Locus 6129

Sequence ID 3L_DroMel_CAF1
Location 16,224,414 – 16,224,654
Length 240
Max. P 0.975755
window9844 window9845 window9846 window9847 window9848

overview

Window 4

Location 16,224,414 – 16,224,534
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -39.09
Consensus MFE -33.17
Energy contribution -34.48
Covariance contribution 1.31
Combinations/Pair 1.03
Mean z-score -2.08
Structure conservation index 0.85
SVM decision value 0.31
SVM RNA-class probability 0.683513
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16224414 120 - 23771897
GCUACCAGCAGCCUUACCUGGGCCCCCAGCCAGAAUCCUACUACUACGGAGGACGGUACCCGGCUGGUGGCUACUACAACAACUACCACAACAGCCCGGGUCCGUACGGCUACCCCUAUC
((.....)).((((.....))))....((((.....(((.((.....)))))((((.(((((((((((((...............))))..))).))))))))))..))))......... ( -39.26)
>DroSec_CAF1 43200 120 - 1
GCUACCAGCAGCCUUACCUGGGCCCCCAGCCAGGAUCCUACUACUACGGAGGACCGUACCCGGCUGGUGGCUACUACAACAACUACCACAACAGCCCGGGUCCGUACGGCUACCCCUAUC
((.....))((((.(((((((....))))...((((((......(((((....)))))...(((((((((...............))))..))))).))))))))).))))......... ( -41.36)
>DroSim_CAF1 44851 120 - 1
GCUACCAGCAGCCUUACCUGGGCCCCCAGCCAGGAUCCUACUACUACGGAGGACCGUACCCGGCUGGUGGCUACUACAACAACUACCACAACAGCCCGGGUCCGUACGGCUACCCCUAUC
((.....))((((.(((((((....))))...((((((......(((((....)))))...(((((((((...............))))..))))).))))))))).))))......... ( -41.36)
>DroEre_CAF1 43009 120 - 1
GCUACCAGCAGCCUUACCUGGGCCCCCAGCCAGGACCCUACUACUACGGAGAAGCGUACCCGGCAGGUGGCUACUACAACAACUACCACAACAGCCCGGGACCGUACGGAUACCCCUAUC
((.....)).......(((((((.....(((.((((.((.((.(....))).)).)).)).))).(((((............)))))......))))))).((....))........... ( -34.40)
>consensus
GCUACCAGCAGCCUUACCUGGGCCCCCAGCCAGGAUCCUACUACUACGGAGGACCGUACCCGGCUGGUGGCUACUACAACAACUACCACAACAGCCCGGGUCCGUACGGCUACCCCUAUC
((.....))((((.(((((((....))))...((((((......(((((....)))))...(((((((((...............))))..))))).))))))))).))))......... (-33.17 = -34.48 +   1.31)

alignment

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secondary structure

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Window 5

Location 16,224,454 – 16,224,574
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.25
Mean single sequence MFE -55.83
Consensus MFE -55.34
Energy contribution -54.90
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -2.29
Structure conservation index 0.99
SVM decision value 1.76
SVM RNA-class probability 0.975755
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16224454 120 + 23771897
GUUGUAGUAGCCACCAGCCGGGUACCGUCCUCCGUAGUAGUAGGAUUCUGGCUGGGGGCCCAGGUAAGGCUGCUGGUAGCUGACACCGAAGGAGACCAGCGGCUUGGCCUUGAUGCAGGU
.(((((...(((.(((((((((....(((((.(......).)))))))))))))).)))(.((((.(((((((((((..((.........))..))))))))))).)))).).))))).. ( -55.50)
>DroSec_CAF1 43240 120 + 1
GUUGUAGUAGCCACCAGCCGGGUACGGUCCUCCGUAGUAGUAGGAUCCUGGCUGGGGGCCCAGGUAAGGCUGCUGGUAGCUGACGCCGAAGGAGACCAGUGGCUUGGCCUUGAUGCAGGU
.(((((...(((.(((((((((....(((((.(......).)))))))))))))).)))(.((((.((((..(((((..((.........))..)))))..)))).)))).).))))).. ( -55.30)
>DroSim_CAF1 44891 120 + 1
GUUGUAGUAGCCACCAGCCGGGUACGGUCCUCCGUAGUAGUAGGAUCCUGGCUGGGGGCCCAGGUAAGGCUGCUGGUAGCUGACGCCGAAGGAGACCAGCGGCUUGGCCUUGAUGCAGGU
.(((((...(((.(((((((((....(((((.(......).)))))))))))))).)))(.((((.(((((((((((..((.........))..))))))))))).)))).).))))).. ( -57.80)
>DroEre_CAF1 43049 120 + 1
GUUGUAGUAGCCACCUGCCGGGUACGCUUCUCCGUAGUAGUAGGGUCCUGGCUGGGGGCCCAGGUAAGGCUGCUGGUAGCCGACGCCGAAGGAGACCAGCGGCUUGGCCUUGAUGCAGGU
.(((((...(((.(((((((((.((.((.((.......)).)).)))))))).))))))(.((((.(((((((((((..((.........))..))))))))))).)))).).))))).. ( -54.70)
>consensus
GUUGUAGUAGCCACCAGCCGGGUACGGUCCUCCGUAGUAGUAGGAUCCUGGCUGGGGGCCCAGGUAAGGCUGCUGGUAGCUGACGCCGAAGGAGACCAGCGGCUUGGCCUUGAUGCAGGU
.(((((...(((.(((((((((....(((((.(......).)))))))))))))).)))(.((((.(((((((((((..((.........))..))))))))))).)))).).))))).. (-55.34 = -54.90 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,224,494 – 16,224,614
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.31
Mean single sequence MFE -52.33
Consensus MFE -48.74
Energy contribution -48.42
Covariance contribution -0.31
Combinations/Pair 1.08
Mean z-score -1.99
Structure conservation index 0.93
SVM decision value 1.30
SVM RNA-class probability 0.939104
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16224494 120 + 23771897
UAGGAUUCUGGCUGGGGGCCCAGGUAAGGCUGCUGGUAGCUGACACCGAAGGAGACCAGCGGCUUGGCCUUGAUGCAGGUGGUGGCCACCACCAGGAGCACUGCUAACUGCAACGGUAGA
(((..((((((.(((.((((.((((.(((((((((((..((.........))..))))))))))).))))....((.....)))))).)))))))))...)))....((((....)))). ( -49.50)
>DroSec_CAF1 43280 120 + 1
UAGGAUCCUGGCUGGGGGCCCAGGUAAGGCUGCUGGUAGCUGACGCCGAAGGAGACCAGUGGCUUGGCCUUGAUGCAGGUGGUGGCCACCACCAGGAGCACUGCUAACUGCAAGGUAUGA
.....((((((.(((.((((.((((.((((..(((((..((.........))..)))))..)))).))))....((.....)))))).)))))))))((..(((.....)))..)).... ( -49.20)
>DroSim_CAF1 44931 120 + 1
UAGGAUCCUGGCUGGGGGCCCAGGUAAGGCUGCUGGUAGCUGACGCCGAAGGAGACCAGCGGCUUGGCCUUGAUGCAGGUGGUGGCCACCACCAGGAGCACUGCUAACUGCAAGGUAAGA
.....((((((.(((.((((.((((.(((((((((((..((.........))..))))))))))).))))....((.....)))))).)))))))))((..(((.....)))..)).... ( -51.70)
>DroEre_CAF1 43089 120 + 1
UAGGGUCCUGGCUGGGGGCCCAGGUAAGGCUGCUGGUAGCCGACGCCGAAGGAGACCAGCGGCUUGGCCUUGAUGCAGGUGGUGGCCACCAGCAGGAGCACUGCUAACUGCAAUAGGAGG
..(((((((.....)))))))((((.(((((((((((..((.........))..))))))))))).))))...(((((((((...)))))(((((.....)))))...))))........ ( -58.90)
>consensus
UAGGAUCCUGGCUGGGGGCCCAGGUAAGGCUGCUGGUAGCUGACGCCGAAGGAGACCAGCGGCUUGGCCUUGAUGCAGGUGGUGGCCACCACCAGGAGCACUGCUAACUGCAAGGGAAGA
...(.((((((.(((.((((.((((.(((((((((((..((.........))..))))))))))).))))....((.....)))))).))))))))).)..(((.....)))........ (-48.74 = -48.42 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,224,494 – 16,224,614
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.31
Mean single sequence MFE -42.24
Consensus MFE -37.60
Energy contribution -38.41
Covariance contribution 0.81
Combinations/Pair 1.09
Mean z-score -1.48
Structure conservation index 0.89
SVM decision value 0.09
SVM RNA-class probability 0.578698
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16224494 120 - 23771897
UCUACCGUUGCAGUUAGCAGUGCUCCUGGUGGUGGCCACCACCUGCAUCAAGGCCAAGCCGCUGGUCUCCUUCGGUGUCAGCUACCAGCAGCCUUACCUGGGCCCCCAGCCAGAAUCCUA
(((...(((((.(.((((.((((....((((((....)))))).))))...(((...((((..((...))..))))))).)))).).))))).....((((....))))..)))...... ( -39.10)
>DroSec_CAF1 43280 120 - 1
UCAUACCUUGCAGUUAGCAGUGCUCCUGGUGGUGGCCACCACCUGCAUCAAGGCCAAGCCACUGGUCUCCUUCGGCGUCAGCUACCAGCAGCCUUACCUGGGCCCCCAGCCAGGAUCCUA
.......((((.....))))...(((((((((.((((.....((((....((((((......)))))).....(((....)))....)))).........)))).))).))))))..... ( -39.14)
>DroSim_CAF1 44931 120 - 1
UCUUACCUUGCAGUUAGCAGUGCUCCUGGUGGUGGCCACCACCUGCAUCAAGGCCAAGCCGCUGGUCUCCUUCGGCGUCAGCUACCAGCAGCCUUACCUGGGCCCCCAGCCAGGAUCCUA
.......((((.....))))...(((((((((.((((....(((......)))....((.((((((.......(((....))))))))).))........)))).))).))))))..... ( -41.91)
>DroEre_CAF1 43089 120 - 1
CCUCCUAUUGCAGUUAGCAGUGCUCCUGCUGGUGGCCACCACCUGCAUCAAGGCCAAGCCGCUGGUCUCCUUCGGCGUCGGCUACCAGCAGCCUUACCUGGGCCCCCAGCCAGGACCCUA
.....((((((.....))))))...((((((((((((....(((......)))....((((..((...))..))))...))))))))))))(((...((((....))))..)))...... ( -48.80)
>consensus
UCUUACCUUGCAGUUAGCAGUGCUCCUGGUGGUGGCCACCACCUGCAUCAAGGCCAAGCCGCUGGUCUCCUUCGGCGUCAGCUACCAGCAGCCUUACCUGGGCCCCCAGCCAGGAUCCUA
.....((((((.....)))))).(((((((((.((((....(((......)))....((.((((((.......(((....))))))))).))........)))).))).))))))..... (-37.60 = -38.41 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,224,534 – 16,224,654
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.16
Mean single sequence MFE -33.97
Consensus MFE -29.35
Energy contribution -29.73
Covariance contribution 0.37
Combinations/Pair 1.07
Mean z-score -1.42
Structure conservation index 0.86
SVM decision value 0.14
SVM RNA-class probability 0.602120
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16224534 120 - 23771897
UCCAUUGGCCAAGUAUCAGCUCCACUUAACUUCUCCACCUUCUACCGUUGCAGUUAGCAGUGCUCCUGGUGGUGGCCACCACCUGCAUCAAGGCCAAGCCGCUGGUCUCCUUCGGUGUCA
....((((((........(((..(((((((................)))).))).))).((((....((((((....)))))).))))...))))))(.((((((......)))))).). ( -34.59)
>DroSec_CAF1 43320 111 - 1
UCCAUUGGCCAAGUACCAGCUCCACU---------CACCUUCAUACCUUGCAGUUAGCAGUGCUCCUGGUGGUGGCCACCACCUGCAUCAAGGCCAAGCCACUGGUCUCCUUCGGCGUCA
....((((((........(((..(((---------((...........)).))).))).((((....((((((....)))))).))))...))))))(((...((...))...))).... ( -31.70)
>DroSim_CAF1 44971 111 - 1
UCCAUUGGCCAAGUACCAGCUCCACU---------CACCUUCUUACCUUGCAGUUAGCAGUGCUCCUGGUGGUGGCCACCACCUGCAUCAAGGCCAAGCCGCUGGUCUCCUUCGGCGUCA
....((((((........(((..(((---------((...........)).))).))).((((....((((((....)))))).))))...))))))((((..((...))..)))).... ( -35.10)
>DroEre_CAF1 43129 114 - 1
UCCAUCAGCC-AGUACCAGCUCCUCUCAG-----CCACCUCCUCCUAUUGCAGUUAGCAGUGCUCCUGCUGGUGGCCACCACCUGCAUCAAGGCCAAGCCGCUGGUCUCCUUCGGCGUCG
.......(((-((.((((((....((..(-----((.........((((((.....))))))....(((.(((((...))))).)))....)))..))..)))))))).....))).... ( -34.50)
>consensus
UCCAUUGGCCAAGUACCAGCUCCACU_________CACCUUCUUACCUUGCAGUUAGCAGUGCUCCUGGUGGUGGCCACCACCUGCAUCAAGGCCAAGCCGCUGGUCUCCUUCGGCGUCA
.......((((((.((((((............................(((.....)))((((....((((((....)))))).))))...(((...)))))))))...))).))).... (-29.35 = -29.73 +   0.37)

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 12:10:51 2006