Locus 7838

Sequence ID	3R_DroMel_CAF1
Location	20,991,006 – 20,991,207
Length	201
Max. P	0.993110

overview

Window 4

Location	20,991,006 – 20,991,113
Length	107
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	91.02
Mean single sequence MFE	-32.02
Consensus MFE	-25.28
Energy contribution	-26.04
Covariance contribution	0.76
Combinations/Pair	1.14
Mean z-score	-1.39
Structure conservation index	0.79
SVM decision value	-0.03
SVM RNA-class probability	0.517207
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20991006 107 + 27905053
GUCGGCACCUGAAACCAAGAGCAUUCUUGUACAUGGUUGCACAAUAAUGAUGCUAGUACAUUAUGUACUAGACUGGGCGCACCUGCUGGGCUAAAUGCAUUAUAGC---C
..(((((..((...(((....((((.((((.((....)).)))).))))...(((((((.....)))))))..)))...))..)))))(((((.........))))---) ( -29.80)
>DroSec_CAF1 31576 107 + 1
GUCGGCACCUGAAACCCAGAGCGUUCUUGUACAUGGUUGCACAAUAAUGAUGCUAGUACAUUAUGUACUAGACUGGGCGCACCUGCUGGGCUAAGUGCAUUAUAGC---C
..(((((..((...(((((..((((.((((.((....)).)))).))))...(((((((.....))))))).)))))..))..)))))(((((.........))))---) ( -34.60)
>DroSim_CAF1 26999 107 + 1
GUCGGCACCUGAAACCCAGAGCGUUCUUGUACAUGGUUGCACAAUAAUGAUGCUAGUACAUUAUGUACUAGACUGGGCGCACCUGCUGGGCUAAGUGCAUUAUAGC---C
..(((((..((...(((((..((((.((((.((....)).)))).))))...(((((((.....))))))).)))))..))..)))))(((((.........))))---) ( -34.60)
>DroEre_CAF1 33557 110 + 1
GUCGGCACCUGAAAUCCCGAACGUUGUUGUACAUGGUUGCACAAUAAUGAUGCAAGUACAUUAUGUACUAAACUGGGCGCACCUGCUGGGCUAAGUGCAUUAUGGCAAUG
((((((((.......((((..(((((((((.((....)).))))))))).....(((((.....)))))....)))).((.((....))))...))))....)))).... ( -29.40)
>DroYak_CAF1 33108 110 + 1
GUGGGCACCUGAAAGCCAGAGCUUUGUUGUACAUGGUUGCACAAUAAUGAUGCAAGUACAUAAUGUACUAAAGUGGCCGCACCUGCUGGGCUAAAUGCAUUAUGGCAAAU
...(((........)))...(((.((((((.((....)).))))))(((((((((((((.....)))))....(((((((....))..)))))..))))))))))).... ( -31.70)
>consensus
GUCGGCACCUGAAACCCAGAGCGUUCUUGUACAUGGUUGCACAAUAAUGAUGCUAGUACAUUAUGUACUAGACUGGGCGCACCUGCUGGGCUAAGUGCAUUAUAGC___C
.((((((..((...(((((..((((.((((.((....)).)))).))))...(((((((.....))))))).)))))..))..))))))((((.(.....).)))).... (-25.28 = -26.04 +   0.76)

alignment

secondary structure

dotplot

Window 5

Location	20,991,006 – 20,991,113
Length	107
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	91.02
Mean single sequence MFE	-32.44
Consensus MFE	-27.56
Energy contribution	-28.04
Covariance contribution	0.48
Combinations/Pair	1.10
Mean z-score	-2.13
Structure conservation index	0.85
SVM decision value	2.20
SVM RNA-class probability	0.990253
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20991006 107 - 27905053
G---GCUAUAAUGCAUUUAGCCCAGCAGGUGCGCCCAGUCUAGUACAUAAUGUACUAGCAUCAUUAUUGUGCAACCAUGUACAAGAAUGCUCUUGGUUUCAGGUGCCGAC
(---((((.........)))))......(.(((((..(.(((((((.....))))))))..((((.(((((((....))))))).))))............))))))... ( -31.10)
>DroSec_CAF1 31576 107 - 1
G---GCUAUAAUGCACUUAGCCCAGCAGGUGCGCCCAGUCUAGUACAUAAUGUACUAGCAUCAUUAUUGUGCAACCAUGUACAAGAACGCUCUGGGUUUCAGGUGCCGAC
(---((......((((((.((...))))))))((((((.(((((((.....)))))))........(((((((....))))))).......)))))).......)))... ( -36.40)
>DroSim_CAF1 26999 107 - 1
G---GCUAUAAUGCACUUAGCCCAGCAGGUGCGCCCAGUCUAGUACAUAAUGUACUAGCAUCAUUAUUGUGCAACCAUGUACAAGAACGCUCUGGGUUUCAGGUGCCGAC
(---((......((((((.((...))))))))((((((.(((((((.....)))))))........(((((((....))))))).......)))))).......)))... ( -36.40)
>DroEre_CAF1 33557 110 - 1
CAUUGCCAUAAUGCACUUAGCCCAGCAGGUGCGCCCAGUUUAGUACAUAAUGUACUUGCAUCAUUAUUGUGCAACCAUGUACAACAACGUUCGGGAUUUCAGGUGCCGAC
............((((((..(((.(((((((((....((.....))....))))))))).......(((((((....)))))))........))).....)))))).... ( -29.30)
>DroYak_CAF1 33108 110 - 1
AUUUGCCAUAAUGCAUUUAGCCCAGCAGGUGCGGCCACUUUAGUACAUUAUGUACUUGCAUCAUUAUUGUGCAACCAUGUACAACAAAGCUCUGGCUUUCAGGUGCCCAC
............((((((((((.(((.((((((........(((((.....)))))))))))....(((((((....)))))))....)))..))))...)))))).... ( -29.00)
>consensus
G___GCUAUAAUGCACUUAGCCCAGCAGGUGCGCCCAGUCUAGUACAUAAUGUACUAGCAUCAUUAUUGUGCAACCAUGUACAAGAACGCUCUGGGUUUCAGGUGCCGAC
............((((((.((((....)).))((((((.(((((((.....)))))))........(((((((....))))))).......))))))...)))))).... (-27.56 = -28.04 +   0.48)

alignment

secondary structure

dotplot

Window 6

Location	20,991,113 – 20,991,207
Length	94
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	93.90
Mean single sequence MFE	-25.82
Consensus MFE	-23.20
Energy contribution	-23.24
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.87
Structure conservation index	0.90
SVM decision value	2.37
SVM RNA-class probability	0.993110
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20991113 94 - 27905053
-----UAUAUAUGCCAUAUAAUGCAUUUCGAUGCGCUCUAAUUGAGGGAUUAGUUAGCCUGAUUAUCGGGUUCAUUAAACUUUCACCAGACAAUG------GGCC
-----.......(((.......((((....))))(.(((...((((((.(((((.((((((.....)))))).))))).))))))..))))....------))). ( -24.50)
>DroSec_CAF1 31683 94 - 1
-----UAUAUGUGCCACAUAAUGCAUUUCGAUGCGCUCUAAUUGAGGGAUUAGUUAGCCUGAUUAUCGGGUUCAUUAAACUUUCACCAGACAAUG------GUCC
-----.......((((......((((....))))(.(((...((((((.(((((.((((((.....)))))).))))).))))))..))))..))------)).. ( -23.30)
>DroSim_CAF1 27106 94 - 1
-----UAUAUGUGCCACAUAAUGCAUUUCGAUGCGCUCUAAUUGAGGGAUUAGUUAGCCUGAUUAUCGGGUUCAUUAAACUUUCACCAGACAAUG------GGCC
-----.......(((.(((...((((....))))(.(((...((((((.(((((.((((((.....)))))).))))).))))))..)))).)))------))). ( -26.00)
>DroEre_CAF1 33667 94 - 1
-----UAUAUGUGCCACAUAAUGCAUUUCGAUGCGCUCUAAUUGAGGGAUUAGUUAGCCUGAUUAUCGGGUUCAUUAAACUUUCACCAGACAAUG------GGCC
-----.......(((.(((...((((....))))(.(((...((((((.(((((.((((((.....)))))).))))).))))))..)))).)))------))). ( -26.00)
>DroYak_CAF1 33218 105 - 1
UUAUGUAUAUGUGCCACAUAAUGCAUUUCGGUGCGCUCUAAUUGAGGGAUUAGUUAGCCUGAUUAUCGGGUUCAUUAAACUUUCACCAGACAAUGCAAAGGGGCC
............(((.(....(((((((((((((.(((.....))).).(((((.((((((.....)))))).))))).....)))).)).))))))...)))). ( -29.30)
>consensus
_____UAUAUGUGCCACAUAAUGCAUUUCGAUGCGCUCUAAUUGAGGGAUUAGUUAGCCUGAUUAUCGGGUUCAUUAAACUUUCACCAGACAAUG______GGCC
............(((.......((((....))))(.(((...((((((.(((((.((((((.....)))))).))))).))))))..))))..........))). (-23.20 = -23.24 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:05 2006