Locus 1998

Sequence ID 3L_DroMel_CAF1
Location 5,475,624 – 5,475,726
Length 102
Max. P 0.850064
window3128 window3129

overview

Window 8

Location 5,475,624 – 5,475,726
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.83
Mean single sequence MFE -33.95
Consensus MFE -18.55
Energy contribution -20.98
Covariance contribution 2.43
Combinations/Pair 1.07
Mean z-score -2.65
Structure conservation index 0.55
SVM decision value 0.44
SVM RNA-class probability 0.738016
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5475624 102 + 23771897
GUUGACUUGAUUAUCAACACUCGCUGCACAUCUUGCA----UGCUCGC--------------AUCUGUAUCUGAUGCUGCAUGUUGCAGCUGGCAGUUGACAGCUGAUGAUGUUGCAUAU
(((((........)))))......((((((((..(((----(((..((--------------(((.......))))).))))))..((((((........))))))..)))).))))... ( -36.50)
>DroSec_CAF1 37112 102 + 1
GUUGACUUGAUUAUCAACACUCGCUGCACAUCUUGCA----UGCUCGC--------------AUCUGUAUCUAAUGCUGCAUGUUGCAGCUGGCAGUUGACAGCUGAUGAUGUUGCAUAU
(((((........)))))......((((((((..(((----(((..((--------------((.........)))).))))))..((((((........))))))..)))).))))... ( -31.80)
>DroSim_CAF1 38798 102 + 1
GUUGACUUGAUUAUCAACACUCGCUGCACAUCUUGCA----UGCUCGC--------------AUCUGUAUCUGAUGCUGCAUGUUGCAGCUGGCAGUUGACAGCUGAUGAUGUUGCAUAU
(((((........)))))......((((((((..(((----(((..((--------------(((.......))))).))))))..((((((........))))))..)))).))))... ( -36.50)
>DroEre_CAF1 36600 108 + 1
GUUGACUUGAUUAUCAACACUCGCUGCACAUCUUGCA----UGCUCGCAUCU--------GCAUCUGUAUCUGAUGCUGCAUGUUGCAGCUGGCAGUUGACAGCUGAUGAUGUUGCAUAU
(((((........)))))......((((((((..(((----(((..((((((--------((....)))...))))).))))))..((((((........))))))..)))).))))... ( -36.40)
>DroYak_CAF1 24960 116 + 1
GUUGACUUGAUUAUCAACACUCGCUGCACAUCUUGCA----UGCUCGCAACUCGCAACUCGCAUCUGUAUCUGAUGCAGCAUGUUGCAGCUGGCAGUUGACAGCUGAUGAUGUUGCAUAU
(((((........)))))......((((((((..(((----((((.((.....)).....(((((.......))))))))))))..((((((........))))))..)))).))))... ( -38.90)
>DroMoj_CAF1 31230 95 + 1
CAUGACUUGAUUAUCACCGCUCGAUGCGC---UUGCACAGCUGAUGGCGACU--------GCAUUUGCAU------UUGCAU-UU-------ACAACUGCCAGCUGAUGAAGUUGCAUGC
((((((((.((((.....((.....))((---(.(((.........((((.(--------((....))).------))))..-..-------.....))).))))))).))))..)))). ( -23.57)
>consensus
GUUGACUUGAUUAUCAACACUCGCUGCACAUCUUGCA____UGCUCGC______________AUCUGUAUCUGAUGCUGCAUGUUGCAGCUGGCAGUUGACAGCUGAUGAUGUUGCAUAU
(((((........)))))......((((((((..(((....)))....................((((..(((..(((((.....)))))...)))...)))).....)))).))))... (-18.55 = -20.98 +   2.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 5,475,624 – 5,475,726
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.83
Mean single sequence MFE -33.71
Consensus MFE -18.16
Energy contribution -20.48
Covariance contribution 2.32
Combinations/Pair 1.07
Mean z-score -3.06
Structure conservation index 0.54
SVM decision value 0.78
SVM RNA-class probability 0.850064
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5475624 102 - 23771897
AUAUGCAACAUCAUCAGCUGUCAACUGCCAGCUGCAACAUGCAGCAUCAGAUACAGAU--------------GCGAGCA----UGCAAGAUGUGCAGCGAGUGUUGAUAAUCAAGUCAAC
...((((.((((..((((((.(....).))))))...(((((.(((((.......)))--------------))..)))----))...))))))))......((((((......)))))) ( -34.90)
>DroSec_CAF1 37112 102 - 1
AUAUGCAACAUCAUCAGCUGUCAACUGCCAGCUGCAACAUGCAGCAUUAGAUACAGAU--------------GCGAGCA----UGCAAGAUGUGCAGCGAGUGUUGAUAAUCAAGUCAAC
...((((.((((..((((((.(....).))))))...(((((.(((((.......)))--------------))..)))----))...))))))))......((((((......)))))) ( -32.80)
>DroSim_CAF1 38798 102 - 1
AUAUGCAACAUCAUCAGCUGUCAACUGCCAGCUGCAACAUGCAGCAUCAGAUACAGAU--------------GCGAGCA----UGCAAGAUGUGCAGCGAGUGUUGAUAAUCAAGUCAAC
...((((.((((..((((((.(....).))))))...(((((.(((((.......)))--------------))..)))----))...))))))))......((((((......)))))) ( -34.90)
>DroEre_CAF1 36600 108 - 1
AUAUGCAACAUCAUCAGCUGUCAACUGCCAGCUGCAACAUGCAGCAUCAGAUACAGAUGC--------AGAUGCGAGCA----UGCAAGAUGUGCAGCGAGUGUUGAUAAUCAAGUCAAC
...((((.((((..((((((.(....).))))))...(((((.(((((............--------.)))))..)))----))...))))))))......((((((......)))))) ( -34.02)
>DroYak_CAF1 24960 116 - 1
AUAUGCAACAUCAUCAGCUGUCAACUGCCAGCUGCAACAUGCUGCAUCAGAUACAGAUGCGAGUUGCGAGUUGCGAGCA----UGCAAGAUGUGCAGCGAGUGUUGAUAAUCAAGUCAAC
...((((((.((...(((((.(....).)))))(((((....((((((.......)))))).))))))))))))).((.----((((.....))))))....((((((......)))))) ( -37.00)
>DroMoj_CAF1 31230 95 - 1
GCAUGCAACUUCAUCAGCUGGCAGUUGU-------AA-AUGCAA------AUGCAAAUGC--------AGUCGCCAUCAGCUGUGCAA---GCGCAUCGAGCGGUGAUAAUCAAGUCAUG
((.((((.......((((((((..((((-------(.-.(((..------..)))..)))--------))..)))...))))))))).---))((.....)).(((((......))))). ( -28.61)
>consensus
AUAUGCAACAUCAUCAGCUGUCAACUGCCAGCUGCAACAUGCAGCAUCAGAUACAGAU______________GCGAGCA____UGCAAGAUGUGCAGCGAGUGUUGAUAAUCAAGUCAAC
...((((.((((.....((((...(((...(((((.....)))))..)))..))))....................(((....)))..))))))))......((((((......)))))) (-18.16 = -20.48 +   2.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:07 2006