Locus 3817

Sequence ID dm3.chr2R
Location 8,130,371 – 8,130,506
Length 135
Max. P 0.934678
window5228 window5229 window5230 window5231

overview

Window 8

Location 8,130,371 – 8,130,487
Length 116
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 74.55
Shannon entropy 0.46383
G+C content 0.45059
Mean single sequence MFE -30.33
Consensus MFE -15.98
Energy contribution -15.68
Covariance contribution -0.30
Combinations/Pair 1.40
Mean z-score -1.81
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.870605
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8130371 116 + 21146708
CGUCGGUUCAGGAACAGAUGCCUCAUGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUUAGCUGAAUGCAAAAAGAUACAAAAGUAUCUUAGAAAUACAAGACCAUUU---
.(((.((((((...(.(((((.(((((((((((.((.......))....))))))))..)))))))).))))))).....(((((((....)))))))..........))).....--- ( -31.00, z-score =  -2.05, R)
>droAna3.scaffold_13266 5426306 100 + 19884421
CAUCGAUUCAGGAACAAUUGUCAGUUGGAACGAACCAAUUGCAAUGCAAGUGGAUCAAGUGAGUCUCAAA-------AAUAGUCUAUAAGGGU-UAUGAGA----CCAAGUU-------
....((((((......((((.(((((((......))))))))))).....))))))...((.((((((..-------..((..((....))..-)))))))----)))....------- ( -25.90, z-score =  -2.41, R)
>droEre2.scaffold_4845 4925493 110 - 22589142
CAACGGUUCAAGAACAGGUGCCUCAUGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUAGGCUGAAUCCAAUGAGAUACAAAAGUAUCUCAGAUAUGCCAGA---------
.....(((....)))..((((.(((((((((((.((.......))....))))))))..))))))).(((...(((...((((((((....)))))))))))..)))...--------- ( -32.00, z-score =  -1.61, R)
>droYak2.chr2R 12319763 119 - 21139217
CAUCGGUUCAAGAACAGGUGCCUCAUGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUUGGCUGAAUCCCAUUAGAUACAAAAGUAUCUUAGAAAUGCCAGAAUACUUGUC
.............(((((((.((((((((((((.((.......))....))))))))..))))..(((((....((.....((((((....))))))..))...)))))..))))))). ( -32.00, z-score =  -1.13, R)
>droSec1.super_1 5679155 104 + 14215200
CGUCGGUUUAGGAACAGGUGCCUCUUGGAGCGGGCCAACUGCCGGACGACCGUUUCAAGUGAGUGUUAGC-------AAUAAGAUACAAAAGUAUCUUAGAAAUACAAGAC--------
.((((((............))).((((((((((.((.......))....))))))))))...(((((...-------..((((((((....))))))))..)))))..)))-------- ( -29.00, z-score =  -1.53, R)
>droSim1.chr2R 6596494 109 + 19596830
CGUCGGUUUAGGAACAGGUGCCUCUUGGAGCGGGCCAACUGCCGGACGACCGUUUCAAGUGAGUGUUAGC-------AAUAAGAUACAAAAGUAUCUUAGAAAUACAAGACCAUUU---
....(((((.(.....((..((.((((((((((.((.......))....)))))))))).).)..))...-------..((((((((....))))))))......).)))))....--- ( -32.10, z-score =  -2.11, R)
>consensus
CAUCGGUUCAGGAACAGGUGCCUCAUGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUUAGC_______AAUAAGAUACAAAAGUAUCUUAGAAAUACAAGAC________
...(((((......(((..((((........))))...)))......)))))...........................((((((((....)))))))).................... (-15.98 = -15.68 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,130,371 – 8,130,487
Length 116
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 74.55
Shannon entropy 0.46383
G+C content 0.45059
Mean single sequence MFE -26.46
Consensus MFE -15.95
Energy contribution -16.82
Covariance contribution 0.86
Combinations/Pair 1.24
Mean z-score -1.19
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.632320
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8130371 116 - 21146708
---AAAUGGUCUUGUAUUUCUAAGAUACUUUUGUAUCUUUUUGCAUUCAGCUAAUACUCACUUGAAACGGUUGUCCGGCAGUUGGCCCGCUCCAUGAGGCAUCUGUUCCUGAACCGACG
---.....(((.((((.....(((((((....)))))))..))))(((((.................(((....)))((((...(((((.....)).)))..))))..)))))..))). ( -27.40, z-score =  -1.02, R)
>droAna3.scaffold_13266 5426306 100 - 19884421
-------AACUUGG----UCUCAUA-ACCCUUAUAGACUAUU-------UUUGAGACUCACUUGAUCCACUUGCAUUGCAAUUGGUUCGUUCCAACUGACAAUUGUUCCUGAAUCGAUG
-------.....((----(((((..-................-------..)))))))...(((((.((...((((((((.((((......)))).)).))).)))...)).))))).. ( -18.95, z-score =  -1.43, R)
>droEre2.scaffold_4845 4925493 110 + 22589142
---------UCUGGCAUAUCUGAGAUACUUUUGUAUCUCAUUGGAUUCAGCCUAUACUCACUUGAAACGGUUGUCCGGCAGUUGGCCCGCUCCAUGAGGCACCUGUUCUUGAACCGUUG
---------...(((..(((((((((((....)))))))...))))...))).............(((((((....(((((...(((((.....)).)))..)))))....))))))). ( -32.20, z-score =  -1.78, R)
>droYak2.chr2R 12319763 119 + 21139217
GACAAGUAUUCUGGCAUUUCUAAGAUACUUUUGUAUCUAAUGGGAUUCAGCCAAUACUCACUUGAAACGGUUGUCCGGCAGUUGGCCCGCUCCAUGAGGCACCUGUUCUUGAACCGAUG
..(((((....((((..(((((((((((....))))))..)))))....))))......)))))...(((((....(((((...(((((.....)).)))..)))))....)))))... ( -32.20, z-score =  -1.18, R)
>droSec1.super_1 5679155 104 - 14215200
--------GUCUUGUAUUUCUAAGAUACUUUUGUAUCUUAUU-------GCUAACACUCACUUGAAACGGUCGUCCGGCAGUUGGCCCGCUCCAAGAGGCACCUGUUCCUAAACCGACG
--------(((..(((....((((((((....)))))))).)-------)).................(((.....(((((...((((.......).)))..))))).....)))))). ( -23.70, z-score =  -1.09, R)
>droSim1.chr2R 6596494 109 - 19596830
---AAAUGGUCUUGUAUUUCUAAGAUACUUUUGUAUCUUAUU-------GCUAACACUCACUUGAAACGGUCGUCCGGCAGUUGGCCCGCUCCAAGAGGCACCUGUUCCUAAACCGACG
---...((((((((......((((((((....))))))))..-------((((((..((....))..(((....)))...))))))......))))(((........)))..))))... ( -24.30, z-score =  -0.63, R)
>consensus
________GUCUGGUAUUUCUAAGAUACUUUUGUAUCUUAUU_______GCUAAUACUCACUUGAAACGGUUGUCCGGCAGUUGGCCCGCUCCAAGAGGCACCUGUUCCUGAACCGACG
....................((((((((....))))))))...........................(((((....(((((...(((..........)))..)))))....)))))... (-15.95 = -16.82 +   0.86)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,130,411 – 8,130,506
Length 95
Sequences 5
Columns 125
Reading direction forward
Mean pairwise identity 68.33
Shannon entropy 0.50223
G+C content 0.36831
Mean single sequence MFE -22.98
Consensus MFE -11.06
Energy contribution -10.42
Covariance contribution -0.64
Combinations/Pair 1.25
Mean z-score -2.03
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.39
SVM RNA-class probability 0.934678
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8130411 95 + 21146708
GCCGGACAACCGUUUCAAGUGAGUAUUAGCUGAAUGCAAAAAGAUACAAAAGUAUCUUAGAAAUACAAGA------CCAUU-UAUAUGAUU--------UCUGUGAAAAU---------------
..(((....)))(((((...(((((((.((.....))...(((((((....)))))))...)))))....------.(((.-...)))...--------))..)))))..--------------- ( -17.20, z-score =  -1.72, R)
>droEre2.scaffold_4845 4925533 99 - 22589142
GCCGGACAACCGUUUCAAGUGAGUAUAGGCUGAAUCCAAUGAGAUACAAAAGUAUCUCAGAUAUGCCAGA------ACGUA-UCUCAGACUAGC----ACUUGUGGAAAC---------------
.((((....))....((((((....(((.((((......((((((((....))))))))((((((.....------.))))-)))))).))).)----))))).))....--------------- ( -31.00, z-score =  -3.76, R)
>droYak2.chr2R 12319803 114 - 21139217
GCCGGACAACCGUUUCAAGUGAGUAUUGGCUGAAUCCCAUUAGAUACAAAAGUAUCUUAGAAAUGCCAGA------AUACU-UGUCUGAAUUAC----AUAUCUGAGACUAGCAUAUGCAAAAGU
..(((....))).((((.(..(((((((((....((.....((((((....))))))..))...))))..------)))))-..).))))...(----(((((((....))).)))))....... ( -24.40, z-score =  -1.38, R)
>droSec1.super_1 5679195 98 + 14215200
GCCGGACGACCGUUUCAAGUGAGUGUUAGC-------AAUAAGAUACAAAAGUAUCUUAGAAAUACAAGAC-----AUAUGCUGUUUGACUUUUUUACACUUGUGAAUGU---------------
..........(((((((((((.(((((...-------..((((((((....))))))))..))))).((((-----(.....)))))..........)))))).))))).--------------- ( -22.00, z-score =  -1.56, R)
>droSim1.chr2R 6596534 101 + 19596830
GCCGGACGACCGUUUCAAGUGAGUGUUAGC-------AAUAAGAUACAAAAGUAUCUUAGAAAUACAAGACCAUUUAUAUGAUUUUUGAGACUU--ACACAUGUGAAUGU---------------
..(((....)))......((((((.((((.-------..((((((((....))))))))............(((....)))....)))).))))--))((((....))))--------------- ( -20.30, z-score =  -1.71, R)
>consensus
GCCGGACAACCGUUUCAAGUGAGUAUUAGCUGAAU_CAAUAAGAUACAAAAGUAUCUUAGAAAUACAAGA______AUAUG_UGUCUGACUUUC____ACAUGUGAAAAU_______________
..(((....)))..........(((((............((((((((....))))))))..)))))........................................................... (-11.06 = -10.42 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,130,411 – 8,130,506
Length 95
Sequences 5
Columns 125
Reading direction reverse
Mean pairwise identity 68.33
Shannon entropy 0.50223
G+C content 0.36831
Mean single sequence MFE -22.64
Consensus MFE -10.76
Energy contribution -10.92
Covariance contribution 0.16
Combinations/Pair 1.09
Mean z-score -1.89
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.894676
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8130411 95 - 21146708
---------------AUUUUCACAGA--------AAUCAUAUA-AAUGG------UCUUGUAUUUCUAAGAUACUUUUGUAUCUUUUUGCAUUCAGCUAAUACUCACUUGAAACGGUUGUCCGGC
---------------..(((((.((.--------.(((((...-.))))------)..((((.....(((((((....)))))))..))))...............)))))))(((....))).. ( -15.60, z-score =  -0.89, R)
>droEre2.scaffold_4845 4925533 99 + 22589142
---------------GUUUCCACAAGU----GCUAGUCUGAGA-UACGU------UCUGGCAUAUCUGAGAUACUUUUGUAUCUCAUUGGAUUCAGCCUAUACUCACUUGAAACGGUUGUCCGGC
---------------.......(((((----(.(((.((((((-((.((------....)).))))((((((((....))))))))......)))).)))....))))))...(((....))).. ( -28.70, z-score =  -2.32, R)
>droYak2.chr2R 12319803 114 + 21139217
ACUUUUGCAUAUGCUAGUCUCAGAUAU----GUAAUUCAGACA-AGUAU------UCUGGCAUUUCUAAGAUACUUUUGUAUCUAAUGGGAUUCAGCCAAUACUCACUUGAAACGGUUGUCCGGC
....((((((((.((......))))))----))))(((((...-(((((------..((((..(((((((((((....))))))..)))))....)))))))))...))))).(((....))).. ( -28.80, z-score =  -2.14, R)
>droSec1.super_1 5679195 98 - 14215200
---------------ACAUUCACAAGUGUAAAAAAGUCAAACAGCAUAU-----GUCUUGUAUUUCUAAGAUACUUUUGUAUCUUAUU-------GCUAACACUCACUUGAAACGGUCGUCCGGC
---------------.......((((((......((.(((...(((...-----....))).....((((((((....))))))))))-------)))......))))))...(((....))).. ( -20.60, z-score =  -2.08, R)
>droSim1.chr2R 6596534 101 - 19596830
---------------ACAUUCACAUGUGU--AAGUCUCAAAAAUCAUAUAAAUGGUCUUGUAUUUCUAAGAUACUUUUGUAUCUUAUU-------GCUAACACUCACUUGAAACGGUCGUCCGGC
---------------...((((...((((--.(((.......(((((....)))))..........((((((((....))))))))..-------))).)))).....)))).(((....))).. ( -19.50, z-score =  -2.03, R)
>consensus
_______________ACUUUCACAAGU____AAAAGUCAAACA_AAUAU______UCUUGUAUUUCUAAGAUACUUUUGUAUCUUAUUG_AUUCAGCUAAUACUCACUUGAAACGGUUGUCCGGC
..................................................................((((((((....))))))))...........................(((....))).. (-10.76 = -10.92 +   0.16)

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 22:17:19 2011