Locus 7319

Sequence ID	3R_DroMel_CAF1
Location	19,338,504 – 19,338,638
Length	134
Max. P	0.795973

overview

Window 0

Location	19,338,504 – 19,338,600
Length	96
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	83.12
Mean single sequence MFE	-36.95
Consensus MFE	-32.51
Energy contribution	-32.85
Covariance contribution	0.34
Combinations/Pair	1.17
Mean z-score	-1.69
Structure conservation index	0.88
SVM decision value	0.60
SVM RNA-class probability	0.795973
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19338504 96 + 27905053
--------UGGAGCGGGAAUUAUGACCCGCGGGGCCAAGUGGCUGGAGUUGAGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGUCGGAGGCAAA
--------....(((((........)))))....((((((((((.......))))))))))(((((((.(((((....))))).))))))).((.....))... ( -41.70)
>DroPse_CAF1 155941 89 + 1
--------U-GGGGGGGAGUUAUGACCUACGGGUUGGAGUGGAUGG-----AGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGCCACAG-CUAA
--------.-.......((((..((((....))))...((((....-----..((....))(((((((.(((((....))))).)))))))..))))))-)).. ( -30.70)
>DroEre_CAF1 137818 96 + 1
--------UGGAGCGGGAAUUAUGACCCGCGGGGCCAAGUGGCCGGAGCUGAGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGUCGGAGGCAAA
--------....(((((........)))))....(((((((((((....)).)))))))))(((((((.(((((....))))).))))))).((.....))... ( -41.20)
>DroYak_CAF1 140727 96 + 1
--------UGGAGCGGGAAUUAUGACCCGCGGGGCCAAGUGGCUGGAGUUGAGCCAUUUGGGUGGCGCCUUUUGUCUUUGAAACGUGCCACAGUCGGAGGCAAA
--------....(((((........)))))....((((((((((.......))))))))))(((((((.((((......)))).))))))).((.....))... ( -39.70)
>DroAna_CAF1 139076 98 + 1
UUGGGAGGUAGUGCGGGAAUUAUGACCUGCGGGG-CAAGUGGCUGC-----AGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGUCGGAGGCACA
..........(((((((........))).(((..-((((((((...-----.)))))))).(((((((.(((((....))))).)))))))..)))...)))). ( -36.70)
>DroPer_CAF1 156233 89 + 1
--------U-GGGGGGGAGUUGUGACCUGCGGGUUGGAGUGGAUGG-----AGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGCCACAG-CUAA
--------.-.......((((((((((....)))(.((((((....-----..)))))).)(((((((.(((((....))))).)))))))...)))))-)).. ( -31.70)
>consensus
________UGGAGCGGGAAUUAUGACCCGCGGGGCCAAGUGGCUGG_____AGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGUCGGAGGCAAA
............(((((........)))))((..((((((((((.......))))))))))(((((((.(((((....))))).)))))))..))......... (-32.51 = -32.85 +   0.34)

alignment

secondary structure

dotplot

Window 1

Location	19,338,533 – 19,338,638
Length	105
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	80.59
Mean single sequence MFE	-33.92
Consensus MFE	-24.29
Energy contribution	-24.65
Covariance contribution	0.36
Combinations/Pair	1.18
Mean z-score	-1.21
Structure conservation index	0.72
SVM decision value	0.06
SVM RNA-class probability	0.561435
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19338533 105 + 27905053
AGUGGCUGGAGUUGAGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGUCGGAGGCAAAGUCGCAGUUGAAGUCGCAA--AAAUAGUGUGCCACAUGCG
.(((((((((.((..(((.((((.(((((((.(((((....))))).)))))))...))))))).)).)).))........(((..--.....))).)))))..... ( -34.40)
>DroPse_CAF1 155969 91 + 1
AGUGGAUGG-----AGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGCCACAG-CUAAGCCGAAGUCAU----------AGCCAGAGUGCCACAUGCG
.((((.(((-----.....((((((((((((.(((((....))))).)))))))(((....)-))...))))).....----------..))).....))))..... ( -31.30)
>DroEre_CAF1 137847 105 + 1
AGUGGCCGGAGCUGAGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGUCGGAGGCAAAGUCGCAGUUGAAAUCGCAA--AAAUAGUGUGCCACAUGCG
.(((((....((((.(((.((((.(((((((.(((((....))))).)))))))...)))))))......((..........))..--...))))..)))))..... ( -35.00)
>DroYak_CAF1 140756 107 + 1
AGUGGCUGGAGUUGAGCCAUUUGGGUGGCGCCUUUUGUCUUUGAAACGUGCCACAGUCGGAGGCAAAGUCGCAGUUGAAAUCGCAAGAAAAUACUGUGCCACAUGCG
.(((((..((.((..(((.((((.(((((((.((((......)))).)))))))...))))))).)).))(((((.....((....))....))))))))))..... ( -39.70)
>DroAna_CAF1 139112 90 + 1
AGUGGCUGC-----AGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGUCGGAGGCACAGCCGGAGU------CAC----AAAUAA--UGCCACAUGCG
..((((((.-----.(((.((((.(((((((.(((((....))))).)))))))...))))))).))))))....------...----......--.((.....)). ( -31.80)
>DroPer_CAF1 156261 91 + 1
AGUGGAUGG-----AGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGCCACAG-CUAAGCCGAAGUCAU----------AGCCAGAGUGCCACAUGCG
.((((.(((-----.....((((((((((((.(((((....))))).)))))))(((....)-))...))))).....----------..))).....))))..... ( -31.30)
>consensus
AGUGGCUGG_____AGCCAUUUGGGUGGCGCCUUUUGUCUUCGAAACGUGCCACAGUCGGAGGCAAAGCCGCAGUUGA___CGC____AAAUAGUGUGCCACAUGCG
.(((((.........(((.((((((((((((.(((((....))))).)))))))..)))))))).........(((.............))).....)))))..... (-24.29 = -24.65 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:03 2006