Locus 7518

Sequence ID 3R_DroMel_CAF1
Location 20,120,665 – 20,120,759
Length 94
Max. P 0.997642
window12141 window12142

overview

Window 1

Location 20,120,665 – 20,120,759
Length 94
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 75.20
Mean single sequence MFE -26.96
Consensus MFE -18.66
Energy contribution -19.18
Covariance contribution 0.52
Combinations/Pair 1.26
Mean z-score -2.53
Structure conservation index 0.69
SVM decision value 2.90
SVM RNA-class probability 0.997642
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20120665 94 + 27905053
AAUAUCAGUGUGGCCAUGCAUGUUGACUCUAUAUCAAAAUC------------CAGCCAAACCUAGCCAAGCGGACUGGUCACACUGCACCAUAUAUAAGCCCACG
.....(((((((((((......((((.......))))..((------------(.((.............))))).)))))))))))................... ( -20.62)
>DroSec_CAF1 4731 86 + 1
AAUAUCAGUGUGGCCAUGCAUGCUGGACCUGGA--------------------CAGCCAAACCUAGCCAAGCGGACUGGUCACACUGCACCAUAUAUAAGCCCACG
.....((((((((((((((..(((((...(((.--------------------...)))...)))))...)))...)))))))))))................... ( -28.00)
>DroSim_CAF1 4731 94 + 1
AAAAUCAGUGUGGUCAUGCAUGCUGGACCUAUAUCAAAAUC------------CAGCCAAACCCAGCCAAGCGGACUGGUCACACUGCACCAUAUAUAAGCCCACG
.....((((((((........((((((............))------------)))).....((((((....)).))))))))))))................... ( -25.20)
>DroEre_CAF1 4748 96 + 1
CAU-UCAGUGUGACCAUACACGCCGGCUGAGUA-CAAAAUCGAAUGCCGA--------AAACCAAGCCAAGCGAACUGGUCACACUGCACCAUAUAUAAGCCCACG
...-.(((((((((((....(((.((((..((.-.....(((.....)))--------..))..))))..)))...)))))))))))................... ( -28.50)
>DroYak_CAF1 4793 105 + 1
AAUUUUAGUGUGACCAUGCAUGCCGGCUCGGUG-CAAUACCGAAAACCAGAUCCGGCCAAACCAAGCCAAGCGAACUGGUCACACUGCAGCGUAUAUAAGCCAAUG
.....(((((((((((.(..(((.((((.(((.-.....(((...........)))....))).))))..)))..))))))))))))..((........))..... ( -32.50)
>consensus
AAUAUCAGUGUGGCCAUGCAUGCUGGCUCUGUA_CAAAAUC____________CAGCCAAACCAAGCCAAGCGGACUGGUCACACUGCACCAUAUAUAAGCCCACG
.....(((((((((((....((((((((....................................)))).))))...)))))))))))................... (-18.66 = -19.18 +   0.52)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,120,665 – 20,120,759
Length 94
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 75.20
Mean single sequence MFE -33.78
Consensus MFE -17.13
Energy contribution -17.29
Covariance contribution 0.16
Combinations/Pair 1.24
Mean z-score -2.27
Structure conservation index 0.51
SVM decision value 1.76
SVM RNA-class probability 0.976154
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20120665 94 - 27905053
CGUGGGCUUAUAUAUGGUGCAGUGUGACCAGUCCGCUUGGCUAGGUUUGGCUG------------GAUUUUGAUAUAGAGUCAACAUGCAUGGCCACACUGAUAUU
.(((((((.((.((((...((((..((((((((.....)))).))))..))))------------(((((((...)))))))..)))).)))))).)))....... ( -27.20)
>DroSec_CAF1 4731 86 - 1
CGUGGGCUUAUAUAUGGUGCAGUGUGACCAGUCCGCUUGGCUAGGUUUGGCUG--------------------UCCAGGUCCAGCAUGCAUGGCCACACUGAUAUU
((((........))))...(((((((.(((....((...(((.(..((((...--------------------.))))..).)))..)).))).)))))))..... ( -26.90)
>DroSim_CAF1 4731 94 - 1
CGUGGGCUUAUAUAUGGUGCAGUGUGACCAGUCCGCUUGGCUGGGUUUGGCUG------------GAUUUUGAUAUAGGUCCAGCAUGCAUGACCACACUGAUUUU
((((........))))...(((((((.((((((.....))))))((...((((------------(((((......)))))))))..)).....)))))))..... ( -34.00)
>DroEre_CAF1 4748 96 - 1
CGUGGGCUUAUAUAUGGUGCAGUGUGACCAGUUCGCUUGGCUUGGUUU--------UCGGCAUUCGAUUUUG-UACUCAGCCGGCGUGUAUGGUCACACUGA-AUG
((((........))))...(((((((((((...((((.((((.(((..--------(((.....))).....-.))).))))))))....))))))))))).-... ( -35.90)
>DroYak_CAF1 4793 105 - 1
CAUUGGCUUAUAUACGCUGCAGUGUGACCAGUUCGCUUGGCUUGGUUUGGCCGGAUCUGGUUUUCGGUAUUG-CACCGAGCCGGCAUGCAUGGUCACACUAAAAUU
....(((........)))..((((((((((((..(((.((((((((...((((((.......))))))....-.)))))))))))..)).))))))))))...... ( -44.90)
>consensus
CGUGGGCUUAUAUAUGGUGCAGUGUGACCAGUCCGCUUGGCUAGGUUUGGCUG____________GAUUUUG_UACAGAGCCAGCAUGCAUGGCCACACUGAUAUU
...................(((((((.(((((..(((.((((..((............................))..)))))))..)).))).)))))))..... (-17.13 = -17.29 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:54 2006