Locus 4908

Sequence ID dm3.chr2R
Location 16,311,596 – 16,311,698
Length 102
Max. P 0.980888
window6749 window6750

overview

Window 9

Location 16,311,596 – 16,311,698
Length 102
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 74.76
Shannon entropy 0.48181
G+C content 0.58953
Mean single sequence MFE -34.92
Consensus MFE -19.14
Energy contribution -20.75
Covariance contribution 1.61
Combinations/Pair 1.21
Mean z-score -2.21
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.06
SVM RNA-class probability 0.980888
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16311596 102 + 21146708
---GAGCACCGCUAACAGAGCCCUGUUAGCGUGCAGCAUCCACCACUUCGUGCCACAACUUCGGCCACUUGAAGUCUCUCGAUUUUGCUCUCGGUGGCGCUUCUC
---..((((.((((((((....))))))))))))(((..(((((.....(((((........)).)))..((((((....))))))......))))).))).... ( -37.10, z-score =  -3.31, R)
>droSim1.chr2R 14967987 102 + 19596830
---GAGCCCCGCUAACAGAGCCCUGUUAGCGUGCAGCAUCCACCACUUCGUGCCACAUCUUCGGCCGCUGGAAGUCUCUCGAUUCUGCUCUCGGUGGCGCUUCUC
---..(((((((((((((....))))))))(.((((.(((....((((((((((........)).)))..))))).....))).)))).)..)).)))....... ( -36.50, z-score =  -2.08, R)
>droSec1.super_1 13867949 102 + 14215200
---GAGCCCCGCUAACAGAGCCCUGUUAGCGUGCAGCAUCCACCACUUCGUGCCACAUCUUCGUCCGCUGGAAGUCUCUCGAUUCUGCUCUCGGUGGCGCUUCUC
---..(((((((((((((....))))))))(.((((.(((....(((((..((.((......))..))..))))).....))).)))).)..)).)))....... ( -33.80, z-score =  -1.99, R)
>droYak2.chr2R 8250014 102 - 21139217
---GCGAGGCGCUAACAGCGCGCUGUUAGCGUGCAGCAUCCACCACUUCGUGCCACAUCUUCGGCACGUUGAAGUCUCUCGAUUUUGCUCUCGUUGCCGCUUCUC
---..(((((((((((((....))))))))(.(((((...........((((((........))))))..((((((....))))))......))))))))))).. ( -40.60, z-score =  -3.45, R)
>droEre2.scaffold_4845 10456903 102 + 22589142
---GAGCCGCGCUAACAGAGCGCUGUUAGCGUGCAGCAUCCACCACUUCGUGCCACAUCUUCGGUCCGUUGAAGUCUCUCGAUGUUGCUCUCGGUGCCGCUGCUC
---((((.((((((((((....))))))))(.((((((((....((((((.(((........)))....)))))).....)))))))).)........)).)))) ( -39.20, z-score =  -2.25, R)
>dp4.chr3 10376455 87 + 19779522
GGGUACCACUGCUAACAGAGCUCUGUU-GUCCACAGUCUCCGUUUCGUGAUGCCAGCGCAUCGUGCCAUGCCCUCGUCACGUCUCGUC-----------------
(((((.(((.((.(((.(((..((((.-....)))).))).)))..))(((((....))))))))...)))))...............----------------- ( -22.30, z-score =  -0.17, R)
>consensus
___GAGCCCCGCUAACAGAGCCCUGUUAGCGUGCAGCAUCCACCACUUCGUGCCACAUCUUCGGCCCCUGGAAGUCUCUCGAUUCUGCUCUCGGUGGCGCUUCUC
.....((.((((((((((....))))))))(.((((.(((....(((((..(((........))).....))))).....))).)))).).....)).))..... (-19.14 = -20.75 +   1.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 16,311,596 – 16,311,698
Length 102
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 74.76
Shannon entropy 0.48181
G+C content 0.58953
Mean single sequence MFE -37.55
Consensus MFE -18.91
Energy contribution -21.05
Covariance contribution 2.14
Combinations/Pair 1.14
Mean z-score -1.69
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.69
SVM RNA-class probability 0.788729
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16311596 102 - 21146708
GAGAAGCGCCACCGAGAGCAAAAUCGAGAGACUUCAAGUGGCCGAAGUUGUGGCACGAAGUGGUGGAUGCUGCACGCUAACAGGGCUCUGUUAGCGGUGCUC---
....(((((((((..((......)).....(((((..(((.(((......)))))))))))))))).))))((((((((((((....)))))))).))))..--- ( -40.20, z-score =  -2.27, R)
>droSim1.chr2R 14967987 102 - 19596830
GAGAAGCGCCACCGAGAGCAGAAUCGAGAGACUUCCAGCGGCCGAAGAUGUGGCACGAAGUGGUGGAUGCUGCACGCUAACAGGGCUCUGUUAGCGGGGCUC---
....((((((((((...((.(((((....)).)))..)).((((......))))......)))))).))))((.(((((((((....)))))))))..))..--- ( -40.10, z-score =  -1.68, R)
>droSec1.super_1 13867949 102 - 14215200
GAGAAGCGCCACCGAGAGCAGAAUCGAGAGACUUCCAGCGGACGAAGAUGUGGCACGAAGUGGUGGAUGCUGCACGCUAACAGGGCUCUGUUAGCGGGGCUC---
....((((((((((.(.((....((....))((((........)))).....)).)....)))))).))))((.(((((((((....)))))))))..))..--- ( -36.60, z-score =  -1.17, R)
>droYak2.chr2R 8250014 102 + 21139217
GAGAAGCGGCAACGAGAGCAAAAUCGAGAGACUUCAACGUGCCGAAGAUGUGGCACGAAGUGGUGGAUGCUGCACGCUAACAGCGCGCUGUUAGCGCCUCGC---
(((..((((((.(.(..((....((....))......(((((((......)))))))..))..).).)))))).(((((((((....))))))))).)))..--- ( -42.80, z-score =  -2.86, R)
>droEre2.scaffold_4845 10456903 102 - 22589142
GAGCAGCGGCACCGAGAGCAACAUCGAGAGACUUCAACGGACCGAAGAUGUGGCACGAAGUGGUGGAUGCUGCACGCUAACAGCGCUCUGUUAGCGCGGCUC---
((((.(((((((((...((....((....))......((..(((......)))..))..))..))).)))))).(((((((((....)))))))))..))))--- ( -38.70, z-score =  -1.43, R)
>dp4.chr3 10376455 87 - 19779522
-----------------GACGAGACGUGACGAGGGCAUGGCACGAUGCGCUGGCAUCACGAAACGGAGACUGUGGAC-AACAGAGCUCUGUUAGCAGUGGUACCC
-----------------...............(((.((.((..(((((....)))))....(((((((.((.((...-..)).)))))))))....)).)).))) ( -26.90, z-score =  -0.71, R)
>consensus
GAGAAGCGCCACCGAGAGCAAAAUCGAGAGACUUCAAGGGGCCGAAGAUGUGGCACGAAGUGGUGGAUGCUGCACGCUAACAGGGCUCUGUUAGCGGGGCUC___
.....((.((.......(((..(((.(...(((((.....((((......))))..)))))..).)))..)))..((((((((....)))))))))).))..... (-18.91 = -21.05 +   2.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:38:21 2011