Locus 3031

Sequence ID 3L_DroMel_CAF1
Location 8,704,885 – 8,705,021
Length 136
Max. P 0.878433
window4737 window4738 window4739 window4740

overview

Window 7

Location 8,704,885 – 8,704,992
Length 107
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.73
Mean single sequence MFE -40.35
Consensus MFE -29.82
Energy contribution -30.78
Covariance contribution 0.96
Combinations/Pair 1.06
Mean z-score -3.33
Structure conservation index 0.74
SVM decision value 0.86
SVM RNA-class probability 0.868066
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8704885 107 + 23771897
UUC-UGUAUUCUGGCUGGUAAGCAAUCGCAUC--UGCUGACUUGUUUGGGGCCA---AACUCUUGGCCAAGAGCUUCAAUGUUGCUGGCCAUC---GCUUGACAUUCG--AGUCGAGC--
...-.......((((..(((((((........--)))(((...((((..(((((---(....))))))..)))).)))...))))..))))..---(((((((.....--.)))))))-- ( -39.00)
>DroSec_CAF1 10432 108 + 1
UUUAUAUUUUCUGGCUGGUAAGCAAUCGCAUC--UGCUGACUUGUUUGGGGCCA---AACUCUUGGCCACGAGCUUCAAUGCUGCUGGCCAUC---GCUUGACAUUCG--AGUCGAGC--
...........((((..(((.(((...((...--.))(((...(((((.(((((---(....)))))).))))).))).))))))..))))..---(((((((.....--.)))))))-- ( -42.30)
>DroSim_CAF1 11249 108 + 1
UUCAUAUUUUCUGGCUGGUAAGCAAUCGCAUC--UGCUGACUUGUUUGGGGCCA---AACUCUUGGCCAAGAGCUUCAAUGCUGCUGGCCAUC---GCUUGACAUUCG--AGUCGAGC--
...........((((..(((.(((...((...--.))(((...((((..(((((---(....))))))..)))).))).))))))..))))..---(((((((.....--.)))))))-- ( -41.30)
>DroEre_CAF1 10415 105 + 1
---AUAUUUUCUGGCUGCUAAGCAAUCGCAUC--UGCUGACUUGUUUGGGGCCG---AACUCUUGGCCAAGAGCUUCAAUGCUGCUGGCCAGC---GCUUGACAUUCG--AGUCGAGC--
---.....(((.((((.((((((((((((...--.)).)).)))))))))))))---))...(((((((..(((......)))..))))))).---(((((((.....--.)))))))-- ( -40.80)
>DroYak_CAF1 10533 107 + 1
---AUAUUUUCUGGCUGCUAAGCAAUCGCAUC--UGCUGACUUGUUUGGGGCCA---AACUCUUGGCCAAGAGCUUCAAUGCUGCUGGCCAUC---GCUUGACAUUCGACAGUCGAGC--
---........(((((.((((((((((((...--.)).)).)))))))))))))---......((((((..(((......)))..))))))..---(((((((........)))))))-- ( -40.60)
>DroAna_CAF1 10262 107 + 1
UUCUGAUUUUCUGGCUGGUAAGCAAACCGUUCUGUGCUGAUUUCUGUUUGGCCAGAAAACUCUUGGCCAU-----------UUCUUGGCCAUCCAAGCUUGACAUUCG--AGUCGAGCUG
....(((((((((((..(..((((..........)))).........)..))))))))).)).((((((.-----------....))))))....((((((((.....--.)))))))). ( -38.10)
>consensus
UUCAUAUUUUCUGGCUGGUAAGCAAUCGCAUC__UGCUGACUUGUUUGGGGCCA___AACUCUUGGCCAAGAGCUUCAAUGCUGCUGGCCAUC___GCUUGACAUUCG__AGUCGAGC__
...........(((((...((((((((((......)).)).))))))..))))).........((((((..(((......)))..)))))).....(((((((........))))))).. (-29.82 = -30.78 +   0.96)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,704,885 – 8,704,992
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.73
Mean single sequence MFE -32.16
Consensus MFE -25.50
Energy contribution -26.91
Covariance contribution 1.40
Combinations/Pair 1.04
Mean z-score -1.67
Structure conservation index 0.79
SVM decision value 0.04
SVM RNA-class probability 0.552409
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8704885 107 - 23771897
--GCUCGACU--CGAAUGUCAAGC---GAUGGCCAGCAACAUUGAAGCUCUUGGCCAAGAGUU---UGGCCCCAAACAAGUCAGCA--GAUGCGAUUGCUUACCAGCCAGAAUACA-GAA
--(((.(((.--.....))).)))---..((((((((.........))...))))))....((---((((........((((.((.--...))))))........)))))).....-... ( -28.09)
>DroSec_CAF1 10432 108 - 1
--GCUCGACU--CGAAUGUCAAGC---GAUGGCCAGCAGCAUUGAAGCUCGUGGCCAAGAGUU---UGGCCCCAAACAAGUCAGCA--GAUGCGAUUGCUUACCAGCCAGAAAAUAUAAA
--(((.(((.--.....))).)))---..((((((..(((......)))..))))))....((---((((........((((.((.--...))))))........))))))......... ( -32.19)
>DroSim_CAF1 11249 108 - 1
--GCUCGACU--CGAAUGUCAAGC---GAUGGCCAGCAGCAUUGAAGCUCUUGGCCAAGAGUU---UGGCCCCAAACAAGUCAGCA--GAUGCGAUUGCUUACCAGCCAGAAAAUAUGAA
--(((.(((.--.....))).)))---..(((((((.(((......))).)))))))....((---((((........((((.((.--...))))))........))))))......... ( -33.79)
>DroEre_CAF1 10415 105 - 1
--GCUCGACU--CGAAUGUCAAGC---GCUGGCCAGCAGCAUUGAAGCUCUUGGCCAAGAGUU---CGGCCCCAAACAAGUCAGCA--GAUGCGAUUGCUUAGCAGCCAGAAAAUAU---
--(((.(((.--.....))).)))---..(((((((.(((......))).)))))))....((---((((........((((.((.--...))))))........))).))).....--- ( -31.49)
>DroYak_CAF1 10533 107 - 1
--GCUCGACUGUCGAAUGUCAAGC---GAUGGCCAGCAGCAUUGAAGCUCUUGGCCAAGAGUU---UGGCCCCAAACAAGUCAGCA--GAUGCGAUUGCUUAGCAGCCAGAAAAUAU---
--(((.((((((.....(((((((---..(((((((.(((......))).)))))))...)))---)))).....)).))))))).--..(((.........)))............--- ( -34.30)
>DroAna_CAF1 10262 107 - 1
CAGCUCGACU--CGAAUGUCAAGCUUGGAUGGCCAAGAA-----------AUGGCCAAGAGUUUUCUGGCCAAACAGAAAUCAGCACAGAACGGUUUGCUUACCAGCCAGAAAAUCAGAA
.((((.(((.--.....))).))))....((((((....-----------.)))))).((.(((((((((..........((......))..(((......))).))))))))))).... ( -33.10)
>consensus
__GCUCGACU__CGAAUGUCAAGC___GAUGGCCAGCAGCAUUGAAGCUCUUGGCCAAGAGUU___UGGCCCCAAACAAGUCAGCA__GAUGCGAUUGCUUACCAGCCAGAAAAUAUGAA
..(((((((........))).........(((((((.(((......))).))))))).))))....((((........((((.((......))))))........))))........... (-25.50 = -26.91 +   1.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,704,922 – 8,705,021
Length 99
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 85.42
Mean single sequence MFE -38.38
Consensus MFE -30.70
Energy contribution -30.68
Covariance contribution -0.02
Combinations/Pair 1.33
Mean z-score -2.76
Structure conservation index 0.80
SVM decision value 0.90
SVM RNA-class probability 0.878433
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8704922 99 + 23771897
CUUGUUUGGGGCCAAACUCUUGGCCAAGAGCUUCAAUGUUGCUGGCCAUCGCUUGACAUUCG--AGUCGAGCGGUGAAUCACGGCAAGAAUUCUGGCAUCG
.........((((((....))))))..(((((..(((.((((((..(((((((((((.....--.))))))))))).....))))))..)))..))).)). ( -39.10)
>DroPse_CAF1 10667 88 + 1
CUGGUUUACGUCCGAGCUGUGGGCCA----------UAUUGCC-ACCUUCGGUUGACAUUCG--AGUCGCUUGGUGAAUCACCAAGAGAAUUCUUGACUUG
...(((.....(((((..((((....----------.....))-)).)))))..)))...((--((((.(((((((...)))))))((....)).)))))) ( -24.00)
>DroSec_CAF1 10470 99 + 1
CUUGUUUGGGGCCAAACUCUUGGCCACGAGCUUCAAUGCUGCUGGCCAUCGCUUGACAUUCG--AGUCGAGCGGUGAAUCACGGCAAGAAUUCUGGCUUCG
.......(((((((((.(((((((((..(((......)))..))))(((((((((((.....--.)))))))))))........))))).)).))))))). ( -42.30)
>DroSim_CAF1 11287 99 + 1
CUUGUUUGGGGCCAAACUCUUGGCCAAGAGCUUCAAUGCUGCUGGCCAUCGCUUGACAUUCG--AGUCGAGCGGUGAAUCACGGCAAGAAUUCUGGCUUCG
.......(((((((((.(((((((((..(((......)))..))))(((((((((((.....--.)))))))))))........))))).)).))))))). ( -42.70)
>DroEre_CAF1 10450 99 + 1
CUUGUUUGGGGCCGAACUCUUGGCCAAGAGCUUCAAUGCUGCUGGCCAGCGCUUGACAUUCG--AGUCGAGCGGUGAAUCACGGCAAGAAUUCUGGCUUCG
.......(((((((((.(((((((((..(((......)))..))))((.((((((((.....--.)))))))).))........))))).))).)))))). ( -42.60)
>DroYak_CAF1 10568 101 + 1
CUUGUUUGGGGCCAAACUCUUGGCCAAGAGCUUCAAUGCUGCUGGCCAUCGCUUGACAUUCGACAGUCGAGCGGUGAAUCACGGCUAAAAUUCUGGCUUCG
.......(((((((.....((((((.(((((......))).))...(((((((((((........)))))))))))......)))))).....))))))). ( -39.60)
>consensus
CUUGUUUGGGGCCAAACUCUUGGCCAAGAGCUUCAAUGCUGCUGGCCAUCGCUUGACAUUCG__AGUCGAGCGGUGAAUCACGGCAAGAAUUCUGGCUUCG
.......(((((((......((((((..(((......)))..)))))).((((((((........))))))))....................))))))). (-30.70 = -30.68 +  -0.02)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,704,922 – 8,705,021
Length 99
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 85.42
Mean single sequence MFE -31.43
Consensus MFE -25.03
Energy contribution -26.37
Covariance contribution 1.34
Combinations/Pair 1.21
Mean z-score -1.64
Structure conservation index 0.80
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8704922 99 - 23771897
CGAUGCCAGAAUUCUUGCCGUGAUUCACCGCUCGACU--CGAAUGUCAAGCGAUGGCCAGCAACAUUGAAGCUCUUGGCCAAGAGUUUGGCCCCAAACAAG
.(..((((((.(((((((((.((((((.((((.(((.--.....))).))))(((........)))))))..)).))).))))))))))))..)....... ( -29.50)
>DroPse_CAF1 10667 88 - 1
CAAGUCAAGAAUUCUCUUGGUGAUUCACCAAGCGACU--CGAAUGUCAACCGAAGGU-GGCAAUA----------UGGCCCACAGCUCGGACGUAAACCAG
...............(((((((...))))))).(((.--.....)))..((((..((-(((....----------..).))))...))))........... ( -21.70)
>DroSec_CAF1 10470 99 - 1
CGAAGCCAGAAUUCUUGCCGUGAUUCACCGCUCGACU--CGAAUGUCAAGCGAUGGCCAGCAGCAUUGAAGCUCGUGGCCAAGAGUUUGGCCCCAAACAAG
....((((((.(((((............((((.(((.--.....))).))))..(((((..(((......)))..)))))))))))))))).......... ( -33.30)
>DroSim_CAF1 11287 99 - 1
CGAAGCCAGAAUUCUUGCCGUGAUUCACCGCUCGACU--CGAAUGUCAAGCGAUGGCCAGCAGCAUUGAAGCUCUUGGCCAAGAGUUUGGCCCCAAACAAG
....((((((.(((((............((((.(((.--.....))).))))..((((((.(((......))).))))))))))))))))).......... ( -34.90)
>DroEre_CAF1 10450 99 - 1
CGAAGCCAGAAUUCUUGCCGUGAUUCACCGCUCGACU--CGAAUGUCAAGCGCUGGCCAGCAGCAUUGAAGCUCUUGGCCAAGAGUUCGGCCCCAAACAAG
....(((.((((((((............((((.(((.--.....))).))))..((((((.(((......))).))))))))))))))))).......... ( -35.90)
>DroYak_CAF1 10568 101 - 1
CGAAGCCAGAAUUUUAGCCGUGAUUCACCGCUCGACUGUCGAAUGUCAAGCGAUGGCCAGCAGCAUUGAAGCUCUUGGCCAAGAGUUUGGCCCCAAACAAG
................((((.(((((..((((.(((........))).)))).(((((((.(((......))).))))))).))))))))).......... ( -33.30)
>consensus
CGAAGCCAGAAUUCUUGCCGUGAUUCACCGCUCGACU__CGAAUGUCAAGCGAUGGCCAGCAGCAUUGAAGCUCUUGGCCAAGAGUUUGGCCCCAAACAAG
.(..(((.((((((((............((((.(((........))).))))..((((((.(((......))).)))))))))))))))))..)....... (-25.03 = -26.37 +   1.34)

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 10:48:00 2006