Locus 111

Sequence ID	2R_DroMel_CAF1
Location	1,357,380 – 1,357,471
Length	91
Max. P	0.913906

overview

Window 1

Location	1,357,380 – 1,357,471
Length	91
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	83.82
Mean single sequence MFE	-21.79
Consensus MFE	-17.55
Energy contribution	-17.91
Covariance contribution	0.36
Combinations/Pair	1.07
Mean z-score	-1.99
Structure conservation index	0.81
SVM decision value	0.52
SVM RNA-class probability	0.766543
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1357380 91 + 20766785
---------U---CCGUUUCCUAU--CGCUUCUUGCG--AAGUUUUAUUACUGUUGCCUACUUCCAGGCAUAAUAUAAUUCACACGCCUAAGCCGCAGGCAGCUGAC
---------.---...........--.(((.((((((--..(..((((......(((((......)))))....))))..)....((....)))))))).))).... ( -20.70)
>DroVir_CAF1 87505 94 + 1
---------G---CC-AUUUCUAUUUUGCUUUUUGCUCCAAGUUAUAUUACAGUUGCCUAUUUUCAGGCAUUAUAUAAUUCACACGCCUAAACCGCAGGCGGCUGAC
---------(---((-...........((.....))....((((((((......(((((......)))))..)))))))).....((((.......))))))).... ( -20.20)
>DroGri_CAF1 79469 91 + 1
---------G---CC-AUUUCCAU--UGCUUUUUGCG-CAAGUUUUAUUACAGUUGCCUACUUUCAGGCAUAAUAUAAUUCACACGCCUAAGCCGCAGGCAGCUGAC
---------.---..-.......(--(((.......)-))).........(((((((((......((((................)))).......))))))))).. ( -20.91)
>DroEre_CAF1 2425 91 + 1
---------C---CCGCUUGCCUU--CGCUUCUGGCG--AAGUUUUAUUACACUUGCCUACUUCCAGGCAUAAUAUAAUUCACACGCCUAAGCCGCAGGCAGCCGAC
---------.---.((.((((((.--(((((..((((--..(..((((......(((((......)))))....))))..)...)))).))).)).)))))).)).. ( -28.40)
>DroWil_CAF1 89159 104 + 1
UACUACUGUUUUGCCCAUUUCUAU--UGCUUUUUGCU-CAAGUUUUAUUACAGUUGCCUACUUUCAGGCAUAAUAUAAUUCACACGCCUAAGCCGCAGGCAGCUGAC
........................--.((.....)).-............(((((((((......((((................)))).......))))))))).. ( -19.41)
>DroAna_CAF1 2925 95 + 1
---------UGUGUCCUUUUCUAU--CGCUUUUUGCG-CAAGUUUUAUUACAGUUGCCUACUUUCAGGCAUAAUAUAAUUCACACGCCUAAGCCGAAGGCAGCUGAC
---------...............--(((.....)))-............(((((((((......((((................)))).......))))))))).. ( -21.11)
>consensus
_________U___CC_AUUUCUAU__CGCUUUUUGCG_CAAGUUUUAUUACAGUUGCCUACUUUCAGGCAUAAUAUAAUUCACACGCCUAAGCCGCAGGCAGCUGAC
...........................((.....))..............(((((((((......((((................)))).......))))))))).. (-17.55 = -17.91 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	1,357,380 – 1,357,471
Length	91
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	83.82
Mean single sequence MFE	-29.00
Consensus MFE	-22.93
Energy contribution	-23.60
Covariance contribution	0.67
Combinations/Pair	1.10
Mean z-score	-2.93
Structure conservation index	0.79
SVM decision value	1.09
SVM RNA-class probability	0.913906
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1357380 91 - 20766785
GUCAGCUGCCUGCGGCUUAGGCGUGUGAAUUAUAUUAUGCCUGGAAGUAGGCAACAGUAAUAAAACUU--CGCAAGAAGCG--AUAGGAAACGG---A---------
(((.(.(((((((..((.(((((((..........)))))))))..))))))).)..........(((--(....)))).)--)).(....)..---.--------- ( -31.20)
>DroVir_CAF1 87505 94 - 1
GUCAGCCGCCUGCGGUUUAGGCGUGUGAAUUAUAUAAUGCCUGAAAAUAGGCAACUGUAAUAUAACUUGGAGCAAAAAGCAAAAUAGAAAU-GG---C---------
....((((((((...(((((((((............)))))))))..)))))...................((.....))...........-))---)--------- ( -23.90)
>DroGri_CAF1 79469 91 - 1
GUCAGCUGCCUGCGGCUUAGGCGUGUGAAUUAUAUUAUGCCUGAAAGUAGGCAACUGUAAUAAAACUUG-CGCAAAAAGCA--AUGGAAAU-GG---C---------
..(((.(((((((...(((((((((..........)))))))))..))))))).))).........(((-(.......)))--).......-..---.--------- ( -28.70)
>DroEre_CAF1 2425 91 - 1
GUCGGCUGCCUGCGGCUUAGGCGUGUGAAUUAUAUUAUGCCUGGAAGUAGGCAAGUGUAAUAAAACUU--CGCCAGAAGCG--AAGGCAAGCGG---G---------
..(.(((((((...((((.((((.((..((((((((.((((((....))))))))))))))...))..--))))..)))).--.)))).))).)---.--------- ( -36.40)
>DroWil_CAF1 89159 104 - 1
GUCAGCUGCCUGCGGCUUAGGCGUGUGAAUUAUAUUAUGCCUGAAAGUAGGCAACUGUAAUAAAACUUG-AGCAAAAAGCA--AUAGAAAUGGGCAAAACAGUAGUA
....(((((((((...(((((((((..........)))))))))..)))))).(((((...........-.((.....)).--.((....))......)))))))). ( -27.80)
>DroAna_CAF1 2925 95 - 1
GUCAGCUGCCUUCGGCUUAGGCGUGUGAAUUAUAUUAUGCCUGAAAGUAGGCAACUGUAAUAAAACUUG-CGCAAAAAGCG--AUAGAAAAGGACACA---------
(((((.(((((.(...(((((((((..........)))))))))..).))))).)).........((..-(((.....)))--..)).....)))...--------- ( -26.00)
>consensus
GUCAGCUGCCUGCGGCUUAGGCGUGUGAAUUAUAUUAUGCCUGAAAGUAGGCAACUGUAAUAAAACUUG_CGCAAAAAGCA__AUAGAAAU_GG___A_________
..(((.(((((((...(((((((((..........)))))))))..))))))).)))..............((.....))........................... (-22.93 = -23.60 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:27:40 2006