Locus 13748

Sequence ID dm3.chrX
Location 8,880,114 – 8,880,231
Length 117
Max. P 0.864937
window18913 window18914

overview

Window 3

Location 8,880,114 – 8,880,231
Length 117
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 75.51
Shannon entropy 0.47887
G+C content 0.42146
Mean single sequence MFE -32.13
Consensus MFE -17.76
Energy contribution -20.57
Covariance contribution 2.81
Combinations/Pair 1.32
Mean z-score -1.64
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.97
SVM RNA-class probability 0.864937
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8880114 117 + 22422827
UUCUAAACAAGUGCACAUUUCAAAUGCACAAAGCCAUUUUGGAAGGCUGAACAGUG-AGUUUUUUUGUUUUGUGGCUACAGAAAUGGCAGCUUUAAUGUGCACACACAUUGGGGAAAA
((((...((((((((((((.....(((....((((((...((((((((........-))))))))......)))))).((....))))).....))))))))).....))).)))).. ( -33.40, z-score =  -1.73, R)
>droEre2.scaffold_4690 12517163 116 - 18748788
AUCUAAGCAAGUGCACAUUUCAAAUGCACAAAGCCAUUUCAGAAAACUGAACAGGGGAGUUUUUUG--UUUGUGGCUACAAAAAUGGCAGCUUUAAUAUGCACAUACAUUGGGGAAAA
.(((((....(((((.(((.....(((....((((((..(((((((((.........)))))))))--...)))))).((....))))).....))).))))).....)))))..... ( -29.30, z-score =  -1.73, R)
>droYak2.chrX 9338225 99 - 21770863
UUCUAAGCAAGUGCACAUUUCAAAUGCACAAAGCCAUUUCAGAAAACUGAACAGGG-AGUUUUUUG--UUUGCGGCUACAGAAAUGACAGCAUUGGGGAAAA----------------
((((((((..(((((.........)))))..((((....(((((((((........-)))))))))--.....)))).((....))...)).))))))....---------------- ( -24.70, z-score =  -1.43, R)
>droSec1.super_34 243644 115 + 457129
UUCUAAACAAGUGCACAUUUCAAAUGCACAAAGCCAUUUGAGAAGGCUGAACAGGG-AGUUUUUUG--UUUGUGGCUUCAGAAAUGGCAGCUUUAAUGUGCACACACAUUGGGGAAAA
..........(((((.........)))))...(((((((..((((.((((((((((-....)))))--)))).).))))..)))))))..((((((((((....)))))))))).... ( -35.20, z-score =  -2.38, R)
>droSim1.chrX 7077839 115 + 17042790
UUCUAAACAAGUGCACAUUUCAAAUGCACAAAGCUAUUUGAGAAGGCUGAACAGGG-AGUUUUUUG--UUUGUGGCUACAGAAAUGGCAGCUUUAAUGUGCACACACAUUGGGGAAAA
((((...((((((((((((((((((((.....)).)))))).(((((((.(((((.-((....)).--))))).....((....)).)))))))))))))))).....))).)))).. ( -32.10, z-score =  -2.07, R)
>droAna3.scaffold_13047 707298 102 + 1816235
-------------CCCAUUCCGAAUGCACAAAGCCAUUU--GGCAGCUGCCGGAGGCGGGGAGUUCG-UUUGCGGCUACACAAAUGGCGACUUUAAUGGGCCCACUUGUGGGGGCGGA
-------------.....((((..(.(((((.(((((((--(......((((.((((((.....)))-))).))))....))))))))........((....)).))))).)..)))) ( -38.10, z-score =  -0.48, R)
>consensus
UUCUAAACAAGUGCACAUUUCAAAUGCACAAAGCCAUUUCAGAAAGCUGAACAGGG_AGUUUUUUG__UUUGUGGCUACAGAAAUGGCAGCUUUAAUGUGCACACACAUUGGGGAAAA
..........(((((((((.....(((....((((((...((((((((.........))))))))......)))))).((....))))).....)))))))))............... (-17.76 = -20.57 +   2.81)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 8,880,114 – 8,880,231
Length 117
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 75.51
Shannon entropy 0.47887
G+C content 0.42146
Mean single sequence MFE -26.07
Consensus MFE -15.74
Energy contribution -15.97
Covariance contribution 0.23
Combinations/Pair 1.38
Mean z-score -1.34
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.805784
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8880114 117 - 22422827
UUUUCCCCAAUGUGUGUGCACAUUAAAGCUGCCAUUUCUGUAGCCACAAAACAAAAAAACU-CACUGUUCAGCCUUCCAAAAUGGCUUUGUGCAUUUGAAAUGUGCACUUGUUUAGAA
...............(((((((((...(((((.......)))))((((((.......(((.-....)))..(((.........))))))))).......))))))))).......... ( -25.90, z-score =  -1.06, R)
>droEre2.scaffold_4690 12517163 116 + 18748788
UUUUCCCCAAUGUAUGUGCAUAUUAAAGCUGCCAUUUUUGUAGCCACAAA--CAAAAAACUCCCCUGUUCAGUUUUCUGAAAUGGCUUUGUGCAUUUGAAAUGUGCACUUGCUUAGAU
...........(((.((((((((((((((.(((((((((((........)--)))))).........(((((....))))).)))).....)).)))))..))))))).)))...... ( -27.10, z-score =  -2.20, R)
>droYak2.chrX 9338225 99 + 21770863
----------------UUUUCCCCAAUGCUGUCAUUUCUGUAGCCGCAAA--CAAAAAACU-CCCUGUUCAGUUUUCUGAAAUGGCUUUGUGCAUUUGAAAUGUGCACUUGCUUAGAA
----------------...........((((.((....)))))).((((.--.........-.((..(((((....)))))..))....((((((.......))))))))))...... ( -19.40, z-score =  -0.84, R)
>droSec1.super_34 243644 115 - 457129
UUUUCCCCAAUGUGUGUGCACAUUAAAGCUGCCAUUUCUGAAGCCACAAA--CAAAAAACU-CCCUGUUCAGCCUUCUCAAAUGGCUUUGUGCAUUUGAAAUGUGCACUUGUUUAGAA
........((((((....)))))).((((.(((((((..((((.(...((--((.......-...))))..).))))..)))))))...((((((.......))))))..)))).... ( -26.80, z-score =  -1.66, R)
>droSim1.chrX 7077839 115 - 17042790
UUUUCCCCAAUGUGUGUGCACAUUAAAGCUGCCAUUUCUGUAGCCACAAA--CAAAAAACU-CCCUGUUCAGCCUUCUCAAAUAGCUUUGUGCAUUUGAAAUGUGCACUUGUUUAGAA
...............(((((((((...(((((.......)))))......--.........-...............((((((.((.....))))))))))))))))).......... ( -24.00, z-score =  -1.51, R)
>droAna3.scaffold_13047 707298 102 - 1816235
UCCGCCCCCACAAGUGGGCCCAUUAAAGUCGCCAUUUGUGUAGCCGCAAA-CGAACUCCCCGCCUCCGGCAGCUGCC--AAAUGGCUUUGUGCAUUCGGAAUGGG-------------
((((....((((((..(((........)))((((((((.(((((((....-))........(((...))).))))))--)))))))))))))....)))).....------------- ( -33.20, z-score =  -0.78, R)
>consensus
UUUUCCCCAAUGUGUGUGCACAUUAAAGCUGCCAUUUCUGUAGCCACAAA__CAAAAAACU_CCCUGUUCAGCCUUCUCAAAUGGCUUUGUGCAUUUGAAAUGUGCACUUGUUUAGAA
...............(((((((((...(((((.......)))))(((((........(((......))).((((.........))))))))).......))))))))).......... (-15.74 = -15.97 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:27:03 2011