Locus 1008

Sequence ID 2L_DroMel_CAF1
Location 2,893,375 – 2,893,483
Length 108
Max. P 0.999137
window1618 window1619

overview

Window 8

Location 2,893,375 – 2,893,483
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.54
Mean single sequence MFE -26.80
Consensus MFE -22.59
Energy contribution -23.71
Covariance contribution 1.12
Combinations/Pair 1.04
Mean z-score -2.91
Structure conservation index 0.84
SVM decision value 3.39
SVM RNA-class probability 0.999137
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2893375 108 + 22407834
UGGCCACGCUGCCAACUGUGAAUCAUCAGAGUGGGCCACCUUGUCCUUUCACC-----UCAAUC-------GCAUUGGCCCACUUUAACUAUUGACCCACACACCUAAUUGAUAUGCCUC
((((......))))..((((..(((..(((((((((((...(((.........-----......-------))).)))))))))))......)))..))))................... ( -26.96)
>DroSec_CAF1 12025 108 + 1
UGGCCACGCUGCCAACUGUGAAUCAUCAGAGUGGGCCACCUUGCCCUUUCACC-----UCAAUC-------GCAUUGGCCCACUUAAACUAUUGACCCACACACCUAAUUGAUAUGCCUC
((((......))))..((((..(((..(((((((((((...(((.........-----......-------))).)))))))))....))..)))..))))................... ( -28.06)
>DroSim_CAF1 12357 108 + 1
UGGCCACGCUGCCAACUGUGAAUCAUCAGAGUGGGCCACCUUGCCCUUUCACC-----UCAAUC-------GCAUUGGCCCACUUAAACUAUUGACCCACACACCUAAUUGAUAUGCCUC
((((......))))..((((..(((..(((((((((((...(((.........-----......-------))).)))))))))....))..)))..))))................... ( -28.06)
>DroEre_CAF1 12270 113 + 1
UGGCCACGCUGCCAACUGUGAAUCAUCA--GUGGGCCACCUUGCCAUUUCACC-----UCCAUCGCAUUGGCCAUUGGCCCACUUAAACUAUUGACCCACACACCUAAUUGAUAUGCCUC
((((......))))..((((..(((..(--((((((((....((((.......-----..........))))...)))))))))........)))..))))................... ( -28.93)
>DroYak_CAF1 12408 111 + 1
UGGCCACGCUGCCAACUGUGAAUCAUCA--GUGGGCCACCUUGCCCUUUCACCUCACCUCCAUC-------CCAUUGGCCCACUUAAACUAUUGACCCACACACCUAAUUGAUAUGCCUC
((((......))))..((((..(((..(--((((((((..........................-------....)))))))))........)))..))))................... ( -22.01)
>consensus
UGGCCACGCUGCCAACUGUGAAUCAUCAGAGUGGGCCACCUUGCCCUUUCACC_____UCAAUC_______GCAUUGGCCCACUUAAACUAUUGACCCACACACCUAAUUGAUAUGCCUC
((((......))))..((((..(((...((((((((((...(((...........................))).)))))))))).......)))..))))................... (-22.59 = -23.71 +   1.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,893,375 – 2,893,483
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.54
Mean single sequence MFE -36.74
Consensus MFE -30.91
Energy contribution -31.71
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.34
Structure conservation index 0.84
SVM decision value 2.54
SVM RNA-class probability 0.995065
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2893375 108 - 22407834
GAGGCAUAUCAAUUAGGUGUGUGGGUCAAUAGUUAAAGUGGGCCAAUGC-------GAUUGA-----GGUGAAAGGACAAGGUGGCCCACUCUGAUGAUUCACAGUUGGCAGCGUGGCCA
..((((((((.....)))))((((((((.(((....(((((((((....-------..(((.-----..........)))..)))))))))))).)))))))).............))). ( -34.40)
>DroSec_CAF1 12025 108 - 1
GAGGCAUAUCAAUUAGGUGUGUGGGUCAAUAGUUUAAGUGGGCCAAUGC-------GAUUGA-----GGUGAAAGGGCAAGGUGGCCCACUCUGAUGAUUCACAGUUGGCAGCGUGGCCA
..((((((((.....)))))((((((((.(((....(((((((((.(((-------..((..-----.....))..)))...)))))))))))).)))))))).............))). ( -38.80)
>DroSim_CAF1 12357 108 - 1
GAGGCAUAUCAAUUAGGUGUGUGGGUCAAUAGUUUAAGUGGGCCAAUGC-------GAUUGA-----GGUGAAAGGGCAAGGUGGCCCACUCUGAUGAUUCACAGUUGGCAGCGUGGCCA
..((((((((.....)))))((((((((.(((....(((((((((.(((-------..((..-----.....))..)))...)))))))))))).)))))))).............))). ( -38.80)
>DroEre_CAF1 12270 113 - 1
GAGGCAUAUCAAUUAGGUGUGUGGGUCAAUAGUUUAAGUGGGCCAAUGGCCAAUGCGAUGGA-----GGUGAAAUGGCAAGGUGGCCCAC--UGAUGAUUCACAGUUGGCAGCGUGGCCA
..((((((((.....)))))((..((((((((((..(((((((((...((((...((.....-----..))...))))....))))))))--)...))))....)))))).))...))). ( -39.20)
>DroYak_CAF1 12408 111 - 1
GAGGCAUAUCAAUUAGGUGUGUGGGUCAAUAGUUUAAGUGGGCCAAUGG-------GAUGGAGGUGAGGUGAAAGGGCAAGGUGGCCCAC--UGAUGAUUCACAGUUGGCAGCGUGGCCA
...(((((((.....))))))).(((((.........((..((((((..-------(.((((.....(((....((((......))))))--).....))))).)))))).)).))))). ( -32.50)
>consensus
GAGGCAUAUCAAUUAGGUGUGUGGGUCAAUAGUUUAAGUGGGCCAAUGC_______GAUUGA_____GGUGAAAGGGCAAGGUGGCCCACUCUGAUGAUUCACAGUUGGCAGCGUGGCCA
..((((((((.....)))))((((((((.(((....(((((((((.((.............................))...)))))))))))).)))))))).............))). (-30.91 = -31.71 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:56 2006