Locus 2812

Sequence ID X_DroMel_CAF1
Location 7,518,885 – 7,519,018
Length 133
Max. P 0.949951
window4614 window4615 window4616

overview

Window 4

Location 7,518,885 – 7,518,999
Length 114
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 82.68
Mean single sequence MFE -57.73
Consensus MFE -43.28
Energy contribution -43.47
Covariance contribution 0.19
Combinations/Pair 1.20
Mean z-score -1.70
Structure conservation index 0.75
SVM decision value 0.38
SVM RNA-class probability 0.714351
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7518885 114 + 22224390
UUCCCUAUCCGCCGUACUUUGCUGCCGCUGCCAUUUUGGGUCGCAGUCUGGCGGGGAUUCCCGGUGCGGCAGCGGCCGCUGGAGCAGCUGCAGCA---GCCGCCGCAGUUGGCGCCU
.........(((((.(((..((((((((.((((..(((.....)))..))))(((....)))...))))))))(((.((((..((....))..))---)).)))..))))))))... ( -53.00)
>DroGri_CAF1 108225 117 + 1
UUCCCUACCCACCGUAUUUCGCUGCUGCUGCACUGCUCGGUCGCAGCCUGGCCGGCAUACCGGGUGCGGCGGCUGCUGCCGGUGCAGCGGCAGCUGCGGCUGCCGCAGUGGGUGCCG
.....(((((((........(((((((((((((....((((.((((((..((((.(((.....))))))))))))).)))))))))))))))))(((((...))))))))))))... ( -70.00)
>DroEre_CAF1 21314 114 + 1
UUCCCUAUCCGCCGUACUUUGCUGCCGCCGCCAUUUUGGGCCGCAGUCUGGCGGGGAUUCCCGGCGCAGCAGCGGCCGCUGGAGCAGCUGCAGCU---GCUGCCGCAGUUGGCGCCU
.........(((((.(((.((((((.(((((((..(((.....)))..))))(((....))))))))))))(((((......((((((....)))---))))))))))))))))... ( -55.40)
>DroYak_CAF1 15069 114 + 1
UACCCUAUCCGCCCUACUUUGCGGCCGCUGCCAUUUUGGGACGCAGUCUGGCGGGGAUUCCCGGUGCCGCUGCGGCCGCUGGAGCAGCUGCAGCA---GCUGCCGCUGUUGGCGCCA
.........((((..((...(((((.(((((((..(((.....)))..))))(((....)))......((((((((.((....)).)))))))))---)).))))).)).))))... ( -52.50)
>consensus
UUCCCUAUCCGCCGUACUUUGCUGCCGCUGCCAUUUUGGGUCGCAGUCUGGCGGGGAUUCCCGGUGCGGCAGCGGCCGCUGGAGCAGCUGCAGCA___GCUGCCGCAGUUGGCGCCU
.........(((((......(((((.(((((.......((((((.(((((.((((....)))).)).))).))))))......))))).(((((....))))).))))))))))... (-43.28 = -43.47 +   0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,518,885 – 7,518,999
Length 114
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 82.68
Mean single sequence MFE -56.83
Consensus MFE -43.74
Energy contribution -43.05
Covariance contribution -0.69
Combinations/Pair 1.22
Mean z-score -2.22
Structure conservation index 0.77
SVM decision value 1.40
SVM RNA-class probability 0.949951
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7518885 114 - 22224390
AGGCGCCAACUGCGGCGGC---UGCUGCAGCUGCUCCAGCGGCCGCUGCCGCACCGGGAAUCCCCGCCAGACUGCGACCCAAAAUGGCAGCGGCAGCAAAGUACGGCGGAUAGGGAA
...((((...((((((.((---((..((....))..)))).)))((((((((...(((....)))((((...((.....))...)))).))))))))...))).))))......... ( -54.60)
>DroGri_CAF1 108225 117 - 1
CGGCACCCACUGCGGCAGCCGCAGCUGCCGCUGCACCGGCAGCAGCCGCCGCACCCGGUAUGCCGGCCAGGCUGCGACCGAGCAGUGCAGCAGCAGCGAAAUACGGUGGGUAGGGAA
....(((((((((((...)))).(((((.((((((((((..((((((((((((.......)).))))..))))))..)))....))))))).))))).......)))))))...... ( -63.50)
>DroEre_CAF1 21314 114 - 1
AGGCGCCAACUGCGGCAGC---AGCUGCAGCUGCUCCAGCGGCCGCUGCUGCGCCGGGAAUCCCCGCCAGACUGCGGCCCAAAAUGGCGGCGGCAGCAAAGUACGGCGGAUAGGGAA
...((((..((((((.(((---(((....)))))))).))))..((((((((((((((....)))(((.......))).......))).)))))))).......))))......... ( -55.70)
>DroYak_CAF1 15069 114 - 1
UGGCGCCAACAGCGGCAGC---UGCUGCAGCUGCUCCAGCGGCCGCAGCGGCACCGGGAAUCCCCGCCAGACUGCGUCCCAAAAUGGCAGCGGCCGCAAAGUAGGGCGGAUAGGGUA
(((((((......))).((---((((((.(((((....))))).))))))))...(((....)))))))..((((...((.....))..))))((((........))))........ ( -53.50)
>consensus
AGGCGCCAACUGCGGCAGC___AGCUGCAGCUGCUCCAGCGGCCGCUGCCGCACCGGGAAUCCCCGCCAGACUGCGACCCAAAAUGGCAGCGGCAGCAAAGUACGGCGGAUAGGGAA
...((((....((((((((....))))).(((((....))))))))((((((..((((....))))...(.((((...........))))).))))))......))))......... (-43.74 = -43.05 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,518,925 – 7,519,018
Length 93
Sequences 3
Columns 93
Reading direction reverse
Mean pairwise identity 91.40
Mean single sequence MFE -42.77
Consensus MFE -35.72
Energy contribution -36.17
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.83
Structure conservation index 0.84
SVM decision value -0.08
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7518925 93 - 22224390
UGCAACUCAUCACCACCAGAGGCGCCAACUGCGGCGGCUGCUGCAGCUGCUCCAGCGGCCGCUGCCGCACCGGGAAUCCCCGCCAGACUGCGA
.(((..((.((.......))(((((.....(((((((((((((.((...)).))))))))))))).))...(((....)))))).)).))).. ( -39.50)
>DroEre_CAF1 21354 93 - 1
UGCAACUCAUCGCCGCCGGAGGCGCCAACUGCGGCAGCAGCUGCAGCUGCUCCAGCGGCCGCUGCUGCGCCGGGAAUCCCCGCCAGACUGCGG
.(((......((((......))))....(((((((.(((((.((.(((((....))))).)).))))))))(((....)))).)))..))).. ( -44.00)
>DroYak_CAF1 15109 93 - 1
UGCAACUCAUCACCGCCAGUGGCGCCAACAGCGGCAGCUGCUGCAGCUGCUCCAGCGGCCGCAGCGGCACCGGGAAUCCCCGCCAGACUGCGU
.............(((.(((((((((......))).((((((((.(((((....))))).))))))))...(((....))))))..)))))). ( -44.80)
>consensus
UGCAACUCAUCACCGCCAGAGGCGCCAACUGCGGCAGCUGCUGCAGCUGCUCCAGCGGCCGCUGCCGCACCGGGAAUCCCCGCCAGACUGCGA
.(((..((.....((((...))))........(((.(((((.((.(((((....))))).)).)))))...(((....)))))).)).))).. (-35.72 = -36.17 +   0.45)

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 10:44:09 2006