Locus 8530

Sequence ID 3L_DroMel_CAF1
Location 22,314,125 – 22,314,405
Length 280
Max. P 0.905468
window13973 window13974 window13975 window13976

overview

Window 3

Location 22,314,125 – 22,314,245
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -33.60
Consensus MFE -28.66
Energy contribution -29.23
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.02
Structure conservation index 0.85
SVM decision value 0.64
SVM RNA-class probability 0.808237
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22314125 120 - 23771897
ACGAAAUACAAAUGUAUCUCUUGCCGGGACUCGGCGUUGGGCGGAAACAAAUGACCCAAAAAUAAUGUUCGAGGACGGAAGUCGCUGGGCAAGACAAACUAUCGGCGAUUAGCUAAGCAA
.(((.((((....)))).(((((((.((.((((((((((((((........)).))))......))).)))))(((....))).)).))))))).......)))((.....))....... ( -35.80)
>DroSec_CAF1 72811 116 - 1
ACGAAAUACAAAUGUAUCUCUUGCCGGGACUCGGCGUUG----GAAACAAAUGACCCAAAAAUAAUGUUCGAGGACGGAAGUCGCUGGGCAAGACAAACUAUCGGCGAUUAGCUAAGCAA
.(((.((((....)))).((((((((((..(((...(((----....))).))))))..............(((((....))).)).))))))).......)))((.....))....... ( -32.30)
>DroEre_CAF1 71169 120 - 1
ACGAAAUACAAAUGUAUCUCUGGCCGGGACUCGGCAUUGGGCGGAAACAAAUGACCCAAAAAUAAUGUUCGAGGACGGAAGUCGCUGGGCAAGACAAACUAUCGGCGAUUAGCUAAGCAA
.(((.((((....)))).(((.(((.((.((((((((((((((........)).))))......))).)))))(((....))).)).))).))).......)))((.....))....... ( -32.10)
>DroYak_CAF1 51308 120 - 1
ACGAAAUACAAAUGUAUCUCUGUCUGGGACUCGGCAUUGAGUGGAAACAAAUGACCCAAAAAUAAUGUUCGAGGACGGAAGUCUCUGGGCAAGACAAACUAUCGGCGAUUAGCUAAGGAA
..((.((((....)))).))(((((((((((((....)))))(....)......)))........((((((..(((....)))..))))))))))).......(((.....)))...... ( -34.20)
>consensus
ACGAAAUACAAAUGUAUCUCUGGCCGGGACUCGGCAUUGGGCGGAAACAAAUGACCCAAAAAUAAUGUUCGAGGACGGAAGUCGCUGGGCAAGACAAACUAUCGGCGAUUAGCUAAGCAA
.(((.((((....)))).(((((((.((.((((((((((...((...........)).....))))).)))))(((....))).)).))))))).......)))((.....))....... (-28.66 = -29.23 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,314,165 – 22,314,285
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.17
Mean single sequence MFE -35.23
Consensus MFE -31.06
Energy contribution -31.62
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.60
Structure conservation index 0.88
SVM decision value 0.30
SVM RNA-class probability 0.678369
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22314165 120 + 23771897
UUCCGUCCUCGAACAUUAUUUUUGGGUCAUUUGUUUCCGCCCAACGCCGAGUCCCGGCAAGAGAUACAUUUGUAUUUCGUGCUAAUCCUUUCUGGUGGAAAUAGAGAUGUGGCUCGGCGA
.....................((((((...........))))))(((((((((.(((((.(((((((....))))))).))))..(((........))).........).))))))))). ( -38.80)
>DroSec_CAF1 72851 116 + 1
UUCCGUCCUCGAACAUUAUUUUUGGGUCAUUUGUUUC----CAACGCCGAGUCCCGGCAAGAGAUACAUUUGUAUUUCGUGCUAAUCCUUUCUGGUGGAAAUAGAGCUGUGGCUCGGCGA
....(.(((.(((......))).))).).........----...(((((((((.((((..(((((((....)))))))...(((.(((........)))..))).)))).))))))))). ( -38.60)
>DroEre_CAF1 71209 120 + 1
UUCCGUCCUCGAACAUUAUUUUUGGGUCAUUUGUUUCCGCCCAAUGCCGAGUCCCGGCCAGAGAUACAUUUGUAUUUCGUGCUAAUCCUUUCUGCUGCAAAUAGAGCUGUGGCUCGCCGA
........(((..........((((((...........))))))...((((((.(((((.(((((((....))))))).(((..............)))....).)))).)))))).))) ( -30.04)
>DroYak_CAF1 51348 120 + 1
UUCCGUCCUCGAACAUUAUUUUUGGGUCAUUUGUUUCCACUCAAUGCCGAGUCCCAGACAGAGAUACAUUUGUAUUUCGUGCUAAUCCUUUCUGGUGGAAAUAGAGCUGUGGCUCGGCGA
....(.(((.(((......))).))).)................(((((((((.(((.(.(((((((....)))))))...(((.(((........)))..))).)))).))))))))). ( -33.50)
>consensus
UUCCGUCCUCGAACAUUAUUUUUGGGUCAUUUGUUUCCGCCCAACGCCGAGUCCCGGCAAGAGAUACAUUUGUAUUUCGUGCUAAUCCUUUCUGGUGGAAAUAGAGCUGUGGCUCGGCGA
....(.(((.(((......))).))).)................(((((((((.((((..(((((((....)))))))...(((.(((........)))..))).)))).))))))))). (-31.06 = -31.62 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,314,205 – 22,314,325
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.19
Mean single sequence MFE -44.64
Consensus MFE -37.12
Energy contribution -38.25
Covariance contribution 1.12
Combinations/Pair 1.08
Mean z-score -2.28
Structure conservation index 0.83
SVM decision value 1.04
SVM RNA-class probability 0.905468
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22314205 120 + 23771897
CCAACGCCGAGUCCCGGCAAGAGAUACAUUUGUAUUUCGUGCUAAUCCUUUCUGGUGGAAAUAGAGAUGUGGCUCGGCGAGCGGUCUCAUCCAUCAGGGCAACCUCAACGGGGGGAUUAG
...((((((.....))))..(((((((....))))))))).((((((((..((((((((....(((((...((((...)))).))))).)))))))((....)).....)..)))))))) ( -48.20)
>DroSec_CAF1 72888 119 + 1
-CAACGCCGAGUCCCGGCAAGAGAUACAUUUGUAUUUCGUGCUAAUCCUUUCUGGUGGAAAUAGAGCUGUGGCUCGGCGAGCGGUCUCAUCCAUCAGGGCAACCUCAACGGGGGGAUUAG
-..((((((.....))))..(((((((....))))))))).((((((((..((((((((....((((....))))(((.....)))...)))))))((....)).....)..)))))))) ( -48.60)
>DroEre_CAF1 71249 120 + 1
CCAAUGCCGAGUCCCGGCCAGAGAUACAUUUGUAUUUCGUGCUAAUCCUUUCUGCUGCAAAUAGAGCUGUGGCUCGCCGAGCGGUCUCAUCCAUCAGCGCAACCUCAACGGGCGGAUUAU
......(((...((((....(((((((....)))))))(((((..........(((((.....((((....)))).....)))))..........)))))........)))))))..... ( -35.85)
>DroYak_CAF1 51388 119 + 1
UCAAUGCCGAGUCCCAGACAGAGAUACAUUUGUAUUUCGUGCUAAUCCUUUCUGGUGGAAAUAGAGCUGUGGCUCGGCGAGCGGUCCCAUCCAUUAGGGCAACC-CAACGGGGGGAUUAG
....(((((((((.(((.(.(((((((....)))))))...(((.(((........)))..))).)))).)))))))))...((((((.(((.((.((....))-.)).))))))))).. ( -45.90)
>consensus
CCAACGCCGAGUCCCGGCAAGAGAUACAUUUGUAUUUCGUGCUAAUCCUUUCUGGUGGAAAUAGAGCUGUGGCUCGGCGAGCGGUCUCAUCCAUCAGGGCAACCUCAACGGGGGGAUUAG
....(((((((((.((((..(((((((....)))))))...(((.(((........)))..))).)))).)))))))))...((((((.(((...(((....)))....))))))))).. (-37.12 = -38.25 +   1.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,314,285 – 22,314,405
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.22
Mean single sequence MFE -38.56
Consensus MFE -31.14
Energy contribution -32.95
Covariance contribution 1.81
Combinations/Pair 1.03
Mean z-score -1.70
Structure conservation index 0.81
SVM decision value 0.27
SVM RNA-class probability 0.659913
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22314285 120 - 23771897
AUAAUCAUUUUCAAAUGCAUCCUUAGAUGGCACAAACUUCUACCGUUGUCAGUCAGGGAAGAAGUUUAUCGGGGGCCAAACUAAUCCCCCCGUUGAGGUUGCCCUGAUGGAUGAGACCGC
.................(((((...((..((.............))..)).(((((((...((.((((.((((((...........)))))).)))).)).))))))))))))....... ( -36.52)
>DroSec_CAF1 72967 120 - 1
AUAAUCAUUUUCAAAUGCAUCCUUAGACGGCACAAACUUCUGCCGUUGUCAGUCAGGGAAGCAGUUUAUCGGGGGCCAAACUAAUCCCCCCGUUGAGGUUGCCCUGAUGGAUGAGACCGC
.................(((((...(((((((........)))))))....(((((((.(((...(((.((((((...........)))))).))).))).))))))))))))....... ( -42.40)
>DroEre_CAF1 71329 120 - 1
AUAAUCAUUUUCAAAUGCAUCCCCAGACGGCACAAACCUCUGCCGCUGUCAGUCAGGGAAGCAGUUUAUCGGGGGCUAAAAUAAUCCGCCCGUUGAGGUUGCGCUGAUGGAUGAGACCGC
........((((...(((.(((((((.(((((........)))))))).......)))).)))(((((((((((((...........))))((.......)).))))))))))))).... ( -35.11)
>DroYak_CAF1 51468 119 - 1
AUAAUGAUUUUCAAAUGCAUCCUCAGACGGCACAAAUUUCUGCCGUUGUCAGUCAGGGCAGCAGUUUAUAGGGGGCUAAACUAAUCCCCCCGUUG-GGUUGCCCUAAUGGAUGGGACCGC
...............(.(((((...(((((((........))))))).......((((((((.....(..(((((..........)))))..)..-.))))))))...))))).)..... ( -40.20)
>consensus
AUAAUCAUUUUCAAAUGCAUCCUCAGACGGCACAAACUUCUGCCGUUGUCAGUCAGGGAAGCAGUUUAUCGGGGGCCAAACUAAUCCCCCCGUUGAGGUUGCCCUGAUGGAUGAGACCGC
.................(((((...(((((((........)))))))....(((((((.(((...(((.((((((...........)))))).))).))).))))))))))))....... (-31.14 = -32.95 +   1.81)

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 13:18:13 2006