Locus 10698

Sequence ID dm3.chr3R
Location 15,806,917 – 15,807,053
Length 136
Max. P 0.897377
window14705 window14706 window14707

overview

Window 5

Location 15,806,917 – 15,807,016
Length 99
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 85.39
Shannon entropy 0.23501
G+C content 0.55784
Mean single sequence MFE -27.02
Consensus MFE -22.21
Energy contribution -22.27
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.73
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.828927
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15806917 99 + 27905053
GCAUACUUUUGAGCGUGUUUCGGCCCCGGAUCGUGUUUCACAGCUCCCGUUGGAGCUGUUUCCCCAACCAGGUCUGUUC---CAUGCUGCUCUGUGCUGUAC
(((((.....(((((.((...((...((((((.((....((((((((....)))))))).....))....))))))..)---)..))))))))))))..... ( -31.70, z-score =  -2.04, R)
>droSim1.chr3R 21850105 102 - 27517382
GCAUACUUUUGAGCGUGUUUCGUCACCGGAUCGUGUUUCACAGCUCCCGUUGGAGCUGUAUCCCCAACCUGGCCUGUCCCACCAUGCUACUCUGUGCUGUAC
(((((......((((((....(.((((((....((....((((((((....)))))))).....))..))))..)).)....))))))....)))))..... ( -28.40, z-score =  -1.42, R)
>droSec1.super_58 47979 102 - 188520
GCAUACUUUUGAGCGUGUUUCGUCCCCGGAUCGCGUUUCACAGCUCCCGUUGGAGCUGUAUCCCCAACCUGGCCUCUCCCACCAUGCUACUCUGUGCUGUAC
(((((.....(((((((.((((....)))).))))))).((((((((....))))))))..........(((......)))...........)))))..... ( -28.40, z-score =  -2.09, R)
>droEre2.scaffold_4770 11892161 86 - 17746568
GCAUACUUUUGAGCGUGUUUCGUCCCCGGAUCGUGUUUCACAGCUCCCAUUGGAGCUGU-UCCCCGACCUCGCCUGUCC---CAUUCUAC------------
((........(..((.....))..)..((.(((.(....((((((((....))))))))-...))))))..))......---........------------ ( -19.60, z-score =  -1.36, R)
>consensus
GCAUACUUUUGAGCGUGUUUCGUCCCCGGAUCGUGUUUCACAGCUCCCGUUGGAGCUGUAUCCCCAACCUGGCCUGUCC___CAUGCUACUCUGUGCUGUAC
((((......(((((((.((((....)))).))))))).((((((((....))))))))........................))))............... (-22.21 = -22.27 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,806,917 – 15,807,016
Length 99
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 85.39
Shannon entropy 0.23501
G+C content 0.55784
Mean single sequence MFE -31.26
Consensus MFE -25.27
Energy contribution -25.40
Covariance contribution 0.13
Combinations/Pair 1.10
Mean z-score -1.95
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.13
SVM RNA-class probability 0.897377
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15806917 99 - 27905053
GUACAGCACAGAGCAGCAUG---GAACAGACCUGGUUGGGGAAACAGCUCCAACGGGAGCUGUGAAACACGAUCCGGGGCCGAAACACGCUCAAAAGUAUGC
((((.((.....))(((.((---.......(((((((((....((((((((....))))))))....).))).))))).......)).))).....)))).. ( -32.64, z-score =  -2.03, R)
>droSim1.chr3R 21850105 102 + 27517382
GUACAGCACAGAGUAGCAUGGUGGGACAGGCCAGGUUGGGGAUACAGCUCCAACGGGAGCUGUGAAACACGAUCCGGUGACGAAACACGCUCAAAAGUAUGC
((((.((........))...(((......(((.((((((...(((((((((....)))))))))...).))))).))).......)))........)))).. ( -30.02, z-score =  -0.80, R)
>droSec1.super_58 47979 102 + 188520
GUACAGCACAGAGUAGCAUGGUGGGAGAGGCCAGGUUGGGGAUACAGCUCCAACGGGAGCUGUGAAACGCGAUCCGGGGACGAAACACGCUCAAAAGUAUGC
...............(((((.(..(((.(....(((((.(..(((((((((....)))))))))...).)))))((....)).....).)))...).))))) ( -33.60, z-score =  -2.07, R)
>droEre2.scaffold_4770 11892161 86 + 17746568
------------GUAGAAUG---GGACAGGCGAGGUCGGGGA-ACAGCUCCAAUGGGAGCUGUGAAACACGAUCCGGGGACGAAACACGCUCAAAAGUAUGC
------------........---.....((((.((((((...-((((((((....))))))))....).)))))((....)).....))))........... ( -28.80, z-score =  -2.87, R)
>consensus
GUACAGCACAGAGUAGCAUG___GGACAGGCCAGGUUGGGGAUACAGCUCCAACGGGAGCUGUGAAACACGAUCCGGGGACGAAACACGCUCAAAAGUAUGC
..........((((...................(((((.(...((((((((....))))))))....).)))))((....))......)))).......... (-25.27 = -25.40 +   0.13)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,806,954 – 15,807,053
Length 99
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 77.86
Shannon entropy 0.37354
G+C content 0.47038
Mean single sequence MFE -18.47
Consensus MFE -13.98
Energy contribution -14.22
Covariance contribution 0.24
Combinations/Pair 1.07
Mean z-score -1.23
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.735039
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15806954 99 + 27905053
UCACAGCUCCCGUUGGAGCUGUUUCCCCAACCAGGUCUGUUCCA---UGCUGCUCUGUGCUGUACCGCUGCCACAUUAUGUAUUAUAAAAGCAUAAACAUUA
..((((((((....))))))))...........(((..((....---(((.((.....)).)))..)).)))...((((((.........))))))...... ( -21.90, z-score =  -0.80, R)
>droSim1.chr3R 21850142 102 - 27517382
UCACAGCUCCCGUUGGAGCUGUAUCCCCAACCUGGCCUGUCCCACCAUGCUACUCUGUGCUGUACCACUGCCACAUUAUGUAUUAUAAAAGCAUAAACAUUA
..((((((((....))))))))..........((((.((......)).))))...((((((.......(((........))).......))))))....... ( -22.44, z-score =  -1.53, R)
>droSec1.super_58 48016 102 - 188520
UCACAGCUCCCGUUGGAGCUGUAUCCCCAACCUGGCCUCUCCCACCAUGCUACUCUGUGCUGUACCACUGCCACAUUAUGUAUUAUAAAAGCAUAAAAAUUA
..((((((((....))))))))..........((((......((.(((........))).)).......))))..((((((.........))))))...... ( -21.12, z-score =  -1.87, R)
>droYak2.chr3R 4589114 77 + 28832112
UCACUGCUCCCGUUGGAGCUGU-UCCCCGGCCUCGCCUGUCCUA---------------UUC---------CACAUUAUGUAUUAUAAAAGCAUUAACGUUA
..((.(((((....))))).))-.....(((...))).......---------------...---------............................... ( -10.60, z-score =   0.23, R)
>droEre2.scaffold_4770 11892198 86 - 17746568
UCACAGCUCCCAUUGGAGCUGU-UCCCCGACCUCGCCUGUCCCA---------------UUCUACCGCUACCACAUUGUGUAUUAUAAAAGCAUAAACGUUG
..((((((((....))))))))-....((((...((..((....---------------....)).)).......((((((.........))))))..)))) ( -16.30, z-score =  -2.17, R)
>consensus
UCACAGCUCCCGUUGGAGCUGU_UCCCCAACCUGGCCUGUCCCA___UGCU_CUCUGUGCUGUACCACUGCCACAUUAUGUAUUAUAAAAGCAUAAACAUUA
..((((((((....)))))))).....................................................((((((.........))))))...... (-13.98 = -14.22 +   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 00:28:50 2011