Locus 11525

Sequence ID dm3.chr3R
Location 21,846,393 – 21,846,541
Length 148
Max. P 0.975039
window15833 window15834 window15835 window15836

overview

Window 3

Location 21,846,393 – 21,846,503
Length 110
Sequences 9
Columns 120
Reading direction forward
Mean pairwise identity 94.81
Shannon entropy 0.10698
G+C content 0.47256
Mean single sequence MFE -22.35
Consensus MFE -19.41
Energy contribution -19.41
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.86
SVM RNA-class probability 0.838646
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21846393 110 + 27905053
-UUGAAAUCAACCAGCAGCA---------ACAGCAACAACAUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCA
-.((((((......((....---------...))......))))))(((......(((((.((...........)).))))).......)))((((((((...........)))))))). ( -23.22, z-score =  -2.19, R)
>droAna3.scaffold_13340 12399604 110 - 23697760
-UUGAAAUCAACCAGCAGCA---------ACAGCAACAACAUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCA
-.((((((......((....---------...))......))))))(((......(((((.((...........)).))))).......)))((((((((...........)))))))). ( -23.22, z-score =  -2.19, R)
>droEre2.scaffold_4820 4269968 110 - 10470090
-UUGAAAUCAACCAGCAGCA---------ACAGCAACAACAUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCA
-.((((((......((....---------...))......))))))(((......(((((.((...........)).))))).......)))((((((((...........)))))))). ( -23.22, z-score =  -2.19, R)
>droYak2.chr3R 4202553 110 - 28832112
-UUGAAAUCAACCAGCAGCA---------ACAGCAACAACAUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCA
-.((((((......((....---------...))......))))))(((......(((((.((...........)).))))).......)))((((((((...........)))))))). ( -23.22, z-score =  -2.19, R)
>droSec1.super_13 640913 110 + 2104621
-UUGAAAUCAACCAGCAGCA---------ACAGCAACAACAUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCA
-.((((((......((....---------...))......))))))(((......(((((.((...........)).))))).......)))((((((((...........)))))))). ( -23.22, z-score =  -2.19, R)
>droSim1.chr3R 21697528 110 + 27517382
-UUGAAAUCAACCAGCAGCA---------ACAGCAACAACAUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCA
-.((((((......((....---------...))......))))))(((......(((((.((...........)).))))).......)))((((((((...........)))))))). ( -23.22, z-score =  -2.19, R)
>droWil1.scaffold_181130 15470883 116 + 16660200
----CAACCAACCAGCAGCAACACCAACAACAUCAACAACAUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCA
----..........................................(((......(((((.((...........)).))))).......)))((((((((...........)))))))). ( -19.72, z-score =  -2.05, R)
>droPer1.super_3 5428367 113 - 7375914
UUGAAAAACAACCAGCAGCAGUA------ACAGCAACAACAUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAA-CACACGACAAAUCUGUUUCCCA
................(((((..------..........................(((((.((...........)).))))).....((((((....-))))))......)))))..... ( -21.30, z-score =  -1.22, R)
>dp4.chr2 11592498 114 - 30794189
UUGAAAAACAACCAGCAGCAGUA------ACAGCAACAACAUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCA
.(((((........((.......------...)).......)))))(((......(((((.((...........)).))))).......)))((((((((...........)))))))). ( -20.78, z-score =  -1.12, R)
>consensus
_UUGAAAUCAACCAGCAGCA_________ACAGCAACAACAUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCA
.............(((((.....................................(((((.((...........)).))))).....((((((.....))))))......)))))..... (-19.41 = -19.41 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,846,393 – 21,846,503
Length 110
Sequences 9
Columns 120
Reading direction reverse
Mean pairwise identity 94.81
Shannon entropy 0.10698
G+C content 0.47256
Mean single sequence MFE -33.76
Consensus MFE -29.51
Energy contribution -29.96
Covariance contribution 0.45
Combinations/Pair 1.06
Mean z-score -1.53
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.560721
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21846393 110 - 27905053
UGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAUGUUGUUGCUGU---------UGCUGCUGGUUGAUUUCAA-
(((((((((.((.....)).)))))))))..(((((((((.((.((......)).)).)).)))))))......((((((...((.((...---------.)).))......)))))).- ( -34.00, z-score =  -1.67, R)
>droAna3.scaffold_13340 12399604 110 + 23697760
UGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAUGUUGUUGCUGU---------UGCUGCUGGUUGAUUUCAA-
(((((((((.((.....)).)))))))))..(((((((((.((.((......)).)).)).)))))))......((((((...((.((...---------.)).))......)))))).- ( -34.00, z-score =  -1.67, R)
>droEre2.scaffold_4820 4269968 110 + 10470090
UGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAUGUUGUUGCUGU---------UGCUGCUGGUUGAUUUCAA-
(((((((((.((.....)).)))))))))..(((((((((.((.((......)).)).)).)))))))......((((((...((.((...---------.)).))......)))))).- ( -34.00, z-score =  -1.67, R)
>droYak2.chr3R 4202553 110 + 28832112
UGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAUGUUGUUGCUGU---------UGCUGCUGGUUGAUUUCAA-
(((((((((.((.....)).)))))))))..(((((((((.((.((......)).)).)).)))))))......((((((...((.((...---------.)).))......)))))).- ( -34.00, z-score =  -1.67, R)
>droSec1.super_13 640913 110 - 2104621
UGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAUGUUGUUGCUGU---------UGCUGCUGGUUGAUUUCAA-
(((((((((.((.....)).)))))))))..(((((((((.((.((......)).)).)).)))))))......((((((...((.((...---------.)).))......)))))).- ( -34.00, z-score =  -1.67, R)
>droSim1.chr3R 21697528 110 - 27517382
UGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAUGUUGUUGCUGU---------UGCUGCUGGUUGAUUUCAA-
(((((((((.((.....)).)))))))))..(((((((((.((.((......)).)).)).)))))))......((((((...((.((...---------.)).))......)))))).- ( -34.00, z-score =  -1.67, R)
>droWil1.scaffold_181130 15470883 116 - 16660200
UGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAUGUUGUUGAUGUUGUUGGUGUUGCUGCUGGUUGGUUG----
(((((((((.((.....)).)))))))))...((.(.((.((..(((((((((.....)))))))((.(((.((......)).))).))))..)).)).).)).............---- ( -32.40, z-score =  -1.00, R)
>droPer1.super_3 5428367 113 + 7375914
UGGGAAACAGAUUUGUCGUGUG-UUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAUGUUGUUGCUGU------UACUGCUGCUGGUUGUUUUUCAA
((..((((((.(..(.((((((-....)))))).)..)(((.((((..(((.(..(((((((((...))))))).........))..).))------)...))))))).))))))..)). ( -32.50, z-score =  -0.98, R)
>dp4.chr2 11592498 114 + 30794189
UGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAUGUUGUUGCUGU------UACUGCUGCUGGUUGUUUUUCAA
(((((((((.((.....)).))))))))).......((..((..((..(...((((((((((((...)))))))......((....)).))------))).....)..))..))..)).. ( -34.90, z-score =  -1.78, R)
>consensus
UGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAUGUUGUUGCUGU_________UGCUGCUGGUUGAUUUCAA_
(((((((((.((.....)).)))))))))..(((((((((.((.((......)).)).)).))))))).......(((((......((.((..........)).))......)))))... (-29.51 = -29.96 +   0.45)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,846,423 – 21,846,541
Length 118
Sequences 8
Columns 119
Reading direction forward
Mean pairwise identity 93.12
Shannon entropy 0.13468
G+C content 0.49607
Mean single sequence MFE -26.56
Consensus MFE -25.19
Energy contribution -25.31
Covariance contribution 0.12
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.92
SVM RNA-class probability 0.975039
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21846423 118 + 27905053
AUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCACGGUCUCGUAAAGUAGGCACACCGCA-CACACACACAAA
......((.......(((((.((...........)).)))))......((((((((((((...........)))))))))).(((((.....).))))))...)).-............ ( -27.60, z-score =  -2.17, R)
>droAna3.scaffold_13340 12399634 119 - 23697760
AUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCACGGUCUCGUAAAGUAGGCACAACACAGCGCAACUAUACA
...........((..(((((.((...........)).)))))........((((((((((...........))))))))))))....(((.(((.(((........)).).))).))). ( -29.00, z-score =  -2.64, R)
>droEre2.scaffold_4820 4269998 118 - 10470090
AUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCACGGUCUCGUAAAGUAGGCACACCGCA-CACACACACACA
......((.......(((((.((...........)).)))))......((((((((((((...........)))))))))).(((((.....).))))))...)).-............ ( -27.60, z-score =  -2.10, R)
>droSec1.super_13 640943 118 + 2104621
AUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCACGGUCUCGUAAAGUAGGCACACCGCA-CACACACACACA
......((.......(((((.((...........)).)))))......((((((((((((...........)))))))))).(((((.....).))))))...)).-............ ( -27.60, z-score =  -2.10, R)
>droVir3.scaffold_13047 5427362 111 + 19223366
AUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCACGGUCUCGUAAAGUAGGCACAACACA--ACACA------
......((.((((...)))).))...........(((...((.....))(((((((((((...........))))))))))).............)))........--.....------ ( -25.70, z-score =  -2.17, R)
>droMoj3.scaffold_6540 15798646 111 + 34148556
AUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCACGGUCUCGUAAAGUAGGCACAACACA--ACACA------
......((.((((...)))).))...........(((...((.....))(((((((((((...........))))))))))).............)))........--.....------ ( -25.70, z-score =  -2.17, R)
>droGri2.scaffold_14906 10803545 111 + 14172833
AUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCACGGUCUCGUAAAGUAGGCACAACACA--ACACA------
......((.((((...)))).))...........(((...((.....))(((((((((((...........))))))))))).............)))........--.....------ ( -25.70, z-score =  -2.17, R)
>droPer1.super_3 5428401 105 - 7375914
AUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAA-CACACGACAAAUCUGUUUCCCACGGUCUCGUAAAGUAGGCACCACACA-------------
...............(((((.((...........)).)))))......(((((((((-.(((.((....))))))))))))(((.((........)).)))))...------------- ( -23.60, z-score =  -1.29, R)
>consensus
AUUUCAGCAAUCCAUCGGAUCGCAUCACAAUCCAGCCAUCCGUCCAACGUGUGGGAAACACACGACAAAUCUGUUUCCCACGGUCUCGUAAAGUAGGCACAACACA__ACACA______
......((.((((...)))).))...........(((...((.....))(((((((((((...........))))))))))).............)))..................... (-25.19 = -25.31 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,846,423 – 21,846,541
Length 118
Sequences 8
Columns 119
Reading direction reverse
Mean pairwise identity 93.12
Shannon entropy 0.13468
G+C content 0.49607
Mean single sequence MFE -38.39
Consensus MFE -33.39
Energy contribution -33.51
Covariance contribution 0.12
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.939042
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21846423 118 - 27905053
UUUGUGUGUGUG-UGCGGUGUGCCUACUUUACGAGACCGUGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAU
((((((...(((-.((.....)).)))..))))))...((((((((((.((.....)).)))))))))).(((((((((.((.((......)).)).)).)))))))............ ( -39.30, z-score =  -1.87, R)
>droAna3.scaffold_13340 12399634 119 + 23697760
UGUAUAGUUGCGCUGUGUUGUGCCUACUUUACGAGACCGUGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAU
.(((.(((.((((......))))..))).)))......((((((((((.((.....)).)))))))))).(((((((((.((.((......)).)).)).)))))))............ ( -42.90, z-score =  -3.30, R)
>droEre2.scaffold_4820 4269998 118 + 10470090
UGUGUGUGUGUG-UGCGGUGUGCCUACUUUACGAGACCGUGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAU
.((.((((...(-((.((....)))))..))))..)).((((((((((.((.....)).)))))))))).(((((((((.((.((......)).)).)).)))))))............ ( -38.20, z-score =  -1.39, R)
>droSec1.super_13 640943 118 - 2104621
UGUGUGUGUGUG-UGCGGUGUGCCUACUUUACGAGACCGUGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAU
.((.((((...(-((.((....)))))..))))..)).((((((((((.((.....)).)))))))))).(((((((((.((.((......)).)).)).)))))))............ ( -38.20, z-score =  -1.39, R)
>droVir3.scaffold_13047 5427362 111 - 19223366
------UGUGU--UGUGUUGUGCCUACUUUACGAGACCGUGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAU
------.((.(--((((..((....))..))))).)).((((((((((.((.....)).)))))))))).(((((((((.((.((......)).)).)).)))))))............ ( -39.10, z-score =  -3.01, R)
>droMoj3.scaffold_6540 15798646 111 - 34148556
------UGUGU--UGUGUUGUGCCUACUUUACGAGACCGUGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAU
------.((.(--((((..((....))..))))).)).((((((((((.((.....)).)))))))))).(((((((((.((.((......)).)).)).)))))))............ ( -39.10, z-score =  -3.01, R)
>droGri2.scaffold_14906 10803545 111 - 14172833
------UGUGU--UGUGUUGUGCCUACUUUACGAGACCGUGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAU
------.((.(--((((..((....))..))))).)).((((((((((.((.....)).)))))))))).(((((((((.((.((......)).)).)).)))))))............ ( -39.10, z-score =  -3.01, R)
>droPer1.super_3 5428401 105 + 7375914
-------------UGUGUGGUGCCUACUUUACGAGACCGUGGGAAACAGAUUUGUCGUGUG-UUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAU
-------------...(..((.................((((((((((((....)).))).-))))))).(((((((((.((.((......)).)).)).))))))).))..)...... ( -31.20, z-score =  -0.74, R)
>consensus
______UGUGU__UGUGUUGUGCCUACUUUACGAGACCGUGGGAAACAGAUUUGUCGUGUGUUUCCCACACGUUGGACGGAUGGCUGGAUUGUGAUGCGAUCCGAUGGAUUGCUGAAAU
.....................((...............((((((((((.((.....)).)))))))))).(((((((((.((.((......)).)).)).)))))))....))...... (-33.39 = -33.51 +   0.12)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:44:34 2011