCUGCUGCCGUC
((((((.((((((.(((.(((.((((------(((((((((.(......).))))))))....(((((........))))))))))..))).)).---).))..)))))))))).... ( -54.60)
>DroAna_CAF1 36933 112 - 1
UUAGCAUGCUCUGAGACUCCCGAUCC------CGGGGAUCGUCGAAGAAGUCCGGUCGCAGAAAGCGGGAGAUGCGUCGCUGAGACGAGCGUCCAAUCCUCAAGGAGCUGGAGCCCUC
...((.(((((.....(((((((..(------((((..((......))..)))))))((.....)))))))....(((.....))))))))((((.(((....)))..)))))).... ( -39.60)
>consensus
GCAGCACGCUCUGAGAGUCACGCUCG______CGUGGCUCGUCAAAGAAGUCGGGCCGCAGAAAGCGUGAGAUUCGACGCUGCGAGGAGCGUCCA___CGCAAGGAGCUGCUGCCAUC
(((((...(((((.(..(((((((.........((((((((.(......).))))))))....))))))).....((((((......)))))).....).))))).)))))....... (-29.68 = -30.27 +   0.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:30 2006