Locus 116

Sequence ID dm3.chr2L
Location 799,880 – 800,023
Length 143
Max. P 0.965697
window165 window166 window167 window168

overview

Window 5

Location 799,880 – 799,983
Length 103
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 80.80
Shannon entropy 0.29567
G+C content 0.42433
Mean single sequence MFE -30.62
Consensus MFE -21.90
Energy contribution -23.77
Covariance contribution 1.88
Combinations/Pair 1.10
Mean z-score -1.79
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.68
SVM RNA-class probability 0.785216
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 799880 103 + 23011544
UUUCAUUAAUACUGUUUUUAUU-----------CCUAGGUAACAGAUGCUGUGACCCAACUGCCGGGAGAAAGUGCACCUGGGCCCAUUAACAUUUUAAUGGGUUAUUAUUUGU
......(((((...........-----------(((((((.((((...))))..(((.......))).........)))))))((((((((....)))))))).)))))..... ( -24.20, z-score =  -0.41, R)
>droYak2.chr2L 782627 108 + 22324452
UUUUAUUGAUCCUGUUUUUAAUAGCUCCUUGCACCUUGGUCACAGAUGCUGGG--CGGAGUGCAAGGUGGU----CACCUGGGCCGCUUAAGAUUUUAAUGGGUUAUUAUUUGU
..................((((((((((((((((.((.(((.(((...)))))--).)))))))))(((((----(.....)))))).............)))))))))..... ( -33.00, z-score =  -1.44, R)
>droSec1.super_14 769811 103 + 2068291
UUUCAUUAAUACUGUUUCUAUU-----------CCUAGGUCACAGAUGCUGUGACCCAACUGCCGGGCGAAAGUGCACCCGGGCCCAUUAACAUUUUAAUGGGUCAUUAUUUGU
......................-----------....((((((((...))))))))......(((((.(......).)))))(((((((((....))))))))).......... ( -31.80, z-score =  -2.53, R)
>droSim1.chr2L 801285 103 + 22036055
UUUCAUUAAUACUGUUCUUAUU-----------CCUAGGUCACAGAUGCUGUGACCCAAGUGCCGGGAGAAAGUGCACCCGGGCCCAUUAACGUUUUAAUGGGUCAUUAUUUGU
......................-----------....((((((((...))))))))((((((.((((.(......).))))((((((((((....))))))))))..)))))). ( -33.50, z-score =  -2.80, R)
>consensus
UUUCAUUAAUACUGUUUUUAUU___________CCUAGGUCACAGAUGCUGUGACCCAACUGCCGGGAGAAAGUGCACCCGGGCCCAUUAACAUUUUAAUGGGUCAUUAUUUGU
.....................................((((((((...))))))))(((((((((((.(......).)))))(((((((((....)))))))))...)))))). (-21.90 = -23.77 +   1.88)

alignment

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secondary structure

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dotplot

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Window 6

Location 799,880 – 799,983
Length 103
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 80.80
Shannon entropy 0.29567
G+C content 0.42433
Mean single sequence MFE -29.13
Consensus MFE -21.11
Energy contribution -24.30
Covariance contribution 3.19
Combinations/Pair 1.07
Mean z-score -2.06
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.17
SVM RNA-class probability 0.904471
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 799880 103 - 23011544
ACAAAUAAUAACCCAUUAAAAUGUUAAUGGGCCCAGGUGCACUUUCUCCCGGCAGUUGGGUCACAGCAUCUGUUACCUAGG-----------AAUAAAAACAGUAUUAAUGAAA
.............((((((.(((((....(((((((.(((.(........)))).)))))))..)))))(((((.......-----------......)))))..))))))... ( -23.52, z-score =  -0.66, R)
>droYak2.chr2L 782627 108 - 22324452
ACAAAUAAUAACCCAUUAAAAUCUUAAGCGGCCCAGGUG----ACCACCUUGCACUCCG--CCCAGCAUCUGUGACCAAGGUGCAAGGAGCUAUUAAAAACAGGAUCAAUAAAA
.....(((((.(((.............((((.(.((((.----...)))).)....)))--)...((((((.......))))))..)).).))))).................. ( -21.00, z-score =  -0.21, R)
>droSec1.super_14 769811 103 - 2068291
ACAAAUAAUGACCCAUUAAAAUGUUAAUGGGCCCGGGUGCACUUUCGCCCGGCAGUUGGGUCACAGCAUCUGUGACCUAGG-----------AAUAGAAACAGUAUUAAUGAAA
...((((.((.((((((((....)))))))).(((((((......)))))))...(((((((((((...))))))))))).-----------........)).))))....... ( -36.20, z-score =  -3.53, R)
>droSim1.chr2L 801285 103 - 22036055
ACAAAUAAUGACCCAUUAAAACGUUAAUGGGCCCGGGUGCACUUUCUCCCGGCACUUGGGUCACAGCAUCUGUGACCUAGG-----------AAUAAGAACAGUAUUAAUGAAA
...((((.((.((((((((....)))))))).(((((.(......).)))))..((((((((((((...))))))))))))-----------........)).))))....... ( -35.80, z-score =  -3.82, R)
>consensus
ACAAAUAAUAACCCAUUAAAAUGUUAAUGGGCCCAGGUGCACUUUCUCCCGGCACUUGGGUCACAGCAUCUGUGACCUAGG___________AAUAAAAACAGUAUUAAUGAAA
...........((((((((....)))))))).(((((((......)))))))..((((((((((((...))))))))))))................................. (-21.11 = -24.30 +   3.19)

alignment

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secondary structure

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dotplot

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Window 7

Location 799,909 – 800,023
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 82.60
Shannon entropy 0.28201
G+C content 0.50949
Mean single sequence MFE -36.87
Consensus MFE -28.23
Energy contribution -29.35
Covariance contribution 1.12
Combinations/Pair 1.10
Mean z-score -1.51
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.677869
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 799909 114 + 23011544
AACAGAUGCUGUGACCCAACUGCCGGGAGAAAGUGCACCUGGGCCCAUUAACAUUUUAAUGGGUUAUUAUUUGUCUCUGUGCAUCUGCAUCUGCUGGCGUUUUCGGGAGUUUCG
....((.(((....((((((.(((((.(((.(((((((..(((((((((((....)))))))))..........))..))))).))...))).))))))))...)))))).)). ( -35.60, z-score =  -1.22, R)
>droYak2.chr2L 782667 98 + 22324452
CACAGAUGCUGGG--CGGAGUGCAAGGUGGU----CACCUGGGCCGCUUAAGAUUUUAAUGGGUUAUUAUUUGUCUCCGUGCAUCUGCAUCUGGUGGCGCUUUG----------
..(((((((((.(--(((((.((((((((((----(.....))))))))..(((((....)))))......))))))))).))...)))))))...........---------- ( -34.90, z-score =  -1.62, R)
>droSec1.super_14 769840 114 + 2068291
CACAGAUGCUGUGACCCAACUGCCGGGCGAAAGUGCACCCGGGCCCAUUAACAUUUUAAUGGGUCAUUAUUUGUCUCUGUGCAUCUGCAUCUGUCGGCGUUUUCGGGAGUUUCG
..(((((((.(.(((........((((.(......).))))((((((((((....)))))))))).......))).)...)))))))...((.((((.....)))).))..... ( -37.20, z-score =  -1.30, R)
>droSim1.chr2L 801314 114 + 22036055
CACAGAUGCUGUGACCCAAGUGCCGGGAGAAAGUGCACCCGGGCCCAUUAACGUUUUAAUGGGUCAUUAUUUGUCUCUGUGCAUCUGCAUCUGUCGGCGUUUUCGGGAGUUUCG
(((((...))))).((((((((((((.(((.(((((((...((((((((((....)))))))))).............))))).))...))).)))))))))..)))....... ( -39.79, z-score =  -1.90, R)
>consensus
CACAGAUGCUGUGACCCAACUGCCGGGAGAAAGUGCACCCGGGCCCAUUAACAUUUUAAUGGGUCAUUAUUUGUCUCUGUGCAUCUGCAUCUGUCGGCGUUUUCGGGAGUUUCG
..(((((((...((..(((((((((((.(......).)))))(((((((((....)))))))))...))))))..))...)))))))........................... (-28.23 = -29.35 +   1.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 799,909 – 800,023
Length 114
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 82.60
Shannon entropy 0.28201
G+C content 0.50949
Mean single sequence MFE -32.62
Consensus MFE -26.60
Energy contribution -28.47
Covariance contribution 1.87
Combinations/Pair 1.04
Mean z-score -2.12
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.75
SVM RNA-class probability 0.965697
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 799909 114 - 23011544
CGAAACUCCCGAAAACGCCAGCAGAUGCAGAUGCACAGAGACAAAUAAUAACCCAUUAAAAUGUUAAUGGGCCCAGGUGCACUUUCUCCCGGCAGUUGGGUCACAGCAUCUGUU
...................(((((((((.......................((((((((....))))))))(((((.(((.(........)))).))))).....))))))))) ( -33.20, z-score =  -2.01, R)
>droYak2.chr2L 782667 98 - 22324452
----------CAAAGCGCCACCAGAUGCAGAUGCACGGAGACAAAUAAUAACCCAUUAAAAUCUUAAGCGGCCCAGGUG----ACCACCUUGCACUCCG--CCCAGCAUCUGUG
----------................((((((((..(....).........................((((.(.((((.----...)))).)....)))--)...)))))))). ( -24.10, z-score =  -1.72, R)
>droSec1.super_14 769840 114 - 2068291
CGAAACUCCCGAAAACGCCGACAGAUGCAGAUGCACAGAGACAAAUAAUGACCCAUUAAAAUGUUAAUGGGCCCGGGUGCACUUUCGCCCGGCAGUUGGGUCACAGCAUCUGUG
..........................((((((((...((..(((....((.((((((((....)))))))).(((((((......))))))))).)))..))...)))))))). ( -36.90, z-score =  -2.18, R)
>droSim1.chr2L 801314 114 - 22036055
CGAAACUCCCGAAAACGCCGACAGAUGCAGAUGCACAGAGACAAAUAAUGACCCAUUAAAACGUUAAUGGGCCCGGGUGCACUUUCUCCCGGCACUUGGGUCACAGCAUCUGUG
..........................((((((((.................((((((((....))))))))(((((((((.(........)))))))))).....)))))))). ( -36.30, z-score =  -2.58, R)
>consensus
CGAAACUCCCGAAAACGCCAACAGAUGCAGAUGCACAGAGACAAAUAAUAACCCAUUAAAAUGUUAAUGGGCCCAGGUGCACUUUCUCCCGGCACUUGGGUCACAGCAUCUGUG
..........................((((((((.................((((((((....))))))))(((((((((...........))))))))).....)))))))). (-26.60 = -28.47 +   1.87)

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 21:06:58 2011