Locus 13401

Sequence ID dm3.chrX
Location 6,357,912 – 6,358,028
Length 116
Max. P 0.682790
window18450 window18451

overview

Window 0

Location 6,357,912 – 6,358,028
Length 116
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 70.58
Shannon entropy 0.56968
G+C content 0.37352
Mean single sequence MFE -23.03
Consensus MFE -13.51
Energy contribution -12.98
Covariance contribution -0.52
Combinations/Pair 1.38
Mean z-score -0.75
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.682790
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6357912 116 + 22422827
GGUUUCAGUUUCAGUUUUCAACAAGCC-UGUCCGAAAAA-GGCAUGCCAUAAAUAGGUUCAUUAAUUGAACCGAAAAGGAAAUAAUGCUCAUGGACACAACUCUUGGAAUUUCGAAUA
((((((((((((..(((((.....(((-(.........)-)))............((((((.....))))))))))).)))))........((....)).....)))))))....... ( -23.70, z-score =  -0.56, R)
>droSim1.chrX 5002079 112 + 17042790
--UUUUGGUUUCAGUUU-CAACGAGC--UGUCCGAAAAA-GGCAUGCCAUAAAUAGGUUCAUUAAUUGAACCGAAAAGAAAAUAUUGCCCAUGGACACAACUCUUGGAAUUUCGAAUG
--.(((((....(((((-(((.(((.--((((((.....-((((...........((((((.....)))))).............))))..))))))...)))))))))))))))).. ( -27.75, z-score =  -2.05, R)
>droSec1.super_4 5748107 114 - 6179234
--UUUUGGUUUCAGUUUUCAACGAGCC-UGUCCGAAAAA-GGCAUGCCAUAAAUAGGUUCAUUAAUUGAACCGAAAUGAAAAUAUUGCUCAUGGACACAACUCUUGGAAUUUCGAAUG
--.....((((.((.((((((.(((..-((((((.....-((....)).......((((((.....))))))...................))))))...))))))))).)).)))). ( -25.60, z-score =  -1.19, R)
>droYak2.chrX 2334021 117 + 21770863
AGUUUAAGUUUCAGUUUUCAACGAGCCCCGUCCGAAAAA-GGCAUGCCAUAAAUAGGUUCAUUAAUUGAACCGAAAGGAAAAUAAUGCUCUUGGACACAACUCUUGGAAUGUCGAAUA
.......((((....((((((.(((....((((((....-(((((..........((((((.....))))))............))))).))))))....)))))))))....)))). ( -26.45, z-score =  -1.19, R)
>droEre2.scaffold_4690 15302474 100 + 18748788
AGUUUCAGUUUCAGUUUUCAACGAGCC-CGUCCGAAAAAAGGCAUGCCAUAAAUAGGUUCAUUAAUUGAACUGGAAAGAAAACAUUGCCAAUGGACACAAC-----------------
.((((((....((((((((..((....-))(((.......((....)).......((((((.....)))))))))..))))))..))....)))).))...----------------- ( -18.00, z-score =  -0.15, R)
>droAna3.scaffold_13335 1325476 105 - 3335858
-------GAUUUUUUUCUCAUUUUAC--UCUUCGGAUUUCGG-AGGACAUAAUGAACUUUAUUUUGUAAAUUGCCAAGCAAACGCCAAAGCAAAAGGUCAAUCGGGGAGUUUUAA---
-------......((((((.......--(((((.(....).)-)))).....(((.((((.(((((....((((...))))....)))))..)))).)))...))))))......--- ( -16.70, z-score =   0.61, R)
>consensus
__UUUCAGUUUCAGUUUUCAACGAGCC_UGUCCGAAAAA_GGCAUGCCAUAAAUAGGUUCAUUAAUUGAACCGAAAAGAAAAUAUUGCUCAUGGACACAACUCUUGGAAUUUCGAAU_
.............................(((((......((....)).......((((((.....))))))...................)))))...................... (-13.51 = -12.98 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,357,912 – 6,358,028
Length 116
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 70.58
Shannon entropy 0.56968
G+C content 0.37352
Mean single sequence MFE -21.97
Consensus MFE -14.47
Energy contribution -14.87
Covariance contribution 0.39
Combinations/Pair 1.39
Mean z-score -0.46
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.627921
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6357912 116 - 22422827
UAUUCGAAAUUCCAAGAGUUGUGUCCAUGAGCAUUAUUUCCUUUUCGGUUCAAUUAAUGAACCUAUUUAUGGCAUGCC-UUUUUCGGACA-GGCUUGUUGAAAACUGAAACUGAAACC
..((((...(((...(((((.(((((....................((((((.....)))))).......((....))-......)))))-)))))...)))...))))......... ( -22.60, z-score =  -0.24, R)
>droSim1.chrX 5002079 112 - 17042790
CAUUCGAAAUUCCAAGAGUUGUGUCCAUGGGCAAUAUUUUCUUUUCGGUUCAAUUAAUGAACCUAUUUAUGGCAUGCC-UUUUUCGGACA--GCUCGUUG-AAACUGAAACCAAAA--
..((((...(((...((((..(((((..(((((.............((((((.....))))))...........))))-).....)))))--))))...)-))..)))).......-- ( -24.85, z-score =  -1.00, R)
>droSec1.super_4 5748107 114 + 6179234
CAUUCGAAAUUCCAAGAGUUGUGUCCAUGAGCAAUAUUUUCAUUUCGGUUCAAUUAAUGAACCUAUUUAUGGCAUGCC-UUUUUCGGACA-GGCUCGUUGAAAACUGAAACCAAAA--
..((((...(((...(((((.((((((((((.......)))))...((((((.....)))))).......((....))-......)))))-)))))...)))...)))).......-- ( -24.40, z-score =  -0.88, R)
>droYak2.chrX 2334021 117 - 21770863
UAUUCGACAUUCCAAGAGUUGUGUCCAAGAGCAUUAUUUUCCUUUCGGUUCAAUUAAUGAACCUAUUUAUGGCAUGCC-UUUUUCGGACGGGGCUCGUUGAAAACUGAAACUUAAACU
..((((...(((...(((((.(((((....................((((((.....)))))).......((....))-......))))).)))))...)))...))))......... ( -27.30, z-score =  -1.28, R)
>droEre2.scaffold_4690 15302474 100 - 18748788
-----------------GUUGUGUCCAUUGGCAAUGUUUUCUUUCCAGUUCAAUUAAUGAACCUAUUUAUGGCAUGCCUUUUUUCGGACG-GGCUCGUUGAAAACUGAAACUGAAACU
-----------------....((((....))))..(((((..((.(((((...(((((((.((.......))...((((.((....)).)-)))))))))).))))).))..))))). ( -18.20, z-score =   0.37, R)
>droAna3.scaffold_13335 1325476 105 + 3335858
---UUAAAACUCCCCGAUUGACCUUUUGCUUUGGCGUUUGCUUGGCAAUUUACAAAAUAAAGUUCAUUAUGUCCU-CCGAAAUCCGAAGA--GUAAAAUGAGAAAAAAAUC-------
---............((((......(((((..(((....))).)))))..............((((((.((..((-.((.....)).)).--.)).)))))).....))))------- ( -14.50, z-score =   0.25, R)
>consensus
_AUUCGAAAUUCCAAGAGUUGUGUCCAUGAGCAAUAUUUUCUUUUCGGUUCAAUUAAUGAACCUAUUUAUGGCAUGCC_UUUUUCGGACA_GGCUCGUUGAAAACUGAAACUAAAA__
...............(((((.(((((....................((((((.....)))))).......((....)).......))))).)))))...................... (-14.47 = -14.87 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:20:40 2011