Locus 183

Sequence ID 3R_DroMel_CAF1
Location 843,309 – 843,668
Length 359
Max. P 0.945983
window303 window304 window305 window306 window307

overview

Window 3

Location 843,309 – 843,429
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.75
Mean single sequence MFE -33.48
Consensus MFE -29.75
Energy contribution -30.00
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.89
SVM decision value 0.11
SVM RNA-class probability 0.588221
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 843309 120 - 27905053
AGACAUGACUGUAACUUUGUCGUGGCUGCCACUUCCACUUCCUUUUCCUCCUCCACUUGCGAUUCCCCUACGUCCUGGCAGCCAUGUCCUCAUUGAGCUGUUCGCCUAAGUGGGCGACUG
.(((..(((.........)))((((((((((..............(((..........).)).............))))))))))))).............((((((....))))))... ( -29.63)
>DroSec_CAF1 19083 120 - 1
AGACAUGGCUGUAACUUUGUCGUGGCUGCCACUUCCACCUCCUUUUCCCCCGCCACUGGCAAUUCCCCUACGUCCUGGCAGCCAUGUCCUCAUUGAGCUGUUCGCCUAAGUGGGCGACUG
.((((((((((.....((((((((((.........................))))).)))))....((........)))))))))))).............((((((....))))))... ( -37.91)
>DroSim_CAF1 18296 120 - 1
AGACAUGGCUGUAACUUUGUCGUGGCUGCCACUUCCACCUCCUUUUCCCCCGCCACUUGCAAUUCCCCUACGUCCUGGCAGCCAUGUCCUCAUUGAGCUGUUCGCCUAAGUGGGCGACUG
.((((((((((.....((((.(((((.........................)))))..))))....((........)))))))))))).............((((((....))))))... ( -34.81)
>DroEre_CAF1 20031 104 - 1
AGACAUGGCUGUAACUUUGUCGUGGCUGCCACUUCCACUUCCUCCUCCAC----------------CUUCCGUCUUGGCAGCCAUGUCCUCAUUGAGCUGUUCGCCUAAGUGGGCGACUG
....((((((.(((....(.(((((((((((...................----------------.........))))))))))).)....)))))))))((((((....))))))... ( -31.59)
>consensus
AGACAUGGCUGUAACUUUGUCGUGGCUGCCACUUCCACCUCCUUUUCCCCCGCCACUUGCAAUUCCCCUACGUCCUGGCAGCCAUGUCCUCAUUGAGCUGUUCGCCUAAGUGGGCGACUG
.((((.((......)).))))((((((((((............................................))))))))))(((((((((..((.....))...)))))).))).. (-29.75 = -30.00 +   0.25)

alignment

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secondary structure

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Window 4

Location 843,389 – 843,509
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.86
Mean single sequence MFE -38.55
Consensus MFE -33.86
Energy contribution -34.17
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.42
Structure conservation index 0.88
SVM decision value 1.36
SVM RNA-class probability 0.945983
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 843389 120 + 27905053
AAGUGGAAGUGGCAGCCACGACAAAGUUACAGUCAUGUCUUGGCUCUUGGCAAACAAACCCAUGUCGUCAUCAUGGAAAUGGCCAUAAGAAGUUUCCACAAACGCACACAUCCUGCCAUU
..((((((((((((((((.((((............)))).)))))..............(((((.......))))).....))))).......))))))....(((.......))).... ( -31.01)
>DroSec_CAF1 19163 120 + 1
AGGUGGAAGUGGCAGCCACGACAAAGUUACAGCCAUGUCUUGGCUCUUGGCAAACAAACCCAUGUCGUCAUCAUGGGAGUGGCCAUAAGAAGUUUCCACAAAGGCACACAUCCUGCCAUU
..((((((((((((((((.((((..((....))..)))).))))).........((..((((((.......))))))..))))))).......))))))...((((.......))))... ( -41.81)
>DroSim_CAF1 18376 120 + 1
AGGUGGAAGUGGCAGCCACGACAAAGUUACAGCCAUGUCUUGGCUCUUGGCAAACAAACCCAUGUCGUCAUCAUGGGAGUGGCCAUAAGAAGUUUCCACAAACGCACACAUCCUGCCAUU
.((((((.(((((.(((((......((((.(((((.....)))))..)))).......((((((.......)))))).)))))........((((....)))))).))).))).)))... ( -41.90)
>DroEre_CAF1 20095 120 + 1
AAGUGGAAGUGGCAGCCACGACAAAGUUACAGCCAUGUCUUGGCUCUUGGCAAACAAGCCCAUGUCGUCAUCCUGGGAGUGGCCACAAGAAGUUUCCCCGAACGCACACUUCCUUCCAUU
....(((((((((.(((((((((.......(((((.....)))))...(((......)))..))))....((....)))))))........((((....)))))).)))))))....... ( -39.50)
>consensus
AAGUGGAAGUGGCAGCCACGACAAAGUUACAGCCAUGUCUUGGCUCUUGGCAAACAAACCCAUGUCGUCAUCAUGGGAGUGGCCAUAAGAAGUUUCCACAAACGCACACAUCCUGCCAUU
....(((.(((((.((((.((((..((....))..)))).))))(((((((...((..((((((.......))))))..))))))..))).............)).))).)))....... (-33.86 = -34.17 +   0.31)

alignment

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secondary structure

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Window 5

Location 843,389 – 843,509
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.86
Mean single sequence MFE -39.70
Consensus MFE -36.44
Energy contribution -36.75
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -1.39
Structure conservation index 0.92
SVM decision value -0.03
SVM RNA-class probability 0.516041
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 843389 120 - 27905053
AAUGGCAGGAUGUGUGCGUUUGUGGAAACUUCUUAUGGCCAUUUCCAUGAUGACGACAUGGGUUUGUUUGCCAAGAGCCAAGACAUGACUGUAACUUUGUCGUGGCUGCCACUUCCACUU
.......(((.(((.((......(....)......((((((..((((((.......))))))..))...))))..(((((.((((............)))).)))))))))).))).... ( -35.90)
>DroSec_CAF1 19163 120 - 1
AAUGGCAGGAUGUGUGCCUUUGUGGAAACUUCUUAUGGCCACUCCCAUGAUGACGACAUGGGUUUGUUUGCCAAGAGCCAAGACAUGGCUGUAACUUUGUCGUGGCUGCCACUUCCACCU
...((((.......))))...((((((........((((((..((((((.......))))))..))...))))..(((((.((((.((......)).)))).))))).....)))))).. ( -39.60)
>DroSim_CAF1 18376 120 - 1
AAUGGCAGGAUGUGUGCGUUUGUGGAAACUUCUUAUGGCCACUCCCAUGAUGACGACAUGGGUUUGUUUGCCAAGAGCCAAGACAUGGCUGUAACUUUGUCGUGGCUGCCACUUCCACCU
...((..(((.(((.((......(....)......((((((..((((((.......))))))..))...))))..(((((.((((.((......)).)))).)))))))))).))).)). ( -39.70)
>DroEre_CAF1 20095 120 - 1
AAUGGAAGGAAGUGUGCGUUCGGGGAAACUUCUUGUGGCCACUCCCAGGAUGACGACAUGGGCUUGUUUGCCAAGAGCCAAGACAUGGCUGUAACUUUGUCGUGGCUGCCACUUCCACUU
.......(((((((.((....(((....))).....((((((((....)).(((((....(((......))).(.(((((.....))))).)....)))))))))))))))))))).... ( -43.60)
>consensus
AAUGGCAGGAUGUGUGCGUUUGUGGAAACUUCUUAUGGCCACUCCCAUGAUGACGACAUGGGUUUGUUUGCCAAGAGCCAAGACAUGGCUGUAACUUUGUCGUGGCUGCCACUUCCACCU
.......(((.(((.((......(....)......((((((..((((((.......))))))..))...))))..(((((.((((.((......)).)))).)))))))))).))).... (-36.44 = -36.75 +   0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 843,429 – 843,549
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.78
Mean single sequence MFE -40.69
Consensus MFE -34.22
Energy contribution -36.10
Covariance contribution 1.88
Combinations/Pair 1.06
Mean z-score -1.43
Structure conservation index 0.84
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 843429 120 - 27905053
GCUGCAUUUGCAGGGCUCACUCACACGACUGCACAUGGAAAAUGGCAGGAUGUGUGCGUUUGUGGAAACUUCUUAUGGCCAUUUCCAUGAUGACGACAUGGGUUUGUUUGCCAAGAGCCA
.((((....))))(((((((.((((((.((((.(((.....)))))))..)))))).))....(....)......((((((..((((((.......))))))..))...)))).))))). ( -45.50)
>DroSec_CAF1 19203 120 - 1
GCUGCAUUUGCUGGGCUCACUCACACGACUGCACAUGGAAAAUGGCAGGAUGUGUGCCUUUGUGGAAACUUCUUAUGGCCACUCCCAUGAUGACGACAUGGGUUUGUUUGCCAAGAGCCA
...((....))..(((((...((((((.((((.(((.....)))))))..)))))).......(....)......((((((..((((((.......))))))..))...)))).))))). ( -41.00)
>DroSim_CAF1 18416 120 - 1
GCUGCAUUUCCUGGGCUCACUCACACGACUGCACAUGGAAAAUGGCAGGAUGUGUGCGUUUGUGGAAACUUCUUAUGGCCACUCCCAUGAUGACGACAUGGGUUUGUUUGCCAAGAGCCA
.............(((((((.((((((.((((.(((.....)))))))..)))))).))....(....)......((((((..((((((.......))))))..))...)))).))))). ( -41.80)
>DroEre_CAF1 20135 120 - 1
GCUGCAGUUGCAGGACUCGCUCAAAGGACUGCACAUGGAAAAUGGAAGGAAGUGUGCGUUCGGGGAAACUUCUUGUGGCCACUCCCAGGAUGACGACAUGGGCUUGUUUGCCAAGAGCCA
.((((....)))).....((((...((((.((((((...............)))))))))).((.((((..((..((..((.((....))))....))..))...)))).))..)))).. ( -34.46)
>consensus
GCUGCAUUUGCAGGGCUCACUCACACGACUGCACAUGGAAAAUGGCAGGAUGUGUGCGUUUGUGGAAACUUCUUAUGGCCACUCCCAUGAUGACGACAUGGGUUUGUUUGCCAAGAGCCA
.((((....))))(((((((.(((((..((((.(((.....)))))))...))))).))....(....)......((((((..((((((.......))))))..))...)))).))))). (-34.22 = -36.10 +   1.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 843,549 – 843,668
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.92
Mean single sequence MFE -32.30
Consensus MFE -23.29
Energy contribution -25.35
Covariance contribution 2.06
Combinations/Pair 1.04
Mean z-score -1.92
Structure conservation index 0.72
SVM decision value 1.14
SVM RNA-class probability 0.921249
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 843549 119 - 27905053
AUGGUUAAUUUAGGUUUGCAUAAAUUAAGUUUCCCAUAUGGCUAUCUGGAAAUAUCCUGUCCAGCCAAGACACCA-AUGUCCAGGCUGCGGAGCUUUUCCUCCCCGGUAUGUUGGUAGCA
((((..(((((((.((.....)).)))))))..))))...((((((.....(((((.....(((((..((((...-.))))..))))).((((......))))..)))))...)))))). ( -33.60)
>DroSec_CAF1 19323 98 - 1
AAGAUAAAUUUAGG----------------------UAUGGCUAUCUGGAAAUAUCCUGUCCAGCCAAGACACCAAAUGUCCAGGCUGCGGAGCUUUUCCUCCUCGGGAUGUUGGUAGCA
..............----------------------....((((((....(((((((((..(((((..((((.....))))..))))).((((......)))).))))))))))))))). ( -33.20)
>DroSim_CAF1 18536 116 - 1
AAGGUAAAUUUAGG----CAUAAAUUAAGUUGCCCAUAUGGCUAUCUGGAAAUAUCCUGUCCAGCCAAGACACCAAAUGUCCAGGCUGCGGAGCUUUUCCUCCUCGGGAUGUGGGUAGCA
..((..(((((((.----......)))))))..)).....(((((((....((((((((..(((((..((((.....))))..))))).((((......)))).))))))))))))))). ( -38.90)
>DroEre_CAF1 20255 107 - 1
AUAGCAAACUCAAGUUCGCAUAAAUUAAGUU------------GUCUGGAAAUAUCCUGACCAGCCAAGACACCAAGUAUCCA-GCUGCGGAACUUUUCCUCCCCGGGAUGUUAGUAGCA
...((.(((....))).)).........(((------------(((.(((....))).)).))))..................-(((((..(((...((((....)))).))).))))). ( -23.50)
>consensus
AAGGUAAAUUUAGG____CAUAAAUUAAGUU_____UAUGGCUAUCUGGAAAUAUCCUGUCCAGCCAAGACACCAAAUGUCCAGGCUGCGGAGCUUUUCCUCCCCGGGAUGUUGGUAGCA
........................................((((((....(((((((((..(((((..((((.....))))..))))).((((......)))).))))))))))))))). (-23.29 = -25.35 +   2.06)

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 09:36:31 2006