Locus 5504

Sequence ID 2R_DroMel_CAF1
Location 17,655,076 – 17,655,413
Length 337
Max. P 0.991872
window8799 window8800 window8801 window8802 window8803 window8804 window8805 window8806

overview

Window 9

Location 17,655,076 – 17,655,189
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.54
Mean single sequence MFE -28.42
Consensus MFE -26.00
Energy contribution -25.72
Covariance contribution -0.28
Combinations/Pair 1.14
Mean z-score -1.70
Structure conservation index 0.91
SVM decision value 1.93
SVM RNA-class probability 0.983098
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655076 113 - 20766785
CAGGUGGCCGCUUUGGAUUUCUAAUAGUUUCGACUGCCGUAGCGGUGGUUCUCUGUUUGAAAACGGAAGCAAAGCCCAAACAAAAAAUGAAAAUAAACACCAA-------ACUCACAUCC
..((((...(((((.(.((((.(((((....(((..(((...)))..)))..))))).)))).).)))))................((....))...))))..-------.......... ( -28.60)
>DroSec_CAF1 8635 113 - 1
CAGGUGGCCGCUUUGGAUUUCUAAUAGUUUCGACCGCCGUAGCGGUGGUUCUCUGUUCGAAAACGGAAGCAAAGCCCAAACAAAAAAUGAAAAUAAACACCAA-------ACUCACAGCC
..((((...(((((.(.((((.(((((....((((((((...))))))))..))))).)))).).)))))................((....))...))))..-------.......... ( -31.40)
>DroSim_CAF1 14566 113 - 1
CAGGUGGCCGCUUUGGAUUUCUAAUAGUUUCGAACGCCGUAGCGGUGGUUCUCUGUUCGAAAACGGAAGCAAAGCCCAAACAAAAAAUGAAAAUAAACACCAA-------ACUCACAGCC
..((((((((((.(((..(((.((....)).)))..))).)))))).(((.((((((....)))))))))...........................))))..-------.......... ( -26.70)
>DroEre_CAF1 8871 113 - 1
CAGGUGGCUGCUUUUUAUUUCUAAUGGUUUAGACCGCCGUAGCGGUGGUUCCCUGUUUGAAAACGGAAGCAAAGCCCAAACAAGAAAUAAAAAUAAACACCAA-------ACUCACAUCC
..((((..((.(((((((((((...(((((.((((((((...))))))))..(((((....))))).....)))))......)))))))))))))..))))..-------.......... ( -32.30)
>DroYak_CAF1 20305 120 - 1
CAGGUGGCAGCUUUGGAUUUCUAAUGGUUUCGAUCGUCGUAGCGGUGGUUCUCUGUUUGAAAACGGAAGCAAAGCCCAAACAAAAAAUACAAAUAAACACCAAACACAAAACUCACAUCC
..((((...(((((.(.((((.(((((...(.(((((....))))).)....))))).)))).).)))))...(......)................))))................... ( -23.10)
>consensus
CAGGUGGCCGCUUUGGAUUUCUAAUAGUUUCGACCGCCGUAGCGGUGGUUCUCUGUUUGAAAACGGAAGCAAAGCCCAAACAAAAAAUGAAAAUAAACACCAA_______ACUCACAUCC
..((((...(((((.(.((((.(((((....((((((((...))))))))..))))).)))).).)))))................((....))...))))................... (-26.00 = -25.72 +  -0.28)

alignment

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secondary structure

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Window 0

Location 17,655,109 – 17,655,223
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.44
Mean single sequence MFE -35.58
Consensus MFE -29.78
Energy contribution -29.90
Covariance contribution 0.12
Combinations/Pair 1.15
Mean z-score -1.39
Structure conservation index 0.84
SVM decision value 0.32
SVM RNA-class probability 0.686629
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655109 114 - 20766785
UGAUU------GUGCACUUGCCACAGAAAAUCGCCGUCUACAGGUGGCCGCUUUGGAUUUCUAAUAGUUUCGACUGCCGUAGCGGUGGUUCUCUGUUUGAAAACGGAAGCAAAGCCCAAA
...((------(.((..((((..((((.((((((((.((((.((..(.((((((((....)))).))...)).)..)))))))))))))).))))((((....)))).)))).)).))). ( -34.90)
>DroSec_CAF1 8668 114 - 1
UGAUU------GUGCACUUGCCACAGAAAAUCGCCGACUACAGGUGGCCGCUUUGGAUUUCUAAUAGUUUCGACCGCCGUAGCGGUGGUUCUCUGUUCGAAAACGGAAGCAAAGCCCAAA
...((------(.((..((((..((((.((((((((.((((.(((((.((((((((....)))).))...)).))))))))))))))))).))))((((....)))).)))).)).))). ( -39.70)
>DroSim_CAF1 14599 114 - 1
UGAUU------GUGCACUUGCCACAGAAAAUCGCCGACUACAGGUGGCCGCUUUGGAUUUCUAAUAGUUUCGAACGCCGUAGCGGUGGUUCUCUGUUCGAAAACGGAAGCAAAGCCCAAA
...((------(.((..((((..((((.((((((((.((((.((((..((((((((....)))).))...))..)))))))))))))))).))))((((....)))).)))).)).))). ( -37.60)
>DroEre_CAF1 8904 114 - 1
UGAUU------GUGCACUUGCCAUAGAAAAACGCCGACUACAGGUGGCUGCUUUUUAUUUCUAAUGGUUUAGACCGCCGUAGCGGUGGUUCCCUGUUUGAAAACGGAAGCAAAGCCCAAA
...((------(.((..((((....(((...(((((.((((.((((((((((..(((....))).)))..)).)))))))))))))).))).(((((....)))))..)))).)).))). ( -32.70)
>DroYak_CAF1 20345 120 - 1
UGAUUGCAUUUGUGCACUUGCCACAGAAAAACGCCGACUACAGGUGGCAGCUUUGGAUUUCUAAUGGUUUCGAUCGUCGUAGCGGUGGUUCUCUGUUUGAAAACGGAAGCAAAGCCCAAA
...((((.(((((((....).))))))....(((((.((((.(((.(.((((((((....)))).)))).).)))...)))))))))....((((((....)))))).))))........ ( -33.00)
>consensus
UGAUU______GUGCACUUGCCACAGAAAAUCGCCGACUACAGGUGGCCGCUUUGGAUUUCUAAUAGUUUCGACCGCCGUAGCGGUGGUUCUCUGUUUGAAAACGGAAGCAAAGCCCAAA
...........(.((..((((..((((.((((((((.((((.((((((.(((((((....)))).)))...).))))))))))))))))).))))((((....)))).)))).)).)... (-29.78 = -29.90 +   0.12)

alignment

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secondary structure

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Window 1

Location 17,655,189 – 17,655,303
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.59
Mean single sequence MFE -31.44
Consensus MFE -21.36
Energy contribution -22.32
Covariance contribution 0.96
Combinations/Pair 1.04
Mean z-score -1.74
Structure conservation index 0.68
SVM decision value 0.02
SVM RNA-class probability 0.544204
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655189 114 + 20766785
UAGACGGCGAUUUUCUGUGGCAAGUGCAC------AAUCAACUGCAAUUGCAGUGGCAAUAGCAAUAGCAACCGCGUCGUUUCCGCUGCUCUUGGCCAAAAAAGGCAUUCGACAAUUAUU
.((((((((......(((((....(((..------.....(((((....))))).((....))....))).))))).......))))).)))..(((......))).............. ( -28.52)
>DroSec_CAF1 8748 114 + 1
UAGUCGGCGAUUUUCUGUGGCAAGUGCAC------AAUCAACUGCAAUUGCAGUGGCAACAGCAAUAGCAACCGCGUCGUUUCCGCUGCUCUUGGCCAAAAAAGGCAUUCGACAAUUAUU
..(((((...((((...(((((((.(((.------.......(((.(((((..((....))))))).)))...(((.......)))))).))).))))..))))....)))))....... ( -31.40)
>DroSim_CAF1 14679 114 + 1
UAGUCGGCGAUUUUCUGUGGCAAGUGCAC------AAUCAACUGCAAUUGCAGUGGCAACAGCAAUAGCAACCGCGUCGUUUCCGCUGCUCUUGGCCAAAAAAGGCAUUCGACAAUUAUU
..(((((...((((...(((((((.(((.------.......(((.(((((..((....))))))).)))...(((.......)))))).))).))))..))))....)))))....... ( -31.40)
>DroEre_CAF1 8984 96 + 1
UAGUCGGCGUUUUUCUAUGGCAAGUGCAC------AAUCAACUGCAAUUGC------A------------ACCGCAGCAUUUCCGCUGCUUUUGGCCAAAAAAGGCAUUCGACAAUUAUU
..((((((.(((((...((((...((((.------.......))))....(------(------------(..(((((......)))))..)))))))))))).))...))))....... ( -27.90)
>DroYak_CAF1 20425 108 + 1
UAGUCGGCGUUUUUCUGUGGCAAGUGCACAAAUGCAAUCAACUGCAAUUGCAGUGGCA------------AUUGCAGCGUUUCCGCUGCUUUUGGCCAAAAAAGGCAUUCGACAAUUAUU
..(((((.((((((...((((...((((....))))....(((((....)))))..((------------(..((((((....))))))..)))))))..))))))..)))))....... ( -38.00)
>consensus
UAGUCGGCGAUUUUCUGUGGCAAGUGCAC______AAUCAACUGCAAUUGCAGUGGCAA_AGCAAUAGCAACCGCGUCGUUUCCGCUGCUCUUGGCCAAAAAAGGCAUUCGACAAUUAUU
..(((((.............((((.(((............(((((....)))))...................(((.......)))))).))))(((......)))..)))))....... (-21.36 = -22.32 +   0.96)

alignment

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secondary structure

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Window 2

Location 17,655,189 – 17,655,303
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.59
Mean single sequence MFE -32.82
Consensus MFE -23.06
Energy contribution -24.72
Covariance contribution 1.66
Combinations/Pair 1.12
Mean z-score -1.82
Structure conservation index 0.70
SVM decision value 0.23
SVM RNA-class probability 0.644902
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655189 114 - 20766785
AAUAAUUGUCGAAUGCCUUUUUUGGCCAAGAGCAGCGGAAACGACGCGGUUGCUAUUGCUAUUGCCACUGCAAUUGCAGUUGAUU------GUGCACUUGCCACAGAAAAUCGCCGUCUA
..........((..((.((((((((.((((.((((((....)).)((((((((....((....))....))))))))........------.))).)))).).)))))))..))..)).. ( -31.70)
>DroSec_CAF1 8748 114 - 1
AAUAAUUGUCGAAUGCCUUUUUUGGCCAAGAGCAGCGGAAACGACGCGGUUGCUAUUGCUGUUGCCACUGCAAUUGCAGUUGAUU------GUGCACUUGCCACAGAAAAUCGCCGACUA
.......((((...((.((((((((.((((.((((((....)).)((((((((....((....))....))))))))........------.))).)))).).)))))))..)))))).. ( -34.60)
>DroSim_CAF1 14679 114 - 1
AAUAAUUGUCGAAUGCCUUUUUUGGCCAAGAGCAGCGGAAACGACGCGGUUGCUAUUGCUGUUGCCACUGCAAUUGCAGUUGAUU------GUGCACUUGCCACAGAAAAUCGCCGACUA
.......((((...((.((((((((.((((.((((((....)).)((((((((....((....))....))))))))........------.))).)))).).)))))))..)))))).. ( -34.60)
>DroEre_CAF1 8984 96 - 1
AAUAAUUGUCGAAUGCCUUUUUUGGCCAAAAGCAGCGGAAAUGCUGCGGU------------U------GCAAUUGCAGUUGAUU------GUGCACUUGCCAUAGAAAAACGCCGACUA
.......((((...((.((((((((((....((((((....)))))))))------------)------((((.((((.......------.)))).))))....)))))).)))))).. ( -26.60)
>DroYak_CAF1 20425 108 - 1
AAUAAUUGUCGAAUGCCUUUUUUGGCCAAAAGCAGCGGAAACGCUGCAAU------------UGCCACUGCAAUUGCAGUUGAUUGCAUUUGUGCACUUGCCACAGAAAAACGCCGACUA
.......((((...((.(((((((((.....((((((....))))))...------------(((((.(((((((......)))))))..)).)))...))))...))))).)))))).. ( -36.60)
>consensus
AAUAAUUGUCGAAUGCCUUUUUUGGCCAAGAGCAGCGGAAACGACGCGGUUGCUAUUGCU_UUGCCACUGCAAUUGCAGUUGAUU______GUGCACUUGCCACAGAAAAUCGCCGACUA
.......((((...((.((((((((.((((.(((.((....))..((((((((....((....))....))))))))...............))).)))).).)))))))..)))))).. (-23.06 = -24.72 +   1.66)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,655,223 – 17,655,343
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.31
Mean single sequence MFE -34.92
Consensus MFE -21.24
Energy contribution -23.05
Covariance contribution 1.81
Combinations/Pair 1.04
Mean z-score -1.95
Structure conservation index 0.61
SVM decision value 0.18
SVM RNA-class probability 0.622719
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655223 120 + 20766785
ACUGCAAUUGCAGUGGCAAUAGCAAUAGCAACCGCGUCGUUUCCGCUGCUCUUGGCCAAAAAAGGCAUUCGACAAUUAUUGCUAUUGAGUGUGAGUGUUAGAGGAAAGGAAAGGAAAGGC
..(((.(((((.((....)).))))).))).((...((.(((((..(.((((..(((......)))....((((....(..(........)..).)))))))).)..))))).))..)). ( -33.00)
>DroSec_CAF1 8782 119 + 1
ACUGCAAUUGCAGUGGCAACAGCAAUAGCAACCGCGUCGUUUCCGCUGCUCUUGGCCAAAAAAGGCAUUCGACAAUUAUUGCUAUUGAGUGUGAGUGUGAGUGG-GAGGAAAGGAAAGGC
..(((.(((((..((....))))))).))).((...((.(((((.(..(((...(((......)))((((.(((.(((.......))).)))))))..)))..)-..))))).))..)). ( -37.20)
>DroSim_CAF1 14713 120 + 1
ACUGCAAUUGCAGUGGCAACAGCAAUAGCAACCGCGUCGUUUCCGCUGCUCUUGGCCAAAAAAGGCAUUCGACAAUUAUUGCUAUUGAGUGUGAGUGUGAGUGGAGAGGAAAGGAAAGGC
..(((.(((((..((....))))))).))).((...((.(((((.(..(((...(((......)))((((.(((.(((.......))).)))))))..)))..)...))))).))..)). ( -37.50)
>DroYak_CAF1 20465 90 + 1
ACUGCAAUUGCAGUGGCA------------AUUGCAGCGUUUCCGCUGCUUUUGGCCAAAAAAGGCAUUCGACAAUUAUUGUUAUUGAAUGUGA------------------GGAAAGGC
..(((((((((....)))------------))))))((.(((((....(((((......)))))((((((((.(((....))).))))))))..------------------))))).)) ( -32.00)
>consensus
ACUGCAAUUGCAGUGGCAACAGCAAUAGCAACCGCGUCGUUUCCGCUGCUCUUGGCCAAAAAAGGCAUUCGACAAUUAUUGCUAUUGAGUGUGAGUGUGAGUGG_GAGGAAAGGAAAGGC
(((((....))))).(((....(((((((((..(((.((....)).))).....(((......)))............)))))))))..)))............................ (-21.24 = -23.05 +   1.81)

alignment

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secondary structure

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Window 4

Location 17,655,223 – 17,655,343
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.31
Mean single sequence MFE -30.62
Consensus MFE -23.23
Energy contribution -25.35
Covariance contribution 2.12
Combinations/Pair 1.04
Mean z-score -2.50
Structure conservation index 0.76
SVM decision value 1.79
SVM RNA-class probability 0.977338
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655223 120 - 20766785
GCCUUUCCUUUCCUUUCCUCUAACACUCACACUCAAUAGCAAUAAUUGUCGAAUGCCUUUUUUGGCCAAGAGCAGCGGAAACGACGCGGUUGCUAUUGCUAUUGCCACUGCAAUUGCAGU
.................................(((((((((((..........(((......)))(((..((..((....))..))..))).)))))))))))..(((((....))))) ( -31.00)
>DroSec_CAF1 8782 119 - 1
GCCUUUCCUUUCCUC-CCACUCACACUCACACUCAAUAGCAAUAAUUGUCGAAUGCCUUUUUUGGCCAAGAGCAGCGGAAACGACGCGGUUGCUAUUGCUGUUGCCACUGCAAUUGCAGU
...............-.................(((((((((((..........(((......)))(((..((..((....))..))..))).)))))))))))..(((((....))))) ( -31.00)
>DroSim_CAF1 14713 120 - 1
GCCUUUCCUUUCCUCUCCACUCACACUCACACUCAAUAGCAAUAAUUGUCGAAUGCCUUUUUUGGCCAAGAGCAGCGGAAACGACGCGGUUGCUAUUGCUGUUGCCACUGCAAUUGCAGU
.................................(((((((((((..........(((......)))(((..((..((....))..))..))).)))))))))))..(((((....))))) ( -31.00)
>DroYak_CAF1 20465 90 - 1
GCCUUUCC------------------UCACAUUCAAUAACAAUAAUUGUCGAAUGCCUUUUUUGGCCAAAAGCAGCGGAAACGCUGCAAU------------UGCCACUGCAAUUGCAGU
(((.....------------------...(((((.((((......)))).)))))........))).....((((((....))))))...------------....(((((....))))) ( -29.49)
>consensus
GCCUUUCCUUUCCUC_CCACUCACACUCACACUCAAUAGCAAUAAUUGUCGAAUGCCUUUUUUGGCCAAGAGCAGCGGAAACGACGCGGUUGCUAUUGCUGUUGCCACUGCAAUUGCAGU
.................................(((((((((((..........(((......))).....((..((....))..))......)))))))))))..(((((....))))) (-23.23 = -25.35 +   2.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,655,303 – 17,655,413
Length 110
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 87.10
Mean single sequence MFE -27.32
Consensus MFE -21.23
Energy contribution -21.60
Covariance contribution 0.37
Combinations/Pair 1.08
Mean z-score -1.44
Structure conservation index 0.78
SVM decision value 0.05
SVM RNA-class probability 0.557996
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655303 110 + 20766785
GCUAUUGAGUGUGAGUGUUAGAGGAAAGGAAAGGAAAGGCAACAAAUGCAAUACACUGCACUUAAAUUGCGCCCACUAAUAACCCAGUCGAUGGGUAAAAGGGACAGCGG
....((((((((.(((((....................(((.....)))...)))))))))))))..(((.(((.......(((((.....)))))....)))...))). ( -26.40)
>DroSec_CAF1 8862 109 + 1
GCUAUUGAGUGUGAGUGUGAGUGG-GAGGAAAGGAAAGGCAACAAGUGCAAUACACUGCACUUAAAUUGCGCCCACUAAUAACCCAGUCGAUGGGUAAAAGGGACAGCGG
.(((((((.((.(..(((.(((((-(.(.((......(....)(((((((......)))))))...)).).)))))).)))..))).)))))))................ ( -33.50)
>DroSim_CAF1 14793 110 + 1
GCUAUUGAGUGUGAGUGUGAGUGGAGAGGAAAGGAAAGGCAACAAGUGCAAUACACUGCACUUAAAUUGCGCCCACUAAUAACCCAGUCGAUGGGUAAAAGGGACAGCGG
.(((((((.((.(..(((.(((((.(.(.((......(....)(((((((......)))))))...)).).)))))).)))..))).)))))))................ ( -29.70)
>DroYak_CAF1 20533 92 + 1
GUUAUUGAAUGUGA------------------GGAAAGGCAACAAGUGCAAUGCACUGCACUUAAAUUGCGCCCACUUAUAAUCCAGUCGAUGAGUAAAAGGGACAGCAG
..............------------------.....(....)(((((((......)))))))....(((.(((..((((.(((.....)))..))))..)))...))). ( -19.70)
>consensus
GCUAUUGAGUGUGAGUGUGAGUGG_GAGGAAAGGAAAGGCAACAAGUGCAAUACACUGCACUUAAAUUGCGCCCACUAAUAACCCAGUCGAUGGGUAAAAGGGACAGCGG
....((((((((.........................(....).((((.....))))))))))))..(((.(((.......(((((.....)))))....)))...))). (-21.23 = -21.60 +   0.37)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,655,303 – 17,655,413
Length 110
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 87.10
Mean single sequence MFE -25.90
Consensus MFE -24.25
Energy contribution -24.12
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -2.42
Structure conservation index 0.94
SVM decision value 2.29
SVM RNA-class probability 0.991872
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17655303 110 - 20766785
CCGCUGUCCCUUUUACCCAUCGACUGGGUUAUUAGUGGGCGCAAUUUAAGUGCAGUGUAUUGCAUUUGUUGCCUUUCCUUUCCUUUCCUCUAACACUCACACUCAAUAGC
..(((((((((...(((((.....)))))....)).))))(((((..((((((((....)))))))))))))...................................))) ( -26.00)
>DroSec_CAF1 8862 109 - 1
CCGCUGUCCCUUUUACCCAUCGACUGGGUUAUUAGUGGGCGCAAUUUAAGUGCAGUGUAUUGCACUUGUUGCCUUUCCUUUCCUC-CCACUCACACUCACACUCAAUAGC
..(((((((((...(((((.....)))))....)).))))(((((..((((((((....))))))))))))).............-.....................))) ( -28.30)
>DroSim_CAF1 14793 110 - 1
CCGCUGUCCCUUUUACCCAUCGACUGGGUUAUUAGUGGGCGCAAUUUAAGUGCAGUGUAUUGCACUUGUUGCCUUUCCUUUCCUCUCCACUCACACUCACACUCAAUAGC
..(((((((((...(((((.....)))))....)).))))(((((..((((((((....)))))))))))))...................................))) ( -28.30)
>DroYak_CAF1 20533 92 - 1
CUGCUGUCCCUUUUACUCAUCGACUGGAUUAUAAGUGGGCGCAAUUUAAGUGCAGUGCAUUGCACUUGUUGCCUUUCC------------------UCACAUUCAAUAAC
.....(((((((.((.((........)).)).))).))))(((((..((((((((....)))))))))))))......------------------.............. ( -21.00)
>consensus
CCGCUGUCCCUUUUACCCAUCGACUGGGUUAUUAGUGGGCGCAAUUUAAGUGCAGUGUAUUGCACUUGUUGCCUUUCCUUUCCUC_CCACUCACACUCACACUCAAUAGC
.....((((((...(((((.....)))))....)).))))(((((..((((((((....)))))))))))))...................................... (-24.25 = -24.12 +  -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 11:46:56 2006