Locus 6984

Sequence ID dm3.chr3L
Location 11,293,132 – 11,293,235
Length 103
Max. P 0.832892
window9612 window9613

overview

Window 2

Location 11,293,132 – 11,293,235
Length 103
Sequences 12
Columns 116
Reading direction forward
Mean pairwise identity 80.61
Shannon entropy 0.40582
G+C content 0.48606
Mean single sequence MFE -30.40
Consensus MFE -15.69
Energy contribution -15.44
Covariance contribution -0.25
Combinations/Pair 1.24
Mean z-score -2.07
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.84
SVM RNA-class probability 0.832892
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11293132 103 + 24543557
CAAGUU-AGCCGCGUGCUAACGGGAAGUCGAC-----GUUGAGUGA--GCGGCCAAAGGAAGUGCAUUUGAAUGAAUGCACAUCUGAUAAAGCCUAAUACCCAUAGACAGG-----
...(((-(((.....))))))(((..((..((-----.....))..--))(((....(((.((((((((....)))))))).)))......))).....))).........----- ( -30.80, z-score =  -2.33, R)
>droPer1.super_20 1505985 100 - 1872136
----UGGGUCUAGGUGCUAACGGGAAGUCGCC-----GUUGAGUGA--GCGGCCAAAGGAAGUGCAUUUGAAUGAAUGCACAUCUGAUAAAGCCUAAUACCCAUAGACAGC-----
----(((((.(((((..((.((((.....(((-----(((.....)--)))))........((((((((....)))))))).)))).))..)))))..)))))........----- ( -34.60, z-score =  -3.00, R)
>dp4.chrXR_group6 2900253 100 - 13314419
----UGGGUCUAGGUGCUAACGGGAAGUCGCC-----GUUGAGUGA--GCGGCCAAAGGAAGUGCAUUUGAAUGAAUGCACAUCUGAUAAAGCCUAAUACCCAUAGACAGC-----
----(((((.(((((..((.((((.....(((-----(((.....)--)))))........((((((((....)))))))).)))).))..)))))..)))))........----- ( -34.60, z-score =  -3.00, R)
>droAna3.scaffold_13337 5577601 105 + 23293914
----GGGGCUUAGGUGCUAACGGGAAGUCGCCUCGCCGUUGAGUGA--GCGGCCAAAGGAAGUGCAUUUGAAUGAAUGCACAUCUGAUAAAGCCUAAUACCCAUGGACAGG-----
----(((..((((((..((.((((..(((((.((((......))))--)))))........((((((((....)))))))).)))).))..))))))..))).........----- ( -38.30, z-score =  -2.43, R)
>droEre2.scaffold_4784 11296912 102 + 25762168
CAAGUU-AGCCGCGUGCUAACGGGAAGUCGAC-----GUUGAGUGA--GCGGCCAAAGGAAGUGCAUUUGAAUGAAUGCACAUCUGAUAAAGCCUAAUACCCAUAGACAG------
...(((-(((.....))))))(((..((..((-----.....))..--))(((....(((.((((((((....)))))))).)))......))).....)))........------ ( -30.80, z-score =  -2.64, R)
>droYak2.chr3L 11328009 103 + 24197627
CAAGUU-AGCCGCGUGCUAACGGGAAGUCGAC-----GUUGAGUGA--GCGGCCAAAGGAAGUGCAUUUGAAUGAAUGCACAUCUGAUAAAGCCUAAUACCCAUAGACAGG-----
...(((-(((.....))))))(((..((..((-----.....))..--))(((....(((.((((((((....)))))))).)))......))).....))).........----- ( -30.80, z-score =  -2.33, R)
>droSec1.super_0 3506202 104 + 21120651
CAAGUUUAGCCGCGUGCUAACGGGAAGUCGAC-----GUUGAGUGA--GCGGCCAAAGGAAGUGCAUUUGAAUGAAUGCACAUCUGAUAAAGCCUAAUACCCAUAGACAGG-----
...((((((((((..(((((((.........)-----))).)))..--)))))....(((.((((((((....)))))))).)))..................)))))...----- ( -31.20, z-score =  -2.35, R)
>droSim1.chr3L 10681664 104 + 22553184
CAAGUUUAGCCGCGUGCUAACGGGAAGUCGAC-----GUUGAGUGA--GCGGCCAAAGGAAGUGCAUUUGAAUGAAUGCACAUCUGAUAAAGCCUAAUACCCAUAGACAGG-----
...((((((((((..(((((((.........)-----))).)))..--)))))....(((.((((((((....)))))))).)))..................)))))...----- ( -31.20, z-score =  -2.35, R)
>droWil1.scaffold_180698 9744984 103 - 11422946
---------GUAGGUGCUAACGGGAAAUGGCCUGGCCAUUGAGCGA--GUC-CGAAAGGAAGUGCAUUUCAAUGAAUGCACAUCUGAUAAA-CGUAAUAUCCAUGGACAGAGAGUC
---------....((((...((((......))))..(((((((((.--.((-(....)))..)))...))))))...)))).((((.....-(((.......)))..))))..... ( -28.40, z-score =  -1.44, R)
>droVir3.scaffold_13049 1582870 90 - 25233164
-----------CAGCUCUAACGGGAAGUCGCC-----GUUGAG----UGCGCCCAAAGGAAGUGCAUUCGAAUGAAUGCACAUCUGAUAAA-CAUAAUGCCCAUAGACAGC-----
-----------..((((.((((((....).))-----))))))----).........(((.((((((((....)))))))).)))......-...................----- ( -24.20, z-score =  -1.36, R)
>droMoj3.scaffold_6680 6503479 104 - 24764193
-CUGCUUCGCUUCGCUCUAACGGGAAAUCGCA-----CUCGACGGACUGCGCUCAAAGGAAGUGCAUUCGAAUGGCUGCACAUCUGAUAAA-CAUGAUACCCAUAGACAGC-----
-.......(((....((((..(((....((((-----.((....)).))))......(((.(((((..(....)..))))).)))......-.......))).)))).)))----- ( -21.70, z-score =   0.84, R)
>droGri2.scaffold_15110 14020347 93 + 24565398
----UAGUUGUGGCUGCUAACGGGAAGUCGCC-----GUUGAGUGC--GCC-CCAAAGGAAGUGCAUUCGAAUGAAUGCACAUCUGAUAAA-UAUAAUACCCAUAA----------
----...(((.(((((((((((((....).))-----))).)))).--)))-.))).(((.((((((((....)))))))).)))......-..............---------- ( -28.20, z-score =  -2.48, R)
>consensus
____UU_AGCUGCGUGCUAACGGGAAGUCGCC_____GUUGAGUGA__GCGGCCAAAGGAAGUGCAUUUGAAUGAAUGCACAUCUGAUAAAGCCUAAUACCCAUAGACAGG_____
.....................(((...(((.........)))...............(((.((((((((....)))))))).)))..............))).............. (-15.69 = -15.44 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,293,132 – 11,293,235
Length 103
Sequences 12
Columns 116
Reading direction reverse
Mean pairwise identity 80.61
Shannon entropy 0.40582
G+C content 0.48606
Mean single sequence MFE -28.44
Consensus MFE -12.30
Energy contribution -12.62
Covariance contribution 0.31
Combinations/Pair 1.18
Mean z-score -2.14
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.583598
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11293132 103 - 24543557
-----CCUGUCUAUGGGUAUUAGGCUUUAUCAGAUGUGCAUUCAUUCAAAUGCACUUCCUUUGGCCGC--UCACUCAAC-----GUCGACUUCCCGUUAGCACGCGGCU-AACUUG
-----...(((..(((((....((((......((.(((((((......))))))).))....))))..--..)))))..-----...))).....((((((.....)))-)))... ( -27.80, z-score =  -2.23, R)
>droPer1.super_20 1505985 100 + 1872136
-----GCUGUCUAUGGGUAUUAGGCUUUAUCAGAUGUGCAUUCAUUCAAAUGCACUUCCUUUGGCCGC--UCACUCAAC-----GGCGACUUCCCGUUAGCACCUAGACCCA----
-----...(((((.((......((((......((.(((((((......))))))).))....))))((--(.....(((-----((.(....))))))))).)))))))...---- ( -30.00, z-score =  -2.76, R)
>dp4.chrXR_group6 2900253 100 + 13314419
-----GCUGUCUAUGGGUAUUAGGCUUUAUCAGAUGUGCAUUCAUUCAAAUGCACUUCCUUUGGCCGC--UCACUCAAC-----GGCGACUUCCCGUUAGCACCUAGACCCA----
-----...(((((.((......((((......((.(((((((......))))))).))....))))((--(.....(((-----((.(....))))))))).)))))))...---- ( -30.00, z-score =  -2.76, R)
>droAna3.scaffold_13337 5577601 105 - 23293914
-----CCUGUCCAUGGGUAUUAGGCUUUAUCAGAUGUGCAUUCAUUCAAAUGCACUUCCUUUGGCCGC--UCACUCAACGGCGAGGCGACUUCCCGUUAGCACCUAAGCCCC----
-----.........((((....((((......((.(((((((......))))))).))....))))((--(.....(((((.(((....))).))))))))......)))).---- ( -32.80, z-score =  -2.32, R)
>droEre2.scaffold_4784 11296912 102 - 25762168
------CUGUCUAUGGGUAUUAGGCUUUAUCAGAUGUGCAUUCAUUCAAAUGCACUUCCUUUGGCCGC--UCACUCAAC-----GUCGACUUCCCGUUAGCACGCGGCU-AACUUG
------..(((..(((((....((((......((.(((((((......))))))).))....))))..--..)))))..-----...))).....((((((.....)))-)))... ( -27.80, z-score =  -2.26, R)
>droYak2.chr3L 11328009 103 - 24197627
-----CCUGUCUAUGGGUAUUAGGCUUUAUCAGAUGUGCAUUCAUUCAAAUGCACUUCCUUUGGCCGC--UCACUCAAC-----GUCGACUUCCCGUUAGCACGCGGCU-AACUUG
-----...(((..(((((....((((......((.(((((((......))))))).))....))))..--..)))))..-----...))).....((((((.....)))-)))... ( -27.80, z-score =  -2.23, R)
>droSec1.super_0 3506202 104 - 21120651
-----CCUGUCUAUGGGUAUUAGGCUUUAUCAGAUGUGCAUUCAUUCAAAUGCACUUCCUUUGGCCGC--UCACUCAAC-----GUCGACUUCCCGUUAGCACGCGGCUAAACUUG
-----...(((((.......))))).......((.(((((((......))))))).)).(((((((((--...((.(((-----(.........))))))...))))))))).... ( -27.90, z-score =  -2.22, R)
>droSim1.chr3L 10681664 104 - 22553184
-----CCUGUCUAUGGGUAUUAGGCUUUAUCAGAUGUGCAUUCAUUCAAAUGCACUUCCUUUGGCCGC--UCACUCAAC-----GUCGACUUCCCGUUAGCACGCGGCUAAACUUG
-----...(((((.......))))).......((.(((((((......))))))).)).(((((((((--...((.(((-----(.........))))))...))))))))).... ( -27.90, z-score =  -2.22, R)
>droWil1.scaffold_180698 9744984 103 + 11422946
GACUCUCUGUCCAUGGAUAUUACG-UUUAUCAGAUGUGCAUUCAUUGAAAUGCACUUCCUUUCG-GAC--UCGCUCAAUGGCCAGGCCAUUUCCCGUUAGCACCUAC---------
........((((...((((.....-..)))).((.(((((((......))))))).)).....)-)))--..(((.(((((............))))))))......--------- ( -23.10, z-score =  -1.06, R)
>droVir3.scaffold_13049 1582870 90 + 25233164
-----GCUGUCUAUGGGCAUUAUG-UUUAUCAGAUGUGCAUUCAUUCGAAUGCACUUCCUUUGGGCGCA----CUCAAC-----GGCGACUUCCCGUUAGAGCUG-----------
-----(((((((((((((.....)-))))).))))((((((((....))))))))........)))((.----((.(((-----((.(....)))))))).))..----------- ( -29.00, z-score =  -2.39, R)
>droMoj3.scaffold_6680 6503479 104 + 24764193
-----GCUGUCUAUGGGUAUCAUG-UUUAUCAGAUGUGCAGCCAUUCGAAUGCACUUCCUUUGAGCGCAGUCCGUCGAG-----UGCGAUUUCCCGUUAGAGCGAAGCGAAGCAG-
-----(((.((((((((.(((..(-((((...((.(((((..(....)..))))).))...)))))(((.((....)).-----))))))..)))).))))....))).......- ( -31.00, z-score =  -0.86, R)
>droGri2.scaffold_15110 14020347 93 - 24565398
----------UUAUGGGUAUUAUA-UUUAUCAGAUGUGCAUUCAUUCGAAUGCACUUCCUUUGG-GGC--GCACUCAAC-----GGCGACUUCCCGUUAGCAGCCACAACUA----
----------.....((((.....-..)))).((.((((((((....)))))))).))..(((.-(((--...((.(((-----((.(....))))))))..))).)))...---- ( -26.20, z-score =  -2.32, R)
>consensus
_____CCUGUCUAUGGGUAUUAGGCUUUAUCAGAUGUGCAUUCAUUCAAAUGCACUUCCUUUGGCCGC__UCACUCAAC_____GGCGACUUCCCGUUAGCACGCAGCU_AA____
........(((((((((...............((.(((((((......))))))).))..((((..........))))..............)))).))).))............. (-12.30 = -12.62 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:18:14 2011