Locus 3491

Sequence ID	X_DroMel_CAF1
Location	9,383,510 – 9,383,609
Length	99
Max. P	0.993585

overview

Window 5

Location	9,383,510 – 9,383,609
Length	99
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	79.94
Mean single sequence MFE	-23.77
Consensus MFE	-20.37
Energy contribution	-20.27
Covariance contribution	-0.11
Combinations/Pair	1.10
Mean z-score	-2.44
Structure conservation index	0.86
SVM decision value	2.41
SVM RNA-class probability	0.993585
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9383510 99 + 22224390
AAUGGAUUUGCG--UGCACAUAAUCAUGCUAUCC--------AUCC-------UCCAAGUUGUCGCCA----UCCACACGCAGUGGACAUCUGGCAAUCCAUUCAUAUUCCCGCAAUUAA
.((((((..(((--((........))))).))))--------))..-------...........((((----(((((.....)))))....))))......................... ( -23.20)
>DroSim_CAF1 763 92 + 1
AAUGGAUUUGCG--UGCGCAUAAUCAUGCUAUCC--------AUCC--------------UGUCGCCA----UCCACACGCAGUGGACAUCUGGCAAUCCAUUCAUAUUCCCGCAAUUAA
.((((((..(((--((........))))).))))--------))..--------------....((((----(((((.....)))))....))))......................... ( -23.20)
>DroYak_CAF1 950 120 + 1
AAUGGAGUUGUGUGUGUACAUAACCAUGCUAUCCAACUAUCCAUCCUAUCCAUUCCAAGUUGUCGCCAUCCAUCCACACGCAGUGGACAUCUGGCAAUCCAUUCAUAUUCCCACAAUUAA
(((((((((((((....))))))).........(((((...................)))))..((((....(((((.....)))))....))))..))))))................. ( -24.91)
>consensus
AAUGGAUUUGCG__UGCACAUAAUCAUGCUAUCC________AUCC_______UCCAAGUUGUCGCCA____UCCACACGCAGUGGACAUCUGGCAAUCCAUUCAUAUUCCCGCAAUUAA
((((((((.......(((........)))...................................((((....(((((.....)))))....))))))))))))................. (-20.37 = -20.27 +  -0.11)

alignment

secondary structure

dotplot

Window 6

Location	9,383,510 – 9,383,609
Length	99
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	79.94
Mean single sequence MFE	-26.23
Consensus MFE	-23.70
Energy contribution	-23.03
Covariance contribution	-0.66
Combinations/Pair	1.10
Mean z-score	-0.40
Structure conservation index	0.90
SVM decision value	0.08
SVM RNA-class probability	0.571198
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9383510 99 - 22224390
UUAAUUGCGGGAAUAUGAAUGGAUUGCCAGAUGUCCACUGCGUGUGGA----UGGCGACAACUUGGA-------GGAU--------GGAUAGCAUGAUUAUGUGCA--CGCAAAUCCAUU
....(((((...(((((((((..((((((....(((((.....)))))----))))))((.((....-------)).)--------).....)))..))))))...--)))))....... ( -24.50)
>DroSim_CAF1 763 92 - 1
UUAAUUGCGGGAAUAUGAAUGGAUUGCCAGAUGUCCACUGCGUGUGGA----UGGCGACA--------------GGAU--------GGAUAGCAUGAUUAUGCGCA--CGCAAAUCCAUU
....((((((.(((........))).))....((((((.....)))))----).))))..--------------.(((--------((((.((((....))))(..--..)..))))))) ( -24.00)
>DroYak_CAF1 950 120 - 1
UUAAUUGUGGGAAUAUGAAUGGAUUGCCAGAUGUCCACUGCGUGUGGAUGGAUGGCGACAACUUGGAAUGGAUAGGAUGGAUAGUUGGAUAGCAUGGUUAUGUACACACACAACUCCAUU
....(((((.(.(((((((((..((((((..(((((((.....)))))))..))))))(((((....((.......))....))))).....)))..)))))).)...)))))....... ( -30.20)
>consensus
UUAAUUGCGGGAAUAUGAAUGGAUUGCCAGAUGUCCACUGCGUGUGGA____UGGCGACAACUUGGA_______GGAU________GGAUAGCAUGAUUAUGUGCA__CGCAAAUCCAUU
....(((((..............((((((....(((((.....)))))....)))))).................................((((....)))).....)))))....... (-23.70 = -23.03 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:35 2006