Locus 5099

Sequence ID	X_DroMel_CAF1
Location	13,319,670 – 13,319,797
Length	127
Max. P	0.784338

overview

Window 3

Location	13,319,670 – 13,319,767
Length	97
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	76.91
Mean single sequence MFE	-23.07
Consensus MFE	-15.38
Energy contribution	-15.62
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.75
Structure conservation index	0.67
SVM decision value	0.57
SVM RNA-class probability	0.784338
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13319670 97 - 22224390
CUUGAUUGCCACGUGUGGUAAUUUCCUCGCCCCGAUAAAUUU-GGGGCUUAUCCCCAUACCCCUCCCCACCCGCCAC-----ACGAUUUGC-----------CGCCCAGCCGCA
...........((((((((.........(((((((.....))-))))).(((....))).............)))))-----)))...(((-----------.((...)).))) ( -26.90)
>DroSec_CAF1 32292 89 - 1
CUUGAUUGCCACGUGUGGUAAUUUCCUCGUCCCGAUAAAUUU-GGGCCUUAUCCCCAC-----UCCCUUCCCACCGA-----ACGAUUUG--------------CCCAGCCGCA
...((((((((....)))))))).................((-((((...(((.....-----..............-----..)))..)--------------)))))..... ( -15.60)
>DroSim_CAF1 25038 89 - 1
CUUGAUUGCCACGUGUGGUAAUUUCCUCGCCCCGAUAAAUUU-GGGGCUUAUCCCCAC-----UCCCUUCCCACCGA-----GCGAUUUG--------------CCCAGCCGCA
...((((((((....)))))))).....(((((((.....))-)))))..........-----..............-----(((.....--------------......))). ( -23.50)
>DroEre_CAF1 23714 106 - 1
CUUGAUUGCCACGUGUGGUAAUUUCCUCGCCCCGAUAAAUUUUGGGGCUCAUUCCCC--------CGAUUCCACCGAUUCCACCGAAUCGCCCAGCCCCCAUCCCCCAGCCUCA
...((((((((....)))))))).....(((((((......))))))).........--------.........((((((....))))))........................ ( -26.30)
>consensus
CUUGAUUGCCACGUGUGGUAAUUUCCUCGCCCCGAUAAAUUU_GGGGCUUAUCCCCAC_____UCCCUUCCCACCGA_____ACGAUUUG______________CCCAGCCGCA
...((((((((....)))))))).....(((((.(......).))))).................................................................. (-15.38 = -15.62 +   0.25)

alignment

secondary structure

dotplot

Window 4

Location	13,319,693 – 13,319,797
Length	104
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	83.76
Mean single sequence MFE	-20.32
Consensus MFE	-13.68
Energy contribution	-14.32
Covariance contribution	0.64
Combinations/Pair	1.06
Mean z-score	-1.66
Structure conservation index	0.67
SVM decision value	-0.00
SVM RNA-class probability	0.531392
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13319693 104 - 22224390
UUGCAA-ACAUUCCAUAGCCGAAUAUUUCCGCUUGAUUGCCACGUGUGGUAAUUUCCUCGCCCCGAUAAAUUU--GGGGCUUAUCCCCAUACCCCUCCCCACCCGCC
..((..-.((.((...(((.((.....)).))).)).))....((((((..((......(((((((.....))--)))))..))..))))))............)). ( -24.30)
>DroSec_CAF1 32312 99 - 1
UUGCAA-ACAUUCCAUAUCCGAAUAUUUCCGCUUGAUUGCCACGUGUGGUAAUUUCCUCGUCCCGAUAAAUUU--GGGCCUUAUCCCCAC-----UCCCUUCCCACC
..((((-(.((((.......)))).)))..))..((((((((....)))))))).....(.(((((.....))--))).)..........-----............ ( -14.60)
>DroSim_CAF1 25058 99 - 1
UUGCAA-ACAUUCCAUAGCCGAAUAUUUCCGCUUGAUUGCCACGUGUGGUAAUUUCCUCGCCCCGAUAAAUUU--GGGGCUUAUCCCCAC-----UCCCUUCCCACC
......-.........(((.((.....)).))).((((((((....)))))))).....(((((((.....))--)))))..........-----............ ( -22.90)
>DroEre_CAF1 23753 97 - 1
UUGCAA-GCAUUCCAUAGCCGAAUAUUUCCGCUUGAUUGCCACGUGUGGUAAUUUCCUCGCCCCGAUAAAUUU-UGGGGCUCAUUCCCC--------CGAUUCCACC
...(((-((((((.......))))......)))))(((((((....)))))))......(((((((......)-)))))).........--------.......... ( -24.30)
>DroYak_CAF1 23464 86 - 1
CUGCAAAACAUUCCAUAGUCGAAUAUUUCCGCUUGAUUGCCACGUGUGGUAAUUUCCUCGCACCGAUAAAUUUGUGGGCCUUAUUC---------------------
....................(((((..(((((..((((((((....))))))))...(((...))).......)))))...)))))--------------------- ( -15.50)
>consensus
UUGCAA_ACAUUCCAUAGCCGAAUAUUUCCGCUUGAUUGCCACGUGUGGUAAUUUCCUCGCCCCGAUAAAUUU__GGGGCUUAUCCCCA______UCCCUUCCCACC
................(((.((.....)).))).((((((((....)))))))).....(((((...........)))))........................... (-13.68 = -14.32 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:07 2006