Locus 6685

Sequence ID	2L_DroMel_CAF1
Location	18,721,765 – 18,721,962
Length	197
Max. P	0.998824

overview

Window 7

Location	18,721,765 – 18,721,885
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.66
Mean single sequence MFE	-29.75
Consensus MFE	-24.52
Energy contribution	-24.96
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.73
Structure conservation index	0.82
SVM decision value	0.49
SVM RNA-class probability	0.757869
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18721765 120 + 22407834
CAGCAACGGAAUCGUUUAAAAUUUGCUCAAGUUAUAGCCAAGGGCGAGCUGGCAAAUCAGGCCUUAAUUCAUUCCGCCAACUCAUCAUCUGCCAAAAACUCCCGUUGGCACAUGUUGGAA
(((((..(((((...((((.(((((((..((((...(((...))).)))))))))))......))))...)))))((((((......................))))))...)))))... ( -28.25)
>DroSec_CAF1 14439 120 + 1
CAGCAACGGAAUCGUUUAAAAUUUGCUCAAGUUAUAGGCAAGGGCGAGCUGGCAAAUCAGGCCUUAAUUCAUUCCGCCAACUCAUCAUCUGCCAAAAACUCCCUUUGGCACAUGUUGGAA
(((((.((((((.(((((.(((((....))))).))))).(((((...((((....))))))))).....)))))).............(((((((.......)))))))..)))))... ( -29.80)
>DroSim_CAF1 12915 120 + 1
CAGCAACGGAAUCGUUUAAAAUUUGCUCAAGUUAUAGCCAAGGGCGAGCUGGCAAAUCAGGCCUUAAUUCAUUCCGCCAACUCAUCAUCUGCCAAAAACUCCCUUUGGCACAUGUUGGAA
(((((.((((((...((((.(((((((..((((...(((...))).)))))))))))......))))...)))))).............(((((((.......)))))))..)))))... ( -29.00)
>DroEre_CAF1 14621 119 + 1
CACCAACG-AAUCGUUUAAAAUUUGCUCAAGCUAUAGCCAAGGGCGAGCUGGCAAAUCAGGCCUUAAUUCAUUCCGCCAACUCAUCAUCUGCCAAAAACUCCCUUUGGCACAUGUUGGAA
..((((((-(..........(((((((..((((...(((...))).)))))))))))..(((.............)))......))...(((((((.......)))))))...))))).. ( -31.72)
>DroYak_CAF1 14682 119 + 1
CACCAACG-AAUCGUUUAAAAUUUGCUCAACUUAAAGCCAAGGGCGAGCUGGCAAAUCAGGCCUUAAUUCAUUCUGCCUACUCAUCAUCUGCCAAAAACUCCCUUUGGCACAUGUUGGAA
..((((((-....((.........))..........((((((((.(((.(((((....((((.............))))..........)))))....)))))))))))...)))))).. ( -29.96)
>consensus
CAGCAACGGAAUCGUUUAAAAUUUGCUCAAGUUAUAGCCAAGGGCGAGCUGGCAAAUCAGGCCUUAAUUCAUUCCGCCAACUCAUCAUCUGCCAAAAACUCCCUUUGGCACAUGUUGGAA
......((((((...((((..(((((((.............)))))))..(((.......)))))))...)))))).....(((.(((.(((((((.......))))))).))).))).. (-24.52 = -24.96 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	18,721,845 – 18,721,962
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.43
Mean single sequence MFE	-22.58
Consensus MFE	-20.10
Energy contribution	-19.98
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-2.37
Structure conservation index	0.89
SVM decision value	3.24
SVM RNA-class probability	0.998824
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18721845 117 + 22407834
CUCAUCAUCUGCCAAAAACUCCCGUUGGCACAUGUUGGAAUCA---CCAACUUACGACCGCAAACGAGGCACUUCCAUGUCAACCCACAAUUCAGAUCGUGCCACACUCCAAAAGAAACA
.((..(((.((((((.........)))))).)))(((((....---........((........)).(((((.((..(((......))).....))..)))))....)))))..)).... ( -19.90)
>DroSec_CAF1 14519 117 + 1
CUCAUCAUCUGCCAAAAACUCCCUUUGGCACAUGUUGGAACCA---CCAGCUUACGACCGCAAACGAGGCACUUCCAUGUCAACCCACAAUUCAGAUCGUGCCACACUCCAAAAGAAACA
.((..(((.(((((((.......))))))).)))(((((....---...((........))......(((((.((..(((......))).....))..)))))....)))))..)).... ( -23.10)
>DroSim_CAF1 12995 117 + 1
CUCAUCAUCUGCCAAAAACUCCCUUUGGCACAUGUUGGAACCA---CCAGCUUACGACCGCAAACGAGGCACUUCCAUGUCAACCCACAAUUCAGAUCGUGCCACACUCCAAAAGAAACA
.((..(((.(((((((.......))))))).)))(((((....---...((........))......(((((.((..(((......))).....))..)))))....)))))..)).... ( -23.10)
>DroEre_CAF1 14700 120 + 1
CUCAUCAUCUGCCAAAAACUCCCUUUGGCACAUGUUGGAACCACCACCAACUUAUGACCGCAAACGAGGCACUUUCAUGUCAACCCACAAUUCAGUUCGUGCCACACUCCGAAAGAAACA
....((((.(((((((.......)))))))...(((((........)))))..))))..........(((((.....((.............))....)))))......(....)..... ( -21.92)
>DroYak_CAF1 14761 117 + 1
CUCAUCAUCUGCCAAAAACUCCCUUUGGCACAUGUUGGAACCA---CCAACUUAUGACCGCAAACGAGGCACUUUCGUGUCAACCCACAAUUCAGAUCGUGCCACACUUCAAAAGAAACA
.(((.(((.(((((((.......))))))).))).))).....---....(((.(((.((....)).(((((..((.(((......))).....))..))))).....))).)))..... ( -24.90)
>consensus
CUCAUCAUCUGCCAAAAACUCCCUUUGGCACAUGUUGGAACCA___CCAACUUACGACCGCAAACGAGGCACUUCCAUGUCAACCCACAAUUCAGAUCGUGCCACACUCCAAAAGAAACA
.((..(((.(((((((.......))))))).)))(((((...................((....)).(((((.....((.............))....)))))....)))))..)).... (-20.10 = -19.98 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:23 2006