Locus 8624

Sequence ID	3R_DroMel_CAF1
Location	23,051,557 – 23,051,707
Length	150
Max. P	0.932745

overview

Window 7

Location	23,051,557 – 23,051,670
Length	113
Sequences	3
Columns	119
Reading direction	reverse
Mean pairwise identity	78.31
Mean single sequence MFE	-37.27
Consensus MFE	-22.59
Energy contribution	-22.60
Covariance contribution	0.01
Combinations/Pair	1.10
Mean z-score	-2.30
Structure conservation index	0.61
SVM decision value	1.22
SVM RNA-class probability	0.932745
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23051557 113 - 27905053
AGUUUCGCCGGCAGCAGGCCAUUACGGCUGCAGCUAUCGCCGCUGCGUUUGCAGCAGAUGCUGCUUCAGUU------GCAGUUACAGUUGCAGUUGCUUCCUCAUCGUACUGAAACCCA
.(((((...(((.....)))....((((((((((((((...(((((....))))).)))(((((.......------)))))...)))))))))))...............)))))... ( -39.90)
>DroSec_CAF1 53352 94 - 1
AGUUUCGC-GGCAGCAGCCCAUUACUG---------------CUGCGUUCGCAGU---UGCUGCUGCAGUU------GCAGUUACAGUUGCAGUUGCUUCCUCAUCGCCAUGAAAUGCA
.((((((.-(((((((((.....((((---------------(.......)))))---.))))))(((..(------((((......)))))..))).........))).))))))... ( -35.40)
>DroSim_CAF1 36847 100 - 1
AGUUUCGC-GGCAGCAGCCCGUUACUG---------------CUGCGUUCGCAGU---UGCUGCUGCAGUUGCAGUUGCAGUUACAGUUGCAGUUGCUUCCUCAUCGCACUGAAAUCCA
.(((((((-(((((((((.....((((---------------(.......)))))---.))))))))....(((..(((((......)))))..)))........)))...)))))... ( -36.50)
>consensus
AGUUUCGC_GGCAGCAGCCCAUUACUG_______________CUGCGUUCGCAGU___UGCUGCUGCAGUU______GCAGUUACAGUUGCAGUUGCUUCCUCAUCGCACUGAAAUCCA
.(((((((.((.((((((........................(((((...(((((....))))))))))........((((......)))).)))))).)).....))...)))))... (-22.59 = -22.60 +   0.01)

alignment

secondary structure

dotplot

Window 8

Location	23,051,597 – 23,051,707
Length	110
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	74.42
Mean single sequence MFE	-26.85
Consensus MFE	-9.37
Energy contribution	-9.73
Covariance contribution	0.36
Combinations/Pair	1.24
Mean z-score	-2.18
Structure conservation index	0.35
SVM decision value	0.28
SVM RNA-class probability	0.665335
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23051597 110 + 27905053
GC------AACUGAAGCAGCAUCUGCUGCAAACGCAGCGGCGAUAGCUGCAGCCGUAAUGGCCUGCUGCCGGCGAAACUGUCGCCAGACAAAUCAAAAGAAAUCGCUCUGGAAUAC
..------.......(((((....))))).....(((.((((((.((.((((((.....)).)))).)).(((((.....)))))................)))))))))...... ( -38.00)
>DroSec_CAF1 53392 91 + 1
GC------AACUGCAGCAGCA---ACUGCGAACGCAG---------------CAGUAAUGGGCUGCUGCC-GCGAAACUGUCGCCAGACAAAUCAAAAGAAAUCGCUCUGGAAUAC
..------....((((((((.---.((((....))))---------------((....)).)))))))).-((((...((((....))))..((....))..)))).......... ( -30.30)
>DroSim_CAF1 36887 97 + 1
GCAACUGCAACUGCAGCAGCA---ACUGCGAACGCAG---------------CAGUAACGGGCUGCUGCC-GCGAAACUGUCGCCAGACAAAUCAAAAGAAAUCGCUCUGGAAUAC
((....))....((((((((.---(((((.......)---------------)))).....)))))))).-((((...((((....))))..((....))..)))).......... ( -31.50)
>DroEre_CAF1 59078 83 + 1
--------AGCAGCAGCGAUA---UCU------GCAG---------------CAGUAAUAGGUUGCAGCC-GCGAAUCUGUCGCCAGACAAAUCAAAAGAAAUCGCUCUGGAAUAC
--------..(((.((((((.---(((------((.(---------------(.((((....)))).)).-))((...((((....))))..))...))).)))))))))...... ( -24.80)
>DroYak_CAF1 58449 83 + 1
--------AACUGCAGCAGCA---UCU------GCAG---------------CAGUAAUAGGCUGCAGCC-GCGAAACUGUCGCCAGACAAAUCAAAAGAAAUCGCUCUGGAAUAC
--------.(((((.((((..---.))------)).)---------------))))....(((....)))-((((...((((....))))..((....))..)))).......... ( -24.10)
>DroAna_CAF1 58062 84 + 1
GA------AACCUCAGAA-AA---UCA------GCAG---------------CCAUAAGUCUCAGCCGCC-ACGAAACUGUCGCCAGACAAAUCAAACCAAUUCGCUGUGGGACAC
..------..((.(((..-((---(..------((.(---------------(...........)).)).-..((...((((....))))..))......)))..))).))..... ( -12.40)
>consensus
GC______AACUGCAGCAGCA___UCU______GCAG_______________CAGUAAUGGGCUGCUGCC_GCGAAACUGUCGCCAGACAAAUCAAAAGAAAUCGCUCUGGAAUAC
...............(((((.........................................)))))..((.((((...((((....))))..((....))..))))...))..... ( -9.37 =  -9.73 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:15:45 2006