Locus 1416

Sequence ID 3L_DroMel_CAF1
Location 4,120,535 – 4,120,815
Length 280
Max. P 0.986113
window2200 window2201 window2202 window2203

overview

Window 0

Location 4,120,535 – 4,120,655
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.67
Mean single sequence MFE -42.72
Consensus MFE -38.26
Energy contribution -39.10
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -1.66
Structure conservation index 0.90
SVM decision value 1.59
SVM RNA-class probability 0.966186
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4120535 120 - 23771897
GACCAAUGCGGUUCGCAAUUGGGAGGUCCUUGUUGGCUCUUCGCACAUCCUGUCGCCCGAAAUCUUCCUCAGCGAUUUGGGCAGUCUCUCGAAGGAGGACUAAGGAACUUAUUGGGUCAU
((((..(((((...(((((.(((....))).))).))...)))))..((((...((((.(((((.........)))))))))((((.(((....))))))).))))........)))).. ( -43.20)
>DroSec_CAF1 2154 120 - 1
GACCAAUGCGGUUCGCAAUUGGGAGGUCCUUGUGGGCUCUUCGCACAUCCUGUCGCCCGAAAUCUUCCUCAGCGAUUUGGGCAGUCUCUCGAAGGAGGACUAAGGAACUUAUUCGGUCAU
((((..(((((((((((...(((....))))))))))....))))..((((...((((.(((((.........)))))))))((((.(((....))))))).))))........)))).. ( -44.40)
>DroSim_CAF1 2450 120 - 1
GACCAAUGCUGUUCGCAAUUGGGAGGUCCUUGUGGGCUCUUCGCACAUCCUGUCGCCCGAAAUCUUCCUCAGCGAUUUGGGCAGUCUCUCGAAGGAGGACUAAGGAACUUAUUCGGUCAU
((((..(((((....))....((((((((....)))).)))))))..((((...((((.(((((.........)))))))))((((.(((....))))))).))))........)))).. ( -43.20)
>DroEre_CAF1 2350 120 - 1
GACCAAUGCGGUUCGCAAUUGGGAGGUCCUUGUGGGCUCUUCGCACAUCCUGUCGCCCGAAAUCUUCCUCAGCGAUUUGGGCAGUCUCUCAAAGGAGGACUAAAGAACUUAUUGGGUCGU
((((((((.(((((((...((((((((((....)))).)))).))...((.(((((..((........)).)))))..))))((((.(((....)))))))...))))))))).)))).. ( -39.80)
>DroYak_CAF1 2800 120 - 1
GACCAAUGCGGUUCGCAAUUGGGAAGUCCUUGUGGGCUCCUCGCACAUCCUGUCGCCCGAAAUAUUCCUCAGCGAUUUGGGUAGUCUCUCGAAGGAGGACUAAAGAGCUAAUUGGGUCAU
(((((((..(((((((....((((.((((....)))))))).))..((((.(((((..((........)).)))))..))))((((.(((....)))))))...))))).))).)))).. ( -43.00)
>consensus
GACCAAUGCGGUUCGCAAUUGGGAGGUCCUUGUGGGCUCUUCGCACAUCCUGUCGCCCGAAAUCUUCCUCAGCGAUUUGGGCAGUCUCUCGAAGGAGGACUAAGGAACUUAUUGGGUCAU
((((..(((((((((((...(((....))))))))))....))))..((((...((((.(((((.........)))))))))((((.(((....))))))).))))........)))).. (-38.26 = -39.10 +   0.84)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,120,615 – 4,120,735
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.00
Mean single sequence MFE -47.30
Consensus MFE -46.48
Energy contribution -46.36
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -1.08
Structure conservation index 0.98
SVM decision value 0.13
SVM RNA-class probability 0.596546
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4120615 120 - 23771897
CAGGUAAAGAACGUGCCCAGGCUUAUUGUCUUCAUCGUGGGCGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGUGACCAAUGCGGUUCGCAAUUGGGAGGUCCUUGUUGGCUCU
.......(((..(..((.((((.....)))).((((.((((((((....)).)))))).)))).))..)(((.((((((...((((((((...))).))))).....)))))).)))))) ( -44.80)
>DroSec_CAF1 2234 120 - 1
CAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUCGUGGGCGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGUGACCAAUGCGGUUCGCAAUUGGGAGGUCCUUGUGGGCUCU
.......(((..(..((.((((.....)))).((((.((((((((....)).)))))).)))).))..)((((((((((...((((((((...))).))))).....))))))))))))) ( -49.00)
>DroSim_CAF1 2530 120 - 1
CAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUCGUGGGUGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGUGACCAAUGCUGUUCGCAAUUGGGAGGUCCUUGUGGGCUCU
.......(((..(..((.((((.....)))).((((.((((..((....))...)))).)))).))..)((((((((((...(((((((.....)).))))).....))))))))))))) ( -44.90)
>DroEre_CAF1 2430 120 - 1
CAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUUGUGGGCGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGUGACCAAUGCGGUUCGCAAUUGGGAGGUCCUUGUGGGCUCU
.......(((..(..((.((((.....)))).((((.((((((((....)).)))))).)))).))..)((((((((((...((((((((...))).))))).....))))))))))))) ( -47.30)
>DroYak_CAF1 2880 120 - 1
CAGGUGAAGAAUGUGCCCAGGCUCAUUGUCUUCAUCGUGGGCGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGUGACCAAUGCGGUUCGCAAUUGGGAAGUCCUUGUGGGCUCC
..(((((((((((.((....)).)))..)))))))).((((((((....)).))))))......((...((((((((((...((((((((...))).))))).....)))))))))).)) ( -50.50)
>consensus
CAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUCGUGGGCGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGUGACCAAUGCGGUUCGCAAUUGGGAGGUCCUUGUGGGCUCU
............(..((.((((.....)))).((((.((((((((....)).)))))).)))).))..)((((((((((...(((((((.....)).))))).....))))))))))... (-46.48 = -46.36 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,120,655 – 4,120,775
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.50
Mean single sequence MFE -49.62
Consensus MFE -49.20
Energy contribution -48.76
Covariance contribution -0.44
Combinations/Pair 1.09
Mean z-score -1.09
Structure conservation index 0.99
SVM decision value 0.11
SVM RNA-class probability 0.589426
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4120655 120 - 23771897
UGCCCGCUACGGUCACUGGCACAAGGACAAGGGACAGGCGCAGGUAAAGAACGUGCCCAGGCUUAUUGUCUUCAUCGUGGGCGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGU
((((.((....))....))))..((((((((((...((.(((.((.....)).)))))...))).)))))))..(((((((((((....))....(((.....)))..)))))))))... ( -42.60)
>DroSec_CAF1 2274 120 - 1
UGCCCGCUACGGUCACUGGCACAAGGACAAGGGCCAGGCGCAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUCGUGGGCGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGU
((((.((....))....))))..((((((((((((.((.(((.((.....)).))))).))))).)))))))..(((((((((((....))....(((.....)))..)))))))))... ( -52.50)
>DroSim_CAF1 2570 120 - 1
UGCCCGCUACGGUCACUGGCACAAGGACAAGGGCCAGGCGCAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUCGUGGGUGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGU
((((.((....))....))))..((((((((((((.((.(((.((.....)).))))).))))).)))))))..(((((((((((....))....(((.....)))..)))))))))... ( -50.60)
>DroEre_CAF1 2470 120 - 1
UGCCCGCUAUGGUCACUGGCACAAGGACAAGGGCCAGGCGCAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUUGUGGGCGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGU
.((((((.(((((.....))...((((((((((((.((.(((.((.....)).))))).))))).)))))))))).))))))((((((.((((.......))))..))))))........ ( -50.80)
>DroYak_CAF1 2920 120 - 1
UGCCCGCUAUGGUCACUGGCACAAGGACAAGGGCCAGGCGCAGGUGAAGAAUGUGCCCAGGCUCAUUGUCUUCAUCGUGGGCGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGU
.(((((.((.((((((((.....((((((((((((.((((((.........))))))..))))).)))))))((((.((((((((....)).)))))).))))))))).))))))).))) ( -51.60)
>consensus
UGCCCGCUACGGUCACUGGCACAAGGACAAGGGCCAGGCGCAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUCGUGGGCGGCGUGAGUAUGUCCGAGAUGCGGUGCGCCUACGAGGU
.(((((.((.((((((((.....((((((((((((.((.(((.((.....)).))))).))))).)))))))((((.((((((((....)).)))))).))))))))).))))))).))) (-49.20 = -48.76 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,120,695 – 4,120,815
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.83
Mean single sequence MFE -44.20
Consensus MFE -43.86
Energy contribution -43.50
Covariance contribution -0.36
Combinations/Pair 1.08
Mean z-score -1.56
Structure conservation index 0.99
SVM decision value 2.03
SVM RNA-class probability 0.986113
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4120695 120 - 23771897
AGGGCAGGGCCCAAAAUACCAAUUAUCAUGCCCCAACCAGUGCCCGCUACGGUCACUGGCACAAGGACAAGGGACAGGCGCAGGUAAAGAACGUGCCCAGGCUUAUUGUCUUCAUCGUGG
.(((((.((.........))........)))))...((((((.(((...))).))))))(((.((((((((((...((.(((.((.....)).)))))...))).)))))))....))). ( -36.50)
>DroSec_CAF1 2314 120 - 1
AGGGCAGGGCCCAGAAUACCAAUUAUCAUGCCCCAACCAGUGCCCGCUACGGUCACUGGCACAAGGACAAGGGCCAGGCGCAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUCGUGG
.(((((.((.........))........)))))...((((((.(((...))).))))))(((.((((((((((((.((.(((.((.....)).))))).))))).)))))))....))). ( -46.40)
>DroSim_CAF1 2610 120 - 1
AGGGCAGGGCCCAGAAUACCAAUUAUCAUGCCCCAACCAGUGCCCGCUACGGUCACUGGCACAAGGACAAGGGCCAGGCGCAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUCGUGG
.(((((.((.........))........)))))...((((((.(((...))).))))))(((.((((((((((((.((.(((.((.....)).))))).))))).)))))))....))). ( -46.40)
>DroEre_CAF1 2510 120 - 1
AGGGCAGGGCCCAGAACACCAAUUAUCAUGCCCCAACCAGUGCCCGCUAUGGUCACUGGCACAAGGACAAGGGCCAGGCGCAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUUGUGG
.(((((.((.........))........)))))...((((((.((.....)).))))))((((((((((((((((.((.(((.((.....)).))))).))))).))))))...))))). ( -47.40)
>DroYak_CAF1 2960 120 - 1
AGGGCAGGGCACAGAAUACCAAUUAUCAUGCCCCAACCAGUGCCCGCUAUGGUCACUGGCACAAGGACAAGGGCCAGGCGCAGGUGAAGAAUGUGCCCAGGCUCAUUGUCUUCAUCGUGG
.(((((.((.........))........)))))...((((((.((.....)).))))))(((.((((((((((((.((((((.........))))))..))))).)))))))....))). ( -44.30)
>consensus
AGGGCAGGGCCCAGAAUACCAAUUAUCAUGCCCCAACCAGUGCCCGCUACGGUCACUGGCACAAGGACAAGGGCCAGGCGCAGGUGAAGAACGUGCCCAGGCUCAUUGUCUUCAUCGUGG
.(((((.((.........))........)))))...((((((.(((...))).))))))(((.((((((((((((.((.(((.((.....)).))))).))))).)))))))....))). (-43.86 = -43.50 +  -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 10:06:59 2006