Locus 4045

Sequence ID 3L_DroMel_CAF1
Location 11,794,449 – 11,794,809
Length 360
Max. P 0.925988
window6294 window6295 window6296 window6297 window6298 window6299

overview

Window 4

Location 11,794,449 – 11,794,569
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -40.97
Consensus MFE -39.77
Energy contribution -39.33
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -2.13
Structure conservation index 0.97
SVM decision value 1.17
SVM RNA-class probability 0.925988
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11794449 120 + 23771897
CUUUUUCGGUUUCCUUGGCUGCGGUUUGGAGUGCAGCGCCUGCGCUUCGAACACUUUAAAAUCAUAAUCGCCAGCAGCAUUUAAGCGCAGAAUAGCCGCUUUGUUGCCGCAGCGAUAGCA
........(((....(.(((((((((((((((((((...))))))))))))).....................((((((...((((((......).))))))))))))))))).).))). ( -43.10)
>DroSec_CAF1 3470 120 + 1
CUUUUUCAGUUUCCUUGGCUGCGGUUUGGAGUGCAGCGCCUGCGCUUCGAACACUUCAAAAUCGUAAUCGCCAACAGAAUUUAAGCGCAGAAUUGCCGCUUUGUUGCCGCAGCGAUAGCA
........(((....(.(((((((((((((((((((...)))))))))))))...................(((((......((((((......).)))))))))).)))))).).))). ( -38.70)
>DroSim_CAF1 3347 120 + 1
CUUUUUCAGCUUCCUUGGCUGCGGUUUGGAGUGCAGCGCCUGCGCUUCGAACACUUCAAAAUCGUAAUCGCCAACAGAAUUUAAGCGCAGAAUUGCCGCUUUGUUGCCGCAGCGAUAGCA
........(((....(.(((((((((((((((((((...)))))))))))))...................(((((......((((((......).)))))))))).)))))).).))). ( -41.10)
>consensus
CUUUUUCAGUUUCCUUGGCUGCGGUUUGGAGUGCAGCGCCUGCGCUUCGAACACUUCAAAAUCGUAAUCGCCAACAGAAUUUAAGCGCAGAAUUGCCGCUUUGUUGCCGCAGCGAUAGCA
........(((....(.(((((((((((((((((((...)))))))))))))...................(((((......((((((......).)))))))))).)))))).).))). (-39.77 = -39.33 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,794,449 – 11,794,569
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -39.14
Consensus MFE -36.31
Energy contribution -36.09
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.73
Structure conservation index 0.93
SVM decision value 0.19
SVM RNA-class probability 0.625893
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11794449 120 - 23771897
UGCUAUCGCUGCGGCAACAAAGCGGCUAUUCUGCGCUUAAAUGCUGCUGGCGAUUAUGAUUUUAAAGUGUUCGAAGCGCAGGCGCUGCACUCCAAACCGCAGCCAAGGAAACCGAAAAAG
.....(((((((((.......(((((...(((((((((.((((((....................))))))..))))))))).)))))........)))))))...(....).))..... ( -38.01)
>DroSec_CAF1 3470 120 - 1
UGCUAUCGCUGCGGCAACAAAGCGGCAAUUCUGCGCUUAAAUUCUGUUGGCGAUUACGAUUUUGAAGUGUUCGAAGCGCAGGCGCUGCACUCCAAACCGCAGCCAAGGAAACUGAAAAAG
.....(((((((((.......(((((...(((((((((...(((.((((.......))))...))).......))))))))).)))))........)))))))..((....))))..... ( -39.86)
>DroSim_CAF1 3347 120 - 1
UGCUAUCGCUGCGGCAACAAAGCGGCAAUUCUGCGCUUAAAUUCUGUUGGCGAUUACGAUUUUGAAGUGUUCGAAGCGCAGGCGCUGCACUCCAAACCGCAGCCAAGGAAGCUGAAAAAG
.(((.(((((((((.......(((((...(((((((((...(((.((((.......))))...))).......))))))))).)))))........)))))))...)).)))........ ( -39.56)
>consensus
UGCUAUCGCUGCGGCAACAAAGCGGCAAUUCUGCGCUUAAAUUCUGUUGGCGAUUACGAUUUUGAAGUGUUCGAAGCGCAGGCGCUGCACUCCAAACCGCAGCCAAGGAAACUGAAAAAG
.....(((((((((.......(((((...(((((((((.....(....).(((.(((.........))).)))))))))))).)))))........)))))))...(....).))..... (-36.31 = -36.09 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,794,529 – 11,794,649
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -40.53
Consensus MFE -37.87
Energy contribution -38.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.93
SVM decision value 0.03
SVM RNA-class probability 0.548761
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11794529 120 + 23771897
UUAAGCGCAGAAUAGCCGCUUUGUUGCCGCAGCGAUAGCAAUAGUUGGGUGCUGACCAUAUGGUAACAAGAAGUUGGCCAAAAUGCCAACGGAAGCCAUCCUGGGCCAACUGAUGAGCGC
....((((...........(((((((((((((((.((((....))))..)))))......)))))))))).((((((((...(((....(....).)))....)))))))).....)))) ( -39.20)
>DroSec_CAF1 3550 120 + 1
UUAAGCGCAGAAUUGCCGCUUUGUUGCCGCAGCGAUAGCAAUAGUUGGGUGCUGACCAGAUGGUAACAAGCAGUUGGCCAAAAUGCCAACGGAAGCCAUCCUUGGCCAACUGAUGAGCCC
....((.(((.....((((((.((((((((((((.((((....))))..)))))......))))))))))).((((((......))))))))..((((....))))...)))....)).. ( -41.20)
>DroSim_CAF1 3427 120 + 1
UUAAGCGCAGAAUUGCCGCUUUGUUGCCGCAGCGAUAGCAAUAGUUGGGUGCUGACCAGAUGGUAACAAGCAGUUGGCCAAAAUGCCAACGGAAGCCAUCCUUGGCCAACUGAUGAGCCC
....((.(((.....((((((.((((((((((((.((((....))))..)))))......))))))))))).((((((......))))))))..((((....))))...)))....)).. ( -41.20)
>consensus
UUAAGCGCAGAAUUGCCGCUUUGUUGCCGCAGCGAUAGCAAUAGUUGGGUGCUGACCAGAUGGUAACAAGCAGUUGGCCAAAAUGCCAACGGAAGCCAUCCUUGGCCAACUGAUGAGCCC
....((.(((.....((((((.((((((((((((.((((....))))..)))))......))))))))))).((((((......))))))))..(((......)))...)))....)).. (-37.87 = -38.20 +   0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,794,529 – 11,794,649
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -41.97
Consensus MFE -37.67
Energy contribution -38.33
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.90
SVM decision value 0.63
SVM RNA-class probability 0.803808
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11794529 120 - 23771897
GCGCUCAUCAGUUGGCCCAGGAUGGCUUCCGUUGGCAUUUUGGCCAACUUCUUGUUACCAUAUGGUCAGCACCCAACUAUUGCUAUCGCUGCGGCAACAAAGCGGCUAUUCUGCGCUUAA
((((........(((((...((((((....((((((......))))))....(((((((....))).))))..........))))))(((..(....)..))))))))....)))).... ( -40.50)
>DroSec_CAF1 3550 120 - 1
GGGCUCAUCAGUUGGCCAAGGAUGGCUUCCGUUGGCAUUUUGGCCAACUGCUUGUUACCAUCUGGUCAGCACCCAACUAUUGCUAUCGCUGCGGCAACAAAGCGGCAAUUCUGCGCUUAA
(((.....(((((((((((((...(((......))).)))))))))))))..(((((((....))).))))))).......((...((((..(....)..))))(((....))))).... ( -42.70)
>DroSim_CAF1 3427 120 - 1
GGGCUCAUCAGUUGGCCAAGGAUGGCUUCCGUUGGCAUUUUGGCCAACUGCUUGUUACCAUCUGGUCAGCACCCAACUAUUGCUAUCGCUGCGGCAACAAAGCGGCAAUUCUGCGCUUAA
(((.....(((((((((((((...(((......))).)))))))))))))..(((((((....))).))))))).......((...((((..(....)..))))(((....))))).... ( -42.70)
>consensus
GGGCUCAUCAGUUGGCCAAGGAUGGCUUCCGUUGGCAUUUUGGCCAACUGCUUGUUACCAUCUGGUCAGCACCCAACUAUUGCUAUCGCUGCGGCAACAAAGCGGCAAUUCUGCGCUUAA
(((.....(((((((((.((((((.(.......).)))))))))))))))..(((((((....))).))))))).......((...((((..(....)..))))((......)))).... (-37.67 = -38.33 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,794,569 – 11,794,689
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -41.37
Consensus MFE -37.97
Energy contribution -38.63
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.92
SVM decision value 0.39
SVM RNA-class probability 0.715621
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11794569 120 - 23771897
GAGGAGUUUACGCGCGCAAAUGGAAUCUCUCUCAUAUGCCGCGCUCAUCAGUUGGCCCAGGAUGGCUUCCGUUGGCAUUUUGGCCAACUUCUUGUUACCAUAUGGUCAGCACCCAACUAU
((.(((....((((.(((.(((((.....)).))).)))))))))).))((((((((.((((((.(.......).))))))))))))))...(((((((....))).))))......... ( -39.30)
>DroSec_CAF1 3590 120 - 1
GAGGAGUUUACGCGCGCAAAUGGGAUCUCUCUCAUAUGCCGGGCUCAUCAGUUGGCCAAGGAUGGCUUCCGUUGGCAUUUUGGCCAACUGCUUGUUACCAUCUGGUCAGCACCCAACUAU
....((((.....(.(((.((((((....)))))).))))(((.....(((((((((((((...(((......))).)))))))))))))..(((((((....))).))))))))))).. ( -42.40)
>DroSim_CAF1 3467 120 - 1
GAGGAGUUUACGCGCGCAAAUGGGAUCUCUCUCAUAUGCCGGGCUCAUCAGUUGGCCAAGGAUGGCUUCCGUUGGCAUUUUGGCCAACUGCUUGUUACCAUCUGGUCAGCACCCAACUAU
....((((.....(.(((.((((((....)))))).))))(((.....(((((((((((((...(((......))).)))))))))))))..(((((((....))).))))))))))).. ( -42.40)
>consensus
GAGGAGUUUACGCGCGCAAAUGGGAUCUCUCUCAUAUGCCGGGCUCAUCAGUUGGCCAAGGAUGGCUUCCGUUGGCAUUUUGGCCAACUGCUUGUUACCAUCUGGUCAGCACCCAACUAU
((.(((((....((.(((.((((((....)))))).)))))))))).))((((((((.((((((.(.......).))))))))))))))...(((((((....))).))))......... (-37.97 = -38.63 +   0.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,794,689 – 11,794,809
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -48.13
Consensus MFE -41.63
Energy contribution -41.97
Covariance contribution 0.34
Combinations/Pair 1.07
Mean z-score -1.85
Structure conservation index 0.86
SVM decision value -0.02
SVM RNA-class probability 0.524406
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11794689 120 - 23771897
UGCCACGAGAUACCCGAAAGUGGAAUUAUAGCUGAUCUUCUCUGGAGCGAUCCACAGGAAGCGCCUGGAUGGGCGGCAUCGCCACGAGGACAUGGAAAACUCUUCGGUGGCGAUGUUGUU
..((((.((...(((....).)).......(((....((((.((((....)))).)))))))..)).).)))((((((((((((((((((..(....)..))))).))))))))))))). ( -44.70)
>DroSec_CAF1 3710 120 - 1
UGCCUCGAGAUACCCGAAAGGGGAGUUAUAGCUGAUCUCCUCUGGAGCGAUCCCCAGGAAGCGCCUGGAUGGGCGGCGUCGCCACGUGGACAUGGAAAACUCUUCGGUGGCGAUGUCGUU
.((((.(((((.(((....))).(((....))).))))).((..(.(((.(((...)))..))))..)).))))(((((((((((.((((...(.....)..)))))))))))))))... ( -50.30)
>DroSim_CAF1 3587 120 - 1
UUCCUCGAGAUACCCGAAAGGGGAGUUAUAGCUGAUCUCCUCUGGAGCGAUCCCCAGGAAGCGCCUGGAUGGUCGGCGUCGCCACGUGGACAUGGAAAACUCUUCGGUGGCGAUGUCGUU
((((..(((((.(((....))).(((....))).)))))....)))).((((.(((((.....)))))..))))(((((((((((.((((...(.....)..)))))))))))))))... ( -49.40)
>consensus
UGCCUCGAGAUACCCGAAAGGGGAGUUAUAGCUGAUCUCCUCUGGAGCGAUCCCCAGGAAGCGCCUGGAUGGGCGGCGUCGCCACGUGGACAUGGAAAACUCUUCGGUGGCGAUGUCGUU
..((..(((((.(((....))).(((....))).))))).((..(.(((.(((...)))..))))..)).))((((((((((((((.(((..(....)..))).).))))))))))))). (-41.63 = -41.97 +   0.34)

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 11:13:11 2006