Locus 3764

Sequence ID dm3.chr2R
Location 7,684,810 – 7,684,968
Length 158
Max. P 0.923150
window5156 window5157 window5158

overview

Window 6

Location 7,684,810 – 7,684,900
Length 90
Sequences 7
Columns 97
Reading direction forward
Mean pairwise identity 74.35
Shannon entropy 0.49349
G+C content 0.45669
Mean single sequence MFE -17.55
Consensus MFE -6.19
Energy contribution -6.80
Covariance contribution 0.61
Combinations/Pair 1.12
Mean z-score -2.69
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.30
SVM RNA-class probability 0.923150
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7684810 90 + 21146708
AACCCACCACAUGCCCCA-UAGCUAUCCGAUUAUCUGUGAGAUAAUCGA---GUCCAGACCCAUCUCAGACUCAUAACUGUAGCACACUCCAUA---
..................-..(((((..(((((((.....)))))))((---(((.(((....)))..)))))......)))))..........--- ( -19.70, z-score =  -3.62, R)
>droAna3.scaffold_13266 6663845 97 - 19884421
AACCCACCAUGUGACCCACUCCCUGUCUGAUUAUCUGUGAGAUAAUCGAUAGGUAGAGACCCAACUCAGACUCAUAACUAUAGCACACUCCACAAAA
.........((((........((((((.(((((((.....)))))))))))))..(((......))).......................))))... ( -20.90, z-score =  -2.38, R)
>droEre2.scaffold_4845 4477440 77 - 22589142
------------AACCCG-CCAC-AUCCGAUUAUCUGUGAGAUAAUCGA---GUCCAGACCCAUCCCAGACUCAUAACUGUAGCACACUCCAUG---
------------.....(-(.((-(...(((((((.....)))))))((---(((..((....))...))))).....))).))..........--- ( -17.20, z-score =  -3.55, R)
>droYak2.chr2R 11870312 90 - 21139217
AACCCACCACAUGCCCCA-UAGCCAACCGAUUAUCUGUGAGAUAAUCGA---GUCCAGACCCAUCUCAGACUCAUAACUGUAGCACACUCCAUG---
...........(((..((-.........(((((((.....)))))))((---(((.(((....)))..))))).....))..))).........--- ( -17.90, z-score =  -3.19, R)
>droSec1.super_1 5236840 90 + 14215200
AACUCACCUCAUGCCCCA-UAGCUAUCCGAUUAUCUGUGAGAUAAUCGA---GUCCAGACCCAUCUCAGACUCAUAACUGUAGCACACUCCAUG---
.........((((.....-..(((((..(((((((.....)))))))((---(((.(((....)))..)))))......)))))......))))--- ( -19.92, z-score =  -2.97, R)
>droSim1.chr2R 6212568 90 + 19596830
AACCCACCACAUGCCCCA-UAGCUAUCCGAUUAUCUGUGAGAUAAUCGA---GUCCAGACCCAUCUCAGACUCAUAACUGUAGCACACUCCAUG---
.........((((.....-..(((((..(((((((.....)))))))((---(((.(((....)))..)))))......)))))......))))--- ( -20.32, z-score =  -3.71, R)
>droWil1.scaffold_181009 3303029 75 - 3585778
-----------AUCCCUUUUUGUCCUUGCAUCAUCGAUAA--UCAUCAA---GUUGGGCUUGAA---AUAUUCAUAACUAUAGCACACUUCAAG---
-----------..(((..((((.......(((...)))..--....)))---)..)))((((((---.....................))))))--- (  -6.92, z-score =   0.61, R)
>consensus
AACCCACCACAUGCCCCA_UAGCUAUCCGAUUAUCUGUGAGAUAAUCGA___GUCCAGACCCAUCUCAGACUCAUAACUGUAGCACACUCCAUG___
...........................((((((((.....))))))))................................................. ( -6.19 =  -6.80 +   0.61)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,684,810 – 7,684,900
Length 90
Sequences 7
Columns 97
Reading direction reverse
Mean pairwise identity 74.35
Shannon entropy 0.49349
G+C content 0.45669
Mean single sequence MFE -26.83
Consensus MFE -10.10
Energy contribution -12.31
Covariance contribution 2.21
Combinations/Pair 1.32
Mean z-score -1.88
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.01
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr2R 7684810 90 - 21146708
---UAUGGAGUGUGCUACAGUUAUGAGUCUGAGAUGGGUCUGGAC---UCGAUUAUCUCACAGAUAAUCGGAUAGCUA-UGGGGCAUGUGGUGGGUU
---(((.(.((((.(((.((((((((((((.(((....)))))))---))(((((((.....)))))))..)))))).-))).)))).).))).... ( -30.30, z-score =  -2.54, R)
>droAna3.scaffold_13266 6663845 97 + 19884421
UUUUGUGGAGUGUGCUAUAGUUAUGAGUCUGAGUUGGGUCUCUACCUAUCGAUUAUCUCACAGAUAAUCAGACAGGGAGUGGGUCACAUGGUGGGUU
..((((((......))))))....(((.((......)).))).((((((((((((((.....))))))).(((.........)))....))))))). ( -22.90, z-score =   0.81, R)
>droEre2.scaffold_4845 4477440 77 + 22589142
---CAUGGAGUGUGCUACAGUUAUGAGUCUGGGAUGGGUCUGGAC---UCGAUUAUCUCACAGAUAAUCGGAU-GUGG-CGGGUU------------
---.......(.(((((((.....(((((..((.....))..)))---))(((((((.....)))))))...)-))))-)).)..------------ ( -27.40, z-score =  -2.84, R)
>droYak2.chr2R 11870312 90 + 21139217
---CAUGGAGUGUGCUACAGUUAUGAGUCUGAGAUGGGUCUGGAC---UCGAUUAUCUCACAGAUAAUCGGUUGGCUA-UGGGGCAUGUGGUGGGUU
---(((.(.((((.(((.(((((.((((((.(((....)))))))---))(((((((.....)))))))...))))).-))).)))).).))).... ( -30.60, z-score =  -2.44, R)
>droSec1.super_1 5236840 90 - 14215200
---CAUGGAGUGUGCUACAGUUAUGAGUCUGAGAUGGGUCUGGAC---UCGAUUAUCUCACAGAUAAUCGGAUAGCUA-UGGGGCAUGAGGUGAGUU
---(((...((((.(((.((((((((((((.(((....)))))))---))(((((((.....)))))))..)))))).-))).))))...))).... ( -31.20, z-score =  -2.71, R)
>droSim1.chr2R 6212568 90 - 19596830
---CAUGGAGUGUGCUACAGUUAUGAGUCUGAGAUGGGUCUGGAC---UCGAUUAUCUCACAGAUAAUCGGAUAGCUA-UGGGGCAUGUGGUGGGUU
---(((.(.((((.(((.((((((((((((.(((....)))))))---))(((((((.....)))))))..)))))).-))).)))).).))).... ( -32.40, z-score =  -3.08, R)
>droWil1.scaffold_181009 3303029 75 + 3585778
---CUUGAAGUGUGCUAUAGUUAUGAAUAU---UUCAAGCCCAAC---UUGAUGA--UUAUCGAUGAUGCAAGGACAAAAAGGGAU-----------
---((((((((((..(((....))).))))---))))))(((..(---(((((.(--((...))).)).))))........)))..----------- ( -13.00, z-score =  -0.38, R)
>consensus
___CAUGGAGUGUGCUACAGUUAUGAGUCUGAGAUGGGUCUGGAC___UCGAUUAUCUCACAGAUAAUCGGAUAGCUA_UGGGGCAUGUGGUGGGUU
.........((((.(((..(((((((.((......)).))........(((((((((.....))))))))))))))...))).)))).......... (-10.10 = -12.31 +   2.21)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,684,865 – 7,684,968
Length 103
Sequences 7
Columns 117
Reading direction reverse
Mean pairwise identity 69.93
Shannon entropy 0.55780
G+C content 0.44147
Mean single sequence MFE -26.09
Consensus MFE -16.53
Energy contribution -18.71
Covariance contribution 2.19
Combinations/Pair 1.28
Mean z-score -1.12
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.27
SVM RNA-class probability 0.919724
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7684865 103 - 21146708
------------UCUGGCUUUGG--AUUUGGUUUUUUCGAUUGGUUUCGGGCUCGUAAAAUGCACAGUUUAACGGUGUGCGGUAUGGAGUGUGCUACAGUUAUGAGUCUGAGAUGGG
------------.......((((--(.........))))).(.(((((((((((((((...(((((.((((((.(....).)).)))).))))).....))))))))))))))).). ( -32.20, z-score =  -2.88, R)
>droEre2.scaffold_4845 4477482 101 + 22589142
------------UCUGGCUUUGG--AUUUGG--UUUUGGAUUGCUUUUGGGCUCGUAAAAUGCUCAGUUUAACGGUGUGCGGCAUGGAGUGUGCUACAGUUAUGAGUCUGGGAUGGG
------------....((((..(--(.....--.))..))..))(((..(((((((((...((.((.(.....).)).))(((((.....)))))....)))))))))..))).... ( -24.40, z-score =   0.08, R)
>droYak2.chr2R 11870367 114 + 21139217
UCUGUCUUUGGAUUUGGUUUUGA--UUUUGG-UUUUAGGAUUGCUUUUGGGCUCGUAAAAUGCACAGUUUAACGGUGUGCGGCAUGGAGUGUGCUACAGUUAUGAGUCUGAGAUGGG
.(((((((.(((..(((((((((--......-..)))))))))..)))((((((((((...(((((.(.....).)))))(((((.....)))))....))))))))))))))))). ( -31.10, z-score =  -1.64, R)
>droSec1.super_1 5236895 102 - 14215200
------------UCUGGCUUUGG--AUUUGG-UUUUUCGAUUGGUUUCGGGCUCGUAAAAUGCACAGUUUAACGGUGUGCGGCAUGGAGUGUGCUACAGUUAUGAGUCUGAGAUGGG
------------.......((((--(.....-...))))).(.(((((((((((((((...(((((.(.....).)))))(((((.....)))))....))))))))))))))).). ( -31.80, z-score =  -2.29, R)
>droSim1.chr2R 6212623 103 - 19596830
------------UCUGGCUUUGG--AUUUGGUUUUUUCGAUUGCUUUCGGGCUCGUAAAAUGCACAGUUUAACGGUGUGCGGCAUGGAGUGUGCUACAGUUAUGAGUCUGAGAUGGG
------------....((.((((--(.........)))))..))((((((((((((((...(((((.(.....).)))))(((((.....)))))....)))))))))))))).... ( -31.20, z-score =  -1.76, R)
>droWil1.scaffold_181009 3303072 101 + 3585778
------UUUUCCACUGUUGUCGGCUCUUUUGUAGUCUCAUUUCUGUUGGUGAACAUAAAAUGCACAAUUUAAUGG-------CUUGAAGUGUGCUAUAGUUAUGAAUAUUUCAA---
------..........(..(((((.....((......)).....)))))..).(((((...(((((.(((((...-------.))))).))))).....)))))..........--- ( -17.00, z-score =   0.30, R)
>droVir3.scaffold_12875 15418151 79 + 20611582
-------------UUAUCUUUCU-GGUCUGG--UUCUGGUCUGGUCUGCGACUCGUAAAAUGCGCUAUUUAAUGG-------CUUGGAGUGUG--GCUAGUAUG-------------
-------------........(.-.(.....--..)..).((((((.((.((((((.....))(((((...))))-------)...)))))))--)))))....------------- ( -14.90, z-score =   0.36, R)
>consensus
____________UCUGGCUUUGG__AUUUGG_UUUUUCGAUUGCUUUCGGGCUCGUAAAAUGCACAGUUUAACGGUGUGCGGCAUGGAGUGUGCUACAGUUAUGAGUCUGAGAUGGG
............................................((((((((((((((...(((((.((((.((.....))...)))).))))).....)))))))))))))).... (-16.53 = -18.71 +   2.19)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:16:16 2011