Locus 7209

Sequence ID 2L_DroMel_CAF1
Location 20,247,890 – 20,248,210
Length 320
Max. P 0.987386
window11519 window11520 window11521 window11522 window11523 window11524

overview

Window 9

Location 20,247,890 – 20,248,010
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -38.53
Consensus MFE -34.22
Energy contribution -34.22
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.12
Structure conservation index 0.89
SVM decision value 0.52
SVM RNA-class probability 0.767729
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20247890 120 - 22407834
AAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUGGCGGAGCCUCCAACUGGCAGCCAUGGCAACAAUGGCCCACAAUGGGCCACAAUGGGCAGGCACCCCAUGGGAAGAAUAUG
..((((.....((((((...(((((((....))))(((((((...(((.......))).)))).))).))).((((((.....))))))...))))))....(((...)))..))))... ( -40.30)
>DroSec_CAF1 6421 110 - 1
AAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUGGCGGAGCCUCCAACUGGCAGCCAUGGCAACAAUGGCCCACA----------AUGGGCAGGCACCCCAUGGGAAGAAUAUG
..((((.....((((((...(((((.......((((..(((.(....).)))..)))).((((((....).))))))))))----------.))))))....(((...)))..))))... ( -35.00)
>DroSim_CAF1 6863 120 - 1
AAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUGGCGGAGCCUCCAACUGGCAGCCAUGGCAACAAUGGCCCACAAUGGGCCACAAUGGGCAGGCACCCCAUGGGAAGAAUAUG
..((((.....((((((...(((((((....))))(((((((...(((.......))).)))).))).))).((((((.....))))))...))))))....(((...)))..))))... ( -40.30)
>consensus
AAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUGGCGGAGCCUCCAACUGGCAGCCAUGGCAACAAUGGCCCACAAUGGGCCACAAUGGGCAGGCACCCCAUGGGAAGAAUAUG
..((((.....(((((....(((((((....))))(((((((...(((.......))).)))).))).)))...(((((.............))))))))))(((...)))..))))... (-34.22 = -34.22 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,247,930 – 20,248,050
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -43.00
Consensus MFE -43.00
Energy contribution -43.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.17
Structure conservation index 1.00
SVM decision value 1.27
SVM RNA-class probability 0.937987
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20247930 120 + 22407834
GUGGGCCAUUGUUGCCAUGGCUGCCAGUUGGAGGCUCCGCCAGACGGCCUAUUAACCACAUUUUAAGCAUAAUUGAAUUUCGUGCAUAAAUUUCGGUUUAUGGGUCGUCGCAGGGAGACC
(((((((......((....))..((....)).))).))))..((((((((((.((((....((((.(((..(.......)..))).))))....)))).))))))))))...((....)) ( -43.00)
>DroSec_CAF1 6451 120 + 1
GUGGGCCAUUGUUGCCAUGGCUGCCAGUUGGAGGCUCCGCCAGACGGCCUAUUAACCACAUUUUAAGCAUAAUUGAAUUUCGUGCAUAAAUUUCGGUUUAUGGGUCGUCGCAGGGAGACC
(((((((......((....))..((....)).))).))))..((((((((((.((((....((((.(((..(.......)..))).))))....)))).))))))))))...((....)) ( -43.00)
>DroSim_CAF1 6903 120 + 1
GUGGGCCAUUGUUGCCAUGGCUGCCAGUUGGAGGCUCCGCCAGACGGCCUAUUAACCACAUUUUAAGCAUAAUUGAAUUUCGUGCAUAAAUUUCGGUUUAUGGGUCGUCGCAGGGAGACC
(((((((......((....))..((....)).))).))))..((((((((((.((((....((((.(((..(.......)..))).))))....)))).))))))))))...((....)) ( -43.00)
>consensus
GUGGGCCAUUGUUGCCAUGGCUGCCAGUUGGAGGCUCCGCCAGACGGCCUAUUAACCACAUUUUAAGCAUAAUUGAAUUUCGUGCAUAAAUUUCGGUUUAUGGGUCGUCGCAGGGAGACC
(((((((......((....))..((....)).))).))))..((((((((((.((((....((((.(((..(.......)..))).))))....)))).))))))))))...((....)) (-43.00 = -43.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,247,930 – 20,248,050
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -37.60
Consensus MFE -37.60
Energy contribution -37.60
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 1.00
SVM decision value 1.29
SVM RNA-class probability 0.938365
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20247930 120 - 22407834
GGUCUCCCUGCGACGACCCAUAAACCGAAAUUUAUGCACGAAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUGGCGGAGCCUCCAACUGGCAGCCAUGGCAACAAUGGCCCAC
((.(((((((.((((.((.((.(((((...((((.(((..(.......)..))).))))...))))).)).)).))))))).))))))......(((..((((((....).)))))))). ( -37.60)
>DroSec_CAF1 6451 120 - 1
GGUCUCCCUGCGACGACCCAUAAACCGAAAUUUAUGCACGAAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUGGCGGAGCCUCCAACUGGCAGCCAUGGCAACAAUGGCCCAC
((.(((((((.((((.((.((.(((((...((((.(((..(.......)..))).))))...))))).)).)).))))))).))))))......(((..((((((....).)))))))). ( -37.60)
>DroSim_CAF1 6903 120 - 1
GGUCUCCCUGCGACGACCCAUAAACCGAAAUUUAUGCACGAAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUGGCGGAGCCUCCAACUGGCAGCCAUGGCAACAAUGGCCCAC
((.(((((((.((((.((.((.(((((...((((.(((..(.......)..))).))))...))))).)).)).))))))).))))))......(((..((((((....).)))))))). ( -37.60)
>consensus
GGUCUCCCUGCGACGACCCAUAAACCGAAAUUUAUGCACGAAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUGGCGGAGCCUCCAACUGGCAGCCAUGGCAACAAUGGCCCAC
((.(((((((.((((.((.((.(((((...((((.(((..(.......)..))).))))...))))).)).)).))))))).))))))......(((..((((((....).)))))))). (-37.60 = -37.60 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,247,970 – 20,248,090
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 99.44
Mean single sequence MFE -39.33
Consensus MFE -38.72
Energy contribution -38.50
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -3.18
Structure conservation index 0.98
SVM decision value 2.08
SVM RNA-class probability 0.987386
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20247970 120 + 22407834
CAGACGGCCUAUUAACCACAUUUUAAGCAUAAUUGAAUUUCGUGCAUAAAUUUCGGUUUAUGGGUCGUCGCAGGGAGACCACAACCCGGCCAGAUUAUUACAUUAUUUACUGGGUGUGUG
..((((((((((.((((....((((.(((..(.......)..))).))))....)))).))))))))))...((....))(((((((((..((((.........)))).)))))).))). ( -39.60)
>DroSec_CAF1 6491 120 + 1
CAGACGGCCUAUUAACCACAUUUUAAGCAUAAUUGAAUUUCGUGCAUAAAUUUCGGUUUAUGGGUCGUCGCAGGGAGACCACAACCCGGCCAGAUUAUUACAUUAUUUACUGGGCGUGUG
..((((((((((.((((....((((.(((..(.......)..))).))))....)))).))))))))))...((....))...((.((.((((...((......))...)))).)).)). ( -39.20)
>DroSim_CAF1 6943 120 + 1
CAGACGGCCUAUUAACCACAUUUUAAGCAUAAUUGAAUUUCGUGCAUAAAUUUCGGUUUAUGGGUCGUCGCAGGGAGACCACAACCCGGCCAGAUUAUUACAUUAUUUACUGGGCGUGUG
..((((((((((.((((....((((.(((..(.......)..))).))))....)))).))))))))))...((....))...((.((.((((...((......))...)))).)).)). ( -39.20)
>consensus
CAGACGGCCUAUUAACCACAUUUUAAGCAUAAUUGAAUUUCGUGCAUAAAUUUCGGUUUAUGGGUCGUCGCAGGGAGACCACAACCCGGCCAGAUUAUUACAUUAUUUACUGGGCGUGUG
..((((((((((.((((....((((.(((..(.......)..))).))))....)))).))))))))))...((....))...((.((.((((...((......))...)))).)).)). (-38.72 = -38.50 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,247,970 – 20,248,090
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -31.00
Consensus MFE -31.00
Energy contribution -31.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 1.00
SVM decision value 0.24
SVM RNA-class probability 0.647242
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20247970 120 - 22407834
CACACACCCAGUAAAUAAUGUAAUAAUCUGGCCGGGUUGUGGUCUCCCUGCGACGACCCAUAAACCGAAAUUUAUGCACGAAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUG
.............................(((((((((((.((......)).)))))))...(((((...((((.(((..(.......)..))).))))...)))))....))))..... ( -31.00)
>DroSec_CAF1 6491 120 - 1
CACACGCCCAGUAAAUAAUGUAAUAAUCUGGCCGGGUUGUGGUCUCCCUGCGACGACCCAUAAACCGAAAUUUAUGCACGAAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUG
.............................(((((((((((.((......)).)))))))...(((((...((((.(((..(.......)..))).))))...)))))....))))..... ( -31.00)
>DroSim_CAF1 6943 120 - 1
CACACGCCCAGUAAAUAAUGUAAUAAUCUGGCCGGGUUGUGGUCUCCCUGCGACGACCCAUAAACCGAAAUUUAUGCACGAAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUG
.............................(((((((((((.((......)).)))))))...(((((...((((.(((..(.......)..))).))))...)))))....))))..... ( -31.00)
>consensus
CACACGCCCAGUAAAUAAUGUAAUAAUCUGGCCGGGUUGUGGUCUCCCUGCGACGACCCAUAAACCGAAAUUUAUGCACGAAAUUCAAUUAUGCUUAAAAUGUGGUUAAUAGGCCGUCUG
.............................(((((((((((.((......)).)))))))...(((((...((((.(((..(.......)..))).))))...)))))....))))..... (-31.00 = -31.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,248,090 – 20,248,210
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.06
Mean single sequence MFE -45.50
Consensus MFE -42.94
Energy contribution -43.50
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.81
Structure conservation index 0.94
SVM decision value 0.38
SVM RNA-class probability 0.714013
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20248090 120 - 22407834
AAACAACAGAGGGAGGCAGGACGAAACGUGGAAUCAUGAAAAAUUGAUGCCCCUGUCGUCUGGUGGCGCCACCUGGUCUGCCCUCUCUCUCGCACGGCAGCUGGCCGUCUCUUUCGUGCA
.......(((((((((((((((((...(.((.((((........)))).)))...))))).((((....))))....))).))))))))).(((((((.....)))(.......))))). ( -45.60)
>DroSec_CAF1 6611 120 - 1
AAACAACAGAGGGAAGCAGGCCGAAACGUGGAAUCAUGAAAAAUUGAUGCCCCUGUCGUCUGGUGGCGCCACCUGGUCUGCCCUCUCUCUCGCACGGCAUCUGGCCGUCUCUUUCGUGCA
.......(((((((.((((((((....((((.((((........))))(((((........)).))).)))).))))))))..))))))).(((((((.....)))(.......))))). ( -45.00)
>DroSim_CAF1 7063 120 - 1
AAACAACAGAGGGAGGCAGGUCGAAACGUGGAAUCAUGAAAAAUUGAUGCCCCUGUCGUCUGGUGGCGCCACCUGGUCUGCCCUCUCUCUCGCACGGCAUCUGGCCGUCUCUUUCGUGCA
.......((((((((((((..((....((((.((((........))))(((((........)).))).)))).))..))).))))))))).(((((((.....)))(.......))))). ( -45.90)
>consensus
AAACAACAGAGGGAGGCAGGACGAAACGUGGAAUCAUGAAAAAUUGAUGCCCCUGUCGUCUGGUGGCGCCACCUGGUCUGCCCUCUCUCUCGCACGGCAUCUGGCCGUCUCUUUCGUGCA
.......((((((((((((((((....((((.((((........))))(((((........)).))).)))).))))))).))))))))).(((((((.....)))(.......))))). (-42.94 = -43.50 +   0.56)

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 12:30:18 2006