Locus 1028

Sequence ID 2R_DroMel_CAF1
Location 4,233,814 – 4,233,951
Length 137
Max. P 0.940183
window1826 window1827

overview

Window 6

Location 4,233,814 – 4,233,919
Length 105
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 84.60
Mean single sequence MFE -37.52
Consensus MFE -28.75
Energy contribution -29.00
Covariance contribution 0.25
Combinations/Pair 1.23
Mean z-score -3.73
Structure conservation index 0.77
SVM decision value 1.28
SVM RNA-class probability 0.940183
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4233814 105 + 20766785
UUUGCUCAGAUGGCUGCCGUUGGAUAUCCGAUUCAGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCGAGAUGCGGCAACUUGCCAUCUUUAGUUAAA
...(((.(((((((((((.((((((((........))))))))(((((((.(((((...((...)-----------)..))))).)))))))))))....)))))))..))).... ( -40.20)
>DroSec_CAF1 3294 105 + 1
UUUGCUCAGAUGGCUGCCGUUGGAUAUCCGAUUCGGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAA
...(((.(((((((((((.(((((((((......)))))))))((((((..(((((...((...)-----------)..)))))..))))))))))....)))))))..))).... ( -39.00)
>DroSim_CAF1 3301 105 + 1
UUUGCUCAGAUGGCUGCCGUUGAAUACCCGAUUCGGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAA
...(((.(((((((((((.(((.(((((......))))).)))((((((..(((((...((...)-----------)..)))))..))))))))))....)))))))..))).... ( -35.40)
>DroEre_CAF1 3283 105 + 1
UUUGCUCAGAUGGCUGCCGUUGGAUAUCCGAUUCGGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCUUAGAUGCGGCAGCUUGCCAUCUUUAGUUUAA
...(((.(((((((((((.(((((((((......)))))))))((((((.((((((...((...)-----------)..)))))).))))))))))....)))))))..))).... ( -41.00)
>DroYak_CAF1 3324 105 + 1
UUUGCUCAGAUGGCUGCCAUUGGAUAUCCCAUUCGGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGAUCUUAGAUGCGACAACUUGCCAUCAUUAGUUUAA
........((((((.....(((((((((......)))))))))((((((.((((((...((...)-----------)..)))))).))))))........)))))).......... ( -32.10)
>DroAna_CAF1 19880 111 + 1
UUUGCACAAAUGGCCGUGCUUGGAUAUCCGAUUUUGUGUCCAAGUAUCUCAGGUUGAUGGCUUUGUUUUCAACACGCCUCGACCUUUGAUGCGGCAU----UCAUUUCUCAUAUA-
............(((((((((((((((........))))))))))(((..(((((((.(((..(((.....))).))))))))))..))))))))..----..............- ( -37.40)
>consensus
UUUGCUCAGAUGGCUGCCGUUGGAUAUCCGAUUCGGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG___________CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAA
........((((((((((.(((((((((......)))))))))((((((..(((((.......................)))))..))))))))))....)))))).......... (-28.75 = -29.00 +   0.25) 

alignment

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secondary structure

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dotplot

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Window 7

Location 4,233,853 – 4,233,951
Length 98
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 77.26
Mean single sequence MFE -22.34
Consensus MFE -12.55
Energy contribution -12.80
Covariance contribution 0.25
Combinations/Pair 1.14
Mean z-score -1.98
Structure conservation index 0.56
SVM decision value 0.84
SVM RNA-class probability 0.864578
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4233853 98 + 20766785
CUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCGAGAUGCGGCAACUUGCCAUCUUUAGUUAAAUUAUUCA--UCAGAAAUUCAU-CAUGAAAUUUAA-----U
....(((((((.(((((...((...)-----------)..))))).)))))))(((.....))).......((((((((..(((--(..((......)-))))))))))))-----) ( -25.60)
>DroSec_CAF1 3333 98 + 1
CUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAAUUAUUCA--UCAGAAAUCCAU-CAUGAAAUUUAA-----U
((((((((((..(((((...((...)-----------)..)))))..))))))(((.....)))....))))........((((--(..((......)-))))))......-----. ( -20.90)
>DroSim_CAF1 3340 98 + 1
CUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAAUUAUUCA--UCAGAAAUCCAU-CAUGAAAUUUAA-----U
((((((((((..(((((...((...)-----------)..)))))..))))))(((.....)))....))))........((((--(..((......)-))))))......-----. ( -20.90)
>DroEre_CAF1 3322 90 + 1
CUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCUUAGAUGCGGCAGCUUGCCAUCUUUAGUUUAAUUAUUCA--CCAG---------UGUGAAAUUUAA-----U
((((((((((.((((((...((...)-----------)..)))))).))))))(((.....)))....))))........((((--(...---------.)))))......-----. ( -25.20)
>DroYak_CAF1 3363 90 + 1
CUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGAUCUUAGAUGCGACAACUUGCCAUCAUUAGUUUAAUUAUUCA--UCAG---------UGUGAAAUUUAA-----U
....((((((.((((((...((...)-----------)..)))))).))))))...........................((((--(...---------.)))))......-----. ( -15.30)
>DroAna_CAF1 19919 112 + 1
CCAAGUAUCUCAGGUUGAUGGCUUUGUUUUCAACACGCCUCGACCUUUGAUGCGGCAU----UCAUUUCUCAUAUA-UUCUUCUCCCCAUUACCCCCUGAAGGAAAUUGAAUCUUAU
....(((((..(((((((.(((..(((.....))).))))))))))..))))).....----.......(((....-((((((...............))))))...)))....... ( -26.16)
>consensus
CUAAGUAUCUCAGGUUGAAGGCCUUG___________CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAAUUAUUCA__UCAGAAAUCCAU_CAUGAAAUUUAA_____U
....((((((..(((((.......................)))))..))))))(((.....)))..................................................... (-12.55 = -12.80 +   0.25) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:41 2006