Locus 9642

Sequence ID	dm3.chr3R
Location	7,957,023 – 7,957,165
Length	142
Max. P	0.998931

overview

Window 5

Location	7,957,023 – 7,957,165
Length	142
Sequences	11
Columns	153
Reading direction	forward
Mean pairwise identity	67.76
Shannon entropy	0.70249
G+C content	0.49468
Mean single sequence MFE	-44.43
Consensus MFE	-32.85
Energy contribution	-31.85
Covariance contribution	-1.00
Combinations/Pair	1.42
Mean z-score	-1.66
Structure conservation index	0.74
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.46
SVM RNA-class probability	0.998705
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7957023 142 + 27905053
-------UCAAAUAACCUGCAGUCCUAUUAGUCGGGUGUUUUGGC-GGGUGACCUUCACAUGCCCGGAUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGGCCAUCUUUUUUUGCC---
-------.((((..((((((..........).)))))....((((-((....))......((((((((((((((........))))..(((((((((.....)))))))))(((.......)))))))))))))))))......))))..--- ( -48.60, z-score =  -1.64, R)
>droSim1.chr3R 14082390 137 - 27517382
------------UAACCUGCCGUCGUAUUAGCAAUGUUUUUUGGC-GGACGACUUUCACCUGCCCGGAUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGGCCAUCUUUUUUUGAU---
------------......((((((((....((((......)).))-..)))))........(((((((((((((........))))..(((((((((.....)))))))))(((.......)))))))))))))))..............--- ( -45.70, z-score =  -1.76, R)
>droSec1.super_0 7101578 127 - 21120651
------------CAACCUGCAGUCGUAUUAGUAAUGUUUUUUGGC-GGACGACUUUCACCUGCUCGGAUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGGUCAUC-------------
------------........((((((....((...........))-..)))))).....(((((((((((((((........))))..(((((((((.....)))))))))(((.......)))))))))))))).....------------- ( -39.20, z-score =  -1.29, R)
>droYak2.chr3R 7764400 132 + 28832112
----------------UUGCAAUCUUAUUAGUAGUGUUUUUAGAU-GGAUGACGUACACGUGCCCGGAUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGGCAAUCUUUUUUUAG----
----------------((((.............((((..(((...-...)))...)))).((((((((((((((........))))..(((((((((.....)))))))))(((.......)))))))))))))))))...........---- ( -40.50, z-score =  -2.07, R)
>droEre2.scaffold_4770 14848456 130 - 17746568
-----------------UGCAAUCUUAUUAGUAAGGAUUUUUGGG-CAAUGACGUGUACAUGCCCGGAUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGGCAACUUUUUUUCC-----
-----------------(((((((((.......))))))..((..-((......))..))((((((((((((((........))))..(((((((((.....)))))))))(((.......))))))))))))))))...........----- ( -39.00, z-score =  -1.25, R)
>droAna3.scaffold_13340 5404152 139 + 23697760
-------UCGAAGGAGGUCUAGUUUUGUUAGCA-----UUUCGGC-AGGAGGCAACCAAAUGCCCGGGUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGAUCG-ACUUUUUUUACUAU
-------..((((((((((..((((.(((.((.-----((((...-.))))))))).))))(((((((((((((........))))..(((((((((.....)))))))))(((.......))))))))))))....)-)))))))))..... ( -50.20, z-score =  -2.71, R)
>dp4.chr2 19721640 132 + 30794189
---------AUCAGAACGUUGGUUUUGUUAGUA-----CUUUGGC-UAGCGUCGGUUGAAUGCCCGGGUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGAA---AACUUUUUGAU---
---------(((((((((((((((..((....)-----)...)))-)))))).((((...((((((((((((((........))))..(((((((((.....)))))))))(((.......)))))))))))))..---)))).))))))--- ( -49.80, z-score =  -3.39, R)
>droPer1.super_3 2464834 146 + 7375914
UUUGGGAUGCUGGGGUGGGCAUUAUUCUGAGAAGAAGGCGUUGGC-GGGAGUGGCCCAAGUGCCCGGGUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGAUUUCUUUUUGCU------
...(..(((((.(((..((.....((((....))))(((.(((((-..((((.((((........)))).)))).)))))..((((.((((((((((.....)))))))))).))))..)))))..))).))).))..)........------ ( -53.90, z-score =  -0.43, R)
>anoGam1.chr2R 51278841 141 + 62725911
--------CGGAAAAAUGUGGGUUGUGUUAAUAUGGUGCAUUGGCGUGGGGGCUGGUAAGAGCCCGGGUAGCUCAGUCGGUAGAGCGUUGGACUUUUAAUCCAACGGUCUAGGGUUCAAGUCCCUAUUCGGGCGGGCG-AAUUUUUUUGC---
--------(((((((((.(.(.((((((((((.......))))))(((((((((.....(((((((((...)))......((((.(((((((.......))))))).)))))))))).)))))))))....)))).).-)))))))))).--- ( -47.50, z-score =  -1.65, R)
>droGri2.scaffold_14906 11425882 124 + 14172833
------------------------UUAUCAGAAGUGUUCCUUGAC-CAUCAGCAAAUGUAUGCCCGGGUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGAGCUCUAUUUUUUUA----
------------------------........((.((((.(((..-...))).........(((((((((((((........))))..(((((((((.....)))))))))(((.......)))))))))))))))).)).........---- ( -39.40, z-score =  -1.83, R)
>droVir3.scaffold_13047 1772746 129 + 19223366
-------------------CACUACAAUUUGAUGCGUAGUUUGCU-CCCAGUUGCUCACCGGCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCCGGUUCAAUCCCGGGUUUCGGCAGAACACUUUUUUUUA----
-------------------..((((..........))))((((((-..(((((((((.(((((.((......)).)))))..))))....)))))..........((..(((((.......)))))..)))))))).............---- ( -34.90, z-score =  -0.30, R)
>consensus
______________A_CUGCAGUCUUAUUAGUAGUGUUUUUUGGC_GGGCGACGUUCACAUGCCCGGAUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGGCCAUCUUUUUUUUA____
.............................................................((((((((.((((........))))...((((((((.....))))))))((((.......)))))))))))).................... (-32.85 = -31.85 +  -1.00)

alignment

secondary structure

dotplot

Window 6

Location	7,957,023 – 7,957,165
Length	142
Sequences	11
Columns	153
Reading direction	reverse
Mean pairwise identity	67.76
Shannon entropy	0.70249
G+C content	0.49468
Mean single sequence MFE	-36.42
Consensus MFE	-29.18
Energy contribution	-28.28
Covariance contribution	-0.90
Combinations/Pair	1.30
Mean z-score	-1.83
Structure conservation index	0.80
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.56
SVM RNA-class probability	0.998931
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7957023 142 - 27905053
---GGCAAAAAAAGAUGGCCGCCCGAACAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAUCCGGGCAUGUGAAGGUCACCC-GCCAAAACACCCGACUAAUAGGACUGCAGGUUAUUUGA-------
---.........((((((((((((((.(((((.......))))).....))))......(((((...((((........))))....((((..(((...(((.....-)))...))))))).......))))))).))))))))..------- ( -42.20, z-score =  -1.37, R)
>droSim1.chr3R 14082390 137 + 27517382
---AUCAAAAAAAGAUGGCCGCCCGAACAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAUCCGGGCAGGUGAAAGUCGUCC-GCCAAAAAACAUUGCUAAUACGACGGCAGGUUA------------
---............((((.(((((..(((((.......))))).....((((((.....)))))).((((........))))....))))).((((.....)).))-))))...(((.(((((........)))))))).------------ ( -41.90, z-score =  -1.65, R)
>droSec1.super_0 7101578 127 + 21120651
-------------GAUGACCGCCCGAACAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAUCCGAGCAGGUGAAAGUCGUCC-GCCAAAAAACAUUACUAAUACGACUGCAGGUUG------------
-------------((((((((((....(((((.......)))))....(((((((............((((........)))).)))))))..))))...)))))).-....................((((.....))))------------ ( -31.92, z-score =  -1.18, R)
>droYak2.chr3R 7764400 132 - 28832112
----CUAAAAAAAGAUUGCCGCCCGAACAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAUCCGGGCACGUGUACGUCAUCC-AUCUAAAAACACUACUAAUAAGAUUGCAA----------------
----...........((((.(((((..(((((.......))))).....((((((.....)))))).((((........))))....)))))..((((.........-........)))).............))))---------------- ( -33.23, z-score =  -2.42, R)
>droEre2.scaffold_4770 14848456 130 + 17746568
-----GGAAAAAAAGUUGCCGCCCGAACAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAUCCGGGCAUGUACACGUCAUUG-CCCAAAAAUCCUUACUAAUAAGAUUGCA-----------------
-----(((............(((((..(((((.......))))).....((((((.....)))))).((((........))))....))))).((..((......))-..))....))).................----------------- ( -31.90, z-score =  -1.25, R)
>droAna3.scaffold_13340 5404152 139 - 23697760
AUAGUAAAAAAAGU-CGAUCGCCCGAGCAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUACCCGGGCAUUUGGUUGCCUCCU-GCCGAAA-----UGCUAACAAAACUAGACCUCCUUCGA-------
.(((((........-.....(((((..(((((.......))))).....((((((.....)))))).((((........))))....))))).((((((........-)))))).-----))))).....................------- ( -37.80, z-score =  -1.70, R)
>dp4.chr2 19721640 132 - 30794189
---AUCAAAAAGUU---UUCGCCCGAGCAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUACCCGGGCAUUCAACCGACGCUA-GCCAAAG-----UACUAACAAAACCAACGUUCUGAU---------
---((((.((.(((---...(((((..(((((.......))))).....((((((.....)))))).((((........))))....)))))...........(((.-.....))-----)............))).)).))))--------- ( -30.90, z-score =  -0.92, R)
>droPer1.super_3 2464834 146 - 7375914
------AGCAAAAAGAAAUCGCCCGAGCAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUACCCGGGCACUUGGGCCACUCCC-GCCAACGCCUUCUUCUCAGAAUAAUGCCCACCCCAGCAUCCCAAA
------.((...........(((((..(((((.......))))).....((((((.....)))))).((((........))))....)))))...(((((.......-((....)).((((....))))....))))).....))........ ( -40.10, z-score =  -1.46, R)
>anoGam1.chr2R 51278841 141 - 62725911
---GCAAAAAAAUU-CGCCCGCCCGAAUAGGGACUUGAACCCUAGACCGUUGGAUUAAAAGUCCAACGCUCUACCGACUGAGCUACCCGGGCUCUUACCAGCCCCCACGCCAAUGCACCAUAUUAACACAACCCACAUUUUUCCG--------
---(((........-.....(((((..(((((.......)))))....(((((((.....)))))))((((........))))....)))))........((......))...))).............................-------- ( -34.30, z-score =  -3.67, R)
>droGri2.scaffold_14906 11425882 124 - 14172833
----UAAAAAAAUAGAGCUCGCCCGAGCAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUACCCGGGCAUACAUUUGCUGAUG-GUCAAGGAACACUUCUGAUAA------------------------
----........((((((((....)))).(...(((((.((((((....((((((.....)))))).((((........))))...))))(((......)))....)-))))))...)...))))....------------------------ ( -34.10, z-score =  -1.71, R)
>droVir3.scaffold_13047 1772746 129 - 19223366
----UAAAAAAAAGUGUUCUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUCCCAACUGAGCUAUUUCGGCCGGUGAGCAACUGGG-AGCAAACUACGCAUCAAAUUGUAGUG-------------------
----..........((((((((((((((((((.......))))).....((((((.....)))))).((((........))))..)))))))((((.....))))))-)))).((((((........)))))).------------------- ( -42.30, z-score =  -2.76, R)
>consensus
____UAAAAAAAAGAUGGCCGCCCGAACAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAUCCGGGCAUGUGAACGUCGCCC_GCCAAAAAACACUACUAAUAAGACUGCAG_U______________
....................(((((..(((((.......))))).....((((((.....)))))).((((........))))....)))))............................................................. (-29.18 = -28.28 +  -0.90)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:08:17 2011