Locus 6064

Sequence ID 3R_DroMel_CAF1
Location 15,931,763 – 15,932,035
Length 272
Max. P 0.875077
window9892 window9893 window9894

overview

Window 2

Location 15,931,763 – 15,931,879
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.03
Mean single sequence MFE -27.24
Consensus MFE -21.44
Energy contribution -21.64
Covariance contribution 0.20
Combinations/Pair 1.26
Mean z-score -1.90
Structure conservation index 0.79
SVM decision value 0.89
SVM RNA-class probability 0.875077
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15931763 116 - 27905053
----AUGGGCGGCAGCAGGGCGCGGCACAAGUAAUACAAACUAUAUGAAAAUAAAGAAUCCAGAUUGCUGAGGGGGCUAAGCAAUCGCCGAGAGAAAUGCUGUAAAAAUAAGUUUAAUAU
----.(((((.((((((...(.((((..............((.(((....))).))......(((((((.((....)).)))))))))))...)...))))))........))))).... ( -30.70)
>DroSec_CAF1 61437 116 - 1
----AUGGGCGGCAGCAGGGCGCGGCACAAGUAAUACAAAGUAUAUGAAAAUAAAGAAUCCAGAUUGCUGAGGGGGCUAAGCAAUCGCCGAGAGAAAUGCUGUAAAAAUAAGUUUAAUAU
----.(((((.((((((...(.((((.................(((....))).........(((((((.((....)).)))))))))))...)...))))))........))))).... ( -29.30)
>DroSim_CAF1 38926 116 - 1
----AUGGGCGGCAGCAGGGCGCGGCACAAGUAAUACAAAGUAUAUGAAAAUAAAGAAUCCAGAUUGCUGAGGGGGCUAAGCAAUCGCCGAAAGAAAUGCUGUAAAAAUAAGUUUAAUAU
----.(((((.((((((...(.((((.................(((....))).........(((((((.((....)).)))))))))))...)...))))))........))))).... ( -29.30)
>DroEre_CAF1 38317 120 - 1
GAUUCUGGGCGGCAGCAGGGCGCUGCACAAGUAAUACAAAGUAUAUGAAAAUAAAGAAUCCAGAUCGUUGAGGGCUCUAAGCAAUCGCCCAGCGAAAUGCUGUAAAAAUAAGUUUAAUAU
....((((((((((((.....)))))..............((.(((....))).(((..((..........))..)))..))...)))))))............................ ( -27.20)
>DroAna_CAF1 32790 113 - 1
----GUGGAAGGCACAGGGGCAAGGCGCAAGUAAUACAAAGUAUAUGAAAAUAAAGAAUCCAGAUUGGGGAG---GCGAUUCGGUCGCCGAGAGAAAUGCUGUAAAAAUAAGUUUAAUAU
----(((.....)))..((((...((....))..((((..((((..............(((.......)))(---(((((...)))))).......)))))))).......))))..... ( -19.70)
>consensus
____AUGGGCGGCAGCAGGGCGCGGCACAAGUAAUACAAAGUAUAUGAAAAUAAAGAAUCCAGAUUGCUGAGGGGGCUAAGCAAUCGCCGAGAGAAAUGCUGUAAAAAUAAGUUUAAUAU
...........((((((...(.((((.................(((....))).........(((((((.((....)).)))))))))))...)...))))))................. (-21.44 = -21.64 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,931,879 – 15,931,995
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.67
Mean single sequence MFE -44.07
Consensus MFE -28.18
Energy contribution -29.38
Covariance contribution 1.20
Combinations/Pair 1.31
Mean z-score -1.87
Structure conservation index 0.64
SVM decision value 0.14
SVM RNA-class probability 0.602200
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15931879 116 - 27905053
CCCACUGCACCACUUACUGUCU--GUCUGCCAGUGUUGAAAAGCGCCAAGGGGUGGGGCUGGCAGGCAGGCAGGCAGUUAGUUUAUCGCGCUUUCGAAAUCUGAGGAACUAGCAGGAU--
....((((...(((..((((((--(((((((((((((....)))(((....)))...))))))))))))))))..)))((((((.(((.............))).))))))))))...-- ( -47.82)
>DroSec_CAF1 61553 112 - 1
CCCACUGCACCACUUACUGUCU--GUCUGCCAGUGUUGAAAAGCGCCCAGGGGUGGGGCUGGCAGG----CAGGCAGUUAGUUUAUCGCGCUUUCGAAAUCUGAGGAACUAGCAGUAU--
...(((((.......(((((((--(((((((((((((....))).((((....)))))))))))))----))))))))((((((.(((.............))).)))))))))))..-- ( -50.32)
>DroSim_CAF1 39042 112 - 1
CCCACUGCACCACUUACUGUCU--GUCUGCCAGUGUUGAAAAGCGCCCAGGGGUGGGGCUGGCAGG----CAGGCAGUUAGUUUAUCGCGCUUUCGAAAUCUGAGGAACUAGCAGGAU--
....((((.......(((((((--(((((((((((((....))).((((....)))))))))))))----))))))))((((((.(((.............))).))))))))))...-- ( -49.42)
>DroEre_CAF1 38437 113 - 1
CCCACUGCACCACUUACUGUCU--GUCUGCCAGUGCUGAAAGGCGCCCAGGGGCGGGGG-GGCUGG----CGGGCGGUUAGUUUAUCGCGCUUUCGAAAUCUGAGGAACUGGCAGCAUGC
..................((.(--(.(((((((((((....))).((((((..((..((-.((.((----..(((.....)))..)))).))..))...)))).)).)))))))))).)) ( -42.20)
>DroAna_CAF1 32903 108 - 1
CUCUACACACCACUUACUGCCUGUGUCUGCCAGUGUUGAAAAGUGCCCAGAGGAAAAGG-GGCGGG-----GUG----CAGUUUAUCGCGCUCACUAAAUCUGAAGAGCCGGCAGGAU--
................(((((.((.(((..(((.(((....(((((((..........)-))).((-----(((----(........))))))))).)))))).))))).)))))...-- ( -30.60)
>consensus
CCCACUGCACCACUUACUGUCU__GUCUGCCAGUGUUGAAAAGCGCCCAGGGGUGGGGCUGGCAGG____CAGGCAGUUAGUUUAUCGCGCUUUCGAAAUCUGAGGAACUAGCAGGAU__
....((((.......(((((((...((((((((((((....)))(((....)))...))))))))).....)))))))((((((.(((.............))).))))))))))..... (-28.18 = -29.38 +   1.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,931,917 – 15,932,035
Length 118
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 82.60
Mean single sequence MFE -40.17
Consensus MFE -29.01
Energy contribution -28.82
Covariance contribution -0.19
Combinations/Pair 1.22
Mean z-score -1.91
Structure conservation index 0.72
SVM decision value 0.72
SVM RNA-class probability 0.831910
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15931917 118 - 27905053
CCCACCGAGCCACCCAAUAUCAGCCAACCUUACACCACCACCCACUGCACCACUUACUGUCUGUCUGCCAGUGUUGAAAAGCGCCAAGGGGUGGGGCUGGCAGGCAGGCAGGCAGUUA
...........................................(((((........(((((((((((((((((((....)))(((....)))...))))))))))))))))))))).. ( -39.20)
>DroSec_CAF1 61591 102 - 1
CC------------CACCAUCAGACAACCUUACACCACCACCCACUGCACCACUUACUGUCUGUCUGCCAGUGUUGAAAAGCGCCCAGGGGUGGGGCUGGCAGG----CAGGCAGUUA
..------------.........................................((((((((((((((((((((....))).((((....)))))))))))))----)))))))).. ( -38.90)
>DroSim_CAF1 39080 114 - 1
CCCACCAAGCCACCCACCAUCAGACAACCUUACACCACCACCCACUGCACCACUUACUGUCUGUCUGCCAGUGUUGAAAAGCGCCCAGGGGUGGGGCUGGCAGG----CAGGCAGUUA
.......................................................((((((((((((((((((((....))).((((....)))))))))))))----)))))))).. ( -38.90)
>DroEre_CAF1 38477 100 - 1
CC------------CACCGGCAGCCAACCUU-CAAUGCCGCCCACUGCACCACUUACUGUCUGUCUGCCAGUGCUGAAAGGCGCCCAGGGGCGGGGG-GGCUGG----CGGGCGGUUA
..------------.((((.(.((((.((((-(....((((((.(((........((((.(.....).))))(((....)))...))))))))))))-)).)))----).).)))).. ( -43.70)
>consensus
CC____________CACCAUCAGACAACCUUACACCACCACCCACUGCACCACUUACUGUCUGUCUGCCAGUGUUGAAAAGCGCCCAGGGGUGGGGCUGGCAGG____CAGGCAGUUA
.......................................................((((((((((((((((((((....)))(((....)))...)))))))))....)))))))).. (-29.01 = -28.82 +  -0.19)

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 12:11:47 2006