Locus 7318

Sequence ID 3L_DroMel_CAF1
Location 19,607,634 – 19,607,789
Length 155
Max. P 0.990497
window11891 window11892 window11893

overview

Window 1

Location 19,607,634 – 19,607,733
Length 99
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 84.08
Mean single sequence MFE -47.86
Consensus MFE -34.32
Energy contribution -36.00
Covariance contribution 1.68
Combinations/Pair 1.14
Mean z-score -2.23
Structure conservation index 0.72
SVM decision value 1.02
SVM RNA-class probability 0.900829
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19607634 99 - 23771897
ACUCAGGAGGCGGAAGUGGCGAGGAUCCGGCGGUUGGAUCCGCAUCUGGAGCUGCUG------------CUUCGGAUACCGAUUCACUUGCUUCUUCGCCUGACGAAGGAG
.(((.(.(((((.(((.((((((((..((((((......))))(((((((((....)------------))))))))..))..)).)))))).))))))))..)....))) ( -44.00)
>DroSec_CAF1 22645 105 - 1
ACUGCGGAGGCGGAAGUGGCGAGGAUCCGGCGGUUGGAUCCGCUUCUGGAGCUGCUG------CUGCGGCUUCGGAUACUGAUUCACUUGCUUCUUCGCCCGACGAAGCAG
.((((...(((....))((((((((...(((((.((((((.(..(((((((((((..------..)))))))))))..).)))))).)))))))))))))...)...)))) ( -51.80)
>DroSim_CAF1 22490 105 - 1
ACUCCGGAGGCGGAAGUGGCGAGGAUCCGGCGGUUGGAUCCGCUUCUGGAGCUGCUG------CUGCGGCUUCGGAUACUGAUUCACUUGCUUCUUCGCCCGACGAAGCAG
.((.((..(((....))((((((((...(((((.((((((.(..(((((((((((..------..)))))))))))..).)))))).))))))))))))))..)).))... ( -49.30)
>DroEre_CAF1 22844 111 - 1
ACCCCGGAAACGGAAGUGCCGAGGAUCCGGCGGCUGGAUCCGCAUCUGGAGCUGCUGCUGCUGCUGCGGCUUCGGACCCCGAUUCACCUGCUUCUACGCCCGAGGAAGCAG
...(((....)))....((((......))))((.((((((.(..(((((((((((.((....)).)))))))))))..).))))))))(((((((.(....).))))))). ( -52.60)
>DroYak_CAF1 22387 105 - 1
ACUCCGGAAACGGAAGUGCCGAGGACGCGGCGGCUGGAUCUGCACCUGGACCUGAUG------CUGCAGAUUCGGAUCUUGAUUCACCUGCUGCUACGCCCGAGGAAGCAG
..((((....)))).((.((..((.((..(((((.(((((((((.(..........)------.)))))))))((((....))))....)))))..)).))..))..)).. ( -41.60)
>consensus
ACUCCGGAGGCGGAAGUGGCGAGGAUCCGGCGGUUGGAUCCGCAUCUGGAGCUGCUG______CUGCGGCUUCGGAUACUGAUUCACUUGCUUCUUCGCCCGACGAAGCAG
....(((..((....)).(((((((...(((((.((((((.(..(((((((((((..........)))))))))))..).)))))).)))))))))))))))......... (-34.32 = -36.00 +   1.68)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,607,693 – 19,607,789
Length 96
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 84.80
Mean single sequence MFE -53.52
Consensus MFE -40.34
Energy contribution -43.40
Covariance contribution 3.06
Combinations/Pair 1.09
Mean z-score -3.02
Structure conservation index 0.75
SVM decision value 2.22
SVM RNA-class probability 0.990497
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19607693 96 + 23771897
GAUCCAACCGCCGGAUCCUCGCCACUUCCGCCUCCUGAGUGGGCUGCAGCUGCCGCCGC------CGCAGCAGCAGCAGCAGAAGUGGAGGGCGAGACGCAA
(((((.......)))))((((((.((.((((..((.....))(((((.(((((.((...------.)).))))).)))))....))))))))))))...... ( -46.40)
>DroSec_CAF1 22710 102 + 1
GAUCCAACCGCCGGAUCCUCGCCACUUCCGCCUCCGCAGUGGGCUGCAGUCGCCGCAGCUGCGGCCGUUGCAGCAGCAGCGGAAGUGGAGGGCGAGAGGCAA
(((((.......)))))((((((.((.((((.(((((.((..(((((((..(((((....)))))..))))))).)).))))).))))))))))))...... ( -60.20)
>DroSim_CAF1 22555 102 + 1
GAUCCAACCGCCGGAUCCUCGCCACUUCCGCCUCCGGAGUGGGCUGCAGUCGCCGCAGCUGCGGCCGUUGCAGCAGCAGCGGAAGUGGAGGGCGAGAGGCAA
(((((.......)))))((((((.((.((((.((((..((..(((((((..(((((....)))))..))))))).))..)))).))))))))))))...... ( -56.90)
>DroYak_CAF1 22452 96 + 1
GAUCCAGCCGCCGCGUCCUCGGCACUUCCGUUUCCGGAGUGGGCUGCAGCCGCAGC---UGCCGC---CGCCGCAGCAGCGGAAGUGGAGGGCGACAGGCAA
.........(((.(((((((..((((((((((..(((....(((.(((((....))---))).))---).)))....)))))))))))))))))...))).. ( -50.60)
>consensus
GAUCCAACCGCCGGAUCCUCGCCACUUCCGCCUCCGGAGUGGGCUGCAGCCGCCGCAGCUGCGGCCGUUGCAGCAGCAGCGGAAGUGGAGGGCGAGAGGCAA
.........(((...(((((.((((((((((..((.....))((((((((.(((((....))))).))))))))....)))))))))).))).))..))).. (-40.34 = -43.40 +   3.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,607,693 – 19,607,789
Length 96
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 84.80
Mean single sequence MFE -52.90
Consensus MFE -38.92
Energy contribution -40.67
Covariance contribution 1.75
Combinations/Pair 1.12
Mean z-score -2.47
Structure conservation index 0.74
SVM decision value 1.48
SVM RNA-class probability 0.957474
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19607693 96 - 23771897
UUGCGUCUCGCCCUCCACUUCUGCUGCUGCUGCUGCG------GCGGCGGCAGCUGCAGCCCACUCAGGAGGCGGAAGUGGCGAGGAUCCGGCGGUUGGAUC
......((((((((((.((((((((((.((((((((.------...)))))))).))))).......))))).)).)).))))))((((((.....)))))) ( -50.51)
>DroSec_CAF1 22710 102 - 1
UUGCCUCUCGCCCUCCACUUCCGCUGCUGCUGCAACGGCCGCAGCUGCGGCGACUGCAGCCCACUGCGGAGGCGGAAGUGGCGAGGAUCCGGCGGUUGGAUC
......((((((((((.(((((((....((((((...(((((....)))))...)))))).....))))))).)).)).))))))((((((.....)))))) ( -55.00)
>DroSim_CAF1 22555 102 - 1
UUGCCUCUCGCCCUCCACUUCCGCUGCUGCUGCAACGGCCGCAGCUGCGGCGACUGCAGCCCACUCCGGAGGCGGAAGUGGCGAGGAUCCGGCGGUUGGAUC
...((..((((((.(((((((((((...((((((...(((((....)))))...))))))((.....)).))))))))))).).(....))))))..))... ( -52.00)
>DroYak_CAF1 22452 96 - 1
UUGCCUGUCGCCCUCCACUUCCGCUGCUGCGGCG---GCGGCA---GCUGCGGCUGCAGCCCACUCCGGAAACGGAAGUGCCGAGGACGCGGCGGCUGGAUC
..(((.(((((((((((((((((((((.((.(((---((....---))))).)).))))).......(....))))))))..))))..))))))))...... ( -54.10)
>consensus
UUGCCUCUCGCCCUCCACUUCCGCUGCUGCUGCAACGGCCGCAGCUGCGGCGACUGCAGCCCACUCCGGAGGCGGAAGUGGCGAGGAUCCGGCGGUUGGAUC
...((..((((((.(((((((((((...((((((...(((((....)))))...))))))((.....)).))))))))))).).(....))))))..))... (-38.92 = -40.67 +   1.75)

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 12:43:55 2006