Locus 6218

Sequence ID	3L_DroMel_CAF1
Location	16,526,892 – 16,526,991
Length	99
Max. P	0.984154

overview

Window 7

Location	16,526,892 – 16,526,991
Length	99
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	82.90
Mean single sequence MFE	-25.02
Consensus MFE	-14.77
Energy contribution	-14.85
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-3.16
Structure conservation index	0.59
SVM decision value	1.81
SVM RNA-class probability	0.978270
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16526892 99 + 23771897
UCCAUUUUCCACACACGCACUGAACACCCACACACCUGCGCGUGUGCGUGUGUUUGUGUGUGUAUG---GUUGCUCUUGACUUCUGCGUUGGAAAAUUAAUA
((((....(((.((((((((.((((((.(.(((((......))))).).)))))))))))))).))---)..((...........))..))))......... ( -33.70)
>DroSec_CAF1 140344 85 + 1
UCCAUUUUCCACACACGCACUGAACACCCACACACCUGCGCGUGUG--------------UGUGUG---AUUCCUCUUGACUUCUACGUUGGAAAAUUAAUA
...(((((((...........((((((.(((((((......)))))--------------)).)))---.))).....(((......))))))))))..... ( -21.10)
>DroSim_CAF1 143322 85 + 1
UCCAUUUUCCACACACGCACUGAACACCCACACACCUGCGCGUGUG--------------UGUGUG---AUUCCUCUUGACUUCUACGUUGGAAAAUUAAUA
...(((((((...........((((((.(((((((......)))))--------------)).)))---.))).....(((......))))))))))..... ( -21.10)
>DroEre_CAF1 137930 79 + 1
UCCAUUUUCCACACACGCACUGCUCGCCCACACACCUGUGUGUGUG-----------------------CCUGCUUUUGACUCCUACGUUGGAAAAUUAAUA
...(((((((...........((..((.((((((....)))))).)-----------------------)..))....(((......))))))))))..... ( -19.90)
>DroYak_CAF1 140861 88 + 1
UCCAUUUUCCACACACGCACUGGACGCCCACACACCUGUGAGUGUG--------------UGUGUGUGUCUUGCUCUUGACUCCUACGUUGGAAAAUUAAUA
...((((((((((((((((((((....)).(((....)))))))))--------------)))))..(((........))).........)))))))..... ( -29.30)
>consensus
UCCAUUUUCCACACACGCACUGAACACCCACACACCUGCGCGUGUG______________UGUGUG___AUUGCUCUUGACUUCUACGUUGGAAAAUUAAUA
...(((((((.(((((((.(.................).)))))))................................(((......))))))))))..... (-14.77 = -14.85 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	16,526,892 – 16,526,991
Length	99
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	82.90
Mean single sequence MFE	-28.50
Consensus MFE	-19.48
Energy contribution	-19.40
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-2.87
Structure conservation index	0.68
SVM decision value	1.97
SVM RNA-class probability	0.984154
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16526892 99 - 23771897
UAUUAAUUUUCCAACGCAGAAGUCAAGAGCAAC---CAUACACACACAAACACACGCACACGCGCAGGUGUGUGGGUGUUCAGUGCGUGUGUGGAAAAUGGA
.........((((..((...........))..(---(((((((.(((....((((.(((((((....))))))).))))...))).))))))))....)))) ( -37.70)
>DroSec_CAF1 140344 85 - 1
UAUUAAUUUUCCAACGUAGAAGUCAAGAGGAAU---CACACA--------------CACACGCGCAGGUGUGUGGGUGUUCAGUGCGUGUGUGGAAAAUGGA
.....((((((((((((((....).....(((.---(((.((--------------(((((......))))))).))))))..)))))...))))))))... ( -26.70)
>DroSim_CAF1 143322 85 - 1
UAUUAAUUUUCCAACGUAGAAGUCAAGAGGAAU---CACACA--------------CACACGCGCAGGUGUGUGGGUGUUCAGUGCGUGUGUGGAAAAUGGA
.....((((((((((((((....).....(((.---(((.((--------------(((((......))))))).))))))..)))))...))))))))... ( -26.70)
>DroEre_CAF1 137930 79 - 1
UAUUAAUUUUCCAACGUAGGAGUCAAAAGCAGG-----------------------CACACACACAGGUGUGUGGGCGAGCAGUGCGUGUGUGGAAAAUGGA
.....((((((((((((((....)....((..(-----------------------(.((((((....)))))).))..))..)))))...))))))))... ( -23.30)
>DroYak_CAF1 140861 88 - 1
UAUUAAUUUUCCAACGUAGGAGUCAAGAGCAAGACACACACA--------------CACACUCACAGGUGUGUGGGCGUCCAGUGCGUGUGUGGAAAAUGGA
.....(((((((((((((((((((........))).....((--------------((((((....))))))))....)))..)))))...))))))))... ( -28.10)
>consensus
UAUUAAUUUUCCAACGUAGAAGUCAAGAGCAAG___CACACA______________CACACGCGCAGGUGUGUGGGUGUUCAGUGCGUGUGUGGAAAAUGGA
.....((((((((((((((....)................................(((((((....))))))).........)))))...))))))))... (-19.48 = -19.40 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:59 2006