Locus 7398

Sequence ID dm3.chr3L
Location 14,563,286 – 14,563,413
Length 127
Max. P 0.999653
window10186 window10187 window10188 window10189

overview

Window 6

Location 14,563,286 – 14,563,384
Length 98
Sequences 9
Columns 98
Reading direction forward
Mean pairwise identity 70.09
Shannon entropy 0.63765
G+C content 0.50639
Mean single sequence MFE -30.24
Consensus MFE -15.88
Energy contribution -16.02
Covariance contribution 0.14
Combinations/Pair 1.14
Mean z-score -1.62
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.25
SVM RNA-class probability 0.986767
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14563286 98 + 24543557
UGCCAGAGGAAAGAGUAUAUCCAACUGCCUAUGACUUGCGGGGCAUUUUUAGACGCGGCCUGUGAGCGAAUUGGCGACACGUGACCGGAUCACGUGUC
.((((((((....(((.......))).))).((.((..((((.(............).))))..))))..)))))(((((((((.....))))))))) ( -33.20, z-score =  -1.70, R)
>droSim1.chr3L 13889231 98 + 22553184
UGCCAUAGGAAAGAGUAUAUCCAGCUGCCUAUGACUUGCAUGGCAUUUUUAGACGCGGCCUGUGGGCGAAUUGGCGACACGCGACCGGAUCACGUGUC
..(((((((...(.((.........((((.(((.....))))))).......)).)..)))))))((......))((((((.((.....)).)))))) ( -28.79, z-score =   0.02, R)
>droSec1.super_0 6688430 98 + 21120651
UGCCAAAGGAAAGAGUAUAUCCAGCUGCCUAUGACUUGCAGGGCAUUUUUAGACGCGGCCUGUGGGCGAAUUGGCGACACGUGACCGGAUCACGUGUC
.((((((((....(((.......))).))).((.((..((((.(............).))))..))))..)))))(((((((((.....))))))))) ( -34.40, z-score =  -1.70, R)
>droYak2.chr3L 14650275 98 + 24197627
UGACAGAAGCAAGGGUAUUCCCAGCUGGCUGUGACUUGCAGGAAAUAUUUAGACGCGGCCUGUGGGCGAAUUGGCGACACGUGACCGGAUCACGUGUC
..((((.(((..(((....))).)))..))))(.((..((((................))))..)))........(((((((((.....))))))))) ( -33.29, z-score =  -1.29, R)
>droEre2.scaffold_4784 14532908 98 + 25762168
UGCAAGAAGAAAGGGUAUACACAGCCGUCUGUGACUUGCAGCGCAUUUUUAGACGCGGCCUGUGGGCGAAUUGGCGACACGUGACCGGAUCACGUGUC
((((((.(((...(((.......))).)))....))))))((((.......).))).(((.((......)).)))(((((((((.....))))))))) ( -31.00, z-score =  -0.26, R)
>droAna3.scaffold_13337 18764782 96 - 23293914
-UCUCGUUUAAAGAGUAUACCAAGUCUGCUAUUUCCCUU-GACCAUUUUUGGCUGUGGCCUGCAAGCGAAUUGGUGACACGUGACCGGAUCACGUGUC
-.(((.......)))...(((((.((.(((.....((..-(.(((....))))...))......))))).)))))(((((((((.....))))))))) ( -26.80, z-score =  -1.30, R)
>dp4.chrXR_group6 6053976 91 - 13314419
-------UGCCGAAUCAAAGAAAAAAGAGUAGAGCUUGUAAAACAUUUUUGUUUGCGGCCUGUGGGCGAAUUGGCGACACGUGACCAGAUCACGUGUC
-------.(((((.((....................((((((.((....))))))))(((....))))).)))))(((((((((.....))))))))) ( -29.80, z-score =  -2.80, R)
>droPer1.super_41 112038 91 - 728894
-------UGCCGAAUCAAGGAAAAAAGAGUAGAGCUUGUAAAACAUUUUUGUUUGCGGCCUGUGGGCGAAUUGGCGACACGUGACCAGAUCACGUGUC
-------.(((((.((....................((((((.((....))))))))(((....))))).)))))(((((((((.....))))))))) ( -29.80, z-score =  -2.53, R)
>droWil1.scaffold_181136 1712443 81 + 2313701
------------UACCAGGGCUAAA----UAAAACUUGUAGCACAAUUUAGUUUGUGGCAAAUUU-CGAAUUGGCGACACGUGACCAAGUCACGUGUC
------------.......(((((.----..(((.((((..(((((......))))))))).)))-....)))))((((((((((...)))))))))) ( -25.10, z-score =  -3.06, R)
>consensus
UGCCAGAGGAAAGAGUAUACCCAGCUGCCUAUGACUUGCAGGACAUUUUUAGACGCGGCCUGUGGGCGAAUUGGCGACACGUGACCGGAUCACGUGUC
.........................................................(((.((......)).)))(((((((((.....))))))))) (-15.88 = -16.02 +   0.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,563,286 – 14,563,384
Length 98
Sequences 9
Columns 98
Reading direction reverse
Mean pairwise identity 70.09
Shannon entropy 0.63765
G+C content 0.50639
Mean single sequence MFE -29.95
Consensus MFE -17.53
Energy contribution -17.00
Covariance contribution -0.53
Combinations/Pair 1.47
Mean z-score -2.65
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.14
SVM RNA-class probability 0.999653
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14563286 98 - 24543557
GACACGUGAUCCGGUCACGUGUCGCCAAUUCGCUCACAGGCCGCGUCUAAAAAUGCCCCGCAAGUCAUAGGCAGUUGGAUAUACUCUUUCCUCUGGCA
((((((((((...))))))))))((((....(((....)))...((((((...((((.(....).....)))).)))))).............)))). ( -33.50, z-score =  -2.88, R)
>droSim1.chr3L 13889231 98 - 22553184
GACACGUGAUCCGGUCGCGUGUCGCCAAUUCGCCCACAGGCCGCGUCUAAAAAUGCCAUGCAAGUCAUAGGCAGCUGGAUAUACUCUUUCCUAUGGCA
((((((((((...))))))))))((((....(((....)))...(((((....(((((((.....))).))))..))))).............)))). ( -33.80, z-score =  -2.17, R)
>droSec1.super_0 6688430 98 - 21120651
GACACGUGAUCCGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCGUCUAAAAAUGCCCUGCAAGUCAUAGGCAGCUGGAUAUACUCUUUCCUUUGGCA
((((((((((...))))))))))(((((...(((....))).(((((((....(((...))).....))))).)).(((.........))).))))). ( -33.10, z-score =  -2.42, R)
>droYak2.chr3L 14650275 98 - 24197627
GACACGUGAUCCGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCGUCUAAAUAUUUCCUGCAAGUCACAGCCAGCUGGGAAUACCCUUGCUUCUGUCA
((((((((((...))))))))))............(((((..(((......(((((((.((..((....))..)).)))))))....))).))))).. ( -28.60, z-score =  -1.57, R)
>droEre2.scaffold_4784 14532908 98 - 25762168
GACACGUGAUCCGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCGUCUAAAAAUGCGCUGCAAGUCACAGACGGCUGUGUAUACCCUUUCUUCUUGCA
((((((((((...))))))))))((......(((....))).((((......)))))).(((((.(((((....))))).............))))). ( -32.44, z-score =  -2.19, R)
>droAna3.scaffold_13337 18764782 96 + 23293914
GACACGUGAUCCGGUCACGUGUCACCAAUUCGCUUGCAGGCCACAGCCAAAAAUGGUC-AAGGGAAAUAGCAGACUUGGUAUACUCUUUAAACGAGA-
((((((((((...))))))))))(((((.(((((......((...((((....)))).-...))....))).)).)))))...(((.......))).- ( -31.50, z-score =  -3.01, R)
>dp4.chrXR_group6 6053976 91 + 13314419
GACACGUGAUCUGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCAAACAAAAAUGUUUUACAAGCUCUACUCUUUUUUCUUUGAUUCGGCA-------
((((((((((...))))))))))(((.....(((....)))..((((.(((((.((............))...))))).))))....))).------- ( -25.60, z-score =  -3.00, R)
>droPer1.super_41 112038 91 + 728894
GACACGUGAUCUGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCAAACAAAAAUGUUUUACAAGCUCUACUCUUUUUUCCUUGAUUCGGCA-------
((((((((((...))))))))))(((...(((((....))).(((((((....))))).....)).................))...))).------- ( -25.50, z-score =  -2.96, R)
>droWil1.scaffold_181136 1712443 81 - 2313701
GACACGUGACUUGGUCACGUGUCGCCAAUUCG-AAAUUUGCCACAAACUAAAUUGUGCUACAAGUUUUA----UUUAGCCCUGGUA------------
((((((((((...))))))))))((((....(-(((((((.(((((......)))))...)))))))).----........)))).------------ ( -25.52, z-score =  -3.64, R)
>consensus
GACACGUGAUCCGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCGUCUAAAAAUGCCCUGCAAGUCAUAGGCAGCUGGAUAUACUCUUUCAUCUGGCA
((((((((((...))))))))))........(((....))).((((......)))).......................................... (-17.53 = -17.00 +  -0.53)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,563,312 – 14,563,413
Length 101
Sequences 9
Columns 101
Reading direction forward
Mean pairwise identity 82.30
Shannon entropy 0.37106
G+C content 0.56237
Mean single sequence MFE -35.51
Consensus MFE -26.86
Energy contribution -26.71
Covariance contribution -0.15
Combinations/Pair 1.26
Mean z-score -1.55
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.10
SVM RNA-class probability 0.891208
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14563312 101 + 24543557
GCCUAUGACUUGCGGGGCAUUUUUAGACGCGGCCUGUGAGCGAAUUGGCGACACGUGACCGGAUCACGUGUCCACACCAACCAGGCGGCGUGUCAACUCUC
((((..........))))........((((.(((((.(.((......))(((((((((.....)))))))))........)))))).)))).......... ( -37.10, z-score =  -1.20, R)
>droSim1.chr3L 13889257 101 + 22553184
GCCUAUGACUUGCAUGGCAUUUUUAGACGCGGCCUGUGGGCGAAUUGGCGACACGCGACCGGAUCACGUGUCCACACCAACCAGGCAGCGUGUCAACUCUC
(((.(((.....)))))).......((((((((((((((((......))((((((.((.....)).))))))....)))..)))))..))))))....... ( -36.80, z-score =  -1.62, R)
>droSec1.super_0 6688456 101 + 21120651
GCCUAUGACUUGCAGGGCAUUUUUAGACGCGGCCUGUGGGCGAAUUGGCGACACGUGACCGGAUCACGUGUCCACACCAACCAGGCGGCGUGUCAACUCUC
((((.((.....))))))........((((.((((((((((......))(((((((((.....)))))))))....)))..))))).)))).......... ( -40.20, z-score =  -2.05, R)
>droYak2.chr3L 14650301 101 + 24197627
GGCUGUGACUUGCAGGAAAUAUUUAGACGCGGCCUGUGGGCGAAUUGGCGACACGUGACCGGAUCACGUGUCCACACCAACCAGGCGGCGUGUCAACUCUC
..((((.....))))...........((((.((((((((((......))(((((((((.....)))))))))....)))..))))).)))).......... ( -38.40, z-score =  -1.54, R)
>droEre2.scaffold_4784 14532934 101 + 25762168
GUCUGUGACUUGCAGCGCAUUUUUAGACGCGGCCUGUGGGCGAAUUGGCGACACGUGACCGGAUCACGUGUCCACACCAACCAGGCGGCGUGUCAACUCUC
.....((((.(((...))).......((((.((((((((((......))(((((((((.....)))))))))....)))..))))).))))))))...... ( -39.00, z-score =  -1.31, R)
>droAna3.scaffold_13337 18764807 100 - 23293914
UGCUAUUUCCC-UUGACCAUUUUUGGCUGUGGCCUGCAAGCGAAUUGGUGACACGUGACCGGAUCACGUGUCCACACCGACCAGGCGGCGUGUCAACUCUC
.((((.(((.(-(((.((((........))))....)))).))).))))(((((((((.....)))))))))(((.(((......))).)))......... ( -33.00, z-score =  -0.99, R)
>dp4.chrXR_group6 6054002 94 - 13314419
-------GCUUGUAAAACAUUUUUGUUUGCGGCCUGUGGGCGAAUUGGCGACACGUGACCAGAUCACGUGUCCACACCAACCAGGCGGCGUGUCAACUCGC
-------((..((.(((((....)))))((.((((((((((......))(((((((((.....)))))))))....)))..))))).))......))..)) ( -34.70, z-score =  -1.59, R)
>droPer1.super_41 112064 94 - 728894
-------GCUUGUAAAACAUUUUUGUUUGCGGCCUGUGGGCGAAUUGGCGACACGUGACCAGAUCACGUGUCCACACCAACCAGGCGGCGUGUCAACUCGC
-------((..((.(((((....)))))((.((((((((((......))(((((((((.....)))))))))....)))..))))).))......))..)) ( -34.70, z-score =  -1.59, R)
>droWil1.scaffold_181136 1712460 90 + 2313701
-------ACUUGUAGCACAAUUUAGUUUGUGGCAAAUUU-CGAAUUGGCGACACGUGACCAAGUCACGUGUCCACACCAAU---GCAACAUGUCAACUCUC
-------..(((((((.((((((((((((...)))))).-.))))))))((((((((((...))))))))))........)---))))............. ( -25.70, z-score =  -2.05, R)
>consensus
G_CUAUGACUUGCAGGACAUUUUUAGACGCGGCCUGUGGGCGAAUUGGCGACACGUGACCGGAUCACGUGUCCACACCAACCAGGCGGCGUGUCAACUCUC
...........................(((.(((((...((......))(((((((((.....))))))))).........))))).)))........... (-26.86 = -26.71 +  -0.15)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 14,563,312 – 14,563,413
Length 101
Sequences 9
Columns 101
Reading direction reverse
Mean pairwise identity 82.30
Shannon entropy 0.37106
G+C content 0.56237
Mean single sequence MFE -36.83
Consensus MFE -32.24
Energy contribution -31.24
Covariance contribution -0.99
Combinations/Pair 1.40
Mean z-score -1.78
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.97
SVM RNA-class probability 0.977354
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14563312 101 - 24543557
GAGAGUUGACACGCCGCCUGGUUGGUGUGGACACGUGAUCCGGUCACGUGUCGCCAAUUCGCUCACAGGCCGCGUCUAAAAAUGCCCCGCAAGUCAUAGGC
......((((((((.(((((((((((...((((((((((...)))))))))))))))).......))))).)))).......(((...))).))))..... ( -37.71, z-score =  -1.38, R)
>droSim1.chr3L 13889257 101 - 22553184
GAGAGUUGACACGCUGCCUGGUUGGUGUGGACACGUGAUCCGGUCGCGUGUCGCCAAUUCGCCCACAGGCCGCGUCUAAAAAUGCCAUGCAAGUCAUAGGC
......((((((((.(((((...((((.(((((((((((...)))))))))).).....))))..))))).)))).......(((...))).))))..... ( -38.10, z-score =  -1.29, R)
>droSec1.super_0 6688456 101 - 21120651
GAGAGUUGACACGCCGCCUGGUUGGUGUGGACACGUGAUCCGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCGUCUAAAAAUGCCCUGCAAGUCAUAGGC
......((((((((.(((((...((((.(((((((((((...)))))))))).).....))))..))))).)))).......(((...))).))))..... ( -38.50, z-score =  -1.63, R)
>droYak2.chr3L 14650301 101 - 24197627
GAGAGUUGACACGCCGCCUGGUUGGUGUGGACACGUGAUCCGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCGUCUAAAUAUUUCCUGCAAGUCACAGCC
..((.(((..((((.(((((...((((.(((((((((((...)))))))))).).....))))..))))).))))..............))).))...... ( -35.99, z-score =  -1.45, R)
>droEre2.scaffold_4784 14532934 101 - 25762168
GAGAGUUGACACGCCGCCUGGUUGGUGUGGACACGUGAUCCGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCGUCUAAAAAUGCGCUGCAAGUCACAGAC
....((.(((((((.(((((...((((.(((((((((((...)))))))))).).....))))..))))).)))).......(((...))).))))).... ( -38.50, z-score =  -1.35, R)
>droAna3.scaffold_13337 18764807 100 + 23293914
GAGAGUUGACACGCCGCCUGGUCGGUGUGGACACGUGAUCCGGUCACGUGUCACCAAUUCGCUUGCAGGCCACAGCCAAAAAUGGUCAA-GGGAAAUAGCA
..((((((.(((((((......)))))))((((((((((...))))))))))..))))))(((......((...((((....))))...-.))....))). ( -40.50, z-score =  -2.61, R)
>dp4.chrXR_group6 6054002 94 + 13314419
GCGAGUUGACACGCCGCCUGGUUGGUGUGGACACGUGAUCUGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCAAACAAAAAUGUUUUACAAGC-------
((((((((.(((((((......)))))))((((((((((...))))))))))..))))))(((....))).))(((((....))))).......------- ( -37.00, z-score =  -2.33, R)
>droPer1.super_41 112064 94 + 728894
GCGAGUUGACACGCCGCCUGGUUGGUGUGGACACGUGAUCUGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCAAACAAAAAUGUUUUACAAGC-------
((((((((.(((((((......)))))))((((((((((...))))))))))..))))))(((....))).))(((((....))))).......------- ( -37.00, z-score =  -2.33, R)
>droWil1.scaffold_181136 1712460 90 - 2313701
GAGAGUUGACAUGUUGC---AUUGGUGUGGACACGUGACUUGGUCACGUGUCGCCAAUUCG-AAAUUUGCCACAAACUAAAUUGUGCUACAAGU-------
..((((((.((..((..---...))..))((((((((((...))))))))))..)))))).-..(((((.(((((......)))))...)))))------- ( -28.20, z-score =  -1.61, R)
>consensus
GAGAGUUGACACGCCGCCUGGUUGGUGUGGACACGUGAUCCGGUCACGUGUCGCCAAUUCGCCCACAGGCCGCGUCUAAAAAUGCCCUGCAAGUCAUAG_C
..((((((.(((((((......)))))))((((((((((...))))))))))..))))))(((....))).((((......))))................ (-32.24 = -31.24 +  -0.99)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:26:11 2011