Locus 8720

Sequence ID dm3.chr3R
Location 1,019,481 – 1,019,606
Length 125
Max. P 0.994972
window11968 window11969 window11970 window11971

overview

Window 8

Location 1,019,481 – 1,019,575
Length 94
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 69.33
Shannon entropy 0.52931
G+C content 0.50218
Mean single sequence MFE -34.70
Consensus MFE -16.70
Energy contribution -18.28
Covariance contribution 1.58
Combinations/Pair 1.18
Mean z-score -2.08
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.74
SVM RNA-class probability 0.964722
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1019481 94 + 27905053
AGUGUUUGAGCUUG-GCGCUAGUGUUGGUGCUGGUGUGUCUGAGUGCGUUUGCUCUUUGGUCCUUU-GCAUGACACACCAGCACCAU----UACCACCAC------------
((((((.......)-))))).(((.(((((((((((((((...(((((...(((....)))....)-))))))))))))))))))).----)))......------------ ( -40.60, z-score =  -3.52, R)
>droSec1.super_6 1142485 94 + 4358794
AGUGUUUGAGCUUG-GCGCUAGUGUUGGUGCUGGUGUGUCUAAGUGCGUUUGCUCUUUGGUCCUUU-GCAUGACACACCAGCACCAU----UGCCAGCAC------------
.........(((.(-((((....))(((((((((((((((...(((((...(((....)))....)-))))))))))))))))))).----.))))))..------------ ( -42.60, z-score =  -3.68, R)
>droYak2.chr3R 1379632 93 + 28832112
AGUGUUUGAGCUCG-GCGCUGGUAUUAGUGCUGGUGUGUCUAACUGCGUUUGCUCUUUGGUCCUU--GCAUGACACACCAGCACCAU----UACCAUUAC------------
((((((.......)-)))))((((...(((((((((((((....((((...(((....)))...)--))).)))))))))))))...----)))).....------------ ( -38.20, z-score =  -4.03, R)
>droEre2.scaffold_4770 1294812 109 + 17746568
AGUGUUUGAGCUCG-GCACUGGUGUUGGUGCUGGUGUGUCUAAGUGCGUUUGCUCUUUGGUCCUU--GCAUGACACACCAGCACAUCAGCACACCAGCACCAUUACCAACAC
.(((((.......(-(..(((((((..(((((((((((((...(((((...(((....)))...)--)))))))))))))))))......)))))))..))......))))) ( -45.32, z-score =  -2.74, R)
>droAna3.scaffold_13340 23214166 85 + 23697760
GGUGUUUGCUGAAGGGUGAUGGUGUUGGUG----UGUGCUCAAGUGCGUUUGCUUUUGGUCCUUUUUGCCUGACACACUGCCAU-AU----UAC------------------
.(((((.((.((((((.(((.(....((((----..(((......)))..))))..).)))))))))))..)))))........-..----...------------------ ( -19.10, z-score =   1.04, R)
>dp4.chr2 9022104 85 - 30794189
------UGUGUGUGUGUGCUGGUAUUGGUG----UGUGCUUAAGUGCGUUUGCUUUUGG-CCCUUUUGCAUGACACACAACUUUUGC----UGCCAGAGA------------
------..(((((((((((.(((...((((----..(((......)))..))))....)-)).....)))).)))))))..(((((.----...))))).------------ ( -22.40, z-score =   0.45, R)
>consensus
AGUGUUUGAGCUUG_GCGCUGGUGUUGGUGCUGGUGUGUCUAAGUGCGUUUGCUCUUUGGUCCUUU_GCAUGACACACCAGCACCAU____UACCAGCAC____________
...........................(((((((((((((...((((....................)))))))))))))))))............................ (-16.70 = -18.28 +   1.58)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,019,481 – 1,019,575
Length 94
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 69.33
Shannon entropy 0.52931
G+C content 0.50218
Mean single sequence MFE -32.83
Consensus MFE -15.28
Energy contribution -17.33
Covariance contribution 2.06
Combinations/Pair 1.12
Mean z-score -2.71
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.75
SVM RNA-class probability 0.994972
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1019481 94 - 27905053
------------GUGGUGGUA----AUGGUGCUGGUGUGUCAUGC-AAAGGACCAAAGAGCAAACGCACUCAGACACACCAGCACCAACACUAGCGC-CAAGCUCAAACACU
------------(((.((((.----.(((((((((((((((.((.-.......))..(((........))).)))))))))))))))..)))).)))-.............. ( -39.00, z-score =  -4.04, R)
>droSec1.super_6 1142485 94 - 4358794
------------GUGCUGGCA----AUGGUGCUGGUGUGUCAUGC-AAAGGACCAAAGAGCAAACGCACUUAGACACACCAGCACCAACACUAGCGC-CAAGCUCAAACACU
------------(((((((..----.(((((((((((((((.((.-.......))(((.((....)).))).)))))))))))))))...)))))))-.............. ( -41.90, z-score =  -5.05, R)
>droYak2.chr3R 1379632 93 - 28832112
------------GUAAUGGUA----AUGGUGCUGGUGUGUCAUGC--AAGGACCAAAGAGCAAACGCAGUUAGACACACCAGCACUAAUACCAGCGC-CGAGCUCAAACACU
------------....(((((----.(((((((((((((((.(((--..................)))....))))))))))))))).)))))((..-...))......... ( -37.67, z-score =  -4.66, R)
>droEre2.scaffold_4770 1294812 109 - 17746568
GUGUUGGUAAUGGUGCUGGUGUGCUGAUGUGCUGGUGUGUCAUGC--AAGGACCAAAGAGCAAACGCACUUAGACACACCAGCACCAACACCAGUGC-CGAGCUCAAACACU
((((((((..(((..(((((((......(((((((((((((.((.--......))(((.((....)).))).)))))))))))))..)))))))..)-)).)))..))))). ( -50.80, z-score =  -4.17, R)
>droAna3.scaffold_13340 23214166 85 - 23697760
------------------GUA----AU-AUGGCAGUGUGUCAGGCAAAAAGGACCAAAAGCAAACGCACUUGAGCACA----CACCAACACCAUCACCCUUCAGCAAACACC
------------------...----..-.(((..(((((((((((......).))....((....))...))).))))----).)))......................... ( -13.30, z-score =   0.50, R)
>dp4.chr2 9022104 85 + 30794189
------------UCUCUGGCA----GCAAAAGUUGUGUGUCAUGCAAAAGGG-CCAAAAGCAAACGCACUUAAGCACA----CACCAAUACCAGCACACACACACA------
------------.........----......((.((((((..(((......(-(.....))....((......))...----...........))).)))))))).------ ( -14.30, z-score =   1.13, R)
>consensus
____________GUGCUGGUA____AUGGUGCUGGUGUGUCAUGC_AAAGGACCAAAGAGCAAACGCACUUAGACACACCAGCACCAACACCAGCGC_CAAGCUCAAACACU
............................(((((((((((((.((.........))....((....)).....)))))))))))))........................... (-15.28 = -17.33 +   2.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,019,504 – 1,019,606
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 62.99
Shannon entropy 0.58747
G+C content 0.51692
Mean single sequence MFE -35.88
Consensus MFE -15.38
Energy contribution -17.18
Covariance contribution 1.80
Combinations/Pair 1.20
Mean z-score -1.92
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.51
SVM RNA-class probability 0.945691
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1019504 102 + 27905053
UUGGUGCUGGUGUGUCUGAGUGCGUUUGCUCUUUGGUCCUUU--GCAUGACACACCAGCAC----------------CAUUACCACCACGCCACCAGCGGCAGUGGCAGUGGCAGUAGCA
.(((((((((((((((...(((((...(((....)))....)--)))))))))))))))))----------------))((((..(((((((((........))))).))))..)))).. ( -50.30, z-score =  -3.63, R)
>droYak2.chr3R 1379655 89 + 28832112
UUAGUGCUGGUGUGUCUAACUGCGUUUGCUCUUUGGUCCUU---GCAUGACACACCAGCAC----------------CAUUACCAUUACGCCCCCAGUGGCAUUGGCA------------
...(((((((((((((....((((...(((....)))...)---))).)))))))))))))----------------.....(((....(((......)))..)))..------------ ( -34.70, z-score =  -3.33, R)
>droEre2.scaffold_4770 1294835 105 + 17746568
UUGGUGCUGGUGUGUCUAAGUGCGUUUGCUCUUUGGUCCUU---GCAUGACACACCAGCACAUCAGCACACCAGCACCAUUACCAACACGCCACCAGUGGCAGUGCCA------------
.((((((((((((((....((((...(((............---)))((......))))))....)))))))))))))).......(((((((....)))).)))...------------ ( -42.40, z-score =  -2.63, R)
>droAna3.scaffold_13340 23214190 92 + 23697760
UUGGUG----UGUGCUCAAGUGCGUUUGCU-UUUGGUCCUUUUUGCCUGACACACUGCCAU-----------------AUUACAGUAGCAGUGGCAGUGGCAGUUUCAGGAUAU------
..((((----..(((......)))..))))-....(((((..(((((.....((((((.((-----------------......)).)))))).....)))))....)))))..------ ( -26.50, z-score =   0.06, R)
>dp4.chr2 9022122 90 - 30794189
UUGGUG----UGUGCUUAAGUGCGUUUGCU-UUUGGCCCUUUU-GCAUGACACACAACUUU----------------UGCUGCCAGAGAGCGAGAGAGAGAGAGGACACUCA--------
((((((----(((((..(((.((.......-....)).)))..-)))).)))).)))((((----------------((((.......)))))))).....(((....))).-------- ( -25.50, z-score =  -0.08, R)
>consensus
UUGGUGCUGGUGUGUCUAAGUGCGUUUGCUCUUUGGUCCUUU__GCAUGACACACCAGCAC________________CAUUACCAUAACGCCACCAGUGGCAGUGGCA____________
...(((((((((((((...((((....(((....))).......)))))))))))))))))........................................................... (-15.38 = -17.18 +   1.80)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,019,504 – 1,019,606
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 62.99
Shannon entropy 0.58747
G+C content 0.51692
Mean single sequence MFE -36.68
Consensus MFE -13.48
Energy contribution -17.16
Covariance contribution 3.68
Combinations/Pair 1.20
Mean z-score -2.34
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.68
SVM RNA-class probability 0.960767
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1019504 102 - 27905053
UGCUACUGCCACUGCCACUGCCGCUGGUGGCGUGGUGGUAAUG----------------GUGCUGGUGUGUCAUGC--AAAGGACCAAAGAGCAAACGCACUCAGACACACCAGCACCAA
...(((..((((.((((((......))))))))))..))).((----------------(((((((((((((.((.--.......))..(((........))).))))))))))))))). ( -54.30, z-score =  -4.89, R)
>droYak2.chr3R 1379655 89 - 28832112
------------UGCCAAUGCCACUGGGGGCGUAAUGGUAAUG----------------GUGCUGGUGUGUCAUGC---AAGGACCAAAGAGCAAACGCAGUUAGACACACCAGCACUAA
------------((((((((((......)))))..))))).((----------------(((((((((((((.(((---..................)))....))))))))))))))). ( -39.97, z-score =  -4.03, R)
>droEre2.scaffold_4770 1294835 105 - 17746568
------------UGGCACUGCCACUGGUGGCGUGUUGGUAAUGGUGCUGGUGUGCUGAUGUGCUGGUGUGUCAUGC---AAGGACCAAAGAGCAAACGCACUUAGACACACCAGCACCAA
------------.(((((.((((....))))))))).....(((((((((((((((((.((((...((((((....---...)))......)))...)))))))).))))))))))))). ( -49.00, z-score =  -2.93, R)
>droAna3.scaffold_13340 23214190 92 - 23697760
------AUAUCCUGAAACUGCCACUGCCACUGCUACUGUAAU-----------------AUGGCAGUGUGUCAGGCAAAAAGGACCAAA-AGCAAACGCACUUGAGCACA----CACCAA
------...((((....((((((((((((.(((....)))..-----------------.)))))))).).)))......)))).(((.-.((....))..)))......----...... ( -24.30, z-score =  -1.23, R)
>dp4.chr2 9022122 90 + 30794189
--------UGAGUGUCCUCUCUCUCUCUCGCUCUCUGGCAGCA----------------AAAGUUGUGUGUCAUGC-AAAAGGGCCAAA-AGCAAACGCACUUAAGCACA----CACCAA
--------.(((((..............)))))....(((((.----------------...)))))((((..(((-..(((.((....-.......)).)))..))).)----)))... ( -15.84, z-score =   1.39, R)
>consensus
____________UGCCACUGCCACUGGUGGCGUGAUGGUAAUG________________GUGCUGGUGUGUCAUGC__AAAGGACCAAAGAGCAAACGCACUUAGACACACCAGCACCAA
............(((((.((((......))))...)))))...................(((((((((((((...(......)........((....)).....)))))))))))))... (-13.48 = -17.16 +   3.68)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:50:52 2011