Locus 9952

Sequence ID	dm3.chr3R
Location	10,086,500 – 10,086,615
Length	115
Max. P	0.758813

overview

Window 7

Location	10,086,500 – 10,086,615
Length	115
Sequences	10
Columns	116
Reading direction	forward
Mean pairwise identity	67.57
Shannon entropy	0.70679
G+C content	0.67217
Mean single sequence MFE	-52.11
Consensus MFE	-19.46
Energy contribution	-19.95
Covariance contribution	0.49
Combinations/Pair	1.47
Mean z-score	-1.06
Structure conservation index	0.37
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.10
SVM RNA-class probability	0.541101
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10086500 115 + 27905053
UGCCGCCUCCGCCGCACGAGCGGAUUGAGCUGCCUUGGCGGCCAGUUCGUUUUUGACC-UGGGAUGCAGCCGCCUCGGCAGCUGCCAUCUGCGAAUCGCUGGCUGCCUUGGCCUCC
....((.((..((((....))))...)))).(((..((((((((((((((........-..(((((((((.((....)).)))).)))))))))...))))))))))..))).... ( -53.30, z-score =  -1.71, R)
>droSim1.chr3R 16152480 115 - 27517382
UGCCGCCUCCGCCGCCCGAGCGGAUUGAGCUGCCUUGGCGGCCAGUUCAUUUUUGACC-UGGGAUGCAGCCGCCUCGGCAGCUGCCAUCUGCGAAUCGCUGGCUGCCUUGGCCUCC
....(((...((.((((((((((((.((((((((..(((((((((.(((....))).)-))(....).))))))..))))))).).))))))...)))..))).))...))).... ( -52.70, z-score =  -1.76, R)
>droSec1.super_0 9166967 115 - 21120651
UGCCGCCUCCGCCGCCCGAGCGGAUUGAGCUGCCUUGGCGGCCAGUUCAUUUUUGACC-UGGGAUGCAGCCGCCUCGGCAGCUGCCAUCUGCGAAUCGCUGGCUGCCUUGGCCUCC
....(((...((.((((((((((((.((((((((..(((((((((.(((....))).)-))(....).))))))..))))))).).))))))...)))..))).))...))).... ( -52.70, z-score =  -1.76, R)
>droYak2.chr3R 12470708 115 - 28832112
CGCUGCCUCCGCUGCUCGAGCGGAUUGAGCUGCCUUGGCGGCCAGUUCGGAUUUGACC-UGGGAUGCAGCCGCCUCGGCAGCUGCCAUCUGGGAAUCGCUGGCUGCCUUGGCUUCC
.(((...((((((.....))))))...))).(((..((((((((((...((((...((-..((..(((((.((....)).)))))..))..))))))))))))))))..))).... ( -58.80, z-score =  -2.66, R)
>droEre2.scaffold_4770 9619525 115 + 17746568
UGCUGCCUCCGCCGCCCGAGCGGAUUGAGCUGCCUUGGCGGCCAGUUCGGAUUUGACC-UGGGAUGCAGCCGCCUCGGCUGCUGCCAUCUGGGAAUCGCUGGCUGCCUUCGCCUCC
.(((...((((((....).)))))...))).((...((((((((((...((((...((-..((..(((((.((....)).)))))..))..))))))))))))))))...)).... ( -51.80, z-score =  -1.06, R)
>droVir3.scaffold_13047 18142405 115 + 19223366
CGCUGCCUCUGCGGCGCGAGCGGAUUGAGCCGCCCUCUCGGCCAGCUCCUGCUUGACC-UGCGUGGCAGCUGCCUCUGCGGCGGCCAUUUGUGCAUCACUGGCAGCCCUCGCCUCC
.((((((...((((.((((((((((((.((((......))))))).))).))))).))-)))(((((.(((((....))))).)))))............)))))).......... ( -51.40, z-score =  -0.58, R)
>droMoj3.scaffold_6540 20561826 115 - 34148556
CGCUGCCUCGGCGGCACGUGCCGACUGCGCCGCCCGCUCGGCCAACUGCUGCUUGACC-UGUGUGGCAGCUGCCUCUGCGGCGGCCAUUUGCGCAUCGCUGGCGGCCCUCGCCUCC
.(((((....))))).((((((((.((.((((((.((..(((...((((..(......-...)..))))..)))...)))))))))).))).))).))..((((.....))))... ( -53.00, z-score =  -0.41, R)
>droGri2.scaffold_15074 5747217 115 + 7742996
UGCCGCCUCCGCUGCUUUGGCAGCUGCAUAUGCUCGAUCCGCCAGCUGCUUCUUAACCAUGCG-GGCGACCUCCGCGGCAGCAGCCUGUUGUGUUCCAUAUGCCUGCUCUGCCUCG
...((((..(((((.((.((((((((.....((.......))))))))))....)).)).)))-)))).....((.(((((.(((..((((((...)))).))..)))))))).)) ( -37.00, z-score =   0.38, R)
>anoGam1.chr2R 10468409 115 + 62725911
GGCGGCCUGGGCCGUGGCGGCCGCCUGGGAAGCCGCCUGGGCGAGCGUGUUCUGCGCCACGUA-CGCAGCCUGCUUGGCUGCGGCAUGCUGGUUAGCGACGGCCGAGUUGGCCUGA
(((.(.((.((((((.(((((((((..((......))..))).(((((((..((((...))))-(((((((.....)))))))))))))))))).)).)))))).)).).)))... ( -67.10, z-score =  -1.76, R)
>apiMel3.GroupUn 75929369 115 + 399230636
UGCUGCAGCCGCAGUUGCCGCGGAUUGAGCAGCAGCUUGCGCCAAUGUGUUUUUCGCAACGAA-CGCAGCUUGUCCGGCCGCGGAAUGUUGAUUGCUCAAUUGCGUGUGCGCUUGU
.(((((....))))).((((((((((((((((((((((.(((...(((((((........)))-))))(((.....))).))).)).)))).)))))))))).)))).))...... ( -43.30, z-score =   0.68, R)
>consensus
UGCUGCCUCCGCCGCCCGAGCGGAUUGAGCUGCCUUGGCGGCCAGUUCGUUUUUGACC_UGGGAUGCAGCCGCCUCGGCAGCUGCCAUCUGCGAAUCGCUGGCUGCCUUGGCCUCC
.((.(((.((((.......)))).....(((((....(((((..........................)))))....)))))..................))).)).......... (-19.46 = -19.95 +   0.49)

alignment

secondary structure

dotplot

Window 8

Location	10,086,500 – 10,086,615
Length	115
Sequences	10
Columns	116
Reading direction	reverse
Mean pairwise identity	67.57
Shannon entropy	0.70679
G+C content	0.67217
Mean single sequence MFE	-51.56
Consensus MFE	-23.64
Energy contribution	-23.43
Covariance contribution	-0.21
Combinations/Pair	1.69
Mean z-score	-0.81
Structure conservation index	0.46
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.60
SVM RNA-class probability	0.758813
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10086500 115 - 27905053
GGAGGCCAAGGCAGCCAGCGAUUCGCAGAUGGCAGCUGCCGAGGCGGCUGCAUCCCA-GGUCAAAAACGAACUGGCCGCCAAGGCAGCUCAAUCCGCUCGUGCGGCGGAGGCGGCA
....((....)).(((.((..(((((.(((.(.(((((((..((((((.......((-(.((......)).)))))))))..)))))))).)))(((....)))))))).))))). ( -51.81, z-score =  -0.55, R)
>droSim1.chr3R 16152480 115 + 27517382
GGAGGCCAAGGCAGCCAGCGAUUCGCAGAUGGCAGCUGCCGAGGCGGCUGCAUCCCA-GGUCAAAAAUGAACUGGCCGCCAAGGCAGCUCAAUCCGCUCGGGCGGCGGAGGCGGCA
....(((..((((((..((.(((....))).)).))))))..))).(((((.(((((-(.(((....))).)))((((((..(((..........)))..))))))))).))))). ( -56.10, z-score =  -1.52, R)
>droSec1.super_0 9166967 115 + 21120651
GGAGGCCAAGGCAGCCAGCGAUUCGCAGAUGGCAGCUGCCGAGGCGGCUGCAUCCCA-GGUCAAAAAUGAACUGGCCGCCAAGGCAGCUCAAUCCGCUCGGGCGGCGGAGGCGGCA
....(((..((((((..((.(((....))).)).))))))..))).(((((.(((((-(.(((....))).)))((((((..(((..........)))..))))))))).))))). ( -56.10, z-score =  -1.52, R)
>droYak2.chr3R 12470708 115 + 28832112
GGAAGCCAAGGCAGCCAGCGAUUCCCAGAUGGCAGCUGCCGAGGCGGCUGCAUCCCA-GGUCAAAUCCGAACUGGCCGCCAAGGCAGCUCAAUCCGCUCGAGCAGCGGAGGCAGCG
....(((..(((.(((((.........((((.(((((((....)))))))))))...-((......))...))))).)))..))).(((...((((((.....))))))...))). ( -53.30, z-score =  -2.04, R)
>droEre2.scaffold_4770 9619525 115 - 17746568
GGAGGCGAAGGCAGCCAGCGAUUCCCAGAUGGCAGCAGCCGAGGCGGCUGCAUCCCA-GGUCAAAUCCGAACUGGCCGCCAAGGCAGCUCAAUCCGCUCGGGCGGCGGAGGCAGCA
((..((....))..)).((..(((((((.(((..(((((((...)))))))...)))-((......))...)))((((((..(((..........)))..))))))))))...)). ( -51.10, z-score =  -0.56, R)
>droVir3.scaffold_13047 18142405 115 - 19223366
GGAGGCGAGGGCUGCCAGUGAUGCACAAAUGGCCGCCGCAGAGGCAGCUGCCACGCA-GGUCAAGCAGGAGCUGGCCGAGAGGGCGGCUCAAUCCGCUCGCGCCGCAGAGGCAGCG
....(((((((((((..(((...)))...((((((((.....))).((......)).-))))).))))((((((.((....)).))))))...)).)))))(((.....))).... ( -53.00, z-score =  -0.23, R)
>droMoj3.scaffold_6540 20561826 115 + 34148556
GGAGGCGAGGGCCGCCAGCGAUGCGCAAAUGGCCGCCGCAGAGGCAGCUGCCACACA-GGUCAAGCAGCAGUUGGCCGAGCGGGCGGCGCAGUCGGCACGUGCCGCCGAGGCAGCG
...(((....)))(((((((...)))...)))).(((.....))).((((((.....-((((((.......)))))).....((((((((.((....))))))))))..)))))). ( -52.90, z-score =   0.48, R)
>droGri2.scaffold_15074 5747217 115 - 7742996
CGAGGCAGAGCAGGCAUAUGGAACACAACAGGCUGCUGCCGCGGAGGUCGCC-CGCAUGGUUAAGAAGCAGCUGGCGGAUCGAGCAUAUGCAGCUGCCAAAGCAGCGGAGGCGGCA
((.(((((....(((...((........)).))).))))).))...((((((-(((((((((.....((.....))......))).))))).(((((....))))).).)))))). ( -44.40, z-score =  -0.34, R)
>anoGam1.chr2R 10468409 115 - 62725911
UCAGGCCAACUCGGCCGUCGCUAACCAGCAUGCCGCAGCCAAGCAGGCUGCG-UACGUGGCGCAGAACACGCUCGCCCAGGCGGCUUCCCAGGCGGCCGCCACGGCCCAGGCCGCC
...((((.....((((((.(((....)))....(((((((.....)))))))-...(.((((.((......))))))).(((((((.(....).)))))))))))))..))))... ( -56.20, z-score =  -1.73, R)
>apiMel3.GroupUn 75929369 115 - 399230636
ACAAGCGCACACGCAAUUGAGCAAUCAACAUUCCGCGGCCGGACAAGCUGCG-UUCGUUGCGAAAAACACAUUGGCGCAAGCUGCUGCUCAAUCCGCGGCAACUGCGGCUGCAGCA
....((((...(((((((((....)))......((((((.......))))))-...)))))).....(.....))))).....(((((.....(((((....).))))..))))). ( -40.70, z-score =  -0.10, R)
>consensus
GGAGGCCAAGGCAGCCAGCGAUUCGCAGAUGGCAGCUGCCGAGGCGGCUGCAUCCCA_GGUCAAAAACGAACUGGCCGACAAGGCAGCUCAAUCCGCUCGAGCGGCGGAGGCAGCA
....((.......((((.(........).)))).(((........((((((.......(((((.........)))))......))))))....(((((.....))))).))).)). (-23.64 = -23.43 +  -0.21)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:14:34 2011