Locus 5882

Sequence ID 2R_DroMel_CAF1
Location 18,582,328 – 18,582,468
Length 140
Max. P 0.997920
window9443 window9444 window9445

overview

Window 3

Location 18,582,328 – 18,582,437
Length 109
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 72.30
Mean single sequence MFE -27.32
Consensus MFE -11.28
Energy contribution -10.96
Covariance contribution -0.32
Combinations/Pair 1.31
Mean z-score -2.61
Structure conservation index 0.41
SVM decision value 2.96
SVM RNA-class probability 0.997920
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18582328 109 + 20766785
UGAUAAUAUACAGAAGUACAAAGGCGAAAAUACCAAGAGAAUGAUGUUAGUGUGUGUGUUAGG-UGGGAAACUUGGCUGGGACUGUAGCUAAGUUCAACACCAGGCGGAG
...(((((((((.(...(((.(..(.............)..)..)))...).)))))))))((-((...((((((((((......))))))))))...))))........ ( -26.92)
>DroSec_CAF1 7131 109 + 1
GGAUAAAAUACCGAAGUGCGCACGGAAAAAUACCAAGAGGAUGAUGUUAGUGUGGAUGUUUGG-UGGGAAACUUGGCUGGGGAUGUAGCUGAGUUCAACACCAGGCGGAG
..........((...((.(((((.((...((.((....))))....)).))))).))((((((-((...((((..((((......))))..))))...)))))))))).. ( -34.10)
>DroSim_CAF1 4232 108 + 1
GGA-AAAAUACCGAAGUACGCACGGAAAAAUACCAAGAGGAUGAUGUUAGUGUGGAUGUUUGG-UGGGAAACUUGGUUGGGGAUGUAGCUGAGUUCAACACCAGGCGGAG
...-......((......(((((.((...((.((....))))....)).)))))...((((((-((...((((..((((......))))..))))...)))))))))).. ( -30.60)
>DroEre_CAF1 7128 87 + 1
GGA-GAUAUACCGGAGAGCA-ACGGAAAAAUACCGAAAG----GUGU-----------AUGGGGUGGAAAACUUGGCUGAGGAUGUAGCAAAGAUCGAAACCAC------
...-......(((.......-.)))....(((((....)----))))-----------.(((..(.((...(((.((((......)))).))).)).)..))).------ ( -22.20)
>DroYak_CAF1 7276 95 + 1
GGA-UAAAUACCGAAGACCG-GCGGAAAAAUACCAAAAG----AUAUUAGAGUGGGUGUUGGGGUGGA-AACUUUGCUGAGGAUGUAGCAAGGUUCAAAACC--------
...-......((((..(((.-((.....((((.(....)----.))))...)).))).))))(((.((-(.((((((((......)))))))))))...)))-------- ( -22.80)
>consensus
GGA_AAAAUACCGAAGUACG_ACGGAAAAAUACCAAGAG_AUGAUGUUAGUGUGGAUGUUGGG_UGGGAAACUUGGCUGGGGAUGUAGCUAAGUUCAACACCAGGCGGAG
((........)).................................................((.((...((((((((((......))))))))))...))))........ (-11.28 = -10.96 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,582,328 – 18,582,437
Length 109
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 72.30
Mean single sequence MFE -17.30
Consensus MFE -4.44
Energy contribution -6.04
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.26
SVM decision value 1.11
SVM RNA-class probability 0.917414
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18582328 109 - 20766785
CUCCGCCUGGUGUUGAACUUAGCUACAGUCCCAGCCAAGUUUCCCA-CCUAACACACACACUAACAUCAUUCUCUUGGUAUUUUCGCCUUUGUACUUCUGUAUAUUAUCA
....((..((((..((((((.(((........))).))))))..))-))................((((......))))......))...(((((....)))))...... ( -19.50)
>DroSec_CAF1 7131 109 - 1
CUCCGCCUGGUGUUGAACUCAGCUACAUCCCCAGCCAAGUUUCCCA-CCAAACAUCCACACUAACAUCAUCCUCUUGGUAUUUUUCCGUGCGCACUUCGGUAUUUUAUCC
....((.(((((..(((((..(((........)))..)))))..))-)))........(((.........((....)).........))).))((....))......... ( -20.97)
>DroSim_CAF1 4232 108 - 1
CUCCGCCUGGUGUUGAACUCAGCUACAUCCCCAACCAAGUUUCCCA-CCAAACAUCCACACUAACAUCAUCCUCUUGGUAUUUUUCCGUGCGUACUUCGGUAUUUU-UCC
...(((.(((.((((....))))..........((((((.......-..........................))))))......))).)))(((....)))....-... ( -17.11)
>DroEre_CAF1 7128 87 - 1
------GUGGUUUCGAUCUUUGCUACAUCCUCAGCCAAGUUUUCCACCCCAU-----------ACAC----CUUUCGGUAUUUUUCCGU-UGCUCUCCGGUAUAUC-UCC
------((((.......(((.(((........))).)))....)))).....-----------....----.....(((((....(((.-.......))).)))))-... ( -13.10)
>DroYak_CAF1 7276 95 - 1
--------GGUUUUGAACCUUGCUACAUCCUCAGCAAAGUU-UCCACCCCAACACCCACUCUAAUAU----CUUUUGGUAUUUUUCCGC-CGGUCUUCGGUAUUUA-UCC
--------(((...((((.(((((........))))).)))-)..)))..............(((((----(....)))))).....((-((.....)))).....-... ( -15.80)
>consensus
CUCCGCCUGGUGUUGAACUUAGCUACAUCCCCAGCCAAGUUUCCCA_CCAAACACCCACACUAACAUCAU_CUCUUGGUAUUUUUCCGU_CGCACUUCGGUAUUUU_UCC
........((((..((((((.(((........))).))))))..)).))............................................................. ( -4.44 =  -6.04 +   1.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,582,360 – 18,582,468
Length 108
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 64.26
Mean single sequence MFE -26.58
Consensus MFE -10.64
Energy contribution -11.33
Covariance contribution 0.69
Combinations/Pair 1.29
Mean z-score -2.17
Structure conservation index 0.40
SVM decision value 0.42
SVM RNA-class probability 0.729530
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18582360 108 + 20766785
CCAAGAGAAUGAUGUUAGUGUGUGUGUUAGG-UGGGAAACUUGGCUGGGACUGUAGCUAAGUUCAACACCAGGCGGAGAGGCAAUUGUGCAUAGUGGUACAAAGGUUGA
((...............((.(.(.(((..((-((...((((((((((......))))))))))...))))..))).).).))..((((((......)))))).)).... ( -32.40)
>DroSim_CAF1 4263 108 + 1
CCAAGAGGAUGAUGUUAGUGUGGAUGUUUGG-UGGGAAACUUGGUUGGGGAUGUAGCUGAGUUCAACACCAGGCGGAGUGGCCAUUGUGCACAGUGGUACAAAGGUUGA
(((....(((...)))....))).(((((((-((...((((..((((......))))..))))...)))))))))....((((.((((((......)))))).)))).. ( -33.20)
>DroEre_CAF1 7158 83 + 1
CCGAAAG----GUGU-----------AUGGGGUGGAAAACUUGGCUGAGGAUGUAGCAAAGAUCGAAACCAC-----------CGCGUCCACAGUGGUAUAAAAGUAUA
(((....----(((.-----------(((.(((((....(((.((((......)))).))).......))))-----------).))).)))..)))............ ( -21.60)
>DroYak_CAF1 7306 84 + 1
CCAAAAG----AUAUUAGAGUGGGUGUUGGGGUGGA-AACUUUGCUGAGGAUGUAGCAAGGUUCAAAACC--------------------ACAGUGGUACAAAAAUAUA
(((....----.........)))(((..(..((((.-((((((((((......)))))))))).....))--------------------))..)..)))......... ( -19.12)
>consensus
CCAAAAG____AUGUUAGUGUGGGUGUUGGG_UGGAAAACUUGGCUGAGGAUGUAGCAAAGUUCAAAACCAG___________AUUGUGCACAGUGGUACAAAAGUAGA
..............................((((...((((((((((......))))))))))...))))....................................... (-10.64 = -11.33 +   0.69)

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 11:57:12 2006