Locus 1617

Sequence ID 2L_DroMel_CAF1
Location 4,345,094 – 4,345,263
Length 169
Max. P 0.972402
window2595 window2596 window2597 window2598

overview

Window 5

Location 4,345,094 – 4,345,184
Length 90
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 93.96
Mean single sequence MFE -26.38
Consensus MFE -22.10
Energy contribution -21.98
Covariance contribution -0.13
Combinations/Pair 1.09
Mean z-score -2.28
Structure conservation index 0.84
SVM decision value 0.98
SVM RNA-class probability 0.893967
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4345094 90 + 22407834
CAGCAGCGUGCAAUCAAACGGAAGUUAGGGCGAGCGUGUAAAGCGGAAACGGAAAC--AGAAAUCAUUCCCUUGUGAUAGCAAGCGGUGCAG
..(((.(((((.(((((((....)))((((...((.......))(....)(....)--..........))))..)))).))..))).))).. ( -26.20)
>DroSec_CAF1 13835 90 + 1
ACGCAGCGUGCAAUCAAACGGAAGUUAGGGCGAGCGUGGAAAGCGGAAACGGAAAC--AGAAAUCAUUCCCUUGUGAUAGAAAGCGGUGCAG
..(((.(((.(.(((.(((....)))...(((((...((((...(....)(....)--........)))))))))))).)...))).))).. ( -25.80)
>DroSim_CAF1 14588 90 + 1
ACGCAGCGUGCAAUCAAACGGAAGUUAGGGCGAGCGUGGAAAGCGGAAACGGAAAC--AGAAAUCAUUCCCUUGUGAUAGAAAGCGGUGCAG
..(((.(((.(.(((.(((....)))...(((((...((((...(....)(....)--........)))))))))))).)...))).))).. ( -25.80)
>DroYak_CAF1 14398 92 + 1
ACGCAGCGUGCAAACAAACGGAAGUUGGGGCGAGUGUGGAAAGCGGAAACGGAAACGAAGGAAACAUUCCCUUGUGAUAGAAAGCGGUGCAG
..(((.(((((...(.(((....))).).))...(((.(.(((.((((.((....))..(....).))))))).).)))....))).))).. ( -27.70)
>consensus
ACGCAGCGUGCAAUCAAACGGAAGUUAGGGCGAGCGUGGAAAGCGGAAACGGAAAC__AGAAAUCAUUCCCUUGUGAUAGAAAGCGGUGCAG
..(((.(((.(.(((((((....)))((((...((.......))(....)(....)............))))..)))).)...))).))).. (-22.10 = -21.98 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,345,134 – 4,345,224
Length 90
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 95.05
Mean single sequence MFE -30.77
Consensus MFE -27.12
Energy contribution -27.62
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.98
Structure conservation index 0.88
SVM decision value 1.69
SVM RNA-class probability 0.972402
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4345134 90 + 22407834
AAGCGGAAACGGAAAC--AGAAAUCAUUCCCUUGUGAUAGCAAGCGGUGCAGUCCGGGCUGGAGAAUCCACAUACCGGACGGGAAAGGUAGA
...((....)).....--....(((.(((((........(((.....))).((((((..(((.....)))....))))))))))).)))... ( -29.70)
>DroSec_CAF1 13875 90 + 1
AAGCGGAAACGGAAAC--AGAAAUCAUUCCCUUGUGAUAGAAAGCGGUGCAGUCCGGGCUGGGGAAUCCACAUCCCGGACGGGAAAGGUAGA
...((....)).....--....(((.(((((((((........))))....(((((((.((((....)).)).)))))))))))).)))... ( -30.80)
>DroSim_CAF1 14628 90 + 1
AAGCGGAAACGGAAAC--AGAAAUCAUUCCCUUGUGAUAGAAAGCGGUGCAGUCCGGGCUGGGGAAUCCACAUCCCGGACGGGAAAGGUAGA
...((....)).....--....(((.(((((((((........))))....(((((((.((((....)).)).)))))))))))).)))... ( -30.80)
>DroYak_CAF1 14438 92 + 1
AAGCGGAAACGGAAACGAAGGAAACAUUCCCUUGUGAUAGAAAGCGGUGCAGUCCGGGCUGGGAAAUCCAGAUCCCGGACGGGAAAGGUAGA
.........((....))..(....).(((((((((........))))....(((((((((((.....))))..))))))))))))....... ( -31.80)
>consensus
AAGCGGAAACGGAAAC__AGAAAUCAUUCCCUUGUGAUAGAAAGCGGUGCAGUCCGGGCUGGGGAAUCCACAUCCCGGACGGGAAAGGUAGA
...((....))...........(((.(((((.((((...(....)..))))(((((((.(((.....)))...)))))))))))).)))... (-27.12 = -27.62 +   0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,345,134 – 4,345,224
Length 90
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 95.05
Mean single sequence MFE -24.45
Consensus MFE -22.38
Energy contribution -22.62
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.92
SVM decision value 1.07
SVM RNA-class probability 0.909457
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4345134 90 - 22407834
UCUACCUUUCCCGUCCGGUAUGUGGAUUCUCCAGCCCGGACUGCACCGCUUGCUAUCACAAGGGAAUGAUUUCU--GUUUCCGUUUCCGCUU
.......(((((((((((....(((.....)))..)))))).(((.....)))........)))))........--................ ( -22.10)
>DroSec_CAF1 13875 90 - 1
UCUACCUUUCCCGUCCGGGAUGUGGAUUCCCCAGCCCGGACUGCACCGCUUUCUAUCACAAGGGAAUGAUUUCU--GUUUCCGUUUCCGCUU
............(((((((.((.((....)))).)))))))....................(((((((......--.....))))))).... ( -24.70)
>DroSim_CAF1 14628 90 - 1
UCUACCUUUCCCGUCCGGGAUGUGGAUUCCCCAGCCCGGACUGCACCGCUUUCUAUCACAAGGGAAUGAUUUCU--GUUUCCGUUUCCGCUU
............(((((((.((.((....)))).)))))))....................(((((((......--.....))))))).... ( -24.70)
>DroYak_CAF1 14438 92 - 1
UCUACCUUUCCCGUCCGGGAUCUGGAUUUCCCAGCCCGGACUGCACCGCUUUCUAUCACAAGGGAAUGUUUCCUUCGUUUCCGUUUCCGCUU
............(((((((..((((.....)))))))))))....................(((((((.......))))))).......... ( -26.30)
>consensus
UCUACCUUUCCCGUCCGGGAUGUGGAUUCCCCAGCCCGGACUGCACCGCUUUCUAUCACAAGGGAAUGAUUUCU__GUUUCCGUUUCCGCUU
.......((((((((((((...(((.....))).))))))).((...))............))))).......................... (-22.38 = -22.62 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,345,146 – 4,345,263
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.43
Mean single sequence MFE -34.32
Consensus MFE -28.52
Energy contribution -28.76
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.49
Structure conservation index 0.83
SVM decision value 0.43
SVM RNA-class probability 0.732114
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4345146 117 + 22407834
AAAC--AGAAAUCAUUCCCUUGUGAUAGCAAGCGGUGCAGUCCGGGCUGGAGAAUCCACAUACCGGACGGGAAAGGUAGAACCAAC-AAAUCGGAGAAGGGAACCUGGCCAACUGGUGAU
...(--((..(((.(((((........(((.....))).((((((..(((.....)))....))))))))))).))).........-.....((...(((...)))..))..)))..... ( -33.20)
>DroSec_CAF1 13887 118 + 1
AAAC--AGAAAUCAUUCCCUUGUGAUAGAAAGCGGUGCAGUCCGGGCUGGGGAAUCCACAUCCCGGACGGGAAAGGUAGAACCAAAAAAAUCGUAGAAGGGAACCUGGCCAACUGGUGAU
....--....(((.(((((((.((...((..........(((((((.((((....)).)).)))))))......((.....)).......)).)).)))))))....(((....)))))) ( -34.50)
>DroSim_CAF1 14640 118 + 1
AAAC--AGAAAUCAUUCCCUUGUGAUAGAAAGCGGUGCAGUCCGGGCUGGGGAAUCCACAUCCCGGACGGGAAAGGUAGAACCAAAAAAAUCGGAGAAGGGAACCUGGCCAACUGGUGAU
...(--((..(((.(((((((((........))))....(((((((.((((....)).)).)))))))))))).)))...............((...(((...)))..))..)))..... ( -34.30)
>DroEre_CAF1 14157 117 + 1
AAAC--AGAAAUCAUUCCCUUGUGAUAGAAAGCGGUGCAGUCCGGGCUGGGAAAUCCACAUCCCGGACAGGAAAGGUAGAACCAAC-AAAUCGGAGAAGGGAACCUGGCCAACUGGUGAU
....--....(((((......)))))......((((...(((((((.((((....)).)).))))))).((..((((....((..(-........)..))..))))..)).))))..... ( -34.30)
>DroYak_CAF1 14450 119 + 1
AAACGAAGGAAACAUUCCCUUGUGAUAGAAAGCGGUGCAGUCCGGGCUGGGAAAUCCAGAUCCCGGACGGGAAAGGUAGAAGCAAC-AAGUCGGAGAAGGGAACCUGGCCAACUGGUGAU
.......(....).(((((((((........))))....(((((((((((.....))))..)))))))))))).........((..-.(((.((...(((...)))..)).)))..)).. ( -35.30)
>consensus
AAAC__AGAAAUCAUUCCCUUGUGAUAGAAAGCGGUGCAGUCCGGGCUGGGGAAUCCACAUCCCGGACGGGAAAGGUAGAACCAAC_AAAUCGGAGAAGGGAACCUGGCCAACUGGUGAU
..............(((((((.((((.............(((((((.(((.....)))...)))))))......((.....))......))))...)))))))....(((....)))... (-28.52 = -28.76 +   0.24)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:48 2006