Locus 6985

Sequence ID	3R_DroMel_CAF1
Location	18,420,777 – 18,420,870
Length	93
Max. P	0.999165

overview

Window 5

Location	18,420,777 – 18,420,870
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	70.31
Mean single sequence MFE	-18.72
Consensus MFE	-12.45
Energy contribution	-13.77
Covariance contribution	1.32
Combinations/Pair	1.25
Mean z-score	-2.65
Structure conservation index	0.66
SVM decision value	3.41
SVM RNA-class probability	0.999165
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18420777 93 + 27905053
AUAGCUGGCAAACUUUAUCCCCAAGUCGAGUUACUAAAUUUGCUUGCGAUAUAAUUACCAUACAUUGCCCCACAAAAUAUGCGGCAAAAAUGU
.....(((.......((((..((((.((((((....)))))))))).))))......)))....(((((.((.......)).)))))...... ( -15.92)
>DroSec_CAF1 6492 80 + 1
-UAGCUGGC------------CAAAUUAAAUUACUAAAUUUGCUUGCGAUAUAAUUACCAUACUUUGCCCCACGAAAUAUGGGGCAACAAUUU
-..((.(((------------.(((((.........)))))))).)).................((((((((.......))))))))...... ( -18.70)
>DroSim_CAF1 6911 80 + 1
-UAGCUGGC------------CAAAUUAAAUUACUAAAUUUGCUUGCAAUAUAAUUAACAUACUUUGCCCCACGAAAUAUGGGGCAAAAAUUU
-..((.(((------------.(((((.........)))))))).))................(((((((((.......)))))))))..... ( -19.80)
>DroEre_CAF1 6852 78 + 1
-UAGCUAGCGAAUUU--ACCCCAAGCCAAAUUACUAAAUUUGCUUGCGAUAU------------UUGCUCCACAAAAAGUGGGGCAAAAAUGU
-..((.(((((((((--(................)))))))))).))....(------------(((((((((.....))))))))))..... ( -25.69)
>DroYak_CAF1 6902 77 + 1
-UAGCUGGCAAACUUUAACCCAAAGUCUAAUUAC---AUUUGCUUGCGAUAU------------AUGGACCACGUAAAAGGGGCCAAAAAUGU
-....((((...((((.((.....(((((((..(---(......))..))..------------.)))))...)).))))..))))....... ( -13.50)
>consensus
_UAGCUGGC_AA_UU___CCCCAAGUCAAAUUACUAAAUUUGCUUGCGAUAUAAUUA_CAUAC_UUGCCCCACGAAAUAUGGGGCAAAAAUGU
...((.((((((..........................)))))).)).................((((((((.......))))))))...... (-12.45 = -13.77 +   1.32)

alignment

secondary structure

dotplot

Window 6

Location	18,420,777 – 18,420,870
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	70.31
Mean single sequence MFE	-20.78
Consensus MFE	-10.23
Energy contribution	-10.75
Covariance contribution	0.52
Combinations/Pair	1.15
Mean z-score	-2.26
Structure conservation index	0.49
SVM decision value	2.19
SVM RNA-class probability	0.989886
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18420777 93 - 27905053
ACAUUUUUGCCGCAUAUUUUGUGGGGCAAUGUAUGGUAAUUAUAUCGCAAGCAAAUUUAGUAACUCGACUUGGGGAUAAAGUUUGCCAGCUAU
.(((..(((((.(((.....))).)))))...)))...........((..((((((((.((..((......))..)).))))))))..))... ( -23.70)
>DroSec_CAF1 6492 80 - 1
AAAUUGUUGCCCCAUAUUUCGUGGGGCAAAGUAUGGUAAUUAUAUCGCAAGCAAAUUUAGUAAUUUAAUUUG------------GCCAGCUA-
......(((((((((.....)))))))))(((.((((........(....)((((((.........))))))------------))))))).- ( -22.70)
>DroSim_CAF1 6911 80 - 1
AAAUUUUUGCCCCAUAUUUCGUGGGGCAAAGUAUGUUAAUUAUAUUGCAAGCAAAUUUAGUAAUUUAAUUUG------------GCCAGCUA-
......(((((((((.....)))))))))(((..((((((((.(((((...........))))).))).)))------------))..))).- ( -20.70)
>DroEre_CAF1 6852 78 - 1
ACAUUUUUGCCCCACUUUUUGUGGAGCAA------------AUAUCGCAAGCAAAUUUAGUAAUUUGGCUUGGGGU--AAAUUCGCUAGCUA-
.....(((((.((((.....)))).))))------------)((((.((((((((((....))))).))))).)))--).............- ( -23.60)
>DroYak_CAF1 6902 77 - 1
ACAUUUUUGGCCCCUUUUACGUGGUCCAU------------AUAUCGCAAGCAAAU---GUAAUUAGACUUUGGGUUAAAGUUUGCCAGCUA-
......(((((..((((.(((((((....------------..)))))...((((.---((......)))))).)).))))...)))))...- ( -13.20)
>consensus
ACAUUUUUGCCCCAUAUUUCGUGGGGCAA_GUAUG_UAAUUAUAUCGCAAGCAAAUUUAGUAAUUUGACUUGGGG___AA_UU_GCCAGCUA_
......(((((((((.....))))))))).................((..((................................))..))... (-10.23 = -10.75 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:51 2006