Locus 6328

Sequence ID	X_DroMel_CAF1
Location	15,987,637 – 15,987,742
Length	105
Max. P	0.857061

overview

Window 4

Location	15,987,637 – 15,987,742
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.01
Mean single sequence MFE	-22.96
Consensus MFE	-4.25
Energy contribution	-4.37
Covariance contribution	0.12
Combinations/Pair	1.30
Mean z-score	-1.87
Structure conservation index	0.19
SVM decision value	0.81
SVM RNA-class probability	0.857061
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15987637 105 + 22224390
AAAGUAAA------------UGCACUUUUUUCACAGUGAAUUUGAAACUUAAUUGCAGAU-GAUAGCAUUAAAAAGUG--CCAAAGUAUAGGCAGUGCAAUAUACUGUGAAUUAGAUGAC
........------------..((((...(((((((((...(((.......(((((..((-(...(((((....))))--).....)))..))))).)))..)))))))))..)).)).. ( -21.90)
>DroSec_CAF1 55563 105 + 1
AAAGUAAA------------UGCACUUUUUGUACAGUGCAUUUGAAACUUAAUUGCAGAU-GAUAGCAUUAAAAAGUG--CCAAAGUAUAGGCUUUGCAAUGAACUGUGAAUUAGAUGAC
....((((------------((((((........))))))))))....((((((((((..-....(((((....))))--)((((((....)))))).......)))).))))))..... ( -24.50)
>DroSim_CAF1 46662 94 + 1
AGAGUAAA------------UGCACUUUUUGUACAGUGCAUUUGAAACUUAAUUGCAGAU-GAUAGCAUUAAAAAGUG--CCAAAGUAUAGGUCUUGCAAU-----------AAGAUGAC
....((((------------((((((........))))))))))...((((.((((((((-.((((((((....))))--).....)))..))).))))))-----------)))..... ( -22.60)
>DroEre_CAF1 54406 120 + 1
AGAGUAAAAUCUAUAUGCUAUGUUUUUUUUUCACAGUGAGUUUGAAACUUAAUUGCAGAUAGAUAACAUUAAAAAGUCCCCCAAAGUAUAGGUUUUGGAAUGGACAGUGAACUAAAUGAC
........((((((.(((...(((((...(((.....)))...)))))......))).))))))..((((.....((((.((((((......))))))...))))((....)).)))).. ( -24.20)
>DroYak_CAF1 38361 111 + 1
AGAGUAAAAUCUGUUUGCUAUGCACUUUUUUCACAGUGCAAUUGAAACUUAAUUGCAGAUAGAUAACAUUCAAAAGUC--CCAAAGUAUAGGUUUAGGUUU-------AAUUGAAAUUAC
...((((.((((((((((...(((((........)))))((((((...))))))))))))))))....(((((..(..--((.(((......))).))..)-------..))))).)))) ( -21.60)
>consensus
AGAGUAAA____________UGCACUUUUUUCACAGUGCAUUUGAAACUUAAUUGCAGAU_GAUAGCAUUAAAAAGUG__CCAAAGUAUAGGUUUUGCAAU__AC_GUGAAUUAGAUGAC
...((((.............((((((........))))))............))))................................................................ ( -4.25 =  -4.37 +   0.12)

alignment

secondary structure

dotplot

Window 5

Location	15,987,637 – 15,987,742
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.01
Mean single sequence MFE	-19.55
Consensus MFE	-6.08
Energy contribution	-7.24
Covariance contribution	1.16
Combinations/Pair	1.06
Mean z-score	-1.96
Structure conservation index	0.31
SVM decision value	0.69
SVM RNA-class probability	0.823424
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15987637 105 - 22224390
GUCAUCUAAUUCACAGUAUAUUGCACUGCCUAUACUUUGG--CACUUUUUAAUGCUAUC-AUCUGCAAUUAAGUUUCAAAUUCACUGUGAAAAAAGUGCA------------UUUACUUU
.........((((((((..(((....((((........))--))...((((((((....-....)).)))))).....)))..)))))))).((((((..------------..)))))) ( -20.60)
>DroSec_CAF1 55563 105 - 1
GUCAUCUAAUUCACAGUUCAUUGCAAAGCCUAUACUUUGG--CACUUUUUAAUGCUAUC-AUCUGCAAUUAAGUUUCAAAUGCACUGUACAAAAAGUGCA------------UUUACUUU
...................((((((..(((........))--)........(((....)-)).)))))).((((...(((((((((........))))))------------))))))). ( -19.70)
>DroSim_CAF1 46662 94 - 1
GUCAUCUU-----------AUUGCAAGACCUAUACUUUGG--CACUUUUUAAUGCUAUC-AUCUGCAAUUAAGUUUCAAAUGCACUGUACAAAAAGUGCA------------UUUACUCU
.....(((-----------((((((.((.........(((--((........)))))..-.))))))).))))....(((((((((........))))))------------)))..... ( -19.30)
>DroEre_CAF1 54406 120 - 1
GUCAUUUAGUUCACUGUCCAUUCCAAAACCUAUACUUUGGGGGACUUUUUAAUGUUAUCUAUCUGCAAUUAAGUUUCAAACUCACUGUGAAAAAAAAACAUAGCAUAUAGAUUUUACUCU
...............((((...(((((........))))).))))........((.((((((.(((.......(((((.........)))))..........))).))))))...))... ( -18.13)
>DroYak_CAF1 38361 111 - 1
GUAAUUUCAAUU-------AAACCUAAACCUAUACUUUGG--GACUUUUGAAUGUUAUCUAUCUGCAAUUAAGUUUCAAUUGCACUGUGAAAAAAGUGCAUAGCAAACAGAUUUUACUCU
((((..((....-------...((((((.......)))))--)....((((.(((.........))).))))((((....((((((........))))))....)))).))..))))... ( -20.00)
>consensus
GUCAUCUAAUUCAC_GU__AUUGCAAAACCUAUACUUUGG__CACUUUUUAAUGCUAUC_AUCUGCAAUUAAGUUUCAAAUGCACUGUGAAAAAAGUGCA____________UUUACUCU
...................................(((((...((((.....(((.........)))...)))).)))))((((((........)))))).................... ( -6.08 =  -7.24 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:44 2006