Locus 2179

Sequence ID	3L_DroMel_CAF1
Location	5,939,913 – 5,940,036
Length	123
Max. P	0.923630

overview

Window 9

Location	5,939,913 – 5,940,004
Length	91
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	83.44
Mean single sequence MFE	-25.60
Consensus MFE	-15.47
Energy contribution	-16.64
Covariance contribution	1.17
Combinations/Pair	1.15
Mean z-score	-2.56
Structure conservation index	0.60
SVM decision value	0.09
SVM RNA-class probability	0.578727
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5939913 91 + 23771897
AGUUGCAGUGAAAGGGGCAAAAA------------AGUCAGCAUACAUUGCCGAUGAAAGCACUUCAUUAGCGAGGAUGCUGAAUGUUUAUUUCCACAUAUGC
.......((((((..((((....------------..(((((((...((((..(((((.....)))))..))))..))))))).))))..))).)))...... ( -26.30)
>DroSec_CAF1 49894 91 + 1
AGUUGCAGUGAAAGGGGCAAAAA------------AGUCAGCAUACAUUGCCGAUGAAAGCACUUCAUUAGCGAGGAUGCUGAAUGUUUAUUCCCACAUAUGC
....((((((...((((..(((.------------..(((((((...((((..(((((.....)))))..))))..)))))))...)))..)))).))).))) ( -28.80)
>DroSim_CAF1 34625 91 + 1
AGUUGCAGUGAAAGGGGCAAAAA------------AGUCAGCAUACAUUGCCGAUGAAAGCACUUCAUUAGCGAGGAUGCUGAAUGUUUAUUCCCACAUAUGC
....((((((...((((..(((.------------..(((((((...((((..(((((.....)))))..))))..)))))))...)))..)))).))).))) ( -28.80)
>DroEre_CAF1 32096 90 + 1
AGUUGCAGUGAAAGGGGCAAA-A------------AGUCAGCAUACAUUGCAGAUGAAAGCACUUCAUUAGCGAGAAGGCUGAAUGUUUAUUUCCCCAUAUGC
....(((......((((.(((-.------------..(((((.....((((.((((((.....)))))).))))....)))))...)))....))))...))) ( -24.80)
>DroYak_CAF1 34530 91 + 1
AUUCGCAGUGAAAGGGGCAAAAA------------AGUCAGCAUGCAUUGCAGAUGAAAGCACUUCAUUAGCGAGAAUGCUGAAUGUUUAUUCCCACAUAUGC
....((((((...((((..(((.------------..(((((((...((((.((((((.....)))))).))))..)))))))...)))..)))).))).))) ( -28.40)
>DroAna_CAF1 61972 96 + 1
AUUUCAAGUGAUGGGGGAAACAAAAAUAAAUAUAAACGUAGCAUACAUUUCAGAUGAAAACACUUCAUUAGCGGG-------AAUGUUUGUUUUUACAUAUCU
.........((((..(....)................((((((.(((((((.((((((.....))))))....))-------))))).)))...))).)))). ( -16.50)
>consensus
AGUUGCAGUGAAAGGGGCAAAAA____________AGUCAGCAUACAUUGCAGAUGAAAGCACUUCAUUAGCGAGGAUGCUGAAUGUUUAUUCCCACAUAUGC
....((((((...((((....................(((((((...((((..(((((.....)))))..))))..)))))))........)))).))).))) (-15.47 = -16.64 +   1.17)

alignment

secondary structure

dotplot

Window 0

Location	5,939,936 – 5,940,036
Length	100
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	88.65
Mean single sequence MFE	-24.35
Consensus MFE	-21.68
Energy contribution	-21.64
Covariance contribution	-0.04
Combinations/Pair	1.05
Mean z-score	-1.67
Structure conservation index	0.89
SVM decision value	1.16
SVM RNA-class probability	0.923630
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5939936 100 + 23771897
AGUCAGCAUACAUUGCCGAUGAAAGCACUUCAUUAGCGAGGAUGCUGAAUGUUUAUUUCCACAUAUGCCUGGACACACAUUUCCGGU-------UCCCUUUUGAAAC
..(((((((...((((..(((((.....)))))..))))..))))))).......((((.......(((.(((........))))))-------........)))). ( -26.36)
>DroSec_CAF1 49917 94 + 1
AGUCAGCAUACAUUGCCGAUGAAAGCACUUCAUUAGCGAGGAUGCUGAAUGUUUAUUCCCACAUAUGCCUGAAC------UUCCGGU-------UCCCUUUUGAAAC
..(((((((...((((..(((((.....)))))..))))..)))))))((((........))))......((((------.....))-------))........... ( -23.50)
>DroSim_CAF1 34648 94 + 1
AGUCAGCAUACAUUGCCGAUGAAAGCACUUCAUUAGCGAGGAUGCUGAAUGUUUAUUCCCACAUAUGCCUGAAC------UUCCGGU-------ACCCUUUUGAAAC
..(((((((...((((..(((((.....)))))..))))..)))))))((((........)))).((((.(...------..).)))-------)............ ( -24.20)
>DroEre_CAF1 32118 107 + 1
AGUCAGCAUACAUUGCAGAUGAAAGCACUUCAUUAGCGAGAAGGCUGAAUGUUUAUUUCCCCAUAUGCCUGGACACACACUUCCGGUUUGAAAUUCCCUUUUGAAAU
..(((((.....((((.((((((.....)))))).))))....))))).............((...(((.(((........)))))).))................. ( -22.30)
>DroYak_CAF1 34553 100 + 1
AGUCAGCAUGCAUUGCAGAUGAAAGCACUUCAUUAGCGAGAAUGCUGAAUGUUUAUUCCCACAUAUGCCUGGACACACACUUCCGGU-------UCCCUUUUGCAAU
..(((((((...((((.((((((.....)))))).))))..)))))))((((........)))).((((((((........))))).-------........))).. ( -25.40)
>consensus
AGUCAGCAUACAUUGCCGAUGAAAGCACUUCAUUAGCGAGGAUGCUGAAUGUUUAUUCCCACAUAUGCCUGGACACACA_UUCCGGU_______UCCCUUUUGAAAC
..(((((((...((((..(((((.....)))))..))))..)))))))..................(((.(((.......))).))).................... (-21.68 = -21.64 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:11 2006