Locus 10370

Sequence ID dm3.chr3R
Location 13,429,541 – 13,429,660
Length 119
Max. P 0.924935
window14260 window14261 window14262

overview

Window 0

Location 13,429,541 – 13,429,636
Length 95
Sequences 9
Columns 114
Reading direction forward
Mean pairwise identity 55.77
Shannon entropy 0.87720
G+C content 0.51477
Mean single sequence MFE -22.68
Consensus MFE -8.29
Energy contribution -9.01
Covariance contribution 0.72
Combinations/Pair 1.12
Mean z-score -1.11
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.21
SVM RNA-class probability 0.909718
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13429541 95 + 27905053
-------------GCAGCUACCAACACCACCCCUU--ACAUACAAGCAUGUUUACGCUCAUGUGUGUGCGUUCGGCUCACGCACACUGAUUCCAUUAGACGCACACAUGG----
-------------.......(((............--........(((((........)))))((((((((...((....))...(((((...))))))))))))).)))---- ( -21.60, z-score =  -0.75, R)
>droEre2.scaffold_4770 9544498 108 - 17746568
GCAGCCACCCUUGUGAGGCAGAAACUCCACCCCUU--GCAUACAGGCGUGUUUAGCCGCAUGUGUGUGCGUUCGGCGCACGCACACUGAUUCCAUUAGACGCACACAUGG----
........((.((((.(((.(((....(((.(((.--......))).)))))).)))((.((((((((((.....))))))))))(((((...)))))..)).)))).))---- ( -35.90, z-score =  -0.92, R)
>droYak2.chr3R 1984196 102 + 28832112
GCAGUCACUCUUGUGAGGCAGGGA----ACACCUU--ACAUACAGGCAUGUUUACCCGCAUGGGUGUGCGUUC--CGCACUAUAACUGAUUCCAUUAGCCGCACACAUGG----
((..((((....))))((((((..----...))).--.....(((..(((...((((....))))(((((...--))))))))..))).........)))))........---- ( -27.80, z-score =  -0.07, R)
>droSec1.super_12 1391806 95 - 2123299
-------------GCAGCCACCAACACCACCCCUU--ACAUACAAGCAUGUUUACGCUCAUGUGUGUGCGUUUGGCUCACGCACACUGAUUCCAUUAGACGCACACAUGG----
-------------.......(((............--........(((((........)))))((((((((((((.(((.......)))..)))...))))))))).)))---- ( -22.70, z-score =  -0.92, R)
>droSim1.chr3R 19469109 97 - 27517382
-------------GCAGCCACCAACACCACCCCUUUUACAUACAAGCAUGUUUACGCUCAUGUGUGUGCGUUCUGCUCACGCACACUGAUUCCAUUAGACGCGCACAUGG----
-------------.......(((......................(((((........)))))((((((((..(((....)))..(((((...))))))))))))).)))---- ( -21.70, z-score =  -0.83, R)
>droAna3.scaffold_13340 5964897 85 - 23697760
--------------------CACACAAAAA----GACAUAUAGAAACAUCCCU-CUUGCAUACGGGUUCGCUU-GCACACGCACACUAAUUCCAUUAGCC-CACACACAUGU--
--------------------..........----.((((..(((........)-)).......(((......(-((....)))..(((((...)))))))-)......))))-- (  -6.90, z-score =   1.18, R)
>dp4.chr2 27095366 94 - 30794189
-------------------UCACGCGACACCCCCAUCUCGCACACACACACAUGCCCGCACAUGUGUGCGUAC-GCACACGCACACUAAUUCCAUUAGCCACGCGCACACAUGG
-------------------....((((..........))))...................(((((((((((..-((....))...(((((...)))))....))))))))))). ( -25.20, z-score =  -2.79, R)
>droPer1.super_7 651305 94 + 4445127
-------------------UCACGCGACACCCCCUUCUCGCACACACACACAUGCUCGCACAUGUGUGCGUAC-GCACACGCACACUAAUUCCAUUAGCCACGCGCACACAUGG
-------------------....((((..........))))...................(((((((((((..-((....))...(((((...)))))....))))))))))). ( -25.20, z-score =  -2.92, R)
>droWil1.scaffold_181130 12456852 83 + 16660200
-------AUAACCACCCCCAAAAAUGUCAAAUUCUCUGCAUAUGUGAAAAAGUGUAUGUGUGUGUGUGUGUCU--UAUUCACACACAGAUCG----------------------
-------..............................(((((..(......)..)))))((.((((((((...--....)))))))).))..---------------------- ( -17.10, z-score =  -1.92, R)
>consensus
______________CAGCCACAAACACCACCCCUU__ACAUACAAGCAUGUUUACCCGCAUGUGUGUGCGUUC_GCACACGCACACUGAUUCCAUUAGACGCACACAUGG____
...............................................................((((((((.......))))))))............................ ( -8.29 =  -9.01 +   0.72)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,429,566 – 13,429,660
Length 94
Sequences 9
Columns 98
Reading direction forward
Mean pairwise identity 64.46
Shannon entropy 0.74418
G+C content 0.52645
Mean single sequence MFE -31.22
Consensus MFE -10.62
Energy contribution -11.83
Covariance contribution 1.21
Combinations/Pair 1.23
Mean z-score -1.36
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.763935
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13429566 94 + 27905053
UACAAGCAUGUUUACGCUCAUGUGUGUGCGUUCGGCUCACGCACACUGAUUCCAUUAGAC----GCACACAUGGGCAGCUGUGCGUGGAACAUUCCAA
.....(((((((...(((((((((((((.((.((.....)).)).(((((...))))).)----))))))))))))))).)))).((((....)))). ( -33.10, z-score =  -1.66, R)
>droEre2.scaffold_4770 9544536 94 - 17746568
UACAGGCGUGUUUAGCCGCAUGUGUGUGCGUUCGGCGCACGCACACUGAUUCCAUUAGAC----GCACACAUGGGCAGCUGUGCGUUGCACAGUCCAA
....(((.......)))((.((((((((((.....))))))))))(((((...)))))..----)).....(((...(((((((...)))))))))). ( -36.90, z-score =  -0.83, R)
>droYak2.chr3R 1984230 92 + 28832112
UACAGGCAUGUUUACCCGCAUGGGUGUGCGUUC--CGCACUAUAACUGAUUCCAUUAGCC----GCACACAUGGGCGGCUGUGCGUUGAACAGUCCAA
....(((..((.(((((....))))).))((((--(((((......((....))..((((----((........)))))))))))..)))).)))... ( -30.50, z-score =  -0.57, R)
>droSec1.super_12 1391831 94 - 2123299
UACAAGCAUGUUUACGCUCAUGUGUGUGCGUUUGGCUCACGCACACUGAUUCCAUUAGAC----GCACACAUGGGCAGCUGUGCGUGGAACAUUCCAA
.....(((((((...((((((((((((((...(((.(((.......)))..)))...).)----))))))))))))))).)))).((((....)))). ( -33.50, z-score =  -1.75, R)
>droSim1.chr3R 19469136 94 - 27517382
UACAAGCAUGUUUACGCUCAUGUGUGUGCGUUCUGCUCACGCACACUGAUUCCAUUAGAC----GCGCACAUGGGCAGCUGUGCGUGGAACAUUACAA
..((.(((((((...((((((((((((((((.......)))))).(((((...)))))..----..))))))))))))).)))).))........... ( -30.80, z-score =  -0.68, R)
>droAna3.scaffold_13340 5964913 88 - 23697760
UAGAAACAUCCCUCU-UGCAUACGGGUUCGCUU-GCACACGCACACUAAUUCCAUUAGCC---CACACACAUGUGAAUCUG-GUGCGUCCGGGC----
.........(((...-(((((.(((((((((.(-((....)))..(((((...)))))..---.........)))))))))-)))))...))).---- ( -23.00, z-score =  -1.07, R)
>dp4.chr2 27095391 88 - 30794189
CACACACAUGCCC----GCACAUGUGUGCGUAC-GCACACGCACACUAAUUCCAUUAGCCACGCGCACACAUGGGCGACUGUGCGUGUCGGAA-----
.((((.((((..(----((.(((((((((((..-((....))...(((((...)))))....))))))))))).)))..)))).)))).....----- ( -33.40, z-score =  -1.46, R)
>droPer1.super_7 651330 88 + 4445127
CACACACAUGCUC----GCACAUGUGUGCGUAC-GCACACGCACACUAAUUCCAUUAGCCACGCGCACACAUGGGCGACUGUGCGUGUCGGAA-----
(((.((((.(.((----((.(((((((((((..-((....))...(((((...)))))....))))))))))).))))))))).)))......----- ( -35.70, z-score =  -2.38, R)
>droWil1.scaffold_181130 12456881 76 + 16660200
UGCAUAUGUGAAAAAGUGUAUGUGUGUGUGUGUGUCUUAUUCACACACAGAUCGGGGUGUGCGUGUGCGUGUGGAA----------------------
..((((((((.....(..(((.(((.((((((((.......)))))))).))..).)))..)...))))))))...---------------------- ( -24.10, z-score =  -1.81, R)
>consensus
UACAAGCAUGUUUACGCGCAUGUGUGUGCGUUC_GCUCACGCACACUGAUUCCAUUAGAC____GCACACAUGGGCAGCUGUGCGUGGAACAGU_CAA
.......................((((((((.......))))))))..................(((((..........))))).............. (-10.62 = -11.83 +   1.21)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,429,566 – 13,429,660
Length 94
Sequences 9
Columns 98
Reading direction reverse
Mean pairwise identity 64.46
Shannon entropy 0.74418
G+C content 0.52645
Mean single sequence MFE -31.85
Consensus MFE -13.77
Energy contribution -15.17
Covariance contribution 1.40
Combinations/Pair 1.21
Mean z-score -1.18
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.31
SVM RNA-class probability 0.924935
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13429566 94 - 27905053
UUGGAAUGUUCCACGCACAGCUGCCCAUGUGUGC----GUCUAAUGGAAUCAGUGUGCGUGAGCCGAACGCACACACAUGAGCGUAAACAUGCUUGUA
.......((((((((((((.(.......))))))----)).....)))))..((((((((.......))))))))..(..(((((....)))))..). ( -32.20, z-score =  -1.02, R)
>droEre2.scaffold_4770 9544536 94 + 17746568
UUGGACUGUGCAACGCACAGCUGCCCAUGUGUGC----GUCUAAUGGAAUCAGUGUGCGUGCGCCGAACGCACACACAUGCGGCUAAACACGCCUGUA
..((.((((((...))))))))((((((((((((----(.(...((....))..))))(((((.....)))))))))))).))).............. ( -32.70, z-score =   0.25, R)
>droYak2.chr3R 1984230 92 - 28832112
UUGGACUGUUCAACGCACAGCCGCCCAUGUGUGC----GGCUAAUGGAAUCAGUUAUAGUGCG--GAACGCACACCCAUGCGGGUAAACAUGCCUGUA
.((((((((((.......((((((.(....).))----))))....))).))))....(((((--...)))))..)))((((((((....)))))))) ( -31.80, z-score =  -0.82, R)
>droSec1.super_12 1391831 94 + 2123299
UUGGAAUGUUCCACGCACAGCUGCCCAUGUGUGC----GUCUAAUGGAAUCAGUGUGCGUGAGCCAAACGCACACACAUGAGCGUAAACAUGCUUGUA
.......((((((((((((.(.......))))))----)).....)))))..((((((((.......))))))))..(..(((((....)))))..). ( -32.20, z-score =  -1.15, R)
>droSim1.chr3R 19469136 94 + 27517382
UUGUAAUGUUCCACGCACAGCUGCCCAUGUGCGC----GUCUAAUGGAAUCAGUGUGCGUGAGCAGAACGCACACACAUGAGCGUAAACAUGCUUGUA
.......((((((((((((........)))))).----......))))))..((((((((.......))))))))..(..(((((....)))))..). ( -32.51, z-score =  -1.05, R)
>droAna3.scaffold_13340 5964913 88 + 23697760
----GCCCGGACGCAC-CAGAUUCACAUGUGUGUG---GGCUAAUGGAAUUAGUGUGCGUGUGC-AAGCGAACCCGUAUGCA-AGAGGGAUGUUUCUA
----.(((..((((((-(.(((((.(((..((...---.))..)))))))).).)))))).(((-(.(((....))).))))-...)))......... ( -27.40, z-score =  -0.42, R)
>dp4.chr2 27095391 88 + 30794189
-----UUCCGACACGCACAGUCGCCCAUGUGUGCGCGUGGCUAAUGGAAUUAGUGUGCGUGUGC-GUACGCACACAUGUGC----GGGCAUGUGUGUG
-----......(((((((((((((.(((((((((.....((((((...))))))(((((....)-))))))))))))).))----.))).)))))))) ( -42.30, z-score =  -1.89, R)
>droPer1.super_7 651330 88 - 4445127
-----UUCCGACACGCACAGUCGCCCAUGUGUGCGCGUGGCUAAUGGAAUUAGUGUGCGUGUGC-GUACGCACACAUGUGC----GAGCAUGUGUGUG
-----......((((((((.((((.(((((((((.....((((((...))))))(((((....)-))))))))))))).))----))...)))))))) ( -43.20, z-score =  -2.64, R)
>droWil1.scaffold_181130 12456881 76 - 16660200
----------------------UUCCACACGCACACGCACACCCCGAUCUGUGUGUGAAUAAGACACACACACACACAUACACUUUUUCACAUAUGCA
----------------------........(((..((.......))...((((((((.......))))))))......................))). ( -12.30, z-score =  -1.84, R)
>consensus
UUG_AAUGUGCCACGCACAGCUGCCCAUGUGUGC____GGCUAAUGGAAUCAGUGUGCGUGAGC_GAACGCACACACAUGCGCGUAAACAUGCUUGUA
.............((((((........))))))...................((((((((.......))))))))....................... (-13.77 = -15.17 +   1.40)

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 00:22:41 2011