Locus 4856

Sequence ID 3L_DroMel_CAF1
Location 13,596,704 – 13,596,847
Length 143
Max. P 0.999399
window7658 window7659 window7660 window7661

overview

Window 8

Location 13,596,704 – 13,596,815
Length 111
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.36
Mean single sequence MFE -32.81
Consensus MFE -24.64
Energy contribution -24.69
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -3.53
Structure conservation index 0.75
SVM decision value 0.58
SVM RNA-class probability 0.788899
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13596704 111 + 23771897
AAUUAAGGCGGCCAAGAAUUUUUGGGCAUCCCC---------GCCGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGC
......((((((((((....)))))......))---------)))((((((((..(....)...........((((((((((((...............))))).))))))))))))))) ( -34.26)
>DroSec_CAF1 3526 114 + 1
AAUUAGGGCGGCCAAGAAUUUUUGGGCAUCCCCAG------CGCCGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGC
.....(((.(.(((((....))))).)...)))..------.(((((((((....)................((((((((((((...............))))).))))))))))))))) ( -33.66)
>DroSim_CAF1 12899 114 + 1
AAUUAAAGCGGCCAAGAAUUUUUGGGCAUCCCCAG------CGCCGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGC
.........(.(((((....))))).)........------.(((((((((....)................((((((((((((...............))))).))))))))))))))) ( -29.86)
>DroEre_CAF1 4714 120 + 1
AAUUAAGGCGGCCAAGAAUUUUUCGGCAUCCCCGCUGCCGUCGCCGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGC
......((((((...((.....))((((.......))))))))))((((((((..(....)...........((((((((((((...............))))).))))))))))))))) ( -38.46)
>DroYak_CAF1 9657 114 + 1
AAUUAAGGCGGCCAAGAAUUUUUCGGCUUCCCCGC------CGCCGCUGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGC
......((((((...((.....))((.....))))------))))((((((((..(....)...........((((((((((((...............))))).))))))))))))))) ( -34.16)
>DroAna_CAF1 39246 107 + 1
AAUUAAGGCUGCACAUAUUUUUUCGGCC--CC-----------CGGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGU
......(((((............)))))--..-----------..((((((((..(....)...........((((((((((((...............))))).))))))))))))))) ( -26.46)
>consensus
AAUUAAGGCGGCCAAGAAUUUUUCGGCAUCCCC________CGCCGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGC
......((..(((...........)))...)).............((((((((..(....)...........((((((((((((...............))))).))))))))))))))) (-24.64 = -24.69 +   0.06)

alignment

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secondary structure

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Window 9

Location 13,596,704 – 13,596,815
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 91.36
Mean single sequence MFE -38.17
Consensus MFE -30.38
Energy contribution -31.11
Covariance contribution 0.72
Combinations/Pair 1.06
Mean z-score -3.57
Structure conservation index 0.80
SVM decision value 1.53
SVM RNA-class probability 0.961754
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13596704 111 - 23771897
GCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCGGC---------GGGGAUGCCCAAAAAUUCUUGGCCGCCUUAAUU
(((((((((..(((........((((((((.((((((.....))))))...)))))))).)))...)))))))))(((---------((......((((......)))))))))...... ( -38.00)
>DroSec_CAF1 3526 114 - 1
GCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCGGCG------CUGGGGAUGCCCAAAAAUUCUUGGCCGCCCUAAUU
(((((((((..(((........((((((((.((((((.....))))))...)))))))).)))...)))))))))((((------(..(((((........)))))..).))))...... ( -42.20)
>DroSim_CAF1 12899 114 - 1
GCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCGGCG------CUGGGGAUGCCCAAAAAUUCUUGGCCGCUUUAAUU
(((((((((..(((........((((((((.((((((.....))))))...)))))))).)))...)))))))))((((------(..(((((........)))))..).))))...... ( -39.80)
>DroEre_CAF1 4714 120 - 1
GCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCGGCGACGGCAGCGGGGAUGCCGAAAAAUUCUUGGCCGCCUUAAUU
((((((((.(((((........((((((((.((((((.....))))))...))))))))......)))))))))))))...(((.((.((((...........)))).)).)))...... ( -41.44)
>DroYak_CAF1 9657 114 - 1
GCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCAGCGGCG------GCGGGGAAGCCGAAAAAUUCUUGGCCGCCUUAAUU
(((((((((((((((.(((((...((.....))...))))))))))))..........(((((.....)))))))))))------))((((..(((((.......)))))..)))).... ( -40.60)
>DroAna_CAF1 39246 107 - 1
ACCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCCG-----------GG--GGCCGAAAAAAUAUGUGCAGCCUUAAUU
.((((((((..(((........((((((((.((((((.....))))))...)))))))).)))...))))))))...-----------((--(((.(............).))))).... ( -27.00)
>consensus
GCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCGGCG________GGGGAUGCCCAAAAAUUCUUGGCCGCCUUAAUU
((((((((.(((((........((((((((.((((((.....))))))...))))))))......))))))))))))).........((((..(((...........)))..)))).... (-30.38 = -31.11 +   0.72)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,596,737 – 13,596,847
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.66
Mean single sequence MFE -38.19
Consensus MFE -33.66
Energy contribution -33.83
Covariance contribution 0.17
Combinations/Pair 1.11
Mean z-score -4.15
Structure conservation index 0.88
SVM decision value 3.57
SVM RNA-class probability 0.999399
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13596737 110 + 23771897
--GCCGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGCGGCAACUGCCG-GGUGGGCAAACA-------ACUAAAAAG
--(((((((((((..(....)...........((((((((((((...............))))).))))))))))))))))))...((((.-....))))....-------......... ( -38.46)
>DroSec_CAF1 3561 112 + 1
-CGCCGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGCGGCAACUGCCGGGGUGGGCAAACA-------ACUAAAAAG
-.(((((((((((..(....)...........((((((((((((...............))))).))))))))))))))))))...((((......))))....-------......... ( -38.96)
>DroSim_CAF1 12934 112 + 1
-CGCCGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGCGGCAACUGCCGGGGUGGGCAAACA-------ACUAAAAAG
-.(((((((((((..(....)...........((((((((((((...............))))).))))))))))))))))))...((((......))))....-------......... ( -38.96)
>DroEre_CAF1 4754 112 + 1
UCGCCGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGCGGCAACUGUCG-GGUGGGCAAACA-------UCUAAAAAG
..(((((((((((..(....)...........((((((((((((...............))))).)))))))))))))))))).......(-((((......))-------)))...... ( -38.16)
>DroYak_CAF1 9692 111 + 1
-CGCCGCUGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGCGGCAACUGUCG-GGUGGGCAAACA-------UCUAAAAAG
-.(((((((((((..(....)...........((((((((((((...............))))).)))))))))))))))))).......(-((((......))-------)))...... ( -35.96)
>DroAna_CAF1 39276 116 + 1
---CGGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGUGGCAGCUGCCU-GGCAAGGAAGCGGCGGUCUGCUCGGGGG
---((((((((((..(....)...........((((((((((((...............))))).)))))))))))))))((((((((((.-.((......))))))).))))))).... ( -38.66)
>consensus
_CGCCGCCGCCGCAAGUCAACAAAUAAUUUCUAUGCAAAUAUUUUACACUAAUUAUUUCAAAUAUUUUGCAUGCGGCGGCGGCAACUGCCG_GGUGGGCAAACA_______ACUAAAAAG
..(((((((((((..(....)...........((((((((((((...............))))).))))))))))))))))))...((((......)))).................... (-33.66 = -33.83 +   0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,596,737 – 13,596,847
Length 110
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.66
Mean single sequence MFE -37.47
Consensus MFE -33.26
Energy contribution -34.28
Covariance contribution 1.03
Combinations/Pair 1.03
Mean z-score -3.27
Structure conservation index 0.89
SVM decision value 3.13
SVM RNA-class probability 0.998540
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13596737 110 - 23771897
CUUUUUAGU-------UGUUUGCCCACC-CGGCAGUUGCCGCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCGGC--
.........-------...(((((....-.)))))..((((((((((((..(((........((((((((.((((((.....))))))...)))))))).)))...))))))))))))-- ( -39.50)
>DroSec_CAF1 3561 112 - 1
CUUUUUAGU-------UGUUUGCCCACCCCGGCAGUUGCCGCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCGGCG-
.........-------...(((((......)))))..((((((((((((..(((........((((((((.((((((.....))))))...)))))))).)))...)))))))))))).- ( -41.40)
>DroSim_CAF1 12934 112 - 1
CUUUUUAGU-------UGUUUGCCCACCCCGGCAGUUGCCGCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCGGCG-
.........-------...(((((......)))))..((((((((((((..(((........((((((((.((((((.....))))))...)))))))).)))...)))))))))))).- ( -41.40)
>DroEre_CAF1 4754 112 - 1
CUUUUUAGA-------UGUUUGCCCACC-CGACAGUUGCCGCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCGGCGA
.........-------((((.(.....)-.)))).((((((((((((((..(((........((((((((.((((((.....))))))...)))))))).)))...)))))))))))))) ( -37.10)
>DroYak_CAF1 9692 111 - 1
CUUUUUAGA-------UGUUUGCCCACC-CGACAGUUGCCGCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCAGCGGCG-
.........-------((((.(.....)-.))))...(((((.((((((..(((........((((((((.((((((.....))))))...)))))))).)))...)))))).))))).- ( -30.30)
>DroAna_CAF1 39276 116 - 1
CCCCCGAGCAGACCGCCGCUUCCUUGCC-AGGCAGCUGCCACCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCCG---
.....(.((((.(.(((((......)).-.))).)))))).((((((((..(((........((((((((.((((((.....))))))...)))))))).)))...))))))))...--- ( -35.10)
>consensus
CUUUUUAGU_______UGUUUGCCCACC_CGGCAGUUGCCGCCGCCGCAUGCAAAAUAUUUGAAAUAAUUAGUGUAAAAUAUUUGCAUAGAAAUUAUUUGUUGACUUGCGGCGGCGGCG_
...................(((((......)))))..((((((((((((..(((........((((((((.((((((.....))))))...)))))))).)))...)))))))))))).. (-33.26 = -34.28 +   1.03)

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 11:35:17 2006