Locus 8666

Sequence ID	3R_DroMel_CAF1
Location	23,155,558 – 23,155,678
Length	120
Max. P	0.718463

overview

Window 6

Location	23,155,558 – 23,155,678
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.36
Mean single sequence MFE	-49.12
Consensus MFE	-41.64
Energy contribution	-41.83
Covariance contribution	0.19
Combinations/Pair	1.14
Mean z-score	-1.65
Structure conservation index	0.85
SVM decision value	0.39
SVM RNA-class probability	0.718463
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23155558 120 + 27905053
UUGGGCAGGUUUCUUUUGAGGAGCUGCCAGUUGAUGCUGGUCGGUGGAGCGGCGGACCGCUGCUUGAUCAGCUUCUUGUGACUAGAUCCCUUCGAGAGUUUGGAGCGGGCGGAACCCAGG
(((((..((..(((..(((((((((((((((....)))))).(((.((((((((...)))))))).)))))))))))).....)))..))((((...((.....))...)))).))))). ( -47.50)
>DroSec_CAF1 6230 120 + 1
UUGGGCAGGUUUCGUUUGAGGAGCUGCCAGUUGAUGCUGGUCGGUGGAGCGGUGGACCGCUGCUUGAUCAGCCUCUUGUGGCUAGAUCCCUUCGAGAUUUUGGAGCGGGCGGUACCCAGG
(((((......(((((((.(((.((((((...((.(((((((((.(.(((((....))))).)))))))))).))...)))).)).)))((((((....)))))))))))))..))))). ( -49.00)
>DroSim_CAF1 10757 120 + 1
UUGGGCAGGUUUCGUUUGAGGAGCUGCCAGUUGAUGCUGGUCGGUGGAGCGGUGGACCGCUGCUUGAUCAGCCUCUUGUGGCUAGAUCCCUUCGAGAUUUUGGAGCGGGCGGAACCCAGG
.......(((((((((((.(((.((((((...((.(((((((((.(.(((((....))))).)))))))))).))...)))).)).)))((((((....))))))))))))))))).... ( -52.40)
>DroYak_CAF1 10741 120 + 1
UUGGGCAGAUUCCGUUUGAGUAGCUGCCAGUUGAUGCUGGUCGGUGGAGGAGCGGACCUCUGCUUGACCAGCUUCUUGUGACUCGAUCCCUUCGAGAGUUUGGAGCGGGCGGAACUUAAG
..(((.....)))..((((((..(((((.(((((.(((((((((..((((......))))..).)))))))).))......(((((.....))))).......))).))))).)))))). ( -47.60)
>consensus
UUGGGCAGGUUUCGUUUGAGGAGCUGCCAGUUGAUGCUGGUCGGUGGAGCGGCGGACCGCUGCUUGAUCAGCCUCUUGUGACUAGAUCCCUUCGAGAGUUUGGAGCGGGCGGAACCCAGG
(((((....(((((((((.(((...((((...((.(((((((((.(.(((((....))))).)))))))))).))...))))....)))((((((....)))))))))))))))))))). (-41.64 = -41.83 +   0.19)

alignment

secondary structure

dotplot

Window 7

Location	23,155,558 – 23,155,678
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.36
Mean single sequence MFE	-34.48
Consensus MFE	-28.24
Energy contribution	-28.67
Covariance contribution	0.44
Combinations/Pair	1.09
Mean z-score	-1.59
Structure conservation index	0.82
SVM decision value	0.15
SVM RNA-class probability	0.606923
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23155558 120 - 27905053
CCUGGGUUCCGCCCGCUCCAAACUCUCGAAGGGAUCUAGUCACAAGAAGCUGAUCAAGCAGCGGUCCGCCGCUCCACCGACCAGCAUCAACUGGCAGCUCCUCAAAAGAAACCUGCCCAA
.(((((((((...((...........))..)))))))))......((.((((.((..(.(((((....))))).)...)).)))).))....(((((....((....))...)))))... ( -33.30)
>DroSec_CAF1 6230 120 - 1
CCUGGGUACCGCCCGCUCCAAAAUCUCGAAGGGAUCUAGCCACAAGAGGCUGAUCAAGCAGCGGUCCACCGCUCCACCGACCAGCAUCAACUGGCAGCUCCUCAAACGAAACCUGCCCAA
..((((((..(....).........(((.(((((((.((((......)))))))).((((((((....))))).....(.((((......))))).))))))....)))....)))))). ( -35.50)
>DroSim_CAF1 10757 120 - 1
CCUGGGUUCCGCCCGCUCCAAAAUCUCGAAGGGAUCUAGCCACAAGAGGCUGAUCAAGCAGCGGUCCACCGCUCCACCGACCAGCAUCAACUGGCAGCUCCUCAAACGAAACCUGCCCAA
..(((((...(....).........(((.(((((((.((((......)))))))).((((((((....))))).....(.((((......))))).))))))....))).....))))). ( -34.20)
>DroYak_CAF1 10741 120 - 1
CUUAAGUUCCGCCCGCUCCAAACUCUCGAAGGGAUCGAGUCACAAGAAGCUGGUCAAGCAGAGGUCCGCUCCUCCACCGACCAGCAUCAACUGGCAGCUACUCAAACGGAAUCUGCCCAA
.....((((((...((((((....(((((.....)))))......((.(((((((.....((((......))))....))))))).))...))).)))........))))))........ ( -34.90)
>consensus
CCUGGGUUCCGCCCGCUCCAAAAUCUCGAAGGGAUCUAGCCACAAGAAGCUGAUCAAGCAGCGGUCCACCGCUCCACCGACCAGCAUCAACUGGCAGCUCCUCAAACGAAACCUGCCCAA
.(((((((((...((...........))..)))))))))......((.((((.((..(.(((((....))))).)...)).)))).))....(((((....((....))...)))))... (-28.24 = -28.67 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:43 2006