Locus 8361

Sequence ID 3R_DroMel_CAF1
Location 22,307,577 – 22,307,705
Length 128
Max. P 0.739783
window13469 window13470 window13471

overview

Window 9

Location 22,307,577 – 22,307,674
Length 97
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 80.33
Mean single sequence MFE -31.57
Consensus MFE -13.89
Energy contribution -15.43
Covariance contribution 1.54
Combinations/Pair 1.08
Mean z-score -2.48
Structure conservation index 0.44
SVM decision value 0.02
SVM RNA-class probability 0.543390
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22307577 97 - 27905053
GAUUCAAGUU----------GCU-GCUGCAGUUGUUGCAGUUGUGCCGUUGCUGGUGCAGCAGCAACACGAGCUACAAGAUACUUUCUGUGCAACCAUAGAACUUCCC
.......(((----------(((-((((((.(.((.((.(.....).)).)).).)))))))))))).................(((((((....)))))))...... ( -31.80)
>DroSec_CAF1 24001 97 - 1
GAUUCAAGUU----------GCU-GCUGCAGUUGUUGCAGUUGUGCAGUUGCUGGUGCAGCAGCAACACGAGCUACAAGAUACUUUCUGUGCAACCAUAGAACUUCCC
.......(((----------(((-((((((((..(((((....)))))..))...)))))))))))).................(((((((....)))))))...... ( -33.30)
>DroSim_CAF1 23489 97 - 1
GAUUCAAGUU----------GCU-GCUGCAGUUGUUGCAGUUGUGCAGUUGCUGGUGCAGCAGCAACACGAGCUACAAGAUACUUUCUGUGCAACCAUAGAACUUCCC
.......(((----------(((-((((((((..(((((....)))))..))...)))))))))))).................(((((((....)))))))...... ( -33.30)
>DroEre_CAF1 25027 97 - 1
GAUUCAAGUU----------GCU-GCUGCAGUUGUUGCAGUUGUGCAGUUGCUGUUGCAGCAGCAACACGAGCUACAAGAUACUUUCUGUGCAACCAUAGAACUUCCC
.......(((----------(((-(((((((..((((((....))))...))..))))))))))))).................(((((((....)))))))...... ( -33.50)
>DroWil_CAF1 26738 107 - 1
GCUUGUUGUUGUUUGUUGUUGCU-GUAGCAAUUGUUAGAGUUGAACGGCAGCAGCAGCAGCAGCAACUUGAGCUACAAGAUACUUUCUGUGCAACCGUAGAACUUCCC
(((((((((((((.(((((((((-((..(((((.....)))))....))))))))))))))))))))..))))...........(((((((....)))))))...... ( -37.40)
>DroAna_CAF1 23808 81 - 1
GAUUCAAGUU----------GCAUAGCGAUGAUGUUGCUGUU--------------GU---UGCAACUUCAGCUACAAGAUACUUUCUGUGCAACCAUAGAACUUCCC
.......(((----------(((((((..(((.(((((....--------------..---.))))).))))))...(((.....))))))))))............. ( -20.10)
>consensus
GAUUCAAGUU__________GCU_GCUGCAGUUGUUGCAGUUGUGCAGUUGCUGGUGCAGCAGCAACACGAGCUACAAGAUACUUUCUGUGCAACCAUAGAACUUCCC
....................((.....))..((((.((.(((((...(((((....))))).)))))....)).))))......(((((((....)))))))...... (-13.89 = -15.43 +   1.54)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,307,614 – 22,307,705
Length 91
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 78.03
Mean single sequence MFE -26.32
Consensus MFE -8.98
Energy contribution -11.17
Covariance contribution 2.18
Combinations/Pair 1.14
Mean z-score -2.56
Structure conservation index 0.34
SVM decision value 0.08
SVM RNA-class probability 0.574681
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22307614 91 + 27905053
UCGUGUUGCUGCUGCACCAGCAACGGCACAACUGCAACAACUGCAGC-AGC----------AACUUGAAUCGCAUCUAUUGAUUGCACACAGUUCAUUGGCG
(((.((((((((((((.........(((....)))......))))))-)))----------))).)))..(((....((.(((((....))))).))..))) ( -29.26)
>DroSec_CAF1 24038 91 + 1
UCGUGUUGCUGCUGCACCAGCAACUGCACAACUGCAACAACUGCAGC-AGC----------AACUUGAAUCGCAUCUAUUGAUUGCACACAGUUCAUUGGCG
(((.((((((((((((........((((....)))).....))))))-)))----------))).)))..(((....((.(((((....))))).))..))) ( -29.72)
>DroSim_CAF1 23526 91 + 1
UCGUGUUGCUGCUGCACCAGCAACUGCACAACUGCAACAACUGCAGC-AGC----------AACUUGAAUCGCAUCUAUUGAUUGCACACAGUUCAUUGGCG
(((.((((((((((((........((((....)))).....))))))-)))----------))).)))..(((....((.(((((....))))).))..))) ( -29.72)
>DroEre_CAF1 25064 91 + 1
UCGUGUUGCUGCUGCAACAGCAACUGCACAACUGCAACAACUGCAGC-AGC----------AACUUGAAUCGCAUCUAUUGAUUGCACACAGUUCAUUGGCG
(((.((((((((((((........((((....)))).....))))))-)))----------))).)))..(((....((.(((((....))))).))..))) ( -29.72)
>DroWil_CAF1 26775 101 + 1
UCAAGUUGCUGCUGCUGCUGCUGCCGUUCAACUCUAACAAUUGCUAC-AGCAACAACAAACAACAACAAGCACAUCUAUUGAUUGCAUGCAGUUCAUUGGCG
((((...(((((((.(((((..((.(((..........))).))..)-)))).))..............(((.(((....))))))..)))))...)))).. ( -23.00)
>DroAna_CAF1 23845 75 + 1
UGAAGUUGCA---AC--------------AACAGCAACAUCAUCGCUAUGC----------AACUUGAAUCGCAUCCAUUGAUUGCACACAGUUCAUUGGCG
(((.(((((.---..--------------....))))).))).(((((((.----------(((((((((((.......))))).))...)))))).))))) ( -16.50)
>consensus
UCGUGUUGCUGCUGCACCAGCAACUGCACAACUGCAACAACUGCAGC_AGC__________AACUUGAAUCGCAUCUAUUGAUUGCACACAGUUCAUUGGCG
....(((((((......))))))).......(((((.....))))).............................(((.((((((....))).))).))).. ( -8.98 = -11.17 +   2.18)

alignment

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secondary structure

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dotplot

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Window 1

Location 22,307,614 – 22,307,705
Length 91
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 78.03
Mean single sequence MFE -31.05
Consensus MFE -12.55
Energy contribution -14.12
Covariance contribution 1.57
Combinations/Pair 1.11
Mean z-score -2.47
Structure conservation index 0.40
SVM decision value 0.45
SVM RNA-class probability 0.739783
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22307614 91 - 27905053
CGCCAAUGAACUGUGUGCAAUCAAUAGAUGCGAUUCAAGUU----------GCU-GCUGCAGUUGUUGCAGUUGUGCCGUUGCUGGUGCAGCAGCAACACGA
........(((((((.((((((....)))(((((....)))----------)))-)))))))))(((((.((((..(((....)))..)))).))))).... ( -32.00)
>DroSec_CAF1 24038 91 - 1
CGCCAAUGAACUGUGUGCAAUCAAUAGAUGCGAUUCAAGUU----------GCU-GCUGCAGUUGUUGCAGUUGUGCAGUUGCUGGUGCAGCAGCAACACGA
......((((.....((((.((....)))))).)))).(((----------(((-((((((((..(((((....)))))..))...)))))))))))).... ( -32.30)
>DroSim_CAF1 23526 91 - 1
CGCCAAUGAACUGUGUGCAAUCAAUAGAUGCGAUUCAAGUU----------GCU-GCUGCAGUUGUUGCAGUUGUGCAGUUGCUGGUGCAGCAGCAACACGA
......((((.....((((.((....)))))).)))).(((----------(((-((((((((..(((((....)))))..))...)))))))))))).... ( -32.30)
>DroEre_CAF1 25064 91 - 1
CGCCAAUGAACUGUGUGCAAUCAAUAGAUGCGAUUCAAGUU----------GCU-GCUGCAGUUGUUGCAGUUGUGCAGUUGCUGUUGCAGCAGCAACACGA
...........((((((((.((....))))).......(((----------(((-((.(((((..(((((....)))))..))))).)))))))).))))). ( -34.70)
>DroWil_CAF1 26775 101 - 1
CGCCAAUGAACUGCAUGCAAUCAAUAGAUGUGCUUGUUGUUGUUUGUUGUUGCU-GUAGCAAUUGUUAGAGUUGAACGGCAGCAGCAGCAGCAGCAACUUGA
............((((...(((....)))))))(((((((((((.(((((((((-((..(((((.....))))).))))))))))))))))))))))..... ( -35.40)
>DroAna_CAF1 23845 75 - 1
CGCCAAUGAACUGUGUGCAAUCAAUGGAUGCGAUUCAAGUU----------GCAUAGCGAUGAUGUUGCUGUU--------------GU---UGCAACUUCA
......((((.(((((.((.....)).))))).))))((((----------((((((((((...)))))))..--------------..---)))))))... ( -19.60)
>consensus
CGCCAAUGAACUGUGUGCAAUCAAUAGAUGCGAUUCAAGUU__________GCU_GCUGCAGUUGUUGCAGUUGUGCAGUUGCUGGUGCAGCAGCAACACGA
.((((((.((((...((((.((....)))))).....))))..........((.....)).))))..)).(((((...(((((....))))).))))).... (-12.55 = -14.12 +   1.57)

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 13:09:39 2006