Locus 2066

Sequence ID	2L_DroMel_CAF1
Location	5,575,329 – 5,575,489
Length	160
Max. P	0.898043

overview

Window 2

Location	5,575,329 – 5,575,449
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.67
Mean single sequence MFE	-28.00
Consensus MFE	-27.80
Energy contribution	-27.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.99
SVM decision value	1.00
SVM RNA-class probability	0.898043
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5575329 120 - 22407834
CAUGCAGCUUGCAUAAAACUUGCAGCUGGAAUUUUCCCCCGAGCAAUUUCAUAUUAGAGUUCCACUCGAGCAACUUUGUAAUUGAAAUCAAAGUGUGUAAAGUGAGCUCGAAAUCAAACC
..(.(((((.(((.......)))))))).).........(((((....((((....(((.....)))..(((((((((..........)))))).)))...))))))))).......... ( -27.80)
>DroSec_CAF1 19381 120 - 1
CAUGCAGCUUGCAUAAAACUUGCAGCUGGAAUUUUCCCCCGAGCAAUUUCAUAUUAGAGUUCCACUCGAGCAACUUUGUAAUUGAAAUCAAAGUGUGUAAAGUGAGCUCGAAAUCAAGCC
...((((((.(((.......)))))))((((((((.....(((....))).....))))))))..((((((.((((((((.(((....)))....))))))))..))))))......)). ( -28.80)
>DroSim_CAF1 21033 120 - 1
CAUGCAGCUUGCAUAAAACUUGCAGCUGGAAUUUUCCCCCGAGCAAUUUCAUAUUAGAGUUCCACUCGAGCAACUUUGUAAUUGAAAUCAAAGUGUGUAAAGUGAGCUCGAAAUCAAACC
..(.(((((.(((.......)))))))).).........(((((....((((....(((.....)))..(((((((((..........)))))).)))...))))))))).......... ( -27.80)
>DroEre_CAF1 19310 120 - 1
CAUGCAGCUUGCAUAAAACUUGCAGCUGGAAUUUUCCCCCGAGCAAUUUCAUAUUAGAGUUCCACUCGAGCAACUUUGUAAUUGAAAUCAAAGUGUGUAAAGUGAGCUCGAAAUCAAACC
..(.(((((.(((.......)))))))).).........(((((....((((....(((.....)))..(((((((((..........)))))).)))...))))))))).......... ( -27.80)
>DroYak_CAF1 19150 120 - 1
CAUGCAGCUUGCAUAAAACUUGCAGCUGGAAUUUUCCCCCGAGCAAUUUCAUAUUAGAGUUCCACUCGAGCAACUUUGUAAUUGAAAUCAAAGUGUGUAAAGUGAGCUCGAAAUCAAACC
..(.(((((.(((.......)))))))).).........(((((....((((....(((.....)))..(((((((((..........)))))).)))...))))))))).......... ( -27.80)
>consensus
CAUGCAGCUUGCAUAAAACUUGCAGCUGGAAUUUUCCCCCGAGCAAUUUCAUAUUAGAGUUCCACUCGAGCAACUUUGUAAUUGAAAUCAAAGUGUGUAAAGUGAGCUCGAAAUCAAACC
..(.(((((.(((.......)))))))).).........(((((....((((....(((.....)))..(((((((((..........)))))).)))...))))))))).......... (-27.80 = -27.80 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	5,575,369 – 5,575,489
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.92
Mean single sequence MFE	-33.40
Consensus MFE	-24.88
Energy contribution	-25.48
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.74
SVM decision value	-0.04
SVM RNA-class probability	0.510710
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5575369 120 + 22407834
UACAAAGUUGCUCGAGUGGAACUCUAAUAUGAAAUUGCUCGGGGGAAAAUUCCAGCUGCAAGUUUUAUGCAAGCUGCAUGGGGAAAUUGCAUUAGCCCCUCCCACCGCCCAGCCGCUUAC
....((((.(((.(((..(...((......))..)..)))((((((......((((((((.......))).)))))...((((..(......)..)))))))).))....))).)))).. ( -35.70)
>DroSec_CAF1 19421 114 + 1
UACAAAGUUGCUCGAGUGGAACUCUAAUAUGAAAUUGCUCGGGGGAAAAUUCCAGCUGCAAGUUUUAUGCAAGCUGCAUGGGCAAAUUGCAUUAGCCCCUCCC------CCUCCGCUUAC
.............(((((((..((......))........((((((......((((((((.......))).)))))...((((...........)))).))))------))))))))).. ( -35.90)
>DroSim_CAF1 21073 114 + 1
UACAAAGUUGCUCGAGUGGAACUCUAAUAUGAAAUUGCUCGGGGGAAAAUUCCAGCUGCAAGUUUUAUGCAAGCUGCAUGGGCAAAUUGCAUUAGCCCCUCCC------CCGCCGCUUAC
....((((.((..(((..(...((......))..)..)))((((((......((((((((.......))).)))))...((((...........)))).))))------)))).)))).. ( -38.60)
>DroEre_CAF1 19350 107 + 1
UACAAAGUUGCUCGAGUGGAACUCUAAUAUGAAAUUGCUCGGGGGAAAAUUCCAGCUGCAAGUUUUAUGCAAGCUGCAUGGGGAAAUUGCAUUUGCCCCUC-------------GGUGGC
......((..((((((..(...((......))..)..))))((((.......(((.(((((.((((((((.....))))))))...))))).)))))))..-------------))..)) ( -30.91)
>DroYak_CAF1 19190 107 + 1
UACAAAGUUGCUCGAGUGGAACUCUAAUAUGAAAUUGCUCGGGGGAAAAUUCCAGCUGCAAGUUUUAUGCAAGCUGCAUGGCGAAAUUGCAUUAACCCCUC-------------GUUGAC
..(((.......((((..(...((......))..)..))))((((.......((((((((.......))).)))))....(((....))).....))))..-------------.))).. ( -25.90)
>consensus
UACAAAGUUGCUCGAGUGGAACUCUAAUAUGAAAUUGCUCGGGGGAAAAUUCCAGCUGCAAGUUUUAUGCAAGCUGCAUGGGGAAAUUGCAUUAGCCCCUCCC______C__CCGCUUAC
.....((((.((((((..(...((......))..)..))))))(((....)))))))((((.((((((((.....))))))))...)))).............................. (-24.88 = -25.48 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:36 2006