Locus 6877

Sequence ID	3R_DroMel_CAF1
Location	18,184,113 – 18,184,256
Length	143
Max. P	0.858460

overview

Window 4

Location	18,184,113 – 18,184,225
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	84.79
Mean single sequence MFE	-35.15
Consensus MFE	-25.74
Energy contribution	-26.05
Covariance contribution	0.31
Combinations/Pair	1.20
Mean z-score	-1.92
Structure conservation index	0.73
SVM decision value	-0.05
SVM RNA-class probability	0.509044
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18184113 112 - 27905053
AA--------GGAAACUCACUUGGAUGCAGUGUGGGCACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUAUGCAAGAGUGUGGUUUUGCCAGCAUUAUCCAGGCCCAGGAACAAUAAUUU
.(--------(....))..(((((..((((((((....))))))))(((.(((((.......))))).........(((((((.....))).)))).....))))))))........... ( -35.20)
>DroPse_CAF1 2884 113 - 1
GA-------CUGCAACUCACUUGGAUGCAGGGUGGGGACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUGUGCAGUAGCGUGGUCUUGCCAGCAUUAUCCAAGCCAAGGAACAACAAUUU
..-------..........(((((((((..((..((..(((((((((((((((((.......))))).)).)).))))))))..))..)).)))...))))))................. ( -41.00)
>DroGri_CAF1 337 120 - 1
UCUGAAUCGCUUUCACUCACUUGGAUGCAGUGUUGGCACAUGCUGCGCUAGCUUAUCAUCUUUGAGCAUAUGCAAUAAUGUGGUUUUACCAGCAUUAUCCAAGCCAAGGAACAAUAGUUU
((((((.....))).....((((((((..((((((((((((..((((...(((((.......)))))...))))...)))))......)))))))))))))))....))).......... ( -30.90)
>DroWil_CAF1 720 113 - 1
AA-------UUUCUACUUACUUGGAUGCAAUGUGGGCACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUAUGCAAUAAUGUGGUUUUACCAGCAUUAUCCAAGCCAAGGAACAAUAAUUU
..-------......(((.((((((((((...((((((.....))).)))(((((.......)))))...)))).((((((((.....))).)))))))))))..)))............ ( -29.40)
>DroAna_CAF1 541 111 - 1
-U--------GAAUACUUACUCGGAUGCAGGGUGGGCACAUGCUGGGCCAGCUUGUCAUCUUUGAGCAUGUGCAACAGUGUGGUUUUUCCAGCAUUGUCCAAGCCGAGGAACAACAACUU
-.--------.........(((((........(((((((((((.(((....))).(((....))))))))))).(((((((((.....))).)))))))))..)))))............ ( -33.40)
>DroPer_CAF1 3618 113 - 1
GA-------CUGCAACUCACUUGGAUGCAGGGUGGGGACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUGUGCAGUAGCGUGGUCUUGCCAGCAUUAUCCAAGCCAAGGAACAACAAUUU
..-------..........(((((((((..((..((..(((((((((((((((((.......))))).)).)).))))))))..))..)).)))...))))))................. ( -41.00)
>consensus
AA_______CUGCAACUCACUUGGAUGCAGGGUGGGCACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUAUGCAAUAGUGUGGUUUUGCCAGCAUUAUCCAAGCCAAGGAACAACAAUUU
...................(((((..((((.(((....))).))))(((((((((.......))))).)).)).(((((((((.....))).)))))).....)))))............ (-25.74 = -26.05 +   0.31)

alignment

secondary structure

dotplot

Window 5

Location	18,184,153 – 18,184,256
Length	103
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	78.84
Mean single sequence MFE	-30.18
Consensus MFE	-20.03
Energy contribution	-21.03
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	0.66
SVM decision value	0.82
SVM RNA-class probability	0.858460
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18184153 103 - 27905053
AGUCACACACAUAACCACUAUUUAGUCCAUG-------AAGGAAACUCACUUGGAUGCAGUGUGGGCACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUAUGCAAGAGUG
.......(((....((((......(((((((-------(.(....))))..))))).....))))(((.((((.((....))...(((....))))))).)))....))) ( -28.20)
>DroVir_CAF1 533 95 - 1
UA----AUACAUAA------UAUAGUAGCUG-----CAUUUAAGACUUACUUGGAUGCAGUGUUGGCACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUAUGCAAUAAUG
..----...((((.------....(((((((-----((((((((.....))))))))))(((....)))..)))))....(((((.......))))).))))........ ( -27.00)
>DroSec_CAF1 917 99 - 1
GU----AUGCACAAUGAGGAUUUUGUCCAGG-------GAGCAGACUCACUUGGAUGCAGUGUGGGCACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUAUGCAAGAGUG
((----((((.(((.((.(((...(((((((-------(((....))).)))))))((((((((....))))))))........))).)).))).))))))......... ( -34.60)
>DroSim_CAF1 802 99 - 1
GU----AUACACAUUGAGGAUUUUGUCCAGG-------GAGCAGACUCACUUGGAUGCAGUGUGGGCACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUAUGCAAGAGUG
((----(((........((.....(((((((-------(((....))).)))))))((((((((....)))))))).)).(((((.......))))).)))))....... ( -33.70)
>DroYak_CAF1 989 104 - 1
AG----UUACACAACGA--AUUCCGUCCAGGAAGGGAGGAGCAGACUCACUUGGAUGCAGUGUGGGCACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUAUGCAAGAGUG
..----...(((.....--..(((..((.....))..)))(((........(((.(((((((((....))))))))))))(((((.......)))))...)))....))) ( -33.20)
>DroMoj_CAF1 433 100 - 1
AG----CUACAGAACAA-UCUGGAGUAGAUG-----AGUUUUACACUUACUUGGAUGCAGUGUUGGGACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUAUGCAAUAAUG
.(----((.((((....-)))).))).((((-----(((............(((.((((((((......))))))))))))))))))........((....))....... ( -24.40)
>consensus
AG____AUACACAACGA__AUUUAGUCCAGG_______GAGCAGACUCACUUGGAUGCAGUGUGGGCACAUGCUGCGCCAGCUUAUCAUCUUUGAGCAUAUGCAAGAGUG
............................................((((...(((.(((((((((....))))))))))))(((((.......)))))........)))). (-20.03 = -21.03 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:14 2006