Locus 5891

Sequence ID 3R_DroMel_CAF1
Location 15,471,076 – 15,471,313
Length 237
Max. P 0.988174
window9625 window9626 window9627 window9628

overview

Window 5

Location 15,471,076 – 15,471,196
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 68.72
Mean single sequence MFE -52.83
Consensus MFE -24.26
Energy contribution -24.88
Covariance contribution 0.62
Combinations/Pair 1.54
Mean z-score -2.32
Structure conservation index 0.46
SVM decision value 2.11
SVM RNA-class probability 0.988174
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15471076 120 - 27905053
GUAUGCCAAAAGCGGGCGUGGCAGCAGCCGUUCCAAAAGCCGGCGCCGCAGUGGAAGUGGCGCCAAAACCAGGCGUGGACGCAGGUGCUCCAAAAGCCGGCGUAGCAGCUGGUGCCCCAA
..(((((.......)))))((((.((((.(((......(((((((((((.......)))))))).......(((.((((.((....))))))...))))))..))).)))).)))).... ( -56.90)
>DroSec_CAF1 1836 120 - 1
GUACGCCAAAAGCGGGCGUGGCAGCAGCCGUCCCAAGAGCCGGCGUCGCAGUGGAAGUGGCGCCAAAACCAGGCGUGGACGCAGGAGCUCCAAAAGCCGGCGUAGCAGCUGGUGCCCCAA
..(((((.......)))))((((.((((.((..(....(((((((((((.......)))))))).......(((.((((.((....))))))...)))))))..)).)))).)))).... ( -55.00)
>DroSim_CAF1 1835 120 - 1
GUACGCCAAAAGCGGGCGUGGCAGCAGCCGUUCCAAAAGCCGGCGUCGCAGUGGAAGUGGCGCCAAAACCAGGCGUGGACGCAGGCGCUCCAAAAGCCGGCGUAGCAGCUGGUGCCCCAA
..(((((.......)))))((((.((((.(((......(((((((((((.......)))))))).......(((.((((((....)).))))...))))))..))).)))).)))).... ( -55.70)
>DroEre_CAF1 1761 120 - 1
GUGCUCCAAAAGCAGCCGUAGCAGCUGGUGCUCCAAAGGCCGGAGUGGCCGCCGGAGCUGCAAACAAGGAAGUGGUGCCCAGAGCAGCACCGAAGGACGUCGUGGAGGUGGCUGCUCCAA
.((((.....))))(((...(.(((....))).)...))).((((..((((((....(..(............(((((........)))))((......)))..).))))))..)))).. ( -46.50)
>DroYak_CAF1 1833 99 - 1
UUGA------A---------------GUUGCGCCAAAGGCAGGCGUAGCAGUUGAAGUUGCGCCAAAGGCAGGCGUAGCAGCUGGUGCUCUAAAAGCCGGCGUAGCAGCUGGUGCUCCGA
....------.---------------((((((((....((.((((((((.......))))))))....)).(((.(((.(((....))))))...)))))))))))(((....))).... ( -42.30)
>DroAna_CAF1 1374 120 - 1
CGGCUCCAAAAGCUGGUGCGGUUGUAGCUGCUCCAAAGGCUGGCGCAGCCGCCGCUGGUGCUCCAAAAGCGGACGUUGCAGCGGGAGCACCAAACGCCGGGGCGGCAGAUACUGCCCCGA
(((((.....)))))..(((((....(((((.(((.....))).))))).)))))(((((((((....((..........)).))))))))).....((((((((......)))))))). ( -60.60)
>consensus
GUACGCCAAAAGCGGGCGUGGCAGCAGCCGCUCCAAAAGCCGGCGUCGCAGUGGAAGUGGCGCCAAAACCAGGCGUGGACGCAGGAGCUCCAAAAGCCGGCGUAGCAGCUGGUGCCCCAA
.................(.((((.((((.((..(.......((((((((.......)))))))).......(((.(((...........)))...)))...)..)).)))).)))).).. (-24.26 = -24.88 +   0.62)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,471,116 – 15,471,233
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 66.67
Mean single sequence MFE -51.94
Consensus MFE -19.14
Energy contribution -21.12
Covariance contribution 1.98
Combinations/Pair 1.67
Mean z-score -1.71
Structure conservation index 0.37
SVM decision value 0.10
SVM RNA-class probability 0.582026
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15471116 117 - 27905053
GUAGCAGCU---GGAGCUCCAAAAGCCGACGUUGCUGCUGGUAUGCCAAAAGCGGGCGUGGCAGCAGCCGUUCCAAAAGCCGGCGCCGCAGUGGAAGUGGCGCCAAAACCAGGCGUGGAC
......((.---...))((((...(((((((..(((((((.((((((.......)))))).))))))))))).........((((((((.......)))))))).......))).)))). ( -54.10)
>DroSec_CAF1 1876 117 - 1
GUAGCAGCU---GGAGCUCCAAAAGCCGACGUUGCUGCUGGUACGCCAAAAGCGGGCGUGGCAGCAGCCGUCCCAAGAGCCGGCGUCGCAGUGGAAGUGGCGCCAAAACCAGGCGUGGAC
......((.---...))((((...(((((((..(((((((.((((((.......)))))).))))))))))).........((((((((.......)))))))).......))).)))). ( -55.50)
>DroSim_CAF1 1875 117 - 1
GUGGCAGCU---GGAGCUCCAAAAGCCGACGUUGCUGCUGGUACGCCAAAAGCGGGCGUGGCAGCAGCCGUUCCAAAAGCCGGCGUCGCAGUGGAAGUGGCGCCAAAACCAGGCGUGGAC
.((((...(---((....)))...))))(((..(((((((.((((((.......)))))).))))))))))((((...(((((((((((.......)))))))).......))).)))). ( -55.11)
>DroEre_CAF1 1801 120 - 1
GCUGCAGUUGAAGUUGCGCCAAAAGCAGGCGUGGACGCAGGUGCUCCAAAAGCAGCCGUAGCAGCUGGUGCUCCAAAGGCCGGAGUGGCCGCCGGAGCUGCAAACAAGGAAGUGGUGCCC
(((((...((...(..((((.......))))..)...))((((((.....)))).))...)))))....(((((...((((.....))))...))))).(((.((......))..))).. ( -45.70)
>DroAna_CAF1 1414 117 - 1
GCAGCUGUA---GCGGCUCCGAAAGCUGGCGCGGCUGUAGCGGCUCCAAAAGCUGGUGCGGUUGUAGCUGCUCCAAAGGCUGGCGCAGCCGCCGCUGGUGCUCCAAAAGCGGACGUUGCA
(((((....---((((((.((..((((((.(((((((((((.((.(((.....))).)).))))))))))).))...))))..)).))))))((((..((...))..))))...))))). ( -58.60)
>DroPer_CAF1 1783 114 - 1
UGUGCCGUA---GGUGCUCCGAAUCCGGGCUGGGCCGUAGGUGCUCCAAAUCCUGGCUGCGCCGUGGGUGCACCAAACCCAGACUGUGCCGUGGG---UGCUCCGAAUCCUGGCUGGGCU
.(..((...---))..).(((....)))(((.((((...(((((.(((.....)))..)))))...((.(((((.....((.....)).....))---))).)).......)))).))). ( -42.60)
>consensus
GUAGCAGCU___GGAGCUCCAAAAGCCGACGUGGCUGCAGGUACGCCAAAAGCGGGCGUGGCAGCAGCCGCUCCAAAAGCCGGCGUCGCAGUGGAAGUGGCGCCAAAACCAGGCGUGGAC
((((((((.......((.......))....))))))))...((((((.......((.(((((....))))).)).......((.(((((.......))))).)).......))))))... (-19.14 = -21.12 +   1.98)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,471,156 – 15,471,273
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 70.68
Mean single sequence MFE -53.00
Consensus MFE -23.42
Energy contribution -23.90
Covariance contribution 0.48
Combinations/Pair 1.85
Mean z-score -2.10
Structure conservation index 0.44
SVM decision value 1.37
SVM RNA-class probability 0.947325
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15471156 117 - 27905053
UCCGAAAGCGGGAGUGGCAGCUGCAGCUCCAAAAGCGGGCGUAGCAGCU---GGAGCUCCAAAAGCCGACGUUGCUGCUGGUAUGCCAAAAGCGGGCGUGGCAGCAGCCGUUCCAAAAGC
.......((.(((((..(((((((.(((((....).))))...))))))---)..)))))....)).((((..(((((((.((((((.......)))))).)))))))))))........ ( -54.10)
>DroSec_CAF1 1916 117 - 1
UCCAAAGGCGGGCGUGGCAGCUGGAGCUCCAAAAGCGGGCGUAGCAGCU---GGAGCUCCAAAAGCCGACGUUGCUGCUGGUACGCCAAAAGCGGGCGUGGCAGCAGCCGUCCCAAGAGC
......((((((((((((...((((((((((...((..((...)).)))---)))))))))...))).)))))(((((((.((((((.......)))))).)))))))))))........ ( -59.90)
>DroSim_CAF1 1915 117 - 1
GCCAAAAGCGGGCGUGGCGGCGGUUGCUCCAAAAGCGGGCGUGGCAGCU---GGAGCUCCAAAAGCCGACGUUGCUGCUGGUACGCCAAAAGCGGGCGUGGCAGCAGCCGUUCCAAAAGC
(((.......))).(((.(((((((((((((...((.((((((.(((((---((....)))..(((.......))))))).))))))....)).....))).)))))))))))))..... ( -52.10)
>DroEre_CAF1 1841 120 - 1
UCCAAAGGCCGGCGUGGCUGCUGGUGCGCCAAAAGCAGGCGCUGCAGUUGAAGUUGCGCCAAAAGCAGGCGUGGACGCAGGUGCUCCAAAAGCAGCCGUAGCAGCUGGUGCUCCAAAGGC
.......((((((.((((((((((.(((((....((.(((((.((.......)).)))))....))..(((....))).))))).))...)))))))).....))))))(((.....))) ( -50.70)
>DroAna_CAF1 1454 117 - 1
UCCAAAGGCUGGUGCGGUUGUAGCAGAUCCAAAGGCUGGUGCAGCUGUA---GCGGCUCCGAAAGCUGGCGCGGCUGUAGCGGCUCCAAAAGCUGGUGCGGUUGUAGCUGCUCCAAAGGC
.((...(((((.((((((((((.(((.((....))))).))))))))))---.)))))........(((.(((((((((((.((.(((.....))).)).))))))))))).)))..)). ( -54.90)
>DroPer_CAF1 1820 117 - 1
UCCGAAUCCGGGCUGGGCCGUGGGAGCUCCAAACCCGGACUGUGCCGUA---GGUGCUCCGAAUCCGGGCUGGGCCGUAGGUGCUCCAAAUCCUGGCUGCGCCGUGGGUGCACCAAACCC
........(((.(..(.((((.(((((.((.....(((......)))..---)).))))).)...))).)..).)))..(((((.(((.....)))..)))))..((((.......)))) ( -46.30)
>consensus
UCCAAAGGCGGGCGUGGCAGCUGGAGCUCCAAAAGCGGGCGUAGCAGCU___GGAGCUCCAAAAGCCGACGUGGCUGCAGGUACGCCAAAAGCGGGCGUGGCAGCAGCCGCUCCAAAAGC
......((((..((((.(((((..((((((...(((..........)))...)))))).....))))).))))(((((((.(((.((.......)).))).)))))))))))........ (-23.42 = -23.90 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,471,196 – 15,471,313
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.92
Mean single sequence MFE -56.33
Consensus MFE -26.22
Energy contribution -25.15
Covariance contribution -1.07
Combinations/Pair 1.65
Mean z-score -2.04
Structure conservation index 0.47
SVM decision value 0.71
SVM RNA-class probability 0.828355
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15471196 117 - 27905053
UAGCGGCGGGUGCUCCAAAAGCGGGCGUGGCGGCGGGUGCUCCGAAAGCGGGAGUGGCAGCUGCAGCUCCAAAAGCGGGCGUAGCAGCU---GGAGCUCCAAAAGCCGACGUUGCUGCUG
(((((((...((((.....))))((((((((....((.((((((...((....))..)((((((.(((((....).))))...))))))---))))).))....))).)))))))))))) ( -53.20)
>DroSec_CAF1 1956 117 - 1
UGGCGGCGGCUGCUCCAAAAGCGGGCGUGGCGGCGGUUGCUCCAAAGGCGGGCGUGGCAGCUGGAGCUCCAAAAGCGGGCGUAGCAGCU---GGAGCUCCAAAAGCCGACGUUGCUGCUG
.(((((((((((((.....))))(((((.((.(((.(((((.....))))).))).)).))((((((((((...((..((...)).)))---)))))))))...)))...))))))))). ( -57.50)
>DroSim_CAF1 1955 117 - 1
UGGCGGCGGGUGCUCCAAAAGCGGGCGUGGCGGCGGUUGCGCCAAAAGCGGGCGUGGCGGCGGUUGCUCCAAAAGCGGGCGUGGCAGCU---GGAGCUCCAAAAGCCGACGUUGCUGCUG
.((((((.((.(((((....((.((.(..((.((.((..((((.......))))..)).)).))..).))....)).(((......)))---))))).))...(((....))))))))). ( -56.40)
>DroEre_CAF1 1881 120 - 1
CGGCAGCUGGCGCUCCAAAGGCCGGCGUGGCUGCUGGCGCUCCAAAGGCCGGCGUGGCUGCUGGUGCGCCAAAAGCAGGCGCUGCAGUUGAAGUUGCGCCAAAAGCAGGCGUGGACGCAG
..(((((((((.((....))))))))(((.((((((((((.(((..((((.....))))..))).)))))...))))).))))))...((...(..((((.......))))..)...)). ( -59.80)
>DroYak_CAF1 1932 114 - 1
UGGAGGCGGGGGCUCCAAAAGCGGAAGUGGCAGCUGGAGCUCCAAAAGCCGGCGUGGCAGCCGCUGCUCCAAAAGCGGGCGUGGCAGU---AGCUGCUCCAAAAGCGGGCGC---CGCAG
....(((.(((((((((...((....))......)))))))))....(((.((.(((.(((.(((((((((...(....).))).)))---))).))))))...)).)))))---).... ( -57.80)
>DroAna_CAF1 1494 117 - 1
UGGAGGUAGCAGCUCCGAACGCUGGUGCAGCUGUAGCUGCUCCAAAGGCUGGUGCGGUUGUAGCAGAUCCAAAGGCUGGUGCAGCUGUA---GCGGCUCCGAAAGCUGGCGCGGCUGUAG
........((((((.((...(((((.(((((....))))).))...(((((.((((((((((.(((.((....))))).))))))))))---.))))).....)))...)).)))))).. ( -53.30)
>consensus
UGGCGGCGGGUGCUCCAAAAGCGGGCGUGGCGGCGGGUGCUCCAAAAGCGGGCGUGGCAGCUGCAGCUCCAAAAGCGGGCGUAGCAGCU___GGAGCUCCAAAAGCCGACGUUGCUGCAG
(((.(((....)))))).........((((((((....(((.....))).(((.(((.(((.((((((((.......))...)))))).......))))))...)))...)))))))).. (-26.22 = -25.15 +  -1.07)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:08 2006