Locus 11679

Sequence ID	dm3.chr3R
Location	23,028,349 – 23,028,446
Length	97
Max. P	0.914228

overview

Window 6

Location	23,028,349 – 23,028,446
Length	97
Sequences	11
Columns	110
Reading direction	forward
Mean pairwise identity	66.90
Shannon entropy	0.66518
G+C content	0.37872
Mean single sequence MFE	-19.14
Consensus MFE	-8.53
Energy contribution	-8.62
Covariance contribution	0.09
Combinations/Pair	1.00
Mean z-score	-1.12
Structure conservation index	0.45
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.80
SVM RNA-class probability	0.822541
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23028349 97 + 27905053
AAAUGAGGCUCAAAUGAAGGGGUAAAUAA------------AAUGUAAAAUAAAUUUACCUUUUGCGUGGCCUGAAACAAGCGACGGACA-AAAAAGCGCACGCACAGAU
...(.(((((...((((((((((((((..------------............))))))))))).)))))))).).....(((.(.....-.....)))).......... ( -19.54, z-score =  -0.99, R)
>droSim1.chr3R 22801774 97 + 27517382
AAAUGAGGCUCAAAUGAAGGGGUAAAUAA------------AAUGUAAAAUAAAUUUACCUUUUGCGUGGCCUGAAACAAGCGACGGACA-AAAAAGCGCACGCACAGAU
...(.(((((...((((((((((((((..------------............))))))))))).)))))))).).....(((.(.....-.....)))).......... ( -19.54, z-score =  -0.99, R)
>droSec1.super_13 1783124 97 + 2104621
AAAUGAGGCUCAAAUGAAGGGGUAAAUAA------------AAUGUAAAAUAAAUUUACCUUUUGCGUGGCCUGAAACAAGCGACGGACA-AAAAAGCGCACGCACAGAU
...(.(((((...((((((((((((((..------------............))))))))))).)))))))).).....(((.(.....-.....)))).......... ( -19.54, z-score =  -0.99, R)
>droYak2.chr3R 5367301 97 - 28832112
AAAUGAGUCUCAAAUGAAGGGGUAAAUAA------------AAUGUAAAAUGAAUUUACCUUUUGCGUGGCCUGAAACAAGCUACGGACA-AAAAAGCGCACGCACAGAU
......(((.......(((((((((((..------------.((.....))..))))))))))).((((((.((...)).))))))))).-.....((....))...... ( -21.40, z-score =  -1.65, R)
>droEre2.scaffold_4820 5461443 98 - 10470090
AAAUGAGGCUCAAAUGAAGGGUUAAAUAA------------AAUGUAAAAUAAAUUUACCUUUUGCGUGGCCUGAAACAAGCAACGGACACAAAAAGCGCACGCACAGAU
...(.((((.((..((((((((.((((..------------............))))))))))))..)))))).).....................((....))...... ( -15.94, z-score =   0.25, R)
>droAna3.scaffold_12911 3965871 109 + 5364042
AAAUGAGCCUCAAAUAAGGUGGUAAAUAAGGCCUCAAAUAAAAUGUAAAAUGAAUUUACCUUUUGCGUGGCCAGAAACAAGCCAGCUACA-AAAAGCCUCACGCACAGAU
...((((.((......((.((((......((((.(...(((((.(((((.....))))).))))).).))))........)))).))...-...)).))))......... ( -20.44, z-score =  -0.31, R)
>dp4.chr2 8651482 107 + 30794189
AAAUGAGCUUCGAAUAAACAACUGGUAAAA--UACGAGUUAAAUGUUAAAUUAACGUACACUUUGCGUGGCUCGAAACCAACCAAAGACU-GAAAUGCGCACGCACAGAU
...((((((.((.......((((.(((...--))).))))..((((((...))))))........)).))))))..............((-(...(((....)))))).. ( -19.50, z-score =  -0.57, R)
>droPer1.super_0 2464977 107 + 11822988
AAAUGAGCUUCGAAUAAACAACUGGUAAAA--UACGAGUUAAAUGUUAAAUUAACGUACACUUUGCGUGGCUCGAAACCAACCAAAGACU-GAAAUGCGCACGCACAGAU
...((((((.((.......((((.(((...--))).))))..((((((...))))))........)).))))))..............((-(...(((....)))))).. ( -19.50, z-score =  -0.57, R)
>droVir3.scaffold_13047 8170492 75 + 19223366
---------------AAAUGAGCC-UCAAA--UAAAGGGUAAAUA--AAAUAAAUUUACGUUUUGCGUGGCGUGAAA---------------AAAUGCGCACGCACAGAU
---------------.........-.....--.((((.((((((.--......)))))).))))(((((((((....---------------..)))).)))))...... ( -18.30, z-score =  -2.16, R)
>droMoj3.scaffold_6540 6127221 75 - 34148556
---------------AAAUGAGCC-UCAAA--UAAAGGGUAAAUA--AAAUAAAUUUACGUUUUGCGUGGCGUGAAA---------------AAAUGCGCACGCACAGAU
---------------.........-.....--.((((.((((((.--......)))))).))))(((((((((....---------------..)))).)))))...... ( -18.30, z-score =  -2.16, R)
>droGri2.scaffold_15074 6299475 75 - 7742996
---------------AAAUGAGCC-UCAUA--UAAAGGGUAAAUA--AAAUAAAUUUACGUUUUGCGUGGCGUGAAA---------------AAAUGCGCACGCACAGAU
---------------..(((....-.))).--.((((.((((((.--......)))))).))))(((((((((....---------------..)))).)))))...... ( -18.50, z-score =  -2.13, R)
>consensus
AAAUGAGGCUCAAAUAAAGGGGUAAAUAA___________AAAUGUAAAAUAAAUUUACCUUUUGCGUGGCCUGAAACAAGC_ACGGACA_AAAAAGCGCACGCACAGAU
...............................................................((((((((.........................)).))))))..... ( -8.53 =  -8.62 +   0.09)

alignment

secondary structure

dotplot

Window 7

Location	23,028,349 – 23,028,446
Length	97
Sequences	11
Columns	110
Reading direction	reverse
Mean pairwise identity	66.90
Shannon entropy	0.66518
G+C content	0.37872
Mean single sequence MFE	-17.99
Consensus MFE	-9.21
Energy contribution	-9.30
Covariance contribution	0.09
Combinations/Pair	1.00
Mean z-score	-1.05
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.24
SVM RNA-class probability	0.914228
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23028349 97 - 27905053
AUCUGUGCGUGCGCUUUUU-UGUCCGUCGCUUGUUUCAGGCCACGCAAAAGGUAAAUUUAUUUUACAUU------------UUAUUUACCCCUUCAUUUGAGCCUCAUUU
........(.(.(((((((-((..(((.(((((...))))).))))))))(((((((..(........)------------..))))))).........))))).).... ( -17.40, z-score =  -1.09, R)
>droSim1.chr3R 22801774 97 - 27517382
AUCUGUGCGUGCGCUUUUU-UGUCCGUCGCUUGUUUCAGGCCACGCAAAAGGUAAAUUUAUUUUACAUU------------UUAUUUACCCCUUCAUUUGAGCCUCAUUU
........(.(.(((((((-((..(((.(((((...))))).))))))))(((((((..(........)------------..))))))).........))))).).... ( -17.40, z-score =  -1.09, R)
>droSec1.super_13 1783124 97 - 2104621
AUCUGUGCGUGCGCUUUUU-UGUCCGUCGCUUGUUUCAGGCCACGCAAAAGGUAAAUUUAUUUUACAUU------------UUAUUUACCCCUUCAUUUGAGCCUCAUUU
........(.(.(((((((-((..(((.(((((...))))).))))))))(((((((..(........)------------..))))))).........))))).).... ( -17.40, z-score =  -1.09, R)
>droYak2.chr3R 5367301 97 + 28832112
AUCUGUGCGUGCGCUUUUU-UGUCCGUAGCUUGUUUCAGGCCACGCAAAAGGUAAAUUCAUUUUACAUU------------UUAUUUACCCCUUCAUUUGAGACUCAUUU
.(((.((((((.((((...-.((.....)).......))))))))))...(((((((............------------..)))))))..........)))....... ( -16.74, z-score =  -0.73, R)
>droEre2.scaffold_4820 5461443 98 + 10470090
AUCUGUGCGUGCGCUUUUUGUGUCCGUUGCUUGUUUCAGGCCACGCAAAAGGUAAAUUUAUUUUACAUU------------UUAUUUAACCCUUCAUUUGAGCCUCAUUU
....(((.(.(((((((((((((.....(((((...))))).)))))))))))................------------............((....))))).))).. ( -17.00, z-score =  -0.37, R)
>droAna3.scaffold_12911 3965871 109 - 5364042
AUCUGUGCGUGAGGCUUUU-UGUAGCUGGCUUGUUUCUGGCCACGCAAAAGGUAAAUUCAUUUUACAUUUUAUUUGAGGCCUUAUUUACCACCUUAUUUGAGGCUCAUUU
....(((.((((((((((.-.((((((((((.......))))).)).....(((((.....)))))....)))..)))))))))).)))..((((....))))....... ( -30.70, z-score =  -2.44, R)
>dp4.chr2 8651482 107 - 30794189
AUCUGUGCGUGCGCAUUUC-AGUCUUUGGUUGGUUUCGAGCCACGCAAAGUGUACGUUAAUUUAACAUUUAACUCGUA--UUUUACCAGUUGUUUAUUCGAAGCUCAUUU
....((((....))))...-.......(((.(((((((((.(((.....))).................(((((.(((--...))).)))))....))))))))).))). ( -17.20, z-score =   1.05, R)
>droPer1.super_0 2464977 107 - 11822988
AUCUGUGCGUGCGCAUUUC-AGUCUUUGGUUGGUUUCGAGCCACGCAAAGUGUACGUUAAUUUAACAUUUAACUCGUA--UUUUACCAGUUGUUUAUUCGAAGCUCAUUU
....((((....))))...-.......(((.(((((((((.(((.....))).................(((((.(((--...))).)))))....))))))))).))). ( -17.20, z-score =   1.05, R)
>droVir3.scaffold_13047 8170492 75 - 19223366
AUCUGUGCGUGCGCAUUU---------------UUUCACGCCACGCAAAACGUAAAUUUAUUU--UAUUUACCCUUUA--UUUGA-GGCUCAUUU---------------
.....((((((.((....---------------......))))))))....((((((......--.))))))((((..--...))-)).......--------------- ( -15.60, z-score =  -2.31, R)
>droMoj3.scaffold_6540 6127221 75 + 34148556
AUCUGUGCGUGCGCAUUU---------------UUUCACGCCACGCAAAACGUAAAUUUAUUU--UAUUUACCCUUUA--UUUGA-GGCUCAUUU---------------
.....((((((.((....---------------......))))))))....((((((......--.))))))((((..--...))-)).......--------------- ( -15.60, z-score =  -2.31, R)
>droGri2.scaffold_15074 6299475 75 + 7742996
AUCUGUGCGUGCGCAUUU---------------UUUCACGCCACGCAAAACGUAAAUUUAUUU--UAUUUACCCUUUA--UAUGA-GGCUCAUUU---------------
.....((((((.((....---------------......))))))))....((((((......--.))))))((((..--...))-)).......--------------- ( -15.60, z-score =  -2.21, R)
>consensus
AUCUGUGCGUGCGCAUUUU_UGUCCGU_GCUUGUUUCAGGCCACGCAAAAGGUAAAUUUAUUUUACAUUU___________UUAUUUACCCCUUUAUUUGAGCCUCAUUU
.....((((((.((.........................))))))))............................................................... ( -9.21 =  -9.30 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:47:30 2011