Locus 12581

Sequence ID dm3.chrX
Location 1,013,352 – 1,013,485
Length 133
Max. P 0.971906
window17301 window17302

overview

Window 1

Location 1,013,352 – 1,013,485
Length 133
Sequences 4
Columns 168
Reading direction forward
Mean pairwise identity 67.48
Shannon entropy 0.53464
G+C content 0.41084
Mean single sequence MFE -41.16
Consensus MFE -17.38
Energy contribution -18.88
Covariance contribution 1.50
Combinations/Pair 1.26
Mean z-score -2.37
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967499
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1013352 133 + 22422827
UUUCAGUGCACUGCAAGAAACCAGACUAGCAAUAGCGAAGGAAUAGUUUGAGAGCGUUCUUCGAGUCGGUAUUG-UAUUUAACGUGUU-AACACAUAGU--------GACCCU-------------------------AGACUGUGCAAUUUUUCUUUCAGUGCACCU
.....((((((((.((((((((.((((.((....))((((((...(((....))).)))))).)))))))((((-(.......(((..-..)))(((((--------......-------------------------..))))))))))..))))).)))))))).. ( -40.90, z-score =  -3.04, R)
>droSec1.super_10 840609 158 + 3036183
UUUCAGUGCACUGCAAGAAACGAGACCAGCUAUACCGAAGGAAUAGUUAGCGAGCGUUCUUCUAGUCAGUAUUG-UAUUUAACGUGUU-AACACAUAGU--------GACCCUUUAAAAAUCAGUAUACCUAAUGCUUAGACUGUGCACUUUUUCUUUCAGUGCAUCU
.....((((((((.((((((.(((............((((((...(((....))).))))))((((((((((((-........(((..-..)))(((.(--------((...........))).)))...)))))))..)))))....))))))))).)))))))).. ( -37.90, z-score =  -1.35, R)
>droYak2.chrX 925714 167 + 21770863
UUUCACUGCACUGCGAGAAACUAGACCAGCCAGUACAAACGAAUACUUAGAGAGCUCUCUUCAAGUCAAUAAUACUAUUUAACAUGUUUAACAUGUAGUAUAAAGAGAACCCUUUAAAAACAAGUACACCUCAAGCUAAGACUGCACUGCUUU-CUCGCAGUGCAACU
......((((((((((((((.(((........((((........((((..(((....)))..))))......((((.....(((((.....)))))))))(((((......))))).......)))).......((.......)).))).)))-)))))))))))... ( -45.00, z-score =  -4.30, R)
>droEre2.scaffold_4644 995921 152 + 2521924
UUUCAGUGCACUGCAAGAAACAAGACCAGCAAGUACGAACGAAUAAUUGGGGAGCGCUCUUGAGGUCAAU--------UUAACAUGU---ACGAGUAC----GAGAGGCCCAUUCGAAAAGAAGUACCCCUCAAGCAGAGAUGGCAUUGUUUU-CUCUCAGUGCAGCU
......(((((((..((((((((..(((....((((..............((.((.((((((.(.((...--------.........---..)).).)----))))))))).(((.....)))))))..(((.....))).)))..))).)))-))..)))))))... ( -40.84, z-score =  -0.81, R)
>consensus
UUUCAGUGCACUGCAAGAAACAAGACCAGCAAGAACGAACGAAUAGUUAGAGAGCGCUCUUCAAGUCAAUAUUG_UAUUUAACAUGUU_AACACAUAGU________GACCCUUUAAAAA_AAGUACACCUCAAGCU_AGACUGCACAGUUUU_CUCUCAGUGCAACU
.....((((((((.((((((...((((........(....)........(((....)))....))))..............(((((.....))))).......................................................)))))).)))))))).. (-17.38 = -18.88 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 1,013,352 – 1,013,485
Length 133
Sequences 4
Columns 168
Reading direction reverse
Mean pairwise identity 67.48
Shannon entropy 0.53464
G+C content 0.41084
Mean single sequence MFE -44.72
Consensus MFE -20.04
Energy contribution -20.23
Covariance contribution 0.19
Combinations/Pair 1.29
Mean z-score -2.26
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.86
SVM RNA-class probability 0.971906
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1013352 133 - 22422827
AGGUGCACUGAAAGAAAAAUUGCACAGUCU-------------------------AGGGUC--------ACUAUGUGUU-AACACGUUAAAUA-CAAUACCGACUCGAAGAACGCUCUCAAACUAUUCCUUCGCUAUUGCUAGUCUGGUUUCUUGCAGUGCACUGAAA
.(((((((((.((((((.......(((.((-------------------------((((((--------.....(((..-..)))((.....)-)......)))))((((..................))))((....))))).))).)))))).))))))))).... ( -37.07, z-score =  -2.41, R)
>droSec1.super_10 840609 158 - 3036183
AGAUGCACUGAAAGAAAAAGUGCACAGUCUAAGCAUUAGGUAUACUGAUUUUUAAAGGGUC--------ACUAUGUGUU-AACACGUUAAAUA-CAAUACUGACUAGAAGAACGCUCGCUAACUAUUCCUUCGGUAUAGCUGGUCUCGUUUCUUGCAGUGCACUGAAA
((.(((((((.((((((.(((((.........)))))((.(((((((((((((....((((--------(.((((((((-((....)).))))-).))).)))))..))))).(....)...........)))))))).)).......)))))).))))))))).... ( -38.50, z-score =  -0.66, R)
>droYak2.chrX 925714 167 - 21770863
AGUUGCACUGCGAG-AAAGCAGUGCAGUCUUAGCUUGAGGUGUACUUGUUUUUAAAGGGUUCUCUUUAUACUACAUGUUAAACAUGUUAAAUAGUAUUAUUGACUUGAAGAGAGCUCUCUAAGUAUUCGUUUGUACUGGCUGGUCUAGUUUCUCGCAGUGCAGUGAAA
..((((((((((((-(((..((..(((((...((..((.(.(((((((.......((((((((((((((((((((((.....))))).....))))).........)))))))))))).))))))).).)).))...)))))..))..)))))))))))))))..... ( -58.10, z-score =  -3.99, R)
>droEre2.scaffold_4644 995921 152 - 2521924
AGCUGCACUGAGAG-AAAACAAUGCCAUCUCUGCUUGAGGGGUACUUCUUUUCGAAUGGGCCUCUC----GUACUCGU---ACAUGUUAA--------AUUGACCUCAAGAGCGCUCCCCAAUUAUUCGUUCGUACUUGCUGGUCUUGUUUCUUGCAGUGCACUGAAA
((.(((((((..((-(((.(((.((((.........((((((..((((.....))).)..))))))----(((...((---((.......--------.(((....)))(((((.............))))))))).))))))).))))))))..))))))))).... ( -45.22, z-score =  -2.00, R)
>consensus
AGAUGCACUGAAAG_AAAACAGCACAGUCU_AGCUUGAGGUGUACUU_UUUUUAAAGGGUC________ACUACGUGUU_AACACGUUAAAUA_CAAUACUGACUUGAAGAACGCUCUCUAACUAUUCCUUCGUAAUUGCUGGUCUAGUUUCUUGCAGUGCACUGAAA
.(((((((((.((((((.......................................................(((((.....)))))..............((((....((....))...............((....)).))))...)))))).))))))))).... (-20.04 = -20.23 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:05:01 2011