Locus 4782

Sequence ID	3R_DroMel_CAF1
Location	12,513,773 – 12,513,935
Length	162
Max. P	0.998523

overview

Window 4

Location	12,513,773 – 12,513,865
Length	92
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	72.78
Mean single sequence MFE	-35.50
Consensus MFE	-12.98
Energy contribution	-12.18
Covariance contribution	-0.80
Combinations/Pair	1.27
Mean z-score	-2.03
Structure conservation index	0.37
SVM decision value	1.15
SVM RNA-class probability	0.923286
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12513773 92 + 27905053
CGCAGCC-UG------AAAACUCGAAAUGAAAUUAAACCCUUUUCGGCGGCUGCUGCUG---CCGCUGACGCUGUUGCAG------CAACAUGGCAACAUGGCGGCUG
.((((((-.(------(....))(...(((((.........))))).)))))))....(---((((....((((...)))------)..((((....))))))))).. ( -33.40)
>DroPse_CAF1 1005 103 + 1
CGCAACG-UGCAACGCGAAACUCGAAAUGAAAUUAAACCCUUUUUGGCGGCGGUGGC---GGCUGCUGCUGCUUCUGCAAAAGACGGACCGC-GGGACGAGGCAAAUA
.((..((-(.(..((((....((.....)).......((.(((((....((((.(((---(((....)))))).)))).))))).))..)))-)).)))..))..... ( -31.80)
>DroSec_CAF1 2866 92 + 1
CGCAGCCUUG------AAAACUCGAAAUGAAAUUAAACCCUUUUUCGGCGCUGCUGCUG----CGCUGCCGCUAUUGCAG------CAACAUGGCAACAUGGCGGCUG
.(((((.(((------((((.....................))))))).))))).((((----((((((.......))))------)..((((....))))))))).. ( -34.20)
>DroSim_CAF1 2930 92 + 1
CGCAGCC-UG------AAAACUCGAAAUGAAAUUAAACCCUUUUCGGCGGCUGCUGCUG---CCGCUGCCGCUGUUGCAG------CAACAUGGCAACAUGGCGGCUG
.((((((-.(------(....))(...(((((.........))))).))))))).((((---(((((((.......))))------)...(((....))))))))).. ( -35.60)
>DroPer_CAF1 4867 106 + 1
CGCAACG-UGCAACGCGAAACUCGAAAUGAAAUUAAACCCUUUUUGGCGGCGGUGGCGGCGGCUGCUGCUGCUUCUGCCAAAGACGGACCGC-GGGACGAGGCAAAUA
.((..((-(.(..((((....((.....)).......((.((((((((((.((..(((((....)))))..)).)))))))))).))..)))-)).)))..))..... ( -42.50)
>consensus
CGCAGCC_UG______AAAACUCGAAAUGAAAUUAAACCCUUUUUGGCGGCUGCUGCUG___CCGCUGCCGCUGUUGCAG______CAACAUGGCAACAUGGCGGCUG
.(((((...............((((((..............))))))..((....)).......)))))(((((((((...............)))..)))))).... (-12.98 = -12.18 +  -0.80)

alignment

secondary structure

dotplot

Window 5

Location	12,513,805 – 12,513,896
Length	91
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	72.11
Mean single sequence MFE	-32.40
Consensus MFE	-17.68
Energy contribution	-18.44
Covariance contribution	0.76
Combinations/Pair	1.33
Mean z-score	-2.23
Structure conservation index	0.55
SVM decision value	2.13
SVM RNA-class probability	0.988690
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12513805 91 + 27905053
CUUUUCGGCGGCUGCUGCUG---CCGCUGACGCUGUUGCAG------CAACAUGGCAACAUGGCGGCUGGCUGCAAGAAAUUAACAUUAUUGCAAUUUCU
......(.((((((((((((---(.((.......)).))))------)).((((....))))))))))).)(((((.............)))))...... ( -34.62)
>DroPse_CAF1 1043 88 + 1
CUUUUUGGCGGCGGUGGC---GGCUGCUGCUGCUUCUGCAAAAGACGGACCGC-GGGACGAGGCAAAUAGUUGCAAAAAAUUAACAUUAUUG--------
((.((((.(.((((.(((---(((....)))))).))))......((..(...-.)..)).).)))).))......................-------- ( -24.70)
>DroSec_CAF1 2899 90 + 1
CUUUUUCGGCGCUGCUGCUG----CGCUGCCGCUAUUGCAG------CAACAUGGCAACAUGGCGGCUGGCUGCAAGAAAUUAACAUUAUUGCAAUUUCU
..........((.(((((((----((((((.......))))------)..((((....))))))))).))).)).(((((((..((....)).))))))) ( -32.40)
>DroSim_CAF1 2962 91 + 1
CUUUUCGGCGGCUGCUGCUG---CCGCUGCCGCUGUUGCAG------CAACAUGGCAACAUGGCGGCUGGCUGCAAGAAAUUAACAUUAUUGCAAUUUCU
......((((((....))))---))((.(((((....))((------(..((((....))))...)))))).)).(((((((..((....)).))))))) ( -35.70)
>DroPer_CAF1 4905 98 + 1
CUUUUUGGCGGCGGUGGCGGCGGCUGCUGCUGCUUCUGCCAAAGACGGACCGC-GGGACGAGGCAAAUAGUUGCAAAAAAUUAACAUUAUUGCAGUUU-U
.((((((((((.((..(((((....)))))..)).))))))))))((..(...-.)..))..((((...((((........))))....)))).....-. ( -34.60)
>consensus
CUUUUUGGCGGCUGCUGCUG___CCGCUGCCGCUGUUGCAG______CAACAUGGCAACAUGGCGGCUGGCUGCAAGAAAUUAACAUUAUUGCAAUUUCU
.....(((((((.((.(......).)).)))))))((((((.........((((....))))((((....))))...............))))))..... (-17.68 = -18.44 +   0.76)

alignment

secondary structure

dotplot

Window 6

Location	12,513,839 – 12,513,935
Length	96
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	80.57
Mean single sequence MFE	-25.72
Consensus MFE	-18.64
Energy contribution	-18.44
Covariance contribution	-0.20
Combinations/Pair	1.19
Mean z-score	-3.32
Structure conservation index	0.72
SVM decision value	3.13
SVM RNA-class probability	0.998523
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12513839 96 + 27905053
GCAG------CAACAUGGCAACAUGGCGGCUGGCUGCAAGAAAUUAACAUUAUUGCAAUUUCUGCAGCUUUAACUAACAAGCGCAGAAAAUACACAAAAAAA
.(((------(..((((....))))...))))..(((((.............))))).(((((((.((((........)))))))))))............. ( -28.72)
>DroSec_CAF1 2932 95 + 1
GCAG------CAACAUGGCAACAUGGCGGCUGGCUGCAAGAAAUUAACAUUAUUGCAAUUUCUGCAGCUUUAACUAACAAGCCCAGAGAAUACACAAU-AAA
.(((------(..((((....))))...))))((((((.((((((..((....)).))))))))))))..............................-... ( -26.90)
>DroSim_CAF1 2996 95 + 1
GCAG------CAACAUGGCAACAUGGCGGCUGGCUGCAAGAAAUUAACAUUAUUGCAAUUUCUGCAGCUUUAACUAACAAGCCCAGAGAAUACACAAA-AAA
.(((------(..((((....))))...))))((((((.((((((..((....)).))))))))))))..............................-... ( -26.90)
>DroEre_CAF1 421 95 + 1
GCAG------CAACAUGGCAACAUGGCGGCUGGCUGCAAGAAAUUAACAUUAUUGCAAUUUCUGCAGCUUUAACUAACAAGCCAAGGGAAUACACGAA-AAA
.(((------(..((((....))))...))))((((((.((((((..((....)).))))))))))))..............................-... ( -26.90)
>DroPer_CAF1 4942 87 + 1
GCCAAAGACGGACCGC-GGGACGAGGCAAAUAGUUGCAAAAAAUUAACAUUAUUGCAGUUU-UGCAGCUUCAACUAGCAAGCCA------UGCCC-------
.((......)).....-(((.((.(((.......(((((((...(((.....)))...)))-))))(((......)))..))).------)))))------- ( -19.20)
>consensus
GCAG______CAACAUGGCAACAUGGCGGCUGGCUGCAAGAAAUUAACAUUAUUGCAAUUUCUGCAGCUUUAACUAACAAGCCCAGAGAAUACACAAA_AAA
((...........((((....))))......(((((((.((((((..((....)).)))))))))))))...........)).................... (-18.64 = -18.44 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:47 2006