Locus 3959

Sequence ID X_DroMel_CAF1
Location 10,517,989 – 10,518,149
Length 160
Max. P 0.962496
window6502 window6503 window6504 window6505

overview

Window 2

Location 10,517,989 – 10,518,109
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.75
Mean single sequence MFE -37.17
Consensus MFE -27.94
Energy contribution -28.10
Covariance contribution 0.16
Combinations/Pair 1.15
Mean z-score -1.95
Structure conservation index 0.75
SVM decision value 0.46
SVM RNA-class probability 0.746633
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10517989 120 + 22224390
UAUUCCGUGGCAGUUAAUAUACACUACUGAAAUAUCCAGUUGCAAAGCCGCCUCAUAAACGGUGGCCAUAUGGCUUCCCCAAACGGCGACACUUACAAACGGCACACGUUCGGUGGCCAA
..(((.((((..((......)).)))).))).......(((((...((((((........))))))....(((.....)))....)))))..........(((.(((.....)))))).. ( -31.90)
>DroSec_CAF1 49524 120 + 1
UAUUCCGUGGCAGUUGAUAUACACUACUGAGAUAUCCAAUUGCAAAGCCGCCUCAUAAACGGUGGCCAUAUGGUUUCCCCAAACGGCGACACUUACAAAUGGUACACGUUCGGUGGCCAA
.........(((((((((((.(.(....).))))).)))))))...((((((.....((((...(((((..(((.((.((....)).)).))).....)))))...)))).))))))... ( -32.40)
>DroSim_CAF1 53048 120 + 1
UAUUCCGUGGCAGUUGAUAUACACUACUGAGAUAUCCAAUUGCAAAGCCGCCUCAUAAACGGUGGCCAUAUGGCUUCCCCAAACGGCGACACUUACAAAUGGCACACGUUCGGUGGCCAA
......((((((((((((((.(.(....).))))).))))))).....((((........((.((((....)))).))......)))).))).......((((.(((.....))))))). ( -34.94)
>DroEre_CAF1 51470 120 + 1
UAUGCCCUGGCAGUUGAUAUACACUACUGAGAUAUCCAGAUGCAAAGCCGCCUCAUAAACGUUGGCCAUUUGGCUGCCCCAAAUGGCGGCACUUACAAAUGGCACACGUUCGGUGGCCAA
..(((.((((((((...........))))......))))..)))..((((((.....(((((..((((((((..((((((....)).))))....))))))))..))))).))))))... ( -42.50)
>DroYak_CAF1 50943 120 + 1
UAUUCCCUGGCAGUUGAUGUAGACCACCGAGAUGUCCAGCUGCAAUGCCGCCUCAUAAACGGUGGCCAUUUGCCUGCCCCAAAUGGCGGCACUUACAAAUGGCACACGUUCGGUGGCCAA
.......((((.(((......)))(((((((.((((((...((((.((((((........))))))...)))).((((((....)).))))........))).)))..))))))))))). ( -44.10)
>consensus
UAUUCCGUGGCAGUUGAUAUACACUACUGAGAUAUCCAGUUGCAAAGCCGCCUCAUAAACGGUGGCCAUAUGGCUUCCCCAAACGGCGACACUUACAAAUGGCACACGUUCGGUGGCCAA
.........(((((((((((...(....)..)))).)))))))...((((((.....((((...(((((.((...((.((....)).))......)).)))))...)))).))))))... (-27.94 = -28.10 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,517,989 – 10,518,109
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.75
Mean single sequence MFE -41.34
Consensus MFE -32.12
Energy contribution -32.28
Covariance contribution 0.16
Combinations/Pair 1.14
Mean z-score -1.64
Structure conservation index 0.78
SVM decision value 0.30
SVM RNA-class probability 0.679940
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10517989 120 - 22224390
UUGGCCACCGAACGUGUGCCGUUUGUAAGUGUCGCCGUUUGGGGAAGCCAUAUGGCCACCGUUUAUGAGGCGGCUUUGCAACUGGAUAUUUCAGUAGUGUAUAUUAACUGCCACGGAAUA
.(((((((((((((.(((.((........)).))))))))))((...))...))))))((((......(((((...((((((((((...))))))..))))......))))))))).... ( -37.60)
>DroSec_CAF1 49524 120 - 1
UUGGCCACCGAACGUGUACCAUUUGUAAGUGUCGCCGUUUGGGGAAACCAUAUGGCCACCGUUUAUGAGGCGGCUUUGCAAUUGGAUAUCUCAGUAGUGUAUAUCAACUGCCACGGAAUA
.((((((.((((((.((..((((....))))..))))))))((....))...))))))((((...(((((...((........))...)))))(((((........))))).)))).... ( -38.40)
>DroSim_CAF1 53048 120 - 1
UUGGCCACCGAACGUGUGCCAUUUGUAAGUGUCGCCGUUUGGGGAAGCCAUAUGGCCACCGUUUAUGAGGCGGCUUUGCAAUUGGAUAUCUCAGUAGUGUAUAUCAACUGCCACGGAAUA
((((...)))).((((..(((.(((((((.((((((....(.((..(((....)))..)).)......))))))))))))).)))........(((((........)))))))))..... ( -38.40)
>DroEre_CAF1 51470 120 - 1
UUGGCCACCGAACGUGUGCCAUUUGUAAGUGCCGCCAUUUGGGGCAGCCAAAUGGCCAACGUUUAUGAGGCGGCUUUGCAUCUGGAUAUCUCAGUAGUGUAUAUCAACUGCCAGGGCAUA
...(((...((((((..((((((((....((((.((....))))))..))))))))..))))))....(((((...(((((((((.....))))..)))))......)))))..)))... ( -43.40)
>DroYak_CAF1 50943 120 - 1
UUGGCCACCGAACGUGUGCCAUUUGUAAGUGCCGCCAUUUGGGGCAGGCAAAUGGCCACCGUUUAUGAGGCGGCAUUGCAGCUGGACAUCUCGGUGGUCUACAUCAACUGCCAGGGAAUA
..(((((((((..((((.(((.((((((.(((((((((..(.((..(((.....))).)).)..))..))))))))))))).))))))).)))))))))..................... ( -48.90)
>consensus
UUGGCCACCGAACGUGUGCCAUUUGUAAGUGUCGCCGUUUGGGGAAGCCAUAUGGCCACCGUUUAUGAGGCGGCUUUGCAACUGGAUAUCUCAGUAGUGUAUAUCAACUGCCACGGAAUA
.......((((..((((.(((.(((((((.((((((....(.((..(((....)))..)).)......))))))))))))).))))))).)).(((((........)))))...)).... (-32.12 = -32.28 +   0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,518,029 – 10,518,149
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.67
Mean single sequence MFE -42.98
Consensus MFE -35.18
Energy contribution -35.50
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -2.02
Structure conservation index 0.82
SVM decision value 1.54
SVM RNA-class probability 0.962496
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10518029 120 + 22224390
UGCAAAGCCGCCUCAUAAACGGUGGCCAUAUGGCUUCCCCAAACGGCGACACUUACAAACGGCACACGUUCGGUGGCCAAAAGACGGGGUAAUUCGGUUGCAUUGCGAAAAGUGUGCAAA
(((((.((((((........))))))....((..((((((....(....)..........(((.(((.....)))))).......)))).))..)).)))))(((((.......))))). ( -35.50)
>DroSec_CAF1 49564 120 + 1
UGCAAAGCCGCCUCAUAAACGGUGGCCAUAUGGUUUCCCCAAACGGCGACACUUACAAAUGGUACACGUUCGGUGGCCAAAAGACGGGGUAAUUCGGUGGCAUUGCGAAAUGUGUGCAAA
......((((((........))))))(((..(((.((.((....)).)).))).....)))(((((((((((...((((.....((((....)))).))))....)).)))))))))... ( -35.60)
>DroSim_CAF1 53088 120 + 1
UGCAAAGCCGCCUCAUAAACGGUGGCCAUAUGGCUUCCCCAAACGGCGACACUUACAAAUGGCACACGUUCGGUGGCCAAAAGACGGGGUAAUUCGGUGGCAUUGCGAAAUGUGUGCAAA
.((((.((((((...........((((....)))).((((....(....).........((((.(((.....)))))))......))))......)))))).)))).............. ( -40.10)
>DroEre_CAF1 51510 120 + 1
UGCAAAGCCGCCUCAUAAACGUUGGCCAUUUGGCUGCCCCAAAUGGCGGCACUUACAAAUGGCACACGUUCGGUGGCCAAAAGGCGGGGUAAUUCGGCGGCAGUGCGGAAAGUGUGCAAA
.(((..((((((.(((.(((((..((((((((..((((((....)).))))....))))))))..)))))..)))(((....)))..........))))))..))).............. ( -49.90)
>DroYak_CAF1 50983 120 + 1
UGCAAUGCCGCCUCAUAAACGGUGGCCAUUUGCCUGCCCCAAAUGGCGGCACUUACAAAUGGCACACGUUCGGUGGCCAAGAGGCGGGGUAACUCGGUGGCAUUGCGAAAAGUGUGCAUA
.(((((((((((.(((.((((...((((((((..((((((....)).))))....))))))))...))))..)))(((....)))(((....)))))))))))))).............. ( -53.80)
>consensus
UGCAAAGCCGCCUCAUAAACGGUGGCCAUAUGGCUUCCCCAAACGGCGACACUUACAAAUGGCACACGUUCGGUGGCCAAAAGACGGGGUAAUUCGGUGGCAUUGCGAAAAGUGUGCAAA
.((((.((((((...........((((....)))).((((....(....).........((((.(((.....)))))))......))))......)))))).)))).............. (-35.18 = -35.50 +   0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,518,029 – 10,518,149
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.67
Mean single sequence MFE -42.62
Consensus MFE -33.02
Energy contribution -33.46
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -2.11
Structure conservation index 0.77
SVM decision value 0.96
SVM RNA-class probability 0.890209
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10518029 120 - 22224390
UUUGCACACUUUUCGCAAUGCAACCGAAUUACCCCGUCUUUUGGCCACCGAACGUGUGCCGUUUGUAAGUGUCGCCGUUUGGGGAAGCCAUAUGGCCACCGUUUAUGAGGCGGCUUUGCA
...((((((..((((...((...(((((..((...))..))))).)).)))).))))))....((((((.((((((....(.((..(((....)))..)).)......)))))))))))) ( -35.20)
>DroSec_CAF1 49564 120 - 1
UUUGCACACAUUUCGCAAUGCCACCGAAUUACCCCGUCUUUUGGCCACCGAACGUGUACCAUUUGUAAGUGUCGCCGUUUGGGGAAACCAUAUGGCCACCGUUUAUGAGGCGGCUUUGCA
..............((((.(((.((..((.....((.....((((((.((((((.((..((((....))))..))))))))((....))...)))))).))...))..)).))).)))). ( -37.60)
>DroSim_CAF1 53088 120 - 1
UUUGCACACAUUUCGCAAUGCCACCGAAUUACCCCGUCUUUUGGCCACCGAACGUGUGCCAUUUGUAAGUGUCGCCGUUUGGGGAAGCCAUAUGGCCACCGUUUAUGAGGCGGCUUUGCA
..............((((.(((..((((..((...))..))))(((.(((((((.(((.((((....)))).))))))))))((..(((....)))..))........)))))).)))). ( -39.10)
>DroEre_CAF1 51510 120 - 1
UUUGCACACUUUCCGCACUGCCGCCGAAUUACCCCGCCUUUUGGCCACCGAACGUGUGCCAUUUGUAAGUGCCGCCAUUUGGGGCAGCCAAAUGGCCAACGUUUAUGAGGCGGCUUUGCA
..............(((..((((((..........(((....)))....((((((..((((((((....((((.((....))))))..))))))))..))))))....))))))..))). ( -49.30)
>DroYak_CAF1 50983 120 - 1
UAUGCACACUUUUCGCAAUGCCACCGAGUUACCCCGCCUCUUGGCCACCGAACGUGUGCCAUUUGUAAGUGCCGCCAUUUGGGGCAGGCAAAUGGCCACCGUUUAUGAGGCGGCAUUGCA
..............((((((((.((..........(((....)))....(((((((.(((((((((...((((.((....)))))).))))))))))).)))))....)).)))))))). ( -51.90)
>consensus
UUUGCACACUUUUCGCAAUGCCACCGAAUUACCCCGUCUUUUGGCCACCGAACGUGUGCCAUUUGUAAGUGUCGCCGUUUGGGGAAGCCAUAUGGCCACCGUUUAUGAGGCGGCUUUGCA
..............((((.(((...(........)(((((.(((((((((((((.(((.((((....)))).))))))))))(.....)...))))))........)))))))).)))). (-33.02 = -33.46 +   0.44)

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 11:12:49 2006