Locus 5738

Sequence ID 3R_DroMel_CAF1
Location 14,949,306 – 14,949,538
Length 232
Max. P 0.964014
window9398 window9399 window9400 window9401

overview

Window 8

Location 14,949,306 – 14,949,426
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.76
Mean single sequence MFE -33.33
Consensus MFE -31.76
Energy contribution -31.45
Covariance contribution -0.31
Combinations/Pair 1.09
Mean z-score -1.57
Structure conservation index 0.95
SVM decision value 0.37
SVM RNA-class probability 0.708370
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14949306 120 + 27905053
UCAUCAUCAGCAAAAUUUCAAUAAUUUCAUUAUCAAGAUGAAGAUUGAUUGAUAAGCUAGCUGCCUGGGCAAAUGGCAGUGUGUGGCCAUGAUUUCGGGGCUGGAUGAUGACCACAUGGC
(((((((((((......(((((..(((((((.....)))))))....))))).......)))((((.((...(((((........)))))....)).))))..))))))))((....)). ( -35.52)
>DroSec_CAF1 85006 116 + 1
UCAUCAUCGGCAAAAUUUCAAUAAUUCCAUUAUCAAGAUGAAGAUUGAUUGAUAAG----CUGCCUGGGCAAAUGGCAGUGUGUGGCCAUGAUUUCGGGGCUGGAUGAUGACCACAUGGC
(((((((((((......(((((...((((((.....))))..))...)))))...)----))((((.((...(((((........)))))....)).))))..))))))))((....)). ( -32.30)
>DroSim_CAF1 77952 116 + 1
UCAUCAUCAGCAAAAUUUCAAUAAUUCCAUUAUCAAGAUGAAGAUUGAUUGAUAAG----CUGCCUGGGCAAAUGGCAGUGUGUGGCCAUGAUUUCGGGGCUGGAUGAUGACCACAUGGC
(((((((((((......(((((...((((((.....))))..))...)))))....----...((((((...(((((........)))))...))))))))).))))))))((....)). ( -32.80)
>DroYak_CAF1 82043 116 + 1
UCAUCAUCAGCAAAAUUUCAAUAAUUCCAUUAUCAAGAUGAAGAUUGAUUGAUAAG----CUGGCCGGGCAAAUGGCAUUUUGUGGCCAUGAUUUCGGGGCUGGAUGAUGACCACAUGGC
(((((((((((...............((((((((((............))))))).----.)))(((((...(((((........)))))...))))).))).))))))))((....)). ( -32.70)
>consensus
UCAUCAUCAGCAAAAUUUCAAUAAUUCCAUUAUCAAGAUGAAGAUUGAUUGAUAAG____CUGCCUGGGCAAAUGGCAGUGUGUGGCCAUGAUUUCGGGGCUGGAUGAUGACCACAUGGC
(((((((((((......(((((...((((((.....))))..))...)))))...........((((((...(((((........)))))...))))))))).))))))))((....)). (-31.76 = -31.45 +  -0.31)

alignment

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secondary structure

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Window 9

Location 14,949,386 – 14,949,506
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.50
Mean single sequence MFE -44.70
Consensus MFE -40.22
Energy contribution -41.48
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.47
Structure conservation index 0.90
SVM decision value 0.97
SVM RNA-class probability 0.893057
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14949386 120 + 27905053
GUGUGGCCAUGAUUUCGGGGCUGGAUGAUGACCACAUGGCCACAUGGCACAGUCGCAAUUGCUGGGCUCAACUUCUCCACUCAAUCAAUAUUGAGUCAUGCGGCAGAAGUUGAGAUUGCG
(((((((((((...(((...(.....).)))...))))))))))).(((((((.......))))..(((((((((((((((((((....))))))).....)).))))))))))..))). ( -46.10)
>DroSec_CAF1 85082 120 + 1
GUGUGGCCAUGAUUUCGGGGCUGGAUGAUGACCACAUGGCCACAUGGCACAGUCGCAAUUGCUGGGCUCAACUUCUCCACUCAAUCAAUAUUGAGUCAUGCGGCAGAAGUUGAGAUUGCG
(((((((((((...(((...(.....).)))...))))))))))).(((((((.......))))..(((((((((((((((((((....))))))).....)).))))))))))..))). ( -46.10)
>DroSim_CAF1 78028 120 + 1
GUGUGGCCAUGAUUUCGGGGCUGGAUGAUGACCACAUGGCCACAUGGCACAGUCGCAAUUGCUGGGCUCAACUUCUCCACUCAAUCAAUAUUGAGUCAUGCGGCAGAAGUUGAGAUUGCG
(((((((((((...(((...(.....).)))...))))))))))).(((((((.......))))..(((((((((((((((((((....))))))).....)).))))))))))..))). ( -46.10)
>DroYak_CAF1 82119 120 + 1
UUGUGGCCAUGAUUUCGGGGCUGGAUGAUGACCACAUGGCCACUUGGCAGAGUCACAAUUGCUGGGCUCAACUUCUGCACUCAAUCAAUAUUAAGUCAUGCGGCAGAAGUUGAGAUUGCG
..(((((((((...(((...(.....).)))...)))))))))(..((((........))))..).((((((((((((.(.((..(........)...)).)))))))))))))...... ( -40.50)
>consensus
GUGUGGCCAUGAUUUCGGGGCUGGAUGAUGACCACAUGGCCACAUGGCACAGUCGCAAUUGCUGGGCUCAACUUCUCCACUCAAUCAAUAUUGAGUCAUGCGGCAGAAGUUGAGAUUGCG
(((((((((((...(((...(.....).)))...))))))))))).(((((((.......))))..(((((((((((((((((((....))))))).....)).))))))))))..))). (-40.22 = -41.48 +   1.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,949,386 – 14,949,506
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.50
Mean single sequence MFE -44.18
Consensus MFE -41.56
Energy contribution -41.43
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -3.58
Structure conservation index 0.94
SVM decision value 1.56
SVM RNA-class probability 0.964014
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14949386 120 - 27905053
CGCAAUCUCAACUUCUGCCGCAUGACUCAAUAUUGAUUGAGUGGAGAAGUUGAGCCCAGCAAUUGCGACUGUGCCAUGUGGCCAUGUGGUCAUCAUCCAGCCCCGAAAUCAUGGCCACAC
((((((((((((((((.((.....(((((((....))))))))))))))))))).......)))))).........((((((((((...((.............))...)))))))))). ( -44.53)
>DroSec_CAF1 85082 120 - 1
CGCAAUCUCAACUUCUGCCGCAUGACUCAAUAUUGAUUGAGUGGAGAAGUUGAGCCCAGCAAUUGCGACUGUGCCAUGUGGCCAUGUGGUCAUCAUCCAGCCCCGAAAUCAUGGCCACAC
((((((((((((((((.((.....(((((((....))))))))))))))))))).......)))))).........((((((((((...((.............))...)))))))))). ( -44.53)
>DroSim_CAF1 78028 120 - 1
CGCAAUCUCAACUUCUGCCGCAUGACUCAAUAUUGAUUGAGUGGAGAAGUUGAGCCCAGCAAUUGCGACUGUGCCAUGUGGCCAUGUGGUCAUCAUCCAGCCCCGAAAUCAUGGCCACAC
((((((((((((((((.((.....(((((((....))))))))))))))))))).......)))))).........((((((((((...((.............))...)))))))))). ( -44.53)
>DroYak_CAF1 82119 120 - 1
CGCAAUCUCAACUUCUGCCGCAUGACUUAAUAUUGAUUGAGUGCAGAAGUUGAGCCCAGCAAUUGUGACUCUGCCAAGUGGCCAUGUGGUCAUCAUCCAGCCCCGAAAUCAUGGCCACAA
((((((((((((((((((......(((((((....))))))))))))))))))).......))))))..........(((((((((...((.............))...))))))))).. ( -43.13)
>consensus
CGCAAUCUCAACUUCUGCCGCAUGACUCAAUAUUGAUUGAGUGGAGAAGUUGAGCCCAGCAAUUGCGACUGUGCCAUGUGGCCAUGUGGUCAUCAUCCAGCCCCGAAAUCAUGGCCACAC
((((((((((((((((.((.....(((((((....))))))))))))))))))).......))))))..........(((((((((...((.............))...))))))))).. (-41.56 = -41.43 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,949,426 – 14,949,538
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 97.32
Mean single sequence MFE -36.83
Consensus MFE -32.33
Energy contribution -32.45
Covariance contribution 0.12
Combinations/Pair 1.05
Mean z-score -2.00
Structure conservation index 0.88
SVM decision value 0.33
SVM RNA-class probability 0.691928
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14949426 112 + 27905053
CACAUGGCACAGUCGCAAUUGCUGGGCUCAACUUCUCCACUCAAUCAAUAUUGAGUCAUGCGGCAGAAGUUGAGAUUGCGUUGCAGGCGGCAGUGAAAGUUAAUUGUGAGCU
.....(((...((((((((.((....(((((((((((((((((((....))))))).....)).))))))))))...))))))).))).(((((........)))))..))) ( -37.70)
>DroSec_CAF1 85122 112 + 1
CACAUGGCACAGUCGCAAUUGCUGGGCUCAACUUCUCCACUCAAUCAAUAUUGAGUCAUGCGGCAGAAGUUGAGAUUGCGUUGCAGGCGGCAGUGAAAGUUAAUUGUGAGCU
.....(((...((((((((.((....(((((((((((((((((((....))))))).....)).))))))))))...))))))).))).(((((........)))))..))) ( -37.70)
>DroSim_CAF1 78068 112 + 1
CACAUGGCACAGUCGCAAUUGCUGGGCUCAACUUCUCCACUCAAUCAAUAUUGAGUCAUGCGGCAGAAGUUGAGAUUGCGUUGCAGGCGGCAGUGAAAGUUAAUUGUGAGCU
.....(((...((((((((.((....(((((((((((((((((((....))))))).....)).))))))))))...))))))).))).(((((........)))))..))) ( -37.70)
>DroYak_CAF1 82159 112 + 1
CACUUGGCAGAGUCACAAUUGCUGGGCUCAACUUCUGCACUCAAUCAAUAUUAAGUCAUGCGGCAGAAGUUGAGAUUGCGUUGCAGGCGGUAGUGAAAGUUAAUUGUGAGCU
((((((((....((((.((((((...((((((((((((.(.((..(........)...)).)))))))))))))..(((...))))))))).))))..)))))..))).... ( -34.20)
>consensus
CACAUGGCACAGUCGCAAUUGCUGGGCUCAACUUCUCCACUCAAUCAAUAUUGAGUCAUGCGGCAGAAGUUGAGAUUGCGUUGCAGGCGGCAGUGAAAGUUAAUUGUGAGCU
.....(((....(((((((((((...(((((((((((((((((((....))))))).....)).))))))))))(((((((.....)).)))))...)).)))))))))))) (-32.33 = -32.45 +   0.12)

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 12:03:28 2006