Locus 4587

Sequence ID 2R_DroMel_CAF1
Location 14,971,770 – 14,972,040
Length 270
Max. P 0.912913
window7360 window7361 window7362 window7363 window7364 window7365

overview

Window 0

Location 14,971,770 – 14,971,890
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.19
Mean single sequence MFE -36.66
Consensus MFE -36.42
Energy contribution -36.48
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.19
Structure conservation index 0.99
SVM decision value 1.09
SVM RNA-class probability 0.912913
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14971770 120 + 20766785
UGAGCGAGAGAGCUAAUAGCUUUUCAGCUUUAGCUUUUCUUGGGCCAAUCGGAAAUUGUAUUUCAUUGGUAAGUACAAGAAGUGGCAGCACCAUAACCAGCAAAUCAAUACUUGGGCUGC
.((((..((((((.....))))))..))))...(.(((((((.((((((.((((......)))))))))).....))))))).)(((((.(((...................)))))))) ( -34.31)
>DroSim_CAF1 1659 120 + 1
UGAGCGAGAGAGCUAAUAGCUUUUCAGCUUUAGCUUUUCUUGGGCCGAUCGGAAAUUGUAUUUGAUUGGUAAGUACAAGAAGUGGCAGCACCAUAACCAGCAAAUCAAUACUUGGGCUGC
.((((..((((((.....))))))..))))...(.(((((((.((((((((((.......)))))))))).....))))))).)(((((.(((...................)))))))) ( -37.11)
>DroEre_CAF1 2089 120 + 1
UGAGCGAGAGAGCGAAUAGCUUUUCAGCUUUAGCUUUUCUUGGGCCGAUCGGAAAUUAUAUUUGAUUGGUAAGUACAAGAAGUGGCAGCACCAUAACCAGCAAAUCAAUACUUGGGCUGC
.((((..((((((.....))))))..))))...(.(((((((.((((((((((.......)))))))))).....))))))).)(((((.(((...................)))))))) ( -37.61)
>DroYak_CAF1 1787 120 + 1
UGAGCGAGAGAGCGAAUAGCUUUUCAGCUUUAGCUUUUCUUGGGCCGAUCGGAAAUUGUAUUUGAUUGGUAAGUACAAGAAGUGGCAGCACCAUAACCAGCAAAUCAAUACUUGGGCUGC
.((((..((((((.....))))))..))))...(.(((((((.((((((((((.......)))))))))).....))))))).)(((((.(((...................)))))))) ( -37.61)
>consensus
UGAGCGAGAGAGCGAAUAGCUUUUCAGCUUUAGCUUUUCUUGGGCCGAUCGGAAAUUGUAUUUGAUUGGUAAGUACAAGAAGUGGCAGCACCAUAACCAGCAAAUCAAUACUUGGGCUGC
.((((..((((((.....))))))..))))...(.(((((((.((((((((((.......)))))))))).....))))))).)(((((.(((...................)))))))) (-36.42 = -36.48 +   0.06)

alignment

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secondary structure

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Window 1

Location 14,971,810 – 14,971,925
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.52
Mean single sequence MFE -34.59
Consensus MFE -30.55
Energy contribution -30.86
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.88
SVM decision value 0.36
SVM RNA-class probability 0.705908
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14971810 115 + 20766785
UGGGCCAAUCGGAAAUUGUAUUUCAUUGGUAAGUACAAGAAGUGGCAGCACCAUAACCAGCAAAUCAAUACUUGGGCUGCCAUUCCGUUU-----CGUUCCGUUCGUCAGUUUUCCUAGC
..(((.((.(((((.(((((((((....).))))))))(.(((((((((.(((...................)))))))))))).)....-----..))))))).)))............ ( -31.21)
>DroSim_CAF1 1699 115 + 1
UGGGCCGAUCGGAAAUUGUAUUUGAUUGGUAAGUACAAGAAGUGGCAGCACCAUAACCAGCAAAUCAAUACUUGGGCUGCCAUUCCGUUU-----CGUUCCGUUCGUUAGUUUUCCUAGC
.((..(((.(((((.(((((((((.....)))))))))....(((((((.(((...................)))))))))))))))..)-----))..))....(((((.....))))) ( -37.71)
>DroEre_CAF1 2129 120 + 1
UGGGCCGAUCGGAAAUUAUAUUUGAUUGGUAAGUACAAGAAGUGGCAGCACCAUAACCAGCAAAUCAAUACUUGGGCUGCCAUUCCGUUUCGUUUCGUUCCGUUCGUUAGUUUUCCUAGC
.((((((((((((.......))))))))))........(.(((((((((.(((...................)))))))))))).).............))....(((((.....))))) ( -32.21)
>DroYak_CAF1 1827 120 + 1
UGGGCCGAUCGGAAAUUGUAUUUGAUUGGUAAGUACAAGAAGUGGCAGCACCAUAACCAGCAAAUCAAUACUUGGGCUGCCAUUCCGUUUCGUUUCGUUCCGUUCGUUAGUUUUCCUAGC
.((..(((.(((((.(((((((((.....)))))))))(.(((((((((.(((...................)))))))))))).).)))))..)))..))....(((((.....))))) ( -37.21)
>consensus
UGGGCCGAUCGGAAAUUGUAUUUGAUUGGUAAGUACAAGAAGUGGCAGCACCAUAACCAGCAAAUCAAUACUUGGGCUGCCAUUCCGUUU_____CGUUCCGUUCGUUAGUUUUCCUAGC
.((((((((((((.......))))))))))........(.(((((((((.(((...................)))))))))))).).............))....(((((.....))))) (-30.55 = -30.86 +   0.31)

alignment

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secondary structure

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Window 2

Location 14,971,810 – 14,971,925
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.52
Mean single sequence MFE -31.12
Consensus MFE -31.56
Energy contribution -31.00
Covariance contribution -0.56
Combinations/Pair 1.08
Mean z-score -1.28
Structure conservation index 1.01
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14971810 115 - 20766785
GCUAGGAAAACUGACGAACGGAACG-----AAACGGAAUGGCAGCCCAAGUAUUGAUUUGCUGGUUAUGGUGCUGCCACUUCUUGUACUUACCAAUGAAAUACAAUUUCCGAUUGGCCCA
(((((.....))).(((.(((((..-----....(((.((((((((((((((......)))).....))).))))))).)))(((((.((.......)).))))).))))).)))))... ( -29.90)
>DroSim_CAF1 1699 115 - 1
GCUAGGAAAACUAACGAACGGAACG-----AAACGGAAUGGCAGCCCAAGUAUUGAUUUGCUGGUUAUGGUGCUGCCACUUCUUGUACUUACCAAUCAAAUACAAUUUCCGAUCGGCCCA
(((((.....))).(((.(((((..-----....(((.((((((((((((((......)))).....))).))))))).)))(((((.((.......)).))))).))))).)))))... ( -32.00)
>DroEre_CAF1 2129 120 - 1
GCUAGGAAAACUAACGAACGGAACGAAACGAAACGGAAUGGCAGCCCAAGUAUUGAUUUGCUGGUUAUGGUGCUGCCACUUCUUGUACUUACCAAUCAAAUAUAAUUUCCGAUCGGCCCA
(((((.....))).(((.(((((((........))(((((((((((((((((......)))).....))).))))))).)))........................))))).)))))... ( -30.60)
>DroYak_CAF1 1827 120 - 1
GCUAGGAAAACUAACGAACGGAACGAAACGAAACGGAAUGGCAGCCCAAGUAUUGAUUUGCUGGUUAUGGUGCUGCCACUUCUUGUACUUACCAAUCAAAUACAAUUUCCGAUCGGCCCA
(((((.....))).(((.(((((...........(((.((((((((((((((......)))).....))).))))))).)))(((((.((.......)).))))).))))).)))))... ( -32.00)
>consensus
GCUAGGAAAACUAACGAACGGAACG_____AAACGGAAUGGCAGCCCAAGUAUUGAUUUGCUGGUUAUGGUGCUGCCACUUCUUGUACUUACCAAUCAAAUACAAUUUCCGAUCGGCCCA
(((((.....))).(((.(((((...........(((.((((((((((((((......)))).....))).))))))).)))(((((.((.......)).))))).))))).)))))... (-31.56 = -31.00 +  -0.56)

alignment

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secondary structure

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Window 3

Location 14,971,890 – 14,972,004
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.40
Mean single sequence MFE -22.84
Consensus MFE -18.72
Energy contribution -18.83
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.21
Structure conservation index 0.82
SVM decision value 0.35
SVM RNA-class probability 0.701636
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14971890 114 + 20766785
CAUUCCGUUU-----CGUUCCGUUCGUCAGUUUUCCUAGCCCAUUCGUUGGCGCUCUCUCUUUUCCGUCAGUCUCUCUCUUUCUCUUCCCCAAAAGAGAGCGAAA-ACCCCCCGCCCGCC
..........-----.....((..((...((((((..((((((.....))).)))(((((((((..(..((.............))..)..))))))))).))))-))....))..)).. ( -20.32)
>DroSim_CAF1 1779 112 + 1
CAUUCCGUUU-----CGUUCCGUUCGUUAGUUUUCCUAGCCCAUUCGUUGGCGCUCUCUCUUUUCCCCCA--CUCUCUCUUUCUCUUCCCCGAAAGAGAGCGAAA-ACCCCCCGCCCGCC
..........-----.....((..((...((((((..((((((.....))).)))...............--..(((((((((........))))))))).))))-))....))..)).. ( -23.90)
>DroYak_CAF1 1907 120 + 1
CAUUCCGUUUCGUUUCGUUCCGUUCGUUAGUUUUCCUAGCCCAUUCGUUGGCGCUCUUUCUUUUCCCCCACACUCUCUCUUUCUCUCUCCCGAAAGAGAGCGAAAAGCCCCCCGCCCGCC
.........................(((((.....)))))......((.((((......((((((.........(((((((((........))))))))).)))))).....)))).)). ( -24.30)
>consensus
CAUUCCGUUU_____CGUUCCGUUCGUUAGUUUUCCUAGCCCAUUCGUUGGCGCUCUCUCUUUUCCCCCA__CUCUCUCUUUCUCUUCCCCGAAAGAGAGCGAAA_ACCCCCCGCCCGCC
....................((..((...((((((..((((((.....))).)))...................(((((((((........))))))))).)))).))....))..)).. (-18.72 = -18.83 +   0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,971,890 – 14,972,004
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.40
Mean single sequence MFE -31.41
Consensus MFE -28.92
Energy contribution -28.70
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.12
Structure conservation index 0.92
SVM decision value 1.03
SVM RNA-class probability 0.903906
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14971890 114 - 20766785
GGCGGGCGGGGGGU-UUUCGCUCUCUUUUGGGGAAGAGAAAGAGAGAGACUGACGGAAAAGAGAGAGCGCCAACGAAUGGGCUAGGAAAACUGACGAACGGAACG-----AAACGGAAUG
..((..((...(((-((((((((((((((..(..((.............))..)....))))))))))(((........)))...)))))))..))..)).....-----.......... ( -30.82)
>DroSim_CAF1 1779 112 - 1
GGCGGGCGGGGGGU-UUUCGCUCUCUUUCGGGGAAGAGAAAGAGAGAG--UGGGGGAAAAGAGAGAGCGCCAACGAAUGGGCUAGGAAAACUAACGAACGGAACG-----AAACGGAAUG
..((..((...(((-((((.(((((((((........)))))))))..--...............(((.(((.....))))))..)))))))..))..)).....-----.......... ( -32.80)
>DroYak_CAF1 1907 120 - 1
GGCGGGCGGGGGGCUUUUCGCUCUCUUUCGGGAGAGAGAAAGAGAGAGUGUGGGGGAAAAGAAAGAGCGCCAACGAAUGGGCUAGGAAAACUAACGAACGGAACGAAACGAAACGGAAUG
..((..((..((..(((((.(((((((((........)))))))))...................(((.(((.....)))))).))))).))..))..)).................... ( -30.60)
>consensus
GGCGGGCGGGGGGU_UUUCGCUCUCUUUCGGGGAAGAGAAAGAGAGAG__UGGGGGAAAAGAGAGAGCGCCAACGAAUGGGCUAGGAAAACUAACGAACGGAACG_____AAACGGAAUG
..((..((..((...((((.(((((((((........)))))))))...................(((.(((.....)))))).))))..))..))..)).................... (-28.92 = -28.70 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,971,925 – 14,972,040
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.30
Mean single sequence MFE -29.87
Consensus MFE -25.37
Energy contribution -25.27
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.20
Structure conservation index 0.85
SVM decision value 0.60
SVM RNA-class probability 0.796595
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14971925 115 + 20766785
CCAUUCGUUGGCGCUCUCUCUUUUCCGUCAGUCUCUCUCUUUCUCUUCCCCAAAAGAGAGCGAAA-ACCCCCCGCCCGCCCACACUCGGUGUAUGUGU----GCUUUGUAAUAACGAGUA
..((((((((..((............((...((.((((((((..........)))))))).))..-)).....((.(((..((((...))))..))).----))...))..)))))))). ( -25.70)
>DroSim_CAF1 1814 113 + 1
CCAUUCGUUGGCGCUCUCUCUUUUCCCCCA--CUCUCUCUUUCUCUUCCCCGAAAGAGAGCGAAA-ACCCCCCGCCCGCCCACACUCGGUGUAUGUGU----GCUUUGUAACAACGAGUA
..((((((((..((................--(.(((((((((........))))))))).)...-.......((.(((..((((...))))..))).----))...))..)))))))). ( -31.20)
>DroYak_CAF1 1947 120 + 1
CCAUUCGUUGGCGCUCUUUCUUUUCCCCCACACUCUCUCUUUCUCUCUCCCGAAAGAGAGCGAAAAGCCCCCCGCCCGCCCCCACUUGGUGCAUGUGUGCGUGCUUUGUAAUAACGAGUA
..(((((((((((......((((((.........(((((((((........))))))))).)))))).....)))).(((.......)))(((((....)))))........))))))). ( -32.70)
>consensus
CCAUUCGUUGGCGCUCUCUCUUUUCCCCCA__CUCUCUCUUUCUCUUCCCCGAAAGAGAGCGAAA_ACCCCCCGCCCGCCCACACUCGGUGUAUGUGU____GCUUUGUAAUAACGAGUA
..((((((((..((..................(.(((((((((........))))))))).)..........(((..((((......)).))..)))..........))..)))))))). (-25.37 = -25.27 +  -0.11)

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 11:23:58 2006