Locus 6829

Sequence ID 3R_DroMel_CAF1
Location 18,057,214 – 18,057,357
Length 143
Max. P 0.986874
window11084 window11085

overview

Window 4

Location 18,057,214 – 18,057,319
Length 105
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 71.31
Mean single sequence MFE -26.13
Consensus MFE -8.55
Energy contribution -9.83
Covariance contribution 1.28
Combinations/Pair 1.19
Mean z-score -2.72
Structure conservation index 0.33
SVM decision value 2.06
SVM RNA-class probability 0.986874
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18057214 105 - 27905053
CAAUCAGUCCUGGUCAAGUGGGUGUGGAAACACCGGAAAAUAAUUUGGCAACAAAGUUGAGGU-UAU-CAAUCAAA----U---AU-AUUAUUUUAACC----UACUAAUCAGUAAAUA
.........(((((..((((((((((....)))...(((((((((((....))))(((((...-..)-))))....----.---..-.))))))).)))----)))).)))))...... ( -26.50)
>DroSec_CAF1 99381 108 - 1
CAAUCAGUCCUGGUCAAGUGGGUGUGGAAACACCGGAAAAUAAUGUGGCAACAAAGUUGAGGA-AAU-CAAUCAAA----U---AU-AUUAUUUUAACCU-UCUACUAAUCAGUAAAAA
.........(((((..(((((((((....)))))(((((((((((((....)...(((((...-..)-))))....----.---))-))))))))..)).-..)))).)))))...... ( -24.30)
>DroSim_CAF1 102234 105 - 1
CAAUCAGUCCUGGUCAAGUGGGUGUGGAAACACCGGAAAAUAAUAUGGCAACAAAGUUGAGAA-AAU-CAAUCAAA----U---AU-AUUAUUUUAACC----UACUAAUCAGUAAAAA
.........(((((..((((((((((....)))...(((((((((((....)...(((((...-..)-))))....----.---))-)))))))).)))----)))).)))))...... ( -27.20)
>DroEre_CAF1 102887 109 - 1
CAAUCAGUCCUGGUCAAGUGGGUGUGGAAACACCGGAAAAUAAUUUGGCAACAAAGCUGGUUG-AAUGCGAAAUAA----U---AU-GUUCUUUUCGCCUACCUACUAAUCAGGAAAA-
.......(((((((..((((((((.(....)(((((.......((((....)))).)))))..-...((((((...----.---..-.....)))))).)))))))).)))))))...- ( -33.90)
>DroYak_CAF1 103814 114 - 1
CAAUCAGUCCUGGUCAAGUGGGCGUGGAAACACCGGAAAAUAAUUUGGUAACAAAGUGGUUUG-CAUAGGAACUAAACUAU---AUAGUUCCUUUAACCUAUUUGCUAAUCAGGAAAA-
.......(((((((((((((((.(((....))).(.(((....((((....))))....))).-)..((((((((......---.))))))))....))))))))...)))))))...- ( -34.60)
>DroAna_CAF1 96621 92 - 1
CAAUCAAACCAGGCUAAGAGGGUAUUCAUGCACUGAGAAAAG---------UUAAGCUGAGGAUUAU-GA---AAA----UGCCAC-AUUAUUAU---------ACAGAUCAAUCUCCA
...........((.(((...((((((((((..((.((.....---------.....)).))...)))-))---..)----))))..-.)))....---------..(((....))))). ( -10.30)
>consensus
CAAUCAGUCCUGGUCAAGUGGGUGUGGAAACACCGGAAAAUAAUUUGGCAACAAAGUUGAGGA_AAU_CAAUCAAA____U___AU_AUUAUUUUAACC____UACUAAUCAGUAAAAA
.........(((((..(((((((((....)))))...........((....))..................................................)))).)))))...... ( -8.55 =  -9.83 +   1.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 18,057,245 – 18,057,357
Length 112
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 77.72
Mean single sequence MFE -27.23
Consensus MFE -13.71
Energy contribution -15.27
Covariance contribution 1.56
Combinations/Pair 1.11
Mean z-score -2.34
Structure conservation index 0.50
SVM decision value 1.03
SVM RNA-class probability 0.904200
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18057245 112 - 27905053
AGAUGAUCAAAUCUAAUGGAAAG--GGCUAGCAAAGCGAGCAAUCAGUCCUGGUCAAGUGGGUGUGGAAACACCGGAAAAUAAUUUGGCAACAAAGUUGAGGU-UAU-CAAUCAAA---
.(((((((...(((..(((..((--((((.((...))((....))))))))..)))....(((((....))))))))......((((....)))).....)))-)))-).......--- ( -33.60)
>DroSec_CAF1 99415 112 - 1
AGAUGAUCAAAUCUAAUGGAAAG--GGCUAGCAAAGCGAGCAAUCAGUCCUGGUCAAGUGGGUGUGGAAACACCGGAAAAUAAUGUGGCAACAAAGUUGAGGA-AAU-CAAUCAAA---
.(((..((((.(((..(((..((--((((.((...))((....))))))))..)))....(((((....))))))))........((....))...))))...-.))-).......--- ( -28.30)
>DroSim_CAF1 102265 112 - 1
AGAUGAUCAAAUCUAAUGGAAAG--GGCUAGCAAAGCGAGCAAUCAGUCCUGGUCAAGUGGGUGUGGAAACACCGGAAAAUAAUAUGGCAACAAAGUUGAGAA-AAU-CAAUCAAA---
.(((..((((.(((..(((..((--((((.((...))((....))))))))..)))....(((((....))))))))........((....))...))))...-.))-).......--- ( -28.40)
>DroEre_CAF1 102921 113 - 1
AGAUGAUCAAAUCUAAUGGAAAG--GGCUGGCUAAGCGAGCAAUCAGUCCUGGUCAAGUGGGUGUGGAAACACCGGAAAAUAAUUUGGCAACAAAGCUGGUUG-AAUGCGAAAUAA---
....(((((..(((..(((..((--((((((((.....)))...)))))))..)))....(((((....))))))))......((((....))))..))))).-............--- ( -30.70)
>DroYak_CAF1 103850 116 - 1
AGAUGAUCAAAUCUAAUGGAAGG--GGCCAGCUAAGCGAGCAAUCAGUCCUGGUCAAGUGGGCGUGGAAACACCGGAAAAUAAUUUGGUAACAAAGUGGUUUG-CAUAGGAACUAAACU
((((......))))..(((....--..))).(((.((((((..((.((((.........))))(((....)))..))......((((....))))...)))))-).))).......... ( -25.20)
>DroAna_CAF1 96650 95 - 1
--------AAAUCUAAUGGGAAGAGUGCUGGCAAAACGAGCAAUCAAACCAGGCUAAGAGGGUAUUCAUGCACUGAGAAAAG---------UUAAGCUGAGGAUUAU-GA---AAA---
--------.(((((..(((...((.((((.(.....).)))).))...)))((((..(((....)))....(((......))---------)..))))..)))))..-..---...--- ( -17.20)
>consensus
AGAUGAUCAAAUCUAAUGGAAAG__GGCUAGCAAAGCGAGCAAUCAGUCCUGGUCAAGUGGGUGUGGAAACACCGGAAAAUAAUUUGGCAACAAAGUUGAGGA_AAU_CAAUCAAA___
...((((((........(((......(((.((...)).)))......)))))))))....(((((....)))))............................................. (-13.71 = -15.27 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:58 2006