Locus 4988

Sequence ID 3R_DroMel_CAF1
Location 13,136,853 – 13,137,048
Length 195
Max. P 0.971719
window8156 window8157 window8158

overview

Window 6

Location 13,136,853 – 13,136,947
Length 94
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 82.13
Mean single sequence MFE -34.35
Consensus MFE -27.43
Energy contribution -27.77
Covariance contribution 0.33
Combinations/Pair 1.05
Mean z-score -1.47
Structure conservation index 0.80
SVM decision value 0.24
SVM RNA-class probability 0.649325
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13136853 94 + 27905053
ACCCGCC---UUU----------CACUUUCCACCUGCCAGUCGCAGGCAGGUGA------GCGAGGCAAAGUUGGACCAGGUUGGUGCAUUCUAGCGCUCACAAAGGUCACUU
....(((---((.----------..((...((((((((.......)))))))))------).))))).......((((..((.(((((......))))).))...)))).... ( -35.60)
>DroPse_CAF1 155545 101 + 1
UUCCGCCACCAUU------------CCAUCCGCCUGCCAGUUGCAUGCAGGCGAGGGCGAGCCGGCCAAAGUUGGACCAGGUUGGUGCAUUCUAGCGCUCACAAAGGUCACUU
....(((......------------.....(((((((.........)))))))..((....)))))........((((..((.(((((......))))).))...)))).... ( -33.90)
>DroEre_CAF1 156554 94 + 1
ACCCGCC---UUU----------CACUUUCCACCUGCCAGUCGCAGGCAGGUGA------GCGAGGCAAAGUUGGACCAGGUUGGUGCAUUCUAGCGCUCACAAAGGUCACUU
....(((---((.----------..((...((((((((.......)))))))))------).))))).......((((..((.(((((......))))).))...)))).... ( -35.60)
>DroYak_CAF1 164659 94 + 1
ACCCGCC---UUU----------CACUUUCCACCUGCCAGUCGCAGGCAGGUGA------GCGAGGCAAAGUUGGACCAGGUUGGUGCAUUCUAGCGCUCACAAAGGUCACUU
....(((---((.----------..((...((((((((.......)))))))))------).))))).......((((..((.(((((......))))).))...)))).... ( -35.60)
>DroAna_CAF1 155763 104 + 1
UAGAACC---UUUUCCUUCUCGGCACUUUCCACCUGCCAGCAGCAGGCAGGCAA------GCAAGGUAAAGUUGGACCAGGUUGGUGCAUUCUAGCGCUCACAAAGGUCACUU
......(---(((.((((((.((......)).((((((.......))))))..)------).)))).))))...((((..((.(((((......))))).))...)))).... ( -31.50)
>DroPer_CAF1 221996 101 + 1
UUCCGCCACCAUU------------CCAUCCGCCUGCCAGUUGCAUGCAGGCGAGGGCGAGCCGGCCAAAGUUGGACCAGGUUGGUGCAUUCUAGCGCUCACAAAGGUCACUU
....(((......------------.....(((((((.........)))))))..((....)))))........((((..((.(((((......))))).))...)))).... ( -33.90)
>consensus
ACCCGCC___UUU__________CACUUUCCACCUGCCAGUCGCAGGCAGGCGA______GCGAGGCAAAGUUGGACCAGGUUGGUGCAUUCUAGCGCUCACAAAGGUCACUU
..............................((((((((.......)))))))).....................((((..((.(((((......))))).))...)))).... (-27.43 = -27.77 +   0.33)

alignment

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secondary structure

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Window 7

Location 13,136,853 – 13,136,947
Length 94
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 82.13
Mean single sequence MFE -36.10
Consensus MFE -25.13
Energy contribution -24.85
Covariance contribution -0.28
Combinations/Pair 1.14
Mean z-score -1.39
Structure conservation index 0.70
SVM decision value -0.02
SVM RNA-class probability 0.523531
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13136853 94 - 27905053
AAGUGACCUUUGUGAGCGCUAGAAUGCACCAACCUGGUCCAACUUUGCCUCGC------UCACCUGCCUGCGACUGGCAGGUGGAAAGUG----------AAA---GGCGGGU
..(.((((....((.(.((......)).)))....)))))...((((((((((------(((((((((.......))))))))...))))----------)..---)))))). ( -35.40)
>DroPse_CAF1 155545 101 - 1
AAGUGACCUUUGUGAGCGCUAGAAUGCACCAACCUGGUCCAACUUUGGCCGGCUCGCCCUCGCCUGCAUGCAACUGGCAGGCGGAUGG------------AAUGGUGGCGGAA
..((.(((...((((((((((((.((.(((.....))).))..))))))..))))))((((((((((.........))))))))..))------------...))).)).... ( -38.70)
>DroEre_CAF1 156554 94 - 1
AAGUGACCUUUGUGAGCGCUAGAAUGCACCAACCUGGUCCAACUUUGCCUCGC------UCACCUGCCUGCGACUGGCAGGUGGAAAGUG----------AAA---GGCGGGU
..(.((((....((.(.((......)).)))....)))))...((((((((((------(((((((((.......))))))))...))))----------)..---)))))). ( -35.40)
>DroYak_CAF1 164659 94 - 1
AAGUGACCUUUGUGAGCGCUAGAAUGCACCAACCUGGUCCAACUUUGCCUCGC------UCACCUGCCUGCGACUGGCAGGUGGAAAGUG----------AAA---GGCGGGU
..(.((((....((.(.((......)).)))....)))))...((((((((((------(((((((((.......))))))))...))))----------)..---)))))). ( -35.40)
>DroAna_CAF1 155763 104 - 1
AAGUGACCUUUGUGAGCGCUAGAAUGCACCAACCUGGUCCAACUUUACCUUGC------UUGCCUGCCUGCUGCUGGCAGGUGGAAAGUGCCGAGAAGGAAAA---GGUUCUA
..(.((((....((.(.((......)).)))....)))))..((((.((((.(------(((((((((.......)))))))((......))))))))).)))---)...... ( -33.00)
>DroPer_CAF1 221996 101 - 1
AAGUGACCUUUGUGAGCGCUAGAAUGCACCAACCUGGUCCAACUUUGGCCGGCUCGCCCUCGCCUGCAUGCAACUGGCAGGCGGAUGG------------AAUGGUGGCGGAA
..((.(((...((((((((((((.((.(((.....))).))..))))))..))))))((((((((((.........))))))))..))------------...))).)).... ( -38.70)
>consensus
AAGUGACCUUUGUGAGCGCUAGAAUGCACCAACCUGGUCCAACUUUGCCUCGC______UCACCUGCCUGCGACUGGCAGGUGGAAAGUG__________AAA___GGCGGGA
((((((((....((.(.((......)).)))....))))..))))..............(((((((((.......)))))))))............................. (-25.13 = -24.85 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,136,947 – 13,137,048
Length 101
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 79.62
Mean single sequence MFE -19.82
Consensus MFE -17.88
Energy contribution -18.12
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.90
SVM decision value 1.68
SVM RNA-class probability 0.971719
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13136947 101 - 27905053
ACCUUCCCAUCCACCUUCACAUCCACAUCCACAUU-CACGACCACGUCCACAUCCACCUGCAGCUGCACGGCAUCGUUUGCCCUGAUAGUUGCUCGUUGACU
...................................-................((.((..(((((((((.((((.....)))).)).)))))))..)).)).. ( -18.90)
>DroSec_CAF1 166301 83 - 1
ACCUU------------CACCUCCGCAUC-------CACGACCACGUCCACAUCCACCUGCAGCUGCACGGCAUCGUUUGCCCUGAUAGUUGCUCGUUGACU
.....------------..........((-------.((((....(....)........(((((((((.((((.....)))).)).))))))))))).)).. ( -19.30)
>DroSim_CAF1 151321 83 - 1
ACCUU------------CACAUCCGCAUC-------CACGACCACGUCCACAUCCACCUGCAGCUGCACGGCAUCGUUUGCCCUGAUAGUUGCUCGUUGACU
.....------------..........((-------.((((....(....)........(((((((((.((((.....)))).)).))))))))))).)).. ( -19.30)
>DroEre_CAF1 156648 89 - 1
ACGUGCACAGCCACCUGCACUU-------------CCACUUCCACAUCCACAUCCACCUGCAGCAGCACGGCAUCGUUUGCCCUGAUAGUUGCUCGUUGACU
..(((((........)))))..-------------.................((.((..(((((..((.((((.....)))).))...)))))..)).)).. ( -21.80)
>consensus
ACCUU____________CACAUCCGCAUC_______CACGACCACGUCCACAUCCACCUGCAGCUGCACGGCAUCGUUUGCCCUGAUAGUUGCUCGUUGACU
....................................................((.((..(((((((((.((((.....)))).)).)))))))..)).)).. (-17.88 = -18.12 +   0.25)

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 11:43:42 2006