Locus 8147

Sequence ID dm3.chr3L
Location 20,583,461 – 20,583,561
Length 100
Max. P 0.933384
window11209 window11210

overview

Window 9

Location 20,583,461 – 20,583,556
Length 95
Sequences 9
Columns 112
Reading direction forward
Mean pairwise identity 51.98
Shannon entropy 0.94251
G+C content 0.47439
Mean single sequence MFE -25.90
Consensus MFE -8.00
Energy contribution -8.67
Covariance contribution 0.67
Combinations/Pair 1.30
Mean z-score -1.42
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.38
SVM RNA-class probability 0.933384
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20583461 95 + 24543557
-----AUAUACAUAAGAACGCCGCUCC-GCUGCUGGCGUACCCGGCAGCGCAGCUACGCGG-AUUAGCC---UAAGUCCAAAUAUAUAAAAAACUGUAAAAUCAG-------
-----...((((.......((.(((.(-((((((((.....))))))))).)))...))((-(((....---..)))))...............)))).......------- ( -29.00, z-score =  -2.70, R)
>droSim1.chr3h_random 884955 77 + 1452968
-----AAACGCAAAUAAGCGUCGCUGC-GCUGCAGGCUAUGCCGGCAGCCCUGCUCCUCGACUUAGGC--------UAAGAAACCAUUGUA---------------------
-----....((...((((((..((.(.-(((((.(((...))).))))).).))....)).)))).))--------...............--------------------- ( -21.80, z-score =   0.28, R)
>droYak2.chrX_random 1263061 86 - 1802292
------------UAAGAGAGCCGCUCC-GCUGCUGUCGUAUCCGGCAGCGCAGCUACGCGG-CUUAGCC---UUCGACGAAAUAUAAUUAAGAAUCACAAAAC---------
------------.....(((((((...-((((((((((....)))))..)))))...))))-)))....---...............................--------- ( -26.00, z-score =  -1.50, R)
>droEre2.scaffold_4855 234983 88 - 242605
-----------AUAAGAGAGCCGCUCC-GCUGCUGGCGUAGCUGGCAGCGCAGCUACGCGGUUUUAGGU---UUAGCCGAAAUAUACUUAAGAAUGUAUCGCC---------
-----------.((((((((((((..(-(((((..((...))..)))))).......)))))))).((.---....))........)))).............--------- ( -28.80, z-score =  -0.23, R)
>droAna3.scaffold_13767 1524744 91 + 1685616
-----ACAUAAGUAAUAAAGUCUCUCC-GCUGCCGGCUUCAAGGGCAGCGCAGCUACGAGGCUCUAAUAAAAUAUGGAAUAAGAUAUUCAUUGUUAA---------------
-----.((((..((.((.((((((...-((((((.(((.....))).).)))))...)))))).)).))...))))(((((...)))))........--------------- ( -23.30, z-score =  -1.51, R)
>droPer1.super_1295 3566 103 + 6930
GAUAAGAACACAUAGUUCUGCCGCUCC-GCUGCCGGCGUCACUGGCAGCGCAGCUCCGCGGCUUUGGGC---U-UACAAAAGCCCAAACCACAAUUGUAAAAUAUAGA----
....(((((.....)))))((.(((.(-((((((((.....))))))))).)))...))((.(((((((---(-(....)))))))))))..................---- ( -42.00, z-score =  -4.49, R)
>droWil1.scaffold_181143 551653 103 + 1323777
-----UUAUUCAUAAGCAGACUGCUCC-UCUGUCGGCGUCUCUGGCAGCGUAACUACACGGUCUUUAGC---UCUACAAGACAAUUGUUAAAGAAUUAAGUAUAUUGAAAAA
-----...((((((.((((((((....-.(((((((.....))))))).((....)).))))))((((.---(((((((.....))))...))).)))))).)).))))... ( -17.90, z-score =   0.58, R)
>droVir3.scaffold_12941 339862 80 - 746104
-----AUAUACAAAAGACUCUCUCUCCCGCUGCUUGCGUAACCGGCACAGCAGCUAUGCGGUCUUAGC------CAUAAGAAUAUAUUGAA---------------------
-----.....(((...............(((((((((.......))).))))))((((...(((((..------..))))).)))))))..--------------------- ( -16.30, z-score =  -0.25, R)
>droMoj3.scaffold_6496 24532205 94 + 26866924
-----AUAUACAUAAGCGGACCGCUGC-UCUGCCGGCGUCACUGGCAGCGCAGCCA-ACCGAUUUUAAC---UGUACUUGACAAUUUUCAUAGAUUUAAGAAUU--------
-----...((((.((((((...(((((-.(((((((.....))))))).)))))..-.))).)))....---))))(((((..((((....)))))))))....-------- ( -28.00, z-score =  -2.98, R)
>consensus
_____AUAUACAUAAGAGAGCCGCUCC_GCUGCCGGCGUAACCGGCAGCGCAGCUACGCGGCUUUAGCC___U_UACAAAAAUAUAUUCAAAAAUUUAA_AA__________
......................(((....(((((((.....)))))))...))).......................................................... ( -8.00 =  -8.67 +   0.67)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,583,461 – 20,583,561
Length 100
Sequences 9
Columns 104
Reading direction forward
Mean pairwise identity 51.74
Shannon entropy 1.02542
G+C content 0.47145
Mean single sequence MFE -25.96
Consensus MFE -8.00
Energy contribution -8.67
Covariance contribution 0.67
Combinations/Pair 1.30
Mean z-score -1.31
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.37
SVM RNA-class probability 0.932027
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20583461 100 + 24543557
AUAUACAUAAGAACGCCGCUCC-GCUGCUGGCGUACCCGGCAGCGCAGCUACGCGG-AUUAGCCUAAGUCCAAAUAUAUAAAAAACUGUAAAAUCAGAGAGA--
(((((.........((.(((.(-((((((((.....))))))))).)))...))((-(((......)))))...)))))......(((......))).....-- ( -29.80, z-score =  -2.36, R)
>droSim1.chr3h_random 884955 77 + 1452968
AAACGCAAAUAAGCGUCGCUGC-GCUGCAGGCUAUGCCGGCAGCCCUGCUCCUCGA-CUUAGGCUAAG--------AAACCAUUGUA-----------------
....((...((((((..((.(.-(((((.(((...))).))))).).))....)).-)))).))....--------...........----------------- ( -21.80, z-score =   0.28, R)
>droYak2.chrX_random 1263061 91 - 1802292
-------UAAGAGAGCCGCUCC-GCUGCUGUCGUAUCCGGCAGCGCAGCUACGCGG-CUUAGCCUUCGACGAAAUAUAAUUAAGAAUCACAAAACAGACA----
-------.....(((((((...-((((((((((....)))))..)))))...))))-)))........................................---- ( -26.00, z-score =  -1.24, R)
>droEre2.scaffold_4855 234983 93 - 242605
------AUAAGAGAGCCGCUCC-GCUGCUGGCGUAGCUGGCAGCGCAGCUACGCGGUUUUAGGUUUAGCCGAAAUAUACUUAAGAAUGUAUCGCCAGAUA----
------.((((((((((((..(-(((((..((...))..)))))).......)))))))).((.....))........))))......((((....))))---- ( -29.90, z-score =  -0.28, R)
>droAna3.scaffold_13767 1524744 96 + 1685616
ACAUAAGUAAUAAAGUCUCUCC-GCUGCCGGCUUCAAGGGCAGCGCAGCUACGAGG-CUCUAAUAAAAUAUGGAAUAAGAUAUUCAUUGUUAAAAACG------
.((((..((.((.((((((...-((((((.(((.....))).).)))))...))))-)).)).))...))))(((((...))))).............------ ( -23.30, z-score =  -1.66, R)
>droPer1.super_1295 3571 101 + 6930
GAACACAUAGUUCUGCCGCUCC-GCUGCCGGCGUCACUGGCAGCGCAGCUCCGCGG-CUUUGGGCUUACAAAAGCCCAAACCACAAUUGUAAAAUAUAGAAGA-
((((.....)))).((.(((.(-((((((((.....))))))))).)))...))((-.(((((((((....))))))))))).....................- ( -40.60, z-score =  -3.97, R)
>droWil1.scaffold_181143 551653 103 + 1323777
UUAUUCAUAAGCAGACUGCUCC-UCUGUCGGCGUCUCUGGCAGCGUAACUACACGGUCUUUAGCUCUACAAGACAAUUGUUAAAGAAUUAAGUAUAUUGAAAAA
...((((((.((((((((....-.(((((((.....))))))).((....)).))))))((((.(((((((.....))))...))).)))))).)).))))... ( -17.90, z-score =   0.58, R)
>droVir3.scaffold_12941 339862 80 - 746104
AUAUACAAAAGACUCUCUCUCCCGCUGCUUGCGUAACCGGCACAGCAGCUAUGCGG-UCUUAGCCAUA------AGAAUAUAUUGAA-----------------
.....(((...............(((((((((.......))).))))))((((...-(((((....))------))).)))))))..----------------- ( -16.30, z-score =  -0.25, R)
>droMoj3.scaffold_6496 24532205 96 + 26866924
AUAUACAUAAGCGGACCGCUGC-UCUGCCGGCGUCACUGGCAGCGCAGCCA-ACCGAUUUUAACUGUACUUGACAAUUUUCAUAGAUUUAAGAAU--UAA----
...((((.((((((...(((((-.(((((((.....))))))).)))))..-.))).)))....))))(((((..((((....)))))))))...--...---- ( -28.00, z-score =  -2.92, R)
>consensus
AUAUACAUAAGAGAGCCGCUCC_GCUGCCGGCGUAACCGGCAGCGCAGCUACGCGG_CUUUGGCUAAACA_AAAAAUAAAUAAAAAUUUAAAAACA_A_A____
.................(((....(((((((.....)))))))...)))....................................................... ( -8.00 =  -8.67 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:40:19 2011