Locus 8221

Sequence ID dm3.chr3L
Location 21,079,445 – 21,079,545
Length 100
Max. P 0.710469
window11300 window11301

overview

Window 0

Location 21,079,445 – 21,079,545
Length 100
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 77.30
Shannon entropy 0.41085
G+C content 0.43732
Mean single sequence MFE -17.04
Consensus MFE -7.43
Energy contribution -8.32
Covariance contribution 0.89
Combinations/Pair 1.08
Mean z-score -2.21
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.710469
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21079445 100 + 24543557
CUCGCUCUAGCUGUCCCUCUCUUCGC--UGAUAUCUCCCAUU------UAUAUAUAUUUUCUCGGCAUCUGGGAA--ACUGCAUAAUUUUCCCGCUUUCCAGCUAUUUUG
.......((((((...........((--(((...........------.............)))))....(((((--(.(.....).))))))......))))))..... ( -18.26, z-score =  -2.27, R)
>droEre2.scaffold_4784 20767459 98 + 25762168
CUCGCUCUAGCUGUCUCUCUCUUUCC--CGAUAUCUCCCAUU--------UAUAUAUUUUCUCGGCAUCUGGGAA--ACUGCAUAAUUUUUCCGCUUUCCAGCUAUUUUG
.......((((((........(((((--((((..(.......--------.............)..))).)))))--)..((...........))....))))))..... ( -14.75, z-score =  -1.44, R)
>droYak2.chr3L 4752175 100 - 24197627
CUCGCUCUAGCUGUCUCUCUCUCUUCACCGAUAUCUCCCAUU--------UAUAUAUUUUCUCGGCAUCUGGGAA--ACUGCAUAAUUUUUCCGCUUUCCAGCUAUUUUG
.......((((((..............((((...........--------...........)))).....(((((--(.(.....).))))))......))))))..... ( -13.15, z-score =  -0.99, R)
>droSec1.super_11 1037151 106 + 2888827
CUCGCUCUAGCUGUCCCUCUCAUCGC--CGAUAUCUCCCAUUUAUAUGUAUAUAUAUUUUCUCGGCAUCUGGGAA--ACUGCAUAAUUUUCCCGCUUUCCAGCUAUUUUG
.......((((((...........((--(((...........(((((....))))).....)))))....(((((--(.(.....).))))))......))))))..... ( -20.29, z-score =  -2.42, R)
>droSim1.chr3L 20434526 106 + 22553184
CUCGCUCUAGCUGUCCCUCUCUUCGC--CGAUAUCUCCCAUUUAUAUGUAUAUAUAUUUUCUCGGCAUCUGGGAA--ACUGCAUAAUUUUCCCGCUUUCCAGCUAUUUUG
.......((((((...........((--(((...........(((((....))))).....)))))....(((((--(.(.....).))))))......))))))..... ( -20.29, z-score =  -2.58, R)
>droVir3.scaffold_13049 9970655 77 - 25233164
--------------CUCCCUCGUC----------CUCCCGUC---------GCAGUUUACCCCAAGCUUCGGCAAUAGCUGCAUCAUUUUCUUGCUUUCCAGCUAUUUUG
--------------..........----------.....(((---------(.(((((.....))))).))))((((((((...((......)).....))))))))... ( -15.50, z-score =  -3.55, R)
>consensus
CUCGCUCUAGCUGUCCCUCUCUUCGC__CGAUAUCUCCCAUU________UAUAUAUUUUCUCGGCAUCUGGGAA__ACUGCAUAAUUUUCCCGCUUUCCAGCUAUUUUG
.......((((((......................(((((.............................)))))......((...........))....))))))..... ( -7.43 =  -8.32 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 21,079,445 – 21,079,545
Length 100
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 77.30
Shannon entropy 0.41085
G+C content 0.43732
Mean single sequence MFE -20.00
Consensus MFE -11.33
Energy contribution -12.08
Covariance contribution 0.75
Combinations/Pair 1.13
Mean z-score -1.56
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.619918
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21079445 100 - 24543557
CAAAAUAGCUGGAAAGCGGGAAAAUUAUGCAGU--UUCCCAGAUGCCGAGAAAAUAUAUAUA------AAUGGGAGAUAUCA--GCGAAGAGAGGGACAGCUAGAGCGAG
.....((((((....(((.........))).((--((((((.....................------..))))))))....--.............))))))....... ( -18.60, z-score =  -0.86, R)
>droEre2.scaffold_4784 20767459 98 - 25762168
CAAAAUAGCUGGAAAGCGGAAAAAUUAUGCAGU--UUCCCAGAUGCCGAGAAAAUAUAUA--------AAUGGGAGAUAUCG--GGAAAGAGAGAGACAGCUAGAGCGAG
.....((((((....(((.........)))..(--(((((.((((((.(...........--------..).))...)))))--)))))........))))))....... ( -19.32, z-score =  -1.82, R)
>droYak2.chr3L 4752175 100 + 24197627
CAAAAUAGCUGGAAAGCGGAAAAAUUAUGCAGU--UUCCCAGAUGCCGAGAAAAUAUAUA--------AAUGGGAGAUAUCGGUGAAGAGAGAGAGACAGCUAGAGCGAG
.....((((((....(((.........))).((--((((((...................--------..))))))))...................))))))....... ( -18.70, z-score =  -1.65, R)
>droSec1.super_11 1037151 106 - 2888827
CAAAAUAGCUGGAAAGCGGGAAAAUUAUGCAGU--UUCCCAGAUGCCGAGAAAAUAUAUAUACAUAUAAAUGGGAGAUAUCG--GCGAUGAGAGGGACAGCUAGAGCGAG
.....((((((......((((((.........)--)))))...((((((.....(((.(((....))).))).......)))--)))..........))))))....... ( -23.80, z-score =  -2.07, R)
>droSim1.chr3L 20434526 106 - 22553184
CAAAAUAGCUGGAAAGCGGGAAAAUUAUGCAGU--UUCCCAGAUGCCGAGAAAAUAUAUAUACAUAUAAAUGGGAGAUAUCG--GCGAAGAGAGGGACAGCUAGAGCGAG
.....((((((......((((((.........)--)))))...((((((.....(((.(((....))).))).......)))--)))..........))))))....... ( -23.80, z-score =  -2.30, R)
>droVir3.scaffold_13049 9970655 77 + 25233164
CAAAAUAGCUGGAAAGCAAGAAAAUGAUGCAGCUAUUGCCGAAGCUUGGGGUAAACUGC---------GACGGGAG----------GACGAGGGAG--------------
...((((((((.(...((......)).).)))))))).(((..((..((......))))---------..)))...----------..........-------------- ( -15.80, z-score =  -0.69, R)
>consensus
CAAAAUAGCUGGAAAGCGGGAAAAUUAUGCAGU__UUCCCAGAUGCCGAGAAAAUAUAUA________AAUGGGAGAUAUCG__GCGAAGAGAGAGACAGCUAGAGCGAG
.....((((((....(((.........))).....((((((.............................)))))).....................))))))....... (-11.33 = -12.08 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:41:35 2011