Locus 1692

Sequence ID 2L_DroMel_CAF1
Location 4,627,591 – 4,627,911
Length 320
Max. P 0.882901
window2704 window2705 window2706

overview

Window 4

Location 4,627,591 – 4,627,704
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 96.81
Mean single sequence MFE -29.34
Consensus MFE -28.01
Energy contribution -28.01
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.33
Structure conservation index 0.95
SVM decision value 0.92
SVM RNA-class probability 0.882901
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4627591 113 - 22407834
UAUUUUAUUGGCGCUCGGGGCGCUGCCGAGAGCACAAAUCAAAACUAACUGGAGUGCUUAGAGUGCCAUAGAGAAACAAACAACAUUAUUCACCGCUCUGAUUUGGUCAAACA
..((((((.(((((((..((((((.(((..((............))...)))))))))..)))))))))))))..................((((........))))...... ( -29.00)
>DroSec_CAF1 64858 113 - 1
UAUUUUAUUGGCGCUCGGGGCGCUGCCGAGAGCACAAAUCAAAACUAACUGGAGUGCUUAGAGUGCCAUAGAGAAACAAACAACAUUAUUCACCGCUCUGAUUUGGCAAAACA
..((((((.(((((((..((((((.(((..((............))...)))))))))..))))))))))))).....................(((.......)))...... ( -29.20)
>DroSim_CAF1 64010 113 - 1
UAUUUUAUUGGCGCUCGGGGCGCUGCCGAGAGCACAAAUCAAAACUAACUGGAGUGCUUAGAGUGCCAUAGAGAAACAAACAACAUUAUUCCCCGCUCUGAUUUGGCCAAACA
.......(((((((((..(((...)))..)))).((((((...(((......)))....((((((............................)))))))))))))))))... ( -28.59)
>DroEre_CAF1 69905 113 - 1
UAUUUCAUUGGCGCUCGGGGCGCUGCCGUAAGCACAAAUCAAAACUAACUGGAGUGCUUAGAGUGCCAUAGAGAAACAAACAACAUUAUUUACCGCUCUGAUUUGGUCAAACA
..((((..((((((((..((((((.(.((.((............)).)).).))))))..))))))))..)))).................((((........))))...... ( -30.60)
>DroYak_CAF1 69520 113 - 1
UAUUUUAUUGGCGCUCGGGGCGCUGCCGAGAGCACAAAUCAAAUCUAACUGGAGUGCUUAGAGUGCCAUAGAGAAACAAACAACAUUAUUCACCGCUCUGAUUUGGACAAACA
..((((((.(((((((..((((((.((((((............)))...)))))))))..)))))))))))))...................(((........)))....... ( -29.30)
>consensus
UAUUUUAUUGGCGCUCGGGGCGCUGCCGAGAGCACAAAUCAAAACUAACUGGAGUGCUUAGAGUGCCAUAGAGAAACAAACAACAUUAUUCACCGCUCUGAUUUGGCCAAACA
........((((((((..((((((.(((..((............))...)))))))))..))))))))(((((......................)))))............. (-28.01 = -28.01 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,627,704 – 4,627,800
Length 96
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 96.47
Mean single sequence MFE -35.84
Consensus MFE -33.30
Energy contribution -33.42
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -1.14
Structure conservation index 0.93
SVM decision value 0.09
SVM RNA-class probability 0.579788
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4627704 96 + 22407834
CAUUUAAGUAGAAACUGUGCCGCUUCUGGUCCGCUCGCCA-ACCCGUGUUACGCGUCGGAGUUUCUGGUGGGGAUCAGACGUGGCCUCAGUCCCGGU
..........(..((((.(((((.((((((((.(.(((((-(((((((.....)).))).))...)))))))))))))).)))))..))))..)... ( -38.60)
>DroSec_CAF1 64971 96 + 1
CAUUUAAGUAGAAACUGUGCCGCUUCUGGUCCGCUCGCCA-ACCCGUGUUACGCGUCGGAGUUUCUGUUGGGGAUCGGACGUGGUCUCAGUCCCGGU
..........(..((((.(((((.((((((((.(.((..(-(((((((.....)).))).)))..))..).)))))))).)))))..))))..)... ( -32.30)
>DroSim_CAF1 64123 96 + 1
CAUUUAAGUAGAAACUGUGCCGCUUCUGGUCCGCUCGCCA-ACCCGUGUUACGCGUCGGAGUUUCUGUUGGGGAUCGGACGUGGUCACAGUCCCGGU
..........(..((((((((((.((((((((.(.((..(-(((((((.....)).))).)))..))..).)))))))).)))).))))))..)... ( -35.80)
>DroEre_CAF1 70018 96 + 1
CAUUUAAGUAAAAACUGUGCCGCUUCUGGUCCGCUCGCCA-ACCCGUGUUACGCGUCGGAGUUUCUGGCGGGGAUCGGACGUGGUCUCAGUCCCGGU
.............((((.(((((.((((((((.(.(((((-(((((((.....)).))).))...)))))))))))))).)))))..))))...... ( -37.40)
>DroYak_CAF1 69633 97 + 1
CAUUUAAGUAGAAACUGUGCCGCUUCUGGUCCGCUCGCCAGACCCGUGUUACGCGUCGGAGUUUCUGGUGGAGAUCGGACGUGGUCUCAGUCCCGGU
..........(..((((.(((((.(((((((...((((((((((((((.....)).))).)..)))))))).))))))).)))))..))))..)... ( -35.10)
>consensus
CAUUUAAGUAGAAACUGUGCCGCUUCUGGUCCGCUCGCCA_ACCCGUGUUACGCGUCGGAGUUUCUGGUGGGGAUCGGACGUGGUCUCAGUCCCGGU
.............((((.(((((.((((((((.(.(((((.(((((((.....)).))).))...)))))))))))))).)))))..))))...... (-33.30 = -33.42 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,627,800 – 4,627,911
Length 111
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 93.84
Mean single sequence MFE -30.73
Consensus MFE -27.25
Energy contribution -27.50
Covariance contribution 0.25
Combinations/Pair 1.12
Mean z-score -1.40
Structure conservation index 0.89
SVM decision value 0.46
SVM RNA-class probability 0.746279
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4627800 111 + 22407834
CC------CAGCUCAUUAAAUCAUCGUAAAAGUGUCCGCUACCGAG--UUGCGGACUCAAUAUUCUGCUCACAUACGACCGUUUAGCGAGUUUGCUCAACGGCUGUUUCGACAUGAGCU
..------.(((((((.......(((((...(.((((((.......--..)))))).).......((....)))))))(((((.((((....)))).)))))..........))))))) ( -31.80)
>DroSec_CAF1 65067 111 + 1
CC------CAGCUCAUUAAAUCAUCGUAAAAGUGUCCGCUACCGAG--UUGCGGACUCAAUAUUCUGCUCACAUACGACCGUUUAGCGAGUUUGCUCAGCGGCUGUUUCGACAUGAGCU
..------.(((((((.......(((((...(.((((((.......--..)))))).).......((....)))))))(((((.((((....)))).)))))..........))))))) ( -31.80)
>DroSim_CAF1 64219 111 + 1
CC------CAGCUCAUUAAAUCAUCGUAAAAGUGUCCGCUACCGAG--UUGCGGACUCAAUAUUCUGCUCACAUACGACCGUUUAGCGAGUUUGCUCAGCGGCUGUUUCGACAUGAGCU
..------.(((((((.......(((((...(.((((((.......--..)))))).).......((....)))))))(((((.((((....)))).)))))..........))))))) ( -31.80)
>DroEre_CAF1 70114 111 + 1
CC------CAGCUCAUUAAAUCAUCGUAAAAUUGUCCGCUACCGAG--UUGCGGACUCAAUAUUCUCCUCACAUACGACCGUUUAGCGAGUUUGCUCAGCGGCUGUUUCGACAUGAGCU
..------.(((((((.................((((((.......--..))))))..................(((.(((((.((((....)))).))))).)))......))))))) ( -29.80)
>DroYak_CAF1 69730 117 + 1
CCCGGUGCCAGCUCAUUAAAUCAUCGUAAAAGUGUCCGCUACCGAG--UUGCGGACUCAAUAUUCUGCUCACAUACGACCGUUUAGCGAGUUUGCUCAGCGGCUGUUUCGCCAUGAGCU
.........(((((.((((((..(((((...(.((((((.......--..)))))).).......((....)))))))..)))))).))))).(((((..(((......))).))))). ( -35.10)
>DroAna_CAF1 67641 113 + 1
GC------CGGAUCAUUAAAUCAUCGUAAAAGUGUCCGCUACCGACUUUUGCGGACUCAAUAUUCAGCUCACAUACAACCGUUUAGCGAGUUUGCUCAGCUGCUAUUUCAACAUGAGCU
..------.......................(.((((((...........)))))).).......((((((............(((((((....))).))))...........)))))) ( -24.10)
>consensus
CC______CAGCUCAUUAAAUCAUCGUAAAAGUGUCCGCUACCGAG__UUGCGGACUCAAUAUUCUGCUCACAUACGACCGUUUAGCGAGUUUGCUCAGCGGCUGUUUCGACAUGAGCU
.........(((((((...............(.((((((...........)))))).)................(((.(((((.((((....)))).))))).)))......))))))) (-27.25 = -27.50 +   0.25)

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 10:08:34 2006