Locus 3795

Sequence ID X_DroMel_CAF1
Location 10,064,734 – 10,064,870
Length 136
Max. P 0.919468
window6234 window6235 window6236

overview

Window 4

Location 10,064,734 – 10,064,841
Length 107
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 87.00
Mean single sequence MFE -27.11
Consensus MFE -21.53
Energy contribution -21.54
Covariance contribution 0.01
Combinations/Pair 1.19
Mean z-score -2.81
Structure conservation index 0.79
SVM decision value 1.13
SVM RNA-class probability 0.919468
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10064734 107 - 22224390
CUUCACUGAAAUUUGCAUAAAUUUGCAUUAUUUUCGGUGAACCGAAAAUCAUAAUGGGCGUGGACAAUGGGCUCAUAAAUUGAGUUUAGCCAA-AAAUAGAAAAAGCC
.((((((((((..((((......))))....))))))))))...............(((.(((....((((((((.....)))))))).))).-...........))) ( -28.32)
>DroSec_CAF1 1278 107 - 1
CAUCACUGAAAUUUGCAUAAAUUUGCAAAAUUUUCGGUGAACCGAAAAUCAUAAUGGGCGUGGACAAUGGGCUCAUAAAUUGAGUUUAGCCGA-AAAUAGAAGAGGCC
..((((.....((((((......))))))((((((((....))))))))..........))))....((((((((.....))))))))(((..-..........))). ( -29.00)
>DroEre_CAF1 865 104 - 1
CAUUACGGAAAUUUGCAUAAAUUUGCAUAAUUUUCGGUGAACCAAAAAUCAUAAUGGGUGUGGACAAUGGGCUCAUAAA----GCUUGCCCAAAAAAUGAAAGAAACC
((((.((((((((((((......)))).)))))))).....(((...(((......))).)))....(((((.......----....)))))...))))......... ( -24.00)
>consensus
CAUCACUGAAAUUUGCAUAAAUUUGCAUAAUUUUCGGUGAACCGAAAAUCAUAAUGGGCGUGGACAAUGGGCUCAUAAAUUGAGUUUAGCCAA_AAAUAGAAGAAGCC
..(((((((((..((((......))))....)))))))))................(((.(((....((((((((.....)))))))).))).............))) (-21.53 = -21.54 +   0.01)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,064,770 – 10,064,870
Length 100
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 83.99
Mean single sequence MFE -15.89
Consensus MFE -10.93
Energy contribution -12.30
Covariance contribution 1.37
Combinations/Pair 1.06
Mean z-score -1.90
Structure conservation index 0.69
SVM decision value 0.54
SVM RNA-class probability 0.773469
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10064770 100 + 22224390
CCCAUUGUCCACGCCCAUUAUGAUUUUCGGUUCACCGAAAAUAAUGCAAAUUUAUGCAAAUUUCAGUGAAGCUUC---CUCAACACAAAUAGC--------GCAAAAACAC
....((((.(((..........((((((((....))))))))..((((......)))).......)))..(((..---............)))--------))))...... ( -17.64)
>DroSec_CAF1 1314 103 + 1
CCCAUUGUCCACGCCCAUUAUGAUUUUCGGUUCACCGAAAAUUUUGCAAAUUUAUGCAAAUUUCAGUGAUGCUUCCUCCUCAACACAAAUAGC--------GCAAAAACAC
....((((.(((.........(((((((((....)))))))))(((((......)))))......)))..(((.................)))--------))))...... ( -18.53)
>DroEre_CAF1 898 108 + 1
CCCAUUGUCCACACCCAUUAUGAUUUUUGGUUCACCGAAAAUUAUGCAAAUUUAUGCAAAUUUCCGUAAUGCUUC---CUCAACCCAAACAGCACAAAAACGCAAAAACAC
...............(((((((((((((((....))))))))..((((......))))......)))))))....---.............((........))........ ( -16.10)
>DroYak_CAF1 32410 98 + 1
CCCAUUGUCCACACCCAUUAUGAUAUUCGGUUCACCAAAAAUGAUGCAAAUUUAUGCAAAUUCCCGUGAGGCUUC---CUCAAACGAAA----------AAAAAAAAACAC
.........................((((...............((((......))))........(((((...)---))))..)))).----------............ ( -11.30)
>consensus
CCCAUUGUCCACACCCAUUAUGAUUUUCGGUUCACCGAAAAUUAUGCAAAUUUAUGCAAAUUUCAGUGAUGCUUC___CUCAACACAAAUAGC________GCAAAAACAC
.........(((.......(((((((((((....)))))))))))(((......)))........)))........................................... (-10.93 = -12.30 +   1.37)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,064,770 – 10,064,870
Length 100
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 83.99
Mean single sequence MFE -26.53
Consensus MFE -16.96
Energy contribution -16.65
Covariance contribution -0.31
Combinations/Pair 1.26
Mean z-score -1.74
Structure conservation index 0.64
SVM decision value 0.09
SVM RNA-class probability 0.580292
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10064770 100 - 22224390
GUGUUUUUGC--------GCUAUUUGUGUUGAG---GAAGCUUCACUGAAAUUUGCAUAAAUUUGCAUUAUUUUCGGUGAACCGAAAAUCAUAAUGGGCGUGGACAAUGGG
.....((..(--------(((..(((((((..(---(....((((((((((..((((......))))....))))))))))))...)).)))))..))))..))....... ( -29.60)
>DroSec_CAF1 1314 103 - 1
GUGUUUUUGC--------GCUAUUUGUGUUGAGGAGGAAGCAUCACUGAAAUUUGCAUAAAUUUGCAAAAUUUUCGGUGAACCGAAAAUCAUAAUGGGCGUGGACAAUGGG
.....((..(--------(((..(((((((..((.(....).(((((((((((((((......))))))..))))))))).))...)).)))))..))))..))....... ( -30.60)
>DroEre_CAF1 898 108 - 1
GUGUUUUUGCGUUUUUGUGCUGUUUGGGUUGAG---GAAGCAUUACGGAAAUUUGCAUAAAUUUGCAUAAUUUUCGGUGAACCAAAAAUCAUAAUGGGUGUGGACAAUGGG
.((((..(((.(..(((((...((((((((...---..)))....((((((((((((......)))).)))))))).....)))))...))))).).)))..))))..... ( -25.90)
>DroYak_CAF1 32410 98 - 1
GUGUUUUUUUUU----------UUUCGUUUGAG---GAAGCCUCACGGGAAUUUGCAUAAAUUUGCAUCAUUUUUGGUGAACCGAAUAUCAUAAUGGGUGUGGACAAUGGG
((((.......(----------(..(((..(((---(...)))))))..))...))))...((..((((...(((((....)))))..........))))..))....... ( -20.02)
>consensus
GUGUUUUUGC________GCUAUUUGGGUUGAG___GAAGCAUCACGGAAAUUUGCAUAAAUUUGCAUAAUUUUCGGUGAACCGAAAAUCAUAAUGGGCGUGGACAAUGGG
.((((..(((................................(((((((((..((((......))))....))))))))).(((..........))))))..))))..... (-16.96 = -16.65 +  -0.31)

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 11:08:48 2006