Locus 303

Sequence ID	2L_DroMel_CAF1
Location	872,785 – 872,887
Length	102
Max. P	0.933296

overview

Window 3

Location	872,785 – 872,887
Length	102
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	80.37
Mean single sequence MFE	-23.02
Consensus MFE	-12.27
Energy contribution	-13.38
Covariance contribution	1.11
Combinations/Pair	1.20
Mean z-score	-2.97
Structure conservation index	0.53
SVM decision value	1.23
SVM RNA-class probability	0.933296
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 872785 102 + 22407834
UCUUCCUCGUCAU------CCUCCUCUUCGAAGAGCAGUUCUUCCAAGAGCUCCUCAUCUUCUUC---CUCUUCCCAUCGCAGUUCUAGCGAUAAAUACCGCGAUAAAGAC
((((..((((...------..........((.(((.((((((....)))))).))).))......---........(((((.......))))).......))))..)))). ( -22.00)
>DroSec_CAF1 1158 105 + 1
UCUUCCUCGUCGU------CCUCCUCUUCGAAGAGCAGUUCUUCCAAGAGCUCCUCCUCUUCUUCCUCCUCUUCCCAUCGCAGUUCUAGCGAUAAAUACCGCGAUAAAGAC
((((..((((.((------..........((((((.((((((....))))))....))))))..............(((((.......)))))....)).))))..)))). ( -24.20)
>DroEre_CAF1 4415 102 + 1
UCAUCCUCGUCGU------CCUCCUCUUCGAAGAGCAGUUCUUCCAAGAGCUCCUCCUCUUCUUC---CUCUUCCCAUCGCAGUUCUAGCGAUAAACACCGCGAUAAAGAC
........(((((------..........((((((.((((((....))))))....))))))...---........(((((.......))))).......)))))...... ( -21.70)
>DroYak_CAF1 919 102 + 1
UCUUCCUCGUCGU------CCUCCUCUUCGAAGAGCAGUUCUUCCAAGAGUUCCUCCUCUUCUUC---CUCUUCCCAUCGCAGUUCUAGCGAUAAACACCGCGAUAAAGAC
((((..((((.((------....(((((.((((((...)))))).)))))...............---........(((((.......)))))....)).))))..)))). ( -22.00)
>DroMoj_CAF1 1100 87 + 1
UCGUC------AU------CCUCUAAUUCAAAGAGC---UCCUCGAAGAGUUCAUCAUCU---------UCGUCCCAUCGUAGCUCGAGCGAUAAGUAUCGUGACAAGGAC
..(((------..------.............((((---((..((((((........)))---------))).......).)))))..(((((....))))))))...... ( -19.50)
>DroAna_CAF1 1137 108 + 1
UCGUCAUCGUCGUCGUCCUCUUCCUCUUCGAAGAGC---UCCUCUAAGAGCUCUUCCUCUUCAUCCUCCUCAUCCCAUCGCAGUUCCAGCGAUAAGUACAGAGACAAGGAC
..............(((((..((.(((..(((((((---((......)))))))))....................(((((.......)))))......)))))..))))) ( -28.70)
>consensus
UCUUCCUCGUCGU______CCUCCUCUUCGAAGAGCAGUUCUUCCAAGAGCUCCUCCUCUUCUUC___CUCUUCCCAUCGCAGUUCUAGCGAUAAAUACCGCGAUAAAGAC
........(((((..........(((((.(((((.....))))).)))))..........................(((((.......))))).......)))))...... (-12.27 = -13.38 +   1.11)

alignment

secondary structure

dotplot

Window 4

Location	872,785 – 872,887
Length	102
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	80.37
Mean single sequence MFE	-30.18
Consensus MFE	-20.36
Energy contribution	-21.17
Covariance contribution	0.81
Combinations/Pair	1.20
Mean z-score	-2.28
Structure conservation index	0.67
SVM decision value	1.05
SVM RNA-class probability	0.906115
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 872785 102 - 22407834
GUCUUUAUCGCGGUAUUUAUCGCUAGAACUGCGAUGGGAAGAG---GAAGAAGAUGAGGAGCUCUUGGAAGAACUGCUCUUCGAAGAGGAGG------AUGACGAGGAAGA
((((((((((((((.((((....))))))))))))))).....---...............(((((.(((((.....))))).)))))....------..)))........ ( -28.00)
>DroSec_CAF1 1158 105 - 1
GUCUUUAUCGCGGUAUUUAUCGCUAGAACUGCGAUGGGAAGAGGAGGAAGAAGAGGAGGAGCUCUUGGAAGAACUGCUCUUCGAAGAGGAGG------ACGACGAGGAAGA
((((((((((((((.((((....))))))))))))..((((((.((....(((((......))))).......)).))))))......))))------))........... ( -31.20)
>DroEre_CAF1 4415 102 - 1
GUCUUUAUCGCGGUGUUUAUCGCUAGAACUGCGAUGGGAAGAG---GAAGAAGAGGAGGAGCUCUUGGAAGAACUGCUCUUCGAAGAGGAGG------ACGACGAGGAUGA
((((((((((((((.((((....))))))))))))........---......((((((.((.(((....))).)).))))))......))))------))........... ( -29.40)
>DroYak_CAF1 919 102 - 1
GUCUUUAUCGCGGUGUUUAUCGCUAGAACUGCGAUGGGAAGAG---GAAGAAGAGGAGGAACUCUUGGAAGAACUGCUCUUCGAAGAGGAGG------ACGACGAGGAAGA
((((((((((((((.((((....))))))))))))........---...............(((((.(((((.....))))).)))))))))------))........... ( -29.70)
>DroMoj_CAF1 1100 87 - 1
GUCCUUGUCACGAUACUUAUCGCUCGAGCUACGAUGGGACGA---------AGAUGAUGAACUCUUCGAGGA---GCUCUUUGAAUUAGAGG------AU------GACGA
((((((.(((((((....))))...(((((.(....)..(((---------(((........))))))...)---))))..)))....))))------))------..... ( -21.80)
>DroAna_CAF1 1137 108 - 1
GUCCUUGUCUCUGUACUUAUCGCUGGAACUGCGAUGGGAUGAGGAGGAUGAAGAGGAAGAGCUCUUAGAGGA---GCUCUUCGAAGAGGAAGAGGACGACGACGAUGACGA
((((((.(((((...((((((((.......)))))))).................((((((((((....)))---)))))))..)))))..)))))).............. ( -41.00)
>consensus
GUCUUUAUCGCGGUAUUUAUCGCUAGAACUGCGAUGGGAAGAG___GAAGAAGAGGAGGAGCUCUUGGAAGAACUGCUCUUCGAAGAGGAGG______ACGACGAGGAAGA
.((((..(((.....((((((((.......)))))))).......................(((((.(((((.....))))).)))))...........)))..))))... (-20.36 = -21.17 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:31 2006