Locus 453

Sequence ID 3R_DroMel_CAF1
Location 1,725,767 – 1,725,878
Length 111
Max. P 0.703178
window732 window733 window734

overview

Window 2

Location 1,725,767 – 1,725,857
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 95.37
Mean single sequence MFE -21.80
Consensus MFE -18.61
Energy contribution -19.43
Covariance contribution 0.81
Combinations/Pair 1.05
Mean z-score -1.83
Structure conservation index 0.85
SVM decision value 0.31
SVM RNA-class probability 0.681895
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1725767 90 + 27905053
UCAGUUUCUCUUCACUUACGCCGCCGACUGCCGUUGGCCUUUAUUGCCAGCCAUUUUGAAUACCAUUUGGUGGCUUAUUACUUCUGCGGC
...................(((((.((..(((((((((.......))))))..........(((....))))))........)).))))) ( -23.10)
>DroSec_CAF1 34892 90 + 1
UCAGAUUCUCUUCACUUACGCCGCCGACUGCCGUUGGCCUUUAUUGCCAGCCAUUUUGAAUACCAUUUGGUGGCUUAUUACUUCUGCGGC
...................(((((.((..(((((((((.......))))))..........(((....))))))........)).))))) ( -23.10)
>DroSim_CAF1 36015 90 + 1
UCAGAUUCUCUUCACUUACGCCGCCGACUGCCGUUGGCCUUUAUUGCCAGCCAUUUUGAAUACCAUUUGGUGGCUUAUUACUUCUGCGGC
...................(((((.((..(((((((((.......))))))..........(((....))))))........)).))))) ( -23.10)
>DroYak_CAF1 34840 90 + 1
UCAGUUGCUCUUCACUUACGCUACCACUUGCCGUUGGCCUUUAUUGCCAGCCAUUUUGAAUACCAUUUUGUGGCUUAUUACUUCUGCGGC
...((.((...........)).)).....(((((((((.......))))(((((..((.....))....)))))...........))))) ( -17.90)
>consensus
UCAGAUUCUCUUCACUUACGCCGCCGACUGCCGUUGGCCUUUAUUGCCAGCCAUUUUGAAUACCAUUUGGUGGCUUAUUACUUCUGCGGC
...................(((((.((..(((((((((.......))))))..........(((....))))))........)).))))) (-18.61 = -19.43 +   0.81)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,725,767 – 1,725,857
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 95.37
Mean single sequence MFE -22.75
Consensus MFE -19.66
Energy contribution -19.98
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -1.58
Structure conservation index 0.86
SVM decision value -0.02
SVM RNA-class probability 0.523582
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1725767 90 - 27905053
GCCGCAGAAGUAAUAAGCCACCAAAUGGUAUUCAAAAUGGCUGGCAAUAAAGGCCAACGGCAGUCGGCGGCGUAAGUGAAGAGAAACUGA
(((((.(((....)..((((((....)))........(((((.........)))))..)))..)).)))))...(((........))).. ( -24.30)
>DroSec_CAF1 34892 90 - 1
GCCGCAGAAGUAAUAAGCCACCAAAUGGUAUUCAAAAUGGCUGGCAAUAAAGGCCAACGGCAGUCGGCGGCGUAAGUGAAGAGAAUCUGA
(((((.(((....)..((((((....)))........(((((.........)))))..)))..)).)))))................... ( -23.70)
>DroSim_CAF1 36015 90 - 1
GCCGCAGAAGUAAUAAGCCACCAAAUGGUAUUCAAAAUGGCUGGCAAUAAAGGCCAACGGCAGUCGGCGGCGUAAGUGAAGAGAAUCUGA
(((((.(((....)..((((((....)))........(((((.........)))))..)))..)).)))))................... ( -23.70)
>DroYak_CAF1 34840 90 - 1
GCCGCAGAAGUAAUAAGCCACAAAAUGGUAUUCAAAAUGGCUGGCAAUAAAGGCCAACGGCAAGUGGUAGCGUAAGUGAAGAGCAACUGA
((((............((((.....))))........(((((.........))))).))))..((....((....)).....))...... ( -19.30)
>consensus
GCCGCAGAAGUAAUAAGCCACCAAAUGGUAUUCAAAAUGGCUGGCAAUAAAGGCCAACGGCAGUCGGCGGCGUAAGUGAAGAGAAACUGA
(((((...(....)..((((((....)))........(((((.........)))))..))).....)))))................... (-19.66 = -19.98 +   0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,725,782 – 1,725,878
Length 96
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 77.47
Mean single sequence MFE -26.17
Consensus MFE -16.19
Energy contribution -16.22
Covariance contribution 0.03
Combinations/Pair 1.28
Mean z-score -1.52
Structure conservation index 0.62
SVM decision value 0.36
SVM RNA-class probability 0.703178
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1725782 96 + 27905053
UUACGCCGCCGACUGCCGUUGGCCUUUAUUGCCAGCCAUUUUGAAUACCAUUUGGUGGCUUAUUACUUCUGCGGCAGAC------CGCUUCUCAAGCAGC------------CG
.......((...(((((((((((.......))))((((((.((.....))...))))))...........)))))))..------.(((.....))).))------------.. ( -27.30)
>DroEre_CAF1 34416 94 + 1
UUGCGCUGCUGGCUGCCGUUGGCCUUUAUUGCCAGCCAUUUUGAAUACCAUUUUGUGGCUUAUUACUUCUGCGG--GAC------CGCUCCUCAAGCAGC------------CA
..........((((((.((((((.......))))))....((((...((((...))))............(((.--...------)))...)))))))))------------). ( -27.80)
>DroWil_CAF1 30495 100 + 1
UU--GCUUCCGUCUGCUGCUGGCUUUUAUUGCCAGCCAUUUUGAAUACCAUUUCGUGGUUUAUUACUUUUGUGGCAGACCGAUUUCGAUUCUCAAGUAGU------------AG
((--((((..(((((((((((((.......))))))..........(((((...))))).............)))))))((....))......)))))).------------.. ( -27.80)
>DroYak_CAF1 34855 96 + 1
UUACGCUACCACUUGCCGUUGGCCUUUAUUGCCAGCCAUUUUGAAUACCAUUUUGUGGCUUAUUACUUCUGCGGCAGAC------CGCUCCUCAAGCAGC------------CA
....(((.....(((((((((((.......))))(((((..((.....))....)))))...........)))))))..------.(((.....))))))------------.. ( -25.30)
>DroAna_CAF1 31090 91 + 1
-----------GCUGGCGUUGGCCUUUAUUGCCACCCAUUUUGAAUACCAUUUUGUGGUUUAUUACUUUUGCGGCAGACCAAUGCCGGUUCUCAAGCAGC------------CA
-----------(((((((((((......(((((.(...........(((((...)))))...........).))))).)))))))))))...........------------.. ( -25.25)
>DroPer_CAF1 30428 111 + 1
U--CCCUUCCGUCUG-CGUUGGCCUUUAUUGCCAGCCAUUUUGAAUACCAUUUUGUGGUUUAUUACUUUUGUGGCAGAGCGAUUCCGAUUCUCAAGUAGCACUGCGGCAUGCCA
.--.....((((.((-(..((((.......))))(((((....((((((((...)))))..)))......)))))((((((....)).))))......)))..))))....... ( -23.60)
>consensus
UU_CGCUGCCGGCUGCCGUUGGCCUUUAUUGCCAGCCAUUUUGAAUACCAUUUUGUGGCUUAUUACUUCUGCGGCAGAC______CGCUUCUCAAGCAGC____________CA
............(((((((((((.......))))(((((..((.....))....)))))...........)))))))..................................... (-16.19 = -16.22 +   0.03)

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 09:43:33 2006