Locus 7394

Sequence ID dm3.chr3L
Location 14,546,187 – 14,546,317
Length 130
Max. P 0.966627
window10179 window10180 window10181

overview

Window 9

Location 14,546,187 – 14,546,287
Length 100
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 65.41
Shannon entropy 0.63615
G+C content 0.43275
Mean single sequence MFE -21.65
Consensus MFE -8.74
Energy contribution -9.39
Covariance contribution 0.65
Combinations/Pair 1.39
Mean z-score -1.22
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.596792
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14546187 100 + 24543557
AGAUAGGUUUCACUUACAUU-----------GGCACCCAUUUUCUACUUCCUUGUCGUCAGGAAUGCCCU-AU--ACCUUUUUU--CAGGGU-GCAUUCAGGCUUCCUAAUUACACA
.((((((............(-----------((...)))...........))))))...(((((.(((..-.(--(((((....--.)))))-)......))))))))......... ( -18.50, z-score =  -0.44, R)
>droAna3.scaffold_13337 18747913 101 - 23293914
---------------AUAUCAGUAUCUUCUCUUC-CCCUUCAGAUACACCCUAUAUCUGAGGUAUGCGUACGUGGCCAUGUAUUCUUAGGGUUGGAAUAGCAUCUUCUCCUUACUUU
---------------......((...((((...(-(((((((((((.......)))))))))...(.((((((....)))))).)...)))..))))..))................ ( -19.40, z-score =  -0.04, R)
>droEre2.scaffold_4784 14515579 112 + 25762168
AGAUAUGCUUUACGUACAUUGCGUUCCGAUUUGCGCCCCUUUUCCACGUCCUUGUAGUCAGGAAUGCCUUCAU--UCCUUUUUU--CAGGGU-GCAUUCAGACUUCCUAAUUACACG
.(..((((............))))..)((..(((((((.......(((....)))....(((((((....)))--)))).....--..))))-))).)).................. ( -22.80, z-score =  -1.53, R)
>droYak2.chr3L 14632045 87 + 24197627
---------------AUAUCA---------UUGC-CCCCUUUCCUACGUCCUUGUAGUCGGGAAUGCCUUCAU--UCCUUUUUU--CAGGGU-GCACUCAGGCUUCCUAAUUACACU
---------------......---------.(((-.((((...(((((....)))))..(((((((....)))--)))).....--.)))).-)))...(((...)))......... ( -19.50, z-score =  -1.91, R)
>droSec1.super_0 6671446 101 + 21120651
UUAUAGGUUUCACUUACAUU-----------GGCGCCCCUUUUCUACUUCCUUGUAGUCAGGAAUGCCUUCAU--UCCUUUUUU--CAGGGU-GCAUUCAGGCUUCCUAAUUACACA
...((((.....((......-----------.((((((.....((((......))))..(((((((....)))--)))).....--..))))-))....))....))))........ ( -24.50, z-score =  -2.77, R)
>droSim1.chr3L 13871859 114 + 22553184
AGAUAGGUUUUCCUUGCAUUUGGCUACGAUUGGCGCCCCUUUUCUACUUCCUUGUCGUCAGGAAUGCCUUCAU--UCCUUUUUUUUCAGGGU-GCAUUCAGGCUUCCUAAUUACACA
...((((....(((.((.....))...((...((((((.......((......))....(((((((....)))--)))).........))))-))..)))))...))))........ ( -25.20, z-score =  -0.61, R)
>consensus
AGAUAGGUUU_ACUUACAUU__________UGGCGCCCCUUUUCUACUUCCUUGUAGUCAGGAAUGCCUUCAU__UCCUUUUUU__CAGGGU_GCAUUCAGGCUUCCUAAUUACACA
....................................................(((.((.(((((.((((......((((........))))........))))))))).)).))).. ( -8.74 =  -9.39 +   0.65)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,546,187 – 14,546,287
Length 100
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 65.41
Shannon entropy 0.63615
G+C content 0.43275
Mean single sequence MFE -24.98
Consensus MFE -12.69
Energy contribution -12.89
Covariance contribution 0.20
Combinations/Pair 1.35
Mean z-score -1.45
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.77
SVM RNA-class probability 0.966627
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14546187 100 - 24543557
UGUGUAAUUAGGAAGCCUGAAUGC-ACCCUG--AAAAAAGGU--AU-AGGGCAUUCCUGACGACAAGGAAGUAGAAAAUGGGUGCC-----------AAUGUAAGUGAAACCUAUCU
..(((..(((((((((((..(((.-..(((.--.....))))--))-.)))).)))))))..)))............((((((..(-----------(.......))..)))))).. ( -24.00, z-score =  -1.36, R)
>droAna3.scaffold_13337 18747913 101 + 23293914
AAAGUAAGGAGAAGAUGCUAUUCCAACCCUAAGAAUACAUGGCCACGUACGCAUACCUCAGAUAUAGGGUGUAUCUGAAGGG-GAAGAGAAGAUACUGAUAU---------------
..((((.((((.((...)).))))..((((..(..(((........)))..).....((((((((.....))))))))))))-..........)))).....--------------- ( -20.30, z-score =  -0.24, R)
>droEre2.scaffold_4784 14515579 112 - 25762168
CGUGUAAUUAGGAAGUCUGAAUGC-ACCCUG--AAAAAAGGA--AUGAAGGCAUUCCUGACUACAAGGACGUGGAAAAGGGGCGCAAAUCGGAACGCAAUGUACGUAAAGCAUAUCU
...(((.....(...(((((.(((-.((((.--.....((((--(((....)))))))..((((......))))....)))).)))..)))))...)....)))............. ( -29.30, z-score =  -1.91, R)
>droYak2.chr3L 14632045 87 - 24197627
AGUGUAAUUAGGAAGCCUGAGUGC-ACCCUG--AAAAAAGGA--AUGAAGGCAUUCCCGACUACAAGGACGUAGGAAAGGGG-GCAA---------UGAUAU---------------
.(((((.(((((...))))).)))-))(((.--.....))).--......((...(((..((((......))))....))).-))..---------......--------------- ( -22.90, z-score =  -1.79, R)
>droSec1.super_0 6671446 101 - 21120651
UGUGUAAUUAGGAAGCCUGAAUGC-ACCCUG--AAAAAAGGA--AUGAAGGCAUUCCUGACUACAAGGAAGUAGAAAAGGGGCGCC-----------AAUGUAAGUGAAACCUAUAA
..((((.(((((((((((..((..-..(((.--.....))).--))..)))).))))))).))))............(((..(((.-----------.......)))...))).... ( -26.50, z-score =  -2.47, R)
>droSim1.chr3L 13871859 114 - 22553184
UGUGUAAUUAGGAAGCCUGAAUGC-ACCCUGAAAAAAAAGGA--AUGAAGGCAUUCCUGACGACAAGGAAGUAGAAAAGGGGCGCCAAUCGUAGCCAAAUGCAAGGAAAACCUAUCU
.(((((.(((((...))))).)))-))(((........((((--(((....))))))).......)))..(((.......(((..........)))...))).(((....))).... ( -26.86, z-score =  -0.95, R)
>consensus
UGUGUAAUUAGGAAGCCUGAAUGC_ACCCUG__AAAAAAGGA__AUGAAGGCAUUCCUGACUACAAGGAAGUAGAAAAGGGGCGCAA__________AAUGUAAGU_AAACCUAUCU
..(((..(((((((((((.........(((........))).......)))).)))))))..))).................................................... (-12.69 = -12.89 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,546,213 – 14,546,317
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.21
Shannon entropy 0.46170
G+C content 0.39543
Mean single sequence MFE -22.30
Consensus MFE -12.69
Energy contribution -12.89
Covariance contribution 0.20
Combinations/Pair 1.35
Mean z-score -1.88
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.41
SVM RNA-class probability 0.936850
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14546213 104 - 24543557
----------UAAUAGCAUAUAAGAGCAAAAAAAGAGAGUUGUGUAAUUAGGAAGCCUGAAUGC-ACCCUGA--AAAAAGGU--AU-AGGGCAUUCCUGACGACAAGGAAGUAGAAAAUG
----------.....((........))...............(((..(((((((((((..(((.-..(((..--....))))--))-.)))).)))))))..)))............... ( -19.90, z-score =  -1.79, R)
>droAna3.scaffold_13337 18747934 119 + 23293914
AGAGAUUUGACAAUCUCUUCUCGGAGA-GACGAAAAGGUAAAAGUAAGGAGAAGAUGCUAUUCCAACCCUAAGAAUACAUGGCCACGUACGCAUACCUCAGAUAUAGGGUGUAUCUGAAG
(((((((....)))))))..(((....-..)))...((((...(((.(..(...(((.(((((.........))))))))..)..).)))...))))((((((((.....)))))))).. ( -25.10, z-score =  -0.08, R)
>droEre2.scaffold_4784 14515616 102 - 25762168
----------UAAUAUC--AUAAGAGC-AACAAAGAGAGUCGUGUAAUUAGGAAGUCUGAAUGC-ACCCUGA--AAAAAGGA--AUGAAGGCAUUCCUGACUACAAGGACGUGGAAAAGG
----------.......--........-..........(((.((((.(((((((((((..((..-..(((..--....))).--))..)))).))))))).))))..))).......... ( -23.10, z-score =  -2.08, R)
>droYak2.chr3L 14632057 104 - 24197627
----------UAAUAUCGUAUAAGAGC-AAAAAAGAGAGAAGUGUAAUUAGGAAGCCUGAGUGC-ACCCUGA--AAAAAGGA--AUGAAGGCAUUCCCGACUACAAGGACGUAGGAAAGG
----------.....((.(((......-.............(((((.(((((...))))).)))-))(((..--.....(((--(((....))))))........)))..))).)).... ( -20.96, z-score =  -1.84, R)
>droSec1.super_0 6671472 104 - 21120651
----------UAAUGGCAUAUAAGAGC-AAAAAAGAGAGUUGUGUAAUUAGGAAGCCUGAAUGC-ACCCUGA--AAAAAGGA--AUGAAGGCAUUCCUGACUACAAGGAAGUAGAAAAGG
----------.....((........))-.............(((((.(((((...))))).)))-))(((..--....((((--(((....)))))))..((((......))))...))) ( -22.90, z-score =  -2.53, R)
>droSim1.chr3L 13871896 106 - 22553184
----------UAAUAGCAUAUAAGAGC-AAAAAAGAGAGUUGUGUAAUUAGGAAGCCUGAAUGC-ACCCUGAAAAAAAAGGA--AUGAAGGCAUUCCUGACGACAAGGAAGUAGAAAAGG
----------.....((........))-.............(((((.(((((...))))).)))-))(((........((((--(((....))))))).......)))............ ( -21.86, z-score =  -2.94, R)
>consensus
__________UAAUAGCAUAUAAGAGC_AAAAAAGAGAGUUGUGUAAUUAGGAAGCCUGAAUGC_ACCCUGA__AAAAAGGA__AUGAAGGCAUUCCUGACUACAAGGAAGUAGAAAAGG
..........................................(((..(((((((((((.........(((........))).......)))).)))))))..)))............... (-12.69 = -12.89 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:26:05 2011