Locus 5424

Sequence ID 3R_DroMel_CAF1
Location 14,306,299 – 14,306,440
Length 141
Max. P 0.998264
window8826 window8827 window8828

overview

Window 6

Location 14,306,299 – 14,306,419
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 97.50
Mean single sequence MFE -32.85
Consensus MFE -30.66
Energy contribution -30.68
Covariance contribution 0.03
Combinations/Pair 1.03
Mean z-score -1.22
Structure conservation index 0.93
SVM decision value 0.95
SVM RNA-class probability 0.887181
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14306299 120 + 27905053
GAAACGCGUGCCACAACGUUGCGGUUGCAGUUGUUUUUAGCGAGUGUUCGUUGCAAAUGCUGCAAAUAAUGCUAAAAGUCUAAAAAGAACACGUCCAGCAACAACUUAGACGACGCGACG
....(((((........(((((((.((..(((.((((((((.((((((..(((((.....)))))..))))))....).))))))).))).)).)).)))))..(......))))))... ( -32.40)
>DroEre_CAF1 88341 120 + 1
GAAACGCGUGCCACAACGUUGCGGUUGCAGUUGUUUUUAGCGAGUGUUCGUUGCAAAUGCUGCAAAUAAUGCUAAAAGUCUAAAAAGAACACGUCCAGCAACAACUUAGACGACGCGACG
....(((((........(((((((.((..(((.((((((((.((((((..(((((.....)))))..))))))....).))))))).))).)).)).)))))..(......))))))... ( -32.40)
>DroWil_CAF1 95620 116 + 1
GAAACGCGUGCCACAACGUUGCGGUUGCAGUUGUUUUUAGCGAGUGUUCGUUGCAAAUGCUGCAAAUAAUGCUAAAAGUCUAAAAAGAACACGUCCAGCAACAACUUCGGU----UGGCG
.........(((.....(((((((.((..(((.((((((((.((((((..(((((.....)))))..))))))....).))))))).))).)).)).)))))(((....))----)))). ( -35.10)
>DroYak_CAF1 83547 120 + 1
GAAACGCGUGCCACAACGUUGCGGUUGCAGUUGUUUUUAGCGAGUGUUCGUUGCAAAUGCUGCAAAUAAUGCUAAAAGUCUAAAAAGAACACGUCCAGCAACAACUUAGACGACGCGACG
....(((((........(((((((.((..(((.((((((((.((((((..(((((.....)))))..))))))....).))))))).))).)).)).)))))..(......))))))... ( -32.40)
>DroAna_CAF1 77341 120 + 1
GAAACGCGUGCCACAACGUUGCGGUUGCAGUUGUUUUUAGCGAGUGUUCGUUGCAAAUGCUGCAAAUAAUGCUAAAAGUCUAAAAAGAACACGUCCAGCAACAACUUAGACGACGCGACG
....(((((........(((((((.((..(((.((((((((.((((((..(((((.....)))))..))))))....).))))))).))).)).)).)))))..(......))))))... ( -32.40)
>DroPer_CAF1 94507 120 + 1
GAAACGCGUGCCACAACGUUGCGGUUGCAGUUGUUUUUAGCGAGUGUUCGUUGCAAAUGCUGCAAAUAAUGCUAAAAGUCUAAAAAGAACACGUCCAGCAACAACUUAGACGACGCGACG
....(((((........(((((((.((..(((.((((((((.((((((..(((((.....)))))..))))))....).))))))).))).)).)).)))))..(......))))))... ( -32.40)
>consensus
GAAACGCGUGCCACAACGUUGCGGUUGCAGUUGUUUUUAGCGAGUGUUCGUUGCAAAUGCUGCAAAUAAUGCUAAAAGUCUAAAAAGAACACGUCCAGCAACAACUUAGACGACGCGACG
....(((((......))(((((((.((..(((.((((((((.((((((..(((((.....)))))..))))))....).))))))).))).)).)).)))))............)))... (-30.66 = -30.68 +   0.03)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,306,299 – 14,306,419
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 97.50
Mean single sequence MFE -35.20
Consensus MFE -33.12
Energy contribution -33.82
Covariance contribution 0.70
Combinations/Pair 1.03
Mean z-score -2.02
Structure conservation index 0.94
SVM decision value 3.05
SVM RNA-class probability 0.998264
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14306299 120 - 27905053
CGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCGCUAAAAACAACUGCAACCGCAACGUUGUGGCACGCGUUUC
...(((((.(((..(((((((..(((..((((((..............(((.....))).((....))...))))))...)))..)))))))(((((......))))))))))))).... ( -35.90)
>DroEre_CAF1 88341 120 - 1
CGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCGCUAAAAACAACUGCAACCGCAACGUUGUGGCACGCGUUUC
...(((((.(((..(((((((..(((..((((((..............(((.....))).((....))...))))))...)))..)))))))(((((......))))))))))))).... ( -35.90)
>DroWil_CAF1 95620 116 - 1
CGCCA----ACCGAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCGCUAAAAACAACUGCAACCGCAACGUUGUGGCACGCGUUUC
.(((.----.....(((((((..(((..((((((..............(((.....))).((....))...))))))...)))..)))))))(((((......))))))))......... ( -31.70)
>DroYak_CAF1 83547 120 - 1
CGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCGCUAAAAACAACUGCAACCGCAACGUUGUGGCACGCGUUUC
...(((((.(((..(((((((..(((..((((((..............(((.....))).((....))...))))))...)))..)))))))(((((......))))))))))))).... ( -35.90)
>DroAna_CAF1 77341 120 - 1
CGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCGCUAAAAACAACUGCAACCGCAACGUUGUGGCACGCGUUUC
...(((((.(((..(((((((..(((..((((((..............(((.....))).((....))...))))))...)))..)))))))(((((......))))))))))))).... ( -35.90)
>DroPer_CAF1 94507 120 - 1
CGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCGCUAAAAACAACUGCAACCGCAACGUUGUGGCACGCGUUUC
...(((((.(((..(((((((..(((..((((((..............(((.....))).((....))...))))))...)))..)))))))(((((......))))))))))))).... ( -35.90)
>consensus
CGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCGCUAAAAACAACUGCAACCGCAACGUUGUGGCACGCGUUUC
...(((((.(((..(((((((..(((..((((((..............(((.....))).((....))...))))))...)))..)))))))(((((......))))))))))))).... (-33.12 = -33.82 +   0.70)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,306,339 – 14,306,440
Length 101
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 93.34
Mean single sequence MFE -36.72
Consensus MFE -29.58
Energy contribution -29.67
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -2.76
Structure conservation index 0.81
SVM decision value 0.81
SVM RNA-class probability 0.857459
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14306339 101 - 27905053
CU-----CUGCCA--GCGGCGACUGCGACGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCG
..-----...(((--(((((((((((((((...))))))...))))))))))))..((((((..............(((.....))).((....))...))))))... ( -38.20)
>DroPse_CAF1 91976 107 - 1
CUUGCGACGGCCGAGGCAGCGAC-GCGACGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCG
((.((((((((..((...(((((-(((....))))))))))..)))))))).))..((((((..............(((.....))).((....))...))))))... ( -39.10)
>DroSim_CAF1 78066 101 - 1
CU-----CUGCCA--GCGGCGACUGCGACGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCG
..-----...(((--(((((((((((((((...))))))...))))))))))))..((((((..............(((.....))).((....))...))))))... ( -38.20)
>DroYak_CAF1 83587 101 - 1
CU-----CUGCCA--GCGGCGACUGCGACGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCG
..-----...(((--(((((((((((((((...))))))...))))))))))))..((((((..............(((.....))).((....))...))))))... ( -38.20)
>DroAna_CAF1 77381 101 - 1
CU-----CUGCCG--ACUUCGACAGCGACGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCG
.(-----((((((--((((((((.(((....)))))))...))))))..)).))).((((((..............(((.....))).((....))...))))))... ( -27.50)
>DroPer_CAF1 94547 107 - 1
CUUGCGACGGCCGAGGCAGCGAC-GCGACGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCG
((.((((((((..((...(((((-(((....))))))))))..)))))))).))..((((((..............(((.....))).((....))...))))))... ( -39.10)
>consensus
CU_____CUGCCA__GCGGCGACUGCGACGUCGCGUCGUCUAAGUUGUUGCUGGACGUGUUCUUUUUAGACUUUUAGCAUUAUUUGCAGCAUUUGCAACGAACACUCG
..........(((..((((((((.((((((...))))))....)))))))))))..((((((..............(((.....))).((....))...))))))... (-29.58 = -29.67 +   0.08)

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 11:54:21 2006