Locus 4019

Sequence ID dm3.chr2R
Location 9,740,290 – 9,740,418
Length 128
Max. P 0.999334
window5496 window5497

overview

Window 6

Location 9,740,290 – 9,740,418
Length 128
Sequences 8
Columns 128
Reading direction forward
Mean pairwise identity 63.97
Shannon entropy 0.71745
G+C content 0.46591
Mean single sequence MFE -42.39
Consensus MFE -13.96
Energy contribution -12.59
Covariance contribution -1.37
Combinations/Pair 1.45
Mean z-score -3.10
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.52
SVM RNA-class probability 0.998851
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9740290 128 + 21146708
AAGUCACCUAAGCACUUAUUUUGUUUCGAUUAGAAAUAGGAGGAUAAUCGGGCUAGCAAGCCGACUGUCAAGUGGCCAUACCAUGUUUAUACUAAUGGAUUACCACCUGACAUGCGGACUAGCAUACC
.((((.............(((((((((.....))))))))).........((((....))))))))((((.((((..((.((((..........))))))..)))).))))((((......))))... ( -34.20, z-score =  -1.84, R)
>droSim1.chr2R 8181856 128 + 19596830
AAGUCACCUAAGCACUUAUUUUGUUUCGACUAGAAGUAGGAGGAUAAUCGGGCUAGCAGGCCGACUGUCAAGUGGCCAUACCAUGUCUAAAGUAAUGGAUUACCACCUGACAUGCGGACUUGCAUGCC
......(((.....((((((((..........))))))))))).......(((..((((((((..(((((.((((..((.((((..........))))))..)))).)))))..))).)))))..))) ( -36.90, z-score =  -1.12, R)
>droSec1.super_1 7267189 128 + 14215200
AAGUCACCUAAGCACUUAUUUUGUUUCGACUAGAAAUAGGAGGAUAAUCGGGCUAGCAAGCCGACUGUCAAGUGGACAUACCAUGUUUAUACUAAUGGAUUACCACCUGACAUGCGGACUUGCAAGCC
(((((......).)))).(((((((((.....))))))))).........((((.((((((((..(((((.((((.....((((..........))))....)))).)))))..))).))))).)))) ( -40.20, z-score =  -3.57, R)
>droYak2.chr2R 13925803 124 - 21139217
AAGUCAUCCAAGCACUUGUUUUGUUUCGACUAAAAGUAGGA---CAAACGGUCAAGCAAGCCGACUGUCAAGUGGCCAUACCAUGUUUAUAGCAAUGGAUUACCACAUGACA-GCGGACUAGCAUGUC
.(((((..(((((....).))))..).))))........((---(.....)))..((.(((((.((((((.((((..((.((((((.....)).))))))..)))).)))))-)))).)).))..... ( -35.00, z-score =  -2.00, R)
>droEre2.scaffold_4845 6509762 125 - 22589142
AACUCGUCCAAGCACUUGUUUUGUUUCGACUAGAAGUAGGA---UAAUCGGUCAAGCAAGCCGACUGUCAAGUGGCUAUACCAUCUUUAUAGAAAUGGAUUACCACCUGACAUGCGGACUAGCAUGUC
..((.(((.(((((.......))))).))).))......((---((.(((((.......))))).))))..((((..((.((((((....)))..)))))..))))..(((((((......))))))) ( -34.90, z-score =  -1.83, R)
>droAna3.scaffold_13266 17041219 125 + 19884421
AAUUUGCAAAAACAUUGUUUUUGUUUCGAUUAGGAAUUAGGC--CAUGCAGCCUGG-AGCCAGACUGCCAGGUGGAUAUUCCACAAGUGACAAAGUGGAAUACCAACUGGCAGUCAGGCUGACAUGCU
((((.((((((((...))))))))...))))........(((--.((((((((((.-...).(((((((((.(((.((((((((..........))))))))))).))))))))))))))).)))))) ( -51.70, z-score =  -5.27, R)
>dp4.chr3 5409889 117 - 19779522
AAGUUGCCUUCAUACAAAUUCUGU---GUUUGGAUGCCCAG----AGGCAGACCGGGACUCUGAUUGCCAGGUGGGAGUAUAUCAUGUACCUCAGCUGGCAACCAGGUGGCCAGUCUGCCUCCG----
.....((.((((.(((.......)---)).)))).))...(----((((((((.((..(((((.(((((((.((((.((((.....)))))))).))))))).)))).).)).)))))))))..---- ( -51.10, z-score =  -3.46, R)
>droPer1.super_4 3236423 117 + 7162766
AAGUUGCCUUCAUACAAAUUUUGU---GUUUGUAUGCCCAG----AGGCAGACCGGAACUCUGAUUGCCAGGUGGGAGUAUAUCGAGUACCUCAGCUGGCAACCAGGUGGCCAGUCUGCCUCCG----
..........(((((((((.....---)))))))))....(----((((((((.((.((.(((.(((((((.((((.((((.....)))))))).))))))).)))))..)).)))))))))..---- ( -55.10, z-score =  -5.69, R)
>consensus
AAGUCACCUAAGCACUUAUUUUGUUUCGACUAGAAGUAGGA___UAAUCGGGCUAGCAAGCCGACUGUCAAGUGGCCAUACCAUGUUUAUAGCAAUGGAUUACCACCUGACAUGCGGACUUGCAUGCC
.((((...........................................(((.........)))...((((..(((..((.((((..........))))))..)))..)))).....))))........ (-13.96 = -12.59 +  -1.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 9,740,290 – 9,740,418
Length 128
Sequences 8
Columns 128
Reading direction reverse
Mean pairwise identity 63.97
Shannon entropy 0.71745
G+C content 0.46591
Mean single sequence MFE -45.00
Consensus MFE -11.21
Energy contribution -10.28
Covariance contribution -0.94
Combinations/Pair 1.31
Mean z-score -3.91
Structure conservation index 0.25
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.80
SVM RNA-class probability 0.999334
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9740290 128 - 21146708
GGUAUGCUAGUCCGCAUGUCAGGUGGUAAUCCAUUAGUAUAAACAUGGUAUGGCCACUUGACAGUCGGCUUGCUAGCCCGAUUAUCCUCCUAUUUCUAAUCGAAACAAAAUAAGUGCUUAGGUGACUU
((((((((((((((..(((((((((((...((((..((....))))))....)))))))))))..)))...)))))).((((((............))))))...........))))).((....)). ( -40.10, z-score =  -2.91, R)
>droSim1.chr2R 8181856 128 - 19596830
GGCAUGCAAGUCCGCAUGUCAGGUGGUAAUCCAUUACUUUAGACAUGGUAUGGCCACUUGACAGUCGGCCUGCUAGCCCGAUUAUCCUCCUACUUCUAGUCGAAACAAAAUAAGUGCUUAGGUGACUU
(((..(((.(((.((.(((((((((((...((((..........))))....))))))))))))).))).)))..)))((((((............)))))).................((....)). ( -39.10, z-score =  -1.86, R)
>droSec1.super_1 7267189 128 - 14215200
GGCUUGCAAGUCCGCAUGUCAGGUGGUAAUCCAUUAGUAUAAACAUGGUAUGUCCACUUGACAGUCGGCUUGCUAGCCCGAUUAUCCUCCUAUUUCUAGUCGAAACAAAAUAAGUGCUUAGGUGACUU
((((.(((((((.((.((((((((((....((((..((....)))))).....)))))))))))).))))))).))))((((((............)))))).................((....)). ( -43.40, z-score =  -4.17, R)
>droYak2.chr2R 13925803 124 + 21139217
GACAUGCUAGUCCGC-UGUCAUGUGGUAAUCCAUUGCUAUAAACAUGGUAUGGCCACUUGACAGUCGGCUUGCUUGACCGUUUG---UCCUACUUUUAGUCGAAACAAAACAAGUGCUUGGAUGACUU
..((.((.((((.((-(((((.((((....((((.(((((....))))))))))))).))))))).)))).)).)).....(..---((((((((................)))))...)))..)... ( -35.29, z-score =  -1.61, R)
>droEre2.scaffold_4845 6509762 125 + 22589142
GACAUGCUAGUCCGCAUGUCAGGUGGUAAUCCAUUUCUAUAAAGAUGGUAUAGCCACUUGACAGUCGGCUUGCUUGACCGAUUA---UCCUACUUCUAGUCGAAACAAAACAAGUGCUUGGACGAGUU
.....(((.((((((((((((((((((.((((((((......)))))).)).))))))))))(((((((......).)))))).---..........................))))..)))).))). ( -40.40, z-score =  -3.23, R)
>droAna3.scaffold_13266 17041219 125 - 19884421
AGCAUGUCAGCCUGACUGCCAGUUGGUAUUCCACUUUGUCACUUGUGGAAUAUCCACCUGGCAGUCUGGCU-CCAGGCUGCAUG--GCCUAAUUCCUAAUCGAAACAAAAACAAUGUUUUUGCAAAUU
.(((....((((.(((((((((.(((((((((((..........)))))))).))).))))))))).))))-..(((((....)--))))...........((((((.......)))))))))..... ( -50.40, z-score =  -5.97, R)
>dp4.chr3 5409889 117 + 19779522
----CGGAGGCAGACUGGCCACCUGGUUGCCAGCUGAGGUACAUGAUAUACUCCCACCUGGCAAUCAGAGUCCCGGUCUGCCU----CUGGGCAUCCAAAC---ACAGAAUUUGUAUGAAGGCAACUU
----((((((((((((((..(((((((((((((.((.((.............)))).))))))))))).)).)))))))))))----)))..(((.((((.---......)))).)))(((....))) ( -53.22, z-score =  -4.61, R)
>droPer1.super_4 3236423 117 - 7162766
----CGGAGGCAGACUGGCCACCUGGUUGCCAGCUGAGGUACUCGAUAUACUCCCACCUGGCAAUCAGAGUUCCGGUCUGCCU----CUGGGCAUACAAAC---ACAAAAUUUGUAUGAAGGCAACUU
----((((((((((((((..(((((((((((((.((.((.............)))).))))))))))).)).)))))))))))----)))..((((((((.---......))))))))(((....))) ( -58.12, z-score =  -6.92, R)
>consensus
GGCAUGCAAGUCCGCAUGUCAGGUGGUAAUCCAUUACUAUAAACAUGGUAUGGCCACUUGACAGUCGGCUUGCUAGCCCGAUUA___UCCUACUUCUAAUCGAAACAAAAUAAGUGCUUAGGCGACUU
.................((((..(((..((((((..........)))).))..)))..))))...(((.........)))................................................ (-11.21 = -10.28 +  -0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:21:04 2011