Locus 6885

Sequence ID 3R_DroMel_CAF1
Location 18,194,882 – 18,195,034
Length 152
Max. P 0.955069
window11176 window11177 window11178

overview

Window 6

Location 18,194,882 – 18,194,994
Length 112
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 92.32
Mean single sequence MFE -31.08
Consensus MFE -22.82
Energy contribution -23.38
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.02
Structure conservation index 0.73
SVM decision value 0.22
SVM RNA-class probability 0.640281
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18194882 112 + 27905053
CCUCU-UGGGC-CC-AAACUCUCUCUCCUCUGCGUUUAUGCUCUCUU-UGCUGUCGGGCUACCGACAUUCUGAGCGCUUUU-UCUGCGGCUAGGAAAAUUUCCGCUUGCCAAA-AAAU
.....-..(((-..-..........(((((((((.....((.(((..-...((((((....))))))....))).))....-..)))))..))))............)))...-.... ( -28.15)
>DroSec_CAF1 2987 113 + 1
CCUCU-UGGGCCCC-AAACUCUCUCUCCUCUUCGUUUGUGCUCUCUU-UUCUGUCGGGCUACCGACAUUCUGAGAGCUUUU-GCUGCGGCUCGGAAAAUUUCCGCUUGCCAAA-AAAU
.....-..(((..(-((((..............))))).((((((..-...((((((....))))))....))))))....-)))..(((.((((.....))))...)))...-.... ( -33.24)
>DroSim_CAF1 2891 113 + 1
CCUCU-UGGGCCCC-AAACUCUCUCUCCUCUUCGUUUGUGCUCUCUU-UUCUGUCGGGCUACCGACAUUCUGAGCGCUUUU-GCUGCGGCUCGGAAAAUUUCCGCUUGCCAAA-AAAU
.....-..(((..(-((((..............))))).((......-...((((((....))))))((((((((((....-...)).)))))))).......))..)))...-.... ( -30.44)
>DroEre_CAF1 3191 116 + 1
CCUCUCUGGGC-CC-AAACUCUCUCGCCUCUGCGAUUGUGCUCUCUUUUUCUUUCGGGCUACCGACAUUCUGAGCGCUUUUCGCUGCGGCUCGGGAAAUUUCCGCUUGCCAAAAAAAU
........(((-..-..........(((.(.((((..((((((..........((((....))))......))))))...)))).).))).(((((...)))))...)))........ ( -33.49)
>DroYak_CAF1 3105 117 + 1
CCUCUCUGGGC-CCGAAACUCUCUCGCCUCUGCGUUGCUGCUCUCUUUUUCUUUCGGGCUACCGACAUUCUGAGCGCUUUUCGCUGCGGCUCGGGAAAUUUCCGCUUGCCAAAAAAAU
........(((-(.((((.((((..(((.(.(((..((.((((..........((((....))))......))))))....))).).)))..))))..)))).)...)))........ ( -30.09)
>consensus
CCUCU_UGGGC_CC_AAACUCUCUCUCCUCUGCGUUUGUGCUCUCUU_UUCUGUCGGGCUACCGACAUUCUGAGCGCUUUU_GCUGCGGCUCGGAAAAUUUCCGCUUGCCAAA_AAAU
........(((........................................((((((....))))))((((((((((........)).))))))))...........)))........ (-22.82 = -23.38 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,194,919 – 18,195,034
Length 115
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 95.05
Mean single sequence MFE -33.94
Consensus MFE -31.20
Energy contribution -31.60
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.27
Structure conservation index 0.92
SVM decision value 0.62
SVM RNA-class probability 0.803577
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18194919 115 + 27905053
CUCUCUU-UGCUGUCGGGCUACCGACAUUCUGAGCGCUUUU-UCUGCGGCUAGGAAAAUUUCCGCUUGCCAAA-AAAUCUGUGUGGCAGUCGAACUUUUUGUCUCGUCCUCGCCGCGU
..(((..-...((((((....))))))....))).......-...(((((.((((..........((((((..-.........)))))).(((((.....)).))))))).))))).. ( -34.70)
>DroSec_CAF1 3025 115 + 1
CUCUCUU-UUCUGUCGGGCUACCGACAUUCUGAGAGCUUUU-GCUGCGGCUCGGAAAAUUUCCGCUUGCCAAA-AAAUCUGUGCGGCAGUCGAACUUUUUGUCUCGUCCUCGCCGCGU
(((((..-...((((((....))))))....))))).....-.....(((.((((.....))))...)))...-........(((((((.(((((.....)).)))..)).))))).. ( -38.60)
>DroSim_CAF1 2929 115 + 1
CUCUCUU-UUCUGUCGGGCUACCGACAUUCUGAGCGCUUUU-GCUGCGGCUCGGAAAAUUUCCGCUUGCCAAA-AAAUCUGUGCGGCAGUCAAACUUUUUGUCUCGUCCUUGCCGCGU
..(((..-...((((((....))))))....))).((....-)).(((((..(((........(((.((((..-.....)).)))))((.(((.....))).))..)))..))))).. ( -33.00)
>DroEre_CAF1 3229 118 + 1
CUCUCUUUUUCUUUCGGGCUACCGACAUUCUGAGCGCUUUUCGCUGCGGCUCGGGAAAUUUCCGCUUGCCAAAAAAAUCUGUGCGGCAGUCGAACUUUUUGUCUCGUCCUCGCCGCGU
.............((((....))))..((((((((((........)).))))))))..........................(((((((.(((((.....)).)))..)).))))).. ( -31.70)
>DroYak_CAF1 3144 118 + 1
CUCUCUUUUUCUUUCGGGCUACCGACAUUCUGAGCGCUUUUCGCUGCGGCUCGGGAAAUUUCCGCUUGCCAAAAAAAUCUGUGCGGCAGUCGAACUUUUUGUCUCGUCCUCGCCGCGU
.............((((....))))..((((((((((........)).))))))))..........................(((((((.(((((.....)).)))..)).))))).. ( -31.70)
>consensus
CUCUCUU_UUCUGUCGGGCUACCGACAUUCUGAGCGCUUUU_GCUGCGGCUCGGAAAAUUUCCGCUUGCCAAA_AAAUCUGUGCGGCAGUCGAACUUUUUGUCUCGUCCUCGCCGCGU
..(((......((((((....))))))....))).((........))(((.(((((...)))))...)))............(((((((.(((((.....)).)))..)).))))).. (-31.20 = -31.60 +   0.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,194,919 – 18,195,034
Length 115
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 95.05
Mean single sequence MFE -36.28
Consensus MFE -30.66
Energy contribution -31.10
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.86
Structure conservation index 0.85
SVM decision value 1.45
SVM RNA-class probability 0.955069
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18194919 115 - 27905053
ACGCGGCGAGGACGAGACAAAAAGUUCGACUGCCACACAGAUUU-UUUGGCAAGCGGAAAUUUUCCUAGCCGCAGA-AAAAGCGCUCAGAAUGUCGGUAGCCCGACAGCA-AAGAGAG
..(((((.((((.((.........((((..(((((.........-..)))))..))))..)).)))).)))))...-.......(((....((((((....))))))...-..))).. ( -36.20)
>DroSec_CAF1 3025 115 - 1
ACGCGGCGAGGACGAGACAAAAAGUUCGACUGCCGCACAGAUUU-UUUGGCAAGCGGAAAUUUUCCGAGCCGCAGC-AAAAGCUCUCAGAAUGUCGGUAGCCCGACAGAA-AAGAGAG
..(((((..(((((((........)))).((((.((.((((...-))))))..))))......)))..)))))...-.....(((((....((((((....))))))...-..))))) ( -39.60)
>DroSim_CAF1 2929 115 - 1
ACGCGGCAAGGACGAGACAAAAAGUUUGACUGCCGCACAGAUUU-UUUGGCAAGCGGAAAUUUUCCGAGCCGCAGC-AAAAGCGCUCAGAAUGUCGGUAGCCCGACAGAA-AAGAGAG
..(((((..........(((((((((((.........)))))))-)))).....((((.....)))).))))).((-....)).(((....((((((....))))))...-..))).. ( -36.40)
>DroEre_CAF1 3229 118 - 1
ACGCGGCGAGGACGAGACAAAAAGUUCGACUGCCGCACAGAUUUUUUUGGCAAGCGGAAAUUUCCCGAGCCGCAGCGAAAAGCGCUCAGAAUGUCGGUAGCCCGAAAGAAAAAGAGAG
..((((((.((((..........))))...)))))).....(((((((((...((.((...(((..((((.((........)))))).)))..)).))...)))))))))........ ( -34.60)
>DroYak_CAF1 3144 118 - 1
ACGCGGCGAGGACGAGACAAAAAGUUCGACUGCCGCACAGAUUUUUUUGGCAAGCGGAAAUUUCCCGAGCCGCAGCGAAAAGCGCUCAGAAUGUCGGUAGCCCGAAAGAAAAAGAGAG
..((((((.((((..........))))...)))))).....(((((((((...((.((...(((..((((.((........)))))).)))..)).))...)))))))))........ ( -34.60)
>consensus
ACGCGGCGAGGACGAGACAAAAAGUUCGACUGCCGCACAGAUUU_UUUGGCAAGCGGAAAUUUUCCGAGCCGCAGC_AAAAGCGCUCAGAAUGUCGGUAGCCCGACAGAA_AAGAGAG
..(((((..((.((((........)))).((((.((.((((....))))))..)))).......))..)))))...........(((....((((((....))))))......))).. (-30.66 = -31.10 +   0.44)

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 12:32:28 2006