Locus 7408

Sequence ID 2L_DroMel_CAF1
Location 20,582,829 – 20,582,921
Length 92
Max. P 0.893866
window11903 window11904

overview

Window 3

Location 20,582,829 – 20,582,921
Length 92
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 79.65
Mean single sequence MFE -22.73
Consensus MFE -10.07
Energy contribution -10.57
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.94
Structure conservation index 0.44
SVM decision value 0.98
SVM RNA-class probability 0.893866
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20582829 92 + 22407834
AAAUAUUUACAAGAUGAAAACUUGUUUCGGC--------------UGUGUGUG--C------AAGGCAUAAAAUUAGCAUUUUUAUGCACACA----CACAUAUAGCACACAAUUAGA
........(((((.(....))))))....((--------------((((((((--.------...((((((((.......)))))))).....----))))))))))........... ( -25.20)
>DroPse_CAF1 145260 105 + 1
AAAUAUUUACAAGAUGAAAACUUGUUUUGGGGUUCGAGAUCGUUGUGUGUGUG--CACUAGUAGGACAUAAAAUUAGCAUUUUUAUGCCGGC-----------CAGCACACAAUUAGA
.......(((((((((((..((......))..)))...))).)))))((((((--(....((.((.(((((((.......))))))))).))-----------..)))))))...... ( -24.80)
>DroSec_CAF1 97515 96 + 1
AAAUAUUUACAAGAUGAAAACUUGUUUCGCC--------------UGUGUGUG--C------GAGGCAUAAAAUUAGCAUUUUUAUGCACACACACACACACAUAGCACACAAUUAGA
........(((((.(....))))))...((.--------------((((((((--.------(.(((((((((.......)))))))).).).))))))))....))........... ( -24.50)
>DroEre_CAF1 88515 87 + 1
AAAUAUUUACAAGAUGGAAACUUGUUUCGGC--------------UGUGUGUG--C------A-GACAUAAAAUUAGCAUUUUUAUGCACA--------CACAUAGCACACAAUUAGA
........(((((.(....))))))....((--------------((((((((--.------.-(.(((((((.......)))))))).))--------))))))))........... ( -23.00)
>DroYak_CAF1 91714 90 + 1
AAAUAUUUACAAGAUGAAAACUUGUUCAGGC--------------UGUGUGUG--C------AAGACAUAAAAUUAGCAUUUUUAUGCACAC------ACACAUAGCACACAAUUAGA
........(((((.(....))))))....((--------------((((((((--.------..(.(((((((.......))))))))...)------)))))))))........... ( -23.10)
>DroAna_CAF1 90831 88 + 1
AAAUAUUUACAAGAUGGAAACUUGUUUUGCC--------------UCUGUCUGUUC-----UAGGACAUAAAAUUAGCAUUUUUAUGCAGGC------CCA-----CACACAAUUAGA
........(((((.(....))))))...(((--------------(.(((((....-----..)))))........((((....))))))))------...-----............ ( -15.80)
>consensus
AAAUAUUUACAAGAUGAAAACUUGUUUCGGC______________UGUGUGUG__C______AAGACAUAAAAUUAGCAUUUUUAUGCACAC______ACACAUAGCACACAAUUAGA
........(((((.......)))))....................(((((((............(.(((((((.......)))))))).................)))))))...... (-10.07 = -10.57 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,582,829 – 20,582,921
Length 92
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 79.65
Mean single sequence MFE -22.90
Consensus MFE -10.93
Energy contribution -10.88
Covariance contribution -0.05
Combinations/Pair 1.05
Mean z-score -2.72
Structure conservation index 0.48
SVM decision value 0.90
SVM RNA-class probability 0.877296
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20582829 92 - 22407834
UCUAAUUGUGUGCUAUAUGUG----UGUGUGCAUAAAAAUGCUAAUUUUAUGCCUU------G--CACACACA--------------GCCGAAACAAGUUUUCAUCUUGUAAAUAUUU
........((.(((....(((----(((((((((((((.......))))))))...------)--))))))))--------------))))..(((((.......)))))........ ( -22.90)
>DroPse_CAF1 145260 105 - 1
UCUAAUUGUGUGCUG-----------GCCGGCAUAAAAAUGCUAAUUUUAUGUCCUACUAGUG--CACACACACAACGAUCUCGAACCCCAAAACAAGUUUUCAUCUUGUAAAUAUUU
......((((..(((-----------(..(((((((((.......))))))).))..))))..--)))).......((....)).........(((((.......)))))........ ( -23.90)
>DroSec_CAF1 97515 96 - 1
UCUAAUUGUGUGCUAUGUGUGUGUGUGUGUGCAUAAAAAUGCUAAUUUUAUGCCUC------G--CACACACA--------------GGCGAAACAAGUUUUCAUCUUGUAAAUAUUU
...............(((.((((((((((.((((((((.......))))))))..)------)--))))))))--------------.)))..(((((.......)))))........ ( -31.00)
>DroEre_CAF1 88515 87 - 1
UCUAAUUGUGUGCUAUGUG--------UGUGCAUAAAAAUGCUAAUUUUAUGUC-U------G--CACACACA--------------GCCGAAACAAGUUUCCAUCUUGUAAAUAUUU
........((.(((.((((--------(((((((((((.......)))))))).-.------)--)))))).)--------------))))..(((((.......)))))........ ( -22.10)
>DroYak_CAF1 91714 90 - 1
UCUAAUUGUGUGCUAUGUGU------GUGUGCAUAAAAAUGCUAAUUUUAUGUCUU------G--CACACACA--------------GCCUGAACAAGUUUUCAUCUUGUAAAUAUUU
...........(((.(((((------(((.((((((((.......))))))))..)------)--)))))).)--------------))....(((((.......)))))........ ( -22.20)
>DroAna_CAF1 90831 88 - 1
UCUAAUUGUGUG-----UGG------GCCUGCAUAAAAAUGCUAAUUUUAUGUCCUA-----GAACAGACAGA--------------GGCAAAACAAGUUUCCAUCUUGUAAAUAUUU
............-----...------((((((((....))))........((((...-----.....)))).)--------------)))...(((((.......)))))........ ( -15.30)
>consensus
UCUAAUUGUGUGCUAUGUGU______GUGUGCAUAAAAAUGCUAAUUUUAUGUCUU______G__CACACACA______________GCCGAAACAAGUUUUCAUCUUGUAAAUAUUU
......((((((..................((((((((.......))))))))............))))))......................(((((.......)))))........ (-10.93 = -10.88 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:03 2006