Locus 175

Sequence ID 3R_DroMel_CAF1
Location 836,953 – 837,142
Length 189
Max. P 0.882768
window289 window290 window291 window292

overview

Window 9

Location 836,953 – 837,072
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.65
Mean single sequence MFE -27.82
Consensus MFE -22.65
Energy contribution -24.52
Covariance contribution 1.87
Combinations/Pair 1.06
Mean z-score -1.24
Structure conservation index 0.81
SVM decision value -0.04
SVM RNA-class probability 0.512809
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 836953 119 + 27905053
CAUCUCUGCGGUUGCCAAUCAAUAAUUUGCCUGGUGAAUGCCUCCGCU-GGCUGUAAUUGUGUUCUGGCCUCUGCCUCUGUUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACU
.......((((..((((....((((((.(((.((((........))))-)))...))))))....))))..))))...((((...(((((((........)))))))..))))....... ( -31.90)
>DroSec_CAF1 12341 119 + 1
CAUCUCUGCGGUUGCCAAUCAAUAAUUUGCCUGGUGAAUGCCUCCGCU-GGCUGUAAUUGUGUUCUGGCCUCUGCCUCUGUUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACU
.......((((..((((....((((((.(((.((((........))))-)))...))))))....))))..))))...((((...(((((((........)))))))..))))....... ( -31.90)
>DroSim_CAF1 11830 119 + 1
CAUCUCUGCGGUUGCCAAUCAAUAAUUUGCCUGGUGAAUGCCUCCGCU-GGCUGUAAUUGUGUUCUGGCCUCUGCCUCUGUUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACU
.......((((..((((....((((((.(((.((((........))))-)))...))))))....))))..))))...((((...(((((((........)))))))..))))....... ( -31.90)
>DroEre_CAF1 14052 119 + 1
CAUCUCUGUGGUUGCCAAUCAAUAAUUUGCCUGGUGAAUGCCUCCGCU-GGCUGUAAUUGUGUUCUGGCCUCUGCCUUUGUUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACU
.......(..(..((((....((((((.(((.((((........))))-)))...))))))....))))..)..).((((((...(((((((........)))))))..))))))..... ( -30.60)
>DroYak_CAF1 12984 120 + 1
CAUCUCUGCGGUUGCCAAUCAAUAAUUUGCCUGGUGAAUGCCUCCGCUCGGUUGUAAUUGUGAUNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
((.((..(((((..(((..(((....)))..)))..)......))))..)).)).................................................................. ( -12.80)
>consensus
CAUCUCUGCGGUUGCCAAUCAAUAAUUUGCCUGGUGAAUGCCUCCGCU_GGCUGUAAUUGUGUUCUGGCCUCUGCCUCUGUUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACU
.......((((..((((....((((((.(((.((((........)))).)))...))))))....))))..))))...((((...(((((((........)))))))..))))....... (-22.65 = -24.52 +   1.87)

alignment

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secondary structure

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Window 0

Location 836,993 – 837,110
Length 117
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 96.19
Mean single sequence MFE -31.52
Consensus MFE -29.31
Energy contribution -29.25
Covariance contribution -0.06
Combinations/Pair 1.06
Mean z-score -1.52
Structure conservation index 0.93
SVM decision value 0.10
SVM RNA-class probability 0.585221
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 836993 117 + 27905053
CCUCCGCUGGCUGUAAUUGUGUUCUGGCCUCUGCCUCUGUUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACUGCCAAUAAGUUGCUUCCACUGCUCUGCAGAGAGAGAAA--
.(((.((.((((..(((...)))..))))...))((((((....(((((((........))))))).(((.((((((((.......))))))))))).......)))))).)))...-- ( -35.00)
>DroSec_CAF1 12381 117 + 1
CCUCCGCUGGCUGUAAUUGUGUUCUGGCCUCUGCCUCUGUUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACUGCCAAUAAGUUGCAUCCACUGCUCUGCAUAGAGAGAAA--
....((.(((.(((((((......((((...(((...((((...(((((((........)))))))..)))).)))...))))...))))))).))).))((((......))))...-- ( -28.70)
>DroSim_CAF1 11870 117 + 1
CCUCCGCUGGCUGUAAUUGUGUUCUGGCCUCUGCCUCUGUUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACUGCCAAUAAGUUGCAUCCACUGCUUUGCAGAGAGAGAAA--
.((((..(((.(((((((......((((...(((...((((...(((((((........)))))))..)))).)))...))))...))))))).)))((((...)))).).)))...-- ( -31.40)
>DroEre_CAF1 14092 119 + 1
CCUCCGCUGGCUGUAAUUGUGUUCUGGCCUCUGCCUUUGUUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACUGCCAAUAAGUUGCAUCCACUGUCCUACAGAGAGAGAAACU
.((((..(((.(((((((......((((...(((..(((((...(((((((........)))))))..))))))))...))))...))))))).)))(((.....))).).)))..... ( -31.00)
>consensus
CCUCCGCUGGCUGUAAUUGUGUUCUGGCCUCUGCCUCUGUUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACUGCCAAUAAGUUGCAUCCACUGCUCUGCAGAGAGAGAAA__
.(((.((.((((..(((...)))..))))...))((((((....(((((((........))))))).(((...((((((.......))))))..))).......)))))).)))..... (-29.31 = -29.25 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 837,032 – 837,142
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.68
Mean single sequence MFE -27.08
Consensus MFE -20.52
Energy contribution -20.02
Covariance contribution -0.50
Combinations/Pair 1.17
Mean z-score -2.15
Structure conservation index 0.76
SVM decision value 0.92
SVM RNA-class probability 0.882768
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 837032 110 + 27905053
UUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACUGCCAAUAAGUUGCUUCCACUGCUCUGCAGAGAGAGAAA-------UGCG---GGUGUACUUAAGUAUCUCAAUAUAAUUU
.......(((.(((((............(((.((((((((.......)))))))))))((((...))))...))))).-------)))(---((.((((....))))))).......... ( -29.20)
>DroSec_CAF1 12420 110 + 1
UUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACUGCCAAUAAGUUGCAUCCACUGCUCUGCAUAGAGAGAAA-------UGCG---GAUGUACUUAAGUAUCUCAAUAUAAUUU
.....(((((((........)))))))((((((......))))))(((((.((((((.(..((((......))))...-------.).)---)))))))))).................. ( -29.30)
>DroSim_CAF1 11909 110 + 1
UUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACUGCCAAUAAGUUGCAUCCACUGCUUUGCAGAGAGAGAAA-------UGCG---GAUGUACUUAAGUAUCUCAAUAUAAUUA
.....(((((((........)))))))((((((......))))))(((((.((((((.((((...))))....(....-------)..)---)))))))))).................. ( -27.20)
>DroEre_CAF1 14131 118 + 1
UUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACUGCCAAUAAGUUGCAUCCACUGUCCUACAGAGAGAGAAACUGAAAAUGUGAAGCAUUUAUUUAAACUUCUGAAUAU--UUA
.....((((.((((((((((..((((.((((((......)))))).....))))(((.(((.....))).).)))))..))))))).....)))).((((((......)))))).--... ( -22.60)
>consensus
UUUUUGUGCAAUUUUCAUUCAUUGCAUUUGGCAAGCAACUGCCAAUAAGUUGCAUCCACUGCUCUGCAGAGAGAGAAA_______UGCG___GAUGUACUUAAGUAUCUCAAUAUAAUUA
.....(((((((........)))))))...(((.((((((.......)))))).(((.((((...)))).).))...........)))....((.((((....)))).)).......... (-20.52 = -20.02 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 837,032 – 837,142
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.68
Mean single sequence MFE -25.20
Consensus MFE -18.41
Energy contribution -18.47
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.90
Structure conservation index 0.73
SVM decision value 0.52
SVM RNA-class probability 0.767009
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 837032 110 - 27905053
AAAUUAUAUUGAGAUACUUAAGUACACC---CGCA-------UUUCUCUCUCUGCAGAGCAGUGGAAGCAACUUAUUGGCAGUUGCUUGCCAAAUGCAAUGAAUGAAAAUUGCACAAAAA
........(((...(((....)))....---.(((-------((((..((..((((......(((((((((((.......)))))))).)))..))))..))..))))..))).)))... ( -24.80)
>DroSec_CAF1 12420 110 - 1
AAAUUAUAUUGAGAUACUUAAGUACAUC---CGCA-------UUUCUCUCUAUGCAGAGCAGUGGAUGCAACUUAUUGGCAGUUGCUUGCCAAAUGCAAUGAAUGAAAAUUGCACAAAAA
........(((.......(((((.((((---(((.-------...((((......))))..)))))))..)))))(((((((....))))))).((((((........)))))))))... ( -28.60)
>DroSim_CAF1 11909 110 - 1
UAAUUAUAUUGAGAUACUUAAGUACAUC---CGCA-------UUUCUCUCUCUGCAAAGCAGUGGAUGCAACUUAUUGGCAGUUGCUUGCCAAAUGCAAUGAAUGAAAAUUGCACAAAAA
........(((.......(((((.((((---(((.-------..........(((...))))))))))..)))))(((((((....))))))).((((((........)))))))))... ( -24.60)
>DroEre_CAF1 14131 118 - 1
UAA--AUAUUCAGAAGUUUAAAUAAAUGCUUCACAUUUUCAGUUUCUCUCUCUGUAGGACAGUGGAUGCAACUUAUUGGCAGUUGCUUGCCAAAUGCAAUGAAUGAAAAUUGCACAAAAA
...--.......(((((..........)))))........((((.(..((.(((.....))).))..).))))..(((((((....))))))).((((((........))))))...... ( -22.80)
>consensus
AAAUUAUAUUGAGAUACUUAAGUACAUC___CGCA_______UUUCUCUCUCUGCAGAGCAGUGGAUGCAACUUAUUGGCAGUUGCUUGCCAAAUGCAAUGAAUGAAAAUUGCACAAAAA
................................(((.......((((..((..((((......(((..((((((.......))))))...)))..))))..))..))))..)))....... (-18.41 = -18.47 +   0.06)

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 09:35:54 2006