Locus 2794

Sequence ID dm3.chr2L
Location 22,414,766 – 22,414,904
Length 138
Max. P 0.999535
window3845 window3846 window3847 window3848

overview

Window 5

Location 22,414,766 – 22,414,864
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.18
Shannon entropy 0.52605
G+C content 0.60177
Mean single sequence MFE -46.06
Consensus MFE -27.04
Energy contribution -28.72
Covariance contribution 1.68
Combinations/Pair 1.15
Mean z-score -2.72
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.44
SVM RNA-class probability 0.998666
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22414766 98 + 23011544
--------CUUGGCUUCAGAAU--A------------CCCGGGCUUGAACUUCGGCCGGCGGUAGUGCUCUACUGACUGGGGUCUCGGAGCUCUACUCACUCCACCACCGCCGGCGGCAA
--------....(((.......--.------------..((((.......))))(((((((((.(((......(((.((((((......)))))).)))...))).)))))))))))).. ( -33.60, z-score =   0.01, R)
>droSim1.chrU 12458103 110 - 15797150
--------UUGGGCUUCAGAAU--ACCACAUACCAUACCCGGGUUUGAACUCCGGCCGGCGGUAGUGCUCUACUGACUGGGGUGUCGGAGCUCUACUCACUCCACUACCGCCGGCGGCAA
--------.(((..((((((..--.((.............)).))))))..)))(((((((((((((......(((.((((((......)))))).)))...)))))))))))))..... ( -45.12, z-score =  -2.57, R)
>droSec1.super_42 16121 110 + 298440
--------UUUGGCUUCAGAAU--ACCACAUACCAUACCUGGGUUUGAACUUCGGCCGGCGGUAGUGCCCUACUGACUGGGGUGUGGGAGCUCUCCUCACUCCACUACCGCCGGCGGCAA
--------....((((((((..--.(((...........))).)))))......((((((((((((((((((.....))))).((((((....))).)))..)))))))))))))))).. ( -47.80, z-score =  -3.22, R)
>droYak2.chr2L 7945874 114 + 22324452
UUUUACCACCGGGAUUAAGUCCCGGUUCCAUACUAUACCUGGGCUUGAACUCCGGCCGGCGUCAGUUCUCU-CCGACAAGGAUGUCGAAGCUG-----ACUCCACUACCGCCGGCGGCAA
.....((..((((.((((((((.(((..........))).)))))))).).)))(((((((..(((((.((-.(((((....))))).))..)-----)....)))..)))))))))... ( -43.70, z-score =  -2.83, R)
>droEre2.scaffold_4929 12734899 115 - 26641161
----CGGAACCGACGUCGGUUCUGGUUCUGUCCCAC-GUAGGGCUUGAACUCCGGCCGGCGGUAGCACUCUCCUAACUGGGGAGACCGAGCUCUACUCACUCCACUACCGCCGGCCCCGA
----((((((((....))))))))((((.((((...-...))))..))))...((((((((((((..((((((.....))))))...(((.....)))......)))))))))))).... ( -60.10, z-score =  -4.99, R)
>consensus
________CUGGGCUUCAGAAU__ACCACAUACCAUACCCGGGCUUGAACUCCGGCCGGCGGUAGUGCUCUACUGACUGGGGUGUCGGAGCUCUACUCACUCCACUACCGCCGGCGGCAA
.......................................((((.......))))((((((((((((((((((.....))))))...((((.........))))))))))))))))..... (-27.04 = -28.72 +   1.68)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,414,766 – 22,414,864
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.18
Shannon entropy 0.52605
G+C content 0.60177
Mean single sequence MFE -48.00
Consensus MFE -30.20
Energy contribution -30.84
Covariance contribution 0.64
Combinations/Pair 1.29
Mean z-score -3.07
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.99
SVM RNA-class probability 0.999535
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22414766 98 - 23011544
UUGCCGCCGGCGGUGGUGGAGUGAGUAGAGCUCCGAGACCCCAGUCAGUAGAGCACUACCGCCGGCCGAAGUUCAAGCCCGGG------------U--AUUCUGAAGCCAAG--------
.(((((((((((((((((((((.......)))))..(((....)))........))))))))))))((..((....)).))))------------)--).............-------- ( -38.20, z-score =  -2.15, R)
>droSim1.chrU 12458103 110 + 15797150
UUGCCGCCGGCGGUAGUGGAGUGAGUAGAGCUCCGACACCCCAGUCAGUAGAGCACUACCGCCGGCCGGAGUUCAAACCCGGGUAUGGUAUGUGGU--AUUCUGAAGCCCAA--------
.(((((((((((((((((((((.......)))))(((......)))........))))))))))))(((.((....))))))))).....((.(((--........))))).-------- ( -46.70, z-score =  -3.12, R)
>droSec1.super_42 16121 110 - 298440
UUGCCGCCGGCGGUAGUGGAGUGAGGAGAGCUCCCACACCCCAGUCAGUAGGGCACUACCGCCGGCCGAAGUUCAAACCCAGGUAUGGUAUGUGGU--AUUCUGAAGCCAAA--------
.(((((((((((((((((..(((.(((....))))))..(((........))))))))))))))))..........((....))..))))..((((--........))))..-------- ( -47.10, z-score =  -3.21, R)
>droYak2.chr2L 7945874 114 - 22324452
UUGCCGCCGGCGGUAGUGGAGU-----CAGCUUCGACAUCCUUGUCGG-AGAGAACUGACGCCGGCCGGAGUUCAAGCCCAGGUAUAGUAUGGAACCGGGACUUAAUCCCGGUGGUAAAA
((((((((((((((...((.((-----(((((((((((....))))))-))....))))).)).))))......((((((.(((..........)))))).)))....)))))))))).. ( -50.30, z-score =  -3.36, R)
>droEre2.scaffold_4929 12734899 115 + 26641161
UCGGGGCCGGCGGUAGUGGAGUGAGUAGAGCUCGGUCUCCCCAGUUAGGAGAGUGCUACCGCCGGCCGGAGUUCAAGCCCUAC-GUGGGACAGAACCAGAACCGACGUCGGUUCCG----
....(((((((((((((.((((.......))))(.(((((.......))))).)))))))))))))).(.((((...(((...-..)))...))))).((((((....))))))..---- ( -57.70, z-score =  -3.53, R)
>consensus
UUGCCGCCGGCGGUAGUGGAGUGAGUAGAGCUCCGACACCCCAGUCAGUAGAGCACUACCGCCGGCCGGAGUUCAAGCCCAGGUAUGGUAUGGAAU__AUUCUGAAGCCAAA________
.(((((((((((((((((((((.......)))))(((......)))........)))))))))))).((.((....)))).))))................................... (-30.20 = -30.84 +   0.64)

alignment

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secondary structure

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dotplot

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Window 7

Location 22,414,784 – 22,414,904
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.17
Shannon entropy 0.36176
G+C content 0.58176
Mean single sequence MFE -43.40
Consensus MFE -28.52
Energy contribution -30.36
Covariance contribution 1.84
Combinations/Pair 1.10
Mean z-score -1.62
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.737379
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22414784 120 + 23011544
GGGCUUGAACUUCGGCCGGCGGUAGUGCUCUACUGACUGGGGUCUCGGAGCUCUACUCACUCCACCACCGCCGGCGGCAAUGGCACAGCAUCCUGGGGUAACCUUGAACUUCGUUUGAUU
..(((((.....(.(((((((((.(((......(((.((((((......)))))).)))...))).))))))))).)......)).))).((..(((....))).))............. ( -38.00, z-score =   0.60, R)
>droSim1.chrU 12458133 120 - 15797150
GGGUUUGAACUCCGGCCGGCGGUAGUGCUCUACUGACUGGGGUGUCGGAGCUCUACUCACUCCACUACCGCCGGCGGCAAUGGCAUAGCAUCCUGGGAUAAACUUGAAUUUCGUCUGAUU
(((((((...(((.(((((((((((((......(((.((((((......)))))).)))...))))))))))))).((....))...........))))))))))............... ( -43.20, z-score =  -1.41, R)
>droSec1.super_42 16151 120 + 298440
GGGUUUGAACUUCGGCCGGCGGUAGUGCCCUACUGACUGGGGUGUGGGAGCUCUCCUCACUCCACUACCGCCGGCGGCAAUGGGAUAGCAUCCUGGGAUAAACUUGAAUUUCGUCUGAUU
(((((((..((.(.((((((((((((((((((.....))))).((((((....))).)))..))))))))))))).)....(((((...)))))))..)))))))............... ( -48.90, z-score =  -2.29, R)
>droYak2.chr2L 7945914 114 + 22324452
GGGCUUGAACUCCGGCCGGCGUCAGUUCUCU-CCGACAAGGAUGUCGAAGCUG-----ACUCCACUACCGCCGGCGGCAAUGGGACAGCAUCCUAGGUUAAACUUGAACUUUGUCUGCCC
((((..........(((((((..(((((.((-.(((((....))))).))..)-----)....)))..)))))))((((((((((.....)))))((((.......))))))))).)))) ( -38.90, z-score =  -0.90, R)
>droEre2.scaffold_4929 12734934 106 - 26641161
GGGCUUGAACUCCGGCCGGCGGUAGCACUCUCCUAACUGGGGAGACCGAGCUCUACUCACUCCACUACCGCCGGCCCCGAUGGGACAGCAUCCUAGGUUUAACUUG--------------
(((.(((((((..((((((((((((..((((((.....))))))...(((.....)))......))))))))))))....(((((.....))))))))))))))).-------------- ( -48.00, z-score =  -4.12, R)
>consensus
GGGCUUGAACUCCGGCCGGCGGUAGUGCUCUACUGACUGGGGUGUCGGAGCUCUACUCACUCCACUACCGCCGGCGGCAAUGGGACAGCAUCCUGGGAUAAACUUGAACUUCGUCUGAUU
(((.(((..((.(.((((((((((((((((((.....))))))...((((.........)))))))))))))))).)....))..)))...))).......................... (-28.52 = -30.36 +   1.84)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,414,784 – 22,414,904
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.17
Shannon entropy 0.36176
G+C content 0.58176
Mean single sequence MFE -45.14
Consensus MFE -31.70
Energy contribution -32.98
Covariance contribution 1.28
Combinations/Pair 1.21
Mean z-score -3.08
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.10
SVM RNA-class probability 0.997407
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22414784 120 - 23011544
AAUCAAACGAAGUUCAAGGUUACCCCAGGAUGCUGUGCCAUUGCCGCCGGCGGUGGUGGAGUGAGUAGAGCUCCGAGACCCCAGUCAGUAGAGCACUACCGCCGGCCGAAGUUCAAGCCC
........(((.(((..(((....((((....))).).....)))(((((((((((((((((.......)))))..(((....)))........)))))))))))).))).)))...... ( -45.50, z-score =  -3.05, R)
>droSim1.chrU 12458133 120 + 15797150
AAUCAGACGAAAUUCAAGUUUAUCCCAGGAUGCUAUGCCAUUGCCGCCGGCGGUAGUGGAGUGAGUAGAGCUCCGACACCCCAGUCAGUAGAGCACUACCGCCGGCCGGAGUUCAAACCC
........(((.(((.(((..(((....))))))...........(((((((((((((((((.......)))))(((......)))........)))))))))))).))).)))...... ( -41.80, z-score =  -3.13, R)
>droSec1.super_42 16151 120 - 298440
AAUCAGACGAAAUUCAAGUUUAUCCCAGGAUGCUAUCCCAUUGCCGCCGGCGGUAGUGGAGUGAGGAGAGCUCCCACACCCCAGUCAGUAGGGCACUACCGCCGGCCGAAGUUCAAACCC
........(((.(((.(((..(((....))))))...........(((((((((((((..(((.(((....))))))..(((........)))))))))))))))).))).)))...... ( -46.00, z-score =  -3.97, R)
>droYak2.chr2L 7945914 114 - 22324452
GGGCAGACAAAGUUCAAGUUUAACCUAGGAUGCUGUCCCAUUGCCGCCGGCGGUAGUGGAGU-----CAGCUUCGACAUCCUUGUCGG-AGAGAACUGACGCCGGCCGGAGUUCAAGCCC
.(((.((((..((((.((......)).))))..))))(((((((((....))))))))).((-----(((((((((((....))))))-))....))))))))(((..(....)..))). ( -47.80, z-score =  -3.06, R)
>droEre2.scaffold_4929 12734934 106 + 26641161
--------------CAAGUUAAACCUAGGAUGCUGUCCCAUCGGGGCCGGCGGUAGUGGAGUGAGUAGAGCUCGGUCUCCCCAGUUAGGAGAGUGCUACCGCCGGCCGGAGUUCAAGCCC
--------------.........((...((((......))))..(((((((((((((.((((.......))))(.(((((.......))))).))))))))))))))))........... ( -44.60, z-score =  -2.19, R)
>consensus
AAUCAGACGAAAUUCAAGUUUAACCCAGGAUGCUGUCCCAUUGCCGCCGGCGGUAGUGGAGUGAGUAGAGCUCCGACACCCCAGUCAGUAGAGCACUACCGCCGGCCGGAGUUCAAGCCC
........(((.(((............((........))......(((((((((((((((((.......)))))(((......)))........)))))))))))).))).)))...... (-31.70 = -32.98 +   1.28)

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 21:58:07 2011