Locus 4878

Sequence ID 3L_DroMel_CAF1
Location 13,615,300 – 13,615,431
Length 131
Max. P 0.909142
window7700 window7701 window7702

overview

Window 0

Location 13,615,300 – 13,615,401
Length 101
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 76.96
Mean single sequence MFE -40.23
Consensus MFE -22.97
Energy contribution -23.33
Covariance contribution 0.36
Combinations/Pair 1.20
Mean z-score -1.59
Structure conservation index 0.57
SVM decision value 0.18
SVM RNA-class probability 0.619466
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13615300 101 + 23771897
CCCCC--CA-----------UGCCAGCGUUGUUGUGGGUGGUCCUUUUUGGGCGG--GGGGCUAUGAUGGGUGCAUGGACCCAUAAACUGCGUUAGUUUAUGAUGCCCAAGCGCUA
(((((--(.-----------.(((.(((....))).))).((((.....))))))--))))........(((((.(((.(.(((((((((...)))))))))..).))).))))). ( -41.30)
>DroSec_CAF1 22296 100 + 1
CCCCCCCCU-----------AGCUAGCGUUGUUGUGGGUGGUCCUUUUUGG---G--GGGGCUGUGCUGGGUGCAUGGACCCAUAAACUGCGUUAGUUUAUGAUGCCCGAGCGCUA
.((((((((-----------(((.......)))).(((....)))....))---)--))))..(((((.((.((((.....(((((((((...))))))))))))))).))))).. ( -40.50)
>DroSim_CAF1 31390 99 + 1
CCCCCCUCU-----------UGCCAGCGUUGUUGUGGGUGGUCCUUUUCGG------GGGGCUGUGCUGGGUGCAUGGACCCAUAAACUGCGUUAGUUUAUGAUGCCCGAGCGCUA
((((((...-----------.(((.(((....))).)))((......))))------))))..(((((.((.((((.....(((((((((...))))))))))))))).))))).. ( -39.10)
>DroEre_CAF1 25116 112 + 1
CUCCCCCCAUUCUCCC--CAUUCU--CGCUGUUGUGGGAGGUCCUUUUUGGGGGGCGGGGGCUGUGCUGGGUGCAUGGACCCAUAAACUGCGUUAGUUUAUGAUGCCCGAGCGCUA
...(((((...(((((--((((((--(((....)))))))........))))))).)))))..(((((.((.((((.....(((((((((...))))))))))))))).))))).. ( -49.90)
>DroYak_CAF1 29426 116 + 1
CCCCUCCCCCACCGCCGGCUUUCCUGCGUUGUUGUGGGAGGUCCUUUUUGGGGAGUUGGGGCUUUGCUGGCUGCAUGGACCCAUAAACUGCGUUAGUUUAUGAUGCCCGAGCGCUA
((((.((((((((((.((....)).))).....))))).))........)))).(((.((((..(((.....)))......(((((((((...)))))))))..)))).))).... ( -41.90)
>DroAna_CAF1 58694 89 + 1
CUCCC----------------GGCAUCUACGAUGUGGCA-GUCA----------GCAUGGAGUGUCCUGGGUGCAUGGACCCAUAAACUCCGUUAGUUUAUGAUGCCCGAGCGCUA
(((..----------------((((((.(((((......-))).----------..(((((((....(((((......)))))...)))))))..))....)))))).)))..... ( -28.70)
>consensus
CCCCCCCCA___________UGCCAGCGUUGUUGUGGGAGGUCCUUUUUGG___G__GGGGCUGUGCUGGGUGCAUGGACCCAUAAACUGCGUUAGUUUAUGAUGCCCGAGCGCUA
.((((................(((..((....))..)))...((.....))......))))..(((((.((.((((.....((((((((.....)))))))))))))).))))).. (-22.97 = -23.33 +   0.36)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,615,300 – 13,615,401
Length 101
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 76.96
Mean single sequence MFE -34.87
Consensus MFE -18.02
Energy contribution -18.63
Covariance contribution 0.61
Combinations/Pair 1.05
Mean z-score -1.84
Structure conservation index 0.52
SVM decision value 0.26
SVM RNA-class probability 0.658139
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13615300 101 - 23771897
UAGCGCUUGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCACCCAUCAUAGCCCC--CCGCCCAAAAAGGACCACCCACAACAACGCUGGCA-----------UG--GGGGG
....((.(((((.(((((((((.....)))))))))))))).))...........((((--(((.((.....)).....((((......).)))..-----------))--))))) ( -33.80)
>DroSec_CAF1 22296 100 - 1
UAGCGCUCGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCACCCAGCACAGCCCC--C---CCAAAAAGGACCACCCACAACAACGCUAGCU-----------AGGGGGGGG
....((..((((.(((((((((.....)))))))))))))..))...........((((--(---((.....((.....))........(....).-----------.))))))). ( -35.00)
>DroSim_CAF1 31390 99 - 1
UAGCGCUCGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCACCCAGCACAGCCCC------CCGAAAAGGACCACCCACAACAACGCUGGCA-----------AGAGGGGGG
....((..((((.(((((((((.....)))))))))))))..))...........((((------((.....((.....)).........((....-----------)).)))))) ( -31.30)
>DroEre_CAF1 25116 112 - 1
UAGCGCUCGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCACCCAGCACAGCCCCCGCCCCCCAAAAAGGACCUCCCACAACAGCG--AGAAUG--GGGAGAAUGGGGGGAG
....(((.((((.(((((((((.....))))))))))))).(((.....))).))).....(((((((........(((((.((......--....))--)))))..))))))).. ( -38.20)
>DroYak_CAF1 29426 116 - 1
UAGCGCUCGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCAGCCAGCAAAGCCCCAACUCCCCAAAAAGGACCUCCCACAACAACGCAGGAAAGCCGGCGGUGGGGGAGGGG
..((((..((((.(((((((((.....)))))))))))))..)).))........((((...(((.......))).(((((((.....(((.((....)).)))))))))).)))) ( -42.60)
>DroAna_CAF1 58694 89 - 1
UAGCGCUCGGGCAUCAUAAACUAACGGAGUUUAUGGGUCCAUGCACCCAGGACACUCCAUGC----------UGAC-UGCCACAUCGUAGAUGCC----------------GGGAG
....((..((((.(((((((((.....)))))))))))))..)).(((.((.....))..((----------...(-(((......))))..)).----------------))).. ( -28.30)
>consensus
UAGCGCUCGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCACCCAGCACAGCCCC__C___CCAAAAAGGACCACCCACAACAACGCUGGCA___________AGGGGGGGG
((((((..((((.(((((((((.....)))))))))))))..))............................((.....))........))))....................... (-18.02 = -18.63 +   0.61)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,615,323 – 13,615,431
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.04
Mean single sequence MFE -30.68
Consensus MFE -21.30
Energy contribution -21.63
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.69
SVM decision value 1.06
SVM RNA-class probability 0.909142
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13615323 108 - 23771897
----------UGUCGCUCUGCGUAUUUCGCUUUGCUCACUUAGCGCUUGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCACCCAUCAUAGCCCC--CCGCCCAAAAAGGACCACC
----------.(((((...(((.....)))...)).......(((...((((...(((((((.....)))))))((((......))))......)))).--.)))........))).... ( -29.20)
>DroPse_CAF1 4660 106 - 1
AUCCGCUCGCUGU--CUCAGCGCACUUCGCUUUGCUCACUUAGCGCUCGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCACCCAAAGCAGAC------------AGGGAACGACA
...((.((.((((--((..((.......(((..(....)..)))((..((((.(((((((((.....)))))))))))))..)).......))))))------------)).)).))... ( -34.80)
>DroSim_CAF1 31415 104 - 1
----------UGUCGCUCUGCGUAUUUCGCUUUGCUCACUUAGCGCUCGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCACCCAGCACAGCCCC------CCGAAAAGGACCACC
----------.(((((...(((.....)))...))...(((..((...((((.(((((((((.....))))))))).....(((.....)))..)))).------.))..)))))).... ( -29.10)
>DroYak_CAF1 29462 110 - 1
----------UGUCGCUCUGCGUAUUUCGCUUUGCUCACUUAGCGCUCGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCAGCCAGCAAAGCCCCAACUCCCCAAAAAGGACCUCC
----------.(((((...)).......((((((((......((((..((((.(((((((((.....)))))))))))))..)).)).)))))))).................))).... ( -29.80)
>DroAna_CAF1 58714 104 - 1
----GAUUGCUGUC-CUCUGCGAUUUUCGCUUUGCUCACUUAGCGCUCGGGCAUCAUAAACUAACGGAGUUUAUGGGUCCAUGCACCCAGGACACUCCAUGC----------UGAC-UGC
----......((((-((..(((.....)))...(((.....)))((..((((.(((((((((.....)))))))))))))..))....))))))........----------....-... ( -29.50)
>DroPer_CAF1 4642 106 - 1
AUCCGCUAGCUGU--CUCAGCGCACUUCGCUUUGCUCACUUAGCGCUCGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCACCCAAAGCAGAC------------AGGGAACGACA
.(((((..((((.--..)))))).....((((((((.....)))((..((((.(((((((((.....)))))))))))))..))....)))))....------------..)))...... ( -31.70)
>consensus
__________UGUC_CUCUGCGUAUUUCGCUUUGCUCACUUAGCGCUCGGGCAUCAUAAACUAACGCAGUUUAUGGGUCCAUGCACCCAGCACAGCCCC__________AAAGGACCACC
...........(((.....(((.....)))...(((.....)))((..((((.(((((((((.....)))))))))))))..)).............................))).... (-21.30 = -21.63 +   0.33)

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 11:35:57 2006