Locus 3990

Sequence ID 2L_DroMel_CAF1
Location 11,617,487 – 11,617,604
Length 117
Max. P 0.975090
window6293 window6294

overview

Window 3

Location 11,617,487 – 11,617,604
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 88.32
Mean single sequence MFE -39.18
Consensus MFE -33.82
Energy contribution -33.88
Covariance contribution 0.06
Combinations/Pair 1.19
Mean z-score -2.70
Structure conservation index 0.86
SVM decision value 1.74
SVM RNA-class probability 0.975090
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11617487 117 + 22407834
GCGGCUAGUUGCGGGCUCGUAAUUCGCAGCAAAGGUAUAAGUUUUAUGACCAUUGCUGCGAUUUUUGUAGCUGAUGUCGCGAGAGUGCUGGCAACUUCGCUUUUUUAUAGCUAAAUG
((((..((((((.(((.(.....(((((((((.((((((.....))).))).))))))))).(((((..((....))..)))))).))).))))))))))................. ( -43.10)
>DroSec_CAF1 70788 117 + 1
GCGGCUAGUUGCGGGCUCGUAAUUCGCAGCAAAGGUAUAAGUUUUAUGACCAUUGCUGCGAUUUUUGUAGCUGAUGUCCCGAGAGUACUGGCAACAUAGCCUUUUUAUAGCUAAAUG
..((((((((((.(((((.....(((((((((.((((((.....))).))).)))))))))...(((..((....))..))))))..)).))))).)))))................ ( -40.40)
>DroSim_CAF1 74574 117 + 1
GCGGCUAGUUGCGGGCUCGUAAUUCGCAGCAAAGGUAUAAGUUUUAUGACCAUUGCUGCGAUUUUUGUAGCUGAUGUCGCGAUAGUGCUGGCAACAUAGCCUUUUUAAAGCUAAAUG
..((((((((((.(((.(.....(((((((((.((((((.....))).))).)))))))))...(((..((....))..)))..).))).))))).)))))................ ( -44.10)
>DroEre_CAF1 101259 116 + 1
GCGGCUAGUUG-GGGCUCGUAAUUCGCAGCAAAGGUAUAAGUUUUAUGACCAUUGCUGCGAUUUUUGUAGCUGGUGUCGCCCGAGUGCUGGCCACUUAGCUUUUUUAUAGCUACACA
..((((((((.-((((.......(((((((((.((((((.....))).))).)))))))))........((....)).)))).)..)))))))...(((((.......))))).... ( -41.40)
>DroYak_CAF1 74001 117 + 1
GCGGCUAGUUGCGGGCUCGUAAUUCGCAGCAGAGGUAUAAGUUUUAUGACCAUUGCUGCGAUUUUUGUAGCUGCUGUCGCCCGAGUGCUGGCAACUCAGCUUUUUUAUAGCUAAAUA
(..((((((..(((((.......(((((((((.((((((.....))).))).)))))))))........((....)).)))))...))))))..)..((((.......))))..... ( -40.70)
>DroAna_CAF1 83965 115 + 1
GCGGCUAGUUGUGGCCUCGUAAUUCGUAGCAAAGGUAUAAGUUUUAUGACCAUUGCCACGAUUUUUGUAGCUCUUGUAAC--UAGUGAUGACAGCUUGGCUAUUUUAUUUGUUUAUU
..(((((((((((((..((.((.((((.((((.((((((.....))).))).)))).)))).)).))..)))........--((....))))))).)))))................ ( -25.40)
>consensus
GCGGCUAGUUGCGGGCUCGUAAUUCGCAGCAAAGGUAUAAGUUUUAUGACCAUUGCUGCGAUUUUUGUAGCUGAUGUCGCGAGAGUGCUGGCAACUUAGCUUUUUUAUAGCUAAAUG
..((((((((((.(((.(.....(((((((((.((((((.....))).))).))))))))).....(..((....))..)....).))).))))).)))))................ (-33.82 = -33.88 +   0.06)

alignment

Postscript

secondary structure

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dotplot

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Window 4

Location 11,617,487 – 11,617,604
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 88.32
Mean single sequence MFE -34.07
Consensus MFE -27.45
Energy contribution -27.32
Covariance contribution -0.13
Combinations/Pair 1.25
Mean z-score -3.64
Structure conservation index 0.81
SVM decision value 1.64
SVM RNA-class probability 0.969102
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11617487 117 - 22407834
CAUUUAGCUAUAAAAAAGCGAAGUUGCCAGCACUCUCGCGACAUCAGCUACAAAAAUCGCAGCAAUGGUCAUAAAACUUAUACCUUUGCUGCGAAUUACGAGCCCGCAACUAGCCGC
.................((..((((((..((......((.......))........(((((((((.(((.(((.....)))))).))))))))).......))..)))))).))... ( -32.20)
>DroSec_CAF1 70788 117 - 1
CAUUUAGCUAUAAAAAGGCUAUGUUGCCAGUACUCUCGGGACAUCAGCUACAAAAAUCGCAGCAAUGGUCAUAAAACUUAUACCUUUGCUGCGAAUUACGAGCCCGCAACUAGCCGC
................(((((.(((((..((.((....))))....(((.......(((((((((.(((.(((.....)))))).)))))))))......)))..)))))))))).. ( -37.02)
>DroSim_CAF1 74574 117 - 1
CAUUUAGCUUUAAAAAGGCUAUGUUGCCAGCACUAUCGCGACAUCAGCUACAAAAAUCGCAGCAAUGGUCAUAAAACUUAUACCUUUGCUGCGAAUUACGAGCCCGCAACUAGCCGC
................(((((.(((((..((......((.......))........(((((((((.(((.(((.....)))))).))))))))).......))..)))))))))).. ( -37.80)
>DroEre_CAF1 101259 116 - 1
UGUGUAGCUAUAAAAAAGCUAAGUGGCCAGCACUCGGGCGACACCAGCUACAAAAAUCGCAGCAAUGGUCAUAAAACUUAUACCUUUGCUGCGAAUUACGAGCCC-CAACUAGCCGC
....(((((.......))))).(((((.((..(((((((.......))).......(((((((((.(((.(((.....)))))).)))))))))....))))...-...)).))))) ( -36.40)
>DroYak_CAF1 74001 117 - 1
UAUUUAGCUAUAAAAAAGCUGAGUUGCCAGCACUCGGGCGACAGCAGCUACAAAAAUCGCAGCAAUGGUCAUAAAACUUAUACCUCUGCUGCGAAUUACGAGCCCGCAACUAGCCGC
...((((((.......))))))((((((........)))))).((.(((.......((((((((..(((.(((.....))))))..))))))))......)))..)).......... ( -36.82)
>DroAna_CAF1 83965 115 - 1
AAUAAACAAAUAAAAUAGCCAAGCUGUCAUCACUA--GUUACAAGAGCUACAAAAAUCGUGGCAAUGGUCAUAAAACUUAUACCUUUGCUACGAAUUACGAGGCCACAACUAGCCGC
..............(((((...)))))..((..((--(((.....)))))......(((((((((.(((.(((.....)))))).))))))))).....))(((........))).. ( -24.20)
>consensus
CAUUUAGCUAUAAAAAAGCUAAGUUGCCAGCACUCUCGCGACAUCAGCUACAAAAAUCGCAGCAAUGGUCAUAAAACUUAUACCUUUGCUGCGAAUUACGAGCCCGCAACUAGCCGC
.................((((.(((((..((......((.......))........(((((((((.(((.(((.....)))))).))))))))).......))..)))))))))... (-27.45 = -27.32 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:37 2006