Locus 7253

Sequence ID	2L_DroMel_CAF1
Location	20,312,573 – 20,312,669
Length	96
Max. P	0.995956

overview

Window 1

Location	20,312,573 – 20,312,669
Length	96
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	75.71
Mean single sequence MFE	-35.48
Consensus MFE	-18.47
Energy contribution	-19.75
Covariance contribution	1.28
Combinations/Pair	1.15
Mean z-score	-1.83
Structure conservation index	0.52
SVM decision value	0.47
SVM RNA-class probability	0.748304
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20312573 96 + 22407834
UGGGUGCGCCAC---------CAACCCGAGGGAAUCGAAGUCGGAGUCCAAGUCGGAAAUCGGUGGCUUUGGCGGCUU-UUUCGGGGCCGCCAAAUAGGAUUACUU
.(((((.(((((---------(...((((.(((.(((....)))..)))...)))).....))))))(((((((((((-.....)))))))))))......))))) ( -39.90)
>DroSec_CAF1 55516 94 + 1
UGGGUGCGCCAC---------CUACCCGAGGGAAUCGAAGUCGGAGUCCAAGUCGGA-AUCGGUGGCUUUGGCGGCUU--UUCGGGGCCGCCAAAUAGGAUAACUU
.((((.((((((---------(...((((.(((.(((....)))..)))...)))).-...))))))(((((((((((--....)))))))))))...)...)))) ( -39.80)
>DroSim_CAF1 54332 94 + 1
UGGGUGCGCCAC---------CUACCCGAGGGAAUCGAAGUCGGAGUCCAAGUCGGA-AUCGGUGGCUUUGGCGGCUU--GUCGGGGCCGCCAAAUAGGAUUACUU
.(((((.(((((---------(...((((.(((.(((....)))..)))...)))).-...))))))((((((((((.--.....))))))))))......))))) ( -40.20)
>DroEre_CAF1 41751 83 + 1
UGGGUGCGCCAC---------CUACCCGAGGGAAUCGAAGUUGGA-----------A-AUCGGUGACUUUGGCGGCUU--UUCGGGGCCGCCAAAUAGGAUUACUU
((((((...)))---------))).((((((..(((((.......-----------.-.)))))..))))((((((((--....)))))))).....))....... ( -29.10)
>DroYak_CAF1 35503 83 + 1
UGGGUGCGCCAC---------CUACCCGAGGGAAUCGAAGUCGGA-----------A-AUCGGUGGCUUUGGCGGCUU--UUCGGGGCCGCCAAAUAGGAUUACUU
.(((((.(((((---------(..((....))..(((....))).-----------.-...))))))(((((((((((--....)))))))))))......))))) ( -34.50)
>DroPer_CAF1 26276 90 + 1
CGGGUGCGGCUCCACAGAUCCCUGCCCCGCAGAGCCGACAC---------------A-UCCGACAGAUGUUGAGGCAAGUCUGAGGUCCGCCAAAUAGGAUUACCU
.((((((((..((.(((((..((((...)))).(((...((---------------(-((.....)))))...)))..))))).)).))))...........)))) ( -29.40)
>consensus
UGGGUGCGCCAC_________CUACCCGAGGGAAUCGAAGUCGGA___________A_AUCGGUGGCUUUGGCGGCUU__UUCGGGGCCGCCAAAUAGGAUUACUU
.(((((..((...........((((((((.....)))..........((.....)).....))))).((((((((((........))))))))))..))..))))) (-18.47 = -19.75 +   1.28)

alignment

secondary structure

dotplot

Window 2

Location	20,312,573 – 20,312,669
Length	96
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	75.71
Mean single sequence MFE	-35.08
Consensus MFE	-18.16
Energy contribution	-18.67
Covariance contribution	0.50
Combinations/Pair	1.24
Mean z-score	-3.03
Structure conservation index	0.52
SVM decision value	2.64
SVM RNA-class probability	0.995956
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20312573 96 - 22407834
AAGUAAUCCUAUUUGGCGGCCCCGAAA-AAGCCGCCAAAGCCACCGAUUUCCGACUUGGACUCCGACUUCGAUUCCCUCGGGUUG---------GUGGCGCACCCA
..((.......(((((((((.......-..)))))))))(((((((((..((((...(((...((....))..))).))))))))---------)))))))..... ( -38.50)
>DroSec_CAF1 55516 94 - 1
AAGUUAUCCUAUUUGGCGGCCCCGAA--AAGCCGCCAAAGCCACCGAU-UCCGACUUGGACUCCGACUUCGAUUCCCUCGGGUAG---------GUGGCGCACCCA
...........(((((((((......--..)))))))))((((((...-(((((...(((...((....))..))).)))))..)---------)))))....... ( -38.50)
>DroSim_CAF1 54332 94 - 1
AAGUAAUCCUAUUUGGCGGCCCCGAC--AAGCCGCCAAAGCCACCGAU-UCCGACUUGGACUCCGACUUCGAUUCCCUCGGGUAG---------GUGGCGCACCCA
..((.......(((((((((......--..)))))))))((((((...-(((((...(((...((....))..))).)))))..)---------)))))))..... ( -38.80)
>DroEre_CAF1 41751 83 - 1
AAGUAAUCCUAUUUGGCGGCCCCGAA--AAGCCGCCAAAGUCACCGAU-U-----------UCCAACUUCGAUUCCCUCGGGUAG---------GUGGCGCACCCA
..((.......(((((((((......--..)))))))))((((((((.-.-----------.......))....((....))..)---------)))))))..... ( -27.20)
>DroYak_CAF1 35503 83 - 1
AAGUAAUCCUAUUUGGCGGCCCCGAA--AAGCCGCCAAAGCCACCGAU-U-----------UCCGACUUCGAUUCCCUCGGGUAG---------GUGGCGCACCCA
..((.......(((((((((......--..)))))))))((((((...-.-----------(((((...........)))))..)---------)))))))..... ( -33.50)
>DroPer_CAF1 26276 90 - 1
AGGUAAUCCUAUUUGGCGGACCUCAGACUUGCCUCAACAUCUGUCGGA-U---------------GUGUCGGCUCUGCGGGGCAGGGAUCUGUGGAGCCGCACCCG
(((....))).....((((.((.((((((((((((.(((((.....))-)---------------))....((...))))))))))..)))).))..))))..... ( -34.00)
>consensus
AAGUAAUCCUAUUUGGCGGCCCCGAA__AAGCCGCCAAAGCCACCGAU_U___________UCCGACUUCGAUUCCCUCGGGUAG_________GUGGCGCACCCA
..((.......(((((((((..........)))))))))((((((((.....................)))...((....))............)))))))..... (-18.16 = -18.67 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:37 2006