Locus 5289

Sequence ID 2R_DroMel_CAF1
Location 17,179,290 – 17,179,424
Length 134
Max. P 0.952473
window8455 window8456 window8457 window8458

overview

Window 5

Location 17,179,290 – 17,179,384
Length 94
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 78.15
Mean single sequence MFE -23.90
Consensus MFE -15.82
Energy contribution -16.46
Covariance contribution 0.64
Combinations/Pair 1.30
Mean z-score -1.77
Structure conservation index 0.66
SVM decision value 0.63
SVM RNA-class probability 0.805488
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17179290 94 + 20766785
AAGUUCAACAAUUAUUGAAAAUGUUUGCAUUCAUAGACACCAUAAAAAAGCCGCCUCUGGG---CGGCCGAAAGUCAUUUAUGCCCAUCCCAGAGGC
...(((((......)))))..((((((......)))))).............(((((((((---.(((..(((....)))..)))...))))))))) ( -25.30)
>DroSec_CAF1 4130 94 + 1
AAGCUCAACAAUUAUUCAAAAUGUUUGCAUUCAUAGAUACCAUAGAAAAGCCGCCUCUGGG---CGGCCGAAAGUCAUUUAUGCCCAUCCCAGAGGC
..((..((((.((.....)).)))).))........................(((((((((---.(((..(((....)))..)))...))))))))) ( -23.70)
>DroSim_CAF1 4123 94 + 1
AAGCUCAACAAUUAUUGAAAAUGUUUGCAUUCAUAGAUACCAUAGAAAAGCCGCCUCUGGG---CGGCCGAAAGUCAUUUAUGCCCAUCCCAGAGGC
..(((.......((((...((((....))))....)))).........))).(((((((((---.(((..(((....)))..)))...))))))))) ( -24.09)
>DroEre_CAF1 4181 94 + 1
AAGGCUAACAAUUAUUGAAAAUGUUUGCAUUUAUAGAGGGCAUACAAAAGCCGCCUCUUGG---CGACCGUAAGUCAUACAUGCCCAUCCCAGAGGC
..((((..((.....))....(((.(((.((....))..))).)))..))))((((((.((---.((..(((.(.....).)))...)))))))))) ( -21.80)
>DroAna_CAF1 4936 95 + 1
AAUCCCA--AAUUACCAAUCAUGUUUUCAUUUCUGGAAAAGAUUGAAAGACCGCCCCUUGAAACGGGUCGGAAGAGUUAUCAGCCGAUAAGGGAGGC
..((((.--......(((((...((((((....)))))).))))).....(((.(((.......))).))).....(((((....)))))))))... ( -24.60)
>consensus
AAGCUCAACAAUUAUUGAAAAUGUUUGCAUUCAUAGAUACCAUAGAAAAGCCGCCUCUGGG___CGGCCGAAAGUCAUUUAUGCCCAUCCCAGAGGC
..............(((..((((....))))..)))................(((((((((....((((....)........)))...))))))))) (-15.82 = -16.46 +   0.64)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,179,290 – 17,179,384
Length 94
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 78.15
Mean single sequence MFE -28.67
Consensus MFE -16.77
Energy contribution -17.89
Covariance contribution 1.12
Combinations/Pair 1.32
Mean z-score -2.17
Structure conservation index 0.58
SVM decision value 1.23
SVM RNA-class probability 0.933887
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17179290 94 - 20766785
GCCUCUGGGAUGGGCAUAAAUGACUUUCGGCCG---CCCAGAGGCGGCUUUUUUAUGGUGUCUAUGAAUGCAAACAUUUUCAAUAAUUGUUGAACUU
(((((((((.(((.(.............).)))---))))))))).((...(((((((...))))))).)).......((((((....))))))... ( -31.52)
>DroSec_CAF1 4130 94 - 1
GCCUCUGGGAUGGGCAUAAAUGACUUUCGGCCG---CCCAGAGGCGGCUUUUCUAUGGUAUCUAUGAAUGCAAACAUUUUGAAUAAUUGUUGAGCUU
(((((((((.(((.(.............).)))---)))))))))(((((..(....((.((...(((((....))))).))))....)..))))). ( -31.02)
>DroSim_CAF1 4123 94 - 1
GCCUCUGGGAUGGGCAUAAAUGACUUUCGGCCG---CCCAGAGGCGGCUUUUCUAUGGUAUCUAUGAAUGCAAACAUUUUCAAUAAUUGUUGAGCUU
(((((((((.(((.(.............).)))---)))))))))(((((....(..((......(((((....)))))......))..).))))). ( -30.82)
>DroEre_CAF1 4181 94 - 1
GCCUCUGGGAUGGGCAUGUAUGACUUACGGUCG---CCAAGAGGCGGCUUUUGUAUGCCCUCUAUAAAUGCAAACAUUUUCAAUAAUUGUUAGCCUU
.......(((.(((((((((.....)))(((((---((....))))))).....)))))))))......((.((((.((.....)).)))).))... ( -27.30)
>DroAna_CAF1 4936 95 - 1
GCCUCCCUUAUCGGCUGAUAACUCUUCCGACCCGUUUCAAGGGGCGGUCUUUCAAUCUUUUCCAGAAAUGAAAACAUGAUUGGUAAUU--UGGGAUU
...((((...((((..((....))..)))).((((((....))))))....((((((.(((.((....)).)))...)))))).....--.)))).. ( -22.70)
>consensus
GCCUCUGGGAUGGGCAUAAAUGACUUUCGGCCG___CCCAGAGGCGGCUUUUCUAUGGUAUCUAUGAAUGCAAACAUUUUCAAUAAUUGUUGAGCUU
(((((((((...(((..............)))....)))))))))(((((...............(((((....)))))............))))). (-16.77 = -17.89 +   1.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,179,307 – 17,179,424
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.09
Mean single sequence MFE -35.88
Consensus MFE -24.44
Energy contribution -26.68
Covariance contribution 2.24
Combinations/Pair 1.21
Mean z-score -2.08
Structure conservation index 0.68
SVM decision value 1.42
SVM RNA-class probability 0.952473
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17179307 117 + 20766785
AAAAUGUUUGCAUUCAUAGACACCAUAAAAAAGCCGCCUCUGGG---CGGCCGAAAGUCAUUUAUGCCCAUCCCAGAGGCCAAGUUAGUUGACGAUGUCGUCAGCUACAUCGCCAAGCCA
.....((((((........................(((((((((---.(((..(((....)))..)))...)))))))))...((.((((((((....))))))))))...).))))).. ( -38.70)
>DroSec_CAF1 4147 117 + 1
AAAAUGUUUGCAUUCAUAGAUACCAUAGAAAAGCCGCCUCUGGG---CGGCCGAAAGUCAUUUAUGCCCAUCCCAGAGGCCAAGUUAGUUGACGAUGUCGUCAGCUACAUCGCCAAACCA
.....((((((........................(((((((((---.(((..(((....)))..)))...)))))))))...((.((((((((....))))))))))...).))))).. ( -38.70)
>DroSim_CAF1 4140 117 + 1
AAAAUGUUUGCAUUCAUAGAUACCAUAGAAAAGCCGCCUCUGGG---CGGCCGAAAGUCAUUUAUGCCCAUCCCAGAGGCCAAGUUAGUUGACGACGUCGUCAGCUACAUCGCCAAACCG
.....((((((........................(((((((((---.(((..(((....)))..)))...)))))))))...((.((((((((....))))))))))...).))))).. ( -38.70)
>DroEre_CAF1 4198 117 + 1
AAAAUGUUUGCAUUUAUAGAGGGCAUACAAAAGCCGCCUCUUGG---CGACCGUAAGUCAUACAUGCCCAUCCCAGAGGCCCAGUUAGUCGACGAUGUCGCGAGCUACAUCGCCAAACCA
.(((((....))))).....((((((.........(((....))---)(((.....)))....))))))........(((...(((....)))((((((....)..))))))))...... ( -31.00)
>DroAna_CAF1 4951 120 + 1
AUCAUGUUUUCAUUUCUGGAAAAGAUUGAAAGACCGCCCCUUGAAACGGGUCGGAAGAGUUAUCAGCCGAUAAGGGAGGCCGAGUACAUUAGCGACAUCGAGAGUCAUCUGGCCCUUCCG
.((...((((((..(((.....))).)))))).(((.(((.......))).)))..)).(((((....)))))((((((((.((...(((..((....))..)))...)))).)))))). ( -32.30)
>consensus
AAAAUGUUUGCAUUCAUAGAUACCAUAGAAAAGCCGCCUCUGGG___CGGCCGAAAGUCAUUUAUGCCCAUCCCAGAGGCCAAGUUAGUUGACGAUGUCGUCAGCUACAUCGCCAAACCA
.....((((((........................(((((((((....((((....)........)))...)))))))))...((.((((((((....))))))))))...).))))).. (-24.44 = -26.68 +   2.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,179,307 – 17,179,424
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.09
Mean single sequence MFE -39.13
Consensus MFE -26.66
Energy contribution -27.22
Covariance contribution 0.56
Combinations/Pair 1.40
Mean z-score -1.75
Structure conservation index 0.68
SVM decision value 0.69
SVM RNA-class probability 0.823052
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17179307 117 - 20766785
UGGCUUGGCGAUGUAGCUGACGACAUCGUCAACUAACUUGGCCUCUGGGAUGGGCAUAAAUGACUUUCGGCCG---CCCAGAGGCGGCUUUUUUAUGGUGUCUAUGAAUGCAAACAUUUU
(((.((((((((((........))))))))))))).....(((((((((.(((.(.............).)))---))))))))).((...(((((((...))))))).))......... ( -42.72)
>DroSec_CAF1 4147 117 - 1
UGGUUUGGCGAUGUAGCUGACGACAUCGUCAACUAACUUGGCCUCUGGGAUGGGCAUAAAUGACUUUCGGCCG---CCCAGAGGCGGCUUUUCUAUGGUAUCUAUGAAUGCAAACAUUUU
(((((.((((((((........))))))))))))).....(((((((((.(((.(.............).)))---))))))))).((..(((.((((...))))))).))......... ( -41.12)
>DroSim_CAF1 4140 117 - 1
CGGUUUGGCGAUGUAGCUGACGACGUCGUCAACUAACUUGGCCUCUGGGAUGGGCAUAAAUGACUUUCGGCCG---CCCAGAGGCGGCUUUUCUAUGGUAUCUAUGAAUGCAAACAUUUU
.((((.((((((((........))))))))))))......(((((((((.(((.(.............).)))---))))))))).((..(((.((((...))))))).))......... ( -39.92)
>DroEre_CAF1 4198 117 - 1
UGGUUUGGCGAUGUAGCUCGCGACAUCGUCGACUAACUGGGCCUCUGGGAUGGGCAUGUAUGACUUACGGUCG---CCAAGAGGCGGCUUUUGUAUGCCCUCUAUAAAUGCAAACAUUUU
(((((.((((((((.(....).)))))))))))))..((.((.....(((.(((((((((.....)))(((((---((....))))))).....)))))))))......))...)).... ( -40.40)
>DroAna_CAF1 4951 120 - 1
CGGAAGGGCCAGAUGACUCUCGAUGUCGCUAAUGUACUCGGCCUCCCUUAUCGGCUGAUAACUCUUCCGACCCGUUUCAAGGGGCGGUCUUUCAAUCUUUUCCAGAAAUGAAAACAUGAU
((((((((..((.((((.......)))))).......((((((.........))))))...))))))))..((((((....))))))....(((...(((((.(....))))))..))). ( -31.50)
>consensus
UGGUUUGGCGAUGUAGCUGACGACAUCGUCAACUAACUUGGCCUCUGGGAUGGGCAUAAAUGACUUUCGGCCG___CCCAGAGGCGGCUUUUCUAUGGUAUCUAUGAAUGCAAACAUUUU
.(((((((((((((........))))))))))........(((((((((...(((..............)))....))))))))).)))............................... (-26.66 = -27.22 +   0.56)

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 11:41:21 2006