Locus 460

Sequence ID 3L_DroMel_CAF1
Location 1,333,460 – 1,333,844
Length 384
Max. P 0.986266
window670 window671 window672 window673 window674 window675 window676

overview

Window 0

Location 1,333,460 – 1,333,574
Length 114
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 77.84
Mean single sequence MFE -35.40
Consensus MFE -18.97
Energy contribution -20.53
Covariance contribution 1.56
Combinations/Pair 1.08
Mean z-score -3.36
Structure conservation index 0.54
SVM decision value 2.04
SVM RNA-class probability 0.986266
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1333460 114 + 23771897
CAAGCAUAAAUAUGCCAAAUACAGGCCAAU---ACACACGCACGAACUCACA--CACACACGCGUUCGAUGGAGAAUGCAAAGUAAAGUGCAGCAGGUGUGCGUGUAUGUGUGUUGGUG
...((((....)))).........((((((---(((((..((((....((((--(......((((((......))))))...((.....)).....)))))))))..))))))))))). ( -40.60)
>DroSec_CAF1 5633 115 + 1
CAAGCAUAAAUAUGCCAAAUACAGGCCAGCAACACGCACGCACGAACACACA----CACACACGUUUGAUGGAGAAUGCAAAGUAAAGUGCAGCAGGUGUGCGCGUGUAUAUGUUGGUG
...((((....)))).........(((((((((((((.(((((...((((.(----(......)).)).)).....((((........))))....))))).))))))...))))))). ( -33.90)
>DroEre_CAF1 5823 94 + 1
CAAGCAUAAAUAAGCCAAAUAC-------------------A------CACACACACACACACGUUUGAUGUAGAAUGCAAAGUAAAGUGCAGCAGGUGUGCGCGUGUGUGUGUUGGUG
.............(((((.(((-------------------(------(((((.(.(((((((((...))))....((((........))))....))))).).)))))))))))))). ( -31.70)
>consensus
CAAGCAUAAAUAUGCCAAAUACAGGCCA_____AC_CACGCACGAAC_CACA__CACACACACGUUUGAUGGAGAAUGCAAAGUAAAGUGCAGCAGGUGUGCGCGUGUGUGUGUUGGUG
...((((....)))).................................(((...(((((((((((...........((((........))))(((....))))))))))))))...))) (-18.97 = -20.53 +   1.56)

alignment

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secondary structure

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Window 1

Location 1,333,460 – 1,333,574
Length 114
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 77.84
Mean single sequence MFE -34.71
Consensus MFE -18.69
Energy contribution -19.37
Covariance contribution 0.67
Combinations/Pair 1.12
Mean z-score -3.27
Structure conservation index 0.54
SVM decision value 1.98
SVM RNA-class probability 0.984470
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1333460 114 - 23771897
CACCAACACACAUACACGCACACCUGCUGCACUUUACUUUGCAUUCUCCAUCGAACGCGUGUGUG--UGUGAGUUCGUGCGUGUGU---AUUGGCCUGUAUUUGGCAUAUUUAUGCUUG
......(((((((((((((........((((........))))(((......))).)))))))))--)))).......(((((.((---((..(((.......))))))).)))))... ( -36.40)
>DroSec_CAF1 5633 115 - 1
CACCAACAUAUACACGCGCACACCUGCUGCACUUUACUUUGCAUUCUCCAUCAAACGUGUGUG----UGUGUGUUCGUGCGUGCGUGUUGCUGGCCUGUAUUUGGCAUAUUUAUGCUUG
(((.((((((((((((((((....)))((((........))))...............)))))----)))))))).)))...(((((......(((.......))).....)))))... ( -34.30)
>DroEre_CAF1 5823 94 - 1
CACCAACACACACACGCGCACACCUGCUGCACUUUACUUUGCAUUCUACAUCAAACGUGUGUGUGUGUGUG------U-------------------GUAUUUGGCUUAUUUAUGCUUG
.....((((((((((((((((((....((((........)))).............)))))))))))))))------)-------------------))....(((........))).. ( -33.43)
>consensus
CACCAACACACACACGCGCACACCUGCUGCACUUUACUUUGCAUUCUCCAUCAAACGUGUGUGUG__UGUG_GUUCGUGCGUG_GU_____UGGCCUGUAUUUGGCAUAUUUAUGCUUG
(((...(((((((((..(((....)))((((........)))).............)))))))))...)))................................(((((....))))).. (-18.69 = -19.37 +   0.67)

alignment

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secondary structure

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Window 2

Location 1,333,496 – 1,333,614
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.75
Mean single sequence MFE -29.56
Consensus MFE -16.86
Energy contribution -17.20
Covariance contribution 0.34
Combinations/Pair 1.16
Mean z-score -3.37
Structure conservation index 0.57
SVM decision value 0.26
SVM RNA-class probability 0.659293
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1333496 118 - 23771897
AAAACAAAAACCCAUGGAAAAGAAUGUACAAACAGAAUAGCACCAACACACAUACACGCACACCUGCUGCACUUUACUUUGCAUUCUCCAUCGAACGCGUGUGUG--UGUGAGUUCGUGC
............((((((......(((....)))............(((((((((((((........((((........))))(((......))).)))))))))--))))..)))))). ( -30.50)
>DroSec_CAF1 5672 116 - 1
AAAACAAAAACCACUGGAAAAGAAUGUACAAACAGAAUAGCACCAACAUAUACACGCGCACACCUGCUGCACUUUACUUUGCAUUCUCCAUCAAACGUGUGUG----UGUGUGUUCGUGC
.............(((................)))....((((.((((((((((((((((....)))((((........))))...............)))))----)))))))).)))) ( -29.49)
>DroEre_CAF1 5845 112 - 1
AAAACAAAAAACACUGAAAAAGAAUGUACAAACAGAAUCUCACCAACACACACACGCGCACACCUGCUGCACUUUACUUUGCAUUCUACAUCAAACGUGUGUGUGUGUGUG------U--
..........((((......(((.(((....)))...))).....(((((((((((((((....)))((((........)))).............)))))))))))))))------)-- ( -28.70)
>consensus
AAAACAAAAACCACUGGAAAAGAAUGUACAAACAGAAUAGCACCAACACACACACGCGCACACCUGCUGCACUUUACUUUGCAUUCUCCAUCAAACGUGUGUGUG__UGUG_GUUCGUGC
........................................(((...(((((((((..(((....)))((((........)))).............)))))))))...)))......... (-16.86 = -17.20 +   0.34)

alignment

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secondary structure

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Window 3

Location 1,333,574 – 1,333,684
Length 110
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 86.48
Mean single sequence MFE -24.26
Consensus MFE -16.19
Energy contribution -16.75
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.12
Structure conservation index 0.67
SVM decision value 0.51
SVM RNA-class probability 0.762505
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1333574 110 + 23771897
CUAUUCUGUUUGUACAUUCUUUUCCAUGGGUUUUUGUUUUUGGCCAAAGCCUGGCUGUUAAAGCAACAACUGCAACAACAACAGCACUGACACACAAUACACACGC--ACAC
......(((.(((.((...........(((((((.((.....)).))))))).((((((...(((.....)))......))))))..))))).)))..........--.... ( -18.90)
>DroSec_CAF1 5748 101 + 1
CUAUUCUGUUUGUACAUUCUUUUCCAGUGGUUUUUGUUUUUGGCCAAAGCCUGGCUGUAUAAGCAG---------CAACAACACCGCUGGCACACAACACACACGC--ACAC
......(((.(((..........((((((((..(((((...(((....)))..(((((....))))---------)))))).))))))))..........))).))--)... ( -27.95)
>DroSim_CAF1 5787 99 + 1
CUAUUCUGUUUGUACAUUCUUUUCCAGUGGUUUUUGUUUUUGGCCAAAGCCUGGCUGUUAAAGCAA---------CAACAACACCGCUGGCACACAACA--CACGA--ACAC
......(((((((..........((((((((..(((((...(((....)))..(((.....)))..---------.))))).)))))))).........--.))))--))). ( -27.15)
>DroYak_CAF1 5931 109 + 1
AGAUUCUGUUUGUACAUUCUUUUUCAGUGGUUUUUGUUUUUGGCCAAAGCCUGGCUGUUAAAGCAACAC---CAACAACAACACCGCUGGCACACAACACACACACACACAC
......(((.(((..........((((((((..(((((.(((((((.....))))(((....)))....---))).))))).))))))))..........))).)))..... ( -23.05)
>consensus
CUAUUCUGUUUGUACAUUCUUUUCCAGUGGUUUUUGUUUUUGGCCAAAGCCUGGCUGUUAAAGCAA_________CAACAACACCGCUGGCACACAACACACACGC__ACAC
......(((.(((...........(((((((..(((((...(((....)))..(((.....)))............))))).)))))))))).)))................ (-16.19 = -16.75 +   0.56)

alignment

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secondary structure

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Window 4

Location 1,333,574 – 1,333,684
Length 110
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 86.48
Mean single sequence MFE -29.45
Consensus MFE -19.61
Energy contribution -20.55
Covariance contribution 0.94
Combinations/Pair 1.07
Mean z-score -1.55
Structure conservation index 0.67
SVM decision value -0.02
SVM RNA-class probability 0.520849
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1333574 110 - 23771897
GUGU--GCGUGUGUAUUGUGUGUCAGUGCUGUUGUUGUUGCAGUUGUUGCUUUAACAGCCAGGCUUUGGCCAAAAACAAAAACCCAUGGAAAAGAAUGUACAAACAGAAUAG
.(((--((((.....(..((.((..(.(((((((..((.((....)).))..)))))))).(((....)))..........)).))..)......))))))).......... ( -26.60)
>DroSec_CAF1 5748 101 - 1
GUGU--GCGUGUGUGUUGUGUGCCAGCGGUGUUGUUG---------CUGCUUAUACAGCCAGGCUUUGGCCAAAAACAAAAACCACUGGAAAAGAAUGUACAAACAGAAUAG
.(((--...((((..((.(...((((.(((.((((((---------(((......))))..(((....)))...)))))..))).))))...).))..)))).)))...... ( -32.20)
>DroSim_CAF1 5787 99 - 1
GUGU--UCGUG--UGUUGUGUGCCAGCGGUGUUGUUG---------UUGCUUUAACAGCCAGGCUUUGGCCAAAAACAAAAACCACUGGAAAAGAAUGUACAAACAGAAUAG
.(((--(.(((--..((.(...((((.((((((((((---------......)))))))..(((....)))..........))).))))...).))..))).))))...... ( -30.60)
>DroYak_CAF1 5931 109 - 1
GUGUGUGUGUGUGUGUUGUGUGCCAGCGGUGUUGUUGUUG---GUGUUGCUUUAACAGCCAGGCUUUGGCCAAAAACAAAAACCACUGAAAAAGAAUGUACAAACAGAAUCU
...(.(((.((((..((.(....(((.(((....((((((---((((((...))))).)).(((....)))...)))))..))).)))....).))..)))).))).).... ( -28.40)
>consensus
GUGU__GCGUGUGUGUUGUGUGCCAGCGGUGUUGUUG_________UUGCUUUAACAGCCAGGCUUUGGCCAAAAACAAAAACCACUGGAAAAGAAUGUACAAACAGAAUAG
.(((.....((((((((.(...((((.(((.(((((............(((.....)))..(((....)))...)))))..))).))))...).)))))))).)))...... (-19.61 = -20.55 +   0.94)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,333,614 – 1,333,724
Length 110
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 87.25
Mean single sequence MFE -31.40
Consensus MFE -28.55
Energy contribution -28.42
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -1.28
Structure conservation index 0.91
SVM decision value -0.03
SVM RNA-class probability 0.517892
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1333614 110 + 23771897
UGGCCAAAGCCUGGCUGUUAAAGCAACAACUGCAACAACAACAGCACUGACACACAAUACACACGC--ACACACGUAAAGCUCGCCGCUGCACUGGUGUUGGUGGUGGAGGC
..(((...(((..((((((...(((.....)))......))))))((..((((.((......(((.--.....)))..(((.....)))....))))))..)))))...))) ( -28.40)
>DroSec_CAF1 5788 101 + 1
UGGCCAAAGCCUGGCUGUAUAAGCAG---------CAACAACACCGCUGGCACACAACACACACGC--ACACACGUAAAGCUCGCCGCUGCACUGGUGUUAGUGGUGGAGGC
........((((.(((((....))))---------).....((((((((((((.((......(((.--.....)))..(((.....)))....)))))))))))))).)))) ( -35.40)
>DroSim_CAF1 5827 99 + 1
UGGCCAAAGCCUGGCUGUUAAAGCAA---------CAACAACACCGCUGGCACACAACA--CACGA--ACACACGUAAAGCUCGCCGCUGCACUGGUGUUAGUGGUGGAGGC
........((((.(((.....)))..---------......((((((((((((.((...--.(((.--.....)))..(((.....)))....)))))))))))))).)))) ( -31.70)
>DroYak_CAF1 5971 109 + 1
UGGCCAAAGCCUGGCUGUUAAAGCAACAC---CAACAACAACACCGCUGGCACACAACACACACACACACACACGUAAAGCUCGCCGAUGCACUUGUGUUGGUGGUGGAGGC
........((((((.((((.....)))))---)........((((((..(((((............((......))...((........))...)))))..)))))).)))) ( -30.10)
>consensus
UGGCCAAAGCCUGGCUGUUAAAGCAA_________CAACAACACCGCUGGCACACAACACACACGC__ACACACGUAAAGCUCGCCGCUGCACUGGUGUUAGUGGUGGAGGC
........((((.(((.....))).................((((((((((((.........(((........)))...((........))....)))))))))))).)))) (-28.55 = -28.42 +  -0.12)

alignment

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secondary structure

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Window 6

Location 1,333,724 – 1,333,844
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.67
Mean single sequence MFE -41.96
Consensus MFE -40.58
Energy contribution -40.66
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.53
Structure conservation index 0.97
SVM decision value 2.03
SVM RNA-class probability 0.986018
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1333724 120 + 23771897
AUCUGCAGAAGCCUUUUGCGCACUCAUCACAUUUUCGUGGAAAUCGGAGCGCCAAGGAGCUGUGGAAAGGUGUAUACUCCGCAUCCGUUGCGAAUCCUUGGCGAAUCGAACUGUGCCACA
....(((((.....)))))((((...((((......))))...((((..(((((((((((..((((..((.(....).))...))))..))...)))))))))..))))...)))).... ( -42.00)
>DroSec_CAF1 5889 120 + 1
AUCUGCAGAAGCCUUUUGCGCACUCAUCACAUUUUCGUGGAAAUCGGAGCGCCAAGGAGCUGUGGAAAGGUGUAUACUCCGCAUCCGUUGCGAAUCCUUGGCGACUCGAAUUGUGCCACA
....(((((.....)))))((((...((((......))))...((((..(((((((((((..((((..((.(....).))...))))..))...)))))))))..))))...)))).... ( -42.10)
>DroSim_CAF1 5926 120 + 1
AUCUGCAGAAGCCUUUUGCGCACUCAUCACAUUUUCGUGGAAAUCGGAGCGCCAAGGAGCUGUGGAAAGGUGUAUACUCCGCAUCCGUUGCGAAUCCUUGGCGACUCGAAUUGUGCCACA
....(((((.....)))))((((...((((......))))...((((..(((((((((((..((((..((.(....).))...))))..))...)))))))))..))))...)))).... ( -42.10)
>DroEre_CAF1 6068 120 + 1
AUCUGCAGAAGCCUUUUGCGCACUCAUCACAUUUUCGUGGAAAUCGGACCGCCAAGGAGCUCUGGAAAGGUGUGUACUCCGCAUCCGUGGCGAAUCCUUGGCGACCCGAGCUAUGCCACA
....(((((.....))))).................((((...((((..((((((((((((.((((..((.(....).))...)))).)))...)))))))))..))))......)))). ( -43.30)
>DroYak_CAF1 6080 120 + 1
AUCUGCAGAAGCCUUUUGCGCACUCAUCACAUUUUCGUGGAAAUCGGACCGCCAAGGAGCUCUGGGAAGGUGUGUACUCCGCAUCCGUGGCGAGUCCUUGGCGACUGGAGCUGUGCCGCA
..........((.....((((((((.((((......))))....(((..(((((((((.(((......((((((.....))))))......)))))))))))).)))))).))))).)). ( -40.30)
>consensus
AUCUGCAGAAGCCUUUUGCGCACUCAUCACAUUUUCGUGGAAAUCGGAGCGCCAAGGAGCUGUGGAAAGGUGUAUACUCCGCAUCCGUUGCGAAUCCUUGGCGACUCGAACUGUGCCACA
....(((((.....)))))((((...((((......))))...((((..(((((((((((..((((..((.(....).))...))))..))...)))))))))..))))...)))).... (-40.58 = -40.66 +   0.08)

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 09:42:26 2006