Locus 10344

Sequence ID dm3.chr3R
Location 13,193,082 – 13,193,210
Length 128
Max. P 0.994935
window14223 window14224 window14225 window14226

overview

Window 3

Location 13,193,082 – 13,193,177
Length 95
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 79.97
Shannon entropy 0.30394
G+C content 0.56662
Mean single sequence MFE -36.37
Consensus MFE -21.89
Energy contribution -21.77
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -1.86
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr3R 13193082 95 + 27905053
AAAGCAUCGCAGCU--CGGC---CCCGGCAACAUUUUUUGGACAAAGUUGCCCAG--------AUACCCGGAUCGCCGGAUAGCCAUAGCCAUAGCCAUGGCCGUGCA------
...........((.--((((---(..(((.......(((((.((....)).))))--------)...((((....))))...............)))..))))).)).------ ( -30.40, z-score =  -0.87, R)
>droEre2.scaffold_4770 9310152 109 - 17746568
AAAGCAUCGCCGCU--CGGC---CCCGGCAACAUUUUUUGGACAAAGUUGCCCGGCAACCCGGAUCCCCGGAUCGCCGGAUAGCUAUAGCUAUAGCUAUAGCCAUGGCCGUGCA
...........((.--((((---((((((.................(((((...)))))((((....))))...)))))...((((((((....))))))))...))))).)). ( -47.50, z-score =  -3.50, R)
>droYak2.chr3R 17283601 91 + 28832112
AAAGCAUCGUUGCUUUCGGC---CCCGGCAACAUUUUUUGGACAAAGUUGCCCAGC--------UACCCGGAUCGCCGGAUAGCUAUAGCAAUGGCCGUGCA------------
((((((....))))))((((---(..((((((..............)))))).(((--------((.((((....)))).)))))........)))))....------------ ( -34.44, z-score =  -2.38, R)
>droSim1.chr3R 19237628 98 - 27517382
AAAGCAUCGCAGCU--CGGCGGCCCCGGCAACAUUUUUUGGACAAAGUUGCCCAG--------AUACCCGGAUCGCCGGAUAGCCAUAGCCAUAGCCAUGGCCGUGCA------
...(((.((....(--(((((..((.((((((..............))))))..(--------.....)))..))))))...(((((.((....)).)))))))))).------ ( -33.14, z-score =  -0.70, R)
>consensus
AAAGCAUCGCAGCU__CGGC___CCCGGCAACAUUUUUUGGACAAAGUUGCCCAG________AUACCCGGAUCGCCGGAUAGCCAUAGCCAUAGCCAUGGCCGUGCA______
..(((......)))...((.....))((((((..............))))))...............((((....))))...(((((.((....)).)))))............ (-21.89 = -21.77 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,193,082 – 13,193,177
Length 95
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 79.97
Shannon entropy 0.30394
G+C content 0.56662
Mean single sequence MFE -46.12
Consensus MFE -30.26
Energy contribution -31.57
Covariance contribution 1.31
Combinations/Pair 1.07
Mean z-score -3.22
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.75
SVM RNA-class probability 0.994935
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13193082 95 - 27905053
------UGCACGGCCAUGGCUAUGGCUAUGGCUAUCCGGCGAUCCGGGUAU--------CUGGGCAACUUUGUCCAAAAAAUGUUGCCGGG---GCCG--AGCUGCGAUGCUUU
------.((..(((((((((....)))))))))(((((((....(((...(--------((.(((((((((.......))).)))))).))---))))--.)))).)))))... ( -39.10, z-score =  -1.62, R)
>droEre2.scaffold_4770 9310152 109 + 17746568
UGCACGGCCAUGGCUAUAGCUAUAGCUAUAGCUAUCCGGCGAUCCGGGGAUCCGGGUUGCCGGGCAACUUUGUCCAAAAAAUGUUGCCGGG---GCCG--AGCGGCGAUGCUUU
.((.((((((((((((((((....)))))))))))((((((((((((....)))))))))).(((((((((.......))).)))))))))---))))--.))........... ( -59.30, z-score =  -5.04, R)
>droYak2.chr3R 17283601 91 - 28832112
------------UGCACGGCCAUUGCUAUAGCUAUCCGGCGAUCCGGGUA--------GCUGGGCAACUUUGUCCAAAAAAUGUUGCCGGG---GCCGAAAGCAACGAUGCUUU
------------....(((((.......(((((((((((....)))))))--------))))(((((((((.......))).))))))..)---))))((((((....)))))) ( -41.60, z-score =  -3.80, R)
>droSim1.chr3R 19237628 98 + 27517382
------UGCACGGCCAUGGCUAUGGCUAUGGCUAUCCGGCGAUCCGGGUAU--------CUGGGCAACUUUGUCCAAAAAAUGUUGCCGGGGCCGCCG--AGCUGCGAUGCUUU
------.(((((((((((((....))))))))....(((((..((.((((.--------(((((((....))))))......).)))).))..)))))--.....)).)))... ( -44.50, z-score =  -2.43, R)
>consensus
______UGCACGGCCAUGGCUAUGGCUAUAGCUAUCCGGCGAUCCGGGUAU________CUGGGCAACUUUGUCCAAAAAAUGUUGCCGGG___GCCG__AGCUGCGAUGCUUU
...........(((((((((....)))))))))...((((...((.((((..........((((((....))))))........)))).))...))))..(((......))).. (-30.26 = -31.57 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,193,111 – 13,193,210
Length 99
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 86.16
Shannon entropy 0.21046
G+C content 0.49234
Mean single sequence MFE -32.50
Consensus MFE -22.31
Energy contribution -22.62
Covariance contribution 0.31
Combinations/Pair 1.09
Mean z-score -2.16
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.44
SVM RNA-class probability 0.698338
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13193111 99 + 27905053
UUUUUGGACAAAGUUGCCCAGAUACCCGGAUCGCCGGAU--------------AGCCAUAGCCAUAGCCAUGGCCGUGCAGUCCGGCCGUAUAUCGCCAUAUAGAUAAAUAUU
....(((.((....)).)))((((..((....(((((((--------------.((.(..(((((....)))))..))).)))))))))..)))).................. ( -29.10, z-score =  -1.71, R)
>droEre2.scaffold_4770 9310181 113 - 17746568
UUUUUGGACAAAGUUGCCCGGCAACCCGGAUCCCCGGAUCGCCGGAUAGCUAUAGCUAUAGCUAUAGCCAUGGCCGUGCAGUUCGGCCGUAUAUCGCCAUAUAGAUAAAUAUU
....(((.(........(((((...((((....))))...)))))...((((((((....)))))))).(((((((.......))))))).....)))).............. ( -42.10, z-score =  -3.10, R)
>droYak2.chr3R 17283632 93 + 28832112
UUUUUGGACAAAGUUGCCCAGCUACCCGGAUCGCCGGAU--------------AGCUAUAGCA------AUGGCCGUGCACUCCGGCCGUAUAUCGCCAUAUAGAUAAAUAUU
....(((.(...(((((..(((((.((((....)))).)--------------))))...)))------))(((((.......))))).......)))).............. ( -29.70, z-score =  -2.11, R)
>droSim1.chr3R 19237660 99 - 27517382
UUUUUGGACAAAGUUGCCCAGAUACCCGGAUCGCCGGAU--------------AGCCAUAGCCAUAGCCAUGGCCGUGCAGUCCGGCCGUAUAUCGCCAUAUAGAUAAAUAUU
....(((.((....)).)))((((..((....(((((((--------------.((.(..(((((....)))))..))).)))))))))..)))).................. ( -29.10, z-score =  -1.71, R)
>consensus
UUUUUGGACAAAGUUGCCCAGAUACCCGGAUCGCCGGAU______________AGCCAUAGCCAUAGCCAUGGCCGUGCAGUCCGGCCGUAUAUCGCCAUAUAGAUAAAUAUU
.....((((.....(((.(......((((....)))).................(((((.((....)).))))).).)))))))(((........)))............... (-22.31 = -22.62 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 13,193,111 – 13,193,210
Length 99
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 86.16
Shannon entropy 0.21046
G+C content 0.49234
Mean single sequence MFE -41.00
Consensus MFE -28.12
Energy contribution -28.62
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -3.47
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.58
SVM RNA-class probability 0.992994
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13193111 99 - 27905053
AAUAUUUAUCUAUAUGGCGAUAUACGGCCGGACUGCACGGCCAUGGCUAUGGCUAUGGCU--------------AUCCGGCGAUCCGGGUAUCUGGGCAACUUUGUCCAAAAA
..................(((((....(((((.(((..(((((((((....)))))))))--------------.....))).))))))))))((((((....)))))).... ( -36.10, z-score =  -2.34, R)
>droEre2.scaffold_4770 9310181 113 + 17746568
AAUAUUUAUCUAUAUGGCGAUAUACGGCCGAACUGCACGGCCAUGGCUAUAGCUAUAGCUAUAGCUAUCCGGCGAUCCGGGGAUCCGGGUUGCCGGGCAACUUUGUCCAAAAA
..............((((((.....(((((.......)))))(((((((((((....)))))))))))((((((((((((....))))))))))))......))).))).... ( -52.10, z-score =  -5.10, R)
>droYak2.chr3R 17283632 93 - 28832112
AAUAUUUAUCUAUAUGGCGAUAUACGGCCGGAGUGCACGGCCAU------UGCUAUAGCU--------------AUCCGGCGAUCCGGGUAGCUGGGCAACUUUGUCCAAAAA
............(((((((((....(((((.......)))))))------)))))))(((--------------((((((....)))))))))((((((....)))))).... ( -39.70, z-score =  -4.12, R)
>droSim1.chr3R 19237660 99 + 27517382
AAUAUUUAUCUAUAUGGCGAUAUACGGCCGGACUGCACGGCCAUGGCUAUGGCUAUGGCU--------------AUCCGGCGAUCCGGGUAUCUGGGCAACUUUGUCCAAAAA
..................(((((....(((((.(((..(((((((((....)))))))))--------------.....))).))))))))))((((((....)))))).... ( -36.10, z-score =  -2.34, R)
>consensus
AAUAUUUAUCUAUAUGGCGAUAUACGGCCGGACUGCACGGCCAUGGCUAUGGCUAUAGCU______________AUCCGGCGAUCCGGGUAGCUGGGCAACUUUGUCCAAAAA
............((((((.(((...(((((.......))))).....))).)))))).................((((((....))))))....(((((....)))))..... (-28.12 = -28.62 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:22:11 2011