Locus 3184

Sequence ID 3L_DroMel_CAF1
Location 9,275,720 – 9,275,812
Length 92
Max. P 0.950524
window4962 window4963

overview

Window 2

Location 9,275,720 – 9,275,812
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.39
Mean single sequence MFE -20.40
Consensus MFE -11.61
Energy contribution -11.92
Covariance contribution 0.31
Combinations/Pair 1.13
Mean z-score -1.73
Structure conservation index 0.57
SVM decision value 0.23
SVM RNA-class probability 0.646107
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9275720 92 + 23771897
GAC-----UUUGGCUG------UAUCUUUUCUAUUGCCACGUUGUUGA-AAUCUAUUAGCCACAUUUAGUGUGGCUCAUAAAAUUCUAUUGCAUCAUUUGUU---UC-------------
...-----..((((.(------((.......))).)))).((.((.((-(.(.(((.((((((((...)))))))).))).).))).)).))..........---..------------- ( -19.10)
>DroPse_CAF1 134803 101 + 1
GACGU---UUUGGCUGUA---GUAUCUUUUCUAUUGCCACGUUGUUGAGAAUCUAUUAGCCACAUUUAGUGUGGCUCAUAAAAUUCUAUUGCAUCAUUUGUUCUCUC-------------
(((((---...(((.(((---(........)))).))))))))((..(((((.(((.((((((((...)))))))).)))..)))))...))...............------------- ( -27.00)
>DroGri_CAF1 124218 111 + 1
GCU-----GCUGUCUGUAUCUGUAUCUUUUCUAUUGCCACAUUGUUAA-AAUCUAUUAGCCACAUUAAGUGCGGCUCGUAAAAUUCGAUUGCAUCAUUUGUU---UGCCUCUCUCUCUCU
(.(-----((.(((.......(((..........)))...........-....(((.((((.(((...))).)))).)))......))).))).).......---............... ( -12.50)
>DroWil_CAF1 213739 97 + 1
GACAGACGCCUGGCUG------UAUCUUUUCUAUUGCCACGUUGUUGA-AAUCUAUUAGCCACAUUUAGUGUGGCUCAUAAAAUUCUAUUGCAUCAUUUGUU---UC-------------
((((((.((.((((.(------((.......))).)))).))(((.((-(.(.(((.((((((((...)))))))).))).).)))....)))...))))))---..------------- ( -22.20)
>DroMoj_CAF1 143823 86 + 1
GCG-----GCUGUCUGUAUCU------UU------UCCACAUUGUUAA-AAUCUAUUAGCCACAUUAAAUGUGGCUCGUAAAAUUCGAUUGCAUCAUUUGUU---UC-------------
...-----((.((((((....------..------...))).......-....(((.((((((((...)))))))).)))......))).))..........---..------------- ( -14.60)
>DroPer_CAF1 135765 101 + 1
GACGU---UUUGGCUGUA---GUAUCUUUUCUAUUGCCACGUUGUUGAGAAUCUAUUAGCCACAUUUAGUGUGGCUCAUAAAAUUCUAUUGCAUCAUUUGUUCUCUC-------------
(((((---...(((.(((---(........)))).))))))))((..(((((.(((.((((((((...)))))))).)))..)))))...))...............------------- ( -27.00)
>consensus
GAC_____UCUGGCUGUA____UAUCUUUUCUAUUGCCACGUUGUUGA_AAUCUAUUAGCCACAUUUAGUGUGGCUCAUAAAAUUCUAUUGCAUCAUUUGUU___UC_____________
..........((((.....................))))..............(((.((((((((...)))))))).)))........................................ (-11.61 = -11.92 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,275,720 – 9,275,812
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.39
Mean single sequence MFE -21.22
Consensus MFE -13.38
Energy contribution -13.85
Covariance contribution 0.47
Combinations/Pair 1.11
Mean z-score -2.28
Structure conservation index 0.63
SVM decision value 1.40
SVM RNA-class probability 0.950524
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9275720 92 - 23771897
-------------GA---AACAAAUGAUGCAAUAGAAUUUUAUGAGCCACACUAAAUGUGGCUAAUAGAUU-UCAACAACGUGGCAAUAGAAAAGAUA------CAGCCAAA-----GUC
-------------..---................(((.(((((.(((((((.....))))))).))))).)-)).......((((..((.......))------..))))..-----... ( -20.30)
>DroPse_CAF1 134803 101 - 1
-------------GAGAGAACAAAUGAUGCAAUAGAAUUUUAUGAGCCACACUAAAUGUGGCUAAUAGAUUCUCAACAACGUGGCAAUAGAAAAGAUAC---UACAGCCAAA---ACGUC
-------------............((((....(((((((....(((((((.....)))))))...)))))))........((((..(((........)---))..))))..---.)))) ( -23.50)
>DroGri_CAF1 124218 111 - 1
AGAGAGAGAGAGGCA---AACAAAUGAUGCAAUCGAAUUUUACGAGCCGCACUUAAUGUGGCUAAUAGAUU-UUAACAAUGUGGCAAUAGAAAAGAUACAGAUACAGACAGC-----AGC
...............---.........(((..(((((.((((..(((((((.....)))))))..)))).)-)).....((((.............))))......))..))-----).. ( -16.52)
>DroWil_CAF1 213739 97 - 1
-------------GA---AACAAAUGAUGCAAUAGAAUUUUAUGAGCCACACUAAAUGUGGCUAAUAGAUU-UCAACAACGUGGCAAUAGAAAAGAUA------CAGCCAGGCGUCUGUC
-------------..---.......(((((....(((.(((((.(((((((.....))))))).))))).)-)).......((((..((.......))------..)))).))))).... ( -27.20)
>DroMoj_CAF1 143823 86 - 1
-------------GA---AACAAAUGAUGCAAUCGAAUUUUACGAGCCACAUUUAAUGUGGCUAAUAGAUU-UUAACAAUGUGGA------AA------AGAUACAGACAGC-----CGC
-------------..---..........((..(((((.((((..((((((((...))))))))..)))).)-)).....((((..------..------...))))))..))-----... ( -16.30)
>DroPer_CAF1 135765 101 - 1
-------------GAGAGAACAAAUGAUGCAAUAGAAUUUUAUGAGCCACACUAAAUGUGGCUAAUAGAUUCUCAACAACGUGGCAAUAGAAAAGAUAC---UACAGCCAAA---ACGUC
-------------............((((....(((((((....(((((((.....)))))))...)))))))........((((..(((........)---))..))))..---.)))) ( -23.50)
>consensus
_____________GA___AACAAAUGAUGCAAUAGAAUUUUAUGAGCCACACUAAAUGUGGCUAAUAGAUU_UCAACAACGUGGCAAUAGAAAAGAUA____UACAGCCAAA_____GUC
..................................((..(((((.(((((((.....))))))).)))))...)).......((((.....................)))).......... (-13.38 = -13.85 +   0.47)

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 10:51:34 2006