Locus 4614

Sequence ID 3L_DroMel_CAF1
Location 13,147,520 – 13,148,029
Length 509
Max. P 0.996479
window7243 window7244 window7245 window7246 window7247 window7248 window7249

overview

Window 3

Location 13,147,520 – 13,147,640
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -47.63
Consensus MFE -44.75
Energy contribution -45.50
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -4.02
Structure conservation index 0.94
SVM decision value 1.04
SVM RNA-class probability 0.905000
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147520 120 - 23771897
CACUCGCUGCAUAUUAAACAGUUUUUGGGAUUCAGUCUCCCGAGUCCCAGAGGCCGCACUUCAUCAACUUGGGGUUCGGUCUCGAAUGUGCUAAAAAAUUGAUUGAUCCUGCAGGAGGCG
..(((.(((((.(((((.(((((((((((((((........))))))).(((((((.((((((......)))))).)))))))..........)))))))).)))))..))))))))... ( -48.70)
>DroSec_CAF1 135176 120 - 1
CACUCGCUGCAUAUUAAACAGUUUUUGGGAUUCAGUCUCCCGAGUCCCAGAGGCCGCACUUCAUCAACUUGGGGUUCGGUCUCGAAUGUGCUAAAAAAUUGAUUGAUCCUGCAGGAGGCG
..(((.(((((.(((((.(((((((((((((((........))))))).(((((((.((((((......)))))).)))))))..........)))))))).)))))..))))))))... ( -48.70)
>DroSim_CAF1 135047 120 - 1
CACUCGCUGCAUAUUAAACAGUUUUUGGGAUUCAGUCUCCCGAGUCCCAGAGGCCGCACUUCAUCAACUUGGGGUUCGGUCUCGAAUGUGCUAAAAAAUUGAUUGAUCCUGCAGGAGGCG
..(((.(((((.(((((.(((((((((((((((........))))))).(((((((.((((((......)))))).)))))))..........)))))))).)))))..))))))))... ( -48.70)
>DroYak_CAF1 136761 120 - 1
CACUCGCUGCAUAUUAAACAGUUUUUGAGAUUCAGUCACCCGAGUCCCAGAGGCCGCACUUCAUCAACUUGGGGCUCGGGCUCGAAUGUGCUAAAAAAUUGAUUGAUCCUGCAGGAGGCG
..(((.(((((.(((((.((((((((.((...((.((.(((((((((((((((.....)))).......)))))))))))...)).))..)).)))))))).)))))..))))))))... ( -44.41)
>consensus
CACUCGCUGCAUAUUAAACAGUUUUUGGGAUUCAGUCUCCCGAGUCCCAGAGGCCGCACUUCAUCAACUUGGGGUUCGGUCUCGAAUGUGCUAAAAAAUUGAUUGAUCCUGCAGGAGGCG
..(((.(((((.(((((.(((((((((((((((........))))))).(((((((.((((((......)))))).)))))))..........)))))))).)))))..))))))))... (-44.75 = -45.50 +   0.75)

alignment

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secondary structure

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Window 4

Location 13,147,600 – 13,147,717
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.94
Mean single sequence MFE -41.30
Consensus MFE -38.24
Energy contribution -37.92
Covariance contribution -0.31
Combinations/Pair 1.08
Mean z-score -1.63
Structure conservation index 0.93
SVM decision value 0.50
SVM RNA-class probability 0.760035
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147600 117 - 23771897
AGGAGGUGGAGACACCUCUUC---CUCUGGCUCACUCCGAAAUUGGUGCAGUUGCUCAAUGUCGUCGCGCUCGGCGGUGUCACUCGCUGCAUAUUAAACAGUUUUUGGGAUUCAGUCUCC
((((((((....)))))))).---....((((.(.(((((((((((((((((......((..(((((....)))))..)).....)))))))......)))))))..))).).))))... ( -39.20)
>DroSec_CAF1 135256 117 - 1
AGGAGGUGGAGACACCUCCUC---CUCUGGCUCACUCCGAAAUUGGUGCGGUUGCUCAAUGUCGUCGCGCUCGGCGGUGUCACUCGCUGCAUAUUAAACAGUUUUUGGGAUUCAGUCUCC
((((((((....)))))))).---....((((.(.((((((((((((((((..((.....))..))))))...((((((.....))))))........)))))))..))).).))))... ( -46.30)
>DroSim_CAF1 135127 117 - 1
AGGAGGUGGAGACACCUCCUC---CUCUGGCUCACUCCGAAAUUGGUGCAGUUGCUCAAUGUCGUCGCGCUCGGCGGUGUCACUCGCUGCAUAUUAAACAGUUUUUGGGAUUCAGUCUCC
((((((((....)))))))).---....((((.(.(((((((((((((((((......((..(((((....)))))..)).....)))))))......)))))))..))).).))))... ( -41.90)
>DroYak_CAF1 136841 120 - 1
AGAAGGUGGAGGCACCUCCUUCCCUUCUGGUUCACUCCGAAAUUGGUGCAGUUGCUCAAUGUCGUCGCGCUCGGCGGUGUCACUCGCUGCAUAUUAAACAGUUUUUGAGAUUCAGUCACC
((((((.((((....))))...))))))......(((.((((((((((((((......((..(((((....)))))..)).....)))))))......))))))).)))........... ( -37.80)
>consensus
AGGAGGUGGAGACACCUCCUC___CUCUGGCUCACUCCGAAAUUGGUGCAGUUGCUCAAUGUCGUCGCGCUCGGCGGUGUCACUCGCUGCAUAUUAAACAGUUUUUGGGAUUCAGUCUCC
((((((((....))))))))......((((....(((.((((((((((((((......((..(((((....)))))..)).....)))))))......))))))).)))..))))..... (-38.24 = -37.92 +  -0.31)

alignment

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secondary structure

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Window 5

Location 13,147,640 – 13,147,751
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.02
Mean single sequence MFE -45.62
Consensus MFE -31.66
Energy contribution -31.97
Covariance contribution 0.31
Combinations/Pair 1.08
Mean z-score -1.77
Structure conservation index 0.69
SVM decision value 0.20
SVM RNA-class probability 0.631565
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147640 111 - 23771897
AGAUGGAUGGCAUCGAAAGCAGUUGGUGCGGA------GUAGGAGGUGGAGACACCUCUUC---CUCUGGCUCACUCCGAAAUUGGUGCAGUUGCUCAAUGUCGUCGCGCUCGGCGGUGU
.........((((((..((((((.(((.((((------(.((((((((....)))))))).---)))))))).))).(((.(((((.((....))))))).)))....)))...)))))) ( -44.60)
>DroSec_CAF1 135296 111 - 1
AGAUGGAUGGGACCGAAUGCAGUUGGUGCGGA------GUAGGAGGUGGAGACACCUCCUC---CUCUGGCUCACUCCGAAAUUGGUGCGGUUGCUCAAUGUCGUCGCGCUCGGCGGUGU
...(((((((((((((......))))).((((------(.((((((((....)))))))).---))))).)))).)))).....(((((((..((.....))..)))))))......... ( -47.80)
>DroSim_CAF1 135167 111 - 1
AGAUGGAUGGCAUCGAAAGCAGUUGGUGCGGA------GUAGGAGGUGGAGACACCUCCUC---CUCUGGCUCACUCCGAAAUUGGUGCAGUUGCUCAAUGUCGUCGCGCUCGGCGGUGU
.........((((((..((((((.(((.((((------(.((((((((....)))))))).---)))))))).))).(((.(((((.((....))))))).)))....)))...)))))) ( -47.30)
>DroYak_CAF1 136881 118 - 1
AGACGGAUGGGAUUGAAUGCAGCA--UGCCAACUGCAUGUAGAAGGUGGAGGCACCUCCUUCCCUUCUGGUUCACUCCGAAAUUGGUGCAGUUGCUCAAUGUCGUCGCGCUCGGCGGUGU
.(((((((((.(((((..((....--.))(((((((((..((((((.((((....))))...))))))((......)).......))))))))).))))).))))).)).))........ ( -42.80)
>consensus
AGAUGGAUGGCAUCGAAAGCAGUUGGUGCGGA______GUAGGAGGUGGAGACACCUCCUC___CUCUGGCUCACUCCGAAAUUGGUGCAGUUGCUCAAUGUCGUCGCGCUCGGCGGUGU
.((((((((((...((..(((.....)))...........((((((((....)))))))).....))...)))).)))((.(((((.((....))))))).)))))(((((....))))) (-31.66 = -31.97 +   0.31)

alignment

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secondary structure

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Window 6

Location 13,147,680 – 13,147,791
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.41
Mean single sequence MFE -35.67
Consensus MFE -25.16
Energy contribution -25.47
Covariance contribution 0.31
Combinations/Pair 1.18
Mean z-score -2.11
Structure conservation index 0.71
SVM decision value 0.96
SVM RNA-class probability 0.889780
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147680 111 + 23771897
UCGGAGUGAGCCAGAG---GAAGAGGUGUCUCCACCUCCUAC------UCCGCACCAACUGCUUUCGAUGCCAUCCAUCUUUUGUCGGUUGACUGCAGUUCAUAAAUUUUUAAAACGCUC
...(((((.((..(((---...((((((....))))))...)------)).))...((((((..(((..(((...((.....))..))))))..))))))...............))))) ( -30.40)
>DroSec_CAF1 135336 111 + 1
UCGGAGUGAGCCAGAG---GAGGAGGUGUCUCCACCUCCUAC------UCCGCACCAACUGCAUUCGGUCCCAUCCAUCUUUUGUCGGUUGACUGCAGUUCAUAAAUUUUUAAAACGCUC
...(((((.((..(((---.((((((((....)))))))).)------)).))...(((((((.((((.((....((.....))..)))))).)))))))...............))))) ( -36.70)
>DroSim_CAF1 135207 110 + 1
UCGGAGUGAGCCAGAG---GAGGAGGUGUCUCCACCUCCUAC------UCCGCACCAACUGCUUUCGAUGCCAUCCAUCUUUUGUCGGUUGACUGCAGUUCAUCCGUAU-AGGGUCGCUC
...((((((.((.(((---.((((((((....)))))))).)------)).(((.(((((((....((((.....))))....).))))))..))).............-.)).)))))) ( -41.60)
>DroYak_CAF1 136921 117 + 1
UCGGAGUGAACCAGAAGGGAAGGAGGUGCCUCCACCUUCUACAUGCAGUUGGCA--UGCUGCAUUCAAUCCCAUCCGUCUUUUGUCGCUUGACUGCAGUUCAUAAAUUUUU-AAACGCUC
.....((((((..((.((((((((((((....))))))))..(((((((.....--.)))))))....)))).))...........((......)).))))))........-........ ( -34.00)
>consensus
UCGGAGUGAGCCAGAG___GAGGAGGUGUCUCCACCUCCUAC______UCCGCACCAACUGCAUUCGAUCCCAUCCAUCUUUUGUCGGUUGACUGCAGUUCAUAAAUUUUUAAAACGCUC
...(((((............((((((((....))))))))................(((((((.((((..((...((.....))..)))))).)))))))...............))))) (-25.16 = -25.47 +   0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,147,680 – 13,147,791
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.41
Mean single sequence MFE -44.92
Consensus MFE -30.33
Energy contribution -31.14
Covariance contribution 0.81
Combinations/Pair 1.16
Mean z-score -4.00
Structure conservation index 0.68
SVM decision value 2.70
SVM RNA-class probability 0.996479
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147680 111 - 23771897
GAGCGUUUUAAAAAUUUAUGAACUGCAGUCAACCGACAAAAGAUGGAUGGCAUCGAAAGCAGUUGGUGCGGA------GUAGGAGGUGGAGACACCUCUUC---CUCUGGCUCACUCCGA
((((............(((.((((((.(((....)))....((((.....))))....)))))).)))((((------(.((((((((....)))))))).---)))))))))....... ( -46.40)
>DroSec_CAF1 135336 111 - 1
GAGCGUUUUAAAAAUUUAUGAACUGCAGUCAACCGACAAAAGAUGGAUGGGACCGAAUGCAGUUGGUGCGGA------GUAGGAGGUGGAGACACCUCCUC---CUCUGGCUCACUCCGA
((((............(((.((((((((((....)))......(((......)))..))))))).)))((((------(.((((((((....)))))))).---)))))))))....... ( -47.60)
>DroSim_CAF1 135207 110 - 1
GAGCGACCCU-AUACGGAUGAACUGCAGUCAACCGACAAAAGAUGGAUGGCAUCGAAAGCAGUUGGUGCGGA------GUAGGAGGUGGAGACACCUCCUC---CUCUGGCUCACUCCGA
(((.((.((.-...((.((.((((((.(((....)))....((((.....))))....)))))).)).))((------(.((((((((....)))))))).---))).)).)).)))... ( -49.50)
>DroYak_CAF1 136921 117 - 1
GAGCGUUU-AAAAAUUUAUGAACUGCAGUCAAGCGACAAAAGACGGAUGGGAUUGAAUGCAGCA--UGCCAACUGCAUGUAGAAGGUGGAGGCACCUCCUUCCCUUCUGGUUCACUCCGA
..((((((-(........))))).)).(((....)))......((((..((((...((((((..--......)))))).(((((((.((((....))))...)))))))))))..)))). ( -36.20)
>consensus
GAGCGUUUUAAAAAUUUAUGAACUGCAGUCAACCGACAAAAGAUGGAUGGCAUCGAAAGCAGUUGGUGCGGA______GUAGGAGGUGGAGACACCUCCUC___CUCUGGCUCACUCCGA
((((............(((.((((((.(((....)))......(((......)))...)))))).)))((((........((((((((....)))))))).....))))))))....... (-30.33 = -31.14 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,147,791 – 13,147,910
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.99
Mean single sequence MFE -38.07
Consensus MFE -33.32
Energy contribution -34.10
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -2.18
Structure conservation index 0.88
SVM decision value 0.47
SVM RNA-class probability 0.747789
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147791 119 + 23771897
GCCGGCGCGAACCAAAACAAACAAGUUUUGAAUCGCCGCCAGGAUCGGUGGAACGCAUCCCAAAAGGUG-GAGUGUGUGGACAGAAGGAGACUGGCAGACACGCAUGUAAUCAAUUUUUA
((((((((((..((((((......))))))..))).)))).((((((......)).)))).....))).-..(((((((......((....))......))))))).............. ( -38.80)
>DroSec_CAF1 135447 119 + 1
GCCGCCGCGAACCAAAACAAACAAGUUUUGAAUCGCCGCCAGGAUCGGCAGAACGCAUCCCAAAAGGUG-GAGUGUGUGGACAGAAGGAGACUGGCAGACACGCAUGUAAUCAAUUUUUA
.(((((((((..((((((......))))))..)))).....((((((......)).)))).....))))-).(((((((......((....))......))))))).............. ( -38.40)
>DroYak_CAF1 137038 120 + 1
GCCGGCGCGAACCAAAACAAACAAGUUUUGAACCGCCGCCAGGAUCGGUGGAACGCAUCCCAAAACGCGAGUGUGUGUGGACAGAAGGAGACUGGCAGACACGCAUAUAAUCAAUUUUUA
((.((((((...((((((......))))))...)).)))).((((((......)).))))......))(((((((((((......((....))......)))))))))..))........ ( -37.00)
>consensus
GCCGGCGCGAACCAAAACAAACAAGUUUUGAAUCGCCGCCAGGAUCGGUGGAACGCAUCCCAAAAGGUG_GAGUGUGUGGACAGAAGGAGACUGGCAGACACGCAUGUAAUCAAUUUUUA
((((((((((..((((((......))))))..))).)))).((((((......)).)))).....)))....(((((((......((....))......))))))).............. (-33.32 = -34.10 +   0.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,147,910 – 13,148,029
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -41.23
Consensus MFE -38.68
Energy contribution -38.46
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.31
Structure conservation index 0.94
SVM decision value 1.00
SVM RNA-class probability 0.898042
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13147910 119 - 23771897
GUAGGAGAAUGCGAGAACAUUCAGUUUAUCGUUUC-CCUCGGCGGCAACGGGUAAUCCAAUUAUAAUAGAGCUGGUCCGCCGGCUGCACCUGCCUCACUUGGGGGCAUUCUUCUAAAAUA
.(((((((((((((((((.....)))).))....(-(((.((.((((...((....))...........((((((....)))))).....))))...)).)))))))))))))))..... ( -40.10)
>DroSec_CAF1 135566 119 - 1
GUAGGAGAAUGCGAGAACAUUCAGUUUAUCGUUUC-CCUCGGCGGCAACGGGUAAUCCAAUUAUAAUAGAGCUGGUCCGCCGGCUGCACCUGCCUCACUUGGGGGCAUUCUUCUAAAAUA
.(((((((((((((((((.....)))).))....(-(((.((.((((...((....))...........((((((....)))))).....))))...)).)))))))))))))))..... ( -40.10)
>DroYak_CAF1 137158 120 - 1
GUAGGAGAAUGCGAGAACAUUCAGUUUAUCGUUUCCCCUUGGCGGCAACGGGUAAUCCAAUUAUAAUAGAGCUGGUCCGCCGGCUGCACCUGCCUCACUUGGGGGCAUUCUUCUAAAAUA
.(((((((((((((((((.....)))).))....((((..((.((((...((....))...........((((((....)))))).....)))).).)..)))))))))))))))..... ( -43.50)
>consensus
GUAGGAGAAUGCGAGAACAUUCAGUUUAUCGUUUC_CCUCGGCGGCAACGGGUAAUCCAAUUAUAAUAGAGCUGGUCCGCCGGCUGCACCUGCCUCACUUGGGGGCAUUCUUCUAAAAUA
.(((((((((((((((((.....)))).))......(((((((((..((.(((.................))).)))))))(((.......)))......)))))))))))))))..... (-38.68 = -38.46 +  -0.22)

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 11:28:38 2006