Locus 1229

Sequence ID X_DroMel_CAF1
Location 3,661,547 – 3,661,760
Length 213
Max. P 0.973844
window1979 window1980 window1981

overview

Window 9

Location 3,661,547 – 3,661,651
Length 104
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 85.87
Mean single sequence MFE -27.90
Consensus MFE -21.06
Energy contribution -22.50
Covariance contribution 1.44
Combinations/Pair 1.11
Mean z-score -2.70
Structure conservation index 0.75
SVM decision value 1.72
SVM RNA-class probability 0.973844
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3661547 104 - 22224390
CGAUACAGAAUACAUC----UAUUGAUAGGCAUGGAUCGAUGUUUUUGUAUAGUGGGUGUGUUAUGCAAAUGCCGCGCAUAAUAACCCCAGUAUAUGCAAAAAAAAAA
((((.((......(((----....))).....)).))))...((((((((((.((((..((((((((.........))))))))..))))...))))))))))..... ( -27.90)
>DroSec_CAF1 13480 98 - 1
CGAUACAGAAUUCAUC----UAUUGAGAGGCAUGGACCGAUGAUUUUGGAUAGUGGGUGUGUUAUGCAAAUGCCGCGCAUAAUCACCCCAGUAUAUGCAAAA------
..........((((..----...))))..((((...((((.....))))(((.((((.(((((((((.........)))))).))))))).)))))))....------ ( -26.60)
>DroEre_CAF1 14356 102 - 1
CGAUACAGAAUACAAC----UAUUGAUAGACAUGGAUCGAUGUUUUUGGAUAGUGGGUGUGUUAUGCAAAUGCCACGCAUAAUAAACCCAGUAUAUCCGAAAUAAA--
................----(((((((........))))))).(((((((((.(((((.((((((((.........)))))))).)))))...)))))))))....-- ( -28.90)
>DroYak_CAF1 14438 106 - 1
CGAUACGGAAUACAUCUAUCUAUUGAUAGACAUGGAUCAAUGUUUUUGGAUAGUGGGUGUGUUAUGCAAAUGCCACGCAUAAAAGACCCAGUAUAUACGAAUUAAA--
.(((.((..((((..(((((((.....((((((......)))))).)))))))(((((.(.((((((.........)))))).).)))))))))...)).)))...-- ( -28.20)
>consensus
CGAUACAGAAUACAUC____UAUUGAUAGACAUGGAUCGAUGUUUUUGGAUAGUGGGUGUGUUAUGCAAAUGCCACGCAUAAUAAACCCAGUAUAUGCAAAAUAAA__
....................(((((((........)))))))..((((((((.(((((.((((((((.........)))))))).)))))...))))))))....... (-21.06 = -22.50 +   1.44)

alignment

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secondary structure

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Window 0

Location 3,661,620 – 3,661,731
Length 111
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 89.97
Mean single sequence MFE -33.20
Consensus MFE -26.90
Energy contribution -26.28
Covariance contribution -0.62
Combinations/Pair 1.19
Mean z-score -1.62
Structure conservation index 0.81
SVM decision value 0.32
SVM RNA-class probability 0.687477
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3661620 111 + 22224390
CCAUGCCUAUCAAUA----GAUGUAUUCUGUAUCGCCGGAUGGAUCUUGUUAGGAGCACCUAGCUUGGAUUUAUGGCUAGUGCCAUAAUUAACUGGUCAAAGGUGUUGCUAAUGG
((((.((.....(((----((.....)))))......))))))...(..((((.(((((((.(((.(...(((((((....)))))))....).)))...))))))).))))..) ( -34.60)
>DroSec_CAF1 13547 111 + 1
CCAUGCCUCUCAAUA----GAUGAAUUCUGUAUCGCCGGAUGGAUCUUGUUAGGAGCACCUAGCUUGGAUUUAUGGCCAGUGCCAUAAUUAACUGGUCGAAGGUGUUGCUAAUGA
((((.((.....(((----((.....)))))......))))))...(..((((.(((((((.(((.(...(((((((....)))))))....).)))...))))))).))))..) ( -33.40)
>DroEre_CAF1 14427 111 + 1
CCAUGUCUAUCAAUA----GUUGUAUUCUGUAUCGCCGGAUAGAUCUUGUUAGGAGCACCCAGCUUCGAUUUAUGGCCGGUACCAUAAUUAACUGGUCGAAGGUGUUGCUAAUGG
((..(((((((....----((.((((...)))).))..)))))))...(((((.((((((....((((((((((((......)))))).......)))))))))))).))))))) ( -29.71)
>DroYak_CAF1 14509 115 + 1
CCAUGUCUAUCAAUAGAUAGAUGUAUUCCGUAUCGCCGGAUAGAUCUCGUUAGGAGUAUCCAGCUUGGAUUUAUGGCUGGUGCCAUAAUUAACUAGUCGAAGGUGUUGCUAAUGG
(((((((((((....))))))).......(((.(((((((((..(((.....))).))))).(((.(...(((((((....)))))))....).)))....)))).)))..)))) ( -35.10)
>consensus
CCAUGCCUAUCAAUA____GAUGUAUUCUGUAUCGCCGGAUAGAUCUUGUUAGGAGCACCCAGCUUGGAUUUAUGGCCAGUGCCAUAAUUAACUGGUCGAAGGUGUUGCUAAUGG
.............................(((.((((..(((((((..((((((....))))))...)))))))(((((((..........)))))))...)))).)))...... (-26.90 = -26.28 +  -0.62)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,661,651 – 3,661,760
Length 109
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 92.81
Mean single sequence MFE -33.41
Consensus MFE -30.01
Energy contribution -28.95
Covariance contribution -1.06
Combinations/Pair 1.21
Mean z-score -1.46
Structure conservation index 0.90
SVM decision value 0.22
SVM RNA-class probability 0.641799
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3661651 109 + 22224390
CCGGAUGGAUCUUGUUAGGAGCACCUAGCUUGGAUUUAUGGCUAGUGCCAUAAUUAACUGGUCAAAGGUGUUGCUAAUGGCCAGUGCCAAACCGAUUCACUAAUGAGUC
..((.(((((((.((((((....))))))..))))(((((((....)))))))...((((((((..((.....))..)))))))).)))..))((((((....)))))) ( -37.40)
>DroSec_CAF1 13578 109 + 1
CCGGAUGGAUCUUGUUAGGAGCACCUAGCUUGGAUUUAUGGCCAGUGCCAUAAUUAACUGGUCGAAGGUGUUGCUAAUGACCAGUGCCAAACCGAUUCACUAAUGAGUC
..((.(((((((.((((((....))))))..))))(((((((....)))))))...((((((((..((.....))..)))))))).)))..))((((((....)))))) ( -36.10)
>DroEre_CAF1 14458 109 + 1
CCGGAUAGAUCUUGUUAGGAGCACCCAGCUUCGAUUUAUGGCCGGUACCAUAAUUAACUGGUCGAAGGUGUUGCUAAUGGCCAGUGCCAAACCGAUUCGCUAAUGAGUC
..((.........(((((.((((((....((((((((((((......)))))).......)))))))))))).)))))(((....)))...))((((((....)))))) ( -30.91)
>DroYak_CAF1 14544 109 + 1
CCGGAUAGAUCUCGUUAGGAGUAUCCAGCUUGGAUUUAUGGCUGGUGCCAUAAUUAACUAGUCGAAGGUGUUGCUAAUGGCCAGUGUCAAACCGAUUCGCUAAUGAGUC
..((...(((((.((((..((((..((.(((.((((((((((....))))))).......))).))).)).))))..)))).)).)))...))((((((....)))))) ( -29.21)
>consensus
CCGGAUAGAUCUUGUUAGGAGCACCCAGCUUGGAUUUAUGGCCAGUGCCAUAAUUAACUGGUCGAAGGUGUUGCUAAUGGCCAGUGCCAAACCGAUUCACUAAUGAGUC
..(((((((((..((((((....))))))...)))))))(((((((..........)))))))...((..(((........)))..))...))((((((....)))))) (-30.01 = -28.95 +  -1.06)

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 10:04:32 2006