Locus 3279

Sequence ID 3L_DroMel_CAF1
Location 9,616,146 – 9,616,314
Length 168
Max. P 0.763329
window5096 window5097 window5098

overview

Window 6

Location 9,616,146 – 9,616,251
Length 105
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 78.22
Mean single sequence MFE -44.68
Consensus MFE -31.25
Energy contribution -31.83
Covariance contribution 0.58
Combinations/Pair 1.36
Mean z-score -1.07
Structure conservation index 0.70
SVM decision value 0.06
SVM RNA-class probability 0.561964
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9616146 105 - 23771897
AAGCAGCCGCAGCUGCUGCCGCCGCUGCAGUUACUCCCGGCUCAAGUGGAAAUCGUCCACCUCGAGGCGCCGAUAAGAUUCGCGCCGCAUCGGGACCUUCCAUAC
..(((((.((.((....)).)).)))))......(((((((....(((((.....))))).....(((((.((......)))))))))..))))).......... ( -41.10)
>DroVir_CAF1 12623 105 - 1
AGGCAGCUGCCGCUGCAGCCGCGGCUGCCGUGACGCCCAUUACGGGGAUCAGUCGCCCGCCUCGCGGCGCUGAUAAAAUUCGCGCUGCAUCGGGCCCCUCCAUAC
.(((((((((.((....)).)))))))))..(((.(((......)))....)))(((((....(((((((.((......)))))))))..))))).......... ( -53.30)
>DroPse_CAF1 10375 105 - 1
AAGCUGCAGCUGCCGCAGCCGCCGCUGCAGUCACGCCCGGUUCUGGUGGAAGUCGCCCGCCGCGCGGUGCAGACAAGAUACGCGCCGCCUCUGGUCCGUCUAUAC
..((((((((.((.......)).)))))))).(((.((((....(((((.......)))))..(((((((...........)))))))..))))..)))...... ( -41.30)
>DroGri_CAF1 13131 105 - 1
AGGCAGCUGCUGCUGCAGCCGCUGCUGCUGUCACGCCCAUCACGGGCGGCAGUCGACCGCCGCGUGGCGCUGAUAAAAUACGUGCUGCAUCGGGUCCCUCGAUAC
..(((((.((....(((((....)))))(((((((((....(((((((((....).))))).))))))).)))))......)))))))((((((...)))))).. ( -44.10)
>DroMoj_CAF1 12453 105 - 1
AGGCAGCCGCGGCUGCGGCUGCCGCUGCUGUUACACCCAUUACCGGAGGCAGUCGGCCGCCUCGGGGUGCUGAUAAAAUACGUGCUGCCUCGGGUCCGUCCAUAC
.(((((((((....)))))))))..................(((.((((((((((((.(((....)))))))...........)))))))).))).......... ( -46.40)
>DroPer_CAF1 10375 105 - 1
AAGCUGCAGCUGCCGCAGCCGCCGCUGCAGUCACGCCCGGUUCUGGUGGAAGUCGCCCGCCGCGCGGUGCAGACAAGAUACGGGCCGCCUCUGGUCCGUCUAUAC
..((((((((.((.......)).))))))))..((((.......))))...(((((((((...)))).)).))).....((((((((....))))))))...... ( -41.90)
>consensus
AAGCAGCAGCUGCUGCAGCCGCCGCUGCAGUCACGCCCAGUACGGGUGGAAGUCGCCCGCCGCGCGGCGCUGAUAAAAUACGCGCCGCAUCGGGUCCGUCCAUAC
..(((((.((.((....)).)).)))))......((((......(((((.......)))))..(((((((...........)))))))...)))).......... (-31.25 = -31.83 +   0.58)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,616,214 – 9,616,314
Length 100
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 84.15
Mean single sequence MFE -39.90
Consensus MFE -28.54
Energy contribution -27.90
Covariance contribution -0.64
Combinations/Pair 1.12
Mean z-score -2.22
Structure conservation index 0.72
SVM decision value 0.19
SVM RNA-class probability 0.626227
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9616214 100 + 23771897
GGAGUAACUGCAGCGGCGGCAGCAGCUGCGGCUGCUUGUGUGUAGGCUCUAAUGCCGCUGUCCGAUUUGCAGGUUCUGCGGGA--AUUGAAUAUUGAAUAUA
(.((...(((((.(((((((((((((....))))))........(((......))))))).)))...)))))...)).)....--................. ( -36.00)
>DroPse_CAF1 10443 101 + 1
GGCGUGACUGCAGCGGCGGCUGCGGCAGCUGCAGCUUGGGUAUAGGCUCGAAUGCCGCUGUCCGACUUGCAGGUUCUGCGGGUGGGAUGAAUAUUA-GUUGG
.....((((((((((((((((((((...)))))))((((((....)))))).))))))))(((.((((((((...)))))))).))).......))-))).. ( -46.80)
>DroSec_CAF1 11863 99 + 1
GAAGUAACUGCAGCGGCGGCAGCAGCUGCGGCUGCUUGUGUGUAGGCUCUAAUACCGCUGUCGGAUUUGCAGGUUCUGCGGGA--AUUGAAUAUUU-AUAUA
.(((((.(((((((((((((....)))))(.((((......)))).)........))))).))).(((((((...))))))).--......)))))-..... ( -31.10)
>DroSim_CAF1 13898 99 + 1
GGAGUAACUGCAGCGGCGGCAGCAGCUGCGGCUGCUUGUGUGUAGGCUCUAAUGCCGCUGUCCGAUUUGCAGGUUCUGCGGGA--AUUGAAUAUUU-AUAUA
(.((...(((((.(((((((((((((....))))))........(((......))))))).)))...)))))...)).)....--...........-..... ( -36.00)
>DroYak_CAF1 11892 99 + 1
GGAGUAACUGCAGCGGCGGCAGCAGCUGCAGCUGCUUGGGUAUACGCCCUAAUGCCGCUGUCUGAUUUGCAGGUGCUGCGGAU--AACAAAUAUUU-GUAUG
..((((.(((((((((((((((((((....)))))..((((....))))...)))))))))......))))).))))((((((--(.....)))))-))... ( -42.70)
>DroPer_CAF1 10443 101 + 1
GGCGUGACUGCAGCGGCGGCUGCGGCAGCUGCAGCUUGGGUAUAGGCUCGAAUGCCGCUGUCCGACUUGCAGGUUCUGCGGGUGGGAUGAACAUUA-GUUGG
.....((((((((((((((((((((...)))))))((((((....)))))).))))))))(((.((((((((...)))))))).))).......))-))).. ( -46.80)
>consensus
GGAGUAACUGCAGCGGCGGCAGCAGCUGCGGCUGCUUGGGUAUAGGCUCUAAUGCCGCUGUCCGAUUUGCAGGUUCUGCGGGA__AAUGAAUAUUU_AUAUA
.........((((((((((((((.......)))))).(.((....)).)....))))))))....(((((((...))))))).................... (-28.54 = -27.90 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,616,214 – 9,616,314
Length 100
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 84.15
Mean single sequence MFE -28.38
Consensus MFE -24.17
Energy contribution -23.58
Covariance contribution -0.58
Combinations/Pair 1.11
Mean z-score -1.78
Structure conservation index 0.85
SVM decision value 0.51
SVM RNA-class probability 0.763329
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9616214 100 - 23771897
UAUAUUCAAUAUUCAAU--UCCCGCAGAACCUGCAAAUCGGACAGCGGCAUUAGAGCCUACACACAAGCAGCCGCAGCUGCUGCCGCCGCUGCAGUUACUCC
.................--....((((...))))......(.(((((((..(((...)))......((((((....))))))...))))))))......... ( -26.20)
>DroPse_CAF1 10443 101 - 1
CCAAC-UAAUAUUCAUCCCACCCGCAGAACCUGCAAGUCGGACAGCGGCAUUCGAGCCUAUACCCAAGCUGCAGCUGCCGCAGCCGCCGCUGCAGUCACGCC
.....-.........(((.((..((((...))))..)).)))..(((((......))).........((((((((.((.......)).))))))))...)). ( -29.20)
>DroSec_CAF1 11863 99 - 1
UAUAU-AAAUAUUCAAU--UCCCGCAGAACCUGCAAAUCCGACAGCGGUAUUAGAGCCUACACACAAGCAGCCGCAGCUGCUGCCGCCGCUGCAGUUACUUC
.....-...........--....((((...))))......(.(((((((..(((...)))......((((((....))))))...))))))))......... ( -24.10)
>DroSim_CAF1 13898 99 - 1
UAUAU-AAAUAUUCAAU--UCCCGCAGAACCUGCAAAUCGGACAGCGGCAUUAGAGCCUACACACAAGCAGCCGCAGCUGCUGCCGCCGCUGCAGUUACUCC
.....-...........--....((((...))))......(.(((((((..(((...)))......((((((....))))))...))))))))......... ( -26.20)
>DroYak_CAF1 11892 99 - 1
CAUAC-AAAUAUUUGUU--AUCCGCAGCACCUGCAAAUCAGACAGCGGCAUUAGGGCGUAUACCCAAGCAGCUGCAGCUGCUGCCGCCGCUGCAGUUACUCC
.....-...........--....(((((..(((.....)))...(((((....(((......))).((((((....))))))))))).)))))......... ( -35.40)
>DroPer_CAF1 10443 101 - 1
CCAAC-UAAUGUUCAUCCCACCCGCAGAACCUGCAAGUCGGACAGCGGCAUUCGAGCCUAUACCCAAGCUGCAGCUGCCGCAGCCGCCGCUGCAGUCACGCC
.....-.........(((.((..((((...))))..)).)))..(((((......))).........((((((((.((.......)).))))))))...)). ( -29.20)
>consensus
CAUAC_AAAUAUUCAAU__ACCCGCAGAACCUGCAAAUCGGACAGCGGCAUUAGAGCCUACACACAAGCAGCCGCAGCUGCUGCCGCCGCUGCAGUUACUCC
.......................((((...))))......(.(((((((....(.(......).)..(((((.......))))).))))))))......... (-24.17 = -23.58 +  -0.58)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:43 2006