Locus 160

Sequence ID	4_DroMel_CAF1
Location	1,016,496 – 1,016,648
Length	152
Max. P	0.902857

overview

Window 7

Location	1,016,496 – 1,016,611
Length	115
Sequences	3
Columns	116
Reading direction	forward
Mean pairwise identity	93.10
Mean single sequence MFE	-27.67
Consensus MFE	-25.46
Energy contribution	-25.13
Covariance contribution	-0.33
Combinations/Pair	1.07
Mean z-score	-2.24
Structure conservation index	0.92
SVM decision value	1.03
SVM RNA-class probability	0.902857
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1016496 115 + 1281640
AAGAAGUAGGAAAUACUUUUGGCCUUCAGUAAUUUAAAACG-CUCUAAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUACUGUUCGAAGGCUCGUACGCACAUCC
.(((((((.....)))))))((((((((((((((((.....-...))))).....))))((((((.(((((((.......)))))))))))))...)))))))............. ( -28.30)
>DroSec_CAF1 5035 116 + 1
AAGAAGUAGGAAAUACUUUUGGUCUUCAGUAAUUUAAAAUGGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCC
.(((((((.....)))))))((((((((....)....((((((...((((......))))......(((((((.......)))))))..)))))).)))))))............. ( -27.60)
>DroSim_CAF1 4954 116 + 1
AAGAAGUAGGAAAUACUUUUGGUCUUCAGUAACUUAAAAUGGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCC
.(((((((.....)))))))(((((((..........((((((...((((......))))......(((((((.......)))))))..)))))).)))))))............. ( -27.10)
>consensus
AAGAAGUAGGAAAUACUUUUGGUCUUCAGUAAUUUAAAAUGGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCC
.(((((((.....)))))))(((((((...................((((......)))).((((.(((((((.......))))))))))).....)))))))............. (-25.46 = -25.13 +  -0.33)

alignment

secondary structure

dotplot

Window 8

Location	1,016,496 – 1,016,611
Length	115
Sequences	3
Columns	116
Reading direction	reverse
Mean pairwise identity	93.10
Mean single sequence MFE	-27.70
Consensus MFE	-24.12
Energy contribution	-23.57
Covariance contribution	-0.55
Combinations/Pair	1.09
Mean z-score	-2.42
Structure conservation index	0.87
SVM decision value	0.81
SVM RNA-class probability	0.856986
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1016496 115 - 1281640
GGAUGUGCGUACGAGCCUUCGAACAGUAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUUAGAG-CGUUUUAAAUUACUGAAGGCCAAAAGUAUUUCCUACUUCUU
(((.((((....(.((((((...((((((..(((((.......)))))...))))))((((....(((......-.)))......)))))))))))....)))).)))........ ( -30.10)
>DroSec_CAF1 5035 116 - 1
GGAUGUGCUUACAAGUCUUCGAACGGCAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUCUAAGCCAUUUUAAAUUACUGAAGACCAAAAGUAUUUCCUACUUCUU
(((.((((((....(((((((((.(((....(((((.......)))))........((((......))))...))).))).........))))))...)))))).)))........ ( -26.30)
>DroSim_CAF1 4954 116 - 1
GGAUGUGCUUACAAGUCUUCGAACGGCAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUCUAAGCCAUUUUAAGUUACUGAAGACCAAAAGUAUUUCCUACUUCUU
(((.((((((....((((((.((((((....(((((.......)))))........((((......))))...))).......)))...))))))...)))))).)))........ ( -26.71)
>consensus
GGAUGUGCUUACAAGUCUUCGAACGGCAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUCUAAGCCAUUUUAAAUUACUGAAGACCAAAAGUAUUUCCUACUUCUU
(((.((((((....((((((...(((.((..(((((.......)))))...)).)))((((.((((.(.....).))))......))))))))))...)))))).)))........ (-24.12 = -23.57 +  -0.55)

alignment

secondary structure

dotplot

Window 9

Location	1,016,536 – 1,016,648
Length	112
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	93.57
Mean single sequence MFE	-28.93
Consensus MFE	-24.84
Energy contribution	-26.40
Covariance contribution	1.56
Combinations/Pair	1.06
Mean z-score	-2.10
Structure conservation index	0.86
SVM decision value	0.31
SVM RNA-class probability	0.681252
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1016536 112 + 1281640
G-CUCUAAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUACUGUUCGAAGGCUCGUACGCACAUCCUU-UUAGGCCUUGCAUUCGCAAGCGUCAGUAAAUAAGA
(-(....((((.((.....((((((.(((((((.......)))))))))))))...)).)))).....))........-...((((((((....))))).)))........... ( -28.30)
>DroSec_CAF1 5075 114 + 1
GGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCCUUUUUAGGCCUUGCAUUCGCUAGCGUCAGUAAAUAAGA
.((((((((((.((..((...((((.(((((((.......))))))))))).))..)).))))).)))))............(((((.((....)).)).)))........... ( -27.20)
>DroSim_CAF1 4994 114 + 1
GGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCCUUUUUAGGCCUUGCAUUCGCAAGCGUCAGUAAAUAAGA
.((((((((((.((..((...((((.(((((((.......))))))))))).))..)).))))).)))))............((((((((....))))).)))........... ( -31.30)
>consensus
GGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCCUUUUUAGGCCUUGCAUUCGCAAGCGUCAGUAAAUAAGA
.((((((((((.((..((...((((.(((((((.......))))))))))).))..)).))))).)))))............((((((((....))))).)))........... (-24.84 = -26.40 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:41 2006