Locus 2835

Sequence ID 3R_DroMel_CAF1
Location 7,605,529 – 7,605,689
Length 160
Max. P 0.932839
window4583 window4584 window4585 window4586

overview

Window 3

Location 7,605,529 – 7,605,649
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -45.73
Consensus MFE -43.57
Energy contribution -43.47
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -2.32
Structure conservation index 0.95
SVM decision value 1.22
SVM RNA-class probability 0.932839
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7605529 120 + 27905053
UAUGUUUGGCUAUAUGCUUGUGUGCAUGUAUCUGGAUCUGUUUGCCCACGGACAUGUGUAGACGAAGGGAAAGGAGAGGCCGAGAGAGCAGAGCGUUCUCGAGCGCAUUGCUCUCGUUGC
.....((((((((((((......)))))).......(((.(((.(((.((.((....))...))..))).))).)))))))))((((((((.(((((....))))).))))))))..... ( -44.10)
>DroSec_CAF1 945 119 + 1
UAUGU-UGGCUAUAUGCUUGUGUGCAUGUAUCUGGAUCUGUUUGCCCACGGACAUGUGUUGACGGAGGGAGAGGAGAGGCCGAGAGAGCAGAGCGUUCUCGAGCGCAUUGCUCUCGUUGC
....(-(((((((((((......)))))).......(((.((..(((.((..((.....)).))..)))..)).)))))))))((((((((.(((((....))))).))))))))..... ( -45.50)
>DroSim_CAF1 946 120 + 1
UAUGUUUGGCUAUAUGCUUGUGUGCAUGUAUCUGGAUCUGUUUGCCCACGGACAUGUGUAGACAGAGGGAGAGGAGAGGCCGAGAGAGCAGAGCGUUCUCGAGCGCAUUGCUCUCGUUGC
.....((((((((((((......)))))).(((...(((((((((.((......)).)))))))))...))).....))))))((((((((.(((((....))))).))))))))..... ( -47.60)
>consensus
UAUGUUUGGCUAUAUGCUUGUGUGCAUGUAUCUGGAUCUGUUUGCCCACGGACAUGUGUAGACGGAGGGAGAGGAGAGGCCGAGAGAGCAGAGCGUUCUCGAGCGCAUUGCUCUCGUUGC
.....((((((((((((......)))))).(((...(((.(((((.((((....))))..).)))).)))..)))..))))))((((((((.(((((....))))).))))))))..... (-43.57 = -43.47 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,605,529 – 7,605,649
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -31.53
Consensus MFE -30.33
Energy contribution -30.67
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.96
SVM decision value 0.80
SVM RNA-class probability 0.854425
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7605529 120 - 27905053
GCAACGAGAGCAAUGCGCUCGAGAACGCUCUGCUCUCUCGGCCUCUCCUUUCCCUUCGUCUACACAUGUCCGUGGGCAAACAGAUCCAGAUACAUGCACACAAGCAUAUAGCCAAACAUA
.....(((((((..(((........)))..)))))))..(((...............((((((........))))))................((((......))))...)))....... ( -31.80)
>DroSec_CAF1 945 119 - 1
GCAACGAGAGCAAUGCGCUCGAGAACGCUCUGCUCUCUCGGCCUCUCCUCUCCCUCCGUCAACACAUGUCCGUGGGCAAACAGAUCCAGAUACAUGCACACAAGCAUAUAGCCA-ACAUA
.....(((((((..(((........)))..)))))))..(((.(((.....(((.(.(.((.....)).).).))).....))).........((((......))))...))).-..... ( -30.10)
>DroSim_CAF1 946 120 - 1
GCAACGAGAGCAAUGCGCUCGAGAACGCUCUGCUCUCUCGGCCUCUCCUCUCCCUCUGUCUACACAUGUCCGUGGGCAAACAGAUCCAGAUACAUGCACACAAGCAUAUAGCCAAACAUA
.....(((((((..(((........)))..)))))))..(((.(((..(((.....(((((((........)))))))...)))...)))...((((......))))...)))....... ( -32.70)
>consensus
GCAACGAGAGCAAUGCGCUCGAGAACGCUCUGCUCUCUCGGCCUCUCCUCUCCCUCCGUCUACACAUGUCCGUGGGCAAACAGAUCCAGAUACAUGCACACAAGCAUAUAGCCAAACAUA
.....(((((((..(((........)))..)))))))..(((...............((((((........))))))................((((......))))...)))....... (-30.33 = -30.67 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,605,569 – 7,605,689
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -43.40
Consensus MFE -41.52
Energy contribution -42.30
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -2.26
Structure conservation index 0.96
SVM decision value 1.15
SVM RNA-class probability 0.922246
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7605569 120 + 27905053
UUUGCCCACGGACAUGUGUAGACGAAGGGAAAGGAGAGGCCGAGAGAGCAGAGCGUUCUCGAGCGCAUUGCUCUCGUUGCAUUCAAUUCUGCCUCUGCUGUAUGUUGUAUUAAUGAAAGU
....(((.((.((....))...))..)))..((.((((((.((((((((((.(((((....))))).))))))))((((....)))))).)))))).))..................... ( -39.60)
>DroSec_CAF1 984 120 + 1
UUUGCCCACGGACAUGUGUUGACGGAGGGAGAGGAGAGGCCGAGAGAGCAGAGCGUUCUCGAGCGCAUUGCUCUCGUUGCAUUCAAUUCUGCCUCUGCUGUAUGUUGUAUUAAUGAAAGU
..........((((((....(.((((((.((((..(((((...((((((((.(((((....))))).))))))))...)).)))..)))).)))))))..)))))).............. ( -43.80)
>DroSim_CAF1 986 120 + 1
UUUGCCCACGGACAUGUGUAGACAGAGGGAGAGGAGAGGCCGAGAGAGCAGAGCGUUCUCGAGCGCAUUGCUCUCGUUGCAUUCAAUUCUGCCUCUGCUGUAUGUUGUAUUAAUGAAAGU
..........((((((..(((.((((((.((((..(((((...((((((((.(((((....))))).))))))))...)).)))..)))).))))))))))))))).............. ( -46.80)
>consensus
UUUGCCCACGGACAUGUGUAGACGGAGGGAGAGGAGAGGCCGAGAGAGCAGAGCGUUCUCGAGCGCAUUGCUCUCGUUGCAUUCAAUUCUGCCUCUGCUGUAUGUUGUAUUAAUGAAAGU
..........((((((..(((.((((((.((((..(((((...((((((((.(((((....))))).))))))))...)).)))..)))).))))))))))))))).............. (-41.52 = -42.30 +   0.78)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,605,569 – 7,605,689
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -34.30
Consensus MFE -33.03
Energy contribution -33.37
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.96
SVM decision value 1.14
SVM RNA-class probability 0.921496
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7605569 120 - 27905053
ACUUUCAUUAAUACAACAUACAGCAGAGGCAGAAUUGAAUGCAACGAGAGCAAUGCGCUCGAGAACGCUCUGCUCUCUCGGCCUCUCCUUUCCCUUCGUCUACACAUGUCCGUGGGCAAA
.....................((.((((((.((.(((....))).(((((((..(((........)))..))))))))).)))))).))........((((((........))))))... ( -34.50)
>DroSec_CAF1 984 120 - 1
ACUUUCAUUAAUACAACAUACAGCAGAGGCAGAAUUGAAUGCAACGAGAGCAAUGCGCUCGAGAACGCUCUGCUCUCUCGGCCUCUCCUCUCCCUCCGUCAACACAUGUCCGUGGGCAAA
......................((.((((.(((...((..((...(((((((..(((........)))..)))))))...)).))...))).)))).)).......((((....)))).. ( -31.90)
>DroSim_CAF1 986 120 - 1
ACUUUCAUUAAUACAACAUACAGCAGAGGCAGAAUUGAAUGCAACGAGAGCAAUGCGCUCGAGAACGCUCUGCUCUCUCGGCCUCUCCUCUCCCUCUGUCUACACAUGUCCGUGGGCAAA
......................(((((((.(((...((..((...(((((((..(((........)))..)))))))...)).))...))).))))))).......((((....)))).. ( -36.50)
>consensus
ACUUUCAUUAAUACAACAUACAGCAGAGGCAGAAUUGAAUGCAACGAGAGCAAUGCGCUCGAGAACGCUCUGCUCUCUCGGCCUCUCCUCUCCCUCCGUCUACACAUGUCCGUGGGCAAA
.....................((.((((((.((.(((....))).(((((((..(((........)))..))))))))).)))))).))........((((((........))))))... (-33.03 = -33.37 +   0.33)

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 10:45:53 2006