Locus 4965

Sequence ID	2R_DroMel_CAF1
Location	16,183,651 – 16,183,828
Length	177
Max. P	0.843707

overview

Window 9

Location	16,183,651 – 16,183,756
Length	105
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	78.86
Mean single sequence MFE	-36.23
Consensus MFE	-19.19
Energy contribution	-19.50
Covariance contribution	0.31
Combinations/Pair	1.30
Mean z-score	-1.83
Structure conservation index	0.53
SVM decision value	0.02
SVM RNA-class probability	0.545205
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16183651 105 - 20766785
UCCAGCUCCCCAUCGGCUAGCACCGAGUUUGGAGCAGGAGGUGACAAGUCGCGCAGCGUUUCCUCGUUGCCCGACUCUACUACCAAGACUCCCUCGCCAAACAAG
(((.(((((...((((......))))....))))).)))(((((...((((.((((((......)))))).))))(((.......))).....)))))....... ( -38.80)
>DroVir_CAF1 36750 105 - 1
AGCGGUUCACGUUCCGCUAGCGAUGAAUUCGGCGCCGGCGGGGACAAAUCACAAAGUGUCUCUUCUGUGCCAGAUUCUACCACCAAAACACCGUCGCCCAUCAAA
(((((........))))).(((((((((..(((((.((.(((((((..........))))))).)))))))..))))...............)))))........ ( -32.26)
>DroSec_CAF1 27541 105 - 1
GCCAGCUCCCCAUCGGAGAGUACCGAGUUUGGAGCAGGAGGUGACAAGUCGUGCAGCGUUUCCUCGGUGCCCGACUCCACUACCAAGACACCCUCGCCAAACAAG
((..(((((...((((......))))....))))).((.((((...(((((.(((.((......)).))).))))).)))).))...........))........ ( -36.00)
>DroEre_CAF1 28138 105 - 1
UCCAGCUCCCGUUCGGCUAGUGCCGAGUUUGGAGCAGGAGGCGACAAGUCGCGUAGCGUUUCCUCGGUGCCAGACUCUACAACCAAGACUCCAUCGCCAAACAAG
(((.(((((..((((((....))))))...))))).)))(((((..((((..((((.((((..........)))).))))......))))...)))))....... ( -38.10)
>DroYak_CAF1 28014 105 - 1
UCCAGUUCCCGAUCGGCUAGUGCCGAGUUUGGAGCAGGAGGUGACAAGUCGCGUAGUGUGUCCUCUGUGCCAGACUCCACUACCAAGACUCCAUCACCAAACAAG
(((.(((((...(((((....)))))....))))).)))(((((..((((..((((((.(...((((...))))..)))))))...))))...)))))....... ( -41.00)
>DroAna_CAF1 47453 105 - 1
GCCAGUUCCCGUUCGGCUAGCGCCGAAUUUGGUGCCGGAGGUGAUAAAUCGCAAAGCGUAUCCUCUGUACCAGAUUCAACCACUAAGUCGCCGUCACCGAAUAAG
....((((.....(((((((.(..(((((((((((.(((((........(((...)))...))))))))))))))))...).)))....)))).....))))... ( -31.20)
>consensus
UCCAGCUCCCGAUCGGCUAGCGCCGAGUUUGGAGCAGGAGGUGACAAGUCGCGAAGCGUUUCCUCGGUGCCAGACUCUACUACCAAGACUCCAUCGCCAAACAAG
.((.(((((...(((((....)))))....))))).)).(((((.....(((...))).....(((.....)))...................)))))....... (-19.19 = -19.50 +   0.31)

alignment

secondary structure

dotplot

Window 0

Location	16,183,719 – 16,183,828
Length	109
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	72.33
Mean single sequence MFE	-36.07
Consensus MFE	-23.57
Energy contribution	-23.55
Covariance contribution	-0.02
Combinations/Pair	1.36
Mean z-score	-1.33
Structure conservation index	0.65
SVM decision value	0.76
SVM RNA-class probability	0.843707
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16183719 109 - 20766785
AGCAACAAUAAUAACAAUU---AUCGUCGUCGCAAUCGACGCGGCGGCCGCCAAUCGGUGAAGGACGCUAGGCCAUCCAGCUCCCCAUCGGCUAGCACCGAGUUUGGAGCAG
(((................---...((((((((.......))))))))((((....))))......))).((....)).(((((...((((......))))....))))).. ( -35.20)
>DroSec_CAF1 27609 112 - 1
GGCAACAACAAUAACAAUAACAAUCGUCGCCGCAAUCGACGCGGCGGCCGCCAUUCAGUGAAGAACGCUAGGUCAGCCAGCUCCCCAUCGGAGAGUACCGAGUUUGGAGCAG
(((......................((((((((.......)))))))).(((....((((.....)))).)))..))).(((((...((((......))))....))))).. ( -39.10)
>DroSim_CAF1 27813 112 - 1
GGCAACAACAAUAACAAUAACAAUCGUCGCCGCAAUCGACGCGGCGGCCGCCAUUCGGUGAAGAACGCUAGGUCAGCCAGCUCCCCAUCGGAGAGUACCGAGUUUGGAGCAG
(((......................((((((((.......))))))))((((....))))...............))).(((((...((((......))))....))))).. ( -40.40)
>DroEre_CAF1 28206 100 - 1
AGCACCAGCA------------AUCGUCGCCGCAAUCGACGCAAUGCCGGCCAGACAGUCAAGAACGCUAUGCCAUCCAGCUCCCGUUCGGCUAGUGCCGAGUUUGGAGCAG
.((.((.(((------------..(((((.......)))))...))).))((((((......(((((....((......))...)))))(((....)))..)))))).)).. ( -32.90)
>DroYak_CAF1 28082 100 - 1
AGCAACAACA------------AUCGUCGCCGCAAUCGUCGCGGCGCCGGCCAGUCGGCCAAGAACGCCAUGUCAUCCAGUUCCCGAUCGGCUAGUGCCGAGUUUGGAGCAG
.((.......------------...(.((((((.......)))))).)((((....))))......))...........(((((...(((((....)))))....))))).. ( -38.10)
>DroAna_CAF1 47521 92 - 1
-----------------UAACAACCGCCGCCGCAAUCGUCGCACUACUGGUCCGCCAACAAAGAAUG---GAGCGGCCAGUUCCCGUUCGGCUAGCGCCGAAUUUGGUGCCG
-----------------........((....)).......((((((((((.((((...((.....))---..)))))))))....(((((((....)))))))..))))).. ( -30.70)
>consensus
AGCAACAACA_______UA___AUCGUCGCCGCAAUCGACGCGGCGCCCGCCAGUCAGUGAAGAACGCUAGGUCAGCCAGCUCCCCAUCGGCUAGUACCGAGUUUGGAGCAG
(((......................(.((((((.......)))))).)(((......)))......)))..........(((((...((((......))))....))))).. (-23.57 = -23.55 +  -0.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:19 2006