Locus 7040

Sequence ID	dm3.chr3L
Location	11,667,867 – 11,667,958
Length	91
Max. P	0.867120

overview

Window 7

Location	11,667,867 – 11,667,958
Length	91
Sequences	8
Columns	98
Reading direction	forward
Mean pairwise identity	65.22
Shannon entropy	0.66088
G+C content	0.68712
Mean single sequence MFE	-37.36
Consensus MFE	-13.70
Energy contribution	-13.88
Covariance contribution	0.17
Combinations/Pair	1.31
Mean z-score	-1.20
Structure conservation index	0.37
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.03
SVM RNA-class probability	0.507910
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11667867 91 + 24543557
GUGUACCUCCAG-CACU---GGCCGCCGCCUUCUGGGCGGCCACCAUGCCCAUGGUGCUGAAGGUGGGC---GAACCGGGAUUUACUCCGCCACCCGG
((.(((((.(((-(...---(((((((........)))))))(((((....))))))))).))))).))---...(((((.............))))) ( -45.52, z-score =  -2.68, R)
>droVir3.scaffold_13049 23883354 79 + 25233164
GAGUACCACCGC----CGCCAGCGGUGGCCUUUUGCGCCGCAACCAUGCCCAUCGUACUGAAGGUGGGC---GAACCGGGCGCCGG------------
........(((.----((((.((((((........)))))).....((((((((........)))))))---).....)))).)))------------ ( -36.30, z-score =  -1.32, R)
>droGri2.scaffold_15110 10777806 85 - 24565398
GUGUACCACCGCCCGACGCUGCCGUCG-CCUUCUGUGCCGCGACCAUGCCCAUUGUGCUGAAUGUGGGCGAUGAGCCGGGCGCUGG------------
.....(((.((((((..(((...((((-(..........)))))(((((((((..........)))))).)))))))))))).)))------------ ( -34.90, z-score =  -1.25, R)
>droMoj3.scaffold_6680 18509648 73 + 24764193
----------GCGUGCCCCCGCCGGCGACUUUCUGUGCCGCGACCAUGCCCAUUGUGCUGAAGGUGGGC---GAGCCGGGCGCUGG------------
----------..((((((.(((.(((.((.....))))))))....((((((((........)))))))---)....))))))...------------ ( -32.50, z-score =  -0.50, R)
>droWil1.scaffold_180949 3690715 79 - 6375548
GUGUCCCAGUGC----CGCCGGCAGCGGCCUUUUGAGCCGCCACCAUGCCCAUGGUGGUAAAUGUGGGC---GAGUUACCUCCUGG------------
.....((((.((----((((.(((((((((....).)))))((((((....)))))).....))).)))---).))......))))------------ ( -33.20, z-score =  -1.48, R)
>droAna3.scaffold_13337 5933876 94 + 23293914
GCGUUCCUCCAG-UGCCUCCACCGGCAGCCUUUUGCGCCGCCACCAUGCCCAUUGUGCUGAAUGUGGGA---GAUCCUGGGCCGACUCCGCCGCCCGG
......((((..-((((......))))((.(((.((((.((......)).....)))).))).)).)))---)...((((((((....))..)))))) ( -26.00, z-score =   1.80, R)
>droSec1.super_0 3854459 91 + 21120651
GUGUACCUCCAG-CACU---GGCCGCCGCCUUCUGGGCGGCCACCAUGCCCAUGGUGCUGAAGGUGGGC---GAGCCGGGAUUUACUCCGCCACCCGG
((.(((((.(((-(...---(((((((........)))))))(((((....))))))))).))))).))---...(((((.............))))) ( -45.22, z-score =  -2.08, R)
>droSim1.chr3L 11037968 91 + 22553184
GUGUACCUCCAG-CACU---GGCCGCCGCCUUCUGGGCGGCCACCAUGCCCAUGGUGCUGAAGGUGGGC---GAGCCGGGAUUUACUCCGCCACCCGG
((.(((((.(((-(...---(((((((........)))))))(((((....))))))))).))))).))---...(((((.............))))) ( -45.22, z-score =  -2.08, R)
>consensus
GUGUACCUCCAC_CACC_CCGGCGGCGGCCUUCUGGGCCGCCACCAUGCCCAUGGUGCUGAAGGUGGGC___GAGCCGGGAGCUAC____________
........((..............(((((.......)))))......((((((..........))))))........))................... (-13.70 = -13.88 +   0.17)

alignment

secondary structure

dotplot

Window 8

Location	11,667,867 – 11,667,958
Length	91
Sequences	8
Columns	98
Reading direction	reverse
Mean pairwise identity	65.22
Shannon entropy	0.66088
G+C content	0.68712
Mean single sequence MFE	-41.02
Consensus MFE	-14.41
Energy contribution	-14.25
Covariance contribution	-0.16
Combinations/Pair	1.46
Mean z-score	-1.78
Structure conservation index	0.35
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.98
SVM RNA-class probability	0.867120
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11667867 91 - 24543557
CCGGGUGGCGGAGUAAAUCCCGGUUC---GCCCACCUUCAGCACCAUGGGCAUGGUGGCCGCCCAGAAGGCGGCGGCC---AGUG-CUGGAGGUACAC
..(((((((((........)))..))---))))(((((((((((........((((.((((((.....)))))).)))---))))-)))))))).... ( -50.00, z-score =  -3.18, R)
>droVir3.scaffold_13049 23883354 79 - 25233164
------------CCGGCGCCCGGUUC---GCCCACCUUCAGUACGAUGGGCAUGGUUGCGGCGCAAAAGGCCACCGCUGGCG----GCGGUGGUACUC
------------...((((((..((.---(((((.(........).)))))..))..).))))).....((((((((.....----)))))))).... ( -35.60, z-score =  -0.39, R)
>droGri2.scaffold_15110 10777806 85 + 24565398
------------CCAGCGCCCGGCUCAUCGCCCACAUUCAGCACAAUGGGCAUGGUCGCGGCACAGAAGG-CGACGGCAGCGUCGGGCGGUGGUACAC
------------(((.((((((((.(((.(((((............))))))))((((((.(......).-)).))))...)))))))).)))..... ( -39.40, z-score =  -2.65, R)
>droMoj3.scaffold_6680 18509648 73 - 24764193
------------CCAGCGCCCGGCUC---GCCCACCUUCAGCACAAUGGGCAUGGUCGCGGCACAGAAAGUCGCCGGCGGGGGCACGC----------
------------...((.((((.(..---(((((............)))))......(((((.......))))).).)))).))....---------- ( -29.00, z-score =   0.29, R)
>droWil1.scaffold_180949 3690715 79 + 6375548
------------CCAGGAGGUAACUC---GCCCACAUUUACCACCAUGGGCAUGGUGGCGGCUCAAAAGGCCGCUGCCGGCG----GCACUGGGACAC
------------(((((((....)))---(((........((.....))((.(((..((((((.....))))))..))))))----)).))))..... ( -37.20, z-score =  -2.78, R)
>droAna3.scaffold_13337 5933876 94 - 23293914
CCGGGCGGCGGAGUCGGCCCAGGAUC---UCCCACAUUCAGCACAAUGGGCAUGGUGGCGGCGCAAAAGGCUGCCGGUGGAGGCA-CUGGAGGAACGC
((((.((((...)))).))(((..((---(((.((..(((((.......)).)))(((((((.......))))))))))))))..-)))..))..... ( -34.00, z-score =   0.99, R)
>droSec1.super_0 3854459 91 - 21120651
CCGGGUGGCGGAGUAAAUCCCGGCUC---GCCCACCUUCAGCACCAUGGGCAUGGUGGCCGCCCAGAAGGCGGCGGCC---AGUG-CUGGAGGUACAC
..((((((((((.....)))..)).)---))))(((((((((((........((((.((((((.....)))))).)))---))))-)))))))).... ( -51.50, z-score =  -3.27, R)
>droSim1.chr3L 11037968 91 - 22553184
CCGGGUGGCGGAGUAAAUCCCGGCUC---GCCCACCUUCAGCACCAUGGGCAUGGUGGCCGCCCAGAAGGCGGCGGCC---AGUG-CUGGAGGUACAC
..((((((((((.....)))..)).)---))))(((((((((((........((((.((((((.....)))))).)))---))))-)))))))).... ( -51.50, z-score =  -3.27, R)
>consensus
____________CCAGAGCCCGGCUC___GCCCACCUUCAGCACCAUGGGCAUGGUGGCGGCCCAGAAGGCCGCCGCCGG_GGCG_CCGGAGGUACAC
...................(((.......(((((............)))))......(((((.......))))).............)))........ (-14.41 = -14.25 +  -0.16)

alignment

secondary structure

dotplot

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