Locus 5983

Sequence ID X_DroMel_CAF1
Location 15,383,901 – 15,384,155
Length 254
Max. P 0.937061
window9722 window9723 window9724 window9725 window9726

overview

Window 2

Location 15,383,901 – 15,384,005
Length 104
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 88.38
Mean single sequence MFE -28.40
Consensus MFE -18.93
Energy contribution -19.26
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.42
Structure conservation index 0.67
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15383901 104 - 22224390
CACUUUAUUACCGCAGGACAUUUGCUG------CUGCUCGUGCGUUGAGGUCCUUGCAGCAAACAAAAACAACAACUGGCAAGGAAAAACGCAAAAGGCCACAAACAACA
............((((........)))------).(((..((((((....(((((((((................)).)))))))..))))))...)))........... ( -26.09)
>DroSec_CAF1 25866 110 - 1
CACUUUAUUACCGCAGGACAUUUGCUGCUGCUGCUGCUCGUGCGUUGAGGUCCUUGCCGCAAACAAAAACAACAACUGGCAAGGAAAAACGCAAAAGGCCGCAAACAACA
............((((........))))(((.(((.....((((((....(((((((((.................)))))))))..))))))...))).)))....... ( -34.23)
>DroEre_CAF1 23419 104 - 1
CACUUUAUUACCGCAGGACAUUUGGUGC---UGCUGCUCGUGCGUUAAGGUCCUUGCCACAAACAAAAAC---AACAAGCAAGGAAAAAGGCAAAAUGCCACCAACAACA
............((((.((.....)).)---))).((....))(((..(((((((((.............---.....)))))))....(((.....))).))...))). ( -24.87)
>consensus
CACUUUAUUACCGCAGGACAUUUGCUGC___UGCUGCUCGUGCGUUGAGGUCCUUGCCGCAAACAAAAACAACAACUGGCAAGGAAAAACGCAAAAGGCCACAAACAACA
............((((.................))))...((((((....(((((((.....................)))))))..))))))................. (-18.93 = -19.26 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,384,005 – 15,384,115
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.14
Mean single sequence MFE -32.55
Consensus MFE -22.66
Energy contribution -22.85
Covariance contribution 0.19
Combinations/Pair 1.12
Mean z-score -2.44
Structure conservation index 0.70
SVM decision value 0.91
SVM RNA-class probability 0.879763
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15384005 110 + 22224390
AAAAACGAAACUCGAGGCAAGAUGGAAGCCAAAGGG------GGAACACC----CUGUUCGGCGAGCAUAAGCAGCUGAAUCUGGGGAAAAGCUGCUGCAGGAAAAUGCAUUUGAAUGGA
...........((((((((........(((.((.((------((....))----)).)).)))..(((...((((((...((....))..))))))))).......))).)))))..... ( -31.70)
>DroSec_CAF1 25976 116 + 1
AAAAACGAAACUCGAGGCAAGAUGAAAGCCAAAGGAGGAGGAGGAAUACC----CCGUUCGGCGAGCAUAAGCAGCUGAAUCUGGGGAAAAGCUGCUGCAGGAAAAUGCAUUUGAAUGGA
.....((((.(((..(((.........)))....))).((.((.....((----(((((((((..((....)).)))))))..)))).....)).))(((......))).))))...... ( -28.60)
>DroEre_CAF1 23523 109 + 1
AAAAACGAAACUCGAGGCAAGAUGAAAGCCAGGGG-------GGAACCCC----UUUUUCGGGGAGCGUAAGCAGCGGAAUCUGGGGAAAAGCUGCUGCAGGAAAAUGCAUUUGAAUGGA
....(((...((((((((.........)))(((((-------....))))----)...)))))...))).((((((....((....))...))))))(((......)))........... ( -36.30)
>DroYak_CAF1 15460 115 + 1
AGGAACGAAACUCGAGGCAAGAUGAAAGCCAAGGGCG-----GAAACCCCCUCCCUGUUCGACGAGCAUAAGCAGCAGAAUCAGGGGAAAAGCUGCUGCAGGAAAAUGCAUUUGAAUGGA
.(((.((.....)).(((.........)))..(((.(-----....).))))))((((((((...((((..(((((((..((....))....)))))))......))))..)))))))). ( -33.60)
>consensus
AAAAACGAAACUCGAGGCAAGAUGAAAGCCAAAGG_______GGAACACC____CUGUUCGGCGAGCAUAAGCAGCUGAAUCUGGGGAAAAGCUGCUGCAGGAAAAUGCAUUUGAAUGGA
.....((.....)).(((.........)))........................((((((((........(((((((...((....))..)))))))(((......)))..)))))))). (-22.66 = -22.85 +   0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,384,005 – 15,384,115
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.14
Mean single sequence MFE -27.30
Consensus MFE -18.44
Energy contribution -18.25
Covariance contribution -0.19
Combinations/Pair 1.10
Mean z-score -2.13
Structure conservation index 0.68
SVM decision value 0.50
SVM RNA-class probability 0.759066
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15384005 110 - 22224390
UCCAUUCAAAUGCAUUUUCCUGCAGCAGCUUUUCCCCAGAUUCAGCUGCUUAUGCUCGCCGAACAG----GGUGUUCC------CCCUUUGGCUUCCAUCUUGCCUCGAGUUUCGUUUUU
.......(((((.(..(((..(((((((((..((....))...))))))........((((((..(----((....))------)..))))))........)))...)))..)))))).. ( -26.60)
>DroSec_CAF1 25976 116 - 1
UCCAUUCAAAUGCAUUUUCCUGCAGCAGCUUUUCCCCAGAUUCAGCUGCUUAUGCUCGCCGAACGG----GGUAUUCCUCCUCCUCCUUUGGCUUUCAUCUUGCCUCGAGUUUCGUUUUU
.......(((((.(..(((..(((((((((..((....))...))))))........((((((.((----((..........)))).))))))........)))...)))..)))))).. ( -26.50)
>DroEre_CAF1 23523 109 - 1
UCCAUUCAAAUGCAUUUUCCUGCAGCAGCUUUUCCCCAGAUUCCGCUGCUUACGCUCCCCGAAAAA----GGGGUUCC-------CCCCUGGCUUUCAUCUUGCCUCGAGUUUCGUUUUU
..........((((......))))(((((...((....))....)))))....((((........(----((((....-------)))))(((.........)))..))))......... ( -25.40)
>DroYak_CAF1 15460 115 - 1
UCCAUUCAAAUGCAUUUUCCUGCAGCAGCUUUUCCCCUGAUUCUGCUGCUUAUGCUCGUCGAACAGGGAGGGGGUUUC-----CGCCCUUGGCUUUCAUCUUGCCUCGAGUUUCGUUCCU
...........((((......(((((((..((......))..)))))))..)))).....((((((((.(((....))-----).)))).(((.........))).........)))).. ( -30.70)
>consensus
UCCAUUCAAAUGCAUUUUCCUGCAGCAGCUUUUCCCCAGAUUCAGCUGCUUAUGCUCGCCGAACAG____GGGGUUCC_______CCCUUGGCUUUCAUCUUGCCUCGAGUUUCGUUUUU
..........((((......))))(((((...((....))....)))))....(((((((..........))).................(((.........)))..))))......... (-18.44 = -18.25 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,384,041 – 15,384,155
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.94
Mean single sequence MFE -40.53
Consensus MFE -24.13
Energy contribution -23.47
Covariance contribution -0.66
Combinations/Pair 1.16
Mean z-score -2.64
Structure conservation index 0.60
SVM decision value 1.26
SVM RNA-class probability 0.937061
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15384041 114 + 22224390
--GGAACACC----CUGUUCGGCGAGCAUAAGCAGCUGAAUCUGGGGAAAAGCUGCUGCAGGAAAAUGCAUUUGAAUGGACUACAACUCAGCCGAGGGGGUGAGGGGGCAGUCGGGGGAA
--......((----((((((((........(((((((...((....))..)))))))(((......)))..)))))).((((.(..((((.((....)).))))..)..))))))))... ( -39.10)
>DroSec_CAF1 26016 104 + 1
GAGGAAUACC----CCGUUCGGCGAGCAUAAGCAGCUGAAUCUGGGGAAAAGCUGCUGCAGGAAAAUGCAUUUGAAUGGACUGCAACGCAGCCGCGGGCGG------------GGGGGAA
........((----(((((((.((.((...(((((((...((....))..)))))))((((....((........))...))))......)))))))))))------------))..... ( -39.90)
>DroYak_CAF1 15497 109 + 1
--GAAACCCCCUCCCUGUUCGACGAGCAUAAGCAGCAGAAUCAGGGGAAAAGCUGCUGCAGGAAAAUGCAUUUGAAUGGACUGCAACUCAGCUGGGG---------GGCAGCCGGGGGAA
--....((((((((.(((((...)))))...(((((((..((....))....))))))).)))..............((.((((..(((....))).---------.))))))))))).. ( -42.60)
>consensus
__GGAACACC____CUGUUCGGCGAGCAUAAGCAGCUGAAUCUGGGGAAAAGCUGCUGCAGGAAAAUGCAUUUGAAUGGACUGCAACUCAGCCGAGGG_G______GGCAG_CGGGGGAA
........((....((((((((........(((((((...((....))..)))))))(((......)))..)))))))).......(((....))).................))..... (-24.13 = -23.47 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,384,041 – 15,384,155
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.94
Mean single sequence MFE -35.47
Consensus MFE -18.75
Energy contribution -19.31
Covariance contribution 0.56
Combinations/Pair 1.10
Mean z-score -2.89
Structure conservation index 0.53
SVM decision value 0.57
SVM RNA-class probability 0.784935
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15384041 114 - 22224390
UUCCCCCGACUGCCCCCUCACCCCCUCGGCUGAGUUGUAGUCCAUUCAAAUGCAUUUUCCUGCAGCAGCUUUUCCCCAGAUUCAGCUGCUUAUGCUCGCCGAACAG----GGUGUUCC--
..................(((((..(((((.((((...............((((......))))((((((..((....))...))))))....)))))))))...)----))))....-- ( -33.30)
>DroSec_CAF1 26016 104 - 1
UUCCCCC------------CCGCCCGCGGCUGCGUUGCAGUCCAUUCAAAUGCAUUUUCCUGCAGCAGCUUUUCCCCAGAUUCAGCUGCUUAUGCUCGCCGAACGG----GGUAUUCCUC
.....((------------(((....((((.(((((((((...................)))))((((((..((....))...))))))..))))..))))..)))----))........ ( -33.41)
>DroYak_CAF1 15497 109 - 1
UUCCCCCGGCUGCC---------CCCCAGCUGAGUUGCAGUCCAUUCAAAUGCAUUUUCCUGCAGCAGCUUUUCCCCUGAUUCUGCUGCUUAUGCUCGUCGAACAGGGAGGGGGUUUC--
..((((((((((..---------...)))))(((((((.(......)...((((......)))))))))))...(((((.(((.((.((....))..)).)))))))).)))))....-- ( -39.70)
>consensus
UUCCCCCG_CUGCC______C_CCCCCGGCUGAGUUGCAGUCCAUUCAAAUGCAUUUUCCUGCAGCAGCUUUUCCCCAGAUUCAGCUGCUUAUGCUCGCCGAACAG____GGUGUUCC__
..........................((((.(((((((((...................)))))((((((..((....))...))))))....))))))))................... (-18.75 = -19.31 +   0.56)

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 12:01:20 2006