Locus 3879

Sequence ID 3R_DroMel_CAF1
Location 10,549,946 – 10,550,106
Length 160
Max. P 0.965817
window6215 window6216 window6217 window6218

overview

Window 5

Location 10,549,946 – 10,550,066
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -37.93
Consensus MFE -36.09
Energy contribution -36.43
Covariance contribution 0.34
Combinations/Pair 1.08
Mean z-score -1.69
Structure conservation index 0.95
SVM decision value 0.30
SVM RNA-class probability 0.677907
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10549946 120 + 27905053
ACCGUCCGAUUCGGAUUCGGAAUUUGUUUUGGUAACAUUCGCUGCUAGUGGUGUAGCAGAAAACAUCGCAUUGCAUAUCGAUACACUCGCGGCGAUGUUAUUCGAUGUAUUGGUUGAUAU
(((((((((.......))))).......((((((((((.((((((..(((((((........)))))))((((.....))))......)))))))))))).)))).....))))...... ( -33.40)
>DroSec_CAF1 24801 120 + 1
ACCGUCCGAUUCGGAUUCGGAAUUUGUUUUGGUAACGUUCGCUGCUAGUGGUGCAGCAGAAAACAUCGCAUCGGGUAUCGAUAUACUCGCGGCGAUGUUAUUCGAUGUGUUGGUUGAUAU
(((((((((.......))))).............(((((.(((((.......))))).(((((((((((..(((((((....)))))))..)))))))).))))))))..))))...... ( -40.20)
>DroSim_CAF1 25141 120 + 1
ACCGUCCGAUUCGGAUUCGGAAUUUGUUUUGGUAACGUUCGCUGCUAGUGGUGCAGCAGAAAACAUCGCAUCGGGUAUCGAUAUACUCGCGGCGAUGUUAUUCGAUGUGUUGGUUGAUAU
(((((((((.......))))).............(((((.(((((.......))))).(((((((((((..(((((((....)))))))..)))))))).))))))))..))))...... ( -40.20)
>consensus
ACCGUCCGAUUCGGAUUCGGAAUUUGUUUUGGUAACGUUCGCUGCUAGUGGUGCAGCAGAAAACAUCGCAUCGGGUAUCGAUAUACUCGCGGCGAUGUUAUUCGAUGUGUUGGUUGAUAU
(((((((((.......))))).............(((((.(((((.......))))).(((((((((((..(((((((....)))))))..)))))))).))))))))..))))...... (-36.09 = -36.43 +   0.34)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,549,946 – 10,550,066
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -32.57
Consensus MFE -29.53
Energy contribution -29.53
Covariance contribution 0.01
Combinations/Pair 1.09
Mean z-score -2.93
Structure conservation index 0.91
SVM decision value 1.46
SVM RNA-class probability 0.955756
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10549946 120 - 27905053
AUAUCAACCAAUACAUCGAAUAACAUCGCCGCGAGUGUAUCGAUAUGCAAUGCGAUGUUUUCUGCUACACCACUAGCAGCGAAUGUUACCAAAACAAAUUCCGAAUCCGAAUCGGACGGU
......(((...((((((...(((((((((....)(((((....)))))..))))))))..((((((......)))))))).)))).............(((((.......))))).))) ( -29.10)
>DroSec_CAF1 24801 120 - 1
AUAUCAACCAACACAUCGAAUAACAUCGCCGCGAGUAUAUCGAUACCCGAUGCGAUGUUUUCUGCUGCACCACUAGCAGCGAACGUUACCAAAACAAAUUCCGAAUCCGAAUCGGACGGU
......((((((.....(((.((((((((..((.((((....)))).))..)))))))))))((((((.......))))))...)))............(((((.......))))).))) ( -34.30)
>DroSim_CAF1 25141 120 - 1
AUAUCAACCAACACAUCGAAUAACAUCGCCGCGAGUAUAUCGAUACCCGAUGCGAUGUUUUCUGCUGCACCACUAGCAGCGAACGUUACCAAAACAAAUUCCGAAUCCGAAUCGGACGGU
......((((((.....(((.((((((((..((.((((....)))).))..)))))))))))((((((.......))))))...)))............(((((.......))))).))) ( -34.30)
>consensus
AUAUCAACCAACACAUCGAAUAACAUCGCCGCGAGUAUAUCGAUACCCGAUGCGAUGUUUUCUGCUGCACCACUAGCAGCGAACGUUACCAAAACAAAUUCCGAAUCCGAAUCGGACGGU
......((((((.....(((.((((((((..((.((((....)))).))..)))))))))))((((((.......))))))...)))............(((((.......))))).))) (-29.53 = -29.53 +   0.01)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,549,986 – 10,550,106
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -42.13
Consensus MFE -39.25
Energy contribution -39.70
Covariance contribution 0.45
Combinations/Pair 1.09
Mean z-score -2.74
Structure conservation index 0.93
SVM decision value 1.59
SVM RNA-class probability 0.965817
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10549986 120 + 27905053
GCUGCUAGUGGUGUAGCAGAAAACAUCGCAUUGCAUAUCGAUACACUCGCGGCGAUGUUAUUCGAUGUAUUGGUUGAUAUCGAUAUUAUAGGCUGUAUUGACGCGGUUGCAGAGAUGCGA
.((((((......))))))......((((((((((.((((...((...(((((..(((...(((((((........)))))))....))).)))))..))...))))))))...)))))) ( -34.80)
>DroSec_CAF1 24841 120 + 1
GCUGCUAGUGGUGCAGCAGAAAACAUCGCAUCGGGUAUCGAUAUACUCGCGGCGAUGUUAUUCGAUGUGUUGGUUGAUAUCGAUAUUAUAGGCUGUAUUGACGCGGCUGCAGAGAUACGA
(((((...(((((((((.(((((((((((..(((((((....)))))))..)))))))).)))...((((((((....)))))))).....)))))))))..)))))............. ( -44.40)
>DroSim_CAF1 25181 120 + 1
GCUGCUAGUGGUGCAGCAGAAAACAUCGCAUCGGGUAUCGAUAUACUCGCGGCGAUGUUAUUCGAUGUGUUGGUUGAUAUCGAUAUUAUAGGCUGUAUUGACGCGGCUGCAGAGAUGCGA
(((((...(((((((((.(((((((((((..(((((((....)))))))..)))))))).)))...((((((((....)))))))).....)))))))))..)))))((((....)))). ( -47.20)
>consensus
GCUGCUAGUGGUGCAGCAGAAAACAUCGCAUCGGGUAUCGAUAUACUCGCGGCGAUGUUAUUCGAUGUGUUGGUUGAUAUCGAUAUUAUAGGCUGUAUUGACGCGGCUGCAGAGAUGCGA
(((((...(((((((((.(((((((((((..(((((((....)))))))..)))))))).)))...((((((((....)))))))).....)))))))))..)))))((((....)))). (-39.25 = -39.70 +   0.45)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,549,986 – 10,550,106
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -27.77
Consensus MFE -25.03
Energy contribution -24.70
Covariance contribution -0.33
Combinations/Pair 1.11
Mean z-score -1.76
Structure conservation index 0.90
SVM decision value 0.07
SVM RNA-class probability 0.568367
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10549986 120 - 27905053
UCGCAUCUCUGCAACCGCGUCAAUACAGCCUAUAAUAUCGAUAUCAACCAAUACAUCGAAUAACAUCGCCGCGAGUGUAUCGAUAUGCAAUGCGAUGUUUUCUGCUACACCACUAGCAGC
((((((...(((....((.........)).....((((((((((............(((......))).(....).)))))))))))))))))))......((((((......)))))). ( -26.90)
>DroSec_CAF1 24841 120 - 1
UCGUAUCUCUGCAGCCGCGUCAAUACAGCCUAUAAUAUCGAUAUCAACCAACACAUCGAAUAACAUCGCCGCGAGUAUAUCGAUACCCGAUGCGAUGUUUUCUGCUGCACCACUAGCAGC
..((((...(((....)))...))))...........(((((............)))))..((((((((..((.((((....)))).))..))))))))....(((((.......))))) ( -28.00)
>DroSim_CAF1 25181 120 - 1
UCGCAUCUCUGCAGCCGCGUCAAUACAGCCUAUAAUAUCGAUAUCAACCAACACAUCGAAUAACAUCGCCGCGAGUAUAUCGAUACCCGAUGCGAUGUUUUCUGCUGCACCACUAGCAGC
..((.....((((((......................(((((............)))))..((((((((..((.((((....)))).))..))))))))....))))))......))... ( -28.40)
>consensus
UCGCAUCUCUGCAGCCGCGUCAAUACAGCCUAUAAUAUCGAUAUCAACCAACACAUCGAAUAACAUCGCCGCGAGUAUAUCGAUACCCGAUGCGAUGUUUUCUGCUGCACCACUAGCAGC
(((((((...((....)).................(((((((((............(((......))).(....).)))))))))...)))))))......((((((......)))))). (-25.03 = -24.70 +  -0.33)

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 11:12:24 2006