Locus 4340

Sequence ID X_DroMel_CAF1
Location 11,409,961 – 11,410,121
Length 160
Max. P 0.634084
window7129 window7130 window7131

overview

Window 9

Location 11,409,961 – 11,410,081
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.83
Mean single sequence MFE -45.47
Consensus MFE -33.73
Energy contribution -33.77
Covariance contribution 0.03
Combinations/Pair 1.40
Mean z-score -1.10
Structure conservation index 0.74
SVM decision value 0.21
SVM RNA-class probability 0.634084
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11409961 120 - 22224390
ACGUUGGGCAACAGUAUGCUAGGUGGCGCCGCUAUGUUCAUUGGCGGUGGAUCGACACCGAGCAUGACGCCACCGAUGACGCCGUGGGCUAACUGCAACACGCCGCGAUACUUCUCUCCA
.((((((.......((((((.((((.((((((((.......))))))))......)))).))))))......)))))).(((.(((.((.....))....))).)))............. ( -42.12)
>DroVir_CAF1 1188 120 - 1
UCCUUGGGCAGCAGCAUGCUGGGCGGCGCUGCCAUCUUUAUGGGCGGCGGCUCCACGCCCAGCAUGACGCCGCCGAUGACGCCUUGGGUGAACUGCCAUACGCCGCGCUACUUCUCACCC
......(((.((..(((((((((((..((((((..((....))..))))))....)))))))))))..)).)))...........((((((...(((.......).))......)))))) ( -53.70)
>DroGri_CAF1 1221 120 - 1
UCCCUUGGUAGCAGUAUGCUUGGCGGUGCUGCCAUCUUUAUGGGCGGCGGUUCCACGCCCAGCAUGACGCCACCAAUGACGCCGUGGGUCAAUUGCCAUACGCCGCGCUACUUCUCACCG
......(((((.((((.((.(((((((((((((((....))))..((((......))))))))))(((.((((..........)))))))..........))))).)))))).)).))). ( -44.80)
>DroWil_CAF1 1196 120 - 1
ACACUGGGCAGCGCAAUGAUGGGCGGUGCUGCCAUGUUUAUUGGAGGCGGUUCCACGCCUAGCAUGACACCGCCAAUGACACCUUGGGUGAACUGUAAUACACCGAGGUACUUCUCUCCG
......((((((((...........)))))))).........(((((((((..((.((...)).))..))))))......((((((((((........))).))))))).......))). ( -42.30)
>DroMoj_CAF1 1245 120 - 1
UCUCUUGGCAGCAGCAUGCUGGGCGGUGCUGCCAUCUUUAUGGGCGGUGGCUCCACGCCAAGUAUGACGCCGCCAAUGACGCCAUGGGUGAAUUGCCAUACACCCCGUUACUUUUCGCCA
....(((((.((..((((((.((((..((..((..((....))..))..))....)))).))))))..)).)))))(((((....(((((..........)))))))))).......... ( -46.10)
>DroPer_CAF1 6744 120 - 1
ACCCUGGGAAGCAGCAUGCUGGGCGGCACGGCCAUGUUCAUUGGCGGUGGCUCUACGCCGAGCAUGACGCCUCCGAUGACACCGUGGGUGAACUGCAAUACGCCACGCUACUNNNNNNNN
......(((.((..((((((.((((.(((.((((.......)))).)))......)))).))))))..)).)))........((((((((........))).)))))............. ( -43.80)
>consensus
ACCCUGGGCAGCAGCAUGCUGGGCGGCGCUGCCAUCUUUAUGGGCGGCGGCUCCACGCCCAGCAUGACGCCGCCAAUGACGCCGUGGGUGAACUGCAAUACGCCGCGCUACUUCUCACCA
......(((.((..((((((.((((.(((((((.........)))))))......)))).))))))..)).)))........((((((((........))).)))))............. (-33.73 = -33.77 +   0.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,410,001 – 11,410,121
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.78
Mean single sequence MFE -49.32
Consensus MFE -32.17
Energy contribution -32.78
Covariance contribution 0.62
Combinations/Pair 1.28
Mean z-score -1.85
Structure conservation index 0.65
SVM decision value 0.05
SVM RNA-class probability 0.560508
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11410001 120 + 22224390
GUCAUCGGUGGCGUCAUGCUCGGUGUCGAUCCACCGCCAAUGAACAUAGCGGCGCCACCUAGCAUACUGUUGCCCAACGUAUUGGGAAUCUCGAUGCCGAAACGACACUUCUCUGCAUCG
(((...(((((((((..((((((((......)))))...........))))))))))))..((((...(...(((((....)))))...)...))))......))).............. ( -39.30)
>DroVir_CAF1 1228 120 + 1
GUCAUCGGCGGCGUCAUGCUGGGCGUGGAGCCGCCGCCCAUAAAGAUGGCAGCGCCGCCCAGCAUGCUGCUGCCCAAGGAGUUGGGUAUCUCGAUGCCGAAACGGCAUUUCUCGGCGUCC
......(((((((.(((((((((((.(..((.((((.(......).)))).)).)))))))))))).)))))))...(((((((((......(((((((...))))))).)))))).))) ( -60.00)
>DroGri_CAF1 1261 120 + 1
GUCAUUGGUGGCGUCAUGCUGGGCGUGGAACCGCCGCCCAUAAAGAUGGCAGCACCGCCAAGCAUACUGCUACCAAGGGAAUUGGGUAUCUCGAUGCCGAAACGGCACUUCUCGGCGUCC
(((.(((((((((..((((((((((((....)).))))).......((((......)))))))))..)))))))))((((((((((...)))))(((((...))))).)))))))).... ( -50.40)
>DroWil_CAF1 1236 120 + 1
GUCAUUGGCGGUGUCAUGCUAGGCGUGGAACCGCCUCCAAUAAACAUGGCAGCACCGCCCAUCAUUGCGCUGCCCAGUGUGUUCGGUAUCUCAAUGCCGAAUCGACAUUUCUCGGCAUCG
(((...((((((..(((((...)))))..))))))........((((((((((...((........))))))))..))))(((((((((....))))))))).))).............. ( -43.60)
>DroMoj_CAF1 1285 120 + 1
GUCAUUGGCGGCGUCAUACUUGGCGUGGAGCCACCGCCCAUAAAGAUGGCAGCACCGCCCAGCAUGCUGCUGCCAAGAGAAUUGGGAAUCUCAAUGCCAAAGCGACACUUCUCCGCGUCC
......((((((......((((((((((.((....))))))......(((((((..((...)).)))))))))))))...((((((...)))))))))...(((.........)))))). ( -40.10)
>DroAna_CAF1 8672 120 + 1
GUCAUCGGAGGCGUCAUGCUCGGCGUGGAGCCGCCGCCAAUGAACAUGGCGGCGCCGCCCAGCAUGCUACUGCCCAGCGUGUUGGGGAUCUCGAUGCCGAAGCGGCACUUCUCGGCGUCG
(.(..((((((.(((..(((((((((.(((.((((((((.......))))))))...(((((((((((.......)))))))))))...))).)))))).)))))).)))).))..).). ( -62.50)
>consensus
GUCAUCGGCGGCGUCAUGCUCGGCGUGGAGCCGCCGCCAAUAAACAUGGCAGCACCGCCCAGCAUGCUGCUGCCCAGCGAAUUGGGUAUCUCGAUGCCGAAACGACACUUCUCGGCGUCC
......(((((((..(((((.((((((....))).(((.........)))......))).)))))..)))))))..................((((((((...........)))))))). (-32.17 = -32.78 +   0.62)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,410,001 – 11,410,121
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.78
Mean single sequence MFE -49.17
Consensus MFE -36.82
Energy contribution -35.85
Covariance contribution -0.97
Combinations/Pair 1.39
Mean z-score -1.52
Structure conservation index 0.75
SVM decision value 0.10
SVM RNA-class probability 0.584745
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11410001 120 - 22224390
CGAUGCAGAGAAGUGUCGUUUCGGCAUCGAGAUUCCCAAUACGUUGGGCAACAGUAUGCUAGGUGGCGCCGCUAUGUUCAUUGGCGGUGGAUCGACACCGAGCAUGACGCCACCGAUGAC
((((((.((((.......)))).))))))............((((((.......((((((.((((.((((((((.......))))))))......)))).))))))......)))))).. ( -43.32)
>DroVir_CAF1 1228 120 - 1
GGACGCCGAGAAAUGCCGUUUCGGCAUCGAGAUACCCAACUCCUUGGGCAGCAGCAUGCUGGGCGGCGCUGCCAUCUUUAUGGGCGGCGGCUCCACGCCCAGCAUGACGCCGCCGAUGAC
....(((((((.......)))))))((((((........)))....(((.((..(((((((((((..((((((..((....))..))))))....)))))))))))..)).))))))... ( -58.10)
>DroGri_CAF1 1261 120 - 1
GGACGCCGAGAAGUGCCGUUUCGGCAUCGAGAUACCCAAUUCCCUUGGUAGCAGUAUGCUUGGCGGUGCUGCCAUCUUUAUGGGCGGCGGUUCCACGCCCAGCAUGACGCCACCAAUGAC
.((.(((((((.......))))))).))..............(.(((((.((..((((((.((((..((((((..((....))..))))))....)))).))))))..)).))))).).. ( -47.20)
>DroWil_CAF1 1236 120 - 1
CGAUGCCGAGAAAUGUCGAUUCGGCAUUGAGAUACCGAACACACUGGGCAGCGCAAUGAUGGGCGGUGCUGCCAUGUUUAUUGGAGGCGGUUCCACGCCUAGCAUGACACCGCCAAUGAC
((((((((((.........)))))))))).....((((..(((...((((((((...........)))))))).)))...)))).((((((..((.((...)).))..))))))...... ( -44.80)
>DroMoj_CAF1 1285 120 - 1
GGACGCGGAGAAGUGUCGCUUUGGCAUUGAGAUUCCCAAUUCUCUUGGCAGCAGCAUGCUGGGCGGUGCUGCCAUCUUUAUGGGCGGUGGCUCCACGCCAAGUAUGACGCCGCCAAUGAC
.(((((......)))))((....))...((((........))))(((((.((..((((((.((((..((..((..((....))..))..))....)))).))))))..)).))))).... ( -49.20)
>DroAna_CAF1 8672 120 - 1
CGACGCCGAGAAGUGCCGCUUCGGCAUCGAGAUCCCCAACACGCUGGGCAGUAGCAUGCUGGGCGGCGCCGCCAUGUUCAUUGGCGGCGGCUCCACGCCGAGCAUGACGCCUCCGAUGAC
....(((((..((.....)))))))((((((...((((......))))..((..((((((.((((.((((((((.......))))))))......)))).))))))..)))).))))... ( -52.40)
>consensus
CGACGCCGAGAAGUGCCGUUUCGGCAUCGAGAUACCCAACACCCUGGGCAGCAGCAUGCUGGGCGGCGCUGCCAUCUUUAUGGGCGGCGGCUCCACGCCCAGCAUGACGCCGCCAAUGAC
.((.((((((.........)))))).))..................(((.((..((((((.((((..((((((.((.....))..))))))....)))).))))))..)).)))...... (-36.82 = -35.85 +  -0.97)

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 11:22:34 2006