Locus 9775

Sequence ID 3R_DroMel_CAF1
Location 25,899,815 – 25,899,943
Length 128
Max. P 0.912984
window15613 window15614 window15615

overview

Window 3

Location 25,899,815 – 25,899,916
Length 101
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 75.68
Mean single sequence MFE -32.02
Consensus MFE -13.70
Energy contribution -14.10
Covariance contribution 0.39
Combinations/Pair 1.20
Mean z-score -2.37
Structure conservation index 0.43
SVM decision value 1.09
SVM RNA-class probability 0.912984
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25899815 101 + 27905053
UGUCCUCUUUAUCGGCGACUUUGGGUUGCAUACUUUUGUGCUCUUGGGUGGGU---AGC-AAAGUUUUGCCGCCUUUGCAAGAUUUU-----CGCAAGUCUUGCAGAAAA
............((((((..((..(((((.(((((..(....)..))))).))---)))-..))..))))))..((((((((((((.-----...))))))))))))... ( -31.10)
>DroVir_CAF1 42920 90 + 1
CU--UUUGCUAUCAGCGUCUU-----UGCAUACUUUUCUGCUCUCAGUCA-G----UUG--AAACUUUGCCGU-UUUGCAAGUUUUU-----CGCAAGUCUUGCAGAAAA
..--.......(((((..((.-----.(((........)))....))...-)----)))--)..........(-((((((((.....-----(....).))))))))).. ( -17.90)
>DroPse_CAF1 28180 99 + 1
UUUGGCCUUUAUCGGGGGCCU-----UGCAUACUUUUGUGCGCUGCCGCUGGUGGAAUG-AAAGUUUUGCCGCCUCUGCAAGUUUUU-----CGCAAGUCUUGCAGAAAA
...(((.......((.(((..-----((((((....))))))..))).))((..((((.-...))))..)))))((((((((.....-----(....).))))))))... ( -39.70)
>DroYak_CAF1 34403 102 + 1
UGUCCUCUUUAUCGGUGGCUUUGGCUUGCAUACUUUUGUGCGCUGGGGUGGGU---GGGCAAAGUUUCGCCGCCUUUGCAAGUUUUU-----CGCAAGUCUUGCAGAAAA
.............((((((....(((..(.(((((..(....)..))))).).---.)))........))))))((((((((.....-----(....).))))))))... ( -32.20)
>DroAna_CAF1 26988 100 + 1
UGUUCGCUUUAUCGGGGGCCU-----UGCAUACUUUUGUGCUUCGGGAU-GGC---AGA-AAAGUUUUGCCGCCUUGGCAAGUUUUUUUUUCUGCAAGUCUUGCAGAAAA
.....((((...(.(((((..-----.(((.((((((.((((.......-)))---).)-)))))..))).))))).).))))....(((((((((.....))))))))) ( -31.50)
>DroPer_CAF1 27984 99 + 1
UUUGGCCUUUAUCGGGGGCCU-----UGCAUACUUUUGUGCGCUGCCGCUGGUGGAAUG-AAAGUUUUGCCGCCUCUGCAAGUUUUU-----CGCAAGUCUUGCAGAAAA
...(((.......((.(((..-----((((((....))))))..))).))((..((((.-...))))..)))))((((((((.....-----(....).))))))))... ( -39.70)
>consensus
UGUCCUCUUUAUCGGGGGCCU_____UGCAUACUUUUGUGCGCUGGGGCGGGU___AGG_AAAGUUUUGCCGCCUUUGCAAGUUUUU_____CGCAAGUCUUGCAGAAAA
.............((.(((........(((((....))))).((......))................))).))((((((((.................))))))))... (-13.70 = -14.10 +   0.39)

alignment

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secondary structure

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dotplot

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Window 4

Location 25,899,849 – 25,899,943
Length 94
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 82.57
Mean single sequence MFE -29.79
Consensus MFE -16.28
Energy contribution -17.26
Covariance contribution 0.98
Combinations/Pair 1.29
Mean z-score -2.69
Structure conservation index 0.55
SVM decision value 0.21
SVM RNA-class probability 0.635274
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25899849 94 + 27905053
UUUGUGCUCUUGGGUGGGUAGC-AAAGUUUUGCCGCCUUUGCAAGAUUUU-----CGCAAGUCUUGCAGAAAAUUAUACAAAAGGCGAAGGCAAAGCUUA
..(((((((......))))).)-)(((((((((((((((((((((((((.-----...)))))))))).............)))))...)))))))))). ( -32.61)
>DroVir_CAF1 42947 90 + 1
UUUCUGCUCUCAGUCA-G-UUG--AAACUUUGCCGU-UUUGCAAGUUUUU-----CGCAAGUCUUGCAGAAAAUUAUACAAAAGGCAAACGUGUUGUGUG
.(((.(((.......)-)-).)--))((((((((.(-((((((((.....-----(....).)))))))))............)))))).))........ ( -19.22)
>DroSim_CAF1 27142 94 + 1
UUUGUGCUCUUGGGUGGGUAGC-AAAGUUUUGCCGCCUUUGCAAGAUUUU-----CGCAAGUCUUGCAGAAAAUUAUACAAAAGGCGAAGGCAAAGCUUA
..(((((((......))))).)-)(((((((((((((((((((((((((.-----...)))))))))).............)))))...)))))))))). ( -32.61)
>DroEre_CAF1 35156 94 + 1
UUUGUGCGCUUGGGUGGGAGGG-AAAGUUUCGCCGCCUUUGCAAGUUUUU-----CGCAAGUCUUGCAGAAAAUUAUACAAAAGGCGAAGGCAAAGCUUA
.......((((.((((..(...-....)..))))((((((((.((((((.-----.(((.....)))..))))))...(....))))))))).))))... ( -28.90)
>DroYak_CAF1 34437 95 + 1
UUUGUGCGCUGGGGUGGGUGGGCAAAGUUUCGCCGCCUUUGCAAGUUUUU-----CGCAAGUCUUGCAGAAAAUUAUACAAAAGGCGAAGGCGAAGCUUA
..(((.((((......)))).)))((((((((((((((((...((((((.-----.(((.....)))..)))))).....))))))...)))))))))). ( -35.10)
>DroAna_CAF1 27017 94 + 1
UUUGUGCUUCGGGAU-GGCAGA-AAAGUUUUGCCGCCUUGGCAAGUUUUUUUUUCUGCAAGUCUUGCAGAAAAUUAUACAAAAGGCGAA----AAGCUUA
....((((..(((.(-((((((-.....)))))))))).)))).((.(..(((((((((.....)))))))))..).))...((((...----..)))). ( -30.30)
>consensus
UUUGUGCUCUUGGGUGGGUAGG_AAAGUUUUGCCGCCUUUGCAAGUUUUU_____CGCAAGUCUUGCAGAAAAUUAUACAAAAGGCGAAGGCAAAGCUUA
........................(((((((((((((((((((((.................)))))).............)))))...)))))))))). (-16.28 = -17.26 +   0.98)

alignment

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secondary structure

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dotplot

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Window 5

Location 25,899,849 – 25,899,943
Length 94
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 82.57
Mean single sequence MFE -24.90
Consensus MFE -12.06
Energy contribution -13.15
Covariance contribution 1.09
Combinations/Pair 1.19
Mean z-score -3.18
Structure conservation index 0.48
SVM decision value 0.34
SVM RNA-class probability 0.694563
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25899849 94 - 27905053
UAAGCUUUGCCUUCGCCUUUUGUAUAAUUUUCUGCAAGACUUGCG-----AAAAUCUUGCAAAGGCGGCAAAACUUU-GCUACCCACCCAAGAGCACAAA
...(((((.....(((((((.(((..((((((.(((.....))))-----)))))..))))))))))((((....))-))..........)))))..... ( -27.50)
>DroVir_CAF1 42947 90 - 1
CACACAACACGUUUGCCUUUUGUAUAAUUUUCUGCAAGACUUGCG-----AAAAACUUGCAAA-ACGGCAAAGUUU--CAA-C-UGACUGAGAGCAGAAA
...........(((((((((((((...(((((.(((.....))))-----))))...))))))-).)))))).(((--((.-.-....)))))....... ( -20.90)
>DroSim_CAF1 27142 94 - 1
UAAGCUUUGCCUUCGCCUUUUGUAUAAUUUUCUGCAAGACUUGCG-----AAAAUCUUGCAAAGGCGGCAAAACUUU-GCUACCCACCCAAGAGCACAAA
...(((((.....(((((((.(((..((((((.(((.....))))-----)))))..))))))))))((((....))-))..........)))))..... ( -27.50)
>DroEre_CAF1 35156 94 - 1
UAAGCUUUGCCUUCGCCUUUUGUAUAAUUUUCUGCAAGACUUGCG-----AAAAACUUGCAAAGGCGGCGAAACUUU-CCCUCCCACCCAAGCGCACAAA
.(((.((((((...((((((.(((...(((((.(((.....))))-----))))...))))))))))))))).))).-...................... ( -22.40)
>DroYak_CAF1 34437 95 - 1
UAAGCUUCGCCUUCGCCUUUUGUAUAAUUUUCUGCAAGACUUGCG-----AAAAACUUGCAAAGGCGGCGAAACUUUGCCCACCCACCCCAGCGCACAAA
...((((((((...((((((.(((...(((((.(((.....))))-----))))...))))))))))))))).....((............))))..... ( -24.80)
>DroAna_CAF1 27017 94 - 1
UAAGCUU----UUCGCCUUUUGUAUAAUUUUCUGCAAGACUUGCAGAAAAAAAAACUUGCCAAGGCGGCAAAACUUU-UCUGCC-AUCCCGAAGCACAAA
...((((----(..(((((..(((...(((((((((.....))))))))).......))).)))))((((.......-..))))-.....)))))..... ( -26.30)
>consensus
UAAGCUUUGCCUUCGCCUUUUGUAUAAUUUUCUGCAAGACUUGCG_____AAAAACUUGCAAAGGCGGCAAAACUUU_CCUACCCACCCAAGAGCACAAA
.(((.(((((...(((((((.(((...((((.((((.....)))).....))))...))))))))))))))).)))........................ (-12.06 = -13.15 +   1.09)

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 13:41:55 2006