Locus 4560

Sequence ID 3L_DroMel_CAF1
Location 13,113,697 – 13,113,814
Length 117
Max. P 0.870645
window7122 window7123

overview

Window 2

Location 13,113,697 – 13,113,814
Length 117
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 95.03
Mean single sequence MFE -34.89
Consensus MFE -30.25
Energy contribution -30.85
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.87
SVM decision value 0.87
SVM RNA-class probability 0.870645
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13113697 117 + 23771897
AAAUGCCCCCGAGCGGCAAGGAGAAGAA--CAACGCUCAAGAAAUUGUUGCAGAAAAUAAUUUUAUGGCUGGCCAAGGGUUGCCCCCUAUUCGGGGUUGGGGGUGGCCAAAGUAAUCUA
....(((.(((((((.............--...)))))..(((((((((......)))))))))..))..)))....(((..(((((...........)))))..)))........... ( -38.29)
>DroSec_CAF1 101357 115 + 1
AAAUGCCCUCGAGCGGCAAGGAGAAGAA--CAACGCUCAAGAAAUUGUUGCAGAAAAUAAUUUUAUUGCUGGCCAAUGGUUGCCCCCUAUUCGGGGUUGGG-G-GGCCAAAGUAAUCUA
..........(((((.............--...)))))..(((((((((......)))))))))((((((((((...))))((((((((........))))-)-)))...))))))... ( -32.89)
>DroSim_CAF1 99098 116 + 1
AAAUGCCCUCGAGCGGCAAGGAGAAGAA--CAACGCUCAAGAAAUUGUUGCAGAAAAUAAUUUUAUGGCUGGCCAAGGGUUGCCCCCUAUUCGGGGUUGGGGG-GGCCAAAGUAAUCUA
....(((((.(((((.............--...)))))..(((((((((......))))))))).(((....)))))))).(((((((..(....)...))))-)))............ ( -34.99)
>DroEre_CAF1 97975 113 + 1
AAAUGCCCUCCAGCGGCAAGGAGAAGAA--CAACGCUCAAGAAAUUGUUGCAGAAAAUAAUUUUAUGGCUGUCCAAGGGUUGCCCCCUAUUCGGGGUUGG----GGCCAAAGUAAUCUA
....(((((...(((((..(((.(....--....((.((.(((((((((......))))))))).))))).)))....)))))((((.....))))..))----)))............ ( -30.20)
>DroYak_CAF1 101372 116 + 1
AAAUGCCCCCGAGCGGCAAGGAGGAGAACACAACGCUCAAGAAAUUGUUGCAGAAAAUAAUUUUAUGGCUGGCCAAGGGUUGCCCCCUAUUUGGGGUUGGG---GGCCAAAGUAAUCUA
....(((((((((((((.....((....((....((.((.(((((((((......))))))))).)))))).))....)))))((((.....)))))))))---)))............ ( -38.10)
>consensus
AAAUGCCCUCGAGCGGCAAGGAGAAGAA__CAACGCUCAAGAAAUUGUUGCAGAAAAUAAUUUUAUGGCUGGCCAAGGGUUGCCCCCUAUUCGGGGUUGGG_G_GGCCAAAGUAAUCUA
....(((...(((((..................)))))..(((((((((......)))))))))..)))(((((.......(((((......))))).......))))).......... (-30.25 = -30.85 +   0.60)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 13,113,697 – 13,113,814
Length 117
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 95.03
Mean single sequence MFE -30.49
Consensus MFE -26.28
Energy contribution -26.64
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.31
Structure conservation index 0.86
SVM decision value 0.22
SVM RNA-class probability 0.638670
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13113697 117 - 23771897
UAGAUUACUUUGGCCACCCCCAACCCCGAAUAGGGGGCAACCCUUGGCCAGCCAUAAAAUUAUUUUCUGCAACAAUUUCUUGAGCGUUG--UUCUUCUCCUUGCCGCUCGGGGGCAUUU
..........((((((.......((((.....))))........))))))(((...(((((.((......)).)))))((((((((..(--..........)..))))))))))).... ( -31.36)
>DroSec_CAF1 101357 115 - 1
UAGAUUACUUUGGCC-C-CCCAACCCCGAAUAGGGGGCAACCAUUGGCCAGCAAUAAAAUUAUUUUCUGCAACAAUUUCUUGAGCGUUG--UUCUUCUCCUUGCCGCUCGAGGGCAUUU
............(((-(-((............))))))........(((.(((..(((....)))..)))........((((((((..(--..........)..))))))))))).... ( -30.90)
>DroSim_CAF1 99098 116 - 1
UAGAUUACUUUGGCC-CCCCCAACCCCGAAUAGGGGGCAACCCUUGGCCAGCCAUAAAAUUAUUUUCUGCAACAAUUUCUUGAGCGUUG--UUCUUCUCCUUGCCGCUCGAGGGCAUUU
..........(((((-.......((((.....)))).........)))))(((...(((((.((......)).)))))((((((((..(--..........)..))))))))))).... ( -30.19)
>DroEre_CAF1 97975 113 - 1
UAGAUUACUUUGGCC----CCAACCCCGAAUAGGGGGCAACCCUUGGACAGCCAUAAAAUUAUUUUCUGCAACAAUUUCUUGAGCGUUG--UUCUUCUCCUUGCCGCUGGAGGGCAUUU
.......(((..((.----.....(((.....)))(((((.....(((((((((..(((((.((......)).)))))..))...))))--)))......)))))))..)))....... ( -27.30)
>DroYak_CAF1 101372 116 - 1
UAGAUUACUUUGGCC---CCCAACCCCAAAUAGGGGGCAACCCUUGGCCAGCCAUAAAAUUAUUUUCUGCAACAAUUUCUUGAGCGUUGUGUUCUCCUCCUUGCCGCUCGGGGGCAUUU
............(((---(((...(((.....)))(((((....(((....)))..............(((((..((....))..)))))..........)))))....)))))).... ( -32.70)
>consensus
UAGAUUACUUUGGCC_C_CCCAACCCCGAAUAGGGGGCAACCCUUGGCCAGCCAUAAAAUUAUUUUCUGCAACAAUUUCUUGAGCGUUG__UUCUUCUCCUUGCCGCUCGAGGGCAUUU
..........(((((........((((.....)))).........)))))(((...(((((.((......)).)))))((((((((..................))))))))))).... (-26.28 = -26.64 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:35 2006