Locus 2944

Sequence ID 2R_DroMel_CAF1
Location 10,169,891 – 10,170,166
Length 275
Max. P 0.938609
window4859 window4860 window4861 window4862 window4863 window4864

overview

Window 9

Location 10,169,891 – 10,170,006
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.38
Mean single sequence MFE -24.19
Consensus MFE -19.37
Energy contribution -20.09
Covariance contribution 0.72
Combinations/Pair 1.09
Mean z-score -1.48
Structure conservation index 0.80
SVM decision value 0.23
SVM RNA-class probability 0.642408
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10169891 115 + 20766785
---CCACAUCCAGUGCAACAUAUUGACCAGCACUUGUUUGCUUUU--UUUUUUAUUAUUGCUGUGGACCAACCCUUCGUGCCAUCUAUACGUCCAAUCUUUGGCUGGUGGUCCACCCAUC
---...((..((((((.............)))).))..)).....--...............((((((((.((......((((.................)))).))))))))))..... ( -24.95)
>DroSec_CAF1 9680 117 + 1
---CCACAUCCAGUGCAACAUAUUGACCAGCACUUGUUUGCUUUUCUUUUUUUAUUAUUGCUGUGGACCAACCCUUCGUGCCAUCUAUACGUCCAAUCUUUGGCUGGUGGUCCACCCAUC
---...((..((((((.............)))).))..))......................((((((((.((......((((.................)))).))))))))))..... ( -24.95)
>DroSim_CAF1 9499 117 + 1
---CCACAUCCAGUGCAACAUAUUGACCAGCACUUGUUUGCUUUUCUUUUUUUAUUAUUGCUGUGGACCAACCCUUCGUGCCAUCUAUACGUCCAAUCUUUGGCUGGUGGUCCACCCAUC
---...((..((((((.............)))).))..))......................((((((((.((......((((.................)))).))))))))))..... ( -24.95)
>DroEre_CAF1 9669 111 + 1
---CCACAUCCAGUGCAACAUAUUGACCAGCACUUGUUUGCUU------UUUUAUUAUUGCUGUGGAGCAACCCUCCUUGCUAUCUAUACGUCCAAACUUUGGCUGGUGGUCCGCCCAUC
---((.....(((((.....)))))((((((....(((((...------..........((...((((.....))))..))............)))))....)))))))).......... ( -23.41)
>DroYak_CAF1 10130 111 + 1
UUGCCACAUCCAGUGCAACAUAUUGGCCAGCACUUGUUUGCUU------UUUUAUUAUUGCUGUGGACCAACACUCCGUGCAAUCUAUAUGUCCAAUCUUUGGCUG---GUCCACCCAUC
((((.((.....)))))).....((((((((....(.(((..(------...(((.(((((.(((......))).....)))))..))).)..))).)....))))---).)))...... ( -22.70)
>consensus
___CCACAUCCAGUGCAACAUAUUGACCAGCACUUGUUUGCUUUU__UUUUUUAUUAUUGCUGUGGACCAACCCUUCGUGCCAUCUAUACGUCCAAUCUUUGGCUGGUGGUCCACCCAUC
......((..((((((.............)))).))..))......................((((((((..((.....((((.................)))).))))))))))..... (-19.37 = -20.09 +   0.72)

alignment

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secondary structure

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Window 0

Location 10,169,928 – 10,170,046
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.15
Mean single sequence MFE -27.02
Consensus MFE -19.43
Energy contribution -21.75
Covariance contribution 2.32
Combinations/Pair 1.07
Mean z-score -2.00
Structure conservation index 0.72
SVM decision value 0.42
SVM RNA-class probability 0.730086
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10169928 118 + 20766785
CUUUU--UUUUUUAUUAUUGCUGUGGACCAACCCUUCGUGCCAUCUAUACGUCCAAUCUUUGGCUGGUGGUCCACCCAUCUGGGGAUAAAUUUAUGCACAUUAUUUGUCCUGUUUGGCAU
.....--...........((((((((((((.((......((((.................)))).)))))))))).......(((((((((...........)))))))))....)))). ( -30.53)
>DroSec_CAF1 9717 120 + 1
CUUUUCUUUUUUUAUUAUUGCUGUGGACCAACCCUUCGUGCCAUCUAUACGUCCAAUCUUUGGCUGGUGGUCCACCCAUCUGGGGAUAAAUUUAUGCACAUUAUUUGUCCUGUUUGGCAU
..................((((((((((((.((......((((.................)))).)))))))))).......(((((((((...........)))))))))....)))). ( -30.53)
>DroSim_CAF1 9536 120 + 1
CUUUUCUUUUUUUAUUAUUGCUGUGGACCAACCCUUCGUGCCAUCUAUACGUCCAAUCUUUGGCUGGUGGUCCACCCAUCUGGGGAUAAAUUUAUGCACAUUAUUUGUCCUGUUUGGCAU
..................((((((((((((.((......((((.................)))).)))))))))).......(((((((((...........)))))))))....)))). ( -30.53)
>DroEre_CAF1 9706 101 + 1
CUU------UUUUAUUAUUGCUGUGGAGCAACCCUCCUUGCUAUCUAUACGUCCAAACUUUGGCUGGUGGUCCGCCCAUCUGGGUAUAAAUUUAUGCACAUUAUUUG-------------
...------.........(((...(((((((......))))...((((.((.(((.....))).)))))))))((((....))))..........))).........------------- ( -17.30)
>DroYak_CAF1 10170 111 + 1
CUU------UUUUAUUAUUGCUGUGGACCAACACUCCGUGCAAUCUAUAUGUCCAAUCUUUGGCUG---GUCCACCCAUCUGGGGAUAAAUUUAUGCACAUUAUUUGUCCUGUUUGGCAU
...------.........((((((((((((.(((...)))..........(.(((.....))))))---)))))).......(((((((((...........)))))))))....)))). ( -26.20)
>consensus
CUUUU__UUUUUUAUUAUUGCUGUGGACCAACCCUUCGUGCCAUCUAUACGUCCAAUCUUUGGCUGGUGGUCCACCCAUCUGGGGAUAAAUUUAUGCACAUUAUUUGUCCUGUUUGGCAU
..................((((((((((((..((.....((((.................)))).)))))))))).......(((((((((...........)))))))))....)))). (-19.43 = -21.75 +   2.32)

alignment

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secondary structure

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Window 1

Location 10,169,928 – 10,170,046
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.15
Mean single sequence MFE -25.72
Consensus MFE -18.62
Energy contribution -20.02
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -1.65
Structure conservation index 0.72
SVM decision value 0.03
SVM RNA-class probability 0.547982
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10169928 118 - 20766785
AUGCCAAACAGGACAAAUAAUGUGCAUAAAUUUAUCCCCAGAUGGGUGGACCACCAGCCAAAGAUUGGACGUAUAGAUGGCACGAAGGGUUGGUCCACAGCAAUAAUAAAAAA--AAAAG
.((((.....)).)).......(((............((....))((((((((.(.((((...((.......))...)))).(....)).)))))))).)))...........--..... ( -25.90)
>DroSec_CAF1 9717 120 - 1
AUGCCAAACAGGACAAAUAAUGUGCAUAAAUUUAUCCCCAGAUGGGUGGACCACCAGCCAAAGAUUGGACGUAUAGAUGGCACGAAGGGUUGGUCCACAGCAAUAAUAAAAAAAGAAAAG
.((((.....)).)).......(((............((....))((((((((.(.((((...((.......))...)))).(....)).)))))))).))).................. ( -25.90)
>DroSim_CAF1 9536 120 - 1
AUGCCAAACAGGACAAAUAAUGUGCAUAAAUUUAUCCCCAGAUGGGUGGACCACCAGCCAAAGAUUGGACGUAUAGAUGGCACGAAGGGUUGGUCCACAGCAAUAAUAAAAAAAGAAAAG
.((((.....)).)).......(((............((....))((((((((.(.((((...((.......))...)))).(....)).)))))))).))).................. ( -25.90)
>DroEre_CAF1 9706 101 - 1
-------------CAAAUAAUGUGCAUAAAUUUAUACCCAGAUGGGCGGACCACCAGCCAAAGUUUGGACGUAUAGAUAGCAAGGAGGGUUGCUCCACAGCAAUAAUAAAA------AAG
-------------.........(((....((((((((((((((.(((((....)).)))...))))))..)))))))).....((((.....))))...))).........------... ( -27.00)
>DroYak_CAF1 10170 111 - 1
AUGCCAAACAGGACAAAUAAUGUGCAUAAAUUUAUCCCCAGAUGGGUGGAC---CAGCCAAAGAUUGGACAUAUAGAUUGCACGGAGUGUUGGUCCACAGCAAUAAUAAAA------AAG
.(((......((((.((((.((((((...((((((((((.....)).)))(---(((.......)))).....)))))))))))...)))).))))...))).........------... ( -23.90)
>consensus
AUGCCAAACAGGACAAAUAAUGUGCAUAAAUUUAUCCCCAGAUGGGUGGACCACCAGCCAAAGAUUGGACGUAUAGAUGGCACGAAGGGUUGGUCCACAGCAAUAAUAAAAAA__AAAAG
..........((((.(((..(((((....((((((..((((.(((.(((....))).)))....))))....)))))).)))))....))).))))........................ (-18.62 = -20.02 +   1.40)

alignment

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secondary structure

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Window 2

Location 10,170,006 – 10,170,126
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 99.58
Mean single sequence MFE -31.60
Consensus MFE -31.60
Energy contribution -31.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.68
Structure conservation index 1.00
SVM decision value 1.12
SVM RNA-class probability 0.918515
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10170006 120 + 20766785
UGGGGAUAAAUUUAUGCACAUUAUUUGUCCUGUUUGGCAUGUCGCGUUGAUUUUUGCGCAAUCCUCUUGCACAUUUCCAAAUGCCAUUUGUAUGCAAACUAACUGCGCUUUAUGCCUCCA
.((((((((((...........)))))))).....((((((..((((.....(((((((((.....))))..........((((.....)))))))))......))))..)))))).)). ( -31.60)
>DroSec_CAF1 9797 120 + 1
UGGGGAUAAAUUUAUGCACAUUAUUUGUCCUGUUUGGCAUGUCGCGUUGAUUUUUGCGCAAUCCUCUUGCACAUUUUCAAAUGCCAUUUGUAUGCAAACUAACUGCGCUUUAUGCCUCCA
.((((((((((...........)))))))).....((((((..((((.....(((((((((.....))))..........((((.....)))))))))......))))..)))))).)). ( -31.60)
>DroSim_CAF1 9616 120 + 1
UGGGGAUAAAUUUAUGCACAUUAUUUGUCCUGUUUGGCAUGUCGCGUUGAUUUUUGCGCAAUCCUCUUGCACAUUUCCAAAUGCCAUUUGUAUGCAAACUAACUGCGCUUUAUGCCUCCA
.((((((((((...........)))))))).....((((((..((((.....(((((((((.....))))..........((((.....)))))))))......))))..)))))).)). ( -31.60)
>DroYak_CAF1 10241 120 + 1
UGGGGAUAAAUUUAUGCACAUUAUUUGUCCUGUUUGGCAUGUCGCGUUGAUUUUUGCGCAAUCCUCUUGCACAUUUCCAAAUGCCAUUUGUAUGCAAACUAACUGCGCUUUAUGCCUCCA
.((((((((((...........)))))))).....((((((..((((.....(((((((((.....))))..........((((.....)))))))))......))))..)))))).)). ( -31.60)
>consensus
UGGGGAUAAAUUUAUGCACAUUAUUUGUCCUGUUUGGCAUGUCGCGUUGAUUUUUGCGCAAUCCUCUUGCACAUUUCCAAAUGCCAUUUGUAUGCAAACUAACUGCGCUUUAUGCCUCCA
.((((((((((...........)))))))).....((((((..((((.....(((((((((.....))))..........((((.....)))))))))......))))..)))))).)). (-31.60 = -31.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,170,006 – 10,170,126
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 99.58
Mean single sequence MFE -33.30
Consensus MFE -33.30
Energy contribution -33.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.07
Structure conservation index 1.00
SVM decision value 1.27
SVM RNA-class probability 0.938609
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10170006 120 - 20766785
UGGAGGCAUAAAGCGCAGUUAGUUUGCAUACAAAUGGCAUUUGGAAAUGUGCAAGAGGAUUGCGCAAAAAUCAACGCGACAUGCCAAACAGGACAAAUAAUGUGCAUAAAUUUAUCCCCA
.((.((.(((((((((((((..(((((((((((((...)))))....))))))))..))))))))..........((.((((.((.....)).......)))))).....))))))))). ( -33.30)
>DroSec_CAF1 9797 120 - 1
UGGAGGCAUAAAGCGCAGUUAGUUUGCAUACAAAUGGCAUUUGAAAAUGUGCAAGAGGAUUGCGCAAAAAUCAACGCGACAUGCCAAACAGGACAAAUAAUGUGCAUAAAUUUAUCCCCA
.((.((.(((((((((((((..(((((((((((((...)))))....))))))))..))))))))..........((.((((.((.....)).......)))))).....))))))))). ( -33.30)
>DroSim_CAF1 9616 120 - 1
UGGAGGCAUAAAGCGCAGUUAGUUUGCAUACAAAUGGCAUUUGGAAAUGUGCAAGAGGAUUGCGCAAAAAUCAACGCGACAUGCCAAACAGGACAAAUAAUGUGCAUAAAUUUAUCCCCA
.((.((.(((((((((((((..(((((((((((((...)))))....))))))))..))))))))..........((.((((.((.....)).......)))))).....))))))))). ( -33.30)
>DroYak_CAF1 10241 120 - 1
UGGAGGCAUAAAGCGCAGUUAGUUUGCAUACAAAUGGCAUUUGGAAAUGUGCAAGAGGAUUGCGCAAAAAUCAACGCGACAUGCCAAACAGGACAAAUAAUGUGCAUAAAUUUAUCCCCA
.((.((.(((((((((((((..(((((((((((((...)))))....))))))))..))))))))..........((.((((.((.....)).......)))))).....))))))))). ( -33.30)
>consensus
UGGAGGCAUAAAGCGCAGUUAGUUUGCAUACAAAUGGCAUUUGGAAAUGUGCAAGAGGAUUGCGCAAAAAUCAACGCGACAUGCCAAACAGGACAAAUAAUGUGCAUAAAUUUAUCCCCA
.((.((.(((((((((((((..(((((((((((((...)))))....))))))))..))))))))..........((.((((.((.....)).......)))))).....))))))))). (-33.30 = -33.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,170,046 – 10,170,166
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.75
Mean single sequence MFE -31.17
Consensus MFE -30.60
Energy contribution -30.85
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.98
SVM decision value 0.23
SVM RNA-class probability 0.644484
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10170046 120 - 20766785
GAUUGGCAUGAGGAUUGAAUUGAGAAUGGCAUGAUGACCAUGGAGGCAUAAAGCGCAGUUAGUUUGCAUACAAAUGGCAUUUGGAAAUGUGCAAGAGGAUUGCGCAAAAAUCAACGCGAC
..............(((..((((..(((((.....).))))...........((((((((..(((((((((((((...)))))....))))))))..)))))))).....))))..))). ( -28.90)
>DroSec_CAF1 9837 120 - 1
GAUUGGCAUGAGGAUUGAGUUGAGAAUGGCAUGAUGACCAUGGAGGCAUAAAGCGCAGUUAGUUUGCAUACAAAUGGCAUUUGAAAAUGUGCAAGAGGAUUGCGCAAAAAUCAACGCGAC
..............(((.(((((..(((((.....).))))...........((((((((..(((((((((((((...)))))....))))))))..)))))))).....))))).))). ( -31.70)
>DroSim_CAF1 9656 120 - 1
GAUUGGCAUGAGGAUUGAGUUGAGAAUGGCAUGAUGACCAUGGAGGCAUAAAGCGCAGUUAGUUUGCAUACAAAUGGCAUUUGGAAAUGUGCAAGAGGAUUGCGCAAAAAUCAACGCGAC
..............(((.(((((..(((((.....).))))...........((((((((..(((((((((((((...)))))....))))))))..)))))))).....))))).))). ( -31.70)
>DroYak_CAF1 10281 120 - 1
GAUUGGCAUCAGGAUUGAGUUGAGAAUGGCAUGAUGACCAUGGAGGCAUAAAGCGCAGUUAGUUUGCAUACAAAUGGCAUUUGGAAAUGUGCAAGAGGAUUGCGCAAAAAUCAACGCGAC
.....((.((......))(((((..(((((.....).))))...........((((((((..(((((((((((((...)))))....))))))))..)))))))).....)))))))... ( -32.40)
>consensus
GAUUGGCAUGAGGAUUGAGUUGAGAAUGGCAUGAUGACCAUGGAGGCAUAAAGCGCAGUUAGUUUGCAUACAAAUGGCAUUUGGAAAUGUGCAAGAGGAUUGCGCAAAAAUCAACGCGAC
..............(((.(((((..(((((.....).))))...........((((((((..(((((((((((((...)))))....))))))))..)))))))).....))))).))). (-30.60 = -30.85 +   0.25)

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 10:43:33 2006