Locus 2216

Sequence ID 2R_DroMel_CAF1
Location 8,157,005 – 8,157,165
Length 160
Max. P 0.762130
window3650 window3651 window3652

overview

Window 0

Location 8,157,005 – 8,157,125
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.28
Mean single sequence MFE -32.18
Consensus MFE -19.11
Energy contribution -20.25
Covariance contribution 1.14
Combinations/Pair 1.24
Mean z-score -1.78
Structure conservation index 0.59
SVM decision value 0.19
SVM RNA-class probability 0.628064
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8157005 120 + 20766785
AACACGCCCAGGAAGAUGUUCUUGACCAGCUUCCACUUGCACACGCCCAGGCGGUCGGGCCACAGAUAGACGGUCUCCACGAAACUGGGCACAAAGAUGCCCAGCAGCGAGAAGAACACG
.....(((((((((....)))))((((.((........))....((....))))))))))..........((.(((.(.((...(((((((......)))))))...)).).)))...)) ( -38.20)
>DroVir_CAF1 7487 120 + 1
AAAACGCCCAAGAGAAUGUUCUUGAUCAGCUUCCACUUGCAGCAGCCCAGACGAUCGGGCCACAGAUAUACAGUCUCCACAAAGCUGGGCACAAAGAUGCCCAGCAGCGAGAAGAAGACG
........((((((....))))))....(((((..(((((....((((........))))...((((.....)))).......((((((((......)))))))).)))))..)))).). ( -38.80)
>DroPse_CAF1 4126 120 + 1
AGAAUGCCCAAAAUAAUAUUCUUUACCAUCUUCCAAUUGCACCAACCCAGACGAUCGGGAUAAAGGUAAACGGUCUCAACGAAGCUGGGAACAAAAAUGCCUAGCAGUGAGAAGAACACG
((((((..........))))))......(((((..(((((.....(((........)))....(((((.....(((((.......))))).......))))).)))))..)))))..... ( -25.20)
>DroGri_CAF1 5016 120 + 1
AAGAUGCCCAAAAGAACGUUCUUGAUCAGCUUCCAUUUGCACCAGCCGAGGCGAUCAGGCCACAGAUACACAGUCUCAAUGAAGCUGGGCACAAAUAUGCCCAGCAGCGAGAAAAACACA
....(((.........(((((((((((.(((((.....((....)).))))))))))))....((((.....)))).))))..((((((((......)))))))).)))........... ( -33.00)
>DroWil_CAF1 5913 117 + 1
AAUACGGCAAGCAAAAUAUUCUUAAUCAGUUUCCAUUUGCACCAUCCCAA---AUUGGGCCACAAGUAGACAGUCUCCACAACACUGGGCACAAAGAUACCCAGCAAGGAGAAGAACACA
.....(((..(((((.....((.....))......))))).(((......---..))))))....((......(((((......(((((..........)))))...))))).....)). ( -23.60)
>DroMoj_CAF1 7338 120 + 1
AAAACUCCCAACAAUAUGUUCUUGAUAAGCUUCCAUUUGCACCAGCCCAGACGAUCGGGCCACAGGUACACGGUCUCCACGAAGCUGGGCACAAAGAUGCCCAGCAGCGAAAAGAAGACG
................(((.((((....((........))....((((........))))..)))).)))..(((((..((..((((((((......))))))))..))....).)))). ( -34.30)
>consensus
AAAACGCCCAAAAAAAUGUUCUUGAUCAGCUUCCAUUUGCACCAGCCCAGACGAUCGGGCCACAGAUACACAGUCUCCACGAAGCUGGGCACAAAGAUGCCCAGCAGCGAGAAGAACACG
...................................(((((....((((........)))).......................((((((((......)))))))).)))))......... (-19.11 = -20.25 +   1.14)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,157,005 – 8,157,125
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.28
Mean single sequence MFE -40.20
Consensus MFE -27.27
Energy contribution -27.42
Covariance contribution 0.15
Combinations/Pair 1.39
Mean z-score -1.66
Structure conservation index 0.68
SVM decision value 0.50
SVM RNA-class probability 0.762130
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8157005 120 - 20766785
CGUGUUCUUCUCGCUGCUGGGCAUCUUUGUGCCCAGUUUCGUGGAGACCGUCUAUCUGUGGCCCGACCGCCUGGGCGUGUGCAAGUGGAAGCUGGUCAAGAACAUCUUCCUGGGCGUGUU
((.((.((((.((..(((((((((....)))))))))..)).))))))))..........((((((((((....))).))......(((((.((........)).))))))))))..... ( -46.40)
>DroVir_CAF1 7487 120 - 1
CGUCUUCUUCUCGCUGCUGGGCAUCUUUGUGCCCAGCUUUGUGGAGACUGUAUAUCUGUGGCCCGAUCGUCUGGGCUGCUGCAAGUGGAAGCUGAUCAAGAACAUUCUCUUGGGCGUUUU
((((..((((.(((((((((((((....)))))))))..((((....).........(..(((((......)))))..).))))))))))).....(((((......))))))))).... ( -45.60)
>DroPse_CAF1 4126 120 - 1
CGUGUUCUUCUCACUGCUAGGCAUUUUUGUUCCCAGCUUCGUUGAGACCGUUUACCUUUAUCCCGAUCGUCUGGGUUGGUGCAAUUGGAAGAUGGUAAAGAAUAUUAUUUUGGGCAUUCU
.(((((((((((((.(((.((.((....)).)).)))...).))))(((((((.((.....(((((((.....)))))).).....)).))))))).))))))))............... ( -28.30)
>DroGri_CAF1 5016 120 - 1
UGUGUUUUUCUCGCUGCUGGGCAUAUUUGUGCCCAGCUUCAUUGAGACUGUGUAUCUGUGGCCUGAUCGCCUCGGCUGGUGCAAAUGGAAGCUGAUCAAGAACGUUCUUUUGGGCAUCUU
...((((((.((((((((((((((....)))))))))((((((.....((..(..(((.(((......))).)))...)..))))))))))).))..))))))((((....))))..... ( -38.70)
>DroWil_CAF1 5913 117 - 1
UGUGUUCUUCUCCUUGCUGGGUAUCUUUGUGCCCAGUGUUGUGGAGACUGUCUACUUGUGGCCCAAU---UUGGGAUGGUGCAAAUGGAAACUGAUUAAGAAUAUUUUGCUUGCCGUAUU
.((((((((((((.((((((((((....))))))))))....)))))...((((.(((((.(((...---..)))....))))).)))).........)))))))............... ( -33.80)
>DroMoj_CAF1 7338 120 - 1
CGUCUUCUUUUCGCUGCUGGGCAUCUUUGUGCCCAGCUUCGUGGAGACCGUGUACCUGUGGCCCGAUCGUCUGGGCUGGUGCAAAUGGAAGCUUAUCAAGAACAUAUUGUUGGGAGUUUU
.((((((....((..(((((((((....)))))))))..)).))))))..((((((...((((((......))))))))))))....(((((((.((((.((....)).))))))))))) ( -48.40)
>consensus
CGUGUUCUUCUCGCUGCUGGGCAUCUUUGUGCCCAGCUUCGUGGAGACCGUCUACCUGUGGCCCGAUCGUCUGGGCUGGUGCAAAUGGAAGCUGAUCAAGAACAUUUUCUUGGGCGUUUU
.(((((((((((((.(((((((((....)))))))))...)).))))((((.((((...((((((......))))))))))...))))..........)))))))............... (-27.27 = -27.42 +   0.15)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,157,045 – 8,157,165
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.94
Mean single sequence MFE -43.22
Consensus MFE -28.93
Energy contribution -29.60
Covariance contribution 0.67
Combinations/Pair 1.30
Mean z-score -1.80
Structure conservation index 0.67
SVM decision value 0.05
SVM RNA-class probability 0.558534
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8157045 120 - 20766785
CUAUCCCCAACCUGGAACCCUUCAUCAGUCUGGUGGGUGCCGUGUUCUUCUCGCUGCUGGGCAUCUUUGUGCCCAGUUUCGUGGAGACCGUCUAUCUGUGGCCCGACCGCCUGGGCGUGU
........(((.(((.((((.(((......))).)))).))).)))((((.((..(((((((((....)))))))))..)).))))((((((((...((((.....)))).)))))).)) ( -44.40)
>DroVir_CAF1 7527 120 - 1
GCAUUCCCAACCUGGAACCGUUCAUCAGUUUGGUGGGCGCCGUCUUCUUCUCGCUGCUGGGCAUCUUUGUGCCCAGCUUUGUGGAGACUGUAUAUCUGUGGCCCGAUCGUCUGGGCUGCU
((.((((......))))..(((((((.....))))))))).((((((....((..(((((((((....)))))))))..)).)))))).........(..(((((......)))))..). ( -48.80)
>DroPse_CAF1 4166 120 - 1
CUAUUCCCAACCUGGAACCGUUCAUCAGCUUGGUGGGCGCCGUGUUCUUCUCACUGCUAGGCAUUUUUGUUCCCAGCUUCGUUGAGACCGUUUACCUUUAUCCCGAUCGUCUGGGUUGGU
......((((((..((..((((((((.....))))))))..(((..(.((((((.(((.((.((....)).)).)))...).)))))..)..)))..............))..)))))). ( -33.90)
>DroGri_CAF1 5056 120 - 1
GCAUACCCAAUCUGGAGCCGUUCAUCAGUUUGGUGGGCGCUGUGUUUUUCUCGCUGCUGGGCAUAUUUGUGCCCAGCUUCAUUGAGACUGUGUAUCUGUGGCCUGAUCGCCUCGGCUGGU
(((((.((.....))(((.(((((((.....)))))))))).......(((((..(((((((((....))))))))).....))))).)))))..(((.(((......))).)))..... ( -40.90)
>DroWil_CAF1 5953 117 - 1
CCAUUCCCGACUUGGAACCGUUCAUCAGUUUGGUGGGAGCUGUGUUCUUCUCCUUGCUGGGUAUCUUUGUGCCCAGUGUUGUGGAGACUGUCUACUUGUGGCCCAAU---UUGGGAUGGU
((((.(((((.((((..(((..((.((((((.....))))))))..).(((((.((((((((((....))))))))))....)))))............)).)))).---))))))))). ( -43.60)
>DroMoj_CAF1 7378 120 - 1
GCAUUCCCAAUCUGGAGCCAUUCAUCAGUCUCGUGGGCGCCGUCUUCUUUUCGCUGCUGGGCAUCUUUGUGCCCAGCUUCGUGGAGACCGUGUACCUGUGGCCCGAUCGUCUGGGCUGGU
....(((......)))((((...........((..(((((.((((((....((..(((((((((....)))))))))..)).)))))).)))..))..))(((((......))))))))) ( -47.70)
>consensus
CCAUUCCCAACCUGGAACCGUUCAUCAGUUUGGUGGGCGCCGUGUUCUUCUCGCUGCUGGGCAUCUUUGUGCCCAGCUUCGUGGAGACCGUCUACCUGUGGCCCGAUCGUCUGGGCUGGU
.....((((..((((.........)))).....))))........(((((.((..(((((((((....)))))))))..)).)))))............((((((......))))))... (-28.93 = -29.60 +   0.67)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:04 2006