Locus 10254

Sequence ID	3R_DroMel_CAF1
Location	27,467,092 – 27,467,242
Length	150
Max. P	0.732598

overview

Window 3

Location	27,467,092 – 27,467,203
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.66
Mean single sequence MFE	-33.44
Consensus MFE	-14.73
Energy contribution	-16.15
Covariance contribution	1.42
Combinations/Pair	1.17
Mean z-score	-1.93
Structure conservation index	0.44
SVM decision value	0.43
SVM RNA-class probability	0.732598
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27467092 111 - 27905053
UGAGCGUGUUUGCGACUGCUUAAGACACUCAACUAGCUGAUGAAAAGCGCGG--GG---GGGGU--GGGGGUGGUAUGGAAG--GGGGAAAGCAGAAACGCUGCAGCGGAAAAGCUAGCG
..(((((.(((((.((..(((....(((((..((.(((.......)))...)--).---.))))--).)))..)).......--.......))))).)))))(((((......))).)). ( -36.46)
>DroSec_CAF1 22980 102 - 1
UGAGCGUGUUUGCGACUGCUUAAGACACUCAACUAGCUGGUGAAAAGCGCGA------------------GGGGAGUGGAAAGCGGGAAAAGCAGAAACGCUGCAGCGGAAAAGCUAGGG
..(((((.(((((..((((((....(((((..((.(((.......)))...)------------------)..)))))..)))))).....))))).)))))..(((......))).... ( -37.30)
>DroSim_CAF1 22844 115 - 1
UGAGCGUGUUUGCGACUGCUUAAGACACUCAACUAGCUGGUGAAAAGCGCGUGGGG---GGGGG--GGGGGGGGAGUGGAAAGCGGGAAAAGCAGAAACGCUGCAGCGGAAAAGCUAGGG
..(((((.(((((..((((((....(((((..((.(((.......))).(......---)....--...))..)))))..)))))).....))))).)))))..(((......))).... ( -34.10)
>DroEre_CAF1 22863 104 - 1
UGAGCGUGUUUGCGACUGCUUAAGACACUCAACUGGCUGGCGAAGAGCGCGG--GG--------------GAAACGCGGAAAAGCGGAAAAGCAGAAACGCUGCAGCGGAAAAGCUGGGG
..(((((.(((((..((((((..(.....)..(((.((.(((.....))).)--)(--------------....).)))..))))))....))))).))))).((((......))))... ( -34.20)
>DroYak_CAF1 23912 114 - 1
UGAGCGUGUUUGCGACUGCUUAAGACACUCAACUAGCUGGCGAAGAGUGCGG--GGAGGGGGAU--GG--GGGUUGUGGAAAAGUGGAAAAGCAGAAACGCAGCAGCGGAAAAGCUAGGG
...((((.(((((..(..(((..(((.((((.((..((.(((.....))).)--)...))...)--))--).)))......)))..)....))))).))))...(((......))).... ( -28.60)
>DroAna_CAF1 35302 99 - 1
UGAGCGUGUUUGCGACUGCUUAAGACACUCAACUAGCAGCCAGAGAUGGAGGAUGGAGUGGUAUUCGCGGGGGGCGUGG-------------CAGGUUGAGUGCAACGGAAG--------
((((((.(((...))))))))).(.(((((((((.((.(((.....(.(.(((((......))))).).)..)))...)-------------).))))))))))..(....)-------- ( -30.00)
>consensus
UGAGCGUGUUUGCGACUGCUUAAGACACUCAACUAGCUGGCGAAAAGCGCGG__GG___GGG_U__GG__GGGGAGUGGAAA__GGGAAAAGCAGAAACGCUGCAGCGGAAAAGCUAGGG
((((.((.((.((....))..)).)).)))).((((((.(((.....))).........................................((((.....))))........)))))).. (-14.73 = -16.15 +   1.42)

alignment

secondary structure

dotplot

Window 4

Location	27,467,130 – 27,467,242
Length	112
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	84.03
Mean single sequence MFE	-25.72
Consensus MFE	-21.25
Energy contribution	-21.25
Covariance contribution	0.00
Combinations/Pair	1.11
Mean z-score	-1.44
Structure conservation index	0.83
SVM decision value	-0.01
SVM RNA-class probability	0.526656
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27467130 112 + 27905053
UCCAUACCACCCCC--ACCCC---CC--CCGCGCUUUUCAUCAGCUAGUUGAGUGUCUUAAGCAGUCGCAAACACGCUCAUAAAUAUUCAUAUAGCUGGGGAGUAUUUGCAAUUGCUUU
..............--....(---((--(.(((((.......)))....(((((((.....((....))....)))))))..............)).))))((((........)))).. ( -22.60)
>DroSec_CAF1 23020 101 + 1
UCCACUCCCC------------------UCGCGCUUUUCACCAGCUAGUUGAGUGUCUUAAGCAGUCGCAAACACGCUCAUAAAUAUUCAUAUAGCUGGGGAGUAUUUGCAAUUGCUUU
...(((((((------------------..(((((.......)))....(((((((.....((....))....)))))))..............)).)))))))....((....))... ( -26.80)
>DroSim_CAF1 22884 114 + 1
UCCACUCCCCCCCC--CCCCC---CCCCACGCGCUUUUCACCAGCUAGUUGAGUGUCUUAAGCAGUCGCAAACACGCUCAUAAAUAUUCAUAUAGCUGGGGAGUAUUUGCAAUUGCUUU
...(((((((....--.....---........((((..((((((....))).)))....))))............(((.(((........)))))).)))))))....((....))... ( -24.20)
>DroEre_CAF1 22903 103 + 1
UCCGCGUUUC--------------CC--CCGCGCUCUUCGCCAGCCAGUUGAGUGUCUUAAGCAGUCGCAAACACGCUCAUAAAUAUUCAUAUAGCUGGGGAGUAUUUGCAAUUGCUUU
...(((.(((--------------((--(.(((((.......)))....(((((((.....((....))....)))))))..............)).))))))....)))......... ( -26.20)
>DroYak_CAF1 23952 113 + 1
UCCACAACCC--CC--AUCCCCCUCC--CCGCACUCUUCGCCAGCUAGUUGAGUGUCUUAAGCAGUCGCAAACACGCUCAUAAAUAUUCAUAUAGCUGGGGAGUAUUUGCAAUUGCUUU
..........--..--..........--..(((..((((.(((((((..(((((((.(((.(.((.((......))))).))))))))))..)))))))))))....)))......... ( -26.50)
>DroAna_CAF1 35322 118 + 1
-CCACGCCCCCCGCGAAUACCACUCCAUCCUCCAUCUCUGGCUGCUAGUUGAGUGUCUUAAGCAGUCGCAAACACGCUCAUAAAUAUUCAUAUAGCUGGGGAGUAUUUGCAAUUGCUUU
-...........((((((((..(((((....(((....)))..((((..(((((((.(((.(.((.((......))))).))))))))))..))))))))).))))))))......... ( -28.00)
>consensus
UCCACACCCC__CC__A_CCC___CC__CCGCGCUCUUCACCAGCUAGUUGAGUGUCUUAAGCAGUCGCAAACACGCUCAUAAAUAUUCAUAUAGCUGGGGAGUAUUUGCAAUUGCUUU
..............................((((((..(........)..))))))...(((((((.(((((.((.(((.....(((....)))....))).)).))))).))))))). (-21.25 = -21.25 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:52:44 2006