Locus 6203

Sequence ID	3R_DroMel_CAF1
Location	16,193,332 – 16,193,490
Length	158
Max. P	0.734771

overview

Window 7

Location	16,193,332 – 16,193,450
Length	118
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	90.47
Mean single sequence MFE	-36.88
Consensus MFE	-30.00
Energy contribution	-30.25
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.81
SVM decision value	0.43
SVM RNA-class probability	0.734771
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16193332 118 - 27905053
UCAGACAUCUGCCAAGUGGCCAAAGGACGAGGACGUGGGCGGUUACUUGGCAAAUGCCAGCUCGGCAAAUCCUCGCCAGCUUCCGACUUCUACCA-CCCCCACCUCCACCGUCAAUAUC
..........(((....))).....((((.(((.(((((.(((....((((....))))(((.(((........))))))..............)-))))))).)))..))))...... ( -39.30)
>DroSec_CAF1 22649 119 - 1
UCAGACAUCUGCCAAGUGGCCAAAGGACGAGGACGUGGGCGGUUACUUGGCAAAUGCCAGCACGGCAAAUCCUCGCCAGCUUCCGACUUCUCCCAACCCCCAUCACCACCGCCAGUCUC
..((((....(((....)))....((.((.((..(((((.((((...((((....))))((..(((........))).))..............)))))))))..))..)))).)))). ( -35.80)
>DroEre_CAF1 21876 110 - 1
UCAGACAUCUGCCAAGUGGCCAAAGGACGAGGACGUGGGCGGUUACUUGGCAAAUGCCAGCUCGGCAAAUCCUCGCCAGCUUCCGACUUC---------CCACCACCGCCUCCAAUCUC
..(((.....(((....)))....(((.(.((..(((((.((((...((((....))))(((.(((........))))))....)))).)---------))))..)).).)))..))). ( -36.10)
>DroYak_CAF1 23296 110 - 1
UCAGACAUCUGCCAAGUGGCCAAAGGACGAGGACGUGGGCGGUUACUUGGCAAAUGCCAGCUCGGCAAAUCCUCGCCAGCUUCCGGCUUG---------CCACCACCACCUCCAAUCUC
..((((.((((((....)))....))).).(((.((((..(((.....(((((..(((((((.(((........)))))))...))))))---------))))).)))).)))..))). ( -36.30)
>consensus
UCAGACAUCUGCCAAGUGGCCAAAGGACGAGGACGUGGGCGGUUACUUGGCAAAUGCCAGCUCGGCAAAUCCUCGCCAGCUUCCGACUUC_________CCACCACCACCGCCAAUCUC
...(.(((.((((((((((((.....(((....)))....)))))))))))).))).)((((.(((........)))))))...................................... (-30.00 = -30.25 +   0.25)

alignment

secondary structure

dotplot

Window 8

Location	16,193,371 – 16,193,490
Length	119
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	99.58
Mean single sequence MFE	-36.04
Consensus MFE	-35.76
Energy contribution	-36.02
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.99
SVM decision value	0.10
SVM RNA-class probability	0.584772
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16193371 119 + 27905053
CUGGCGAGGAUUUGCCGAGCUGGCAUUUGCCAAGUAACCGCCCACGUCCUCGUCCUUUGGCCACUUGGCAGAUGUCUGACUGUCAUUUAUUACAAUUGCUUUGACUUUUGUUAGUUUGU
..(((((....)))))(((((((((((((((((((..(((...(((....)))....)))..)))))))))))))).(((.((((................))))....)))))))).. ( -36.49)
>DroSec_CAF1 22689 119 + 1
CUGGCGAGGAUUUGCCGUGCUGGCAUUUGCCAAGUAACCGCCCACGUCCUCGUCCUUUGGCCACUUGGCAGAUGUCUGACUGUCAUUUAUUACAAUUGCUUUGACUUUUGUUAGUUUGU
..(((((....))))).....((((((((((((((..(((...(((....)))....)))..))))))))))))))((((.((((................))))....))))...... ( -34.69)
>DroEre_CAF1 21907 119 + 1
CUGGCGAGGAUUUGCCGAGCUGGCAUUUGCCAAGUAACCGCCCACGUCCUCGUCCUUUGGCCACUUGGCAGAUGUCUGACUGUCAUUUAUUACAAUUGCUUUGACUUUUGUUAGUUUGU
..(((((....)))))(((((((((((((((((((..(((...(((....)))....)))..)))))))))))))).(((.((((................))))....)))))))).. ( -36.49)
>DroYak_CAF1 23327 119 + 1
CUGGCGAGGAUUUGCCGAGCUGGCAUUUGCCAAGUAACCGCCCACGUCCUCGUCCUUUGGCCACUUGGCAGAUGUCUGACUGUCAUUUAUUACAAUUGCUUUGACUUUUGUUAGUUUGU
..(((((....)))))(((((((((((((((((((..(((...(((....)))....)))..)))))))))))))).(((.((((................))))....)))))))).. ( -36.49)
>consensus
CUGGCGAGGAUUUGCCGAGCUGGCAUUUGCCAAGUAACCGCCCACGUCCUCGUCCUUUGGCCACUUGGCAGAUGUCUGACUGUCAUUUAUUACAAUUGCUUUGACUUUUGUUAGUUUGU
..(((((....)))))(((((((((((((((((((..(((...(((....)))....)))..)))))))))))))).(((.((((................))))....)))))))).. (-35.76 = -36.02 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:27 2006