Locus 595

Sequence ID X_DroMel_CAF1
Location 1,665,786 – 1,666,018
Length 232
Max. P 0.708871
window955 window956 window957 window958

overview

Window 5

Location 1,665,786 – 1,665,905
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.23
Mean single sequence MFE -40.35
Consensus MFE -38.47
Energy contribution -38.72
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.95
SVM decision value 0.37
SVM RNA-class probability 0.708871
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1665786 119 - 22224390
ACUGCCGCGUCCCAAGGCAGUUUAGUGUGCUUCCACGGAAUCGGGCACACAUCUCAUGGCGCACACCGUGCCGCACAUAGCGUACAACAAGUUGUAGGCGCUCCAUGGCGUUACACAAC-
((((((.........))))))...(((((((((....))....)))))))...((((((.((.....(((...)))...((.(((((....))))).)))).))))))...........- ( -39.90)
>DroSec_CAF1 131 119 - 1
ACUGCCGCGUCCCAAGGCAGUUUAGUGUGCUUCCACGGAACCGGGCACACAUCACAUGGCGCACACCGUGCCGCACAUAGCGUACAACAAGUUGUAGGCGCUCCAUGGCGUUACACAAC-
((((((.........))))))...(((((((....((....)))))))))....(((((.((.....(((...)))...((.(((((....))))).)))).)))))............- ( -40.60)
>DroSim_CAF1 988 119 - 1
ACUGCCGCGUCCCAAGGCAGUUUAGUGUGCUUCCACGGAACCGGGCACACAUCACAUGGCGCACACCGUGCCGCACAUAGCGUACAACAAGUUGUAGGCGCUCCAUGGCGUUACACAAC-
((((((.........))))))...(((((((....((....)))))))))....(((((.((.....(((...)))...((.(((((....))))).)))).)))))............- ( -40.60)
>DroYak_CAF1 1001 120 - 1
ACUGCCGCGUCCCAAGGCAGUUUAGUGUGCUUGCACGGAACCGGGCACACAUCACAUGGCGCACACCGUGCCACACAUAACGUACAACAAGUUGUAGGCGCACCAUGGGCUUACACAACA
((((((.........))))))...(((((((((........)))))))))......((((((.....)))))).................((.((((((.(.....).)))))))).... ( -40.30)
>consensus
ACUGCCGCGUCCCAAGGCAGUUUAGUGUGCUUCCACGGAACCGGGCACACAUCACAUGGCGCACACCGUGCCGCACAUAGCGUACAACAAGUUGUAGGCGCUCCAUGGCGUUACACAAC_
((((((.........))))))...(((((((....((....)))))))))....(((((.((.....(((...)))...((.(((((....))))).)))).)))))............. (-38.47 = -38.72 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,665,825 – 1,665,945
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.50
Mean single sequence MFE -43.58
Consensus MFE -40.79
Energy contribution -40.85
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -1.65
Structure conservation index 0.94
SVM decision value 0.12
SVM RNA-class probability 0.593252
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1665825 120 - 22224390
UCUACGUUGCAAUGUGCCAAGGUUCAGGUUCAGUCGUGCAACUGCCGCGUCCCAAGGCAGUUUAGUGUGCUUCCACGGAAUCGGGCACACAUCUCAUGGCGCACACCGUGCCGCACAUAG
.(((.((.((..((((((..(((((.((...((.((..((((((((.........)))))))..)..)))).))...))))).))))))........(((((.....))))))))).))) ( -41.90)
>DroSec_CAF1 170 120 - 1
UCUACGUUGCAAUGUGCCAAGGUUCAGGUUUAGUCGUGCAACUGCCGCGUCCCAAGGCAGUUUAGUGUGCUUCCACGGAACCGGGCACACAUCACAUGGCGCACACCGUGCCGCACAUAG
.(((.((.((..((((((..(((((.((...((.((..((((((((.........)))))))..)..)))).))...))))).))))))........(((((.....))))))))).))) ( -45.20)
>DroSim_CAF1 1027 120 - 1
UCUACGUUGCAAUGUGCCAAGGUUCAGGUUCAGUCGUGCAACUGCCGCGUCCCAAGGCAGUUUAGUGUGCUUCCACGGAACCGGGCACACAUCACAUGGCGCACACCGUGCCGCACAUAG
.(((.((.((..((((((..(((((.((...((.((..((((((((.........)))))))..)..)))).))...))))).))))))........(((((.....))))))))).))) ( -44.50)
>DroYak_CAF1 1041 120 - 1
UCUACGUUGCAAUGUGCCAAGGUUCAGGUUCAGUCGUGCAACUGCCGCGUCCCAAGGCAGUUUAGUGUGCUUGCACGGAACCGGGCACACAUCACAUGGCGCACACCGUGCCACACAUAA
............((((((..(((((..((.(((.((..((((((((.........)))))))..)..)).))).)).))))).)))))).......((((((.....))))))....... ( -42.70)
>consensus
UCUACGUUGCAAUGUGCCAAGGUUCAGGUUCAGUCGUGCAACUGCCGCGUCCCAAGGCAGUUUAGUGUGCUUCCACGGAACCGGGCACACAUCACAUGGCGCACACCGUGCCGCACAUAG
.....((.((..((((((..(((((.(....((.((..((((((((.........)))))))..)..))))....).))))).))))))........(((((.....))))))))).... (-40.79 = -40.85 +   0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,665,905 – 1,666,018
Length 113
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 90.71
Mean single sequence MFE -34.41
Consensus MFE -30.52
Energy contribution -30.52
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 0.89
SVM decision value 0.18
SVM RNA-class probability 0.621869
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1665905 113 + 22224390
UGCACGACUGAACCUGAACCUUGGCACAUUGCAACGUAGACACGUAGACACGCAGACUCGUCGCCCGAGUCGCGCGAUUGCGAUUCUCGUUGCCCAUUUCGGAUGCUAUAUAU
.(((...(((((((........))......((((((.(((..(((((.(.(((.((((((.....))))))))).).)))))..)))))))))....))))).)))....... ( -35.90)
>DroSec_CAF1 250 93 + 1
UGCACGACUAAACCUGAACCUUGGCACAUUGCAACGUAGACACGUAGACACGCAGACUCGUCGCCCGAGUCGCGCGAUUGCGAUUCUCGUUGC--------------------
(((.(((.............))))))....((((((.(((..(((((.(.(((.((((((.....))))))))).).)))))..)))))))))-------------------- ( -29.92)
>DroSim_CAF1 1107 113 + 1
UGCACGACUGAACCUGAACCUUGGCACAUUGCAACGUAGACACGUAGACACGCAGACUCGUCGCCCGAGUCGCGCGAUUGCGAUUCUCGUUGCCCAUUUCGGAUGCUAUAUAU
.(((...(((((((........))......((((((.(((..(((((.(.(((.((((((.....))))))))).).)))))..)))))))))....))))).)))....... ( -35.90)
>DroYak_CAF1 1121 113 + 1
UGCACGACUGAACCUGAACCUUGGCACAUUGCAACGUAGACACGUAGACACGCAGACUCGUCGCCCGAGUCGCGCGAUUGCGAUUCUCGUUGCCCAUUUCGGAUGCUAUAUAU
.(((...(((((((........))......((((((.(((..(((((.(.(((.((((((.....))))))))).).)))))..)))))))))....))))).)))....... ( -35.90)
>consensus
UGCACGACUGAACCUGAACCUUGGCACAUUGCAACGUAGACACGUAGACACGCAGACUCGUCGCCCGAGUCGCGCGAUUGCGAUUCUCGUUGCCCAUUUCGGAUGCUAUAUAU
(((.(((.............))))))....((((((.(((..(((((.(.(((.((((((.....))))))))).).)))))..))))))))).................... (-30.52 = -30.52 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,665,905 – 1,666,018
Length 113
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 90.71
Mean single sequence MFE -38.00
Consensus MFE -35.24
Energy contribution -36.05
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -1.35
Structure conservation index 0.93
SVM decision value 0.19
SVM RNA-class probability 0.626801
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1665905 113 - 22224390
AUAUAUAGCAUCCGAAAUGGGCAACGAGAAUCGCAAUCGCGCGACUCGGGCGACGAGUCUGCGUGUCUACGUGUCUACGUUGCAAUGUGCCAAGGUUCAGGUUCAGUCGUGCA
.......(((..(((.....(((((((((..((....(((((((((((.....)))))).)))))....))..))).))))))..((.(((........))).)).)))))). ( -39.60)
>DroSec_CAF1 250 93 - 1
--------------------GCAACGAGAAUCGCAAUCGCGCGACUCGGGCGACGAGUCUGCGUGUCUACGUGUCUACGUUGCAAUGUGCCAAGGUUCAGGUUUAGUCGUGCA
--------------------(((((((((..((....(((((((((((.....)))))).)))))....))..))).)))))).(((.(((........))).....)))... ( -33.20)
>DroSim_CAF1 1107 113 - 1
AUAUAUAGCAUCCGAAAUGGGCAACGAGAAUCGCAAUCGCGCGACUCGGGCGACGAGUCUGCGUGUCUACGUGUCUACGUUGCAAUGUGCCAAGGUUCAGGUUCAGUCGUGCA
.......(((..(((.....(((((((((..((....(((((((((((.....)))))).)))))....))..))).))))))..((.(((........))).)).)))))). ( -39.60)
>DroYak_CAF1 1121 113 - 1
AUAUAUAGCAUCCGAAAUGGGCAACGAGAAUCGCAAUCGCGCGACUCGGGCGACGAGUCUGCGUGUCUACGUGUCUACGUUGCAAUGUGCCAAGGUUCAGGUUCAGUCGUGCA
.......(((..(((.....(((((((((..((....(((((((((((.....)))))).)))))....))..))).))))))..((.(((........))).)).)))))). ( -39.60)
>consensus
AUAUAUAGCAUCCGAAAUGGGCAACGAGAAUCGCAAUCGCGCGACUCGGGCGACGAGUCUGCGUGUCUACGUGUCUACGUUGCAAUGUGCCAAGGUUCAGGUUCAGUCGUGCA
.......((((.........(((((((((..((....(((((((((((.....)))))).)))))....))..))).))))))..((.(((........))).))...)))). (-35.24 = -36.05 +   0.81)

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 09:48:55 2006