Locus 4050

Sequence ID 3R_DroMel_CAF1
Location 11,042,924 – 11,043,284
Length 360
Max. P 0.964502
window6485 window6486 window6487 window6488 window6489

overview

Window 5

Location 11,042,924 – 11,043,044
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -45.64
Consensus MFE -42.38
Energy contribution -43.28
Covariance contribution 0.89
Combinations/Pair 1.05
Mean z-score -1.59
Structure conservation index 0.93
SVM decision value -0.02
SVM RNA-class probability 0.525268
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11042924 120 + 27905053
UUCCCAGGUCCAGGCCAACCAAACGGGCCGAUCGCAAGCGUGUCACAUGCUUGUACGUACUGAUGGCCAACUCUGCCAGCUCCAGGUAGAGCUUCUGGAAGGCUUGAUUCGAGCCCAGGG
..(((...(((((((((......(((..((...(((((((((...))))))))).))..))).)))))..(((((((.......)))))))....)))).((((((...))))))..))) ( -46.90)
>DroSec_CAF1 5673 120 + 1
UUCCCAGGUCCAGACCAACCAAACGGGCGGAUCGCAAGCGUGUCACAUGCUUGUACGUACUGAUGGCCAGUUCUGCCAGCUCCAGGUAUAGCUUCUGAAAGGCUUGAUUCGAGCCCAGGG
..(((.(((....)))........((((((((((((((((((...)))))))))..(((((..((((.......))))......)))))(((((.....))))).)))))..)))).))) ( -40.20)
>DroSim_CAF1 5693 120 + 1
UUCCCAGGUCCAGACCAACCAAACGGGCCGAUCGCAAGCGUGUCACAUGCUUGUACGUACUGAUGGCCAGUUCUGCCAGCUCCAGGUAGAGCUUCUGGAAGGCUUGGUUCGAGCCCAGGG
..(((...((((((...........((((.((((((((((((...))))))))).......)))))))(((((((((.......))))))))))))))).((((((...))))))..))) ( -49.81)
>consensus
UUCCCAGGUCCAGACCAACCAAACGGGCCGAUCGCAAGCGUGUCACAUGCUUGUACGUACUGAUGGCCAGUUCUGCCAGCUCCAGGUAGAGCUUCUGGAAGGCUUGAUUCGAGCCCAGGG
..(((...((((((...........((((.((((((((((((...))))))))).......)))))))(((((((((.......))))))))))))))).((((((...))))))..))) (-42.38 = -43.28 +   0.89)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,043,004 – 11,043,124
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -53.10
Consensus MFE -49.67
Energy contribution -50.00
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.70
Structure conservation index 0.94
SVM decision value 1.57
SVM RNA-class probability 0.964502
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11043004 120 + 27905053
UCCAGGUAGAGCUUCUGGAAGGCUUGAUUCGAGCCCAGGGCUUCCUUAAGCUGCUCAGCCCCCGAUUUCUUGGGCUUACGAUUGGGAGACCGGUCUCGUAGCUGAGGUGUCGCCUGGAGG
(((((((..(((((..(((((.((((.........)))).)))))..))))).((((((.(((((....))))).....((((((....)))))).....)))))).....))))))).. ( -55.80)
>DroSec_CAF1 5753 120 + 1
UCCAGGUAUAGCUUCUGAAAGGCUUGAUUCGAGCCCAGGGCUUCCUUUAGCUGCUCAGCCCCCGAUUUUUUGGGCUUACGAUUGGGAGACCGUUCUCGGAGCUGAGGUGUCGCCUGGAGG
(((((((..((((.(((...((((((...)))))))))))))..((((((((.(..(((((..........)))))...((.(((....))).))..).))))))))....))))))).. ( -48.20)
>DroSim_CAF1 5773 120 + 1
UCCAGGUAGAGCUUCUGGAAGGCUUGGUUCGAGCCCAGGGCUUCCUUCAGCUGCUCAGCCCCCGAUUUUUUGGGCUUACGAUUGGGAGACCGUUCUCGGAGCUGAGGUGUCGCCUGGAGG
(((((((..((((...(((((.(((((.......))))).)))))...)))).((((((.(((((....)))))....(((.(((....)))...)))..)))))).....))))))).. ( -55.30)
>consensus
UCCAGGUAGAGCUUCUGGAAGGCUUGAUUCGAGCCCAGGGCUUCCUUAAGCUGCUCAGCCCCCGAUUUUUUGGGCUUACGAUUGGGAGACCGUUCUCGGAGCUGAGGUGUCGCCUGGAGG
(((((((..((((...(((((.((((.........)))).)))))...)))).((((((.(((((....)))))....(((.(((....)))...)))..)))))).....))))))).. (-49.67 = -50.00 +   0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,043,004 – 11,043,124
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -40.93
Consensus MFE -38.44
Energy contribution -38.00
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.70
Structure conservation index 0.94
SVM decision value 0.24
SVM RNA-class probability 0.649391
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11043004 120 - 27905053
CCUCCAGGCGACACCUCAGCUACGAGACCGGUCUCCCAAUCGUAAGCCCAAGAAAUCGGGGGCUGAGCAGCUUAAGGAAGCCCUGGGCUCGAAUCAAGCCUUCCAGAAGCUCUACCUGGA
..((((((......(((((((..((((....))))...........(((.(....).)))))))))).(((((..(((((.(.(((.......))).).)))))..)))))...)))))) ( -41.60)
>DroSec_CAF1 5753 120 - 1
CCUCCAGGCGACACCUCAGCUCCGAGAACGGUCUCCCAAUCGUAAGCCCAAAAAAUCGGGGGCUGAGCAGCUAAAGGAAGCCCUGGGCUCGAAUCAAGCCUUUCAGAAGCUAUACCUGGA
..((((((......(((((((((((((....)))).....(....)............))))))))).((((..(((....)))(((((.......)))))......))))...)))))) ( -38.50)
>DroSim_CAF1 5773 120 - 1
CCUCCAGGCGACACCUCAGCUCCGAGAACGGUCUCCCAAUCGUAAGCCCAAAAAAUCGGGGGCUGAGCAGCUGAAGGAAGCCCUGGGCUCGAACCAAGCCUUCCAGAAGCUCUACCUGGA
..((((((......(((((((((((((....)))).....(....)............))))))))).((((...(((((.(.(((.......))).).)))))...))))...)))))) ( -42.70)
>consensus
CCUCCAGGCGACACCUCAGCUCCGAGAACGGUCUCCCAAUCGUAAGCCCAAAAAAUCGGGGGCUGAGCAGCUAAAGGAAGCCCUGGGCUCGAAUCAAGCCUUCCAGAAGCUCUACCUGGA
..((((((......(((((((..((((....))))...........(((........)))))))))).((((...(((((.(.(((.......))).).)))))...))))...)))))) (-38.44 = -38.00 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,043,084 – 11,043,204
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -45.73
Consensus MFE -45.77
Energy contribution -46.10
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 1.00
SVM decision value 0.75
SVM RNA-class probability 0.839687
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11043084 120 - 27905053
ACGCCAACUUCGGAGCAGUUGCACAUAGUGGUGCAGCUAUCGUCGGGAAUUGGAGAUGCGCCGUCCGAGCAGCAUCAGUUCCUCCAGGCGACACCUCAGCUACGAGACCGGUCUCCCAAU
..(((...((((.(((((((((((......)))))))).(((((.(((...(((((((((((....).)).)))))...)))))).))))).......))).))))...)))........ ( -41.20)
>DroSec_CAF1 5833 120 - 1
ACGCCAACUUCGGAGCAGUUGCACAUAGUGGUGCAGCUAUCGUCGGGAAUUGGAGAUGCGCCGUCCGAGCAGCAUCAGUUCCUCCAGGCGACACCUCAGCUCCGAGAACGGUCUCCCAAU
..(((...((((((((((((((((......)))))))).(((((.(((...(((((((((((....).)).)))))...)))))).))))).......))))))))...)))........ ( -48.00)
>DroSim_CAF1 5853 120 - 1
ACGCCAACUUCGGAGCAGUUGCACAUCGUGGUGCAGCUAUCGUCGGGAAUUGGAGAUGCGCCGUCCGAGCAGCAUCAGUUCCUCCAGGCGACACCUCAGCUCCGAGAACGGUCUCCCAAU
..(((...((((((((((((((((......)))))))).(((((.(((...(((((((((((....).)).)))))...)))))).))))).......))))))))...)))........ ( -48.00)
>consensus
ACGCCAACUUCGGAGCAGUUGCACAUAGUGGUGCAGCUAUCGUCGGGAAUUGGAGAUGCGCCGUCCGAGCAGCAUCAGUUCCUCCAGGCGACACCUCAGCUCCGAGAACGGUCUCCCAAU
..(((...((((((((((((((((......)))))))).(((((.(((...(((((((((((....).)).)))))...)))))).))))).......))))))))...)))........ (-45.77 = -46.10 +   0.33)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,043,164 – 11,043,284
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -45.50
Consensus MFE -45.50
Energy contribution -45.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 1.00
SVM decision value 0.65
SVM RNA-class probability 0.813081
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11043164 120 - 27905053
AGCACUGUGCUCCCAUCUGGAACUUGGCCAAGGAUAAGCUCUACGAGCUCGGCAAACUGUGUGGCCUCUUGCCCGGCUGCACGCCAACUUCGGAGCAGUUGCACAUAGUGGUGCAGCUAU
........((((((....)(((.(((((....(...(((((...)))))...).....(((..(((........)))..)))))))).))))))))((((((((......)))))))).. ( -45.50)
>DroSec_CAF1 5913 120 - 1
AGCACUGUGCUCCCAUCUGGAACUUGGCCAAGGAUAAGCUCUACGAGCUCGGCAAACUGUGUGGCCUCUUGCCCGGCUGCACGCCAACUUCGGAGCAGUUGCACAUAGUGGUGCAGCUAU
........((((((....)(((.(((((....(...(((((...)))))...).....(((..(((........)))..)))))))).))))))))((((((((......)))))))).. ( -45.50)
>DroSim_CAF1 5933 120 - 1
AGCACUGUGCUCCCAUCUGGAACUUGGCCAAGGAUAAGCUCUACGAGCUCGGCAAACUGUGUGGCCUCUUGCCCGGCUGCACGCCAACUUCGGAGCAGUUGCACAUCGUGGUGCAGCUAU
........((((((....)(((.(((((....(...(((((...)))))...).....(((..(((........)))..)))))))).))))))))((((((((......)))))))).. ( -45.50)
>consensus
AGCACUGUGCUCCCAUCUGGAACUUGGCCAAGGAUAAGCUCUACGAGCUCGGCAAACUGUGUGGCCUCUUGCCCGGCUGCACGCCAACUUCGGAGCAGUUGCACAUAGUGGUGCAGCUAU
........((((((....)(((.(((((....(...(((((...)))))...).....(((..(((........)))..)))))))).))))))))((((((((......)))))))).. (-45.50 = -45.50 +   0.00)

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 11:16:49 2006