Locus 2056

Sequence ID dm3.chr2L
Location 15,966,303 – 15,966,420
Length 117
Max. P 0.733703
window2827 window2828 window2829

overview

Window 7

Location 15,966,303 – 15,966,401
Length 98
Sequences 12
Columns 118
Reading direction reverse
Mean pairwise identity 72.93
Shannon entropy 0.56875
G+C content 0.47211
Mean single sequence MFE -28.21
Consensus MFE -14.15
Energy contribution -13.76
Covariance contribution -0.39
Combinations/Pair 1.23
Mean z-score -1.18
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.733703
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15966303 98 - 23011544
AAAUCGGAAGCC-GAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAA--CUCCAUUCCGAGAUCGGAAUAGCC-----------------
.....(((...(-....)((((.(((.......)))..........(((.((((....))))..)))..))))..--.)))((((((....))))))....----------------- ( -29.20, z-score =  -1.65, R)
>droSim1.chr2L 15679386 98 - 22036055
AAAUCGGAAGCC-GAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAA--CUCCAUUUCGAGAUCGGAAUAGCC-----------------
...((((...))-)).....((((((.......)))..........(((.((((....))))..)))...((((.--(((......))).))))....)))----------------- ( -26.90, z-score =  -0.95, R)
>droSec1.super_5 4699704 98 - 5866729
AAAUCGGAAGCC-GAAAGCGGGAGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAA--CUCCAUUUCGAGAUCGGAAUAGCC-----------------
.....((...((-((...((((.(((.......)))..........(((.((((....))))..)))..))))..--(((......))).)))).....))----------------- ( -27.10, z-score =  -1.45, R)
>droYak2.chr2L 2953763 97 + 22324452
AAAUCGGAAGCU-GAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGA-CCCGAA--CUCCAUUUCGAGAUCGGAAUAGCC-----------------
.....(((.((.-....))(((.(((.......)))..........(((.((((....))))..))).-)))...--.)))((((((....))))))....----------------- ( -25.90, z-score =  -0.92, R)
>droEre2.scaffold_4929 7663852 98 - 26641161
AAAUCGGAAGCC-GAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAA--CUCCAUUUCGAGAUCGGAAUAGCC-----------------
...((((...))-)).....((((((.......)))..........(((.((((....))))..)))...((((.--(((......))).))))....)))----------------- ( -26.90, z-score =  -0.95, R)
>droAna3.scaffold_12916 15772708 99 + 16180835
AGAUCGGAAGCCAAAAAACGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCUAAA--CUCCAUUUGGUGCUCAGGUUGGCC-----------------
.........(((((.....(((((((.......))).........((((.((((....))))((((((.......--.))))))))))))))...))))).----------------- ( -30.40, z-score =  -1.71, R)
>dp4.chr4_group4 4792767 106 - 6586962
AAAUCGGAAGCC-AAAAACGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCUGAG--CCCCAUAGAGAGUGGGUGCCAUCCGAGGGGCG---------
...(((((....-......(((.(((.......)))..........(((.((((....))))..))).)))((.(--((((((.....))))).)))))))))......--------- ( -33.10, z-score =  -0.80, R)
>droPer1.super_49 229528 106 + 569410
AAAUCGGAAGCC-AAAAACGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCUGAG--CCCCAUAGAGAGUGGGUGCCAUCCGAGGGGCG---------
...(((((....-......(((.(((.......)))..........(((.((((....))))..))).)))((.(--((((((.....))))).)))))))))......--------- ( -33.10, z-score =  -0.80, R)
>droWil1.scaffold_180772 2438658 93 + 8906247
UAAUAGGAAGCCAAAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCUGAA--ACUCCUGUGAAGGAAGCA-----------------------
..((((((.((......))(((.(((.......)))..........(((.((((....))))..))).)))....--..))))))..........----------------------- ( -23.70, z-score =  -0.96, R)
>droMoj3.scaffold_6500 9327960 113 - 32352404
AAAUAGGAAGUC--AAAACGAGCGCAUAAAAAUUGCAUUAAAAUUGCUUUGCGGAUAUCCGCAAUGGAGUCCAU---UUUCGGCUUCUUACAACGUUUGCCUUCAGUUCCAUUUGCCG
.....((((.(.--((..((((((..........(((.......))).((((((....)))))).((((((...---....))))))......))))))..)).).))))........ ( -26.40, z-score =  -1.00, R)
>droVir3.scaffold_12723 3801336 113 + 5802038
AAAUAGGAAGCC--AAAACGAGCGCAUAAAAAUUGCAUUAAAAUAGCCGUGCGGAUAUCCGCAAUGGACUCCAUU---UUCGAGGUUUGUUGGAUUUUUCCUCUUCUUUUUAUUUGUU
((((((((((..--..((((((((((.......)))..........((((((((....)))).)))).(((....---...))))))))))(((....)))....))))))))))... ( -29.50, z-score =  -1.96, R)
>droGri2.scaffold_15252 8132794 116 + 17193109
AAAUAGGAAGCC--AAAACGAGCGCAUAAAAAUUGCAUUAAAAAUGCUGUGCGGAUAUCCGCAAUGGACUCCAUUUCCUUCAGAGCCAAUUCAGAUUUUCAGUUUCAGUUUUUUGGUU
........((((--(((..(((((((.......)))(((.(((((.((((((((....))))).(((.(((...........))))))...)))))))).)))....))))))))))) ( -26.30, z-score =  -0.97, R)
>consensus
AAAUCGGAAGCC_GAAAACGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCCGAA__CUCCAUUUCGAGAUCGGAAUAGCC_________________
...................(((.(((.......)))..........(((.((((....))))..))).)))............................................... (-14.15 = -13.76 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,966,330 – 15,966,420
Length 90
Sequences 10
Columns 113
Reading direction forward
Mean pairwise identity 76.95
Shannon entropy 0.41882
G+C content 0.43245
Mean single sequence MFE -21.34
Consensus MFE -17.07
Energy contribution -16.32
Covariance contribution -0.75
Combinations/Pair 1.28
Mean z-score -0.68
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.543873
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15966330 90 + 23011544
--------GGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGCUUUC-GGCUUCCGAUUUUUU------AUUUAACCCCCCCGUU--------
--------(((((((((.((((....))))))))..........(((.......)))(((.......-)))............------.....)))))......-------- ( -23.10, z-score =  -0.14, R)
>droSim1.chr2L 15679413 89 + 22036055
--------GGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGCUUUC-GGCUUCCGAUUUUUU------AUUUAACCCCCC-GUU--------
--------(((((((((.((((....))))))))..........(((.......)))(((.......-)))............------.....)))))..-...-------- ( -23.10, z-score =  -0.19, R)
>droSec1.super_5 4699731 89 + 5866729
--------GGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCUCCCGCUUUC-GGCUUCCGAUUUUUU------AUUUAACCCCCC-GUU--------
--------(((((((((.((((....))))))))..........(((.......)))........((-((...))))......------.....)))))..-...-------- ( -22.10, z-score =  -0.42, R)
>droYak2.chr2L 2953790 88 - 22324452
---------GGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGCUUUC-AGCUUCCGAUUUUUU------AUUUAACCCCCC-GUU--------
---------((((((((.((((....))))))))..........(((.......)))))))((....-.))............------............-...-------- ( -19.20, z-score =  -0.18, R)
>droEre2.scaffold_4929 7663879 89 + 26641161
--------GGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGCUUUC-GGCUUCCGAUUUUUU------AUUUAACCCCCC-GUU--------
--------(((((((((.((((....))))))))..........(((.......)))(((.......-)))............------.....)))))..-...-------- ( -23.10, z-score =  -0.19, R)
>droAna3.scaffold_12916 15772735 99 - 16180835
--------AGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGUUUUUUGGCUUCCGAUCUUUU------AUUUCGUUCUCUCAUCCUCCCACC
--------.(((.((((.((((....))))))))..........(((.......)))(((........)))............------..................)))... ( -19.70, z-score =  -0.22, R)
>droWil1.scaffold_180772 2438679 90 - 8906247
--------AGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGCUUUUUGGCUUCCUAUUAUAU------AUUCGGUUUUCUUUU---------
--------.((((((((.((((....))))))))..........(((.......)))))))(((....)))............------...............--------- ( -20.60, z-score =  -0.43, R)
>droMoj3.scaffold_6500 9327997 100 + 32352404
--GAAAAUGGACUCCAUUGCGGAUAUCCGCAAAGCAAUUUUAAUGCAAUUUUUAUGCGCUCGUUUU--GACUUCCUAUUUGCCCUGGCUACAAUAUUUUUUAUU---------
--.((((((..(....((((((....)))))).(((.......)))...........)..))))))--............((....))................--------- ( -17.40, z-score =  -0.36, R)
>droVir3.scaffold_12723 3801373 90 - 5802038
--GAAAAUGGAGUCCAUUGCGGAUAUCCGCACGGCUAUUUUAAUGCAAUUUUUAUGCGCUCGUUUU--GGCUUCCUAUUUUCU----------UAUAUUUUAUU---------
--((((((((((.(((..((((....))))(((((.........(((.......))))).)))..)--)).)))).)))))).----------...........--------- ( -21.80, z-score =  -2.25, R)
>droGri2.scaffold_15252 8132832 97 - 17193109
AAGGAAAUGGAGUCCAUUGCGGAUAUCCGCACAGCAUUUUUAAUGCAAUUUUUAUGCGCUCGUUUU--GGCUUCCUAUUUUCG-----UAUUUUAUUUUUUAUU---------
..((((((((((.(((.(((((....)))))..((((.....))))...................)--)).)))).)))))).-----................--------- ( -23.30, z-score =  -2.38, R)
>consensus
________GGGGUCCAUUGCGGAUGUCCGCGUGGCAAUUUUAAUGCAAUUUUUAUGCGCCCGCUUUC_GGCUUCCGAUUUUUU______AUUUAACCCCCC_GUU________
.........((((.((((((((....)))))..(((.......))).......))).))))(((....))).......................................... (-17.07 = -16.32 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,966,330 – 15,966,420
Length 90
Sequences 10
Columns 113
Reading direction reverse
Mean pairwise identity 76.95
Shannon entropy 0.41882
G+C content 0.43245
Mean single sequence MFE -22.67
Consensus MFE -14.16
Energy contribution -13.64
Covariance contribution -0.52
Combinations/Pair 1.23
Mean z-score -1.24
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.07
SVM RNA-class probability 0.530811
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15966330 90 - 23011544
--------AACGGGGGGGUUAAAU------AAAAAAUCGGAAGCC-GAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCC--------
--------......((((((....------........((..(((-.......)))(((.......)))..........))..((((....))))....))))))-------- ( -26.00, z-score =  -0.89, R)
>droSim1.chr2L 15679413 89 - 22036055
--------AAC-GGGGGGUUAAAU------AAAAAAUCGGAAGCC-GAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCC--------
--------...-..((((((....------........((..(((-.......)))(((.......)))..........))..((((....))))....))))))-------- ( -26.00, z-score =  -1.12, R)
>droSec1.super_5 4699731 89 - 5866729
--------AAC-GGGGGGUUAAAU------AAAAAAUCGGAAGCC-GAAAGCGGGAGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCC--------
--------...-..((((((....------......((((...))-))..(((((.(((.......)))........((((....)).)))))))....))))))-------- ( -24.70, z-score =  -1.19, R)
>droYak2.chr2L 2953790 88 + 22324452
--------AAC-GGGGGGUUAAAU------AAAAAAUCGGAAGCU-GAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCC---------
--------...-...(((((....------........((..(((-.......)))(((.......)))..........))..((((....))))....)))))--------- ( -20.20, z-score =  -0.07, R)
>droEre2.scaffold_4929 7663879 89 - 26641161
--------AAC-GGGGGGUUAAAU------AAAAAAUCGGAAGCC-GAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCC--------
--------...-..((((((....------........((..(((-.......)))(((.......)))..........))..((((....))))....))))))-------- ( -26.00, z-score =  -1.12, R)
>droAna3.scaffold_12916 15772735 99 + 16180835
GGUGGGAGGAUGAGAGAACGAAAU------AAAAGAUCGGAAGCCAAAAAACGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCU--------
.((((.((..........(((...------......)))...(((........)))(((.......))).......)).))))((((....))))..........-------- ( -21.70, z-score =  -0.52, R)
>droWil1.scaffold_180772 2438679 90 + 8906247
---------AAAAGAAAACCGAAU------AUAUAAUAGGAAGCCAAAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCU--------
---------.........(((...------........((..(((........)))(((.......)))..........))..((((....))))..))).....-------- ( -18.90, z-score =  -1.05, R)
>droMoj3.scaffold_6500 9327997 100 - 32352404
---------AAUAAAAAAUAUUGUAGCCAGGGCAAAUAGGAAGUC--AAAACGAGCGCAUAAAAAUUGCAUUAAAAUUGCUUUGCGGAUAUCCGCAAUGGAGUCCAUUUUC--
---------................((....)).....(((..((--(........(((.......)))............((((((....)))))))))..)))......-- ( -21.10, z-score =  -1.05, R)
>droVir3.scaffold_12723 3801373 90 + 5802038
---------AAUAAAAUAUA----------AGAAAAUAGGAAGCC--AAAACGAGCGCAUAAAAAUUGCAUUAAAAUAGCCGUGCGGAUAUCCGCAAUGGACUCCAUUUUC--
---------...........----------.((((((.(((..((--(..(((.(((((.......)))((....)).)))))((((....))))..)))..)))))))))-- ( -22.80, z-score =  -3.47, R)
>droGri2.scaffold_15252 8132832 97 + 17193109
---------AAUAAAAAAUAAAAUA-----CGAAAAUAGGAAGCC--AAAACGAGCGCAUAAAAAUUGCAUUAAAAAUGCUGUGCGGAUAUCCGCAAUGGACUCCAUUUCCUU
---------................-----........(((..((--(........(((.......))).............(((((....))))).)))..)))........ ( -19.30, z-score =  -1.93, R)
>consensus
________AAC_AGAGGAUUAAAU______AAAAAAUCGGAAGCC_GAAAGCGGGCGCAUAAAAAUUGCAUUAAAAUUGCCACGCGGACAUCCGCAAUGGACCCC________
....................................................(((.(((.......)))..........(((.((((....))))..))).)))......... (-14.16 = -13.64 +  -0.52)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:43:55 2011