Locus 6142

Sequence ID 3L_DroMel_CAF1
Location 16,260,401 – 16,260,550
Length 149
Max. P 0.932134
window9867 window9868 window9869

overview

Window 7

Location 16,260,401 – 16,260,494
Length 93
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 78.56
Mean single sequence MFE -36.60
Consensus MFE -25.12
Energy contribution -25.90
Covariance contribution 0.78
Combinations/Pair 1.16
Mean z-score -1.99
Structure conservation index 0.69
SVM decision value 1.22
SVM RNA-class probability 0.932134
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16260401 93 - 23771897
GGUGGCCACCUCCUAUGCCAACACCUACAAGGUGGCCACCAAGGCCAUUCCAGUGGUCCAUGCCGCU------------------CCUCUGGUCCAUGCCGUGCCUGCUCU
(((((((((((..((.(......).))..))))))))))).(((((.....((((((....))))))------------------.....(((....)))).))))..... ( -37.10)
>DroVir_CAF1 11544 108 - 1
GGUGGCCACCUCCUAUGCCAACACGUACAAGGUCGCCACCAAGGCCUAUCCCGUGGUGCAUGCCGCGCCCGUCUAUCAUGCACCCGCCGUUGU---CGCUGCCCCAGCUCU
((((((.((((..((((......))))..)))).))))))..(((..((..((.((((((((..((....))....))))))))))..)).))---)((((...))))... ( -40.40)
>DroGri_CAF1 11212 111 - 1
GGUGGCCACAUCCUAUGCCAACACCUACAAGGUGGCGACCAAGGCUUAUCCCGUCGUACAUGCCGCACCCAUCUAUCAUGCACCCGCUGUUGUGCAUGCCGCACCAGCUCU
.(((((...............((((.....))))(((((...((.....)).)))))....)))))...................((((..((((.....))))))))... ( -29.50)
>DroSec_CAF1 11829 111 - 1
AGUGGCCACCUCCUAUGCCAACACCUACAAGGUGGCCACCAAGGCCAUUCCAGUGGUCCAUGCCGCUCCCCUGGUGCACGCUGCUCCUCUGGUCCAUGCCGUGCCUGCUCU
.((((((((((..((.(......).))..))))))))))...(((....((((.((..((.((.((.((...)).))..))))..)).)))).....)))........... ( -39.10)
>DroEre_CAF1 11711 111 - 1
GGUGGCCACCUCCUACGCCAACACCUACAAGGUGGCCACCAAGGCCAUCCCCGUGGUCCAUGCCGCUCCCCUGGUGCACGCCGCUCCUCUGGUCCAUGCCGUGCCUGCUCU
(((((((((((..((.(......).))..))))))))))).((((.((...(((((.(((.((((......))))((.....)).....))).)))))..))))))..... ( -41.70)
>DroAna_CAF1 10995 111 - 1
CGUGGCUACCUCCUACGCCAACACCUACAAGGUGGCCACCAAGGCCAUCCCUGUGGUACACGCCGCCCCUCUGGUCCAUGCUGCUCCUCUGGUCCAUGCUGCCCCUGCUCU
.((((((((((..((.(......).))..))))))))))...(((((.....(..(((...((((......))))...)))..).....)))))...((.......))... ( -31.80)
>consensus
GGUGGCCACCUCCUAUGCCAACACCUACAAGGUGGCCACCAAGGCCAUUCCCGUGGUCCAUGCCGCUCCCCUGGUGCAUGCAGCUCCUCUGGUCCAUGCCGCGCCUGCUCU
(((((((((((..((.(......).))..)))))))))))..(((.......(((((....))))).............(((........)))....)))........... (-25.12 = -25.90 +   0.78)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,260,454 – 16,260,550
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.05
Mean single sequence MFE -41.18
Consensus MFE -29.45
Energy contribution -30.12
Covariance contribution 0.67
Combinations/Pair 1.16
Mean z-score -1.30
Structure conservation index 0.72
SVM decision value 0.24
SVM RNA-class probability 0.649031
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16260454 96 + 23771897
GGUGGCCACCUUGUAGGUGUUGGCAUAGGAGGUGGCCACCGGGUGGGC---------------------GA---CAAUGGGAGCGGCGUAGCUCUUGAUGAUCGGGGCGUGCGAGAUCAC
((((((((((((.((.((....)).)).))))))))))))..((((((---------------------..---(....)..))..(((((((((........))))).))))...)))) ( -41.60)
>DroVir_CAF1 11612 117 + 1
GGUGGCGACCUUGUACGUGUUGGCAUAGGAGGUGGCCACCGGGUGGAUGGUCUUCACGAUGGGCGCAUGCA---CAAUGGGCGCGGCAUAGCUCUUGAUGAUCGGCGCAUGCGAGAUGAC
((((((.(((((.((.((....)).)).))))).)))))).........(((.((.((....((((...((---(((.((((........))))))).))....))))...)).)).))) ( -45.20)
>DroGri_CAF1 11283 117 + 1
GGUCGCCACCUUGUAGGUGUUGGCAUAGGAUGUGGCCACCGGGUGGAUGGUCUUCACGAUGGGUGCAUGGA---CAAUGGGCGCGGCAUAGCUCUUGAUGAUCGGCGCAUGCGAGAUGAC
......((.((((((.((((((((((((((.((.(((.(((.(((((.....)))))..)))((.(((...---..))).))..)))...)))))).))).))))))).)))))).)).. ( -38.50)
>DroSec_CAF1 11900 96 + 1
GGUGGCCACCUUGUAGGUGUUGGCAUAGGAGGUGGCCACUGGGUGGGC---------------------GA---CAAUGGGUGCAGCGUAGCUCUUGAUGAUCGGGGCAUGCGAGAUCAC
((((((((((((.((.((....)).)).))))))))))))..((((((---------------------.(---(.....)))).((((.(((((........)))))))))....)))) ( -38.60)
>DroEre_CAF1 11782 96 + 1
GGUGGCCACCUUGUAGGUGUUGGCGUAGGAGGUGGCCACCGGAUGGGC---------------------CA---CAAUGGGGGCGGCGUAGCUCUUGAUGAUCGGAGCGUGCGAGAUCAG
((((((((((((.((.((....)).)).)))))))))))).(((..((---------------------(.---.......)))..(((((((((........))))).))))..))).. ( -45.60)
>DroAna_CAF1 11066 99 + 1
GGUGGCCACCUUGUAGGUGUUGGCGUAGGAGGUAGCCACGGGGUGGGC---------------------CACGGCGAUGGGGGCAGCGUAGCUCUUGAUGAUCGGGGCGUGGGAGAUCAC
.(((((.(((((.((.((....)).)).))))).)))))...((((.(---------------------((((.((((((((((......))))))....))))...)))))....)))) ( -37.60)
>consensus
GGUGGCCACCUUGUAGGUGUUGGCAUAGGAGGUGGCCACCGGGUGGGC_____________________CA___CAAUGGGCGCGGCGUAGCUCUUGAUGAUCGGGGCAUGCGAGAUCAC
((((((((((((.((.((....)).)).)))))))))))).............................................((((.(((((........)))))))))........ (-29.45 = -30.12 +   0.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,260,454 – 16,260,550
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.05
Mean single sequence MFE -29.58
Consensus MFE -18.99
Energy contribution -20.22
Covariance contribution 1.22
Combinations/Pair 1.05
Mean z-score -1.65
Structure conservation index 0.64
SVM decision value 0.36
SVM RNA-class probability 0.703530
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16260454 96 - 23771897
GUGAUCUCGCACGCCCCGAUCAUCAAGAGCUACGCCGCUCCCAUUG---UC---------------------GCCCACCCGGUGGCCACCUCCUAUGCCAACACCUACAAGGUGGCCACC
(((....)))......(((.((....((((......))))....))---))---------------------).......(((((((((((..((.(......).))..))))))))))) ( -31.20)
>DroVir_CAF1 11612 117 - 1
GUCAUCUCGCAUGCGCCGAUCAUCAAGAGCUAUGCCGCGCCCAUUG---UGCAUGCGCCCAUCGUGAAGACCAUCCACCCGGUGGCCACCUCCUAUGCCAACACGUACAAGGUCGCCACC
(((.((.(((((((((...((.....))((......)).......)---))))))))........)).))).........((((((.((((..((((......))))..)))).)))))) ( -35.70)
>DroGri_CAF1 11283 117 - 1
GUCAUCUCGCAUGCGCCGAUCAUCAAGAGCUAUGCCGCGCCCAUUG---UCCAUGCACCCAUCGUGAAGACCAUCCACCCGGUGGCCACAUCCUAUGCCAACACCUACAAGGUGGCGACC
(((.....(((((.(((.........).))))))).((........---.....(((......(((..(.(((((.....)))))))))......)))...((((.....))))))))). ( -24.10)
>DroSec_CAF1 11900 96 - 1
GUGAUCUCGCAUGCCCCGAUCAUCAAGAGCUACGCUGCACCCAUUG---UC---------------------GCCCACCCAGUGGCCACCUCCUAUGCCAACACCUACAAGGUGGCCACC
((((((...........))))))...(.((.(((.((....)).))---).---------------------)).).....((((((((((..((.(......).))..)))))))))). ( -25.70)
>DroEre_CAF1 11782 96 - 1
CUGAUCUCGCACGCUCCGAUCAUCAAGAGCUACGCCGCCCCCAUUG---UG---------------------GCCCAUCCGGUGGCCACCUCCUACGCCAACACCUACAAGGUGGCCACC
............((((..........))))...(((((.......)---))---------------------))......(((((((((((..((.(......).))..))))))))))) ( -32.00)
>DroAna_CAF1 11066 99 - 1
GUGAUCUCCCACGCCCCGAUCAUCAAGAGCUACGCUGCCCCCAUCGCCGUG---------------------GCCCACCCCGUGGCUACCUCCUACGCCAACACCUACAAGGUGGCCACC
((((((...........))))))...(.((((((..((.......))))))---------------------)).).....((((((((((..((.(......).))..)))))))))). ( -28.80)
>consensus
GUGAUCUCGCACGCCCCGAUCAUCAAGAGCUACGCCGCCCCCAUUG___UC_____________________GCCCACCCGGUGGCCACCUCCUAUGCCAACACCUACAAGGUGGCCACC
((((((...........)))))).....((......))..........................................(((((((((((..((.(......).))..))))))))))) (-18.99 = -20.22 +   1.22)

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 12:11:11 2006