Locus 10706

Sequence ID dm3.chr3R
Location 15,900,569 – 15,900,660
Length 91
Max. P 0.934738
window14716 window14717

overview

Window 6

Location 15,900,569 – 15,900,660
Length 91
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 75.79
Shannon entropy 0.46356
G+C content 0.42752
Mean single sequence MFE -26.53
Consensus MFE -13.85
Energy contribution -14.41
Covariance contribution 0.56
Combinations/Pair 1.24
Mean z-score -1.96
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.21
SVM RNA-class probability 0.909637
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15900569 91 + 27905053
AAAAUAUUGUUUUCGUUU-GUGGGA---UGGCAGCAAAUGCAUGGAUUGAAAUUGAAAUGUGCCCGAGGGCAGUAACAAACUCCCCGAACGAAAA---
.........(((((((((-(.((((---..(((.....)))...................((((....)))).........))))))))))))))--- ( -26.40, z-score =  -2.01, R)
>droSim1.chr3R 21948281 97 - 27517382
AAAAUAUUGUUUUCGUUU-GUGGGAGGAUGACAGCGAAUGCAUGGAUUGAAAUUGAAAUGUGCCCGAGGGCAGUAACAAACUCCCCGAACGAAAGAAA
.........(((((((((-(.(((((..(((((.(((...((.....))...)))...)))(((....))).....))..)))))))))))))))... ( -31.20, z-score =  -3.81, R)
>droSec1.super_58 143732 97 - 188520
AAAAUAUUGUUUCCGUUU-GUGGGAGGAUGGCAGCGAAUGCAUGGAUUGAAAUUGAAAUGUGCCCGAGGGCAGGAACAAACUCCCCGAACGAAAGAAA
......((.((((.((((-(.(((((..(((((.....))).................(.((((....)))).)..))..)))))))))))))).)). ( -30.10, z-score =  -2.53, R)
>droYak2.chr3R 4686864 91 + 28832112
AAAAUAUUGUUUUCGUUUUGUGGGA---UGGCAGGGGAUGCAUGGUUUGAAAUUGAAAUGUGCCUGAGGGCAGCACCAAACUCCCCGAACGAAG----
...........(((((((.(.((((---.(.....((.(((...((((.......)))).((((....)))))))))...))))))))))))).---- ( -22.50, z-score =   0.24, R)
>droEre2.scaffold_4770 11987054 87 - 17746568
AAAAUAUUGUUUUCGUUU-GUGGGA---UGCCAGCGAAUGCAUGGAUCGAAAUUGAAAUGUGCCUGAGGGCA---ACGAAUUCCCCGAACGACA----
............((((((-(.((((---((((..((...(((((..(((....)))..))))).))..))))---......)))))))))))..---- ( -25.00, z-score =  -1.44, R)
>droWil1.scaffold_181108 3906622 83 + 4707319
GGUUUUUUAUUUUUGUUU-GUUACAAAUUGU-----AACGCAUUGGGAAAAUUGAAAAUGGGCUUCAGGGC-----CCAAUUCCC-AAACAAACC---
(((((.............-(((((.....))-----)))...(((((((...(....)((((((....)))-----))).)))))-))..)))))--- ( -24.00, z-score =  -2.18, R)
>consensus
AAAAUAUUGUUUUCGUUU_GUGGGA___UGGCAGCGAAUGCAUGGAUUGAAAUUGAAAUGUGCCCGAGGGCAG_AACAAACUCCCCGAACGAAA____
..........((((((((...((((...((.........((((..............))))(((....))).....))...)))).)))))))).... (-13.85 = -14.41 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 15,900,569 – 15,900,660
Length 91
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 75.79
Shannon entropy 0.46356
G+C content 0.42752
Mean single sequence MFE -22.68
Consensus MFE -11.36
Energy contribution -11.58
Covariance contribution 0.23
Combinations/Pair 1.33
Mean z-score -2.14
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.39
SVM RNA-class probability 0.934738
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15900569 91 - 27905053
---UUUUCGUUCGGGGAGUUUGUUACUGCCCUCGGGCACAUUUCAAUUUCAAUCCAUGCAUUUGCUGCCA---UCCCAC-AAACGAAAACAAUAUUUU
---((((((((.(((((..(((....((((....)))).....)))...........(((.....)))..---)))).)-.))))))))......... ( -21.50, z-score =  -1.83, R)
>droSim1.chr3R 21948281 97 + 27517382
UUUCUUUCGUUCGGGGAGUUUGUUACUGCCCUCGGGCACAUUUCAAUUUCAAUCCAUGCAUUCGCUGUCAUCCUCCCAC-AAACGAAAACAAUAUUUU
....(((((((.((((((..((....((((....))))................((.((....)))).))..))))).)-.))))))).......... ( -24.80, z-score =  -3.49, R)
>droSec1.super_58 143732 97 + 188520
UUUCUUUCGUUCGGGGAGUUUGUUCCUGCCCUCGGGCACAUUUCAAUUUCAAUCCAUGCAUUCGCUGCCAUCCUCCCAC-AAACGGAAACAAUAUUUU
....(((((((.((((((..((....((((....))))...................(((.....)))))..))))).)-.))))))).......... ( -24.90, z-score =  -2.56, R)
>droYak2.chr3R 4686864 91 - 28832112
----CUUCGUUCGGGGAGUUUGGUGCUGCCCUCAGGCACAUUUCAAUUUCAAACCAUGCAUCCCCUGCCA---UCCCACAAAACGAAAACAAUAUUUU
----.((((((.(((((((.((((..((((....))))..............)))).)).)))))((...---.....)).))))))........... ( -20.89, z-score =  -1.24, R)
>droEre2.scaffold_4770 11987054 87 + 17746568
----UGUCGUUCGGGGAAUUCGU---UGCCCUCAGGCACAUUUCAAUUUCGAUCCAUGCAUUCGCUGGCA---UCCCAC-AAACGAAAACAAUAUUUU
----..(((((.(((((....((---.(((....)))))..............(((.((....)))))..---)))).)-.)))))............ ( -19.90, z-score =  -1.00, R)
>droWil1.scaffold_181108 3906622 83 - 4707319
---GGUUUGUUU-GGGAAUUGG-----GCCCUGAAGCCCAUUUUCAAUUUUCCCAAUGCGUU-----ACAAUUUGUAAC-AAACAAAAAUAAAAAACC
---(((((((((-(((((.(((-----((......))))).........))))))).))(((-----((.....)))))-.............))))) ( -24.10, z-score =  -2.69, R)
>consensus
____UUUCGUUCGGGGAGUUUGUU_CUGCCCUCAGGCACAUUUCAAUUUCAAUCCAUGCAUUCGCUGCCA___UCCCAC_AAACGAAAACAAUAUUUU
.....((((((.((((((.(((....((((....)))).....))).))).......((....)).........)))....))))))........... (-11.36 = -11.58 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:28:58 2011