Locus 11685

Sequence ID dm3.chr3R
Location 23,106,099 – 23,106,209
Length 110
Max. P 0.983777
window16053 window16054

overview

Window 3

Location 23,106,099 – 23,106,206
Length 107
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 72.88
Shannon entropy 0.50722
G+C content 0.39963
Mean single sequence MFE -26.23
Consensus MFE -11.02
Energy contribution -11.77
Covariance contribution 0.75
Combinations/Pair 1.35
Mean z-score -1.80
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.684580
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23106099 107 - 27905053
AAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAUUUUUUUUUUAAACCAUCUGCCAAGUGAAUUUCCAGUGGGCAGAAG----UAUACAUAUCAAACGGAAGUC
(((((((....)))))))....((((((.....)))))).................((((((.(.((......)).).))))))..----............((....)). ( -28.30, z-score =  -2.67, R)
>droEre2.scaffold_4820 5542151 107 + 10470090
AAGUCC-AAACUGGAUUUUUUCGCUGGCAGAUAGCCAGCAU-UUUUUUU--AACCAUCUGCCAAGUGAAUUUCGGGUGGGUUGGAGUAUAUGUACAUAUCAAACGGAAGCC
((((((-.....))))))((((((((((.....))))))..-.......--..(((((..((..(......)..))..)).)))....................))))... ( -27.10, z-score =  -0.84, R)
>droYak2.chr3R 5444590 109 + 28832112
AAGUCCAAAACUGGAUUUUUUCGUUGGCACAUAGCCAGCAUAUUUUUUU--AACCAUCUGCCAACUGAAUUUCGGGUGGGUUGAAGUUUCUGUACAUAUCGAACGGAAGCC
(((((((....)))))))....((((((.....)))))).......(((--(((((((((............))))).)))))))((((((((.(.....).)))))))). ( -31.50, z-score =  -2.47, R)
>droSec1.super_13 1860206 105 - 2104621
AAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAUUUUUUUUU--AACCAUCUGCCAAGUGAACUUCCAGUGGGCAGAAG----UAUACAUAUCAAACGGAAGUC
(((((((....)))))))....((((((.....))))))..........--.....((((((.(.((......)).).))))))..----............((....)). ( -28.30, z-score =  -2.53, R)
>droSim1.chr3R_random 34468 104 - 1307089
AAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAUUUUUUUU---AACCAUCUGCCAAGUGAACUUCCAGUGGGCAGAAG----UAUACAUAUCAAACGGAAGUC
(((((((....)))))))....((((((.....)))))).........---.....((((((.(.((......)).).))))))..----............((....)). ( -28.30, z-score =  -2.49, R)
>droVir3.scaffold_13047 7945277 86 - 19223366
-----------UGUACCUAUU-AUGGGUUUCGA---AGUGUUGUUCUC---AUUUGUCAGAUA--UGGGUUUCGAGUAGGAAAAA-----UACGAAAAGUAAAUACGAAAC
-----------....((....-..))(((((..---.(((((.(((..---((((((((....--)))....)))))..))).))-----))).....((....))))))) ( -13.90, z-score =   0.22, R)
>consensus
AAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAUUUUUUUUU__AACCAUCUGCCAAGUGAAUUUCCAGUGGGCAGAAG____UAUACAUAUCAAACGGAAGUC
.(((((......)))))(((((((((((.....))))))..............((((..................)))).........................))))).. (-11.02 = -11.77 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 23,106,102 – 23,106,209
Length 107
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 71.59
Shannon entropy 0.53108
G+C content 0.37893
Mean single sequence MFE -26.75
Consensus MFE -14.22
Energy contribution -14.57
Covariance contribution 0.35
Combinations/Pair 1.35
Mean z-score -2.08
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.15
SVM RNA-class probability 0.983777
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23106102 107 - 27905053
AAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAUUUUUUUUUUAAACCAUCUGCCAAGUGAAUUUCCAGUGGGCAGAAG----UAUACAUAUCAAACGGAA
((((((((((....)))))))))).((((((.....))))))..............((.((((((.(.((......)).).)))))).(----....).........)).. ( -29.80, z-score =  -3.20, R)
>droEre2.scaffold_4820 5542154 107 + 10470090
AAAAAGUCC-AAACUGGAUUUUUUCGCUGGCAGAUAGCCAGCAU-UUUUUUU--AACCAUCUGCCAAGUGAAUUUCGGGUGGGUUGGAGUAUAUGUACAUAUCAAACGGAA
(((((((((-.....))))))))).((((((.....))))))..-.......--..(((((..((..(......)..))..)).))).(((....)))............. ( -28.60, z-score =  -1.69, R)
>droYak2.chr3R 5444593 109 + 28832112
AAAAAGUCCAAAACUGGAUUUUUUCGUUGGCACAUAGCCAGCAUAUUUUUUU--AACCAUCUGCCAACUGAAUUUCGGGUGGGUUGAAGUUUCUGUACAUAUCGAACGGAA
((((((((((....)))))))))).((((((.....))))))......((((--(((((((((............))))).)))))))).((((((.(.....).)))))) ( -30.20, z-score =  -2.41, R)
>droSec1.super_13 1860209 105 - 2104621
AAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAUUUUUUUUU--AACCAUCUGCCAAGUGAACUUCCAGUGGGCAGAAG----UAUACAUAUCAAACGGAA
((((((((((....)))))))))).((((((.....))))))..........--..((.((((((.(.((......)).).)))))).(----....).........)).. ( -29.80, z-score =  -3.10, R)
>droSim1.chr3R_random 34471 104 - 1307089
AAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAUUUUUUUU---AACCAUCUGCCAAGUGAACUUCCAGUGGGCAGAAG----UAUACAUAUCAAACGGAA
((((((((((....)))))))))).((((((.....)))))).........---..((.((((((.(.((......)).).)))))).(----....).........)).. ( -29.80, z-score =  -3.06, R)
>droVir3.scaffold_13047 7945280 86 - 19223366
---------------AUAUGUACCUAUUAUGGGUUUCGAAGUGUUGUUCUC---AUUUGUCAGAUA--UGGGUUUCGAGUAGGAAAAA-----UACGAAAAGUAAAUACGA
---------------...((((((......))........(((((.(((..---((((((((....--)))....)))))..))).))-----)))..........)))). ( -12.30, z-score =   0.96, R)
>consensus
AAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAUUUUUUUUU__AACCAUCUGCCAAGUGAAUUUCCAGUGGGCAGAAG____UAUACAUAUCAAACGGAA
((((((((((....)))))))))).((((((.....))))))..............((((..................))))............................. (-14.22 = -14.57 +   0.35)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:47:36 2011