Locus 8348

Sequence ID dm3.chr3L
Location 22,158,722 – 22,158,881
Length 159
Max. P 0.809892
window11467 window11468 window11469 window11470

overview

Window 7

Location 22,158,722 – 22,158,816
Length 94
Sequences 10
Columns 107
Reading direction reverse
Mean pairwise identity 66.65
Shannon entropy 0.67898
G+C content 0.52654
Mean single sequence MFE -32.27
Consensus MFE -13.34
Energy contribution -12.01
Covariance contribution -1.33
Combinations/Pair 1.47
Mean z-score -1.06
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.658424
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22158722 94 - 24543557
UGUCGCUGGCAUUUUUCCUUUUCCUUAGAUUGCCAGCGACAUUUCGACUGAGCUGCAGGAUUAUUGCG--GCGGUGGCGGUGGCGCUGGCGUUCUC-----------
(((((((((((.(((...........))).)))))))))))....(((...(((((((.....)))))--))(.(((((....))))).))))...----------- ( -37.40, z-score =  -2.18, R)
>droEre2.scaffold_4784 21829762 91 - 25762168
UGUCGUUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGAGACAUUUCGACUGAGCUGCAGGAUUAUUGCG--GCGGUGGCGGUGGCGGUAGCUUC--------------
((((.((((((.(((...........))).)))))).)))).....((((.(((((((.....)))))--)).....))))(((....)))..-------------- ( -26.80, z-score =   0.20, R)
>droYak2.chr3L 22513659 85 - 24197627
UGUCGCUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGAGACAUUUCGACUCAGCUGCAGGAUUAUUGCG--GUGCUAGCGGUGGCUUC--------------------
((((.((((((.(((...........))).)))))).))))..(((.((..(((((((.....)))))--))...))))).......-------------------- ( -25.50, z-score =  -0.65, R)
>droSec1.super_11 2089279 94 - 2888827
UGUCGCUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGCGACAUUUCGACUGAGCUGCAGGAUUAUUGCG--GCGGUGGCGGUGGUGCUGGCGUUCUC-----------
(((((((((((.(((...........))).)))))))))))........((((..(((.((((((((.--......)))))))).)))..))))..----------- ( -36.00, z-score =  -1.80, R)
>droSim1.chr3L 21507420 94 - 22553184
UGUCGCUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGCGACAUUUCGACUGAGCUGCAGGAUUAUUGCG--GCGGUGGCGGUGGUGCUGGCGUUCUC-----------
(((((((((((.(((...........))).)))))))))))........((((..(((.((((((((.--......)))))))).)))..))))..----------- ( -36.00, z-score =  -1.80, R)
>dp4.chrXR_group8 6234253 105 - 9212921
UGUUGCUGGCAUUUUUCUUCUUUCUUAGAUUGCCAGCGACAUUUCGACUGAGUUGCAGGAUUAUUGUG-CGGCAUGGCUGAGUGUGUGGCACAGGCACGGUCACGG-
(((((((((((....(((........))).)))))))))))....(((((.((((((.((...)).))-))))...(((..(((.....))).))).)))))....- ( -40.60, z-score =  -2.91, R)
>droPer1.super_45 369889 105 + 618639
UGUUGCUGGCAUUUUUCUUCUUUCUUAGAUUGCCAGCGACAUUUCGACUGAGUUGCAGGAUUAUUGUG-CGGCAUGGCUGAGUGUGUGGCACAGGCACGGUCACGG-
(((((((((((....(((........))).)))))))))))....(((((.((((((.((...)).))-))))...(((..(((.....))).))).)))))....- ( -40.60, z-score =  -2.91, R)
>droMoj3.scaffold_6680 19489422 94 - 24764193
UGCCAUUGGCGUUUUUCUU-------AGAUUGCUGGCGACGUUCCG-UUGAGUUGCAGGAUUAUUGUGUUGGGGCAGUCA-GACG----GAGGGGGUUGACAAGUGU
.((((...(((.(((....-------))).)))))))..(.(((((-(((((((.(((.((....)).))).)))..)))-.)))----))).)............. ( -22.70, z-score =   0.91, R)
>droVir3.scaffold_13049 14714799 95 - 25233164
UGCCAUUGGCGUUUUUCUU-------AGAUUGCUGGCGACGUUCCG-UUGAGUUGCAGGAUUAUUGUGUUGGGGCAGUCGCGAGG----CGCGGGGCUGACAAGUGU
.((((...(((.(((....-------))).)))))))...((((((-(...(((.(((.((....)).))).))).(((....))----)))))))).......... ( -27.10, z-score =   1.06, R)
>droGri2.scaffold_15110 6559368 101 + 24565398
UGCCUUUGGCGUUUUUUCUUC----CAGAUUGCUGGUGGAGUUCCG-UUGAGUUGCAGGAUUAUUGUAUUGGGGCAGUCGCGUCGCCUCGUAGAGGAUGACAAGUG-
((((((..(((....((((.(----(((....)))).))))...))-)..)..(((((.....)))))...))))).....((((((((...)))).)))).....- ( -30.00, z-score =  -0.54, R)
>consensus
UGUCGCUGGCAUUUUUCCUCUUCCUUAGAUUGCCAGCGACAUUUCGACUGAGCUGCAGGAUUAUUGCG__GGGGUGGCGGUGGCGCUGGCGUGGGC___________
((((.((((((.(((...........))).)))))).)))).............((((.....))))........................................ (-13.34 = -12.01 +  -1.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,158,748 – 22,158,848
Length 100
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 75.62
Shannon entropy 0.41370
G+C content 0.52655
Mean single sequence MFE -28.28
Consensus MFE -15.15
Energy contribution -15.73
Covariance contribution 0.58
Combinations/Pair 1.10
Mean z-score -1.71
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.660765
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22158748 100 + 24543557
---------CGCAAUAAUCCUGCAGCU-CAGUCGAAAUGUCGCUGGCAAUCUAAGGAAAAGGA--AAAAUGCCAGCGACAGCGGUGGGG-AGUGGGUAGGCGGUGGCGUGCCC
---------.(((.......))).(((-(.((((...(((((((((((.(((........)))--....))))))))))).))))...)-)))(((((.((....)).))))) ( -40.50, z-score =  -3.17, R)
>droEre2.scaffold_4784 21829785 90 + 25762168
---------CGCAAUAAUCCUGCAGCU-CAGUCGAAAUGUCUCUGGCAAUCUAAGGAAGAGGA--AAAAUGCCAACGACAGCGGUGAGG-AGCUGGCGUGCCC----------
---------.(((.....((.((..((-((.(((...((((..(((((.(((........)))--....)))))..)))).))))))).-.)).))..)))..---------- ( -25.90, z-score =  -0.44, R)
>droYak2.chr3L 22513676 90 + 24197627
---------CGCAAUAAUCCUGCAGCU-GAGUCGAAAUGUCUCUGGCAAUCUAAGGAAGAGGA--AAAAUGCCAGCGACAGCGGUGGGG-AGAUGGCGUGCCC----------
---------(((.....((((...(((-(........((((.((((((.(((........)))--....)))))).)))).)))).)))-)....))).....---------- ( -26.30, z-score =  -0.25, R)
>droSec1.super_11 2089305 77 + 2888827
---------CGCAAUAAUCCUGCAGCU-CAGUCGAAAUGUCGCUGGCAAUCUAAGGAAGAGGA--AAAAUGCCAGCGACAGCGGUGGGG------------------------
---------.(((.......)))..((-((.(((...(((((((((((.(((........)))--....))))))))))).))))))).------------------------ ( -29.80, z-score =  -3.56, R)
>droSim1.chr3L 21507446 77 + 22553184
---------CGCAAUAAUCCUGCAGCU-CAGUCGAAAUGUCGCUGGCAAUCUAAGGAAGAGGA--AAAAUGCCAGCGACAGCGGUGGGG------------------------
---------.(((.......)))..((-((.(((...(((((((((((.(((........)))--....))))))))))).))))))).------------------------ ( -29.80, z-score =  -3.56, R)
>droWil1.scaffold_180698 11355711 103 - 11422946
CUGCCCCAACACAAUAAUCCUGCAACUUCAGGCAAAACGUCGCUAGCAAUCUAAGAAAGAAGAGAAAAAUGCCAAAGACUGUAGUGGUGUAGCAUGCCCGUUU----------
((((.(((..(((.....((((......))))......(((....(((.(((........)))......)))....))))))..))).))))...........---------- ( -17.40, z-score =   0.70, R)
>consensus
_________CGCAAUAAUCCUGCAGCU_CAGUCGAAAUGUCGCUGGCAAUCUAAGGAAGAGGA__AAAAUGCCAGCGACAGCGGUGGGG_AG__GGC__GC____________
.................((((((.(((...........(((.((((((.(((........)))......)))))).)))))).))))))........................ (-15.15 = -15.73 +   0.58)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,158,748 – 22,158,848
Length 100
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 75.62
Shannon entropy 0.41370
G+C content 0.52655
Mean single sequence MFE -24.70
Consensus MFE -15.33
Energy contribution -14.72
Covariance contribution -0.61
Combinations/Pair 1.22
Mean z-score -1.61
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.76
SVM RNA-class probability 0.809892
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22158748 100 - 24543557
GGGCACGCCACCGCCUACCCACU-CCCCACCGCUGUCGCUGGCAUUUU--UCCUUUUCCUUAGAUUGCCAGCGACAUUUCGACUG-AGCUGCAGGAUUAUUGCG---------
(((...((....))...))).((-(........(((((((((((.(((--...........))).)))))))))))........)-))..((((.....)))).--------- ( -30.19, z-score =  -2.87, R)
>droEre2.scaffold_4784 21829785 90 - 25762168
----------GGGCACGCCAGCU-CCUCACCGCUGUCGUUGGCAUUUU--UCCUCUUCCUUAGAUUGCCAGAGACAUUUCGACUG-AGCUGCAGGAUUAUUGCG---------
----------..(((..((.((.-.((((.((.((((.((((((.(((--...........))).)))))).))))...))..))-))..)).)).....))).--------- ( -23.80, z-score =  -0.32, R)
>droYak2.chr3L 22513676 90 - 24197627
----------GGGCACGCCAUCU-CCCCACCGCUGUCGCUGGCAUUUU--UCCUCUUCCUUAGAUUGCCAGAGACAUUUCGACUC-AGCUGCAGGAUUAUUGCG---------
----------(((..........-.)))..((.((((.((((((.(((--...........))).)))))).))))...))....-....((((.....)))).--------- ( -20.60, z-score =   0.07, R)
>droSec1.super_11 2089305 77 - 2888827
------------------------CCCCACCGCUGUCGCUGGCAUUUU--UCCUCUUCCUUAGAUUGCCAGCGACAUUUCGACUG-AGCUGCAGGAUUAUUGCG---------
------------------------......((((((((((((((.(((--...........))).)))))))))))......(((-.....))).......)))--------- ( -25.00, z-score =  -3.44, R)
>droSim1.chr3L 21507446 77 - 22553184
------------------------CCCCACCGCUGUCGCUGGCAUUUU--UCCUCUUCCUUAGAUUGCCAGCGACAUUUCGACUG-AGCUGCAGGAUUAUUGCG---------
------------------------......((((((((((((((.(((--...........))).)))))))))))......(((-.....))).......)))--------- ( -25.00, z-score =  -3.44, R)
>droWil1.scaffold_180698 11355711 103 + 11422946
----------AAACGGGCAUGCUACACCACUACAGUCUUUGGCAUUUUUCUCUUCUUUCUUAGAUUGCUAGCGACGUUUUGCCUGAAGUUGCAGGAUUAUUGUGUUGGGGCAG
----------.........(((..((.(((....(((.((((((.(((.............))).)))))).)))......((((......))))......))).))..))). ( -23.62, z-score =   0.36, R)
>consensus
____________GC__GCC__CU_CCCCACCGCUGUCGCUGGCAUUUU__UCCUCUUCCUUAGAUUGCCAGCGACAUUUCGACUG_AGCUGCAGGAUUAUUGCG_________
..............................(((.(((.((((((.(((.............))).)))))).))).......(((......))).......)))......... (-15.33 = -14.72 +  -0.61)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,158,778 – 22,158,881
Length 103
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 65.27
Shannon entropy 0.60520
G+C content 0.53294
Mean single sequence MFE -27.64
Consensus MFE -7.35
Energy contribution -6.69
Covariance contribution -0.66
Combinations/Pair 1.57
Mean z-score -2.20
Structure conservation index 0.27
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.37
SVM RNA-class probability 0.662313
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22158778 103 - 24543557
---CAUCUGCUGCUCCACCAGCUGAACAGACUGGUGGGGCACGCCACCGCCUACCCACUCCCCACCGCUGUCGCUGGCAUUUU--UCCUUUUCCUUAGAUUGCCAGCG
---.....(((((((((((((((....)).))))))))))).))...........................((((((((.(((--...........))).)))))))) ( -37.80, z-score =  -4.23, R)
>droEre2.scaffold_4784 21829815 93 - 25762168
---CAUCUGCUGCUCCACCAGCUGAACUGACUGGUGGGGCACGCCA----------GCUCCUCACCGCUGUCGUUGGCAUUUU--UCCUCUUCCUUAGAUUGCCAGAG
---.....((((((((((((((......).))))))))))).))((----------((........))))...((((((.(((--...........))).)))))).. ( -34.10, z-score =  -2.69, R)
>droYak2.chr3L 22513706 93 - 24197627
---CAUCUGCUGCUCCACCAGCUGAACUGACUGGUGGGGCACGCCA----------UCUCCCCACCGCUGUCGCUGGCAUUUU--UCCUCUUCCUUAGAUUGCCAGAG
---.....((((((((((((((......).))))))))))).))..----------.................((((((.(((--...........))).)))))).. ( -32.10, z-score =  -2.57, R)
>dp4.chrXR_group8 6234320 80 - 9212921
---CAGAUGCUGCUCCAGAAGAUGCUCCUCCUC-----------------------CUUCACUACCAAUGUUGCUGGCAUUUU--UCUUCUUUCUUAGAUUGCCAGCG
---..............((((..(......)..-----------------------))))............(((((((....--(((........))).))))))). ( -16.80, z-score =  -0.80, R)
>droPer1.super_45 369956 80 + 618639
---CAGAUGCUGCUCCAGAAGAUGCUCCUCCUC-----------------------CUUCACUACCAAUGUUGCUGGCAUUUU--UCUUCUUUCUUAGAUUGCCAGCG
---..............((((..(......)..-----------------------))))............(((((((....--(((........))).))))))). ( -16.80, z-score =  -0.80, R)
>droWil1.scaffold_180698 11355751 103 + 11422946
GUUCGUUCGUUCGUCCGUCGGUCGGACGGACGGUCUUCUAAAACGGGCA-----UGCUACACCACUACAGUCUUUGGCAUUUUUCUCUUCUUUCUUAGAUUGCUAGCG
(((((((((((((((((.....))))))))))).........)))))).-----..........(((((((((..((...............))..)))))).))).. ( -28.26, z-score =  -2.12, R)
>consensus
___CAUCUGCUGCUCCACCAGCUGAACCGACUGGUGGGGCACGCCA__________CCUCACCACCACUGUCGCUGGCAUUUU__UCCUCUUCCUUAGAUUGCCAGCG
.....((.(((........))).))................................................((((((.(((.............))).)))))).. ( -7.35 =  -6.69 +  -0.66)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:43:58 2011