Locus 4456

Sequence ID 3L_DroMel_CAF1
Location 12,954,377 – 12,954,537
Length 160
Max. P 0.961804
window6937 window6938

overview

Window 7

Location 12,954,377 – 12,954,497
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.31
Mean single sequence MFE -38.86
Consensus MFE -33.58
Energy contribution -34.06
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -1.67
Structure conservation index 0.86
SVM decision value 1.07
SVM RNA-class probability 0.909474
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12954377 120 + 23771897
GGGCGUGGCAGGGCGUGUCUUGACCGGGCUAGUAAACUAUGCAAACAAAUAGCCAACUUAUUUUGGGGGGCCCCGAAGUAAAUUGUACAGAGCAGCGCAAAAUUCGUGCUGCAAAGCAAC
.(((.((((((((....))))).))).))).........(((...........(((.((((((((((....)))))))))).)))......(((((((.......)))))))...))).. ( -43.30)
>DroSec_CAF1 71589 119 + 1
GGGCGUGGCAGGGCGUGUCUUGACCGGGCUAGUAAACUAUGCAAACAAAUAGCCAACUUAUUUUGG-GGGCCCCGAAGUAAAUUGUACAGAGCAGCGCAGAAUUCGUGCUGCAAAGCAAC
.(((.((((((((....))))).))).))).........(((...........(((.(((((((((-(...)))))))))).)))......(((((((.......)))))))...))).. ( -40.30)
>DroSim_CAF1 76421 119 + 1
GGGAGUGGCAGGGCGUGUCUUGACCGGGCUAGUAAACUAUGCAAACAAAUAGCCAACUUAUUUCGG-GGGCCCCGAAGUAAAUUGUACAGAGCAGCGCAGAAUUCGUGCUGCAAAGCAAC
.....((((((((....))))).))).(((.(((..((((........)))).(((.(((((((((-(...)))))))))).))))))...(((((((.......)))))))..)))... ( -38.00)
>DroEre_CAF1 77665 119 + 1
GGGCGUGGCAGGGCGUGUCUUGACCGGGCUAGUAAACUAUGCAAACAAAUAGCCAACUUAUUUUGG-GCGCACCGAAGUAAAUUGUACAGACUAGCGCAGAAUUCGUGCUGCAAAGCAAC
..((...((((.(((..(((.....(.((((((...((((........)))).(((.(((((((((-.....))))))))).))).....)))))).))))...))).))))...))... ( -37.70)
>DroYak_CAF1 75470 119 + 1
GGGCGGGGCAGGGCGUGUCUUGACCGGGCUAGUAAACUAUGCAAACAAAUAGCCAACUUAUUUUGG-GGGUCCGGAAGUAAAUUGUACAGAGCAGCGCAGAAUUCGUGCUGCAAAGCAAC
...(((((((.....))))))).(((((((......((((........))))((((......))))-.)))))))..(((.....)))...(((((((.......)))))))........ ( -35.00)
>consensus
GGGCGUGGCAGGGCGUGUCUUGACCGGGCUAGUAAACUAUGCAAACAAAUAGCCAACUUAUUUUGG_GGGCCCCGAAGUAAAUUGUACAGAGCAGCGCAGAAUUCGUGCUGCAAAGCAAC
.(((.((((((((....))))).))).))).........(((...........(((.(((((((((......))))))))).)))......(((((((.......)))))))...))).. (-33.58 = -34.06 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,954,417 – 12,954,537
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.30
Mean single sequence MFE -33.58
Consensus MFE -27.24
Energy contribution -27.32
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -2.26
Structure conservation index 0.81
SVM decision value 1.53
SVM RNA-class probability 0.961804
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12954417 120 + 23771897
GCAAACAAAUAGCCAACUUAUUUUGGGGGGCCCCGAAGUAAAUUGUACAGAGCAGCGCAAAAUUCGUGCUGCAAAGCAACAGCUGUCGGAAAACUCAAAGUCUGGUCUGUAAAAUAUCAG
.............(((.((((((((((....)))))))))).)))(((((((((((((.......))))))).......(((((....((....))..)).))).))))))......... ( -36.30)
>DroSec_CAF1 71629 119 + 1
GCAAACAAAUAGCCAACUUAUUUUGG-GGGCCCCGAAGUAAAUUGUACAGAGCAGCGCAGAAUUCGUGCUGCAAAGCAACAGCUGUCGGAAAACUCAAAGUCUGGUCUGUAAAAUAUCAG
.............(((.(((((((((-(...)))))))))).)))(((((((((((((.......))))))).......(((((....((....))..)).))).))))))......... ( -33.30)
>DroSim_CAF1 76461 119 + 1
GCAAACAAAUAGCCAACUUAUUUCGG-GGGCCCCGAAGUAAAUUGUACAGAGCAGCGCAGAAUUCGUGCUGCAAAGCAACAGCUGUCGGAAAACUCAAAGUCUGGUCUGUAAAAUAUCAG
.............(((.(((((((((-(...)))))))))).)))(((((((((((((.......))))))).......(((((....((....))..)).))).))))))......... ( -35.40)
>DroEre_CAF1 77705 117 + 1
GCAAACAAAUAGCCAACUUAUUUUGG-GCGCACCGAAGUAAAUUGUACAGACUAGCGCAGAAUUCGUGCUGCAAAGCAACAGCUGUCGGACAACUCAAAG--UGGUCUGUAAAAUAUCGG
.............(((.(((((((((-.....))))))))).)))(((((((((.(((((......((((....))))....))).))((....))....--)))))))))......... ( -29.70)
>DroYak_CAF1 75510 117 + 1
GCAAACAAAUAGCCAACUUAUUUUGG-GGGUCCGGAAGUAAAUUGUACAGAGCAGCGCAGAAUUCGUGCUGCAAAGCAACAGCUGUCGGAAAACUCAAAG--UGGUCUGUAAAAUAUCAG
........(((((((.....((((((-(..((((..(((...((((.....(((((((.......)))))))...))))..)))..))))...)))))))--))).)))).......... ( -33.20)
>consensus
GCAAACAAAUAGCCAACUUAUUUUGG_GGGCCCCGAAGUAAAUUGUACAGAGCAGCGCAGAAUUCGUGCUGCAAAGCAACAGCUGUCGGAAAACUCAAAGUCUGGUCUGUAAAAUAUCAG
.............(((.(((((((((......))))))))).)))(((((((((((((.......)))))))..(((....))).....................))))))......... (-27.24 = -27.32 +   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 11:23:34 2006