Locus 4930

Sequence ID	dm3.chr2R
Location	16,472,820 – 16,472,912
Length	92
Max. P	0.939943

overview

Window 8

Location	16,472,820 – 16,472,912
Length	92
Sequences	7
Columns	106
Reading direction	forward
Mean pairwise identity	53.81
Shannon entropy	0.84586
G+C content	0.35453
Mean single sequence MFE	-19.33
Consensus MFE	-1.86
Energy contribution	-2.80
Covariance contribution	0.95
Combinations/Pair	1.69
Mean z-score	-2.43
Structure conservation index	0.10
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.25
SVM RNA-class probability	0.614044
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16472820 92 + 21146708
-------------UAACUUUCUCGAAGUACUUAGUACCAGAAACGUGUACUUUACAUAAACAUAAAAAAUAACACUUUGCUGAUACCA-GGCACUUGGGAAAAUCA
-------------....((((((.((((.(((.(((.(((....((((.......................))))....))).))).)-)).)))))))))).... ( -17.20, z-score =  -2.00, R)
>droSim1.chr2R 15134514 86 + 19596830
-------------UAAGUUUCUCAAAGGGCUUGGUUCCAAAAAAGGGUACUAUACAA---CA---AAAAUUACACCUCUCUGAAACCA-GGCACUUGCGAAAAUCA
-------------....((((.(((...((((((((.((....((((((........---..---.....))).)))...)).)))))-)))..))).)))).... ( -18.96, z-score =  -2.17, R)
>droSec1.super_1 14027539 89 + 14215200
-------------UAAGUUUCUCAAAGGGCUUGGUUCCAGAAACGUGUACUAUACAAACACA---AAAAUUACACCUAUCUGAUACCA-GGCACUUCCGAAAAUCA
-------------....((((...(((.(((((((..((((...(((((.............---.....)))))...))))..))))-))).)))..)))).... ( -21.77, z-score =  -3.59, R)
>droYak2.chr2R 8415457 89 - 21139217
-------------UAGGUUUCUCGAAGUACGUAGUACCAGUAACGUGUACUUUAACCAAACA---AAAAUUACACCUUGCUGAUACUA-AGCACUUGGGAAAAUCA
-------------..(((((..(.((((.(.(((((.((((((.(((((.(((.........---.))).))))).)))))).)))))-.).)))).)..))))). ( -26.90, z-score =  -4.19, R)
>droEre2.scaffold_4845 10619162 89 + 22589142
-------------CAUGUUUCUCAAAGUACCUAGUACCAGUAACGUGUACUUUACCCAAAUA---AAAAUUACACCUUGCUGAUACUA-UGCACUUGGGAAAAUCA
-------------....((((((((.((.(.(((((.((((((.(((((.(((.........---.))).))))).)))))).)))))-.).)))))))))).... ( -24.80, z-score =  -4.55, R)
>dp4.chr3 11100407 101 - 19779522
UGAAAACAUGAAACGAGCGUUUGGGAACCGAUUACAUUUGAAUUUAACCGUAUGUACA-AAAUGCAUACAUACAUAGUUUAAGCGACGCGACGCGAGAAAGA----
.............((.(((((...(((((((......))).........(((((((..-...))))))).......))))....)))))....)).......---- ( -16.50, z-score =  -0.14, R)
>triCas2.chrUn_95 45657 80 + 72281
-------------CAAGUUUUUUUUAAUUUUUAACAAAAAGCCCAAAUACUAAUUUU---CA----AGGACAUAAGUU-----CAAUG-GACGUUUAAAAAUGUCG
-------------...((((((((((.....))).)))))))...............---..----.((((....)))-----)....-((((((....)))))). (  -9.20, z-score =  -0.36, R)
>consensus
_____________UAAGUUUCUCAAAGUACUUAGUACCAGAAACGUGUACUAUACACA_ACA___AAAAUUACACCUUGCUGAUACCA_GGCACUUGGGAAAAUCA
.................((((((((......((((..((((.....................................))))..))))......)))))))).... ( -1.86 =  -2.80 +   0.95)

alignment

secondary structure

dotplot

Window 9

Location	16,472,820 – 16,472,912
Length	92
Sequences	7
Columns	106
Reading direction	reverse
Mean pairwise identity	53.81
Shannon entropy	0.84586
G+C content	0.35453
Mean single sequence MFE	-23.42
Consensus MFE	-3.12
Energy contribution	-3.66
Covariance contribution	0.54
Combinations/Pair	1.84
Mean z-score	-2.82
Structure conservation index	0.13
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.44
SVM RNA-class probability	0.939943
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16472820 92 - 21146708
UGAUUUUCCCAAGUGCC-UGGUAUCAGCAAAGUGUUAUUUUUUAUGUUUAUGUAAAGUACACGUUUCUGGUACUAAGUACUUCGAGAAAGUUA-------------
(((((((((.((((((.-(((((((((....((((....((((((......)))))).))))....))))))))).)))))).).))))))))------------- ( -30.10, z-score =  -5.36, R)
>droSim1.chr2R 15134514 86 - 19596830
UGAUUUUCGCAAGUGCC-UGGUUUCAGAGAGGUGUAAUUUU---UG---UUGUAUAGUACCCUUUUUUGGAACCAAGCCCUUUGAGAAACUUA-------------
...((((((.(((.((.-((((((((((((((.(((.....---..---........))).)))))))))))))).)).))))))))).....------------- ( -25.76, z-score =  -3.50, R)
>droSec1.super_1 14027539 89 - 14215200
UGAUUUUCGGAAGUGCC-UGGUAUCAGAUAGGUGUAAUUUU---UGUGUUUGUAUAGUACACGUUUCUGGAACCAAGCCCUUUGAGAAACUUA-------------
...((((((((.(.((.-((((.(((((.(.(((((....(---((((....)))))))))).).))))).)))).))).)))))))).....------------- ( -25.20, z-score =  -2.65, R)
>droYak2.chr2R 8415457 89 + 21139217
UGAUUUUCCCAAGUGCU-UAGUAUCAGCAAGGUGUAAUUUU---UGUUUGGUUAAAGUACACGUUACUGGUACUACGUACUUCGAGAAACCUA-------------
....(((((.((((((.-(((((((((.((.(((((...((---((......)))).))))).)).))))))))).)))))).).))))....------------- ( -28.50, z-score =  -3.79, R)
>droEre2.scaffold_4845 10619162 89 - 22589142
UGAUUUUCCCAAGUGCA-UAGUAUCAGCAAGGUGUAAUUUU---UAUUUGGGUAAAGUACACGUUACUGGUACUAGGUACUUUGAGAAACAUG-------------
((.(((((..((((((.-(((((((((.((.(((((...((---(((....))))).))))).)).))))))))).)))))).))))).))..------------- ( -30.00, z-score =  -4.45, R)
>dp4.chr3 11100407 101 + 19779522
----UCUUUCUCGCGUCGCGUCGCUUAAACUAUGUAUGUAUGCAUUU-UGUACAUACGGUUAAAUUCAAAUGUAAUCGGUUCCCAAACGCUCGUUUCAUGUUUUCA
----........(((..((((......((((..((((((((......-.))))))))(((((.((....)).))))))))).....)))).)))............ ( -17.00, z-score =  -0.75, R)
>triCas2.chrUn_95 45657 80 - 72281
CGACAUUUUUAAACGUC-CAUUG-----AACUUAUGUCCU----UG---AAAAUUAGUAUUUGGGCUUUUUGUUAAAAAUUAAAAAAAACUUG-------------
....((((((((..(((-((...-----.(((.((.....----..---...)).)))...)))))......)))))))).............------------- (  -7.40, z-score =   0.75, R)
>consensus
UGAUUUUCCCAAGUGCC_UGGUAUCAGAAAGGUGUAAUUUU___UGU_UGUGUAUAGUACACGUUUCUGGUACUAAGUACUUCGAGAAACUUA_____________
....((((..........(((((((((.((.(.(((.....................))).).)).)))))))))..........))))................. ( -3.12 =  -3.66 +   0.54)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:38:45 2011