Locus 2544

Sequence ID	X_DroMel_CAF1
Location	6,821,132 – 6,821,337
Length	205
Max. P	0.995269

overview

Window 1

Location	6,821,132 – 6,821,222
Length	90
Sequences	3
Columns	119
Reading direction	forward
Mean pairwise identity	78.43
Mean single sequence MFE	-27.57
Consensus MFE	-16.56
Energy contribution	-16.90
Covariance contribution	0.34
Combinations/Pair	1.09
Mean z-score	-3.10
Structure conservation index	0.60
SVM decision value	2.56
SVM RNA-class probability	0.995269
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6821132 90 + 22224390
AACCGAGAUAGGUGUAAAUUUGAAAUUUACUCACACCAUAGAGAUAUGAUAAUUGUAUGUGCAAUUGAAACAUGUGAUUAUCAAGUUUCA-----------------------------
.(((......)))((((((.....))))))..........(((((.(((((((..(((((.........)))))..))))))).))))).----------------------------- ( -23.80)
>DroSec_CAF1 1503 119 + 1
AAACGAGAUAGGUGUAAAUUUGAGAUUUACUCACACCACAGAGAUAUGAUAAUUGUAUGUGCAAUUGAUAUGUGUGAUUACCAAGUUUCAGAUCAACAUCUUUCUGUCUUUAUAACACA
.....(((.((((((..(((((((((((..((((((..((......)).(((((((....)))))))....)))))).....)))))))))))..)))))).))).............. ( -28.40)
>DroSim_CAF1 1517 119 + 1
AAACGAGAUAGGUGUAAAUUUGAGAUUUGCUCACACCAUAGAGAUAUGAUAAUUGUAUGUGCAAUUGAUAUGCGUGAUUACCAAGUUUCAGAUCAACAUCUUUCUGUCUUUAUAAUACA
.....(((.((((((..((((((((((((.((((..((((....)))).(((((((....)))))))......))))....))))))))))))..)))))).))).............. ( -30.50)
>consensus
AAACGAGAUAGGUGUAAAUUUGAGAUUUACUCACACCAUAGAGAUAUGAUAAUUGUAUGUGCAAUUGAUAUGUGUGAUUACCAAGUUUCAGAUCAACAUCUUUCUGUCUUUAUAA_ACA
....(((((.((((((((((...)))))))((((((((((....)))).(((((((....)))))))....))))))..)))..))))).............................. (-16.56 = -16.90 +   0.34)

alignment

secondary structure

dotplot

Window 2

Location	6,821,222 – 6,821,337
Length	115
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	74.24
Mean single sequence MFE	-27.64
Consensus MFE	-20.12
Energy contribution	-19.57
Covariance contribution	-0.55
Combinations/Pair	1.27
Mean z-score	-0.92
Structure conservation index	0.73
SVM decision value	0.36
SVM RNA-class probability	0.705971
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6821222 115 - 22224390
GGCCAAUGAUUUUGGCGACGAGGAUGCCAAGAAGUACUACACCUACUACCAGUGGGUGUGCUUCGUGCUUUUCUUCCAGGUGAGUUUCGUAGCA--UAAGAUUUUACUUCUAGAUUC
.(((((.....))))).............(((((((..((((((((.....))))))))(((.((.((((.((.....)).))))..)).))).--........)))))))...... ( -33.90)
>DroEre_CAF1 1777 107 - 1
GGCCAAUGACUUUGGCGAUGAGGAUGCCAAGAAGUACUACACCUACUAUCAGUGGGUGUGCUUCGUGCUUUUCUUCCAGGUGAGUUUCGCAUUUACUUCUA---C-------GAUUC
.(((((.....)))))...(((((.((...(((((...((((((((.....)))))))))))))..))...))))).((((((((.....))))))))...---.-------..... ( -33.90)
>DroWil_CAF1 1936 96 - 1
GGCCAAUGAUUUUGAUGACGAAGAUGCCAAGAAAUAUUAUACCUACUAUCAAUGGGUUUGCUUUGUGCUCUUCUUUCAGGUAAGUGUCGGCGGA--GA-------------------
.(((.((.((((...(((.(((((.((((((.........(((((.......)))))....)))).)))))))..)))...)))))).)))...--..------------------- ( -18.12)
>DroYak_CAF1 1643 105 - 1
GGCCAAUGAUUUUGGCGAUGAGGAUGCCAAGAAGUACUACACCUACUACCAGUGGGUCUGCUUCGUGCUUUUCUUCCAGGUGAGUUUCCUAUCU--UAAGG---C-------ACUUC
.(((((.....)))))...((((.((((..((((((....((((((.....)))))).))))))..((((.((.....)).)))).........--...))---)-------))))) ( -31.10)
>DroAna_CAF1 2282 96 - 1
GGCCAAUGACUUUGGUGACGAAGAUGCCAAGAAAUACUACACCUACUACCAAUGGGUGUGCUUUGUGCUCUUCUUCCAGGUGAGUUAUAUA---------------CUCCU------
.(((((.....)))))((.(((((.((((((......((((((((.......)))))))).)))).))))))).))..((.((((.....)---------------)))))------ ( -24.90)
>DroPer_CAF1 1625 95 - 1
GUCCAAUGAUUUCGGAGACGAGGAUGCCAAGAAAUACUAUACCUACUACCAGUGGGUAUGCUUUGUGCUCUUCUUUCAGGUGAGUAA-AUA---------------GUCUG------
((((.......(((....)))))))....(((.....(((((((((.....)))))))))((...(((((.((.....)).))))).-..)---------------)))).------ ( -23.91)
>consensus
GGCCAAUGAUUUUGGCGACGAGGAUGCCAAGAAAUACUACACCUACUACCAGUGGGUGUGCUUCGUGCUCUUCUUCCAGGUGAGUUUCGUA_____UA___________________
.(((((.....)))))((.(((((.((...(((....(((((((((.....))))))))).)))..))))))).))......................................... (-20.12 = -19.57 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:17 2006