Locus 6112

Sequence ID dm3.chr3L
Location 3,787,983 – 3,788,105
Length 122
Max. P 0.977830
window8406 window8407 window8408

overview

Window 6

Location 3,787,983 – 3,788,090
Length 107
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 75.33
Shannon entropy 0.45822
G+C content 0.56135
Mean single sequence MFE -42.15
Consensus MFE -26.15
Energy contribution -26.82
Covariance contribution 0.67
Combinations/Pair 1.38
Mean z-score -1.61
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.20
SVM RNA-class probability 0.907881
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3787983 107 + 24543557
-------UGUGACAAAAAAUUGUUUA-UAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGAAUUUGCACCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCG
-------...(((((....)))))..-.....((.(((((((((.(((((....(((((.....)))))................((((....)))))))))..))))))))))) ( -41.70, z-score =  -1.81, R)
>droSim1.chr3L 3328035 107 + 22553184
-------UGUGACAAAAAAUUGUUUA-UAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGACUUUGGCCCGUUUCGCGGCACUUGUCGGCAGCGCGGUCACACUCG
-------...(((((....)))))..-.....((.(((((((((.((((((....((((.....))))(((....(((((...)).)))....)))))))))..))))))))))) ( -45.70, z-score =  -2.57, R)
>droSec1.super_2 3782038 107 + 7591821
-------UGUGACAAAAAAUUGUUUA-UAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGACAUUGGCCCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCG
-------...(((((....)))))..-.....((.(((((((((.((((((....((((.....))))((((...(((((...)).)))...))))))))))..))))))))))) ( -47.40, z-score =  -3.22, R)
>droYak2.chr3L 4343910 106 + 24197627
-------UGUGACAAAAAAUUGUUUA-UAUGGCGCAGUGUGGCCAGCUACUAGGCGGCCGAUGAGGCCGAGUUUCGCCCGUUUGGCGGCAUUCUUCGGCAGCGCGGUCACACCG-
-------((((((........(((..-...)))...((((.(((.(((....)))((((.....))))((((.(((((.....))))).))))...))).)))).))))))...- ( -39.80, z-score =  -0.80, R)
>droEre2.scaffold_4784 6483580 106 + 25762168
-------UGUGACAAAAAAUUGUUUA-UAUGGCGCAGUGUGGCCAGAUACUUGGCGGCCGAUAAGGCCGAGUUGGGCCCGUUUGGCGGCAUUUUUCGGCAGCGCGGUCACACCG-
-------((((((........(((..-...)))...((((.(((.((......((.(((((...((((......))))...))))).)).....))))).)))).))))))...- ( -39.30, z-score =  -0.88, R)
>droAna3.scaffold_13337 13637606 103 - 23293914
GAUGCUAGGCGGCCAUAA-UUGUUUACUUUCAGGCAGUGCA-CGAGUCGCCCUGUGCUGGCUAAAAUGG---CAGCCCUGGUCAGCUGCUUUCG--GCCAGUGCUGCCAU-----
...(((((((((((...(-((((((......)))))))...-.).))))))......))))....((((---((((.((((((..........)--))))).))))))))----- ( -39.00, z-score =  -0.40, R)
>consensus
_______UGUGACAAAAAAUUGUUUA_UAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGACUUUGGCCCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUC_
.......((((((...................(((...((((....))))...)))(((((((((((((................)))).)))))))))......)))))).... (-26.15 = -26.82 +   0.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,787,992 – 3,788,105
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 86.98
Shannon entropy 0.22256
G+C content 0.58365
Mean single sequence MFE -51.24
Consensus MFE -37.00
Energy contribution -38.84
Covariance contribution 1.84
Combinations/Pair 1.06
Mean z-score -2.88
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.98
SVM RNA-class probability 0.977830
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3787992 113 + 24543557
AAAUUGUUUAUAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGAAUUUGCACCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCGAGAAGAGAGCGGCUG
.............(((((.((((((((.(((((....(((((.....)))))................((((....)))))))))..))))))))((.....))..))))).. ( -49.10, z-score =  -2.71, R)
>droSim1.chr3L 3328044 113 + 22553184
AAAUUGUUUAUAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGACUUUGGCCCGUUUCGCGGCACUUGUCGGCAGCGCGGUCACACUCGAGAAGAGAGCGGCUG
.............(((((.((((((((.((((((....((((.....))))(((....(((((...)).)))....)))))))))..))))))))((.....))..))))).. ( -53.10, z-score =  -3.16, R)
>droSec1.super_2 3782047 113 + 7591821
AAAUUGUUUAUAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGACAUUGGCCCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCGAGAAGAGAGCGGCUG
.............(((((.((((((((.((((((....((((.....))))((((...(((((...)).)))...))))))))))..))))))))((.....))..))))).. ( -54.80, z-score =  -3.97, R)
>droYak2.chr3L 4343919 111 + 24197627
AAAUUGUUUAUAUGGCGCAGUGUGGCCAGCUACUAGGCGGCCGAUGAGGCCGAGUUUCGCCCGUUUGGCGGCAUUCUUCGGCAGCGCGGUCACAC-CGCGGCUGUA-UGAAUG
.....(((((((((((((.((((((((.(((.((....((((.....))))((((.(((((.....))))).))))...)).)))..))))))))-.)).))))))-))))). ( -51.90, z-score =  -3.04, R)
>droEre2.scaffold_4784 6483589 112 + 25762168
AAAUUGUUUAUAUGGCGCAGUGUGGCCAGAUACUUGGCGGCCGAUAAGGCCGAGUUGGGCCCGUUUGGCGGCAUUUUUCGGCAGCGCGGUCACAC-CGCGGCUGUAGUGAGCG
.....(((((((((((((.((((((((.((......((.(((((...((((......))))...))))).)).....)).((...))))))))))-.)).))))).)))))). ( -47.30, z-score =  -1.53, R)
>consensus
AAAUUGUUUAUAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGACUUUGGCCCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCGAGAAGAGAGCGGCUG
.............((((((((((((((.((((((....((((.....))))(((....(.(((.....))))....)))))))))..)))))))))..........))))).. (-37.00 = -38.84 +   1.84)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,787,992 – 3,788,105
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 86.98
Shannon entropy 0.22256
G+C content 0.58365
Mean single sequence MFE -42.48
Consensus MFE -32.14
Energy contribution -32.02
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -2.18
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.889966
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3787992 113 - 24543557
CAGCCGCUCUCUUCUCGAGUGUGACCGCGCUGCCGACAAAUGCCGCGAAACGGUGCAAAUUCGGCCUUAUCGGCCGCUAAGCAGCUGGCCACACUGCGGCAUAUAAACAAUUU
..(((((..........((((((.(((.(((((........((((.....)))).......(((((.....)))))....)))))))).)))))))))))............. ( -42.50, z-score =  -2.40, R)
>droSim1.chr3L 3328044 113 - 22553184
CAGCCGCUCUCUUCUCGAGUGUGACCGCGCUGCCGACAAGUGCCGCGAAACGGGCCAAAGUCGGCCUUAUCGGCCGCUAAGCAGCUGGCCACACUGCGGCAUAUAAACAAUUU
..(((((..........((((((.(((.(((((.(((....(((.((...)))))....)))((((.....)))).....)))))))).)))))))))))............. ( -44.70, z-score =  -2.11, R)
>droSec1.super_2 3782047 113 - 7591821
CAGCCGCUCUCUUCUCGAGUGUGACCGCGCUGCCGACAAAUGCCGCGAAACGGGCCAAUGUCGGCCUUAUCGGCCGCUAAGCAGCUGGCCACACUGCGGCAUAUAAACAAUUU
..(((((..........((((((.(((.(((((.((((...(((.((...)))))...))))((((.....)))).....)))))))).)))))))))))............. ( -46.40, z-score =  -3.07, R)
>droYak2.chr3L 4343919 111 - 24197627
CAUUCA-UACAGCCGCG-GUGUGACCGCGCUGCCGAAGAAUGCCGCCAAACGGGCGAAACUCGGCCUCAUCGGCCGCCUAGUAGCUGGCCACACUGCGCCAUAUAAACAAUUU
......-....(.((((-(((((.(((.(((((..........((((.....)))).....(((((.....)))))....)))))))).))))))))).)............. ( -42.40, z-score =  -2.36, R)
>droEre2.scaffold_4784 6483589 112 - 25762168
CGCUCACUACAGCCGCG-GUGUGACCGCGCUGCCGAAAAAUGCCGCCAAACGGGCCCAACUCGGCCUUAUCGGCCGCCAAGUAUCUGGCCACACUGCGCCAUAUAAACAAUUU
.(((......)))((((-(((((.(((....(((((.....(((........))).....))))).....)))..((((......)))))))))))))............... ( -36.40, z-score =  -0.97, R)
>consensus
CAGCCGCUCUCUUCUCGAGUGUGACCGCGCUGCCGACAAAUGCCGCGAAACGGGCCAAACUCGGCCUUAUCGGCCGCUAAGCAGCUGGCCACACUGCGGCAUAUAAACAAUUU
..............(((((((((.(((.(((((.........(((.....)))........(((((.....)))))....)))))))).)))))).))).............. (-32.14 = -32.02 +  -0.12)

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 Tue Apr 19 23:01:28 2011