Locus 7255

Sequence ID 3R_DroMel_CAF1
Location 19,137,187 – 19,137,309
Length 122
Max. P 0.804110
window11738 window11739

overview

Window 8

Location 19,137,187 – 19,137,295
Length 108
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 82.09
Mean single sequence MFE -24.28
Consensus MFE -15.04
Energy contribution -16.84
Covariance contribution 1.80
Combinations/Pair 1.23
Mean z-score -2.13
Structure conservation index 0.62
SVM decision value 0.63
SVM RNA-class probability 0.804110
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19137187 108 + 27905053
CCUAG-------UGCAAUCUAAGCAAUUUUCUUAUCAAUUUGAGGCUAUUUUUAGUUUGCAAAACCAAGCCC--CCCAUCAUAUCUUUAUAGGUCAUGCAUCUGUAAAGUUUAUGGU
.....-------(((((.(((((.(((..(((((......)))))..)))))))).)))))...........--...((((((.((((((((((.....))))))))))..)))))) ( -24.70)
>DroSec_CAF1 20031 115 + 1
CCUAGCUUACGGCGCCAGAAAAACAAUUUUCUUAUCAAUUGUUGGCUAUUUUAAGUUUGCAAAACCAAGCCC--CUCAUCAUAUCUUUAUAGGUCAUGCAUCUGUAAAGUUUAUGGU
..........(((...((((((....))))))......((((..(((......)))..))))......))).--...((((((.((((((((((.....))))))))))..)))))) ( -24.10)
>DroSim_CAF1 20478 114 + 1
CCUAGCUUACGGCGC-AGCUAAGUAAUUUUCUUAUCAAUUGUUUUCUAUUUUAAGUUUGCAAAGCCAAGCCC--CUCAUCAUAUCUUUAUAGGUCAUGCAUCUGUAAAGUUUAUGGU
....((((..(((..-.(.((((.......)))).)..((((...((......))...)))).)))))))..--...((((((.((((((((((.....))))))))))..)))))) ( -23.10)
>DroEre_CAF1 20667 109 + 1
-------GACGGCGC-AGUUAAGCAAUUUUCUUAUCAAUUGCGAACUAUUUUUAUUUUGCAACCCAACCCCCGCGCCAUCAUAUCUUUGUAGGUCAUGCAUCUGUAAAGUUUAUGGC
-------...(((((-.(.((((.......)))).)..(((((((.((....)).)))))))..........))))).(((((.((((((((((.....))))))))))..))))). ( -25.50)
>DroYak_CAF1 21260 109 + 1
-------AACGGCGC-AGUUAAGCAAUUUUCUUAUCAAUUGCAAACUAUUUUUAUUUUGCAAAACCAAGCCCCCCCCAUCAUAUCUUUAUAGGUCAUGCAUCUGUAAAGUUUAUGGC
-------...(((((-......))..............(((((((.((....)).)))))))......))).......(((((.((((((((((.....))))))))))..))))). ( -24.00)
>consensus
CCUAG__UACGGCGC_AGCUAAGCAAUUUUCUUAUCAAUUGCAAACUAUUUUUAGUUUGCAAAACCAAGCCC__CCCAUCAUAUCUUUAUAGGUCAUGCAUCUGUAAAGUUUAUGGU
..........(((((.......))..............((((((((((....))))))))))......))).......(((((.((((((((((.....))))))))))..))))). (-15.04 = -16.84 +   1.80)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,137,218 – 19,137,309
Length 91
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 85.67
Mean single sequence MFE -19.52
Consensus MFE -14.68
Energy contribution -15.96
Covariance contribution 1.28
Combinations/Pair 1.20
Mean z-score -1.61
Structure conservation index 0.75
SVM decision value 0.12
SVM RNA-class probability 0.592708
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19137218 91 + 27905053
UUUGAGGCUAUUUUUAGUUUGCAAAACCAAGCCC--CCCAUCAUAUCUUUAUAGGUCAUGCAUCUGUAAAGUUUAUGGUU-UUCCAGUUCUAGG
((((((((((....)))))).)))).((.((..(--...((((((.((((((((((.....))))))))))..)))))).-.....)..)).)) ( -18.00)
>DroSec_CAF1 20069 91 + 1
UUGUUGGCUAUUUUAAGUUUGCAAAACCAAGCCC--CUCAUCAUAUCUUUAUAGGUCAUGCAUCUGUAAAGUUUAUGGUU-UUGCAAUUCUAAG
...............((.(((((((((((.....--..........((((((((((.....))))))))))....)))))-))))))..))... ( -20.31)
>DroSim_CAF1 20515 91 + 1
UUGUUUUCUAUUUUAAGUUUGCAAAGCCAAGCCC--CUCAUCAUAUCUUUAUAGGUCAUGCAUCUGUAAAGUUUAUGGUU-UUGCAGUUCUAGG
...............((.(((((((((((.....--..........((((((((((.....))))))))))....)))))-))))))..))... ( -20.01)
>DroEre_CAF1 20697 94 + 1
UUGCGAACUAUUUUUAUUUUGCAACCCAACCCCCGCGCCAUCAUAUCUUUGUAGGUCAUGCAUCUGUAAAGUUUAUGGCUUUCGCAGUUCUGCG
(((((((.((....)).)))))))............(((((.....((((((((((.....))))))))))...)))))...((((....)))) ( -20.90)
>DroYak_CAF1 21290 93 + 1
UUGCAAACUAUUUUUAUUUUGCAAAACCAAGCCCCCCCCAUCAUAUCUUUAUAGGUCAUGCAUCUGUAAAGUUUAUGGCU-UCGCAGUUCUAGG
(((((((.((....)).)))))))......((.....((((.....((((((((((.....))))))))))...))))..-..))......... ( -18.40)
>consensus
UUGCAAACUAUUUUUAGUUUGCAAAACCAAGCCC__CCCAUCAUAUCUUUAUAGGUCAUGCAUCUGUAAAGUUUAUGGUU_UUGCAGUUCUAGG
((((((((((....))))))))))................(((((.((((((((((.....))))))))))..)))))................ (-14.68 = -15.96 +   1.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:21 2006