Locus 11053

Sequence ID dm3.chr3R
Location 18,326,993 – 18,327,095
Length 102
Max. P 0.904673
window15184 window15185

overview

Window 4

Location 18,326,993 – 18,327,095
Length 102
Sequences 9
Columns 111
Reading direction forward
Mean pairwise identity 72.47
Shannon entropy 0.56853
G+C content 0.48184
Mean single sequence MFE -33.38
Consensus MFE -13.85
Energy contribution -14.77
Covariance contribution 0.92
Combinations/Pair 1.29
Mean z-score -1.94
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.904673
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18326993 102 + 27905053
--CCAGCCAGCGAGAAAUUGCAGCCAUUAGUUGGCCC-AAAAAGCUGGUAAAGAGGUCUUUUGAGUGUUUACCACUUGGGCGCUGACAUUUUCUUGCUACUGCGG------
--((((..(((((((((.((((((((.....))((((-(...((.(((((((..(.((....)).).)))))))))))))))))).)).))))))))).))).).------ ( -38.50, z-score =  -2.92, R)
>droPer1.super_7 990826 93 + 4445127
--GAAAACAGCGCGAAAUUGCAGCCAUUAGUUGGCCCCAAAAAGCCAUUGAAGAGGCCCAA-GAGUGUUUACCACUUGGGCGCUGACAUUUUUCUG---------------
--(((((((((((....(((..((((.....))))..)))...(((........)))((((-(.(.(....)).)))))))))))....)))))..--------------- ( -28.20, z-score =  -2.00, R)
>dp4.chr2 27443963 93 - 30794189
--GAAAACAGCGCGAAAUUGCAGCCAUUAGUUGGCCCCAAAAAGCCAUUGAAGAGGCCCAA-GAGUGUUUACCACUUGGGCGCUGACAUUUUUCUG---------------
--(((((((((((....(((..((((.....))))..)))...(((........)))((((-(.(.(....)).)))))))))))....)))))..--------------- ( -28.20, z-score =  -2.00, R)
>droAna3.scaffold_13340 21737681 108 + 23697760
CUACUGGCAGCGCGAAAUUGCAGCCAUUAGUUGGCCC-AAAAAGCCGUUGAAGAGGCCCAA-GAGUGUUUACCACUUGGGCGCAUUUUUUCCCCAGCUCUGCCACUGCGG-
....((((((.((((((.(((.((((.....))))..-.................((((((-(.(.(....)).))))))))))...))))....)).))))))......- ( -34.80, z-score =  -0.58, R)
>droEre2.scaffold_4820 718485 102 - 10470090
--CCAGCCAGCGAGAAAUUGCAGCCAUUAGUUGGCCC-AAAAAGCUGGUAAAGAGGUCUUUUGAGUGUUUACCACUUGCGCGCUGACAUUUUCUUGCUACUGCGG------
--((((..(((((((((.((((((((.....))((..-...(((.(((((((..(.((....)).).))))))))))..)))))).)).))))))))).))).).------ ( -31.60, z-score =  -1.07, R)
>droYak2.chr3R 19171532 102 + 28832112
--CCAGCCAGCGAGAAAUUGCAGCCAUUAGUUGGCCC-AAAAAGCUGGUAAAGAGGUCUUUUGAGUGUUUACCACUUGGGCGCUGACAUUUUCUUGCUACUGCGG------
--((((..(((((((((.((((((((.....))((((-(...((.(((((((..(.((....)).).)))))))))))))))))).)).))))))))).))).).------ ( -38.50, z-score =  -2.92, R)
>droSec1.super_0 18679830 102 + 21120651
--CCCGCCAGCGAGAAAUUGCAGCCAUUAGUUGGCCC-AAAAAGCUGGUAAAGAGGUCUUUUGAGUGUUUACCACUUGGGCGCUGACAUUUUCUUGCUACUGCGG------
--.((((.(((((((((.((((((((.....))((((-(...((.(((((((..(.((....)).).)))))))))))))))))).)).)))))))))...))))------ ( -42.00, z-score =  -4.04, R)
>droSim1.chr3R 18134873 102 + 27517382
--CCAGCCAGCGAGAAAUUGCAGCCAUUAGUUGGCCC-AAAAAGCUGGUAAAGAGGUCUUUUGAGUGUUUACCACUUGGGCGCUGACAUUUUCUUGCUACUGCGG------
--((((..(((((((((.((((((((.....))((((-(...((.(((((((..(.((....)).).)))))))))))))))))).)).))))))))).))).).------ ( -38.50, z-score =  -2.92, R)
>droVir3.scaffold_13047 544678 94 - 19223366
----------GGCAAUAUGACAGC--UUGAUAGUUCC---AUGGCAUCUGCACACAUAUGU--AUUAUAUGUUAUGAUGCUGAUGACAUUGUAAUGAUAUUGUAAUCAGCC
----------(((..((((..(((--(....)))).)---)))(((((.....(((((((.--..)))))))...)))))((((.(((.(((....))).))).))))))) ( -20.10, z-score =   0.97, R)
>consensus
__CCAGCCAGCGAGAAAUUGCAGCCAUUAGUUGGCCC_AAAAAGCUGGUAAAGAGGUCUUUUGAGUGUUUACCACUUGGGCGCUGACAUUUUCUUGCUACUGCGG______
.......((((...........((((.....))))....................((((...(((((.....))))))))))))).......................... (-13.85 = -14.77 +   0.92)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 5

Location 18,326,993 – 18,327,095
Length 102
Sequences 9
Columns 111
Reading direction reverse
Mean pairwise identity 72.47
Shannon entropy 0.56853
G+C content 0.48184
Mean single sequence MFE -32.32
Consensus MFE -11.03
Energy contribution -12.28
Covariance contribution 1.25
Combinations/Pair 1.07
Mean z-score -1.90
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.638748
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18326993 102 - 27905053
------CCGCAGUAGCAAGAAAAUGUCAGCGCCCAAGUGGUAAACACUCAAAAGACCUCUUUACCAGCUUUUU-GGGCCAACUAAUGGCUGCAAUUUCUCGCUGGCUGG--
------...(((((((.(((((.((.((((((((((((((((((...((....))....)))))))....)))-))))((.....)))))))).))))).))).)))).-- ( -34.20, z-score =  -2.51, R)
>droPer1.super_7 990826 93 - 4445127
---------------CAGAAAAAUGUCAGCGCCCAAGUGGUAAACACUC-UUGGGCCUCUUCAAUGGCUUUUUGGGGCCAACUAAUGGCUGCAAUUUCGCGCUGUUUUC--
---------------..(((((....(((((((((((.(.......).)-))))(((........)))...(((.(((((.....))))).)))....)))))))))))-- ( -31.70, z-score =  -2.49, R)
>dp4.chr2 27443963 93 + 30794189
---------------CAGAAAAAUGUCAGCGCCCAAGUGGUAAACACUC-UUGGGCCUCUUCAAUGGCUUUUUGGGGCCAACUAAUGGCUGCAAUUUCGCGCUGUUUUC--
---------------..(((((....(((((((((((.(.......).)-))))(((........)))...(((.(((((.....))))).)))....)))))))))))-- ( -31.70, z-score =  -2.49, R)
>droAna3.scaffold_13340 21737681 108 - 23697760
-CCGCAGUGGCAGAGCUGGGGAAAAAAUGCGCCCAAGUGGUAAACACUC-UUGGGCCUCUUCAACGGCUUUUU-GGGCCAACUAAUGGCUGCAAUUUCGCGCUGCCAGUAG
-..((((((.((((((((..(((.....(.(((((((.(.......).)-)))))))..)))..)))))))((-((((((.....))))).)))....)))))))...... ( -39.60, z-score =  -0.97, R)
>droEre2.scaffold_4820 718485 102 + 10470090
------CCGCAGUAGCAAGAAAAUGUCAGCGCGCAAGUGGUAAACACUCAAAAGACCUCUUUACCAGCUUUUU-GGGCCAACUAAUGGCUGCAAUUUCUCGCUGGCUGG--
------...(((((((.(((((.(((.(((((....))((((((...((....))....)))))).)))....-.(((((.....)))))))).))))).))).)))).-- ( -30.20, z-score =  -1.00, R)
>droYak2.chr3R 19171532 102 - 28832112
------CCGCAGUAGCAAGAAAAUGUCAGCGCCCAAGUGGUAAACACUCAAAAGACCUCUUUACCAGCUUUUU-GGGCCAACUAAUGGCUGCAAUUUCUCGCUGGCUGG--
------...(((((((.(((((.((.((((((((((((((((((...((....))....)))))))....)))-))))((.....)))))))).))))).))).)))).-- ( -34.20, z-score =  -2.51, R)
>droSec1.super_0 18679830 102 - 21120651
------CCGCAGUAGCAAGAAAAUGUCAGCGCCCAAGUGGUAAACACUCAAAAGACCUCUUUACCAGCUUUUU-GGGCCAACUAAUGGCUGCAAUUUCUCGCUGGCGGG--
------((((..((((.(((((.((.((((((((((((((((((...((....))....)))))))....)))-))))((.....)))))))).))))).)))))))).-- ( -36.90, z-score =  -3.15, R)
>droSim1.chr3R 18134873 102 - 27517382
------CCGCAGUAGCAAGAAAAUGUCAGCGCCCAAGUGGUAAACACUCAAAAGACCUCUUUACCAGCUUUUU-GGGCCAACUAAUGGCUGCAAUUUCUCGCUGGCUGG--
------...(((((((.(((((.((.((((((((((((((((((...((....))....)))))))....)))-))))((.....)))))))).))))).))).)))).-- ( -34.20, z-score =  -2.51, R)
>droVir3.scaffold_13047 544678 94 + 19223366
GGCUGAUUACAAUAUCAUUACAAUGUCAUCAGCAUCAUAACAUAUAAU--ACAUAUGUGUGCAGAUGCCAU---GGAACUAUCAA--GCUGUCAUAUUGCC----------
(((((((......)))).....(((.((.(.(((((...(((((((..--...)))))))...)))))...---.((....))..--).)).)))...)))---------- ( -18.20, z-score =   0.51, R)
>consensus
______CCGCAGUAGCAAGAAAAUGUCAGCGCCCAAGUGGUAAACACUCAAAAGACCUCUUUACCAGCUUUUU_GGGCCAACUAAUGGCUGCAAUUUCUCGCUGGCUGG__
..........................(((((....((((.....))))...........................(((((.....))))).........)))))....... (-11.03 = -12.28 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:35:29 2011