Locus 7332

Sequence ID dm3.chr3L
Location 13,975,088 – 13,975,239
Length 151
Max. P 0.985802
window10093 window10094 window10095

overview

Window 3

Location 13,975,088 – 13,975,201
Length 113
Sequences 9
Columns 117
Reading direction reverse
Mean pairwise identity 73.29
Shannon entropy 0.53692
G+C content 0.64172
Mean single sequence MFE -44.87
Consensus MFE -24.21
Energy contribution -25.38
Covariance contribution 1.17
Combinations/Pair 1.37
Mean z-score -2.05
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.21
SVM RNA-class probability 0.985802
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13975088 113 - 24543557
-CGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGCUGCAU--CACCUGCAAAUU-GGCGCACUGCCCACGCCGGCGAGUGAAACGCCACGAUUUG
-((..((((.......))))((((....(((.((((....)))).)))(((((((..((((.--....))))..))-)))))........))))((((.......)))).))..... ( -46.90, z-score =  -1.93, R)
>anoGam1.chr2L 42778566 101 + 48795086
----------------CACGGCCGACCCGUUUGUCAAUCACUGCUACAGUUACGAUCUGCACGACAGCAUCGAGCUGGGCGCGUUGCCGACACCGGCGAGCGAGGUGGCUAACGUUG
----------------...((((.(((((((((((...........(((((.(((((((.....))).)))))))))(((.....)))......)))))))).)))))))....... ( -38.00, z-score =  -0.98, R)
>droGri2.scaffold_15110 6170630 86 + 24565398
----------------------------CAGUGGCACUGGCGGCGGUGGUGCCGAGAUGCAU--CAAUUGCAAAUU-GGCGCCCUGCCCACGCCGGCGAGUGAAACGCCCAGAUUUG
----------------------------..(.(((.((((((((((.((((((((..((((.--....))))..))-)))))))))))...)))))...(.....)))))....... ( -39.50, z-score =  -2.34, R)
>droVir3.scaffold_13049 2100772 86 + 25233164
----------------------------CAGCGGCACUGGCGGUGUCGGUGCCGAGCUGCAU--CAUUUGCAAAUU-GGCGCCCUGCCGACGCCGGCGAGUGAAACGCCAAGAUUUG
----------------------------..(((.((((.((((((((((((((((..((((.--....))))..))-))).....))))))))).)).))))...)))......... ( -42.30, z-score =  -3.03, R)
>droAna3.scaffold_13337 11327245 113 + 23293914
-CGAUGCUGACACCAUUGGCGGCGACUCCAGCGGCUGCUAUGCCACUGGCGCCGAGCUGCAG--CAUCUGCAAAUU-GGCGCACUGCCCACGCCGGCGAGUGAAACGCCCCGAUUUG
-.(((((((.((...((((((......((((.(((......))).))))))))))..)))))--))))..((((((-(((((((((((......))).))))...))))..)))))) ( -48.40, z-score =  -2.15, R)
>droEre2.scaffold_4784 13965022 113 - 25762168
-CGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGCUGCAU--CACCUGCAAAUU-GGCGCACUGCCCACGCCGGCGAGUGAAACGCCACGAUUUG
-((..((((.......))))((((....(((.((((....)))).)))(((((((..((((.--....))))..))-)))))........))))((((.......)))).))..... ( -46.90, z-score =  -1.93, R)
>droYak2.chr3L 14062234 114 - 24197627
ACGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGCUGCAU--CACCUGCAAAUU-GGCGCACUGCCCACGCCGGCGAGUGAAACGCCACGAUUUG
.((..((((.......))))((((....(((.((((....)))).)))(((((((..((((.--....))))..))-)))))........))))((((.......)))).))..... ( -47.40, z-score =  -2.04, R)
>droSec1.super_0 6121929 113 - 21120651
-CGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGUUGCAU--CACCUGCAAAUU-GGCGCACUGCCCACGCCGGCGAGUGAAACGCCACGAUUUG
-((..((((.......))))((((....(((.((((....)))).)))(((((((.(((((.--....))))).))-)))))........))))((((.......)))).))..... ( -47.50, z-score =  -2.10, R)
>droSim1.chr3L 13331456 113 - 22553184
-CGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGCUGCAU--CACCUGCAAAUU-GGCGCACUGCCCACGCCGGCGAGUGAAACGCCACGAUUUG
-((..((((.......))))((((....(((.((((....)))).)))(((((((..((((.--....))))..))-)))))........))))((((.......)))).))..... ( -46.90, z-score =  -1.93, R)
>consensus
_CGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGCUGCAU__CACCUGCAAAUU_GGCGCACUGCCCACGCCGGCGAGUGAAACGCCACGAUUUG
....................((((....(((.(((......))).)))(((((((..((((.......))))..)).)))))((((((......))).)))....))))........ (-24.21 = -25.38 +   1.17)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,975,128 – 13,975,239
Length 111
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 96.60
Shannon entropy 0.05721
G+C content 0.62142
Mean single sequence MFE -48.14
Consensus MFE -44.90
Energy contribution -44.90
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.84
SVM RNA-class probability 0.970607
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13975128 111 + 24543557
AAUUUGCAGGUGAUGCAGCUCGGCGCCAGUGGCGAAUCCGCCGCUGGAGUCGCCGCCAUUGGUGUCGGCAUCG---CCGUAACCACCAACCACACCGACAUGGCCAUAGCCGUA
.....(..((((........((((((((((((((....)))))))))...)))))...((((((.((((...)---)))....))))))...))))..)(((((....))))). ( -49.00, z-score =  -2.41, R)
>droEre2.scaffold_4784 13965062 108 + 25762168
AAUUUGCAGGUGAUGCAGCUCGGCGCCAGUGGCGAAUCCGCCGCUGGAGUCGCCGCCAUUGGUGUCGGCAUCG---CCGUAACCACCAACCACACCGACAUGGCCAUAGCC---
....((..((((........((((((((((((((....)))))))))...)))))...((((((.((((...)---)))....))))))...))))..)).(((....)))--- ( -46.40, z-score =  -2.19, R)
>droYak2.chr3L 14062274 111 + 24197627
AAUUUGCAGGUGAUGCAGCUCGGCGCCAGUGGCGAAUCCGCCGCUGGAGUCGCCGCCAUUGGUGUCGGCAUCGUAACCGUAACCACCAACCACACCGACAUGGCCGUAGCC---
....((((.....))))(((((((.(((((((((....))))))))).((((......((((((.(((........)))....))))))......))))...)))).))).--- ( -47.30, z-score =  -2.22, R)
>droSec1.super_0 6121969 111 + 21120651
AAUUUGCAGGUGAUGCAACUCGGCGCCAGUGGCGAAUCCGCCGCUGGAGUCGCCGCCAUUGGUGUCGGCAUCG---CCGUAACCACCAACCACACCGACAUGGCCAUAGCCGUA
.....(..((((........((((((((((((((....)))))))))...)))))...((((((.((((...)---)))....))))))...))))..)(((((....))))). ( -49.00, z-score =  -2.76, R)
>droSim1.chr3L 13331496 111 + 22553184
AAUUUGCAGGUGAUGCAGCUCGGCGCCAGUGGCGAAUCCGCCGCUGGAGUCGCCGCCAUUGGUGUCGGCAUCG---CCGUAACCACCAACCACACCGACAUGGCCAUAGCCGUA
.....(..((((........((((((((((((((....)))))))))...)))))...((((((.((((...)---)))....))))))...))))..)(((((....))))). ( -49.00, z-score =  -2.41, R)
>consensus
AAUUUGCAGGUGAUGCAGCUCGGCGCCAGUGGCGAAUCCGCCGCUGGAGUCGCCGCCAUUGGUGUCGGCAUCG___CCGUAACCACCAACCACACCGACAUGGCCAUAGCCGUA
....((..((((........((((((((((((((....)))))))))...)))))...((((((.(((........)))....))))))...))))..)).(((....)))... (-44.90 = -44.90 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,975,128 – 13,975,239
Length 111
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 96.60
Shannon entropy 0.05721
G+C content 0.62142
Mean single sequence MFE -52.08
Consensus MFE -49.16
Energy contribution -48.84
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -2.30
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.79
SVM RNA-class probability 0.968221
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13975128 111 - 24543557
UACGGCUAUGGCCAUGUCGGUGUGGUUGGUGGUUACGG---CGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGCUGCAUCACCUGCAAAUU
...((((.((((...((((.(((.(((((((....(((---(...)))).))))))).))).)))).((((.((((....)))).)))).))))))))(((.....)))..... ( -51.90, z-score =  -2.15, R)
>droEre2.scaffold_4784 13965062 108 - 25762168
---GGCUAUGGCCAUGUCGGUGUGGUUGGUGGUUACGG---CGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGCUGCAUCACCUGCAAAUU
---((((.((((...((((.(((.(((((((....(((---(...)))).))))))).))).)))).((((.((((....)))).)))).))))))))(((.....)))..... ( -51.60, z-score =  -2.22, R)
>droYak2.chr3L 14062274 111 - 24197627
---GGCUACGGCCAUGUCGGUGUGGUUGGUGGUUACGGUUACGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGCUGCAUCACCUGCAAAUU
---((((.((((...((((.(((.(((((((....((((......)))).))))))).))).)))).((((.((((....)))).)))).))))))))(((.....)))..... ( -53.90, z-score =  -2.92, R)
>droSec1.super_0 6121969 111 - 21120651
UACGGCUAUGGCCAUGUCGGUGUGGUUGGUGGUUACGG---CGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGUUGCAUCACCUGCAAAUU
..((((.........((((.(((.(((((((....(((---(...)))).))))))).))).)))).((((.((((....)))).)))).))))..(((((.....)))))... ( -51.10, z-score =  -2.08, R)
>droSim1.chr3L 13331496 111 - 22553184
UACGGCUAUGGCCAUGUCGGUGUGGUUGGUGGUUACGG---CGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGCUGCAUCACCUGCAAAUU
...((((.((((...((((.(((.(((((((....(((---(...)))).))))))).))).)))).((((.((((....)))).)))).))))))))(((.....)))..... ( -51.90, z-score =  -2.15, R)
>consensus
UACGGCUAUGGCCAUGUCGGUGUGGUUGGUGGUUACGG___CGAUGCCGACACCAAUGGCGGCGACUCCAGCGGCGGAUUCGCCACUGGCGCCGAGCUGCAUCACCUGCAAAUU
...((((.((((...((((.(((.(((((((....(((........))).))))))).))).)))).((((.((((....)))).)))).))))))))(((.....)))..... (-49.16 = -48.84 +  -0.32)

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 23:24:54 2011