Locus 4200

Sequence ID 3R_DroMel_CAF1
Location 11,349,946 – 11,350,085
Length 139
Max. P 0.549845
window6772 window6773

overview

Window 2

Location 11,349,946 – 11,350,046
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.51
Mean single sequence MFE -35.50
Consensus MFE -32.00
Energy contribution -31.68
Covariance contribution -0.32
Combinations/Pair 1.17
Mean z-score -1.41
Structure conservation index 0.90
SVM decision value -0.02
SVM RNA-class probability 0.525378
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11349946 100 + 27905053
GAU--------------UCUGGAUUCGAGCGGAAGUUGCAACUGCAGC------GGCAAAAGGGCGGAAGUGGAUGUUGCAGAUACUAAGCCGGCGGUUGGGGUUAUUCAGCCGAUGGAA
..(--------------((((........)))))(((((....)))))------.((((....((....)).....))))..........(((.((((((((....)))))))).))).. ( -30.00)
>DroSec_CAF1 92195 106 + 1
GAU--------------UCUGGAUUCGAGCGGAAGCUGCAACUGCAGCAGCAGCAGCAGAAGGGCGGAAGUGGAUGUUGCAGAUACUAAGCCGGCGGUUGGGGUUAUUCAACCGAUGGAA
..(--------------((((........)))))(((((....)))))....((((((.....((....))...))))))..........(((.((((((((....)))))))).))).. ( -36.50)
>DroSim_CAF1 87384 106 + 1
GAU--------------UCUGGAUUCGAGCGGAAGUUGCAACUGCAGCAGCAGCAGCAGAAGGGCGGAAGUGGAUGUUGCAGAUACUAAGCCGGCGGUUGGGGUUAUUUAACCGAUGGAA
..(--------------((((........)))))(((((....)))))....((((((.....((....))...))))))..........(((.((((((((....)))))))).))).. ( -32.00)
>DroEre_CAF1 85071 117 + 1
UAUACAGUAUACAGUUUACUGGACGCGAGCGGAAGUUGCAACUGCAGCGGCA---GCAGCAGGGCGGAAGUGGAUGCUGCAGAUACUAAGCCGGCGGUUGGGGUUGUUCAGCCGAUGGAA
.....(((((.(((....)))...((.(((....)))))..((((((((((.---...))...((....))...)))))))))))))...(((.((((((((....)))))))).))).. ( -41.90)
>DroYak_CAF1 87374 109 + 1
AAUUCCGAA-------UUCUGGAUUCGAGCGGAAGUUGCAACUGCAGCAGCA---GCAGAGGGGCGGAAGUGGAUGCUGCAGAUACUAAGCCGGCGGUUGGGGC-AUUCAGCCGAUGGAA
...((((..-------...)))).(((.((.((((((.(((((((.((.(((---(((.....((....))...))))))((...))..))..))))))).)))-.))).)))))..... ( -37.10)
>consensus
GAU______________UCUGGAUUCGAGCGGAAGUUGCAACUGCAGCAGCA___GCAGAAGGGCGGAAGUGGAUGUUGCAGAUACUAAGCCGGCGGUUGGGGUUAUUCAGCCGAUGGAA
...................(((.....(((....)))....((((((((((....))......((....))...))))))))...)))..(((.((((((((....)))))))).))).. (-32.00 = -31.68 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,349,972 – 11,350,085
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.02
Mean single sequence MFE -32.16
Consensus MFE -28.56
Energy contribution -28.40
Covariance contribution -0.16
Combinations/Pair 1.14
Mean z-score -1.17
Structure conservation index 0.89
SVM decision value 0.03
SVM RNA-class probability 0.549845
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11349972 113 + 27905053
ACUGCAGC------GGCAAAAGGGCGGAAGUGGAUGUUGCAGAUACUAAGCCGGCGGUUGGGGUUAUUCAGCCGAUGGAAUCAGAAAUCAGCGAG-AAUGCAAAUACUCGUAAUUAAAUG
.(((((((------(.(......((....)).).))))))))...((...(((.((((((((....)))))))).)))....))......(((((-.((....)).)))))......... ( -31.40)
>DroSec_CAF1 92221 119 + 1
ACUGCAGCAGCAGCAGCAGAAGGGCGGAAGUGGAUGUUGCAGAUACUAAGCCGGCGGUUGGGGUUAUUCAACCGAUGGAAUCAGAAAUCAGCGAA-AAUGCAAAUACUCGUAAUUAAAUG
..((((...((.((((((.....((....))...)))))).(((.((...(((.((((((((....)))))))).)))....))..))).))...-..)))).................. ( -31.80)
>DroSim_CAF1 87410 119 + 1
ACUGCAGCAGCAGCAGCAGAAGGGCGGAAGUGGAUGUUGCAGAUACUAAGCCGGCGGUUGGGGUUAUUUAACCGAUGGAAUCAGAAAUCAGCGAG-AAUGCAAAUACUCGUAAUUAAAUG
.((((((((((....))......((....))...))))))))...((...(((.((((((((....)))))))).)))....))......(((((-.((....)).)))))......... ( -33.20)
>DroEre_CAF1 85111 117 + 1
ACUGCAGCGGCA---GCAGCAGGGCGGAAGUGGAUGCUGCAGAUACUAAGCCGGCGGUUGGGGUUGUUCAGCCGAUGGAAUCAGAAAUCAGCGAGAAAUGCAAAUACUCUUAAUUAAAUG
..((((.(.((.---((((((..((....))...)))))).(((.((...(((.((((((((....)))))))).)))....))..))).))..)...)))).................. ( -34.40)
>DroYak_CAF1 87407 116 + 1
ACUGCAGCAGCA---GCAGAGGGGCGGAAGUGGAUGCUGCAGAUACUAAGCCGGCGGUUGGGGC-AUUCAGCCGAUGGAAUCAGAAAUCAGCGAGAAAUGCAAAUACUCUUAAUUAAAUG
..((((.(.(((---(((.....((....))...)))))).(((.((...(((.(((((((...-..))))))).)))....))..))).....)...)))).................. ( -30.00)
>consensus
ACUGCAGCAGCA___GCAGAAGGGCGGAAGUGGAUGUUGCAGAUACUAAGCCGGCGGUUGGGGUUAUUCAGCCGAUGGAAUCAGAAAUCAGCGAG_AAUGCAAAUACUCGUAAUUAAAUG
.((((((((((....))......((....))...))))))))...((...(((.((((((((....)))))))).)))....))......(((.....)))................... (-28.56 = -28.40 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:27 2006