Locus 6588

Sequence ID 2L_DroMel_CAF1
Location 18,514,024 – 18,514,193
Length 169
Max. P 0.994147
window10515 window10516 window10517 window10518

overview

Window 5

Location 18,514,024 – 18,514,130
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.01
Mean single sequence MFE -24.39
Consensus MFE -16.82
Energy contribution -17.22
Covariance contribution 0.40
Combinations/Pair 1.15
Mean z-score -1.99
Structure conservation index 0.69
SVM decision value 1.12
SVM RNA-class probability 0.918466
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18514024 106 + 22407834
AUAAAAUAGUUAGUCGUUUAAUUUAAAUC----C---------UCAUUA-AAAGCCACAACAAAAGGAAGUUGCCGAAGGAGCAGCCGUUGGCUUCAUCAUGAGGAAGCCAGAAAUGCUG
..........(((.(((((........((----(---------((((..-.(((((((..(....)...((((((....).))))).).))))))....)))))))......)))))))) ( -25.04)
>DroPse_CAF1 41193 119 + 1
AUAAAUUAUUAAGUCGUUUAAUUUAAACCAAUCCCCAACCAUCCCAUAAAACAAACAC-ACAAAAGAGUGUUGCCGAGGGAGCAACCGACUGCUUCGAAAUGACUAAGCAACAAUUGCUU
...........((((((((..................................(((((-........)))))..(((((.(((....).)).)))))))))))))(((((.....))))) ( -22.00)
>DroSec_CAF1 34458 106 + 1
AUAAAUUAGUAAGUCGUUUAAUUUAAAUC----C---------UAAUAA-AAAGCCACAACAAAAGGAAGUUGCCGCAGGAGCAGCCGUUGGCUUCAUCAUGACGAAGCCAGAAAUGCUG
.((((((((........))))))))..((----(---------(.....-...((..((((........))))..)))))).((((..((((((((........))))))))....)))) ( -25.40)
>DroSim_CAF1 33006 106 + 1
AUAAAUUAGUAAGUCGUUUAAUUUAAAUC----C---------UAAUAA-AAAGCCACAACAAAAGGAAGUUGCCGCAGGAGCAGCCGUUGGCUUCAUCAUGACGAAGCCAGAAAUGCUG
.((((((((........))))))))..((----(---------(.....-...((..((((........))))..)))))).((((..((((((((........))))))))....)))) ( -25.40)
>DroYak_CAF1 34436 94 + 1
AUAAAUUAGUAAGUCGUUUAAUUUAAUUC----C---------UCAUAA-A------------AAGGAAGUUGACGCAGGAGUAGCCGCUGGCUUCAUCAUGACGAAGCCAGAAAUGCUG
.((((((((........)))))))).(((----(---------(.....-.------------.)))))......(((((.....)).((((((((........))))))))...))).. ( -24.10)
>consensus
AUAAAUUAGUAAGUCGUUUAAUUUAAAUC____C_________UCAUAA_AAAGCCACAACAAAAGGAAGUUGCCGCAGGAGCAGCCGUUGGCUUCAUCAUGACGAAGCCAGAAAUGCUG
.((((((((........)))))))).......................................................((((....((((((((........))))))))...)))). (-16.82 = -17.22 +   0.40)

alignment

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secondary structure

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Window 6

Location 18,514,024 – 18,514,130
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.01
Mean single sequence MFE -28.18
Consensus MFE -14.16
Energy contribution -15.80
Covariance contribution 1.64
Combinations/Pair 1.16
Mean z-score -2.59
Structure conservation index 0.50
SVM decision value 1.76
SVM RNA-class probability 0.975819
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18514024 106 - 22407834
CAGCAUUUCUGGCUUCCUCAUGAUGAAGCCAACGGCUGCUCCUUCGGCAACUUCCUUUUGUUGUGGCUUU-UAAUGA---------G----GAUUUAAAUUAAACGACUAACUAUUUUAU
.(((.......)))(((((((...((((((..(((........)))(((((........)))))))))))-..))))---------)----))........................... ( -25.80)
>DroPse_CAF1 41193 119 - 1
AAGCAAUUGUUGCUUAGUCAUUUCGAAGCAGUCGGUUGCUCCCUCGGCAACACUCUUUUGU-GUGUUUGUUUUAUGGGAUGGUUGGGGAUUGGUUUAAAUUAAACGACUUAAUAAUUUAU
..(((((((((((((.(......).)))))).)))))))((((..((((((((.(....).-))).)))))....)))).(((((..((((......))))...)))))........... ( -30.80)
>DroSec_CAF1 34458 106 - 1
CAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAACGGCUGCUCCUGCGGCAACUUCCUUUUGUUGUGGCUUU-UUAUUA---------G----GAUUUAAAUUAAACGACUUACUAAUUUAU
((((.....(((((((((....)))))))))...)))).((((((.(((((........))))).))...-.....)---------)----))..(((((((..........))))))). ( -29.70)
>DroSim_CAF1 33006 106 - 1
CAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAACGGCUGCUCCUGCGGCAACUUCCUUUUGUUGUGGCUUU-UUAUUA---------G----GAUUUAAAUUAAACGACUUACUAAUUUAU
((((.....(((((((((....)))))))))...)))).((((((.(((((........))))).))...-.....)---------)----))..(((((((..........))))))). ( -29.70)
>DroYak_CAF1 34436 94 - 1
CAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAGCGGCUACUCCUGCGUCAACUUCCUU------------U-UUAUGA---------G----GAAUUAAAUUAAACGACUUACUAAUUUAU
.(((....((((((((((....))))))))))..)))..............((((((------------.-....))---------)----))).(((((((..........))))))). ( -24.90)
>consensus
CAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAACGGCUGCUCCUGCGGCAACUUCCUUUUGUUGUGGCUUU_UUAUGA_________G____GAUUUAAAUUAAACGACUUACUAAUUUAU
((((.....(((((((((....)))))))))...))))........(((((........)))))...............................(((((((..........))))))). (-14.16 = -15.80 +   1.64)

alignment

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secondary structure

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Window 7

Location 18,514,054 – 18,514,168
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.43
Mean single sequence MFE -26.40
Consensus MFE -15.32
Energy contribution -16.96
Covariance contribution 1.64
Combinations/Pair 1.17
Mean z-score -2.68
Structure conservation index 0.58
SVM decision value 1.52
SVM RNA-class probability 0.961021
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18514054 114 - 22407834
AAUUAAGAAUUUUCA--ACUCACCAUAAAAUUAAACUAAUCAGCAUUUCUGGCUUCCUCAUGAUGAAGCCAACGGCUGCUCCUUCGGCAACUUCCUUUUGUUGUGGCUUU-UAAUGA---
.(((((((.......--.......................((((.....(((((((........)))))))...))))......(.(((((........))))).).)))-))))..--- ( -22.60)
>DroPse_CAF1 41233 119 - 1
AUUUAGGAACUGCCAAAACUCACCAUAAAAUUAAACUAAAAAGCAAUUGUUGCUUAGUCAUUUCGAAGCAGUCGGUUGCUCCCUCGGCAACACUCUUUUGU-GUGUUUGUUUUAUGGGAU
.....((.....)).....((.(((((((((.((((.....((((((((((((((.(......).)))))).)))))))).........((((......))-))))))))))))))))). ( -30.80)
>DroSec_CAF1 34488 114 - 1
AAUUAAGAAUUUUCA--ACUCACCAUAAAAUUAAACUAAUCAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAACGGCUGCUCCUGCGGCAACUUCCUUUUGUUGUGGCUUU-UUAUUA---
...((((((......--.......................((((.....(((((((((....)))))))))...)))).....((.(((((........))))).)))))-)))...--- ( -28.40)
>DroSim_CAF1 33036 114 - 1
AAUUAAGAAUUUUCU--ACUCACCAUAAAAUUAAACUAAUCAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAACGGCUGCUCCUGCGGCAACUUCCUUUUGUUGUGGCUUU-UUAUUA---
...((((((......--.......................((((.....(((((((((....)))))))))...)))).....((.(((((........))))).)))))-)))...--- ( -28.40)
>DroYak_CAF1 34466 102 - 1
AAUUAAAAACUUUCA--ACUCACCAUAAAAUUAAACUAAUCAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAGCGGCUACUCCUGCGUCAACUUCCUU------------U-UUAUGA---
...............--......(((((((............(((...((((((((((....)))))))))).((.....)))))...........)------------)-))))).--- ( -21.80)
>consensus
AAUUAAGAAUUUUCA__ACUCACCAUAAAAUUAAACUAAUCAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAACGGCUGCUCCUGCGGCAACUUCCUUUUGUUGUGGCUUU_UUAUGA___
....................(((.((((((..........((((.....(((((((((....)))))))))...)))).......(....)....)))))).)))............... (-15.32 = -16.96 +   1.64)

alignment

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secondary structure

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Window 8

Location 18,514,090 – 18,514,193
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.23
Mean single sequence MFE -18.61
Consensus MFE -13.46
Energy contribution -13.70
Covariance contribution 0.24
Combinations/Pair 1.31
Mean z-score -2.35
Structure conservation index 0.72
SVM decision value 2.45
SVM RNA-class probability 0.994147
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18514090 103 - 22407834
UCGGA------CAAAUCACAC-AUUAAAUAC--------UAAUUAAGAAUUUUCA--ACUCACCAUAAAAUUAAACUAAUCAGCAUUUCUGGCUUCCUCAUGAUGAAGCCAACGGCUGCU
.....------..........-.........--------................--.......................((((.....(((((((........)))))))...)))).. ( -14.60)
>DroPse_CAF1 41272 97 - 1
UCAU--------------CUA-AAUAAAAAC--------UAUUUAGGAACUGCCAAAACUCACCAUAAAAUUAAACUAAAAAGCAAUUGUUGCUUAGUCAUUUCGAAGCAGUCGGUUGCU
...(--------------(((-((((.....--------))))))))..................................((((((((((((((.(......).)))))).)))))))) ( -19.00)
>DroSec_CAF1 34524 109 - 1
UCGGACUUUAACAAAUCACAC-AUUAAAUAU--------UAAUUAAGAAUUUUCA--ACUCACCAUAAAAUUAAACUAAUCAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAACGGCUGCU
.....................-.........--------................--.......................((((.....(((((((((....)))))))))...)))).. ( -17.80)
>DroSim_CAF1 33072 109 - 1
UCGGACUUUAACAAAUCACAC-AUUAAAUAC--------UAAUUAAGAAUUUUCU--ACUCACCAUAAAAUUAAACUAAUCAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAACGGCUGCU
..((.................-((((.....--------))))..(((....)))--.....))................((((.....(((((((((....)))))))))...)))).. ( -17.90)
>DroYak_CAF1 34490 107 - 1
-----------AAAAUGACACCAACAAAUGCUAAUGGCUUAAUUAAAAACUUUCA--ACUCACCAUAAAAUUAAACUAAUCAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAGCGGCUACU
-----------.........((...(((((((..(((.((((((...........--...........)))))).)))...)))))))((((((((((....)))))))))).))..... ( -23.75)
>consensus
UCGGA______CAAAUCACAC_AUUAAAUAC________UAAUUAAGAAUUUUCA__ACUCACCAUAAAAUUAAACUAAUCAGCAUUUCUGGCUUCGUCAUGAUGAAGCCAACGGCUGCU
................................................................................((((.....(((((((((....)))))))))...)))).. (-13.46 = -13.70 +   0.24)

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 12:15:00 2006