Locus 3718

Sequence ID 2R_DroMel_CAF1
Location 12,323,974 – 12,324,179
Length 205
Max. P 0.761228
window6040 window6041 window6042

overview

Window 0

Location 12,323,974 – 12,324,071
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 88.98
Mean single sequence MFE -23.30
Consensus MFE -20.03
Energy contribution -19.87
Covariance contribution -0.16
Combinations/Pair 1.17
Mean z-score -1.47
Structure conservation index 0.86
SVM decision value 0.00
SVM RNA-class probability 0.535713
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12323974 97 - 20766785
ACAAAUUUCAAUUCCACACCGCGUGAGUGUGCGUUAUAAAUUGCGUAUGCAGGCCCACUUGGUCAGUUU-----------------------GUGAAUACAAAUCUACGCGUUUUACAUA
...................((((((.((((((((........)))))))).((((.....)))).((((-----------------------((....)))))).))))))......... ( -23.20)
>DroSec_CAF1 22760 97 - 1
ACAAAUUUCAAUUCCACACCGCGUGAGUGUGCGUUAUAAAUUGCGUAUGCAGGCCCACUUGGUCAGUUU-----------------------GUGAAUACAAAUCUACGCGUUUUACAUA
...................((((((.((((((((........)))))))).((((.....)))).((((-----------------------((....)))))).))))))......... ( -23.20)
>DroSim_CAF1 20920 97 - 1
ACAAAUUUCAAUUCCACACCGCGUGAGUGUGCGUUAUAAAUUGCGUAUGCAGGCCCACUUGGUCAGUUU-----------------------GUGAAUACAAAUCUACGCGUUUUACAUA
...................((((((.((((((((........)))))))).((((.....)))).((((-----------------------((....)))))).))))))......... ( -23.20)
>DroEre_CAF1 22985 97 - 1
ACAAAUUUCAAUUCCACACCGCGUAAGUGUGCGUUAUAAAUUGCGUAUGCAGACCCACUUGGUCAGUUU-----------------------GUGAAUACAAAUCUACGCGUUUUACAUA
...................((((((.((((((((........)))))))).((((.....)))).((((-----------------------((....)))))).))))))......... ( -24.10)
>DroYak_CAF1 21360 97 - 1
ACAAAUUUCAAUUCCACACCGCGUGAGUGUGCGUUAUAAAUUGCGUAUGCAGGGCCACUUGGUCAGUUU-----------------------GUGAAUACAAAUCUACGCGCUUUACAUA
....................(((((.((((((((........))))))))..((((....)))).((((-----------------------((....))))))...)))))........ ( -24.10)
>DroAna_CAF1 20512 120 - 1
ACAAAUUUCAAUUCCAUUCCGUAUGUGUGUGCGUUAUAAAUUGCGUAUGCAGACCCAUUUGGUCAGUUUUUUUUUUGAUUUUUUUUUAGGUUUUGAAUACAAAUCUACGCGUUUUACAUA
......(((((..((..........(((((((((........)))))))))((((.....))))........................))..)))))....................... ( -22.00)
>consensus
ACAAAUUUCAAUUCCACACCGCGUGAGUGUGCGUUAUAAAUUGCGUAUGCAGGCCCACUUGGUCAGUUU_______________________GUGAAUACAAAUCUACGCGUUUUACAUA
...................((((((.((((((((........)))))))).((((.....)))).........................................))))))......... (-20.03 = -19.87 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,324,071 – 12,324,179
Length 108
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 79.44
Mean single sequence MFE -28.58
Consensus MFE -16.10
Energy contribution -16.18
Covariance contribution 0.08
Combinations/Pair 1.11
Mean z-score -1.79
Structure conservation index 0.56
SVM decision value 0.02
SVM RNA-class probability 0.542264
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12324071 108 + 20766785
CUCAGUCCAGGUCGGUCUCCCGGGUUUCAGGUCCCCAAAGACCCAAAAG-----ACCCGCGUCCACCGACCGGCGCUUCUUGCUUUUCAAUCGACUAAAAGCUAUGAAACCGA
....((((.(((((((..(.(((((((..((((......))))....))-----))))).)...))))))))).))(((..((((((.........))))))...)))..... ( -34.00)
>DroSec_CAF1 22857 94 + 1
CUCAGUCCAGGUCGGUCCCCCGGGUUUCAGGUCCCCAAAGACCCAA-AG-----ACC-------------CGGCGCUUCUUGCUUUUCAAUCGACUAAAAGCUAUGAAACCGA
...........(((((...((((((((..((((......))))...-))-----)))-------------)))...(((..((((((.........))))))...)))))))) ( -27.50)
>DroSim_CAF1 21017 94 + 1
CUCAGUCCAGGUCGGUCCCCCGGGUUUCAGGUCCCCAAAGACCCAA-AG-----ACC-------------CGGCGCUUCUUGCUUUUCAAUCGACUAAAAGCUAUGAAACCGA
...........(((((...((((((((..((((......))))...-))-----)))-------------)))...(((..((((((.........))))))...)))))))) ( -27.50)
>DroEre_CAF1 23082 85 + 1
CUCAGUCCAGGUCGGUCCCCCGGGUUUCAGGUCCCCAAAGACC----------------CGUCCACCGCCCGGCGCUUCUUGCUUUUCAAUCGA------------AAACCGA
...(((((.((.((((....(((((((..((...))..)))))----------------))...)))))).)).)))..(((.(((((....))------------))).))) ( -23.80)
>DroYak_CAF1 21457 113 + 1
CUCAGUCCAGGUCGGUUCCCUGGGUUUCAGGUCCCCAAAGACCCCCGUCCCCUUUCCACCGUCCACCACCCGGCGCUUCUUGCUUUUCAAUCGACUAAAAGCUAUGAAGCCGA
.........((.((((.....(((..(..((((......))))...)..))).....)))).))......((((...((..((((((.........))))))...)).)))). ( -30.10)
>consensus
CUCAGUCCAGGUCGGUCCCCCGGGUUUCAGGUCCCCAAAGACCCAA_AG_____ACC__CGUCCACC__CCGGCGCUUCUUGCUUUUCAAUCGACUAAAAGCUAUGAAACCGA
............(((....)))(((((((((((......))))............................((((.....))))....................))))))).. (-16.10 = -16.18 +   0.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,324,071 – 12,324,179
Length 108
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 79.44
Mean single sequence MFE -38.12
Consensus MFE -20.28
Energy contribution -20.52
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.05
Structure conservation index 0.53
SVM decision value 0.50
SVM RNA-class probability 0.761228
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12324071 108 - 20766785
UCGGUUUCAUAGCUUUUAGUCGAUUGAAAAGCAAGAAGCGCCGGUCGGUGGACGCGGGU-----CUUUUGGGUCUUUGGGGACCUGAAACCCGGGAGACCGACCUGGACUGAG
(((((......((((((.((..........)).)))))).(((((((((...(.(((((-----..((..(((((....)))))..))))))).)..))))))).))))))). ( -43.60)
>DroSec_CAF1 22857 94 - 1
UCGGUUUCAUAGCUUUUAGUCGAUUGAAAAGCAAGAAGCGCCG-------------GGU-----CU-UUGGGUCUUUGGGGACCUGAAACCCGGGGGACCGACCUGGACUGAG
(((((..(...((((((.((..........)).)))))).(((-------------(((-----.(-(..(((((....)))))..)))))))))..)))))........... ( -38.70)
>DroSim_CAF1 21017 94 - 1
UCGGUUUCAUAGCUUUUAGUCGAUUGAAAAGCAAGAAGCGCCG-------------GGU-----CU-UUGGGUCUUUGGGGACCUGAAACCCGGGGGACCGACCUGGACUGAG
(((((..(...((((((.((..........)).)))))).(((-------------(((-----.(-(..(((((....)))))..)))))))))..)))))........... ( -38.70)
>DroEre_CAF1 23082 85 - 1
UCGGUUU------------UCGAUUGAAAAGCAAGAAGCGCCGGGCGGUGGACG----------------GGUCUUUGGGGACCUGAAACCCGGGGGACCGACCUGGACUGAG
(((((..------------...........((.....)).(((((.(((...((----------------(((((....)))))))..)))(((....))).)))))))))). ( -32.80)
>DroYak_CAF1 21457 113 - 1
UCGGCUUCAUAGCUUUUAGUCGAUUGAAAAGCAAGAAGCGCCGGGUGGUGGACGGUGGAAAGGGGACGGGGGUCUUUGGGGACCUGAAACCCAGGGAACCGACCUGGACUGAG
...(((((...((((((.........))))))..))))).(((((((((...(........(....)(((..((...(....)..))..))).)...))).))))))...... ( -36.80)
>consensus
UCGGUUUCAUAGCUUUUAGUCGAUUGAAAAGCAAGAAGCGCCGG__GGUGGACG__GGU_____CU_UUGGGUCUUUGGGGACCUGAAACCCGGGGGACCGACCUGGACUGAG
(((((((.......................((.....))...............................(((((((.(((........))).))))))).....))))))). (-20.28 = -20.52 +   0.24)

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 11:02:39 2006