Locus 7861

Sequence ID 3R_DroMel_CAF1
Location 21,038,002 – 21,038,137
Length 135
Max. P 0.984842
window12663 window12664 window12665

overview

Window 3

Location 21,038,002 – 21,038,097
Length 95
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 72.93
Mean single sequence MFE -38.17
Consensus MFE -28.50
Energy contribution -27.64
Covariance contribution -0.85
Combinations/Pair 1.46
Mean z-score -1.81
Structure conservation index 0.75
SVM decision value 1.99
SVM RNA-class probability 0.984842
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21038002 95 + 27905053
GGAGGUGGUGCCCGCCGUC------------UCGGCGACCAGCAAUCAGAGCAUGCAGAUUGUGGUCUGCAUGCAGUUGGGUGAACCAGGAGAGCCGGAGUAUCCGG
((((((((...))))).((------------.((((..((..........((((((((((....)))))))))).....((....)).))...))))))...))).. ( -40.80)
>DroSim_CAF1 1418 95 + 1
GGAGGUGGUGCCCGCCGUC------------UCGGCGACCAGCAAUCAAAGCAUGCAGAUUGUGGUCUGCAUGCAGUUGGGUGAACCAGGAGAGCCGGAGUAUCCAG
((((((((...))))).((------------.((((..((......(((.((((((((((....))))))))))..)))((....)).))...))))))...))).. ( -40.90)
>DroEre_CAF1 1453 95 + 1
GCAGGUGAUGCCCGUCGUC------------UCAGCAACCAGCAAUCAAAGCAUGCAGAUUGUGGUCUGCAUGCAGUUGGGUGAACCAGGAGAGCCGGUGUAUCCGG
....(.((((((((.(.((------------((.((.....)).......((((((((((....))))))))))..((((.....))))))))).))).)))))).. ( -36.40)
>DroWil_CAF1 1662 95 + 1
GGUGGUAGAGCCGGGUCAG------------UCAUCAAGAACCAAUCAGAGUAUGCAGAUUAUAGUGUGCAUGCAACUUGGCGAGCCGGGAGUACCUACUUGGCCGG
((((((((..((.(((..(------------(((....((.....))...(((((((.((....)).)))))))....))))..))).)).....)))))..))).. ( -30.40)
>DroYak_CAF1 1438 95 + 1
GGAGGUGGUGCCCGUCGUC------------UCGGCCAGCAGCAAUCAGAGCAUGCAAAUUGUGGUCUGCAUGCAGUUGGGUGAACCGGGUGAGCCGCUGUAUCCGG
((((((((((((((..((.------------(((.(((((.(((..((((.(((.......))).))))..))).))))).))))))))))..))))))...))).. ( -40.30)
>DroAna_CAF1 1215 107 + 1
GGUCGUAGUCCCGCCGGUCAAGACUACGGACUCUAGAUCCAAUAACCAGAGCAUGCAGAUAAUCAUUUGCAUGCAGUUGGGAGAGCCAGGGGUACCUACCUGGCCGG
(..(((((((...........)))))))..).......((.....((((.((((((((((....))))))))))..))))..(.((((((........))))))))) ( -40.20)
>consensus
GGAGGUGGUGCCCGCCGUC____________UCGGCAACCAGCAAUCAGAGCAUGCAGAUUGUGGUCUGCAUGCAGUUGGGUGAACCAGGAGAGCCGGAGUAUCCGG
((((((...((((((((...............))))..............((((((((((....))))))))))....))))..))).((....))......))).. (-28.50 = -27.64 +  -0.85)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,038,002 – 21,038,097
Length 95
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 72.93
Mean single sequence MFE -32.32
Consensus MFE -19.24
Energy contribution -18.97
Covariance contribution -0.27
Combinations/Pair 1.52
Mean z-score -1.70
Structure conservation index 0.60
SVM decision value 1.07
SVM RNA-class probability 0.910650
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21038002 95 - 27905053
CCGGAUACUCCGGCUCUCCUGGUUCACCCAACUGCAUGCAGACCACAAUCUGCAUGCUCUGAUUGCUGGUCGCCGA------------GACGGCGGGCACCACCUCC
((((.....))))......((((...(((....(((((((((......))))))))).......((((.((.....------------))))))))).))))..... ( -34.80)
>DroSim_CAF1 1418 95 - 1
CUGGAUACUCCGGCUCUCCUGGUUCACCCAACUGCAUGCAGACCACAAUCUGCAUGCUUUGAUUGCUGGUCGCCGA------------GACGGCGGGCACCACCUCC
.(((.....(((((..((.(((.....)))...(((((((((......)))))))))...))..)))))((((((.------------..))))))...)))..... ( -34.70)
>DroEre_CAF1 1453 95 - 1
CCGGAUACACCGGCUCUCCUGGUUCACCCAACUGCAUGCAGACCACAAUCUGCAUGCUUUGAUUGCUGGUUGCUGA------------GACGACGGGCAUCACCUGC
..((....(((((.....)))))....))....(((((((((......)))))))))..((((.(((.((((....------------..)))).)))))))..... ( -32.20)
>DroWil_CAF1 1662 95 - 1
CCGGCCAAGUAGGUACUCCCGGCUCGCCAAGUUGCAUGCACACUAUAAUCUGCAUACUCUGAUUGGUUCUUGAUGA------------CUGACCCGGCUCUACCACC
...........((((...((((.(((((((...(.(((((..........))))).).....)))))((.....))------------..)).))))...))))... ( -20.20)
>DroYak_CAF1 1438 95 - 1
CCGGAUACAGCGGCUCACCCGGUUCACCCAACUGCAUGCAGACCACAAUUUGCAUGCUCUGAUUGCUGCUGGCCGA------------GACGACGGGCACCACCUCC
.(((...((((((((((...((....)).....(((((((((......)))))))))..)))..))))))).))).------------...((.((......)))). ( -32.60)
>DroAna_CAF1 1215 107 - 1
CCGGCCAGGUAGGUACCCCUGGCUCUCCCAACUGCAUGCAAAUGAUUAUCUGCAUGCUCUGGUUAUUGGAUCUAGAGUCCGUAGUCUUGACCGGCGGGACUACGACC
(((((((((........)))))))...(((...(((((((..........)))))))..))).....)).......(((.(((((((((.....)))))))))))). ( -39.40)
>consensus
CCGGAUACACCGGCUCUCCUGGUUCACCCAACUGCAUGCAGACCACAAUCUGCAUGCUCUGAUUGCUGGUUGCCGA____________GACGGCGGGCACCACCUCC
.(((.....(((((..((..((....)).....(((((((((......)))))))))...))..)))))...)))...................((......))... (-19.24 = -18.97 +  -0.27)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,038,026 – 21,038,137
Length 111
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 71.59
Mean single sequence MFE -39.40
Consensus MFE -16.05
Energy contribution -15.55
Covariance contribution -0.50
Combinations/Pair 1.36
Mean z-score -1.96
Structure conservation index 0.41
SVM decision value 0.63
SVM RNA-class probability 0.804106
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21038026 111 + 27905053
GACCAGCAAUCAGAGCAUGCAGAUUGUGGUCUGCAUGCAGUUGGGUGAACCAGGAGAGCCGGAGUAUCCGGACAAGUGCCGCUACGGGCAGCGGCUAAUGCAGGCCUCCAU
..(((((.......((((((((((....)))))))))).)))))........((((.(((((.....)).(.((...((((((......))))))...))).))))))).. ( -46.00)
>DroPse_CAF1 1728 111 + 1
AUUCAAUAAUCACAGCAUACAAAUAAUUGUUUGUAUGCAAUUGGGCGAACCCGGAGUUCCCACAUGGCCGGAUAAAUGCCGCUACGGACAGCACCUGAGAAACGCGUCUAA
..............((((((((((....))))))))))..(((((((...((((.....((....)))))).....(((.((....).).)))...........))))))) ( -28.70)
>DroWil_CAF1 1686 111 + 1
AAGAACCAAUCAGAGUAUGCAGAUUAUAGUGUGCAUGCAACUUGGCGAGCCGGGAGUACCUACUUGGCCGGACAAGUGCCGCUACGGACAGCGGCUAAGACAAGCGUCCAU
..............(((((((.((....)).))))))).(((((.((.((((((........))))))))..)))))((((((......))))))...(((....)))... ( -38.20)
>DroYak_CAF1 1462 111 + 1
CAGCAGCAAUCAGAGCAUGCAAAUUGUGGUCUGCAUGCAGUUGGGUGAACCGGGUGAGCCGCUGUAUCCGGACAAGUGUCGCUACGGACAACGACUGAUGCAGGCCUCCAU
..(((((.......)).))).......(((((((((.((((((......(((((((........))))))).....((((......)))).)))))))))))))))..... ( -41.50)
>DroMoj_CAF1 1505 111 + 1
CAGUAAUAACCAAAGUAUGCAAAUCAUUGUAUGCAUGCACCUGGGCGUCCCAGGCGUUCCAACCUGGCCCGACAAGUGCCGCUAUGGUCAGCGCUUGCUGCCCGCAUCCAG
..............((((((((....))))))))((((....(((((...(((((((((((...((((.(.....).))))...)))..)))))))).))))))))).... ( -35.20)
>DroAna_CAF1 1251 111 + 1
AUCCAAUAACCAGAGCAUGCAGAUAAUCAUUUGCAUGCAGUUGGGAGAGCCAGGGGUACCUACCUGGCCGGAUAAGUGCCGCUAUGGGCUGCGAUUGAAGCCCGCGUCCGC
((((.....((((.((((((((((....))))))))))..))))..(.((((((........)))))))))))..(((.(((...(((((........))))))))..))) ( -46.80)
>consensus
AAGCAACAAUCAGAGCAUGCAAAUUAUGGUCUGCAUGCAGUUGGGCGAACCAGGAGUACCGACCUGGCCGGACAAGUGCCGCUACGGACAGCGACUGAUGCACGCGUCCAU
..............(((((((.((....)).)))))))......((...(((((....))....((((.((.......)))))))))...))................... (-16.05 = -15.55 +  -0.50)

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 12:56:34 2006