Locus 3293

Sequence ID 3R_DroMel_CAF1
Location 8,824,392 – 8,824,635
Length 243
Max. P 0.999427
window5315 window5316 window5317 window5318 window5319

overview

Window 5

Location 8,824,392 – 8,824,485
Length 93
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 88.02
Mean single sequence MFE -36.90
Consensus MFE -29.33
Energy contribution -29.45
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.95
Structure conservation index 0.79
SVM decision value 0.82
SVM RNA-class probability 0.858247
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8824392 93 + 27905053
UUCCUGCUGCCAUGUGAUGUCUCUGUCCUCCAUGGACGUAGAUGUAGAU------GCGGAUGC------GGAGGGCGAUGUGGAUGCCACAGCGUCCUCCUCCUG
......((((.((.(.((((((.(((((.....))))).))))))).))------))))....------((((((((.(((((...))))).))))))))..... ( -38.40)
>DroSec_CAF1 3000 87 + 1
UUCCUGCUGCCAUGUGAUGUCUCUGUCCUCCAUGGAUG------UAGAU------GUGGAUGC------GGAGGGCGAUGUGGAUGCCACAGCGUCCUCCUCCUG
.....((..((((.....((((..((((.....)))).------.))))------))))..))------((((((((.(((((...))))).))))))))..... ( -34.90)
>DroSim_CAF1 2999 87 + 1
UUCCUGCUGCCAUGUGAUGUCUCUGUCCUCCAUGGAUG------UAGAU------GUGGAUGC------GGAGGGCGAUGUGGAUGCCACAGCGUCCUCCUCCUG
.....((..((((.....((((..((((.....)))).------.))))------))))..))------((((((((.(((((...))))).))))))))..... ( -34.90)
>DroYak_CAF1 2972 99 + 1
UUCCUGCUGCCAUGUGAUGUCCCUGUCCUCCAUGGAUG------UAGAUGCUGAUGUGGAUGCGGAUGCGGAGGGCGAUGUGGAUGCCGCAACGUCCUCCUCCUG
...((((..((((((.(((((..(((((.....)))))------..)))).).))))))..))))....((((((((.(((((...))))).))))))))..... ( -39.40)
>consensus
UUCCUGCUGCCAUGUGAUGUCUCUGUCCUCCAUGGAUG______UAGAU______GUGGAUGC______GGAGGGCGAUGUGGAUGCCACAGCGUCCUCCUCCUG
.....((..((((.....((((.(((((.....))))).......))))......))))..))......((((((((.(((((...))))).))))))))..... (-29.33 = -29.45 +   0.12)

alignment

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secondary structure

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Window 6

Location 8,824,449 – 8,824,557
Length 108
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 94.39
Mean single sequence MFE -50.86
Consensus MFE -47.34
Energy contribution -48.02
Covariance contribution 0.68
Combinations/Pair 1.05
Mean z-score -1.46
Structure conservation index 0.93
SVM decision value 1.45
SVM RNA-class probability 0.954820
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8824449 108 + 27905053
----GGAGGGCGAUGUGGAUGCCACAGCGUCCUCCUCCUGCGUCGCCACCGCUUCCCAGCUGAAUCCGUCGCCACCGCCUGCUGGUGUCCAACAGGCGAAGCCGGCGCGGAG
----((((((((.(((((...))))).))))))))..((((((((.....(((((...((.((.....))))....(((((.(((...))).)))))))))))))))))).. ( -51.60)
>DroSec_CAF1 3051 108 + 1
----GGAGGGCGAUGUGGAUGCCACAGCGUCCUCCUCCUGCGUCGCCACCGCCACCCAGCUGAAUUCGUCGCCACCGCCUGCUGGUGUCCAACAGGCGAAGCCGGCGCGGAG
----((((((((.(((((...))))).))))))))..((((((((.(..((((..(((((.((.....))((....))..)))))((.....))))))..).)))))))).. ( -49.50)
>DroSim_CAF1 3050 108 + 1
----GGAGGGCGAUGUGGAUGCCACAGCGUCCUCCUCCUGCGUCGCCACCGCUUCCCAGCUGAAUUCGUCGCCACCGCCUGCUGGUGUCCAACAGGCGAAGCCGGCGCGGAG
----((((((((.(((((...))))).))))))))..((((((((.....(((((...((.((.....))))....(((((.(((...))).)))))))))))))))))).. ( -51.60)
>DroEre_CAF1 3165 109 + 1
AUG---AGGGCGAUGUGGAUGCCACAACGUCCUCCUCCUGCGGUGCCACCGCUUCCCAGCUGAAUCCGUCGCCACCGCCUGCUGGUGUCCAACAGGCGAAGCCGGCGCGGAG
..(---((((((.(((((...))))).))))))).....((((.....))))............((((.((((..((((((.(((...))).)))))).....)))))))). ( -50.10)
>DroYak_CAF1 3031 112 + 1
AUGCGGAGGGCGAUGUGGAUGCCGCAACGUCCUCCUCCUGCGUCGCCACCGCUUCCCAGCUGAAUCCGUCGCCACCGCCUGCUGGUGUCCAACAGGCGAAGCCGGCGCGGAG
....((((((((.(((((...))))).))))))))..((((((((.....(((((...((.((.....))))....(((((.(((...))).)))))))))))))))))).. ( -51.50)
>consensus
____GGAGGGCGAUGUGGAUGCCACAGCGUCCUCCUCCUGCGUCGCCACCGCUUCCCAGCUGAAUCCGUCGCCACCGCCUGCUGGUGUCCAACAGGCGAAGCCGGCGCGGAG
....((((((((.(((((...))))).))))))))..((((((((.....(((((...((.((.....))))....(((((.(((...))).)))))))))))))))))).. (-47.34 = -48.02 +   0.68)

alignment

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secondary structure

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Window 7

Location 8,824,449 – 8,824,557
Length 108
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 94.39
Mean single sequence MFE -54.48
Consensus MFE -50.92
Energy contribution -51.32
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.93
SVM decision value 2.18
SVM RNA-class probability 0.989731
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8824449 108 - 27905053
CUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGGAUUCAGCUGGGAAGCGGUGGCGACGCAGGAGGAGGACGCUGUGGCAUCCACAUCGCCCUCC----
.(((((((((...(((((((((((...)))))))))))))))).))))(((.(((....))).(((....))).)))(((((.((.(((((...))))).)).)))))---- ( -55.80)
>DroSec_CAF1 3051 108 - 1
CUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGAAUUCAGCUGGGUGGCGGUGGCGACGCAGGAGGAGGACGCUGUGGCAUCCACAUCGCCCUCC----
(.((((.(((((((((((((((((...)))))))))))((....)).....)))))))))).)(((....)))....(((((.((.(((((...))))).)).)))))---- ( -53.80)
>DroSim_CAF1 3050 108 - 1
CUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGAAUUCAGCUGGGAAGCGGUGGCGACGCAGGAGGAGGACGCUGUGGCAUCCACAUCGCCCUCC----
((((((.(((((((((((((((((...)))))))))))((....)).....))))))...)).(((....))).))))((((.((.(((((...))))).)).)))).---- ( -53.30)
>DroEre_CAF1 3165 109 - 1
CUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGGAUUCAGCUGGGAAGCGGUGGCACCGCAGGAGGAGGACGUUGUGGCAUCCACAUCGCCCU---CAU
((((...(((((((((((((((((...)))))))))))((....)).....))))))...((((.....)))).))))((((.((.(((((...))))).)).)))---).. ( -55.40)
>DroYak_CAF1 3031 112 - 1
CUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGGAUUCAGCUGGGAAGCGGUGGCGACGCAGGAGGAGGACGUUGCGGCAUCCACAUCGCCCUCCGCAU
.(((((((((...(((((((((((...)))))))))))))))).))))....((.(((..(((((((((((((........).))))))((...)).))))))..))))).. ( -54.10)
>consensus
CUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGGAUUCAGCUGGGAAGCGGUGGCGACGCAGGAGGAGGACGCUGUGGCAUCCACAUCGCCCUCC____
((((((.(((((((((((((((((...)))))))))))((....)).....))))))...)).(((....))).))))((((.((.(((((...))))).)).))))..... (-50.92 = -51.32 +   0.40)

alignment

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secondary structure

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Window 8

Location 8,824,485 – 8,824,595
Length 110
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 95.31
Mean single sequence MFE -58.62
Consensus MFE -53.34
Energy contribution -54.42
Covariance contribution 1.08
Combinations/Pair 1.05
Mean z-score -2.36
Structure conservation index 0.91
SVM decision value 3.59
SVM RNA-class probability 0.999427
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8824485 110 - 27905053
AGCUGAGCCGCUCCAGGAGCUGGCAUGGCGGUGAG--CUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGGAUUCAGCUGGGAAGCGGUGGCGACG
.(((..((((((((...((((((....((((....--))))(((((((((...(((((((((((...)))))))))))))))).)))).)))))).)).))))))))).... ( -60.20)
>DroSec_CAF1 3087 110 - 1
AGUUGAGCCGCUCCAGGAGCUGGCAUGGCGGUGAG--CUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGAAUUCAGCUGGGUGGCGGUGGCGACG
.((((.((((((((...((((((...(((((....--))))).(((((((...(((((((((((...)))))))))))))))).))...)))))).)).))))))..)))). ( -57.50)
>DroSim_CAF1 3086 112 - 1
AGUUGAGCCGCUCCAGGAGCUGGCAUGGCGGUGCCGUGUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGAAUUCAGCUGGGAAGCGGUGGCGACG
.((((.((((((((.(((((..(((((((...))))))))))))((((((...(((((((((((...)))))))))))))))).)...........)).))))))..)))). ( -62.00)
>DroEre_CAF1 3202 110 - 1
AGUUGAGCCGCUCCAGGAGAUGGCAUGGCGGUGAG--CUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGGAUUCAGCUGGGAAGCGGUGGCACCG
......((((..(((.....)))..))))((((.(--(((((((((((((...(((((((((((...)))))))))))))))).))))(((......))))))))..)))). ( -55.50)
>DroYak_CAF1 3071 110 - 1
AGUUGAGCCGCUCCAGGAGAUGGCAUGGCGGUGAG--CUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGGAUUCAGCUGGGAAGCGGUGGCGACG
.((((.((((((((.....((.((...)).)).((--(((.(((((((((...(((((((((((...)))))))))))))))).))))..))))).)).))))))..)))). ( -57.90)
>consensus
AGUUGAGCCGCUCCAGGAGCUGGCAUGGCGGUGAG__CUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGGUGGCGACGGAUUCAGCUGGGAAGCGGUGGCGACG
.((((.((((((((...((((((....((((......))))(((((((((...(((((((((((...)))))))))))))))).)))).)))))).)).))))))..)))). (-53.34 = -54.42 +   1.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,824,519 – 8,824,635
Length 116
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 95.89
Mean single sequence MFE -52.10
Consensus MFE -49.60
Energy contribution -50.64
Covariance contribution 1.04
Combinations/Pair 1.02
Mean z-score -1.14
Structure conservation index 0.95
SVM decision value 0.33
SVM RNA-class probability 0.690609
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8824519 116 - 27905053
AGGAUCGUGUGCAGCGUGUUGAUGAUGUUGCCGUCGGGAAAGCUGAGCCGCUCCAGGAGCUGGCAUGGCGGUGAG--CUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGG
.(((.((.((.((((...((..(((((....)))))..)).)))).)))).))).(((((((((..(((((....--)))))....)))))))))(((((((((...))))))))).. ( -56.20)
>DroSec_CAF1 3121 116 - 1
AGGAUCGUGUGCAGCGUGUUGAUGAUGUUGCCGUCGGGAAAGUUGAGCCGCUCCAGGAGCUGGCAUGGCGGUGAG--CUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGG
.(((.((.((.((((...((..(((((....)))))..)).)))).)))).))).(((((((((..(((((....--)))))....)))))))))(((((((((...))))))))).. ( -53.80)
>DroSim_CAF1 3120 118 - 1
AGGAUCGUGUGCAGCGUGUUGAUGAUGUUGCCGUCGGGAAAGUUGAGCCGCUCCAGGAGCUGGCAUGGCGGUGCCGUGUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGG
.(((.((.((.((((...((..(((((....)))))..)).)))).)))).))).(((((((((...((((.((.....)).)))))))))))))(((((((((...))))))))).. ( -56.70)
>DroEre_CAF1 3236 116 - 1
AGGAUCGUGUGCAGCGUGUUAAUGAUAUUGCCCUCGGGAAAGUUGAGCCGCUCCAGGAGAUGGCAUGGCGGUGAG--CUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGG
.((..((((.(((((...(((((.......((....))...)))))(((((((((.....)))...))))))..)--))))..)))))).....((((((((((...)))))))))). ( -46.90)
>DroYak_CAF1 3105 116 - 1
AGGAUCGUGUGCAGCGUGUUAAUGAUAUUGCCCUCGGGAAAGUUGAGCCGCUCCAGGAGAUGGCAUGGCGGUGAG--CUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGG
.((..((((.(((((...(((((.......((....))...)))))(((((((((.....)))...))))))..)--))))..)))))).....((((((((((...)))))))))). ( -46.90)
>consensus
AGGAUCGUGUGCAGCGUGUUGAUGAUGUUGCCGUCGGGAAAGUUGAGCCGCUCCAGGAGCUGGCAUGGCGGUGAG__CUGCUCCGCGCCGGCUUCGCCUGUUGGACACCAGCAGGCGG
.(((.((.((.((((...((..(((((....)))))..)).)))).)))).))).(((((((((...((((.(.......).)))))))))))))(((((((((...))))))))).. (-49.60 = -50.64 +   1.04)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:48 2006