Locus 3468

Sequence ID 3L_DroMel_CAF1
Location 10,197,899 – 10,198,128
Length 229
Max. P 0.995017
window5413 window5414 window5415 window5416

overview

Window 3

Location 10,197,899 – 10,198,008
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 87.34
Mean single sequence MFE -55.90
Consensus MFE -38.40
Energy contribution -41.32
Covariance contribution 2.92
Combinations/Pair 1.08
Mean z-score -3.08
Structure conservation index 0.69
SVM decision value 1.34
SVM RNA-class probability 0.943927
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10197899 109 + 23771897
CGGUGGAUAACCGCCGAAUGCGUUUGGUGGUCCUCCUGGUCCUGCUGGUCCGGGAGGAUAUCCGCCGAAGGCCUGGGGCGGUGGUGCUCCUCCUCCGUAGUGUGGCUGU
(((((((((.((((((((....))))))))(((((((((.((....)).))))))))))))))))))..((((....((((.((.......)).)))).....)))).. ( -60.90)
>DroSec_CAF1 74288 109 + 1
CGGUGGAUAACCGGCGAAUGCGUUUGGUGGUCCCCCUGGUCCUGCUGGUCCGGGAGGAUAUCCGCCGAAGGCAUGUGGUGGUGGUGCUCCUCCUCCGUAGGGCGGCUGU
.((.(((..((((.((.((((.(((((((((((.(((((.((....)).))))).)))...)))))))).))))....)).))))..))).)).(((.....))).... ( -51.90)
>DroSim_CAF1 78454 109 + 1
CGGUGGAUAACCGCCGAAUGCGUUUGGUGGUCCCCCUGGUCCUGCUGGUCCGGGAGGAUAUCCGCCGAAGGCAUGUGGUGGUGGUGCUCCUCCUCCGUAGGGCGGCUGU
.((.(((..(((((((.((((.(((((((((((.(((((.((....)).))))).)))...)))))))).))))....)))))))..))).)).(((.....))).... ( -56.70)
>DroEre_CAF1 78970 109 + 1
UGGUGGAUACCCGCCGAAUGCGUUGGCAGGUCCUCCUGGUCCUGCUGGUCCGGGGGGAUAACCGCCGAAGGCCUGUGGAGGUGGUGCUCCUCCUCCGUAGGGUGGCUGU
.(((((...((.(((((.....))))).))(((((((((.((....)).)))))))))...)))))(..(.((((((((((.((....)).)))))))))).)..)... ( -57.30)
>DroYak_CAF1 78355 100 + 1
CGGUGGAUAUCCGCCAAAUGCGCUUGGAGGAC---------CUGCUGGUCCUGGGGGAUACCCUCCAAAGGCCUGUGGAGGUGGUGCUCCUCCUCCGUAGGCUGGCUGU
.(((((....)))))....((..(((((((((---------(....))))))((((....)))))))).((((((((((((.((....)).)))))))))))).))... ( -52.70)
>consensus
CGGUGGAUAACCGCCGAAUGCGUUUGGUGGUCCCCCUGGUCCUGCUGGUCCGGGAGGAUAUCCGCCGAAGGCCUGUGGAGGUGGUGCUCCUCCUCCGUAGGGUGGCUGU
((((((....))))))...((.(((((((((((.(((((.((....)).))))).)))...)))))))).))((((((.((.((....)).)).))))))......... (-38.40 = -41.32 +   2.92)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,197,968 – 10,198,088
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.98
Mean single sequence MFE -55.84
Consensus MFE -29.86
Energy contribution -30.44
Covariance contribution 0.58
Combinations/Pair 1.10
Mean z-score -3.38
Structure conservation index 0.53
SVM decision value 2.53
SVM RNA-class probability 0.995017
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10197968 120 + 23771897
GGCCUGGGGCGGUGGUGCUCCUCCUCCGUAGUGUGGCUGUCCACCAGGACCACCUACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUAAGGUGGCUGACCACCUGGACCACCCAUGUA
.((.((((((((((((.(.........((((.((((...(((....)))))))))))...((((((....))))))).)))).))))...((((((....))))))......)))).)). ( -51.90)
>DroSec_CAF1 74357 120 + 1
GGCAUGUGGUGGUGGUGCUCCUCCUCCGUAGGGCGGCUGUCCACCAGGACCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUACGGGGGCUGACCACCUGGACCACCCAUGUA
.(((((.((((((((((.((..((((((((..((((..(((((...((((...((((.....))))..))))...)))))...)))).))))))))..)).))))...))))))))))). ( -64.10)
>DroSim_CAF1 78523 120 + 1
GGCAUGUGGUGGUGGUGCUCCUCCUCCGUAGGGCGGCUGUCCACCAGGACCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUACGGGGGCUGACCACCUGGUCCACCCAUGUA
.(((((.(((((.((((.((..((((((((..((((..(((((...((((...((((.....))))..))))...)))))...)))).))))))))..)).))))....)))))))))). ( -63.70)
>DroEre_CAF1 79039 108 + 1
GGCCUGUGGAGGUGGUGCUCCUCCUCCGUAGGGUGGCUGUCCACCGGGACCACCUCCAUAAGGUG------------GAGCACCCGCAUAAGGUGGCUGGCCACCUGGACCACCCACGUA
..((((((((((.((....)).))))))))))((((..((((..((((.((((((.....)))))------------)....))))....((((((....))))))))))...))))... ( -54.90)
>DroYak_CAF1 78415 90 + 1
GGCCUGUGGAGGUGGUGCUCCUCCUCCGUAGGCUGGCUGUCCACCUGGACCA------------------------------CCCACAUAAGGUGGCUGUCCACCUGGACCACCCACGUA
((((((((((((.((....)).))))))))))))((..(((((..(((((..------------------------------.((((.....))))..)))))..)))))..))...... ( -44.60)
>consensus
GGCCUGUGGAGGUGGUGCUCCUCCUCCGUAGGGUGGCUGUCCACCAGGACCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUAAGGUGGCUGACCACCUGGACCACCCAUGUA
.((.((.((.(((((((.((..((.((.....((((..((((....))))((((.......))))..................))))....)).))..)).))))...))).)))).)). (-29.86 = -30.44 +   0.58)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,197,968 – 10,198,088
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.98
Mean single sequence MFE -56.36
Consensus MFE -36.25
Energy contribution -38.88
Covariance contribution 2.63
Combinations/Pair 1.06
Mean z-score -2.95
Structure conservation index 0.64
SVM decision value 2.34
SVM RNA-class probability 0.992562
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10197968 120 - 23771897
UACAUGGGUGGUCCAGGUGGUCAGCCACCUUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUAGGUGGUCCUGGUGGACAGCCACACUACGGAGGAGGAGCACCACCGCCCCAGGCC
.....(((((((..((((((....))))))......((((.(((.(((.....))).((((.((((((((((((....))...))))).))))))))).))).)))))))))))...... ( -57.70)
>DroSec_CAF1 74357 120 - 1
UACAUGGGUGGUCCAGGUGGUCAGCCCCCGUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUGGGUGGUCCUGGUGGACAGCCGCCCUACGGAGGAGGAGCACCACCACCACAUGCC
..((((((((((...((((.((..((.(((((.((((.((..(((((......(((((((.....))))))))))))....)).))))..))))).))..)).)))))))))).)))).. ( -63.60)
>DroSim_CAF1 78523 120 - 1
UACAUGGGUGGACCAGGUGGUCAGCCCCCGUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUGGGUGGUCCUGGUGGACAGCCGCCCUACGGAGGAGGAGCACCACCACCACAUGCC
..(((((((((....((((.((..((.(((((.((((.((..(((((......(((((((.....))))))))))))....)).))))..))))).))..)).)))).))))).)))).. ( -61.80)
>DroEre_CAF1 79039 108 - 1
UACGUGGGUGGUCCAGGUGGCCAGCCACCUUAUGCGGGUGCUC------------CACCUUAUGGAGGUGGUCCCGGUGGACAGCCACCCUACGGAGGAGGAGCACCACCUCCACAGGCC
...(((((.(((..((((((....))))))......(((((((------------(.((((.(((.((((((((....))...)))))))))..)))).))))))))))))))))..... ( -54.40)
>DroYak_CAF1 78415 90 - 1
UACGUGGGUGGUCCAGGUGGACAGCCACCUUAUGUGGG------------------------------UGGUCCAGGUGGACAGCCAGCCUACGGAGGAGGAGCACCACCUCCACAGGCC
......(((.(((((..(((...(((((((.....)))------------------------------)))))))..))))).))).((((..(((((.((....)).)))))..)))). ( -44.30)
>consensus
UACAUGGGUGGUCCAGGUGGUCAGCCACCUUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUAGGUGGUCCUGGUGGACAGCCACCCUACGGAGGAGGAGCACCACCACCACAGGCC
.......((((....((((((...((.((((....(((((((.............(((((.....)))))((((....)))).)))))))....)))).))...)))))).))))..... (-36.25 = -38.88 +   2.63)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,198,008 – 10,198,128
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.07
Mean single sequence MFE -47.58
Consensus MFE -32.83
Energy contribution -34.94
Covariance contribution 2.11
Combinations/Pair 1.03
Mean z-score -1.91
Structure conservation index 0.69
SVM decision value 0.57
SVM RNA-class probability 0.786953
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10198008 120 + 23771897
CCACCAGGACCACCUACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUAAGGUGGCUGACCACCUGGACCACCCAUGUAAGGUGGUUGUCCGGCUCCGUAGGGCGGAGCUUCUCCGUAU
...((.(((((((((.....))))))...)))(((.((((..........((((((....)))))).(((((((.......))))))))))))))......))((((((...)))))).. ( -51.80)
>DroSec_CAF1 74397 120 + 1
CCACCAGGACCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUACGGGGGCUGACCACCUGGACCACCCAUGUAAGGUGGUUGUCCGGCUCCGUAGGGCGGAGCUUCUCCGUAC
...(((((..((.((((.....)))).))....)))))..........(((((((((.((((((((..((.......)).))))))))))))(((((((.....)))))))...))))). ( -51.70)
>DroSim_CAF1 78563 120 + 1
CCACCAGGACCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUACGGGGGCUGACCACCUGGUCCACCCAUGUAAGGUGGUUGUCCGGCCCCGUAGGGCGGAGCUUCUCCGUAC
...((.((((...((((.....))))..))))(((.((((...((((.((((.(((..((((....))))..))).))))..))))..)))))))......))((((((...)))))).. ( -51.00)
>DroEre_CAF1 79079 108 + 1
CCACCGGGACCACCUCCAUAAGGUG------------GAGCACCCGCAUAAGGUGGCUGGCCACCUGGACCACCCACGUAAGGUGGUUGUCCGGCUCCGUAGGGCUGAGCUUCUCCGUAC
....(((((((((((......((((------------(.((....))...((((((....))))))...)))))......))))))))(..((((((....))))))..)....)))... ( -45.60)
>DroYak_CAF1 78455 90 + 1
CCACCUGGACCA------------------------------CCCACAUAAGGUGGCUGUCCACCUGGACCACCCACGUAAGGUGGUUGUCCGGCGCCGUAGGGCGGCGCUUCUCCGUAC
......((((..------------------------------........((((((....)))))).(((((((.......)))))))))))(((((((.....)))))))......... ( -37.80)
>consensus
CCACCAGGACCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUAAGGUGGCUGACCACCUGGACCACCCAUGUAAGGUGGUUGUCCGGCUCCGUAGGGCGGAGCUUCUCCGUAC
......((((...........(((((...(((....)))))))).......(((((....)))))..(((((((.......)))))))))))(((((((.....)))))))......... (-32.83 = -34.94 +   2.11)

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 10:58:52 2006