Locus 4463

Sequence ID 3L_DroMel_CAF1
Location 12,958,455 – 12,958,685
Length 230
Max. P 0.991962
window6955 window6956 window6957 window6958 window6959

overview

Window 5

Location 12,958,455 – 12,958,567
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.71
Mean single sequence MFE -32.10
Consensus MFE -23.66
Energy contribution -23.50
Covariance contribution -0.16
Combinations/Pair 1.24
Mean z-score -1.80
Structure conservation index 0.74
SVM decision value 0.36
SVM RNA-class probability 0.703326
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12958455 112 - 23771897
CGCUGAGGGUUUGGAAGAAGUCAAGCCCUCCUUAUUGCACCAGCAAUG-------UGUGUGUGCGGCAAAACUU-UAGUUGAGUUUCGGCUAAGUUAUUCGAAAUUUUAGUAAUUGAUAU
(((.((((((((((......))))))))))......((((((....))-------.))))..)))....(((((-.(((((.....))))))))))........................ ( -31.00)
>DroSec_CAF1 75678 113 - 1
CGCUGAGGGUUUGGAAAAAGUCAAGCCCUCCUUAUUGCACCAGCAAUU-------UGUGGGUGCGGGAAAACUUUUGGUUGAGUUUCGGCUAAGUUAUACGAAAUUUUAGUAAUUUAUAU
.(((((((((((((......))))))))((((....(((((.((....-------.)).))))))))).(((((......))))))))))((((((((...........))))))))... ( -33.20)
>DroSim_CAF1 80424 113 - 1
CGCUGAGGGUUUGGAAAAAGUCAAACCCUCCCUAUUGCACCAGCAAUG-------UGUGGGUGCGGGAAAACUUUUGGUUGAGUUUCGGCUAAGUUAUACGAAAUUUUAGUAAUUGAUAU
....((((((((((......))))))))))(((...(((((.((....-------.)).))))))))....(..(((.(.((((((((...........)))))))).).)))..).... ( -33.90)
>DroEre_CAF1 81728 112 - 1
CUUCGAGGGCUUGGGAAAAGUCAGGCCCUCCUUAUUACAGCAGUAAUG-------UAUGUGGGCGGGAAAACUU-UGGUUGAGUUUCGUCUAAGUUAUCCAACAUUUUAGUAAUUGAUAU
....((((((((((......))))))))))...(((((.(((....))-------)...((((((..(.(((..-..)))...)..)))))).................)))))...... ( -32.40)
>DroYak_CAF1 79555 119 - 1
CUCCGAGGGUUUGGAAAAAGUCAAGCCCUCCGUAUUACAUCAGCAAUGGUACGAGUAUAUGUGCGUGAAAACUU-UGGUUGCGUUUCGACUAAGUUAUCCAACAUUUUAGUAAUUGAUAU
....((((((((((......))))))))))((.(((((....(((...(((....)))...)))(.((.(((((-.(((((.....)))))))))).))).........))))))).... ( -30.00)
>consensus
CGCUGAGGGUUUGGAAAAAGUCAAGCCCUCCUUAUUGCACCAGCAAUG_______UGUGUGUGCGGGAAAACUU_UGGUUGAGUUUCGGCUAAGUUAUACGAAAUUUUAGUAAUUGAUAU
(((.((((((((((......))))))))))..((((((....))))))..............)))....((((..((((((.....))))))))))........................ (-23.66 = -23.50 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,958,495 – 12,958,606
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.64
Mean single sequence MFE -32.92
Consensus MFE -24.44
Energy contribution -25.08
Covariance contribution 0.64
Combinations/Pair 1.10
Mean z-score -1.77
Structure conservation index 0.74
SVM decision value 0.31
SVM RNA-class probability 0.684647
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12958495 111 + 23771897
AACUA-AAGUUUUGCCGCACACACA-------CAUUGCUGGUGCAAUAAGGAGGGCUUGACUUCUUCCAAACCCUCAGCGAGGGCGACAAUGACUUUGUGUAAAUAUA-GGGGGAGAAUU
.((((-((((((((((((((.((..-------......))))))......(((((.(((........))).)))))......)))))....))))))).)).......-........... ( -27.80)
>DroSec_CAF1 75718 112 + 1
AACCAAAAGUUUUCCCGCACCCACA-------AAUUGCUGGUGCAAUAAGGAGGGCUUGACUUUUUCCAAACCCUCAGCGAGGGCGACAAUGACUUUGUGUAAAUAUA-GGGGGAGAAUU
.......(((((((((.(.(((...-------.(((((....)))))...(((((.(((........))).))))).....)))..((((.....)))).........-).))))))))) ( -33.70)
>DroSim_CAF1 80464 112 + 1
AACCAAAAGUUUUCCCGCACCCACA-------CAUUGCUGGUGCAAUAGGGAGGGUUUGACUUUUUCCAAACCCUCAGCGAGGGCGACAAUGACUUUGUGUAAAUAUA-GGGGGAGAAUU
.......(((((((((.(.(((.(.-------.(((((....)))))..)(((((((((........))))))))).....)))..((((.....)))).........-).))))))))) ( -38.20)
>DroEre_CAF1 81768 112 + 1
AACCA-AAGUUUUCCCGCCCACAUA-------CAUUACUGCUGUAAUAAGGAGGGCCUGACUUUUCCCAAGCCCUCGAAGAGGGCGACAAUGACUUUGUGUAAAUAUAUAGGGGAGAAUU
.....-.(((((((((((((.....-------.(((((....)))))...((((((.((........)).)))))).....)))).((((.....))))............))))))))) ( -36.80)
>DroYak_CAF1 79595 118 + 1
AACCA-AAGUUUUCACGCACAUAUACUCGUACCAUUGCUGAUGUAAUACGGAGGGCUUGACUUUUUCCAAACCCUCGGAGAGGACGACAAUGACUUUGUGUAAAUAUA-GGGGGAGAAUU
.....-.(((((((.....(((....((((.(((((((....))))).(.(((((.(((........))).))))).)...))))))..))).(((((((....))))-))).))))))) ( -28.10)
>consensus
AACCA_AAGUUUUCCCGCACACACA_______CAUUGCUGGUGCAAUAAGGAGGGCUUGACUUUUUCCAAACCCUCAGCGAGGGCGACAAUGACUUUGUGUAAAUAUA_GGGGGAGAAUU
.......(((((((((.(...............(((((....)))))...(((((.(((........))).))))).((((((..........))))))..........).))))))))) (-24.44 = -25.08 +   0.64)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,958,495 – 12,958,606
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.64
Mean single sequence MFE -34.11
Consensus MFE -24.10
Energy contribution -24.38
Covariance contribution 0.28
Combinations/Pair 1.19
Mean z-score -2.51
Structure conservation index 0.71
SVM decision value 0.94
SVM RNA-class probability 0.885632
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12958495 111 - 23771897
AAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGCCCUCGCUGAGGGUUUGGAAGAAGUCAAGCCCUCCUUAUUGCACCAGCAAUG-------UGUGUGUGCGGCAAAACUU-UAGUU
...........-...........(((((..(((((((.(.(((.((((((((((......))))))))))..((((((....))))))-------.))).).))))))).))))-).... ( -35.20)
>DroSec_CAF1 75718 112 - 1
AAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGCCCUCGCUGAGGGUUUGGAAAAAGUCAAGCCCUCCUUAUUGCACCAGCAAUU-------UGUGGGUGCGGGAAAACUUUUGGUU
...........-........((.(((((..((.((((.(((((.((((((((((......))))))))))...(((((....))))).-------.))))).)))).)).)))))))... ( -33.30)
>DroSim_CAF1 80464 112 - 1
AAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGCCCUCGCUGAGGGUUUGGAAAAAGUCAAACCCUCCCUAUUGCACCAGCAAUG-------UGUGGGUGCGGGAAAACUUUUGGUU
.....((((..-.........((((.....))))(((((.(((.((((((((((......))))))))))...(((((....))))))-------)).))))).))))............ ( -35.70)
>DroEre_CAF1 81768 112 - 1
AAUUCUCCCCUAUAUAUUUACACAAAGUCAUUGUCGCCCUCUUCGAGGGCUUGGGAAAAGUCAGGCCCUCCUUAUUACAGCAGUAAUG-------UAUGUGGGCGGGAAAACUU-UGGUU
......................((((((..((.((((((.....((((((((((......))))))))))......((((((....))-------).))))))))).)).))))-))... ( -38.10)
>DroYak_CAF1 79595 118 - 1
AAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGUCCUCUCCGAGGGUUUGGAAAAAGUCAAGCCCUCCGUAUUACAUCAGCAAUGGUACGAGUAUAUGUGCGUGAAAACUU-UGGUU
...........-..........((((((((((((.(......(.((((((((((......)))))))))).)........).))))))(((((......)))))......))))-))... ( -28.24)
>consensus
AAUUCUCCCCC_UAUAUUUACACAAAGUCAUUGUCGCCCUCGCUGAGGGUUUGGAAAAAGUCAAGCCCUCCUUAUUGCACCAGCAAUG_______UGUGUGUGCGGGAAAACUU_UGGUU
...................((...((((..((.((((.(.(((.((((((((((......))))))))))..((((((....))))))........))).).)))).)).))))...)). (-24.10 = -24.38 +   0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,958,527 – 12,958,645
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.45
Mean single sequence MFE -25.56
Consensus MFE -24.47
Energy contribution -24.23
Covariance contribution -0.24
Combinations/Pair 1.15
Mean z-score -1.63
Structure conservation index 0.96
SVM decision value 2.30
SVM RNA-class probability 0.991962
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12958527 118 - 23771897
CCCAUUGCAAUAACAAAUAUUGGU-UGCUGGCACAAUUUCAAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGCCCUCGCUGAGGGUUUGGAAGAAGUCAAGCCCUCCUUAUUGCAC
.....((((((((...........-.((.((((((((..(...........-..............)..))))).)))...)).((((((((((......)))))))))).)))))))). ( -28.01)
>DroSec_CAF1 75751 119 - 1
CCCAUUGCAAUAACAAAUAUUGGUUUGCUGGCACAAUUUCAAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGCCCUCGCUGAGGGUUUGGAAAAAGUCAAGCCCUCCUUAUUGCAC
.....((((((((.............((.((((((((..(...........-..............)..))))).)))...)).((((((((((......)))))))))).)))))))). ( -28.01)
>DroSim_CAF1 80497 119 - 1
CCCAUUGCAAUAACAAAUAUUGGUUUGCUGGCACAAUUUCAAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGCCCUCGCUGAGGGUUUGGAAAAAGUCAAACCCUCCCUAUUGCAC
.....(((((((..............((.((((((((..(...........-..............)..))))).)))...)).((((((((((......))))))))))..))))))). ( -27.41)
>DroEre_CAF1 81800 119 - 1
CCCAUUGCAAUAACAAAUAUUGGC-UGCUGGCACAAUUUCAAUUCUCCCCUAUAUAUUUACACAAAGUCAUUGUCGCCCUCUUCGAGGGCUUGGGAAAAGUCAGGCCCUCCUUAUUACAG
.......(((((.....))))).(-((..((((((((..(..........................)..))))).)))......((((((((((......)))))))))).......))) ( -24.07)
>DroYak_CAF1 79634 118 - 1
CCCAUUGCAAUAACAAAUAUUGGU-UGCUGGCACAAUUUCAAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGUCCUCUCCGAGGGUUUGGAAAAAGUCAAGCCCUCCGUAUUACAU
.(((..(((((...........))-))))))....................-......(((((((.....))))..........((((((((((......)))))))))).)))...... ( -20.30)
>consensus
CCCAUUGCAAUAACAAAUAUUGGU_UGCUGGCACAAUUUCAAUUCUCCCCC_UAUAUUUACACAAAGUCAUUGUCGCCCUCGCUGAGGGUUUGGAAAAAGUCAAGCCCUCCUUAUUGCAC
.....(((((((.................((((((((..(..........................)..))))).)))......((((((((((......))))))))))..))))))). (-24.47 = -24.23 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,958,567 – 12,958,685
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.81
Mean single sequence MFE -23.57
Consensus MFE -22.74
Energy contribution -22.18
Covariance contribution -0.56
Combinations/Pair 1.12
Mean z-score -1.45
Structure conservation index 0.96
SVM decision value 1.42
SVM RNA-class probability 0.952666
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12958567 118 - 23771897
AACAAAUCAGCGACAAAUGCAUGGGCGGUGCACAAACUCACCCAUUGCAAUAACAAAUAUUGGU-UGCUGGCACAAUUUCAAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGCCCU
.........(((((((.((((((((.(((......)).).)))).)))).....((((((.((.-........................))-.))))))...........)))))))... ( -24.21)
>DroSec_CAF1 75791 119 - 1
AACAAAUCAGCGACAAAUGCAUGGGCGGUGCACAAACUCACCCAUUGCAAUAACAAAUAUUGGUUUGCUGGCACAAUUUCAAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGCCCU
.........(((((((.((((((((.(((......)).).)))).)))).........(((((((....))).))))..............-..................)))))))... ( -24.30)
>DroSim_CAF1 80537 119 - 1
AACAAAUCAGCGACAAAUGCAUGGGCGGUGCACAAACUCACCCAUUGCAAUAACAAAUAUUGGUUUGCUGGCACAAUUUCAAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGCCCU
.........(((((((.((((((((.(((......)).).)))).)))).........(((((((....))).))))..............-..................)))))))... ( -24.30)
>DroEre_CAF1 81840 119 - 1
AACAAAUCAGCGACAAAUGCAUGGGCGGUGCACGAAUUCACCCAUUGCAAUAACAAAUAUUGGC-UGCUGGCACAAUUUCAAUUCUCCCCUAUAUAUUUACACAAAGUCAUUGUCGCCCU
.........(((((((.((((((((.((.........)).)))).))))...........((((-(..((................................)).))))))))))))... ( -24.35)
>DroYak_CAF1 79674 118 - 1
AACAAAUCAGCGACAAAUGCAUGGGCGGUGCACGAAUACACCCAUUGCAAUAACAAAUAUUGGU-UGCUGGCACAAUUUCAAUUCUCCCCC-UAUAUUUACACAAAGUCAUUGUCGUCCU
......((((((((...((((((((..(((......))).)))).))))....((.....))))-))))))....................-.......((((((.....)))).))... ( -20.70)
>consensus
AACAAAUCAGCGACAAAUGCAUGGGCGGUGCACAAACUCACCCAUUGCAAUAACAAAUAUUGGU_UGCUGGCACAAUUUCAAUUCUCCCCC_UAUAUUUACACAAAGUCAUUGUCGCCCU
.........(((((((.((((((((.(((......)).).)))).)))).........((((((......)).)))).................................)))))))... (-22.74 = -22.18 +  -0.56)

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 11:23:54 2006