Locus 2069

Sequence ID	2R_DroMel_CAF1
Location	7,764,707 – 7,764,833
Length	126
Max. P	0.974715

overview

Window 8

Location	7,764,707 – 7,764,800
Length	93
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	78.48
Mean single sequence MFE	-31.02
Consensus MFE	-16.44
Energy contribution	-17.42
Covariance contribution	0.97
Combinations/Pair	1.15
Mean z-score	-1.90
Structure conservation index	0.53
SVM decision value	0.23
SVM RNA-class probability	0.643539
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7764707 93 - 20766785
CUGUCUG-------GUCAGGGCC--ACAUUGCGUAUACGCGAU--GCGGGCCAA-AGGACCGCUAUCAGUCCGGCAAUUCCUG-UCCCAAUCAUCCUAGACAAAUG
.((((((-------(...((.((--.(((((((....))))))--).)).))..-.((((........))))((((.....))-)).........))))))).... ( -34.50)
>DroPse_CAF1 20916 85 - 1
CUGUCUG-------ACAGCAGCC--ACAUUGCGUAUACGCGAU--GCGGGCGA---GG-UCG-----UGUCCCGCCAUCUAUU-CCCCAAUCAUCCUAGACAAAUG
.((((((-------........(--.(((((((....))))))--).)((((.---((-...-----...)))))).......-............)))))).... ( -25.70)
>DroEre_CAF1 19861 94 - 1
CUGUCUG-------GCCAAGGCC--ACAUUGCGUAUACGCGAU--GCGGGCCAAAAGGACCGCUAUCAGUCCGGCCAUUCCUG-UCCCAAUCAUCCUAGACAAAUG
.((((((-------(((..((((--.(((((((....))))))--)..))))....((((........)))))))).....((-.......))....))))).... ( -35.50)
>DroYak_CAF1 18332 94 - 1
CUGUGUG-------GCCAAGGCC--ACGUUGCGUAUACGCGAU--GCGGGCCAAAAGGACCGGUAUCAGUCCGGCAAUCCCUG-UCCCAAUCAUCCUAGACAAAUG
....(((-------((....)))--))((((((....)))(((--..(((.((...(((((((.......))))...))).))-.))).)))......)))..... ( -30.80)
>DroAna_CAF1 15827 106 - 1
CUCCCUGCCGUCCGACAGCGGUCAUACAGUGCGUAUACGCGAUGUGCGGGCCAAAAGGAUCGCCAUCAGUCGGCCAAUCUCUGGCCCCAAUCAUCCUAGACAAAUG
.........(((.(((.(((...((((.....)))).)))((((.(((..((....))..))))))).)))(((((.....)))))............)))..... ( -33.90)
>DroPer_CAF1 20302 85 - 1
CUGUCUG-------ACAGCAGCC--ACAUUGCGUAUACGCGAU--GCGGGCGA---GG-UCG-----UGUCCCGCCAUCUAUU-CCCCAAUCAUCCUAGACAAAUG
.((((((-------........(--.(((((((....))))))--).)((((.---((-...-----...)))))).......-............)))))).... ( -25.70)
>consensus
CUGUCUG_______ACAACGGCC__ACAUUGCGUAUACGCGAU__GCGGGCCAA_AGGACCGCUAUCAGUCCGGCAAUCCCUG_CCCCAAUCAUCCUAGACAAAUG
.((((((............((((....((((((....)))))).....))))....((((........))))........................)))))).... (-16.44 = -17.42 +   0.97)

alignment

secondary structure

dotplot

Window 9

Location	7,764,732 – 7,764,833
Length	101
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	75.81
Mean single sequence MFE	-32.05
Consensus MFE	-13.81
Energy contribution	-13.82
Covariance contribution	0.00
Combinations/Pair	1.24
Mean z-score	-2.68
Structure conservation index	0.43
SVM decision value	1.74
SVM RNA-class probability	0.974715
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7764732 101 - 20766785
UAAUCAUCCUUGGCCACAAACUUUUCCACUUAACUGUCUG-------GUCAGGGCC--ACAUUGCGUAUACGCGAU--GCGGGCCAA-AGGACCGCUAUCAGUCCGGCAAUUC
.......(((((((((...((..............)).))-------)))))))((--.(((((((....))))))--).))(((..-.((((........)))))))..... ( -32.94)
>DroPse_CAF1 20941 90 - 1
CAAUCU---ACGACCACAAACUUUUCCACUCAACUGUCUG-------ACAGCAGCC--ACAUUGCGUAUACGCGAU--GCGGGCGA---GG-UCG-----UGUCCCGCCAUCU
.....(---((((((..................(((....-------.)))..(((--.(((((((....))))))--)..)))..---))-)))-----))........... ( -27.40)
>DroEre_CAF1 19886 102 - 1
UAAUCAUCCUUGGCCACAAACUUUUCCACUUAACUGUCUG-------GCCAAGGCC--ACAUUGCGUAUACGCGAU--GCGGGCCAAAAGGACCGCUAUCAGUCCGGCCAUUC
.......(((((((((...((..............)).))-------))))))).(--.(((((((....))))))--).)((((....((((........)))))))).... ( -35.64)
>DroYak_CAF1 18357 102 - 1
UAAUCAUCCUUGGCCACAAACUUUUCCACUUAACUGUGUG-------GCCAAGGCC--ACGUUGCGUAUACGCGAU--GCGGGCCAAAAGGACCGGUAUCAGUCCGGCAAUCC
......((((((((((((...((........))...))))-------)))..((((--.(((((((....))))))--)..))))..)))))((((.......))))...... ( -40.20)
>DroAna_CAF1 15853 111 - 1
UAAUCAA--AUGACAAGAAACUCUUCCACUCAACUCCCUGCCGUCCGACAGCGGUCAUACAGUGCGUAUACGCGAUGUGCGGGCCAAAAGGAUCGCCAUCAGUCGGCCAAUCU
.......--.(((...(((....)))...)))..........(.(((((.(((...((((.....)))).)))((((.(((..((....))..))))))).))))).)..... ( -28.70)
>DroPer_CAF1 20327 90 - 1
CAAUCU---ACGACCACAAACUUUUCCACUCAACUGUCUG-------ACAGCAGCC--ACAUUGCGUAUACGCGAU--GCGGGCGA---GG-UCG-----UGUCCCGCCAUCU
.....(---((((((..................(((....-------.)))..(((--.(((((((....))))))--)..)))..---))-)))-----))........... ( -27.40)
>consensus
UAAUCAU__AUGACCACAAACUUUUCCACUCAACUGUCUG_______ACAACGGCC__ACAUUGCGUAUACGCGAU__GCGGGCCAA_AGGACCGCUAUCAGUCCGGCAAUCC
..........(((((............((......))...............((((....((((((....)))))).....))))....)).))).................. (-13.81 = -13.82 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:27 2006