Locus 3245

Sequence ID 3R_DroMel_CAF1
Location 8,658,054 – 8,658,192
Length 138
Max. P 0.811786
window5245 window5246 window5247

overview

Window 5

Location 8,658,054 – 8,658,152
Length 98
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 81.12
Mean single sequence MFE -24.33
Consensus MFE -19.81
Energy contribution -20.42
Covariance contribution 0.61
Combinations/Pair 1.04
Mean z-score -1.58
Structure conservation index 0.81
SVM decision value 0.55
SVM RNA-class probability 0.779028
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8658054 98 + 27905053
CUUCGUCC-----GC-------CAUCGACCAUGCAAUGUUGUUCUUUCCGAUGUCGUUUGUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCA
..(((...-----..-------...)))..(((((.(((.((...((((((((.(((..(((((.....))))).))).)))).))))...)))))..)))))....... ( -22.30)
>DroVir_CAF1 106134 85 + 1
-------------------------CUGGCAUGCAAUGUUGUUCUUUCUGAUGUCGUUUAUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCA
-------------------------((((.(((((.(((.((..(((((((((.(((..(((((.....))))).))).)))))))))...)))))..))))).)))).. ( -25.20)
>DroWil_CAF1 108080 110 + 1
UUCCACUCCGUCAGCCUUCCUUCAUCAGGUAUGCAAUGUUGUUCUUUCUGAUGUCGUUUGUUUUCGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCA
.............((...(((.....))).(((((.(((.((..(((((((((.(((....((((....))))..))).)))))))))...)))))..)))))....)). ( -26.60)
>DroMoj_CAF1 136322 85 + 1
-------------------------GUGCCUGCCAAUGUUGUUCUUUCUGAUGUCGUUUAUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCA
-------------------------(..((((.......(((..(((((((((.(((..(((((.....))))).))).)))))))))...)))))))..)......... ( -24.61)
>DroAna_CAF1 79505 95 + 1
UUCCAC--------C-------CACAGACCAUGCAAUGUUGUUCUUUCCGAUGUCGUUUGUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCA
......--------.-------........(((((.(((.((...((((((((.(((..(((((.....))))).))).)))).))))...)))))..)))))....... ( -21.40)
>DroPer_CAF1 92271 103 + 1
AUUCGCCCACUCACC-------CUUCGAGCAUGCAAUGUUGUUCUUUCUGAUGUCGUUUGUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCA
....((...(((...-------....))).(((((.(((.((..(((((((((.(((..(((((.....))))).))).)))))))))...)))))..)))))....)). ( -25.90)
>consensus
_U_C_C________C_______CAUCGACCAUGCAAUGUUGUUCUUUCUGAUGUCGUUUGUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCA
..............................(((((.(((.((..(((((((((.(((..(((((.....))))).))).)))))))))...)))))..)))))....... (-19.81 = -20.42 +   0.61)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,658,072 – 8,658,192
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 95.22
Mean single sequence MFE -29.17
Consensus MFE -24.87
Energy contribution -25.32
Covariance contribution 0.45
Combinations/Pair 1.06
Mean z-score -1.57
Structure conservation index 0.85
SVM decision value 0.13
SVM RNA-class probability 0.599739
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8658072 120 + 27905053
AUGCAAUGUUGUUCUUUCCGAUGUCGUUUGUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCACAAUAAAAACGUAAUUGCUGGCAAUUUAAUGCUGUUGUUC
..(((((..(((...((((((((.(((..(((((.....))))).))).)))).))))...)))...((((......))))............))))).((((......))))....... ( -27.40)
>DroVir_CAF1 106139 120 + 1
AUGCAAUGUUGUUCUUUCUGAUGUCGUUUAUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCACAAUAAAAACGUAAUUGCUGGCAAUUUAAUACAGUUGUUA
..(((((..(((..(((((((((.(((..(((((.....))))).))).)))))))))...)))...((((......))))............)))))((((((((......)))))))) ( -29.20)
>DroGri_CAF1 85705 120 + 1
AUGCAAUGUUGUUCUUUCUGAUGUCGUUUAUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCACAAUAAAAACGUAAUUGCUGGCAAUUUAAUACAGUUGUUA
..(((((..(((..(((((((((.(((..(((((.....))))).))).)))))))))...)))...((((......))))............)))))((((((((......)))))))) ( -29.20)
>DroWil_CAF1 108110 120 + 1
AUGCAAUGUUGUUCUUUCUGAUGUCGUUUGUUUUCGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCACAAUAAAAACGUAAUUGCUAGCAAUUUAAUGCUGCUCUUG
..(((((..(((..(((((((((.(((....((((....))))..))).)))))))))...)))...((((......))))............)))))(((((......)))))...... ( -31.10)
>DroMoj_CAF1 136327 120 + 1
UGCCAAUGUUGUUCUUUCUGAUGUCGUUUAUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCACAAUAAAAACGUAAUUGCUGGCAAUUUAAUACAGUUGUUA
(((((.(((.((..(((((((((.(((..(((((.....))))).))).)))))))))...))))).((((......)))).................)))))................. ( -29.20)
>DroAna_CAF1 79520 120 + 1
AUGCAAUGUUGUUCUUUCCGAUGUCGUUUGUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCACAAUAAAAACGUAAUUGCCGGCAAUUUAAUGCUGUUGUUC
..(((((..(((...((((((((.(((..(((((.....))))).))).)))).))))...)))...((((......))))............)))))(((((......)))))...... ( -28.90)
>consensus
AUGCAAUGUUGUUCUUUCUGAUGUCGUUUAUUUUUGUUCGAAAUUGCGCCAUCAGGAAUAUGCACAGGUGCAUUUUAGCACAAUAAAAACGUAAUUGCUGGCAAUUUAAUACAGUUGUUA
..(((((..(((..(((((((((.(((..(((((.....))))).))).)))))))))...)))...((((......))))............))))).((((((........)))))). (-24.87 = -25.32 +   0.45)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,658,072 – 8,658,192
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 95.22
Mean single sequence MFE -23.16
Consensus MFE -20.89
Energy contribution -20.58
Covariance contribution -0.31
Combinations/Pair 1.08
Mean z-score -1.34
Structure conservation index 0.90
SVM decision value 0.65
SVM RNA-class probability 0.811786
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8658072 120 - 27905053
GAACAACAGCAUUAAAUUGCCAGCAAUUACGUUUUUAUUGUGCUAAAAUGCACCUGUGCAUAUUCCUGAUGGCGCAAUUUCGAACAAAAACAAACGACAUCGGAAAGAACAACAUUGCAU
........(((......)))..(((((...(((((((((((((((..(((((....)))))........)))))))))(((((................)))))))))))...))))).. ( -24.09)
>DroVir_CAF1 106139 120 - 1
UAACAACUGUAUUAAAUUGCCAGCAAUUACGUUUUUAUUGUGCUAAAAUGCACCUGUGCAUAUUCCUGAUGGCGCAAUUUCGAACAAAAAUAAACGACAUCAGAAAGAACAACAUUGCAU
......................(((((...((((((...((((......))))............((((((.((..((((.......))))...)).)))))).))))))...))))).. ( -21.00)
>DroGri_CAF1 85705 120 - 1
UAACAACUGUAUUAAAUUGCCAGCAAUUACGUUUUUAUUGUGCUAAAAUGCACCUGUGCAUAUUCCUGAUGGCGCAAUUUCGAACAAAAAUAAACGACAUCAGAAAGAACAACAUUGCAU
......................(((((...((((((...((((......))))............((((((.((..((((.......))))...)).)))))).))))))...))))).. ( -21.00)
>DroWil_CAF1 108110 120 - 1
CAAGAGCAGCAUUAAAUUGCUAGCAAUUACGUUUUUAUUGUGCUAAAAUGCACCUGUGCAUAUUCCUGAUGGCGCAAUUUCGAACGAAAACAAACGACAUCAGAAAGAACAACAUUGCAU
.......((((......)))).(((((...((((((...((((......))))............((((((.((...((((....)))).....)).)))))).))))))...))))).. ( -27.20)
>DroMoj_CAF1 136327 120 - 1
UAACAACUGUAUUAAAUUGCCAGCAAUUACGUUUUUAUUGUGCUAAAAUGCACCUGUGCAUAUUCCUGAUGGCGCAAUUUCGAACAAAAAUAAACGACAUCAGAAAGAACAACAUUGGCA
.................((((((.......((((..(((((((((..(((((....)))))........)))))))))...))))..............((.....))......)))))) ( -21.40)
>DroAna_CAF1 79520 120 - 1
GAACAACAGCAUUAAAUUGCCGGCAAUUACGUUUUUAUUGUGCUAAAAUGCACCUGUGCAUAUUCCUGAUGGCGCAAUUUCGAACAAAAACAAACGACAUCGGAAAGAACAACAUUGCAU
......(.(((......))).)(((((...(((((((((((((((..(((((....)))))........)))))))))(((((................)))))))))))...))))).. ( -24.29)
>consensus
UAACAACAGCAUUAAAUUGCCAGCAAUUACGUUUUUAUUGUGCUAAAAUGCACCUGUGCAUAUUCCUGAUGGCGCAAUUUCGAACAAAAACAAACGACAUCAGAAAGAACAACAUUGCAU
........(((......)))..(((((...((((((...((((......))))............((((((.((....................)).)))))).))))))...))))).. (-20.89 = -20.58 +  -0.31)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:34 2006