Locus 1830

Sequence ID	2R_DroMel_CAF1
Location	6,854,672 – 6,854,765
Length	93
Max. P	0.930157

overview

Window 7

Location	6,854,672 – 6,854,765
Length	93
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	80.48
Mean single sequence MFE	-26.73
Consensus MFE	-18.40
Energy contribution	-18.73
Covariance contribution	0.34
Combinations/Pair	1.32
Mean z-score	-1.51
Structure conservation index	0.69
SVM decision value	0.33
SVM RNA-class probability	0.693761
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6854672 93 + 20766785
UUCAAUGAACAUGCCGAUUGAGUUAAUGGUCGGUGCUUAAGAUAGCUUCUGAUAGCGGUGUGAGCAC---AGGGUCCGACCAAGAUAAUGUCAAUC----
...............((((((((((.(((((((((((((.....(((......)))....)))))).---.....)))))))...)))).))))))---- ( -25.70)
>DroSec_CAF1 1899 87 + 1
------GAACAUACCGAUUGACUUAAUGGUCGGUGCUCAAGAUAGCUUUUGAUAGCGGUGUGAGCAC---AGGGUCCGACCAAGAUAAUGUCAUUC----
------.........((.(((((((.(((((((((((((.....(((......)))....)))))).---.....)))))))...))).)))).))---- ( -27.00)
>DroSim_CAF1 3584 87 + 1
------GAACAUACCGAUUGACUUAAUGGUCGGUGCUCAAGAUAGCUUCUGAUAGCGGUGUGAGCAC---AGGGUCCGACCAAGAUAAUGUCAAUC----
------.........((((((((((.(((((((((((((.....(((......)))....)))))).---.....)))))))...))).)))))))---- ( -30.20)
>DroEre_CAF1 1882 97 + 1
UUCCAUGAGCAUACUGAUUGACCUAAUGGUCGGUGCUCGAGAUAGCUUCUGAUAGCGGUGAGAGCAC---UGGGUCCGACCAAGAUAAGGUCAUUCCAUC
...............((.((((((..(((((((.((((......(((......)))((((....)))---)))))))))))).....)))))).)).... ( -31.00)
>DroYak_CAF1 3711 93 + 1
UUCAAUAAACAUACUGAUUGACUUAAUGGUCGGUGCUCGAGAUAGCUUCUGAUAGCGGUGAGAGCAC---AGGGUCCGACCAAGAUAAAGUCAUUC----
...............((.((((((..(((((((.((((......(((......))).((....))..---.))))))))))).....)))))).))---- ( -27.30)
>DroAna_CAF1 1989 95 + 1
CCCAAUGGCGAUAUCGAUUAUCUUAAUGGAAGGUGCUCGAGAUAGCAUCUGAUAACU-UCUUAGCACGGCAGAGUUCGUUCCAGAUAAUGACGUUC----
...((((((....((((.((((((.....)))))).))))....))(((((..(((.-.(((.((...)).)))...))).))))).....)))).---- ( -19.20)
>consensus
UUCAAUGAACAUACCGAUUGACUUAAUGGUCGGUGCUCAAGAUAGCUUCUGAUAGCGGUGUGAGCAC___AGGGUCCGACCAAGAUAAUGUCAUUC____
...............((.((((....(((((((((((((.....(((......)))....)))))).........))))))).......)))).)).... (-18.40 = -18.73 +   0.34)

alignment

secondary structure

dotplot

Window 8

Location	6,854,672 – 6,854,765
Length	93
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	80.48
Mean single sequence MFE	-26.18
Consensus MFE	-18.99
Energy contribution	-19.35
Covariance contribution	0.36
Combinations/Pair	1.21
Mean z-score	-2.40
Structure conservation index	0.73
SVM decision value	1.20
SVM RNA-class probability	0.930157
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6854672 93 - 20766785
----GAUUGACAUUAUCUUGGUCGGACCCU---GUGCUCACACCGCUAUCAGAAGCUAUCUUAAGCACCGACCAUUAACUCAAUCGGCAUGUUCAUUGAA
----((((((..(((...(((((((...((---(.((.......))...)))..(((......))).))))))).))).))))))............... ( -24.80)
>DroSec_CAF1 1899 87 - 1
----GAAUGACAUUAUCUUGGUCGGACCCU---GUGCUCACACCGCUAUCAAAAGCUAUCUUGAGCACCGACCAUUAAGUCAAUCGGUAUGUUC------
----((.((((.(((...(((((((.....---.((((((....(((......))).....))))))))))))).))))))).)).........------ ( -26.80)
>DroSim_CAF1 3584 87 - 1
----GAUUGACAUUAUCUUGGUCGGACCCU---GUGCUCACACCGCUAUCAGAAGCUAUCUUGAGCACCGACCAUUAAGUCAAUCGGUAUGUUC------
----(((((((.(((...(((((((.....---.((((((....(((......))).....))))))))))))).)))))))))).........------ ( -30.50)
>DroEre_CAF1 1882 97 - 1
GAUGGAAUGACCUUAUCUUGGUCGGACCCA---GUGCUCUCACCGCUAUCAGAAGCUAUCUCGAGCACCGACCAUUAGGUCAAUCAGUAUGCUCAUGGAA
....((.((((((.....(((((((.....---.(((((.....(((......)))......))))))))))))..)))))).))............... ( -29.10)
>DroYak_CAF1 3711 93 - 1
----GAAUGACUUUAUCUUGGUCGGACCCU---GUGCUCUCACCGCUAUCAGAAGCUAUCUCGAGCACCGACCAUUAAGUCAAUCAGUAUGUUUAUUGAA
----...((((((.....(((((((...((---(.((.......))...)))..(((......))).)))))))..)))))).((((((....)))))). ( -29.00)
>DroAna_CAF1 1989 95 - 1
----GAACGUCAUUAUCUGGAACGAACUCUGCCGUGCUAAGA-AGUUAUCAGAUGCUAUCUCGAGCACCUUCCAUUAAGAUAAUCGAUAUCGCCAUUGGG
----....((((((((((((...(....)..))(((((.(((-(((........))).)))..))))).........))))))).)))............ ( -16.90)
>consensus
____GAAUGACAUUAUCUUGGUCGGACCCU___GUGCUCACACCGCUAUCAGAAGCUAUCUCGAGCACCGACCAUUAAGUCAAUCGGUAUGUUCAUUGAA
....((.((((.(((...((((((.........((((((.....(((......)))......)))))))))))).))))))).))............... (-18.99 = -19.35 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:12 2006