Locus 3766

Sequence ID	3R_DroMel_CAF1
Location	10,217,078 – 10,217,194
Length	116
Max. P	0.710164

overview

Window 1

Location	10,217,078 – 10,217,194
Length	116
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	87.50
Mean single sequence MFE	-38.20
Consensus MFE	-27.76
Energy contribution	-27.82
Covariance contribution	0.06
Combinations/Pair	1.05
Mean z-score	-1.47
Structure conservation index	0.73
SVM decision value	0.04
SVM RNA-class probability	0.553173
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10217078 116 + 27905053
GCUUUUGCAGACUCGAAUACAGUGUAGUGGCGCCACCUAUGCAGGCAUCACCGGCAAGCGCCACCUACACGGGCACUAGCAACUAGACUUGGCGCCAUCUACAACAACUGAACCGG
((....))...........((((((((((((((((.((((((((((......(((....))).((.....)))).)).)))..)))...)))))))).))))....))))...... ( -37.00)
>DroSec_CAF1 75157 116 + 1
GCUUUUGCAGACUCGAAUACAGUGUAGUGGCGCCACCUAUGCAGGCAUCGCCGGCAAACGCCACCUACACGGGCAUUAGCAAUUAGAGUUGGCGCCAUCUACAACAACUGAACCGG
((....))...........(((((((((((((((((((((((.(((...)))(((....))).(((....))).....)))..))).).)))))))).))))....))))...... ( -37.80)
>DroSim_CAF1 74977 116 + 1
GAUUUUGCACACUCAAAUACAAUGUAGUGGCGCCACCUAUGGAGCCAUAGCCGGCAUACGCCACCUACACGGGCCUUAGCAAUUUGAGUUGGCGCCAUCUACAACAACUGAACCGG
(((..(((..((((((((.(..((((((((((((..(((((....)))))..)))....)))).)))))..)((....)).))))))))..)))..)))................. ( -34.50)
>DroEre_CAF1 76931 115 + 1
GCUCUUGCAGGCUCAAAUACCAUGUAGUGGCGCCACCUGUGCAGGCAUCGCCAGCAGACGCCACCUGCACGGGCA-GAGCAAGUGGAUUGGGCGCCAUCUACAACAGCUGAAUCGG
..((..((.((........)).((((((((((((.((((((((((...((........))...))))))))))..-...(((.....)))))))))).)))))...)).))..... ( -43.50)
>consensus
GCUUUUGCAGACUCAAAUACAAUGUAGUGGCGCCACCUAUGCAGGCAUCGCCGGCAAACGCCACCUACACGGGCAUUAGCAAUUAGAGUUGGCGCCAUCUACAACAACUGAACCGG
......................((((((((((((.((.(((....)))....(((....)))........))((....))..........))))))).)))))............. (-27.76 = -27.82 +   0.06)

alignment

secondary structure

dotplot

Window 2

Location	10,217,078 – 10,217,194
Length	116
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	87.50
Mean single sequence MFE	-44.42
Consensus MFE	-36.90
Energy contribution	-36.90
Covariance contribution	-0.00
Combinations/Pair	1.22
Mean z-score	-1.60
Structure conservation index	0.83
SVM decision value	0.37
SVM RNA-class probability	0.710164
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10217078 116 - 27905053
CCGGUUCAGUUGUUGUAGAUGGCGCCAAGUCUAGUUGCUAGUGCCCGUGUAGGUGGCGCUUGCCGGUGAUGCCUGCAUAGGUGGCGCCACUACACUGUAUUCGAGUCUGCAAAAGC
.(((..((((....((((.(((((((....((((...)))).(((..(((((((..((((....))))..)))))))..))))))))))))))))))...)))............. ( -45.20)
>DroSec_CAF1 75157 116 - 1
CCGGUUCAGUUGUUGUAGAUGGCGCCAACUCUAAUUGCUAAUGCCCGUGUAGGUGGCGUUUGCCGGCGAUGCCUGCAUAGGUGGCGCCACUACACUGUAUUCGAGUCUGCAAAAGC
.(((..((((....((((.((((((((.........((....))((((((((((..(((......)))..)))))))).))))))))))))))))))...)))............. ( -42.30)
>DroSim_CAF1 74977 116 - 1
CCGGUUCAGUUGUUGUAGAUGGCGCCAACUCAAAUUGCUAAGGCCCGUGUAGGUGGCGUAUGCCGGCUAUGGCUCCAUAGGUGGCGCCACUACAUUGUAUUUGAGUGUGCAAAAUC
.............(((((.((((((((.((......((((.((((.(((((.(...).))))).)))).)))).....)).)))))))))))))((((((......)))))).... ( -41.60)
>DroEre_CAF1 76931 115 - 1
CCGAUUCAGCUGUUGUAGAUGGCGCCCAAUCCACUUGCUC-UGCCCGUGCAGGUGGCGUCUGCUGGCGAUGCCUGCACAGGUGGCGCCACUACAUGGUAUUUGAGCCUGCAAGAGC
........(((.((((((..(((((((((.....)))...-.(((.((((((((..((((....))))..)))))))).)))))))))(((....)))........)))))).))) ( -48.60)
>consensus
CCGGUUCAGUUGUUGUAGAUGGCGCCAACUCUAAUUGCUAAUGCCCGUGUAGGUGGCGUUUGCCGGCGAUGCCUGCAUAGGUGGCGCCACUACACUGUAUUCGAGUCUGCAAAAGC
.(((..(((....(((((.((((((((.........((....))(((((((((((.((((....)))).))))))))).))))))))))))))))))...)))............. (-36.90 = -36.90 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:29 2006