Locus 5029

Sequence ID	dm3.chr2R
Location	17,212,695 – 17,212,794
Length	99
Max. P	0.996471

overview

Window 6

Location	17,212,695 – 17,212,794
Length	99
Sequences	8
Columns	99
Reading direction	forward
Mean pairwise identity	75.18
Shannon entropy	0.47233
G+C content	0.31751
Mean single sequence MFE	-21.45
Consensus MFE	-12.81
Energy contribution	-13.06
Covariance contribution	0.25
Combinations/Pair	1.13
Mean z-score	-2.63
Structure conservation index	0.60
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.94
SVM RNA-class probability	0.996471
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17212695 99 + 21146708
AAAAAGUAACACAAAAUAUAGCCAUAUAUAUAUAUGAUGUUAACAUCAUACUGAGUGCCUAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAAAAGG
...............(((((......))))).(((((((....))))))).((((.(((..((((((((.......))))))))..))).))))..... ( -22.60, z-score =  -3.47, R)
>droPer1.super_4 2045276 90 - 7162766
----AUAAACGCCUAGAUAUGUUAG----CCAAGUGAUGUUAAAAUUCAACUGAGCGCCGUUAUCGGUCUAUUUUUGAUUGAUUUUGGCUGUUAAAAG-
----...(((..............(----(((..(((.........)))..)).))((((..(((((((.......)))))))..)))).))).....- ( -19.50, z-score =  -1.47, R)
>dp4.chr3 9978006 90 - 19779522
----AUAAACGCCUAGAUAUGUUAG----CCAAGUGAUGUUACAAUUCAACUGAGCGCCGUUAUCGGUCUAUUUUUGAUUGAUUUUGGCUGUUAAAAG-
----...(((..............(----(((..(((.........)))..)).))((((..(((((((.......)))))))..)))).))).....- ( -19.50, z-score =  -1.21, R)
>droAna3.scaffold_13266 5014908 91 + 19884421
----AAUAAUGCUUAGUUAGAUCAG----CCAAAUGAUGUUACAAUCAUACUGAGUGCCGCUAUCGAUCUAUUUUUGAUUGAUUCUGGCGUAUAAAAGG
----......(((((((........----....(((((......))))))))))))((((..(((((((.......)))))))..)))).......... ( -22.20, z-score =  -2.07, R)
>droEre2.scaffold_4845 11356497 94 + 22589142
-GGAAGUAAUACAAAAUAACGCAAC----AUUUAUGAUGUUCACAUCAUACUGAGUGCCUGAAUCGAUCUAUUCUUGAUUGAUUUUGGCUAUUAUAAGG
-....((((((..............----...(((((((....)))))))......(((.(((((((((.......))))))))).))))))))).... ( -23.40, z-score =  -3.09, R)
>droYak2.chr2R 9163604 94 - 21139217
-GAAAGUAAUGCAAAAUAACACUAC----GUUUAUGAUGUUCACAUCAUACUGAGUGCCUAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAUAAGG
-....(((.((........)).)))----...(((((((....))))))).((((.(((..((((((((.......))))))))..))).))))..... ( -22.60, z-score =  -3.16, R)
>droSec1.super_9 544064 96 + 3197100
AAAAAGUAACACAAAAAAAAAGCAA---UAUAUAUGAUGUUAACAUCAUACUGAGUGCCUAAAUCCAUCUAUUUUUGAUUGAUUCUGGCUUUUAAAAGG
.........................---....(((((((....))))))).((((.(((..((((.(((.......))).))))..))).))))..... ( -17.80, z-score =  -2.24, R)
>droSim1.chr2R 15864910 95 + 19596830
AAAAAGUAACACAAAAAAUAGC-AU---UAUAUAUGAUGUUAACAUCAUACUGAGUGCCUAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAAAAGG
.((((((.............((-((---(...(((((((....)))))))...)))))(..((((((((.......))))))))..)))))))...... ( -24.00, z-score =  -4.36, R)
>consensus
__AAAGUAACACAAAAAAAAGCCAG____AUAUAUGAUGUUAACAUCAUACUGAGUGCCUAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAAAAGG
.................................(((((......))))).......(((...(((((((.......)))))))...))).......... (-12.81 = -13.06 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	17,212,695 – 17,212,794
Length	99
Sequences	8
Columns	99
Reading direction	reverse
Mean pairwise identity	75.18
Shannon entropy	0.47233
G+C content	0.31751
Mean single sequence MFE	-18.29
Consensus MFE	-6.93
Energy contribution	-7.92
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.38
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.05
SVM RNA-class probability	0.521197
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17212695 99 - 21146708
CCUUUUAAAAGCCAGAAUCAAUCAAAAAUAGAUCGAUUUAGGCACUCAGUAUGAUGUUAACAUCAUAUAUAUAUAUGGCUAUAUUUUGUGUUACUUUUU
.........((((((((((.(((.......))).))))).........((((((((....)))))))).......)))))................... ( -19.90, z-score =  -2.27, R)
>droPer1.super_4 2045276 90 + 7162766
-CUUUUAACAGCCAAAAUCAAUCAAAAAUAGACCGAUAACGGCGCUCAGUUGAAUUUUAACAUCACUUGG----CUAACAUAUCUAGGCGUUUAU----
-.........(((.................(.(((....))))(((.(((.((.........))))).))----)...........)))......---- ( -12.80, z-score =  -0.65, R)
>dp4.chr3 9978006 90 + 19779522
-CUUUUAACAGCCAAAAUCAAUCAAAAAUAGACCGAUAACGGCGCUCAGUUGAAUUGUAACAUCACUUGG----CUAACAUAUCUAGGCGUUUAU----
-.........(((.................(.(((....))))(((.(((.((.........))))).))----)...........)))......---- ( -12.80, z-score =  -0.12, R)
>droAna3.scaffold_13266 5014908 91 - 19884421
CCUUUUAUACGCCAGAAUCAAUCAAAAAUAGAUCGAUAGCGGCACUCAGUAUGAUUGUAACAUCAUUUGG----CUGAUCUAACUAAGCAUUAUU----
..........(((...(((.(((.......))).)))...)))..((((((((((......)))))...)----)))).................---- ( -14.00, z-score =  -0.20, R)
>droEre2.scaffold_4845 11356497 94 - 22589142
CCUUAUAAUAGCCAAAAUCAAUCAAGAAUAGAUCGAUUCAGGCACUCAGUAUGAUGUGAACAUCAUAAAU----GUUGCGUUAUUUUGUAUUACUUCC-
..........(((..((((.(((.......))).))))..)))......(((((((....)))))))...----..((((......))))........- ( -18.70, z-score =  -1.86, R)
>droYak2.chr2R 9163604 94 + 21139217
CCUUAUAAAAGCCAGAAUCAAUCAAAAAUAGAUCGAUUUAGGCACUCAGUAUGAUGUGAACAUCAUAAAC----GUAGUGUUAUUUUGCAUUACUUUC-
..........(((.(((((.(((.......))).))))).)))......(((((((....)))))))...----(((((((......)))))))....- ( -26.60, z-score =  -5.08, R)
>droSec1.super_9 544064 96 - 3197100
CCUUUUAAAAGCCAGAAUCAAUCAAAAAUAGAUGGAUUUAGGCACUCAGUAUGAUGUUAACAUCAUAUAUA---UUGCUUUUUUUUUGUGUUACUUUUU
..........(((.(((((.(((.......))).))))).))).....((((((((....))))))))...---......................... ( -19.50, z-score =  -2.14, R)
>droSim1.chr2R 15864910 95 - 19596830
CCUUUUAAAAGCCAGAAUCAAUCAAAAAUAGAUCGAUUUAGGCACUCAGUAUGAUGUUAACAUCAUAUAUA---AU-GCUAUUUUUUGUGUUACUUUUU
..........(((.(((((.(((.......))).))))).))).....((((((((....)))))))).((---((-((........))))))...... ( -22.00, z-score =  -3.66, R)
>consensus
CCUUUUAAAAGCCAGAAUCAAUCAAAAAUAGAUCGAUUUAGGCACUCAGUAUGAUGUUAACAUCAUAUAU____CUAGCUUUAUUUUGCGUUACUUU__
..........(((...(((.(((.......))).)))...))).......(((((......)))))................................. ( -6.93 =  -7.92 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:40:33 2011