Locus 7828

Sequence ID dm3.chr3L
Location 17,663,938 – 17,664,069
Length 131
Max. P 0.808263
window10772 window10773

overview

Window 2

Location 17,663,938 – 17,664,035
Length 97
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 68.23
Shannon entropy 0.55241
G+C content 0.40581
Mean single sequence MFE -23.40
Consensus MFE -11.79
Energy contribution -11.46
Covariance contribution -0.32
Combinations/Pair 1.53
Mean z-score -1.22
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.46
SVM RNA-class probability 0.702504
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17663938 97 + 24543557
-----UCUGCCUUUACUAGGGCUUUUUGUCCAAACAU------UUUCCUACAGCAC----GUUUUAUGGCAUAAAGA-GUGGGUAAGCUCUUCCAAUGAGCUUGGACACUUAA----
-----..((((.......((((.....))))((((..------.............----))))...))))....((-(((..(((((((.......)))))))..)))))..---- ( -26.46, z-score =  -1.80, R)
>droWil1.scaffold_181017 535531 116 - 939937
GCGCCAUACACUUGCUUAAGGUCUUGAAUAUGAAUAUAAUUUAUUUUUUAUUCCAUUAAAGUUUAGCUUCAUUGAGAUAUGUAUAUAGGUUUCCA-UGAAUCUCUACGCUCAUGGCA
..(((((..((((.....))))...(((((.(((((.....)))))..))))).......((..((.(((((.(((((..........))))).)-)))).))..))....))))). ( -20.60, z-score =  -0.37, R)
>droYak2.chr3L 7807870 97 - 24197627
-----UCCUCCUCCGCUUGGCCUUUUUGUCCAAACAU------UUUCCUACAGCGC----GUCUUAUGGCGUAAAGU-GUGGGUAAGCUCUUCCAAUGAGCUUGGGUACUUAA----
-----.......(((.((((.(.....).)))).)..------...((((((..((----(((....)))))....)-)))))(((((((.......))))))))).......---- ( -24.70, z-score =  -0.89, R)
>droEre2.scaffold_4784 9573524 97 - 25762168
-----GCUUCCUCCGCUUGGGCUUUUUGUCCAAACAU------UUUCCCACAGCAC----GUUUUAUGACAUAAAGU-GUGGGUAAGCUCUUCCAAUGAGCUUGGGCACUUAA----
-----(((......(.((((((.....)))))).)..------...((((((....----(((....)))......)-)))))(((((((.......))))))))))......---- ( -26.50, z-score =  -1.43, R)
>droSec1.super_0 9710081 97 + 21120651
-----UCUUCCUCCACAAGGGCUUUUUGUCAAAACAU------UUUCCUACAGCAC----GUUUUAUGACAUAAAGA-GUGGGUAAGCUCCUUCAAUGAGCUUGGACACUUAA----
-----...((((.....))))((((.(((((((((..------.............----))))..))))).))))(-(((..(((((((.......)))))))..))))...---- ( -22.76, z-score =  -1.39, R)
>droSim1.chr3L 17002400 91 + 22553184
-----------UCUUCAUUUGCUUUUUGUCCAAACAU------UUUCCUACAGCAC----GUUUUAUGACAUAAAGA-GUGGGUAAGCUCCUUCAAUGAGCUUGGACACUUAA----
-----------..........((((.((((.((((..------.............----))))...)))).))))(-(((..(((((((.......)))))))..))))...---- ( -19.36, z-score =  -1.42, R)
>consensus
_____UCUUCCUCCACUAGGGCUUUUUGUCCAAACAU______UUUCCUACAGCAC____GUUUUAUGACAUAAAGA_GUGGGUAAGCUCUUCCAAUGAGCUUGGACACUUAA____
..........................(((((...............(((((.........(((....)))........))))).((((((.......)))))))))))......... (-11.79 = -11.46 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 17,663,978 – 17,664,069
Length 91
Sequences 7
Columns 91
Reading direction forward
Mean pairwise identity 62.58
Shannon entropy 0.70574
G+C content 0.39419
Mean single sequence MFE -20.66
Consensus MFE -9.06
Energy contribution -7.83
Covariance contribution -1.24
Combinations/Pair 1.67
Mean z-score -0.99
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.76
SVM RNA-class probability 0.808263
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17663978 91 + 24543557
AGCACGUUUUAUGGCAUAAAGAGUGGGUAAGCUCUUCCAAUGAGCUUGGACACUUAAUUGAAGUUAAUUUCGAUUUAGGGGUUCUCAGGAA
.((.(((...))))).....(((((..(((((((.......)))))))..))))).......(..(((..(......)..)))..)..... ( -21.90, z-score =  -0.96, R)
>droPer1.super_9 1497620 84 - 3637205
-----GUGCCGGGGGGUGGCAUCUAGUUUAUUUGAUUGUAUG-GCGAAAUUACUCCUUUUGAGGCAGUUUCAAUAUAUAAUUCAAUGAAA-
-----((((((.....))))))....((((((.(((((((((-..((((((.(((.....)))..))))))..))))))))).)))))).- ( -22.40, z-score =  -1.88, R)
>dp4.chrXR_group6 9467688 74 - 13314419
-----GUGCCGGGGGGUGGCAUCUAGUUUAUUUGAUUGUAUA-GCGAAAUUACUCCUUUUGAGGCAGUUUCAAUAUGAAA-----------
-----.((((((((((((((((.(((((.....))))).)).-)).....))))))))....)))).((((.....))))----------- ( -14.10, z-score =   0.51, R)
>droYak2.chr3L 7807910 80 - 24197627
AGCGCGUCUUAUGGCGUAAAGUGUGGGUAAGCUCUUCCAAUGAGCUUGGGUACUUAAUUGGAGUUAAUUUCGAUUUAAUG-----------
...(((((....))))).....(((..(((((((.......)))))))..)))..((((((((....)))))))).....----------- ( -19.40, z-score =  -1.06, R)
>droEre2.scaffold_4784 9573564 91 - 25762168
AGCACGUUUUAUGACAUAAAGUGUGGGUAAGCUCUUCCAAUGAGCUUGGGCACUUAAUUGGAGUUAAUUUGGAUUUAAUGGUUCUCUAGAA
.....(((....)))...((((((...(((((((.......))))))).))))))..((((((...(((.......)))....)))))).. ( -19.00, z-score =  -0.08, R)
>droSec1.super_0 9710121 91 + 21120651
AGCACGUUUUAUGACAUAAAGAGUGGGUAAGCUCCUUCAAUGAGCUUGGACACUUAAUUGGAGUUAAUAUCGAUUUAGGGGUGCUCAGAAA
((((((((....))).....(((((..(((((((.......)))))))..))))).........................)))))...... ( -22.80, z-score =  -1.41, R)
>droSim1.chr3L 17002434 91 + 22553184
AGCACGUUUUAUGACAUAAAGAGUGGGUAAGCUCCUUCAAUGAGCUUGGACACUUAAUUGGAGUUAAUUUCGAUUUAGGGGUGCUCAGUAA
((((((((....))).....(((((..(((((((.......)))))))..)))))((((((((....)))))))).....)))))...... ( -25.00, z-score =  -2.03, R)
>consensus
AGCACGUUUUAUGGCAUAAAGUGUGGGUAAGCUCUUUCAAUGAGCUUGGACACUUAAUUGGAGUUAAUUUCGAUUUAAGGGU_CUCAG_AA
......(((((.....))))).(((..(((((((.......)))))))..)))...................................... ( -9.06 =  -7.83 +  -1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:34:15 2011