Locus 8479

Sequence ID dm3.chr3L
Location 23,339,403 – 23,339,637
Length 234
Max. P 0.997981
window11642 window11643 window11644 window11645

overview

Window 2

Location 23,339,403 – 23,339,512
Length 109
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 54.23
Shannon entropy 0.76040
G+C content 0.51425
Mean single sequence MFE -36.60
Consensus MFE -10.61
Energy contribution -11.30
Covariance contribution 0.69
Combinations/Pair 1.54
Mean z-score -1.41
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.17
SVM RNA-class probability 0.577511
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23339403 109 - 24543557
-----CCUGUCAUUUCAGCCCUA-CAGGCGCCCCCACAUGGGAUGCCUGUGGGAAGCAGGGGUUAAAAGUUUCAAG-AUUCACUUCUACAAGACCACGGGUAAUUUUAAAUAUACA
-----(((((.((..(.((((((-(((((((((......))).))))))))))..)).)..)).....((((..((-(......)))...)))).)))))................ ( -32.40, z-score =  -1.44, R)
>droYak2.chr3L 23921230 106 - 24197627
GCGAAUUUGCGUUCACACCCCCU-CGCGC-UCCGCACAUGGGCGGACUAUGGGAGGCAGGUGUGAAAACUGCAAAACACCUACUCCUACGAG-CGGUGGGAAGCGCACU-------
(((..((((((((((((((.(((-(.((.-(((((......)))))...)).))))..))))))))...))))))........((((((...-..))))))..)))...------- ( -44.00, z-score =  -2.87, R)
>dp4.Unknown_group_112 11972 113 + 17658
GCGAAUUUGCGUUAAUACCGCCG-CGAGC-UCCUCACAUGGGAGGGCUAUGGGAGGUAGGUGUAAAAACUGCCAAGGGCCUACUCCUACGGG-CGAUAGGCAGCGCGCUCCUAACC
........(((((....((.(((-..(((-.((((......))))))).)))..(((((.........)))))..))((((((.((....))-.).)))))))))).......... ( -39.80, z-score =  -0.03, R)
>triCas2.ChLG6 13063411 112 - 13544221
---UAUAUGGAAGUCUAUUCCUGCCAAGUCUCCAUAUACCGGGGGAAUUUGGGAAGCGGGGGUUAAAACAUUUAAGCAUCAUUUUAAACGUG-UUGUGGGACUCUCGUUAUUAACA
---.....((((.....))))..((((((((((........)))).))))))..((((((((((..((((((((((......)))))..)))-))....))))))))))....... ( -30.20, z-score =  -1.32, R)
>consensus
___AAUUUGCGAUUACACCCCCG_CAAGC_UCCACACAUGGGAGGACUAUGGGAAGCAGGGGUUAAAACUGCCAAGCACCUACUCCUACGAG_CGAUGGGAAGCGCGCUAUUAACA
........(((((.....((((.....((.(((...(((((.....)))))))).)).))))......................(((((......))))).))))).......... (-10.61 = -11.30 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 23,339,442 – 23,339,543
Length 101
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 54.19
Shannon entropy 0.75753
G+C content 0.49140
Mean single sequence MFE -34.90
Consensus MFE -14.06
Energy contribution -15.12
Covariance contribution 1.06
Combinations/Pair 1.62
Mean z-score -2.32
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.23
SVM RNA-class probability 0.997981
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23339442 101 - 24543557
-----CAAGUUACCUCGUCGAGCCA----UCAAAGCCUAUCCUGUCAUUUCAGCCCUACAGGCGCCCCCACAUGGGAUGCCUGUGGGAAGCAGGGGUUAAAAGUUUCAAG
-----......(((((...((....----))...((.....(((......))).(((((((((((((......))).))))))))))..)).)))))............. ( -31.80, z-score =  -1.48, R)
>droYak2.chr3L 23921262 104 - 24197627
-----CAAUUCGCGAGUUCGCAUCAAAAAGCGGAUGCGAAUUUGCGUUCACACCCCCUCGCGC-UCCGCACAUGGGCGGACUAUGGGAGGCAGGUGUGAAAACUGCAAAA
-----.....((((((((((((((........))))))))))))))((((((((.((((.((.-(((((......)))))...)).))))..)))))))).......... ( -49.50, z-score =  -5.17, R)
>dp4.Unknown_group_112 12011 104 + 17658
-----CAAUUCGCGACUUCGCGUCAAAAAACGGAUGCGAAUUUGCGUUAAUACCGCCGCGAGC-UCCUCACAUGGGAGGGCUAUGGGAGGUAGGUGUAAAAACUGCCAAG
-----.....(((((.((((((((........)))))))).)))))....((((.((.(((((-.((((......))))))).)))).))))(((((....)).)))... ( -38.00, z-score =  -2.83, R)
>triCas2.ChLG6 13063450 110 - 13544221
AAAAGAAAGUAGUCAAAAGAUUAAAUAAUGAAGGUAUUAUAUGGAAGUCUAUUCCUGCCAAGUCUCCAUAUACCGGGGGAAUUUGGGAAGCGGGGGUUAAAACAUUUAAG
.........(((((....))))).............(((.(((.......(((((((((((((((((........)))).)))))....)))))))).....))).))). ( -20.30, z-score =   0.19, R)
>consensus
_____CAAGUCGCCACUUCGCGUCAAAAAGCAGAUGCGAAUUUGCGUUCACACCCCCACAAGC_UCCACACAUGGGAGGACUAUGGGAAGCAGGGGUUAAAACUGCCAAG
...........((((.((((((((........)))))))).))))........((((....((.(((...(((((.....)))))))).)).)))).............. (-14.06 = -15.12 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 23,339,446 – 23,339,547
Length 101
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 54.77
Shannon entropy 0.72356
G+C content 0.50109
Mean single sequence MFE -35.73
Consensus MFE -12.19
Energy contribution -14.25
Covariance contribution 2.06
Combinations/Pair 1.50
Mean z-score -2.20
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.15
SVM RNA-class probability 0.983891
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23339446 101 - 24543557
--------GGCACAAGUUACCUCGUCGAGCCAUCAA----AGCCUAUCCUGUCAUUUCAGCCCUACAGGCGCCCCCACAUGGGAUGCCUGUGGGAAGCAGGGGUUAAAAGUUU
--------(((((.((....)).))...))).....----(((((...(((......))).(((((((((((((......))).))))))))))......)))))........ ( -32.30, z-score =  -0.72, R)
>droYak2.chr3L 23921266 104 - 24197627
--------GACGCAAUUCGCGAGUUCGCAUCAAAAAGCGGAUGCGAAUUUGCGUUCACACCCCCUCGCGC-UCCGCACAUGGGCGGACUAUGGGAGGCAGGUGUGAAAACUGC
--------...(((...((((((((((((((........))))))))))))))((((((((.((((.((.-(((((......)))))...)).))))..))))))))...))) ( -51.10, z-score =  -5.11, R)
>dp4.Unknown_group_112 12015 104 + 17658
--------GACACAAUUCGCGACUUCGCGUCAAAAAACGGAUGCGAAUUUGCGUUAAUACCGCCGCGAGC-UCCUCACAUGGGAGGGCUAUGGGAGGUAGGUGUAAAAACUGC
--------.((((....(((((.((((((((........)))))))).)))))....((((.((.(((((-.((((......))))))).)))).)))).))))......... ( -39.80, z-score =  -3.62, R)
>triCas2.ChLG6 13063454 110 - 13544221
UUUGAAAAGAAAGUAGUCAAAAGAUUAAAUAAUGAA---GGUAUUAUAUGGAAGUCUAUUCCUGCCAAGUCUCCAUAUACCGGGGGAAUUUGGGAAGCGGGGGUUAAAACAUU
.......(((...(((((....))))).((((((..---..)))))).......)))(((((((((((((((((........)))).)))))....))))))))......... ( -19.70, z-score =   0.63, R)
>consensus
________GACACAAGUCACGACUUCGAAUCAAAAA___GAUGCGAAUUUGCGUUCACACCCCCACAAGC_UCCACACAUGGGAGGACUAUGGGAAGCAGGGGUUAAAACUGC
..................((((.((((((((........)))))))).))))........((((....((.(((...(((((.....)))))))).)).)))).......... (-12.19 = -14.25 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 23,339,547 – 23,339,637
Length 90
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 55.17
Shannon entropy 0.76839
G+C content 0.50785
Mean single sequence MFE -28.74
Consensus MFE -7.14
Energy contribution -9.14
Covariance contribution 2.00
Combinations/Pair 1.76
Mean z-score -1.61
Structure conservation index 0.25
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.543768
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23339547 90 - 24543557
--AUGGGUGUCCUCUCAUUCUAUGUGCCGACAACGGAAAGGCCUAUGUGGGCGCGGAAAAAGCCCUCACGGGAGAUUUCUUCGCUACAGGAA---------
--(((((......)))))(((.((((.(((....(((((..((..((.((((.........)))).))..))...)))))))).))))))).--------- ( -26.60, z-score =   0.04, R)
>droSec1.super_41 221023 92 - 296808
AUGAGAGGACACUCUCAUUCUAUGUGGCGACAACGGAAAGACCUGUGCGGGCGCGGAAAAAGCCCUCACGGGAGACUUCCUCGCUACAGGAA---------
(((((((....)))))))(((.((((((((....((((...((((((.((((.........)))).))))))....))))))))))))))).--------- ( -42.00, z-score =  -4.94, R)
>droSim1.chr3L 22460309 92 - 22553184
AUGAGAGGACACUCUCAUUCUAUGUGGCGACAACGGAAAGACCUGUGCGGGCGCGGAAAAAGCCCUUACGGGAGACUUCCUUGCUACAGGAA---------
(((((((....)))))))(((.((((((((....((((...((((((.((((.........)))).))))))....))))))))))))))).--------- ( -37.70, z-score =  -4.19, R)
>droWil1.scaffold_181123 1341468 83 - 1459946
---AGGAGUACCCCGAAUGGUCCACUGCGACAAUGCGACGAAUUUUGUCGGAGCGAGCAGGGAGCU-GCCGGAUCUUCGUCGCAAGA--------------
---.((.....))((((.(((((.((.((((((...........)))))).)).(.((((....))-))))))))))))((....))-------------- ( -27.70, z-score =  -0.46, R)
>triCas2.ChLG6 13063564 91 - 13544221
---AGAAGAGUC---AAU--UAUAUCG-GACAAUGGUACAAAUUUCGUGGGUGCAAACAGAGAGUU-GCAGGAAAUUGAACAUUUAUUUAAGUCAAAUGAA
---.(((...((---(((--(.(((((-.....)))))(((.((((.((........)))))).))-).....))))))...)))................ (  -9.70, z-score =   1.50, R)
>consensus
___AGAGGACACUCUCAUUCUAUGUGGCGACAACGGAAAGACCUGUGUGGGCGCGGAAAAAGCCCU_ACGGGAGAUUUCCUCGCUACAGGAA_________
......................((((((((....((((...(((.((.((((.........)))).)).)))....))))))))))))............. ( -7.14 =  -9.14 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:46:22 2011