Locus 602

Sequence ID X_DroMel_CAF1
Location 1,672,913 – 1,673,055
Length 142
Max. P 0.998533
window975 window976 window977

overview

Window 5

Location 1,672,913 – 1,673,015
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.59
Mean single sequence MFE -45.62
Consensus MFE -30.88
Energy contribution -33.76
Covariance contribution 2.88
Combinations/Pair 1.09
Mean z-score -3.68
Structure conservation index 0.68
SVM decision value 3.13
SVM RNA-class probability 0.998533
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1672913 102 + 22224390
AGGAGCUUGGGGAGACCCAGGCCACGGAGCUUGUGCAGCUCCUGCUCGGUUACCGGGU--------AUCUGUGUGGCUCAUUUGACACUCGAAUGAGCCAAUGUA--UA------G--CA
.(..(((((((....)))))))..)((((((.....))))))(((((((...))))))--------).((((((((((((((((.....)))))))))))...))--))------)--.. ( -52.20)
>DroSec_CAF1 7021 102 + 1
AGGAGCUUGGGGAGACCCAGGCCACGGAGCUUGUGCAGCUCCUGCUCGGUUGCCGGCU--------AUCUGUGUGGCUCAUUUGACACUCGAAUGAGCCAAUGUA--UA------G--CA
.(..(((((((....)))))))..)((((((.....))))))....(((...)))(((--------((.....(((((((((((.....)))))))))))....)--))------)--). ( -50.90)
>DroSim_CAF1 7807 102 + 1
AGGAGCUUGGGGAGACCCAGGCCACGGAGCUUGUGCAGCUCAUGCUCGGUUGCCGGCU--------AUCUGUGUGGCUCAUUUGACACUCGAAUGAGCCAAUGUA--UA------G--CA
..(.(((((((....)))))))).(((((((.(.(((.....))).))))).)))(((--------((.....(((((((((((.....)))))))))))....)--))------)--). ( -49.00)
>DroEre_CAF1 10587 106 + 1
AGGAG--UG--GAGACCCAAGCCAUGGAGCUUGUGCAGCUCCUGCUCGGUUACCGGCU--------ACCUGUGUGGCUCAUUUGACACUCGAAUGAGUCAAUGUA--UAUUCGGUGUACA
(((((--((--(.((((..(((...((((((.....)))))).))).)))).)).)))--------.)))...(((((((((((.....))))))))))).((((--(((...))))))) ( -41.10)
>DroYak_CAF1 9235 105 + 1
AGCAG--UGGGGAGACGGAAGCCA-----------CAGCUCCUGCUCGGUUAUCGGCUAUCUGGCUAUCUGUGUGGCUCAUUUGACACUCGAAUGAGUCAAUGUGUAUAAUCGUGG--CA
.....--...(....)....((((-----------((((....))).(((((((((((....)))).......(((((((((((.....)))))))))))....).))))))))))--). ( -34.90)
>consensus
AGGAGCUUGGGGAGACCCAGGCCACGGAGCUUGUGCAGCUCCUGCUCGGUUACCGGCU________AUCUGUGUGGCUCAUUUGACACUCGAAUGAGCCAAUGUA__UA______G__CA
....(((((((....)))))))(((((((((.....)))))).((.(((...))))).............)))(((((((((((.....))))))))))).................... (-30.88 = -33.76 +   2.88)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,672,913 – 1,673,015
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.59
Mean single sequence MFE -33.74
Consensus MFE -20.58
Energy contribution -24.18
Covariance contribution 3.60
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.61
SVM decision value 0.01
SVM RNA-class probability 0.536579
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1672913 102 - 22224390
UG--C------UA--UACAUUGGCUCAUUCGAGUGUCAAAUGAGCCACACAGAU--------ACCCGGUAACCGAGCAGGAGCUGCACAAGCUCCGUGGCCUGGGUCUCCCCAAGCUCCU
.(--(------(.--.....(((((((((.(.....).)))))))))....((.--------((((((...(((....((((((.....)))))).))).)))))).))....))).... ( -38.90)
>DroSec_CAF1 7021 102 - 1
UG--C------UA--UACAUUGGCUCAUUCGAGUGUCAAAUGAGCCACACAGAU--------AGCCGGCAACCGAGCAGGAGCUGCACAAGCUCCGUGGCCUGGGUCUCCCCAAGCUCCU
.(--(------((--(....(((((((((.(.....).))))))))).....))--------))).(....).((((.((((((.....))))))......((((....)))).)))).. ( -40.50)
>DroSim_CAF1 7807 102 - 1
UG--C------UA--UACAUUGGCUCAUUCGAGUGUCAAAUGAGCCACACAGAU--------AGCCGGCAACCGAGCAUGAGCUGCACAAGCUCCGUGGCCUGGGUCUCCCCAAGCUCCU
.(--(------((--(....(((((((((.(.....).))))))))).....))--------))).(....).((((..(((((.....))))).......((((....)))).)))).. ( -36.10)
>DroEre_CAF1 10587 106 - 1
UGUACACCGAAUA--UACAUUGACUCAUUCGAGUGUCAAAUGAGCCACACAGGU--------AGCCGGUAACCGAGCAGGAGCUGCACAAGCUCCAUGGCUUGGGUCUC--CA--CUCCU
.....((((..((--(....((.((((((.(.....).)))))).)).....))--------)..))))..((((((.((((((.....))))))...)))))).....--..--..... ( -33.80)
>DroYak_CAF1 9235 105 - 1
UG--CCACGAUUAUACACAUUGACUCAUUCGAGUGUCAAAUGAGCCACACAGAUAGCCAGAUAGCCGAUAACCGAGCAGGAGCUG-----------UGGCUUCCGUCUCCCCA--CUGCU
..--..(((..........(((((.(......).)))))..(((((((((.....((......))......((.....)).).))-----------)))))).))).......--..... ( -19.40)
>consensus
UG__C______UA__UACAUUGGCUCAUUCGAGUGUCAAAUGAGCCACACAGAU________AGCCGGUAACCGAGCAGGAGCUGCACAAGCUCCGUGGCCUGGGUCUCCCCAAGCUCCU
....................(((((((((.(.....).)))))))))(((.............((((.....)).)).((((((.....)))))))))((.((((....)))).)).... (-20.58 = -24.18 +   3.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,672,953 – 1,673,055
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.92
Mean single sequence MFE -42.42
Consensus MFE -33.65
Energy contribution -33.29
Covariance contribution -0.36
Combinations/Pair 1.09
Mean z-score -3.10
Structure conservation index 0.79
SVM decision value 2.73
SVM RNA-class probability 0.996679
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1672953 102 + 22224390
CCUGCUCGGUUACCGGGU--------AUCUGUGUGGCUCAUUUGACACUCGAAUGAGCCAAUGUA--UA------G--CAUGGCGAGUGGGUCCAAUGGGUGAGCAAGUCCUCAUGCAUA
((..((((....((((.(--------((.....(((((((((((.....)))))))))))....)--))------.--).)))))))..))....(((.(((((......))))).))). ( -39.40)
>DroSec_CAF1 7061 102 + 1
CCUGCUCGGUUGCCGGCU--------AUCUGUGUGGCUCAUUUGACACUCGAAUGAGCCAAUGUA--UA------G--CAUGGCGAGUGGGUCCAAUGGGUGAGCAAGUCCUCAUGCAUA
...(((((.(((((((((--------((.....(((((((((((.....)))))))))))....)--))------)--).)))))).)))))...(((.(((((......))))).))). ( -46.10)
>DroSim_CAF1 7847 102 + 1
CAUGCUCGGUUGCCGGCU--------AUCUGUGUGGCUCAUUUGACACUCGAAUGAGCCAAUGUA--UA------G--CAUGGCGAGUGGGUCCAAUGGGUGAGCAAGUCCUCAUGCAUA
...(((((.(((((((((--------((.....(((((((((((.....)))))))))))....)--))------)--).)))))).)))))...(((.(((((......))))).))). ( -46.10)
>DroEre_CAF1 10623 110 + 1
CCUGCUCGGUUACCGGCU--------ACCUGUGUGGCUCAUUUGACACUCGAAUGAGUCAAUGUA--UAUUCGGUGUACAUGGCGAGUGGGUCCAAUGGGUGAGCAAGUCCUCAUGCAUA
((..(((((...)).(((--------.......(((((((((((.....)))))))))))(((((--(((...))))))))))))))..))....(((.(((((......))))).))). ( -40.00)
>DroYak_CAF1 9262 118 + 1
CCUGCUCGGUUAUCGGCUAUCUGGCUAUCUGUGUGGCUCAUUUGACACUCGAAUGAGUCAAUGUGUAUAAUCGUGG--CAUGGCGAGUGGGUCCAAUGGGUGAGCAAGUUCUCAUGCAUA
((..((((.(.....(((((..(..((((....(((((((((((.....)))))))))))....).)))..)))))--)..).))))..))....(((.(((((......))))).))). ( -40.50)
>consensus
CCUGCUCGGUUACCGGCU________AUCUGUGUGGCUCAUUUGACACUCGAAUGAGCCAAUGUA__UA______G__CAUGGCGAGUGGGUCCAAUGGGUGAGCAAGUCCUCAUGCAUA
((((((((....(((..............((..(((((((((((.....)))))))))).)..))...............)))))))))))....(((.(((((......))))).))). (-33.65 = -33.29 +  -0.36)

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 09:49:12 2006