Locus 5392

Sequence ID	3R_DroMel_CAF1
Location	14,166,388 – 14,166,501
Length	113
Max. P	0.953686

overview

Window 0

Location	14,166,388 – 14,166,501
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.24
Mean single sequence MFE	-30.53
Consensus MFE	-16.90
Energy contribution	-17.79
Covariance contribution	0.89
Combinations/Pair	1.09
Mean z-score	-2.18
Structure conservation index	0.55
SVM decision value	0.94
SVM RNA-class probability	0.886335
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14166388 113 + 27905053
UUGGCACGGU-GUA---GUUACAAAUGGUCGGGCUAUAAAUUGCCACAGCCAU---AGUGUCCAUCAUGUUGAAAUGCUUGAAUUUUUCAUUGCUUGCAUUUCAAUUUCAUGGCCAGCCA
.((((...((-(..---..)))..(((((.((((........))).).)))))---..((.((((...((((((((((..((((.....))).)..))))))))))...)))).)))))) ( -33.50)
>DroVir_CAF1 42680 113 + 1
U---CAGAGC-GUUCAUUGUGGCAUUGCCUUGGCCAUAAAUUAAAGCCGCUCU---AGUGUCCAUCAUGUUGAAAUGCUUGCAUUUUUCAUAGCUUGCAUUUCAAUUUCAUGGCCAGCCA
.---.(((((-(....(((((((.........)))))))........))))))---..((.((((...((((((((((..((..........))..))))))))))...)))).)).... ( -34.60)
>DroPse_CAF1 46102 111 + 1
GUGGCA------GC---GUUACGAAUGGGCGAGCUAUAAAUUAUCAGAGCCAUAGUAGUGUCCAUCACGUUGAAAUGCUUGAAUUUUUCAUCGCUUGCAUUUCAAUUUCAUGGGCAGCCA
.((((.------..---.((((.....(((...((..........)).)))...))))(((((((.(.((((((((((.(((........)))...)))))))))).).))))))))))) ( -31.90)
>DroWil_CAF1 38237 114 + 1
UUGUUGCUGUCAUU---AUUAUAAAUGCUCAGACUAUAAAUUAUCGGCGCUCU---AGUGUCCAUCAUGUUGAAAUGCUUGAAUUUUUCAUUGCUUGCAUUUCAUUUUCAUGGCCAGCCA
..(((((((.((((---......))))..))).............(((((...---.)))))..(((((.((((((((..((((.....))).)..))))))))....))))).)))).. ( -23.10)
>DroAna_CAF1 35021 112 + 1
UUGGCACAAC-GUU---UUUACAAAUGGCCGAGCUAUAAAUUGCCU-GCCCAU---AGUGUCCAUCAUGUUGAAAUGCUUGAAUUUUUCAUUGCAUGCAUUUCAAUUUCAUGGCCAGCCA
.((((.....-...---.......((((.((.((........)).)-).))))---..((.((((...((((((((((.(((((.....))).)).))))))))))...)))).)))))) ( -29.80)
>DroPer_CAF1 44303 111 + 1
GUGGCA------GC---GUUACGAAUGGGCGAGCUAUAAAUUAUCAGAGCCAUACUAGUGUCCAUCACGUUGAAAUGCUUGAAUUUUUCAUCGCUUGCAUUUCAAUUUCAUGGGCAGCCA
.((((.------..---..........(((...((..........)).))).......(((((((.(.((((((((((.(((........)))...)))))))))).).))))))))))) ( -30.30)
>consensus
UUGGCAC_G__GUU___GUUACAAAUGGCCGAGCUAUAAAUUAUCAGAGCCAU___AGUGUCCAUCAUGUUGAAAUGCUUGAAUUUUUCAUUGCUUGCAUUUCAAUUUCAUGGCCAGCCA
..(((...................((((.....)))).....................((.((((...((((((((((..................))))))))))...)))).))))). (-16.90 = -17.79 +   0.89)

alignment

secondary structure

dotplot

Window 1

Location	14,166,388 – 14,166,501
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.24
Mean single sequence MFE	-30.08
Consensus MFE	-18.17
Energy contribution	-17.15
Covariance contribution	-1.02
Combinations/Pair	1.24
Mean z-score	-2.35
Structure conservation index	0.60
SVM decision value	1.44
SVM RNA-class probability	0.953686
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14166388 113 - 27905053
UGGCUGGCCAUGAAAUUGAAAUGCAAGCAAUGAAAAAUUCAAGCAUUUCAACAUGAUGGACACU---AUGGCUGUGGCAAUUUAUAGCCCGACCAUUUGUAAC---UAC-ACCGUGCCAA
(((((((((((.(..(((((((((..(.(((.....))))..)))))))))..).))))(((..---((((.((.(((........))))).)))).)))...---...-.))).)))). ( -34.00)
>DroVir_CAF1 42680 113 - 1
UGGCUGGCCAUGAAAUUGAAAUGCAAGCUAUGAAAAAUGCAAGCAUUUCAACAUGAUGGACACU---AGAGCGGCUUUAAUUUAUGGCCAAGGCAAUGCCACAAUGAAC-GCUCUG---A
....((.((((.(..(((((((((..((..........))..)))))))))..).)))).)).(---(((((((((.........))))..(((...))).........-))))))---. ( -34.50)
>DroPse_CAF1 46102 111 - 1
UGGCUGCCCAUGAAAUUGAAAUGCAAGCGAUGAAAAAUUCAAGCAUUUCAACGUGAUGGACACUACUAUGGCUCUGAUAAUUUAUAGCUCGCCCAUUCGUAAC---GC------UGCCAC
((((.((((((.(..(((((((((....((........))..)))))))))..).))))..........((((.(((....))).))))..............---))------.)))). ( -27.50)
>DroWil_CAF1 38237 114 - 1
UGGCUGGCCAUGAAAAUGAAAUGCAAGCAAUGAAAAAUUCAAGCAUUUCAACAUGAUGGACACU---AGAGCGCCGAUAAUUUAUAGUCUGAGCAUUUAUAAU---AAUGACAGCAACAA
..((((.((((.(...((((((((..(.(((.....))))..))))))))...).)))).....---...((.(.(((........))).).)).........---.....))))..... ( -23.00)
>DroAna_CAF1 35021 112 - 1
UGGCUGGCCAUGAAAUUGAAAUGCAUGCAAUGAAAAAUUCAAGCAUUUCAACAUGAUGGACACU---AUGGGC-AGGCAAUUUAUAGCUCGGCCAUUUGUAAA---AAC-GUUGUGCCAA
((((...((((.(..(((((((((.((.(((.....))))).)))))))))..).))))(((..---((((.(-..((........))..).)))).)))...---...-.....)))). ( -33.70)
>DroPer_CAF1 44303 111 - 1
UGGCUGCCCAUGAAAUUGAAAUGCAAGCGAUGAAAAAUUCAAGCAUUUCAACGUGAUGGACACUAGUAUGGCUCUGAUAAUUUAUAGCUCGCCCAUUCGUAAC---GC------UGCCAC
((((.((((((.(..(((((((((....((........))..)))))))))..).))))......(..(((((.(((....))).))).))..).........---))------.)))). ( -27.80)
>consensus
UGGCUGGCCAUGAAAUUGAAAUGCAAGCAAUGAAAAAUUCAAGCAUUUCAACAUGAUGGACACU___AUGGCUCUGAUAAUUUAUAGCCCGACCAUUUGUAAC___AAC__C_GUGCCAA
.(((((.((((.(..(((((((((..(.(((.....))))..)))))))))..).))))...((.....)).............)))))............................... (-18.17 = -17.15 +  -1.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:35 2006