Locus 5201

Sequence ID dm3.chr2R
Location 18,479,126 – 18,479,232
Length 106
Max. P 0.978207
window7136 window7137 window7138 window7139

overview

Window 6

Location 18,479,126 – 18,479,226
Length 100
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 67.64
Shannon entropy 0.53571
G+C content 0.40897
Mean single sequence MFE -23.28
Consensus MFE -11.38
Energy contribution -12.22
Covariance contribution 0.84
Combinations/Pair 1.19
Mean z-score -2.14
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.99
SVM RNA-class probability 0.978207
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18479126 100 + 21146708
UUUAGUGCUACCUCGUAAUAUCCUCUUAUAGAGGAUACGUAAUCCAGUAGGGGUACAUCAUAUAUCACACA-CGUGUGAC---C--------AAAUUGCAUAAACUGCGGUC
....(((.((((((......(((((.....)))))(((........))))))))))))......(((((..-..))))).---.--------..((((((.....)))))). ( -25.30, z-score =  -1.65, R)
>droYak2.chr2R 15942998 112 + 21139217
UUUAUUGUCACACCGUAAUAUCCUCUUAUAGAGGAUACGUAAUUCAGUGGUUAUGUACAUCACAUCACACAUCGCACAACACACGUGUGUCGAAAUUGCGUAAACCACGUUU
.............(((....(((((.....)))))(((((((((..(((...((((.....))))..))).(((((((.......)))).))))))))))))....)))... ( -26.50, z-score =  -1.92, R)
>droEre2.scaffold_4845 15113264 90 - 22589142
UUUGGUGUCACAUCGUAAUAUCCUCUUAUAGAGGAUACGUAA---------UUCAGUGGGUAUAUCACAAA-CGUGUGGC---A--------AAAUUGCGUAAACUACGUU-
.....(((((((.(((..(((((((.....))))))).....---------....((((.....))))..)-))))))))---)--------.....(((((...))))).- ( -25.90, z-score =  -3.22, R)
>droSec1.super_9 1777623 81 + 3197100
UUUAGUGCUACCUCGUAAUAUCCUCCUUUAGAGG-UAC---------------------ACAUAUCACACA-CGUGUGACCACC--------AAAUUGCAUAAACUGCGGUC
....(((.((((((.(((.........)))))))-)))---------------------))...(((((..-..))))).....--------..((((((.....)))))). ( -19.50, z-score =  -2.35, R)
>droSim1.chr2R 17063159 81 + 19596830
UUUAGUGCUACCUCGUAAUAUCCUCUUAUAGGGG-UAC---------------------ACAUAUCACACA-CGUGUGACCACC--------AAAUUGCAUAAACUGCGGUC
....(((.((((((...(((......))).))))-)))---------------------))...(((((..-..))))).....--------..((((((.....)))))). ( -19.20, z-score =  -1.55, R)
>consensus
UUUAGUGCUACCUCGUAAUAUCCUCUUAUAGAGGAUACGUAA_________________ACAUAUCACACA_CGUGUGAC___C________AAAUUGCAUAAACUGCGGUC
.............((((.(((((((.....)))))))...........................(((((.....)))))..........................))))... (-11.38 = -12.22 +   0.84)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,479,126 – 18,479,226
Length 100
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 67.64
Shannon entropy 0.53571
G+C content 0.40897
Mean single sequence MFE -23.94
Consensus MFE -13.62
Energy contribution -13.70
Covariance contribution 0.08
Combinations/Pair 1.33
Mean z-score -1.32
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.883584
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18479126 100 - 21146708
GACCGCAGUUUAUGCAAUUU--------G---GUCACACG-UGUGUGAUAUAUGAUGUACCCCUACUGGAUUACGUAUCCUCUAUAAGAGGAUAUUACGAGGUAGCACUAAA
.((((((.....)))...((--------(---((((((..-..)))))).......(((..((....))..)))((((((((.....))))))))..))))))......... ( -26.50, z-score =  -1.46, R)
>droYak2.chr2R 15942998 112 - 21139217
AAACGUGGUUUACGCAAUUUCGACACACGUGUGUUGUGCGAUGUGUGAUGUGAUGUACAUAACCACUGAAUUACGUAUCCUCUAUAAGAGGAUAUUACGGUGUGACAAUAAA
..((((((((((((((....((((((....))))))))))..(((.(.((((.....)))).))))))))))))))((((((.....))))))................... ( -31.40, z-score =  -1.31, R)
>droEre2.scaffold_4845 15113264 90 + 22589142
-AACGUAGUUUACGCAAUUU--------U---GCCACACG-UUUGUGAUAUACCCACUGAA---------UUACGUAUCCUCUAUAAGAGGAUAUUACGAUGUGACACCAAA
-.((((((((((.(((....--------)---))((((..-..))))..........))))---------))))))((((((.....))))))................... ( -20.80, z-score =  -2.67, R)
>droSec1.super_9 1777623 81 - 3197100
GACCGCAGUUUAUGCAAUUU--------GGUGGUCACACG-UGUGUGAUAUGU---------------------GUA-CCUCUAAAGGAGGAUAUUACGAGGUAGCACUAAA
....(((.....)))..(((--------((((((((((..-..)))))).(((---------------------(((-((((.....)))).)).))))......))))))) ( -22.10, z-score =  -1.12, R)
>droSim1.chr2R 17063159 81 - 19596830
GACCGCAGUUUAUGCAAUUU--------GGUGGUCACACG-UGUGUGAUAUGU---------------------GUA-CCCCUAUAAGAGGAUAUUACGAGGUAGCACUAAA
.((((((.....))).....--------((.(((.(((((-(((...))))))---------------------)))-))))..................)))......... ( -18.90, z-score =  -0.03, R)
>consensus
GACCGCAGUUUAUGCAAUUU________G___GUCACACG_UGUGUGAUAUGU_________________UUACGUAUCCUCUAUAAGAGGAUAUUACGAGGUAGCACUAAA
....(((.....))).................(((((((...))))))).........................((((((((.....))))))))................. (-13.62 = -13.70 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,479,132 – 18,479,232
Length 100
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 67.66
Shannon entropy 0.51267
G+C content 0.42641
Mean single sequence MFE -24.70
Consensus MFE -11.51
Energy contribution -12.19
Covariance contribution 0.68
Combinations/Pair 1.18
Mean z-score -2.26
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.83
SVM RNA-class probability 0.970362
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18479132 100 + 21146708
GCUACCUCGUAAUAUCCUCUUAUAGAGGAUACGUAAUCCAGUAGGGGUACAUCAUAUAUCACAC------------ACGUGUGACC---AAAUUGCAUAAACUGCGGUCGAGGAU
....(((((...(((((((.....))))))).(((..((....))..)))........(((((.------------...)))))..---..((((((.....))))))))))).. ( -29.30, z-score =  -2.53, R)
>droYak2.chr2R 15943004 112 + 21139217
GUCACACCGUAAUAUCCUCUUAUAGAGGAUACGUAAUUCAGUGGUUAUGUACAUCACAUCACACAUCGCACAACACACGUGUGUCG---AAAUUGCGUAAACCACGUUUGAAGAU
.(((...(((....(((((.....)))))(((((((((..(((...((((.....))))..))).(((((((.......)))).))---))))))))))....)))..))).... ( -27.60, z-score =  -1.60, R)
>droEre2.scaffold_4845 15113270 90 - 22589142
GUCACAUCGUAAUAUCCUCUUAUAGAGGAUACGUAAUUCAGUGG----GUAUAUCACAA-----------------ACGUGUGGCA---AAAUUGCGUAAACUACGUU-GAAGAU
((((((.(((..(((((((.....))))))).........((((----.....))))..-----------------))))))))).---.....(((((...))))).-...... ( -25.00, z-score =  -3.05, R)
>droSec1.super_9 1777629 81 + 3197100
GCUACCUCGUAAUAUCCUCCUUUAGAGG-UAC---------------------ACAUAUCACAC------------ACGUGUGACCACCAAAUUGCAUAAACUGCGGUCGAGGAU
....(((((......((((.....))))-...---------------------.....(((((.------------...))))).......((((((.....))))))))))).. ( -19.80, z-score =  -1.98, R)
>droSim1.chr2R 17063165 81 + 19596830
GCUACCUCGUAAUAUCCUCUUAUAGGGG-UAC---------------------ACAUAUCACAC------------ACGUGUGACCACCAAAUUGCAUAAACUGCGGUCGAGGAU
....(((((...............((((-(.(---------------------((((.......------------..)))))))).))..((((((.....))))))))))).. ( -21.80, z-score =  -2.15, R)
>consensus
GCUACCUCGUAAUAUCCUCUUAUAGAGGAUACGUAAU_CAGU_G______A__ACAUAUCACAC____________ACGUGUGACC___AAAUUGCAUAAACUGCGGUCGAGGAU
....(((((...(((((((.....)))))))..............................................(((((..................)).)))..))))).. (-11.51 = -12.19 +   0.68)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,479,132 – 18,479,232
Length 100
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 67.66
Shannon entropy 0.51267
G+C content 0.42641
Mean single sequence MFE -26.92
Consensus MFE -14.32
Energy contribution -16.68
Covariance contribution 2.36
Combinations/Pair 1.13
Mean z-score -2.04
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.90
SVM RNA-class probability 0.974241
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18479132 100 - 21146708
AUCCUCGACCGCAGUUUAUGCAAUUU---GGUCACACGU------------GUGUGAUAUAUGAUGUACCCCUACUGGAUUACGUAUCCUCUAUAAGAGGAUAUUACGAGGUAGC
..(((((...(((.....))).....---.((((((...------------.)))))).......(((..((....))..)))((((((((.....))))))))..))))).... ( -30.20, z-score =  -2.32, R)
>droYak2.chr2R 15943004 112 - 21139217
AUCUUCAAACGUGGUUUACGCAAUUU---CGACACACGUGUGUUGUGCGAUGUGUGAUGUGAUGUACAUAACCACUGAAUUACGUAUCCUCUAUAAGAGGAUAUUACGGUGUGAC
....(((.((((((((((((((....---((((((....)))))).....)))))))((((.....)))))))))........((((((((.....))))))))....)).))). ( -32.80, z-score =  -1.44, R)
>droEre2.scaffold_4845 15113270 90 + 22589142
AUCUUC-AACGUAGUUUACGCAAUUU---UGCCACACGU-----------------UUGUGAUAUAC----CCACUGAAUUACGUAUCCUCUAUAAGAGGAUAUUACGAUGUGAC
(((...-.((((((((((.(((....---)))((((...-----------------.))))......----....))))))))))((((((.....)))))).....)))..... ( -21.40, z-score =  -2.62, R)
>droSec1.super_9 1777629 81 - 3197100
AUCCUCGACCGCAGUUUAUGCAAUUUGGUGGUCACACGU------------GUGUGAUAUGU---------------------GUA-CCUCUAAAGGAGGAUAUUACGAGGUAGC
((((((....(((.....)))..(((((.(((.((((((------------((...))))))---------------------)))-)).))))).))))))............. ( -25.90, z-score =  -2.13, R)
>droSim1.chr2R 17063165 81 - 19596830
AUCCUCGACCGCAGUUUAUGCAAUUUGGUGGUCACACGU------------GUGUGAUAUGU---------------------GUA-CCCCUAUAAGAGGAUAUUACGAGGUAGC
((((((....(((.....))).....((.(((.((((((------------((...))))))---------------------)))-)))).....))))))............. ( -24.30, z-score =  -1.71, R)
>consensus
AUCCUCGACCGCAGUUUAUGCAAUUU___GGUCACACGU____________GUGUGAUAUGU__U______C_ACUG_AUUACGUAUCCUCUAUAAGAGGAUAUUACGAGGUAGC
..(((((...(((.....))).........(((((((..............))))))).........................((((((((.....))))))))..))))).... (-14.32 = -16.68 +   2.36)

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 22:43:47 2011