Locus 10574

Sequence ID dm3.chr3R
Location 14,818,460 – 14,818,596
Length 136
Max. P 0.977310
window14536 window14537 window14538

overview

Window 6

Location 14,818,460 – 14,818,557
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 88.72
Shannon entropy 0.18171
G+C content 0.48308
Mean single sequence MFE -13.31
Consensus MFE -12.93
Energy contribution -13.17
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.91
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.97
SVM RNA-class probability 0.977310
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14818460 97 - 27905053
CAGUGCCCAGCCUCCACGGCUGUACGAGUAUGUGUAUCUGCCUCCCCCUUUUUUUUUUUUUUUGUUUCCAUCAUUUCCAUCUUCACGCAUUCUCCCA
..((((..((((.....))))))))(((.((((((.................................................)))))).)))... ( -14.79, z-score =  -2.97, R)
>droSim1.chr3R 20864239 87 + 27517382
CAGUGCCCAGCCUCCACGGCUAUACGAGUAUGUGUAUCUGCCCCCC----------UUUUUUUGUUUCCAUCAUUUCCAUCUUCACGCAUUCUCCCA
..(((...((((.....)))).)))(((.((((((...........----------............................)))))).)))... ( -11.73, z-score =  -1.53, R)
>droSec1.super_166 33072 87 + 36471
CAGUGCCCAGCCUCCACGGCUAUACGAGUAUGUGUAUCUGCCCCCC----------UUUUUUUGUUUCCAUCAUUUCCAUCUUCACGCAUUCUCCCA
..(((...((((.....)))).)))(((.((((((...........----------............................)))))).)))... ( -11.73, z-score =  -1.53, R)
>droYak2.chr3R 3502078 81 - 28832112
CAGUGCCCAGCCUCAACGGCUGUACGAGUAUGUGUAUCUGCCCCC-----------UUUUUUUGU-----UCAUUUUCAUCUUCACGCAUUCUCUCA
..((((..((((.....))))))))(((.((((((..........-----------.........-----..............)))))).)))... ( -15.61, z-score =  -2.23, R)
>droEre2.scaffold_4770 10935523 81 + 17746568
CAGUGCCCAGCUUCCACGGCUGUACGAGUAUGUGUAUCUGCCCCC-----------UUUUUUUGU-----UCAUUUCCAUCUUCACGCAUUCUCCCA
..((((..((((.....))))))))(((.((((((..........-----------.........-----..............)))))).)))... ( -12.71, z-score =  -1.28, R)
>consensus
CAGUGCCCAGCCUCCACGGCUGUACGAGUAUGUGUAUCUGCCCCCC__________UUUUUUUGUUUCCAUCAUUUCCAUCUUCACGCAUUCUCCCA
..((((..((((.....))))))))(((.((((((.................................................)))))).)))... (-12.93 = -13.17 +   0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,818,482 – 14,818,596
Length 114
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 90.69
Shannon entropy 0.15046
G+C content 0.43664
Mean single sequence MFE -26.96
Consensus MFE -24.94
Energy contribution -24.74
Covariance contribution -0.20
Combinations/Pair 1.07
Mean z-score -1.27
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.732764
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14818482 114 + 27905053
AAUGAUGGAAACAAAAAAAAAAAAAAAGGGGGAGGCAGAUACACAUACUCGUACAGCCGUGGAGGCUGGGCACUGUCAGCUUGACUGACAUCAUUUCCGAUGUUUAUCUUUUCA
.....((....))..................((((.(((((.((((....(..(((((.....)))))..)..((((((.....)))))).........)))).))))))))). ( -29.80, z-score =  -1.72, R)
>droSim1.chr3R 20864261 104 - 27517382
AAUGAUGGAAACAAAAAAA----------GGGGGGCAGAUACACAUACUCGUAUAGCCGUGGAGGCUGGGCACUGUCAGCUUGACUGACAUCAUUUCCGAUGUUUAUCUUUUCA
.....((....))......----------..(..(.(((((.((((....((.(((((.....))))).))..((((((.....)))))).........)))).))))))..). ( -27.60, z-score =  -1.19, R)
>droSec1.super_166 33094 104 - 36471
AAUGAUGGAAACAAAAAAA----------GGGGGGCAGAUACACAUACUCGUAUAGCCGUGGAGGCUGGGCACUGUCAGCUUGACUGACAUCAUUUCCGAUGUUUAUCUUUUCA
.....((....))......----------..(..(.(((((.((((....((.(((((.....))))).))..((((((.....)))))).........)))).))))))..). ( -27.60, z-score =  -1.19, R)
>droYak2.chr3R 3502100 98 + 28832112
---AAUG--AACAAAAAAA-----------GGGGGCAGAUACACAUACUCGUACAGCCGUUGAGGCUGGGCACUGUCAGCUUGACUGACAUCAUUUCCGAUGUUUAUCUUUUCA
---....--..........-----------.(..(.(((((.((((....(..(((((.....)))))..)..((((((.....)))))).........)))).))))))..). ( -27.30, z-score =  -1.89, R)
>droEre2.scaffold_4770 10935545 98 - 17746568
---AAUG--AACAAAAAAA-----------GGGGGCAGAUACACAUACUCGUACAGCCGUGGAAGCUGGGCACUGUCAGCUUGACUGACAUCAUUUCCGAUGUUUAUCUUUUCA
---....--..........-----------.(..(.(((((.((((....(..((((.......))))..)..((((((.....)))))).........)))).))))))..). ( -22.50, z-score =  -0.34, R)
>consensus
AAUGAUGGAAACAAAAAAA__________GGGGGGCAGAUACACAUACUCGUACAGCCGUGGAGGCUGGGCACUGUCAGCUUGACUGACAUCAUUUCCGAUGUUUAUCUUUUCA
.....((....))..................((((.(((((.((((....(..(((((.....)))))..)..((((((.....)))))).........)))).))))))))). (-24.94 = -24.74 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,818,482 – 14,818,596
Length 114
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 90.69
Shannon entropy 0.15046
G+C content 0.43664
Mean single sequence MFE -23.62
Consensus MFE -22.06
Energy contribution -22.30
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.34
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.775164
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14818482 114 - 27905053
UGAAAAGAUAAACAUCGGAAAUGAUGUCAGUCAAGCUGACAGUGCCCAGCCUCCACGGCUGUACGAGUAUGUGUAUCUGCCUCCCCCUUUUUUUUUUUUUUUGUUUCCAUCAUU
(((...(((....)))(((((..(((((((.....))))))((((..((((.....))))))))....................................)..))))).))).. ( -25.40, z-score =  -1.57, R)
>droSim1.chr3R 20864261 104 + 27517382
UGAAAAGAUAAACAUCGGAAAUGAUGUCAGUCAAGCUGACAGUGCCCAGCCUCCACGGCUAUACGAGUAUGUGUAUCUGCCCCCC----------UUUUUUUGUUUCCAUCAUU
(((...(((....)))(((((..(((((((.....))))))(((.........)))(((.(((((......)))))..)))....----------.....)..))))).))).. ( -23.20, z-score =  -1.44, R)
>droSec1.super_166 33094 104 + 36471
UGAAAAGAUAAACAUCGGAAAUGAUGUCAGUCAAGCUGACAGUGCCCAGCCUCCACGGCUAUACGAGUAUGUGUAUCUGCCCCCC----------UUUUUUUGUUUCCAUCAUU
(((...(((....)))(((((..(((((((.....))))))(((.........)))(((.(((((......)))))..)))....----------.....)..))))).))).. ( -23.20, z-score =  -1.44, R)
>droYak2.chr3R 3502100 98 - 28832112
UGAAAAGAUAAACAUCGGAAAUGAUGUCAGUCAAGCUGACAGUGCCCAGCCUCAACGGCUGUACGAGUAUGUGUAUCUGCCCCC-----------UUUUUUUGUU--CAUU---
.....(((((.(((((((......((((((.....))))))...))(((((.....))))).....).)))).)))))......-----------..........--....--- ( -24.10, z-score =  -1.49, R)
>droEre2.scaffold_4770 10935545 98 + 17746568
UGAAAAGAUAAACAUCGGAAAUGAUGUCAGUCAAGCUGACAGUGCCCAGCUUCCACGGCUGUACGAGUAUGUGUAUCUGCCCCC-----------UUUUUUUGUU--CAUU---
((((..(((..((((((....))))))..)))((((((........))))))....(((.(((((......)))))..)))...-----------........))--))..--- ( -22.20, z-score =  -0.77, R)
>consensus
UGAAAAGAUAAACAUCGGAAAUGAUGUCAGUCAAGCUGACAGUGCCCAGCCUCCACGGCUGUACGAGUAUGUGUAUCUGCCCCCC__________UUUUUUUGUUUCCAUCAUU
.....(((((.(((((........((((((.....))))))((((..((((.....))))))))..).)))).))))).................................... (-22.06 = -22.30 +   0.24)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:26:29 2011