Locus 3087

Sequence ID 3L_DroMel_CAF1
Location 8,942,402 – 8,942,541
Length 139
Max. P 0.798706
window4810 window4811

overview

Window 0

Location 8,942,402 – 8,942,501
Length 99
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 84.30
Mean single sequence MFE -35.90
Consensus MFE -26.86
Energy contribution -27.18
Covariance contribution 0.32
Combinations/Pair 1.20
Mean z-score -1.89
Structure conservation index 0.75
SVM decision value 0.59
SVM RNA-class probability 0.790978
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8942402 99 + 23771897
UU-UGUUAGUGGCAAUAACGGUUCAUAGGCAAAACGCAGUGUGGUAGUGGACGCCACAACAAAGCUUUCCGGCUCAGUGAGCGACGGGCACACUGGCACA
((-((((.(((((....((...(((((.((.....))..)))))..))....)))))))))))........((.(((((.((.....)).)))))))... ( -31.50)
>DroSec_CAF1 1471 100 + 1
UUUCGUUAGUGGCUAUAACGGUUCAUAGCCGAAACGCAGUGUGAUAGUGCUCACCACAACUGAGCUUUCCGGCUCAGUGAGGGACGGGCACACUGCCGCA
........(((((.....((((.....))))...............((((((.((...((((((((....))))))))...))..))))))...))))). ( -38.60)
>DroSim_CAF1 1325 100 + 1
UUACGUUAGUGGCAAUAACGGUUCAUAGCCGAAACGCAGUGUGAUAGUGCUCACCACAACUGAGCUUUCCGGCUCAGUGAGGGACGGGCACACUGUCGCA
........((((((....((((.....))))...............((((((.((...((((((((....))))))))...))..))))))..)))))). ( -37.20)
>DroEre_CAF1 1751 100 + 1
CUUUAAAAGCGGCAAUAACGGUUCAUAGCCGAAACGCAGUGUGGUAGUGCUUACCGCAGCUGAGCUUUCUGGCUCAGCAAGCGACGGGCACACUGGCGCA
........(((.((....((((.....))))...(((..((((((((...))))))))((((((((....))))))))..)))..........)).))). ( -39.60)
>DroYak_CAF1 1216 100 + 1
UUUCGAAAAUGGCAAUAACGGUGCAUAGCCGAAACGCAGUGUGGUAGUGCCUAGUCCAGCUGAGCUUUAGGGCCCAGCAAGCGACGGGCACACUGGCGCA
...........((.....((((.....))))....)).(((((((.((((((.((((.((((.(((....))).))))..).)))))))))))).)))). ( -32.60)
>consensus
UUUCGUUAGUGGCAAUAACGGUUCAUAGCCGAAACGCAGUGUGGUAGUGCUCACCACAACUGAGCUUUCCGGCUCAGUGAGCGACGGGCACACUGGCGCA
........(((.......((((.....)))).....(((((((...(((.....))).((((((((....))))))))..........))))))).))). (-26.86 = -27.18 +   0.32)

alignment

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secondary structure

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dotplot

Postscript

Window 1

Location 8,942,423 – 8,942,541
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.84
Mean single sequence MFE -36.02
Consensus MFE -18.89
Energy contribution -20.92
Covariance contribution 2.03
Combinations/Pair 1.33
Mean z-score -1.89
Structure conservation index 0.52
SVM decision value 0.61
SVM RNA-class probability 0.798706
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8942423 118 + 23771897
UCAUAGGCAAAACGCAGUGUGGUAGUGGACGCCACAACAAAGCUUUCCGGCUCAGUGAGCGACGGGCACAC--UGGCACAAAGCACAAAACAGAACAGUCGGUCGGAAACGGAAUCGAAA
.((((.((.....))..))))((.((((...)))).))...(((((...((.(((((.((.....)).)))--))))..)))))..............(((((((....))..))))).. ( -33.10)
>DroSec_CAF1 1493 118 + 1
UCAUAGCCGAAACGCAGUGUGAUAGUGCUCACCACAACUGAGCUUUCCGGCUCAGUGAGGGACGGGCACAC--UGCCGCAAAGCACAAAACAGAACAGUCGGACGGAAACGGAAUCGAAA
((....((((...((((((((...((.(((......((((((((....))))))))..)))))...)))))--))).((...))..............)))).((....)).....)).. ( -38.00)
>DroSim_CAF1 1347 118 + 1
UCAUAGCCGAAACGCAGUGUGAUAGUGCUCACCACAACUGAGCUUUCCGGCUCAGUGAGGGACGGGCACAC--UGUCGCAAAGCACAAAACAGAACAGUCGCACGGAAACGGAAUCGAAA
.......(((...((..(((((((((((((.((...((((((((....))))))))...))..))))..))--)))))))..))...................((....))...)))... ( -41.10)
>DroEre_CAF1 1773 118 + 1
UCAUAGCCGAAACGCAGUGUGGUAGUGCUUACCGCAGCUGAGCUUUCUGGCUCAGCAAGCGACGGGCACAC--UGGCGCAAAGCACAAAACAGAACAGUCGGACGGAAACGGAAUCGAAG
((....((((...((..((((.((((((((..(((.((((((((....))))))))..)))..))))..))--)).))))..)).(......).....)))).((....)).....)).. ( -41.10)
>DroYak_CAF1 1238 118 + 1
GCAUAGCCGAAACGCAGUGUGGUAGUGCCUAGUCCAGCUGAGCUUUAGGGCCCAGCAAGCGACGGGCACAC--UGGCGCAAAGCACAAAACAGAACAGUCGGACGGAAACGGAAUCGCAA
((....((((...((..((((.((((((((.((((.((((.(((....))).))))..).)))))))..))--)).))))..)).(......).....)))).((....)).....)).. ( -39.00)
>DroAna_CAF1 1445 99 + 1
UCAUAGCCAGGUUGCAGUGUGCGGAAA------------GGUAUUUCCG--UUGGGAAGCUCUGGCCACACAUCGCAAAAAAGCACAAAACCCA-----CGGACACAAA--AAACUCAAC
.....((....((((.(((((.((...------------((..(((((.--...)))))..))..)).))))).))))....))..........-----..........--......... ( -23.80)
>consensus
UCAUAGCCGAAACGCAGUGUGGUAGUGCUCACCACAACUGAGCUUUCCGGCUCAGUAAGCGACGGGCACAC__UGGCGCAAAGCACAAAACAGAACAGUCGGACGGAAACGGAAUCGAAA
.......(((...((..((((.((((((((......((((((((....)))))))).......))))))....)).))))..))...................((....))...)))... (-18.89 = -20.92 +   2.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:10 2006