Locus 7300

Sequence ID dm3.chr3L
Location 13,721,983 – 13,722,110
Length 127
Max. P 0.745127
window10046 window10047

overview

Window 6

Location 13,721,983 – 13,722,110
Length 127
Sequences 9
Columns 127
Reading direction forward
Mean pairwise identity 91.94
Shannon entropy 0.16733
G+C content 0.46297
Mean single sequence MFE -31.36
Consensus MFE -24.31
Energy contribution -24.98
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.745127
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13721983 127 + 24543557
CUUCUGCGGCUGUGCAGUCAACUGAUGCAGCUACGCAGUUGUAACCCGGCCGCACUCACUAAUAGUUCUAAUUGCAAAAAGCAAUUAAAACUUUCGCCAACUCCAAGAUGCACAUACCCACAGCACG
..((((((((((..(((....))).(((((((....)))))))...)))))))..........((((.(((((((.....))))))).)))).............)))(((...........))).. ( -32.20, z-score =  -1.73, R)
>droEre2.scaffold_4784 13728321 127 + 25762168
CUUCUGCGGCUGUGCAGUCAACUGAUGCAGCUACGCAGUUGUAACCCGGCCACACUCACUAAUAGUUCUAAUUGCAAAAAGCAAUUAAAACUUUCACCAACUCCAAGAUGCACAUACCCACAGCACG
...(((.((.((((((.((..(((.(((((((....)))))))...)))..............((((.(((((((.....))))))).))))..............))))))))...)).))).... ( -29.30, z-score =  -1.68, R)
>droYak2.chr3L 13819095 127 + 24197627
CUUCUGCGGCUGUGCAGUCAACUGAUGCAGCUACGCAGUUGUAACCCGGCCACACUCACUAAUAGUUCUAAUUGCAAAAAGCAAUUAAAACUUUCACCAACUCCAAGAUGCACAUACCCACAGCACG
...(((.((.((((((.((..(((.(((((((....)))))))...)))..............((((.(((((((.....))))))).))))..............))))))))...)).))).... ( -29.30, z-score =  -1.68, R)
>droSec1.super_0 5884017 127 + 21120651
CUUCUGCGGCUGUGCAGUCAACUGAUGCAGCUACGCAGUUGUAACCCGGCCACACUCACUAAUAGUUCUAAUUGCAAAAAGCAAUUAAAACUUUCGCCAACUCCAAGAUGCACAUACCCACAGAACG
.(((((.((.((((((.((......(((((((....)))))))....(((.............((((.(((((((.....))))))).))))...)))........))))))))...)).))))).. ( -34.69, z-score =  -3.27, R)
>droSim1.chr3L 13107726 127 + 22553184
CUUCUGCGGCUGUGCAGUCAACUGAUGCAGCUACGCAGUUGUAACCCGGCCACACUCACUAAUAGUUCUAAUUGCAAAAAGCAAUUAAAACUUUCGCCAACUCCAAGAUGCACAUACCCACAGCACG
...(((.((.((((((.((......(((((((....)))))))....(((.............((((.(((((((.....))))))).))))...)))........))))))))...)).))).... ( -31.79, z-score =  -2.06, R)
>dp4.chrXR_group8 2512714 125 - 9212921
CCUCUGCGGCUGUUCAGUCAACUGAUGCAGCAACGCAGUUGUAACCCGGCCACACUCACUAAUAGUUCUAAUUGCAAAAAGCAAUUAAAACUUUCACCAACUC-AAGAUGCACACAUCCAAGGAAU-
...((((((((((((((....)))).)))))..))))).......((................((((.(((((((.....))))))).))))...........-..((((....))))...))...- ( -30.70, z-score =  -2.59, R)
>droPer1.super_36 608422 125 + 818889
CCUCUGCGGCUGUUCAGUCAACUGAUGCAGCAACGCAGUUGUAACCCGGCCACACUCACUAAUAGUUCUAAUUGCAAAAAGCAAUUAAAACUUUCACCAACUC-AAGAUGCACACAUCCAAGGAAU-
...((((((((((((((....)))).)))))..))))).......((................((((.(((((((.....))))))).))))...........-..((((....))))...))...- ( -30.70, z-score =  -2.59, R)
>droAna3.scaffold_13337 1594959 126 - 23293914
CUUCUGCGGCUCUGCAGUCAACUGAUGCAGCUACGCAUUUGUAACCCGGCCGCACUUACUAAUAGUUCUAAUUGCAAAAAGCAAUUAAAACUUUCGCCAACUCCAAGAUGCACAUAUACCCGGGCA-
....((((...(((((.((....)))))))...)))).......(((((..............((((.(((((((.....))))))).))))...((............))........)))))..- ( -30.50, z-score =  -1.23, R)
>droVir3.scaffold_13049 5568648 125 - 25233164
CUGCUGCGGCUGUGCAGUCAACUGAGGCAGCGACGCAGUUGUAAACCGGC-GCACUCACUAAUAGUUCUAAUUGCAAAAAGCAAUUAAAACUUUCGCCAACUC-AAGACAGACACACACACCACUCA
(((((((((((((.(((....)))..)))))..))))).........(((-(...........((((.(((((((.....))))))).))))..)))).....-....)))................ ( -33.02, z-score =  -1.31, R)
>consensus
CUUCUGCGGCUGUGCAGUCAACUGAUGCAGCUACGCAGUUGUAACCCGGCCACACUCACUAAUAGUUCUAAUUGCAAAAAGCAAUUAAAACUUUCGCCAACUCCAAGAUGCACAUACCCACAGCACG
....((((((((..(((....))).((((((......))))))...)))))............((((.(((((((.....))))))).)))).................)))............... (-24.31 = -24.98 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 13,721,983 – 13,722,110
Length 127
Sequences 9
Columns 127
Reading direction reverse
Mean pairwise identity 91.94
Shannon entropy 0.16733
G+C content 0.46297
Mean single sequence MFE -44.04
Consensus MFE -31.58
Energy contribution -31.56
Covariance contribution -0.02
Combinations/Pair 1.03
Mean z-score -2.23
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.46
SVM RNA-class probability 0.704853
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13721983 127 - 24543557
CGUGCUGUGGGUAUGUGCAUCUUGGAGUUGGCGAAAGUUUUAAUUGCUUUUUGCAAUUAGAACUAUUAGUGAGUGCGGCCGGGUUACAACUGCGUAGCUGCAUCAGUUGACUGCACAGCCGCAGAAG
....((((((...((((((.......((..((...((((((((((((.....)))))))))))).....(((.((((((.(.((.......)).).)))))))))))..)))))))).))))))... ( -47.81, z-score =  -2.67, R)
>droEre2.scaffold_4784 13728321 127 - 25762168
CGUGCUGUGGGUAUGUGCAUCUUGGAGUUGGUGAAAGUUUUAAUUGCUUUUUGCAAUUAGAACUAUUAGUGAGUGUGGCCGGGUUACAACUGCGUAGCUGCAUCAGUUGACUGCACAGCCGCAGAAG
....((((((...((((((.((((((.(((.(((.((((((((((((.....)))))))))))).))).))).)....)))))...((((((.((....))..))))))..)))))).))))))... ( -43.60, z-score =  -1.90, R)
>droYak2.chr3L 13819095 127 - 24197627
CGUGCUGUGGGUAUGUGCAUCUUGGAGUUGGUGAAAGUUUUAAUUGCUUUUUGCAAUUAGAACUAUUAGUGAGUGUGGCCGGGUUACAACUGCGUAGCUGCAUCAGUUGACUGCACAGCCGCAGAAG
....((((((...((((((.((((((.(((.(((.((((((((((((.....)))))))))))).))).))).)....)))))...((((((.((....))..))))))..)))))).))))))... ( -43.60, z-score =  -1.90, R)
>droSec1.super_0 5884017 127 - 21120651
CGUUCUGUGGGUAUGUGCAUCUUGGAGUUGGCGAAAGUUUUAAUUGCUUUUUGCAAUUAGAACUAUUAGUGAGUGUGGCCGGGUUACAACUGCGUAGCUGCAUCAGUUGACUGCACAGCCGCAGAAG
..((((((((...((((((.......((..((...((((((((((((.....)))))))))))).....(((.((..((.(.((.......)).).))..)))))))..)))))))).)))))))). ( -47.81, z-score =  -3.33, R)
>droSim1.chr3L 13107726 127 - 22553184
CGUGCUGUGGGUAUGUGCAUCUUGGAGUUGGCGAAAGUUUUAAUUGCUUUUUGCAAUUAGAACUAUUAGUGAGUGUGGCCGGGUUACAACUGCGUAGCUGCAUCAGUUGACUGCACAGCCGCAGAAG
....((((((...((((((.......((..((...((((((((((((.....)))))))))))).....(((.((..((.(.((.......)).).))..)))))))..)))))))).))))))... ( -45.31, z-score =  -2.17, R)
>dp4.chrXR_group8 2512714 125 + 9212921
-AUUCCUUGGAUGUGUGCAUCUU-GAGUUGGUGAAAGUUUUAAUUGCUUUUUGCAAUUAGAACUAUUAGUGAGUGUGGCCGGGUUACAACUGCGUUGCUGCAUCAGUUGACUGAACAGCCGCAGAGG
-.(((...(((((....))))).-)))(((.(((.((((((((((((.....)))))))))))).))).))).((((((...)))))).(((((..((((..((((....)))).)))))))))... ( -40.20, z-score =  -1.99, R)
>droPer1.super_36 608422 125 - 818889
-AUUCCUUGGAUGUGUGCAUCUU-GAGUUGGUGAAAGUUUUAAUUGCUUUUUGCAAUUAGAACUAUUAGUGAGUGUGGCCGGGUUACAACUGCGUUGCUGCAUCAGUUGACUGAACAGCCGCAGAGG
-.(((...(((((....))))).-)))(((.(((.((((((((((((.....)))))))))))).))).))).((((((...)))))).(((((..((((..((((....)))).)))))))))... ( -40.20, z-score =  -1.99, R)
>droAna3.scaffold_13337 1594959 126 + 23293914
-UGCCCGGGUAUAUGUGCAUCUUGGAGUUGGCGAAAGUUUUAAUUGCUUUUUGCAAUUAGAACUAUUAGUAAGUGCGGCCGGGUUACAAAUGCGUAGCUGCAUCAGUUGACUGCAGAGCCGCAGAAG
-(((....)))..((((..(((.(.(((..((...((((((((((((.....))))))))))))........(((((((.(.((.......)).).)))))))..))..))).))))..)))).... ( -41.40, z-score =  -1.64, R)
>droVir3.scaffold_13049 5568648 125 + 25233164
UGAGUGGUGUGUGUGUCUGUCUU-GAGUUGGCGAAAGUUUUAAUUGCUUUUUGCAAUUAGAACUAUUAGUGAGUGC-GCCGGUUUACAACUGCGUCGCUGCCUCAGUUGACUGCACAGCCGCAGCAG
...(((((.((((((((....((-(((..(((((.((((((((((((.....))))))))))))...........(-((.(((.....)))))))))))..)))))..))).))))))))))..... ( -46.40, z-score =  -2.52, R)
>consensus
CGUGCUGUGGGUAUGUGCAUCUUGGAGUUGGCGAAAGUUUUAAUUGCUUUUUGCAAUUAGAACUAUUAGUGAGUGUGGCCGGGUUACAACUGCGUAGCUGCAUCAGUUGACUGCACAGCCGCAGAAG
........................((.(((((...((((((((((((.....))))))))))))(((....)))...))))).))....(((((..((((...(((....)))..)))))))))... (-31.58 = -31.56 +  -0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:24:15 2011