Locus 5975

Sequence ID dm3.chr3L
Location 2,870,710 – 2,870,875
Length 165
Max. P 0.994040
window8218 window8219 window8220 window8221

overview

Window 8

Location 2,870,710 – 2,870,808
Length 98
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 82.05
Shannon entropy 0.24030
G+C content 0.60017
Mean single sequence MFE -42.70
Consensus MFE -32.61
Energy contribution -32.73
Covariance contribution 0.12
Combinations/Pair 1.17
Mean z-score -1.77
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.714520
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2870710 98 + 24543557
UUUGCAGGGAACUCAUGGCGGUGGG---------UCCCACGGGUCCUGCUACUGAAUUGGGUCCUACGGAGCCAGGAGGUAUGGAACCUGUUGCAGCUGCUACUGCA
.(((((((((.(((((....)))))---------))))((((((((...((((...((((.(((...))).))))..)))).)).)))))))))))..((....)). ( -38.30, z-score =  -0.72, R)
>droYak2.chr3L 15137306 107 - 24197627
UUUGCAGCGAGCUCAUGGCAGUGGGACCCACAGAUCCCACGGAUCCCGUUACUGAGUUUGGUCCCACGGAGCCAGGAGGUAGGACACCUGCAGCAGCUGCGACCGCU
.(((((((...(((.((((.((((((((.((.(((((...))))).((....)).))..))))))))...)))).)))(((((...)))))....)))))))..... ( -45.50, z-score =  -2.40, R)
>droSec1.super_2 2890877 98 + 7591821
UUUGCAGGGAGCUCAUGGCGGUGGG---------UCCCACGGGUCCCACUACUGAAUUGGGACCUACGGAGCCAGGAGGUAUGGAACCUGCAGCAGCUGCUACUGCU
..((((((.(.(((.((((.(((((---------((((((((.........)))...))))))))))...)))).))).)......))))))((((......)))). ( -44.30, z-score =  -2.19, R)
>consensus
UUUGCAGGGAGCUCAUGGCGGUGGG_________UCCCACGGGUCCCGCUACUGAAUUGGGUCCUACGGAGCCAGGAGGUAUGGAACCUGCAGCAGCUGCUACUGCU
...(((((.(.(((.((((.(((((..........)))))(((.((((.........)))).))).....)))).))).)......)))))(((((......))))) (-32.61 = -32.73 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 2,870,741 – 2,870,845
Length 104
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 64.11
Shannon entropy 0.58686
G+C content 0.62946
Mean single sequence MFE -44.80
Consensus MFE -24.25
Energy contribution -25.38
Covariance contribution 1.12
Combinations/Pair 1.39
Mean z-score -1.60
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.85
SVM RNA-class probability 0.971540
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2870741 104 + 24543557
GGGUCCUGCUACUGAAUUGGGUCCUACGGAGCCAGGAGGUAUGGAACCUGUUGCAGCUGCUA-CUGCAGCUGCCGAUCCUGGUGGCACUCCUGCUCCUAUGGGCA
((..((............))..))...(((((.(((((((.....(((.(((((((((((..-..))))))).))))...))).)).))))))))))........ ( -45.00, z-score =  -1.48, R)
>anoGam1.chr2L 5454804 91 - 48795086
------------GGCAGCGGUGGCAGCGGAGUCGGUGUCAGCUGCGUUAGCUGUGUCAGCGAGCCGCCCGUACCGGGUGAGGCGGAGCUC--GGUGAGAUCGGUA
------------.(((((..(((((.((....)).))))))))))....(((((.(((.(((((((((((...)))))).......))))--).))).).)))). ( -40.31, z-score =  -0.86, R)
>droYak2.chr3L 15137346 104 - 24197627
GGAUCCCGUUACUGAGUUUGGUCCCACGGAGCCAGGAGGUAGGACACCUGCAGCAGCUGCGA-CCGCUGCUGCCGAUCCAGGUGGCACUCCUGCUCCUAUGGGCA
....................((((...(((((.(((((....(.(((((((((((((.....-..))))))))......))))).).))))))))))...)))). ( -43.80, z-score =  -0.79, R)
>droSec1.super_2 2890908 104 + 7591821
GGGUCCCACUACUGAAUUGGGACCUACGGAGCCAGGAGGUAUGGAACCUGCAGCAGCUGCUA-CUGCUGCUGCCGAUCCUGGUGGCACUCCUGCUCCUAUGGGCA
((((((((.........))))))))..(((((.(((((((..(((.(..((((((((.....-..)))))))).).))).....)).))))))))))........ ( -50.10, z-score =  -3.29, R)
>consensus
GGGUCCCGCUACUGAAUUGGGUCCUACGGAGCCAGGAGGUAUGGAACCUGCAGCAGCUGCGA_CCGCUGCUGCCGAUCCAGGUGGCACUCCUGCUCCUAUGGGCA
....................((((...(((((.(((((...((.((((..(.(((((.((.....)).))))).).....)))).))))))))))))...)))). (-24.25 = -25.38 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 2,870,741 – 2,870,845
Length 104
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 64.11
Shannon entropy 0.58686
G+C content 0.62946
Mean single sequence MFE -41.05
Consensus MFE -22.11
Energy contribution -26.30
Covariance contribution 4.19
Combinations/Pair 1.23
Mean z-score -2.06
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.66
SVM RNA-class probability 0.994040
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2870741 104 - 24543557
UGCCCAUAGGAGCAGGAGUGCCACCAGGAUCGGCAGCUGCAG-UAGCAGCUGCAACAGGUUCCAUACCUCCUGGCUCCGUAGGACCCAAUUCAGUAGCAGGACCC
(((((...(((((.((....))..(((((...((((((((..-..))))))))....(((.....)))))))))))))...))((........)).)))...... ( -38.80, z-score =  -1.50, R)
>anoGam1.chr2L 5454804 91 + 48795086
UACCGAUCUCACC--GAGCUCCGCCUCACCCGGUACGGGCGGCUCGCUGACACAGCUAACGCAGCUGACACCGACUCCGCUGCCACCGCUGCC------------
........(((.(--((((..(((((..........)))))))))).)))..((((....(((((.((.......)).)))))....))))..------------ ( -29.30, z-score =  -1.31, R)
>droYak2.chr3L 15137346 104 + 24197627
UGCCCAUAGGAGCAGGAGUGCCACCUGGAUCGGCAGCAGCGG-UCGCAGCUGCUGCAGGUGUCCUACCUCCUGGCUCCGUGGGACCAAACUCAGUAACGGGAUCC
..(((((.((((((((((.(.((((((...(((((((.((..-..)).))))))))))))).)....))))).))))))))))......(((......))).... ( -47.80, z-score =  -1.89, R)
>droSec1.super_2 2890908 104 - 7591821
UGCCCAUAGGAGCAGGAGUGCCACCAGGAUCGGCAGCAGCAG-UAGCAGCUGCUGCAGGUUCCAUACCUCCUGGCUCCGUAGGUCCCAAUUCAGUAGUGGGACCC
........((((((((((.(......(((((.((((((((..-.....)))))))).)))))....)))))).)))))...(((((((.........))))))). ( -48.30, z-score =  -3.54, R)
>consensus
UGCCCAUAGGAGCAGGAGUGCCACCAGGAUCGGCAGCAGCAG_UAGCAGCUGCAGCAGGUGCCAUACCUCCUGGCUCCGUAGGACCCAAUUCAGUAGCGGGACCC
..(((((.((((((((((((.((((.....((((((((((.....))))))))))..)))).)))...))))).)))))))))...................... (-22.11 = -26.30 +   4.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 2,870,778 – 2,870,875
Length 97
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 93.13
Shannon entropy 0.09467
G+C content 0.58076
Mean single sequence MFE -37.97
Consensus MFE -33.65
Energy contribution -33.77
Covariance contribution 0.12
Combinations/Pair 1.11
Mean z-score -1.90
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.849980
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2870778 97 - 24543557
AAUUACUACCGGAUGGAACACCAAUGCCUGUGCCCAUAGGAGCAGGAGUGCCACCAGGAUCGGCAGCUGCAGUAGCAGCUGCAACAGGUUCCAUACC
..........(((((((((..((...(((((.((....)).)))))..))((....))....((((((((....)))))))).....))))))).)) ( -37.20, z-score =  -2.45, R)
>droYak2.chr3L 15137383 97 + 24197627
AAUUACUACCGGAUGGAACACCCAUGCCUGUGCCCAUAGGAGCAGGAGUGCCACCUGGAUCGGCAGCAGCGGUCGCAGCUGCUGCAGGUGUCCUACC
..........((..(((.(((((((.(((((.((....)).))))).)))((....))....((((((((.......)))))))).)))))))..)) ( -38.00, z-score =  -0.91, R)
>droSec1.super_2 2890945 97 - 7591821
AAUUACUACCGGAUGGAACACCCAUGCCUGUGCCCAUAGGAGCAGGAGUGCCACCAGGAUCGGCAGCAGCAGUAGCAGCUGCUGCAGGUUCCAUACC
..........(((((((((.......(((((.((....)).)))))..((((.........))))((((((((....))))))))..))))))).)) ( -38.70, z-score =  -2.33, R)
>consensus
AAUUACUACCGGAUGGAACACCCAUGCCUGUGCCCAUAGGAGCAGGAGUGCCACCAGGAUCGGCAGCAGCAGUAGCAGCUGCUGCAGGUUCCAUACC
..........(((((((((.......(((((.((....)).)))))..((((.........))))((((((((....))))))))..))))))).)) (-33.65 = -33.77 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:58:51 2011