Locus 11403

Sequence ID dm3.chr3R
Location 20,873,278 – 20,873,474
Length 196
Max. P 0.975014
window15672 window15673 window15674 window15675 window15676 window15677

overview

Window 2

Location 20,873,278 – 20,873,372
Length 94
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 66.10
Shannon entropy 0.48452
G+C content 0.40931
Mean single sequence MFE -25.90
Consensus MFE -13.79
Energy contribution -15.23
Covariance contribution 1.45
Combinations/Pair 1.06
Mean z-score -1.80
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.19
SVM RNA-class probability 0.906169
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20873278 94 + 27905053
-------------------CAGUACUCAUUAAGUAG-----UCGGCCUAUCUACCAGAAUAUUAGCCAAGGUACACAUUUGUACCUGCAAACGUACCUAGGUACGAAAGCUGUCACCU
-------------------...((((.....))))(-----.((((..................((..(((((((....)))))))))...(((((....)))))...)))).).... ( -23.40, z-score =  -1.83, R)
>droEre2.scaffold_4820 3290680 117 - 10470090
CUGUGCUUAUCAGGCAGUACAAGAUCAGUUAGACAAAAGUUUUUCCUUUGCCACCAAA-UAUCAACCUAGGUACAUGUGUGUACCUGCUACCUUACCUAGGUACGAAAGCUGUCACCU
.((((((........)))))).((.(((((.(.((((.(.....).)))).)......-.....(((((((((...(((.((....)))))..))))))))).....))))))).... ( -25.10, z-score =  -0.07, R)
>droSim1.chr3R 20700635 118 + 27517382
CAGUACUAAUUAAGCAGUUCAAGUCGAGUUAAACAAAAGUUUAUUCCUAUUUACCAAAAUAUUAGCCUAGGUACAGAUUUGUACCUGCAAACGUACCUAGGUUCGAAAGCUGUCACCU
.............((((((....((((..(((((....))))).....................((((((((((.(.(((((....)))))))))))))))))))).))))))..... ( -29.20, z-score =  -3.49, R)
>consensus
C_GU_CU_AU_A_GCAGU_CAAGACCAGUUAAACAAAAGUUUAUCCCUAUCUACCAAAAUAUUAGCCUAGGUACACAUUUGUACCUGCAAACGUACCUAGGUACGAAAGCUGUCACCU
................................................................((((((((((...(((((....))))).)))))))))).(....)......... (-13.79 = -15.23 +   1.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,873,299 – 20,873,412
Length 113
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 83.26
Shannon entropy 0.30320
G+C content 0.44173
Mean single sequence MFE -28.66
Consensus MFE -18.07
Energy contribution -17.87
Covariance contribution -0.20
Combinations/Pair 1.12
Mean z-score -2.77
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.92
SVM RNA-class probability 0.975014
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20873299 113 + 27905053
-----CCUAUCUACCAGAAUAUUAGCCAAGGUACACAUUUGUACCUGCAAACGUACCUAGGUACGAAAGCUGUCACCUUGCGCAUCACUGGCGACGAUACAUUUCGCCGACUAUCGAU
-----...........((......((((((((((((.((((((((((..........)))))))))).).))).)))))).)).....((((((.........))))))....))... ( -31.30, z-score =  -3.06, R)
>droEre2.scaffold_4820 3290720 117 - 10470090
UUUUCCUUUGCCACCAAA-UAUCAACCUAGGUACAUGUGUGUACCUGCUACCUUACCUAGGUACGAAAGCUGUCACCUUUCGCAUCACUGGCGACGAUACAUUUUGCCGACUAUCGAU
.......((((((.....-.....(((((((((...(((.((....)))))..))))))))).((((((.......))))))......))))))(((((............))))).. ( -28.10, z-score =  -2.38, R)
>droYak2.chr3R 3207589 115 - 28832112
--UUUCUUUCCCACCAAAAUAUCAUCAUAGGUACACACUUGUACCUAC-GCCUUACCUAGGUACGAAAGCUGUCACCUUACGCAUCACUGGCGACGAUACAUUUCGCCGACUAUCGAU
--...(((((.................((((((((....)))))))).-((((.....))))..)))))..(((......(((.......))).(((......)))..)))....... ( -23.80, z-score =  -2.47, R)
>droSec1.super_33 135055 112 + 478481
UUAUUCCUAUUUACCAAAAUAUUACCCUAGGUACAGAUUUGUACCUG------UAUCUAGGUACGAAAGCUGCAACCUUGCACAUCACUGGCGGCGAUACAUUUCGCAGACUAUCGAU
.........................(((((((((((........)))------))))))))..(((.((((((....((((.((....)))))).((......)))))).)).))).. ( -29.40, z-score =  -3.16, R)
>droSim1.chr3R 20700675 118 + 27517382
UUAUUCCUAUUUACCAAAAUAUUAGCCUAGGUACAGAUUUGUACCUGCAAACGUACCUAGGUUCGAAAGCUGUCACCUUGCGCAUCACUGGCGACGAUACAUUUCGCAGACUAUCGAU
........................((((((((((.(.(((((....))))))))))))))))((((.((((((.......(((.......)))..((......)))))).)).)))). ( -30.70, z-score =  -2.78, R)
>consensus
UUAUUCCUAUCUACCAAAAUAUUAGCCUAGGUACACAUUUGUACCUGC_AACGUACCUAGGUACGAAAGCUGUCACCUUGCGCAUCACUGGCGACGAUACAUUUCGCCGACUAUCGAU
............(((............((((((((....))))))))............))).(((.(((.(((.((............)).)))((......))...).)).))).. (-18.07 = -17.87 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,873,299 – 20,873,412
Length 113
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 83.26
Shannon entropy 0.30320
G+C content 0.44173
Mean single sequence MFE -35.40
Consensus MFE -23.38
Energy contribution -23.58
Covariance contribution 0.20
Combinations/Pair 1.10
Mean z-score -2.20
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.892892
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20873299 113 - 27905053
AUCGAUAGUCGGCGAAAUGUAUCGUCGCCAGUGAUGCGCAAGGUGACAGCUUUCGUACCUAGGUACGUUUGCAGGUACAAAUGUGUACCUUGGCUAAUAUUCUGGUAGAUAGG-----
.......((((((((......)))))(((((....(((((((....)......(((((....))))).))))(((((((....)))))))..)).......))))).)))...----- ( -35.50, z-score =  -1.55, R)
>droEre2.scaffold_4820 3290720 117 + 10470090
AUCGAUAGUCGGCAAAAUGUAUCGUCGCCAGUGAUGCGAAAGGUGACAGCUUUCGUACCUAGGUAAGGUAGCAGGUACACACAUGUACCUAGGUUGAUA-UUUGGUGGCAAAGGAAAA
.......((((.(((...(((((((((((............)))))).(((.((.(((....))).)).)))(((((((....))))))).....))))-)))).))))......... ( -33.70, z-score =  -1.55, R)
>droYak2.chr3R 3207589 115 + 28832112
AUCGAUAGUCGGCGAAAUGUAUCGUCGCCAGUGAUGCGUAAGGUGACAGCUUUCGUACCUAGGUAAGGC-GUAGGUACAAGUGUGUACCUAUGAUGAUAUUUUGGUGGGAAAGAAA--
.......((((.(...((((((((.(....)))))))))..).))))..(((((.((((.(((((...(-(((((((((....))))))))))....))))).)))).)))))...-- ( -41.00, z-score =  -4.02, R)
>droSec1.super_33 135055 112 - 478481
AUCGAUAGUCUGCGAAAUGUAUCGCCGCCAGUGAUGUGCAAGGUUGCAGCUUUCGUACCUAGAUA------CAGGUACAAAUCUGUACCUAGGGUAAUAUUUUGGUAAAUAGGAAUAA
..(((.((.((((((..((((((((.....)))))..)))...)))))))).)))..(((((.((------(((((....))))))).)))))....((((((........)))))). ( -32.90, z-score =  -2.19, R)
>droSim1.chr3R 20700675 118 - 27517382
AUCGAUAGUCUGCGAAAUGUAUCGUCGCCAGUGAUGCGCAAGGUGACAGCUUUCGAACCUAGGUACGUUUGCAGGUACAAAUCUGUACCUAGGCUAAUAUUUUGGUAAAUAGGAAUAA
.....((((((((.(((((((((...((((....)).)).((((............)))).)))))))))))(((((((....))))))))))))).((((((........)))))). ( -33.90, z-score =  -1.70, R)
>consensus
AUCGAUAGUCGGCGAAAUGUAUCGUCGCCAGUGAUGCGCAAGGUGACAGCUUUCGUACCUAGGUAAGGU_GCAGGUACAAAUCUGUACCUAGGCUAAUAUUUUGGUAGAUAGGAAAAA
..(((.(((..((.....))...((((((............)))))).))).)))((((.(((((.......(((((((....))))))).......))))).))))........... (-23.38 = -23.58 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,873,372 – 20,873,473
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 89.50
Shannon entropy 0.19240
G+C content 0.55106
Mean single sequence MFE -39.02
Consensus MFE -29.18
Energy contribution -29.46
Covariance contribution 0.28
Combinations/Pair 1.04
Mean z-score -2.36
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.894159
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20873372 101 - 27905053
CACUGGCGAAUGCGAAUGAAUCCGAUCGCAACUUGGAUGCGGACGCAGAGUGAGCCCGUCUAUCGAUAGUCGGCGAAAUGUAUCGUCGCCAGUGAUGCGCA
(((((((((.(((((.((....)).))))).....((((((..(((...))).(((.(.(((....))).))))....)))))).)))))))))....... ( -35.40, z-score =  -0.70, R)
>droEre2.scaffold_4820 3290797 95 + 10470090
CACUGGCGAAU------GAAUCCGAUCGGAACUUGGAUGCCGACGGCCAGUGAGCCCGACUAUCGAUAGUCGGCAAAAUGUAUCGUCGCCAGUGAUGCGAA
(((((((((.(------((((((((.......))))))(((((((((......)))((.....))...))))))........))))))))))))....... ( -39.30, z-score =  -3.60, R)
>droYak2.chr3R 3207664 101 + 28832112
CACUGGCAAAUGAAUCCGAAUCCGAUCGGAACUUGGAUGCCGACGGUCAGUGAGCCCGGCUAUCGAUAGUCGGCGAAAUGUAUCGUCGCCAGUGAUGCGUA
(((((((......((((((.(((....)))..))))))...((((((((....(((.(((((....))))))))....)).)))))))))))))....... ( -41.30, z-score =  -3.01, R)
>droSec1.super_33 135127 101 - 478481
CACUGGCGAAUGCGAAUGAAUCCGAUCGCAACUUGGAUGCGGACGCAGAGUGAGCCCGGCUAUCGAUAGUCUGCGAAAUGUAUCGCCGCCAGUGAUGUGCA
((((((((..(((((.((....)).))))).....((((((..((((((.(((((...))).....)).))))))...))))))..))))))))....... ( -38.80, z-score =  -2.17, R)
>droSim1.chr3R 20700753 101 - 27517382
CACUGGCGAAUGCGAAUGAAUCCGAUCGCAACUUGGAUGCGGACGCAGAGUGAGCCCGGCUAUCGAUAGUCUGCGAAAUGUAUCGUCGCCAGUGAUGCGCA
(((((((((.(((((.((....)).))))).....((((((..((((((.(((((...))).....)).))))))...)))))).)))))))))....... ( -40.30, z-score =  -2.30, R)
>consensus
CACUGGCGAAUGCGAAUGAAUCCGAUCGCAACUUGGAUGCGGACGCAGAGUGAGCCCGGCUAUCGAUAGUCGGCGAAAUGUAUCGUCGCCAGUGAUGCGCA
(((((((((..........((((((.......))))))((((((........((.....)).......))))))...........)))))))))....... (-29.18 = -29.46 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,873,373 – 20,873,474
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 89.50
Shannon entropy 0.19240
G+C content 0.55106
Mean single sequence MFE -36.00
Consensus MFE -24.88
Energy contribution -24.80
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -2.20
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.37
SVM RNA-class probability 0.663569
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20873373 101 + 27905053
GCGCAUCACUGGCGACGAUACAUUUCGCCGACUAUCGAUAGACGGGCUCACUCUGCGUCCGCAUCCAAGUUGCGAUCGGAUUCAUUCGCAUUCGCCAGUGA
.....(((((((((((((......((((.((((...(((.(.(((((.(.....).)))))))))..)))))))))))((.....))....)))))))))) ( -34.30, z-score =  -1.45, R)
>droEre2.scaffold_4820 3290798 95 - 10470090
UCGCAUCACUGGCGACGAUACAUUUUGCCGACUAUCGAUAGUCGGGCUCACUGGCCGUCGGCAUCCAAGUUCCGAUCGGAUUC------AUUCGCCAGUGA
.....((((((((((..........(((((((...((.....))((((....))))))))))).......(((....)))...------..)))))))))) ( -38.40, z-score =  -3.36, R)
>droYak2.chr3R 3207665 101 - 28832112
ACGCAUCACUGGCGACGAUACAUUUCGCCGACUAUCGAUAGCCGGGCUCACUGACCGUCGGCAUCCAAGUUCCGAUCGGAUUCGGAUUCAUUUGCCAGUGA
.....((((((((((...........((((((..(((..(((...)))...)))..))))))........(((((......))))).....)))))))))) ( -36.00, z-score =  -2.19, R)
>droSec1.super_33 135128 101 + 478481
GCACAUCACUGGCGGCGAUACAUUUCGCAGACUAUCGAUAGCCGGGCUCACUCUGCGUCCGCAUCCAAGUUGCGAUCGGAUUCAUUCGCAUUCGCCAGUGA
.....(((((((((((((......)))).((((...(((.((.((((.(.....).)))))))))..))))((((..........))))...))))))))) ( -36.70, z-score =  -2.43, R)
>droSim1.chr3R 20700754 101 + 27517382
GCGCAUCACUGGCGACGAUACAUUUCGCAGACUAUCGAUAGCCGGGCUCACUCUGCGUCCGCAUCCAAGUUGCGAUCGGAUUCAUUCGCAUUCGCCAGUGA
.....(((((((((((((......((((((.((...(((.((.((((.(.....).)))))))))..)))))))))))((.....))....)))))))))) ( -34.60, z-score =  -1.57, R)
>consensus
GCGCAUCACUGGCGACGAUACAUUUCGCCGACUAUCGAUAGCCGGGCUCACUCUGCGUCCGCAUCCAAGUUGCGAUCGGAUUCAUUCGCAUUCGCCAGUGA
.....(((((((((((((......)))..((((...(((.(.(((((.........)))))))))..))))....................)))))))))) (-24.88 = -24.80 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,873,373 – 20,873,474
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 89.50
Shannon entropy 0.19240
G+C content 0.55106
Mean single sequence MFE -40.42
Consensus MFE -30.58
Energy contribution -30.86
Covariance contribution 0.28
Combinations/Pair 1.04
Mean z-score -2.76
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.83
SVM RNA-class probability 0.970258
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20873373 101 - 27905053
UCACUGGCGAAUGCGAAUGAAUCCGAUCGCAACUUGGAUGCGGACGCAGAGUGAGCCCGUCUAUCGAUAGUCGGCGAAAUGUAUCGUCGCCAGUGAUGCGC
((((((((((.(((((.((....)).))))).....((((((..(((...))).(((.(.(((....))).))))....)))))).))))))))))..... ( -36.80, z-score =  -1.19, R)
>droEre2.scaffold_4820 3290798 95 + 10470090
UCACUGGCGAAU------GAAUCCGAUCGGAACUUGGAUGCCGACGGCCAGUGAGCCCGACUAUCGAUAGUCGGCAAAAUGUAUCGUCGCCAGUGAUGCGA
((((((((((.(------((((((((.......))))))(((((((((......)))((.....))...))))))........)))))))))))))..... ( -40.70, z-score =  -3.77, R)
>droYak2.chr3R 3207665 101 + 28832112
UCACUGGCAAAUGAAUCCGAAUCCGAUCGGAACUUGGAUGCCGACGGUCAGUGAGCCCGGCUAUCGAUAGUCGGCGAAAUGUAUCGUCGCCAGUGAUGCGU
((((((((......((((((.(((....)))..))))))...((((((((....(((.(((((....))))))))....)).))))))))))))))..... ( -42.70, z-score =  -3.29, R)
>droSec1.super_33 135128 101 - 478481
UCACUGGCGAAUGCGAAUGAAUCCGAUCGCAACUUGGAUGCGGACGCAGAGUGAGCCCGGCUAUCGAUAGUCUGCGAAAUGUAUCGCCGCCAGUGAUGUGC
(((((((((..(((((.((....)).))))).....((((((..((((((.(((((...))).....)).))))))...))))))..)))))))))..... ( -40.20, z-score =  -2.71, R)
>droSim1.chr3R 20700754 101 - 27517382
UCACUGGCGAAUGCGAAUGAAUCCGAUCGCAACUUGGAUGCGGACGCAGAGUGAGCCCGGCUAUCGAUAGUCUGCGAAAUGUAUCGUCGCCAGUGAUGCGC
((((((((((.(((((.((....)).))))).....((((((..((((((.(((((...))).....)).))))))...)))))).))))))))))..... ( -41.70, z-score =  -2.82, R)
>consensus
UCACUGGCGAAUGCGAAUGAAUCCGAUCGCAACUUGGAUGCGGACGCAGAGUGAGCCCGGCUAUCGAUAGUCGGCGAAAUGUAUCGUCGCCAGUGAUGCGC
((((((((((..........((((((.......))))))((((((........((.....)).......))))))...........))))))))))..... (-30.58 = -30.86 +   0.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:42:19 2011