Locus 7869

Sequence ID	3L_DroMel_CAF1
Location	21,016,314 – 21,016,461
Length	147
Max. P	0.961344

overview

Window 7

Location	21,016,314 – 21,016,421
Length	107
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	69.27
Mean single sequence MFE	-23.07
Consensus MFE	-11.57
Energy contribution	-12.58
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.72
Structure conservation index	0.50
SVM decision value	0.27
SVM RNA-class probability	0.662443
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21016314 107 - 23771897
GCCGGCUAAUAUCCAGCCCACGGAUAAGCCGAACAAAUUGCAUACAACACUCCCCC-AUCGGAGGAUACAAACACAUACAUACAAUGUAUACAUAGU------------ACGAAUAUCGA
..(((((..(((((.......))))))))))...........(((....((((...-...))))...........((((((...)))))).....))------------)((.....)). ( -21.30)
>DroSim_CAF1 42215 95 - 1
GCCGGCUAAUAUCCAGCCCACGGAUAAGCCGAACAAAUUGCAUACAACACUCCCCC-AUCGCAGGAUACAAACAUAUAUA-------CAUACAUAGU------------AUGAAU-----
..(((((..(((((.......)))))))))).........(((((.........((-......))...........(((.-------.....)))))------------)))...----- ( -16.50)
>DroYak_CAF1 43233 89 - 1
GCCGGCUAAUAUCCAGCCCACGGAUAAGCCUAACAAAUUGCAUAUAACACUCCCCC-AUCGGAGAAUAUA------UAUA-------C-----UGGU------------ACGAAUAUCGA
(((((((..(((((.......)))))))))...........(((((...((((...-...))))..))))------)...-------.-----.)))------------.((.....)). ( -19.40)
>DroAna_CAF1 30308 105 - 1
CCCGGC--GUAUCCAGCCCACGGAUAAGCCGAACAAAUUGCAAACAUCACUGCCCCUCUUGGAGGAUGGAGG-AUAGAGG-------C-----UGGAGGAUAGAGGAUGUCGGAUGUCGG
.(((((--((.((((((((.(((.....)))........(((........))).(((((........)))))-...).))-------)-----)))).((((.....))))..))))))) ( -35.10)
>consensus
GCCGGCUAAUAUCCAGCCCACGGAUAAGCCGAACAAAUUGCAUACAACACUCCCCC_AUCGGAGGAUACAAA_AUAUAUA_______C_____UAGU____________ACGAAUAUCGA
..(((((..(((((.......))))))))))..................((((.......))))........................................................ (-11.57 = -12.58 +   1.00)

alignment

secondary structure

dotplot

Window 8

Location	21,016,342 – 21,016,461
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.85
Mean single sequence MFE	-37.66
Consensus MFE	-26.72
Energy contribution	-27.84
Covariance contribution	1.12
Combinations/Pair	1.08
Mean z-score	-2.23
Structure conservation index	0.71
SVM decision value	0.71
SVM RNA-class probability	0.830773
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21016342 119 + 23771897
UGUAUGUGUUUGUAUCCUCCGAU-GGGGGAGUGUUGUAUGCAAUUUGUUCGGCUUAUCCGUGGGCUGGAUAUUAGCCGGCGGUUGUUGCCACCCCGUUGCAAUUAAAAUUAAUAAACGAA
......(((((((......((((-(((((((.((((....))))...)))(((....((((.(((((.....))))).)))).....))).)))))))).(((....))).))))))).. ( -37.60)
>DroSim_CAF1 42231 119 + 1
UAUAUAUGUUUGUAUCCUGCGAU-GGGGGAGUGUUGUAUGCAAUUUGUUCGGCUUAUCCGUGGGCUGGAUAUUAGCCGGCGGUUGUUGCCACCCCGUUGCAAUUAAAAUUAAUAAACGAA
......(((((((....((((((-(((((((.((((....))))...)))(((....((((.(((((.....))))).)))).....))).))))))))))..((....))))))))).. ( -42.20)
>DroEre_CAF1 42811 109 + 1
----------UAUAUCCUCCGAU-GGGGGAGUGUUGUGUGCAAUUUGUUCGGCUUAUCCGUGGGCUGGAUAUUAGCCGGCGGUUGUUGCCACCCCGUUGCAAUUAAAAUUAAUAAACGAA
----------.........((((-(((((((.((((....))))...)))(((....((((.(((((.....))))).)))).....))).))))))))..................... ( -36.20)
>DroYak_CAF1 43249 113 + 1
UAUA------UAUAUUCUCCGAU-GGGGGAGUGUUAUAUGCAAUUUGUUAGGCUUAUCCGUGGGCUGGAUAUUAGCCGGCGGUUGUUGCCACCCCGUUGCAAUUAAAAUUAAUAAACGAA
((((------.(((((((((...-.)))))))))))))((((((......(((....((((.(((((.....))))).)))).....))).....))))))................... ( -35.90)
>DroAna_CAF1 30336 117 + 1
CCUCUAU-CCUCCAUCCUCCAAGAGGGGCAGUGAUGUUUGCAAUUUGUUCGGCUUAUCCGUGGGCUGGAUAC--GCCGGGGGGCGUUAACACCCCGUUGCAAUUAAAAUUAAUAAACGAA
....(((-(((((..((((...)))))).)).)))).(((((((....(((((.((((((.....)))))).--)))))((((.(....).))))))))))).................. ( -36.40)
>consensus
UAUAU_U___UAUAUCCUCCGAU_GGGGGAGUGUUGUAUGCAAUUUGUUCGGCUUAUCCGUGGGCUGGAUAUUAGCCGGCGGUUGUUGCCACCCCGUUGCAAUUAAAAUUAAUAAACGAA
..............((((((....))))))........((((((......(((....((((.((((((...)))))).)))).....))).....))))))................... (-26.72 = -27.84 +   1.12)

alignment

secondary structure

dotplot

Window 9

Location	21,016,342 – 21,016,461
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.85
Mean single sequence MFE	-30.52
Consensus MFE	-23.92
Energy contribution	-24.04
Covariance contribution	0.12
Combinations/Pair	1.11
Mean z-score	-2.33
Structure conservation index	0.78
SVM decision value	1.53
SVM RNA-class probability	0.961344
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21016342 119 - 23771897
UUCGUUUAUUAAUUUUAAUUGCAACGGGGUGGCAACAACCGCCGGCUAAUAUCCAGCCCACGGAUAAGCCGAACAAAUUGCAUACAACACUCCCCC-AUCGGAGGAUACAAACACAUACA
...((((............((((((((..((....)).))).(((((..(((((.......))))))))))......))))).......((((...-...)))).....))))....... ( -30.80)
>DroSim_CAF1 42231 119 - 1
UUCGUUUAUUAAUUUUAAUUGCAACGGGGUGGCAACAACCGCCGGCUAAUAUCCAGCCCACGGAUAAGCCGAACAAAUUGCAUACAACACUCCCCC-AUCGCAGGAUACAAACAUAUAUA
...((((............((((((((..((....)).))).(((((..(((((.......))))))))))......)))))............((-......))....))))....... ( -26.50)
>DroEre_CAF1 42811 109 - 1
UUCGUUUAUUAAUUUUAAUUGCAACGGGGUGGCAACAACCGCCGGCUAAUAUCCAGCCCACGGAUAAGCCGAACAAAUUGCACACAACACUCCCCC-AUCGGAGGAUAUA----------
...................((((((((..((....)).))).(((((..(((((.......))))))))))......))))).......((((...-...))))......---------- ( -28.80)
>DroYak_CAF1 43249 113 - 1
UUCGUUUAUUAAUUUUAAUUGCAACGGGGUGGCAACAACCGCCGGCUAAUAUCCAGCCCACGGAUAAGCCUAACAAAUUGCAUAUAACACUCCCCC-AUCGGAGAAUAUA------UAUA
...................(((((...(((((......)))))((((..(((((.......))))))))).......))))).......((((...-...))))......------.... ( -27.50)
>DroAna_CAF1 30336 117 - 1
UUCGUUUAUUAAUUUUAAUUGCAACGGGGUGUUAACGCCCCCCGGC--GUAUCCAGCCCACGGAUAAGCCGAACAAAUUGCAAACAUCACUGCCCCUCUUGGAGGAUGGAGG-AUAGAGG
..(.((((((........((((((.((((((....)))))).((((--.(((((.......))))).))))......)))))).((((.((.((......))))))))...)-))))).) ( -39.00)
>consensus
UUCGUUUAUUAAUUUUAAUUGCAACGGGGUGGCAACAACCGCCGGCUAAUAUCCAGCCCACGGAUAAGCCGAACAAAUUGCAUACAACACUCCCCC_AUCGGAGGAUACA___A_AUAUA
......((((.........(((((.((((((....)).)).))((((..(((((.......))))))))).......))))).......((((.......))))))))............ (-23.92 = -24.04 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:05 2006