Locus 8999

Sequence ID dm3.chr3R
Location 3,267,990 – 3,268,222
Length 232
Max. P 0.951384
window12352 window12353 window12354 window12355

overview

Window 2

Location 3,267,990 – 3,268,096
Length 106
Sequences 8
Columns 108
Reading direction forward
Mean pairwise identity 69.79
Shannon entropy 0.57530
G+C content 0.49205
Mean single sequence MFE -21.86
Consensus MFE -10.12
Energy contribution -10.28
Covariance contribution 0.16
Combinations/Pair 1.20
Mean z-score -1.09
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.03
SVM RNA-class probability 0.508496
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3267990 106 + 27905053
UGACACUGAAAGCCGCUGUCAGCUGCCAAAUAGCUACAAACGGU-UUAGCCCCC-GGCUAGCACACAAAUACAUUCAUAUACAUAACACGGCACCCGGCACACAAAUC
...........((((.(((((((((.....))))).......((-((((((...-)))))).)).........................))))..))))......... ( -21.20, z-score =  -0.72, R)
>droSim1.chr3R 3312414 107 + 27517382
UGACACUGAAAGCCGCUGUCAGCUGCCAAAUAGCUGCAAACGGU-UUAGCCCCCUGGCUAACACACAAAUACAUACAUAUACAUAAUACGGCACCCGGCACACAAAUC
.....(((...((((.((.((((((.....))))))))...(..-((((((....))))))..)........................))))...))).......... ( -22.50, z-score =  -0.79, R)
>droSec1.super_6 3359105 107 + 4358794
UGACACUGAAAGCCGCUGUCAGCUGCCAAAUAGCUGCAAACGGU-UUAGCCCCCUGGCUAACACACAAAUACCUACAUAUACAUAAUACGGCACCCGGCACACAAAUC
.....(((...((((.((.((((((.....))))))))...(..-((((((....))))))..)........................))))...))).......... ( -22.50, z-score =  -0.80, R)
>droYak2.chr3R_random 962713 100 + 3277457
UGACACUGAAAGCCGCUGUCAACUGCCAAAUAGCUGCAAACGGC-UGAGCCCCC-GGCUAAUAUGC-----UAUACACAUGCAUAUUACGGCACCCA-UACACAAGUC
(((((.((.....)).)))))..((((...((((((....))))-))((((...-))))(((((((-----.........)))))))..))))....-.......... ( -26.30, z-score =  -1.74, R)
>droEre2.scaffold_4770 3533579 80 + 17746568
UGAAACUGAGAGCCGCUGUCAGCUGCCAAAUAGCUGCAAACGGC-UUAGCCCCC-GGCUAAUAUGC-----UAUACACAUGCAAAUC---------------------
.........((((((.((.((((((.....))))))))..))))-))((((...-))))....(((-----.........)))....--------------------- ( -22.00, z-score =  -1.48, R)
>droAna3.scaffold_13340 3051501 85 + 23697760
UGACACUGAAAGCCGCUGUCAGCUUGGAAAUUGCUACAAGCCCUUUCAGGCCCUCGGCUAAUAUAC------AUAUUAUGACGCCG----GAACC-------------
.....(((((((..(((((.(((.........))))).))).)))))))....(((((..(((...------....)))...))))----)....------------- ( -21.10, z-score =  -1.17, R)
>dp4.chr2 26670829 95 + 30794189
UGACACUGAAAGCCGCUGUCAGCUGCCAAAUAGCUACAAACGCUCUUAG-CCCCCGGCUAAUAUAC------AUAUUAUGGCGCCCUCUCGAAUCUCGAAUC------
(((((.((.....)).)))))((.((((...(((.......))).((((-((...)))))).....------......))))))....(((.....)))...------ ( -20.50, z-score =  -1.18, R)
>droPer1.super_6 1988585 89 + 6141320
UGACACUGAAAGCCGCUGUCAGCUGCCAAAUAGCUACAAACGCUCUUAG-CCCCCGGCUAAUAUAC------AUAUUAUGGCGCCCUCUCGAAUCU------------
(((((.((.....)).)))))((.((((...(((.......))).((((-((...)))))).....------......))))))............------------ ( -18.80, z-score =  -0.82, R)
>consensus
UGACACUGAAAGCCGCUGUCAGCUGCCAAAUAGCUACAAACGGU_UUAGCCCCC_GGCUAAUAUAC______AUACAAAUACAUAAUACGGCACCC___ACA______
..........((((..(((.(((((.....))))))))...(((....)))....))))................................................. (-10.12 = -10.28 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,268,096 – 3,268,194
Length 98
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 75.00
Shannon entropy 0.43373
G+C content 0.47134
Mean single sequence MFE -30.46
Consensus MFE -16.84
Energy contribution -19.40
Covariance contribution 2.56
Combinations/Pair 1.38
Mean z-score -1.95
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.895257
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3268096 98 - 27905053
------AAUUAGCAUUUAGCAUGUUGAGCAAA-UGUCAAGCGAUGGGUUUGGGUUUACGCUUGAAAUUUGGAGCUGAGUUCGGUUUGAGCCUGGUUUUGGGCUUG
------..(((((((.....))))))).((((-(.(((((((.((..(....)..))))))))).)))))((((((....))))))((((((......)))))). ( -30.20, z-score =  -2.15, R)
>droSim1.chr3R 3312521 98 - 27517382
------AAUUAGCAUUUAGCAGGUUGAGCGAA-UGUCAAGCGAUGGGUUCGGGUUCACGCUUGAAAUUCGGAACCGAGUUCGGUUUGAGCCUGGUUUUGGGCUUG
------....(((....(.((((((...((((-(.(((((((.((..(....)..))))))))).)))))((((((....)))))).)))))).).....))).. ( -36.80, z-score =  -3.34, R)
>droSec1.super_6 3359212 98 - 4358794
------AAUUAGCAUUUAGCAGGUUGAGCGAA-UGUCAAGCGAUGGGUUCGGGUUCACGCUUGAAAUUCGGAACCGAGUUCGGCUUGAGCCAGGUUUUGGGCUUG
------.............(((((((((((((-(.(((((((.((..(....)..))))))))).))))(....)..))))))))))((((........)))).. ( -33.80, z-score =  -2.13, R)
>droYak2.chr3R_random 962813 98 - 3277457
------AAUUAGCAUUUAGCAGGUUGAGCGAA-UGUCAAGCGAUGGGUUCGAGUUCACGCUUGAAAUUUGAAGCCGAGUUCGGUUUAAGCCUGGUUUUGGGUUUG
------......((...(.((((((...((((-(.(((((((.((..(....)..))))))))).)))))((((((....)))))).)))))).)..))...... ( -31.80, z-score =  -2.57, R)
>droWil1.scaffold_181089 7147233 96 - 12369635
GGCAAUAAUUAGCAUUUAGCAGGUUGAACCAGCUGUCAAGAGGCGGAAUUGAAU---------AACAAAAGGGUGGCUCGUGGCAUGAAGCUAGUGAGGGGGGAA
..(....((((((....(((.((.....)).)))((((.(((.((...(((...---------..))).....)).))).)))).....))))))....)..... ( -19.70, z-score =   0.43, R)
>consensus
______AAUUAGCAUUUAGCAGGUUGAGCGAA_UGUCAAGCGAUGGGUUCGGGUUCACGCUUGAAAUUCGGAGCCGAGUUCGGUUUGAGCCUGGUUUUGGGCUUG
......(((..((.....))..)))...((((...(((((((.((((......)))))))))))..))))((((((....))))))((((((......)))))). (-16.84 = -19.40 +   2.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,268,130 – 3,268,222
Length 92
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 94.93
Shannon entropy 0.08142
G+C content 0.46196
Mean single sequence MFE -22.06
Consensus MFE -20.70
Energy contribution -20.76
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -2.06
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.57
SVM RNA-class probability 0.951384
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3268130 92 + 27905053
CCAAAUUUCAAGCGUAAACCCAAACCCAUCGCUUGACAUUUGCUCAACAUGCUAAAUGCUAAUUACUUGGCGUUGAUGAUGUCGCCGACAUU
.(((((.(((((((...............))))))).))))).(((((((.....))(((((....)))))))))).((((((...)))))) ( -21.36, z-score =  -2.47, R)
>droSim1.chr3R 3312555 92 + 27517382
CCGAAUUUCAAGCGUGAACCCGAACCCAUCGCUUGACAUUCGCUCAACCUGCUAAAUGCUAAUUACUUGGCGUUGAUGAUGUCGCCGACAUU
.(((((.(((((((((..........)).))))))).)))))............((((((((....))))))))...((((((...)))))) ( -24.00, z-score =  -2.77, R)
>droSec1.super_6 3359246 92 + 4358794
CCGAAUUUCAAGCGUGAACCCGAACCCAUCGCUUGACAUUCGCUCAACCUGCUAAAUGCUAAUUACUUGGCGUUGAUGAUGUCGCCGACAUU
.(((((.(((((((((..........)).))))))).)))))............((((((((....))))))))...((((((...)))))) ( -24.00, z-score =  -2.77, R)
>droYak2.chr3R_random 962847 92 + 3277457
UCAAAUUUCAAGCGUGAACUCGAACCCAUCGCUUGACAUUCGCUCAACCUGCUAAAUGCUAAUUACUUGGCGUCGAUGGUGUCGCCGACAUU
.......(((((((((..........)).)))))))((((.((.......))..))))........((((((.((....)).)))))).... ( -18.90, z-score =  -0.25, R)
>consensus
CCAAAUUUCAAGCGUGAACCCGAACCCAUCGCUUGACAUUCGCUCAACCUGCUAAAUGCUAAUUACUUGGCGUUGAUGAUGUCGCCGACAUU
.(((((.(((((((...............))))))).)))))............((((((((....))))))))...((((((...)))))) (-20.70 = -20.76 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,268,130 – 3,268,222
Length 92
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 94.93
Shannon entropy 0.08142
G+C content 0.46196
Mean single sequence MFE -25.68
Consensus MFE -25.42
Energy contribution -24.80
Covariance contribution -0.62
Combinations/Pair 1.12
Mean z-score -1.24
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.86
SVM RNA-class probability 0.838444
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3268130 92 - 27905053
AAUGUCGGCGACAUCAUCAACGCCAAGUAAUUAGCAUUUAGCAUGUUGAGCAAAUGUCAAGCGAUGGGUUUGGGUUUACGCUUGAAAUUUGG
......((((..........))))......(((((((.....))))))).(((((.(((((((.((..(....)..))))))))).))))). ( -23.00, z-score =  -0.72, R)
>droSim1.chr3R 3312555 92 - 27517382
AAUGUCGGCGACAUCAUCAACGCCAAGUAAUUAGCAUUUAGCAGGUUGAGCGAAUGUCAAGCGAUGGGUUCGGGUUCACGCUUGAAAUUCGG
......((((..........))))...((((..((.....))..))))..(((((.(((((((.((..(....)..))))))))).))))). ( -27.10, z-score =  -1.74, R)
>droSec1.super_6 3359246 92 - 4358794
AAUGUCGGCGACAUCAUCAACGCCAAGUAAUUAGCAUUUAGCAGGUUGAGCGAAUGUCAAGCGAUGGGUUCGGGUUCACGCUUGAAAUUCGG
......((((..........))))...((((..((.....))..))))..(((((.(((((((.((..(....)..))))))))).))))). ( -27.10, z-score =  -1.74, R)
>droYak2.chr3R_random 962847 92 - 3277457
AAUGUCGGCGACACCAUCGACGCCAAGUAAUUAGCAUUUAGCAGGUUGAGCGAAUGUCAAGCGAUGGGUUCGAGUUCACGCUUGAAAUUUGA
......((((.(......).))))...((((..((.....))..))))..(((((.(((((((.((..(....)..))))))))).))))). ( -25.50, z-score =  -0.74, R)
>consensus
AAUGUCGGCGACAUCAUCAACGCCAAGUAAUUAGCAUUUAGCAGGUUGAGCGAAUGUCAAGCGAUGGGUUCGGGUUCACGCUUGAAAUUCGG
......((((..........))))...((((..((.....))..))))..(((((.(((((((.((..(....)..))))))))).))))). (-25.42 = -24.80 +  -0.62)

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 23:56:13 2011