Locus 9627

Sequence ID	3R_DroMel_CAF1
Location	25,434,149 – 25,434,309
Length	160
Max. P	0.969071

overview

Window 1

Location	25,434,149 – 25,434,269
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.75
Mean single sequence MFE	-38.64
Consensus MFE	-31.66
Energy contribution	-33.34
Covariance contribution	1.69
Combinations/Pair	1.09
Mean z-score	-2.51
Structure conservation index	0.82
SVM decision value	1.64
SVM RNA-class probability	0.969071
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25434149 120 + 27905053
UAGCAGUGCAGCAGGAGAAGAUUAUUCAGAUUCCUCUGAAUCUCUCGCCAUGAACCAGCUAACAAUCGCGAUUUUCUGGCUGGCAUGCAUUAACUUCGCCUCUUCGACUUGCUGCACUUU
....(((((((((((.(((((..(((((((....))))))).....((.(((..(((((((..(((....)))...))))))))))))............)))))..))))))))))).. ( -41.80)
>DroSec_CAF1 116985 119 + 1
UAGCA-UGCAGCUGGAGAAGAUAAUUCAGAUUCCCGUGGAUCUCUCGCCAUGAAGCAGCUUACAAUCGCGAUUUUCUGGCUGGCAUGCAUUAACUUCGCCUCUUCGACUUGCUGCACUUC
.....-((((((.(..(((((......((((((....))))))...((((.((((..((........))...)))))))).(((.............))))))))..)..)))))).... ( -32.82)
>DroSim_CAF1 118915 120 + 1
UAGCAGUGCAGCAGGAGAAGAUUAUUCAGAUUCCUCUAGAUCUCUCGCCAUGAACCGGCUCACAACCGCGAUUUUCUGGCUGGCAUGCAUUAACUUCGCCUCUUCGACUUGCUGCACUUC
....(((((((((((.(((((......(((((......)))))...(((.......)))........((((.......((......)).......)))).)))))..))))))))))).. ( -36.84)
>DroYak_CAF1 127231 120 + 1
UAGCAGUGCAGUAGGAGAAGACGAAUCAGAUGUCUCUGGAUCGCUCGCCAUGAAGCGGCUUACAAUCGCGGUUUUCUGGCUGGCAUGUAUAAACUUGGCUUCCACGACUUGCUGCACUUC
....(((((((((((.((((.(((.(((((....))))).))(((.((((.(((((.((........)).))))).)))).))).............))))).....))))))))))).. ( -43.10)
>consensus
UAGCAGUGCAGCAGGAGAAGAUUAUUCAGAUUCCUCUGGAUCUCUCGCCAUGAACCAGCUUACAAUCGCGAUUUUCUGGCUGGCAUGCAUUAACUUCGCCUCUUCGACUUGCUGCACUUC
....(((((((((((.(((((..((((((......)))))).....((((.((((..((........))...)))))))).(((.............))))))))..))))))))))).. (-31.66 = -33.34 +   1.69)

alignment

secondary structure

dotplot

Window 2

Location	25,434,149 – 25,434,269
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.75
Mean single sequence MFE	-37.95
Consensus MFE	-30.10
Energy contribution	-30.85
Covariance contribution	0.75
Combinations/Pair	1.12
Mean z-score	-1.73
Structure conservation index	0.79
SVM decision value	0.47
SVM RNA-class probability	0.749330
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25434149 120 - 27905053
AAAGUGCAGCAAGUCGAAGAGGCGAAGUUAAUGCAUGCCAGCCAGAAAAUCGCGAUUGUUAGCUGGUUCAUGGCGAGAGAUUCAGAGGAAUCUGAAUAAUCUUCUCCUGCUGCACUGCUA
..(((((((((.(..(((((((((..((....)).)))).((((...((((((........)).))))..)))).....(((((((....)))))))..)))))..)))))))))).... ( -43.60)
>DroSec_CAF1 116985 119 - 1
GAAGUGCAGCAAGUCGAAGAGGCGAAGUUAAUGCAUGCCAGCCAGAAAAUCGCGAUUGUAAGCUGCUUCAUGGCGAGAGAUCCACGGGAAUCUGAAUUAUCUUCUCCAGCUGCA-UGCUA
...(((((((..(..(((((((((..((....)).))))...((((...(((.((((....(((.......)))....))))..)))...)))).....)))))..).))))))-).... ( -32.40)
>DroSim_CAF1 118915 120 - 1
GAAGUGCAGCAAGUCGAAGAGGCGAAGUUAAUGCAUGCCAGCCAGAAAAUCGCGGUUGUGAGCCGGUUCAUGGCGAGAGAUCUAGAGGAAUCUGAAUAAUCUUCUCCUGCUGCACUGCUA
..(((((((((.(..(((((((((..((....)).))))...((((...((..((((....((((.....))))....))))..))....)))).....)))))..)))))))))).... ( -39.30)
>DroYak_CAF1 127231 120 - 1
GAAGUGCAGCAAGUCGUGGAAGCCAAGUUUAUACAUGCCAGCCAGAAAACCGCGAUUGUAAGCCGCUUCAUGGCGAGCGAUCCAGAGACAUCUGAUUCGUCUUCUCCUACUGCACUGCUA
..(((((((...((((((.((((...(((((((..(((.............)))..))))))).))))))))))((((((..((((....))))..))).)))......))))))).... ( -36.52)
>consensus
GAAGUGCAGCAAGUCGAAGAGGCGAAGUUAAUGCAUGCCAGCCAGAAAAUCGCGAUUGUAAGCCGCUUCAUGGCGAGAGAUCCAGAGGAAUCUGAAUAAUCUUCUCCUGCUGCACUGCUA
..(((((((((.(..((((((((...((....))..))).(((((((....((........))...))).))))........((((....)))).....)))))..)))))))))).... (-30.10 = -30.85 +   0.75)

alignment

secondary structure

dotplot

Window 3

Location	25,434,189 – 25,434,309
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.94
Mean single sequence MFE	-39.37
Consensus MFE	-31.51
Energy contribution	-31.70
Covariance contribution	0.19
Combinations/Pair	1.09
Mean z-score	-1.69
Structure conservation index	0.80
SVM decision value	0.24
SVM RNA-class probability	0.648422
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25434189 120 + 27905053
UCUCUCGCCAUGAACCAGCUAACAAUCGCGAUUUUCUGGCUGGCAUGCAUUAACUUCGCCUCUUCGACUUGCUGCACUUUUGCGGCGACUCUGCACUUCAAGAUCCGUGGCGGAGUCUGU
.(((.(((((((..(((((((..(((....)))...)))))))..((((......(((......))).((((((((....))))))))...))))..........))))))))))..... ( -37.70)
>DroSec_CAF1 117024 120 + 1
UCUCUCGCCAUGAAGCAGCUUACAAUCGCGAUUUUCUGGCUGGCAUGCAUUAACUUCGCCUCUUCGACUUGCUGCACUUCUGCGGCAACGCUGCACUUCAAGAUCCGUGGCGGAGUCAGU
.(((.(((((((..(((((........((((.......((......)).......)))).........((((((((....)))))))).))))).(.....)...))))))))))..... ( -40.64)
>DroSim_CAF1 118955 120 + 1
UCUCUCGCCAUGAACCGGCUCACAACCGCGAUUUUCUGGCUGGCAUGCAUUAACUUCGCCUCUUCGACUUGCUGCACUUCUGCGGCGACUCUGCACUUCAAGAUCCGUGGCGGAGUCUGU
.(((.(((((((...(((.......))).((((((..(((.(((.............))).....((.((((((((....)))))))).)).)).)...))))))))))))))))..... ( -36.22)
>DroYak_CAF1 127271 120 + 1
UCGCUCGCCAUGAAGCGGCUUACAAUCGCGGUUUUCUGGCUGGCAUGUAUAAACUUGGCUUCCACGACUUGCUGCACUUCUGCGGCGACUCUGCACUUCAAGAUCCGUGGAGGAGUCUGC
..(((.((((.(((((.((........)).))))).)))).)))..............((((((((..((((((((....)))))))).(((........)))..))))))))....... ( -42.90)
>consensus
UCUCUCGCCAUGAACCAGCUUACAAUCGCGAUUUUCUGGCUGGCAUGCAUUAACUUCGCCUCUUCGACUUGCUGCACUUCUGCGGCGACUCUGCACUUCAAGAUCCGUGGCGGAGUCUGU
.(((.(((((((.....((........))((((((..(((.(((.............))).....((.((((((((....)))))))).)).)).)...))))))))))))))))..... (-31.51 = -31.70 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:39 2006