Locus 7772

Sequence ID	3R_DroMel_CAF1
Location	20,817,129 – 20,817,221
Length	92
Max. P	0.791913

overview

Window 5

Location	20,817,129 – 20,817,221
Length	92
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	91.06
Mean single sequence MFE	-26.22
Consensus MFE	-20.61
Energy contribution	-20.85
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-1.73
Structure conservation index	0.79
SVM decision value	0.59
SVM RNA-class probability	0.791913
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20817129 92 + 27905053
GGUCUACAAAACUGGGCUCAUUAUG-GCCUCUGCUGAUUUCUUAUUGCGGUUCGCAUAGAAGCUGGCUGAAAUCCCUAAUGAGCUGGAAGC------UU
............(.(((((((((.(-(..((.(((..(((((...((((...)))).)))))..))).))...)).))))))))).)....------.. ( -27.40)
>DroSec_CAF1 32760 92 + 1
CGUCUAUAAAACUGAGCUCAUUAUG-GCCUAUGCUGAUUUCUUAUUGCGGUUCGCAUAGAAGCUGGCUAAAAUCCAUAAUGAGCUGGAAGC------UU
...........((.(((((((((((-(.....(((..(((((...((((...)))).)))))..)))......))))))))))))))....------.. ( -30.40)
>DroSim_CAF1 32689 92 + 1
CGUCUAUAAAACUGAGCUCAUUAUG-GCCUAUGCUGAUUUCUUAUUGCGCUUCGCAUAGAAGCUGGCUGAAAUCCCUAAUGAGCUGGAAGC------UU
...........((.(((((((((.(-(.....(((..(((((...((((...)))).)))))..)))......)).)))))))))))....------.. ( -26.10)
>DroEre_CAF1 30527 99 + 1
GGUCUAUAAAAUUGAACUCAUUAUGGGCCUAUGCUGAUUUCUUAUUGCGGUUCACAUAGAAGCUGGCUGAAAUCCCUAAUGAGCUGGAAGCUCCCGCUU
(((((((((...((....)))))))))))...((.((((((.....((...((.....)).)).....))))))......((((.....))))..)).. ( -22.40)
>DroYak_CAF1 26114 93 + 1
AGUCCAUAAAAUUGAGCUCAUUACGAGCCUAUGCUGAUUUCUUAUUGCGGUUCGCAUAGAAGCUGGCUGAAAUCCCUAAUGAGCUGGAAGC------UU
...........((.(((((((((.((......(((..(((((...((((...)))).)))))..))).....))..))))))))).))...------.. ( -24.80)
>consensus
CGUCUAUAAAACUGAGCUCAUUAUG_GCCUAUGCUGAUUUCUUAUUGCGGUUCGCAUAGAAGCUGGCUGAAAUCCCUAAUGAGCUGGAAGC______UU
............(.(((((((((.........(((..(((((...((((...)))).)))))..))).........))))))))).)............ (-20.61 = -20.85 +   0.24)

alignment

secondary structure

dotplot

Window 6

Location	20,817,129 – 20,817,221
Length	92
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	91.06
Mean single sequence MFE	-23.86
Consensus MFE	-17.92
Energy contribution	-17.44
Covariance contribution	-0.48
Combinations/Pair	1.13
Mean z-score	-1.59
Structure conservation index	0.75
SVM decision value	0.00
SVM RNA-class probability	0.536037
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20817129 92 - 27905053
AA------GCUUCCAGCUCAUUAGGGAUUUCAGCCAGCUUCUAUGCGAACCGCAAUAAGAAAUCAGCAGAGGC-CAUAAUGAGCCCAGUUUUGUAGACC
((------(((....((((((((.((.((((.((....((((.((((...))))...))))....)).)))))-).))))))))..)))))........ ( -22.50)
>DroSec_CAF1 32760 92 - 1
AA------GCUUCCAGCUCAUUAUGGAUUUUAGCCAGCUUCUAUGCGAACCGCAAUAAGAAAUCAGCAUAGGC-CAUAAUGAGCUCAGUUUUAUAGACG
((------(((...((((((((((((.....((....))(((((((......(.....)......))))))))-))))))))))).)))))........ ( -26.00)
>DroSim_CAF1 32689 92 - 1
AA------GCUUCCAGCUCAUUAGGGAUUUCAGCCAGCUUCUAUGCGAAGCGCAAUAAGAAAUCAGCAUAGGC-CAUAAUGAGCUCAGUUUUAUAGACG
((------(((...(((((((((..((((((.....(((((.....))))).......)))))).((....))-..))))))))).)))))........ ( -24.60)
>DroEre_CAF1 30527 99 - 1
AAGCGGGAGCUUCCAGCUCAUUAGGGAUUUCAGCCAGCUUCUAUGUGAACCGCAAUAAGAAAUCAGCAUAGGCCCAUAAUGAGUUCAAUUUUAUAGACC
((((....))))..((((((((((((.....((....))(((((((......(.....)......)))))))))).))))))))).............. ( -22.90)
>DroYak_CAF1 26114 93 - 1
AA------GCUUCCAGCUCAUUAGGGAUUUCAGCCAGCUUCUAUGCGAACCGCAAUAAGAAAUCAGCAUAGGCUCGUAAUGAGCUCAAUUUUAUGGACU
..------...((((((((((((.(((((((((....))....((((...))))....))))))(((....)))).)))))))).........)))).. ( -23.30)
>consensus
AA______GCUUCCAGCUCAUUAGGGAUUUCAGCCAGCUUCUAUGCGAACCGCAAUAAGAAAUCAGCAUAGGC_CAUAAUGAGCUCAGUUUUAUAGACC
...............((((((((.(((((((((....))....((((...))))....)))))).((....)).).))))))))............... (-17.92 = -17.44 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:20 2006