Locus 1113

Sequence ID dm3.chr2L
Location 8,371,018 – 8,371,152
Length 134
Max. P 0.943596
window1518 window1519 window1520

overview

Window 8

Location 8,371,018 – 8,371,119
Length 101
Sequences 7
Columns 106
Reading direction forward
Mean pairwise identity 57.17
Shannon entropy 0.78072
G+C content 0.55924
Mean single sequence MFE -18.05
Consensus MFE -9.25
Energy contribution -8.03
Covariance contribution -1.22
Combinations/Pair 1.50
Mean z-score -0.61
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.905739
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 8371018 101 + 23011544
-CCGAUUUCCCC--AAGUGGCGCGUUUCGCUAAGCGUUAUUAUUU-UUACCUUCCGCUAAACAC-UUGGCGCCGAUUCGAUUCCCUCCUUACCCUCGAAACCAGUG
-.........((--((((((((.....)))..((((.........-........))))...)))-))))(((.(.(((((..............))))).)..))) ( -17.17, z-score =  -0.28, R)
>droPer1.super_1 2172231 77 + 10282868
-----CUGUGCCUAAAGUGGCGUGUUUCAUGGAACGAGCUU------GGCGCUCCGCUCUGUCCCCCUACGCUGCCCCUCCCCUUACC------------------
-----..(((.....((.(((((((.....(((..((((..------((....))))))..)))....)))).))).)).....))).------------------ ( -17.40, z-score =  -0.23, R)
>dp4.chr4_group3 696081 77 + 11692001
-----CUGUGCCUAAAGUGGCGUGUUUCAUGGAACGAGCUU------GGCGCUCCGCUCUUUCCCCCUACGCUGCCCCUCCCCUCUCC------------------
-----..........((.(((((((.....((((.((((..------((....)))))).))))....)))).))).)).........------------------ ( -18.80, z-score =  -1.15, R)
>droAna3.scaffold_12916 5455602 93 + 16180835
AUUAUUUUCGCUUAAAGUGGCGCGUUUCACUAAGCACUUUGCCU---UUCCGUCCGUUAAACGCCUUGGCGCCUAACCACCUCUACCCACUUCCCG----------
..............((((((.((..........)).........---........((((..(((....)))..)))).........))))))....---------- ( -14.60, z-score =  -0.42, R)
>droYak2.chr2L 11009140 99 + 22324452
-CCGAUUUCCCC--AAGUGGCGCGUUUCGCUAAGCGUUAUUUUUCGUUACCUUCCGCCAAGCAC-UUGGCGCCGAUCCGAUCCCCUCGAAUCCACUGAUACCC---
-...........--.((((((((((((....))))))..................(((((....-))))))))(((.(((.....))).))).))).......--- ( -20.00, z-score =  -0.53, R)
>droEre2.scaffold_4929 17280496 90 + 26641161
-CCGAUUUCCCC--AAGUGGCGCGUUUCGCUAAGCGUUAUUUUU---UACCUUCCGCCAAGCAC-UUGGCGCCGAUCCGAUCCCCUCGAGCUCAGUG---------
-..((.......--(((((((((..........)))))))))..---.....))((((((....-))))))..((.((((.....))).).))....--------- ( -19.04, z-score =  -0.01, R)
>droSec1.super_3 3867605 99 + 7220098
-CCGAUUUCCCC--AAGUGGCGCGUUUCGCUAAGCGUUAUU--UU-UUACCUUCCGCCAAACAC-UUGGCGCCGAUUCGAACCCCUCCAUACCCUCGAAACCACUG
-...........--.(((((.((((((....))))))....--..-........((((((....-))))))....(((((..............))))).))))). ( -19.34, z-score =  -1.66, R)
>consensus
_CCGAUUUCCCC__AAGUGGCGCGUUUCGCUAAGCGUUAUU__U___UACCUUCCGCUAAACAC_UUGGCGCCGAUCCGACCCCCUCCA__CCC__G_________
..................(((((((((....))))....................(.....)......)))))................................. ( -9.25 =  -8.03 +  -1.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 8,371,018 – 8,371,119
Length 101
Sequences 7
Columns 106
Reading direction reverse
Mean pairwise identity 57.17
Shannon entropy 0.78072
G+C content 0.55924
Mean single sequence MFE -26.78
Consensus MFE -12.36
Energy contribution -12.06
Covariance contribution -0.30
Combinations/Pair 1.62
Mean z-score -1.00
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.49
SVM RNA-class probability 0.943596
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 8371018 101 - 23011544
CACUGGUUUCGAGGGUAAGGAGGGAAUCGAAUCGGCGCCAA-GUGUUUAGCGGAAGGUAA-AAAUAAUAACGCUUAGCGAAACGCGCCACUU--GGGGAAAUCGG-
..((((((((..((((...((.....)).....(((((...-.((((.((((........-.........)))).))))....)))))))))--...))))))))- ( -28.03, z-score =  -1.16, R)
>droPer1.super_1 2172231 77 - 10282868
------------------GGUAAGGGGAGGGGCAGCGUAGGGGGACAGAGCGGAGCGCC------AAGCUCGUUCCAUGAAACACGCCACUUUAGGCACAG-----
------------------......((((.((((.((....(....)...))((....))------..)))).)))).........(((......)))....----- ( -23.50, z-score =  -0.98, R)
>dp4.chr4_group3 696081 77 - 11692001
------------------GGAGAGGGGAGGGGCAGCGUAGGGGGAAAGAGCGGAGCGCC------AAGCUCGUUCCAUGAAACACGCCACUUUAGGCACAG-----
------------------...(...((((.(((.(.((....((((.((((((....))------..)))).)))).....)).)))).))))...)....----- ( -19.90, z-score =   0.33, R)
>droAna3.scaffold_12916 5455602 93 - 16180835
----------CGGGAAGUGGGUAGAGGUGGUUAGGCGCCAAGGCGUUUAACGGACGGAA---AGGCAAAGUGCUUAGUGAAACGCGCCACUUUAAGCGAAAAUAAU
----------((.(((((((((...(.(.(((((((((....))))))))).).)....---((((.....))))........)).)))))))...))........ ( -26.70, z-score =  -1.60, R)
>droYak2.chr2L 11009140 99 - 22324452
---GGGUAUCAGUGGAUUCGAGGGGAUCGGAUCGGCGCCAA-GUGCUUGGCGGAAGGUAACGAAAAAUAACGCUUAGCGAAACGCGCCACUU--GGGGAAAUCGG-
---.(((.((....(((((((.....)))))))(((((...-.((((.((((..................)))).))))....)))))....--...)).)))..- ( -31.67, z-score =  -1.45, R)
>droEre2.scaffold_4929 17280496 90 - 26641161
---------CACUGAGCUCGAGGGGAUCGGAUCGGCGCCAA-GUGCUUGGCGGAAGGUA---AAAAAUAACGCUUAGCGAAACGCGCCACUU--GGGGAAAUCGG-
---------..((((.(((.(((.(((...)))(((((...-.((((.((((.......---........)))).))))....))))).)))--.)))...))))- ( -29.86, z-score =  -1.45, R)
>droSec1.super_3 3867605 99 - 7220098
CAGUGGUUUCGAGGGUAUGGAGGGGUUCGAAUCGGCGCCAA-GUGUUUGGCGGAAGGUAA-AA--AAUAACGCUUAGCGAAACGCGCCACUU--GGGGAAAUCGG-
(.((..(..(((((((.....((.(((......))).))..-((((((.((..(((((..-..--....)).))).)).))))))))).)))--)..)..)).).- ( -27.80, z-score =  -0.65, R)
>consensus
_________C__GGG__UGGAGGGGAUCGGAUCGGCGCCAA_GUGCUUAGCGGAAGGUA___A__AAUAACGCUUAGCGAAACGCGCCACUU__GGGGAAAUCGG_
.................................(((((.....((((.((((..................)))).))))....))))).................. (-12.36 = -12.06 +  -0.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 8,371,054 – 8,371,152
Length 98
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 59.93
Shannon entropy 0.72874
G+C content 0.52962
Mean single sequence MFE -13.90
Consensus MFE -4.81
Energy contribution -4.87
Covariance contribution 0.06
Combinations/Pair 1.67
Mean z-score -1.66
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.25
SVM RNA-class probability 0.916850
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8371054 98 + 23011544
-UUAUUUUUACCUUCCGCUAAACACUUGGCGCCGAUUCGAUUCCCUCCUUACCCUCGAAACCAGUGAUACUCCA--UC--GUGCGACUGA--GCAUUAUCUGACG
-..............((((((....))))))....(((((..............)))))..(((((((.(((..--((--....))..))--).)))).)))... ( -15.34, z-score =  -1.15, R)
>droAna3.scaffold_12916 5455641 85 + 16180835
--------UGCCUUUCCGUC--CGUUAAACGCCUUGGCGC--CUAACCACCUCUACCCACUUCCCGAUUUCCCC--------CCAACUGAUGCCAUUAUCUGACG
--------........((((--.((((..(((....))).--.))))...........................--------......((((....)))).)))) ( -10.70, z-score =  -1.93, R)
>droYak2.chr2L 11009176 94 + 22324452
UUUUUCGUUACCUUCCGCCAAGCACUUGGCGC-----CGA----UCCGAUCCCCUCGAAUCCACUGAUACCCCAUACCCCUCAUGCACCA--GCAUUAUCUGACG
.....(((((.....((((((....)))))).-----.((----(.(((.....))).))).....................((((....--))))....))))) ( -15.90, z-score =  -2.40, R)
>droEre2.scaffold_4929 17280532 84 + 26641161
---UUUUUUACCUUCCGCCAAGCACUUGGCGC-----CGA----UCCGAUCCCCUCGAGCUCAGUGAUACCCCU--CG---UGCGAC--A--CCAUUAUCUCACG
---....((((....((((((....)))))).-----.((----.((((.....))).).)).)))).......--((---((.((.--.--......)).)))) ( -15.60, z-score =  -1.43, R)
>droSec1.super_3 3867641 98 + 7220098
---UUUUUUACCUUCCGCCAAACACUUGGCGCCGAUUCGAACCCCUCCAUACCCUCGAAACCACUGAUACCCUC--CUCCGUGCGACAGA--GCAUUAUCUGACG
---............((((((....)))))).((.(((((..............)))))..(((.((.......--.)).))))).((((--......))))... ( -16.14, z-score =  -2.64, R)
>droSim1.chr2L 8156987 80 + 22036055
--------UAUUUUACUCGCAACACUGCGCGA----UCGA--CCCUCCAU-CCCUCGAA-UCACUGAUACCUCU--CU----GCGACUGA--GCAU-AUCUGACG
--------.......(.((((....)))).).----((((--........-...)))).-(((..((((...((--(.----......))--)..)-)))))).. (  -9.70, z-score =  -0.38, R)
>consensus
___UUUUUUACCUUCCGCCAAACACUUGGCGC____UCGA__CCCUCCAUCCCCUCGAAACCACUGAUACCCCA__CC___UGCGACUGA__GCAUUAUCUGACG
...............((((((....)))))).......................................................................... ( -4.81 =  -4.87 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:25:50 2011